Some Budding Yeast I Used to Grow (Gotye Parody)
Some Budding Yeast I Used to Grow (Parody of Somebody that I Used to Know by Gotye feat. Kimbra) Submission for UC-Berkeley MCB Follies 2012-2013 (UC-Berkeley, Dept. of Molecular and Cell Biology) LYRICS, VOCALS, EDITING STARRING: Nathaniel Krefman STORYLINE: Lydia Thé, Haomiao Huang, Nathaniel Krefman ANIMATION: Lydia Thé Nathaniel Krefman DIRECTION PHOTOGRAPHY: Lydia Thé Haomiao Huang ________________________________________________ LYRICS: Now and then I think of things that I could have done better. Like when I forgot to give you glucose, and you just died. An organism that was right for me. The awesome power of genetics in yeast. But now I think I #39;ll have to use a metazoan. You can get addicted to the haploid-diploid cycle. And recombination in a site-specific way. So when they showed yeast could do anti-sense, It didn #39;t change any experiments. A recessive loss-of-function, try to find one in a Hela cell. But NIH, don #39;t cut me off. Just cuz yeast aren #39;t motile doesn #39;t mean I don #39;t need funding. And I don #39;t even need that much, But you say they don #39;t have neurons, and your budget #39;s tough. Did you know that we have auxotrophs? Synthetic genetic arrays. Try doing that with a fish or monkey. You say they don #39;t get develop though. Now you #39;re just some budding yeast I used to grow. Now you #39;re just some budding yeast I used to grow. Now you #39;re just some budding yeast I used to grow. Now and then I think of all we #39;ve learned with Saccharomyces. Cuz of all that ...

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Some Budding Yeast I Used to Grow (Gotye Parody) - Video

Scientific Explanation on How and Why Cannabis can Cure Cancer
Health Professionals, Doctors and Scientists Interviewed on the subject of cannabis. They are listed in order of appearance in this video... Jeffrey Hergenrather MD President of the Society of Cannabis Clinicians thesethgroup.org Dr. Robert Melamed Ph.D. Associate Professor and Biology Chairman in the Biology Department at the University of Colorado and of Cannabis Science Dr. Manuel Guzman Professor of Biochemistry - University of Madrid Paul Armentano Deputy Director NORML Prakash Nagarkatti, Ph.D. Vice President for Research University of South Carolina Columbia Distinguished Professor Dr. Donald Tashkin MD Professor of Pulmonary Medicine, UCLA

By: Lincoln Horsley

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Scientific Explanation on How and Why Cannabis can Cure Cancer - Video

Focus on Both Undergraduate and Graduate Students
Dr. Ann Hagerman, Professor of Biochemistry, talks about Miami #39;s focus on undergraduate and graduate education and research.

By: miamiuniversitycas

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Focus on Both Undergraduate and Graduate Students - Video

How to Pronounce Coded
Learn how to say Coded correctly with EmmaSaying #39;s "how do you pronounce" free tutorials. Definition of code (oxford dictionary): noun 1a system of words, letters, figures, or symbols used to represent others, especially for the purposes of secrecy: the Americans cracked their diplomatic code [mass noun]: messages written in code a phrase or concept used to represent another in an indirect way: researching #39;the family #39; is usually a code for studying women a series of letters, numbers, or symbols assigned to something for the purposes of classification or identification: each box had a label with the code SC 90 short for dialling code. I was given the number, but not the code for Guildford 2 [mass noun] Computing program instructions: assembly code 3a systematic collection of laws or statutes: a revision of the penal code a set of conventions or moral principles governing behaviour in a particular sphere: a strict dress code a stern code of honour verb [with object] 1convert (the words of a message) into a code so as to convey a secret meaning: only Mitch knew how to read the message mdash;even the name was coded express the meaning of (a statement) in an indirect way: (as adjective coded) journalists made coded allusions to his deficiencies assign a code to (something) for purposes of classification or identification: she coded the samples and sent them for dissection 2write code for (a computer program). 3 [no object] (code for) Biochemistry be the genetic code for (an amino ...

By: Emma Saying

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How to Pronounce Coded - Video

How to Pronounce Coder
Learn how to say Coder correctly with EmmaSaying #39;s "how do you pronounce" free tutorials. Definition of code (oxford dictionary): noun 1a system of words, letters, figures, or symbols used to represent others, especially for the purposes of secrecy: the Americans cracked their diplomatic code [mass noun]: messages written in code a phrase or concept used to represent another in an indirect way: researching #39;the family #39; is usually a code for studying women a series of letters, numbers, or symbols assigned to something for the purposes of classification or identification: each box had a label with the code SC 90 short for dialling code. I was given the number, but not the code for Guildford 2 [mass noun] Computing program instructions: assembly code 3a systematic collection of laws or statutes: a revision of the penal code a set of conventions or moral principles governing behaviour in a particular sphere: a strict dress code a stern code of honour verb [with object] 1convert (the words of a message) into a code so as to convey a secret meaning: only Mitch knew how to read the message mdash;even the name was coded express the meaning of (a statement) in an indirect way: (as adjective coded) journalists made coded allusions to his deficiencies assign a code to (something) for purposes of classification or identification: she coded the samples and sent them for dissection 2write code for (a computer program). 3 [no object] (code for) Biochemistry be the genetic code for (an amino ...

By: Emma Saying

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How to Pronounce Coder - Video

How to Pronounce Coders
Learn how to say Coders correctly with EmmaSaying #39;s "how do you pronounce" free tutorials. Definition of code (oxford dictionary): noun 1a system of words, letters, figures, or symbols used to represent others, especially for the purposes of secrecy: the Americans cracked their diplomatic code [mass noun]: messages written in code a phrase or concept used to represent another in an indirect way: researching #39;the family #39; is usually a code for studying women a series of letters, numbers, or symbols assigned to something for the purposes of classification or identification: each box had a label with the code SC 90 short for dialling code. I was given the number, but not the code for Guildford 2 [mass noun] Computing program instructions: assembly code 3a systematic collection of laws or statutes: a revision of the penal code a set of conventions or moral principles governing behaviour in a particular sphere: a strict dress code a stern code of honour verb [with object] 1convert (the words of a message) into a code so as to convey a secret meaning: only Mitch knew how to read the message mdash;even the name was coded express the meaning of (a statement) in an indirect way: (as adjective coded) journalists made coded allusions to his deficiencies assign a code to (something) for purposes of classification or identification: she coded the samples and sent them for dissection 2write code for (a computer program). 3 [no object] (code for) Biochemistry be the genetic code for (an amino ...

By: Emma Saying

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How to Pronounce Coders - Video

How to Pronounce Codes
Learn how to say Codes correctly with EmmaSaying #39;s "how do you pronounce" free tutorials. Definition of code (oxford dictionary): noun 1a system of words, letters, figures, or symbols used to represent others, especially for the purposes of secrecy: the Americans cracked their diplomatic code [mass noun]: messages written in code a phrase or concept used to represent another in an indirect way: researching #39;the family #39; is usually a code for studying women a series of letters, numbers, or symbols assigned to something for the purposes of classification or identification: each box had a label with the code SC 90 short for dialling code. I was given the number, but not the code for Guildford 2 [mass noun] Computing program instructions: assembly code 3a systematic collection of laws or statutes: a revision of the penal code a set of conventions or moral principles governing behaviour in a particular sphere: a strict dress code a stern code of honour verb [with object] 1convert (the words of a message) into a code so as to convey a secret meaning: only Mitch knew how to read the message mdash;even the name was coded express the meaning of (a statement) in an indirect way: (as adjective coded) journalists made coded allusions to his deficiencies assign a code to (something) for purposes of classification or identification: she coded the samples and sent them for dissection 2write code for (a computer program). 3 [no object] (code for) Biochemistry be the genetic code for (an amino ...

By: Emma Saying

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How to Pronounce Codes - Video

Crystal structure of the piRNA biogenesis factor Zucchini from mouse
Animation of X-ray crystallographic structure determined for the protein mZuc (Zucchini / PLD6 from mouse) which has been implicated as a nuclease in piRNA biogenesis. The protein forms a homodimer which displays a narrow, positively-charged groove running through the active site which is capable of accommodating single-stranded nucleic acids. These data are available on the PDB with accession codes 4GGJ and 4GGK. The full research article is: The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Ipsaro JJ, Haase AD, Knott SR, Joshua-Tor L, Hannon GJ. Nature. 2012 Nov 8;491(7423):279-83. doi: 10.1038/nature11502. Epub 2012 Oct 14.

By: jonipsaro

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Crystal structure of the piRNA biogenesis factor Zucchini from mouse - Video

Associate professor Masaya Fujita and doctoral candidate Sarem Davi study B. subtilis cells grown on an agar plate. | File photo/The Daily Cougar

Novel research in UHs biochemistry department is unfolding previously misunderstood and seemingly simple pathways in bacterial sporulation.

Biochemistry associate professor Masaya Fujitaand doctoral candidateSarem Davirecently published a paper in Proceedings of the National Academy of Sciences that outlines a mechanism for spore formation in bacillus subtilis, a common bacteria that is harmless to humans. The pathway was previously assumed by other scientists to involve only one protein: Spo0A. Fujita and Davi discovered that multiple checkpoints were involved that caused this bacteria to form into a spore.

For the bacterial system, people thought it was much simpler than a eukaryotic system. Of course, the eukaryotic systems like our body are very complicated andhave checkpoints or critical points to decide their future fate, Fujita said.

However, B. subtilis undergoes either a growing cell or a spore, depending on the environmental conditions. Its just two choices so people thought that this was very simple: that a single protein Spo0A molecule can make thesedecisions. However, the cells expressing Spo0A only kick off the sporulation process and begin making preparations, but the cells are not yet committed to this survival strategy.

The research was published in the PNAS journal because of the surprise that the previous assumptions were debunked,Fujita said. Instead of a simple network, the process involves many different steps.

The research team found that the ultimate decision process for sporulation is a result of a series of nested feed forward loops network motifs in which one master regulator controls another by directly regulating its amount and indirectly regulating its activity,Fujita said.

Using such integrated and sophisticated genetic networks, the cells can process information, and if needed, change their mind, though without a brain. This strategy allows them to make an accurate decision under unpredictable environmental conditions. Thus, the cells can postpone their final decision-making until the point of no return.

This process is difficult to study with in the wild B. subtilis, Davi said. Artificial techniques needed to be used to study the processes.

Its very difficult to study in the wild-type cells so thats why we use this artificial sporulation system so we can decouple the pathways. We can dissect different pathways and use IPCT as the inducer to study different parts. We can study it in more detail. That is how we can find out that there are different steps going on. Its very complex, Davi said.

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Biochemists left cell-shocked by UH study

Jan. 22, 2013 While working out the structure of a cell-killing protein produced by some strains of the bacterium Enterococcus faecalis, researchers stumbled on a bit of unusual biochemistry. They found that a single enzyme helps form distinctly different, three-dimensional ring structures in the protein, one of which had never been observed before.

The new findings, reported in Nature Chemical Biology, should help scientists find new ways to target the enterococcal cytolysin protein, a "virulence factor that is associated with acute infection in humans," said University of Illinois chemistry and Institute for Genomic Biology professor Wilfred van der Donk, who conducted the study with graduate student Weixin Tang.

Enterococcus faecalis (EN-ter-oh-cock-us faye-KAY-liss) is a normal microbial inhabitant of the gastrointestinal tracts of humans and other mammals and generally does not harm its host. Some virulent strains, however, produce cytolysin (sigh-toe-LIE-sin), a protein that, once assembled, attacks other microbes and kills mammalian cells.

"The cytolysin protein made by Enterococcus faecalis consists of two compounds that have no activity by themselves but when combined kill human cells," van der Donk said. "We know from epidemiological studies that if you are infected with a strain of E. faecalis that has the genes to make cytolysin, you have a significantly higher chance of dying from your infection." E. faecalis contributes to root canal infections, urinary tract infections, endocarditis, meningitis, bacteremia and other infections.

Enterococcal cytolysin belongs to a class of antibiotic proteins, called lantibiotics, which have two or more sulfur-containing ring structures. Scientists had been unable to determine the three-dimensional structure of this cytolysin because the bacterium produces it at very low concentrations. Another problem that has stymied researchers is that the two protein components of cytolysin tend to clump together when put in a lab dish.

Van der Donk and Tang got around these problems by producing the two cytolysin components separately in another bacterium, Escherichia coli (esh-uh-REE-kee-uh KOH-lie), and analyzing them separately.

"The two components are both cyclic peptides, one with three rings and the other with two rings," van der Donk said. "Curiously, a single enzyme makes both compounds."

In a series of experiments, the researchers found that one ring on each of the proteins adopted a (D-L) stereochemistry that is common in lantibiotics (see image, above). But the other rings all had an unusual (L-L) configuration, something van der Donk had never seen before.

Scientists had assumed that the enzyme that shaped enterococcal cytolysin, a lantibiotic synthetase, acted like a three-dimensional mold that gave the ring structures of cytolysin the exact same stereochemistry, van der Donk said.

"But we found that the enzyme, enterococcal cytolysin synthetase, makes the rings with different stereochemistry," he said. "I don't know of any other examples where one enzyme can make very similar products but with different stereochemistries."

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Odd biochemistry yields lethal bacterial protein

Public release date: 22-Jan-2013 [ | E-mail | Share ]

Contact: Diana Yates diya@illinois.edu 217-333-5802 University of Illinois at Urbana-Champaign

CHAMPAIGN, Ill. While working out the structure of a cell-killing protein produced by some strains of the bacterium Enterococcus faecalis, researchers stumbled on a bit of unusual biochemistry. They found that a single enzyme helps form distinctly different, three-dimensional ring structures in the protein, one of which had never been observed before.

The new findings, reported in Nature Chemical Biology, should help scientists find new ways to target the enterococcal cytolysin protein, a "virulence factor that is associated with acute infection in humans," said University of Illinois chemistry and Institute for Genomic Biology professor Wilfred van der Donk, who conducted the study with graduate student Weixin Tang.

Enterococcus faecalis (EN-ter-oh-cock-us faye-KAY-liss) is a normal microbial inhabitant of the gastrointestinal tracts of humans and other mammals and generally does not harm its host. Some virulent strains, however, produce cytolysin (sigh-toe-LIE-sin), a protein that, once assembled, attacks other microbes and kills mammalian cells.

"The cytolysin protein made by Enterococcus faecalis consists of two compounds that have no activity by themselves but when combined kill human cells," van der Donk said. "We know from epidemiological studies that if you are infected with a strain of E. faecalis that has the genes to make cytolysin, you have a significantly higher chance of dying from your infection." E. faecalis contributes to root canal infections, urinary tract infections, endocarditis, meningitis, bacteremia and other infections.

Enterococcal cytolysin belongs to a class of antibiotic proteins, called lantibiotics, which have two or more sulfur-containing ring structures. Scientists had been unable to determine the three-dimensional structure of this cytolysin because the bacterium produces it at very low concentrations. Another problem that has stymied researchers is that the two protein components of cytolysin tend to clump together when put in a lab dish.

Van der Donk and Tang got around these problems by producing the two cytolysin components separately in another bacterium, Escherichia coli (esh-uh-REE-kee-uh KOH-lie), and analyzing them separately.

"The two components are both cyclic peptides, one with three rings and the other with two rings," van der Donk said. "Curiously, a single enzyme makes both compounds."

In a series of experiments, the researchers found that one ring on each of the proteins adopted a (D-L) stereochemistry that is common in lantibiotics (see image, above). But the other rings all had an unusual (L-L) configuration, something van der Donk had never seen before.

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Study: Odd biochemistry yields lethal bacterial protein