Biology

From Things and Stuff Wiki
Revision as of 21:27, 1 November 2023 by Milk (talk | contribs) (→‎Bioinformatics)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search


General

oof

















Amino acids

  • https://en.wikipedia.org/wiki/Amino_acid - biologically important organic compounds containing amine (-NH2) and carboxylic acid (-COOH) functional groups, usually along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.

In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids (generic formula H2NCHRCOOH in most cases, where R is an organic substituent known as a "side-chain"); often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins. These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes and some antibiotics. Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids. The other three ("non-standard" or "non-canonical") are selenocysteine (present in many noneukaryotes as well as most eukaryotes, but not coded directly by DNA), pyrrolysine (found only in some archea and one bacterium) and N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts). Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element. Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids.

Many important proteinogenic and non-proteinogenic amino acids also play critical non-protein roles within the body. For example, in the human brain, glutamate (standard glutamic acid) and gamma-amino-butyric acid ("GABA", non-standard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters; hydroxyproline (a major component of the connective tissue collagen) is synthesised from proline; the standard amino acid glycine is used to synthesise porphyrins used in red blood cells; and the non-standard carnitine is used in lipid transport.

Nine proteinogenic amino acids are called "essential" for humans because they cannot be created from other compounds by the human body and, so, must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species.

Because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, and chiral catalysts.


  • https://en.wikipedia.org/wiki/Essential_amino_acid - or indispensable amino acid is an amino acid that cannot be synthesized de novo (from scratch) by the organism being considered, and therefore must be supplied in its diet. The nine amino acids humans cannot synthesize are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine (i.e., F V T W M L I K H).

Six amino acids are considered conditionally essential in the human diet, meaning their synthesis can be limited under special pathophysiological conditions, such as prematurity in the infant or individuals in severe catabolic distress.[2] These six are arginine, cysteine, glycine, glutamine, proline and tyrosine (i.e. R C G Q P Y). Five amino acids are dispensable in humans, meaning they can be synthesized in the body. These five are alanine, aspartic acid, asparagine, glutamic acid and serine (i.e., A D N E S)


DNA



  • https://en.wikipedia.org/wiki/DNA_barcoding - a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections (also called "sequences"), an individual sequence can be used to uniquely identify an organism to species, just as a supermarket scanner uses the familiar black stripes of the UPC barcode to identify an item in its stock against its reference database. These "barcodes" are sometimes used in an effort to identify unknown species or parts of an organism, simply to catalog as many taxa as possible, or to compare with traditional taxonomy in an effort to determine species boundaries.


  • https://en.wikipedia.org/wiki/Barcode_of_Life_Data_System - commonly known as BOLD or BOLDSystems, is a web platform specifically devoted to DNA barcoding. It is a cloud-based data storage and analysis platform developed at the Centre for Biodiversity Genomics in Canada. It consists of four main modules, a data portal, an educational portal, a registry of BINs (putative species), and a data collection and analysis workbench which provides an online platform for analyzing DNA sequences. Since its launch in 2005, BOLD has been extended to provide a range of functionality including data organization, validation, visualization and publication. The most recent version of the system, version 4, launched in 2017, brings a set of improvements supporting data collection and analysis but also includes novel functionality improving data dissemination, citation, and annotation. Before November 16, 2020, BOLD already contained barcode sequences for 318,105 formally described species covering animals, plants, fungi, protists (with ~8.9 million specimens).


Genes

to sort!







Sequence
  • https://en.wikipedia.org/wiki/Nucleic_acid_sequence a succession of letters that indicate the order of nucleotides within a DNA (using GACT) or RNA (GACU) molecule. By convention, sequences are usually presented from the 5' end to the 3' end. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.
  • https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism - also known as simple nucleotide polymorphism, (SNP, pronounced snip; plural snips) is a DNA sequence variation occurring commonly within a population (e.g. 1%) in which a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes.


  • https://en.wikipedia.org/wiki/Allele - one of a number of alternative forms of the same gene or same genetic locus. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. However, most genetic variations result in little or no observable variation. The word "allele" is a short form of allelomorph ("other form"), which was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes. It derives from the Greek prefix ἀλλήλ, allel, meaning "reciprocal" or "each other", which itself is related to the Greek adjective ἄλλος (allos; cognate with Latin "alius"), meaning "other".


  • https://en.wikipedia.org/wiki/Locus_(genetics) - plural loci, the specific location or position of a gene, DNA sequence, on a chromosome, in the field of genetics. Each chromosome carries many genes; humans' estimated 'haploid' protein coding genes are 20,000-25,000, on the 23 different chromosomes. A variant of the similar DNA sequence located at a given locus is called an allele. The ordered list of loci known for a particular genome is called a gene map. Gene mapping is the process of determining the locus for a particular biological trait. Diploid and polyploid cells whose chromosomes have the same allele of a given gene at some locus are called homozygous with respect to that gene, while those that have different alleles of a given gene at a locus, are called heterozygous with respect to that gene.



  • https://en.wikipedia.org/wiki/Reading_frame - way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.


  • https://en.wikipedia.org/wiki/Open_reading_frame - In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA). An AUG codon within the ORF (not necessarily the first) may indicate where translation starts. The transcription termination site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons, ORFs may span exons. These would be spliced into an ORF in the mRNA.



  • https://en.wikipedia.org/wiki/DNA - Deoxyribonucleic acid (Listeni/diˌɒksiˌraɪbɵ.njuːˌkleɪ.ɨk ˈæsɪd/; DNA) is a molecule that carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses. DNA is a nucleic acid; alongside proteins and carbohydrates, nucleic acids compose the three major macromolecules essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are known as polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of a nitrogen-containing nucleobase—either cytosine (C), guanine (G), adenine (A), or thymine (T)—as well as a monosaccharide sugar called deoxyribose and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. According to base pairing rules (A with T, and C with G), hydrogen bonds bind the nitrogenous bases of the two separate polynucleotide strands to make double-stranded DNA.


  • https://en.wikipedia.org/wiki/Base_pair - which form between specific nucleobases (also termed nitrogenous bases), are the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a backup copy of all genetic information encoded within double-stranded DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA, and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes.
  • https://en.wikipedia.org/wiki/Nucleobase - nitrogen-containing biological compounds (nitrogenous bases) found linked to a sugar within nucleosides—the basic building blocks of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Often simply called bases in genetics, their ability to form base pairs and to stack upon one another lead directly to the helical structure of DNA and RNA. Use of the word base is historical, in reference to the chemical properties of nucleobases in acid-base reactions within the test tube, and is not especially important for understanding most of their biological functions.


  • https://en.wikipedia.org/wiki/DNA_codon_table - The genetic code is traditionally represented as an RNA codon table because, when proteins are made in a cell by ribosomes, it is mRNA that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. With the rise of computational biology and genomics, most genes are now discovered at the DNA level, so a DNA codon table is becoming increasingly useful.[1] The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5' → 3' direction.


  • https://en.wikipedia.org/wiki/Chromatin - a complex of macromolecules found in cells, consisting of DNA, protein and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells (cells with defined nuclei). Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore and is localized within the nucleoid region).
Creation
  • https://en.wikipedia.org/wiki/DNA_polymerase - enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase “reads” the existing DNA strands to create two new strands that match the existing ones.

Every time a cell divides, DNA polymerase is required to help duplicate the cell’s DNA, so that a copy of the original DNA molecule can be passed to each of the daughter cells. In this way, genetic information is transmitted from generation to generation. Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form. This opens up or “unzips” the double-stranded DNA to give two single strands of DNA that can be used as templates for replication.


  • https://en.wikipedia.org/wiki/Oligonucleotide - short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, library construction and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression (e.g. microRNA), or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.

Oligonucleotides are characterized by the sequence of nucleotide residues that make up the entire molecule. The length of the oligonucleotide is usually denoted by "-mer" (from Greek meros, "part"). For example, an oligonucleotide of six nucleotides (nt) is a hexamer, while one of 25 nt would usually be called a "25-mer". Oligonucleotides readily bind, in a sequence-specific manner, to their respective complementary oligonucleotides, DNA, or RNA to form duplexes or, less often, hybrids of a higher order. This basic property serves as a foundation for the use of oligonucleotides as probes for detecting DNA or RNA. Examples of procedures that use oligonucleotides include DNA microarrays, Southern blots, ASO analysis, fluorescent in situ hybridization (FISH), and the synthesis of artificial genes. Oligonucleotides are also indispensable elements in antisense therapy.



  • Is there a sixth DNA base? methyl-adenine could regulate the expression of certain genes in eukaryotic cells could have a specific role in stem cells and in early stages of development. [7]


  • https://en.wikipedia.org/wiki/Holliday_junction - a branched nucleic acid structure that contains four double-stranded arms joined together. These arms may adopt one of several conformations depending on buffer salt concentrations and the sequence of nucleobases closest to the junction. The structure is named after the molecular biologist Robin Holliday, who proposed its existence in 1964. In biology, Holliday junctions are a key intermediate in many types of genetic recombination, as well as in double-strand break repair. These junctions usually have a symmetrical sequence and are thus mobile, meaning that the four individual arms may slide though the junction in a specific pattern that largely preserves base pairing. Additionally, four-arm junctions similar to Holliday junctions appear in some functional RNA molecules.


  • https://en.wikipedia.org/wiki/Primary_transcript - the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor messenger RNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing.




  • Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products across databases. Founded in 1998, the project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database (SGD) and the Mouse Genome Database (MGD). The GO Consortium (GOC) has since grown to incorporate many databases, including several of the world's major repositories for plant, animal, and microbial genomes. The GO Contributors page lists all member organizations.






  • https://en.wikipedia.org/wiki/Chromatin - a complex of macromolecules found in cells, consisting of DNA, protein and RNA. The primary functions of chromatin are 1) to package DNA into a smaller volume to fit in the cell, 2) to reinforce the DNA macromolecule to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replication. The primary protein components of chromatin are histones that compact the DNA. Chromatin is only found in eukaryotic cells, (a cell with a defined nucleus). Prokaryotic cells have a different organization of their DNA (the prokaryotic chromosome equivalent is called genophore) and is localized within the nucleoid region.



  • https://www.quantamagazine.org/20141002-in-social-spiders-evidence-that-groups-evolve/ [9] - TL;DR: Different colonies of these spiders had different ratios of nanny spiders to warrior spiders, based on the specific pressures of the habitat they grew up in. When these colonies were transplanted to a new habitat with different pressures, and then their ratio of nannies to warriors was forcibly changed to match the new habitat, the ratio quickly changed back to one that was suited to their old habitat, leading to the death of the colony.


Expression



  • https://en.wikipedia.org/wiki/Phenotype - the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird's nest).






  • https://en.wikipedia.org/wiki/Copy-number_variation - a form of structural variation—are alterations of the DNA of a genome that results in the cell having an abnormal or, for certain genes, a normal variation in the number of copies of one or more sections of the DNA. CNVs correspond to relatively large regions of the genome that have been deleted (fewer than the normal number) or duplicated (more than the normal number) on certain chromosomes. For example, the chromosome that normally has sections in order as A-B-C-D might instead have sections A-B-C-C-D (a duplication of "C") or A-B-D (a deletion of "C"). This variation accounts for roughly 13% of human genomic DNA and each variation may range from about one kilobase (1,000 nucleotide bases) to several megabases in size. CNVs contrast with single-nucleotide polymorphisms (SNPs), which affect only one single nucleotide base.



Sequencing









Cells


  • Allen Integrated Cell - a predictive, 3D model of human induced pluripotent stem cell (hiPSC) organization. It provides a realistic, data-driven 3D visualization of a living hiPSC in its pluri-potent state. The visualization shows the many molecular machines and structures (organelles) inside the cell, simultaneously. This integrated organization drives the cell’s basic functions, and these models provide a baseline for new models of different cell types, disease, drug responses, and cellular environments.





Metabolism

  • https://en.wikipedia.org/wiki/Metabolism - the set of life-sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter by way of cellular respiration, and anabolism, the building up of components of cells such as proteins and nucleic acids. Usually, breaking down releases energy and building up consumes energy.

  • https://en.wikipedia.org/wiki/Metabolic_pathway - in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or to signals from other cells.


  • https://en.wikipedia.org/wiki/Catabolism - the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy, or used in other anabolic reactions. Catabolism breaks down large molecules (such as polysaccharides, lipids, nucleic acids and proteins) into smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively).

Proteins



  • https://en.wikipedia.org/wiki/Proteinogenic_amino_acid - amino acids that are precursors to proteins, and are incorporated into proteins cotranslationally — that is, during translation. There are 22 proteinogenic amino acids in prokaryotes, but only 21 are encoded by the nuclear genes of eukaryotes. Of the 22, pyrrolysine (O/Pyl) is incorporated into proteins by distinct post-translational biosynthetic mechanisms; all the other 21 are directly encoded by the genetic code, including selenocysteine (U/Sec), that uses a special case of insertion during the translational incorporation, but that is not considered a post-translational modification . Humans can synthesize 11 of these 20 from each other or from other molecules of intermediary metabolism. The other nine must be consumed (usually as their protein derivatives), and so they are called essential amino acids.


  • https://en.wikipedia.org/wiki/Glutamic_acid - one of the 20-23 proteinogenic amino acids, and its codons are GAA and GAG. It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates. In neuroscience, glutamate is an important neurotransmitter that plays the principal role in neural activation. Glutamate is the most abundant excitatory neurotransmitter in the vertebrate nervous system. At chemical synapses, glutamate is stored in vesicles. Nerve impulses trigger release of glutamate from the pre-synaptic cell. Glutamate acts on ionotropic and metabotropic (G-protein coupled) receptors. In the opposing post-synaptic cell, glutamate receptors, such as the NMDA receptor or the AMPA receptor, bind glutamate and are activated. Because of its role in synaptic plasticity, glutamate is involved in cognitive functions like learning and memory in the brain. The form of plasticity known as long-term potentiation takes place at glutamatergic synapses in the hippocampus, neocortex, and other parts of the brain. Glutamate works not only as a point-to-point transmitter but also through spill-over synaptic crosstalk between synapses in which summation of glutamate released from a neighboring synapse creates extrasynaptic signaling/volume transmission. In addition, glutamate plays important roles in the regulation of growth cones and synaptogenesis during brain development as originally described by Mark Mattson.



  • https://en.wikipedia.org/wiki/Proteasome - are protein complexes inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into shorter amino acid sequences and used in synthesizing new proteins. Proteins are tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein.

In structure, the proteasome is a cylindrical complex containing a "core" of four stacked rings forming a central pore. Each ring is composed of seven individual proteins. The inner two rings are made of seven β subunits that contain three to seven protease active sites. These sites are located on the interior surface of the rings, so that the target protein must enter the central pore before it is degraded. The outer two rings each contain seven α subunits whose function is to maintain a "gate" through which proteins enter the barrel. These α subunits are controlled by binding to "cap" structures or regulatory particles that recognize polyubiquitin tags attached to protein substrates and initiate the degradation process. The overall system of ubiquitination and proteasomal degradation is known as the ubiquitin-proteasome system.


  • https://en.wikipedia.org/wiki/Protein_(nutrient) - are essential nutrients for the human body. They are one of the building blocks of body tissue, and can also serve as a fuel source. As a fuel, proteins contain 4 kcal per gram, just like carbohydrates and unlike lipids, which contain 9 kcal per gram. The most important aspect and defining characteristic of protein from a nutritional standpoint is its amino acid composition.

Proteins are polymer chains made of amino acids linked together by peptide bonds. During human digestion, proteins are broken down in the stomach to smaller polypeptide chains via hydrochloric acid and protease actions. This is crucial for the synthesis of the essential amino acids that cannot be biosynthesized by the body.

There are nine essential amino acids which humans must obtain from their diet in order to prevent protein-energy malnutrition. They are phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine. There are five dispensable amino acids which humans are able to synthesize in the body. These five are alanine, aspartic acid, asparagine, glutamic acid and serine. There are six conditionally essential amino acids whose synthesis can be limited under special pathophysiological conditions, such as prematurity in the infant or individuals in severe catabolic distress. These six are arginine, cysteine, glycine, glutamine, proline and tyrosine.

Humans need the essential amino acids in certain ratios. Some protein sources contain amino acids in a more or less 'complete' sense. This has given rise to various ranking systems for protein sources, as described in the article. Animal sources of protein include meats, dairy products, fish and eggs. Vegan sources of protein include whole grains, pulses, legumes, soy, and nuts. Vegetarians and vegans can get enough essential amino acids by eating a variety of plant proteins. It is commonly believed that athletes should consume a higher-than-normal protein intake to maintain optimal physical performance.

Peptide


Microorganism



  • https://en.wikipedia.org/wiki/Archaea - Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species forms spores.

Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.




  • https://en.wikipedia.org/wiki/Bacteriophage - a virus that infects and replicates within a bacterium. The term is derived from "bacteria" and the Greek: φαγεῖν (phagein), "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have relatively simple or elaborate structures. Their genomes may encode as few as four genes, and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere.



Evolution


Classification












  • Eating viruses can power growth, reproduction of microorganism | Nebraska Today | University of Nebraska–Lincoln - Chloroviruses, a career-defining discovery by Nebraska’s James Van Etten, are known to infect microscopic green algae. Eventually, the invading chloroviruses burst their single-celled hosts like balloons, spilling carbon and other life-sustaining elements into the open water. That carbon, which might have gone to predators of the tiny creatures, instead gets vacuumed up by other microorganisms — a grim recycling program in miniature and, seemingly, in perpetuity. [23]


to sort













Galaxy

  • Galaxy - an open source, web-based platform for data intensive biomedical research. If you are new to Galaxy start here or consult our help resources. You can install your own Galaxy by following the tutorial and choose from thousands of tools from the Tool Shed.
  • Galaxy Training! - a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Biorhythm

Yeast

Plants


Viscera




Birds

  • Avibase - The World Bird Database - an extensive database information system about all birds of the world, containing over 37 million records about 10,000 species and 22,000 subspecies of birds, including distribution information for 20,000 regions, taxonomy, synonyms in several languages and more. This site is managed by Denis Lepage and hosted by Bird Studies Canada, the Canadian copartner of Birdlife International. Avibase has been a work in progress since 1992 and I am now pleased to offer it as a service to the bird-watching and scientific community.

Human

See Being.


Bioinformatics

  • MultiQC - Aggregate results from bioinformatics analyses across many samples into a single reportMultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.


  • https://en.wikipedia.org/wiki/Biological_database - are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.



  • https://en.wikipedia.org/wiki/Minimum_information_required_in_the_annotation_of_models - Minimum Information Required In The Annotation of Models, is a community-level effort to standardize the annotation and curation processes of quantitative models of biological systems. It consists of a set of guidelines suitable for use with any structured format, allowing different groups to collaborate and share resulting models. Adherence to these guidelines also facilitates the sharing of software and service infrastructures built upon modeling activities. The idea of "a set of good practices" including "some obligatory metadata" was first proposed by Nicolas Le Novère in October 2004 as part of a discussion to develop a common database of models in systems biology (which led to the creation of BioModels Database). These initial ideas were further refined at a meeting in Heidelberg, during ICSB 2004, with representatives from many other interested groups. MIRIAM is a registered project of the MIBBI (minimum information for biological and biomedical investigations).


  • https://en.wikisource.org/wiki/Data_reuse_and_the_open_data_citation_advantage - Sharing information facilitates science. Publicly sharing detailed research data – sample attributes, clinical factors, patient outcomes, DNA sequences, raw mRNA microarray measurements – with other researchers allows these valuable resources to contribute far beyond their original analysis. In addition to being used to confirm original results, raw data can be used to explore related or new hypotheses, particularly when combined with other publicly available data sets. Real data is indispensable when investigating and developing study methods, analysis techniques, and software implementations. The larger scientific community also benefits: sharing data encourages multiple perspectives, helps to identify errors, discourages fraud, is useful for training new researchers, and increases efficient use of funding and patient population resources by avoiding duplicate data collection.

Making research data publicly available also has challenges and costs. Some costs are borne by society: For example, data archives must be created and maintained. Many costs, however, are borne by the data-collecting investigators: Data must be documented, formatted, and uploaded. Investigators may be afraid that other researchers will find errors in their results, or “scoop” additional analyses they have planned for the future.


Scanning

  • https://github.com/dafne-imaging/dafne - Dafne (Deep Anatomical Federated Network) is a collaborative platform to annotate MRI images and train machine learning models without your data ever leaving your machine.
Retrieved from "https://wiki.thingsandstuff.org/index.php?title=Biology&oldid=63088"