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G8. General Links and References - Biology

G8. General Links and References - Biology


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  1. Bradley, P. et al. Toward high-resolution de novo structure prediction for small proteins. Science. 309, 1868 (2005)
  2. Boyle J. A. Bioinformatics in Undergraduate Education. Biochemistry and Molecular Biology Education. 32, 236 (2004)
  3. Feig, A. L., & Jabri, E. Incorporation of Bioinformatics Exercises into the Undergraduate Biochemistry. 30, 224 (2002)
  4. Mayor et al. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421, pg 863 (2003)
  5. Zhou and Karplus. Interpreting the folding kinetics of helical proteins. Nature 401, pg 400(1999)

First on the list is setting up the G8’s impressive time of flight (ToF) sensor, which facilitates palm recognition unlocking as well as air gesture controls. These can take some getting used to when it comes to finding that sweet spot. You can head to Settings > General > Lock screen & security to set up Hand ID, but we’re specifically talking about using Air Motion controls here.

Head to Settings > General > Air Motion > Shortcut and capture and toggle it on. Now, you can hold your hand out flat about 6 or 7 inches above the ToF sensor on top of the screen. Once you see the green and purple indicator pop up, change your hand to a claw-like gesture, still pointed at the screen, and you should see the Air Motion menu appear. Move your wrist left or right to open the shortcut of your choice. These options can be configured in Settings > General > Air Motion > Shortcut and capture, just look at the bottom for Swipe left and Swipe right.

When it comes to choosing shortcuts, it’s up to you to choose which apps will be most helpful, but we do have two particular suggestions. First is a music application, as music playback can be controlled through Air Motion, and it also supports volume controls (Apple Music can only be opened, not controlled). You will have to touch the screen to choose the song or album you want to play, even if you open the app via air gestures, but after that Air Motions can be a useful tool for when your hands are wet or dirty and you’d rather not pick up your phone to pause or play a song or turn up the volume. Make sure you toggle on Control music and video in the same system settings menu.

Next, we recommend the camera app — particularly if you take a lot of selfies. By default, the camera app opens to the last mode used so if you’re regularly snapping selfies then opening the camera via Air Motion will pop you right into selfie mode, where you can then trigger the shutter with another hand gesture — an open palm changed to a fist — a reliable and quick way to snap that perfect pic without having to tap the shutter button.


Facts about Stachybotrys chartarum

Stachybotrys chartarum is a greenish-black mold. It can grow on material with a high cellulose content, such as fiberboard, gypsum board, and paper. Growth occurs when there is moisture from water damage, water leaks, condensation, water infiltration, or flooding. Constant moisture is required for its growth.

Does Stachybotrys chartarum cause acute idiopathic pulmonary hemorrhage among infants?

To date, a possible association between acute idiopathic pulmonary hemorrhage among infants and Stachybotrys chartarum has not been proven. Further studies are needed to determine what causes acute idiopathic hemorrhage.

What if my child has acute idiopathic pulmonary hemorrhage?

Parents should ensure that their children get proper medical treatment.

Is there a test for Stachybotrys chartarum?

At present, no test exists that proves an association between Stachybotrys chartarum and particular health symptoms. Individuals with persistent symptoms should see their physician. However, if Stachybotrys chartarum or other molds are found in a building they should be removed.

Stachybotrys chartarum and other molds may cause health symptoms that are nonspecific. It is not necessary to determine what type of mold you may have growing in your home or other building. All molds should be treated the same with respect to potential health risks and removal.


Results

Expression of MyoD protein and Myf5 mRNA in the epiblast

MyoD mRNA is expressed in a small subpopulation of cells in the pregastrulating epiblast (George-Weinstein et al., 1996 Gerhart et al., 2000, 2006 Strony et al., 2005). To determine whether these cells produce MyoD protein, stage 1–4 embryos were double labeled with mAbs to MyoD and the G8 antigen. The G8 mAb binds to a cell surface antigen and is a specific marker for cells that express MyoD mRNA in the epiblast (Fig. 1 A Gerhart et al., 2001, 2004a Strony et al., 2005). MyoD protein was not detected in stage 1 or 2 embryos, and only a single G8-positive (G8 pos ) cell in the stage 4 epiblast was labeled with the MyoD antibody (Fig. 1, B–D). These results were confirmed with a rabbit polyclonal antiserum to MyoD. Therefore, MyoD mRNA either is not translated or the protein does not accumulate to detectable levels in the early epiblast.

MyoD pos epiblast cells were further characterized by determining whether they express Myf5 mRNA. In agreement with the results of Kiefer and Hauschka (2001), Myf5 mRNA was not detected by in situ hybridization in the stage 1 or 2 epiblast (Fig. 1 E). The lack of detection of Myf5 mRNA in the pregastrulating epiblast suggests that MyoD is expressed before Myf5 in the chick embryo, although analyses of the embryo before laying would be required to demonstrate this definitively. Myf5 mRNA was detected in only a subpopulation of G8 pos cells in the stage 4 epiblast (Fig. 1 F). Interestingly, a few stage 4 epiblast cells that did not appear to express the G8 antigen expressed Myf5 (Fig. 1 F). Therefore, epiblast cells of gastrulating embryos may be heterogeneous with respect to their expression of muscle regulatory factors.

Behavior of MyoD pos epiblast cells tracked into the heart and nervous system

Cells expressing MyoD mRNA in the stage 2 epiblast were tracked into the heart and nervous system by fluorescently labeling them with the G8 mAb and incubating the embryos for 3 d in ovo (stage 16). Although the majority of G8 pos cells were incorporated into the somites (56%), ∼9 labeled cells were found in the heart, 10 were found in the neural tube, 9 were in the brain, and 27 were found in other nonsomitic tissues of the embryo, including the mesenchyme of the head. Most were present as single cells surrounded by G8-negative (G8 neg ) cells. Within the somites, all of the G8 pos cells contained MyoD protein (Fig. 2 A), and the majority (73%) had synthesized sarcomeric myosin.

All of the G8 pos cells tracked into the heart continued to express MyoD mRNA, and a subpopulation (59%) was stained with the MyoD mAb (Fig. 2, B–D). Although most cells lacking the G8 label had synthesized cardiac troponin T, this marker for cardiac muscle differentiation was not detected in any G8 pos cells in the stage 16 heart (Fig. 2 E). Within the central nervous system (CNS) of the stage 16 embryo, all G8 pos cells that originated in the epiblast continued to express MyoD mRNA, and ∼50% were stained with the MyoD mAb (Fig. 2, F and G). Only a single G8 pos cell contained sarcomeric myosin (Fig. 2 H). None of the G8 pos cells were labeled with an antibody to neurofilament-associated antigen (Fig. 2 I).

The CNS (Fig. 2 J) and heart contained a few cells that expressed MyoD but lacked the G8 tag that had been applied in the stage 2 embryo. This is consistent with the observation that more G8 pos cells (∼36 cells) were found in hearts directly labeled with the G8 mAb than the number of G8 pos epiblast cells tracked into the heart (nine cells). Some cells with MyoD mRNA but lacking the G8 tag applied in the epiblast were present in clusters containing G8-labeled cells, whereas others were surrounded by G8 neg cells (Fig. 2 J). Although it is possible that the G8 signal was lost in some cells as a result of proliferation, the expression of MyoD may have been initiated in a separate population after application of the antibody (Gerhart et al., 2006).

Importantly, no cell that expressed MyoD mRNA and the G8 antigen within the epiblast and were tracked into the heart or nervous system or any cells that may have initiated G8 synthesis sometime after stage 2 of development contained detectable levels of cardiac troponin T or neurofilament-associated antigen. These results indicate that G8 pos epiblast cells are not induced to differentiate into cardiac muscle or neurons in the developing heart and nervous system.

Microinjection of MyoD pos and MyoD neg epiblast cells into the precardiac mesoderm and neural plate

In the aforementioned tracking experiments, it is possible that the restriction of developmental potential may have occurred in cells on route to their final destination. Therefore, a second approach was taken to challenge the behavior of MyoD pos epiblast cells that involved microinjecting them directly into the precardiac mesoderm and neural plate. Stage 1 epiblasts were removed from the embryo, dissociated, labeled with the G8 mAb, and the G8 pos and G8 neg populations were isolated by magnetic cell sorting. The purity of both sorted populations was >97% (Gerhart et al., 2004a). Sorted cells were labeled with Hoechst dye, a procedure that did not affect their viability or ability to differentiate in vitro (unpublished data). 60 G8 pos or G8 neg Hoechst-labeled epiblast cells were microinjected into six sites (10 cells per site) of the precardiac mesoderm of stage 4–5 embryos (Fig. 3 A) or the neural plate of stage 6–7 embryos (Fig. 4 A). The microinjection procedure did not appear to affect morphogenesis of the heart or nervous system during the course of the experiment (Figs. 3, B and C and 4, B–D). The expression of cell type–specific markers was analyzed in tissue sections and after the dissociation of tissues and centrifugation of the cell suspensions onto slides.

Behavior of MyoD pos and MyoD neg epiblast cells microinjected into the precardiac mesoderm

After microinjecting cells into the precardiac mesoderm of stage 4–5 embryos, ∼94% of the Hoechst-labeled cells were later found in stage 12–14 hearts (Fig. 3 C). Microinjected G8 pos cells increased in number to a greater extent than G8 neg cells (2.5- and 1.9-fold, respectively P ≤ 0.05). Some clusters of two to four G8 pos cells were found within the myocardium, although most were present as single cells surrounded by host cells (Fig. 3, D–K). The majority of microinjected G8 neg cells was present within the middle of the myocardium (Fig. 3, L and M), whereas G8 pos epiblast cells often were found toward the periphery of the myocardium (Fig. 3, D–K), suggesting that some cell sorting may have occurred.

None of the Hoechst-labeled G8 pos cells contained detectable levels of cardiac troponin T (Fig. 3, D and E and Table I). Instead, 99% contained MyoD mRNA (Fig. 3, F and G), and most were labeled with the MyoD mAb (Fig. 3, H and I and Table I). Some of the microinjected G8 pos cells differentiated into skeletal muscle, as indicated by staining with the 12101 mAb (Fig. 3, J and K), although the percentage of these cells that expressed 12101 in vivo varied greatly between experiments (Table I). This may reflect a delay in the accumulation of this antigen after terminal differentiation because the majority of G8 pos cells contained sarcomeric myosin (Table I).

G8 pos epiblast cells microinjected into the precardiac mesoderm displayed a greater tendency to differentiate into skeletal muscle than those that were tracked from the epiblast into the heart. This suggests that the procedure for isolating and dissociating the epiblast in preparation for sorting and microinjection may have enhanced the ability of MyoD pos cells to differentiate in foreign environments. Cell–cell interactions within the epiblast epithelium and a factor produced in the mesoderm are inhibitory for skeletal myogenesis (George-Weinstein et al., 1996).

The procedure for isolating epiblast cells is not sufficient to trigger skeletal myogenesis in epiblast cells that lack MyoD mRNA. Less than 1% of microinjected G8 neg cells or their progeny contained detectable levels of MyoD mRNA (Fig. 3, L and M) or MyoD protein, and none appeared to synthesize the 12101 antigen (Table I). Unlike the G8 pos cells, nearly all of the G8 neg cells that were microinjected into the precardiac mesoderm differentiated into cardiomyocytes (Fig. 3, N and O and Table I). A greater percentage of G8 neg epiblast cells were labeled with the cardiac troponin antibody than host cells (P ≤ 0.03), illustrating their proclivity for differentiation.

A small decrease was found in the number of host cells that differentiated into cardiac muscle in embryos microinjected with G8 pos cells than G8 neg cells (Table I). Slightly more host cells were stained with mAbs to MyoD and 12101 in hearts implanted with G8 pos cells than G8 neg cells (Table I). This raises the possibility that microinjected G8 pos cells influence the pathway of the differentiation of host cells in the heart. The results obtained when epiblast cells were microinjected into the developing heart were consistent with the cell-tracking experiments. That is, cells expressing MyoD mRNA in the epiblast continued to do so in the heart and were not redirected to the cardiac muscle lineage. In contrast, cells that lacked MyoD mRNA in the epiblast were capable of differentiating into cardiac muscle.

Behavior of G8 pos and G8 neg cells microinjected into the neural plate

The fate of epiblast cells that express MyoD mRNA was also tested in the developing nervous system. As was the case with implantations into the heart, the microinjected G8 pos cells increased in number to a greater extent than G8 neg cells (10-fold and ninefold, respectively). The higher rates of proliferation of cells microinjected into the neural plate than in the precardiac mesoderm is consistent with the observation that cardiomyocyte differentiation was nearly complete by the time the embryos were fixed for analysis (Manasek, 1968).

Greater than 80% of the microinjected cells were found in the head (Fig. 4 C). Within the head, 75% of Hoechst-labeled cells were present in the brain. Approximately 60% of the Hoechst-labeled cells in the trunk were found in the neural tube (Fig. 4 D). Most of the microinjected cells were surrounded by host cells, although some were present in clusters of two to four cells in the brain and neural tube (Fig. 4, E–P).

Neurofilament-associated antigen was not detected in any of the G8 pos cells microinjected into the neural plate even when they were surrounded by host cells containing this marker of neuronal differentiation (Fig. 4, E and F and Table II). Instead, all G8 pos cells found within the CNS (Fig. 4, G and H) and other embryonic tissues contained MyoD mRNA. Within the CNS, some G8 pos cells were labeled with mAbs to MyoD protein (∼70% Fig. 4, I and J), sarcomeric myosin (∼13% Fig. 4, K and L), and the 12101 antigen (∼7%). The majority (∼55%) of Hoechst-labeled G8 pos cells present in the mesenchyme of the head or myogenic region of the somite had differentiated into skeletal muscle. A few host cells were found to express MyoD mRNA in the brain (Fig. 4, G and H).

In contrast to the behavior of G8 pos cells, ∼70% of G8 neg cells that were microinjected into the neural plate and incorporated into nervous tissue expressed neurofilament-associated antigen (Fig. 4, M and N). Only 1% of the Hoechst-labeled G8 neg cells contained MyoD mRNA (Fig. 4, O and P), and none were stained with mAbs to MyoD protein or the 12101 antigen. All Hoechst-labeled G8 neg cells found in the myogenic region of the somite did express MyoD mRNA (unpublished data).

A precise determination of the percentages of cells microinjected into the neural plate that later differentiated into neurons or skeletal muscle throughout the embryo was calculated by separating the head from the trunk, dissociating the tissues to produce a single-cell suspension, centrifuging the cells onto slides, and staining with antibodies (Table II). Significantly more Hoechst-labeled G8 pos than G8 neg cells were stained with the MyoD mAb (head, P ≤ 0.000005 trunk, P ≤ 0.0003) and differentiated into skeletal muscle (head, P ≤ 0.02). Importantly, no microinjected G8 pos epiblast cells were stained with the antibody to neurofilament-associated antigen, whereas approximately one third of the microinjected G8 neg cells in the head and 10% in the remainder of the embryo expressed this marker of neurogenesis.

The results of experiments involving the microinjection of epiblast cells into the neural plate were consistent with those in which cells were tracked into the nervous system. They also mirrored the data obtained when epiblast cells were microinjected or tracked into the heart. Regardless of whether MyoD pos cells were incorporated into the nervous system or heart, they either remained as skeletal muscle precursors or formed skeletal muscle. They did not differentiate into neurons or cardiac muscle.

Behavior of microinjected MyoD pos epiblast cells in culture

Although G8 pos epiblast cells microinjected into the precardiac mesoderm and neural plate continued to express MyoD mRNA in the heart and nervous system, only a subpopulation synthesized sarcomeric myosin and the 12101 antigen. To test whether the population of microinjected G8 pos epiblast cells that remained undifferentiated was capable of undergoing skeletal myogenesis, cell cultures were prepared from hearts, heads, and trunks. Because epiblast cells lacking MyoD mRNA in vivo do not form skeletal muscle in this culture system, the conditions are permissive and not instructive for skeletal myogenesis (Gerhart et al., 2004a Strony et al., 2005). 4 d after plating, 90–100% of Hoechst-labeled G8 pos epiblast cells that had been microinjected into the embryo synthesized the 12101 antigen (90 ± 5% from the heart, 95 ± 4% from the head, and 100% from the trunk n = 3 cultures per region Fig. 5, A–C). Therefore, MyoD pos epiblast cells microinjected into the precardiac mesoderm and neural plate are able to differentiate into skeletal muscle in a permissive environment.


About Parasites

A parasite is an organism that lives on or in a host organism and gets its food from or at the expense of its host. There are three main classes of parasites that can cause disease in humans: protozoa, helminths, and ectoparasites.

Entamoeba histolytica is a protozoan. A microscope is necessary to view this parasite. Credit: CDC.

Protozoa are microscopic, one-celled organisms that can be free-living or parasitic in nature. They are able to multiply in humans, which contributes to their survival and also permits serious infections to develop from just a single organism. Transmission of protozoa that live in a human&rsquos intestine to another human typically occurs through a fecal-oral route (for example, contaminated food or water or person-to-person contact). Protozoa that live in the blood or tissue of humans are transmitted to other humans by an arthropod vector (for example, through the bite of a mosquito or sand fly).

The protozoa that are infectious to humans can be classified into four groups based on their mode of movement:

  • Sarcodina &ndash the ameba, e.g., Entamoeba
  • Mastigophora &ndash the flagellates, e.g., Giardia, Leishmania
  • Ciliophora &ndash the ciliates, e.g., Balantidium
  • Sporozoa &ndash organisms whose adult stage is not motile e.g., Plasmodium, Cryptosporidium

An adult Ascaris lumbriocoides worm. They can range from 15 to 35 cm.
Credit: CDC.

Helminths are large, multicellular organisms that are generally visible to the naked eye in their adult stages. Like protozoa, helminths can be either free-living or parasitic in nature. In their adult form, helminths cannot multiply in humans. There are three main groups of helminths (derived from the Greek word for worms) that are human parasites:

  • Flatworms (platyhelminths) &ndash these include the trematodes (flukes) and cestodes (tapeworms).
  • Thorny-headed worms (acanthocephalins) &ndash the adult forms of these worms reside in the gastrointestinal tract. The acanthocephala are thought to be intermediate between the cestodes and nematodes.
  • Roundworms (nematodes) &ndash the adult forms of these worms can reside in the gastrointestinal tract, blood, lymphatic system or subcutaneous tissues. Alternatively, the immature (larval) states can cause disease through their infection of various body tissues. Some consider the helminths to also include the segmented worms (annelids)&mdashthe only ones important medically are the leeches. Of note, these organisms are not typically considered parasites.

An adult louse. Acutal size is about as big as a sesame seed.
Credit: CDC.

Although the term ectoparasites can broadly include blood-sucking arthropods such as mosquitoes (because they are dependent on a blood meal from a human host for their survival), this term is generally used more narrowly to refer to organisms such as ticks, fleas, lice, and mites that attach or burrow into the skin and remain there for relatively long periods of time (e.g., weeks to months). Arthropods are important in causing diseases in their own right, but are even more important as vectors, or transmitters, of many different pathogens that in turn cause tremendous morbidity and mortality from the diseases they cause.

Parasitic infections cause a tremendous burden of disease in both the tropics and subtropics as well as in more temperate climates. Of all parasitic diseases, malaria causes the most deaths globally. Malaria kills more than 400,000 people each year, most of them young children in sub-Saharan Africa.

The Neglected Tropical Diseases (NTDs), which have suffered from a lack of attention by the public health community, include parasitic diseases such as lymphatic filariasis, onchocerciasis, and Guinea worm disease. The NTDs affect more than 1 billion people worldwide, largely in rural areas of low-income countries. These diseases extract a large toll on endemic populations, including lost ability to attend school or work, stunting of growth in children, impairment of cognitive skills and development in young children, and the serious economic burden placed on entire countries.

However, parasitic infections also affect persons living in developed countries, including the United States.


What to Include on Your Resume

As you review them, you’ll see that there are creative ways to compensate for a lack of substantial work experience. Resumes for students and / or new graduates can be quite effective if they showcase one’s education, internships, volunteer work, and both academic and personal achievements.

It is also important to emphasize soft skills in lieu of work experience. Everyone has individual, innate talents, and personality traits that can help become valued employees. Soft traits include characteristics like work ethic, a can-do attitude, personal and social networking, oral and written communications talents, creative thinking, positivity, teamwork, good decision-making skills, motivational talents, flexibility, time management, problem-solving, conflict resolution, and critical thinking skills.

Finally, if you are a recent college graduate, your resume should be crafted to describe your major field of study and it should be presented in the format that’s expected by employers in your industry – resumes for jobs in the sciences (lab technicians, bench scientists, research assistants) will be formatted differently, for example, than those designed for communications jobs (editors, social media specialists, marketing specialists).

A well-written resume will help you to stand out from the competition and spark an employer’s interest. It should be clear, concise, and free of spelling and grammatical errors.

The links below will give you strategies for creating a resume and cover letter targeted for your specific field of expertise. The links below also provide useful writing, formatting, and job search tips.


Format and Style of Supplementary Materials

Supplementary Materials (SM) are posted permanently at the Science web sites, are linked to the manuscript, and are freely available. Supplementary Materials must be essential to the scientific integrity and excellence of the paper, and their use is restricted to Reports and Research Articles. The material is subject to the same editorial standards and peer-review procedures as the print publication. To aid in the organization of Supplementary Materials, we recommend using or following the Microsoft Word template supplied here.

In general, the Supplementary Materials may comprise

Materials and Methods: The materials and methods section should provide sufficient information to allow replication of the study. It should be cited at relevant points in the text using a citation number that refers to a note in the reference list that reads “Materials and methods are available as supplementary materials at the Science website.” Study design should be described in detail and descriptions of reagents and equipment should facilitate replication (for example source and purity of reagents should be specified, there should be evidence that antibodies have been validated, and cell lines should be authenticated). Clinical and preclinical studies should include a section titled Experimental Design at the beginning of materials and methods in which the objectives and design of the study, as well as prespecified components, are described. Statistical methods must be described with enough detail to enable a knowledgeable reader with access to the original data to verify the results. The values for N, P, and the specific statistical test performed for each experiment should be included in the appropriate figure legend or main text. Please see our editorial policies for additional guidelines for specific types of studies as well as further details on reporting of statistical analysis. For papers in the life sciences that involve a method that would benefit from the publication of a step-by-step protocol, we encourage authors to consider submitting a detailed protocol to our collaborative partner Bio-protocol .

Supplementary Text: Additional information regarding control or supplemental experiments, field sites, observations, hypotheses, etc., that bear directly on the arguments of the print paper. Further discussion or development of arguments beyond those in the main text is not permitted in supplementary text. This can be referred to in the main text as “supplementary text” with no reference note required.

Figures: Figures that cannot be accommodated in the print version but that are integral to the paper’s arguments. Figures should meet the same standards as print figures. See below These are numbered starting at 1, with the prefix S (eg Fig S1) All figures should be called out in the main text, No reference note is required.

Tables: Extensive data tables useful in assessing the arguments of the print paper. Authors wishing to post presentations of data more complex than flat text files or tables that can be converted to PDF format need to consult with their editor.

Multimedia files: Online video clips should be in QuickTime (preferred) or AVI format MPEG movies may also be acceptable. For Quicktime h264 compression is the preferred format. Authors should opt for the minimum frame size and number of images that are consistent with a reasonably effective on-screen presentation. Animated GIFs are not accepted. Authors should submit online videos or movies with accompanying captions. For audio files WAV, AIFF, or AU formats are accepted.

References only cited in the supplementary materials should be included at the end of the reference section of the main text, and the reference numbering should continue as if the Supplementary Materials was a continuation of the main text.

Both at initial submission, and at the revision stage, authors should submit the supplementary sections, materials and methods, text, tables and figures, as a single docx or PDF file that should not exceed 25 MB. For ease of reading, the text and tables should be single spaced figures should be individually numbered, and each figure should have its legend on the page on which the figure appears, immediately beneath the figure. Supplementary multimedia or large data files that cannot be included in the Supplementary Materials file should be uploaded as Auxiliary Supplementary Materials or Movies. There is a 25 MB combined size limit on auxiliary or movie files and a limit of 10 auxiliary or movie files. Video clips should be in .mp4 format. Quicktime (.mov) files are acceptable provided the h.264 compression setting is used. Where possible please use HD frame size (1920x1080 pixels). Animated GIFs are not accepted. For audio files, WAV AIFF, AU or .m4a are preferred. MP3 or AAC files are acceptable but a bit rate of at least 160kb/s must be used. Authors should submit video and audio with clearly identifiable accompanying captions and credit information. If you have files essential to the evaluation of your manuscript that exceed these limits, please contact [email protected] . See Submitting your manuscript for further details on how to submit.


G8. General Links and References - Biology

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What are reference proteomes?

Last modified February 23, 2021

Proteomes

UniProt provides several sets of proteins thought to be expressed by organisms whose genomes have been completely sequenced, termed "proteomes".

As more and more genomes of the same organism are being sequenced, we introduced unique proteome identifiers to distinguish individual proteomes from the same taxonomy identifier.

These proteomes can be queried and downloaded from the Proteomes section of the UniProt website. UniProtKB entries that are part of a proteome have a cross-reference to their proteome.

Reference proteomes

With the significant increase in the number of complete genomes sequenced and thus for the number of proteomes as described above, it is critically important to organise this data in a way that allows users to effectively navigate the growing number of available proteome sequences. The approach adopted by UniProt to meet this challenge is to define a set of "reference proteomes" which are "landmarks" in proteome space.

Reference proteomes have been selected among all proteomes (manually and algorithmically, according to a number of criteria) to provide broad coverage of the tree of life. Reference proteomes constitute a representative cross-section of the taxonomic diversity to be found within UniProtKB. They include the proteomes of well-studied model organisms and other proteomes of interest for biomedical and biotechnological research. Species of particular importance may be represented by numerous reference proteomes for specific ecotypes or strains of interest.

UniProtKB entries from these reference proteomes are tagged with the keyword Reference proteome.

Reference proteome download

Our FTP server allows to download precomputed data sets for reference proteomes, based on a gene-centric perspective.


Weathering Process: Physical, Chemical and Biological Weathering

It is a process in which the massive consolidated rocks are broken down into smaller particles and eventually into the individual minerals of which they are composed.

As a result of Lathering the rock fragments and the minerals are changed to new minerals either by alteration or by complete chemical changes.

Weathering processes are distinguished into the following three types on the basis of nature of agencies which bring about weathering:

(2) Chemical weathering, and

(3) Biological weathering or biogeochemical weathering.

1. Physical Weathering:

Physical weathering of rocks is a mechanical process which is brought about by a number of factors, such as:

It causes breakdown of rocks in the following ways:

(i) Differential expansion and contraction of materials:

Minerals composing the rock show different degrees of expansion (coefficient of expansion). These minerals expand in the high temperature of day and contract when the temperature falls. The differential expansion and contraction of different minerals set up internal tension and produce cracks in the rocks and thus the rocks weather into finer and finer particles.

The arrangement of layers in rock is called stratification. Layer differentiation is not common in all types of rocks. The upper layer of rocks expand and contract faster than those of deeper region. The temperature changes bring about separation and disintegration of the layers of rocks. This process is known as exfoliation.

Sometimes, temperature of rocks reaches below freezing point. This causes accumulation and freezing of water in the crevices and rock joints. In freezing water expands to about 9 per cent of its original volume and exerts a pressure of approximately 150 tons per square feet which is more than enough to break the rocks.

Water causes weathering of rocks in the following ways:

Natural water falling either in the form of rain drops or as hail storm on the surface of rocks with beating effect bring about abrasion of massive rocks into smaller particles.

Rapidly flowing water rolls the heavy rock masses (rock boulders) along the bottom of stream and grinds them into finer particles.

It is most active in sea shores. The water waves striking with great force on the rock surface break and grind the rock into pieces.

At mountain tops, ice formation takes place in the winter season. When the summer approaches, ice starts melting and glaciers (huge sliding masses of ice) move downwardly on the slopes. In the glacier movement, the rocks are corroded and finally broken into sand particles (Fig. 22.1).

Rapid stormy wind carrying suspended sand particles causes the abrasion of exposed rock. The Fig. 22.2 shows rocks which were subjected to wind erosion.

2. Chemical Weathering:

Chemical weathering brings about disappearance of original rock minerals either completely or partly. In this process secondary products may be formed from parent materials. This process IS also known as chemical transformation. Presence of moisture and air is very essential in the chemical weathering. This is why chemical weathering is not so effective in desert.

The chemical weathering takes place in the following ways:

Solvent action of water helps in the weathering of rocks. It dissolves soluble minerals of rocks. Solution helps in the removal of weathered materials but total loss is negligible Solvent action is increased in presence of CO2 and organic acids formed by decomposing dead organic remains of plants and animals. Sodium, potassium, calcium and magnesium are easily removed from rocks in dissolved state.

It is essentially an exchange of constituent parts between water and rock minerals. When water reacts with strong base it produces hydroxides. The soluble products of hydrolysis are usually removed by water. Sometimes soluble products may react with insoluble ones and form clays. Hydroxides in presence of CO2 change to carbonates and bicarbonates. Water in ionized state acts as a weak acid on siliceous matter, e.g.,

It means addition of oxygen to mineral compounds. The reaction produces oxides which when dissolve in water weaken the rock and bring about weathering. Iron, aluminum foil, manganese oxides and sulphides are easily oxidized.

It means removal of oxygen from minerals, e.g.,

Reduction takes place in the deep zone where oxygen is not available.

It occurs simultaneously with hydrolysis. In this process, CO2 unites with water to produce carbonic acid which is a weak acid.

The carbonic acid reacts with hydroxides of soil forming minerals and forms insoluble carbonates. Sometimes it dissolves minerals and thus weakens the rock promoting thereby the weathering. Carbonation of hydroxides results in the formation of carbonates and bicarbonates, e.g.

In this process, water molecules become chemically attached to particular rock material, for example

Soil forming minerals in the rock do not contain any water. They undergo hydration when they come in contact with water. In this process, the volume of the parental material increases and hydrated materials become soft and more readily weather able.

3. Biological Weathering:

Many organisms play important roles in the weathering of rocks through physical and chemical means important organisms concerned with the decomposition of rocks are lichens, bacteria, fungi, higher plants, nematodes and other soil microbes. Lichens and some other organism’s in presence of moisture secrete carbonic acid which corrodes the rock.

The presence of roots on the surface of rock exerts a considerable pressure by which rocks are broken into smaller fragments. The root exudates also weaken the rocks and weather them to a small extent. Joffe (1949) states that there is no biogeochemical weathering. According to him, it is either physical or chemical weathering by biological agencies.


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Star Wars quiz questions and answers

  1. What day of the year is known by fans as Star Wars Day?
  2. Who does John Boyega play in the most recent Star Wars films?
  3. The showrunners of which mega TV series reportedly walked away from a planned Star Wars trilogy?
  4. What is the name of the top secret order given by Palpatine in Revenge of the Sith, calling for all Jedi leaders to be killed?
  5. What type of creature does Luke Skywalker fight underneath Jabba the Hutt’s throne in Return of the Jedi?

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Comments:

  1. Kaarlo

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  2. Eweheorde

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  4. Croydon

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