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Culturomics (microbiology)
Culturomics is the high-throughput cell culture of bacteria that aims to comprehensively identify strains or species in samples obtained from tissues such as the human gut or from the environment. This approach was conceived as an alternative, complementary method to metagenomics, which relies on the presence of homologous sequences to identify new bacteria. Due to the limited phylogenetic information available on bacteria, metagenomic data generally contains large amounts of "microbial dark matter", sequences of unknown origin. Culturomics provides some of the missing gaps with the added advantage of enabling the functional study of the generated cultures. Its main drawback is that many bacterial species remain effectively uncultivable until their growth conditions are better understood. Therefore, optimization of the culturomics approach has been done by improving culture conditions. Unlike metagenomics, which relies on direct shotgun sequencing or 16S rRNA gene sequencing, cu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
High Throughput Biology
High throughput biology (or high throughput cell biology) is the use of automation equipment with classical cell biology techniques to address biological questions that are otherwise unattainable using conventional methods. It may incorporate techniques from optics, chemistry, biology or image analysis to permit rapid, highly parallel research into how cells function, interact with each other and how pathogens exploit them in disease. High throughput cell biology has many definitions, but is most commonly defined by the search for active compounds in natural materials like in medicinal plants. This is also known as high throughput screening (HTS) and is how most drug discoveries are made today, many cancer drugs, antibiotics, or viral antagonists have been discovered using HTS.Kalinina MA, Skvortsov DA, Rubtsova MP, Komarova ES, Dontsova OA. Cytotoxicity Test Based on Human Cells Labeled with Fluorescent Proteins: Fluorimetry, Photography, and Scanning for High-Throughput Assay. M ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Shotgun Sequencing
In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The Sanger sequencing#Method, chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are sequence assembly, assembled to give the overall sequence. In shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain ''reads''. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing was one of the precursor technologies that was resp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microbiota
Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host. The term ''microbiome'' describes either the collective genomes of the microbes that reside in an ecological niche or else the microbes themselves. The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genetic characteristics, sometimes collectively referred to as a holobiont. The presence of microbiota in human and other metazoan guts has been critical for understanding the co-evolution between metazoans and bacteria. Microbiota play key roles in the intestinal immune and metabolic responses via their fermentation product ( short-chain fatty acid), acetate. Introduction All plants and animals, from simple life fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genomics
Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of ''individual'' genes and their roles in inheritance, genomics aims at the collective characterization and quantification of ''all'' of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionization, ionized, for example by bombarding it with a Electron ionization, beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragmen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Time-of-flight Mass Spectrometry
Time-of-flight mass spectrometry (TOFMS) is a method of mass spectrometry in which an ion's mass-to-charge ratio is determined by a time of flight measurement. Ions are accelerated by an electric field of known strength. This acceleration results in an ion having the same kinetic energy as any other ion that has the same charge. The velocity of the ion depends on the mass-to-charge ratio (heavier ions of the same charge reach lower speeds, although ions with higher charge will also increase in velocity). The time that it subsequently takes for the ion to reach a detector at a known distance is measured. This time will depend on the velocity of the ion, and therefore is a measure of its mass-to-charge ratio. From this ratio and known experimental parameters, one can identify the ion. Theory The potential energy of a charged particle in an electric field is related to the charge of the particle and to the strength of the electric field: where ''E''p is potential energy, ''q'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Matrix-assisted Laser Desorption/ionization
In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy-absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of biomolecules (biopolymers such as DNA, proteins, peptides and carbohydrates) and various organic molecules (such as polymers, dendrimers and other macromolecules), which tend to be fragile and fragment when ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft (low fragmentation) ways of obtaining ions of large molecules in the gas phase, though MALDI typically produces far fewer multi-charged ions . MALDI methodology is a three-step process. First, the sample is mixed with a suitable matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
16S Ribosomal RNA
16S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rRNA genes and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977. Multiple sequences of the 16S rRNA gene can exist within a single bacterium. Terminology The descriptor ''16S'' refers to the size of these ribosomal subunits as reflected indirectly by the speed at which they sediment when samples are centrifuged. Thus ''16S'' means 16 Svedburg units. Functions * Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. * The 3-end contains the anti- Shine-Dalgarno sequence, which binds upstream ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetic Sequence
Genetic may refer to: *Genetics, in biology, the science of genes, heredity, and the variation of organisms **Genetic, used as an adjective, refers to genes *** Genetic disorder, any disorder caused by a genetic mutation, whether inherited or de novo ***Genetic mutation, a change in a gene **** Heredity, genes and their mutations being passed from parents to offspring ** Genetic recombination, refers to the recombining of alleles resulting in a new molecule of DNA * Genetic relationship (linguistics), in linguistics, a relationship between two languages with a common ancestor language *Genetic algorithm In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to g ..., in computer science, a kind of search technique modeled on evolutionary biology See also * Genetic memory (other) {{ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell Culture
Cell culture or tissue culture is the process by which cell (biology), cells are grown under controlled conditions, generally outside of their natural environment. After cells of interest have been Cell isolation, isolated from living tissue, they can subsequently be maintained under carefully controlled conditions. They need to be kept at body temperature (37 °C) in an incubator. These conditions vary for each cell type, but generally consist of a suitable vessel with a substrate or rich growth medium, medium that supplies the essential nutrients (amino acids, carbohydrates, vitamins, minerals), growth factors, hormones, and gases (Carbon dioxide, CO2, Oxygen, O2), and regulates the physio-chemical environment (Buffer solution, pH buffer, osmotic pressure, temperature). Most cells require a surface or an artificial substrate to form an adherent culture as a monolayer (one single-cell thick), whereas others can be grown free floating in a medium as a suspension culture. T ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Homology (biology)
In biology, homology is similarity in anatomical structures or genes between organisms of different taxa due to shared ancestry, ''regardless'' of current functional differences. Evolutionary biology explains homologous structures as retained heredity from a common descent, common ancestor after having been subjected to adaptation (biology), adaptive modifications for different purposes as the result of natural selection. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this from Aristotle's biology onwards, and it was explicitly analysed by Pierre Belon in 1555. A common example of homologous structures is the forelimbs of vertebrates, where the bat wing development, wings of bats and origin of avian flight, birds, the arms of primates, the front flipper (anatomy), flippers of whales, and the forelegs of quadrupedalis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metagenomics
Metagenomics is the study of all genetics, genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the microbial composition of Natural environment, environmental and clinical samples without the need for time-consuming Microbiological culture, culture of individual species. Metagenomics has transformed microbial ecology and evolutionary biology by uncovering previously hidden biodiversity and metabolic capabilities. As the cost of DNA sequencing continues to decline, metagenomic studies now routinely profile hundreds to thousands of samples, enabling large-scale exploration of microbial communities and their roles in health and global ecosystems. Metagenomic studies most commonly employ shotgun sequencing though Third-generation sequencing, long-read sequencing is being increasingly utilised as technologies advance. The field is also referre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
