Topic: Molecular Biology

You are looking at all articles with the topic "Molecular Biology". We found 10 matches.

Hint: To view all topics, click here. Too see the most popular topics, click here instead.

πŸ”— Burrows–Wheeler Transform

πŸ”— Molecular Biology πŸ”— Molecular Biology/Computational Biology

The Burrows–Wheeler transform (BWT, also called block-sorting compression) rearranges a character string into runs of similar characters. This is useful for compression, since it tends to be easy to compress a string that has runs of repeated characters by techniques such as move-to-front transform and run-length encoding. More importantly, the transformation is reversible, without needing to store any additional data except the position of the first original character. The BWT is thus a "free" method of improving the efficiency of text compression algorithms, costing only some extra computation. The Burrows–Wheeler transform is an algorithm used to prepare data for use with data compression techniques such as bzip2. It was invented by Michael Burrows and David Wheeler in 1994 while Burrows was working at DEC Systems Research Center in Palo Alto, California. It is based on a previously unpublished transformation discovered by Wheeler in 1983. The algorithm can be implemented efficiently using a suffix array thus reaching linear time complexity.

Discussed on

πŸ”— Peto's Paradox

πŸ”— Physiology πŸ”— Molecular Biology πŸ”— Physiology/cell πŸ”— Molecular Biology/Molecular and Cell Biology

Peto's paradox is an observation that at the species level, the incidence of cancer does not appear to correlate with the number of cells in an organism. For example, the incidence of cancer in humans is much higher than the incidence of cancer in whales, despite whales having more cells than humans. If the probability of carcinogenesis were constant across cells, one would expect whales to have a higher incidence of cancer than humans. Peto's paradox is named after English statistician and epidemiologist Richard Peto, who first observed the connection.

Discussed on

πŸ”— Sonic Hedgehog Protein (encoded by the SHH gene)

πŸ”— Video games πŸ”— Molecular Biology πŸ”— Video games/Sega πŸ”— Molecular Biology/Molecular and Cell Biology πŸ”— Molecular Biology/Genetics πŸ”— Molecular Biology/Cell Signaling

Sonic hedgehog protein (SHH) is encoded for by the SHH gene. The protein is named after the character Sonic the Hedgehog.

This signaling molecule is key in regulating embryonic morphogenesis in all animals. SHH controls organogenesis and the organization of the central nervous system, limbs, digits and many other parts of the body. Sonic hedgehog is a morphogen that patterns the developing embryo using a concentration gradient characterized by the French flag model. This model has a non-uniform distribution of SHH molecules which governs different cell fates according to concentration. Mutations in this gene can cause holoprosencephaly, a failure of splitting in the cerebral hemispheres, as demonstrated in an experiment using SHH knock-out mice in which the forebrain midline failed to develop and instead only a single fused telencephalic vesicle resulted.

Sonic hedgehog still plays a role in differentiation, proliferation, and maintenance of adult tissues. Abnormal activation of SHH signaling in adult tissues has been implicated in various types of cancers including breast, skin, brain, liver, gallbladder and many more.

Discussed on

πŸ”— Foldit

πŸ”— Video games πŸ”— Molecular Biology πŸ”— Molecular Biology/Molecular and Cell Biology

Foldit is an online puzzle video game about protein folding. It is part of an experimental research project developed by the University of Washington, Center for Game Science, in collaboration with the UW Department of Biochemistry. The objective of Foldit is to fold the structures of selected proteins as perfectly as possible, using tools provided in the game. The highest scoring solutions are analyzed by researchers, who determine whether or not there is a native structural configuration (native state) that can be applied to relevant proteins in the real world. Scientists can then use these solutions to target and eradicate diseases and create biological innovations. A 2010 paper in the science journal Nature credited Foldit's 57,000 players with providing useful results that matched or outperformed algorithmically computed solutions.

Discussed on

πŸ”— Confocal microscopy

πŸ”— Technology πŸ”— Physics πŸ”— Neuroscience πŸ”— Molecular Biology πŸ”— Molecular Biology/Molecular and Cell Biology

Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser scanning confocal microscopy (LSCM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a spatial pinhole to block out-of-focus light in image formation. Capturing multiple two-dimensional images at different depths in a sample enables the reconstruction of three-dimensional structures (a process known as optical sectioning) within an object. This technique is used extensively in the scientific and industrial communities and typical applications are in life sciences, semiconductor inspection and materials science.

Light travels through the sample under a conventional microscope as far into the specimen as it can penetrate, while a confocal microscope only focuses a smaller beam of light at one narrow depth level at a time. The CLSM achieves a controlled and highly limited depth of field.

Discussed on

πŸ”— Miraculin

πŸ”— Chemicals πŸ”— Food and drink πŸ”— Pharmacology πŸ”— Molecular Biology πŸ”— Molecular Biology/Molecular and Cell Biology

Miraculin is a taste modifier, a glycoprotein extracted from the fruit of Synsepalum dulcificum. The berry, also known as the miracle fruit, was documented by explorer Chevalier des Marchais, who searched for many different fruits during a 1725 excursion to its native West Africa.

Miraculin itself does not taste sweet. When taste buds are exposed to miraculin, the protein binds to the sweetness receptors. This causes normally sour-tasting acidic foods, such as citrus, to be perceived as sweet. The effect can last for one or two hours.

Discussed on

πŸ”— Baum-Welch Algorithm

πŸ”— Computing πŸ”— Mathematics πŸ”— Statistics πŸ”— Molecular Biology πŸ”— Molecular Biology/Computational Biology

In electrical engineering, statistical computing and bioinformatics, the Baum–Welch algorithm is a special case of the expectation–maximization algorithm used to find the unknown parameters of a hidden Markov model (HMM). It makes use of the forward-backward algorithm to compute the statistics for the expectation step.

πŸ”— Folding@Home

πŸ”— Computing πŸ”— Biology πŸ”— Computing/Software πŸ”— Stanford University πŸ”— Pharmacology πŸ”— Molecular Biology πŸ”— Molecular Biology/Molecular and Cell Biology πŸ”— Molecular Biology/Computational Biology

Folding@home (FAH or F@h) is a distributed computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements of proteins, and is reliant on simulations run on volunteers' personal computers. Folding@home is currently based at the University of Pennsylvania and led by Greg Bowman, a former student of Vijay Pande.

The project utilizes graphics processing units (GPUs), central processing units (CPUs), and ARM processors like those on the Raspberry Pi for distributed computing and scientific research. The project uses statistical simulation methodology that is a paradigm shift from traditional computing methods. As part of the client–server model network architecture, the volunteered machines each receive pieces of a simulation (work units), complete them, and return them to the project's database servers, where the units are compiled into an overall simulation. Volunteers can track their contributions on the Folding@home website, which makes volunteers' participation competitive and encourages long-term involvement.

Folding@home is one of the world's fastest computing systems. With heightened interest in the project as a result of the COVID-19 pandemic, the system achieved a speed of approximately 1.22 exaflops by late March 2020 and reached 2.43 exaflops by April 12, 2020, making it the world's first exaflop computing system. This level of performance from its large-scale computing network has allowed researchers to run computationally costly atomic-level simulations of protein folding thousands of times longer than formerly achieved. Since its launch on OctoberΒ 1, 2000, Folding@home was involved in the production of 226 scientific research papers. Results from the project's simulations agree well with experiments.

Discussed on

πŸ”— Wikipedia tests a new UI design

πŸ”— Religion πŸ”— Biology πŸ”— History of Science πŸ”— Science πŸ”— Evolutionary biology πŸ”— Molecular Biology πŸ”— Creationism πŸ”— Tree of Life πŸ”— Molecular Biology/Genetics

Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or rare within a population. The evolutionary pressures that determine whether a characteristic would be common or rare within a population constantly change, resulting in a change in heritable characteristics arising over successive generations. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms and molecules.

The theory of evolution by natural selection was conceived independently by Charles Darwin and Alfred Russel Wallace in the mid-19th century and was set out in detail in Darwin's book On the Origin of Species. Evolution by natural selection was first demonstrated by the observation that more offspring are often produced than can possibly survive. This is followed by three observable facts about living organisms: (1) traits vary among individuals with respect to their morphology, physiology and behaviour (phenotypic variation), (2) different traits confer different rates of survival and reproduction (differential fitness) and (3) traits can be passed from generation to generation (heritability of fitness). Thus, in successive generations members of a population are more likely to be replaced by the progenies of parents with favourable characteristics that have enabled them to survive and reproduce in their respective environments. In the early 20th century, other competing ideas of evolution such as mutationism and orthogenesis were refuted as the modern synthesis reconciled Darwinian evolution with classical genetics, which established adaptive evolution as being caused by natural selection acting on Mendelian genetic variation.

All life on Earth shares a last universal common ancestor (LUCA) that lived approximately 3.5–3.8Β billion years ago. The fossil record includes a progression from early biogenic graphite, to microbial mat fossils, to fossilised multicellular organisms. Existing patterns of biodiversity have been shaped by repeated formations of new species (speciation), changes within species (anagenesis) and loss of species (extinction) throughout the evolutionary history of life on Earth. Morphological and biochemical traits are more similar among species that share a more recent common ancestor, and can be used to reconstruct phylogenetic trees.

Evolutionary biologists have continued to study various aspects of evolution by forming and testing hypotheses as well as constructing theories based on evidence from the field or laboratory and on data generated by the methods of mathematical and theoretical biology. Their discoveries have influenced not just the development of biology but numerous other scientific and industrial fields, including agriculture, medicine, and computer science.

Discussed on

πŸ”— Eigen's Paradox

πŸ”— Evolutionary biology πŸ”— Molecular Biology πŸ”— Molecular Biology/Genetics

In evolutionary biology and population genetics, the error threshold (or critical mutation rate) is a limit on the number of base pairs a self-replicating molecule may have before mutation will destroy the information in subsequent generations of the molecule. The error threshold is crucial to understanding "Eigen's paradox".

The error threshold is a concept in the origins of life (abiogenesis), in particular of very early life, before the advent of DNA. It is postulated that the first self-replicating molecules might have been small ribozyme-like RNA molecules. These molecules consist of strings of base pairs or "digits", and their order is a code that directs how the molecule interacts with its environment. All replication is subject to mutation error. During the replication process, each digit has a certain probability of being replaced by some other digit, which changes the way the molecule interacts with its environment, and may increase or decrease its fitness, or ability to reproduce, in that environment.

Discussed on