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Scientists from US Have Successfully Edited Human DNA – News4C
Posted: July 31, 2017 at 9:49 am
Scientists from U.S Have Successfully Edited Human DNA By using CRISPR technology, a team of scientists from Oregon has edited the genes in human embryos and made huge steps in reaching new results. They tried to eradicate genetically transmitted diseases.
CRISPR isnt a new technology but it has started being used in human genetics recently. CRISPR is a DNA sequence that was found in bacteria and could protect the immune system, detecting and destroying invaders such as viruses that try to infect the bacteria. Scientists try to use CRISPS so that they target mutations that would cause diseases, this way treating them from the root of DNA encoding.
Major issues were solved using gene-altering technology.
The lead researcher Shoukhrat Mitalipov from the Oregan Health and Science University stated that they solved their previous problems they had with CRISPR gene-altering technology. In 2015 they faced a problem using this technology, resulting in embryos suffering a condition named mosaicism due to CRISPR that aligned edited and unedited cells.
In the early 2017 China went through a similar problem at the Hospital Guangzhou Medical University.
They tried to repair abnormal embryos and the results were not satisfying. They also used normal embryos resulted from immature eggs and fertilized them with sperm that carried genetic disease. Before the cell division started, they injected CRISPR and out of 6 embryos, half were repaired but with a problem: two of them were suffering from mosaicism.
New ground has been broken later by Mitalipov and his team.
In Oregon Mitalipov and his team were able to inject CRISPR into the eggs while they fertilized them with sperm and avoided moisaicism. They also solved the problem of genetic disease transmission, correcting the genes.
Were still waiting for official results from the Oregon Health and Science University and Shoukhrat Mitalipov through a published paper which will soon appear in a scientific journal.
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Scientists from US Have Successfully Edited Human DNA - News4C
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Biblical mystery solved: Ancient Canaanites DNA lives on in Lebanese – Genetic Literacy Project
Posted: at 9:49 am
The Canaanites lived at the crossroads of the ancient world. They experienced wars, conquests and occupations for millennia, and as a result evolutionary geneticists expected that their DNA would become substantially mixed with incoming populations.
Astonishingly, new genetic analysis shows that scientists were wrong. According to a new study in the American Journal of Human Genetics, todays Lebanese share a whopping 93% of their DNA with the ancient Canaanites.
One of five Canaanites found buried in present-day Lebanon from which scientists extracted and sequenced DNA. Photo by Dr. Claude Doumet-Serhal/the Sidon excavation
Archaeologists at the Sidon excavation site have been unearthing ancient Canaanite secrets for the last 19 years in the still-inhabited Lebanese port city
They sequenced the whole genomes of five individuals found in Sidon who lived about 3,700 years ago. The team then compared the genomes of these ancient Canaanites with those of 99 Lebanese people currently living in the country, along with the previously published genetic information from modern and ancient populations across Europe and Asia.
This evidence supports the idea that different Levantine cultural groups such as the Moabites, Israelites, and Phoenicians may have had a common genetic background, the authors said.
The findings have powerful cultural implicationsIn a country struggling with the ramifications of war and a society fiercely divided along political and sectarian lines, religious groups have often looked to an uncertain history for their identities.
The GLP aggregated and excerpted this article to reflect the diversity of news, opinion, and analysis. Read full, original post: The DNA of ancient Canaanites lives on in modern-day Lebanese, genetic analysis shows
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Biblical mystery solved: Ancient Canaanites DNA lives on in Lebanese - Genetic Literacy Project
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Wade genealogy info boosted by DNA test – Fairfield Daily Republic
Posted: at 9:49 am
My oldest brother Orvis recently submitted his DNA to Mountain View personal genomics and biotechnology company 23andMe. Hed been interested in finding out details of his genealogy for some time and finally bit the bullet.
Orvis submitted his saliva samples and got his results back in about six weeks. The cool thing is that he got a special deal where the regular $100 price was reduced to $80. The cooler thing is that brothers unless they are identical twins share 50 percent of the same DNA. Thats close enough for me to pay $0 and get a column out of it.
Here are Orviss test results:
Sub-Saharan African 72.7%European 23.4%East Asian & Native American 2.9%South Asian 0.5%Unassigned 0.6%
The fact that our ancestors were from Africa is not a surprise. The website breaks it down further. The lions share (68.9 percent) of our distant relatives came from West Africa. This is what the website says: Expanding from Senegal to Nigeria, West Africa composes about a fifth of the African continent. West Africans have a long shared history, and were united by large empires such as the Ghana Empire, dating as far back as the eighth century AD.
The great thing about the DNA results is that they can be combined with another chunk of information we already had, a 20-page document called The Wade Genealogy. I got it from a Texas Landman (an intermediary for an energy company) in 2010 whod used it to find me because of a parcel of land in the Lone Star state my late father had owned. Most of its information came from a file in (where else?) Salt Lake City called the wills of San Augustine (Texas, where both my parents were born and grew up).
The first part of the genealogy is rather detailed and the second part is less so, but lists six generations of my family. The names are just that to me, names, but then suddenly there is my grandfather whom I never met, Booker T. Wade. He married Corine Dennis and then it lists their children including my dad, Orvis T. Wade Sr.
I wish I knew more of my relatives, but I dont. One name that jumped out from the document was Carla Nicole Wade, my cousin, whom I know from Facebook.
The first time I saw the names of my brothers and myself in the document it was sort of like the part in the book Roots where Alex Haley changes the tense of the narrative as he entered into the history of his own book. The genealogy has errors and omissions. My youngest brother Scott was not listed and Kelvins name was misspelled as Kevin the story of his life.
I wrote a column about the genealogy in 2010 and here is a part:
My great-great-grandmothers name was . . . wait for it . . . Anarchy. Seriously. Ned and Anarchy Wade were listed together in the 1870 census. Her name sounds like a Marvel Comics Super Villain.
Ned and Anarchy had been the property of a man named Edward Teal and when he died in 1858 he left no will so the courts had to settle the estate. This is what it says in the genealogy:
The appointed commissioners of the courts ordered that the heirs of the estate separate the Negro property into two lots, 1 & 2, and place them in a hat and draw, and whichever one drew that lot would own those Negroes.
That is still horrifying for me to actually picture happening, but it did.
Orvis DNA test results showing our mixed heritage is boosted by the Wade Genealogy. In it, Ned was described as a Negro man of yellow complexion. Ned, Anarchy and their childrens race was listed as mulatto, meaning one-half negro blood.
The .6 percent unassigned made me scratch my head. Pod people? Borg? 23andMes explanation: There is a wide range of human diversity and sometimes our algorithm is unable to assign a region of DNA to a specific population. As we collect more data and update our algorithm, we expect that the amount of unassigned ancestry will decrease.
The ancestry DNA thing is very interesting and informative and I recommend that everyone have their sibling pay for it and then check out the results.
Reach Fairfield writer Tony Wade at toekneeweighed@gmail.com.
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How scientists redesign DNA codes – ABC News
Posted: at 9:49 am
Scientists are working to create yeast that operates with custom-made DNA.
They have long been able to make specific changes in an organism's DNA. Now, they're pushing into the more radical step of starting over, and building redesigned versions from scratch.
Their work is part of a bold and controversial pursuit aimed at creating custom-made DNA codes to be inserted into living cells to change how they function, or even provide treatments for diseases. It could also someday help give scientists the profound and unsettling ability to create entirely new organisms.
The genetic code is like a book written with an alphabet of only four letters: A, C, G, and T. Chemical building blocks that correspond to these letters line up in DNA molecules like links in a chain; genes are made up of specific sequences of those building blocks. These sequences tell the yeast cell how to build particular proteins.
The complete DNA code for yeast, called its genome, contains about 12 million letters. An international scientific team aims to add, delete or alter about a million of the DNA letters.
Yeast DNA is spread across 16 large chunks called chromosomes, which were parceled out among the team's labs to tackle.
So how do you redesign and build a chromosome? We asked Leslie Mitchell, a researcher at New York University. She created a 240,000-letter synthetic yeast chromosome, starting while she was at Johns Hopkins University in Baltimore.
Here's the recipe:
1. On a computer, start with the natural DNA sequence of the letters across a chromosome.
2. Tell the computer to make specific alterations, such as:
Every time it sees the letter series TAG at the end of a gene, change it to TAA. Both triplets deliver the same message to the yeast's machinery for making protein, so the change doesn't affect the yeast. But the TAG triplet could be used in a different place to make the yeast produce a protein from building blocks not found in nature, for example.
Delete a class of genes called 'tRNA genes' from their normal positions, where they can impair the process of duplicating the genome before a yeast cell divides. These genes will be relocated to their own, new chromosome, where they can do their jobs without causing trouble.
Insert bits of DNA code that will let researchers rearrange the order of genes on the chromosomes, like shuffling a deck of cards. This way, scientists can experiment with many different reshufflings to see which one makes yeast grow best, or perform best in some other way.
3. Once the alterations are done, break the redesigned code into lengths of about 10,000 letters apiece and have a company create chunks of DNA that reflect each of these segments. Chunks of that size can be easily manipulated in a laboratory.
4. In the test tube, use a chemical reaction to glue three to six of these chunks together into a "megachunk."
5. Take ordinary yeast and use this 30,000-60,000-letter megachunk to replace the corresponding segment of natural DNA. Yeast will do this without much coaxing.
6. If the yeast doesn't grow normally, identify and fix the problem in the megachunk. This is called debugging. If it's fine, add the next megachunk.
7. Repeat steps 4-6 until the entire chromosome has been replaced with megachunks of synthetic DNA.
Mitchell said it took her a couple months to build her chromosome but longer to debug. "The tiniest change in the code can have dramatic effect on growth," she said. "We are learning new rules about how cells operate by building from scratch."
Follow Malcolm Ritter at http://twitter.com/malcolmritter His recent work can be found at http://tinyurl.com/RitterAP
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How scientists redesign DNA codes - ABC News
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Scientists hide a real movie within a germ’s DNA – Science News for Students
Posted: at 9:49 am
(for more about Power Words, clickhere)
audioHaving to do with sound.
bacterialHaving to do with bacteria, single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside animals.
bit(in computer science) The term is short for binary digit. It has a value of either 0 or 1.
code(in computing) To use special language to write or revise a program that makes a computer do something.
colleagueSomeone who works with another; a co-worker or team member.
CRISPRAn abbreviation pronounced crisper for the term clustered regularly interspaced short palindromic repeats. These are pieces of RNA, an information-carrying molecule. They are copied from the genetic material of viruses that infect bacteria. When a bacterium encounters a virus that it was previously exposed to, it produces an RNA copy of the CRISPR that contains that virus genetic information. The RNA then guides an enzyme, called Cas9, to cut up the virus and make it harmless. Scientists are now building their own versions of CRISPR RNAs. These lab-made RNAs guide the enzyme to cut specific genes in other organisms. Scientists use them, like a genetic scissors, to edit or alter specific genes so that they can then study how the gene works, repair damage to broken genes, insert new genes or disable harmful ones.
dataFacts and/or statistics collected together for analysis but not necessarily organized in a way that gives them meaning. For digital information (the type stored by computers), those data typically are numbers stored in a binary code, portrayed as strings of zeros and ones.
DNA(short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.
E. coli(short for Escherichia coli) A common bacterium that researchers often harness to study genetics. Some naturally occurring strains of this microbe cause disease, but many othersdo not.
gene(adj. genetic) A segment of DNA that codes, or holds instructions, for a cells production of a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.
geneticHaving to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.
GIF (short for Graphics Interchange Format) This is a format used to send images, especially movies, on the internet. An animated GIF file is one that can move on the internet, such as a swirling flag or jumping frog.
moleculeAn electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).
nucleotidesThe four chemicals that, like rungs on a ladder, link up the two strands that make up DNA. They are: A (adenine), T (thymine), C (cytosine) and G (guanine). A links with T, and C links with G, to form DNA. In RNA, uracil takes the place of thymine.
organismAny living thing, from elephants and plants to bacteria and other types of single-celled life.
pixelShort for picture element . A tiny area of illumination on a computer screen, or a dot on a printed page, usually placed in an array to form a digital image. Photographs are made of thousands of pixels, each of different brightness and color, and each too small to be seen unless the image is magnified.
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Love Island fans spot Britain’s Got Talent stars DNA on reunion show but did you see them? – The Sun
Posted: at 9:49 am
LOVE Island fans noticed Kem Cetinays homecoming bash had two very special guests of honour waiting to welcome him back.
During tonights reunion show, eagle eyed viewers spotted Britains Got Talent double act DNA loitering in the background during a clip of Kem and Amber Davies visiting his salon in Essex.
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Some fans couldnt believe their eyes as they saw Darren, 29, and Andrew,43, mingling with the barbers friends and family.
One tweeted: Wtf! Was it just me who just saw DNA in Kems barbers shop?
Another wrote: Anyone know why DNA were in @KemCetinay barber shop on Love Island?
Darren and Andrew, who made it to the final of Britains Got Talent earlier this year, stayed pretty low key during Kems arrival and didnt speak during the short clip.
It turns out the pair are pretty chummy with Kem, and actually hinted they would be performing with them at a later date.
They told their Twitter followers: Great seeing Kem and Amber! So happy for them, worthy #LoveIsland winners!! Video of us performing on them coming soon! #KemandAmber.
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Tonight's reunion show had it's far share of surprises, with Chyna Ellis left stunned when Jonny Mitchell appeared to dump her live on air.
She got her revenge and later branded him a p***k - filming him secretly on her phone and uploading it to Instagram.
In another shot, she wrote over the smiling reality stars face, What a little p***k.
Jonny and Chyna had jetted off on a romantic break away to Budapest, giving fans the impression they were dating.
When Caroline Flack asked them what was happening however, Jonny denied they were dating leaving Chyna looking stunned.
As Caroline told them it was the most awkward moment of the night so far, Chyna blushed and said the pair were just having fun.
Caroline then quizzed Jonny on why hed taken Chyna on holiday which he had boasted cost 100,000 to which he replied: I just like holidays.
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The show became more awkward when Montana Brown and Alex Beattie tried to persuade Caroline they were still dating.
Since leaving the villa, the pair have tried to convince fans theyre dating despite The Sun revealing the couple had broken up.
A source told The Sun: Montana is keen to follow her dreams as a TV presenter and has been attending meetings this week to get the wheels in motion.
She doesnt like partying and isnt a big drinker so personal appearances in nightclubs arent really her thing.
Instead she is ambitious and very much a career woman her relationship with Alex is going to take a back seat.
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Love Island fans spot Britain's Got Talent stars DNA on reunion show but did you see them? - The Sun
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Seeing double in arachnid genomes: new insights into the consequences of whole genome duplication in animals – BMC Blogs Network (blog)
Posted: at 9:48 am
Research published today in BMC Biology finds that whole genome duplication, a process in which an organisms entire genome duplicates, occurred in the lineage leading to spiders but not their distant arachnid relatives, ticks and mites. Here to discuss this research and whole genome duplication in the ancestors of vertebrates and other chelicerates is author of the study, Alistair P. McGregor.
Alistair P. McGregor 31 Jul 2017
Luka Miles
It is thought that gene duplication plays an important role in generating new genetic material for the evolutionary diversification of species. Gene duplication can be caused by several mechanisms and in the extreme case two copies of all of the genes in a genome can be generated by whole genome duplication (WGD).
In a recent study published in BMC Biology, my colleagues and I analyzed the genome of the common house spider Parasteatoda tepidariorum and we have found evidence for a WGD in the lineage leading to spiders.
This event was likely shared with scorpions and probably other arachnopulmonates like whip-scorpions and whip spiders, but not with more distantly related arachnids such as ticks and mites. This suggests that the approximately 45,000 extant species of arachnopulmonates evolved from a polyploid ancestor over 400 million years ago.
Our study also suggests that this WGD in arachnids was likely independent of WGD in another group of chelicerates, the horseshoe crabs. Our findings thus offer an exciting opportunity to discover more about the outcomes of WGD in terms of gene content and regulation, and how such events may contribute to animal diversification.
In the ancestor of vertebrates there were two rounds of WGD and these events may have led to the diversification of these animals through the retention and utilization of duplicated genes. For example, while most animals contain a single cluster of Hox genes, vertebrates, like ourselves, have four Hox clusters and these additional genes play many important roles in development. However, genes can be retained or lost for many reasons after WGD events, including random mutation, recombination and dosage effects.
A better understanding of the patterns of gene retention and loss after WGD and identification of commonalities, as well as potentially the genes that may underlie evolutionary innovation, requires the study of independent events. This comparison, however, suffers from the fact that only a few examples of WGD have been described in animals to date.
Our identification of a WGD in arachnids, consequently, provides a much-needed new data point for understanding the general and lineage specific impact of WGD events.
Our identification of a WGD in arachnids, consequently, provides a much-needed new data point for understanding the general and lineage specific impact of WGD events. The duplicated genes that have been retained in both spiders and scorpions represent many that encode proteins with important roles in development, including two copies of most Hox genes arranged in two (nearly) complete clusters.
Furthermore the paralogs of each of the spider Hox genes differ in their timing and spatial expression during embryogenesis suggesting that some of the new copies perform novel functions with respect to the single copy ancestral gene. Therefore our study reveals an intriguing parallel between the outcomes of WGD in arachnids and vertebrates.
Interestingly, our study and previous work also reveals a high rate of retention of duplicated microRNAs. These genes are thought to modulate the expression levels of their target genes and they have perhaps been retained in high numbers after WGD to buffer the dosage effects of targeted duplicated protein coding genes, rather than contributing to the emergence of novel traits. Indeed, a possible outcome of gene duplication is developmental systems drift, whereby different genes and interactions can be used to achieve the same phenotypic outcome, but this remains to be investigated systematically.
Cave Whip Spiders Damon variegates
Wikimedia commons
More fully understanding the consequences WGD event in arachnids requires the analysis of additional arachnid genomes to determine exactly when this event occurred and which lineages were affected. For example, it would be interesting to explore whether there is any evidence for WGD in other arachnid orders like camel spiders, harvestmen and pseudoscorpions.
In addition, comparing the genomes of whip spiders and whip scorpions with spiders and scorpions could help reveal genes that have been retained by most groups after WGD versus lineage specific retentions and losses. These data will not only provide insights into arachnid genomes before and after the WGD event, but a better understanding of how duplicated genes produced by this event have contributed to the evolution of innovations in these animals, for example, silk production in spiders and the booklungs (novel breathing organs) of arachnopulmonates.
Finally, a more detailed understanding of the patterns of gene retention and loss after WGD in arachnids will provide an excellent comparison to such events in vertebrates to better understand the broader implications and consequences of WGD for the evolution of animal genomes and their biology.
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Seeing double in arachnid genomes: new insights into the consequences of whole genome duplication in animals - BMC Blogs Network (blog)
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Maryland scientists research gene linked to depression | The … – The Spokesman-Review
Posted: at 9:45 am
Sun., July 30, 2017, 8:58 p.m.
Dr. Mary Kay Lobo and her colleagues at the University of Maryland School of Medicine have been examining the gene known as Slc6a15 and researching the role it plays in either protecting from stress or contributing to depression. (Karl Merton Ferron / Karl Merton Ferron/Baltimore Sun)
BALTIMORE Although there are medications to treat depression, many scientists arent sure why theyre effective and why they dont work for everyone.
Researchers at the University of Maryland School of Medicine believe they may have found a key to the puzzle of major depression that could lead to therapies for those who dont respond to medications already on the market.
A study by the researchers has identified the central role a gene known as Slc6a15 plays in either protecting from stress or contributing to depression, depending on its level of activity in a part of the brain associated with motivation, pleasure and reward seeking.
Published in the Journal of Neuroscience in July, the study is the first to illuminate in detail how the gene works in a kind of neuron that plays a key role in depression, the according to the medical school.
Specifically, the researchers found that mice with depression had reduced levels of the genes activity, while those with high levels of the genes activity handled chronic stress better.
Though senior researcher Mary Kay Lobos primary studies were done with mice, she also examined the brains of people who had committed suicide and found reduced levels of the genes activity, confirming a likely link.
She hopes now that drugs could be developed that would encourage the genes activity.
I thought it was fascinating we had this system in place that allows us to go after things or be motivated or have pleasure and I was interested in how it becomes dysfunctional in certain diseases like depression, Lobo said. I hope that we can identify molecules that could potentially be therapeutically treated or targeted to treat depression.
Lobo and her colleagues have been examining the gene for years. In 2006, they discovered that it was more common among specific neurons in the brain that they later learned were related to depression. Five years later, other researchers learned that the gene played a role in depression and Lobo and her research colleagues decided to investigate what that role is in those specific neurons.
About 15 million adults, or 6.7 percent of all U.S. adults, experience major depression in a given year, according to the Anxiety and Depression Association of America. It is the leading cause of disability for Americans ages 15 to 44. It is more prevalent in women and can develop at any age, but the median age of onset is 32.5.
David Dietz, an associate professor in the Department of Pharmacology and Toxicology at the State University of New York at Buffalo, said little was known previously about the biological basis of depression in the brain. Many drugs used to treat depression were discovered serendipitously, he said, and it wasnt clear why they worked.
Were starting to really get an idea of what does the depressed brain look like, Dietz said. When you put the whole puzzle together, you see where the problem is. For too long weve been throwing things at individual pieces. Its so complex and we have so little information that it was almost bound to be that way. For the first time this is one of those bigger pieces you can slide into the jigsaw puzzle.
Lobo said its not clear yet how Slc6a15 works in the brain, but she believes it may be transporting three types of amino acids into a subset of neurons called D2 neurons in a part of the brain called the nucleus accumbens. The nucleus accumbens and D2 neurons are known to play a role in pleasure, activating when one eats a delicious meal, has sex or drinks alcohol.
The amino acids would then be synthesized into neurotransmitters. Depression previously has been linked to imbalances of the neurotransmitters serotonin, norepinephrine and dopamine.
So even though people may have proper levels of amino acids in their bodies, the neurons in their brains that need them may not be getting enough if the transporter is not working as it should.
This gene is critical for putting very specific amino acids in the right place so that neurotransmitters can be synthesized, said A.J. Robison, an assistant professor in the Department of Physiology at Michigan State University. Its the location, location, location idea. Its not the amino acids, its where theyre at and in which cells.
Robison said Lobos next step would be discovering more about how the transporter gene works.
The fact that this transporter seems to be important is what the paper shows and how it does it is not shown, and thats a challenge for her, he said. Figuring out the how of it is the next step and Dr. Lobo is particularly positioned to do it.
Lobos team was able to use gene therapy, a form of therapy in the early stages of being studied in humans, in the mice to boost the genes activity. The mice were exposed to larger, more aggressive mice, which usually causes depressive symptoms. But the gene therapy helped protect the mice against the stress, the team found. When the team reduced the genes activity in the mice, just one day of exposure to the aggressive mice was enough to cause symptoms of depression.
Gene therapy is starting to be used in the treatment of some types of cancers, but Lobo said science had not yet advanced to the point where it can be used for treating neurological issues in human patients. A more likely treatment would be a drug that targets the genes activity directly, she said.
I think this is a major step toward our understanding of the precise maladaptive changes that occur in response to stress, said Vanna Zachariou, an associate professor in the Department of Neuroscience at the Icahn School of Medicine at Mount Sinai. It can be a more efficient way to target depression because its not simply targeting monoamine receptors or dopamine but targeting molecular adaptations that occur. It doesnt act necessarily as the drugs we have available, so it might create an alternative avenue to treat depression.
Lobo said she wouldnt refer to Slc6a15 as a depression gene, saying the disease was complex and could have many factors.
I wouldnt say theres one depression gene she said. A number of things play a role, and also theres no depression neuron, theres multiple depression neurons.
There also may be different types of depression with different symptoms, she said. With the disease, some sufferers sleep a lot, while others sleep a lot less, for example.
With all these complex diseases, its hard to link it to something, she said. Like Huntingtons disease, we know theres a specific gene that causes Huntingtons disease. For depression we dont have that.
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Gene Markers Can Predict Your Outcome of Cancer or Immune Disease – Technology Networks
Posted: at 9:45 am
Publishing in the July 24, 2017, issue of Nature Communications, Professor Klaus Ley, M.D., who led the study, and his team identify gene markers that directly correlate with the outcome of inflammatory and malignant diseases in humans, including survival of osteosarcoma, melanoma, chronic lymphocytic leukemia (CLL), Burkitt lymphoma and large-cell lung carcinoma. Their findings emphasize that accounting for immune diversity is a critical factor to increase the success rate of predicting disease outcomes based on immune cell measurements.
Traditionally, researchers have relied on inbred mouse strains to gain insight into the complex world of human diseases while reducing what is known as experimental noise. If you take a black, a brown or a white mouse each one will give you a different answer in the same assay. For example, if you vaccinate them, their responses will be different, which creates a lot of experimental noise, says Ley. However, when you think about patients, or even healthy people, we are all different.
To mine those differences for valuable information, the LJI researchers actively embraced the experimental noise. Instead of analyzing a single inbred mouse strain, Buscher turned to the hybrid mouse diversity panel (HDMP). The panel was developed by co-author Aldons J. Lusis, Ph.D., a professor in the Departments of Medicine, Human Genetics, and Microbiology, Immunology, and Molecular Genetics at the University of California, Los Angeles.
The HDMP is a panel of about 100 different inbred mouse strains that mirror the breadth of genetic and immunological diversity found in the human population. You can think of the panel as a hundred different patients, or healthy people, explain Buscher.
Buscher, Lusis, Ley and others studied the natural variation in the activation pattern of abdominal macrophages, versatile members of the immune system. Professional phagocytes, they clear worn-out cells and cellular debris; survey tissue surfaces for foreign invaders; engulf bacteria and cancer cells; increase or quiet down inflammation and recruit other members of the immune system.
Macrophages isolated from 83 different mouse strains from the HDMP were exposed to lipopolysaccharide (LPS), a major component of the outer wall of gram-negative bacteria, to gauge their reaction to the strong inflammatory. Gram-negative bacteria are the cause of wide range of different illnesses, including food poisoning, cholera, tuberculosis and periodontitis, among many others.
Fundamentally, when the immune system is confronted with gram-negative bacteria, it can deal with the situation in two ways: Either, it gets very angry and tries to kill the bacteria or it can wall them off in an attempt to live with it, explains Ley. Both strategies carry a certain risk but a long evolutionary history has insured that mice and people can survive with either strategy.
The LPS-induced reactions of the macrophages analyzed as part of the study covered the whole spectrum from very aggressive (LPS+) to very tolerant (LPS-) depending on the mouse strain. This LPS+ and LPS- designation is related to the M1 and M2 designation introduced by Charles D. Mills, another co-author of the study. Next, the researchers asked which genes were active during each response type to identify gene signatures that correlated with LPS-responsiveness. Ley and his team then ran these gene signatures across various human gene expression data sets and discovered that they strongly correlated with human disease outcomes.
For example, macrophages isolated from healthy joints were enriched in LPS-tolerant genes, whereas macrophages from rheumatoid arthritis patients were strongly skewed towards LPS-aggressive. The same held true for macrophages found in the kidneys of healthy people versus lupus erythematosus patients.
Since it had been known that mice and people with the aggressive phenotype are better at fighting canceralthough they are more susceptible to cardiovascular diseasethe scientists specifically asked whether the level of LPS-responsiveness could predict tumor survival.
After analyzing data from 18,000 biopsies across 39 different tumor types, they found that the LPS+ gene signature strongly correlated with survival while the LPS- signature correlated with cancer death. The pattern was significant across many different types of cancer, including osteosarcoma, melanoma, chronic lymphocytic leukemia, Burkitt lymphoma and large-cell lung carcinoma.
This article has been republished frommaterialsprovided byLa Jolla Institute for Allergy and Immunology. Note: material may have been edited for length and content. For further information, please contact the cited source.
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Not many in ‘Valley’ buy Trump’s job promises – The-review
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By RANDY LUDLOW The Columbus Dispatch Published: July 31, 2017 3:00 AM
YOUNGSTOWN -- If only it was as simple as President Donald Trump makes it sound.
It never has been. The long-suffering Mahoning Valley was a charter member of the "rust belt" long before the phrase became politically incorrect.
All those old, shuttered hulks of the valley's steel-making heyday -- what Trump called "big, once incredible job-producing factories" -- will come roaring back to life, the president told his supporters Tuesday.
Don't sell your homes, Trump told a packed house of 8,000 at a Covelli Centre rally. Don't move in search of employment. Those long-lost jobs, "they're all coming back." It was similar to his promises to coal miners and others from the 2016 campaign.
The specifics of how the fortunes of the Youngstown-Warren area will suddenly and dramatically improve did not accompany Trump's remarks last week.
The Valley, a traditional Democratic stronghold long hungry for good jobs, cast a larger share of its votes for the Republican last fall. It has heard promises from politicians and presidents across generations.
But they have only sporadically translated into bottom-line improvement for residents of the Youngstown-Warren region, which has lost nearly 20 percent of its population since the mills began closing more than three decades ago.
Few, beyond perhaps Trump's most hard-core supporters, expect a return of a lot of high-paying factory jobs. Instead, the area's advocates are concentrating on diversifying the Valley economy beyond blast furnaces and assembly lines.
Youngstown Mayor John McNally, a Democrat, was polite, saying it would be a "challenge" to resurrect all those long-gone jobs in heavy industry.
"It's one of those promises that the previous Democratic campaigns have tried with residents around here. Unless you can deliver on that promise, coming back the next time the response may be different from folks," he said. "I don't think this area as a whole believes those jobs are coming back. I don't know why we keep hearing it."
But Trump supporters say he deserves a chance to deliver on his promises.
"He came back to the area to check on the people. He hasn't forgotten Youngstown," said Marleah Campbell, auxiliary chair of the Trumbull County Republican Party. "He's trying to do what he wants to do, but getting no cooperation. The Republicans need to get behind him."
It's hard to envision a manufacturing revival when the Mahoning Valley is fighting to hang on to what it already has amid an area economy that has bled some of its better jobs just since the start of Trump's presidency.
United Auto Workers Local 1417 trustee Jeff Terrace, a survivor from the stamping-line at one of the pair of General Motors' plants at Lordstown, saw the speech as typical untempered, over-promising Trump.
"I've been a gambler all my life. He's one of those guys who's all-in on every hand regardless of what he holds. We haven't seen any action. It's all talk," said the 57-year-old Terrace.
The lack of demand for small cars led General Motors in March to eliminate the third shift at the plants that build the Chevrolet Cruze. More than 1,000 jobs were lost, including some at area suppliers of seats and bumpers.
The area's unemployment rate stands at 5.9 percent, 20 percent higher than the statewide average. Even after a slight comeback, 700 fewer manufacturing jobs exist now than in January, according to federal figures. The overall jobs picture, however, has improved from 8.2 percent unemployment rate of March due to growth in many lower-paying positions.
Terrace and fellow stamping-line worker Ernie Long, 39, are disappointed that Trump and his administration have not yet abandoned or renegotiated the North American Free Trade Agreement with Mexico and Canada, as he promised.
Addressing NAFTA might help retrieve the production of the Cruze hatchback model from Mexico might help restore the lost third shift at Lordstown, the men said. Trump told the Youngstown crowd that if he doesn't get a "great deal," he will terminate the pact.
Noting that Trump's overseas-made, Trump-branded products and his moves to hire more foreign workers at a golf property, Long was displeased that Trump has not demonstrated an all-out commitment -- quoting the signs held by his rally supporters -- to "Buy American, Hire American."
"He's supposed to be bringing all these steel jobs back. Where are they?" he asked. "It's all smoke."
Sen. Sherrod Brown, D-Ohio, asked the same question last week at Wheatland Tube in Warren, where he implored Trump to amend an executive order to implement legislation he introduced with Sen. Rob Portman, R-Ohio, to require American-made steel and products in all federally funded infrastructure and public works projects.
Sarah Boyarko, senior vice president of economic development for the Youngstown/Warren Regional Chamber, stresses diversity and support jobs for emerging industry and trades as the key to Valley job growth.
"We learned from our past experience with the steel industry about having most of our eggs in one basket, and it just doesn't look that way anymore," she said.
A $70 million Obama administration initiative established America Makes in Youngstown to attract investments and provide job training and ongoing development of 3-D printing in metals.
Efforts continue to attract jobs in health care, warehouse distribution and logistics, well-drilling support and high-tech manufacturing, and the area is already attempting to position itself to capture petrochemical and plastic support jobs related to the proposed PTT Global Chemical America $6 billion ethane cracker plant in Belmont County, she said.
The chamber also is attempting to attract more support service jobs for the aluminum industry. The Youngstown-Warren area produces the second-largest amount in the nation.
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