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Unlocking herbaria biodiversity using a QR code sampling-to-sequencing workflow

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Within the past decade, next-generation sequencing technologies have revolutionized the way in which genetic data are generated and analyzed. In the field of phylogenetics, this has meant that researchers are rapidly reconstructing the tree of life, a goal that biologists have been working toward since Darwin sketched the first phylogeny in his notebook in 1837.

Yet despite the relative ease with which DNA can now be sequenced in large quantities, scientists must first extract that DNA from an organism, often relying on vast numbers of curated specimens in museums and herbaria. With over 250,000 species in the plant kingdom alone, the acquisition and documentation of specimen material is now by far the most time-consuming and error-prone process in large studies.

In a research article published in a recent issue of Applications in Plant Sciences, researchers undertook the goal of automating the collecting process by using a combination of unique object identifiers, QR codes, and citizen science.

“Our goal was to create a resource for the scientific community,” said lead author Ryan Folk, an assistant professor and herbarium curator at Mississippi State University. “In the future, we hope that all such collection information will be available online, where it’s easy to find and the work won’t need to be repeated.”

Folk and his colleagues are working to create a partial — 50 percent coverage — phylogeny of seed plants that harbor nitrogen-fixing bacteria in specialized root nodules. This symbiotic relationship spans several disparate seed plant groups that collectively contain more than 30,000 species, for which the team relied entirely on herbarium specimens.

For a project of this scale, that meant members of the team worked for weeks at a time at multiple herbaria, focusing their efforts primarily at the New York and Missouri Botanical Gardens and the California Academy of Sciences.

Ordinarily, this would involve sifting through specimen material and manually transcribing or copying voucher information (such as the specimen locality, date, and name of the collector(s)) into a spreadsheet, as well as manually copying labels onto the samples themselves.

This process is absolutely essential for downstream analyses, but it requires large amounts of time and creates the potential for error. The biggest drawback, however, is the information garnered at this stage is typically only useful to the researchers who collected it and cannot be easily shared between groups. If a different group of researchers wanted to extract DNA from the same specimens, they would have to re-collect all of the same data.

Folk and his colleagues, wanting to curtail this duplication of effort, devised a digitization workflow whereby voucher information would only need to be collected once.

“Our workflow is made up of essentially several strategies — more or less connected — that takes you straight from walking into a museum all the way through data analysis and publication,” said Folk.

At a glance, the process has three steps. First, a unique object identifier is assigned and physically attached to each herbarium voucher, and the specimen is photographed with the identifier clearly visible.

To transcribe the data from the roughly 15,000 specimens they used for the study, they used the citizen science platform Notes From Nature, which offers an online, interactive workspace where volunteers can join specific projects from home and communicate with researchers involved in the study.

By itself, this digitization of specimen information with unique object identifiers will be a valuable tool for researchers in the future and may ultimately complement the monumental effort being undertaken in museums around the world to digitize collections. But the researchers didn’t stop there.

In the third step, QR codes were assigned to each specimen to further streamline data collection. This meant that when extracting and amplifying DNA in the lab, the researchers no longer had to manually enter specimen data into spreadsheets. Instead, that information was auto-populated when they scanned a given QR code.

“Scanning QR codes was basically effortless and didn’t require any training or set up,” said study co-author Heather Kates, a post-doctoral associate at the University of Florida. “But more important than the time-saving aspect of this approach was the reduction of errors. The errors introduced through illegibility and typos are a pain when you’re doing a set of 20 extractions; you can imagine how important it is with 15,000 that those errors are avoided as much as possible.”

Rather than keeping all of this information in spreadsheets, which have limited utility for specialized queries or data analysis, the team also created their own database using Python scripts.

The detailed workflow and Python scripts have been made freely available online so that researchers can access and fine-tune them for personalized use in their own studies.

“Although we have seen large DNA datasets published in recent years, reuse of data from many projects has been minimal due to the difficulty of accessing data online,” said Folk. “In the long-term, we will release the data to the community in a form more easily amenable to future researchers. My hope is that our efforts will jump-start major projects focused on other organisms as well as establish a new baseline for biodiversity in the nitrogen-fixing clade of seed plants.”

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Citation: Folk, R. A., H. R. Kates, R. LaFrance, D. E. Soltis, P. S. Soltis, and R. P. Guralnick. 2021. High-throughput methods for efficiently building massive phylogenies from natural history collections. Applications in Plant Sciences 9(2): e11410. https://doi.org/10.1002/aps3.11410

Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal focusing on new tools, technologies, and protocols in all areas of the plant sciences. It is published by the Botanical Society of America, a nonprofit membership society with a mission to promote botany, the field of basic science dealing with the study and inquiry into the form, function, development, diversity, reproduction, evolution, and uses of plants and their interactions within the biosphere. APPS is available as part of the Wiley Online Library.

For further information, please contact the APPS staff at [email protected]

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Source: https://bioengineer.org/unlocking-herbaria-biodiversity-using-a-qr-code-sampling-to-sequencing-workflow/

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Alzheimer Europe calls for people with dementia and carers to be prioritized for vaccine

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Alzheimer Europe calls for prioritisation of people with dementia and carers in COVID-19 vaccination programs across Europe

Luxembourg, 7 May 2021 – In a new position statement, Alzheimer Europe has issued a call for prioritisation of people with dementia and their carers in national COVID-19 vaccination strategies, urging governments to recognise the disproportionate effect of the pandemic on these groups.

Alzheimer Europe has today issued a call for people with dementia and their carers to be given priority in the ongoing COVID-19 vaccination campaigns across Europe.

In its position statement, Alzheimer Europe notes that people with dementia have almost twice the risk for developing COVID-19 compared to their peers without dementia, with high rates of hospitalisation and a risk of mortality within six months of approximately 20% in certain populations. Those who become infected are also more prone to developing delirium, which can complicate the management of their current and future cognitive health.

Currently, countries vary significantly in their prioritisation of different groups for COVID-19 vaccination. The vast majority of European countries have prioritised frontline healthcare workers, long-term care facility residents and the oldest old in the first phases of vaccination, with a smaller number also prioritising social care personnel and professional carers. A small number of European countries, recognising dementia per se as a risk category for severe COVID-19, have prioritised people with dementia for COVID-19 vaccination. However, in the majority of countries, neither people with dementia, nor informal carers have been specifically identified as priority groups for the COVID-19 vaccination, despite their increased risk.

Alzheimer Europe notes the disproportionate impact of the pandemic already experienced by people with dementia and their carers, as a result of service cancellations, care home restrictions etc., and accordingly, makes the following three demands of European governments:

  • Include dementia as a risk category for severe COVID-19, prioritising people with dementia for the COVID-19 vaccine, independent of age, place of residence or other risk factors for severe COVID-19.
  • Prioritise informal carers for the COVID-19 vaccine, acknowledging their important contribution during the pandemic to the care, support and even survival of people with dementia, as well as the indirect protection vaccination can confer for the people for whom they care.
  • Ensure that reasonable accommodations are made and that support mechanisms are in place when organising and rolling out the vaccine to people with dementia, such as the possibility to be vaccinated at home and to have decision-making support, if required.

Commenting further, Alzheimer Europe’s Executive Director, Jean Georges, stated:

“People with dementia and their carers have often been overlooked and forgotten during this pandemic. Particularly during the early stages of the outbreak, public health measures designed to control the spread of the virus have had profound and often tragic consequences for people with dementia, their families and carers.

Governments must recognise that people with dementia, their families and carers have already been disproportionately affected by the pandemic and ensure that people with dementia and their carers will not be overlooked again in the development and implementation of vaccination strategies.

We urge governments across Europe to revise their approaches to vaccination campaigns and prioritise people with dementia and their carers, allowing a return to some semblance of normality for this vulnerable group.”

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To download the position paper and the briefing document visit:
http://bit.ly/AEPositionCOVIDVaccine

For further information, contact: Jean Georges, Executive Director, Alzheimer Europe, 14, rue Dicks, L-1417 Luxembourg, Tel.: +352-29 79 70, Fax: +352-29 79 72, [email protected], http://www.alzheimer-europe.org

Notes to editors:

To support people with dementia, carers and Alzheimer’s associations during the COVID-19 pandemic, the organisation has dedicated a special section of its website to useful resources and links: https://www.alzheimer-europe.org/Living-with-dementia/COVID-19

A detailed briefing document has been included alongside the position statement, providing further details and references demonstrating the disproportionate impact of the pandemic on people with dementia. This paper also explores the ethical, legal and human rights issues associated with public health interventions and the current vaccination campaigns. This is also available to download at: https://www.alzheimer-europe.org/Policy/Our-opinion-on/COVID-19-Vaccinations-and-People-with-Dementia

The position and briefing document received funding under an operating grant from the European Union’s Health Programme (2014-2020). The contents represent the views of the author only and is his/her sole responsibility; it cannot be considered to reflect the views of the European Commission and/or the Consumers, Health, Agriculture and Food Executive Agency or any other body of the European Union. The European Commission and the Agency do not accept any responsibility for use that may be made of the information it contains.

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Source: https://bioengineer.org/alzheimer-europe-calls-for-people-with-dementia-and-carers-to-be-prioritized-for-vaccine/

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Rare genetic disease caused by mutations in protein that controls RNA metabolism

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PITTSBURGH, May 7, 2021 – In a paper published today in Nature Communications, an international group of collaborators led by researchers at UPMC Children’s Hospital of Pittsburgh have identified a genetic cause of a rare neurological disorder marked by developmental delay and loss of coordination, or ataxia.

The disorder, scientists found, is caused by mutations in a protein called GEMIN5–one of the key building blocks of a protein complex that controls RNA metabolism in neurons. No mutations in GEMIN5 were previously linked to any genetic disease.

“It’s just like building a house,” said senior author Udai Pandey, Ph.D., associate professor of pediatrics, human genetics and neurology at the University of Pittsburgh School of Medicine. “You take out the most important brick at the base and the whole building falls apart.”

GEMIN5 is part of a protein complex that regulates a slew of important cellular processes, including development of specialized outgrowths from nerve cells called dendrites and axons. Interestingly, mutations in another key protein of the complex, named survival motor neuron protein, cause a different devastating disorder–spinal muscular atrophy.

To gather material for the study, Pittsburgh researchers contacted pediatricians, geneticists and neurologists from all over the globe, eventually collecting data from 30 patient families in 12 different countries.

Because isolating live neurons from people isn’t possible, researchers had to come up with another way of getting samples for future testing. They collected blood samples from pediatric patients who were referred to neurogenetic clinics with undiagnosed neurological symptoms. Blood samples were then processed to isolate cells that, with careful tinkering in the lab, were reprogrammed into neurons.

After comparing genetic material of reprogrammed neurons from sick children with that of unaffected relatives, scientists linked neurologic manifestations of the disease to 26 mutations in the GEMIN5 gene that cause damage to the structure of the protein.

“Children came into the clinic with non-specific symptoms, such as developmental delay and abnormal gait. Their doctors ran all the possible tests, including assessing a child’s metabolic function, to no avail–their conditions had no easy explanation,” said Deepa Rajan, M.D., assistant professor of pediatrics, Pitt School of Medicine, neurologist at UPMC Children’s Hospital and a co-first author of the study. “It was not until we did an extensive genome analysis that we found that these patients had mutations in the GEMIN5 gene.”

“Many genetic disorders seem individually rare, but collectively they are relatively common,” added Rajan, who also is director of the Neurogenetics Clinic at UPMC Children’s Hospital. “We now are able to harness next-generation technology to help diagnose previously undiagnosed children, and each new gene discovery is the start of the journey to understanding each of these diseases better.”

Additional experiments linked damage to GEMIN5 protein to disease manifestations more definitively. Scientists found that depleting an analog of human neuronal GEMIN5 protein in fruit flies was deadly if it happened in early stages of the fly’s life cycle, or drastically delayed its development if such disruption happened later.

“The most exciting part of being a researcher is working on a project that directly helps families,” said Pandey. “We are hopeful that because of our study, neurologists will now consider testing for GEMIN5 mutations and that labs will include GEMIN5 in their testing for ataxic disorders. Genetic diseases are challenging to identify and treat, but if we find a cure, it will make a massive difference in someone’s life.”

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Other authors on the manuscript include Sukhleen Kour, Ph.D., Tyler Fortuna, Ph.D., Eric Anderson, Ph.D., Dhivyaa Rajasundaram, Ph.D., and Caroline Ward, all of Pitt, among 70 total authors.

This work was supported by a University of Pittsburgh Children’s Neuroscience Institute research grant.

To read this release online or share it, visit https://www.upmc.com/media/news/050721-Pandey-GEMIN5 [when embargo lifts].

About UPMC Children’s Hospital of Pittsburgh

Regionally, nationally, and globally, UPMC Children’s Hospital of Pittsburgh is a leader in the treatment of childhood conditions and diseases, a pioneer in the development of new and improved therapies, and a top educator of the next generation of pediatricians and pediatric subspecialists. With generous community support, UPMC Children’s Hospital has fulfilled this mission since its founding in 1890. UPMC Children’s is recognized consistently for its clinical, research, educational, and advocacy-related accomplishments, including ranking in the top 10 on the 2020-2021 U.S. News & World Report Honor Roll of America’s Best Children’s Hospitals. UPMC Children’s also ranks 15th among children’s hospitals and schools of medicine in funding for pediatric research provided by the National Institutes of Health (FY2019).

About the University of Pittsburgh Schools of the Health Sciences

The University of Pittsburgh Schools of the Health Sciences include the schools of Medicine, Nursing, Dental Medicine, Pharmacy, Health and Rehabilitation Sciences and the Graduate School of Public Health. The schools serve as the academic partner to the UPMC (University of Pittsburgh Medical Center). Together, their combined mission is to train tomorrow’s health care specialists and biomedical scientists, engage in groundbreaking research that will advance understanding of the causes and treatments of disease and participate in the delivery of outstanding patient care. Since 1998, Pitt and its affiliated university faculty have ranked among the top 10 educational institutions in grant support from the National Institutes of Health. For additional information about the Schools of the Health Sciences, please visit http://www.health.pitt.edu.

http://www.upmc.com/media

Contact: Anastasia Gorelova

Mobile: 412-491-9411

E-mail: [email protected]

Contact: Andrea Kunicky

Mobile: 412-552-7448

E-mail: [email protected]

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Source: https://bioengineer.org/rare-genetic-disease-caused-by-mutations-in-protein-that-controls-rna-metabolism/

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Learning on the fly

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Computational model demonstrates similarity in how humans and insects learn about their surroundings

Even the humble fruit fly craves a dose of the happy hormone, according to a new study from the University of Sussex which shows how they may use dopamine to learn in a similar manner to humans.

Informatics experts at the University of Sussex have developed a new computational model that demonstrates a long sought after link between insect and mammalian learning, as detailed in a new paper published today in Nature Communications.

Incorporating anatomical and functional data from recent experiments, Dr James Bennett and colleagues modelled how the anatomy and physiology of the fruit fly’s brain can support learning according to the reward prediction error (RPE) hypothesis.

The computational model indicates how dopamine neurons in an area of a fruit fly’s brain, known as the mushroom body, can produce similar signals to dopamine neurons in mammals, and how these dopamine signals can reliably instruct learning.

The academics believe that establishing whether flies also use prediction errors to learn could lead to more humane animal research allowing researchers to replace animals with more simple insect species for future studies into the mechanisms of learning.

By opening up new opportunities to study neural mechanisms of learning, the researchers hope the model could also be helpful in illuminating greater understanding of mental health issues such as depression or addiction which are underpinned by the RPE hypothesis.

Dr Bennett, research fellow in the University of Sussex’s School of Engineering and Informatics, said: “Using our computational model, we were able to show that data from insect experiments did not necessarily conflict with predictions from the RPE hypothesis, as had been thought previously.

“Establishing a bridge between insect and mammal studies on learning may open up the possibility to exploit the powerful genetic tools available for performing experiments in insects, and the smaller scale of their brains, to make sense of brain function and disease in mammals, including humans.”

Understanding of how mammals learn has come a long way thanks to the RPE hypothesis, which suggests that associative memories are learned in proportion to how inaccurate they are.

The hypothesis has had considerable success explaining experimental data about learning in mammals, and has been extensively applied to decision-making and mental health illnesses such as addiction and depression. But scientists have encountered difficulties when applying the hypothesis to learning in insects due to conflicting results from different experiments.

The University of Sussex research team created a computational model to show how the major features of mushroom body anatomy and physiology can implement learning according to the RPE hypothesis.

The model simulates a simplification of the mushroom body, including different neuron types and the connections between them, and how the activity of those neurons promote learning and influence the decisions a fly makes when certain choices are rewarded.

To further understanding of learning in fly brains, the research team used their model to make five novel predictions about the influence different neurons in the mushroom body have on learning and decision-making, in the hope that they promote future experimental work.

Dr Bennett said: “While other models of the mushroom body have been created, to the best of our knowledge no other model until now has included connections between dopamine neurons and another set of neurons that predict and drive behaviour towards rewards. For example, when the reward is the sugar content of food, these connections would allow the predicted sugar availability to be compared with the actual sugar ingested, allowing more accurate predictions and appropriate sugar-seeking behaviours to be learned.

“The model can explain a large array of behaviours exhibited by fruit flies when the activity of particular neurons in their brains are either silenced or activated artificially in experiments. We also propose connections between dopamine neurons and other neurons in the mushroom body, which have not yet been reported in experiments, but would help to explain even more experimental data.”

Thomas Nowotny, Professor of Informatics at the University of Sussex, said: “The model brings together learning theory and experimental knowledge in a way that allows us to think systematically how fly brains actually work. The results show how learning in simple flies might be more similar to how we learn than previously thought.”

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Source: https://bioengineer.org/learning-on-the-fly/

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A bridge from classroom to providing actual patient care: A study of the Regenstrief tEMR

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Anonymized real-world platform gives learners realistic experience with health IT

INDIANAPOLIS – As electronic medical records (EMRs) are increasingly used across the United States, the next generation of physicians, nurses, social workers, pharmacists and other clinicians need to acquire new knowledge and competencies related to use of EMRs early in their clinical education. But training is not routinely provided.

A new study presents the functions and application of the novel, scalable Regenstrief teaching electronic medical record (tEMR) platform which contains a unique, large, anonymized patient database enabling health professions students to learn how to use health information technology (HIT) to best manage the complex issues presented by real-world patients.

“HIPAA [Health Insurance Portability and Accountability Act of 1996] has restricted access to EMRs so, ironically, the more EMRs are used, the less access students have to patient data, but the more they need to know,” said Regenstrief Institute Research Scientist Debra Litzelman, M.D., M.A., corresponding author of the new study and a professor of medicine at Indiana University School of Medicine. “Regenstrief tEMR offers detailed, anonymized data on complex patients as well as unique real-world functionality including patient sharing among care team members.”

“Medical, nursing, social work and other clinical trainees who have early exposure to EMRs will think differently about patient care and about future EMR development because of that early exposure. It creates a different mindset.”

Regenstrief tEMR offers a realistic virtual patient care experience, which the study noted was especially helpful during the early months of the COVID pandemic when students’ access to patients in health care settings was limited. The tEMR platform also enables and encourages interprofessional collaboration between learners pursuing different careers at diverse locations working at the same or different times.

Professional schools often have simulation centers teaching various skills such as CPR, intubation or robotic surgery procedures which trainees need to learn before they are on the job. Similarly, Regenstrief tEMR provides real-life simulation which prepares individuals for the real-world health IT environments they will enter.

The Regenstrief tEMR was created by the Regenstrief Institute along with IU School of Medicine, Eskenazi Health and the American Medical Association (AMA). Since 2013, the Regenstrief tEMR has been used at 12 health profession educational institutions. More than 11,800 students have accessed the system.

“Regenstrief teaching electronic medical record (tEMR) platform: a novel tool for teaching and evaluating applied health information technology” is published in JAMIA Open. Co-authors in addition to Dr. Litzelman are Blaine Y. Takesue, M.D., of IU School of Medicine and Regenstrief Institute; William M. Tierney, M.D., of IU Fairbanks School of Public Health at IUPUI and IU School of Medicine; Peter J. Embí, M.D., and Burke W. Mamlin, M.D., of Regenstrief Institute and IU School of Medicine and Jeff Warvel of Regenstrief Institute.

“With the exponential growth of health-related data and the impact of health information technology (HIT) on work-life balance, it is critical for students to get early EHR skills practice and understand how EHRs work. The ultimate tEMR project aim is to create tools through which our students — future educators, administrators, practice leaders, and front-line physicians — can develop enough HIT savvy to influence how HIT should be used in health care rather than HIT dictating how health care is delivered,” the study authors concluded.

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This project was supported by funding from the American Medical Association Accelerating Change in Medical Education initiative, a program that has provided more than $14 million to innovative projects at 37 medical schools since 2013, and the Regenstrief Institute.

About Regenstrief Institute

Founded in 1969 in Indianapolis, the Regenstrief Institute is a local, national and global leader dedicated to a world where better information empowers people to end disease and realize true health. A key research partner to Indiana University, Regenstrief and its research scientists are responsible for a growing number of major healthcare innovations and studies. Examples range from the development of global health information technology standards that enable the use and interoperability of electronic health records to improving patient-physician communications, to creating models of care that inform practice and improve the lives of patients around the globe.

About IU School of Medicine

IU School of Medicine is the largest medical school in the U.S. and is annually ranked among the top medical schools in the nation by U.S. News & World Report. The school offers high-quality medical education, access to leading medical research and rich campus life in nine Indiana cities, including rural and urban locations consistently recognized for livability.

About Debra Litzelman, M.D., M.A.

Debra Litzelman, M.D., M.A., is the associate director of the Regenstrief Institute William M. Tierney Center for Health Services Research and Indiana University Center for Health Services and Outcomes Research. She is also the D. Craig Brater Professor of Global Health Education at Indiana University School of Medicine.

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Source: https://bioengineer.org/a-bridge-from-classroom-to-providing-actual-patient-care-a-study-of-the-regenstrief-temr/

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