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UC Santa Cruz genetics lab helps solve the mystery of ‘Miranda Eve’ – UC Santa Cruz (press release)

The coffin of a little girl was found buried beneath a San Francisco home during renovation work in 2016. (Photo courtesy of Garden of Innocence)

Richard E. (Ed) Green, associate professor of biomolecular engineering, helped identify the remains. (Photo by C. Lagattuta)

On May 9, 2016, a contractor discovered the casket of a child while excavating the backyard of the Karner family in the Lone Mountain neighborhood of San Francisco, setting off a search for the child's identity that garnered international attention.

It was determined that the lost child was a little girl, approximately 2 to 3 years of age, but who was she? What happened to her? When UC Davis anthropology professor Jelmer Eerkens heard about the little girldubbed Miranda Evehe knew he had to help.

I read they were planning to just rebury the body without any analysis, Eerkens told the New York Times in June. As an archaeologist, I thought, thats not right. At some point, these things from the past become our collective heritage.

To unravel the mystery, Eerkens worked with more than 30 specialists and volunteers, including UC Santa Cruz biomolecular engineering professor Ed Green and genealogist and Garden of Innocence founder Elissa Davey. Green's DNA analysis ultimately enabled the investigators to make a definite identification of the child in the casket.

The type of casket Miranda Eve was found in, along with the clothes she was wearing, indicated she was buried approximately 140 to 150 years ago. Researchers discovered that from 1865 until the early 20th century, the present day Lone Mountain neighborhood of San Francisco had been a cemetery owned by the Independent Order of Odd Fellows. The cemetery closed to new burials in 1902, and in the early 1930s, those interred there were removed and reburied in the Greenlawn Cemetery in Colma, Calif. Somehow, the little girl's casket was missed and left behind.

Historical maps

Using an 1865 plan for the development of the cemetery (a map for a time after 1902 could not be located), researchers pinpointed two sections of the cemetery that most likely intersected with the location of the Karners home. Historical maps were then digitally layered on top of each other and cross-referenced against photographs to identify any family plots in that location.

Before she was reinterred, samples of hair were taken for chemical and DNA testing in the hopes of finding a match with a living relative and learning what led to her death at such a young age. In the clean-room facilities in Green's Paleogenomics lab at UC Santa Cruz, DNA was extracted from the Miranda Eve hair samples using standard ancient DNA techniques.

Meanwhile, Eerkens and his students at UC Davis analyzed the nitrogen isotopes in the hair, which revealed that she had suffered from malnourishment for several months before her death. This indicates she was suffering from a chronic illness that caused wasting or starvation, rather than something more sudden such as smallpox, which was common during this time, or an injury, he said. While the exact illness is still unknown, we suspect an illness caused her to eat less and less until she was unable to eat at all.

DNA analysis

Green's initial analysis of the nuclear DNA confirmed little Miranda Eve to be a girl of likely European ancestry, and her mitochondrial DNA was found to be a type most common on the British Isles.

Research on internment records narrowed the search to two highly likely candidates for Miranda Eve's true identity, and an exhaustive search of genealogical records eventually found living family descendants for both candidates. The descendants were contacted and agreed to provide DNA samples for comparison. Green then was able to find a clear match between the DNA from the hair sample and that obtained from the living family member of one of the candidates.

After a year-long search, the mystery was solved: Miranda Eve was born on November 28, 1873, as Edith Howard Cook, the eldest daughter of Horatio Nelson and Edith Scooffy Cook, members of two prominent San Francisco families during the late 19th and early 20th centuries. Edith died just short of her third birthday in October 1876. Her three siblings, two brothers and a sister, survived her. Her older brother Milton H. Cooks grandson, Peter Cook, resides in the San Francisco Bay Area today.

Peter Cooks father passed away when he was just three years old, so he didnt know much about his fathers family history until Eerkens contacted him about Edith. When the DNA testing came back as a match, It hit the roof for me. I was beaming ear-to-ear with the news, Cook said. Now the 82-year-old can share the Cook family history with his eight children, 13 grandchildren, and 10 great-grandchildren.

Principle researchers on this project in addition to Professors Eerkens and Green and Ms. Davey, include Dave Frederick, genealogist and cold case investigator based in Billings, Mt., genealogist Bob Phillips of Seattle, Wa., and Alex Snyder, transportation planner and public historian in San Francisco.

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UC Santa Cruz genetics lab helps solve the mystery of 'Miranda Eve' - UC Santa Cruz (press release)

Direct-to-consumer genetics a new era in personalized medicine? – The Pharma Letter (registration)

Direct-to-consumer (DTC) genetics company 23andMe was recently granted approval by the Food and Drug

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Direct-to-consumer genetics a new era in personalized medicine? - The Pharma Letter (registration)

Striking demos speak volumes at Ag Fest – Holyoke Enterprise

Holyoke fifth-graders participated in Ag Fest at the Phillips County Event Center last Thursday, May 4, along with students from Julesburg, Revere and Creek Valley schools. Students took turns at nine different stations led by Colorado State University Extension agents who are passionate about agriculture. Instruction and hands-on activities featured range ecology, GPS, butter, honey, power and simple tools, groundwater, microbes, embryology and plant science. Ag Fest is in its eighth year of teaching important agricultural lessons to youth so they can make informed decisions in the future, even if they dont live on a farm.

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Striking demos speak volumes at Ag Fest - Holyoke Enterprise

Scientists unveil the UK’s largest resource of human stem cells from healthy donors – Medical Xpress

May 10, 2017 Eye stem cells. Credit: University of Southampton

Reported in Nature today, one of the largest sets of high quality human induced pluripotent stem cell lines from healthy individuals has been produced by a consortium involving the Wellcome Trust Sanger Institute. Comprehensively annotated and available for independent research, the hundreds of stem cell lines are a powerful resource for scientists studying human development and disease.

With collaborative partners from King's College London, the European Bioinformatics Institute, the University of Dundee and the University of Cambridge, the study also investigates in unprecedented detail the extensive variation between stem cells from different healthy people.

Technological advancements have made it possible to take an adult cell and use specific growth conditions to turn back the clock - returning it to an early embryonic state. This results in an induced pluripotent stem cell (iPSC), which can develop into any type of cell in the body. These iPSCs have huge scientific potential for studying the development and the impact of diseases including cancer, Alzheimer's, and heart disease.

However, the process of creating an iPSC is long and complicated and few laboratories have the facilities to characterise their cells in a way that makes them useful for other scientists to use.

The Human Induced Pluripotent Stem Cell Initiative (HipSci) project used standardised methods to generate iPSCs on a large scale to study the differences between healthy people. Reference sets of stem cells were generated from skin biopsies donated by 301 healthy volunteers, creating multiple stem cell lines from each person.

The researchers created 711 cell lines and generated detailed information about their genome, the proteins expressed in them, and the cell biology of each cell line. Lines and data generated by this initiative are available to academic researchers and industry.

Dr Daniel Gaffney, a lead author on the paper, from the Wellcome Trust Sanger Institute, said: "We have created a comprehensive, high quality reference set of human induced pluripotent stem cell lines from healthy volunteers. Each of these stem cell lines has been extensively characterised and made available to the wider research community along with the annotation data. This resource is a stepping stone for researchers to make better cell models of many diseases, because they can study disease risk in many cell types, including those that are normally inaccessible."

By creating more than one stem cell line from each healthy individual, the researchers were able to determine the similarity of stem cell lines from the same person.

Prof Fiona Watt, a lead author on the paper and co-principal investigator of HipSci, from King's College London, said: "Many other efforts to create stem cells focus on rare diseases. In our study, stem cells have been produced from hundreds of healthy volunteers to study common genetic variation. We were able to show similar characteristics of iPS cells from the same person, and revealed that up to 46 per cent of the differences we saw in iPS cells were due to differences between individuals. These data will allow researchers to put disease variations in context with healthy people."

The project, which has taken 4 years to complete, required a multidisciplinary approach with many different collaborators, who specialised in different aspects of creating the cell lines and characterising the data.

Dr Oliver Stegle, a lead author on the paper, from the European Bioinformatics Institute, said: "This study was only possible due to the large scale, systematic production and characterisation of the stem cell lines. To help us to understand the different properties of the cells, we collected extensive data on multiple molecular layers, from the genome of the lines to their cell biology. This type of phenotyping required a whole facility rather than just a single lab, and will provide a huge resource to other scientists. Already, the data being generated have helped to gain a clearer picture of what a typical human iPSC cell looks like."

Dr Michael Dunn, Head of Genetics and Molecular Sciences at Wellcome, said: "This is the fantastic result of many years of work to create a national resource of high quality, well-characterised human induced pluripotent stem cells. This has been a significant achievement made possible by the collaboration of researchers across the country with joint funding provided by Wellcome and the MRC. It will help to provide the knowledge base to underpin a huge amount of future research into the effects of our genes on health and disease. By ensuring this resource is openly available to all, we hope that it will pave the way for many more fascinating discoveries."

Explore further: Stem cell consortium tackles complex genetic diseases

More information: Helena Kilpinen et al, Common genetic variation drives molecular heterogeneity in human iPSCs, Nature (2017). DOI: 10.1038/nature22403

http://www.yourgenome.org/facts/what-is-a-stem-cell

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Scientists unveil the UK's largest resource of human stem cells from healthy donors - Medical Xpress

This Grey’s Anatomy Teaser Hints at [SPOILER]’s Exit – TV Guide (blog)

Now Playing 9 Things You Didn't Know About Grey's Anatomy

It's been rumored for months that actress Jerrika Hinton might be taking leave of Grey Sloan Memorial Hospital sometime this season, and the newest teaser for Grey's Anatomy's upcoming episode certainly paints a grim picture for her very near future on the show.

Hinton, who's played Dr. Stephanie Edwards since the series' ninth season, is the focus of this clip from TVLine, which shows the halls of the hospital swarming with police as Chief Bailey (Chandra Wilson) frantically searches for Edwards while Jackson Avery (Jesse Williams) laments his decision to leave Edwards with the apparently dangerous patient she's shown wheeling around.

When it was first reported that Hinton might be leaving Grey's, the news was that she wouldn't return as a series regular, leaving open the possibility of her still coming in as a guest star. However, if this teaser is any indication, her departure might just be more final than anyone expected ... which wouldn't be too much of a surprise, given how murder-happy the Grey's writers have been with their medical staff over the years.

Hinton is expected to star in Wes Ball's new HBO dramedy series, Here, Now later this year.

Grey's Anatomy airs Thursday nights at 8/7c on ABC.

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This Grey's Anatomy Teaser Hints at [SPOILER]'s Exit - TV Guide (blog)

Q&A with Greg Dunn, neuroscientist turned artist – PLoS Blogs (blog)

For most neuroscientists, long days in the lab pipetting or recording from cellsdoesnt inspire one to pick up a paintbrush or sketchpad. But for others,the still-mysteriousand often breathtakingly beautifulworkings of the brain are a source of awe. One such individual is neuroscientist-turned-artist Greg Dunn. As a graduate student at the University of Pennsylvania, his own researchmerged withexperimental forays into painting, adapting neural forms to the principles of Asian art. Greg joins us to discuss his personal journey to becominga science artist, his visionsfor the burgeoning field of science-inspired art, and his advice for aspiringbrain-loving artists.

You followed a unique career path compared to most scientists. Could you share a bit about your transition from scientist to artist and what inspired you to pursue this path?

GD: I had always needed an artistic outlet in my life, and that became more true than ever when working on very complex biological systems in the lab. When experiments dont work after a massive expenditure in your efforts, its nice to have something going in parallel that produces something tangible, such as art. Ive always loved Asian art and the neuroscience images I saw every day in grad school began to merge with that interest, and over the course of several months in my first year of grad school I began to develop my aesthetic in earnest.

I never felt that I was doing anything at the lab bench that others couldnt have, but I do feel like I have a useful voice in combining science and art. I hope that my career trajectory serves as an example that specialized scientific knowledge can be applied to many different fields and can help to refine a persons individual voice.

Art based on science (including neuroscience) is becoming increasingly popular. Why do you suspect this field is so appealing, even to non-scientists?

GD: The brain is the ultimate frontier, it is more fundamentally US than anything else we possess. It is at the fundamental root of everything we could possibly be interested in or do with our lives. It is similar to why astronomy is popular to the lay public in this sense, it holds such great philosophical mysteries to explore. And on top of its conceptual and metaphorical meaning, it is aesthetically beautiful. It is so rich in possibility that it is the sort of thing a person can comfortably spend their whole life exploring.

How, if at all, do you believe that neuroscience-inspired art can serve as an effective outreach tool? Have you witnessed this with your own work?

GD: Yes. Art harnesses the power of emotions and direct perceptions in a way that hard data and dry explanations cant. I deliberately use the power of composition and design to try and make my works appealing on an instinctive level. With the world at our fingertips, people need to be given a reason to care about what they are looking at. Making compelling paintings is about drawing the viewer in initially and then giving them something to chew on in the long term, in this case pondering the nature of the brain and mind.

In the case of Self Reflected, my latest work done in collaboration with Dr. Brian Edwards, the point was to demonstrate directly what complexity looks like. Telling somebody that the brain has 86 billion neurons is essentially meaningless because we have no ability to grasp what that number means. Showing somebody directly what the activity of 500,000 neurons looks like at once in a huge, wall sized microetching gives a person a stepping stone to begin to comprehend this astonishing fact. When you then tell them that the brain is actually hundreds of millions of times MORE complicated than that, thats when a light goes on.

How do you select the subject matter for your work? Do you have any favorite pieces that were particularly meaningful, or that youre especially proud of?

GD:Im attracted by a variety of compelling images and subjects in neuroscience and meditation. I try to choose subjects that are of interest to different categories of people- some are more specialized neuro, others more general, some more abstract, etc. Id say that some of my favorites are Basket and Pyramidals as I think it is a clear statement about how neurons fit in the fractal like organization of nature and how they are similar in form to trees, branches, etc that have been painted in gold leaf in Asia for centuries. Cortex in Metallic Pastels also turned out very well and is one of the first examples of my deep reflective gold leaf technique. And, of course, Self Reflected is the most ambitious project of any kind Id ever attempted. Its scope and attention to detail I think will make it a useful visualization of the brain for a very long time.

The overlapping fields of art and neuroscience are evolving rapidly. How to do you see the field changing over the next decade?

GD: Representing brain aesthetics is only one part of it. There is a lot of art/sci work going on in using EEG signals or other neurofeedback devices to direct tasks of various sorts. I am looking forward to seeing some of the work that will come out of collecting unconscious brain activity data that will direct image generation software. I personally plan to try to elucidate states of consciousness that arise in deeper states of meditation through art, as this is more of a subjectively and experientially directed bit of neuroscience art. I think that it is important that art poke our brains into different types of perceptions to teach us a bit more about how it works.

Do you have any advice for others hoping to pursue a career in science-inspired art?

GD: Find your own unique voice! Make a Venn diagram of what your passions are and think hard about how and where they intersect. That is where you will be more effective, motivated, and unique. Really strive to make something categorically new. Dont always trust your first idea on how to do something, give yourself the time to really iterate an idea in your mind before you realize it. If you are trying to make a living at it, be smart about how to balance your passion with financial realities. Overall, work to convince the world that the barriers between science and art are indistinct at best, and that multifaceted approaches to problems are the most effective solutions.

You can learn more about Greg Dunns work atgregadunn.com

Feature image:Basket and Pyramidals, ink on 22K gold leaf, 18 X 24, 2013

Any views expressed are those of the author, and do not necessarily reflect those of PLOS.Emilie Reas received her PhD in Neuroscience from UC San Diego, where she used fMRI to study memory. As a postdoc at UCSD, she currently studies how the brain changes with aging and disease. In addition to her tweets for@PLOSNeuroshe is@etreas.

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Q&A with Greg Dunn, neuroscientist turned artist - PLoS Blogs (blog)

Doomtree’s Dessa has neuroscience on the brain at NYC residency – amNY

The songwriter, rapper, essayist and whiskey enthusiast Dessa was a part of a chart-topping album last fall, performing the previously-unreleased Congratulations on The Hamilton Mixtape. That record made it to the top of the Billboard 200, so the obvious follow-up is a four-week performance residency involving neuroscience.

Part of the last six months of my life has been spent lying on my back, in a 7 Tesla MRI scanner, to see if I could find the love in my own brain, she says, as an introduction to her Heartbreakers series at The Greene Space. And if I could, then how to get rid of it.

Mixing song with science, Dessa has put together lineups for each evening that look as much like a fascinating dinner party as a performance. Paper Tiger, her cohort from the Minneapolis hip-hop collective Doomtree, will be joining Dessa on the same night as Columbia University professor of psychology Geraldine Downey, for instance, and also taking the stage will be rappers, singers and cognitive neuroscientists.

amNewYork caught up with Dessa in advance of the first night of her residency to talk breakups, connections and the passion shared by both artists and researchers.

What was the spark for this?

A breakup. Id had a really lousy breakup with a really awesome dude. I found that I was healing really slowly. You expect that youre going to eat ice cream and sulk around for a while, but eventually youre going to perk back up. I was just blue for a really long time. So partly out of vested interest in my own well-being and partly out of scholarly interest I started reading some of the research on what happens to the brain and the body during and after love. I got really into the work of Dr. Helen Fisher, an anthropologist who uses fMRI technology to investigate what the human brain looks like in love, when its a reciprocal love and when its not a reciprocal love. And I was hooked. Every one of my interests seemed to coalesce there; Ive been long interested in science, human connection, better understanding the human condition I studied philosophy in college and it all came wrapped up in a neat bow. And I thought, Id love to put out an event that investigates heartbreak both from an artistic and from a really robust scientific viewpoint.

You debuted some of this in Minneapolis, right?

I had this orchestral debut a couple of months ago with the Minneapolis Orchestra. And part of that concert included a mini-TED talk that investigated some of these ideas. But on that stage there were only a few minutes to talk about some of the work Id been researching. The events at The Greene Space are going to have some music and a lot of conversation, and opportunity to ask questions of the researchers present.

From the outside, combining songwriters and researchers seems like an odd match.

Both fields, music and science, are very often driven by the spirit of inquiry and lifelong driving passion and curiosity. Very few researchers and very few musicians at a dinner party would say, I did it for the money. Its a passion-driven field, and in the particular artists and scientists Ive invited to participate in the residency, Ive asked those people who have really been driven to try and understand interpersonal relations, to try and understand why and how people connect, why we fall in love, out of love and what to do if were left holding one end of a love that someone else released. Theyre approaching the same phenomenon, but from different vantage points.

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Doomtree's Dessa has neuroscience on the brain at NYC residency - amNY

Home | Cancer Immunology Research

Research Articles

Elena Lo Presti, Francesca Toia, Sebastiano Oieni, Simona Buccheri, Alice Turdo, Laura Rosa Mangiapane, Giuseppina Campisi, Valentina Caputo, Matilde Todaro, Giorgio Stassi, Adriana Cordova, Francesco Moschella, Gaetana Rinaldi, Serena Meraviglia and Francesco Dieli

Cancer Immunol Res May 1 2017 5 (5) 397-407; DOI:10.1158/2326-6066.CIR-16-0348

Tumor-infiltrating lymphocytes contain T cells. In early-stage SCC tumors, T cells had antitumor properties, such as production of IFN. However, clinically advanced tumors contained many more T cells that produced IL-17 and promoted tumor growth.

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BRIEF-Atossa Genetics says second positive interim review on Phase 1 study of endoxifen may advance to final topical … – Reuters

UPDATE 2-Brazil inflation hits lowest in nearly 10 years in April

(Adds data, market reaction, economist's comment) By Silvio Cascione BRASILIA, May 10 Brazil's annual inflation rate fell in April to its lowest level in nearly 10 years, bolstering the view of a steep interest rate cut by the central bank at the end of this month. Consumer prices rose 4.08 percent in the 12 months through April, slightly below market forecasts for a 4.10 percent increase and compared with an increase of 4.57 percent in the year to March, the national st

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BRIEF-Atossa Genetics says second positive interim review on Phase 1 study of endoxifen may advance to final topical ... - Reuters

Experts say the Microbiome could overtake Genetics as the Next Big Thing – Labiotech.eu (blog)

Yesterday, a panel of experts at BioTrinity discussed the huge possibilities offered by the young microbiome field, which could soon overtake genetics.

Scientists and investors worldwide are starting to turn to the microbiome, which many believe hold the key to human health. The microorganisms that live in us and on us have shown to play a role in conditions ranging from obesity to cancer and neurodegenerative disease. I think it is a bigger deal than genetics, says Tim Spector, CEO of Map my gut, a company that offers direct-to-consumer microbiome sequencing services. But he reckons that being such a new field, still driven by small companies, very few are collecting samples of the microbiome as they should.

Back in the early days of genetics, companies would not collect DNA samples because it was too much trouble regarding ethical permissions, storage, he says. Something very similar seems to be happening with the microbiome despite the huge links with health that have been observed. The science is now there, and its obvious that anyone doing a big trial should measure how patients with different microbiome profiles respond to drugs.

Theres good evidence that efficacy and adverse effects of checkpoint inhibitors are linked to specific bacteria, agrees Mike Romanos, CEO of Microbiotica. BMScertainly believes this, as it recently signed a partnership with Enterome to study checkpoint inhibitors in the context of micrbiome-related biomarkers.

But we still have to find out how to mine such a huge potential. We need to know whats going on with the bacteria down to the strain level to fully understand their phenotype, Romanos says. With that aim, his company is building a data repository, similar to those for the human genome.

It seems that the field is rapidly growing and overcoming the challenges. The number of publications has risen exponentially in the last couple of years, says Denise Kelly from Seventure, a French VC with the first and only fund fully dedicated to microbiome companies. In a chat with her later, she explained that France is a hub with excellent microbiology research, counting with companies like MaaT Pharmaand Eligo Biosciencein addition toEnterome. France also led the European MetaHIT project, which was one of the first to sequence the microbiome, much like the Human Genome Project did before.

Kelly highlighted the main challenge at the moment is understanding the mode of action of specific organisms and the metabolites they produce. The field is in a very early stage, there are just 6 or 7 companies in clinical stage worldwide. (Indeed, when we scouted companies to include in our microbiome infographic, they seemed to be few and far between!)

For her, the next step is getting from studying correlation to identifying causality, and she knows a couple of companies that can pinpoint causality, but couldnt disclose their names. She did mention, though, the progress made with FishTaco, a system developed at the University of Washington that can discern how much each species contribute to a disease phenotype.

Furthermore, Kelly thinks that the public is more motivated than ever to look after themselves, not just regarding disease but also maintaining a healthy lifestyle. The microbiome affects every aspect of human physiology. The market is currently at 500M, but it can be much bigger if we make the right discoveries quickly, she concluded.

Images from royaltystockphoto.com, WhiteDragon /Shutterstock

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Experts say the Microbiome could overtake Genetics as the Next Big Thing - Labiotech.eu (blog)