Topic: Molecular and Cell Biology
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Alan Turing's 100th Birthday - Mathematician, logician, cryptanalyst, scientist
Alan Mathison Turing (; 23 June 1912 – 7 June 1954) was an English mathematician, computer scientist, logician, cryptanalyst, philosopher, and theoretical biologist. Turing was highly influential in the development of theoretical computer science, providing a formalisation of the concepts of algorithm and computation with the Turing machine, which can be considered a model of a general-purpose computer. Turing is widely considered to be the father of theoretical computer science and artificial intelligence. Despite these accomplishments, he was not fully recognised in his home country during his lifetime, due to his homosexuality, and because much of his work was covered by the Official Secrets Act.
During the Second World War, Turing worked for the Government Code and Cypher School (GC&CS) at Bletchley Park, Britain's codebreaking centre that produced Ultra intelligence. For a time he led Hut 8, the section that was responsible for German naval cryptanalysis. Here, he devised a number of techniques for speeding the breaking of German ciphers, including improvements to the pre-war Polish bombe method, an electromechanical machine that could find settings for the Enigma machine.
Turing played a crucial role in cracking intercepted coded messages that enabled the Allies to defeat the Nazis in many crucial engagements, including the Battle of the Atlantic, and in so doing helped win the war. Due to the problems of counterfactual history, it is hard to estimate the precise effect Ultra intelligence had on the war, but at the upper end it has been estimated that this work shortened the war in Europe by more than two years and saved over 14 million lives.
After the war Turing worked at the National Physical Laboratory, where he designed the Automatic Computing Engine. The Automatic Computing Engine was one of the first designs for a stored-program computer. In 1948 Turing joined Max Newman's Computing Machine Laboratory, at the Victoria University of Manchester, where he helped develop the Manchester computers and became interested in mathematical biology. He wrote a paper on the chemical basis of morphogenesis and predicted oscillating chemical reactions such as the Belousov–Zhabotinsky reaction, first observed in the 1960s.
Turing was prosecuted in 1952 for homosexual acts; the Labouchere Amendment of 1885 had mandated that "gross indecency" was a criminal offence in the UK. He accepted chemical castration treatment, with DES, as an alternative to prison. Turing died in 1954, 16 days before his 42nd birthday, from cyanide poisoning. An inquest determined his death as a suicide, but it has been noted that the known evidence is also consistent with accidental poisoning.
In 2009, following an Internet campaign, British Prime Minister Gordon Brown made an official public apology on behalf of the British government for "the appalling way he was treated". Queen Elizabeth II granted Turing a posthumous pardon in 2013. The Alan Turing law is now an informal term for a 2017 law in the United Kingdom that retroactively pardoned men cautioned or convicted under historical legislation that outlawed homosexual acts.
- "Alan Turing's 100th Birthday - Mathematician, logician, cryptanalyst, scientist" | 2012-06-22 | 146 Upvotes 19 Comments
- "Happy Birthday, Alan Turing" | 2011-06-23 | 78 Upvotes 6 Comments
DNA Digital Data Storage
DNA digital data storage is the process of encoding and decoding binary data to and from synthesized strands of DNA.
While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently severely limited because of its high cost and very slow read and write times.
In June 2019, scientists reported that all 16 GB of text from Wikipedia's English-language version have been encoded into synthetic DNA.
- "DNA Digital Data Storage" | 2019-10-09 | 31 Upvotes 9 Comments
DNA origami is the nanoscale folding of DNA to create non-arbitrary two- and three-dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs make DNA a useful construction material, through design of its base sequences. DNA is a well-understood material that is suitable for creating scaffolds that hold other molecules in place or to create structures all on its own.
DNA origami was the cover story of Nature on March 16, 2006. Since then, DNA origami has progressed past an art form and has found a number of applications from drug delivery systems to uses as circuitry in plasmonic devices; however, most applications remain in a concept or testing phase.
- "DNA origami" | 2016-12-22 | 37 Upvotes 5 Comments
Evolution of metal ions in biological systems
Evolution of metal ions in biological systems refers to the incorporation of metallic ions into living organisms and how it has changed over time. Metal ions have been associated with biological systems for billions of years, but only in the last century have scientists began to truly appreciate the scale of their influence. Major (iron, manganese, magnesium and zinc) and minor (copper, cobalt, nickel, molybdenum, tungsten) metal ions have become aligned with living organisms through the interplay of biogeochemical weathering and metabolic pathways involving the products of that weathering. The associated complexes have evolved over time.
Natural development of chemicals and elements challenged organisms to adapt or die. Current organisms require redox reactions to induce metabolism and other life processes. Metals have a tendency to lose electrons and are important for redox reactions.
Metals have become so central to cellular function that the collection of metal-binding proteins (referred to as the metallomes) accounts for over 30% of all proteins in the cell. Metals are known to be involved in over 40% of enzymatic reactions, and metal-binding proteins carry out at least one step in almost all biological pathways.
Metals are also toxic so a balance must be acquired to regulate where the metals are in an organism as well as in what quantities. Many organisms have flexible systems in which they can exchange one metal for another if one is scarce. Metals in this discussion are naturally occurring elements that have a tendency to undergo oxidation. Vanadium, molybdenum, cobalt, copper, chromium, iron, manganese, nickel, and zinc are deemed essential because without them biological function is impaired.
Har Gobind Khorana
Har Gobind Khorana (9 January 1922 – 9 November 2011) was an Indian-American biochemist. While on the faculty of the University of Wisconsin–Madison, he shared the 1968 Nobel Prize for Physiology or Medicine with Marshall W. Nirenberg and Robert W. Holley for research that showed the order of nucleotides in nucleic acids, which carry the genetic code of the cell and control the cell's synthesis of proteins. Khorana and Nirenberg were also awarded the Louisa Gross Horwitz Prize from Columbia University in the same year.
Born in British India, Khorana served on the faculties of three universities in North America. He became a naturalized citizen of the United States in 1966, and received the National Medal of Science in 1987.
HeLa, the oldest and most commonly used human cell line
HeLa (; also Hela or hela) is an immortal cell line used in scientific research. It is the oldest and most commonly used human cell line. The line was derived from cervical cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who died of cancer on October 4, 1951. The cell line was found to be remarkably durable and prolific, which gives rise to its extensive use in scientific research.
The cells from Lacks's cancerous cervical tumor were taken without her knowledge or consent, which was common practice at the time. Cell biologist George Otto Gey found that they could be kept alive, and developed a cell line. Previously, cells cultured from other human cells would only survive for a few days. Scientists would spend more time trying to keep the cells alive than performing actual research on them. Cells from Lacks' tumor behaved differently. As was custom for Gey's lab assistant, she labeled the culture 'HeLa', the first two letters of the patient's first and last name; this became the name of the cell line.
These were the first human cells grown in a lab that were naturally "immortal", meaning that they do not die after a set number of cell divisions (i.e. cellular senescence). These cells could be used for conducting a multitude of medical experiments—if the cells died, they could simply be discarded and the experiment attempted again on fresh cells from the culture. This represented an enormous boon to medical and biological research, as previously stocks of living cells were limited and took significant effort to culture.
The stable growth of HeLa enabled a researcher at the University of Minnesota hospital to successfully grow polio virus, enabling the development of a vaccine, and by 1952, Jonas Salk developed a vaccine for polio using these cells. To test Salk's new vaccine, the cells were put into mass production in the first-ever cell production factory.
In 1953, HeLa cells were the first human cells successfully cloned and demand for the HeLa cells quickly grew in the nascent biomedical industry. Since the cells' first mass replications, they have been used by scientists in various types of investigations including disease research, gene mapping, effects of toxic substances on organisms, and radiation on humans. Additionally, HeLa cells have been used to test human sensitivity to tape, glue, cosmetics, and many other products.
Scientists have grown an estimated 50 million metric tons of HeLa cells, and there are almost 11,000 patents involving these cells.
The HeLa cell lines are also notorious for invading other cell cultures in laboratory settings. Some have estimated that HeLa cells have contaminated 10–20% of all cell lines currently in use.
- "HeLa, the oldest and most commonly used human cell line" | 2015-10-30 | 54 Upvotes 12 Comments
- "Immortal cells of Henrietta Lacks" | 2010-02-01 | 36 Upvotes 7 Comments
Horizontal Gene Transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HGT is an important factor in the evolution of many organisms.
Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, and plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence. It often involves temperate bacteriophages and plasmids. Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms of HGT such as transformation, transduction and conjugation, subsequently arming the antibiotic resistant genes' recipient against antibiotics. The rapid spread of antibiotic resistance genes in this manner is becoming medically challenging to deal with. Ecological factors may also play a role in the LGT of antibiotic resistant genes. It is also postulated that HGT promotes the maintenance of a universal life biochemistry and, subsequently, the universality of the genetic code.
Most thinking in genetics has focused upon vertical transfer, but the importance of horizontal gene transfer among single-cell organisms is beginning to be acknowledged.
Gene delivery can be seen as an artificial horizontal gene transfer, and is a form of genetic engineering.
- "Horizontal gene transfer" | 2014-04-29 | 14 Upvotes 1 Comments
Mirror life (also called mirror-image life, chiral life, or enantiomeric life) is a hypothetical form of life with mirror-reflected molecular building blocks. The possibility of mirror life was first discussed by Louis Pasteur. Although this alternative life form has not been discovered in nature, efforts to build a mirror-image version of biology's molecular machinery are already underway.
- "Mirror life" | 2018-09-09 | 145 Upvotes 35 Comments
The Needleman–Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences. It was one of the first applications of dynamic programming to compare biological sequences. The algorithm was developed by Saul B. Needleman and Christian D. Wunsch and published in 1970. The algorithm essentially divides a large problem (e.g. the full sequence) into a series of smaller problems, and it uses the solutions to the smaller problems to find an optimal solution to the larger problem. It is also sometimes referred to as the optimal matching algorithm and the global alignment technique. The Needleman–Wunsch algorithm is still widely used for optimal global alignment, particularly when the quality of the global alignment is of the utmost importance. The algorithm assigns a score to every possible alignment, and the purpose of the algorithm is to find all possible alignments having the highest score.
- "Needleman-Wunsch Algorithm" | 2015-06-20 | 10 Upvotes 2 Comments
Brainbow is a process by which individual neurons in the brain can be distinguished from neighboring neurons using fluorescent proteins. By randomly expressing different ratios of red, green, and blue derivatives of green fluorescent protein in individual neurons, it is possible to flag each neuron with a distinctive color. This process has been a major contribution to the field of connectomics, traditionally known as hodology, which is the study of neural connections in the brain.
The technique was originally developed in 2007 by a team led by Jeff W. Lichtman and Joshua R. Sanes, both at Harvard University. The original technique has recently been adapted for use with other model organisms including Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana.
While earlier labeling techniques allowed for the mapping of only a few neurons, this new method allows more than 100 differently mapped neurons to be simultaneously and differentially illuminated in this manner. The resulting images can be quite striking and have won awards in science photography competitions.
- "Brainbow" | 2020-07-26 | 16 Upvotes 3 Comments