Monthly Archives: May 2017

May 30, 2017 Map of Egypt, showing the archaeological site of Abusir-el Meleq (orange X), and the location of the modern Egyptian samples used in the study (orange circles). Credit: Graphic: Annette Guenzel. Credit: Nature Communications, DOI: 10.1038/NCOMMS15694

An international team of scientists, led by researchers from the University of Tuebingen and the Max Planck Institute for the Science of Human History in Jena, successfully recovered and analyzed ancient DNA from Egyptian mummies dating from approximately 1400 BCE to 400 CE, including the first genome-wide nuclear data from three individuals, establishing ancient Egyptian mummies as a reliable source for genetic material to study the ancient past. The study, published today in Nature Communications, found that modern Egyptians share more ancestry with Sub-Saharan Africans than ancient Egyptians did, whereas ancient Egyptians were found to be most closely related to ancient people from the Near East.

Egypt is a promising location for the study of ancient populations. It has a rich and well-documented history, and its geographic location and many interactions with populations from surrounding areas, in Africa, Asia and Europe, make it a dynamic region. Recent advances in the study of ancient DNA present an intriguing opportunity to test existing understandings of Egyptian history using ancient genetic data.

However, genetic studies of ancient Egyptian mummies are rare due to methodological and contamination issues. Although some of the first extractions of ancient DNA were from mummified remains, scientists have raised doubts as to whether genetic data, especially nuclear genome data, from mummies would be reliable, even if it could be recovered. "The potential preservation of DNA has to be regarded with skepticism," confirms Johannes Krause, Director at the Max Planck Institute for the Science of Human History in Jena and senior author of the study. "The hot Egyptian climate, the high humidity levels in many tombs and some of the chemicals used in mummification techniques, contribute to DNA degradation and are thought to make the long-term survival of DNA in Egyptian mummies unlikely." The ability of the authors of this study to extract nuclear DNA from such mummies and to show its reliability using robust authentication methods is a breakthrough that opens the door to further direct study of mummified remains.

For this study, an international team of researchers from the University of Tuebingen, the Max Planck Institute for the Science of Human History in Jena, the University of Cambridge, the Polish Academy of Sciences, and the Berlin Society of Anthropology, Ethnology and Prehistory, looked at genetic differentiation and population continuity over a 1,300 year timespan, and compared these results to modern populations. The team sampled 151 mummified individuals from the archaeological site of Abusir el-Meleq, along the Nile River in Middle Egypt, from two anthropological collections hosted and curated at the University of Tuebingen and the Felix von Luschan Skull Collection at the Museum of Prehistory of the Staatliche Museen zu Berlin, Stiftung Preussicher Kulturbesitz.

In total, the authors recovered mitochondrial genomes from 90 individuals, and genome-wide datasets from three individuals. They were able to use the data gathered to test previous hypotheses drawn from archaeological and historical data, and from studies of modern DNA. "In particular, we were interested in looking at changes and continuities in the genetic makeup of the ancient inhabitants of Abusir el-Meleq," said Alexander Peltzer, one of the lead authors of the study from the University of Tuebingen. The team wanted to determine if the investigated ancient populations were affected at the genetic level by foreign conquest and domination during the time period under study, and compared these populations to modern Egyptian comparative populations. "We wanted to test if the conquest of Alexander the Great and other foreign powers has left a genetic imprint on the ancient Egyptian population," explains Verena Schuenemann, group leader at the University of Tuebingen and one of the lead authors of this study.

Close genetic relationship between ancient Egyptians and ancient populations in the Near East

The study found that ancient Egyptians were most closely related to ancient populations in the Levant, and were also closely related to Neolithic populations from the Anatolian Peninsula and Europe. "The genetics of the Abusir el-Meleq community did not undergo any major shifts during the 1,300 year timespan we studied, suggesting that the population remained genetically relatively unaffected by foreign conquest and rule," says Wolfgang Haak, group leader at the Max Planck Institute for the Science of Human History in Jena. The data shows that modern Egyptians share approximately 8% more ancestry on the nuclear level with Sub-Saharan African populations than with ancient Egyptians. "This suggests that an increase in Sub-Saharan African gene flow into Egypt occurred within the last 1,500 years," explains Stephan Schiffels, group leader at the Max Planck Institute for the Science of Human History in Jena. Possible causal factors may have been improved mobility down the Nile River, increased long-distance trade between Sub-Saharan Africa and Egypt, and the trans-Saharan slave trade that began approximately 1,300 years ago.

This study counters prior skepticism about the possibility of recovering reliable ancient DNA from Egyptian mummies. Despite the potential issues of degradation and contamination caused by climate and mummification methods, the authors were able to use high-throughput DNA sequencing and robust authentication methods to ensure the ancient origin and reliability of the data. The study thus shows that Egyptian mummies can be a reliable source of ancient DNA, and can greatly contribute to a more accurate and refined understanding of Egypt's population history.

Explore further: 17 mummies discovered in central Egypt

More information: Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods, Nature Communications (2017). nature.com/articles/doi:10.1038/ncomms15694

Egyptian archaeologists have discovered 17 mummies in desert catacombs in Minya province, an "unprecedented" find for the area south of Cairo, the antiquities ministry announced Saturday.

New research published in Global Heart (the journal of the World Heart Federation) shows that there are no significant differences in the incidence or severity of atherosclerotic disease (narrowing of the arteries with fatty ...

(AP) -- Archeologists have unearthed 57 ancient Egyptian tombs, most of which hold an ornately painted wooden sarcophagus with a mummy inside, Egypt's Supreme Council of Antiquities said Sunday.

(Phys.org) The study and popular perception of Egyptian antiquities focuses too much on the unwrapping of mummies and the use of technologies such as scanning, according to an academic from the University of East Anglia.

As silent witnesses to the past, ancient Egyptian mummies can add to our knowledge of their society well beyond what we can learn from the study of texts, art and funerary rituals.

Egyptian archaeologists have unearthed several mummies, colourful wooden sarcophagi and more than 1,000 funerary statues in a 3,500-year-old tomb near the city of Luxor, hailing an "important discovery".

An international team of scientists, led by researchers from the University of Tuebingen and the Max Planck Institute for the Science of Human History in Jena, successfully recovered and analyzed ancient DNA from Egyptian ...

About 1 to 2 million years ago, early humans in East Africa periodically faced very dry conditions, with little or no water in sight. But they likely had access to hundreds of springs that lingered despite long dry spells, ...

The origin of animals was one of the most important events in the history of Earth. Beautifully preserved fossil embryos suggest that our oldest ancestors might have existed a little more than half a billion years ago.

In human history, the transition from hunting and gathering to farming is a significant one. As such, hunter-gatherers and farmers are usually thought about as two entirely different sets of people. But researchers reporting ...

A new species of a fossil pliosaur (large predatory marine reptile from the 'age of dinosaur') has been found in Russia and profoundly change how we understand the evolution of the group, says an international team of scientists.

People using smartphones are more likely to make rational and unemotional decisions compared to PC users when presented with a moral dilemma on their device, according to a new study from City, University of London.

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The first genome data from ancient Egyptian mummies - Phys.Org

Ness Ziona, Israel May 30, 2017NRGene, the worldwide leader in genomic mapping, assembly, and referencing, has assembled 300 genomes of major crop plants in less than two years, enabling the highly accurate genome comparisons required to breed better seeds.

Before NRGenes technology, individual genomes took years to produce and then many more years to improve genome accuracy. With NRGenesDeNovoMAGICTM, the highest level of genome completeness and accuracy is achieved with a single assembly.

Over the past two years, assemblies have been created in cooperation with many of the worlds leading universities, government research institutes and non-for-profit organizations, as well as global companies like Syngenta and Monsanto.

DeNovoMAGIC 3.0delivers reference genomes quickly, accurately, and cost effectively, without requiring external data. It accelerates downstream analysis and reduces unnecessary technical work. DeNovoMAGIC assembles Illumina reads into long, phased sequences, delivering accurate assembly results, even from complex genomes, no matter the size, ploidy, or zygosity, for high quality genome mapping and productive breeding.

For crops with an existing reference genome, theDeNovoMAGICassemblies enable researchers to elucidate the vast genomic diversity that exists within the crop species. Scientists are using this critical information to breed more productive new varieties with the highest nutritional values.

Many full genomes now exist in most of the key crops, and NRGenesPanMAGICTMcombines the initial assemblies into an accurate genome-to-genome mapping to capture the full diversity of the crop varieties, including all types of sequence differences within the studied population, e.g. SNPs, InDels of any size, inversions, translocations, gene PAVs, and gene CNVs.

Breeding is all about making the most of a given genomic diversity in a given crop. If your goal is to make genomics applicable for breeding you must describe crop diversity accurately and affordably, says NRGene CEO Gil Ronen. Based on the feedback we get from our customers, were doing that and more allowing them to make major breakthroughs in the quest to increase the worlds food supply with more productive, hardier seeds.

About NRGene

NRGeneis a genomic big data company developing cutting-edge software and algorithms to reveal the complexity and diversity of crop plants, animals, and aquatic organisms for supporting the most advanced and sophisticated breeding programs. NRGene tools have already been employed by some of the leading seed companies worldwide as well as the most influential research teams in academia.www.nrgene.com.

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NRGene Assembles its 300th Crop Genome - DirectionsMag.com

New York, May 30 (IANS) The CRISPR-Cas9 gene-editing technology can introduce hundreds of unintended mutations into the genome, warns a new study.

"We feel it's critical that the scientific community consider the potential hazards of all off-target mutations caused by CRISPR, including single nucleotide mutations and mutations in non-coding regions of the genome," said co-author Stephen Tsang, Associate Professor at Columbia University Medical Centre in the US.

CRISPR-Cas9 editing technology -- by virtue of its speed and unprecedented precision -- has been a boon for scientists trying to understand the role of genes in disease.

The technique has also raised hope for more powerful gene therapies that can delete or repair flawed genes, not just add new genes.

The first clinical trial to deploy CRISPR is now underway in China, and a US trial is slated to start next year.

But even though CRISPR can precisely target specific stretches of DNA, it sometimes hits other parts of the genome.

Most studies that search for these off-target mutations use computer algorithms to identify areas most likely to be affected and then examine those areas for deletions and insertions.

"These predictive algorithms seem to do a good job when CRISPR is performed in cells or tissues in a dish, but whole genome sequencing has not been employed to look for all off-target effects in living animals," co-author Alexander Bassuk, Professor at the University of Iowa, said.

In the new study, published in the journal Nature Methods, the researchers sequenced the entire genome of mice that had undergone CRISPR gene editing in the team's previous study and looked for all mutations, including those that only altered a single nucleotide.

The researchers determined that CRISPR had successfully corrected a gene that causes blindness, but they also found that the genomes of two independent gene therapy recipients had sustained more than 1,500 single-nucleotide mutations and more than 100 larger deletions and insertions.

None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.

"We're still upbeat about CRISPR," co-author of the study Vinit Mahajan, Associate Professor at Stanford University, said.

"We're physicians, and we know that every new therapy has some potential side effects - but we need to be aware of what they are," Mahajan added.

--IANS

gb/dg

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CRISPR gene tool can cause unintended flaws in genome - The ... - Economic Times

Local diagnostics company One BioMed Pte Ltd and A*STARs Genome Institute of Singapore (GIS) have established a joint laboratory to develop molecular diagnostic assays for the Asian clinical infectious disease testing market.

The joint laboratory will focus on the full development and integration of the initial assays for the One BioMed platform. Each panel will be multiplexed and syndromic, and is expected to address clinically important infectious diseases in Asia, including pediatric respiratory infections, drug resistant tuberculosis and mosquito-borne illnesses. The laboratory will be located in the Genome building at Biopolis and will leverage the genomic expertise of GIS to improve the delivery of clinical medicine.

One BioMed recently spun-out of A*STARs Institute of Microelectronics (IME) is developing a point-of-care diagnostic platform deploying two proprietary technologies: a chemistry-based nucleic acid extraction and a silicon biophotonics dual-ring sensor. Integrated into a consumable cartridge design and run on a portable instrument, these approaches are expected to enable simple, cost-effective, rapid and highly multiplexed molecular testing outside of a central laboratory setting.

Dr Alexander Lezhava, Group Leader, Translational Research will lead the lab for GIS, and Dr Park Mi Kyoung, founder and Chief Technology Officer of One BioMed, will lead the lab for the company. We allied with the GIS Translational Research group because they combine extensive molecular diagnostics assay development expertise with regulatory and commercialisation experience, said Dr Park.

Prof Ng Huck Hui, Executive Director of GIS said, Our collaboration with One BioMed helps us address one of the most difficult problems facing patients and healthcare providers across the region poor access to accurate testing for infectious diseases like influenza, dengue and tuberculosis.

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One BioMed and A*STAR's Genome Institute of Singapore establish joint lab - Enterprise Innovation

US scientists have delayed cancer cell growth by using genome editing to remove a protein.

Removing an enzyme known as Tudor-SN delayed the replication of cellsfrom human kidney and cervical cancers in the lab.

'We know that Tudor-SN is more abundant in cancer cells than healthy cells, and our study suggests that targeting this protein could inhibit fast-growing cancer cells,' said Dr Reyad Elbarbary of the University of Rochester, New York, and lead author.

Normal cells divide and replicate through the process known as the cell cycle. If the cycle is disrupted, cells can become cancerousand replicate uncontrollably, forming tumours.

One regulatory component of the cell cycle is micro RNA (miRNA) - small noncoding RNA molecules which adjust gene expression. The Rochester team showed that removing Tudor-SN through genome editing increased the amount of miRNA present. The miRNA reduced the expression of genes critical to the progression of the cell cycle from the 'preparatory' phase to the replication phase.

Although the research is at a very early stage, the team hope their findings could lead to a new treatment option for cancer. They next plan to investigate how Tudor-SN works with other molecules in the cell cycle, in order to develop drugs to target it.

'Because cancer cells have a faulty cell cycle, pursuing factors involved in the cell cycle is a promising avenue for cancer treatment,' said Professor Lynne Maquat of the University of Rochester, and senior author.

Dr Thomas Cox of the Garvan Institute of Medical Research,Australia, who was not involved in the study, told Cosmos magazine that targeting miRNAis difficult and technically challenging. 'This study is saying: "Well, if we cant target microRNAs directly, can we target something regulating them?"'

The study was published in Science.

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Genome editing used to slow cancer growth - BioNews