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1.0: Overview - Biology

1.0: Overview - Biology


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Genetics – is the scientific study of heredity and the variation of inherited characteristics. It includes the study of genes, themselves, how they function, interact, and produce the visible and measurable characteristics we see in individuals and populations of species as they change from one generation to the next, over time, and in different environments.

Heredity – Humans have always been aware that the characteristics of an individual plant or animal in a population could be passed down through the generations. Offspring look more like their parents.Humans also knew that some heritable characteristics (such as the size or color of fruit) varied between individuals, and that they could select or breed crops and animals for the most favorable traits. Knowledge of these hereditary properties has been of significant value in the history of human development. In the past, humans could only manipulate and select from naturally existing combinations of genes. More recently, with the discovery of the substance and nature of genetic material, DNA, we can now identify, clone, and create novel, better combinations of genes that will serve our goals. Understanding the mechanisms of genetics is fundamental to using it wisely and for the betterment of all.

Fig.1-1: Parent and offspring. Wolf’s Monkey. (Flickr-eclectic echos-CC:AND)


1.2 Nature of Science Overview

Science is a fact-based way of understanding natural phenomena. Science is really two things: (1) a collection of facts that have been established through observation or experimentation and (2) a process for advancing knowledge about the natural world. We’ll discuss both established facts and science process in this text, but our emphasis will be on science as a process.

Figure 1.1 How science works: The flowchart.

The process of science

Simply, the process of science includes making observations, generating questions and hypotheses about these observations, making and testing predictions, and revising the collective understanding through communication of our findings.

A hypothesis is a proposed explanation for some sort of natural phenomenon (such as male masturbation, female orgasm, or same-sex sexual preferences). By definition, a hypothesis sets the stage for further exploration, either through more observations or experimentation.


Genomics & Comp. Biology (GCB)

Epigenetic alterations encompass heritable, non-genetic changes to chromatin (the polymer of DNA plus histone proteins) that influence cellular and organismal processes. This course will examine epigenetic mechanisms in directing development from the earliest stages of growth, and in maintaining normal cellular homeostasis during life. We will also explore how diverse epigenetic processes are at the heart of numerous human disease states. We will review topics ranging from a historical perspective of the discovery of epigenetic mechanisms to the use of modern technology and drug development to target epigenetic mechanisms toincrease healthy lifespan and combat human disease. The course will involve a ccombination of didactic lectures, primary scientific literature and research lectures, and student-led presentations. Prerequisite: BIOL 483 recommended

Course offered spring odd-numbered years

GCB 533 Statistics for Genomics and Biomedical Informatics

GCB 533 is an introductory course in probability theory and statistical inference for graduate students in Genomics and Computational Biology. The goal of the course is to provide foundation of basic concepts and tools as well as hands-on practice in their application to problems in genomics. At the completion of the course, students should have an intuitive understanding of basic probability and statistical inference and be prepared to select and execute appropriate statistical approaches in their future research.

Taught by: Pablo Camara and Laura Almasy

GCB 534 Experimental Genome Science

This course will survey methods and questions in experimental genomics, including next generation sequencing methods, genomic sequencing in humans and model organisms, functional genomics, proteomics, and applications of genomics methods. Students will be expected to review and discuss current literature and to propose new experiments based on material learned in the course. Prerequisite: Undergraduates and Masters students need BIOL 431.

Taught by: C. Brown, J. Murray

GCB 535 Introduction to Bioinformatics

This course provides overview of bioinformatics and computational biology as applied to biomedical research. A primary objective of the course is to enable students to integrate modern bioinformatics tools into their research activities. Course material is aimed to address biological questions using computational approaches and the analysis of data. A basic primer in programming and operating in a UNIX enviroment will be presented, and students will also be introduced to Python R, and tools for reproducible research. This course emphasizes direct, hands-on experience with applications to current biological research problems. Areas include DNA sequence alignment, genetic variation and analysis, motif discovery, study design for high-throughput sequencing RNA, and gene expression, single gene and whole-genome analysis, machine learning, and topics in systems biology. The relevant principles underlying methods used for analysis in these areas will be introduced and discussed at a level appropriate for biologists without a background in computer science. The course is not intended for computer science students who want to learn about biologically motivated algorithmic problems BIOL 437/GCB 536 and GCB/CIS/BIOL537 are more appropriate. Prerequisites: An advanced undergraduate course such as BIOL 421 or a graduate course in biology such as Biol 526 (Experimental Principles in Cell and Molecular Biology), BIOL 527 (Advanced Moleclar Genetics), BIOL 540 (Genetic Systems), or equivalent, is a prerequisite.

Course usually offered in spring term

Prerequisite: BIOL 421 OR BIOL 526 OR BIOL 527 OR BIOL 528 OR BIOL 540

GCB 536 Fundamentals of Computational Biology

Introductory computational biology course designed for both biology students and computer science, engineering students. The course will cover fundamentals of algorithms, statistics, and mathematics as applied to biological problems. In particular, emphasis will be given to biological problem modeling and understanding the algorithms and mathematical procedures at the "pencil and paper" level. That is, practical implementation of the algorithms is not taught but principles of the algorithms are covered using small sized examples. Topics to be covered are: genome annotation and string algorithms, pattern search and statistical learning, molecular evolution and phylogenetics, functional genomics and systems level analysis. Prerequisite: College level introductory biology required undergraduate or graduate level statistics taken previously or concurrently required molecular biology and/or genetics encouraged programming experience encouraged

Course usually offered in fall term

GCB 567 Mathematical Computation Methods for Modeling Biological Systems

This course will cover topics in systems biology at the molecular/cellular scale. The emphasis will be on quantitative aspects of molecular biology, with possible subjects including probabilistic aspects of DNA replication, transcription, translation, as well as gene regulatory networks and signaling. The class will involve analyzing and simulating models of biological behavior using MATLAB. Prereqisite: Graduate standing or permission of the instructor.

One-term course offered either term

GCB 577 Advanced Epigenetics Technology

Second year students in GCB, CAMB (G&E), or IGG programs using genomics methods to measure transcriptomics and epigenomics changes in their experimental systems. The goal is to familiarize students with the latest cutting-edge genomics tools and cover solutions to major experimental and computational challenges in the investigation of genome-wide epigenetic data sets. Students will develop competence in (i) variations of experimental techniques improving resolution and throughout, (ii) issues related to the computational analyses closely related to the various genome-wide assays used to probe epigenetic processes and signals, (iii) computational approaches useful to overcome pitfalls associated to the analysis of a given epigenetic data modality, (iv) methods, techniques and studies on the integration of multi-layer epigenetic data sets.

Course usually offered in spring term

GCB 585 Wistar Institute Cancer Biology Course: Signaling Pathways in Cancer

This course is intended to provide foundational information about the molecular basis of cancer. When necessary the significance of this information for clinical aspects of cancer is also discussed. The main theme centers around cell cycle checkpoints with specific emphasis on the biochemistry and genetics of DNA damage signaling pathways, DNA damage checkpoints, mitotic checkpoints and their relevance to human cancer. The course is taught by the organizers and guest lecturers from universities and research institutions in the Northeast.Following every lecture, students present a research paper related to the topic of that lecture. The course is intended for first and second year graduate students but all graduate students are welcome to attend. Prerequisite: Undergraduates and Master's degree candidates require permission from the course directors.

Taught by: Skordalakes and Murphy

Course usually offered in fall term

GCB 699 Lab Rotation

GCB 752 Genomics

Recent advances in molecular biology, computer science, and engineering have opened up new possibilities for studying the biology of organisms. Biologists now have access to the complete genomic sequence and set of cellular instructions encoded in the DNA of specific organisms, including homo sapiens, dozens of bacterial species, the yeast Saccharomyces cerevisiae, the nematode C. elegans, and the fruit fly Drosophila melanogaster. The goals of the course include the following: 1. introduce the basic principles involved in sequencing genomes, 2. familiarize the students with new instrumentation, informative tools, and laboratory automation technologies related to genomics, 3. teach the students how to access the information and biological materials that are being developed in genomics and 4. examine how these new tools and resources are being applied to basic and translational research. This will be accomplished through in depth discussion of classic and recent papers. Prerequisite: Permission of Instructor.


Biology (BIO)

Prerequisite: Graduate standing. This course provides a basic overview of the requirements for ethical conduct within the research laboratory. The grade report for this course is either “CR” (satisfactory completion) or “NC” (unsatisfactory completion). (Credit cannot be earned for both BIO� and BIO 7413.) Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Epigenetics and Metabolism. (3-0) 3 Credit Hours.

Scientific overview and discussion course related topics including stem cells, diseases, and interaction between metabolism and different epigenetic mechanisms. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Biotechnology Laboratory. (0-6) 3 Credit Hours.

Prerequisite: Graduate standing. Concurrent enrollment in BIO 5323 is strongly recommended for M.S. in Biotechnology students. An organized course offering an introduction to routine procedures employed in the modern research laboratory. Differential Tuition: $150. Course Fees: GS01 $90 IUB1 $10 L001 $30.

BIO�. Principles of Molecular Biology. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. Molecular structure and function of genes and nucleic acids, and the processes of DNA replication, mutation and repair, as well as transcription and translation of genetic material. Genome projects, functional genomics and the genetic control of development will also be covered. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Principles of Cell Biology. (3-0) 3 Credit Hours.

Prerequisites: BIO� and BIO�, or their equivalents. Basic structure, organization and differentiation of cells. Cell cycle, signaling, growth and movement of cells, as well as cellular immunology and cellular aspects of infectious disease will also be covered. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Advanced Nucleic Acids Laboratory. (0-6) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. BIO� recommended. An introduction to advanced techniques of molecular biology dealing with manipulations and analyses of DNA, including preparation and analysis of genomic DNA, genomic cloning, the polymerase chain reaction (PCR), Southern blotting, DNA sequencing and computational analysis of DNA sequence data. (Formerly titled "Advanced Molecular Biology Laboratory – DNA Techniques.") Differential Tuition: $150. Course Fees: GS01 $90 IUB1 $10 L001 $30.

BIO�. Recombinant Protein Biotechnology Laboratory. (0-6) 3 Credit Hours.

Prerequisite: Satisfactory completion of BIO�. Small- to large-scale growth of microorganisms and eukaryotic cells followed by downstream processing of supernatants and/or cell pellets, protein purification and protein analysis. (Formerly BIO 7542 and BIO 7543. Credit cannot be earned for both BIO� and BIO 7542 or BIO 7543.) Differential Tuition: $150. Course Fees: GS01 $90 IUB1 $10 L001 $30.

BIO�. Principles of Chemical Biology. (3-0) 3 Credit Hours.

Prerequisites: BIO� and BIO�, or equivalents. The role of chemistry in prokaryotic and eukaryotic biological systems. Topics will cover the probing and controlling biological systems using chemical methods and the manipulation of biological systems via novel chemistries to advance fundamental knowledge which serve as a basis for translational approaches. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Medicinal Plants. (3-0) 3 Credit Hours.

Prerequisite: Graduate standing in Biology or Chemistry. An overview of plant secondary metabolism, and the ethnobotany, biochemistry, and pharmacology of some of our most important plant-derived pharmaceuticals. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Proteins and Nucleic Acids. (3-0) 3 Credit Hours.

Prerequisite: BIO� or equivalent. Protein sequences, domains, folding, proteomics, glycoproteins, protein-DNA interaction, RNA conformations. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Neuroanatomy. (3-0) 3 Credit Hours.

Prerequisite: Consent of instructor. The anatomy of the vertebrate nervous system. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Systems Neuroscience. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. The fundamentals of neurophysiology are presented from the cellular to the systems level. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Molecular Neurobiology. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. BIO� or an equivalent recommended. An introduction to the biochemical basis of synaptic transmission, and the pathological changes in synaptic transmission associated with neurobiological diseases and disorders. (Formerly titled "Neurochemistry.") Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Reproductive Biology. (3-0) 3 Credit Hours.

Prerequisite: Graduate standing in Biology. Mammalian reproduction including mechanisms involved in sexual differentiation, fertilization, and fetal development. Endocrine regulation and environmental influences with a focus on human reproduction. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Computational Neuroscience. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. A non-mathematical approach to the computational functions of the brain, including sensory coding, neural control of movement, and the computational properties of neurons and neuronal networks. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Cognitive Neuroscience. (3-0) 3 Credit Hours.

Prerequisite: BIO� (or PSY�) recommended, or consent of instructor. The biological foundations of mental phenomena, including perception, attention, learning, memory, language, motor control, and executive function, as well as functional specialization, development and plasticity, through various methodologies. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Enzymes. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. A study of enzyme structure and mechanism, inhibitors, cofactor, kinetics, and regulation. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Pharmacology and Toxicology. (3-0) 3 Credit Hours.

Prerequisite: Graduate standing in Biology. Mechanisms of action of major classes of therapeutic drugs. Clinical uses, drug comparisons, beneficial and adverse effects involved in clinical therapeutics. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Neurodegenerative Disease. (3-0) 3 Credit Hours.

Prerequisite: BIO�, BIO�, or consent of instructor BIO� or BIO� is recommended. The pathogenesis of neurodegenerative diseases will be covered with an emphasis on the molecular mechanisms and experimental approaches. Current research progress will be covered. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Bioinformatics and Computational Biology. (3-0) 3 Credit Hours.

Prerequisites: BIO� or an equivalent enrollment in Biology Ph.D. program required, or permission of the Biology Department or instructor. Computational analysis of sequences, protein structures, and gene expression network on a large scale. Comparative genomics, functional genomics, and proteomics will also be covered. (Credit cannot be earned for both BIO� and BIO 5623.) Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Applications of Recombinant DNA Technology. (3-0) 3 Credit Hours.

A course on recombinant DNA technology, concentrating on major DNA manipulation methods, including their use in vaccine and bioactive protein production, gene therapy, plant genetic engineering along with ethical and safety considerations. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Ornithology. (3-0) 3 Credit Hours.

A course covering various aspects of the biology of birds, including anatomy, physiology, systematics, evolution, behavior, ecology, and biogeography. Field trips may be included. (Same as ES�. Credit cannot be earned for both BIO� and ES�.) Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Advanced Medical Mycology. (3-0) 3 Credit Hours.

Prerequisites: BIO� and BIO�. This course is a comprehensive study of the etiological agents and host factors that lead to fungal disease in humans. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Advanced Virology. (3-0) 3 Credit Hours.

Prerequisite: Graduate standing in Biology. A detailed study of the diversity of viruses and biochemical mechanisms for their replication. (Formerly titled "Biochemical Virology.") Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Conservation Biology. (3-0) 3 Credit Hours.

The class topics will include the nature of the biosphere, threats to its integrity, and ecologically sound responses to these threats. Also included will be the origin and preservation of biotic diversity, how the rich variety of plant and animal life arose, how it has been maintained by natural processes, and how its destruction can be prevented. (Same as ES�. Credit cannot be earned for both BIO� and ES�.) Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Fundamentals of Immunology for Biotechnology. (2-0) 2 Credit Hours.

An integrated examination of the principles of immunology pertaining to the Biotechnology Industry. An emphasis on current immunological techniques, including: recombinant antibody, flow cytometry and elispot technology. Issues related to vaccine production and therapeutics will also be considered. Differential Tuition: $100. Course Fees: GS01 $60.

BIO�. Introduction to Good Manufacturing Practices and Good Laboratory Practices. (3-0) 3 Credit Hours.

Review of FDA and U.S. Pharmacopia regulations. Practical considerations for the implementation of GMP/GLP systems data management and reporting, as well as problem solving and interpretive skills, will be emphasized. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Frontiers in Human Pluripotent Stem Cells. (3-0) 3 Credit Hours.

Integrates the fundamental aspects of developmental biology with emerging concepts in embryonic and adult stem cells and regenerative medicine. A discussion of various stem cell applications in industry, military, medicine, and ethics of regenerative medicine is presented. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Membrane Structure and Function. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. A study of the composition, organization, transport functions, and permeability of natural and model membranes. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Plant Biotechnology. (3-0) 3 Credit Hours.

Prerequisite: BIO� or equivalent. BIO� is recommended. The principles of plant physiology and genetics, and techniques used in plant modification, and principles of plant breeding and quantitative genetics as applied to plant biotechnology. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Directed Research. (0-0) 1 Credit Hour.

Prerequisites: Admission to either the Biology or Biotechnology Master’s program or admission as a special graduate or non-degree-seeking student, and permission in writing (form available) of the instructor and the student’s Graduate Advisor of Record. The directed research course may involve either a laboratory or a theoretical problem. May be repeated for credit, but not more than 6 hours, regardless of discipline, in combination with BIO�-3 (Independent Study), will apply to the Master’s degree. Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Directed Research. (0-0) 2 Credit Hours.

Prerequisites: Admission to either the Biology or Biotechnology Master’s program or admission as a special graduate or non-degree-seeking student, and permission in writing (form available) of the instructor and the student’s Graduate Advisor of Record. The directed research course may involve either a laboratory or a theoretical problem. May be repeated for credit, but not more than 6 hours, regardless of discipline, in combination with BIO�-3 (Independent Study), will apply to the Master’s degree. Differential Tuition: $100. Course Fees: GS01 $60.

BIO�. Directed Research. (0-0) 3 Credit Hours.

Prerequisites: Admission to either the Biology or Biotechnology Master’s program or admission as a special graduate or non-degree-seeking student, and permission in writing (form available) of the instructor and the student’s Graduate Advisor of Record. The directed research course may involve either a laboratory or a theoretical problem. May be repeated for credit, but not more than 6 hours, regardless of discipline, in combination with BIO�-3 (Independent Study), will apply to the Master’s degree. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Methods in Field Biology. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. Examination of techniques to collect, identify, and preserve plants and animals. Field methods used in the analysis of populations and communities are considered. (Same as ES�. Credit cannot be earned for both BIO� and ES�.) Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Advanced Ecology. (3-0) 3 Credit Hours.

Prerequisite: BIO� or an equivalent. Interaction of organisms with their environment, allelopathy, competition, distribution, succession, and factors that control growth and dispersal. Special consideration is given to the concepts of climax, succession, and land management. (Same as ES�. Credit cannot be earned for both BIO� and ES�.) Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Quantitative Biology. (3-0) 3 Credit Hours.

Prerequisite: Graduate standing or consent of instructor. An introduction of quantitative analysis of biological data and design of experiments. Topics include probability theory and distributions descriptive statistics hypothesis testing and confidence intervals for means, variances, and proportions chi-square statistic categorical data analysis linear correlation and regression model analysis of variance and nonparametric methods. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Molecular Biology and Biophysics of Ion Channels. (3-0) 3 Credit Hours.

Prerequisites: BIO� and BIO�, or permission of instructor. A study of the molecular composition and biophysical properties of ion channels. The course emphasizes three families of ion channels: voltage-gated, ligand-gated and metabotropically-stimulated channels. Their structure and function will be related to how ion channels mediate cellular actions in excitable cells. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Essentials of Biostatistics for Biotechnology. (3-0) 3 Credit Hours.

Basic, intermediate, and advanced (but not bioinformatics) statistical vocabulary, concepts, and methods commonly used in the biotechnology industry. A focus on tests for quality control and assurance of equipment and test systems to assess accuracy, precision, and bias related to test validations. Concepts and appropriate selections of test/study design using power analyses and estimations of sample sizes also for clinical trials. Analytical calibration curves, frequency distributions, descriptive statistics, measures of central tendency and dispersion/error, probability, paired and unpaired, one-tailed and two-tailed t-tests, correlations, regression, one-way and two-way analysis of variance with repeated measures, parametric and nonparametric tests, post hoc tests for significance, reporting and interpretations of statistical results, validations of clinical tests for specificity, sensitivity, predictive values, likelihood ratios, receiver operating characteristic curves. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Animal Behavior. (3-0) 3 Credit Hours.

Prerequisite: BIO� or consent of instructor. An examination of neural, endocrine, genetic, and environmental determinants of behavior. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Drug Development. (3-0) 3 Credit Hours.

This course will provide students with an overview of the early drug discovery process, including target identification, validation, assay development and high throughput screening up to pre-clinical trials. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Vaccine Development. (3-0) 3 Credit Hours.

Prerequisites: BIO� and permission of instructor. This course will provide students with an overview of issues about the roles of vaccines in the control of infectious diseases, vaccine development, clinical trials and implementation of vaccine programs. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Microbial Pathogenesis. (3-0) 3 Credit Hours.

The student will gain an understanding of the cellular and molecular mechanisms by which eukaryotic and viral pathogens cause disease and the host immune responses against these pathogens. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Advanced Immunology and Immunochemistry. (3-0) 3 Credit Hours.

Prerequisite: BIO� or consent of instructor. The study of current concepts of humoral and cell-mediated immunity, with emphasis on molecular mechanisms. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Bacterial Pathogenesis. (3-0) 3 Credit Hours.

Prerequisites: BIO� and BIO�, or consent of instructor. This course will present a selection of topics in the field of bacterial pathogenesis. Lectures will cover regulation of virulence colonization and host tissue damage vaccines, antibiotics and novel antimicrobials evasion of the immune system intracellular pathogens pathogenic mechanisms of Gram-negative and Gram-positive bacteria pathogenic mycobacteriology and experimental tools in bacterial pathogenesis. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Independent Study. (0-0) 1 Credit Hour.

Prerequisites: Graduate standing and permission in writing of the instructor and the student’s Graduate Advisor of Record. Independent reading, research, discussion, and/or writing under the direction of a faculty member. For students needing specialized work not normally or not often available as part of the regular course offerings. May be repeated for credit, but not more than 6 hours, regardless of discipline, in combination with BIO�-3 Directed Research will apply to the Master’s degree. Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Independent Study. (0-0) 2 Credit Hours.

Prerequisites: Graduate standing and permission in writing of the instructor and the student’s Graduate Advisor of Record. Independent reading, research, discussion, and/or writing under the direction of a faculty member. For students needing specialized work not normally or not often available as part of the regular course offerings. May be repeated for credit, but not more than 6 hours, regardless of discipline, in combination with BIO�-3 Directed Research will apply to the Master’s degree. Differential Tuition: $100. Course Fees: GS01 $60.

BIO�. Independent Study. (0-0) 3 Credit Hours.

Prerequisites: Graduate standing and permission in writing of the instructor and the student’s Graduate Advisor of Record. Independent reading, research, discussion, and/or writing under the direction of a faculty member. For students needing specialized work not normally or not often available as part of the regular course offerings. May be repeated for credit, but not more than 6 hours, regardless of discipline, in combination with BIO�-3 Directed Research will apply to the Master’s degree. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Comprehensive Examination. (0-0) 1 Credit Hour.

Prerequisite: Approval of the appropriate Graduate Program Committee to take the Comprehensive Examination. Independent study course for the purpose of taking the Comprehensive Examination. May be repeated as many times as approved by the Graduate Program Committee. Enrollment is required each term in which the Comprehensive Examination is taken if no other courses are being taken that term. The grade report for the course is either “CR” (satisfactory performance on the Comprehensive Examination) or “NC” (unsatisfactory performance on the Comprehensive Examination). Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Special Problems. (3-0) 3 Credit Hours.

Prerequisite: Consent of instructor. An organized course offering the opportunity for specialized study not normally or not often available as part of the regular course offerings. Special Problems courses may be repeated for credit when the topics vary, but not more than 6 hours, regardless of discipline, may be applied to the Master’s degree. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Master's Thesis. (0-0) 1 Credit Hour.

Prerequisites: Permission of the Graduate Advisor of Record and thesis director. Thesis research and preparation. May be repeated for credit, but not more than 6 hours will apply to the Master’s degree. Credit will be awarded upon completion of the thesis. Enrollment in BIO�, BIO�, or BIO� is required each term in which the thesis is in progress. Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Master's Thesis. (0-0) 2 Credit Hours.

Prerequisites: Permission of the Graduate Advisor of Record and thesis director. Thesis research and preparation. May be repeated for credit, but not more than 6 hours will apply to the Master’s degree. Credit will be awarded upon completion of the thesis. Enrollment in BIO�, BIO�, or BIO� is required each term in which the thesis is in progress. Differential Tuition: $100. Course Fees: GS01 $60.

BIO�. Master’s Thesis. (0-0) 3 Credit Hours.

Prerequisites: Permission of the Graduate Advisor of Record and thesis director. Thesis research and preparation. May be repeated for credit, but not more than 6 hours will apply to the Master’s degree. Credit will be awarded upon completion of the thesis. Enrollment in BIO�, BIO�, or BIO� is required each term in which the thesis is in progress. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Biology Colloquium. (1-0) 1 Credit Hour.

Prerequisite: Graduate standing. Oral presentations, discussions, critical evaluation of students’ research in progress, or discussions of current journal articles or reviews of recent scientific advances. May be repeated for credit. The grade report for this course is either “CR” (satisfactory participation in the colloquium) or “NC” (unsatisfactory participation in the colloquium). (Formerly BIO 5041. Same as ES�. Unless topic varies, credit cannot be earned for both BIO� and ES�.) Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Seminar in Life Sciences. (1-0) 1 Credit Hour.

Prerequisite: Graduate standing. Formal presentations of research by outside authorities in the biological sciences. May be repeated for credit. The grade report for this course is either “CR” (satisfactory participation in the seminar) or “NC” (unsatisfactory participation in the seminar). Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Principles of Biological Scientific Teaching. (0-0) 3 Credit Hours.

Prerequisite: Admission to candidacy for the Doctoral degree. Required course for Biology doctoral students. The student will be responsible for all aspects of leading a discussion section or laboratory course. Approval by the chair of the appropriate Doctoral Studies committee required. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Principles of Biological Scientific Writing. (3-0) 3 Credit Hours.

Prerequisite: Graduate standing. This course will provide an overview of scientific grant and manuscript preparation. The class will be directed toward producing a Ph.D. dissertation proposal and a predoctoral fellowship application. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Doctoral Research. (0-0) 1 Credit Hour.

Prerequisite: Admission to either the Neurobiology or Cell and Molecular Biology Doctoral program. May be repeated for credit, but no more than 52 hours may be applied to the Doctoral degree. Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Doctoral Research. (0-0) 2 Credit Hours.

Prerequisite: Admission to either the Neurobiology or Cell and Molecular Biology Doctoral program. May be repeated for credit, but no more than 52 hours may be applied to the Doctoral degree. Differential Tuition: $100. Course Fees: GS01 $60.

BIO�. Doctoral Research. (0-0) 3 Credit Hours.

Prerequisite: Admission to either the Neurobiology or Cell and Molecular Biology Doctoral program. May be repeated for credit, but no more than 52 hours may be applied to the Doctoral degree. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Doctoral Dissertation. (0-0) 1 Credit Hour.

Prerequisites: Admission to candidacy for the Doctoral degree and completion of at least 18 semester credit hours of BIO�-3. May be repeated for credit. Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Doctoral Dissertation. (0-0) 2 Credit Hours.

Prerequisites: Admission to candidacy for the Doctoral degree and completion of at least 18 semester credit hours of BIO�-3. May be repeated for credit. Differential Tuition: $100. Course Fees: GS01 $60.

BIO�. Doctoral Dissertation. (0-0) 3 Credit Hours.

Prerequisites: Admission to candidacy for the Doctoral degree and completion of at least 18 semester credit hours of BIO�-3. May be repeated for credit. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Practicum in Biotechnology. (0-0) 3 Credit Hours.

Prerequisites: Enrollment in Master’s in Biotechnology program and at least 18 hours credit including satisfactory completion of BIO� and one other organized laboratory course. An internship in a Biotechnology company. Must have approval of Biotechnology Graduate Studies Committee. Differential Tuition: $150. Course Fees: GS01 $90.

BIO�. Experimental Techniques in Biology. (0-2) 1 Credit Hour.

Prerequisite: Consent of instructor. Topics include research methods in cell and molecular biology, molecular neurobiology, and microbiology. May be repeated for credit as topics vary. (Formerly BIO 5571.) Differential Tuition: $50. Course Fees: GS01 $30.

BIO�. Experimental Techniques in Biology. (0-4) 2 Credit Hours.

Prerequisite: Consent of instructor. Topics include research methods in cell and molecular biology, molecular neurobiology, and microbiology. May be repeated for credit as topics vary. (Formerly BIO 5572.) Differential Tuition: $100. Course Fees: GS01 $60.


EIU Department of Biological Sciences

BIO 1001G - Biological Principles and Issues. (2-2-3) An introduction to the study of living organisms with emphasis upon an appreciation for their behavioral, functional, and structural adaptations, their diversity and relationship to the environment. In addition, strong emphasis on current issues dealing with the field of biology. Does not count toward the Biological Sciences major or minor. Credit for BIO 1001G will not be granted if the student already has credit for or registration in BIO 1091G or BIO 1500. L1 900L Credits: 3

BIO 1002G - Practical Botany. (2-2-3) This course will introduce students to the importance of plants in their daily lives. General botanical principles will be taught with emphasis on instructing students in methods of identification, growth and maintenance of plants used in landscaping, gardening, and interiorscaping. Does not count toward the Biological Sciences major or minor. Credit for BIO 1002G will not be granted if the student already has credit for or registration in BIO 1092G or BIO 1550G. Credits: 3

BIO 1003G - Life of Animals. (2-2-3) An introduction to the study of animals and animal diversity with emphasis on behavioral, functional, and structural adaptations as they relate to specific habitats. Does not count toward the Biological Sciences major or minor. Credit for BIO 1003G will not be granted if the student already has credit for or registration in BIO 1093G or BIO 1550G. Credits: 3

BIO 1004G - Practical Microbiology. (2-2-3) Using practical laboratory experiences students learn characteristics and activities of microorganisms with special emphasis on their significance to society. This course targets students majoring in Family and Consumer Sciences, Pre-Nursing, and Health Promotion. Does not count in the Biological Sciences major or minor. Credit for BIO 1004G will not be granted if the student already has credit for or registration in BIO 1094G or BIO 3300. L1 903L Credits: 3

BIO 1091G - Biological Principles and Issues, Honors. (2-2-3) The study of the fundamental processes and structures common to all living things. Current issues in the biological sciences will be addressed. Does not count toward the Biological Sciences major or minor. Credit for BIO 1091G will not be granted if the student already has credit for or registration in BIO 1001G or BIO 1500. L1 900L WI Credits: 3 Prerequisites & Notes: Admission to the University Honors College.

BIO 1092G - Practical Botany, Honors. (2 -2-3) This course will introduce students to the importance of plants in their daily lives. Emphasis will be placed on students learning methods for the identification, growth and maintenance of plants used in landscaping, gardening and the home. Does not count toward the Biological Sciences major or minor. Credit for BIO 1092G will not be granted if the student already has credit for or registration in BIO 1002G or BIO 1550G. Credits: 3 Prerequisites & Notes: Admission to the University Honors College.

BIO 1093G - Life of Animals, Honors. (2-2 -3) An introduction to the study of animals with an emphasis upon an appreciation for their behavioral, functional, and structural adaptations, their diversity and relationships to their environment. Does not count toward the Biological Sciences major or minor. Credit for BIO 1093G will not be granted if the student already has credit for or registration in BIO 1003G or BIO 1550G. WI Credits: 3 Prerequisites & Notes: Admission to the University Honors College.

BIO 1094G - Practical Microbiology, Honors. (1-4-3) Using practical laboratory experiences student will learn characteristics and activities of microorganisms with emphasis on the performance of standard procedures and techniques used to study microbes. The course culminates with a student designed original research project. Does not count toward the Biological Sciences major or minor. Credit for BIO 1094G will not be granted if the student already has credit for or registration in BIO 1004G or BIO 3300. Credits: 3 Prerequisites & Notes: Admission to the University Honors College.

BIO 1150 - Biology Forum (1-0-1) The course is designed for freshmen and transfer students majoring in the Biological Sciences to enhance their transition to Eastern Illinois University by introducing them to the Biological Sciences program, providing an overview of the major and core requirements, and addressing specific skill sets necessary for success in the major. These skills include: library expertise, computer competence, and ability to produce and interpret graphs and tables, and critical scientific reading. Students will also meet the Biological Sciences faculty and discover departmental research opportunities and internship opportunities, summer and study abroad programs, career opportunities, and student clubs. Credits: 1

BIO 1180. Principles of Biological Investigations. (1-3-1) On Demand. This is a half-semester course that offers hands-on, guided research opportunity in the context of early stage college experience to allow students in Biological Sciences major to be immersed in the process of scientific inquiry outside of a lecture format. This course will be restricted to students majoring in Biological Sciences. A limit of 1 hour may be applied to a major. Prerequisite: BIO 1500 and permission of the instructor. BIO 1500 can be repeated after BIO 1180 for credit and a grade recalculation. WA

BIO 1500 - General Biology I(3-3-4) F, S. The first in a two-course introduction series for students majoring or minoring in the Biological Sciences, with emphasis on understanding the fundamental aspects of life. This course has a significant laboratory component that requires additional fees to offset the costs of supplies and reagents. Grade and credit hours for this course will be removed if student already has credit for or is registered in BIO 1100.

BIO 1550G - General Biology II(3-3-4) F, S. The second in a two-course introduction series for students majoring or minoring in the Biological Sciences, with emphasis on taxonomic groups, form and function, and life history. Note: This course is open to all students, but it is intended for Biological Sciences majors and minors, as well as Chemistry majors (Biochemistry concentration). It has a significant laboratory component that requires additional fees to offset the costs of supplies and reagents. Grade and credit hours for this course will be removed if student already has credit for or is registered in BIO 1200G and BIO 1300G. Prerequisite: BIO 1500.

BIO 2001G - Human Physiology. (3-2-4) An organ systems approach to the function of the human body. Does not count toward the Biological Sciences major or minor. Credit for BIO 2001G will not be granted if the student already has credit for or registration in BIO 2091G or BIO 3520. L1 904L Credits: 4

BIO 2002G - Environmental Life Sciences. (3-0-3) A study of the interrelationships of the living and non- living components of the environment, the ecology of humankind, and the interaction of humans with the environment. The course emphasizes current environmental issues and possible solutions and courses of action. Does not count towards the Biological Sciences major or minor. Credit for BIO 2002G will not be granted if the student already has credit for or registration in BIO 2092G or BIO 3850. Credits: 3

BIO 2003G - Heredity and Society. (3-0-3) A course for non-science majors that addresses the ethical, political, and social implications of heredity and modern genetic technology. Basic genetic principles as well as contemporary issues in biotechnology will be studied. Does not count toward the Biological Sciences major or minor. Credit for BIO 2003G will not be granted if the student already has credit for or registration in BIO 2093G or BIO 3200. Credits: 3

BIO 2091G - Human Physiology, Honors. (3 -2-4) An organ systems approach to the function of the human body. Does not count toward the Biological Sciences major or minor. Credit for BIO 2091G will not be granted if the student already has credit for or registration in BIO 2001G or BIO 3520. WI Credits: 4 Prerequisites & Notes: Admission to the University Honors College.

BIO 2092G - Environmental Life Sciences, Honors. (4-0-4) A study of the interrelationships of the living and non-living components of the environment, the ecology of humankind, and the interaction of humans with the environment. The course emphasizes current environmental issues and possible solutions and courses of action. Does not count towards the Biological Sciences major or minor. Credit for BIO 2092G will not be granted if the student already has credit for or registration in BIO 2002G or BIO 3850. Credits: 4 Prerequisites & Notes: Admission to the University Honors College.

BIO 2093G - Heredity and Society, Honors. (4-0-4) A course for non-science majors that addresses the ethical, political, and social implications of heredity and modern genetic technology. Basic genetic principles as well as contemporary issues in biotechnology will be studied. Does not count toward the Biological Sciences major or minor. Not open to those students with credit for, or registration in, BIO 3200. WI Credits: 4 Prerequisites & Notes: Admission to the University Honors College.

BIO 2210. Anatomy and Physiology I. (3-3- 4) Comprehensive survey of human anatomy and physiology. First of a two- semester sequential course that covers the structure and function of cells and tissues, and a systematic approach to the integumentary, skeletal, muscular, nervous, and endocrine systems. Includes a laboratory component with identification of anatomical structures in models and cadavers and hands-on physiological experiments. Equivalent course: BIO 2200. Prerequisites: BIO 1001G, or BIO 1500 or BIO 1550G or KSS 2440.

BIO 2220. Anatomy and Physiology II. (3- 3-4) Comprehensive survey of human anatomy and physiology. Second of a two- semester sequential course that covers the structure and function of cardiovascular, lymphatic, respiratory, digestive, urinary and reproductive systems, metabolism and energetics, and development. Includes a laboratory component with identification of anatomical structures in models and cadavers and hands-on physiological experiments. Equivalent Course: BIO 2200. Prerequisite: BIO 2210.

BIO 2320 - Economic Botany - Role of Plants in the World Economy. (3-0-3) S. The impact of plants and plant products on the world economy, with emphasis on the U. S. economy. Course also includes information on the origin, development, diversity and future impact of plants and plant products on the world economy. Credits: 3 Prerequisites and Notes: BIO 1550G or permission of the instructor.

BIO 3003G - An Introduction to Evolution. (3-0-3). A survey of the history, evidence, mechanisms and implications of evolutionary theory. Topics covered include natural selection, fossil formation, Mendelian genetics, attitudes towards evolutionary theory, and evolution of Homo sapiens. This course does not count toward Biological Sciences major or minor.

BIO 3120 - Molecular and Cellular Biology. (2-4-4) F, S. A class on the biology of cells, with respect to the structures, functions, and interactions of biomolecules and organelles, to help students understand the molecular underpinnings of life. The laboratory portion of the class provides integrated experiments to allow students to learn and practice basic molecular biology techniques. Course replaces former courses BIO 3100 and BIO 3101. Prerequisites: BIO 1500, CHM 1410, and CHM 1415.

BIO 3155G. Introduction to Evolutionary Medicine. (3-0-3) On Demand. A survey of current topics in evolutionary medicine, such as cancer treatment, antibiotic resistance, asthma and diseases of civilization will be explored and analyzed using the mechanisms of evolution natural selection, generation of biological traits and evolutionary history "mismatch" to current lifestyles affecting human biology today. This course does not count toward Biological Sciences major or minor.

BIO 3180. Introduction to Ecology and Evolution. (3-3-4) F, S. Introduction to fundamental concepts in ecology and evolution with a focus on the interconnections among organisms, the environment, and evolution. The laboratory portion of this course provides students with a hands-on application of concepts, including demonstration of techniques for collecting, analyzing, and interpreting ecological data. Students also will gain experience in scientific writing. Prerequisites: BIO 1500 and BIO 1550G. Credit for BIO 3180 will not be granted if the student already has credit for or registration in BIO 3800. WI

BIO 3200 - Genetics. (3-2-4) The fundamental principles of genetics (classical, molecular, and population) stressing applications to all organisms. Credits: 4 Prerequisites & Notes: BIO 3120 or CHM 3450.

BIO 3210. Immunology. (3-3-4) S. Basic principles and laboratory procedures for the study of immune responses. Prerequisites: BIO 3120 or BIO 3200.

BIO 3300 - General Microbiology. (2-4-4) An introduction to the biology of prokaryotic and eukaryotic microorganisms. Emphasis is placed on bacteria and their chemical composition and structure, classification, growth, physiology, genetics, diversity, pathogenicity, ecology, and economic importance. The laboratory will include principles and techniques for the isolation, cultivation, enumeration, and characterization of microorganisms. Credits: 4 Prerequisites & Notes: BIO 1500.

BIO 3312 - Horticulture. (2-2-3) The principles and practices of indoor and outdoor home gardening with emphasis on practical applications of horticulture. Credits: 3 Prerequisites & Notes: BIO 1550G.

BIO 3322 - Dendrology. (2-3-3) The identification of common native, naturalized, and planted trees, shrubs, and vines of Illinois, their life histories, wood structure, ecology, and economic significance. The biotic divisions of Illinois and major forest regions of North America are also stressed. Credits: 3 Prerequisites & Notes: BIO 1550G.

BIO 3333G. Sustainable Energy and the Environment. (3-0-3) Su. An exploration of current renewable energy technologies, including bioenergy, with emphasis on their environmental impact and sustainability. The course is restricted to off- campus students that are non-Biological Sciences majors and minors.

BIO 3400 - Methods of Teaching Biological Sciences in High School. (2-2-3) A study of teaching techniques including the collection and use of materials for demonstrations and laboratory experiments. Thirty clock hours in pre-student teaching are required. Credits: 3 Prerequisites & Notes: EDP 2330 and SED 3330 for Middle Level Education majors, MLE 3110.

BIO 3450A - Independent Study I. (Arr.-Arr.-1-3) (Credit/No Credit) Individual study on a topic in biology selected by the student under the supervision of an instructor. May be repeated once for credit. Prerequisites & Notes: BIO 1550G, and permission of the department chairperson and instructor. This course is not intended for students who wish to complete a research project. Credits: 1 to 3

BIO 3450B - Independent Study II (Arr.-Arr.-1 -3) (Credit/No Credit) Individual study on a topic in biology selected by the student under the supervision of an instructor. May not be repeated for elective credit. Prerequisites & Notes: BIO 1550G and permission of the department chairperson and instructor. This course is not intended for students who wish to complete a research project. Must complete BIO 3450A twice. Credits: 1 to 3

BIO 3451A - Undergraduate Research I. (Arr.-Arr.-1-3) (Credit/No Credit) Original research in Biological Sciences conducted in consultation with a faculty mentor. Students will conduct a research project using current scientific protocols. Hypothesis formation, bench work, data collection/analysis become the responsibility of each student. Written report required. May be repeated once for credit to a maximum of three semester hours for elective credit in the major from BIO 3451A and 3451B. Prerequisites & Notes: BIO 1550G and approval of instructor and department chairperson. Credits: 1 to 3

BIO 3451B - Undergraduate Research II (Arr.-Arr.-1-2) (Credit/No Credit) Original research in Biological Sciences conducted in consultation with a faculty mentor. Students will conduct a research project using current scientific protocols. Hypothesis formation, bench work, data collection/analysis become the responsibility of each student. Written report required. May be repeated once for credit to a maximum of three semester hours for elective credit in the major from BIO 3451A and 3451B. Prerequisites & Notes: BIO 1500G and approval of instructor and department chairperson. Must have completed BIO 3451A twice. Credits: 1 to 2

BIO 3460 - Clinical Rotation. (3-3-4) Practical experience for pre-health professional tract students to obtain the hands-on experience needed to be competitive for admission to professional schools. The course requires at least 3 hours of clinical time per week that is arranged over the semester. Students will rotate between different health professional settings. In addition to the clinical rotation, students will meet with the course instructor 3 hours per week to reflect on components of their rotation. Prerequisites: A grade of &ldquoB&rdquo or better in BIO 2210 and BIO 2220, or BIO 3620. May not have previously taken BIO3960A-001 (CRN#93104 or CRN#39559 or CRN#99378).

BIO 3510 - Plant Physiology. (2-4-4) The study of water relations, mineral nutrition, phytohormones, photosynthesis, respiration and physiological ecology. Credits: 4 Prerequisites & Notes: BIO 1500G and BIO 3120 or CHM 3450.

BIO 3520 - Animal Physiology. (3-3-4) A study of basic principles of animal physiology with emphasis on mammalian organ systems. WI Credits: 4 Prerequisites & Notes: BIO 3120 or CHM 3450.

BIO 3612 - Plant Evolution and Diversity. (2-3-3) The morphology, anatomy, life cycles, and evolutionary history of plants, including bryophytes, ferns and fern allies, gymnosperms, and angiosperms. WI Credits: 3 Prerequisites and Notes: BIO 1550G.

BIO 3620 - Functional Comparative Anatomy. (2-4-4) A study of vertebrate anatomy, emphasizing the evolution of form and function of structures. Laboratory dissection of representative vertebrates. Credits: 4 Prerequisites & Notes: BIO 1550G and junior-level standing.

BIO 3622 - Embryology. (2-4-4) Systematic examination of the mechanisms that underlie animal development from a single-cell to a multicellular organism. Morphological studies emphasize selected embryonic stages in echinoderms, amphibians, birds, and mammals. Credits: 4 Prerequisites & Notes: BIO 1550G.

BIO 3624 - HistologyBIO 3624 - Histology. (1-4-3) The structure and function of tissues, primarily human. Laboratory study is combined with discussion of normal tissue structures. Credits: 3 Prerequisites & Notes: BIO 2210 and BIO 2220, or permission of the instructor.

BIO 3710 - Plant - Animal Interactions. (3-0-3) S-even-numbered years. The course examines diverse interactions between plants and animals, including exploitative, commensal, and mutualistic relationships, as well as those indirectly affecting or mediated by third parties involved in multi-trophic interactions, such as fungi and bacteria. Credits: 3 Prerequisites and Notes: BIO 1550G.

BIO 3740 - Clinical Mycology. (3-0-3) F. An introduction to the fungi which cause superficial, subcutaneous and systemic infections in humans and other vertebrate organisms with an emphasis on the history, classification, morphology, epidemiology, pathogenesis, histopathology, clinical treatment and prevention of the diseases fungi cause. Prerequisites: BIO 1550G or permission of instructor.

BIO 3810 - Freshwater Ecology. (1-4-3) The physical environment and biological communities involved in fresh water ecosystems. Credits: 3 Prerequisites & Notes: BIO 1550G, CHM 1310G, and 1315G.

BIO 3850 - Environmental Health and Sustainability. (3-3-4) On Demand. An introduction to the principles of environmental sciences for biology majors. This course investigates the foundations of environmental science with particular attention to environmental problems from a biological perspective and the costs and benefits to their &ldquosolutions&rdquo from the local to global scale. This course pays particular attention to how to analyze, interpret and present scientific information in the life sciences. Prerequisites & Notes: BIO 1550G.

BIO 3888G - Subtropical and Marine Ecology. (Arr.-Arr.-4) S. The identification, natural history, and ecology of the flora and fauna of the Bahamas. This course will include a mandatory, week- long field experience to Fofar Field Station on Andros Island, Bahamas. Preference given to students with relevant experience in biology. Credits: 4 Prerequisites and Notes: Permission of instructor.

BIO 3950 - Vertebrate Natural History. (2-3-3) The natural history of vertebrates including distribution, reproduction, behavior, evolution, and phylogeny. WI Prerequisites & Notes: BIO 1550G. Credits: 3

BIO 3952 - Invertebrate Natural History. (2-3-3) Natural history, including distribution and habitat utilization reproduction, behavior, and life histories identification, classification and evolution of terrestrial and aquatic invertebrates. Emphasis on major groups in the Midwest. WI Credits: 3 Prerequisites & Notes: BIO 1550G.

BIO 3960A - Special Topics. (Arr.-Arr.-1-4) On Demand. Reading discussions, reports, on-campus and off-campus fieldwork on topics in biological sciences not ordinarily treated in existing courses. Topics to be announced. May be repeated once to a maximum of eight semester hours of credit in BIO 3960 courses with permission of the department chairperson. Prerequisites: BIO 1500, 1550G and permission of the department chairperson and instructor. Credits: 1 to 4

BIO 3960B - Special Topics. (Arr.-Arr.-1-4) On Demand. Reading discussions, reports, on-campus and off-campus fieldwork on topics in biological sciences not ordinarily treated in existing courses. Topics to be announced. May be repeated once to a maximum of eight semester hours of credit in BIO 3960 courses with permission of the department chairperson. Prerequisites: BIO 3960A (twice) and permission of the department chairperson and instructor. Credits: 1 to 4

BIO 3970 - Study Abroad. (Arr.-Arr.-1-15) See STA 3970. Credits: 1 to 15.

BIO 3985 - Vertebrate Zoology. (3-0-3) A survey of the evolution, diversity and conservation of fish, amphibians, reptiles, birds and mammals, with special focus on North American and Illinois species. This course is designed for non-Biological Science majors, specifically non- traditional EIU students, and has no lab component.

BIO 3986 - Biotechnology: Hype/Reality. (3-0-3) A study of the current state of biotechnology. This course begins with understanding genes and gene expression and leads into a variety of current topics including the Human Genome Project, gene therapy, cloning, stem cell research, genetically modified organisms, and the advantages and potential threats of biotechnology.

BIO 3987 - Introduction to Evolution (3-0-3) A survey of the history, supporting evidence, mechanisms and implications of evolutionary theory. This is a course for non-majors interested in understanding one of the seminal ideas of modern civilization. Does not count towards the Biological Sciences major or minor.

BIO 3988 - Animal Welfare: Ethics and Issues. (3-0-3) An Introduction to animal welfare and related issues including behavior, physiology, human- animal interaction, ethics and standards. This course is for students interested in developing the ability to objectively assess animal welfare of species in production, zoos, research, and companion animals. Does not count towards the Biological Sciences major or minor.

BIO 3989 - Biology of the Human Body. (3- 0-3) A course for non-science majors that covers basic human biology. The course will cover a brief background of the levels of organization (molecular, cellular, tissue). The main focus will be over the functions and physiology of the organ systems. Does not count toward Biological Sciences Major or Minor, and does not have a lab component. Not open to those with credit for, or registration in BIO 2001G (Human Physiology). Does not count towards the Biological Sciences major or minor.

BIO 3990 - A Survey of Human Diseases: An Organ System Approach to the Human Body. (3-0-3) This course will focus on the clinical manifestations of various diseases. It will also introduce students to the physiology and anatomy of the human body, system by system. We will survey most diseases that afflict the major eleven systems of the body. No prerequisites, but an introductory Biology course is highly recommended. Does not count towards the Biological Sciences major or minor.

BIO 3991 - Introduction to Sustainability. (3-0-3) The course will focus on the impacts of human populations on the environment with particular focus on energy, sustainable resource consumption, and pollution. The course will develop a general understanding of how humans exploit natural resources and the technologies used in traditional and alternative energy production and the biogeochemistry of sustainable agriculture and freshwater usage. We will spend considerable time detailing the processes of extracting, refining, and distributing fossil fuels. We will then study the technologies being used to generate alternative energy solutions, including an explanation of how gasification of biomass, refining of bio-fuels, photovoltaic cells and wind turbines function. We will compare these traditional technologies to the alternative solutions to assess their impact on carbon cycling as well as the economic feasibility and efficiency of these technologies, considering both energy output and cost savings through the possible reduction of economic externalities. Additionally, we will analyze the biogeochemical processes that are associated with agriculture, development, and resource extraction that influence pollution and eutrophication of waterways. We will then examine the biochemical processes that cause algal blooms, acidification, and die-offs resulting from this run off. Lastly, the class will examine environmental pollutants with an emphasis on greenhouse gas emissions and particulate matter resulting from energy consumption with a specific focus on energy generation, carbon sequestration, atmospheric carbon level, and ocean acidification.

BIO 3995 - Introductory Statistics for the Health Sciences. (3-0-3) This course is designed to give the students an introduction to simple analytical techniques for the statistical analysis of data from the health sciences. Basic descriptive statistics, graphical data analysis, hypothesis testing of means, correlation, regression, simple analysis of variance and categorical data analysis will be covered. Emphasis will be on assumptions and when to use the specific procedures rather than on proofs or statistical theory. Correct use and interpretation of statistical procedures will be emphasized in the laboratory exercises. NOTE: this course does NOT count toward the Biological Sciences majors or minor.

BIO 3996 - Antibiotic Resistant Bacteria.This course will describe the cellular targets of antibiotics, the genetic basis of antibiotic resistance, the evolution of drug-resistant bacteria, and steps that can be taken to slow this process.

BIO 4275 - Internship. (Arr.-Arr.-6 OR 12) (Credit/No Credit) Employment experience in one or more phases of the Biological Sciences for one semester with an agency or firm approved by the environmental biology coordinator. A formal written report of the internship experience is required. The course may be repeated once for a total of not more than 12 hours. Prerequisites & Notes: Only open to students in Environmental Biology option. At least 90 semester hours of work in Biological Sciences program completion of at least one advanced ecology course minimum cumulative GPA or major GPA of 2.25 approval of the environmental biology coordinator. Credits: 6 or 12

BIO 4400A - Teaching in the Lab I. (Arr.- Arr.-1) (Credit/No Credit) Experience assisting and supervising in a biological lab setting. Students work under the direction of the course instructor. May be repeated for credit once. Prerequisites & Notes: Completion of the course in which the student is assisting with a grade of B or higher and permission of the instructor. Credits: 1

All Sections for this Course

BIO 4400B - Teaching in the Lab II. (Arr.- Arr.-1) (Credit/No Credit) Experience assisting and supervising in a biological lab setting. Students work under the direction of the course instructor. May not be repeated. Prerequisites & Notes: Completion of 2 semester hours of BIO 4400A Credits: 1

All Sections for this Course

BIO 4444A - Honors Independent Study I. (Arr.-Arr.-1-3) Consideration of special topics in Biological Sciences. Special emphasis on an area of interest to the student approved by faculty supervisor and Departmental Honors Coordinator. Prerequisites & Notes Admission to the Departmental Honors Program and permission of the Departmental Honors Coordinator. May be taken twice for credit. Credits: 1 to 3

BIO 4444B - Honors Independent Study II. (Arr.-Arr.-1-3) Consideration of special topics in Biological Sciences. Special emphasis on an area of interest to the student approved by faculty supervisor and Departmental Honors Coordinator. Prerequisites & Notes Admission to the Departmental Honors Program and permission of the Departmental Honors Coordinator. May be taken twice for credit. Must have completed BIO 4444A twice. Credits: 1 to 3

BIO 4444D - Honors Independent Study IIII. (Arr.-Arr.-1-3) Consideration of special topics in Biological Sciences. Special emphasis on an area of interest to the student approved by faculty supervisor and Departmental Honors Coordinator. Prerequisites & Notes Admission to the Departmental Honors Program and permission of the Departmental Honors Coordinator. Must have completed BIO 4444B twice. Credits: 1 to 3

BIO 4555A - Honors Research I. (Arr.-Arr.-1-3) Original experimental or theoretical research in Biological Sciences conducted in consultation with a faculty mentor. Students will conduct a research project using current scientific protocols. Prerequisites & Notes Admission to the Departmental Honors Program and permission of the Departmental Honors coordinator. May be taken for credit up to six semester hours. May be taken twice for credit. Credits: 1 to 3

BIO 4555B - Honors Research II. (Arr.-Arr.-1-3) Original experimental or theoretical research in Biological Sciences conducted in consultation with a faculty mentor. Students will conduct a research project using current scientific protocols.Prerequisites & Notes Admission to the Departmental Honors Program and permission of the Departmental Honors coordinator. May be taken for credit up to six semester hours. Must have completed BIO 4555A twice. Credits: 1 to 3

BIO 4555D - Honors Research III. (Arr.-Arr.-1 -3) Original experimental or theoretical research in Biological Sciences conducted in consultation with a faculty mentor. Students will conduct a research project using current scientific protocols. Prerequisites & Notes Admission to the Departmental Honors Program and permission of the Departmental Honors coordinator. May be taken for credit up to six semester hours. Must have completed BIO 4555B twice. Credits: 1 to 3

BIO 4644 - Honors Thesis. (Arr.-Arr.-3) Original research in preparation of a thesis on a topic in Biological Sciences approved by faculty supervisor and the Departmental Honors Coordinator. Students in the Biological Sciences Honors Program must take at least 3 credit hours of thesis. Credits: 3 Prerequisites & Notes Admission to the Departmental Honors Program and permission of the Departmental Honors Coordinator.

BIO 4666 - Honors Seminar. (2-0-1) Areas of investigation which require integration of Biological Sciences and research will be addressed. Credits: 1 Prerequisites & Notes: Admission to the Departmental Honors Program and permission of the Departmental Honors coordinator. May be taken twice for credit.

BIO 4750 - Statistical Analysis of Scientific Data. (2-2-3) Methods of quantitative analysis of biological data at the population level. Emphasis placed on practical applications of statistical analysis. Credits: 3 Prerequisites & Notes: College algebra or permission of instructor.

BIO 4751 - Advanced Molecular Cell Biology. (3-0-3) A study of the molecular basis of intracellular processes, including gene regulation and expression molecular biosyntheses and transport cell motility and adhesion cell cycle regulation and intracellular signaling, using case studies from current scientific literature. Credits: 3 Prerequisites & Notes: BIO 3120 and 3200.

BIO 4810 - Plant Ecology. (1-4-3) The application of investigative techniques to the study of the structure and successional patterns of plant communities. WI Credits: 3 Prerequisites & Notes: Two years of Biological Sciences.

BIO 4812 - Fisheries Ecology and Management. (2-3-3) Relationships of fish with biotic and abiotic components of their environment. Role of fishes in aquatic ecosystems and current management strategies. Credits: 3 Prerequisites & Notes: BIO 3180 BIO 4750 recommended.

BIO 4814 - Conservation Biology. (3-0-3) Study of the application of ecological and genetic principles to the preservation and conservation of biological diversity. Topics will include the demography and genetics of small populations, population viability, island biogeography, and the design of nature reserves. WI Credits: 3 Prerequisites & Notes: BIO 3200 and 3180.

BIO 4816 - Study of Biotic Communities. (2-Arr.-3) The study of selected biotic communities in Illinois and surrounding states. May be repeated for credit if a different topic is taught. Credits: 3 Prerequisites and Notes: Major in Biological Sciences 12 semester hours in Biological Sciences including BIO 3180 or 4810 or permission of the instructor.

BIO 4818 - Environmental Microbiology. (2-4-4) An introduction to the principles, applications, and methodologies of environmental microbiology with emphasis on microbial interactions with animals and plants, on the microbiology of air, water, sewage, and soils, and on the role of microorganisms in biogeochemical cycling. The use of microorganisms in the bioremediation of environmental pollutants and in the recovery and enhancement of environmental resources will also be considered. Credits: 4 Prerequisites & Notes: BIO 3300 or equivalent or permission of the instructor.

BIO 4820 - Spatial Analysis for Environmental Sciences. (3-3-4) F. An introduction to how spatial data are synthesized and interpreted in the environmental sciences. The course will focus on interpretation of remotely sensed data, point pattern analysis, and digital elevation models. Students will become familiar using appropriate software such as Geographic Information Systems (GIS), statistical and modeling software. Credits: 4 Prerequisites & Notes Permission of the instructor.

BIO 4830 - Comparative Vertebrate Physiology. (3-0-3) A comparison of physiological activities of vertebrates and adaptations to their natural environment. Credits: 3 Prerequisites & Notes: BIO 3520 and CHM 2430 CHM 3300 recommended.

BIO 4832 - Animal Behavior. (3-3-4) Theoretical and experimental studies of the principles of animal behavior. Credits: 4 Prerequisites & Notes: Sixteen semester hours of Biological Sciences or permission of the instructor.

BIO 4833 - Neurobiology of Diseases. (4-0- 4) Su. This course will cover in- depth the biology of important neurological and psychiatric diseases. Prerequisite: A grade of &ldquoC&rdquo or better in BIO 3120. May not have previously taken BIO5970D-001 (CRN#60736).

BIO 4834 - Neurobiology. (3-0-3) A study of the structure and function of neurons, the principal cells of the nervous system, at the molecular and cellular level. This course will emphasize neurobiological aspects of learning, memory, and behavior. Credits: 3 Prerequisites & Notes: BIO 3120 or permission of the instructor.

BIO 4835 - Advanced Neurobiology. (3-0-3) S. This course will cover advanced topics on molecular, cellular and physiological aspects of brain structure and function during health and diseases. Prerequisite: A grade of &ldquoC&rdquo or better in BIO 4834. May not have previously taken BIO5460H-001 (CRN#33735) or BIO3960A-003 (CRN#32704).

BIO 4836 - Pathogenic Microbiology. (2-4-4) An introduction to the role and activities of pathogenic microorganisms in the diseases of humans, animals, and plants with emphasis on the history, classification, morphology, nutrition and growth, metabolism, genetics, and virulence factors of disease-causing prokaryotes as well as the epidemiology, diagnosis, treatment, and prevention of the diseases they cause. The laboratory will emphasize clinical techniques required for the isolation, cultivation, and identification of pathogenic microorganisms. Credits: 4 Prerequisites & Notes: BIO 3300 or equivalent or permission of the instructor.

BIO 4840 - Resource Management and Environmental Assessment. (2-3-3) S. This course will explore the concepts in natural resource management including data acquisition and how environmental regulations are used in integrated ecological assessments at the federal and state level. Credits: 3 Prerequisites and Notes: Permission of the instructor.

BIO 4842 - Wildlife Ecology and Management. (3-0-3) S. Wildlife Ecology. Principles of managing wildlife resources with emphasis on population ecology, habitat management and the social context of wildlife management. Prerequisite: BIO 3180 or permission of instructor.

BIO 4850 - Wildlife Techniques. (2-3-3) F. Instruction in current field, lab and analytical techniques in wildlife biology. This will include: population and biodiversity estimation, capture and marking, behavioral observations, age estimation, condition assessment, biotelemetry, and habitat assessment. BIO 5372 and BIO 3960 are equivalent courses. Students will not be allowed to earn credit in BIO 4850 if they already have received credit for BIO 5372 or BIO 3960. Grade and credit hours for this course will be removed if student already has credit for those courses. Prerequisites: Junior-level standing and &ldquoC&rdquo or better in BIO 3950 or BIO 3180 or permission of instructor. BIO 4750 recommended. WI

BIO 4892 - Introduction to Paleobotany. (3-2-4) Introduction to the origin and theories of evolution, diversification, radiation, and paleogeography of plants through time, with special reference to vascular plants. Field work. Credits: 4 Prerequisites & Notes: BIO 1550G or permission of instructor. Credit not granted for both GEO 4892 and BIO 4892.

BIO 4914 - Plant Anatomy. (2-3-3) F. A comprehensive study of the internal structure of vascular plants, focusing primarily on the anatomy of seed plants. The course emphasizes plant development and structural-functional relationships. The laboratory component of this class will introduce students to basic microtechniques and emphasize microscopic plant structure. Restriction: Junior status. Prerequisite: BIO 1550G or at least 9 semester hours in the biological sciences major.

BIO 4920 - Medicinal Plants. (3-0-3) On Demand. A worldwide survey of the past and present human utilization of plants and plant products as medicines, including their chemical constituents and natural and cultural history. WI Prerequisite: BIO 1550G or equivalent.

BIO 4940 - Phycology. (2-3-3) Introduction to algal biology emphasis is placed on freshwater algae including the study of classification, life-history, physiology, ecology, and evolution. Credits: 3 Prerequisites & Notes: BIO 1550G.

BIO 4942 - Mycology. (2-3-3) Survey of the fungi specifically the characteristics and phylogenetic relationships of the major groups of fungi, their structure, growth and development, physiology, reproduction and dispersal, genetics, ecological role and economic importance. WI Credits: 3 Prerequisites & Notes: BIO 1550G.

BIO 4944 - Lichens. (2-3-3) Systematic survey of the lichens, including their physiology, growth and development, reproduction, ecology, economic importance, and classification. Field trips required. WI Credits: 3 Prerequisites & Notes: BIO 1550G.

BIO 4946 - Bryology. (1-4-3) The structure, identification, life-history, and importance of the mosses and liverworts. Fall field trip is required. Credits: 3 Prerequisites & Notes: BIO 1550G.

BIO 4948 - Plant Taxonomy. (1-4-3) The classification and evolution of flowering plants. Emphasis on learning common families and field techniques, especially specimen preparation. Saturday field trip required. Credits: 3 Prerequisites & Notes: BIO 1550G

BIO 4950 - Ichthyology. (2-3-3) Study of the anatomy, physiology, systematics and zoogeography of fishes. Credits: 3 Prerequisites & Notes: BIO 3180 or BIO 3950 or permission of instructor.

BIO 4952 - Herpetology. (2-3-3) S-even-numbered years. A survey of the amphibian and reptilian classes, with emphasis on the extant herpetofauna of ¿Mid-West¿ region of the North America. Material presented in lecture will be supplemented with laboratory examinations of preserved specimens and field trips to regional sites for surveying available taxa. Prerequisites & Notes: BIO 3180 or BIO 3950 and junior-level standing.

BIO 4954 - Ornithology. (2-3-3) The identification, classification, distribution, and natural history of Midwestern birds. WI Credits: 3 Prerequisites & Notes: BIO 3180 or BIO 3950 or permission of instructor.

BIO 4956 - Mammalogy. (2-3-3) F. A study of mammals with emphasis on mammalian evolution, classification, distribution, physiology, natural history and ecology. Prerequisite: BIO 3180 or permission of instructor.

BIO 4958 - Parasitology. (3-3-4) F. A study of parasitism as a symbiotic relationship to include identification, systematics, life histories, pathology, and control of common parasites of animals, including humans. Prerequisite: BIO 1550G or permission of instructor.

BIO 4960 - Wetland and Aquatic Vascular Plants. (2-3-3) F-odd-numbered years. The study of the taxonomy and ecology of wetland and aquatic plants, emphasizing those occurring in the Midwest. Field trips required. Credits: 3 Prerequisites & Notes: BIO 1550G

BIO 4964 - Entomology. (3-3-4) F. A study of insects, and closely related arthropods, with regard to identification, ecology, morphology, physiology, and evolution. Methods of collection and specimen preparation are included. WI Prerequisites and Notes: BIO 1550G or permission of instructor. Course may not be repeated. Credits: 4

BIO 4984 - Organic Evolution. (3-0-3) Fundamental principles of organic evolution stressing historical fact, evidences for and processes common to all biota. WI Credits: 3 Prerequisites & Notes BIO 1550G, 3200, and senior-level standing.

BIO 5150 - Graduate Seminar. (2-0-1). Seminar in current biological sciences literature. Required of all biological sciences graduate students. May be repeated, with maximum of two hours credit applied to graduate degree.

BIO 5200 - Stream Ecology. (3-0-3) A description of the physical, chemical, and biological characteristics in streams and rivers including an integrated study of the environmental factors affecting the composition and distribution of biota. The course will also emphasize the application of ecological principles in aquatic ecosystem protection and management. Prerequisites and Notes: BIO 3800. Credits: 3

BIO 5202 - Behavioral Ecology. (3-0-3) The study of natural selection and how it relates to adaptive strategies of behavioral phenomena in animal populations in response to the biotic and abiotic environment. Emphasis will be placed on theoretical aspects of current topics in behavioral ecology.

BIO 5204 - Ecotoxicology and Biological Monitoring of Pollution.(1-4-3) Characterization of pollutants and their qualitative and quantitative effects on biota. Includes laboratory investigation of biological and ecotoxicological effects of pollution. Prerequisites and Notes: 12 semester hours in the biological sciences and one year of college chemistry.

BIO 5206 - Advanced Limnology. (2-3-3) Investigation of the functioning of lakes and reservoirs with specific regard to the relative roles of physical, chemical and biological factors in determining species distribution and abundance. Emphasis will be placed on lake and reservoir management and restoration.

BIO 5208 - Population Ecology. (3-0-3) This course covers the structure and dynamics of populations with an emphasis on understanding how reproduction, mortality and dispersal interact to control fluctuations in population size and structure. Special emphasis will be placed on the use of models to address specific applications in conservation biology and natural resource management. Prerequisites and Notes: BIO 3800.

BIO 5210 - Insect Morphology and Physiology. (3-3-4) An in-depth examination of the physiological processes and morphological adaptations by which insects function in their physical, chemical, and biological environments. Experimental methods and research equipment appropriate to the discipline will be introduced. Course available Spring 2006. Prerequisites and Notes: BIO 3720 or equivalent, or consent of instructor.

BIO 5225 - Systematics. (3-2-3) The course provides a comprehensive survey of the theory and methodology of biological systematics as currently practiced. The course emphasizes practical experience in the acquisition and analysis of systematic data, understanding of biological patterns in the context of phylogenetic hypotheses, and hands-on experience using several computer programs in systematic studies. Prerequisites and Notes: 16 semester hours of biological science.

BIO 5232 - Plant Cell and Tissue Culture. (2-3-3) Techniques in the initiation, propagation, maintenance, preservation, and genetic improvement of plant cells, tissues, and organs in vitro. Prerequisites and Notes: BIO 3200 is recommended, but it is not required.

BIO 5250 - Biological Microtechnique. (3- 3-4) F. Techniques in preparing biological specimens for sectioning, staining, and visualization with a microscope. Light and scanning electron microscopy will be utilized. Prerequisite: At least 16 semester hours of biological sciences or permission of the instructor.

BIO 5333 - Bioenergy and Bioresources. (2-2-3) This course explores the components and properties of algae and plants that make them useful for bioenergy applications. Sustainable production of crops and species is discussed, along with the environmental impact of their growth, harvest and utilization. Prerequisite: Admission to an MS in the College of Sciences or admission to the MS in Sustainable Energy.

BIO 5340 - Population Genetics. (3-2-3) Theoretical principles of population genetics and application of experimental methodology using quantitative and analytical methods. Laboratory topics: nucleic acid analyses, enzyme electrophoresis, polytene chromosome examinations, and statistical analyses. Prerequisites and Notes: BIO 3200 and either BIO 4750, MAT 2250C or equivalent.

BIO 5360 - Field Mycology. (3-3-4) The collection, identification, and ecology of macrofungi. Prerequisites and Notes: BIO 1200G.

BIO 5366 - Biogeography. (3-0-3) The study of the geographical distribution of organisms, their habitats, and the historical and biological factors that produced them. Prerequisites and Notes: 16 semester hours of biological sciences or permission of the instructor.

BIO 5380 - Landscape Ecology. (2-2-3) Introduction to the principles and application of landscape ecology, the study of pattern and heterogeneity across large spatial scales. Emphasis is placed on how to characterize pattern, how it develops and changes through time, and its implications for populations, communities, and ecosystem processes. Prerequisites and Notes: BIO 3800 or permission of instructor.

BIO 5381 - Advanced Biostatistics. (3-0-3) Survey of methods of analysis of univariate and multivariate data from biological systems. Techniques will include: survival analysis, ANOVA, MANOVA, ordination methods and regression analysis. Focus will be on the practical application of techniques. Prerequisites and Notes: BIO 4750 or MAT 2250G or permission of instructor

BIO 5385 - Experimental Design for the Laboratory and Field. (2-2-3) F. Experimental Design. This course will explore the design, implementation and analysis of scientific experiments in biology from a statistical perspective for field and laboratory based studies. The course will focus on the use of modern statistical approaches that include mixed-model, permutational and multi- model procedures within the context of readily available statistical software packages. Prerequisite(s): BIO 4750 or MAT 2250G Not concurrently.

BIO 5400 - Cell Physiology. (3-3-4) A study of the fundamental physical and chemical processes which underlie cellular structure and function. Prerequisites and Notes: BIO 3520 and one course in organic chemistry.

BIO 5402 - Advanced Plant Physiology I, Plant Growth and Development. (2-3-3) The growth and development of seed plants from germination through maturation with emphasis on water relations, nitrogen metabolism, and environmental influences. Prerequisites and Notes: BIO 3510 and CHM 2430 biochemistry recommended.

BIO 5404 - Advanced Plant Physiology II, Metabolism. (2-3-3) The principles of photosynthesis, respiration, and organic translocation. Prerequisites and Notes: BIO 3510 and CHM 2430 biochemistry recommended.

BIO 5406 - Endocrinology. (3-3-4) A study of endocrine glands and mechanisms of hormone action. Prerequisites and Notes: BIO 3520 and CHM 2430.

BIO 5460A - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460B - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460D - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460E - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460F - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460H - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460I - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460J - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460K - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460L - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460M - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460O - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460P - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460Q - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460T - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460U - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460V - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460W - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460X - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460Y - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5460Z - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5900A - Research in Biological Sciences. (Arr.-Arr.-1 to 6) (Credit/No Credit) Intended for thesis option students conducting original research in consultation with a thesis advisor. May be repeated once for a maximum of eight semester hours in BIO 5900A and BIO 5900B. NOTE: A maximum of nine semester hours in combination of 5900, 5950, and 5990 A/B may be applied to the graduate degree. Students not writing a thesis are ineligible to register for this course. Prerequisites & Notes: Completion of the thesis proposal form and permission of the Coordinator, Biological Sciences Graduate Program Committee. Credits: 1 to 6

BIO 5900B - Research in Biological Sciences. (Arr.-Arr.-1 to 6) (Credit/No Credit) Intended for thesis option students conducting original research in consultation with a thesis advisor. May be repeated once for a maximum of eight semester hours in BIO 5900A and BIO 5900B. NOTE: A maximum of nine semester hours in combination of 5900A/B, 5950, and 5990 may be applied to the graduate degree. Students not writing a thesis are ineligible to register for this course. Prerequisites & Notes: Completion of BIO 5900A twice. Credits: 1 to 6

BIO 5900L - Research in Biological Sciences. (Arr.-Arr.-1 to 6) (Credit/No Credit) Intended for thesis option students conducting original research in consultation with a thesis advisor. May be repeated once for a maximum of eight semester hours in BIO 5900A, BIO 5900B, BIO 5900L and BIO 5900M. NOTE: A maximum of nine semester hours in combination of 5900, 5950, and 5990 A/B may be applied to the graduate degree. Students not writing a thesis are ineligible to register for this course. Prerequisites & Notes: Completion of the thesis proposal form and permission of the Coordinator, Biological Sciences Graduate Program Committee. Credits: 1 to 6

BIO 5900M - Researching Biological Sciences. (Arr.-Arr.-1 to 6) (Credit/No Credit) Intended for thesis option students conducting original research in consultation with a thesis advisor. May be repeated once for a maximum of eight semester hours in BIO 5900A, BIO 5900B, BIO 5900L, and BIO 5900M. NOTE: A maximum of nine semester hours in combination of 5900, 5950, and 5990 may be applied to the graduate degree. Students not writing a thesis are ineligible to register for this course. Prerequisites & Notes: Completion of BIO 5900A or BIO 5900L twice. Credits: 1 to 6

BIO 5950 - Thesis. (Arr.-Arr.-3 or 6) (Credit/No Credit) May be repeated for credit up to six semester hours. NOTE: For thesis option students, a maximum of nine semester hours in a combination of 5900, 5950, and 5990 may be applied to the graduate degree.

BIO 5951 - Non-credit Thesis. (0-0-0). Non-credit Thesis. The purpose of this course is to allow a graduate student to remain continuously enrolled and access services required to complete the thesis after completing the maximum number of hours of credit for thesis [5950], research [5900], and independent study [5990] in a thesis option. Credits: 0

BIO 5970A - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970B - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970D - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970E - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970F - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970H - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970I - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970J - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970L - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970M - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970O - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970P - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970Q - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970T - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970U - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970V - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970W - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970X - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970Y - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5970Z - Special Topics in Biological Sciences. (Arr.-Arr.-1-4) On Demand. Specific areas within the cohort disciplines will be given intensive study through lectures, lab, readings, reports, papers, and discussion. Prerequisites & Notes: Student must be eligible to take graduate courses and permission from instructor. Credits: 1 to 4

BIO 5980A - Graduate Internship in Biological Sciences. (Arr.-Arr.- 1-6) (Credit/No Credit) A graduate-level employment experience in the biological sciences with an agency, firm or facility approved by a faculty advisor and the coordinator of the Biological Sciences Graduate Program Committee. A written report on the internship experience is required at the completion of 6 credit hours. Prerequisites and Notes: For internship option students, at least 20 semester hours of graduate credit in the Biological Sciences Graduate Program. May be repeated once for a maximum of six semester hours in BIO 5980A, BIO 5980B and BIO 5980D. Note: For internship option students, a maximum of nine semester hours in a combination of 5980A/B/D and 5990 may be applied to the graduate program. Credits: 1 - 6

BIO 5980B - Graduate Internship in Biological Sciences. (Arr.-Arr.- 1-6) (Credit/No Credit) A graduate-level employment experience in the biological sciences with an agency, firm or facility approved by a faculty advisor and the coordinator of the Biological Sciences Graduate Program Committee. A written report on the internship experience is required at the completion of 6 credit hours. Prerequisites and Notes: For internship option students, at least 20 semester hours of graduate credit in the Biological Sciences Graduate Program. May be repeated once for a maximum of six semester hours in BIO 5980A, BIO 5980B and BIO 5980D. Note: For internship option students, a maximum of nine semester hours in a combination of 5980A/B/D and 5990 may be applied to the graduate program. Credits: 1 - 6

BIO 5980D - Graduate Internship in Biological Sciences. (Arr.-Arr.- 1-6) (Credit/No Credit) A graduate-level employment experience in the biological sciences with an agency, firm or facility approved by a faculty advisor and the coordinator of the Biological Sciences Graduate Program Committee. A written report on the internship experience is required at the completion of 6 credit hours. Prerequisites and Notes: For internship option students, at least 20 semester hours of graduate credit in the Biological Sciences Graduate Program. May be repeated once for a maximum of six semester hours in BIO 5980A, BIO 5980B and BIO 5980D. Note: For internship option students, a maximum of nine semester hours in a combination of 5980A/B/D and 5990 may be applied to the graduate program. Credits: 1 - 6

BIO 5990A - Independent Study I. (Arr.-Arr.-1 to 6) (Credit/No Credit) Advanced studies in a selected field of the biological sciences other than the thesis or internship. May be repeated once for a maximum of six semester hours of credit. NOTE: Students who do not write a thesis may apply a maximum of three semester hours of credit toward the graduate degree. Credits: 1 to 6

BIO 5990B - Independent Study II. (Arr.-Arr.-1 to 6) (Credit/No Credit) Advanced studies in a selected field of the biological sciences other than the thesis or internship. May be repeated once for a maximum of six semester hours of credit. NOTE: Students who do not write a thesis may apply a maximum of three semester hours of credit toward the graduate degree. Prerequisites & Notes: Completion of BIO 5990A twice Credits: 1 to 6

BIO 5991 - Non-credit Independent Study. (0-0-0) The purpose of this course is to allow a graduate student to remain continuously enrolled as an auditor and access services required to complete the degree after completing all degree requirements except for completion of examinations or other non-course capstone requirements. Candidates in thesis options use non-credit thesis (5951). Prerequisites: Candidate must retain degree seeking status and secure permission of the department chair or graduate coordinator. Credits: Audit only.


Proteus species- Overview

Proteus species are Gram-negative aerobic bacteria . Their scale is between 0.4 and 0.8 μm in diameter and between 1.0 and 3.0 μm in length. They are named on the basis of their capacity to undergo colonial morphological changes. Proteus strains are able to grow in temperatures ranging from 10 to 43 °C. The optimal temperature for Proteus is 25 °C. The swarming occurs between 20 and 37 °C.

History of Discovery

  • The first representatives of genus Proteus (P. mirabilis, P. vulgaris) were isolated in 1885 by the German bacteriologist G. Hauser from putrefied meat.
  • The name of genus, proposed by Hauser, goes back to the sea-god of Greek mythology Proteus, famous by his active body transformations. Similarly, discovered microbial culture was capable of rapid changing of its morphology and growth characteristics.

Classification

  • Genus Proteus belongs to the family Enterobacteriaceae.It comprises microbial species P. vulgaris, P. mirabilis, P. myxofaciens, P. рenneri, and P. hauseri.
  • Some other closely related bacteria pertain to genus Providencia (type species – P. rettgeri), and genus Morganella (species M. morganii).

Structure and Properties

  • The bacteria look like straight rods 0.5-2 μm in size without spores and capsule.
  • Most of microbial cells demonstrate striking motility due to the multiple peritrichous flagella.
  • They easily grow on basic nutrient media at 35-37оС, pH 7.2-7.4. Motile bacteria designated as microbial H forms (from German hauch – mist or breath) render swarming growth, when cultured on solid media.
  • Non-motile O-variants produce round-shaped semitransparent colonies. Microbial growth is followed by fishy odor.Culturing on Endo or McConkey agar results in lactose-negative bacterial colonies.
  • Some characteristics of a Proteus culture are swarming and an ammonia smell.
  • Type of respiration – facultatively anaerobic.
  • The bacteria possess versatile biochemical activities. They ferment numerous carbohydrates with acid and gas end products, liquefy gelatin, produce H2S, reduce nitrates to nitrites.
  • The members of Proteus genus have catalase and marked urease activity.
  • Unlike other enterobacteria, they are capable of phenylalanine deamination.

Differentiation of genera Proteus, Morganella and Providencia rests on a number of tests indicated in table

Environmental resistance of Proteus species is rather high. At low temperatures they stay viable for a long time. When heated at 60oС bacteria maintain viability near to 1 h.


Wikipedia:Version 1.0 Editorial Team

In late 2003, Jimmy Wales had proposed making an offline release version of Wikipedia. This group was formed in late 2004 to meet this challenge. Our work involves identifying and organizing articles, and improving and maintaining a core set. Our work does not hinder the existing wiki process for creating and editing articles, but rather it supports that work by providing additional organization. We aim to produce collections that can be used in places where the internet coverage is expensive or non-existent.

See these more detailed related articles:

You are encouraged to join us and help out with one of the projects, or to discuss Wikipedia 1.0 on the talk page. A significant part of our work centers around maintaining the assessment scheme, which is now used on more than six million articles by over 2000 WikiProjects [ dead link ] on the English Wikipedia. It is also being used on other language projects. Generally work on this team is sporadic – periods of hectic activity followed by long periods of waiting! Often work is long and tedious – checking through a list of 22,000 instances of profanities one by one, organizing 10,000 keywords taken from category names, or dealing with technical bugs when the assessment bot fails for no apparent reason. However, it is all worth it in the end.

Our strategy has been intensely debated, but the group has reached a consensus. We elected not to follow the German model. Instead we chose to start with a core of quality articles on key subjects and expand from there. We have produced three test versions: Version 0.5, Version 0.7, and Version 0.8 with the goal of releasing better collections of articles in due course. The next general release is generically referred to as "Release Version" while our first "official" comprehensive release will be called Version 1.0. These collections are then made available for offline use using a reader such as Kiwix, which was chosen as Sourceforge project of the month. The project was on hiatus for several years because of the loss of our main developer. However, as of February 2016, a new group of developers has begun work on upgrading the code and the process, in order to start producing new collections again, especially collections for schools.

Current needs

Although we have much of the requisite system automated, there are still some outstanding tasks:

  • Preparation of a reliable index. If you can write code and you're interested in how to map category trees into a useful index (not as easy as it sounds!) please contact Walkerma.
  • Reviewing manual nominations. Whenever there is a new release being planned, we need volunteers to review a few articles and process them.
  • Propose useful "guide" pages to be added, such as lists and disambiguation pages.
  • Check for vandalism in the selected version-IDs of the articles.
  • Develop nice pages for navigation through the content, such as subject portals.
  • Test the reader software, and find and report bugs.
  • Help with distribution, especially in remote areas without Internet access.

Please let us know on the Talk page if you can help with any of these.

At present, the only active components are:

  • The assessment scheme, which is used by WikiProjects for organizing their content. We are currently looking for someone who can maintain the WP 1.0 bot which updates assessment lists daily as of April 1, 2017, the bot is stalled, and must be run manually. Please contact Walkerma if you wish to help.
  • Production of article selections for schools, in collaboration with various people from Kiwix the One Laptop Per Child organization. Please contact Walkerma if you wish to help.

The last "official" general selection was Version 0.8, which was released on 3 March 2011. We had intended to develop version 0.9, but problems with the code prevented this. One of the long term goals is to produce Version 1.0, which is intended to include a comprehensive index and a version (RevID) quality control system (the latter was used on 0.8).

To select articles, we are mainly using a bot-assisted selection process based on assessment by individual WikiProjects, where articles are selected automatically based on quality and importance project rankings. We have also developed a method to automate the version selection using WikiTrust, to ensure that vandalism does not remain in our offline releases we may also use Flagged Revisions if feasible.

RevID selection

Based on recent discussions (at the 2017 Potsdam hackathon and since), we plan to reactivate RevID selection. Previously code based on WikiTrust was used in Version 0.8, and this appeared to produce a largely vandalism-free collection of articles. This worked by scoring each RevID based on the edits remaining in it, and choosing the most "trustworthy" recent RevID based on the WikiTrust algorithm.

For Versions 0.9 and 1.0, the current proposal is to use a combination of both mw:ORES and WikiTrust, which appear to be somewhat complementary in their methods. As of September 2017, discussions are under way with Prof. Luca de Alfaro (the developer of WikiTrust), who plans to update the code just for RevID scoring/selection (without text markup).

Active projects

If you would like to start a new project, please discuss it on the talk page first before adding it here.


Biology

In this course, students will expand their understanding of God’s complex creation. Students will classify systems to survey living organisms. They will participate in lab activities and simulations to examine the structures and processes in living organisms. By applying concepts in statistics and probability, students will explore the mechanisms for inheritance and variation. Students will also analyze interactions within ecosystems and the effects of human activity. This course has a lab component.

FROM THE TEACHER

“In the beginning, God created the heavens and the earth.” Genesis 1:1

Ever since humans were first created, we have been exploring the wonders of Creation around us. As a child, you were probably curious about all the plants and animals around you. You were acting as a biologist without even knowing it! In this Biology course, we will take a closer look at God’s Creation and discover intricate details about the plant and animal kingdoms.

Just as Adam named all the organisms in the Garden of Eden, we will also be learning how biologists today classify and name all the organisms in Creation.

Join me as we embark on an in-depth adventure into exploring the wonders of God’s Creation!

If there are books and materials for this course, they can be purchased from our Online Bookstore.

Student Feedback

I really liked the fact that there weren’t tests every week, and that the models were split up over a couple weeks. I found this setup very helpful!

Nastassia

I felt like there was a good work load overall, and I loved that the weeks were only four days.

Kaitlyn

This is a great course and I like how it is organized. I am really enjoying science.


Bug fixes

General

  • Copy-Paste:
    • A long-standing, very annoying bug where, when copying an object to the clipboard while also running certain other programs on Linux desktops (mainly clipboard managers), caused multiple export extension dialogs to open, has been fixed, so you can now again use your favorite clipboard manager while also using Inkscape (Commit fe7c68, Bug #575)
    • When copy-pasting some items along with their originals/frames/paths (clones, text-on-path, text-in-a-shape, linked offsets), they are no longer displaced in relation to the pasted original (Commit b93f21, Bug #853)

    MacOS

    • Performance: Packaging has been updated for macOS, which removes a performance regression in Inkscape 1.0.1 (Commit 643286)
    • Icons: File system icons look correct again now (Commit 643286, Bug #1893)
    • Export: PDF export no longer produces unprintable PDF files (Bug #827, Commit 643286)

    Circle Tool

    • Arcs from Inkscape files created with versions older than 1.0 are no longer rendered as slices (Bug #1900)
    • When dragging on an ellipse's handles inside the ellipse to create an arc, Inkscape no longer renders it as a closed slice (Commit def938)

    Eraser Tool

    • A long-standing issue with the Eraser tool painting red lines instead of erasing as soon as the user has interacted with a menu or dialog or another user interface element has been fixed (Bug #2068, Commit 2057bf)

    Live Path Effects

    Mesh Gradient tool

    Filter Editor dialog

    Objects dialog

    Selectors and CSS dialog

    • In addition to multiple crash fixes (see below), the dialog now correctly recognizes style tags inside the documents defs section (Commit 12f4d6, Bug #905)
    • A series of related bugs with text objects was fixed (MR #2434).
      All of the affected actions required a text object to behave like a path, but it behaved like a group, and the action failed. This series of bugs mostly affected new users who were following tutorials which did not work as expected.
      Specifically, the following actions now work again:
      • A text object unioned with itself results in a single path again.
      • Text objects can again be used with other objects in all Boolean operations.
      • Text objects can again be inset and outset.
      • Text objects can again be used to create a Dynamic Offset or a Linked Offset.

      Other Bug fixes

      Packaging

      • AppImage now comes with Python 3.8 (Commit)
      • Snap now uses the system's font cache and thus finds all installed fonts (Commit). Additionally, it can now make use of extensions with custom user interfaces (e.g. InkStitch) (Commit)

      Canvas

      • The zoom correction factor no longer depends on the display unit, so correction works properly for documents that are not in mm (Commit)

      Dialogs

      • The document properties dialog can now be resized even if one is using display scaling on a hidpi screen on Linux

      Rendering

      • Zooming no longer causes artifacts when there is a path with an arc segment with a radius of 0 in the drawing (Commit)

      Tools

      • 3D-box tool:
        • Keyboard shortcuts for changing angles in the 3D-box tool were adjusted to work as documented, even with the Y-axis inverted (Commit)
        • Duplicated circles are now closed properly (Commit)
        • The mass value field is no longer greyed out and can be used (Commit)
        • Simplifying selected gradient stops with Ctrl+L works now (Commit)
        • Path > Reverse now works on subpaths again (Commit)
        • The 'flatten simplify (LPE)' button now only shows up when it can be used (Commit)
        • Keyboard shortcuts with Alt key for rotating objects also work as documented again with the Y-axis inversion (Commit)
        • Objects no longer seemingly jump or scale up when moving multiple of them with snapping turned on (Commit)
        • Default snap delay was set to 0 so snapping will work more precisely (Commit)
        • Line height doesn't change spontaneously when switching tools while having text selected (Commit)

        Import / Export / Save

        • when saving as PDF / PS / EPS + LaTeX, % signs are now properly escaped (Commit)
        • the dpi value for exporting to PNG can be specified as a decimal number again
        • attribute order is no longer reversed when saving as SVG, so comparing two SVG files is easier now (Commit)

        Masking / Clipping

        • When releasing or undoing a mask, objects will no longer become unselectable and will use their own bounding box (Commit)

        Live Path Effects

        • LPE selection dialog looks better now with some desktop themes (Commit)
        • Clone original LPE items now get the cloned or linked item's style by default instead of starting with a black fill. A regression that made it impossible to use text elements as source was fixed. Transforms (moving, stretching, shearing) are handled correctly now. (Commit)
        • Fill between many: option 'fuse coincident points' has been replaced with good defaults (Commit)
        • The Knot LPE allows to switch the direction of self-crossings (Commit)
        • When using the PowerStroke LPE with the join type 'extrapolated arc', the corners no longer have a dent, but are smooth again (Commit)
        • Roughen LPE now works more reliably (Commit)
        • Inkscape no longer becomes unresponsive when selecting an object that is used for the Pattern-Along-Path LPE (Commit)

        Performance

        • Inkscape no longer becomes unresponsive when opening a document with lots of style tags in it (Commit)

        Extensions

        General

        • Relative paths to linked images no longer break when using an extension (Commit)
        • Path elements are now transformed correctly when applying transformation matrices to them (Commit)
        • Text element coordinates are now interpreted correctly, even if they use a different unit than px (Commit) and their (guessed) bounding boxes now consider transforms
        • Extensions that adjust colors now work on groups again (Commit)

        Specific extensions

        • Plot extension and HPGL Output extension no longer have an option to automatically convert objects to path, this is now always done (except for texts) (Commit).
        • When switching plotter pens using the HPGL output extension, the plotter no longer makes a dot with the new pen at the end of the old pen's line (Commit). The extension now works with multiple pens (marked by their layer name in Inkscape) again (Commit).
        • The Interpolate extension now works with the tutorial files again (Commit).
        • The extension Render > Barcode > Datamatrix now renders 64 x 64 datamatrices correctly (Commit).
        • Rendering a 3D Polyhedron no longer gives deprecation warnings (Commit).
        • The Measure Path extension now also works when the Help tab is open when clicking on Apply (Commit
        • Color > Randomize extension now works correctly for the Hue and Lightness parameters
        • The unnecessary Live preview was removed from the Interactive Mockup extension (Commit)
        • The Perspective / Envelope extension now considers transforms (Commit).
        • The Hershey text extension fonts now contain letters needed to plot in Danish (Commit). Additionally, the extension can now better handle line heights (Commit).

        Extension failure fixes

        • … when exporting a document with unknown SVG tags to HTML5 canvas (Commit)
        • … when trying to access a document node with an unknown tag (Commit)
        • … when trying to import a dxf file with a circle / ellipse (Commit)
        • … when using the Perfect Bound Cover extension (Commit)
        • … when using the Mesh Gradient to Path extension (Commit)
        • … when using the JessyInk extension (Commit).
        • … when using the DPI Switcher extension (Commit)

        Extension API changes / Improvements for Extension Developers

        • Shape objects now have an is_visible method (Commit)
        • Documentation extended and improved (Commit, []https://gitlab.com/inkscape/extensions/-/commit/9b21776f7c3d746911dac7305b8e1f2a08e38b70 Commit], Commit, Commit)
        • Use an underscore in front of the name attribute value to mark things that do not need to be available in the .py file (Commit)
        • Shape coordinates are now reported in user units (Commit)
        • inkex.addNS() is no longer required, attributes like inkscape:groupmode can now be used directly, too (Commit)
        • added method getElementByName() to get an object by Inkscape label (Commit)
        • added method getElementsByClass() to get objects by their class name (Commit)
        • added method to create Star shapes (Commit)

        Upcoming deprecations (1.1 will issue a warning, while both the old and the new version will just work in 1.0.1):

        Filters

        Templates

        Markers

        Color management

        Command line

        • the pre-1.0 options --export-[type]= , --file= and --without-gui= now have a fallback and print out a warning (Commit)
        • when converting a pdf to svg on the command line, the poppler text import method no longer changes randomly (Commit)
        • opening files with Windows drive paths (with colons) works again (Commit)
        • background color is now exported to PNG when using --export-background even when --export-background-opacity is not set explicitly (Commit)
        • the tab key can now be used to automatically complete Inkscape command line commands in a Linux terminal (bash completion) (Commit)
        • in command line arguments, "0" and "1" had been inverted. They now mean the correct thing (0 = False, 1 = True) (Commit)

        Contents

        Synthetic biology currently has no generally accepted definition. Here are a few examples:

        • "the use of a mixture of physical engineering and genetic engineering to create new (and, therefore, synthetic) life forms" [2]
        • "an emerging field of research that aims to combine the knowledge and methods of biology, engineering and related disciplines in the design of chemically synthesized DNA to create organisms with novel or enhanced characteristics and traits" [3]
        • "designing and constructing biological modules, biological systems, and biological machines or, re-design of existing biological systems for useful purposes" [4]
        • “applying the engineering paradigm of systems design to biological systems in order to produce predictable and robust systems with novel functionalities that do not exist in nature” (The European Commission, 2005) This can include the possibility of a molecular assembler, based upon biomolecular systems such as the ribosome[5]

        Synthetic biology has traditionally been divided into two different approaches: top down and bottom up.

        1. The top down approach involves using metabolic and genetic engineering techniques to impart new functions to living cells.
        2. The bottom up approach involves creating new biological systems in vitro by bringing together 'non-living' biomolecular components, [6] often with the aim of constructing an artificial cell.

        Biological systems are thus assembled module-by-module. Cell-free protein expression systems are often employed, [7] [8] [9] as are membrane-based molecular machinery. There are increasing efforts to bridge the divide between these approaches by forming hybrid living/synthetic cells, [10] and engineering communication between living and synthetic cell populations. [11]

        1910: First identifiable use of the term "synthetic biology" in Stéphane Leduc's publication Théorie physico-chimique de la vie et générations spontanées. [12] He also noted this term in another publication, La Biologie Synthétique in 1912. [13]

        1961: Jacob and Monod postulate cellular regulation by molecular networks from their study of the lac operon in E. coli and envisioned the ability to assemble new systems from molecular components. [14]

        1973: First molecular cloning and amplification of DNA in a plasmid is published in P.N.A.S. by Cohen, Boyer et al. constituting the dawn of synthetic biology. [15]

        1978: Arber, Nathans and Smith win the Nobel Prize in Physiology or Medicine for the discovery of restriction enzymes, leading Szybalski to offer an editorial comment in the journal Gene:

        The work on restriction nucleases not only permits us easily to construct recombinant DNA molecules and to analyze individual genes, but also has led us into the new era of synthetic biology where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated. [16]

        1988: First DNA amplification by the polymerase chain reaction (PCR) using a thermostable DNA polymerase is published in Science by Mullis et al. [17] This obviated adding new DNA polymerase after each PCR cycle, thus greatly simplifying DNA mutagenesis and assembly.

        2000: Two papers in Nature report synthetic biological circuits, a genetic toggle switch and a biological clock, by combining genes within E. coli cells. [18] [19]

        2003: The most widely used standardized DNA parts, BioBrick plasmids, are invented by Tom Knight. [20] These parts will become central to the international Genetically Engineered Machine competition (iGEM) founded at MIT in the following year.

        2003: Researchers engineer an artemisinin precursor pathway in E. coli. [21]

        2004: First international conference for synthetic biology, Synthetic Biology 1.0 (SB1.0) is held at the Massachusetts Institute of Technology, USA.

        2005: Researchers develop a light-sensing circuit in E. coli. [22] Another group designs circuits capable of multicellular pattern formation. [23]

        2006: Researchers engineer a synthetic circuit that promotes bacterial invasion of tumour cells. [24]

        2010: Researchers publish in Science the first synthetic bacterial genome, called M. mycoides JCVI-syn1.0. [25] [26] The genome is made from chemically-synthesized DNA using yeast recombination.

        2011: Functional synthetic chromosome arms are engineered in yeast. [27]

        2012: Charpentier and Doudna labs publish in Science the programming of CRISPR-Cas9 bacterial immunity for targeting DNA cleavage. [28] This technology greatly simplified and expanded eukaryotic gene editing.

        2019: Scientists at ETH Zurich report the creation of the first bacterial genome, named Caulobacter ethensis-2.0, made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist. [29] [30]

        2019: Researchers report the production of a new synthetic (possibly artificial) form of viable life, a variant of the bacteria Escherichia coli, by reducing the natural number of 64 codons in the bacterial genome to 59 codons instead, in order to encode 20 amino acids. [31] [32]

        Engineers view biology as a technology (in other words, a given system includes biotechnology or its biological engineering) [33] Synthetic biology includes the broad redefinition and expansion of biotechnology, with the ultimate goals of being able to design and build engineered live biological systems that process information, manipulate chemicals, fabricate materials and structures, produce energy, provide food, and maintain and enhance human health, as well as advance fundamental knowledge of biological systems (see Biomedical Engineering) and our environment. [34]

        Studies in synthetic biology can be subdivided into broad classifications according to the approach they take to the problem at hand: standardization of biological parts, biomolecular engineering, genome engineering, metabolic engineering. [ citation needed ]

        Biomolecular engineering includes approaches that aim to create a toolkit of functional units that can be introduced to present new technological functions in living cells. Genetic engineering includes approaches to construct synthetic chromosomes or minimal organisms like Mycoplasma laboratorium.

        Biomolecular design refers to the general idea of de novo design and additive combination of biomolecular components. Each of these approaches share a similar task: to develop a more synthetic entity at a higher level of complexity by inventively manipulating a simpler part at the preceding level. [35] [36]

        On the other hand, "re-writers" are synthetic biologists interested in testing the irreducibility of biological systems. Due to the complexity of natural biological systems, it would be simpler to rebuild the natural systems of interest from the ground up In order to provide engineered surrogates that are easier to comprehend, control and manipulate. [37] Re-writers draw inspiration from refactoring, a process sometimes used to improve computer software.

        Several novel enabling technologies were critical to the success of synthetic biology. Concepts include standardization of biological parts and hierarchical abstraction to permit using those parts in synthetic systems. [38] Basic technologies include reading and writing DNA (sequencing and fabrication). Measurements under multiple conditions are needed for accurate modeling and computer-aided design (CAD).

        DNA and gene synthesis Edit

        Driven by dramatic decreases in costs of oligonucleotide ("oligos") synthesis and the advent of PCR, the sizes of DNA constructions from oligos have increased to the genomic level. [39] In 2000, researchers reported synthesis of the 9.6 kbp (kilo bp) Hepatitis C virus genome from chemically synthesized 60 to 80-mers. [40] In 2002 researchers at Stony Brook University succeeded in synthesizing the 7741 bp poliovirus genome from its published sequence, producing the second synthetic genome, spanning two years. [41] In 2003 the 5386 bp genome of the bacteriophage Phi X 174 was assembled in about two weeks. [42] In 2006, the same team, at the J. Craig Venter Institute, constructed and patented a synthetic genome of a novel minimal bacterium, Mycoplasma laboratorium and were working on getting it functioning in a living cell. [43] [44] [45]

        In 2007 it was reported that several companies were offering synthesis of genetic sequences up to 2000 base pairs (bp) long, for a price of about $1 per bp and a turnaround time of less than two weeks. [46] Oligonucleotides harvested from a photolithographic- or inkjet-manufactured DNA chip combined with PCR and DNA mismatch error-correction allows inexpensive large-scale changes of codons in genetic systems to improve gene expression or incorporate novel amino-acids (see George M. Church's and Anthony Forster's synthetic cell projects. [47] [48] ) This favors a synthesis-from-scratch approach.

        Additionally, the CRISPR/Cas system has emerged as a promising technique for gene editing. It was described as "the most important innovation in the synthetic biology space in nearly 30 years". [49] While other methods take months or years to edit gene sequences, CRISPR speeds that time up to weeks. [49] Due to its ease of use and accessibility, however, it has raised ethical concerns, especially surrounding its use in biohacking. [50] [51] [52]

        Sequencing Edit

        DNA sequencing determines the order of nucleotide bases in a DNA molecule. Synthetic biologists use DNA sequencing in their work in several ways. First, large-scale genome sequencing efforts continue to provide information on naturally occurring organisms. This information provides a rich substrate from which synthetic biologists can construct parts and devices. Second, sequencing can verify that the fabricated system is as intended. Third, fast, cheap, and reliable sequencing can facilitate rapid detection and identification of synthetic systems and organisms. [53]

        Microfluidics Edit

        Microfluidics, in particular droplet microfluidics, is an emerging tool used to construct new components, and to analyse and characterize them. [54] [55] It is widely employed in screening assays. [56]

        Modularity Edit

        The most used [57] : 22–23 standardized DNA parts are BioBrick plasmids, invented by Tom Knight in 2003. [58] Biobricks are stored at the Registry of Standard Biological Parts in Cambridge, Massachusetts. The BioBrick standard has been used by thousands of students worldwide in the international Genetically Engineered Machine (iGEM) competition. [57] : 22–23

        While DNA is most important for information storage, a large fraction of the cell's activities are carried out by proteins. Tools can send proteins to specific regions of the cell and to link different proteins together. The interaction strength between protein partners should be tunable between a lifetime of seconds (desirable for dynamic signaling events) up to an irreversible interaction (desirable for device stability or resilient to harsh conditions). Interactions such as coiled coils, [59] SH3 domain-peptide binding [60] or SpyTag/SpyCatcher [61] offer such control. In addition it is necessary to regulate protein-protein interactions in cells, such as with light (using light-oxygen-voltage-sensing domains) or cell-permeable small molecules by chemically induced dimerization. [62]

        In a living cell, molecular motifs are embedded in a bigger network with upstream and downstream components. These components may alter the signaling capability of the modeling module. In the case of ultrasensitive modules, the sensitivity contribution of a module can differ from the sensitivity that the module sustains in isolation. [63] [64]

        Modeling Edit

        Models inform the design of engineered biological systems by better predicting system behavior prior to fabrication. Synthetic biology benefits from better models of how biological molecules bind substrates and catalyze reactions, how DNA encodes the information needed to specify the cell and how multi-component integrated systems behave. Multiscale models of gene regulatory networks focus on synthetic biology applications. Simulations can model all biomolecular interactions in transcription, translation, regulation and induction of gene regulatory networks. [65] [66] [67]

        Synthetic transcription factors Edit

        Studies have considered the components of the DNA transcription mechanism. One desire of scientists creating synthetic biological circuits is to be able to control the transcription of synthetic DNA in unicellular organisms (prokaryotes) and in multicellular organisms (eukaryotes). One study tested the adjustability of synthetic transcription factors (sTFs) in areas of transcription output and cooperative ability among multiple transcription factor complexes. [68] Researchers were able to mutate functional regions called zinc fingers, the DNA specific component of sTFs, to decrease their affinity for specific operator DNA sequence sites, and thus decrease the associated site-specific activity of the sTF (usually transcriptional regulation). They further used the zinc fingers as components of complex-forming sTFs, which are the eukaryotic translation mechanisms. [68]

        Biological computers Edit

        A biological computer refers to an engineered biological system that can perform computer-like operations, which is a dominant paradigm in synthetic biology. Researchers built and characterized a variety of logic gates in a number of organisms, [69] and demonstrated both analog and digital computation in living cells. They demonstrated that bacteria can be engineered to perform both analog and/or digital computation. [70] [71] In human cells research demonstrated a universal logic evaluator that operates in mammalian cells in 2007. [72] Subsequently, researchers utilized this paradigm to demonstrate a proof-of-concept therapy that uses biological digital computation to detect and kill human cancer cells in 2011. [73] Another group of researchers demonstrated in 2016 that principles of computer engineering, can be used to automate digital circuit design in bacterial cells. [74] In 2017, researchers demonstrated the 'Boolean logic and arithmetic through DNA excision' (BLADE) system to engineer digital computation in human cells. [75] In 2019, researchers implemented a perceptron in biological systems opening the way for machine learning in these systems. [76]

        Biosensors Edit

        A biosensor refers to an engineered organism, usually a bacterium, that is capable of reporting some ambient phenomenon such as the presence of heavy metals or toxins. One such system is the Lux operon of Aliivibrio fischeri, [77] which codes for the enzyme that is the source of bacterial bioluminescence, and can be placed after a respondent promoter to express the luminescence genes in response to a specific environmental stimulus. [78] One such sensor created, consisted of a bioluminescent bacterial coating on a photosensitive computer chip to detect certain petroleum pollutants. When the bacteria sense the pollutant, they luminesce. [79] Another example of a similar mechanism is the detection of landmines by an engineered E.coli reporter strain capable of detecting TNT and its main degradation product DNT, and consequently producing a green fluorescent protein (GFP). [80]

        Modified organisms can sense environmental signals and send output signals that can be detected and serve diagnostic purposes. Microbe cohorts have been used. [81]

        Cell transformation Edit

        Cells use interacting genes and proteins, which are called gene circuits, to implement diverse function, such as responding to environmental signals, decision making and communication. Three key components are involved: DNA, RNA and Synthetic biologist designed gene circuits that can control gene expression from several levels including transcriptional, post-transcriptional and translational levels.

        Traditional metabolic engineering has been bolstered by the introduction of combinations of foreign genes and optimization by directed evolution. This includes engineering E. coli and yeast for commercial production of a precursor of the antimalarial drug, Artemisinin. [82]

        Entire organisms have yet to be created from scratch, although living cells can be transformed with new DNA. Several ways allow constructing synthetic DNA components and even entire synthetic genomes, but once the desired genetic code is obtained, it is integrated into a living cell that is expected to manifest the desired new capabilities or phenotypes while growing and thriving. [83] Cell transformation is used to create biological circuits, which can be manipulated to yield desired outputs. [18] [19]

        By integrating synthetic biology with materials science, it would be possible to use cells as microscopic molecular foundries to produce materials with properties whose properties were genetically encoded. Re-engineering has produced Curli fibers, the amyloid component of extracellular material of biofilms, as a platform for programmable nanomaterial. These nanofibers were genetically constructed for specific functions, including adhesion to substrates, nanoparticle templating and protein immobilization. [84]

        Designed proteins Edit

        Natural proteins can be engineered, for example, by directed evolution, novel protein structures that match or improve on the functionality of existing proteins can be produced. One group generated a helix bundle that was capable of binding oxygen with similar properties as hemoglobin, yet did not bind carbon monoxide. [86] A similar protein structure was generated to support a variety of oxidoreductase activities [87] while another formed a structurally and sequentially novel ATPase. [88] Another group generated a family of G-protein coupled receptors that could be activated by the inert small molecule clozapine N-oxide but insensitive to the native ligand, acetylcholine these receptors are known as DREADDs. [89] Novel functionalities or protein specificity can also be engineered using computational approaches. One study was able to use two different computational methods – a bioinformatics and molecular modeling method to mine sequence databases, and a computational enzyme design method to reprogram enzyme specificity. Both methods resulted in designed enzymes with greater than 100 fold specificity for production of longer chain alcohols from sugar. [90]

        Another common investigation is expansion of the natural set of 20 amino acids. Excluding stop codons, 61 codons have been identified, but only 20 amino acids are coded generally in all organisms. Certain codons are engineered to code for alternative amino acids including: nonstandard amino acids such as O-methyl tyrosine or exogenous amino acids such as 4-fluorophenylalanine. Typically, these projects make use of re-coded nonsense suppressor tRNA-Aminoacyl tRNA synthetase pairs from other organisms, though in most cases substantial engineering is required. [91]

        Other researchers investigated protein structure and function by reducing the normal set of 20 amino acids. Limited protein sequence libraries are made by generating proteins where groups of amino acids may be replaced by a single amino acid. [92] For instance, several non-polar amino acids within a protein can all be replaced with a single non-polar amino acid. [93] One project demonstrated that an engineered version of Chorismate mutase still had catalytic activity when only 9 amino acids were used. [94]

        Researchers and companies practice synthetic biology to synthesize industrial enzymes with high activity, optimal yields and effectiveness. These synthesized enzymes aim to improve products such as detergents and lactose-free dairy products, as well as make them more cost effective. [95] The improvements of metabolic engineering by synthetic biology is an example of a biotechnological technique utilized in industry to discover pharmaceuticals and fermentive chemicals. Synthetic biology may investigate modular pathway systems in biochemical production and increase yields of metabolic production. Artificial enzymatic activity and subsequent effects on metabolic reaction rates and yields may develop "efficient new strategies for improving cellular properties . for industrially important biochemical production". [96]

        Designed nucleic acid systems Edit

        Scientists can encode digital information onto a single strand of synthetic DNA. In 2012, George M. Church encoded one of his books about synthetic biology in DNA. The 5.3 Mb of data was more than 1000 times greater than the previous largest amount of information to be stored in synthesized DNA. [97] A similar project encoded the complete sonnets of William Shakespeare in DNA. [98] More generally, algorithms such as NUPACK, [99] ViennaRNA, [100] Ribosome Binding Site Calculator, [101] Cello, [102] and Non-Repetitive Parts Calculator [103] enables the design of new genetic systems.

        Many technologies have been developed for incorporating unnatural nucleotides and amino acids into nucleic acids and proteins, both in vitro and in vivo. For example, in May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA. By including individual artificial nucleotides in the culture media, they were able to exchange the bacteria 24 times they did not generate mRNA or proteins able to use the artificial nucleotides. [104] [105] [106]

        Space exploration Edit

        Synthetic biology raised NASA's interest as it could help to produce resources for astronauts from a restricted portfolio of compounds sent from Earth. [107] [108] [109] On Mars, in particular, synthetic biology could lead to production processes based on local resources, making it a powerful tool in the development of manned outposts with less dependence on Earth. [107] Work has gone into developing plant strains that are able to cope with the harsh Martian environment, using similar techniques to those employed to increase resilience to certain environmental factors in agricultural crops. [110]

        Synthetic life Edit

        One important topic in synthetic biology is synthetic life, that is concerned with hypothetical organisms created in vitro from biomolecules and/or chemical analogues thereof. Synthetic life experiments attempt to either probe the origins of life, study some of the properties of life, or more ambitiously to recreate life from non-living (abiotic) components. Synthetic life biology attempts to create living organisms capable of carrying out important functions, from manufacturing pharmaceuticals to detoxifying polluted land and water. [112] In medicine, it offers prospects of using designer biological parts as a starting point for new classes of therapies and diagnostic tools. [112]

        A living "artificial cell" has been defined as a completely synthetic cell that can capture energy, maintain ion gradients, contain macromolecules as well as store information and have the ability to mutate. [113] Nobody has been able to create such a cell. [113]

        A completely synthetic bacterial chromosome was produced in 2010 by Craig Venter, and his team introduced it to genomically emptied bacterial host cells. [25] The host cells were able to grow and replicate. [114] [115] The Mycoplasma laboratorium is the only living organism with completely engineered genome.

        The first living organism with 'artificial' expanded DNA code was presented in 2014 the team used E. coli that had its genome extracted and replaced with a chromosome with an expanded genetic code. The nucleosides added are d5SICS and dNaM. [106]

        In May 2019, researchers, in a milestone effort, reported the creation of a new synthetic (possibly artificial) form of viable life, a variant of the bacteria Escherichia coli, by reducing the natural number of 64 codons in the bacterial genome to 59 codons instead, in order to encode 20 amino acids. [31] [32]

        In 2017 the international Build-a-Cell large-scale research collaboration for the construction of synthetic living cell was started, [116] followed by national synthetic cell organizations in several countries, including FabriCell, [117] MaxSynBio [118] and BaSyC. [119] The European synthetic cell efforts were unified in 2019 as SynCellEU initiative. [120]

        Drug delivery platforms Edit

        Engineered bacteria-based platform Edit

        Bacteria have long been used in cancer treatment. Bifidobacterium and Clostridium selectively colonize tumors and reduce their size. [121] Recently synthetic biologists reprogrammed bacteria to sense and respond to a particular cancer state. Most often bacteria are used to deliver a therapeutic molecule directly to the tumor to minimize off-target effects. To target the tumor cells, peptides that can specifically recognize a tumor were expressed on the surfaces of bacteria. Peptides used include an affibody molecule that specifically targets human epidermal growth factor receptor 2 [122] and a synthetic adhesin. [123] The other way is to allow bacteria to sense the tumor microenvironment, for example hypoxia, by building an AND logic gate into bacteria. [124] The bacteria then only release target therapeutic molecules to the tumor through either lysis [125] or the bacterial secretion system. [126] Lysis has the advantage that it can stimulate the immune system and control growth. Multiple types of secretion systems can be used and other strategies as well. The system is inducible by external signals. Inducers include chemicals, electromagnetic or light waves.

        Multiple species and strains are applied in these therapeutics. Most commonly used bacteria are Salmonella typhimurium, Escherichia Coli, Bifidobacteria, Streptococcus, Lactobacillus, Listeria and Bacillus subtilis. Each of these species have their own property and are unique to cancer therapy in terms of tissue colonization, interaction with immune system and ease of application.

        Cell-based platform Edit

        The immune system plays an important role in cancer and can be harnessed to attack cancer cells. Cell-based therapies focus on immunotherapies, mostly by engineering T cells.

        T cell receptors were engineered and ‘trained’ to detect cancer epitopes. Chimeric antigen receptors (CARs) are composed of a fragment of an antibody fused to intracellular T cell signaling domains that can activate and trigger proliferation of the cell. A second generation CAR-based therapy was approved by FDA. [ citation needed ]

        Gene switches were designed to enhance safety of the treatment. Kill switches were developed to terminate the therapy should the patient show severe side effects. [127] Mechanisms can more finely control the system and stop and reactivate it. [128] [129] Since the number of T-cells are important for therapy persistence and severity, growth of T-cells is also controlled to dial the effectiveness and safety of therapeutics. [130]

        Although several mechanisms can improve safety and control, limitations include the difficulty of inducing large DNA circuits into the cells and risks associated with introducing foreign components, especially proteins, into cells.

        The creation of new life and the tampering of existing life has raised ethical concerns in the field of synthetic biology and are actively being discussed. [131] [132]

        Common ethical questions include:

        • Is it morally right to tamper with nature?
        • Is one playing God when creating new life?
        • What happens if a synthetic organism accidentally escapes?
        • What if an individual misuses synthetic biology and creates a harmful entity (e.g., a biological weapon)?
        • Who will have control of and access to the products of synthetic biology?
        • Who will gain from these innovations? Investors? Medical patients? Industrial farmers?
        • Does the patent system allow patents on living organisms? What about parts of organisms, like HIV resistance genes in humans? [133]
        • What if a new creation is deserving of moral or legal status?

        The ethical aspects of synthetic biology has 3 main features: biosafety, biosecurity, and the creation of new life forms. [134] Other ethical issues mentioned include the regulation of new creations, patent management of new creations, benefit distribution, and research integrity. [135] [131]

        Ethical issues have surfaced for recombinant DNA and genetically modified organism (GMO) technologies and extensive regulations of genetic engineering and pathogen research were in place in many jurisdictions. Amy Gutmann, former head of the Presidential Bioethics Commission, argued that we should avoid the temptation to over-regulate synthetic biology in general, and genetic engineering in particular. According to Gutmann, "Regulatory parsimony is especially important in emerging technologies. where the temptation to stifle innovation on the basis of uncertainty and fear of the unknown is particularly great. The blunt instruments of statutory and regulatory restraint may not only inhibit the distribution of new benefits, but can be counterproductive to security and safety by preventing researchers from developing effective safeguards.". [136]

        The "creation" of life Edit

        One ethical question is whether or not it is acceptable to create new life forms, sometimes known as "playing God". Currently, the creation of new life forms not present in nature is at small-scale, the potential benefits and dangers remain unknown, and careful consideration and oversight are ensured for most studies. [131] Many advocates express the great potential value—to agriculture, medicine, and academic knowledge, among other fields—of creating artificial life forms. Creation of new entities could expand scientific knowledge well beyond what is currently known from studying natural phenomena. Yet there is concern that artificial life forms may reduce nature's "purity" (i.e., nature could be somehow corrupted by human intervention and manipulation) and potentially influence the adoption of more engineering-like principles instead of biodiversity- and nature-focused ideals. Some are also concerned that if an artificial life form were to be released into nature, it could hamper biodiversity by beating out natural species for resources (similar to how algal blooms kill marine species). Another concern involves the ethical treatment of newly created entities if they happen to sense pain, sentience, and self-perception. Should such life be given moral or legal rights? If so, how?

        Biosafety and biocontainment Edit

        What is most ethically appropriate when considering biosafety measures? How can accidental introduction of synthetic life in the natural environment be avoided? Much ethical consideration and critical thought has been given to these questions. Biosafety not only refers to biological containment it also refers to strides taken to protect the public from potentially hazardous biological agents. Even though such concerns are important and remain unanswered, not all products of synthetic biology present concern for biological safety or negative consequences for the environment. It is argued that most synthetic technologies are benign and are incapable of flourishing in the outside world due to their "unnatural" characteristics as there is yet to be an example of a transgenic microbe conferred with a fitness advantage in the wild.

        In general, existing hazard controls, risk assessment methodologies, and regulations developed for traditional genetically modified organisms (GMOs) are considered to be sufficient for synthetic organisms. "Extrinsic" biocontainment methods in a laboratory context include physical containment through biosafety cabinets and gloveboxes, as well as personal protective equipment. In an agricultural context they include isolation distances and pollen barriers, similar to methods for biocontainment of GMOs. Synthetic organisms may offer increased hazard control because they can be engineered with "intrinsic" biocontainment methods that limit their growth in an uncontained environment, or prevent horizontal gene transfer to natural organisms. Examples of intrinsic biocontainment include auxotrophy, biological kill switches, inability of the organism to replicate or to pass modified or synthetic genes to offspring, and the use of xenobiological organisms using alternative biochemistry, for example using artificial xeno nucleic acids (XNA) instead of DNA. [137] [138] Regarding auxotrophy, bacteria and yeast can be engineered to be unable to produce histidine, an important amino acid for all life. Such organisms can thus only be grown on histidine-rich media in laboratory conditions, nullifying fears that they could spread into undesirable areas.

        Biosecurity Edit

        Some ethical issues relate to biosecurity, where biosynthetic technologies could be deliberately used to cause harm to society and/or the environment. Since synthetic biology raises ethical issues and biosecurity issues, humanity must consider and plan on how to deal with potentially harmful creations, and what kinds of ethical measures could possibly be employed to deter nefarious biosynthetic technologies. With the exception of regulating synthetic biology and biotechnology companies, [139] [140] however, the issues are not seen as new because they were raised during the earlier recombinant DNA and genetically modified organism (GMO) debates and extensive regulations of genetic engineering and pathogen research are already in place in many jurisdictions. [141]

        European Union Edit

        The European Union-funded project SYNBIOSAFE [142] has issued reports on how to manage synthetic biology. A 2007 paper identified key issues in safety, security, ethics and the science-society interface, which the project defined as public education and ongoing dialogue among scientists, businesses, government and ethicists. [143] [144] The key security issues that SYNBIOSAFE identified involved engaging companies that sell synthetic DNA and the biohacking community of amateur biologists. Key ethical issues concerned the creation of new life forms.

        A subsequent report focused on biosecurity, especially the so-called dual-use challenge. For example, while synthetic biology may lead to more efficient production of medical treatments, it may also lead to synthesis or modification of harmful pathogens (e.g., smallpox). [145] The biohacking community remains a source of special concern, as the distributed and diffuse nature of open-source biotechnology makes it difficult to track, regulate or mitigate potential concerns over biosafety and biosecurity. [146]

        COSY, another European initiative, focuses on public perception and communication. [147] [148] [149] To better communicate synthetic biology and its societal ramifications to a broader public, COSY and SYNBIOSAFE published SYNBIOSAFE, a 38-minute documentary film, in October 2009. [150]

        The International Association Synthetic Biology has proposed self-regulation. [151] This proposes specific measures that the synthetic biology industry, especially DNA synthesis companies, should implement. In 2007, a group led by scientists from leading DNA-synthesis companies published a "practical plan for developing an effective oversight framework for the DNA-synthesis industry". [139]

        United States Edit

        In January 2009, the Alfred P. Sloan Foundation funded the Woodrow Wilson Center, the Hastings Center, and the J. Craig Venter Institute to examine the public perception, ethics and policy implications of synthetic biology. [152]

        On July 9–10, 2009, the National Academies' Committee of Science, Technology & Law convened a symposium on "Opportunities and Challenges in the Emerging Field of Synthetic Biology". [153]

        After the publication of the first synthetic genome and the accompanying media coverage about "life" being created, President Barack Obama established the Presidential Commission for the Study of Bioethical Issues to study synthetic biology. [154] The commission convened a series of meetings, and issued a report in December 2010 titled "New Directions: The Ethics of Synthetic Biology and Emerging Technologies." The commission stated that "while Venter's achievement marked a significant technical advance in demonstrating that a relatively large genome could be accurately synthesized and substituted for another, it did not amount to the “creation of life”. [155] It noted that synthetic biology is an emerging field, which creates potential risks and rewards. The commission did not recommend policy or oversight changes and called for continued funding of the research and new funding for monitoring, study of emerging ethical issues and public education. [141]

        Synthetic biology, as a major tool for biological advances, results in the "potential for developing biological weapons, possible unforeseen negative impacts on human health . and any potential environmental impact". [156] These security issues may be avoided by regulating industry uses of biotechnology through policy legislation. Federal guidelines on genetic manipulation are being proposed by "the President's Bioethics Commission . in response to the announced creation of a self-replicating cell from a chemically synthesized genome, put forward 18 recommendations not only for regulating the science . for educating the public". [156]

        Opposition Edit

        On March 13, 2012, over 100 environmental and civil society groups, including Friends of the Earth, the International Center for Technology Assessment and the ETC Group issued the manifesto The Principles for the Oversight of Synthetic Biology. This manifesto calls for a worldwide moratorium on the release and commercial use of synthetic organisms until more robust regulations and rigorous biosafety measures are established. The groups specifically call for an outright ban on the use of synthetic biology on the human genome or human microbiome. [157] [158] Richard Lewontin wrote that some of the safety tenets for oversight discussed in The Principles for the Oversight of Synthetic Biology are reasonable, but that the main problem with the recommendations in the manifesto is that "the public at large lacks the ability to enforce any meaningful realization of those recommendations". [159]

        The hazards of synthetic biology include biosafety hazards to workers and the public, biosecurity hazards stemming from deliberate engineering of organisms to cause harm, and environmental hazards. The biosafety hazards are similar to those for existing fields of biotechnology, mainly exposure to pathogens and toxic chemicals, although novel synthetic organisms may have novel risks. [160] [137] For biosecurity, there is concern that synthetic or redesigned organisms could theoretically be used for bioterrorism. Potential risks include recreating known pathogens from scratch, engineering existing pathogens to be more dangerous, and engineering microbes to produce harmful biochemicals. [161] Lastly, environmental hazards include adverse effects on biodiversity and ecosystem services, including potential changes to land use resulting from agricultural use of synthetic organisms. [162] [163]

        Existing risk analysis systems for GMOs are generally considered sufficient for synthetic organisms, although there may be difficulties for an organism built "bottom-up" from individual genetic sequences. [138] [164] Synthetic biology generally falls under existing regulations for GMOs and biotechnology in general, and any regulations that exist for downstream commercial products, although there are generally no regulations in any jurisdiction that are specific to synthetic biology. [165] [166]


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Comments:

  1. Innocent

    It's simply incomparable topic

  2. Turan

    the main thing is ingenuity

  3. Darren

    So you can argue endlessly ..



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