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How to build tiny models of human tissues, called organoids, more precisely than ever before

How to build tiny models of human tissues, called organoids, more precisely than ever before | Amazing Science | Scoop.it

A UCSF-led team has developed a technique to build tiny models of human tissues, called organoids, more precisely than ever before using a process that turns human cells into a biological equivalent of LEGO bricks. These mini-tissues in a dish can be used to study how particular structural features of tissue affect normal growth or go awry in cancer. They could be used for therapeutic drug screening and to help teach researchers how to grow whole human organs.


The new technique — called DNA Programmed Assembly of Cells (DPAC) and reported in the journal Nature Methods on Aug. 31 — allows researchers to create arrays of thousands of custom-designed organoids, such as models of human mammary glands containing several hundred cells each, which can be built in a matter of hours.


There are few limits to the tissues this technology can mimic, said Zev Gartner, PhD, the paper’s senior author and an associate professor of pharmaceutical chemistry at UCSF. “We can take any cell type we want and program just where it goes. We can precisely control who’s talking to whom and who’s touching whom at the earliest stages. The cells then follow these initially programmed spatial cues to interact, move around, and develop into tissues over time.”


“One potential application,” Gartner said, “would be that within the next couple of years, we could be taking samples of different components of a cancer patient’s mammary gland and building a model of their tissue to use as a personalized drug screening platform. Another is to use the rules of tissue growth we learn with these models to one day grow complete organs.”


Our bodies are made of more than 10 trillion cells of hundreds of different kinds, each of which plays its unique role in keeping us alive and healthy. The way these cells organize themselves structurally in different organ systems helps them coordinate their amazingly diverse behaviors and functions, keeping the whole biological machine running smoothly. But in diseases such as breast cancer, the breakdown of this order has been associated with the rapid growth and spread of tumors.


“Cells aren’t lonely little automatons,” Gartner said. “They communicate through networks to make group decisions. As in any complex organization, you really need to get the group’s structure right to be successful, as many failed corporations have discovered. In the context of human tissues, when organization fails, it sets the stage for cancer.”


But studying how the cells of complex tissues like the mammary gland self-organize, make decisions as groups, and break down in disease has been a challenge to researchers. The living organism is often too complex to identify the specific causes of a particular cellular behavior. On the other hand, cells in a dish lack the critical element of realistic 3-D structure.


“This technique lets us produce simple components of tissue in a dish that we can easily study and manipulate,” said Michael Todhunter, PhD, who led the new study with Noel Jee, PhD, when both were graduate students in the Gartner research group. “It lets us ask questions about complex human tissues without needing to do experiments on humans.”

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Rethinking RNA: Thousands of long noncoding RNAs are physically attached to DNA

Rethinking RNA: Thousands of long noncoding RNAs are physically attached to DNA | Amazing Science | Scoop.it

It’s a new day for RNA. In a study published in Cell Reports on Aug 18, Michael Werner, sixth-year graduate student in Cell and Molecular Biology, and Alex Ruthenburg, PhD, Neubauer Family Foundation Assistant Professor of Molecular Genetics and Cell Biology, detail their discovery of a new class of RNA molecule that could perhaps be considered the “dark matter” of the genome. They identified thousands of long noncoding RNAs that are physically attached to DNA (quite literally coating the genome), which may play important but yet unidentified roles in gene regulation.


At some point in high school and college introductory biology classes you probably learned the “Central Dogma.” It posits that in all organisms, genetic information is coded within DNA, which is converted to a ‘messenger’ molecule called RNA, which is then converted into proteins – and it is proteins that perform the various functions of the cell as molecular machines. Advances in next-generation sequencing technologies during the last decade have revealed that this is only part of the story, however.


It turns out that only ~1.5 percent of our genome contains the information to make proteins. Most of the DNA in our genome is processed into RNA ‘transcripts’ that don’t code for proteins – referred to as noncoding RNA. Some have even been shown to perform functions in the cell as RNA molecules, without the need to be turned into a protein.


Now, together with Alex Ruthenburg, Werner discovered a class of noncoding RNA that establishes a new paradigm for how RNA acts inside cells. In a recent Cell Reports paper, the two scientists show that the majority of long noncoding RNA molecules are actually associated with DNA, as opposed to messenger RNAs that are loosely dispersed throughout the nucleus.


Remarkably, they identified several thousand RNAs that are actually physically tethered to DNA and coat the human genome, which they called chromatin-enriched RNAs (cheRNAs). The discovery of these RNAs was possible through biochemical enrichment of the genome, to the exclusion of other parts of the cell that predominately contained messenger RNA. Although they didn’t intend to find these cheRNA molecules, they decided to see if there was anything else they could learn about them. To their excitement and considerable surprise, they found tantalizing hints that cheRNAs are involved in regulating the expression of nearby genes. The sheer number of these RNAs suggest that they could be a relatively common way to control genes throughout the human genome, possibly contributing to the complexity of tissues seen across our bodies.

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The human genome takes shape and shifts over time

The human genome takes shape and shifts over time | Amazing Science | Scoop.it

If you could unravel all the DNA in a single human cell and stretch it out, you’d have a molecular ribbon about 2 meters long and 2 nanometers across. Now imagine packing it all back into the cell’s nucleus, a container only 5 to 10 micrometers wide. That would be like taking a telephone cord that runs from Manhattan to San Francisco and cramming it into a two-story suburban house.


Fitting all that genetic material into a cramped space is step one. Just as important is how the material is organized. The cell’s complete catalog of DNA — its genome — must be configured in a specific three-dimensional shape to work properly. That 3-D organization of nuclear material — a configuration called the nucleome — helps control how and when genes are activated, defining the cell’s identity and its job in the body.


Researchers have long realized the importance of DNA’s precisely arranged structure. But only recently have new technologies made it possible to explore this architecture deeply. With simulations, indirect measurements and better imaging, scientists hope to reveal more about how the nucleome’s intricate folds regulate healthy cells. Better views will also help scientists understand the role that disrupted nucleomes play in aging and diseases, such as progeria and cancer.


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DNA And Protein Self-Assemble Into Biodegradable Solar Antenna

DNA And Protein Self-Assemble Into Biodegradable Solar Antenna | Amazing Science | Scoop.it

A new light-harvesting antenna complex could pave the way for making biologically based solar cells. Challa V. Kumar and his team at the University of Connecticut made the biodegradable antenna from DNA, modified bovine serum albumin (BSA), and four fluorescent dyes.

Kumar reported the research Monday at the American Chemical Society national meeting in Boston during a session sponsored by the Division of Analytical Chemistry.


The antenna is inexpensive to make because it doesn’t require complicated assembly procedures: The components arrange themselves. Each dye binds to a specific site on the DNA or protein. One dye binds to the minor groove of the DNA double helix; the other three bind to specific sites on the albumin. The dye-loaded protein in turn binds to the negatively charged DNA because the researchers chemically modified the albumin to be positively charged. The resulting DNA-protein matrix holds the dyes close enough, but not too close, for efficient energy transfer between the dyes.


In the resulting “bucket brigade,” the dyes transfer excitation energy from one to the next until it reaches the lowest energy acceptor dye. With the current set of dyes, the antenna absorbs blue light and then emits mostly red. The overall efficiency of the antenna in converting blue to red photons is only 23%. But that efficiency is still remarkable for a system that involves energy transfer between four dye molecules and has a relatively inefficient final dye that sets an upper limit of 39% for the whole antenna, Kumar said. The team plans to find a more efficient final dye.


The complex acts as an antenna that amplifies energy capture relative to the final dye alone, which can absorb blue light and emit red. The multiple dyes allow the antenna to capture a wider range of wavelengths and thus more energy that can be funneled to the final dye. Excitation with blue light results in 2.3 times more red emission with the entire antenna than with the final dye alone, Kumar said.


The antenna also functions efficiently after exposure to 80 °C for more than 169 days, which mimics the harsh conditions under which solar cells operate. “It’s a very intriguing idea to use DNA as a matrix for dye-associated BSA,” commented Ishita Mukerji, a professor of molecular biology and biochemistry at Wesleyan University who studies DNA-protein interactions. The complex “has a lot of promise for making an antenna for solar cells.”



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King's College London - Study offers first genetic analysis of people with extremely high intelligence

King's College London - Study offers first genetic analysis of people with extremely high intelligence | Amazing Science | Scoop.it

The first ever genetic analysis of people with extremely high intelligence has revealed small but important genetic differences between some of the brightest people in the United States and the general population.


Published today in Molecular Psychiatry, the King's College London study selected 1,400 high-intelligence individuals from the Duke University Talent Identification Program. Representing the top 0.03 per cent of the ‘intelligence distribution’, these individuals have an IQ of 170 or more - substantially higher than that of Nobel Prize winners, who have an average IQ of around 145.


Genetic research on intelligence consistently indicates that around half of the differences between people can be explained by genetic factors. This study’s unique design, which focused on the positive end of the intelligence distribution and compared genotyping data against more than 3,000 people from the general population, greatly enhanced the study’s power to detect genes responsible for the heritability of intelligence.


Researchers analyszd single nucleotide polymorphisms (SNPs), which are DNA differences (polymorphisms) between individuals in the 3 billion nucleotide base pairs of DNA - steps in the spiral staircase of the double helix of DNA that make up the human genome. Each SNP represents a difference in a single nucleotide base pair, and these SNPs account for inherited differences between people, including intelligence. The study focused, for the first time, on rare, functional SNPs – rare because previous research had only considered common SNPs and functional because these are SNPs that are likely to cause differences in the creation of proteins.


The researchers did not find any individual protein-altering SNPs that met strict criteria for differences between the high-intelligence group and the control group. However, for SNPs that showed some difference between the groups, the rare allele was less frequently observed in the high intelligence group. This observation is consistent with research indicating that rare functional alleles are more often detrimental than beneficial to intelligence.


Professor Robert Plomin from the Institute of Psychiatry, Psychology & Neuroscience (IoPPN) at King’s College London, said: ‘Rare functional alleles do not account for much on their own but in combination, their impact is significant.


‘Our research shows that there are not genes for genius. However, to have super-high intelligence you need to have many of the positive alleles and importantly few of the negative rare effects, such as the rare functional alleles identified in our study.’ The researchers also analysed genome-wide similarity to explore the genetic architecture of intelligence.


Professor Plomin added: ‘Previous research suggests that common SNPs in total account for around 25 per cent of the variance in intelligence. The question we asked, for the first time, was - how much will these functional variants account for? We found that the functional SNPs in our study explain around 17 per cent of the differences between people in intelligence.’


The authors acknowledge that environmental influences also have an impact, often interacting with genetic factors. Professor Plomin said: ‘Clearly super-bright people such as those in our study are more likely to select environments conducive to their genetic propensity, so they might have grown up reading books that present intellectual problems or be more likely to attend a university.’


Professor Michael Simpson from the Division of Genetic and Molecular Medicine at King’s College London, said: ‘Our study demonstrates the challenges in identifying specific genetic variants that contribute to this complex trait, but provides potential insight into its genetic architecture that will inform future studies.’

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A cellular puzzle: The weird and wonderful architecture of RNA

A cellular puzzle: The weird and wonderful architecture of RNA | Amazing Science | Scoop.it
Cells contain an ocean of twisting and turning RNA molecules. Now researchers are working out the structures — and how important they could be.


When Philip Bevilacqua decided to work out the shapes of all the RNA molecules in a living plant cell, he faced two problems. First, he had not studied plant biology since high school. And second, biochemists had tended to examine single RNA molecules; tackling the multitudes that waft around in a cell was a much thornier challenge.


Bevilacqua, an RNA chemist at Pennsylvania State University in University Park, was undeterred. He knew that RNA molecules were vital regulators of cell biology and that their structures might offer broad lessons about how they work. He brushed up on plant anatomy in an undergraduate course and worked with molecular plant biologist Sarah Assmann to develop a technique that could cope with RNAs at scale.


In November 2013, they and their teams became the first to describe the shapes of thousands of RNAs in a living cell — revealing a veritable sculpture garden of different forms in the weedy thale cress, Arabidopsis thaliana1.


One month later, a group at the University of California, San Francisco, reported a comparable study of yeast and human cells2. The number of RNA structures they managed to resolve was “unprecedented”, says Alain Laederach, an RNA biologist at the University of North Carolina at Chapel Hill (UNC).


Scientists' view of RNA has transformed over the past few decades. Once, most RNAs were thought to be relatively uninteresting pieces of limp spaghetti that ferried information between the molecules that mattered, DNA and protein. Now, biologists know that RNAs serve many other essential functions: they help with protein synthesis, control gene activity and modify other RNAs. At least 85% of the human genome is transcribed into RNA, and there is vigorous debate about what, if anything, it does.


But a key mystery has remained: its convoluted structures. Unlike DNA, which forms a predictable double helix, RNA comprises a single strand that folds up into elaborate loops, bulges, pseudo-knots, hammerheads, hairpins and other 3D motifs. These structures flip and twist between different forms, and are thought to be central to the operation of RNA, albeit in ways that are not yet known. “It's a big missing piece of the puzzle of understanding how RNAs work,” says Jonathan Weissman, a biophysicist and leader of the yeast and human RNA study.


In the past few years, researchers have begun to get a toehold on the problem. Bevilacqua, Weissman and others have devised techniques that allow them to take snapshots of RNA configurations en masse inside cells — and found that the molecules often look nothing like what is seen when RNA folds under artificial conditions. The work is helping them to decipher some of the rules that govern RNA structure, which might be useful in understanding human variation and disease — and even in improving agricultural crops.


“It gets at the very basic problem of how do living things evolve and how do these molecular rules affect what we look like and how we function,” says Laederach. “And that, fundamentally as a biologist, is really exciting.” The best-described RNA structures are what Kevin Weeks, a chemical biologist at the UNC, calls “RNA rocks”: molecules that have changed little in their sequence or structure over evolutionary time. These include transfer RNAs and ribosomal RNAs (both involved in protein synthesis) as well as enzymatic RNAs known as ribozymes. “But in the world of RNAs,” Weeks says, “these are probably huge outliers.”

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Engineered ribosomes could pave way for designer enzymes and synthetic cells

Engineered ribosomes could pave way for designer enzymes and synthetic cells | Amazing Science | Scoop.it

By hijacking the cellular machinery that makes proteins, bioengineers have developed a tool that could allow them to better understand protein synthesis, explore how antibiotics work and convert cells into custom chemical factories.


All life owes its existence to the ribosome, a huge, hardworking molecular machine that reads RNA templates transcribed from DNA, and uses the information to string together amino acids into proteins. A cell requires functioning ribosomes to survive — but they are difficult to engineer. If the engineered molecules deviate too far from the standard design, the cell will die.


“An engineered ribosome learns to do better what you want, but it starts to forget how to do its normal job,” says biochemist Alexander Mankin of the University of Illinois in Chicago.


Mankin teamed up with biochemical engineer Michael Jewett of Northwestern University in Evanston, Illinois, and others to create a ribosome that engineers could tinker with. The results of their handiwork are published in Nature1.


Ribosomes are conglomerates of RNA and protein, hundreds of times larger than typical enzymes. RNA is thought to be responsible for the bulk of a ribosome’s work, which is is considerable — it produces protein at a rate of up to 20 amino acids a second with a remarkably low error rate. “The ribosome deserves all possible respect,” says Mankin.


It is these properties that draw the attention of bioengineers such as Jewett. These researchers would like to create ribosomes that could do other chemical reactions and spit out novel polymers, or incorporate unnatural amino acids into proteins that could be used as drugs.


Each ribosome contains two clumps of snarled RNA molecules, a small subunit and a large one. The subunits come together to translate a messenger RNA sequence into protein, and then separate. They assemble again when it is time to make another protein, although not necessarily with the same partners. “In a way they are very promiscuous,” says Mankin.


That promiscuity hindered efforts to engineer ribosomes to incorporate unnatural amino acids or other compounds. Engineered and natural subunits mixed and matched, reducing the cell's ability to produce normal proteins. The solution, Mankin and Jewett's team decided, was to marry together two engineered subunits. It was unclear whether the approach would work: it was thought that ribosomes exist in two distinct units because it is necessary for their function.


The researchers used a strand of RNA to tether the large and the small subunit together, toiling for months to get the length and location of the link just right so that the machine could still function. “We certainly came close, several times, to saying ‘OK, biology wins',” says Jewett. The team screened its tethered ribosomes in Escherichia coli cells that lacked functioning RNA, and eventually found engineered ribosomes that worked well enough to support some growth, albeit slow. They then tested their platform to confirm that a tethered ribosome could operate side-by-side with natural ribosomes.


The result unlocks a molecular playground for bioengineers: by tethering the artificial subunits together, they can tweak the engineered machines to their liking without halting cell growth, says Joseph Puglisi, a structural biologist at Stanford University in California. Puglisi hopes to harness the system to study how the ribosome functions. James Collins, a bioengineer at the Massachusetts Institute of Technology in Cambridge, says that his lab may use the system to study antibiotics — many of which work by binding to bacterial ribosomes.

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Next-Gen Shotgun Cloning Using the Gibson Assembly Method

Next-Gen Shotgun Cloning Using the Gibson Assembly Method | Amazing Science | Scoop.it
Traditional cloning and sequencing methods can be laborious, expensive, and time-consuming techniques, especially when applied to large sample numbers. Even for the routine cloning of small sample sizes, however, many research laboratories have yet to discover the power, ease, and efficiency of the Gibson Assembly® method. First described by Dan Gibson at the J. Craig Venter Institute (JCVI) in 2009, the Gibson Assembly method is a sequence-independent, seamless cloning method that offers many advantages over traditional cloning, most notably the ability to assemble multiple DNA fragments quickly, accurately, and efficiently in a single-tube reaction.

  • SGI-DNA, a Synthetic Genomics company, offers Gibson Assembly reagent kits: the Gibson Assembly HiFi 1-Step Kit can be used for the simultaneous assembly of up to 5 fragments and the Gibson Assembly Ultra Kit can be used for the simultaneous assembly of up to 15 fragments. The Gibson Assembly method can be leveraged for a variety of applications, including routine cloning, site-directed mutagenesis, and whole-genome synthesis.
  • Here, we discuss the results and advantages of coupling the Gibson Assembly method with shotgun cloning and next-generation sequencing. The combined technologies of the Gibson Assembly method, shotgun cloning, and next-generation sequencing constitute Gibson Assembly next-generation shotgun cloning.
  • Shotgun cloning and next-generation sequencing methods offer significant time and cost savings relative to traditional (Sanger) sequencing methods and independent, repetitive cloning methods. Shotgun cloning drastically reduces sample number and next-generation sequencing drastically reduces the amount of time required for high-throughput sample processing. Combining the highly-efficient, error-correcting Gibson Assembly method with shotgun cloning and next-generation sequencing harnesses the advantages of the combined technologies, yielding substantial time and resource savings in comparison to traditional methods.
Traditional cloning and sequencing methods require the processing of individual samples through the following steps:

Preparation of insert and vector DNA by PCR amplification or restriction enzyme digestion → Vector Dephosphorylation → Ligation Cloning → Transformation → Plating → Picking Colonies → Plasmid Preparation  → Sequencing → Analysis → Construct Retrieval

The sequencing and cloning of n constructs (where n = the number of constructs) requires individually manipulating all n samples through the 10 workflow steps outlined on the previous page in n tubes (i.e., cloning 12 constructs requires handling 12 samples during every workflow stage). See Figure 1A for a schematic overview.

Combining Gibson Assembly shotgun cloning with next-generation sequencing is achieved by processing samples through the following steps:

Preparation of insert and vector DNA by PCR amplification → Gel Purification → The Gibson Assembly Method → Transformation → Plating → Picking Colonies → Plasmid Preparation → Next-Generation Sequencing → Analysis → Construct Retrieval

In the Gibson Assembly next-generation shotgun cloning workflow, samples are pooled prior to gel purification and processed in size-correlated batches. Therefore, to sequence and clone n samples using Gibson Assembly shotgun cloning, n constructs will be individually PCR-amplified. Following amplification, however, samples are pooled. For convenience and processing using 96-well plates, pools are typically batched with 8 samples per batch. Because of batching, for the remaining workflow steps, instead of processing n samples, only n/8 sample batches are manipulated for each step, which translates into substantial reagent savings (see Figures 1B & 2).
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Researchers find short tracks of DNA may aid in regulating human gene expression

Researchers find short tracks of DNA may aid in regulating human gene expression | Amazing Science | Scoop.it

A team of researchers with members from Washington University, Johns Hopkins School of Medicine, the Howard Hughes Medical Institute and the Polish Academy of Sciences has found that problems with RNA appear to be behind protein translation interruptions and that short segments of DNA may assist in regulating gene expression. They have published a paper describing their research and findings in the journal Science Advances.


Scientists have known for some time that the mechanism that controls protein translation, known as polyadenylate A aka, poly(A) is sometimes interrupted, causing degradation of messenger RNA (mRNA) and the proteins under development, leading to some ailments such as neurodegenerative diseases. Past research has suggested the problem lies with amino acids involved in the encoding, but now it appears that the problem is actually with the RNA itself—specifically strings of multiple adenosine (A) nucleotides.


In this new effort the team, noting that approximately 2 percent of genes in the human genome may be impacted, found that in studying bacterial ribosomes, that they were more likely to be interrupted on strings of lysines if they were encoded by AAA codons, as opposed to AAG codons. They showed that making shorter or longer runs of adenosine nucleotides, without modifying amino acid sequences, changed the protein output and also the stability of the mRNA. They noted also that doing so also sometimes led to the creation of what they termed "frameshifted" protein products.


The researchers also studied poly(A) tracks in human cells and found some as short as just nine basses long might influence gene expression. They discovered that poly(A) lowered the expression of protein in two different ways. The first was by halting translation, which led to degradation of the protein and mRNA itself. The second was when frameshifts occurred during translation, which led to early termination of the production of proteins.


The work by the team, and another also at Washington University looking into the impact of nucleotides on Poly(A) offer a fresh insight into the creation of disease-causing states in cells and by extension, possible ways to prevent it from happening, offering patients with such ailments hope of recovery.

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Researchers folded DNA into the shape of a nanoscale bunny and other 3D structures

Researchers folded DNA into the shape of a nanoscale bunny and other 3D structures | Amazing Science | Scoop.it

Folding DNA into the shape of a tiny bunny rabbit is now easier than ever, according to a study published in Nature today. Folding DNA isn’t new — it’s known as DNA origami — but automating the process is. Thanks to a set of computer algorithms, researchers have developed a way to streamline the design phase that comes before the DNA assembly — a substantial step toward 3D printing at the nanoscale.


This has not been done before, it is novel and surprising," says Thorsten Schmidt, a chemist at the Dresden University of Technology who didn't work on the study. "In fact, we have a very related study under review at the moment and the only bad aspect of Björn Högberg’s study is that they were faster than us."


The bunny, while cute, wasn’t the point of the study. Rather, it’s a demonstration that scientists can automatically generate a DNA sequence to form a complex shape — the closest thing to 3D printing on a very tiny scale. "It’s almost a one-click procedure," Högberg says. And if scientists can fully automate the process, they’ll have a real DNA printer at their disposal — one that could, among other things, make drugs easier to deliver to the right places in the body.

Actually, there are a lot of ideas about how these techniques could be used. In addition to drug delivery, researchers are working on coating the DNA structures with non-biological materials, like gold, that react when the structure comes in contact with light.


But at this point, the bunny and the bottle don't do all that much. "We're not really concerned with the genetic information," Högberg says. "We're using DNA purely as a construction material."


Now that the study has been published, the researchers want to find a way to make their own construction materials. That may mean using natural DNA — taken from a plant or bacteria that they cultivate themselves — instead of synthetic DNA, Högberg says. "We're getting very good at making structures at the nanoscale," Högberg says. Researchers just need to find a way to make lots tiny DNA bunnies cheaply — and all at once.


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Present-day Amazonians share an unexpected genetic link with Asian islanders, hinting at unknown migration track

Present-day Amazonians share an unexpected genetic link with Asian islanders, hinting at unknown migration track | Amazing Science | Scoop.it

A mysterious group of humans crossed the Bering land bridge from Siberia into the Americas thousands of years ago, genetic analysis reveals. Modern-day signatures of this ‘unknown population’ survive in people who live deep in the Brazilian Amazon, but the two research teams who have made the discovery have different ideas about when and how these migrants reached the Americas12.


"This is an unexpected finding," says Jennifer Raff, an anthropological geneticist at the University of Texas at Austin who was not involved in either study. "It’s honestly one of the most exciting results we’ve seen in a while."


North and South America were the last continents that humans settled. Previous studies of DNA from modern and ancient Native Americans suggest that the trek was made at least 15,000 years ago (although the timing is not clear-cut) by a single group dubbed the ‘First Americans’, who crossed the Bering land bridge linking Asia and North America.


“The simplest hypothesis would be that a single population penetrated the ice sheets and gave rise to most of the Americans,” says David Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts. In 2012, his team found evidence for a single founding migration in the genomes from members of 52 Native American groups3.


So Reich was flabbergasted when a colleague called Pontus Skoglund mentioned during a conference last year that he had found signs of a second ancient migration to the Americas lurking in the DNA of contemporary Native Amazonians. Reich wasted no time in verifying the discovery. “During the session afterward, he passed his laptop over the crowd, and he had corroborated the results,” says Skoglund, who is now a researcher in Reich’s lab.


Skoglund’s discovery — which is published online on 21 July in Nature2 — was that members of two Amazonian groups, the Suruí and the Karitiana, are more closely related to Papua New Guineans and Aboriginal Australians than other Native Americans are to these Australasian  groups. The team confirmed the finding with several statistical methods used to untangle genetic ancestry, as well as additional genomes from Amazonians and Papuans. “We spent a lot of time being sceptical and incredulous about the finding and trying to make it go away, but it just got stronger,” says Reich.


Their explanation is that distant ancestors of Australasians also crossed the Bering land bridge, only to be replaced by the First Americans in most of North and South America. Other genetic evidence suggests that modern-day Australasians descend from humans who once lived more widely across Asia. “We think this is an ancestry that no longer exists in Asia, which crossed Beringia at some point, but has been overwritten by later events,” Reich says. The team calls this ghost population “Population Y”, after the word for ancestor, Ypykuéra, in the languages spoken by the Suruí and Karitiana. They contend that Population Y reached the Americas either before or around the same time as the First Americans, more than 15,000 years ago.

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Yeast can optimize its genome in response to environmental factors

Yeast can optimize its genome in response to environmental factors | Amazing Science | Scoop.it

Researchers at the Babraham Institute and Cambridge Systems Biology Centre, University of Cambridge have shown that yeast can modify their genomes to take advantage of an excess of calories in the environment and attain optimal growth.
 
The ability to sense environmental nutrient availability and act accordingly is a critical process for all organisms. Changing behaviour in response to nutrients can occur at many levels: the activity of proteins can be varied or new genes can be activated to produce a different set of proteins. Research published in the latest issue of PNAS reveals that yeast go one step further and actually modify their genomes to act optimally in the current environment.
 
We think of the information in our genome as stable, only changing occasionally through random mutation. However, a handful of genes in organisms from yeast to mammals are known to change rapidly at specific times and in specific cell types. A good example of this is the system which creates immune diversity in vertebrates. How these systems are controlled is a major question as mechanisms that cause genome change can be very dangerous if mis-directed. This is especially true for single-celled organisms like yeast, for which a genome change affects not just an individual but is passed down to all its descendants.
 
This research looked at the genes encoding ribosomes - the factories that produce proteins in cells. To create an entire new cell requires the synthesis of a huge amount of proteins by the ribosomes, and a vast proportion of cellular resources are used in producing enough ribosomes to allow cells to divide at the maximum possible speed. TOR is a signalling pathway that coordinates growth rate in response to nutrient availability and controls the rate of ribosome synthesis. TOR signalling is conserved from yeast to mammals and controls numerous processes, one notable example being the response to caloric restriction which slows growth and can extend lifespan.
 
In the paper published in PNAS, the researchers show that TOR also responds to caloric excess, instigating a pathway that increases the number of ribosomal DNA genes in the genome. Yeast engineered to carry a sub-optimal complement of ribosomal DNA genes are known to undergo gene amplification to correct this deficit, but it was not known why. The researchers found that these cells perceive the normal environment as containing an excess of calories because they struggle to produce enough ribosomes to maintain normal levels of protein synthesis. TOR signalling responds to this caloric excess and initiates ribosomal DNA gene amplification. Amplification of the ribosomal DNA genes provides a long term, heritable increase in ribosome synthesis capacity to enable optimum reproduction rate and make best use of available nutrients. It will be fascinating to now ask whether TOR can also drive genome changes in higher organisms in response to an excess of calories, and what effects this might have on health and lifespan.


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Shape-shifting molecular cousins are the key to DNA repair

Shape-shifting molecular cousins are the key to DNA repair | Amazing Science | Scoop.it

It’s taken years of frustration and dedication (not to mention countless hours spent in a small room roughly the temperature of a domestic fridge) but the hard work has finally paid off. Our researchers Martin Taylor and Simon Boulton at the Francis Crick Institute have solved a decades-old biological mystery, publishing the results of their molecular sleuthing in the journal Cell.


The story centres on a protein called RAD51 and its closely-related molecular ‘cousins’, known as paralogs, which are involved in helping cells repair DNA damage. It’s been known for some time that people who inherit a single faulty version of one of the genes that makes these proteins are at higher risk of developing breast and ovarian tumors – for example, our researchers found that inheriting a mistake in a paralog gene called RAD51D increases a woman’s chances of developing ovarian cancer six-fold. Inheriting two broken copies causes a severe genetic syndrome known as Fanconi anaemia, which usually leads to leukaemia. But until now, exactly how RAD51’s molecular cousins work – and how they contribute to cancer – was completely unknown, until no.


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Temples hidden dangers: Incense could be more harmful than cigarette smoke, researchers find

Temples hidden dangers: Incense could be more harmful than cigarette smoke, researchers find | Amazing Science | Scoop.it

In the future, incense might need to carry a health warning, just like tobacco. That’s the conclusion of researchers who for the first time have compared the effects of burning incense indoors to inhaling tobacco smoke. Previous research has already shown how incense smoke can be harmful to a person’s health, but these new findings suggest that it’s worse than cigarettes by several measurements – a result that may alarm some in Asian countries, where incense burning is a common practice in the home and a traditional ritual in many temples.


Clearly, there needs to be greater awareness and management of the health risks associated with burning incense in indoor environments,” said Rong Zhou of the South China University of Technology, in a statement to the press.


The researchers tested two types of incense against cigarette smoke to see their effects on bacteria and the ovary cells of Chinese hamsters. Both the incense products contained the common ingredients agarwood and sandalwood, which are used in incense for their fragrances.


The findings, published in Environmental Chemistry Letters, showed that incense smoke is mutagenic, which means it can cause mutations to genetic material, primarily DNA. Compared to the cigarette smoke, the incense products were found to be more cytotoxic (toxic to cells) and genotoxic (toxic to DNA). Of the 64 compounds identified in the incense smoke, two were singled out as highly toxic.


Obviously none of this sounds very good, and for people frequently exposed to incense smoke in indoor environments, hopefully it serves as a wake-up call: mutagenics, genotoxins, and cytotoxins are all linked to the development of cancers.

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New DNA code makes synthetic proteins

New DNA code makes synthetic proteins | Amazing Science | Scoop.it

The world's first functioning organism with an expanded DNA alphabet has now met another milestone in artificial life: making proteins that don't exist in nature. The organism, a bacterium created by scientists at The Scripps Research Institute, incorporates two synthetic DNA letters, called X and Y, along with the four natural ones, A, T, C and G. A team led by Floyd Romesberg published a study last year demonstrating that the organism, an engineered strain of E. coli, can function and replicate with the synthetic DNA.


Synthorx, a biotech startup that licensed the technology from Scripps, has now used the bacterium to produce proteins incorporating artificial amino acids, the building blocks of proteins. These are placed at precisely specified intervals along the protein sequence, obeying the code of the expanded DNA alphabet.


The La Jolla startup plans to make drugs out of these artificial proteins with properties that can be adjusted, such as the length of action inside the body, and how tightly they bind to their target. By using the bacterium as living factories, Synthorx plans to make these drugs far more efficiently and cheaply than by traditional chemistry.


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Meteorite Impacts Can Create DNA Building Blocks

Meteorite Impacts Can Create DNA Building Blocks | Amazing Science | Scoop.it

The emergence of life's building blocks on the prebiotic Earth was the first crucial step for the origins of life. Extraterrestrial delivery of intact amino acids and nucleobases is the prevailing hypothesis for their availability on prebiotic Earth because of the difficulties associated with the production of these organics from terrestrial carbon and nitrogen sources under plausible prebiotic conditions. However, the variety and amounts of these intact organics delivered by meteorites would have been limited. Previous shock–recovery experiments have demonstrated that meteorite impact reactions could have generated organics on the prebiotic Earth.


A new study shown that meteorite impacts on ancient oceans may have created nucleobases and amino acids. Researchers from Tohoku University, National Institute for Materials Science and Hiroshima University discovered this after conducting impact experiments simulating a meteorite hitting an ancient ocean. A new study shown that meteorite impacts on ancient oceans may have created nucleobases and amino acids. Researchers from Tohoku University, National Institute for Materials Science and Hiroshima University discovered this after conducting impact experiments simulating a meteorite hitting an ancient ocean. 


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Illumina wants to enable any developer with a computer to start a genomics company

Illumina wants to enable any developer with a computer to start a genomics company | Amazing Science | Scoop.it

The CEO of the world’s leading DNA sequencing company says he knows how to finally get consumers interested in their genomes: by creating an enormous app store for genetic information. 


Recently, Illumina said that along with Warburg Pincus and Sutter Hill Ventures it was investing $100 million in a new company called Helix to make consumer genomics part of the Internet mainstream. Illumina’s CEO, Jay Flatley, said in an interview that Helix will subsidize the cost of decoding people’s genomes in hopes of spurring the creation of consumer apps that will draw on the DNA data repeatedly. “You saw what happened with the Apple app store: it just unleashed the consumer side because apps are so cheap to make,” says Flatley, who will be chairman of the new company.


Flatley says that when Helix goes live next year it will sequence and store consumers’ DNA, then sell them pay-as-you-go access to it through the apps, which will be offered by partners, the first of which are LabCorp and the Mayo Clinic. Profits will get shared, in a model similar to the one for Apple’s app store. If Helix succeeds, it will operate the largest sequencing laboratory of any kind, Flatley predicts.


Everyone is trying to unlock the value of the genome, most of all Illumina (see“50 Smartest Companies 2014”). The San Diego-based company, whose sleek-looking sequencing machines are also said to be inspired by Apple’s designs, is the big winner so far. It dominates the market and last year sold $1.8 billion of DNA sequencing machines, chemicals, and tests. The more sequencing happens, the better for Illumina.


So how do you get consumers to participate? The idea behind Helix is to make it pay-as-you-go. Here’s how it might work. Say you download an app from a Helix partner to find out if you have a specific genetic variant, for example the “speed gene,” known to be possessed by many athletes (nicely described here by 23andMe). And imagine that app costs $20. You send in a spit sample; Helix will return just that information to you through the app.


But Helix will sequence much more of your genome, says Flatley. He says Helix will do “an exome plus” – that is, decode all your genes and a few more key spots, but not parts of the genome without clear medical relevance. That will cost Helix perhaps $500. But then, if you order a new app that draws on your genes, Helix will already have your DNA information, ready to be quickly served up.


“We are betting on the consumer coming back and asking for more, and then you don’t have to sequence a second time,” says Flatley. In contrast, if you wanted to sign up for both Ancestry.com and 23andMe, two different companies offering genetic genealogy, you’d have to get tested twice.


Flatley says Helix will be a “neutral” player, storing DNA and serving it up to any app on the platform. Like Apple’s app store, which takes a 30 percent cut of every copy of Angry Birds that is sold, revenue will be shared by Helix and by app makers, although Flatley didn’t say what the percentages would be. He did describe one important twist: whichever affiliate (say, the Mayo Clinic) first convinces a consumer to send in a spit sample will also get paid each time that person’s genome is accessed again, by any other app. That’s basically a bounty for dragging people into the genome age.


Storing thousands or millions of genomes could also put Helix in a good position as biologists make more discoveries about what genetic information is good for. “As the science gets better and better the content is going to be better, and the consumer will be charged for that,” says Flatley.


Illumina’s prior foray into apps wasn’t a big success. It launched a system called BaseSpace—an app store for researchers—that didn’t really take off. Scientists tell me it does a little of everything, but nothing very well. But times change. Now everyone is anticipating an explosion of consumer activity around genomics, cloud computing, and apps (see “Google Wants to Store Your Genome” and “Apple Has Plans for Your DNA”). To succeed, Helix may need a killer app.


The Mayo Clinic is working on one app related to educating people about DNA, the organization confirmed, and Flatley says other early apps could be “educational, to do with nutrition, or sports-related.” It sounds like lightweight stuff. There are reasons for that. To dispense real diagnostic information an app maker would probably need approval from the U.S. Food and Drug Administration—something that would take time to obtain. Flatley says he’s been talking to the FDA about Helix.


Right now, the most important consumer-facing uses of genetics are in cancer predisposition testing, genealogy, and carrier screening. The genealogy tests tell you to whom you are related, your ethnic origins, and how much Neanderthal DNA you have. Carrier screening is about what’s next: when you are ready to have a baby, you can check whether you and your partner share dangerous disease mutations.


Companies offering these types of consumer tests, such as 23andMe and Counsyl, have spent millions building out labs, analytical software, or just paying Illumina to analyze the DNA. With Helix, says Flatley, companies won’t have to invest in starting a laboratory anymore. Instead, he says, any developer with a computer will be able to start a genomics company.

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Photonic heating and cooling with light leads to ultrafast PCR-based DNA diagnostics

Photonic heating and cooling with light leads to ultrafast PCR-based DNA diagnostics | Amazing Science | Scoop.it

A new technology developed by UC Berkeley bioengineers promises to make a workhorse lab tool cheaper, more portable and many times faster by accelerating the heating and cooling of genetic samples with the switch of a light. This turbocharged thermal cycling, described in a paper published July 31 in the journal Light: Science & Application, greatly expands the clinical and research applications of the polymerase chain reaction (PCR) test, with results ready in minutes instead of an hour or more.


The PCR test, which amplifies a single copy of a DNA sequence to produce thousands to millions of copies, has become vital in genomics applications, ranging from cloning research to forensic analysis to paternity tests. PCR is used in the early diagnosis of hereditary and infectious diseases, and for analysis of ancient DNA samples of mummies and mammoths.


Using light-emitting diodes, or LEDs, the UC Berkeley researchers were able to heat electrons at the interface of thin films of gold and a DNA solution. They clocked the speed of heating the solution at around 55 degrees Fahrenheit per second. The rate of cooling was equally impressive, coming in at about 43.9 degrees per second.


“PCR is powerful, and it is widely used in many fields, but existing PCR systems are relatively slow,” said study senior author Luke Lee, a professor of bioengineering. “It is usually done in a lab because the conventional heater used for this test requires a lot of power and is expensive. Because it takes an hour or longer to complete each test, it is not practical for use for point-of-care diagnostics. Our system can generate results within minutes.”


To pick up the pace of this thermal cycling, Lee and his team of researchers took advantage of plasmonics, or the interaction between light and free electrons on a metal’s surface. When exposed to light, the free electrons get excited and begin to oscillate, generating heat. Once the light is off, the oscillations and the heating stop.


Gold, it turns out, is a popular metal for this plasmonic photothermal heating because it is so efficient at absorbing light. It has the added benefit of being inert to biological systems, so it can be used in biomedical applications.


For their experiments, the researchers used thin films of gold that were 120 nanometers thick, or about the width of a rabies virus. The gold was deposited onto a plastic chip with microfluidic wells to hold the PCR mixture with the DNA sample.


The light source was an array of off-the-shelf LEDs positioned beneath the PCR wells. The peak wavelength of the blue LED light was 450 nanometers, tuned to get the most efficient light-to-heat conversion. The researchers were able to cycle from 131 degrees to 203 degrees Fahrenheit 30 times in less than five minutes.


They tested the ability of the photonic PCR system to amplify a sample of DNA, and found that the results compared well with conventional PCR tests. “This photonic PCR system is fast, sensitive and low-cost,” said Lee, who is also co-director of the Berkeley Sensor and Actuator Center. “It can be integrated into an ultrafast genomic diagnostic chip, which we are developing for practical use in the field. Because this technology yields point-of-care results, we can use this in a wide range of settings, from rural Africa to a hospital ER.”


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A Giant Burst on Tree of Life Comes into View

A Giant Burst on Tree of Life Comes into View | Amazing Science | Scoop.it

A new technique for finding and characterizing microbes has boosted the number of known bacteria by almost 50 percent, revealing a hidden world all around us.


A team of microbiologists based at the University of California, Berkeley, recently figured out one such new way of detecting life. At a stroke, their work expanded the number of known types — or phyla — of bacteria by nearly 50 percent, a dramatic change that indicates just how many forms of life on earth have escaped our notice so far.


“Some of the branches in the tree of life had been noted before,” said Chris Brown, a student in the lab of Jill Banfield and lead author of the paper. “With this study we were able to fill in many gaps.”


As an organizational tool, the tree of life has been around for a long time. Lamarck had his version. Darwin had another. The basic structure of the current tree goes back 40 years to the microbiologist Carl Woese, who divided life into three domains: eukaryotes, which include all plants and animals; bacteria; and archaea, single-celled microorganisms with their own distinct features. After a point, discovery came to hinge on finding new ways of searching. “We used to think there were just plants and animals,” said Edward Rubin, director of the U.S. Department of Energy’s Joint Genome Institute. “Then we got microscopes, and got microbes. Then we got small levels of DNA sequencing.”


DNA sequencing is at the heart of this current study, though the researchers’ success also owes a debt to more basic technology. The team gathered water samples from a research site on the Colorado River near the town of Rifle, Colo. Before doing any sequencing, they passed the water through a pair of increasingly fine filters — with pores 0.2 and 0.1 microns wide — and then analyzed the cells captured by the filters. At this point they already had undiscovered life on their hands, for the simple reason that scientists had not thought to look on such a tiny scale before. “Most people assumed that bacteria were bigger, and most bacteria are bigger,” Rubin said. “Banfield has shown that there are whole populations that are very small.”


The researchers extracted the DNA from the cellular material and sent it to the Joint Genome Institute for sequencing. What they got back was a mess. Imagine being handed a box of pieces from thousands of different jigsaw puzzles and having to assemble them without knowing what any of the final images look like. That’s the challenge researchers face when performing metagenomic analysis — sequencing scrambled genetic material from many organisms at once.


The Berkeley team began the reassembly process with algorithms that assembled bits of the sequenced genetic code into slightly longer strings called contigs. “You no longer have tiny pieces of DNA, you have bigger pieces,” Brown said. “Then you figure out which of these larger pieces are part of a single genome.”


This part of the process, in which contigs are combined to reconstruct the genome sequence, is called genome binning. To execute it, the researchers relied on another set of algorithms, customized for the task by Itai Sharon, a co-author of the study. They also assembled some of the genomes manually, making decisions about what goes where based on the fact that some characteristics are consistent for a given genome. For example, the percentage of Gs and Cs will be similar on any part of an organism’s DNA.


When the assembly was complete, the researchers had eight full bacterial genomes and 789 draft genomes that were roughly 90 percent complete. Some of the organisms had been glimpsed before; many others were completely new.


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How many species of giant sea spiders do we have?

How many species of giant sea spiders do we have? | Amazing Science | Scoop.it

Sea spiders belong to a group of arthropods called the pycnogonids, which are found scuttling along the bottom of many of the world’s oceans and seas. They are crustaceans and not spiders. Most are relatively small – it’s only around the poles that sea spiders grow large, which is a trait they share with many marine species. Exactly why this happens remains a mystery.


Many sea spiders are carnivorous, dining on worms, jellyfish and sponges. “They have a giant proboscis to suck up their food,” says Florian Leese at Ruhr University Bochum in Germany. Like true spiders, some sea spiders have eight legs. But not all do. “Some have 10 and even 12 legs,” says Leese.


Curiously, though, their bodies don’t appear to have much else apart from their long legs and proboscis. “They don’t really have a body,” says Leese. “They have their organs in their legs.” These creatures are sometimes called the pantopoda – meaning “all legs” – because of their bizarre anatomy.


The lack of an obvious body means sea spiders don’t need to bother with a respiratory system. Simple diffusion can deliver gases to all of the tissues. The Southern Ocean giant sea spider is one of the most common sea spiders in the waters around Antarctica. It also lives in coastal waters off South America, South Africa and Madagascar, down to a depth of 4.9 kilometers.


It is so widespread that some have wondered whether it really is a single species. To find out, Leese and his colleagues examined DNA taken from 300 specimens. Animal cells usually carry two forms of DNA: most is in the form of nuclear DNA in the cell’s nucleus, but there is a second form of DNA in the mitochondria – often called the “powerhouse of the cell”. Mitochondrial DNA is usually only inherited down the female line.


The mitochondrial genes fell into about 20 distinct groups, apparently suggesting the Southern Ocean giant sea spider should really be broken up into 20 distinct species. But the nuclear DNA showed that many of these apparently distinct species can and have interbred in the recent past. In fact, the team says, if the Southern Ocean giant sea spider is divided into several distinct species, we should probably recognise only five – not 20.


Why is this? The mitochondrial DNA sequences are so distinct that the sea spiders probably began to diverge about a million years ago – perhaps during glacial periods when a deterioration in conditions left small populations of sea spiders isolated from one another in ice-free “refugia”, where they could each develop their own genetic mutations.


But when environmental conditions improved and the spider lineages began expanding out of those refugia, they began to interbreed and hybridise. That’s not unlike the way different human lineages like the Neanderthals, Denisovans and our species interbred when they came into contact after thousands of years of isolation.


The results are important for conservation. Mitochondrial and nuclear DNA often show the same general pattern, says Leese, so when easier-to-analyse mitochondrial DNA indicates one species actually breaks down into several “cryptic” species, conservationists want to protect all of the lineages. But nuclear DNA sequences might show that many of those cryptic species don’t really exist. “The study advises caution in calling distinct mitochondrial lineages species,” says Leese.


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Simple technology makes CRISPR-Cas9 gene editing cheaper

Simple technology makes CRISPR-Cas9 gene editing cheaper | Amazing Science | Scoop.it

University of California, Berkeley, researchers have discovered a much cheaper and easier way to target a hot new gene editing tool, CRISPR-Cas9, to cut or label DNA. The CRISPR-Cas9 technique, invented three years ago at UC Berkeley, has taken genomics by storm, with its ability to latch on to a very specific sequence of DNA and cut it, inactivating genes with ease. This has great promise for targeted gene therapy to cure genetic diseases, and for discovering the causes of disease.


The technology can also be tweaked to latch on without cutting, labeling DNA with a fluorescent probe that allows researchers to locate and track a gene among thousands in the nucleus of a living, dividing cell. The newly developed technique now makes it easier to create the RNA guides that allow CRISPR-Cas9 to target DNA so precisely. In fact, for less than $100 in supplies, anyone can make tens of thousands of such precisely guided probes covering an organism’s entire genome. The process, which they refer to as CRISPR-EATING – for “Everything Available Turned Into New Guides” – is reported in a paper to appear in the August 10 issue of the journal Developmental Cell.


As proof of principle, the researchers turned the entire genome of the common gut bacterium E. coli into a library of 40,000 RNA guides that covered 88 percent of the bacterial genome. Each RNA guide is a segment of 20 RNA base pairs: the template used by CRISPR-Cas9 as it seeks out complementary DNA to bind and cut.


These libraries can be employed in traditional CRISPR-Cas9 editing to target any specific DNA sequence in the genome and cut it, which is what researchers do to pin down the function of a gene: knock it out and see what bad things happen in the cell. This can help pinpoint the cause of a disease, for example. The process is called genetic screening and is done in batches: each of the thousands of probes is introduced into a single cell on a plate filled with hundreds of thousands of cells.


“We can make these libraries for a lot less money, which makes genetic screening potentially accessible in organisms less well studied,” such as those that have not yet had their genomes sequenced, said first author Andrew Lane, a UC Berkeley post-doctoral fellow.

But Lane and colleague Rebecca Heald, UC Berkeley professor of molecular and cell biology, developed the technology in order to track chromosomes in real-time in living cells, in particular during cell division, a process known as mitosis. This is part of a larger project by Heald to find out what regulates the size of the nucleus and other subcellular components as organisms grow from just a few cells to many cells.


“This technology will allow us to paint a whole chromosome and look at it live and really follow it in the nucleus during the cell cycle or as it goes through developmental transitions, for example in an embryo, to see how it changes in size and structure,” Heald said.


The new technique uses standard PCR (polymerase chain reaction) to generate many short lengths of DNA from whatever segment of DNA a researcher is interested in, up to and including an entire genome.


These fragments are then precisely snipped at a region called a PAM, which is critical to CRISPR binding. Simple restriction enzymes are then used to cut each piece 20 base pairs from the PAM end, generating the exact size of RNA guide that CRISPR uses in searching the genome for complementary sites. These guide RNAs are then easily incorporated into the CRISPR-Cas9 complex, yielding tens of thousands of probes for labeling or cutting DNA.


“By using the genome itself as a source for guide RNAs, their approach puts the creation of libraries that target contiguous regions in reach of almost any lab,” said Jacob Corn, managing and scientific director of the Innovative Genomics Initiative at UC Berkeley. “This could be very useful for genome imaging and certain kinds of screens, and I’m very interested to see how it enables biological discovery using Cas9 tools.”


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Sophia Nguyen's curator insight, July 28, 11:01 PM

As before, CRISPR is something that I am interested in studying since it is relatively new in the gene editing world. Also, UC Berkeley is a college that I am considering  applying and attending so it would be good to contribute to this research.

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How Viruses Feign Death to Survive and Thrive

How Viruses Feign Death to Survive and Thrive | Amazing Science | Scoop.it

Billions of cells die each day in the human body in a process called "apoptosis" or "programmed cell death". When cells encounter stress such as inflammation, toxins or pollutants, they initiate an internal repair program which gets rid of the damaged proteins and DNA molecules. But if the damage exceeds their capacity for repair then cells are forced to activate the apoptosis program. Apoptotic cells do not suddenly die and vanish, instead they execute a well-coordinated series of molecular and cellular signals which result in a gradual disintegration of the cell over a period of several hours.


What happens to the cellular debris that is generated when a cell dies via apoptosis? It consists of fragmented cellular compartments, proteins, fat molecules that are released from the cellular corpse. This "trash" could cause even more damage to neighboring cells because it exposes them to molecules that normally reside inside a cell and could trigger harmful reactions on the outside. Other cells therefore have to clean up the mess as soon as possible. Macrophages are cells which act as professional garbage collectors and patrol our tissues, on the look-out for dead cells and cellular debris. The remains of the apoptotic cell act as an "Eat me!" signal to which macrophages respond by engulfing and gobbling up the debris ("phagocytosis") before it can cause any further harm. Macrophages aren't always around to clean up the debris which is why other cells such as fibroblasts or epithelial cells can act as non-professional phagocytes and also ingest the dead cell's remains. Nobody likes to be surrounded by trash.

Clearance of apoptotic cells and their remains is thus crucial to maintain the health and function of a tissue. Conversely, if phagocytosis is inhibited or prevented, then the lingering debris can activate inflammatory signals and cause disease. Multiple autoimmune diseases, lung diseases and even neurologic diseases such as Alzheimer's disease are associated with reduced clearance. The cause and effect relationship is not always clear because these diseases can promote cell death. Are the diseases just killing so many cells that the phagocytosis capacity is overwhelmed, does the debris actually promote the diseased state, or is it a bit of both, resulting in a vicious cycle of apoptotic debris resulting in more cell death and more trash buildup? Researchers are currently investigating whether specifically tweaking phagocytosis could be used as a novel way to treat diseases with impaired clearance of debris.

During the past decade, multiple groups of researchers have come across a fascinating phenomenon by which viruses hijack the phagocytosis process in order to thrive. One of the "Eat Me!" signals for phagocytes is that debris derived from an apoptotic cell is coated by a membrane enriched with phosphatidylserines which are negatively charged molecules. Phosphatidylserines are present in all cells but they are usually tucked away on the inside of cells and are not seen by other cells. When a cell undergoes apoptosis, phosphatidylserines are flipped inside out. When particles or cell fragments present high levels of phosphatidylserines on their outer membranes then a phagocyte knows that it is encountering the remains of a formerly functioning cell that needs to be cleared by phagocytosis.

However, it turns out that not all membranes rich in phosphatidylserines are remains of apoptotic cells. Recent research studies suggest that certain viruses invade cells, replicate within the cell and when they exit their diseased host cell, they cloak themselves in membranes rich in phosphatidylserines. How the viruses precisely appropriate the phosphatidylserines of a cell that is not yet apoptotic and then adorn their viral membranes with the cell's "Eat Me!" signal is not yet fully understood and a very exciting area of research at the interface of virology, immunology and the biology of cell death.

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Altering RNA helicases in roundworms doubles their lifespan, something that could be tried in humans

Altering RNA helicases in roundworms doubles their lifespan, something that could be tried in humans | Amazing Science | Scoop.it
The things we do to extend our lives -- quitting smoking, cutting back on carbs, taking up jogging -- all have some impact on our longevity, if only just a little. But no matter how hard we work towards chasing the dream of forever staying fit and youthful, our efforts all end the same way and we must come to terms with the fact that we are mortal beings living on a finite timeline. There is nothing we can do to stop the aging process, and most things people do only serve to delay the inevitable: we can't stop death.


If someone was going to attempt to stop it, what would be the first step? Researchers at the Center for Plant Aging Research with support from the Institute for Basic Science (IBS) in Korea have made a breakthrough in decoding the aging process and how to dramatically slow it down.


The team used a mutated form of the roundworm in which they restricted a gene called daf-2 which is responsible for the rate of aging, reproductive development, resistance to oxidative stress, thermotolerance, resistance to hypoxia, and resistance to bacterial pathogens. In this case the daf-2 gene was altered so its IIS (insulin/insulin-like growth factor 1 (IGF1) signaling) would be restricted. These daf-2 mutants display increased resistance against diverse stresses, including heat stress, pathogenic bacteria, and oxidative stress and most importantly, the daf-2 mutants displayed double the lifespan compared to wild Caenorhabditis elegans roundworms.


The team believes that HEL-1 may act as a transcription regulator, which control how cells convert DNA to RNA since other RNA helicases do the same thing now. According to the team, "In contrast to the expectation that RNA helicases have general housekeeping roles in RNA metabolism, our findings reveal that the RNA helicase HEL-1 has specific roles in a specific longevity pathway."


Even if immortality isn't an immediate result of this work, there are other possible applications. Something called DDX39 (the mammalian version of the roundworm's HEL-1) is found in increased levels in the frontal cortex of patients with Alzheimer's disease. The ability to regulate DDX39 and other RNA helicases may give us an insight into finding the ability to control Alzheimer's disease, among other brain disorders.


Using the technique of altering RNA helicases to extend life in humans looks promising as human and roundworm both have HEL-1 and IIS which can be manipulated in similar ways. It isn't clear if the same mechanism is responsible for cellular aging regulation in humans, but evidence suggests that it might be. This research hasn't given humanity a cure to any diseases or made any claims of human life extension but it is an important first step in more fully understanding the lifecycle and function of cells.


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Next Generation Genomic Sequencing Technologies Speed Pathogen Detection

Next Generation Genomic Sequencing Technologies Speed Pathogen Detection | Amazing Science | Scoop.it

Earlier this year, researchers reported details of 2 curious medical cases that left clinicians stumped. In one, after sustaining numerous tick bites, a Kansas man began experiencing fever, fatigue, anorexia, nausea, and vomiting. Doxycycline, prescribed because some tickborne illnesses respond to this drug, brought no improvement. His condition rapidly deteriorated, and despite hospitalization and additional treatment with antimicrobials, he experienced multiorgan failure and shock, dying about a week later.


In the second case, 3 men in Germany were hospitalized for and later died of encephalitis of unknown cause. An intriguing clue to a possible cause was an unusual activity the men had in common: they all bred variegated squirrels, an animal native to Central America. In both cases, diagnostic testing for a range of known infections failed to reveal the causes. Instead, answers emerged only when researchers applied powerful genomics tools to their investigations, which ultimately identified 2 novel viruses.


In the US case, the Centers for Disease Control and Prevention (CDC) sent a blood sample to its virology laboratory in Fort Collins, Colorado, to determine if the Kansas man had been infected with tickborne Heartland virus, identified in 2012 in the Midwest. The laboratory found no signs of this pathogen, but cultures showed evidence of an unknown virus (Kosoy OI et al. Emerg Infect Dis. 2015;21[5]:760-764). The team then turned to next-generation sequencing (NGS), which allows for high-throughput sequencing of millions of snippets of DNA in parallel, to sequence the mystery virus and to bioinformatic analysis to compare the data with reference sequences cataloged in genomic databases, explained J. Erin Staples, MD, PhD, one of the report’s coauthors. The results revealed the novel virus, named the Bourbon virus after the county in which the patient lived, to be most closely related to 2 tickborne Thogotoviruses never before found in the Americas.


To search for the pathogen that killed the 3 squirrel breeders, researchers in Germany turned to metagenomics, which uses NGS to sequence genetic material from uncultured samples that might contain many species of microbes. This approach led to the discovery of a novel Bornavirus in brain tissue samples from the deceased patients and from the carcass of a squirrel owned by one of them (http://bit.ly/1LQh0Qe).


  • Next-generation sequencing (NGS): High-throughput DNA sequencing that allows rapid parallel sequencing of millions of DNA fragments in a sample; multiple rounds of sequencing improve accuracy and completeness of a reconstructed genome sequence. Bioinformatics tools are then needed to map the sequence data to a reference genome or to reconstruct the genome of a novel microbe.

  • Whole-genome sequencing: Sequencing an organism’s entire genetic sequence, including protein coding, noncoding, and regulatory sequences. Next-generation sequencing has greatly reduced the time necessary for whole-genome sequencing.

  • Metagenomic sequencing: High-throughput simultaneous sequencing of random fragments of genetic material (eg, whole genome, transcriptome, or 16S ribosomal RNA) recovered directly from an uncultured environmental sample that makes it possible to profile microbial communities. In contrast to PCR-based approaches, metagenomic sequencing relies on NGS technology and is “unbiased” in that it does not target any specific microbe.



Via Integrated DNA Technologies
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DNA Origami: Novel rare structures built from DNA emerge

DNA Origami: Novel rare structures built from DNA emerge | Amazing Science | Scoop.it

Scientists have worked for many years to refine the technique of DNA origami. The aim is to compose new sets of design rules, vastly expanding the range of nanoscale architectures generated by the method. In a new research, a variety of innovative nanoforms are described, each displaying unprecedented design control. The technique promises to bring futuristic microelectronics and biomedical innovations to market.


Hao Yan, a researcher at Arizona State University's Biodesign Institute, has worked for many years to refine the technique. His aim is to compose new sets of design rules, vastly expanding the range of nanoscale architectures generated by the method. In new research, a variety of innovative nanoforms are described, each displaying unprecedented design control.


In the current study, complex nano-forms displaying arbitrary wireframe architectures have been created, using a new set of design rules. "Earlier design methods used strategies including parallel arrangement of DNA helices to approximate arbitrary shapes, but precise fine-tuning of DNA wireframe architectures that connect vertices in 3D space has required a new approach," Yan says.


Yan has long been fascinated with Nature's seemingly boundless capacity for design innovation. The new study describes wireframe structures of high complexity and programmability, fabricated through the precise control of branching and curvature, using novel organizational principles for the designs. (Wireframes are skeletal three-dimensional models represented purely through lines and vertices.)


The resulting nanoforms include symmetrical lattice arrays, quasicrystalline structures, curvilinear arrays, and a simple wire art sketch in the 100-nm scale, as well as 3D objects including a snub cube with 60 edges and 24 vertices and a reconfigurable Archimedean solid that can be controlled to make the unfolding and refolding transitions between 3D and 2D.


In previous investigations, the Yan group created subtle architectural forms at an astonishingly minute scale, some measuring only tens of nanometers across--roughly the diameter of a virus particle. These nano-objects include spheres, spirals, flasks, Möbius forms, and even an autonomous spider-like robot capable of following a prepared DNA track.


Although DNA origami originally produced nanoarchitectures of purely aesthetic interest, refinements of the technique have opened the door to a range of exciting applications including molecular cages for the encapsulation of molecules, enzyme immobilization and catalysis, chemical and biological sensing tools, drug delivery mechanisms, and molecular computing devices.


The technique described in the new study takes this approach a step further, allowing researchers to overcome local symmetry restrictions, creating wireframe architectures with higher order arbitrariness and complexity. Here, each line segment and vertex is individually designed and controlled. The number of arms emanating from each vertex may be varied from 2 to 10 and the precise angles between adjacent arms can be modified.


In the current study, the method was first applied to symmetrical, regularly repeating polygonal designs, including hexagonal, square and triangular tiling geometries. Such common designs are known as tessellation patterns. A clever strategy involving a series of bridges and loops was used to properly route the scaffold strand, allowing it to pass through the entire structure, touching all lines of the wireframe once and only once. Staple strands were then applied to complete the designs.


In subsequent stages, the researchers created more complex wireframe structures, without the local translational symmetry found in the tessellation patters. Three such patterns were made, including a star shape, a 5-fold Penrose tile and an 8-fold quasicrystalline pattern. (Quasicrystals are structures that are highly ordered but non-periodic. Such patterns can continuously fill available space, but are not translationally symmetric.) Loop structures inserted into staple strands and unpaired nucleotides at the vertex points of the scaffold strands were also used, allowing researchers to perform precision modifications to the angles of junction arms.


The new design rules were next tested with the assembly of increasingly complex nanostructures, involving vertices ranging from 2 to 10 arms, with many different angles and curvatures involved, including a complex pattern of birds and flowers. The accuracy of the design was subsequently confirmed by AFM imaging, proving that the method could successfully yield highly sophisticated wireframe DNA nanostructures.

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