Monthly Archives: January 2014

‘Man’-hunt for ‘Adam’

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A pair of scientific studies using the latest genetic evidence are seeking to identify the very first man to walk the Earth, the so-called "Adam."

The studies delve into phylogenetics, a forensic hunt through the Xs and Ys of our chromosomes to find the genetic Adam, to borrow the name from the Bible. And Eran Elhaik from the University of Sheffield says he knows exactly when that first man lived.

"We can say with some certainty that modern humans emerged in Africa a little over 200,000 years ago," Elhaik said in a press release. That directly contradicts a March 2013 studyfrom Arizona Research Labs at the University of Arizona, which found that the human Y chromosome (the hereditary factor determining male sex) originated through interbreeding among species and dates back even further than 200 millennia.

"Our analysis indicates this lineage diverged from previously known Y chromosomes about 338,000 years ago, a time when anatomically modern humans had not yet evolved," said Michael Hammer, an associate professor in the University of Arizona's Department of Ecology and Evolutionary Biology.

Elhaik published a paper in the January 2014 issue of the European Journal of Human Genetics on his work; he used the opportunity to take a swipe at Hammer's paper, published in the American Journal of Human Genetics.

"We have shown that the University of Arizona study lacks any scientific merit," Elhaik claimed. "In fact, their hypothesis creates a sort of 'space-time paradox' whereby the most ancient individual belonging to the Homo sapiens species has not yet been born."

Think of the Michael J. Fox film, Back to the Future. Marty was worried that his parents would not meet and so he would not be born in the future. "It's the same idea," Elhaik said.

Hammer told FoxNews.com he stands by his work.

The paper by Elhaik and colleagues does not present a convincing argument against our paper and unfortunately at times appears to display a lack of technical understanding of the subject area. We are in the process of submitting a rebuttal," he said.

Identifying the very first Y chromosome of a genetic Adam would not mean scientists had located the Biblical figure Adam, explained Werner Arber, the Vaticans top scientist, told FoxNews.com.

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'Man'-hunt for 'Adam'

Canada’s public health care future in jeopardy

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The future of public health care in Canada is in serious jeopardy. A health care crisis is looming because of decisions being made by the federal government. Unfortunately, this looming crisis is flying below the radar. Few seem to pay attention to what will bring an end to public health care as we know it today.

In a world where we seem to be moving from one crisis to the next, it seems the public has become desensitized to issues that are not affecting them in the here and now. Decisions being made today will lead to a gradual deterioration of Canadas public health care system. If the Canadian public allows the federal government to continue on its current path our health care system will become vulnerable to things like for-profit medical services or a multi-tiered health system this is defined by a persons ability to pay.

Canada is facing an important next step in our medicare history. In 2014, the current health care accord deal that sets funding and health care service delivery agreements between the federal and provincial and territorial governments expires and must be renegotiated. The federal government is ignoring the calls of the provinces and territories to work on a deal, and shockingly announced $36 billion worth of health care cuts which will come into effect after the next federal election in 2015. The provinces and territories will thus be forced to reduce health services, increase taxes, and/or privatize services; health care will vary widely across the country.

In December 2011, the federal government unilaterally announced a withdrawal from anything but a reduced financing role: in 2017 the transfer of health care funds will be cut from the current annual six per cent increase to a percentage pegged to the GDP, with a guarantee base of three per cent.

This is a time of an aging population and an increasing demand for health care services; unless transfer funding is stable and certain our cherished public health care system is in danger. Unless a new health accord is re-negotiated to establish community health centres and to include universal home and palliative care, health services cost will continue to skyrocket; and elderly Canadians will continue to suffer, facing the end of their lives in unfamiliar environments while society pays billions for their care.

More than 94 per cent of Canadians believe health care is a core social right, a symbol of Canada as a compassionate and caring society. Canadians want governments to work together to share information about how to best deliver public heath care and to ensure that every Canadian has equal access to quality care provide by a national, public system. The federal, provincial, and territorial governments need to negotiate a new health accord that protects and strengthens our universal public health care system. Our elected representatives need to advocate for a new accord and stop the federal government from undermining our health care system by refusing to come back to the bargaining table. Each of us needs to stand up and demand the federal government negotiate with the premiers to ensure every Canadian has access to quality health care services as needed.

Rennie Maierle

Burnaby

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Canada’s public health care future in jeopardy

Refugee health-care cuts challenged in court

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TORONTO - Ottawa's cutbacks to health-care coverage for refugee claimants may leave some of them dependent on the charity of provincial officials, a judge said Thursday.

Justice Anne Mactavish raised the issue on the last day of a legal challenge launched by Canadian Doctors for Refugee Care and the Canadian Association of Refugee Lawyers.

The groups argue the changes announced 18 months ago are unlawful and inhumane, and want the court to strike them down.

Government lawyers say the new rules bring health benefits for newcomers in line with what other Canadians receive, and deter those who would abuse Canada's health-care system.

They have argued refugee claimants can still access health care through other programs, including those put in place by some provinces to reinstate access to essential and emergency care.

But though Alberta, Manitoba, Saskatchewan, Nova Scotia, Quebec and Ontario have all taken steps to bridge the gap, not all offer the same level of coverage.

While Ontario has put forth a "coherent program," Mactavish said, Quebec offers assistance on an ad-hoc basis, which can leave refugee claimants dependent on the "whims" and "charity" of officials.

"Is that filling the gap?" the judge asked. And "is it humane to put people through that?"

Neeta Logsetty, one of the government lawyers, said many refugee claimants had also received donations from pharmaceutical companies and help from doctors, as well as provincial assistance.

Of those involved in the court case, "everyone got the treatment they required, at little or no cost," she told the judge.

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Refugee health-care cuts challenged in court

Health-care cuts for refugees challenged in court

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TORONTO - Ottawa's cutbacks to health-care coverage for refugee claimants may leave some of them dependent on the charity of provincial officials, a judge said Thursday.

Justice Anne Mactavish raised the issue on the last day of a legal challenge launched by Canadian Doctors for Refugee Care and the Canadian Association of Refugee Lawyers.

The groups argue the changes announced 18 months ago are unlawful and inhumane, and want the court to strike them down.

Government lawyers say the new rules bring health benefits for newcomers in line with what other Canadians receive, and deter those who would abuse Canada's health-care system.

They have argued refugee claimants can still access health care through other programs, including those put in place by some provinces to reinstate access to essential and emergency care.

But though Alberta, Manitoba, Saskatchewan, Nova Scotia, Quebec and Ontario have all taken steps to bridge the gap, not all offer the same level of coverage.

While Ontario has put forth a "coherent program," Mactavish said, Quebec offers assistance on an ad-hoc basis, which can leave refugee claimants dependent on the "whims" and "charity" of officials.

"Is that filling the gap?" the judge asked. And "is it humane to put people through that?"

Neeta Logsetty, one of the government lawyers, said many refugee claimants had also received donations from pharmaceutical companies and help from doctors, as well as provincial assistance.

Of those involved in the court case, "everyone got the treatment they required, at little or no cost," she told the judge.

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Health-care cuts for refugees challenged in court

Scientists discover new genetic forms of neurodegeneration

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PUBLIC RELEASE DATE:

30-Jan-2014

Contact: Scott LaFee slafee@ucsd.edu 619-543-6163 University of California - San Diego

In a study published in the January 31, 2014 issue of Science, an international team led by scientists at the University of California, San Diego School of Medicine report doubling the number of known causes for the neurodegenerative disorder known as hereditary spastic paraplegia. HSP is characterized by progressive stiffness and contraction of the lower limbs and is associated with epilepsy, cognitive impairment, blindness and other neurological features.

Over several years, working with scientific colleagues in parts of the world with relatively high rates of consanguinity or common ancestry, UC San Diego researchers recruited a cohort of more than 50 families displaying autosomal recessive HSP the largest such cohort assembled to date. The scientists analyzed roughly 100 patients from this cohort using a technique called whole exome sequencing, which focuses on mapping key portions of the genome. They identified a genetic mutation in almost 75 percent of the cases, half of which were in genes never before linked with human disease.

"After uncovering so many novel genetic bases of HSP, we were in the unique position to investigate how these causes link together. We were able to generate an 'HSP-ome,' a map that included all of the new and previously described causes," said senior author Joseph G. Gleeson, MD, Howard Hughes Medical Institute investigator, professor in the UC San Diego departments of Neurosciences and Pediatrics and at Rady Children's Hospital-San Diego, a research affiliate of UC San Diego.

The HSP-ome helped researchers locate and validate even more genetic mutations in their patients, and indicated key biological pathways underlying HSP. The researchers were also interested in understanding how HSP relates to other groups of disorders. They found that the HSP-ome links HSP to other more common neurodegenerative disorders, such as Alzheimer's disease and amyotrophic lateral sclerosis.

"Knowing the biological processes underlying neurodegenerative disorders is seminal to driving future scientific studies that aim to uncover the exact mechanisms implicated in common neurodegenerative diseases, and to indicate the path toward development of effective treatments," said Gleeson.

"I believe this study is important for the neurodegenerative research community," said co-lead author Gaia Novarino, PhD, a post-doctoral scholar in Gleeson's lab. "But more broadly, it offers an illustrative example of how, by utilizing genomics in specific patient populations, and then building an 'interactome,' we greatly expand knowledge around unknown causes of disease."

"This is very exciting since identifying the biological processes in neurological disorders is the first step toward the development of new treatments," agreed co-lead author Ali G. Fenstermaker. "We identified several promising targets for development of new treatments."

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Scientists discover new genetic forms of neurodegeneration

Dartmouth researchers develop new tool to identify genetic risk factors

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PUBLIC RELEASE DATE:

30-Jan-2014

Contact: Donna Dubuc Donna.M.Dubuc@Dartmouth.edu 603-653-3615 The Geisel School of Medicine at Dartmouth

(Lebanon, NH, 1/30/14) Dartmouth researchers developed a new biological pathway-based computational model, called the Pathway-based Human Phenotype Network (PHPN), to identify underlying genetic connections between different diseases as reported in BioDataMining this week. The PHPN mines the data present in large publicly available disease datasets to find shared SNPs, genes, or pathways and expresses them in a visual form.

"The PHPN offers a bird's eye view of the diseases and phenotype's relationships at the systems level," said Christian Darabos, PhD, post-doctoral fellow, Institute for Quantitative Biomedical Sciences (iQBS), Dartmouth College.

The PHPN uses information in human disease networks in conjunction with network science tools to show clusters of related disorders sharing common genetic backgrounds. It does so without the typical clinical classification of disease, in which all heart disease or all cancers are grouped together, based on clinical presentation. Dartmouth geneticists instead rely on the information contained in the PHPN's topology to automatically classify traits and diseases by their shared genetic mechanisms, such as common genes or pathways. PHPN explores the connections between the layers of the networks to find patterns and relationships.

"The intuitive network representation of the knowledge mined from several large-scale datasets makes the information accessible to anyone. It lies at the crossroads of computational genetics, systems biology, information theory, and network science," Darabos said.

PHPN supports the integration of genomic and phenotypic data to uncover significant links between traits, attributes, and disease. This offer tremendous potential in identifying risk factors for certain diseases. At the same time, it can reveal important targets for therapeutic intervention.

"As a proof of concept, the PHPN has proven capable of identifying well documented interactions, and many novel links that remain to be explored in depth," said Darabos.

The PHPN reveals biological connections between seemingly disparate displays of genetic properties and offers a unique view of the architecture of disease.

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Dartmouth researchers develop new tool to identify genetic risk factors

Puzzling question in bacterial immune system answered

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A central question has been answered regarding a protein that plays an essential role in the bacterial immune system and is fast becoming a valuable tool for genetic engineering. A team of researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley have determined how the bacterial enzyme known as Cas9, guided by RNA, is able to identify and degrade foreign DNA during viral infections, as well as induce site-specific genetic changes in animal and plant cells. Through a combination of single-molecule imaging and bulk biochemical experiments, the research team has shown that the genome-editing ability of Cas9 is made possible by the presence of short DNA sequences known as "PAM," for protospacer adjacent motif.

"Our results reveal two major functions of the PAM that explain why it is so critical to the ability of Cas9 to target and cleave DNA sequences matching the guide RNA," says Jennifer Doudna, the biochemist who led this study. "The presence of the PAM adjacent to target sites in foreign DNA and its absence from those targets in the host genome enables Cas9 to precisely discriminate between non-self DNA that must be degraded and self DNA that may be almost identical. The presence of the PAM is also required to activate the Cas9 enzyme."

With genetically engineered microorganisms, such as bacteria and fungi, playing an increasing role in the green chemistry production of valuable chemical products including therapeutic drugs, advanced biofuels and biodegradable plastics from renewables, Cas9 is emerging as an important genome-editing tool for practitioners of synthetic biology.

"Understanding how Cas9 is able to locate specific 20-base-pair target sequences within genomes that are millions to billions of base pairs long may enable improvements to gene targeting and genome editing efforts in bacteria and other types of cells," says Doudna who holds joint appointments with Berkeley Lab's Physical Biosciences Division and UC Berkeley's Department of Molecular and Cell Biology and Department of Chemistry, and is also an investigator with the Howard Hughes Medical Institute (HHMI).

Doudna is one of two corresponding authors of a paper describing this research in the journal Nature. The paper is titled "DNA interrogation by the CRISPR RNA-guided endonuclease Cas9." The other corresponding author is Eric Greene of Columbia University. Co-authoring this paper were Samuel Sternberg, Sy Redding and Martin Jinek.

Bacterial microbes face a never-ending onslaught from viruses and invasive snippets of nucleic acid known as plasmids. To survive, the microbes deploy an adaptive nucleic acid-based immune system that revolves around a genetic element known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. Through the combination of CRISPRs and RNA-guided endonucleases, such as Cas9, ("Cas" stands for CRISPR-associated), bacteria are able to utilize small customized crRNA molecules (for CRISPR RNA) to guide the targeting and degradation of matching DNA sequences in invading viruses and plasmids to prevent them from replicating. There are three distinct types of CRISPR-Cas immunity systems. Doudna and her research group have focused on the Type II system which relies exclusively upon RNA-programmed Cas9 to cleave double-stranded DNA at target sites.

"What has been a major puzzle in the CRISPR-Cas field is how Cas9 and similar RNA-guided complexes locate and recognize matching DNA targets in the context of an entire genome, the classic needle in a haystack problem," says Samuel Sternberg, lead author of the Nature paper and a member of Doudna's research group. "All of the scientists who are developing RNA-programmable Cas9 for genome engineering are relying on its ability to target unique 20-base-pair long sequences inside the cell. However, if Cas9 were to just blindly bind DNA at random sites across a genome until colliding with its target, the process would be incredibly time-consuming and probably too inefficient to be effective for bacterial immunity, or as a tool for genome engineers. Our study shows that Cas9 confines its search by first looking for PAM sequences. This accelerates the rate at which the target can be located, and minimizes the time spent interrogating non-target DNA sites."

Doudna, Sternberg and their colleagues used a unique DNA curtains assay and total internal reflection fluorescence microscopy (TIRFM) to image single molecules of Cas9 in real time as they bound to and interrogated DNA. The DNA curtains technology provided unprecedented insights into the mechanism of the Cas9 target search process. Imaging results were verified using traditional bulk biochemical assays.

"We found that Cas9 interrogates DNA for a matching sequence using RNA-DNA base-pairing only after recognition of the PAM, which avoids accidentally targeting matching sites within the bacterium's own genome," Sternberg says. "However, even if Cas9 somehow mistakenly binds to a matching sequence on its own genome, the catalytic nuclease activity is not triggered without a PAM being present. With this mechanism of DNA interrogation, the PAM provides two redundant checkpoints that ensure that Cas9 can't mistakenly destroy its own genomic DNA."

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Puzzling question in bacterial immune system answered

Thinking Strategically About Big Data by Business Technology Futurist and Speaker Jack Shaw – Video

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Thinking Strategically About Big Data by Business Technology Futurist and Speaker Jack Shaw
Hi. I #39;m Jack Shaw, the Business Technology Futurist. This is one in a series of brief videos in which I will discuss intelligent systems and how you, and you...

By: Jack Shaw

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Thinking Strategically About Big Data by Business Technology Futurist and Speaker Jack Shaw - Video

‘Radical idealists’ highlighted

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A new local exhibit spotlights an influential and controversial group of early 20th century Italian artists.

"Futurism: Concepts and Imaginings" at the Boca Raton Museum of Art contains almost 40 paintings, drawings and collages from seven artists that depict the Italian Futurism movement's emphasis on portraying energy and motion.

These artists advanced a confrontational credo that embraced the new technology of the period, especially airplanes, as a path toward cultural advancement and military conquests.

"Their vision of the future was machine-driven," said museum assistant curator Kelli Bodle. "They thought machines would take over, do the work for you that you would work less."

The Italian Futurists also advocated controversial ideas like abolishing libraries and museums and supported a fascist political philosophy, Bodle said.

"They were radical idealists. They felt that there was a new age, and that as artists, rather than recycling old ideas and old themes they should be embracing new technologies and new ideas and new approaches," said museum director Steven Maklansky. "The Futurists' legacy was their aggressive pursuit of novelty and experimentation in art."

The exhibit on the museum's second floor begins with an introductory text panel explaining the artistic and political movement. On the same wall is a television screen that plays a video of an actor reciting some of movement leader F.T. Marinetti's important 1909 document, "The Futurist Manifesto."

Although exact dates for the works are unknown, they are believed to have been completed from 1930-1950, according to exhibit materials.

Pippo Rizzo's "Homage to Depero," a collage on cardboard, is one of a handful of works in this show that were completed to honor an esteemed individual. The piece features a man in a theatrical costume with sheet music in the background. In the blue sky with two white clouds is a descending black airplane trailed by its cloud of green and red smoke.

Rizzo's "Squad," an eye-catching tempera on wood painting with geometric shapes and vibrant black and blue colors, reflects the movement's fascination with military culture. The piece depicts four uniformed military members marching in lockstep, each holding a blackjack, or billy club.

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'Radical idealists' highlighted