Category Archives: Transhuman News

Have you ever wondered why you wash your rice or soak it overnight before cooking it? Perhaps you wash your rice grains to enhance taste, reduce starch levels, or maybe that's just the way your family has always prepped rice. Thanks to a tip from science communicator Samantha Yammine who came across Dr. Nausheen Sadiq's neat finding while live-tweeting a forum on Diversity and Excellence in Science it turns out there is another reason why, as washing rice actually helps reduce the concentration of heavy metals, like chromium, cadmium, arsenic, and lead.

Heavy metal contamination in crops can be caused by human activities, such as mining, fertilizers, pesticides, and sewage sludge. Compared to most cereal crops though, rice (Oryza sativa L.) actually accumulates more heavy materials, like cadmium or arsenic, where long-term heavy metal intake can cause health risks. For example, long-term arsenic exposure leads to skin disease, high blood pressure, and neurological effects. This is especially important to consider as rice is a staple food across the globe.

Heavy metal contamination in crops can be caused by human activities, such as mining, fertilizers, pesticides, and sewage sludge.

Photo by TUAN ANH TRAN on Unsplash

In a recent study, researchers investigated the effects of different cooking methods (normal, high-pressure and microwave cooking) on the concentration, bio-accessibility and health risks posed by three heavy metals (cadmium, arsenic and lead) in two strains of brown rice. After cooking 100 grams of brown rice grains, researchers evaluated bioaccessibility (i.e. how much of the heavy metal is released for absorption) by mixing rice samples with simulated gastric fluid, and then used spectrometery to measure heavy metal concentration. Lastly, the researchers calculated the health risk posed by the heavy metals by calculating values such as the average daily dose.

Overall, the researchers found that instead of the three different cooking methods, it was the washing process which significantly reduced concentrations of cadmium, arsenic and lead, suggesting that the reduction may be due to rice morphology. For example, lead is found largely in the outer compartments of rice kernels, so lead is more likely to be removed during rice washing.

In contrast, the three cooking methods did impact bioaccessibility i.e. how much of the heavy metal would be released for absorption by the body. Here, washing and soaking isn't enough as rice absorbs water poorly at 25C. This finding was also reflected in calculated values: the average daily doses of cadmium, arsenic and lead were lower in washed and cooked rice, compared to raw rice.

It's worth noting that the European Commission has enforced limits on heavy metal levels - for example, arsenic is currently limited to 200 parts per billion (ppb) for adults and 100 ppb for infants. Both the U.S. and Canada currently have no limits in place for arsenic in food though Canada is currently reviewing a proposal to add maximum levels for arsenic found in white and brown rice, while the U.S. FDA has previously released a (non-binding) risk assessment, suggesting the same 100 ppb levels as Europe.

So the takeaway here is that yes, your family and all those professional chefs have been right all along. Yes, washing rice involves sacrificing some of its nutritional value, but doing so means you can reduce the levels of heavy metals present in grains, and still enjoy dishes like rice cakes. And returning back to Yammine's reporting, Saudiq actually shared that by soaking and washing rice for ~5 mins, you can get rid of 50-100% of these elements. (Thanks Sam!)

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Vaccine-laced snacks are being scattered in the wilderness to protect wildlife from rabies - Massive Science

Findings to be presented cover broad range of scientifically and clinically relevant areas including schizophrenia, sex development, cancer and muscular dystrophy

SAN DIEGO, Oct. 16, 2019 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (BNGO) today announced that disease researchers using Bionanos Saphyr system for whole genome imaging will present their results at the American Society of Human Genetics (ASHG) Annual Meeting, between October 15-19 in Austin, Texas.

The impact of analysis using the Saphyr system for ultra-sensitive and ultra-specific genome-wide detection of structural variation will be presented at ASHG with 22 oral and poster presentations and an Educational Event hosted by Bionano.

ASHG 2019 represents a milestone for Bionano, with a record number of presentations demonstrating novel discoveries through our genome mapping technology, said Erik Holmlin, Ph.D., CEO of Bionano. The growing use of the Saphyr system in disease research illustrates the value in identifying genomic variations for deep understanding of disease origin and diagnostic development.

Optical mapping through Saphyr enables the direct observation of large genomic variations through imaging of fluorescently labeled, megabase-size native DNA molecules. Next-generation sequencing (NGS), in contrast, relies on short-reads that piece together sequence fragments in an attempt to rebuild the actual structure of the genome. NGS often misses large DNA variations, such as deletions, insertions, duplications, and translocations and inversions. Genome mapping resolves these structural variations for more insight into the genetic variations that cause disease.

Below is a summary of key presentations to be given at ASHG 2019 featuring the use of optical genome mapping:

Genetic diagnosis of sex development disorders through optical mappingHalf of disorders of sex development (DSD) patients lack a firm diagnosis. Prof. Eric Vilain, from George Washington University and Childrens National Medical Center, will present research validating the diagnostic and gene discovery use of Bionano genome mapping to identify structural variants in patients with DSD. The talk, entitled Integration of optical genome mapping and sequencing technologies for identification of structural variants in DSD, will be presented on Wed. Oct. 16 at 5:15 - 5:30 pm in the convention center Level 3, Room 361D.

Genomic mapping has the potential to replace a combination of current cytogenetic techniquesCurrently, a comprehensive clinical analysis of genomic aberrations requires a combination of various assays such as CNV-microarrays, karyotyping and fluorescence in situ hybridization (FISH). Dr. Tuomo Mantere, from Radboud University Medical Center, will present data directly comparing traditional cytogenetic assays with Bionano mapping in leukemia patient samples to illustrate that genome mapping can identify all aberrations found by the three conventional technologies combined, and additional variants as well. The poster, entitled Next-generation cytogenetics: High-resolution optical mapping to replace FISH, karyotyping and CNV-microarrays will be presented on Thurs. Oct. 17, between 2 - 3pm, PgmNr 2533/T.

Genomic architecture reveals critical factors that may contribute to schizophrenia-associated 3q29 chromosomal deletionDeletions at the 3q29 chromosomal locus are associated with a 40-fold increase in risk for schizophrenia. Knowing the features that contribute to genomic instability is critical for identifying risk factors of chromosomal deletions. Trenel Mosley, from Emory University, will present the discovery of novel genomic structural characteristics found in 12 patients with 3q29 deletion and their parents using Saphyr. The poster entitled, Optical mapping of the schizophrenia-associated 3q29 deletion reveals new features of genomic architecture, will be presented on Wed. Oct. 16, between 2 - 3pm, PgmNr 1389/W.

Bionano and NGS resolve complex rearrangements in extrachromosomal, circular DNA in glioblastoma The rapid growth of aggressive tumors such as glioblastoma is partially caused by the rapid amplification of oncogenes in circular structures outside of native chromosomes. Because these structures do not occur in the reference genome, standard analysis methods fail to correctly assemble them. Jens Luebeck, from the University of California, San Diego, demonstrates that a combination of Bionano genome mapping and NGS resolves important breakpoints and gene amplifications in extrachromosomal DNA. The talk, entitled Integrated Analysis of NGS and Optical Mapping Resolves the Complex Structure of Highly Rearranged Focal Amplifications in Cancer, will be presented on Sat. Oct. 19, from 10:15 - 10:30am PgmNr: 323

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Bionano Educational Event will feature research on muscular dystrophy, prenatal development & neurodegenerative disordersAt Bionanos educational event, Dr. Alka Chaubey from Perkin Elmer Genomics, Dr. Frances High from Mass General Hospital for Children, and Dr. Mark Ebbert from the Mayo Clinic will present findings from their work using the Saphyr system for structural genomic resolution. Analysis of chromosomal repeats, complex genomic haplotypes, and risk loci found in genetic disease will be highlighted by the speakers. Entitled Resolving Structural Variants Across the Whole Genome to Power Your Next Discovery in Human Genetics, the event will take place on Thurs. Oct 17, from 12:45 - 2:00pm at the Marriott Marquis, Houston, River Oaks, Level 3, and include a complimentary lunch.

Additional presentations featuring optical genome mapping:

High Throughput Analysis of Tandem Repeat Contraction Associated with Facioscapulohumeral Muscular Dystrophy (FSHD) by Optical MappingPresented by Jian Wang, Bionano GenomicsWed. Oct. 16, 2 - 3pm PgmNr: 2535/W

Full Genome Analysis for Identification of Single Nucleotide and Structural Variants in Genes that Cause Developmental DelayPresented by Hsiao-Jung Kao, Academia SINICAWed. Oct. 16, 2 - 3pm PgmNr: 2547/W

A Robust Benchmark for Germline Structural Variant DetectionPresented by Justin Zook, National Institute of Standards and TechnologyWed. Oct. 16, 2 - 3pm PgmNr: 1695/W

De Novo Genome Assembly and Phasing for Undiagnosed ConditionsPresented by Joseph Shieh, University of California, San FranciscoWed. Oct. 16, 2 -3 pm PgmNr: 2529/W

Bionano Prep SP Isolates High Quality Ultra-high Molecular Weight (UHMW) Genomic DNA to Improve Research of Cancer and Undiagnosed DisordersPresented by Henry Sadowski, Bionano GenomicsWed. Oct. 16, 3 - 4pm PgmNr: 2598/W

nanotatoR: An Annotation Tool for Genomic Structural VariantsPresented by Surajit Bhattacharya, Childrens National Medical CenterWed. Oct. 16, 3 - 4pm PgmNr: 1506/W

Detection, Characterization, and Breakpoint Refinement of Balanced Rearrangements by Optical Mapping in Clinical CasesPresented by Alex Hastie, Bionano Genomics + LabCorpThurs. Oct. 17, 2 - 3pm PgmNr: 2569/T

Genetic/epigenetic Diagnosis of Facioscapulohumeral Muscular Dystrophy (FSHD) via Optical MappingPresented by Yi-Wen Chen, Childrens National Medical CenterThurs. Oct. 17, 2 - 3pm PgmNr: 2533/T

Comprehensive Analysis of Structural Variants in Clinical Cancer SamplesPresented by Ernest Lam, Bionano GenomicsThurs. Oct. 17, 3 - 4pm PgmNr: 1060/T

Advanced Structural Analysis of CDH Risk Loci with Optical Genome Mapping TechnologyPresented by Mauro Longoni, Massachusetts General HospitalThurs. Oct. 17, 3 - 4pm PgmNr: 2578/T

Structural Variants Associated with GWAS SNPs Provide Mechanistic Explanation of Phenotypic AssociationsPresented by Seth Berger, Childrens National Medical CenterThurs. Oct. 17, 3 - 4pm PgmNr: 2254/T

The Complete Linear Assembly and Methylation Map of Human Chromosome 8Presented by Glennis Logsdon, University of WashingtonFri. Oct. 18, 1 - 2pm PgmNr: 1703/F

High Throughput High Molecular Weight DNA Extraction from Human Tissues for Long-read SequencingPresented by Kelvin Liu, CirculomicsFri. Oct. 18, 1 - 2pm PgmNr: 1769/F

Optical Mapping for Chromosomal Abnormalities: A Pilot Feasibility Study for Clinical UsePresented by Gokce Toruner, UT MD Anderson Cancer CenterFri. Oct. 18, 1 - 2pm PgmNr: 2447/F

Comprehensive Detection of Germline and Somatic Structural Mutation in Cancer Genomes by Bionano Genomics Optical MappingPresented by Mark Ebbert, Mayo ClinicFri. Oct. 18, 2 - 3pm PgmNr: 1760/F

Dark and Camouflaged Genes May Harbor Disease-relevant Variants that Long-read Sequencing Can ResolvePresented by Andy Pang, Bionano GenomicsFri. Oct. 18, 2 - 3pm PgmNr: 1814/F

Bionano Genomics Sample to Answer Workflow for Single Molecule Analysis of Variation in Genome StructurePresented by Sven Bocklandt, Bionano GenomicsFri. Oct. 18, 2 - 3pm PgmNr: 1838/F

Draft Assembly of an Armenian GenomePresented by Hayk Barseghyan, Childrens National Medical CenterFri. Oct. 18, 2 - 3pm PgmNr: 2342/F

About Bionano GenomicsBionano is a life sciences instrumentation company in the genome analysis space. Bionano develops and markets the Saphyr system, a platform for ultra-sensitive and ultra-specific structural variation detection that enables researchers and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline digital cytogenetics, which is designed to be a more systematic, streamlined and industrialized form of traditional cytogenetics. The Saphyr system comprises an instrument, chip consumables, reagents and a suite of data analysis tools. For more information, visit http://www.bionanogenomics.com.

Forward-Looking StatementsThis press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, including among other things: the timing and content of the presentations identified in this press release; and the ability of genome mapping to perform comprehensive clinical analysis as well as conventional technologies. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks that our sales, revenue, expense and other financial guidance may not be as expected, as well as risks and uncertainties associated with general market conditions; changes in the competitive landscape and the introduction of competitive products; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the ability of key clinical studies to demonstrate the effectiveness of our products; the loss of key members of management and our commercial team; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2018 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on management's assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

ContactsCompany Contact:Mike Ward, CFOBionano Genomics, Inc.+1 (858) 888-7600mward@bionanogenomics.com

Investor Relations Contact:Ashley R. RobinsonLifeSci Advisors, LLC+1 (617) 775-5956arr@lifesciadvisors.com

Media Contact:Kirsten ThomasThe Ruth Group+1 (508) 280-6592kthomas@theruthgroup.com

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Top Researchers to Present Discoveries Made Possible by Bionanos Saphyr System for Genome Imaging Technology at the ASHG 2019 Annual Meeting - Yahoo...

My 65-pound black mutt is feeling playful. She rams her headinto the couch cushions and launches her butt into the air, snuffling andgrowling excitedly. She achieves a partial headstand and her hind legs kickwildly. She is the embodiment of joy, and that joy is infectious.

Dogs have been jubilantly kicking their legs in the air forat least 14,000 years, and during that time they became our devoted companions.Two new books offer different takes on this interspecies bond. The first makesa compelling case that dogs do far more than just obey us they love us. Theother book offers a broader look at all the complexities and contradictions ofthe human-dog relationship.

Clive Wynne, a canine behaviorist and founding director of the Canine Science Collaboratory at Arizona State University in Tempe, has always loved dogs, but it took him many years to become convinced that the feeling is reciprocated. In Dog Is Love, readers accompany Wynne on his scientific journey from skeptic to believer. Not only do dogs love us, he argues, but it is their capacity and desire to connect with humans that makes dogs unique.

Many scientists are loath to talk about the emotional lives of animals, love in particular (SN: 3/2/19, p. 28). The concept seems too soppy and imprecise, Wynne writes, and we risk anthropomorphizing dogs. But acknowledging their capacity for love is the only way to make sense of why dogs are so devoted to us and thrive in our company, he argues. Dog Is Love takes readers all the way from theories about how dogs became domesticated to recent behavioral, biological and genetics research that provides convincing evidence that our canine companions feel affection. Dogs genetic makeup predisposes them to be loving (SN: 8/19/17, p. 8), Wynne argues, and early exposure to humans (or even other animals) solidifies the connection.

Our Dogs, Ourselvesoffers a more comprehensive exploration of the human-dog relationship. AlexandraHorowitz, head of Barnard Colleges Dog Cognition Lab in New York City andauthor of the 2009 New York Timesbestseller Inside of a Dog, gives an overviewof the culture of dogdom the way people acquire, name, train, raise, treat,talk to and see dogs. She explores the lighter side of this culture, includingour fixation with dog accessories everything from dog bathrobes and caninebody sprays to fake testicles.

But Horowitz also tackles the darker side and poses somethought-provoking ethical questions: Should we view dogs as property? Is spayingand neutering dogs the right way to deal with overpopulation? Should dogs beused in research?

Both books address a particularly thorny problem: dog breeds. Initially, dogs were bred for specific purposes hunting or providing comfort, for example. But in the late 1800s, the emphasis became purity, Horowitz writes. Today, purebred dogs are descended from a relatively small pool of founders and inbreeding is rampant. A purebreds family tree might reveal that his father is also his grandfather and his mothers uncle to boot, Wynne writes. Because the gene pool for each breed is closed, genetic defects crop up. Dalmatians are predisposed to deafness and a heritable urinary tract disorder. German shepherds are prone to hip problems.

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Some of the defining physical characteristics of certainbreeds can also present serious health challenges. Bulldogs have such enormousheads that puppies must typically be delivered via cesarean section. Pugs andother flat-faced dogs often have trouble breathing. Breed standards, whichdescribe how a breed should look, glorify disease and deformity, Horowitzwrites. The puzzling thing isnt that these animals are diseased, she adds,its that it is we who made themsick.

Horowitz and Wynne agree that we can do better for dogs. Thatmight mean changing the laws that govern dog ownership and how we treat dogs, rethinkingour devotion to purebreds and finding better ways to control overpopulation anddeal with strays. Wynne argues that no-kill shelters often become little morethan canine warehouses, housing dogs that have no hope of being adopted. He proposes some modest changes that mighthelp improve the lives of shelter dogs and adoption rates.

We also must help our dogs lead richer, more satisfyinglives. Dogs are suited to be companions, but many spend the majority of theirlives alone, awaiting the return of their humans. The cruelest thing you cando to a highly social being is shut him up all day where he cannot interactwith anyone, Wynne writes. Yet that has become the norm in many countries.

If you want a deep dive into the research that suggests dogs are capable of love, how this capability came to be and what dog owners can do to foster it, grab Dog Is Love. For a wide-ranging exploration of the human-dog relationship, including its perils and pitfalls, pick up Our Dogs, Ourselves. Both books will make you see canine companions in new ways. And both are best enjoyed with a dogs head in your lap.

BuyDog Is Love orOur Dogs, Ourselvesfrom Amazon.com. Science Newsis a participant in the Amazon Services LLC Associates Program. Please see ourFAQfor more details.

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New books explore why dogs and humans have such a special bond - Science News

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Few areas of science have seen such a dramatic development in the last decade as genomics. It is now possible to read the genomes of millions of people in so-called genome-wide association studies. These studies have identified thousands of small differences in our genome that are linked to diseases, such as cancer, heart disease and mental health.

Most of these genetic studies use data from white people over 78% of participants are of European descent. This doesnt mean that they represent Europe. In fact, only three nationalities make up most of the participants: the US, UK, and Iceland. Even though the UK and the US have very diverse populations, their non-white citizens have rarely been included in genetic research.

In recent years, efforts to collect multi-ethnic data have increased. One example is the UK Biobank, a collection of data from half a million British people accessible to any bona fide researcher. It includes some 35,000 DNA samples from people who are either non-European or mixed-race. Yet 92% of research papers on UK Biobank only used the data from the European-descent samples. So collecting data doesnt automatically solve the problem of non-white representation in research.

The under-representation of non-European groups is problematic for scientific and ethical reasons. The effects of gene variants that are present only in the unstudied groups remain unknown, which means important clues about the causes of diseases might be missed. Such undiscovered genes would not be included when testing for genetic diseases. So a person carrying one of them could wrongly get a negative genetic test result and might be told that they are not at increased risk of developing the disease.

Our recent work also shows that existing genetic findings might not apply equally to non-European populations. We found that some gene variants predicting high cholesterol in white populations do not lead to the same heart problems in people from rural Uganda. These findings should serve as a major warning to the field of genetics one cannot blindly apply findings from ancestrally European groups to everyone else.

Also read: In a single week, 3 giant strides made towards detecting and curing cancer

It is important to support the global application of research because scientists have a moral responsibility to develop science for the benefit of the whole of humanity, not restricted by ethnic, cultural, economic or educational boundaries. Some 80% of the worlds population live in low and middle-income countries where healthcare and research are constrained by limited financial and human resources. We should not overlook this part of the world.

Studying different populations has advanced the medical field for everyones benefit. For example, the first disease gene mapped in humans was the gene for Huntingtons disease in 1983, identified through examining a large population of patients in villages surrounding Lake Maracaibo in Venezuela. The area was found to have the largest concentration of Huntingtons disease sufferers in the world, which helped them to find the gene.

More recently, a study of schizophrenia found new risk genes by using African and Latino American samples. Genetic risk scores based on results from these groups improved the ability to predict who would develop schizophrenia in all ethnic groups.

Two things need to happen if we want to avoid increasing health disparities and instead share the medical benefits of genomic science across countries and ethnic groups. First, we need more large diverse studies. First steps in this direction are being taken by the Human Hereditary and Health in Africa Initiative. PAGE and All of Us are paving the way to recruit more diverse ethnic groups in the US, and East London Genes and Health focuses on people of South Asian origin in London.

And second, to make sure diverse ethnic data resources are widely used by researchers, the challenges of analysing genetic data from ancestrally diverse samples need to be addressed. While there are statistical solutions, more work is needed to make them easy to use and give clear guidance about the best approach.

Understanding how genetic risk and social inequality interact to influence disparities in disease risk and outcomes will be critical to improving public health for all.

Also read:What makes nanoscience so crucial and how it can impact our lives

Karoline Kuchenbaecker, Associate Professor, Psychiatry, UCL; Evangelos Vassos, Senior Clinical Research Fellow, Psychiatry, Kings College London, and Roseann Peterson, Assistant Professor, Statistical Geneticist, Virginia Commonwealth University

This article is republished from The Conversation under a Creative Commons license.

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Most genetic studies use only white participants and that affects public health - ThePrint

We often think of culture as solely human. We think of our music, our clothes, our food, our languages. However, culture stretches far beyond Homo sapiens. As evidence of the existence of culture in other animal groups emerges (from insects, rats, fish to land mammals, primates and dolphins), humans need to rethink what it means to have culture. We must accept that what we have long considered our own might be shared.

This is especially important because culture can have important implications for conservation. Understanding an animals culture might be the only way to save them.

As a PhD candidate studying culture in a non-human species, the sperm whale, I have had the chance to witness its implications. The more time I spend with whales and learning from them, the more I am convinced that acknowledging their culture is necessary to understand and protect them.

While most people have a general idea of what culture is, defining it can prove difficult. Culture is pervasive and, at the same time, it can express itself in such small, almost non-perceptible ways. Biology defines culture as shared information (or behaviour) that you acquire socially from your peers.

The importance of culture has long been recognized in humans. It is how we successfully inhabited all the biomes of our planet. Culture dictates our social interactions; the spontaneity of fashion and music; the laws that govern our societies and civilizations; the causes of our wars; the reason why, right now, you are reading this article instead of foraging in the forest.

Culture shapes every aspect of our lives and has allowed us to become the dominant species we are today. However, although humans might be the most cultural species, they are not the only cultural species.

Instead, culture expressed in small and big ways is found throughout the animal kingdom: chimpanzees in West Africa use tools to crack nuts, capuchin monkeys have group-specific social rituals, dolphins cooperate with fishermen to obtain food, songbirds and humpback whales have ever-changing songs, bighorn sheep follow cultural migratory routes, reef fishes have preferred mating sites, bumblebees learn from each other to solve complex puzzles.

And this is only the very tip of the iceberg. Every year, more evidence emerges on to the presence of culture in animals.

Beyond primates, the animal group for which we have the most evidence of culture are the cetaceans (whales and dolphins). Among them, the sperm whale has received particular attention.

Like us, sperm whales have families, they have strong affiliations with a few individuals and they are extremely social. Such a social environment is the perfect substrate for culture.

Sperm whales are matrilineal, which means that females stay with their mothers, forming groups called social units. These social units are comprised of one or two families and are stable over their entire lives. They travel together, socialize together, forage together and learn from each other. Beyond social units, sperm whale societies are also organized at a higher tier called vocal clans. Vocal clans include thousands of individuals and can be recognized acoustically.

Whales from different vocal clans sound incredibly different!

The most exciting part, however, is that individuals from different vocal clans not only have extremely different repertoires but also do not associate with each other, even if they live in the same environment. For example, in the Eastern Caribbean where I study sperm whales, we know about two vocal clans: EC1 and EC2. These two vocal clans have been identified in the same area (around the island of Dominica) but have never been seen interacting with each other: not even once in the 15 years the Dominica Sperm Whale Project has been studying the population.

In contrast, social units that belong to the same vocal clans are regularly observed foraging and socializing together.

Why is that? They live in the same environment, so surely, these differences are not the result of geographic adaptations. Could it be genetics? The evidence says otherwise: genetics cant explain the variation in vocal repertoire. The only remaining explanation is culture. Perhaps whales actively choose to avoid whales from different vocal clans. They learn a specific vocal repertoire from their mothers and then only associate with individuals that share that same repertoire.

EC1 vocal clan audio clip.

EC2 vocal clan audio clip.

These short audio clips are from the two vocal clans present in the Caribbean: EC1 and EC2. While EC1 whales often make clicks in the pattern click-click-click-click-click, EC2 whales often make clicks in the pattern click-click-click-click-click. These patterns have the same number of clicks, but different tempos.

Culture has important implications for conservation. If a population is subdivided into cultural groups, then conservation efforts targeting only one group will lead to a loss of diversity.

If cultural knowledge is mostly obtained from older matriarchs, then protecting these individuals at all costs should be our priority. If species are able to learn socially, they might respond differently to anthropogenic stressors. And yet, we seldom hear about it.

Acknowledging the presence of culture in other species would go against our anthropocentric view of the world: a world where humans are at the end of the evolutionary tree, smarter, more advanced and more important than other species.

It would blur the line between us and them. Once this occurs, how could we justify putting these cultural beings in cages, treating them as legal property and destroying their habitats? Perhaps it is time to re-think culture and acknowledge that other species might share what we long considered our own.

[ Youre smart and curious about the world. So are The Conversations authors and editors. You can read us daily by subscribing to our newsletter. ]

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We need to understand the culture of whales so we can save them - The Conversation CA

Male and female mouse brains could have significant differences that reach right down to the cellular level, according to a new discovery.

Based on a reading of their genetic activity, neurons in a part of the mouse nervous system responsible for aggression and mating behaviours appear to be chemically structured in subtle but distinctly different ways between the two sexes.

These findings haven't been tested in other mammal species as yet, so we can't read too much into them. But it's a fascinating study that warrants further investigation in the brains of other animals.

Researchers from the California Institute of Technology and the Allen Institute for Brain Science in Seattle looked at a region of the brain called the ventrolateral subdivision of the ventromedial hypothalamus (VMHvl) in both male and female mice.

The VMHvl is tiny, made up of a mere 4,000 cells in mice, but still has quite a schedule on its hands, playing an important role in metabolism and complex sexual and social behaviours.

To identify cell types in the region, the researchers usedsingle cell RNA reading technology, which identifies genes that have been actively translated into RNA.

This is important, because while a species' full genome is kept in the nucleus of each cell, only a limited number of these genes will actually be expressed into proteins that meet the needs of the specific cell type. For example, a blood cell has different needs and therefore will activate different genes than a skin cell.

This technology provided the scientists with a snapshot of the 'books' being read in each cell's genetic library, giving them a clear idea of how each cell's individual physical make-up and activity differs.

Cells are considered to be of a certain type if clusters of genes in close proximity are expressed together to carry out a task.

In total the team identified 17 distinct types of brain cells in this tiny bit of brain tissue, which they then verified using glowing genetic tags in a process called fluoro in-situ hybridisation.

While that might sound like a lot of brain cell types, uncovering such a level of diversity shouldn't be all that surprising. Similar research has already identified scores of cell types across the entire hypothalamus.

What hadn't been seen before in mammals, at least were clear differences in neuron types between the male and female brains they analysed.

Some of these cell types were found in vastly greater numbers among mice of one gender or the other. One in particular was already known to make an enzyme that was present only in male mouse brains.

But another newly identified cell type was specific to female mice, not being found at all in male mice.

Importantly, these differences weren't a direct result of contrasting sex chromosomes, with the distinct brain cell types traced back to patterns of genes on parts of the genome both sexes possess.

Having genes that are generally active in one sex but not the other is hardly shocking. The small but significant leap in this case is finding clusters of activity large enough in brain cells to make them physically different types.

One thing that did come as a surprise was that only a few of these specific variations seemed to match specific behaviours, posing questions on just what it is many of these gender-biased cell types do.

"The results show that there are differences between male and female mammalian brains at the level of cellular composition as well as gene expression but that those differences are subtle, and their functional significance remains to be explained," says California Institute of Technology biologist, David Anderson.

It's a conclusion that's sure to polarise opinions on what is already a controversial topic. Research on the culture and biology of human gender is a divisive topic marked by a history of stereotypes and misinformation

On top of that, it's difficult to know how studies on lab animals might apply to humans. We're unlikely to be unique, but it's an assumption that would require further research to support.

Treading cautiously, studies like this one can't be dismissed out of hand either.

Like mice, there's a good chance our own brains not only promote different behaviours depending on whether we have a Y chromosome, but have fundamentally different cell types that just might be responsible for sex-specific functions.

That doesn't mean men are from Mars and women are from Venus. Genetics is complicated, and while we can generalise based on patterns, it doesn't dismiss the significance of individual variations or cultural influences.

Technology that can provide a detailed library list of genes being actively read in individual cells is changing what we know about everything from mental health to evolution to our own developing bodies.

We're almost certain to be surprised by just how diverse human biology can be.

This research was published in Cell.

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Gender-Specific Brain Cells Have Just Been Discovered Inside The Brains of Mice - ScienceAlert

Stem cell therapy for animals has seen breakthroughs

Stem cell therapy is increasingly becoming a more mainstream form of medicine. Usually applied to humans, the use of this regenerative treatment is now also being extended to animals including cats and dogs. Regenerative medicine, particularly stem cell treatment has seen many advancements in recent years with some groundbreaking studies coming to light.

Taking the cells from bone marrow, umbilical cords, blood or fat, stem cells can grow to become any kind of cell and the treatment has seen many successes in animals. The regenerative therapy has been useful particularly for treatment of spinal cord and bone injuries as well as problems with tendons, ligaments and joints.

Expanded Potential Stem Cells (EPSCs) have been obtained from pig embryos for the first time. The cells offer groundbreaking potential for studying embryonic development and producing transnational research in genomics and regenerative medicine, biotechnology and agriculture.

The cells have been efficiently derived from pig preimplantation embryos and a new culture medium developed in Hong Kong and Cambridge enabled researchers from the FLI to establish permanent embryonic stem cell lines. The cells have been discovered in a collaboration between research groups from the Institute of Farm Animal Genetics at the Friedrich-Loeffler-Institut (FLI) in Mariensee, Germany, the Wellcome Trust Sanger Institute in Cambridge, UK and the University of Hong Kong, Li Ka Shing Faculty of Medicine, School of Biomedical Sciences.

Embryonic stem cells (ESC) are derived from the inner cells of very early embryos, the so-called blastocysts. Embryonic stem cells are all-rounders and can develop into various cell types of the body in the culture dish. This characteristic is called pluripotency. Previous attempts to establish pluripotent embryonic stem cell lines from farm animals such as pigs or cattle have resulted in cell lines that have not really fulfilled all properties of pluripotency and were therefore called ES-like.

Dr Monika Nowak-Imialek of the FLI said: Our porcine EPSCs isolated from pig embryos are the first well-characterized cell lines worldwide. EPSCs great potential to develop into any type of cell provides important implications for developmental biology, regenerative medicine, organ transplantation, disease modelling and screening for drugs.

The stem cells can renew themselves meaning they can be kept in culture indefinitely, and also show the typical morphology and gene expression patterns of embryonic stem cells. Somatic cells have a limited lifespan, so these new stem cells are much better suited for long selection processes. It has been shown that these porcine stem cell lines can easily be modified with new genome editing techniques such as CRISPR/Cas, which is particularly interesting for the generation of porcine disease models.

The EPSCs have a high capacity to develop not only into numerous cell types of the organism, but also into extraembryonic tissue, the trophoblasts, making them very unique and lending them their name. This capacity could prove valuable for the future promising organoid technology, where organ-like small cell aggregations are grown in 3D aggregates that can be used for research into early embryo development, various disease models and testing of new drugs in petri dishes. In addition, the authors were able to show that trophoblast stem cells can be generated from their porcine stem cells, offering a unique possibility to investigate functions or diseases of the placenta in vitro.

A major hurdle to using neural stem cells derived from genetically different donors to replace damaged or destroyed tissues, such as in a spinal cord injury, has been the persistent rejection of the introduced material (cells), necessitating the use of complex drugs and techniques to suppress the hosts immune response.

Earlier this year, an international team led by scientists at University of California San Diego School of Medicine successfully grafted induced pluripotent stem cell (iPSC)-derived neural precursor cells back into the spinal cords of genetically identical adult pigs with no immunosuppression efforts. The grafted cells survived long-term, displayed differentiated functionality and caused no tumours.

The researchers also demonstrated that the same cells showed similar long-term survival in adult pigs with different genetic backgrounds after only short course use of immunosuppressive treatment once injected into injured spinal cord.

Senior author of the paper Martin Marsala, MD, professor in the Department of Anesthesiology at UC San Diego School of Medicine said: The promise of iPSCs is huge, but so too have been the challenges. In this study, weve demonstrated an alternate approach.

We took skin cells from an adult pig, an animal species with strong similarities to humans in spinal cord and central nervous system anatomy and function, reprogrammed them back to stem cells, then induced them to become neural precursor cells (NPCs), destined to become nerve cells. Because they are syngeneic genetically identical with the cell-graft recipient pig they are immunologically compatible. They grow and differentiate with no immunosuppression required.

Co-author Samuel Pfaff, PhD, professor and Howard Hughes Medical Institute Investigator at Salk Institute for Biological Studies, said: Using RNA sequencing and innovative bioinformatic methods to deconvolute the RNAs species-of-origin, the research team demonstrated that pig iPSC-derived neural precursors safely acquire the genetic characteristics of mature CNS tissue even after transplantation into rat brains.

NPCs were grafted into the spinal cords of syngeneic non-injured pigs with no immunosuppression finding that the cells survived and differentiated into neurons and supporting glial cells at all observed time points. The grafted neurons were detected functioning seven months after transplantation.

Then researchers grafted NPCs into genetically dissimilar pigs with chronic spinal cord injuries, followed by a transient four-week regimen of immunosuppression drugs again finding long-term cell survival and maturation.

Marsala continued: Our current experiments are focusing on generation and testing of clinical grade human iPSCs, which is the ultimate source of cells to be used in future clinical trials for treatment of spinal cord and central nervous system injuries in a syngeneic or allogeneic setting.

Because long-term post-grafting periods between one and two years are required to achieve a full grafted cells-induced treatment effect, the elimination of immunosuppressive treatment will substantially increase our chances in achieving more robust functional improvement in spinal trauma patients receiving iPSC-derived NPCs.

In our current clinical cell-replacement trials, immunosuppression is required to achieve the survival of allogeneic cell grafts. The elimination of immunosuppression requirement by using syngeneic cell grafts would represent a major step forward said co-author Joseph Ciacci, MD, a neurosurgeon at UC San Diego Health and professor of surgery at UC San Diego School of Medicine.

Other recent advancements include the advancement toward having a long-lasting repair caulk for blood vessels. A new method has been for generating endothelial cells, which make up the lining of blood vessels, from human induced pluripotent stem cells. When endothelial cells are surrounded by a supportive gel and implanted into mice with damaged blood vessels, they become part of the animals blood vessels, surviving for more than 10 months.

The research was carried out by stem cell researchers at Emory University School of Medicine and could form the basis of a treatment for peripheral artery disease, derived from a patients own cells.

Young-sup Yoon, MD, PhD, who led the team, said: We tried several different gels before finding the best one. This is the part that is my dream come true: the endothelial cells are really contributing to endogenous vessels.

When cells are implanted on their own, many of them die quickly, and the main therapeutic benefits are from growth factors they secrete. When these endothelial cells are delivered in a gel, they are protected. It takes several weeks for most of them to migrate to vessels and incorporate into them.

Other groups had done this type of thing before, but the main point is that all of the culture components we used would be compatible with clinical applications.

This research is particularly successful as previous attempts to achieve the same effect elsewhere had implanted cells lasting only a few days to weeks, using mostly adult stem cells, such as mesenchymal stem cells or endothelial progenitor cells. The scientists also designed a gel to mimic the supportive effects of the extracellular matrix. When encapsulated by the gel, cells could survive oxidative stress inflicted by hydrogen peroxide that killed unprotected cells. The gel is biodegradable, disappearing over the course of several weeks.

The scientists tested the effects of the encapsulated cells by injecting them into mice with hindlimb ischemia (restricted blood flow in the leg), a model of peripheral artery disease.

After 4 weeks, the density of blood vessels was highest in mice implanted with gel-encapsulated endothelial cells. The mice were nude, meaning genetically immunodeficient, facilitating acceptance of human cells.

The scientists found that implanted cells produce pro-angiogenic and vasculogenic growth factors. In addition, protection by the gel augmented and prolonged the cells ability to contribute directly to blood vessels. To visualise the implanted cells, they were labelled beforehand with a red dye, while functioning blood vessels were labelled by infusing a green dye into living animals. Implanted cells incorporated into vessels, with the highest degree of incorporation occurring at 10 months.

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Stem cell therapy is for animals too - SciTech Europa

The aim of the new exhibition is to explore trust, identity and health in a changing world, according to the Turner-winning architectural collective Assemble, who have designed and curated the space.The exhibition, in the building designed to promote the best in medicine and science, presents over fifty artworks and medical related items, divided into four thematic groups; Genetics, Minds and Bodies, Infection and Environmental Breakdown.

Transparent woman, by an unknown artist, at the Wellcome Collection in London - the aim is to present the human body in a different way.

A traveler in an unknown world, the Refugee astronaut seems both under- and over-prepared for his trip.

Jukebox that plays songs about disease at the Wellcome Collection, by Kin Design.

Heather Dewey-Hagborgs three-dimensional printed portrait - Sequencing the DNA from chucked cigarette butts and spat-out lumps of gum that she found on the street, she has picked out the genetic markers that influence physical appearance and created a portrait.

Example of a prosthetic leg, from the Wellcome Collection, London.

The PPE Portrait Project is an art intervention designed to improve Ebola care.

Batoul S'Himi's work takes major global issues and situates them in a global setting.

A CRISPR kit - CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. Its many potential applications include correcting genetic defects, treating and preventing the spread of diseases and improving crops.

The London Freedom Seed Bank is a network of food growers and gardeners dedicated to saving, storing and distributing open-pollinated seed.

Commissioned for the Wellcome Collections new exhibition, Being Human, 5318008, a sculpture designed to symbolize breast milk.

A transparent orange symbol of a person in a chair to express personhood, leaning forward with a double wheel to suggest movement.

Latai Taumoepeau - Artist portrait / collage.

Link:
Review: What does it mean to be human? New London exhibit reveals all (Includes first-hand account) - Digital Journal