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The human genome is larger and more complex than bacterial genomes. This is not particularly surprising since one would expect to find more genes in humans than in bacteria. However, the genome size of many eukaryotes does not appear to be related to an organism’s genetic complexity; for example, the salamander genome is ten times larger than the human genome. This apparent paradox was resolved by the discovery that many organisms contain not only genes but also large amounts of so-called junk DNA that does not code for proteins at all. In particular, most human genes are broken into pieces called exons that are separated by this junk DNA. The difference in the sizes of the salamander and human genomes thus presumably reflects larger amounts of junk DNA and repeats in the salamander genome.

Split genes are analogous to a magazine article that begins on page 1, continues on page 13, then takes up again on pages 43, 51, 74, 80, and 91, with pages of advertising appearing in between. We do not understand why these jumps occur. and a significant portion of the human genome is this junk “advertising” that separates exons.

More confusing is that the jumps between different parts of split genes are inconsistent from species to species. A gene in an insect edition of the genome will be organized differently than the related gene in a worm genome. The number of parts (exons) may be different: the information that appears in one part in the human edition may be broken up into two in the mouse version, or vice versa. While the genes themselves are related, they may be quite different in terms of the parts’ structure.

Gene prediction is the problem of locating genes in a genomic sequence. Human genes constitute only 3% of the human genome, and no existing in silico gene recognition algorithm provides completely reliable gene recognition. The intron-exon model of a gene seems to prevail in eukaryotic organisms; prokaryotic organisms (like bacteria) do not have broken genes. As a result, gene prediction algorithms for prokaryotes tend to be somewhat simpler than those for eukaryotes.

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Природни канцероген, изазивач мутација

 

Вучја јабука (лат. Aristolochia clematitis) је зељаста биљка из фамилије Aristolochiaceae. Раније се сматрала лековитом и употребљавана је широм Балкана, али се у последње време (као извор аристолохинске киселине) сматра узрочником балканске ендемске нефропатије.

 

 

640px-Balkan_endemic_nephropathy_map.svg

 

Mapa balkanske endemske nefropatije

 
Balkanska endemska nefropatija upalna je bolest bubrega (oblik intersticijskog nefritisa) nepoznatog uzroka koja se javlja na točno određenim područjima naBalkanu. Prvi puta je prepoznata 1920ih godina, među malim zajednicam duž rijeke Dunav i njenih pritoka, na području današnjih zemalja HrvatskeBosneSrbije,Rumunjske i Bugarske. Najiznendađujuća značajka ove bolesti je lokaliziranost. Postoji otprilike desetak manjih područja gdje se bolest pojavljuje, koja su uglavnom ruralna. Između područja ne postoje nikakve poveznice osim bolesti. Balkanska endemska nefropatija je spora i napredujuća bolest, koja obično završava letalnim ishodom. Od bolesti jednako oboljevaju došljaci kao i starosjedioci, zbog čega se smatra da je uzročnik bolesti neki agens (tvar) iz okoliša.

 

 

640px-Aristolochia_clematitis_002.JPG

 

Aristolochia clematitis, the plant responsible for Balkan endemic nephropathy

 

Aristolochic acids are a family of carcinogenicmutagenic, and nephrotoxic compounds commonly found in the birthwort (Aristolochiaceae) family of plants. Aristolochic acid (AA) I is the most abundant one.The Aristolochiaceae family includes the Aristolochia genus and the Asarum (wild ginger) genus, which are commonly used in Chinese herbal medicine.Although these compounds are widely associated with kidney problems and urothelial cancers, the use of AA-containing plants for medicinal purposes has a long history. Nevertheless, the FDA has issued warnings regarding consumption of AA-containing supplements.

 

Aristolochic acid poisoning was first diagnosed at a clinic in Brussels, Belgium, when cases of nephritis leading to rapid kidney failure were seen in a group of women who had all taken the same weight-loss supplement, Aristolochia fangchi, which contained aristolochic acid. This nephritis was termed “Chinese herbs nephropathy” (CHN) due to the origin of the weight-loss supplement. A similar condition previously known as Balkan endemic nephropathy (BEN), first characterized in the 1950s in southeastern Europe, was later discovered to be also the result of aristolochic acid (AA) consumption. BEN is more slowly progressive than the nephritis that is seen in CHN, but is likely caused by low-level AA exposure, possibly from contamination of wheat flour seeds by a plant of the birthwort family, Aristolochia clematitis. CHN and BEN fall under the umbrella of what is now known as aristolochic acid nephropathy, the prevalent symptom of AA poisoning.

 

Transversion, in molecular biology, refers to the substitution of a (two ring) purine for a (one ring) pyrimidine orvice versa, in deoxyribonucleic acid (DNA). It can only be reversed by a spontaneous reversion.

Although there are two possible transversions but only one possible transition, transition mutations are more likely than transversions because substituting a single ring structure for another single ring structure is more likely than substituting a double ring for a single ring. Also, transitions are less likely to result in amino acid substitutions (due to wobble base pair), and are therefore more likely to persist as "silent substitutions" in populations as single nucleotide polymorphisms (SNPs). A transversion usually has a more pronounced effect than a transition because the third nucleotide codon position of the DNA, which to a large extent is responsible for the degeneracy of the code, is more tolerant of transition than a transversion: that is, a transition is more likely to encode for the same amino acid.

Transversions can be spontaneous, or can be caused by ionizing radiation or alkylating agents.

473px-Transitions-transversions-v4.svg.p

 

Aristolochic acid, a natural plant chemical causing A:T transversions in humans

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Još jedan prirodan kancerogen, aflatoksin. I on izaziva mutacije...

 

Aflatoxin B1 induces the transversion of G-->T in codon 249 of the p53 tumor suppressor gene in human hepatocytes.

Half of hepatocellular carcinoma (HCC) from regions in the world with high contamination of food with the mycotoxin aflatoxin B1 (AFB1) contain a mutation in codon 249 of the p53 tumor suppressor gene. The mutation almost exclusively consists of a G-->T transversion in the third position of this codon, resulting in the insertion of serine at position 249 in the mutant protein. 

 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC47402/

 

Aflatoksini su prirodni mikotoksini koje proizvode mnoge vrste Aspergillus gljiva, od kojih su najznačajnije Aspergillus flavus i Aspergillus parasiticus. Aflatoksini su otrovni i spadaju među najkancerogenije poznate supstance.[5] Aflatoksini se stvaraju na polju i tokom skladištenja, a najčešće se mogu naći u kukuruzu, susamu, kikirikiju, pamuku, pirinču, pistaćima, semenkama bundeve, bademu, lešniku, suncokretu, soji, sušenom voću, začinima, mleku i mlečnim proizvodima i mesu.

B1 aflatoksin je jedina supstanca iz grupe aflatoksina koja se nalazi na listi kancerogenih materija. Pokazuje štetne uticaje pre svega na ćelije jetre, kako u smislu toksičnosti, tako i u smislu povećanja rizika za pojavu raka jetre. Ipak, medicinske studije ukazuju na to da se rak jetre retko javlja samo kao posledica intoksikacije aflatoksinom B1, već je potrebno da ona bude udružena sa drugim faktorima rizika poput hronične infekcije virusom hepatitisa i sl.

 

 
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mutation-and-dna-repair-mechanisms-28-72

 

100.000 mutacija po ćeliji ljudskog organizma dnevno ?! WTF

 

Current estimation of human total cell number calculated for a variety of organs and cell types is presented. These partial data correspond to a total number of 3.72 × 1013

 

(3.72 × 1013) x 103.72 × 1019 mutacija u jednom ljudskom organizmu dnevno!

 

37200000000000000000

 

37 triliona (milion x milion x milion)

 

red veličina:

 

Mathematics – Answer to the wheat and chessboard problem: When doubling the grains of wheat on each successive square of a chessboard, beginning with one grain of wheat on the first square, the final number of grains of wheat on all 64 squares of the chessboard when added up is 264−1 = 18,446,744,073,709,551,615 (≈1.84×1019)

 

BioMed – Insects: It has been estimated that the insect population of the Earth is about 1019

 

 

Broj dnevnih mutacija u organizmu čoveka jednak je 3,7 ukupnih populacija insekata na Zemlji!

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Genetski stražar, p53

 

368px-P53.png

All cancers begin when one or more genes in a cell are mutated, or changed. This creates an abnormal protein or no protein at all. The most commonly mutated gene in people who have cancer is p53. In fact, more than 50% of all cancers involve a missing or damaged p53 gene. Most p53 gene mutations are acquired mutations. Germline p53 mutations are rare.

 

Tumor protein p53, also known as p53 is any isoform of a protein encoded by homologous genes in various organisms, such as TP53 (humans) and Trp53 (mice). This homolog (originally thought to be, and often spoken of as, a single protein) is crucial in multicellular organisms, where it prevents cancer formation, thus, functions as a tumor suppressor. As such, p53 has been described as "the guardian of the genome" because of its role in conserving stability by preventing genome mutation.Hence TP53 is classified as a tumor suppressor gene.

 

Fig-7-18-p53-Gene.jpg

 

 

 

 

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original.JPG


Non-healing wounds make it more difficult to provide effective treatment to patients and are therefore a serious problem faced by doctors. These wounds can be caused by damage to blood vessels in the case of diabetes, failure of the immune system resulting from an HIV infection or cancers, or slow cell division in elderly people. Treatment of non-healing wounds by conventional methods is very difficult, and in some cases impossible.

Cold atmospheric-pressure plasma refers to a partially ionized gas—the proportion of charged particles in the gas is close to 1 percent, with a temperature below 100,000 K. Its application in biology and medicine is possible through the advent of plasma sources generating jets at 30-40?°C.

 

 

 

An earlier study established the bactericidal properties of low-temperature plasma, as well as the relatively high resistance of cells and tissues to its influence. The results of plasma treatment of patients with non-healing wounds varied from positive to neutral. The authors’ previous work prompted them to investigate the possibility that the effect of plasma treatment on wound healing could depend on application pattern (the interval between applications and the total number of applications).

Two types of cells were used in this study: fibroblasts (connective tissue cells) and keratinocytes (epithelial cells). Both play a central role in wound healing.

 

Xdf86QN.jpg

 

 
Fig. 2. Experimental design. The first set of samples (cells) was treated by plasma once [A], while the second and the third sets were treated two and three [C] times with 48 and 24 hour intervals respectively. Credit: MIPT

The effect of plasma treatment on cells was measured. In fibroblast samples, the number of cells increased by 42.6 percent after one application [A] and by 32 percent after two applications , as compared to the untreated controls. While no signs of DNA breaks were detected following plasma application, an accumulation of cells in the active phases of the cell cycle was observed, alongside a prolonged growth phase (30 hours). This means that the effect of plasma could be characterized as regenerative, as opposed to harmful.

The proliferation of cells that had been treated daily over a period of three days (group C) was reduced by 29 percent relative to the controls. Keratinocytes did not show noticeable changes in proliferation.

The researchers also performed an assay of the senescence-associated β-galactosidase, which is measured at pH 6.0. The concentration of this enzyme in a cell increases with age. Plasma treatment significantly reduced the content of this substance in the samples. This, together with a prolonged exponential growth phase of the culture, suggests a functional activation of cells—their rejuvenation.

“The positive response to plasma treatment that we observed could be linked to the activation of a natural destructive mechanism called autophagy, which removes damaged organelles from the cell and reactivates cellular metabolic processes,” says Elena Petersen, a co-author of the paper and the head of the Laboratory of Cellular and Molecular Technologies at MIPT.

The scientists are planning additional research into the molecular mechanisms underlying the effects of plasma on cells. They also aim to determine the influence of a patient’s age on the effectiveness of plasma therapy.

Source: Moscow Institute of Physics and Technology

 

 

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Brain training can alter opinions of faces

 

Neurofeedback technique nudges people to shift neutral judgments to like or dislike human faces

 

BY LAURA SANDERS 2:01PM, SEPTEMBER 8, 2016

 

 

By sneakily influencing brain activity, scientists changed people’s opinions of faces. This covert neural sculpting relied on a sophisticated brain training technique in which people learn to direct their thoughts in specific ways.

 

The results, published September 8 in PLOS Biology, support the idea that neurofeedback methods could help reveal how the brain’s behavior gives rise to perceptions and emotions. What’s more, the technique may ultimately prove useful for easing traumatic memories and treating disorders such as depression. The research is still at an early stage, says neurofeedback researcher Michelle Hampson of Yale University, but, she notes, “I think it has great promise.”

 

Takeo Watanabe of Brown University and colleagues used functional MRI to measure people’s brain activity in an area called the cingulate cortex as participants saw pictures of faces. After participants had rated each face, a computer algorithm sorted their brain responses into patterns that corresponded to faces they liked and faces they disliked. With this knowledge in hand, the researchers then attempted to change people’s face preferences by subtly nudging brain activity in the cingulate cortex.

 

In step 2 of the experiment, returning to the fMRI scanner, participants saw an image of a face that they had previously rated as neutral. Just after that, they were shown a disk. The goal, the participants were told, was simple: make the disk bigger by using their brains. They had no idea that the only way to make the disk grow was to think in a very particular way.

 

For 12 people, the researchers made the disk grow when the participants’ brain activity looked like the activity that corresponded to faces they had liked in the first round. For 12 other people, the disk grew when their brain activity mirrored activity elicited by previously unliked faces. Another six people saw the faces, but didn’t do any disk training. This training lasted an hour each day for three days.

 

At the end of the training, people induced to call up brain activity similar to positive responses rated previously neutral faces as slightly more positive. “By doing this again and again, subjects began to like what was neutral before,” Watanabe says. And people who had called up activity associated with negative responses rated previously neutral faces as slightly more negative. People who hadn’t trained on the disk didn’t change their ratings. These opinion shifts lasted at least three months, later experiments showed.

 

Participants were simply told to make the disk bigger; they had no idea what the disk actually represented. “These results are fascinating in showing how nonconscious brain activity can be utilized to modify brain function and behavior in a targeted way,” says neuroscientist Rafi Malach of the Weizmann Institute of Science in Israel.

 

By showing that neurofeedback can influence complex mental processes, this study and others raise the possibility that similar methods could change the brain in desirable ways. Perhaps this sort of neural training could get rid of problematic patterns of thinking, such as those that come with abnormal fear and depression, Watanabe says. 

 


 

Još jedan korak ka razmevanju mašinskog jezika mozga. Problem je što će ovo prvo biti upotrebljeno u predizbornim kampanjama. 

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Microbial matter comes out of the dark

 

Scientists identify bacteria that defy rules of biochemistry
BY 
7:00AM, SEPTEMBER 7, 2016

 

 

DARK MATTER  Most microbes have stayed hidden from scientists, but new technologies are revealing unknown species of bacteria, some of which may hold medicinal promise.

ASHLEY MACKENZIE

Few people today could recite the scientific accomplishments of 19th century physician Julius Petri. But almost everybody has heard of his dish.

For more than a century, microbiologists have studied bacteria by isolating, growing and observing them in a petri dish. That palm-sized plate has revealed the microbial universe — but only a fraction, the easy stuff, the scientific equivalent of looking for keys under the lamppost.

But in the light — that is, the greenhouse-like conditions of a laboratory — most bacteria won’t grow. By one estimate, a staggering 99 percent of all microbial species on Earth have yet to be discovered, remaining in the shadows. They’re known as “microbial dark matter,” a reference to astronomers’ description of the vast invisible matter in space that makes up most of the mass in the cosmos.

 

091716_darkmatter_ichip_free.jpg
Using a device they named the iChip, researchers at Northeastern University and colleagues have found 50,000 new strains of soil bacteria. One new bacterium yielded a potential new class of antibiotics in 2015.
SLAVA EPSTEIN/NORTHEASTERN UNIV.

 

In the last decade or so, though, scientists have developed new tools for growing bacteria and collecting genetic data, allowing faster and better identifications of microbes without ever removing them from natural conditions. A device called the iChip, for instance, encourages bacteria to grow in their home turf. (That device led to the discovery of a potential new antibiotic, in a time when infections are fast outwitting all the old drugs.) Recent genetic explorations of land, water and the human body have raised the prospect of finding hundreds of thousands of new bacterial species.

Already, the detection of these newfound organisms is challenging what scientists thought they knew about the chemical processes of biology, the tree of life and the manner in which microbes live and grow. The secrets of microbial dark matter may redefine how life evolved and exists, and even improve the understanding of, and treatments, for many diseases.

“Everything is changing,” says Kelly Wrighton, a microbiologist at Ohio State University in Columbus. “The whole field is full of enthusiasm and discovery.”

Counter culture

Microbiologists have in the past discovered new organisms without petri dishes, but those experiments were slow going. In one of her first projects, Tanja Woyke analyzed the bacterial community huddled inside a worm that lives in the Mediterranean Sea. Woyke, a microbiologist at the U.S. Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., and colleagues published the report in Nature in 2006. It was two years in the making.

They relied on metagenomics, which involves gathering a sample of DNA from the environment — in soil, water or, in this case, worm insides. After extracting the genetic material of every microbe the worm contained, Woyke and colleagues determined the order, or sequences, of all the DNA units, or bases. Analyzing that sequence data allowed the researchers to infer the existence of four previously unknown microbes. It was a bit like obtaining boxes of jigsaw puzzle pieces that need assembly without knowing what the pictures look like or how many different puzzles they belong to, she says. The project involved 300 million bases and cost more than $100,000, using the time-consuming methods available at the time.

99 percent

of all microbial species on Earth have yet to be discovered

Just as Woyke was wrapping up the worm endeavor, new technology came online that gave genetic analysis a turbo boost. Sequencing a genome — the entirety of an organism’s DNA — became faster and cheaper than most scientists ever predicted. With next-generation sequencing, Woyke can analyze more than 100 billion bases in the time it takes to turn around an Amazon order, she says, and for just a few thousand dollars. By scooping up random environmental samples and searching for DNA with next-generation sequencing, scientists have turned up entirely new phyla of bacteria in practically every place they look. In 2013 inNature, Woyke and her colleagues described more than 200 members of almost 30 previously unknown phyla. Finding so many phyla, the first big groupings within a kingdom, tells biologists that there’s a mind-boggling amount of uncharted diversity.

Woyke has shifted from these broad genetic fishing expeditions to working on individual bacterial cells. Gently breaking them open, she catalogs the DNA inside. Many of the organisms she has found defy previous rules of biological chemistry. Two genomes taken from a hydrothermal vent in the Pacific Ocean, for example, contained the code UGA, which stands for the bases uracil, guanine and adenine in a strand of RNA. UGA normally separates the genes that code for different proteins, acting like a period at the end of a sentence. In most other known species of animal or microbe, UGA means “stop.” But in these organisms, and one found about the same time in a human mouth, instead of “stop,” the sequence codes for the amino acid glycine. “That was something we had never seen before,” Woyke says. “The genetic code is not as rigid as we thought.”

Other recent finds also defy long-held notions of how life works. This year in the ISME Journal, Ohio State’s Wrighton reported a study of the enzyme RubisCO taken from a new microbial species that had never been grown in a laboratory. RubisCO, considered the most abundant protein on Earth, is key to photosynthesis; it helps convert carbon from the atmosphere into a form useful to living things. Because the majority of life on the planet would not exist without it, RubisCO is a familiar molecule — so familiar that most scientists thought they had found all the forms it could take. Yet, Wrighton says, “we found so many new versions of this protein that were entirely different from anything we had seen before.”

The list of oddities goes on. Some newly discovered organisms are so small that they barely qualify as bacteria at all. Jillian Banfield, a microbiologist at the University of California, Berkeley, has long studied the microorganisms in the groundwater pumped out of an aquifer in Rifle, Colo. To filter this water, she and her colleagues used a mesh with openings 0.2 micrometers wide — tiny enough that the water coming out the other side is considered bacteria-free. Out of curiosity, Banfield’s team decided to use next-generation sequencing to identify cells that might have slipped through. Sure enough, the water contained extremely minuscule sets of genes.

091716_darkmatter_bacteria1_free.jpg
This tiny groundwater bacterium can slip through filters.
B. LUEF ET AL/NATURE COMMUNICATIONS 2015

 

“We realized these genomes were really, really tiny,” Banfield says. “So we speculated if something has a tiny genome, the cells are probably pretty tiny, too.” And she has pictures to prove it. Last year in Nature Communications, she and her team published the first images (taken with an electron microscope) and detailed description of these ultrasmall microbes (see, right). They are probably difficult to isolate in a petri dish, Banfield says, because they are slow-growing and must scavenge many of the essential nutrients they need from the environment around them. Part of the price of a minigenome is that you don’t have room for the DNA to make everything you need to live.

Relationship status: It’s complicated

Banfield predicts that an “unimaginably large number” of species await in every cranny of the globe — soil, rocks, air, water, plants and animals. The human microbiome alone is probably teeming with unfamiliar microbial swarms. As a collection of organisms that live on and in the body, the human microbiome affects health in ways that science is just beginning to comprehend (SN: 2/6/16, p. 6).

Scientists from UCLA, the University of Washington in Seattle and colleagues recently offered the most detailed descriptions yet of a human mouth bacterium belonging to a new phylum: TM7. (TM stands for “Torf, mittlere Schicht,” German for a middle layer of peat; organisms in this phylum were first detected in the mid-1990s in a bog in northern Germany.) German scientists found TM7 by sifting through soil samples, using a test that’s specific for the genetic information in bacteria. In the last decade, TM7 species have been found throughout the human body. An overabundance of TM7 appears to be correlated with inflammatory bowel disease and gum disease, plus other conditions.

Until recently, members of TM7 have stubbornly resisted scientists’ efforts to study them. In 2015, Jeff McLean, a microbiologist at the University of Washington, and his collaborators finally isolated a TM7 species in a lab and deciphered its full genome. To do so, the team combined the best of old and new technology: First the researchers figured out how to grow most known oral bacteria together, and then they gradually thinned down the population until only two species remained: TM7 and a larger organism.

“The really remarkable thing is we finally found out how it lives,” McLean says, and why it wouldn’t grow in the lab. They discovered that this species of TM7, like the miniature bacteria in Colorado groundwater, doesn’t have the cellular machinery to get by on its own. Even more unusual, these bacteria pilfer missing amino acids and whatever else they need by latching on, like parasites, to a larger bacterium. Eventually they can kill their host. “We think this is the first example of a bacterium that lives in this manner,” McLean says.

He expects to see more unusual relationships among microbes as the dark matter comes to light. Many have evaded detection, he suspects, because of their small size (sometimes perhaps mistaken for bacterial debris) and dependence on other organisms for survival. In 2013 in the Proceedings of the National Academy of Sciences, McLean and colleagues were the first to describe a member of another uncultivated phylum, TM6. They found this group growing in the slime in a hospital sink drain. Later studies determined that the organism lives by tucking itself inside an amoeba.

 

091716_darkmatter_bacteria_free.jpg
Some bacteria live in untraditional ways. One, from a newly discovered phylum called TM7 (left, red dots), lives parasitically on another bacterium. Another, from phylum TM6 (right, dark blobs), lives in an amoeba.
FROM LEFT: BATBILEG BOR AND XUESONG HE/UCLA; V. DELAFONT ET AL/ENVIRONMENTAL MICROBIAL REPORTS 2015

 

One of the greatest hopes for microbial dark matter exploration is that newly found microbes might provide desperately needed antibiotics. From the 1940s to the 1960s, scientists discovered 10 new classes of drugs by testing chemicals found in soil and elsewhere for action against common infections. But only two classes of medically important antibiotics have been discovered in the last 30 years, and none since 1997. Some major infections are at the brink of being unstoppable because they’ve become resistant to most existing drugs (SN Online: 5/27/16). Many experts think that natural sources of antibiotics have been exhausted.

Maybe not. In 2015, a research team led by scientists from Northeastern University in Boston captured headlines after describing in Nature a new chemical extracted from a ground-dwelling bacterium in Maine. The scientists isolated the organism using the iChip, a thumb-sized tool that contains almost 400 separate wells, each large enough to hold only an individual bacterial cell plus a smidgen of its home dirt. The bacteria grow on this scaffold in part because they never leave their natural surroundings. In lauding the discovery, Francis Collins, director of the National Institutes of Health, called the iChip “an ingenious approach that enhances our ability to search one of nature’s richest sources of potential antibiotics: soil.” So far, the research team has discovered about 50,000 new strains of bacteria.

One strain held an antibiotic, named teixobactin (SN: 2/7/15, p. 10). In laboratory experiments, it killed two major pathogens in a way that did not appear easily vulnerable to the development of resistance. Most antibiotics work by disrupting a microbe’s survival mechanism. Over time, the bacteria genetically adapt, find a work-around and overcome the threat. This new antibiotic, however, prevents a microbe from assembling the molecules it needs to form an outer wall. Since the antibiotic interrupts a mechanical process and not just a specific chemical reaction, “there’s no obvious molecular target” for resistance, says Kim Lewis, a microbiologist at Northeastern.

The small reveal

For more than a century, bacteria — the few scientists managed to culture — were grown on petri dishes or in flasks. Recent technological advances now allow scientists to quickly and cheaply reveal a microbe’s genetic identity without ever having to grow the organism in a laboratory. 

 

091716_darkmatter_flowchart-730-NEW.png
ADAPTED BY J. HIRSHFELD

 

Source:  R.S. Lasken and J.S. McLean/Nature Reviews Genetics 2014

Everything is illuminated

Some microbiologists feel like astronomers who, after years of staring up into the dark, were just handed the Hubble Space Telescope. Billions of galaxies are coming into view. Banfield expects this new microbial universe to be mapped over the next few years. Then, she says, an even more exciting era begins, as science explores how these dark matter bacteria make a living. “They are doing a lot of things, and we have no idea what,” she says.

Part of the excitement comes from knowing that microbes have a history of granting unexpected solutions to problems that scientists never expected to solve. Consider that the enzyme that makes the laboratory technique PCR possible came from organisms that live inside the thermal vents at Yellowstone National Park. PCR, which works like a photocopier to make multiple copies of DNA segments, is now used across a range of situations, from diagnosing cancer to paternity testing. CRISPR, a powerful gene-editing technology, relies on “molecular scissors” that were found in bacteria (SN: 9/3/16, p. 22).

Banfield estimates that 30 to 50 percent of newly discovered organisms contain proteins that never met a petri dish. Their function in the chemistry of life is an obscure mystery. Since microbes are the world’s most abundant organism, Banfield says, “the vast majority of life consists of biochemistry we don’t understand.” But once we do, the future could be very bright.

 

https://www.sciencenews.org/article/microbial-matter-comes-out-dark

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Gospodin Slucaj

http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0156905

Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe. This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.

....

 

 

prevod ovde
 
 
Edited by Gospodin Slucaj

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 British Prime Minister Benjamin Disraeli: "There are three kinds of lies: lies, damned lies, and statistics."

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Caesarean births 'affecting human evolution'

 

 

The regular use of Caesarean sections is having an impact on human evolution, say scientists.

 

More mothers now need surgery to deliver a baby due to their narrow pelvis size, according to a study.

 

Researchers estimate cases where the baby cannot fit down the birth canal have increased from 30 in 1,000 in the 1960s to 36 in 1,000 births today.

 

Historically, these genes would not have been passed from mother to child as both would have died in labour.

 

Researchers in Austria say the trend is likely to continue, but not to the extent that non-surgical births will become obsolete.

 

Dr Philipp Mitteroecker, of the department of theoretical biology at the University of Vienna, said there was a long standing question in the understanding of human evolution.

 

"Why is the rate of birth problems, in particular what we call fetopelvic disproportion - basically that the baby doesn't fit through the maternal birth canal - why is this rate so high?" he said.

 

"Without modern medical intervention such problems often were lethal and this is, from an evolutionary perspective, selection.

 

"Women with a very narrow pelvis would not have survived birth 100 years ago. They do now and pass on their genes encoding for a narrow pelvis to their daughters."


 

Opposing forces

It has been a long standing evolutionary question why the human pelvis has not grown wider over the years.
 

The head of a human baby is large compared with other primates, meaning animals such as chimps can give birth relatively easily.
 

The researchers devised a mathematical model using data from the World Health Organization and other large birth studies.
 

They found opposing evolutionary forces in their theoretical study.
 

One is a trend towards larger newborns, which are more healthy.
 

However, if they grow too large, they get stuck during labour, which historically would have proved disastrous for mother and baby, and their genes would not be passed on.
 

"One side of this selective force - namely the trend towards smaller babies - has vanished due to Caesarean sections," said Dr Mitteroecker.
 

"Our intent is not to criticise medical intervention," he said. "But it's had an evolutionary effect. "
 

Future trends

The researchers estimated that the global rate of cases where the baby could not fit through the maternal birth canal was 3%, or 30 in 1,000 births.
 

Over the past 50 or 60 years, this rate has increased to about 3.3-3.6%, so up to 36 in 1,000 births.
 

That is about a 10-20% increase of the original rate, due to the evolutionary effect.
 

"The pressing question is what's going to happen in the future?" Dr Mitteroecker said.
 

"I expect that this evolutionary trend will continue but perhaps only slightly and slowly.
 

"There are limits to that. So I don't expect that one day the majority of children will have to be born by [Caesarean] sections."
 

The research is published in the journal, Proceedings of the National Academy of Sciences.
 

Commenting on the study, Smithsonian paleoanthropologist Dr Briana Pobiner said there are "probably many other biological and cultural issues that factor into the Caesarean sections rate, which varies widely across the developed and developing world".
 

And Daghni Rajasingam, a consultant obstetrician and a spokesman for the Royal College of Obstetricians, said factors such as diabetes and obesity, are having an impact on the number of Caesarean sections.
 

"I think what is important to take into the [question of] evolution is that things like diabetes are much more common at a younger age so we see many more women of reproductive age who have diabetes," she said.
 

"That has consequences as to whether or not they may need a caesarean section.

 

"In addition, the rates of obesity are increasing so more and more women of reproductive age have a higher body mass index and this again has an impact on caesarean section rates."

Edited by miki.bg

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