in silico

Examples of in silico in the following topics:

• Annotating Genomes

  • The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism.
  • Ideally, these approaches co-exist and complement each other in the same annotation pipeline (process).
  • These steps may involve both biological experiments and in silico analysis.
  • Scientists are still at an early stage in the process of delineating this parts list and in understanding how all the parts "fit together. "
  • The annotation of an entire genome would entail a similar in depth analysis of thousand even millions of such DNA sequences.

• Carboxysomes

  • Carboxysomes are intracellular structures that contain enzymes involved in carbon fixation and found in many autotrophic bacteria.
  • They are proteinaceous structures resembling phage heads in their morphology; they contain the enzymes of carbon dioxide fixation in these organisms.
  • Using electron microscopy the first carboxysomes were seen in 1956, in the cyanobacterium Phormidium uncinatum.
  • In the early 1960s, similar polyhedral objects were observed in other cyanobacteria.
  • These structures were named polyhedral bodies in 1961; over the next few years they were also discovered in some chemotrophic bacteria that fixed carbon dioxide.

• Control of Transcription in Archaea

  • Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria.
  • Transcription and translation in archaea resemble these processes in eukaryotes more than in bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in eukaryotes.
  • However, other archaean transcription factors are closer to those found in bacteria.
  • Post-transcriptional modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few protein-encoding genes.
  • Compare the archaea with bacteria and eukaryotes in terms of their general mechanisms of gene expression

• In Vivo Testing

  • In vivo testing follows strict guidelines and humane animal use ethics.
  • Polyclonal antibodies have various applications in the clinic and in research laboratories.
  • Animals are also used to model human diseases in the research field.
  • In addition to having bodies that work similar to humans and other animals, rodents are small in size, easy to handle, relatively inexpensive to buy and keep, and produce many offspring in a short period of time.
  • Animals are used in laboratory experiments to translate in vitro findings.

• Methane-Producing Archaea: Methanogens

  • In deep basaltic rocks near the mid-ocean ridges, methanogens can obtain their hydrogen from the serpentinization reaction of olivine as observed in the Lost City hydrothermal field.
  • They are responsible for the methane in the belches of ruminants, as in , the flatulence in humans, and the marsh gas of wetlands.
  • Because of this, methanogens thrive in environments in which all electron acceptors other than CO2 (such as oxygen, nitrate, trivalent iron, and sulfate) have been depleted.
  • Methanogens have been found buried under kilometers of ice in Greenland, as well as in the "solid" rock of the Earth's crust, kilometers below the surface.
  • Cows also burp methane due to methanogens in their digestive systems.

• Size Variation and ORF Contents in Genomes

  • An open reading frame (ORF) is the part of a reading frame that varies in size and content in bacterial genomes.
  • Open reading frames are used as one piece of evidence to assist in gene prediction.
  • Possible stop codons in DNA are "TGA", "TAA", and "TAG".
  • These microorganisms have very little noncoding or repetitive DNA, as the variation in their genome size usually reflects differences in gene repertoire.
  • Frame +1 is the ORF predicted in the database to encode a protein. +2 and +3 are the other two potential ORFs in the same strand and -1, -2, and -3 are the three potential ORFs in the antisense strand.

• Industrial Microorganisms

  • Currently, the debate in the use of genetically modified organisms (GMOs) in food sources is gaining both momentum, with more and more supporters on both sides.
  • They are found in numerous ecological niches and are most often used in industry for the mass production of amino acids and nutritional factors.
  • Corynebacterium can also be used in steroid conversion and in the degradation of hydrocarbons.
  • Aspergillus is also commonly used in large-scale fermentation in the production of alcoholic beverages such as Japanese sake.
  • Describe how microorganisms are used in industry to manufacture food or products in large quantities

• Distribution and Importance of Parasitic Worms

  • An overactive immune response is often seen in individuals with allergies and hay-fever, specifically in developed countries where parasites have been under strict prevention and control.
  • An additional study links an increase in metabolic syndrome in the Western world and the success in preventing and eliminating parasites.
  • The study demonstrates that immune system cells, eosinophils, that are present in fat tissue play a role in the prevention of insulin resistance via secretion of interleukin 4.
  • The study showed that parasitic worm infection results in an increase in eosinophils, thus, promoting control of glucose maintenance .
  • Infectious Necator americanus larva are applied to the skin in therapy, either in a single dose or in multiple smaller doses over the course of two or three months.

• Planctomycetes

  • They are found in samples of brackish, marine, and fresh water.
  • Murein is an important heteropolymer present in most bacterial cell walls that serves as a protective component in the cell wall skeleton.
  • Instead, their walls are made up of glycoprotein rich in glutamate.
  • While they do not have a nucleus in the eukaryotic sense, the nuclear material can sometimes be enclosed in a double membrane.
  • One such example is a gene sequence (in Gemmata obscuriglobus) that was found to have significant homology to the integrin alpha-V, a protein that is important in transmembrane signal transduction in eukaryotes.

• Enzymes Used in Industry

  • Almost all chemical reactions in a biological cell need enzymes in order to occur at rates sufficient for life.
  • However, enzymes in general are limited in the number of reactions they have evolved to catalyze, and by their lack of stability in organic solvents and at high temperatures.
  • These enzymes are used in the production of sugars from starch, such as in making high-fructose corn syrup.
  • In baking, they catalyze the breakdown of starch in the flour to sugar.
  • Industrially-produced barley enzymes are widely used in the brewing process to substitute for the natural enzymes found in barley.