Posted on Leave a comment

Model can more naturally detect depression in conversations

To diagnose depression, clinicians interview patients, asking specific questions — about, say, past mental illnesses, lifestyle, and mood — and identify the condition based on the patient’s responses.

In recent years, machine learning has been championed as a useful aid for diagnostics. Machine-learning models, for instance, have been developed that can detect words and intonations of speech that may indicate depression. But these models tend to predict that a person is depressed or not, based on the person’s specific answers to specific questions. These methods are accurate, but their reliance on the type of question being asked limits how and where they can be used.

In a paper being presented at the Interspeech conference, MIT researchers detail a neural-network model that can be unleashed on raw text and audio data from interviews to discover speech patterns indicative of depression. Given a new subject, it can accurately predict if the individual is depressed, without needing any other information about the questions and answers.

The researchers hope this method can be used to develop tools to detect signs of depression in natural conversation. In the future, the model could, for instance, power mobile apps that monitor a user’s text and voice for mental distress and send alerts. This could be especially useful for those who can’t get to a clinician for an initial diagnosis, due to distance, cost, or a lack of awareness that something may be wrong.

“The first hints we have that a person is happy, excited, sad, or has some serious cognitive condition, such as depression, is through their speech,” says first author Tuka Alhanai, a researcher in the Computer Science and Artificial Intelligence Laboratory (CSAIL). “If you want to deploy [depression-detection] models in scalable way … you want to minimize the amount of constraints you have on the data you’re using. You want to deploy it in any regular conversation and have the model pick up, from the natural interaction, the state of the individual.”

The technology could still, of course, be used for identifying mental distress in casual conversations in clinical offices, adds co-author James Glass, a senior research scientist in CSAIL. “Every patient will talk differently, and if the model sees changes maybe it will be a flag to the doctors,” he says. “This is a step forward in seeing if we can do something assistive to help clinicians.”

The other co-author on the paper is Mohammad Ghassemi, a member of the Institute for Medical Engineering and Science (IMES).

Context-free modeling

The key innovation of the model lies in its ability to detect patterns indicative of depression, and then map those patterns to new individuals, with no additional information. “We call it ‘context-free,’ because you’re not putting any constraints into the types of questions you’re looking for and the type of responses to those questions,” Alhanai says.

Other models are provided with a specific set of questions, and then given examples of how a person without depression responds and examples of how a person with depression responds — for example, the straightforward inquiry, “Do you have a history of depression?” It uses those exact responses to then determine if a new individual is depressed when asked the exact same question. “But that’s not how natural conversations work,” Alhanai says.

The researchers, on the other hand, used a technique called sequence modeling, often used for speech processing. With this technique, they fed the model sequences of text and audio data from questions and answers, from both depressed and non-depressed individuals, one by one. As the sequences accumulated, the model extracted speech patterns that emerged for people with or without depression. Words such as, say, “sad,” “low,” or “down,” may be paired with audio signals that are flatter and more monotone.

Individuals with depression may also speak slower and use longer pauses between words. These text and audio identifiers for mental distress have been explored in previous research. It was ultimately up to the model to determine if any patterns were predictive of depression or not.

“The model sees sequences of words or speaking style, and determines that these patterns are more likely to be seen in people who are depressed or not depressed,” Alhanai says. “Then, if it sees the same sequences in new subjects, it can predict if they’re depressed too.”

This sequencing technique also helps the model look at the conversation as a whole and note differences between how people with and without depression speak over time.

Detecting depression

The researchers trained and tested their model on a dataset of 142 interactions from the Distress Analysis Interview Corpus that contains audio, text, and video interviews of patients with mental-health issues and virtual agents controlled by humans. Each subject is rated in terms of depression on a scale between 0 to 27, using the Personal Health Questionnaire. Scores above a cutoff between moderate (10 to 14) and moderately severe (15 to 19) are considered depressed, while all others below that threshold are considered not depressed. Out of all the subjects in the dataset, 28 (20 percent) are labeled as depressed.

In experiments, the model was evaluated using metrics of precision and recall. Precision measures which of the depressed subjects identified by the model were diagnosed as depressed. Recall measures the accuracy of the model in detecting all subjects who were diagnosed as depressed in the entire dataset. In precision, the model scored 71 percent and, on recall, scored 83 percent. The averaged combined score for those metrics, considering any errors, was 77 percent. In the majority of tests, the researchers’ model outperformed nearly all other models.

One key insight from the research, Alhanai notes, is that, during experiments, the model needed much more data to predict depression from audio than text. With text, the model can accurately detect depression using an average of seven question-answer sequences. With audio, the model needed around 30 sequences. “That implies that the patterns in words people use that are predictive of depression happen in shorter time span in text than in audio,” Alhanai says. Such insights could help the MIT researchers, and others, further refine their models.

This work represents a “very encouraging” pilot, Glass says. But now the researchers seek to discover what specific patterns the model identifies across scores of raw data.

“Right now it’s a bit of a black box,” Glass says. “These systems, however, are more believable when you have an explanation of what they’re picking up. … The next challenge is finding out what data it’s seized upon.”

The researchers also aim to test these methods on additional data from many more subjects with other cognitive conditions, such as dementia. “It’s not so much detecting depression, but it’s a similar concept of evaluating, from an everyday signal in speech, if someone has cognitive impairment or not,” Alhanai says.

Posted on Leave a comment

Mechanism of Marburg virus sexual transmission identified in nonhuman primates

Research published today by a team of Army scientists sheds light on the mechanism of sexual transmission of filoviruses, including Ebola and Marburg virus, which have been shown to persist in the testes and other immune privileged sites. Their work appears online in the journal Cell Host and Microbe.

Sexual transmission of filoviruses was first reported in 1968 after an outbreak of Marburg virus disease and recently caused flare-ups of Ebola virus disease in the 2013-2016 outbreak, according to the authors. How filoviruses establish testicular persistence and are shed in semen, however, was unknown.

Led by Dr. Xiankun (Kevin) Zeng, investigators at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) conducted a study using cynomolgus macaques to examine the persistence of Marburg virus in the testes of animals that survived infection after being treated with antiviral compounds.

The team found that Marburg virus persists in the seminiferous tubules, which are the sites of immune privilege and sperm production in the testes. Persistence leads to severe testicular damage, including cell depletion and breakdown of the blood-testis barrier, according to the authors. In addition, they identified a type of specialized cells, known as the Sertoli cells, as the reservoir for the Marburg virus.

“Importantly, we also identified local infiltration of immunosuppressive regulatory T cells, which may play an important role in sustaining Marburg virus persistence,” said Zeng. “Targeting these T cells may help to clear Marburg virus from the testes, thereby preventing sexual transmission of the virus.”

About 30 percent of cynomolgus monkeys that survived Marburg virus infection after antiviral treatment had persistent Marburg virus infection in the testes, but not in other common target organs such as the liver, spleen, and lymph nodes, according to the authors. The fact that it takes longer for Marburg virus to infect the testes strongly suggests that early intervention with therapeutics can prevent testicular persistence.

The 2013-2016 outbreak of Ebola virus disease in Western Africa resulted in about 11,000 deaths, and left behind the biggest cohort (over 17,000 individuals) of Ebola survivors in history, according to the World Health Organization. Many follow-up studies have detected Ebola virus RNA in the semen of survivors up to 18 months after recovery.

“Sexual transmission of Ebola virus has been implicated in the initiation of entirely new transmission chains,” Zeng explained. “Our study illustrates the mechanism behind testicular filovirus persistence and sexual transmission of filoviruses.”

According to Zeng, the team’s next step is to develop animal models to evaluate the efficacy of medical countermeasures to prevent and clear Marburg and Ebola viral persistence in the testes.

Story Source:

Materials provided by US Army Medical Research Institute of Infectious Diseases. Note: Content may be edited for style and length.

Posted on Leave a comment

Inhibiting nuclear factor kappa B improves heart function in a mouse model of Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is a devastating genetic disease that impairs cardiac and skeletal muscle development. People with DMD gradually lose ambulation in childhood, acquire respiratory and heart failure in young adulthood and succumb to the disease by their mid-thirties. Until recently, there has been no effective treatment for the characteristic muscle-wasting progression of this disease. Provisional FDA approval of the first DMD therapy (eteplirsen) and improved disease management strategies have extended the life span of DMD patients and expanded the field of DMD research into later-stage outcomes such as cardiomyopathy (heart failure).

Overall, little is known about the mechanisms of DMD cardiomyopathy, particularly how individual signaling pathways contribute to its development. Breakthrough research published August 24, 2018 in Nature Communications by a large, interdisciplinary team of Medical University of South Carolina (MUSC) and Ohio State University investigators has uncovered an unexpected mechanism that underlies cardiomyopathy in DMD. The team was led by Denis Guttridge, Ph.D., professor in MUSC’s Department of Pediatrics, director of the Darby Children’s Research Institute, and associate director of Translational Sciences for the Hollings Cancer Center.

“Understanding cardiomyopathy is a significant achievement,” explains Guttridge. “About 95 percent of patients with dystrophin gene mutations (like the one that causes DMD) develop heart failure and up to 25 percent of these patients die from it. As we’ve gotten better at managing patients on ventilators and with other types of care, they’re living longer but extending life is also thought to put more stress on their hearts. So, heart failure needs to be considered in the overall management of this disease.”

The team had previously focused on the NF-κB transcription factor in skeletal muscle and, with others, showed that it regulates both physiological (differentiation, growth, and metabolism) and pathophysiological (cachexia, atrophy, and dystrophy) aspects of skeletal muscle biology. Their finding that inhibiting NF-κB improved functioning in dystrophic limb and diaphragm muscles and reduced inflammatory damage laid the foundation for investigations into NF-κB as a potential therapeutic target in DMD.

“We’d been using skeletal muscle as a platform to understand NF-κB,” explains Guttridge. “We know it drives inflammation and DMD has an inflammatory component, so then we started looking at what it does in DMD. There’s also some evidence that NF-κB plays a role in heart failure, but results differ widely based on the type of heart disease-which suggests that it may act differently in various cardiac conditions. So, we began wondering how it might contribute to cardiomyopathy in DMD.”

Using a mouse model of DMD (mdx), the team first established that NF-κB does, indeed, contribute to cardiac dysfunction in this disease. Specifically, their first set of experiments showed that cardiomyocyte NF-κB impairs cardiac response to beta-adrenergic stress. This is the first evidence to establish that cardiomyocyte-derived NF-κB signaling is instrumental in promoting dystrophic cardiac dysfunction.

Their next experiments found that cardiomyocyte NF-κB, though not required for the development of cardiac fibrosis or myocyte injury in mdx mice, still contributes to cardiac dysfunction. The question then became “How?” Published evidence indicated that genes related to calcium were enriched in the absence of NF-κB. The team followed this proposed link between NF-κB and calcium using microarray analyses to compare the hearts of NF-κB knock-out mice (mdxHRTΔIKKβ) with littermates that had intact NF-κB (mdxIKKβf/f).

They found that cardiomyocyte NF-κB ablation normalized calcium handling and significantly increased calcium gene expression.

Taking a broader look at overall gene expression patterns in dystrophic hearts lacking NF-κB, they found that it played a previously unreported functional role as a global repressor in mdx hearts.

“This mechanism was unexpected,” says Guttridge. “We thought that when the pathway was ablated, the global gene expression pattern would be down-regulated because NF-κB is supposed to be an activator. Surprisingly, we saw the opposite-about 75 percent of genes were upregulated. That told us that NF-κB was acting as a transcriptional repressor.”

The team’s next series of experiments uncovered that, although NF-κB was activated in dystrophic hearts, it was not playing its canonical role as a direct transcriptional activator but rather was modulating chromatin conformation to deplete H3K27ac. A reduction of this chromatin mark indicates that there is a repression on gene expression. This depletion, in turn, repressed the Slc8a1 gene, which codes for the NCX1 protein. And, here’s the rub — NCX1 plays a crucial role in maintaining calcium homeostasis in multiple cell types, including muscle.

“When we dug deeper to find out how and exactly what genes it was repressing, we saw that the ones that were going up were mostly calcium-handling genes like Slc8a1. Without proper mobilization of calcium, the heart doesn’t contract normally,” says Guttridge, “The reason NF-κB was acting as a repressor of calcium genes now made a lot of sense.”

While it is understood that the pathology of dystrophic hearts is caused by disruption of calcium homeostasis, the exact mechanisms driving this disruption have not previously been explored. Furthermore, these findings have important implications for the treatment of heart failure in multiple conditions including diabetes and after ischemia-reperfusion injuries. Perhaps most important, these findings highlight that targeting NF-κB could benefit both skeletal and cardiac muscle.

“I’m very excited about these findings!” says Guttridge. “As a scientist, you follow your hunches and try to vigorously test your hypotheses — it’s so satisfying to have found a pathway that we believe contributes to the pathology of DMD, not just in skeletal muscle but also in the heart. This gives us hope that a drug can be developed that has the possibility of improving patients’ lives.”

Posted on Leave a comment

A master switch controls aggressive breast cancer

A team at the Salk Institute has identified a master switch that appears to control the dynamic behavior of tumor cells that makes some aggressive cancers so difficult to treat. The gene Sox10 directly controls the growth and invasion of a significant fraction of hard-to-treat triple-negative breast cancers.

Recently, the Salk lab led by Professor Geoffrey Wahl discovered that aggressive breast cancers return to a flexible, earlier state found in fetal breast tissue. This cellular reprogramming may be the key to cancer’s ability to form new cell types, evolve drug resistance and metastasize to other locations in the body. The new work documenting Sox10’s role in this process, which was reported in the journal Cancer Cell on August 30, 2018, represents a major milestone in researchers’ understanding of cancer and could open new avenues for diagnosing and treating aggressive breast cancer as well as other types of intractable cancers.

“Two things that make triple-negative breast cancers so hard to treat are their heterogeneity — they have many different cell types within a single tumor — and their ability to move around and colonize new areas, the process of metastasis,” says Wahl, holder of the Daniel and Martina Lewis Chair and senior author of the work. “It’s what you could call the imprecision in precision medicine, in the sense that we might target one type of cell, but there are other cells within the tumor that can change to become drug resistant, analogous to how a chameleon changes colors to evade predators.”

In order to develop from a single cell into a complete organism such as a mouse or human, embryonic and fetal cells have the ability to divide rapidly, move throughout the body and change into multiple different cell types — properties known as “plasticity.” But adults cells turn off this plasticity, which, for reasons that aren’t fully understood, can get reawakened and turn cells cancerous.

“The embryo will supercharge certain cells to rapidly start critical developmental processes that spawn the growths of new tissues, but it’s very important that these cells get shut off when your body no longer needs this to occur,” says Christopher Dravis, a Salk staff scientist and the paper’s co-first author. “In aggressive breast cancers, we’re finding that safety mechanisms that regulate these powerful development genetic programs are lost, so these processes underlying cellular plasticity are being reactivated to drive tumor development and ultimately the malignancy that’s associated with the disease.”

In the new study, the Wahl lab began by examining which parts of mouse mammary cells’ DNA — which is tightly coiled in a package called chromatin — was uncoiling to make specific genes more accessible. This was the team’s first clue to which genes might be active during development. The chromatin analysis revealed that in both fetal cells and a subpopulation of breast tumor cells, the same areas of the genome were becoming accessible — areas where a master gene regulator called Sox10 is known to bind to DNA to initiate a variety of developmental processes. It seemed like a gene regulation “smoking gun.”

“In fetal cells, which are the most ‘plastic,’ we saw that binding sites for Sox10 were very open and accessible compared to healthy adult cells, which are mostly inflexible and the chromatin is very closed,” says Chi-Yeh Chung, a Salk research associate and the paper’s co-first author.

Next the team showed that Sox10 actually bound to genes in the open regions to activate them, thereby directly regulating genes responsible for cell type, mobility and other features relevant to breast cancer’s ability to evolve and metastasize. Breast cancer cells with high levels of Sox10 changed to become much more primitive and acquired the ability to move. The results were so dramatic that the team repeated the experiment with a technique to keep Sox10 from binding to those genes. This time, without access to Sox10, none of the breast cells that had been programmed to turn cancerous were now able to form tumors.

“When you’re talking about metastasis, a result like this is huge,” says Bianca Lundien Kennedy, a two-time breast cancer survivor and patient/research advocate who has worked with the Wahl lab for seven years. “It drastically alters the research landscape and will be such a personally significant thing for any breast cancer survivor or person with cancer to hear. It really hits home.”

The researchers caution that strategies to block Sox10 will require further development and will have to be tested for safety to determine if they impact normal cellular functions. However, the fact that Sox10 regulates many genes potentially linked to aggressive breast cancer offers the potential to target one or more of them as the basis for developing “personalized” therapies for metastatic breast cancer. Additionally, the findings could lead to diagnostic tests for breast and other cancers by checking adult tissues for proteins that normally would only be produced by fetal cells.

The team next plans to explore potential therapeutic drug targets among the genes regulated by Sox10.

Other authors included: Nikki K. Lytle and Tannishtha Reya of Sanford Consortium for Regenerative Medicine and UC San Diego Moores Cancer Center; and Jaslem Herrera-Valdez, Gidsela Luna and Christy L. Trejo of Salk.

The work was funded by the National Institutes of Health/National Cancer Institute (R35 CA197687); the Susan G. Komen Foundation (SAC110036); the Breast Cancer Research Foundation; and NIH National Research Service Award fellowships F32CA174430, GM007752, CA206416, CA186043 and CA197699.

Posted on Leave a comment

Study illustrates challenges of lowering tetanus mortality

The overall mortality in patients suffering non-neonatal tetanus is high. Efforts to reduce mortality in one sub-Saharan African intensive care unit (ICU) by implementing a standard tetanus protocol did little to change mortality rates, although they shifted causes of deaths, researchers have now reported in PLOS Neglected Tropical Diseases.

Tetanus is a vaccine-preventable neglected disease that mostly occurs in regions where vaccination coverage is incomplete. The World Health Organization recommends treating tetanus with patient monitoring, antibody injections, sedation, pain relief, and general supportive care.

In the new work, Jennifer Downs of Weill Cornell Medicine, New York, and colleagues looked at a tetanus patient care protocol implemented in the ICU of Bugando Medical Centre in Tanzania in 2006. The stepwise protocol, which was modified in 2012, emphasized airway control, early administration of medications, and wound care. Patient care and outcomes were analyzed for tetanus patients in three groups — those admitted pre-protocol in 2001 to 2006, those in an Early group, admitted in 2006 to 2011, and a Late group admitted after the protocol was modified, in 2012 to 2016.

The researchers saw a significant increase in utilized care between the Early and Late groups, with more mechanical ventilation, surgical wound care, and tracheostomies used in the Late group. Despite this increase in care, there was no significant change to overall mortality or 7-day mortality between the pre-protocol and post-protocol groups or Early and Late groups, with mortality rates ranging from 40.3% to 60.7% in all groups. There was, however, a decrease in deaths related to airway compromise and increase in deaths due to sepsis in the post-protocol groups.

“Implementation of protocolized care in resource-limited settings is highly complex and requires in-depth monitoring and assessment of patients, staff, and procedures,” the researchers say. “We strongly call from an increase in vaccination coverage for at-risk men in sub-Saharan Africa… with the aim of eliminating this preventable, lethal disease,” they add.

Story Source:

Materials provided by PLOS. Note: Content may be edited for style and length.

Posted on Leave a comment

How damaging immune cells develop during tuberculosis

Insights into how harmful white blood cells form during tuberculosis infection point to novel targets for pharmacological interventions, according to a study published in the open-access journal PLOS Pathogens by Valentina Guerrini and Maria Laura Gennaro of Rutgers New Jersey Medical School, and colleagues.

Foam cells are a type of white blood cell, known as macrophages, that have accumulated fatty, waxy, or oily compounds called lipids. These cells contribute to maladaptive immune responses such as chronic inflammation and tissue damage in a variety of diseases. The formation of foam cells has been most thoroughly studied in the context of atherosclerosis, or hardening of the arteries. During atherosclerosis, macrophages develop into foam cells by accumulating a waxy, fat-like substance called cholesterol. But it has been unclear how these cells form during chronic infectious diseases such as tuberculosis — a contagious and often severe airborne disease caused by infection with Mycobacterium tuberculosis bacteria.

Gennaro and colleagues provide evidence that foam cells in lung tissue from rabbits, non-human primates, and humans with tuberculosis form by primarily accumulating a type of fat called triglycerides, rather than cholesterol as seen in atherosclerosis. Moreover, triglyceride accumulation in human macrophages infected with M. tuberculosis is mediated by distinct signaling pathways from those associated with cholesterol storage in macrophages during atherosclerosis. The findings demonstrate that foam cells store different types of lipids and form through distinct mechanisms, depending on the disease.

According to the authors, the findings may have translational implications. For example, molecules involved in triglyceride synthesis may be used as novel biomarkers of progression to active tuberculosis. In addition, manipulating factors that affect macrophage lipid content might be an effective way to treat tuberculosis. Because many of these factors have been extensively studied in the context of cancer, cardiovascular diseases, and metabolic diseases, it may be possible to repurpose pharmacological compounds as therapies against tuberculosis. Such therapies may shorten the duration of antibiotic regimens and help restrict the emergence of antibiotic resistance.

“The finding that foam cells found in tuberculosis differ from those present in atherosclerosis,” states Gennaro, “demonstrates that these dysfunctional cells, which are associated with many diseases, are generated through biological processes that differ from one disease to another.”

Story Source:

Materials provided by PLOS. Note: Content may be edited for style and length.

Posted on Leave a comment

DNA accessibility, gene expression jointly profiled in thousands of cells

Scientists have now developed an assay that concurrently profiles both the epigenome and transcriptome of each of thousands of single cells.

The epigenome and transcriptome are part of the molecular biology that converts a genetic blueprint into tools and materials for living cells.

The genomes of different types of cells may be identical, while their epigenomes and transcriptomes are not. The epigenome consists of a set of marks that shape what each cell’s genome will do, while the transcriptome is the set of copies of the instructions themselves. These encode the production of proteins. The flow of information from the inherited plan to the making of proteins is critical for forming and maintaining life.

Cells can access only certain portions of their chromatin-packaged, double-stranded genome during RNA transcription. Because this access varies among different cell types, chromatin accessibility is what helps determine the shape, function and variety of the diverse cells in a multi-cellular, living organism.

The researchers call their assay sci-CAR. Sci stands for single-cell combinatorial indexing, a means of studying large numbers of single cells at once. In a research report Aug. 30 in Science, the scientists describe how the new assay merges two other genomic assays into one protocol.

These assays, among their other features, incorporate unique barcodes for the nucleic acid contents of cells or of the cell nucleus, which contains the main control center for living cells. The scientists’ method for labeling and sorting cells lets them link the messenger RNA and chromatin accessibility profiles of individual cells.

Most assays of what goes on genetically inside single cells, the scientists noted, can survey only one aspect of cellular biology. The ability to investigate several classes of molecules concurrently could uncover, for example, how certain genetic mechanisms are related and regulated.

It could also improve the usefulness of cell atlases of complex organisms, like those of the worm or mouse. Eventually, it could be helpful in compiling a human cell atlas.

The new method was developed by scientists at the Brotman Baty Institute for Precision Medicine in Seattle, University of Washington School of Medicine Department of Genome Sciences, Oregon Health Sciences University, Illumina, Inc., in California, Allen Discovery Center for Cell Lineage Tracing, and Howard Hughes Medical Institute.

The first author of the study is Junyue Cao, a graduate student in the Molecular and Cellular Biology program and in genome sciences at the University of Washington School of Medicine. The study was led by Jay Shendure and Cole Trapnell. Both are faculty in the Department of Genome Sciences at the UW School of Medicine and investigators at the Brotman Baty Institute, where Shendure is the director.

The researchers first tried their co-assay on more than 4,800 cells in a lung-cancer-derived cell culture model of cortisol response. In this model, the cells are treated with the corticosteroid dexamethasone. This synthetic steroid can activate the binding of thousands of locations on the genome and change the expression of hundreds of genes.

The scientists then examined the time course of dexamethasone’s effects on gene expression, as well as dynamic changes that occurred in chromatin accessibility in the same cells.

In related work, the researchers sought to study the gene-control landscape that underlies the messenger RNA collections found in the different types of cells in the mammalian kidney.

In applying their co-assay to the nuclei from whole mouse kidneys, they recovered both transcriptome and chromatin accessibility profiles from 11,296 cells. They clustered their mouse kidney cells into 14 groups, and characterized cell-type specific epigenome landscapes and linked transcriptome features.

Based on the covariance between epigenome and transcriptome, the researchers also learned that they could draw links between distant genomic regulatory elements and their targeted genes to explain some of the differences in gene expression across various cell types.

Looking forward, there are clear advantages of a joint assay over assays that only profile either RNA transcription or DNA accessibility. One advantage of sci-CAR specifically is that this method could potentially be used to jointly assay millions of single cells at once.

Among its limitations is the sparseness of some of the chromatin accessibility data. The researchers suggested that this might be overcome in future experiments by optimizing some aspects of the current protocol.

The researchers hope to continue to combine additional co-assays so that molecular biologists could concurrently trace the flow of genetic information from DNA to RNA to specific proteins in each of the many single cells that can exist in complex living things.

Posted on Leave a comment

Simple test detects disease-carrying mosquitoes, presence of biopesticide

A new diagnostic tool has been developed by researchers at The University of Texas at Austin that can easily, quickly and cheaply identify whether a mosquito belongs to the species that carries dangerous diseases such as Zika virus, dengue, chikungunya or yellow fever. It can also determine whether the bug has come into contact with a mosquito-control strategy known as Wolbachia.

“Many of these diseases are spreading in areas where they weren’t common before,” said Sanchita Bhadra, a research associate in the Department of Molecular Biosciences and first author on the paper. “Having surveillance is important in conjunction with any kind of outbreak, and this method allows a rapid test in the field.”

The tool uses a smartphone camera, a small 3D-printed box and a simple chemical test to show whether a dead mosquito belongs to the Aedes aegypti species. Aedes aegypti carries Zika and other devastating viruses that afflict an estimated 100 million people worldwide each year. The species also is closely linked to the tripling of cases of mosquito-borne diseases in the United States since 2004.

The research appears in the journal PLOS Neglected Tropical Diseases.

The tool developed by scientists and students at UT Austin also detects the presence of a biopesticide called Wolbachia, a type of bacteria that keeps mosquitoes from spreading diseases. In countries around the world and in 20 U.S. states where the Aedes aegypti mosquito is found, scientists working in public health agencies have started to infect mosquitoes with Wolbachia by introducing the bacteria into a local mosquito population to help curb transmission of viruses.

Because mosquitoes show no outward signs of having the bacteria — and because existing diagnostic tests are hard to read, expensive and logistically cumbersome — the new tool represents a significant step forward for those hoping to monitor the effectiveness of Wolbachia.

“This test can happen without involving a lot of staff and equipment to make sure Wolbachia is effective and spreading as anticipated,” Bhadra said.

Public health groups trap and kill mosquitoes routinely in conjunction with monitoring efforts, but existing technology requires a complex process to extract nucleic acid from inside mosquitoes, often after they have been dead for days and have started to decay, leading to greater expense and the possibility of more errors in lab tests than the new technology.

The new diagnostic tool uses a smartphone’s camera and a simple test that can be done anywhere. It tests mosquitoes’ nucleic acid without requiring a complicated process to remove it. Officially known as a loop-mediated isothermal amplification and oligonucleotide strand displacement, or LAMP OSD, the probe delivers a simple yes-or-no readout on a cellphone, with accuracy of greater than 97 percent.

In addition to the tests to detect mosquito species and Wolbachia, the team also is exploring use of the technology to easily identify whether trapped mosquitoes are carrying Zika, dengue and other pathogens.

Story Source:

Materials provided by University of Texas at Austin. Note: Content may be edited for style and length.

Posted on Leave a comment

CRISPR halts Duchenne muscular dystrophy progression in dogs

Scientists for the first time have used CRISPR gene editing to halt the progression of Duchenne muscular dystrophy (DMD) in a large mammal, according to a study by UT Southwestern that provides a strong indication that a lifesaving treatment may be in the pipeline.

The research published in Science documents unprecedented improvement in the muscle fibers of dogs with DMD — the most common fatal genetic disease in children, caused by a mutation that inhibits the production of dystrophin, a protein critical for muscle function.

Researchers used a single-cut gene-editing technique to restore dystrophin in muscle and heart tissue by up to 92 percent of normal levels. Scientists have estimated a 15 percent threshold is needed to significantly help patients.

“Children with DMD often die either because their heart loses the strength to pump, or their diaphragm becomes too weak to breathe,” said Dr. Eric Olson, Director of UT Southwestern’s Hamon Center for Regenerative Science and Medicine. “This encouraging level of dystrophin expression would hopefully prevent that from happening.”

DMD, which affects one in 5,000 boys, leads to muscle and heart failure, and premature death by the early 30s. Patients are forced into wheelchairs as their muscles degenerate and eventually onto respirators as their diaphragms weaken. No effective treatment exists, though scientists have known for decades that a defect in the dystrophin gene causes the condition.

The Science study establishes the proof-of-concept for single-cut gene editing in dystrophic muscle and represents a major step toward a clinical trial. Already Dr. Olson’s team has corrected DMD mutations in mice and human cells by making single cuts at strategic points of the mutated DNA.

The latest research applied the same technique in four dogs that shared the type of mutation most commonly seen in DMD patients. Scientists used a harmless virus called adeno-associated virus (AAV) to deliver CRISPR gene-editing components to exon 51, one of the 79 exons that comprise the dystrophin gene.

CRISPR edited the exon, and within several weeks the missing protein was restored in muscle tissue throughout the body, including 92 percent correction in the heart and 58 percent in the diaphragm, the main muscle needed for breathing.

“Our strategy is different from other therapeutic approaches for DMD because it edits the mutation that causes the disease and restores normal expression of the repaired dystrophin,” said Dr. Leonela Amoasii, lead author of the study and Assistant Instructor of Molecular Biology in Dr. Olson’s lab. “But we have more to do before we can use this clinically.”

The lab will next conduct longer-term studies to measure whether the dystrophin levels remain stable and to ensure the gene edits do not have adverse side effects.

Dr. Olson hopes the next step beyond dogs is a clinical trial, which would be among several that UT Southwestern’s gene therapy center aims to launch in the coming years to address numerous deadly childhood diseases.

In the meantime, Dr. Olson’s recent work has spawned a biotechnology company, Exonics Therapeutics Inc., which is working to further optimize and bring this technology to the clinic. Exonics intends to extend the approach to additional DMD mutations, as well as other neuromuscular diseases. Exonics has licensed the technology from UT Southwestern.

Story Source:

Materials provided by UT Southwestern Medical Center. Note: Content may be edited for style and length.

Posted on Leave a comment

How our brain and personality provide protection against emotional distress

If you feel anxious prior to exams, take note: studies suggest that you can learn how to be resilient and manage your stress and anxiety.

Researchers at the Beckman Institute for Advanced Science and Technology at the University of Illinois recently examined a sample of 85 healthy college students to see how a number of personality traits can protect an individual’s brain against symptoms of emotional distress, namely depression and anxiety.

“In this study, we wanted to look at commonalities across brain regions and across personality traits that contribute to protective factors,” said Matt Moore, a Beckman Institute Graduate Fellow and co-author of the study. “We targeted a number of regions in the prefrontal cortex, looking specifically at the volume of those regions using structural magnetic resonance imaging. We did a confirmatory factor analysis, which is basically a statistical approach for testing whether there is a common factor underlying the observed measurements.”

The study, “Neuro-Behavioral Mechanisms of Resilience against Emotional Distress: An Integrative Brain-Personality-Symptom Approach using Structural Equation Modeling,” was recently published in Personality Neuroscience.

In order to examine resiliency in young adults, previous research has looked at the relationship between specific brain regions and certain personality traits, such as optimism, positive affect, and cognitive reappraisal, all of which factor into how an individual copes with emotional challenges.

“We knew from the clinical literature that there are relationships between brain volume and certain personality traits,” said Sanda Dolcos, a research scientist in psychology, and one of the study’s authors. “Lower brain volume in certain areas is associated with increased anxiety.”

Coupled with questionnaires that identified the personality traits, the structural information of the prefrontal cortical regions provided evidence that there are common factors in brain structure and personality that can help provide adaptive behavior in order to avoid negative emotions.

“In a statistical model, we extracted these factors, one at the brain level, one at the personality level, and we found that if you have larger volume in this set of brain regions, you had higher levels of these protective personality traits,” Moore said.

The researchers are interested in identifying these brain regions along with specific personality traits in order to create ways for individuals to learn how to combat anxiety and depression.

“We are interested in cognitive behavioral intervention,” Dolcos said. “We have identified a resilience factor, which relates to detailed components in the prefrontal cortex, so cognitive interventions would target those brain areas.”

The fact that the brain volume can change based on developing skills that might alter traits such as optimism indicates that brain training is one way to combat emotional distress.

“People are not necessarily aware of how plastic the brain is,” Dolcos said. “We can change the volume of the brain through experience and training. I teach brain and cognition, and students are so empowered at the end of the course because they realize that they are in charge.

“It means that we can work on developing new skills, for instance, new emotion regulation strategies that have a more positive approach, and can actually impact the brain.”

“This study gives us the coordinates of the brain regions that are important as well as some traits that are important,” Moore said. “As the next step, we can then try and engage this plasticity at each of these levels and then train against a negative outcome.”