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Numerous viruses found living in and on the bodies of healthy humans

Numerous viruses found living in and on the bodies of healthy humans | Amazing Science | Scoop.it
Human herpesvirus 6, pictured above, is just one of numerous viruses found living in and on the bodies of healthy humans. The virus commonly causes illness in young children but is found in the mouths of some healthy young adults, where its presence indicates an active viral infection despite a lack of symptoms.


On average, healthy individuals carry about five types of viruses on their bodies, the researchers report online in BioMed Central Biology. The study is the first comprehensive analysis to describe the diversity of viruses in healthy people.


The research was conducted as part of the Human Microbiome Project, a major initiative funded by the National Institutes of Health (NIH) that largely has focused on cataloging the body's bacterial ecosystems. "Most everyone is familiar with the idea that a normal bacterial flora exists in the body," said study co-author Gregory Storch, MD, a virologist and chief of the Division of Pediatric Infectious Diseases. "Lots of people have asked whether there is a viral counterpart, and we haven't had a clear answer. But now we know there is a normal viral flora, and it's rich and complex."


In 102 healthy young adults ages 18 to 40, the researchers sampled up to five body habitats: nose, skin, mouth, stool and vagina. The study's subjects were nearly evenly split by gender. At least one virus was detected in 92 percent of the people sampled, and some individuals harbored 10 to 15 viruses.


"We were impressed by the number of viruses we found," said lead author Kristine M. Wylie, PhD, an instructor of pediatrics. "We only sampled up to five body sites in each person and would expect to see many more viruses if we had sampled the entire body."


Scientists led by George Weinstock, PhD, at Washington University's Genome Institute, sequenced the DNA of the viruses recovered from the body, finding that each individual had a distinct viral fingerprint. (Weinstock is now at The Jackson Laboratory in Connecticut.) About half of people were sampled at two or three points in time, and the researchers noted that some of the viruses established stable, low-level infections.


The researchers don't know yet whether the viruses have a positive or negative effect on overall health but speculate that in some cases, they may keep the immune system primed to respond to dangerous pathogens while in others, lingering viruses increase the risk of disease.

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Schizophrenia is not a single disease but rather consists of eight different genetically distinct classes

Schizophrenia is not a single disease but rather consists of eight different genetically distinct classes | Amazing Science | Scoop.it

New research shows that schizophrenia isn’t a single disease but a group of eight genetically distinct disorders, each with its own set of symptoms. The finding could be a first step toward improved diagnosis and treatment for the debilitating psychiatric illness.


The research at Washington University School of Medicine in St. Louis is reported online Sept. 15 in The American Journal of Psychiatry. About 80 percent of the risk for schizophrenia is known to be inherited, but scientists have struggled to identify specific genes for the condition.


Now, in a novel approach analyzing genetic influences on more than 4,000 people with schizophrenia, the research team has identified distinct gene clusters that contribute to eight different classes of schizophrenia.


“Genes don’t operate by themselves,” said C. Robert Cloninger, MD, PhD, one of the study’s senior investigators. “They function in concert much like an orchestra, and to understand how they’re working, you have to know not just who the members of the orchestra are but how they interact.” 

Cloninger, the Wallace Renard Professor of Psychiatry and Genetics, and his colleagues matched precise DNA variations in people with and without schizophrenia to symptoms in individual patients. In all, the researchers analyzed nearly 700,000 sites within the genome where a single unit of DNA is changed, often referred to as a single nucleotide polymorphism (SNP). They looked at SNPs in 4,200 people with schizophrenia and 3,800 healthy controls, learning how individual genetic variations interacted with each other to produce the illness. 

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Plant genomics: Methods for obtaining large, phylogenomic data sets

Plant genomics: Methods for obtaining large, phylogenomic data sets | Amazing Science | Scoop.it

The use of next-generation sequencing (NGS) technologies in phylogenetic studies is in a state of continual development and improvement. Though the botanically-inclined have historically focused on markers from the chloroplast genome, the importance of incorporating nuclear data is becoming increasingly evident. Nuclear genes provide not only the potential to resolve relationships between closely related taxa, but also the means to disentangle hybridization and better understand incongruences caused by incomplete lineage sorting and introgression.

By harnessing the power of NGS—which has increased sequencing capacity by several orders of magnitude over the past few years—scientists are now able to easily sequence enormous amounts of DNA or RNA from any genome within an organism, a practice that is transforming many areas of plant biology.


A team of international scientists, led by researchers at Oregon State University, has utilized a recently developed method to assemble a phylogenomic data set containing hundreds of nuclear loci and plastomes for milkweeds.


"This approach, termed Hyb-Seq, uses targeted sequence capture via hybridization-based enrichment and has shown great promise for obtaining large nuclear data sets," explains Dr. Aaron Liston, principal investigator of the study. "Sequencing low-copy nuclear genes has traditionally required a large amount of effort for each gene. Hyb-Seq eliminates the need for PCR optimization and cloning—two time-consuming and sometimes problematic steps."


The protocol is freely available in the September issue of Applications in Plant SciencesWhile it would be ideal to simply sequence entire genomes for every organism being studied, this is not yet feasible across large numbers of species. The Hyb-Seq approach reduces genomic complexity of the organism-of-interest by targeting only a small portion of the total genome. This is achieved by hybridizing DNA or RNA probes to specific regions of the genome, then simply discarding the remaining, unwanted regions.


"The probe design was done bioinformatically by comparing our draft sequence of the milkweed genome and transcriptome (expressed genes) to another genome in the same family and to genes that are conserved across the asterids and the angiosperms," explains Liston. "This allowed us to eliminate duplicated genes that can complicate phylogenetic inference and select relatively conserved genes, so that they could be obtained from divergent milkweed species with a single probe set."


This approach enabled Liston and colleagues to sequence over 700 genes for 10 Asclepias species and two related genera. "Furthermore," says Liston, "we were able to assemble complete plastomes from the off-target reads."


"It is likely that as sequencing technology advances, it will be feasible in the next decade or so to sequence complete genomes routinely and inexpensively. However, until that time, the ability to sequence hundreds of genes at a time—as is possible with the Hyb-Seq method—represents a significant and exciting advance over previous methods."

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Parasitic Plant Strangleweed Injects Host With Over 9,000 RNA Transcripts

Parasitic Plant Strangleweed Injects Host With Over 9,000 RNA Transcripts | Amazing Science | Scoop.it

Virginia Tech professor and Fralin Life Institute affiliate Jim Westwood has made a discovery about plant-to-plant communication: enormous amounts of genetic messages in the form of mRNA transcripts are transmitted from the parasitic plant Cuscuta (known more commonly as dodder and strangleweed) to its hosts.


Using Illumina next generation sequencing technologies to sequence the tissues of the host and an attached parasite, the team found that the number of genes that gets passed into the host depends on the identity of the host.  The tomato plant received 347 of the strangleweed’s mRNAs, whereas the Arabidopsis received an astonishing 9514 mRNAs.  When Arabidopsis plant receives this many mRNAs, the total genetic material of tissues in contact with the strangleweed is about 45% from the parasite.


The new quantitative result builds on Professor Westwood’s prior discovery of RNA transfer between the parasitic plant and its host plants.  In the prior study, Westwood found that when the strangleweed uses its haustorium (piercing appendage) to penetrate the stems of its host plants, it passes on its own RNA to the host, though only tens of mRNAs were identified.  The discovery challenged our understanding that mRNAs are mainly kept within cells.


But now the research team has quantified the extent to which the messages are passed.  mRNA stands for “messenger RNA” and are the snippets of genetic information that are created from DNA.  Typically an mRNA molecule is “read” by a molecule machine known as a ribosome and turned into a protein which carries out particular functions in the cell.  And usually, more mRNAs means more protein.  Therefore, the conversion from DNA to mRNA is one way to amplify or control the activation of a gene.


It is not yet clear what are the functions of the transmitted genes but bioinformatic analysis shows that hydrolase activity, metabolism and response to stimulus gene groups were among the most represented in those that crossed the species bridge.


Westwood has determined that the host plant may be receiving orders of a kind from the parasitic plant, such as lowering its natural defense system so that the strangleweed can more easily attack them.


The findings by Westwood, Professor of weed science, plant pathology and physiology at the College of Agriculture and Life Sciences, is even more surprising when considered against prior thought that mRNA is unstable, short-lived and fragile.


The discoveries also opens new avenues in the research of the eradication of parasitic plants such as broomrape and witchweed, two plants that pose serious threats to legumes and other crops.  This also has intriguing implications for increasing efficiency of yields.


Future plans include expansion of such research to other organismal domains, such as fungi and bacteria, also exchange the mRNA.  But the meaning and the outcome of the transmitted messages remain yet unclear and work must be done to find out what the plants are saying to each other.

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Plants may use RNA language to communicate with each other, Virginia Tech researcher finds

Plants may use RNA language to communicate with each other, Virginia Tech researcher finds | Amazing Science | Scoop.it

A Virginia Tech scientist has discovered a potentially new form of plant communication, one that allows them to share an extraordinary amount of genetic information with one another. 


The finding by Jim Westwood, a professor of plant pathology, physiology, and weed science in the College of Agriculture and Life Sciences, throws open the door to a new arena of science that explores how plants communicate with each other on a molecular level. It also gives scientists new insight into ways to fight parasitic weeds that wreak havoc on food crops in some of the poorest parts of the world. His findings were published on Aug. 15 in the journal Science.


“The discovery of this novel form of inter-organism communication shows that this is happening a lot more than any one has previously realized,” said Westwood, who is an affiliated researcher with the Fralin Life Science Institute. “Now that we have found that they are sharing all this information, the next question is, ‘What exactly are they telling each other?’.” 


Westwood examined the relationship between a parasitic plant, dodder, and two host plants, Arabidopsis and tomatoes. In order to suck the moisture and nutrients out the host plants, dodder uses an appendage called a haustorium to penetrate the plant. Westwood previously broke new ground when he found that during this parasitic interaction, there is a transport of RNA between the two species. RNA translates information passed down from DNA, which is an organism’s blueprint. 


His new work expands this scope of this exchange and examines the mRNA, or messenger RNA, which sends messages within cells telling them which actions to take, such as which proteins to code. It was thought that mRNA was very fragile and short-lived, so transferring it between species was unimaginable. 


But Westwood found that during this parasitic relationship, thousands upon thousands of mRNA molecules were being exchanged between both plants, creating this open dialogue between the species that allows them to freely communicate. Through this exchange, the parasitic plants may be dictating what the host plant should do, such as lowering its defenses so that the parasitic plant can more easily attack it. Westwood’s next project is aimed at finding out exactly what the mRNA are saying.


“Parasitic plants such as witchweed and broomrape are serious problems for legumes and other crops that help feed some of the poorest regions in Africa and elsewhere,” said Julie Scholes, a professor at the University of Sheffield, U.K., who is familiar with Westwood’s work but was not part of this project. “In addition to shedding new light on host-parasite communication, Westwood’s findings have exciting implications for the design of novel control strategies based on disrupting the mRNA information that the parasite uses to reprogram the host." 

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DNA sequencing with nanopores reaches new lengths

DNA sequencing with nanopores reaches new lengths | Amazing Science | Scoop.it

Researchers from the University of Washington’s Departments of Physics and Genome Sciences have developed a nanopore sequencing technique reaching read lengths of several thousand bases. The result is the latest in a series of advances in nanopore technology developed at the university.


The team, led by Jens Gundlach, published their findings in Nature Biotechnology as an advanced online publication on June 25, 2014 ("Decoding long nanopore sequencing reads of natural DNA").


“This is the first time anyone has shown that nanopores can be used to generate interpretable signatures corresponding to very long DNA sequences from real-world genomes,” said co-author Jay Shendure, an associate professor in Genome Sciences, “It’s a major step forward.


”The idea for nanopore sequencing originated in the 90s: a lipid membrane, similar to the material that makes up the cell wall, acts as a barrier separating two liquids. Inserted into the membrane is a tiny gap, just nanometers across, called a nanopore. By applying a voltage difference across the barrier, ions in the liquid try to move between the two sides of the barrier and the only way to do this is to flow through the nanopore. The movement of the charged molecules between the two liquids is a current, just like electrons moving along a wire in an electrical circuit, and can be recorded.


Any DNA in the system is also pulled towards the other side of the barrier by the voltage difference, since DNA is negatively charged, and just like the ions it has to pass through the nanopore. The difference is that the DNA is much bigger than the ions and partially blocks the nanopore, making it harder for the smaller molecules to pass through. As the ions are blocked by the DNA, there is a measurable difference in the current flowing across the membrane which is dependent on the DNA base passing through the nanopore. By measuring the changing current, information can be gained on the bases passing through.


The researchers created the nanopore by inserting a single protein called Mycobacterium smegmatis porin A, or MspA, in the membrane. MspA is normally found lining the membrane of a species of bacteria, controlling the intake of nutrients.


One challenge the researchers faced was the control of the DNA passing through the nanopore. Normally, the DNA would zip through the MspA nanopore too fast to detect the changes in the current. The researchers slowed the DNA movement through the pore using a second protein called phi29 DNA polymerase (DNAP), which captures DNA and slows its movement through the pore.


The shape of the protein MspA meant that several bases passed through the nanopore at one time and the current changes were the result of a combination of those bases. This presented another challenge. Since several bases passed through the nanopore at one time, the researchers needed a way to decipher what the current changes meant. To do this, they first made a library of DNA sequences that contains all possible combinations of 4 nucleotides (for the mathematically inclined, the library is 44 = 256 bases long – a string of 4 bases with 4 possible choices for each DNA base). The library, whose sequence was already known, was run though the nanopore first to find the current associated with each set of DNA base combinations. They combined the library measurements with known genome sequences to generate a set of expected current changes that could be compared to experimental measurements.


The researchers tested their approach by sequencing the entire genome of bacteriophage Phi X 174, a virus that infects bacteria and is used as a benchmark for evaluating new sequencing technologies. The impressive feat here is the length of the genome they sequenced – the Phi X 174 genome is 4,500 bases long. Other nanopore technologies have been limited to sequencing DNA fragments that were much shorter.


“Despite the remaining hurdles, our demonstration that a low-cost device can reliably read the sequences of naturally occurring DNA and can interpret DNA segments as long as 4,500 nucleotides in length represents a major advance in nanopore DNA sequencing,” explained Gundlach.

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DNA Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of citrus domestication

DNA Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of citrus domestication | Amazing Science | Scoop.it
Genome sequences of nine species of citrus, including oranges, pummelos and mandarins, reveal pathways of domestication and provide resources for breeding.


Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Researchers now sequenced and compared citrus genomes— a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and showed that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species.


Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement. Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources of vitamin C and other health-promoting compounds. Global production in 2012 exceeded 86 million metric tons, with an estimated value of $9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes them highly vulnerable to disease outbreaks, including citrus greening disease (also known as Huanglongbing or HLB), which is rapidly spreading throughout the world's major citrus-producing regions1. Understanding the population genomics and domestication of citrus will enable strategies for improvements, including resistance to greening and other diseases.

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Diet Affects Men’s and Women’s Intestinal Microbes Differently

Diet Affects Men’s and Women’s Intestinal Microbes Differently | Amazing Science | Scoop.it

 The microbes living in the guts of males and females react differently to diet, even when the diets are identical, according to a study by scientists from The University of Texas at Austin and six other institutions published this week in the journal Nature CommunicationsThese results suggest that therapies designed to improve human health and treat diseases through nutrition might need to be tailored for each sex.


The researchers studied the gut microbes in two species of fish and in mice, and also conducted an in-depth analysis of data that other researchers collected on humans. They found that in fish and humans diet affected the microbiota of males and females differently. In some cases, different species of microbes would dominate, while in others, the diversity of bacteria would be higher in one sex than the other.

These results suggest that any therapies designed to improve human health through diet should take into account whether the patient is male or female.


Only in recent years has science begun to completely appreciate the importance of the human microbiome, which consists of all the bacteria that live in and on people’s bodies. There are hundreds or even thousands of species of microbes in the human digestive system alone, each varying in abundance.


Genetics and diet can affect the variety and number of these microbes in the human gut, which can in turn have a profound influence on human health. Obesity, diabetes, and inflammatory bowel disease have all been linked to low diversity of bacteria in the human gut.


One concept for treating such diseases is to manipulate the microbes within a person’s gut through diet. The idea is gaining in popularity because dietary changes would make for a relatively cheap and simple treatment.


Much has to be learned about which species, or combination of microbial species, is best for human health. In order to accomplish this, research has to illuminate how these microbes react to various combinations of diet, genetics and environment. Unfortunately, to date most such studies only examine one factor at a time and do not take into account how these variables interact.


“Our study asks not just how diet influences the microbiome, but it splits the hosts into males and females and asks, do males show the same diet effects as females?” said Daniel Bolnick, professor in The University of Texas at Austin's College of Natural Sciences and lead author of the study.

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Eric Chan Wei Chiang's curator insight, August 2, 11:36 PM

Previously, it was assumed that men and women have mostly similar biological functions. This is an interesting paradigm shift indeed. 

 

This has future implication with our diet and how we treat diseases.

http://www.scoop.it/t/food-health-and-nutrition/?tag=Diet

http://www.scoop.it/t/biotech-and-beyond/?tag=Novel+Therapies

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Removing parasitic retroviruses from the genome is a critical step in evolving larger bodies and longer lifespans

Removing parasitic retroviruses from the genome is a critical step in evolving larger bodies and longer lifespans | Amazing Science | Scoop.it
Cancer has left its 'footprint' on our evolution, according to a study which examined how the relics of ancient viruses are preserved in the genomes of 38 mammal species. The team found that as animals increased in size they 'edited out' potentially cancer-causing relics from their genomes so that mice have almost ten times as many ERVs as humans. The findings offer a clue as to why larger animals have a lower incidence of cancer than expected compared to smaller ones, and could help in the search for new anti-viral therapies.


Viral relics are evidence of the ancient battles our genes have fought against infection. Occasionally the retroviruses that infect an animal get incorporated into that animal's genome and sometimes these relics get passed down from generation to generation -- termed 'endogenous retroviruses' (ERVs). Because ERVs may be copied to other parts of the genome they contribute to the risk of cancer-causing mutations.


Now a team from Oxford University, Plymouth University, and the University of Glasgow has identified 27,711 ERVs preserved in the genomes of 38 mammal species, including humans, over the last 10 million years. The team found that as animals increased in size they 'edited out' these potentially cancer-causing relics from their genomes so that mice have almost ten times as many ERVs as humans. The findings offer a clue as to why larger animals have a lower incidence of cancer than expected compared to smaller ones, and could help in the search for new anti-viral therapies.


We set out to find as many of these viral relics as we could in everything from shrews and humans to elephants and dolphins,' said Dr Aris Katzourakis of Oxford University's Department of Zoology, lead author of the report. 'Viral relics are preserved in every cell of an animal: Because larger animals have many more cells they should have more of these endogenous retroviruses (ERVs) -- and so be at greater risk of ERV-induced mutations -- but we've found this isn't the case. In fact larger animals have far fewer ERVs, so they must have found ways to remove them.'


A combination of mathematical modelling and genome research uncovered some striking differences between mammal genomes: mice (c.19 grams) have 3331 ERVs, humans (c.59 kilograms) have 348 ERVs, whilst dolphins (c.281 kilograms) have just 55 ERVs.


'This is the first time that anyone has shown that having a large number of ERVs in your genome must be harmful -- otherwise larger animals wouldn't have evolved ways of limiting their numbers,' said Dr Katzourakis. 'Logically we think this is linked to the increased risk of ERV-based cancer-causing mutations and how mammals have evolved to combat this risk. So when we look at the pattern of ERV distribution across mammals it's like looking at the 'footprint' cancer has left on our evolution.'


Dr Robert Belshaw of Plymouth University Peninsula Schools of Medicine and Dentistry, School of Biomedical and Healthcare Sciences, added: "Cancer is caused by errors occurring in cells as they divide, so bigger animals -- with more cells -- ought to suffer more from cancer. Put simply, the blue whale should not exist. However, larger animals are not more prone to cancer than smaller ones: this is known as Peto's Paradox (named after Sir Richard Peto, the scientist credited with first spotting this). A team of scientists at Oxford, Plymouth and Glasgow Universities had been studying endogenous retroviruses, viruses like HIV but which have become part of their host's genome and which in other animals can cause cancer. Surprisingly, they found that bigger mammals have fewer of these viruses in their genome. This suggests that similar mechanism might be involved in fighting both cancer and the spread of these viruses, and that these are better in bigger animals (like humans) than smaller ones (like laboratory mice)."

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Who's your daddy? Researchers program computer to find out

Who's your daddy? Researchers program computer to find out | Amazing Science | Scoop.it
A University of Central Florida research team has developed a facial recognition tool that promises to be useful in rapidly matching pictures of children with their biological parents and in potentially identifying photos of missing children as they age.


The work verifies that a computer is capable of matching pictures of parents and their children. The study will be presented at the nation's premier event for the science of computer vision - the IEEE Computer Vision and Pattern Recognition conference in Columbus, Ohio, which begins Monday, June 23. Graduate Student Afshin Dehfghan and a team from UCF's Center for Research in Computer Vision started the project with more than 10,000 online images of celebrities, politicians and their children.


"We wanted to see whether a machine could answer questions, such as 'Do children resemble their parents?' 'Do children resemble one parent more than another?' and 'What parts of the face are more genetically inspired?'" he said.


Anthropologists have typically studied these questions. However Dehghan and his team are advancing a new wave of computational science that uses the power of a mechanical "mind" to evaluate data completely objectively – without the clutter of subjective human emotions and biases. The tool could be useful to law enforcement and families in locating missing children.


"As this tool is developed I could see it being used to identify long-time missing children as they mature," said Ross Wolf, associate professor of criminal justice at UCF.


Wolf said that facial recognition technology is already heavily used by law enforcement, but that it has not been developed to the point where it can identify the same characteristics in photos over time, something this technology could have the capability to do. Dehghan said he is planning to expand on the work in that area by studying how factors such as age and ethnicity affect the resemblance of facial features.

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Intestinal bacterial ecosystem: Identification of 741 bacteria, 181 new species, and 848 bacterial viruses

Intestinal bacterial ecosystem: Identification of 741 bacteria, 181 new species, and 848 bacterial viruses | Amazing Science | Scoop.it

Researchers at DTU (Technical University of Denmark) in collaboration with an international team from countries including France and China devised a method based on the co-abundance principle to easily identify the genomes (or genetic material) of unknown intestinal microorganisms. The scientists demonstrated this method on 396 human stool samples and uncovered 741 microbial species of which 181 are proposed to be completely novel.  Unlike prior methods to identify bacterial species, the use of CAGs obviates the need for assembly as well the need for a database of reference genomes.


The new approach also identified 848 viruses that infect each bacterium (called bacteriophages). The balance of intestinal fauna affects human health as it is increasingly recognized disrupting such balance for example by use of antibiotics leads to disease states.  Therefore modulation of the bacterial composition by viral agents is an attractive means to restore the balance.  Moreover, the new insight makes possible the exploitation of viruses to attack specific bacteria, thereby adding another tool to our pharmacological arsenal which is under increasing pressure from antibiotic resistance.


The human intestine is home to many microorganisms, whose cell population is estimated to be 10 times greater than the number of human cells in an individual.  Only a few species that can be cultivated in the laboratory to be sequenced by traditional methods.  Identification of the different microbial species in the intestinal ecology and their interactions will lead to better understanding of relevant disease conditions such as type 2 diabetes, asthma and obesity.

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Untangling whole genomes of individual species from a microbial mix

Untangling whole genomes of individual species from a microbial mix | Amazing Science | Scoop.it

Scientists at the University of Washington have developed a new approach to study microbes in the wild, which will allow researchers to sequence the genomes of individual species from highly complex mixtures. It marks a big advance for understanding the enormous diversity of microbial communities —including the human microbiome. This new method can cluster sequence fragments from a mixed sample of yeasts into species. In the shown graph, each of the 12 species with a substantial presence in the mix are represented by a cluster. Each fragment is shown as a dot, with size indicating length, colored by species. Line widths represent the densities of links between the fragment shown.


The work is described in an article published May 22 in Early Online form in the journal G3: Genes|Genomes|Genetics, published by the Genetics Society of America.


"This new method will allow us to discover many currently unknown microbial species that can't be grown in the lab, while simultaneously assembling their genome sequences," says co-author Maitreya Dunham, a biologist at the University of Washington's Department of Genome Sciences.


Microbial communities, whether sampled from the ocean floor or a human mouth, are made up of many different species living together. Standard methods for sequencing these communities combine the information from all the different types of microbes in the sample. The result is a hodgepodge of genes that is challenging to analyze, and unknown species in the sample are difficult to discover.


"Our approach tells us which sequence fragments in a mixed sample came from the same genome, allowing us to construct whole genome sequences for individual species in the mix," says co-author Jay Shendure, also of the University of Washington's Department of Genome Sciences.


The key advance was to combine standard approaches with a method that maps out which fragments of sequence were once near each other inside a cell. The cells in the sample are first treated with a chemical that links together DNA strands that are in close proximity. Only strands that are inside the same cell will be close enough to link. The DNA is then chopped into bits, and the linked portions are isolated and sequenced.


Reference:

Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps Joshua N. Burton, Ivan Liachko, Maitreya J. Dunham, and Jay Shendure. G3: Genes|Genomes|Genetics g3.114.011825; Early Online May 22, 2014, DOI: 10.1534/g3.114.011825 ; PMID 24855317

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Friends Are the Family You Choose: Genome-Wide Analysis Reveals Genetic Similarities Among Friends

Friends Are the Family You Choose: Genome-Wide Analysis Reveals Genetic Similarities Among Friends | Amazing Science | Scoop.it

If you consider your friends family, you may be on to something. A study from the University of California, San Diego, and Yale University finds that friends who are not biologically related still resemble each other genetically.


Published in the Proceedings of the National Academy of Sciences, the study is coauthored by James Fowler, professor of medical genetics and political science at UC San Diego, and Nicholas Christakis, professor of sociology, evolutionary biology, and medicine at Yale.


“Looking across the whole genome,” Fowler said, “we find that, on average, we are genetically similar to our friends. We have more DNA in common with the people we pick as friends than we do with strangers in the same population.”


The study is a genome-wide analysis of nearly 1.5 million markers of gene variation, and relies on data from the Framingham Heart Study. The Framingham dataset is the largest the authors are aware of that contains both that level of genetic detail and information on who is friends with whom.


The researchers focused on 1,932 unique subjects and compared pairs of unrelated friends against pairs of unrelated strangers. The same people, who were neither kin nor spouses, were used in both types of samples. The only thing that differed between them was their social relationship.


The findings are not, the researchers say, an artifact of people’s tendency to befriend those of similar ethnic backgrounds. The Framingham data is dominated by people of European extraction. While this is a drawback for some research, it may be advantageous to the study here: because all the subjects, friends and not, were drawn from the same population. The researchers also controlled for ancestry, they say, by using the most conservative techniques currently available. The observed genetic go beyond what you would expect to find among people of shared heritage – these results are “net of ancestry,” Fowler said.

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European gene pools seems to be derived from three ancient populations

European gene pools seems to be derived from three ancient populations | Amazing Science | Scoop.it

The modern European gene pool was formed when three ancient populations mixed within the last 7,000 years, Nature reports.


Blue-eyed, swarthy hunters mingled with brown-eyed, pale skinned farmers as the latter swept into Europe from the Near East. But another, mysterious population with Siberian affinities also contributed to the genetic landscape of the continent. The findings are based on analysis of genomes from nine ancient Europeans. Agriculture originated in the Near East - in modern Syria, Iraq and Israel - before expanding into Europe around 7,500 years ago.


Multiple lines of evidence suggested this new way of life was spread by a wave of migrants, who interbred with the indigenous European hunter-gatherers they encountered on the way. But assumptions about European origins were based largely on the genetic patterns of living people. The science of analysing genomic DNA from ancient bones has put some of the prevailing theories to the test, throwing up a few surprises.


In the new paper, Prof David Reich from the Harvard Medical School and colleagues studied the genomes of seven hunter-gatherers from Scandinavia, one hunter whose remains were found in a cave in Luxembourg and an early farmer from Stuttgart, Germany. The hunters arrived in Europe thousands of years before the advent of agriculture, hunkered down in southern refuges during the Ice Age and then expanded during a period called the Mesolithic, after the ice sheets had retreated from central and northern Europe.


Their genetic profile is not a good match for any modern group of people, suggesting they were caught up in the farming wave of advance. However, their genes live on in modern Europeans, to a greater extent in the north-east than in the south.


The early farmer genome showed a completely different pattern, however. Her genetic profile was a good match for modern people in Sardinia, and was rather different from the indigenous hunters.

But, puzzlingly, while the early farmers share genetic similarities with Near Eastern people at a global level, they are significantly different in other ways. Prof Reich suggests that more recent migrations in the farmers' "homeland" may have diluted their genetic signal in that region today.


Prof Reich explained: "The only way we'll be able to prove this is by getting ancient DNA samples along the potential trail from the Near East to Europe... and seeing if they genetically match these predictions or if they're different.


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Oxytricha trifallax breaks its own DNA into a quarter-million pieces and rapidly reassemble those for mating

Oxytricha trifallax breaks its own DNA into a quarter-million pieces and rapidly reassemble those for mating | Amazing Science | Scoop.it

Life can be so intricate and novel that even a single cell can pack a few surprises, according to a study led by Princeton University researchers. The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it's time to mate, the researchers report in the journal Cell.


The organism internally stores its genome as thousands of scrambled, encrypted gene pieces. Upon mating with another of its kind, the organism rummages through these jumbled genes and DNA segments to piece together more than 225,000 tiny strands of DNA. This all happens in about 60 hours.


The organism's ability to take apart and quickly reassemble its own genes is unusually elaborate for any form of life, explained senior author Laura Landweber, a Princeton professor of ecology and evolutionary biology. That such intricacy exists in a seemingly simple organism accentuates the "true diversity of life on our planet," she said.


"It's one of nature's early attempts to become more complex despite staying small in the sense of being unicellular," Landweber said. "There are other examples of genomic jigsaw puzzles, but this one is a leader in terms of complexity. People might think that pond-dwelling organisms would be simple, but this shows how complex life can be, that it can reassemble all the building blocks of chromosomes."


From a practical standpoint, Oxytricha is a model organism that could provide a template for understanding how chromosomes in more complex animals such as humans break apart and reassemble, as can happen during the onset of cancer, Landweber said. While chromosome dynamics in cancer cells can be unpredictable and chaotic, Oxytricha presents an orderly step-by-step model of chromosome reconstruction, she said.


"It's basically bad when human chromosomes break apart and reassemble in a different order," Landweber said. "The process in Oxytricha recruits some of the same biological mechanisms that normally protect chromosomes from falling apart and uses them to do something creative and constructive instead."


Gertraud Burger, a professor of biochemistry at the University of Montreal, said that the "rampant and diligently orchestrated genome rearrangements that take place in this organism" demonstrate a unique layer of complexity for scientists to consider when it comes to studying an organism's genetics.


"This work illustrates in an impressive way that the genetic information of an organism can undergo substantial change before it is actually used for building the components of a living cell," said Burger, who is familiar with the work but had no role in it.


"Therefore, inferring an organism's make-up from the genome sequence alone can be a daunting task and maybe even impossible in certain instances," Burger said. "A few cases of minor rearrangements have been described in earlier work, but these are dilettantes compared to [this] system."

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Coffee Genome Sequenced and Annotated

Coffee Genome Sequenced and Annotated | Amazing Science | Scoop.it

The coffee genome has been sequenced for the first time, brewing up a better understanding of that flavor, aroma, and buzz we love (and need) so much. According to the findings, published in Science this week, the caffeine-producing enzymes in coffee evolved independently from those in tea and chocolate. 


“The coffee genome helps us understand what’s exciting about coffee -- other than that it wakes me up in the morning,” says SUNY Buffalo’s Victor Albert in a news release. “By looking at which families of genes expanded in the plant, and the relationship between the genome structure of coffee and other species, we were able to learn about coffee’s independent pathway in evolution, including -- excitingly -- the story of caffeine.”


Commonly known as robusta coffee, Coffea canephora makes up 30 percent of the coffee produced worldwide -- which totals 8.7 million tons a year or 2.25 billion cups a day. The less acidic-tasting Coffea arabica makes up most of the rest, but this lower caffeine variety has a more complicated genome. 


So, to derive a draft genome of Coffea canephora, a huge consortium led by Albert and researchers from the French Institute of Research for Development and the French National Sequencing Center pieced together DNA sequences and assembled a total length of 568.6 megabases -- that’s 80 percent of the plant’s 710-megabase genome.


After running a comparative genomics software on protein sequences from coffee, grape, tomato, and a flowering plant called Arabidopsis, the team identified 16,000 genes that originated from a single gene in their last common ancestor. They were also able to pinpoint adaptations in genes for disease resistance and caffeine production that were unique to coffee. Overall, the team isolated 25,574 protein-making genes in the Coffea canephora genome and 23 new genes that are only found in coffee.


The robusta coffee genome also revealed that the enzymes involved in coffee’s caffeine production -- called N-methyltransferases -- adapted independently from those in cacao and tea. That is, they didn’t inherit their caffeine-linked genes from a common ancestor: The ability to produce caffeine must have evolved at least twice, and long before we started depending on it.


But what good is caffeine for plants? It may protect the coffee plant from predators like leaf-eating bugs, and when their leaves fall on the ground, the high caffeine concentration stunts the growth of rival plants trying to develop near them. “Caffeine also habituates pollinators and makes them want to come back for more, which is what it does to us, too,”Albert tells Nature. Furthermore, over evolutionary time, the coffee genome wasn't triplicated or duplicated en masse. Instead, the team team thinks that the duplication of individual genes, including the caffeine ones, spurred innovations, Science explains.

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21 Species of Metabolically Active Microbes In Hydrocarbon Lakes On Earth Boost Chances For Extraterrestrial Life

21 Species of Metabolically Active Microbes In Hydrocarbon Lakes On Earth Boost Chances For Extraterrestrial Life | Amazing Science | Scoop.it

In a ground-breaking discovery released by the journal Science, researchers have revealed microhabitats of metabolically active, thriving microbes living in the world’s largest asphalt lake, Pitch Lake, on the island of Trinidad in the Caribbean.  Asphalt lakes are large reservoirs of a sticky, black, viscous hydrocarbons (known as asphalt, bitumen or pitch) where no life was expected to be found.


The international team discovered the microbes in tiny water droplets recovered from the lake in 2011.  Each sample, measuring only one to three microliters, has the equivalent volume of approximately 1/50 of a conventional “drop” of water.


The team’s only United States-based researcher, Dirk Schulze-Makuch, is a professor at Washington University School of the Environment.  Using advanced sequencing technologies, the team extracted all the DNA of all organisms in each droplet simultaneously.  Reading through 12 microdroplets, they found 21 species of bacteria and archaebacteria.


Professor Schulze-Makuch explained that each water droplet seems representative of an entire ecosystem because of the observed diversity in bacteria and archaea.  Moreover, remarkably there was very little measurable ammonia or phosphates, both ingredients thought to be essential for life.


These microbes, the researchers report, are actively degrading oils in the lake, most likely to exploit it as a source of bioenergy.  One bioengineering implication of this discovery is to use these active microbes to clean up oil spills with as little impact to the environment as possible.


The water droplets also had an unusually high salt content.  By studying the isotope composition of droplets from Pitch Lake, the team was able to say that the microbes did not originate from surface waters that are part of the hydrologic cycle, but rather from much deeper, for example ancient underground seawater or another deep source of brine.


Professor Schulze-Makuch went on to explain that these microbes could mean life on other planets as well.  One well-known example is Saturn’s moon, Titan.  Its surface is characterized as being saturated with hydrocarbons, in liquid lakes on the ground and also in vapor form and liquid rain in the atmosphere.  Schulze-Makuch explains that this discovery has implications for astrobiology, the study of life on other planets.


Reference: Science 8 August 2014: Vol. 345 no. 6197 pp. 673-676

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Parenting from before conception: Babies' health doesn't 'start from scratch'

Parenting from before conception: Babies' health doesn't 'start from scratch' | Amazing Science | Scoop.it
There's now overwhelming evidence that a child's future health is influenced by more than just their parents' genetic material, and that children born of unhealthy parents will already be pre-programmed for greater risk of poor health, according to researchers. "The reality is, the child doesn't quite start from scratch -- they already carry over a legacy of factors from their parents' experiences that can shape development in the fetus and after birth. Depending on the situation, we can give our children a burden before they've even started life," experts say.


At fertilization, the gametes endow the embryo with a genomic blueprint, the integrity of which is affected by the age and environmental exposures of both parents. Recent studies reveal that parental history and experiences also exert effects through epigenomic information not contained in the DNA sequence, including variations in sperm and oocyte cytosine methylation and chromatin patterning, noncoding RNAs, and mitochondria. Transgenerational epigenetic effects interact with conditions at conception to program the developmental trajectory of the embryo and fetus, ultimately affecting the lifetime health of the child. These insights compel us to revise generally held notions to accommodate the prospect that biological parenting commences well before birth, even prior to conception.

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Bert Vogelstein’s Liquid Biopsy Blood Test for DNA Could Stop Cancer in its Tracks

Bert Vogelstein’s Liquid Biopsy Blood Test for DNA Could Stop Cancer in its Tracks | Amazing Science | Scoop.it

He watched his brother die from a cancer that no drug could cure. Globally, eight million people died of cancer in 2012. Now one of the world’s most renowned cancer researchers says it’s time for Plan B. The answers Bert Vogelstein needed and feared were in the blood sample.


Vogelstein is among the most highly cited scientists in the world. He was described, in the 1980s, as having broken into “the cockpit of cancer” after he and coworkers at Johns Hopkins University showed for the first time exactly how a series of DNA mutations, adding up silently over decades, turn cells cancerous. Damaged DNA, he helped prove, is the cause of cancer.


Now imagine you could see these mutations—see cancer itself—in a vial of blood. Nearly every type of cancer sheds DNA into the bloodstream, and Vogelstein’s laboratory at Johns ­Hopkins has developed a technique, called a “liquid biopsy,” that can find the telltale genetic material.


The technology is made possible by instruments that speedily sequence DNA in a blood sample so researchers can spot tumor DNA even when it’s present in trace amounts. The ­Hopkins scientists, working alongside doctors who treat patients in Baltimore’s largest oncology center, have now studied blood from more than a thousand people. They say liquid biopsies can find cancer long before symptoms of the disease arise.


This particular blood sample, though, was personal. It was from Vogelstein’s brother, an orthopedic surgeon one year younger. He was fighting skin cancer, and the disease was already spreading. There was hope he’d respond to a new type of drug, but the treatment causes swelling, and it’s difficult to tell from an x-ray or CT scan whether the cancer is melting away or not. So Vogelstein used his lab’s new technology. If the cancer DNA had disappeared from the blood, they might celebrate. If it was still there, maybe he could steer his brother to some last-ditch drug.


“We tried to guide the treatment. That was the hope, anyway,” says Vogelstein. His voice tightens. He doesn’t say what happened next.

The obituary of Barry Vogelstein, born in Baltimore, appeared on July 3, 2013.


We’re not winning the war on cancer, and the death of ­Vogelstein’s brother shows why. Too many cancers are caught when they have become incurable. Each year, $91 billion is spent on cancer drugs worldwide, but most of those medicines are given to patients when it’s too late. The newest treatments, created at staggering expense, cost $10,000 a month and often extend life by only a few weeks. Pharmaceutical firms develop and test more drugs for late-stage cancer than for any other kind of disease.


“We as the public and as scientists have been entranced by this idea of curing advanced cancers,” says Vogelstein. “That is society’s Plan A. I don’t think that has to be the case.” There are other ways to reduce cancer deaths: wearing sunscreen, not smoking, and getting screened to catch cancer early. To ­Vogelstein, all these preventive steps represent “Plan B” because they receive so much less attention and funding. Yet when prevention works, it has better results than any drug. In the United States, the chance of dying from colorectal cancer is 40 percent lower than it was in 1975, a decrease mostly due to colonoscopy screening. Melanoma skin cancer, too, is treatable with surgery if caught early. “We think Plan B needs to be Plan A,” says Vogelstein.


The new blood tests could make that possible. For the first time, Hopkins researchers say, they are within reach of a general screening tool that could be used to scan broadly—perhaps at an annual physical—for molecular traces of cancer in people with no symptoms. “We think we’ve solved early detection,” says Victor Velculescu, a Hopkins researcher who runs a lab in the building next to Vogelstein’s.


Making such screening a routine practice in medicine will be challenging. One difficulty is that while the test may detect the presence of cancer DNA in the body, physicians might not know where the tumor is, how dangerous it is, or even whether it is worth treating. “We have to be cautious about how we talk about that,” says Daniel Haber, director of the Massachusetts General Hospital Cancer Center. He believes the DNA blood tests are “far from ready” and says very large studies will be needed to prove that they are useful. “There is a huge bar to get over,” he says.


Despite such skepticism, the technology is gaining attention. Tony Dickherber, head of the Innovative Molecular Analysis Technologies Program at the National Cancer Institute, says the idea of scanning blood for tumor DNA was “fringe at best” only three years ago. But now labs and companies from California to London are jumping in, producing a stream of improvements to the blood screening technology and new data supporting it. “People are starting to think that Vogelstein is right—this could be the best way to do early diagnosis,” he says. “[It] could be done much more widely than other screening technology we have, and you could screen for an incredible range of cancers.”

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End of chemotherapy within 20 years as pioneering DNA sequencing project is launched in the UK

End of chemotherapy within 20 years as pioneering DNA sequencing project is launched in the UK | Amazing Science | Scoop.it

Cancer patients will no longer have to put up with the debilitating side-effects of chemotherapy after David Cameron launched a new landmark project to map the genetic causes of the disease.


David Cameron, the prime minister, said the venture would ‘unlock the power of DNA’ to deliver ‘better tests, better drugs and better care for patients.’ "As our plan becomes a reality, I believe we will be able to transform how devastating diseases are diagnosed and treated in the NHS and across the world,” he said.


The first few hundred pilot participants in London, Cambridge and Newcastle have already donated DNA samples and the project is expected to be completed 2018. "20 years from now there will be therapies, instead of chemo, that will be a much more targeted approach to treatment,” said Prof Jeremy Farrer, head of the Wellcome Trust.


“We will look back in 20 years time and the blockbuster chemotherapy drugs that gave you all those nasty side effects will be a thing of the past and we will think ‘gosh what an era that was’. “Understanding humanity’s genetic code is not only going to be fundamental to the medicine of the future. It is essential part of medicine today. In rare congenital disease, in cancer and in infections, genomic insights are already transforming diagnosis and treatment.” Prof Farrer also predicted that genome sequencing to find the causes of the disease will become standard within our lifetime.


The first human genome was sequenced in 2003 following 13 years of work at a cost of £2 billion. Now it takes around two days and costs just £1,000.


A genome consists of a person’s 20,000 or so genes and the DNA in between. Each genome consists of a code of 3 billion letters. Over the next four years, about 75,000 patients with cancer and rare diseases, plus their close relatives, will have their whole genetic codes, or genomes, sequenced.


Cancer patients will have the DNA of both healthy and tumour cells mapped, making up the 100,000 total. Scientists expect the project to be pivotal to the development of future personalised treatments based on genetics, with the potential to revolutionise medicine.


A £78 million partnership between Genomics England, the body set up by the Department of Health to oversee the project, and the Californian DNA sequencing technology company Illumina was unveiled by Mr Cameron today.


Illumina, originally "spun out" by Cambridge University scientists, will invest around £162 million into the project over its lifetime. By the end of next year that figure is expected to have risen to about 10,000.

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Christofer Toumazou's 'lab on a chip' makes preventing illness possible

Christofer Toumazou's 'lab on a chip' makes preventing illness possible | Amazing Science | Scoop.it

The Chairman and CEO of DNA Electronics, a provider of point-of-care genomic diagnostics solutions for medical and healthcare applications, Chris Toumazou, has been awarded the European Inventor Award 2014 in the Research category, for his rapid USB-based  DNA testing device.


Announced at the European Inventor Awards ceremony in Berlin on June 17th 2014, Toumazou’s win recognises his contribution to medical research with his ground-breaking invention. The device, which can show the results of a DNA test within minutes, uses silicon transistors to identify DNA and RNA, offering a simpler, cheaper and more discrete alternative to existing DNA analysis equipment.


The invention involves the amplification and detection of DNA and other biomolecules using pH measurement, providing the ground work for DNA Electronics’ molecular diagnostics platform Genalysis®. With the capability of identifying genomic sequences, not only in patients, but also in infectious agents, the company is developing products   that will provide clinicians with rapid actionable diagnosis of life-threatening conditions.


DNA Electronics is a developer of semiconductor solutions for real-time nucleic acid detection which enables faster, simpler and more cost-effective DNA analysis platforms.


A spin-out of Imperial College London, DNA Electronics was founded by Professor Toumazou following his invention of the company’s core technology that allows CMOS transistors to be switched on and off with DNA – the key invention enabling semiconductor-based sequencing.   Prof. Toumazou’s innovation has culminated in the world’s first DNA logic on standard CMOS technology.


The company’s IP portfolio includes techniques for monitoring nucleotide insertions using ion-sensitive transistors, enabling label-free electronic DNA sequencing and diagnostics platforms. DNA Electronics (DNAe) has developed the ground-breaking Genalysis® platform of disposable silicon chip-based solutions for real-time nucleic acid sequence detection at the point of care, providing end users with technology as yet unavailable outside a laboratory.


DNA Electronics has a non-exclusive, field-limited licensing agreement with Ion Torrent (now part of Thermo Fisher Scientific), whose next generation sequencing technology is based on DNA Electronics’ semiconductor sequencing IP. DNA Electronics has also licensed its Genalysis® technology platform to GENEU™, a company that is delivering on-the-spot genetic analytics services for cosmetics and skincare applications.


For more information: http://www.dnae.co.uk


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Elephants possess a sense of smell that is likely the strongest ever identified in a single species

Elephants possess a sense of smell that is likely the strongest ever identified in a single species | Amazing Science | Scoop.it

The African elephant's genome contains the largest number of smell receptor genes - nearly 2,000 - say the researchers in the journal Genome Research.


Olfactory receptors detect odors in the environment. That means elephants' sniffers are five times more powerful than people's noses, twice that of dogs, and even stronger than the previous known record-holder in the animal kingdom: rats.


"Apparently, an elephant's nose is not only long but also superior," says lead study author Dr Yoshihito Niimura of the University of Tokyo.


Just how these genes work is not well understood, but they likely helped elephants survive and navigate their environment over the ages.


The ability to smell allows creatures to find mates and food - and avoid predators.


The study compared elephant olfactory receptor genes to those of 13 other animals, including horses, rabbits, guinea pigs, cows, rodents and chimpanzees.


Primates and people actually had very low numbers of olfactory receptor genes compared to other species, the study found.

This could be "a result of our diminished reliance on smell as our visual acuity improved," sats Niimura.

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Researchers develop powerful single-cell epigenetic methylation mapping to study environmental effects on DNA

Researchers develop powerful single-cell epigenetic methylation mapping to study environmental effects on DNA | Amazing Science | Scoop.it

Researchers at the BBSRC-funded Babraham Institute, in collaboration with the Wellcome Trust Sanger Institute Single Cell Genomics Centre, have developed a powerful new single-cell technique to help investigate how the environment affects our development and the traits we inherit from our parents. The technique can be used to map all of the ‘epigenetic marks’ on the DNA within a single cell.  This single-cell approach will boost understanding of embryonic development, could enhance clinical applications like cancer therapy and fertility treatments, and has the potential to reduce the number of mice currently needed for this research.


‘Epigenetic marks’ are chemical tags or proteins that mark DNA and act as a kind of cellular memory. They do not change the DNA sequence but record a cell’s experiences onto the DNA, which allows cells to remember an experience long after it has faded. Placing these tags is part of normal development; they tell genes whether to be switched on or off and so can determine how the cell develops. Different sets of active genes make a skin cell different from a brain cell, for example. However, environmental cues such as diet can also alter where epigenetic tags are laid down on DNA and influence an organism’s long-term health.


Dr Gavin Kelsey, from the Babraham Institute, said: “The ability to capture the full map of these epigenetic marks from individual cells will be critical for a full understanding of early embryonic development, cancer progression and aid the development of stem cell therapies.


“Epigenetics research has mostly been reliant on using the mouse as a model organism to study early development. Our new single-cell method gives us an unprecedented ability to study epigenetic processes in human early embryonic development, which has been restricted by the very limited amount of tissue available for analysis.”


The new research, published in Nature Methods, offers a new single-cell technique capable of analysing DNA methylation – one of the key epigenetic marks – across the whole genome. The method treats the cellular DNA with a chemical called bisulphite. Treated DNA is then amplified and read on high-throughput sequencing machines to show up the location of methylation marks and the genes being affected.


These analyses will help to define how epigenetic changes in individual cells during early development drive cell fate. Current methods observe epigenetic marks in multiple, pooled cells. This can obscure modifications taking place in individual cells at a time in development when each cell has the potential to form in a unique way. The new method has already revealed that many of the methylation marks that differ between individual cells are precisely located in sites that control gene activity.

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Genome Sequencing Moving to the Clinic: Massive British Sequencing Project Will Run on Illumina Machines

Genome Sequencing Moving to the Clinic: Massive British Sequencing Project Will Run on Illumina Machines | Amazing Science | Scoop.it
The world’s largest genome project will be carried out on instruments from the California sequencing company.


The British government says that it plans to hire the U.S. gene-sequencing company Illumina to sequence 100,000 human genomes in what is the largest national project to decode the DNA of a populace.


In a regulatory filing with the U.S. Securities and Exchange Commission, Illumina said it had been picked as the “preferred partner” for the £100 million project.


Genomics England confirmed that it had chosen the California company to carry out the sequencing project. “We’ve been through the ‘bake-off’ process to find the right company to do the sequencing, and will now be entering detailed negotiations,” says Vivienne Parry, a spokesperson for Genomics England. One in 17 people are born with or will develop a rare disease in their lifetime, with 80 percent of rare diseases having an identified genetic component. By sequencing 100,000 genomes, the project’s other aims are to kickstart the development of a U.K. genomics industry and introduce the technology into its mainstream health system, according to the Genomics England website.


Illumina’s sequencing instruments dominate the market for unraveling DNA (see “50 Smartest Companies”). Parry says fewer than five other companies bid for the job, one of the largest sequencing projects ever undertaken.


Some other countries are also considering large national sequencing projects. The U.K. project will focus on people with cancer, as well as adults and children with rare diseases. Because all Britons are members of the National Health Service, the project expects to be able to compare DNA data with detailed centralized health records (see “Why the U.K. Wants a Genomic National Health Service”).


While the number of genomes to be sequenced is 100,000, the total number of Britons participating in the study is smaller, about 70,000. That is because for cancer patients Genomics England intends to obtain the sequence of both their inherited DNA as well as that of their cancers.


Genomics England began talking early this year to potential bidders, including Chinese company and Illumina rival BGI (see “Inside China’s Genome Factory”). At the time, the average cost of completing a genome was about $3,000 to $4,000.


Completing all 100,000 genomes would have cost more than twice Genomics England’s budget. The agency said in December it intended to use its negotiating power to drive prices down.


Why Illumina is #1 (Technology Review, MIT)

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A Draft Map of the Human Proteome

A Draft Map of the Human Proteome | Amazing Science | Scoop.it

Two international teams have independently produced the first drafts of the human proteome. These curated catalogs of the proteins expressed in most non-diseased human tissues and organs can be used as a baseline to better understand changes that occur in disease states. Their findings were published today (May 29) in Nature.


Both teams uncovered new complexities of the human genome, identifying novel proteins from regions of the genome previously thought to be non-coding.


“While other large proteomic data sets have been collected that cataloged up to 10,000 proteins, the real breakthrough with these two projects is the comprehensive coverage of more than 80 percent of the expected human proteome which has not been achieved previously,” said Hanno Steen, director of proteomics at Boston Children's Hospital, who was not involved in the work. “These efforts clearly show that to get to this deep level of proteome coverage, many different tissue types must be probed.”


Analyzing 30 different tissue types, Akhilesh Pandey, a proteomics researcher at Johns Hopkins University in Baltimore, Maryland, and his colleagues at the Institute of Bioinformatics in Bangalore, India, and elsewhere cataloged proteins encoded by about 84 percent of all human genes predicted to code for proteins. The researchers published the results of their Human Proteome Map online, and the data will also soon be accessible through the National Center for Biotechnology Information database, said Pandey.


Meanwhile, proteomics researcher Bernhard Küster of the Technische Universität München in Germany and his colleagues created ­ProteomicsDB, a searchable, public database that catalogs 92 percent of the estimated 19,629 human proteins.


Both teams analyzed human tissue samples using mass spectrometry. Pandey’s team generated all new data, analyzing a variety of healthy human tissues, including seven types of fetal tissues and six types of hematopoetic cells. The Küster group took a slightly different approach, compiling already available raw mass spec data from databases and colleagues’ contributions, which currently makes up about 60 percent of the ProteomicsDB. To fill in the data gaps, the Küster lab generated its own mass spec data, analyzing 60 human tissues, 13 body fluids, and 147 cancer cell lines. According to Küster, the team only selected high-resolution public data, which was computationally processed for strict quality control.


“These two papers are very complimentary,” said Anne-Claude Gingras, a proteomics researcher at the Lunenfeld-Tanenbaum Research Institute in Toronto, Canada, who was not involved in either study. “The Hopkins group really addressed what was missing in proteomics, providing a survey of human proteins from a single source, which allows for easy comparisons within their data.” In contrast, the ProteomeDB effort connected new information with existing data from the proteomics community. The goal, said Küster, is to continue to grow and refine the database, further engaging the community and pooling more resources.


  • M. Wilhelm et al., “Mass-spectrometry-based draft of the human proteome,” Nature, doi:10.1038/nature13319, 2014.
  • M.S. Kim et al. “A draft map of the human proteome,” Nature, doi:10.1038/nature13302, 2014.
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