vania-janet/multiturn-rag-retrieval-data huggingface dataset:
Corynebacterium
L - Lysine production is specific to C. glutamicum in which core metabolic enzymes are manipulated through genetic engineering to drive metabolic flux towards the production of NADPH from the pentose phosphate pathway , and L - 4 - aspartyl phosphate , the commitment step to the synthesis of L - lysine , lysC , dapA , dapC , and dapF . These enzymes are up - regulated in industry through genetic engineering to ensure adequate amounts of lysine precursors are produced to increase metabolic flux . Unwanted side reactions such as threonine and asparagine production can occur if a buildup of intermediates occurs , so scientists have developed mutant strains of C. glutamicum through PCR engineering and chemical knockouts to ensure production of side - reaction enzymes are limited . Many genetic manipulations conducted in industry are by traditional cross-over methods or inhibition of transcriptional activators .
Vector (molecular biology)
In molecular cloning , a vector is a DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell , where it can be replicated and / or expressed ( e.g. - plasmid , cosmid , Lambda phages ) . A vector containing foreign DNA is termed recombinant DNA . The four major types of vectors are plasmids , viral vectors , cosmids , and artificial chromosomes . Of these , the most commonly used vectors are plasmids . Common to all engineered vectors are an origin of replication , a multicloning site , and a selectable marker .
Vinegar
Cane vinegars from Ilocos are made in two different ways . One way is to simply place sugar cane juice in large jars ; it becomes sour by the direct action of bacteria on the sugar . The other way is through fermentation to produce a local wine known as basi . Low - quality basi is then allowed to undergo acetic acid fermentation that converts alcohol into acetic acid . Contaminated basi also becomes vinegar .
Protein folding
The duration of the folding process varies dramatically depending on the protein of interest . When studied outside the cell , the slowest folding proteins require many minutes or hours to fold primarily due to proline isomerization , and must pass through a number of intermediate states , like checkpoints , before the process is complete . On the other hand , very small single - domain proteins with lengths of up to a hundred amino acids typically fold in a single step . Time scales of milliseconds are the norm and the very fastest known protein folding reactions are complete within a few microseconds .
Gram-positive bacteria
Transformation is one of three processes for horizontal gene transfer , in which exogenous genetic material passes from a donor bacterium to a recipient bacterium , the other two processes being conjugation ( transfer of genetic material between two bacterial cells in direct contact ) and transduction ( injection of donor bacterial DNA by a bacteriophage virus into a recipient host bacterium ) . In transformation , the genetic material passes through the intervening medium , and uptake is completely dependent on the recipient bacterium .
Germ cell
A 10 - 20 μm large somatic cell generally needs 24 hours to double its mass for mitosis . By this way it would take a very long time for that cell to reach the size of a mammalian egg with a diameter of 100 μm ( some insects have eggs of about 1,000 μm or greater ) . Eggs have therefore special mechanisms to grow to their large size . One of these mechanisms is to have extra copies of genes : meiotic division I is paused so that the oocyte grows while it contains two diploid chromosome sets . Some species produce many extra copies of genes , such as amphibians , which may have up to 1 or 2 million copies . A complementary mechanism is partly dependent on syntheses of other cells . In amphibians , birds , and insects , yolk is made by the liver ( or its equivalent ) and secreted into the blood . Neighboring accessory cells in the ovary can also provide nutritive help of two types . In some invertebrates some oogonia become nurse cells . These cells are connected by cytoplasmic bridges with oocytes . The nurse cells of insects provide oocytes macromolecules such as proteins and mRNA . Follicular granulosa cells are the second type of accessory cells in the ovary in both invertebrates and vertebrates . They form a layer around the oocyte and nourish them with small molecules , no macromolecules , but eventually their smaller precursor molecules , by gap junctions .
Nephron
The four mechanisms used to create and process the filtrate ( the result of which is to convert blood to urine ) are filtration , reabsorption , secretion and excretion . Filtration occurs in the glomerulus and is largely passive : it is dependent on the intracapillary blood pressure . About one - fifth of the plasma is filtered as the blood passes through the glomerular capillaries ; four - fifths continues into the peritubular capillaries . Normally the only components of the blood that are not filtered into Bowman 's capsule are blood proteins , red blood cells , white blood cells and platelets . Over 150 liters of fluid enter the glomeruli of an adult every day : 99 % of the water in that filtrate is reabsorbed . Reabsorption occurs in the renal tubules and is either passive , due to diffusion , or active , due to pumping against a concentration gradient . Secretion also occurs in the tubules and is active . Substances reabsorbed include : water , sodium , chloride , glucose , amino acids , lactate , magnesium , calcium , phosphate , uric acid , and bicarbonate . Substances secreted include urea , creatinine , potassium , hydrogen , and uric acid . Some of the hormones which signal the tubules to alter the reabsorption or secretion rate , and thereby maintain homeostasis , include ( along with the substance affected ) antidiuretic hormone ( water ) , aldosterone ( sodium , potassium ) , parathyroid hormone ( calcium , phosphate ) , atrial natriuretic peptide ( sodium ) and brain natriuretic peptide ( sodium ) . A countercurrent system in the renal medulla provides the mechanism for generating a hypertonic interstitium , which allows the recovery of solute - free water from within the nephron and returning it to the venous vasculature when appropriate .
Tooth decay
Bacteria in a person 's mouth convert glucose , fructose , and most commonly sucrose ( table sugar ) into acids such as lactic acid through a glycolytic process called fermentation . If left in contact with the tooth , these acids may cause demineralization , which is the dissolution of its mineral content . The process is dynamic , however , as remineralization can also occur if the acid is neutralized by saliva or mouthwash . Fluoride toothpaste or dental varnish may aid remineralization . If demineralization continues over time , enough mineral content may be lost so that the soft organic material left behind disintegrates , forming a cavity or hole . The impact such sugars have on the progress of dental caries is called cariogenicity . Sucrose , although a bound glucose and fructose unit , is in fact more cariogenic than a mixture of equal parts of glucose and fructose . This is due to the bacteria utilising the energy in the saccharide bond between the glucose and fructose subunits . S. mutans adheres to the biofilm on the tooth by converting sucrose into an extremely adhesive substance called dextran polysaccharide by the enzyme dextransucranase .
Incandescent light bulb
The first successful light bulb filaments were made of carbon ( from carbonized paper or bamboo ) . Early carbon filaments had a negative temperature coefficient of resistance -- as they got hotter , their electrical resistance decreased . This made the lamp sensitive to fluctuations in the power supply , since a small increase of voltage would cause the filament to heat up , reducing its resistance and causing it to draw even more power and heat even further . In the `` flashing '' process , carbon filaments were heated by current passing through them while in an evacuated vessel containing hydrocarbon vapor ( usually gasoline ) . The carbon deposited on the filament by this treatment improved the uniformity and strength of filaments as well as their efficiency . A metallized or `` graphitized '' filament was first heated in a high - temperature oven before flashing and lamp assembly . This transformed the carbon into graphite , which further strengthened and smoothed the filament . This also changed the filament to have a positive temperature coefficient , like a metallic conductor , and helped stabilize the lamp 's power consumption , temperature and light output against minor variations in supply voltage .
Bacterial conjugation
When conjugation is initiated by a signal the relaxase enzyme creates a nick in one of the strands of the conjugative plasmid at the oriT . Relaxase may work alone or in a complex of over a dozen proteins known collectively as a relaxosome . In the F - plasmid system the relaxase enzyme is called TraI and the relaxosome consists of TraI , TraY , TraM and the integrated host factor IHF . The nicked strand , or T - strand , is then unwound from the unbroken strand and transferred to the recipient cell in a 5 ' - terminus to 3 ' - terminus direction . The remaining strand is replicated either independent of conjugative action ( vegetative replication beginning at the oriV ) or in concert with conjugation ( conjugative replication similar to the rolling circle replication of lambda phage ) . Conjugative replication may require a second nick before successful transfer can occur . A recent report claims to have inhibited conjugation with chemicals that mimic an intermediate step of this second nicking event . 1.
Microphone
Early microphones did not produce intelligible speech , until Alexander Graham Bell made improvements including a variable - resistance microphone / transmitter . Bell 's liquid transmitter consisted of a metal cup filled with water with a small amount of sulfuric acid added . A sound wave caused the diaphragm to move , forcing a needle to move up and down in the water . The electrical resistance between the wire and the cup was then inversely proportional to the size of the water meniscus around the submerged needle . Elisha Gray filed a caveat for a version using a brass rod instead of the needle . Other minor variations and improvements were made to the liquid microphone by Majoranna , Chambers , Vanni , Sykes , and Elisha Gray , and one version was patented by Reginald Fessenden in 1903 . These were the first working microphones , but they were not practical for commercial application . The famous first phone conversation between Bell and Watson took place using a liquid microphone .
UNICEF
In May 2010 , Crucell N.V. announced an additional US $110 million award from UNICEF to supply its pentavalent pediatric vaccine Quinvaxem to the developing world .
Precursor mRNA
When a pre-mRNA strand has been properly processed to an mRNA sequence , it is exported out of the nucleus and eventually translated into a protein -- a process accomplished in conjunction with ribosomes .
Fermentation
Homolactic fermentation ( producing only lactic acid ) is the simplest type of fermentation . The pyruvate from glycolysis undergoes a simple redox reaction , forming lactic acid . It is unique because it is one of the only respiration processes to not produce a gas as a byproduct . Overall , one molecule of glucose ( or any six - carbon sugar ) is converted to two molecules of lactic acid : C H O → 2 CH CHOHCOOH It occurs in the muscles of animals when they need energy faster than the blood can supply oxygen . It also occurs in some kinds of bacteria ( such as lactobacilli ) and some fungi . It is this type of bacteria that converts lactose into lactic acid in yogurt , giving it its sour taste . These lactic acid bacteria can carry out either homolactic fermentation , where the end - product is mostly lactic acid , or
Cellular respiration
The potential of NADH and FADH is converted to more ATP through an electron transport chain with oxygen as the `` terminal electron acceptor '' . Most of the ATP produced by aerobic cellular respiration is made by oxidative phosphorylation . This works by the energy released in the consumption of pyruvate being used to create a chemiosmotic potential by pumping protons across a membrane . This potential is then used to drive ATP synthase and produce ATP from ADP and a phosphate group . Biology textbooks often state that 38 ATP molecules can be made per oxidised glucose molecule during cellular respiration ( 2 from glycolysis , 2 from the Krebs cycle , and about 34 from the electron transport system ) . However , this maximum yield is never quite reached because of losses due to leaky membranes as well as the cost of moving pyruvate and ADP into the mitochondrial matrix , and current estimates range around 29 to 30 ATP per glucose .
Gene
Genetic engineering is now a routine research tool with model organisms . For example , genes are easily added to bacteria and lineages of knockout mice with a specific gene 's function disrupted are used to investigate that gene 's function . Many organisms have been genetically modified for applications in agriculture , industrial biotechnology , and medicine .
Citric acid cycle
The carbon skeletons of many non-essential amino acids are made from citric acid cycle intermediates . To turn them into amino acids the alpha keto - acids formed from the citric acid cycle intermediates have to acquire their amino groups from glutamate in a transamination reaction , in which pyridoxal phosphate is a cofactor . In this reaction the glutamate is converted into alpha - ketoglutarate , which is a citric acid cycle intermediate . The intermediates that can provide the carbon skeletons for amino acid synthesis are oxaloacetate which forms aspartate and asparagine ; and alpha - ketoglutarate which forms glutamine , proline , and arginine .
Candle
Prior to the candle , people used oil lamps , in which a lit wick rested in a container of liquid oil . Liquid oil lamps had a tendency to spill , and the wick had to be advanced by hand . The earliest surviving candles originated in Han China around 200 BC , and were made from whale fat . European candles of antiquity were made from various forms of natural fat , tallow , and wax . In Ancient Rome , candles were made of tallow due to the prohibitive cost of beeswax . It is possible that they also existed in Ancient Greece , but imprecise terminology makes it difficult to determine .
Ship
Hull materials and vessel size play a large part in determining the method of construction . The hull of a mass - produced fiberglass sailboat is constructed from a mold , while the steel hull of a cargo ship is made from large sections welded together as they are built .
Protein folding
Minimizing the number of hydrophobic side - chains exposed to water is an important driving force behind the folding process . The hydrophobic effect is the phenomenon in which the hydrophobic chains of a protein collapse into the core of the protein ( away from the hydrophilic environment ) . In an aqueous environment , the water molecules tend to aggregate around the hydrophobic regions or side chains of the protein , creating water shells of ordered water molecules . An ordering of water molecules around a hydrophobic region increases order in a system and therefore contributes a negative change in entropy ( less entropy in the system ) . The water molecules are fixed in these water cages which drives the hydrophobic collapse , or the inward folding of the hydrophobic groups . The hydrophobic collapse introduces entropy back to the system via the breaking of the water cages which frees the ordered water molecules . The multitude of hydrophobic groups interacting within the core of the globular folded protein contributes a significant amount to protein stability after folding , because of the vastly accumulated van der Waals forces ( specifically London Dispersion forces ) . The hydrophobic effect exists as a driving force in thermodynamics only if there is the presence of an aqueous medium with an amphiphilic molecule containing a large hydrophobic region . The strength of hydrogen bonds depends on their environment ; thus , H - bonds enveloped in a hydrophobic core contribute more than H - bonds exposed to the aqueous environment to the stability of the native state . Chaperones
Virus
Replication of viruses involves primarily multiplication of the genome . Replication involves synthesis of viral messenger RNA ( mRNA ) from `` early '' genes ( with exceptions for positive sense RNA viruses ) , viral protein synthesis , possible assembly of viral proteins , then viral genome replication mediated by early or regulatory protein expression . This may be followed , for complex viruses with larger genomes , by one or more further rounds of mRNA synthesis : `` late '' gene expression is , in general , of structural or virion proteins .
Insulin
Insulin is produced by beta cells of the pancreatic islets in most vertebrates and by the Brockmann body in some teleost fish . Cone snails Conus geographus and Conus tulipa , venomous sea snails that hunt small fish , use modified forms of insulin in their venom cocktails . The insulin toxin , closer in structure to fishes ' than to snails ' native insulin , slows down the prey fishes by lowering their blood glucose levels .
Spinal cord
The spinal cord is made from part of the neural tube during development . There are four stages of the spinal cord that arises from the neural tube : The neural plate , neural fold , neural tube , and the spinal cord . Neural differentiation occurs within the spinal cord portion of the tube . As the neural tube begins to develop , the notochord begins to secrete a factor known as Sonic hedgehog or SHH . As a result , the floor plate then also begins to secrete SHH , and this will induce the basal plate to develop motor neurons . During the maturation of the neural tube , its lateral walls thicken and form a longtitudinal groove called the sulcus limitans . This extends the length of the spinal cord into dorsal and ventral portions as well . Meanwhile , the overlying ectoderm secretes bone morphogenetic protein ( BMP ) . This induces the roof plate to begin to secrete BMP , which will induce the alar plate to develop sensory neurons . Opposing gradients of such morphogens as BMP and SHH form different domains of dividing cells along the dorsal ventral axis . Dorsal root ganglion neurons differentiate from neural crest progenitors . As the dorsal and ventral column cells proliferate , the lumen of the neural tube narrows to form the small central canal of the spinal cord . The alar plate and the basal plate are separated by the sulcus limitans . Additionally , the floor plate also secretes netrins . The netrins act as chemoattractants to decussation of pain and temperature sensory neurons in the alar plate across the anterior white commissure , where they then ascend towards the thalamus . Following the closure of the caudal neuropore and formation of the brain 's ventricles that contain the choroid plexus tissue , the central canal of the caudal spinal cord is filled with cerebrospinal fluid .
Bacterial cell structure
The bacterial flagellum consists of three basic components : a whip - like filament , a motor complex , and a hook that connects them . The filament is approximately 20 nm in diameter and consists of several protofilaments , each made up of thousands of flagellin subunits . The bundle is held together by a cap and may or may not be encapsulated . The motor complex consists of a series of rings anchoring the flagellum in the inner and outer membranes , followed by a proton - driven motor that drives rotational movement in the filament .
Xenon
In 1995 , M. Räsänen and co-workers , scientists at the University of Helsinki in Finland , announced the preparation of xenon dihydride ( HXeH ) , and later xenon hydride - hydroxide ( HXeOH ) , hydroxenoacetylene ( HXeCCH ) , and other Xe - containing molecules . In 2008 , Khriachtchev et al. reported the preparation of HXeOXeH by the photolysis of water within a cryogenic xenon matrix . Deuterated molecules , HXeOD and DXeOH , have also been produced .
Carbon dioxide
All aerobic organisms produce CO when they oxidize carbohydrates , fatty acids , and proteins . The large number of reactions involved are exceedingly complex and not described easily . Refer to ( cellular respiration , anaerobic respiration and photosynthesis ) . The equation for the respiration of glucose and other monosaccharides is :
Virus
Uncoating is a process in which the viral capsid is removed : This may be by degradation by viral enzymes or host enzymes or by simple dissociation ; the end - result is the releasing of the viral genomic nucleic acid .
Evidence of common descent
Not only has life evolved , but life has evolved to evolve . That is , correlations within protein structure have evolved , and mechanisms to manipulate these correlations have evolved in tandem . The rates at which the various events within the hierarchy of evolutionary moves occur are not random or arbitrary but are selected by Darwinian evolution . Sensibly , rapid or extreme environmental change leads to selection for greater evolvability . This selection is not forbidden by causality and is strongest on the largest - scale moves within the mutational hierarchy . Many observations within evolutionary biology , heretofore considered evolutionary happenstance or accidents , are explained by selection for evolvability . For example , the vertebrate immune system shows that the variable environment of antigens has provided selective pressure for the use of adaptable codons and low - fidelity polymerases during somatic hypermutation . A similar driving force for biased codon usage as a result of productively high mutation rates is observed in the hemagglutinin protein of influenza A .
Endomembrane system
Vesicles sent off by the ER containing proteins are further altered at the Golgi apparatus and then prepared for secretion from the cell or transport to other parts of the cell . Various things can happen to the proteins on their journey through the enzyme covered space of the Golgi apparatus . The modification and synthesis of the carbohydrate portions of glycoproteins is common in protein processing . The Golgi apparatus removes and substitutes sugar monomers , producing a large variety of oligosaccharides . In addition to modifying proteins , the Golgi also manufactures macromolecules itself . In plant cells , the Golgi produces pectins and other polysaccharides needed by the plant structure .
Vinegar
Apple cider vinegar is made from cider or apple must , and has a brownish - gold color . It is sometimes sold unfiltered and unpasteurized with the mother of vinegar present , as a natural product . It can be diluted with fruit juice or water or sweetened ( usually with honey ) for consumption .
Carbon monoxide poisoning
Carbon monoxide is produced naturally by the body as a byproduct of converting protoporphyrin into bilirubin . This carbon monoxide also combines with hemoglobin to make carboxyhemoglobin , but not at toxic levels .
Glow stick
The glow stick contains two chemicals and a suitable dye ( sensitizer , or fluorophor ) . This creates an exothermic reaction . The chemicals inside the plastic tube are a mixture of the dye and diphenyl oxalate . The chemical in the glass vial is hydrogen peroxide . By mixing the peroxide with the phenyl oxalate ester , a chemical reaction takes place , yielding two moles of phenol and one mole of peroxyacid ester ( 1 , 2 - dioxetanedione ) . The peroxyacid decomposes spontaneously to carbon dioxide , releasing energy that excites the dye , which then relaxes by releasing a photon . The wavelength of the photon -- the color of the emitted light -- depends on the structure of the dye . The reaction releases energy mostly as light , with very little heat . The reason for this is that the reverse 2 + 2 photocycloaddition of 1 , 2 - dioxetanedione is a forbidden transition ( it violates Woodward -- Hoffmann rules ) and can not proceed through a regular thermal mechanism . Oxidation