9 Ocak 2015 Cuma

Dynamic Duo, a Dimeric Enzyme, Clobbers Oxidative Stress

  • Dynamic Duo, a Dimeric Enzyme, Clobbers Oxidative Stress
  • Alternating conformations and switching tasks, a dimer’s oppositely oriented halves relieve the cellular stress that can build up when molecular oxygen is used for power generation. When one half of the dimer acts like a proton pump, the other half converts NADH to NADP+—and vice versa.
    Both of these mutually exclusive tasks are necessary to create NADPH, which is used for amino acid biosynthesis and to remove reactive oxygen species. Yet somehow both tasks are accomplished by one enzyme, nicotinamide nucleotide transhydrogenase (TH).
    The details of TH’s task juggling ways emerged from structural studies of the ancient enzyme, which is found throughout the animal kingdom as well as in plants and many simpler species. In humans and other higher organisms, TH works within mitochondria, the tiny double-hulled oxygen reactors that help power most cellular processes.
    Although oxygen is great for efficient energy production, it has a serious downside: the accumulation of reactive oxygen species. These have been linked with diseases such as diabetes, cancer, and Alzheimer's and Parkinson's diseases, as well as with cell death and aging. To support their use of oxygen, cells have had to evolve defense mechanisms, of which TH is a part.
    TH has long been thought to participate in the production of NADPH, which is crucial for defusing oxygen-free radicals. But TH has been hard to study. It has exceptionally loose structural components, and so it is difficult to evaluate using X-ray crystallography. With its structure poorly understood, TH has given up few functional secrets.
    Until recently. In the January 9 issue of Science, researchers based at The Scripps Research Institute (TSRI) presented a new structural model for TH, which they used to support speculation about TH’s mechanisms. The details, which appeared in an article entitled, “Division of labor in transhydrogenase by alternating proton translocation and hydride transfer,” included the structure of TH’s transmembrane portion and the way in which TH’s parts relate to the enzyme’s whole.
    “We present the 2.8 Å crystal structure of the transmembrane proton channel domain of TH from Thermus thermophilus and the 6.9 Å crystal structure of the entire enzyme (holo-TH),” wrote the authors. “The membrane domain crystallized as a symmetric dimer, with each protomer containing a putative proton channel.”
    Most interesting were revelations about TH’s “domain III” structures. These appear directly above TH’s transmembrane structure, just inside the mitochondrial matrix. They serve to bind NDPH’s precursor molecule, NADP+, during conversion to NADPH. Structural biologists haven't understood how two such structures could work side by side in the TH dimer and not interfere with each other's activity. The new structural data suggest that these side-by-side structures are highly flexible and always have different orientations.
    “Our most striking finding was that the two domain III structures are not symmetric—one of them faces up while the other faces down," said Josephine H. Leung, first author of the Science article and a graduate student in the laboratory of C. David Stout, Ph.D., an associate professor at TSRI.
    One of structures is oriented apparently to catalyze the production of NADPH, while the other is turned toward the membrane, perhaps to facilitate transit of a proton. The new structural model suggests that with each proton transit, the two domain III structures flip and switch their functions. "We suspect that the passage of the proton is what somehow causes this flipping of the domain III structures," Leung noted.
    "Despite its importance, TH has been one of the least studied of mitochondrial enzymes," stated Dr. Stout. "Our new study helps clear up some mysteries—suggesting how the enzyme structure might harness protons and indicating that its two sides are able to alternate functions, always staying in balance."
  • Kaynak: http://www.genengnews.com/gen-news-highlights/dynamic-duo-a-dimeric-enzyme-clobbers-oxidative-stress/81250786/

6 Ocak 2015 Salı

Fructose is more toxic than table sugar, and cuts lifespan and reproduction of female mice

The sugar in corn syrup is more toxic to female mice than regular table sugar, new research has found.
FIONA MACDONALD   6 JAN 2015

 
Female mice that are fed a comparable human dose of fructose have both their reproductive abilities and their lifespans cut shorter than those that are fed regular table sugar or sucrose, new research shows.
“This is the most robust study showing there is a difference between high-fructose corn syrup and table sugar at human-relevant doses,” said biologist Wayne Potts from the University of Utah in the US, who led the study, in a press release.
Interestingly, the study found that there was no difference in the affects of fructose and normal sugar in male mice, which the researchers believe may indicate that both sugars are equally toxic to males. 
The results which are being published in The Journal of Nutrition, and they’re worrying, as high-fructose corn syrup is now found in many processed foods, from soft drinks to muesli bars.
While many studies have shown that both types of sugar aren’t great for you, the team was interested in investigating whether their affects differed. Previous studies had suggested that fructose was worse for animals - but hadn’t tested the sugars in the way humans normally consume them.
And it turns out that high-fructose sugar blends and table sugar are chemically quite distinct. Corn syrup contains far higher levels of fructose than glucose, which means the two remain as separate molecules called monosaccharides. But, in the white powdered table sugar we use when baking, there are roughly equal parts of fructose and glucose, and they bond to form a disaccharide compound.
To figure out how the two sugars affected mice, the researchers looked at mice that were either fed a diet where 25 percent of the calories were in the form of high-fructose and glucose monosccharides, like the type found in corn syrup, or where 25 percent came from table sugar.
This is comparable to the percentage of calories the average American consumes each day from added sugar, which ranges from 13 to 25 percent. And almost half of that comes from high-fructose sugars found in cane syrup.
“When the diabetes-obesity-metabolic syndrome epidemics started in the mid-1970s, they corresponded with both a general increase in consumption of added sugar and the switchover from sucrose being the main added sugar in the American diet to high-fructose corn syrup making up half our sugar intake,” explained Potts in the release.
The team then studied the two groups of mice for 40 weeks and observed how long the mice lived, how many children they had and how well they managed to hang on to their mice “houses” while competing with other individuals.
The female on the high-fructose diet had 1.87 times higher death rates than those on the sucrose diet, and they also produced 26.4 percent fewer children, suggesting that their reproductive rates had been affected.
The males showed no difference, but a study by the same group in 2013 found that males that were fed a high-fructose diet were less likely to be able to reproduce and hold their territory than those that were fed starch, which suggests that sugar in general is bad for the guys.
But regardless of the sex of the mice, there was no difference between the two diet groups when it came to how much they ate, weight gain and glucose intolerance. 
The scientists still aren’t sure exactly what’s causing the difference in the two types of sugars, but table sugar, or sucrose, is broken down into monosaccharides before the body absorbs it, so whatever is causing the difference must be occurring before the food is absorbed.
“So we speculate that the different sugars could favour different microbes in the guts of mice. Other research has shown differences in bacterial communities in the gut to be associated with metabolic diseases in rodents and in humans. It’s possible one form of sugar causes more bacteria to get across your gut than another,” said James Ruff, the study’s first author, in the release.
Obviously there's a lot more research to be done on what the affect of these sugars is on humans, but it's interesting research to consider next time you reach for a second can of coke.
Kaynak:http://www.sciencealert.com/fructose-is-more-toxic-than-table-sugar-and-cuts-lifespan-and-reproduction-of-female-mice

KONUŞMAYI ÖĞRENMENİN SIRRI GENLERDE!

Bristol Üniversitesi Tıbbi Araştırmalar Konseyi (Medical Research Council-MRC) Bütüncül Epidemiyoloji Bölümü’nden biliminsanları, dünyanın çeşitli yerlerindeki meslektaşlarıyla birlikte, ROBO2 geni yakınındaki genetik değişimlerle dil gelişiminin erken evrelerinde çocukların söyleyebildiği kelime sayıları arasında önemli bir bağlantı keşfettiler.
Bizler 10-15 aylıkken kelimeleri söylemeye başlarız ve kelime hazinemiz bizimle birlikte büyür. 15-18 aylıkken 50, 18-30 aylıkken 200, altı yaşındayken 14.000 civarında kelime biliriz. Ortaokuldan ayrıldığımızda ise dağarcığımız 50.000’in üzerinde kelimeye sahiptir.
Araştırmacılar konuşmayı öğrenmeyle genetik yapı arasındaki bağlantıyı, iki kelimeyi birleştirmeye ve daha karmaşık grametik yapıları kurmaya başlamamış, sadece birer kelimeyle iletişim kuran 15-18 aylık çocuklarda buldular.
16 Eylül’de Nature Communications’da yayımlanan araştırmanın sonuçları yakın zaman önce disleksi ve konuşma bozukluklarıyla ilgili araştırmalarda incelenen “kromozom 3” üzerindeki belirli genetik bölgelere ışık tutuyor.
ROBO2 geni, ROBO2 proteinini yapmak üzere talimatlar taşır. Bu protein, bebeklerde dil gelişimiyle birlikte ses üretimini de sağlayan beyin hücreleri ve diğer nöronal hücre yapılanmalarındaki kimyasalları yönlendirir. Aynı zamanda ROBO2 proteini, okumayla ve konuşma seslerinin depolanmasıyla bağlantılı olduğu bulunmuş diğer ROBO proteinleriyle sık sık etkileşimde bulunur.
Araştırmayı, MRC Bütüncül Epidemiyoloji Bölümü’nden Profesör Davey Smith ile ortaklaşa yürüten Dr. Beate St. Pourcain, “Bu araştırma, sağlıklı çocuklarda dil gelişiminin erken evrelerinde, özellikle sadece birer kelime ile konuşulan dönemde etkili olabilecek genetik faktörlerin daha iyi anlaşılmasına yardımcı oluyor ve ROBO proteini ile insanlardaki dilsel yeteneklerin çeşitliliği arasındaki bağı güçlendiriyor” diyor.
Warwick Üniversitesi’nde görev yapan, çalışmanın başyazarlarından Dr. Claire Haworth ise sonuçları şöyle yorumluyor: “Bu araştırmada DNA kullanılarak elde edilen sonuçların, dil gelişiminde genetik etkilerin önemine ilişkin yaptığımız ikiz çalışmalarının sonuçlarını doğruladığını bulduk. Bu iyi bir haber; çünkü dil gelişiminin erken evrelerinde etkili olan pek çok genetik faktörün yakalanmasında, yürütülmekte olan DNA bazlı araştırmaların kullanılabileceği anlamına geliyor.”
10.000’i aşkın çocuğun verilerinin kullanıldığı araştırma, Erken Genetik ve Yaşam Seyri Epidemiyolojisi Birliği’nde (EArly Genetics and Lifecourse Epidemiology Consortium; EAGLE) çalışan biliminsanlarının oluşturduğu uluslararası bir takım tarafından yapıldı.
Çeviri: Şule Dede / Bilim ve Gelecek
Kaynak: http://bilimfili.com/konusmayi-ogrenmenin-sirri-genlerde/

5 Ocak 2015 Pazartesi

DNA Replication(DNA Replikasyonu)

http://www.biology101.org/biologystudyguides/dnareplication.php

Human Body Ingredients

Our entire composition comes from the cosmic dust of exploding stars. You are literally the stuff of stars...

Kaynak: http://imgur.com/r/Infographics/wORsdRm

Surprise! 20 Percent of Neanderthal Genome Lives On in Modern Humans, Scientists Find

Two new studies suggest that the contribution from Neanderthal DNA was vital.

Comparison of Neanderthal anatomy to modern human anatomy.
 A comparison of Neanderthal anatomy to modern human anatomy.
PHOTOGRAPH JOE MCNALLY, NATIONAL GEOGRAPHIC
Ed Yong
PUBLISHED JANUARY 29, 2014
When modern humans migrated out of Africa some 60,000 years ago, they found the Eurasian continent already inhabited by brawny, big-browed Neanderthals. We know that at least some encounters between the two kinds of human produced offspring, because the genomes of people living outside Africa today are composed of some 1 to 4 percent Neanderthal DNA.
Two studies published concurrently in Nature andScience on Wednesday suggest that while the Neanderthal contribution to our genomes was modest, it may have proved vitally important.
Some parts of non-African genomes are totally devoid of Neanderthal DNA, but other regions abound with it, including those containing genes that affect our skin and hair. This hints that the Neanderthal gene versions conferred some benefit, and were kept during evolution.
"It seems quite compelling that as modern humans left Africa, met Neanderthals, and exchanged genes, we picked up adaptive variants in some genes that conferred an advantage in local climatic conditions," says Joshua Akey, who led the study in Science.
"The adaptive things from Neanderthals are very interesting because they are not obvious," says John Hawks of the University of Wisconsin-Madison, who was not involved in either study. Based on fossil bones alone, anthropologists would never have predicted that Neanderthals contributed to the keratin filaments and immune systems of modern people.
The fact that Neanderthal DNA is totally absent from other stretches of the modern non-African genome suggests that their versions of the genes in these regions would have caused problems in modern humans, and were weeded out by natural selection.
In the Nature study, Sriram Sankararaman and David Reich of Harvard Medical School used the previously sequenced Neanderthal genome to screen 1,004 modern genomes for sequences with distinctive Neanderthal features.
For example, if a fragment of DNA is shared by Neanderthals and non-Africans, but not Africans or other primates, it is likely to be a Neanderthal heirloom. Also, Neanderthal sequences are typically inherited in large batches, since they were imported into the modern human genome relatively recently and have not had time to break apart.
In the Science study, Akey and Benjamin Vernot, both of the University of Washington in Seattle, used similar statistical features to search for Neanderthal DNA in the genomes of 665 living people—but they initially did so without the Neanderthal genome as a reference. They still managed to identify fragments that collectively amount to 20 percent of the full Neanderthal genome.
Neanderthal Influence on Skin, Hair, Common Diseases
Despite their different approaches, both teams converged on similar results. They both found that genes involved in making keratin—the protein found in our skin, hair, and nails—are especially rich in Neanderthal DNA.
For example, the Neanderthal version of the skin gene POU2F3 is found in around 66 percent of East Asians, while the Neanderthal version of BNC2, which affects skin color, among other traits, is found in 70 percent of Europeans.
The Neanderthal version of these genes may have helped our ancestors thrive in parts of the world that they were not familiar with but that Neanderthals had already adapted to. "Neanderthals had been in these environments for hundreds or thousands of years," says Sankararaman. "As modern human ancestors moved into these areas, one way to quickly adapt would be to get genes from the Neanderthals."
"Unfortunately, skin and hair do so many things that it's hard to speculate on what specifically that adaptive trait was," says Akey.
Sankararaman also found Neanderthal variants in genes that affect the risk of several diseases, including lupus, biliary cirrhosis, Crohn's disease, and type 2 diabetes. The significance of these sequences is "even less clear."
Both teams found that non-African genomes have large continuous "deserts" that are totally devoid of Neanderthal DNA. These regions include genes such as FOXP2, which is involved in motor coordination and could play an important role in human language and speech.
The Neanderthal-poor deserts are especially big in the X chromosome, and include genes that are specifically activated in testes. This hints that some Neanderthal genes may have reduced the fertility of male modern humans and were eventually lost. However, Hawks cautions that this probably happened over hundreds of generations—it was very unlikely that the sons of Neanderthals and modern humans were obviously infertile.
DNA Hints at Other Mystery Humans
Both teams are now planning to apply their methods to other hominids like the Denisovans—an enigmatic group whose presence in Asia some 40,000 years ago is known just from DNA from a finger bone and some teeth found in a single cave in Russia.
And Akey's work shows that it may even be possible to partially reconstruct the genomes of unknown groups of ancient humans without any prehistoric DNA samples.
"That's one of the things that I'm most excited about," he says. "Paleogenomics is a difficult field because it often requires finding suitable fossils with well-preserved DNA. "Maybe we're not always beholden to bones. We can look at the genomes of present-day individuals."
It is becoming increasingly clear that the Pleistocene was awash with many different groups of early humans, hooking up with each other to various degrees. Recent studies, for instance, have found tantalizing hints of unknown groups from Asia and Africa that left genes in Denisovans and modern humans, respectively. Akey's method could give us our first glimpse at these mystery humans.
"If there is no fossil evidence and potentially never will be, this will be the only way of finding out about groups that were important in human history," he added.
Kaynak:http://news.nationalgeographic.com/news/2014/01/140129-neanderthal-genes-genetics-migration-africa-eurasian-science/