Culture

The cover for issue 4 of Oncotarget features Figure 8, "Model for biological function categorization of PMEPA1 isoforms (c, d, and e) in the context of prostate cancer," by Sharad, et al.

In addition to 4 reported PMEPA1 isoforms, one novel isoform PMEPA1-e was identified with RNA Seq analysis of hormone-responsive VCa P, LNCa P cells and human prostate cancer samples from The Cancer Genome Atlas dataset.

The researchers analyzed the structures, expressions, biological functions and clinical relevance of PMEPA1-e isoform and less characterized isoforms c and d in the context of prostate cancer and AR/TGF- signaling.

The expression of PMEPA1-e was induced by androgen and AR.

Taken together, their findings first defined the prostate tumorigenesis mediated by PMEPA1-d and -e isoforms, providing novel insights into the new strategies for prognostic evaluation and therapeutics of prostate tumor.

Dr. Hua Li and Dr. Shashwat Sharad from the Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences as well as the Walter Reed National Military Medical Center, Bethesda, Maryland, USA said in their Oncotarget article, "Prostate cancer is the most commonly diagnosed male malignancy and second leading cause of cancer-related deaths in the USA."

It was shown that the methylation of PMEPA1 gene promoter accounted for the silencing of PMEPA1 in prostate cancer cells in vitro and in vivo.

PMEPA1 was also reported as a TGF- regulated gene in the context of both prostate cancer and non-prostate solid tumors including colon, lung and breast cancers.

Further, a recent study showed that the loss of membrane-anchored PMEPA1 protein facilitated metastasis of prostate cancer via activating TGF- signaling by sequestering SMAD2/3 in proteasome independent way.

Cumulatively, these findings underscored the multi-function features of the PMEPA1 gene and further suggested its expressions and biological functions were dependent on the cellular context centering androgen and TGF- signaling.

The alternative splicing variant mechanism had also been shown to be important for diversifying functions of tumor-associated genes.

Further, earlier studies from their and other groups explored PMEAP1 gene isoforms in the initiation and development of prostate tumors via interrupting AR and/or TGF- signaling.

Here, the Oncotarget authors focused on defining the expressions, regulations and biological behaviors/functions of understudied PMEPA1 isoforms in the context of both androgen and TGF- signaling, and further exploration of the clinical significances and relevance of these isoforms in prostate tumor.

The Li/Sharad Research Team concluded in their Oncotarget study that gene isoform ratio could potentially predict the gene functional consequences and disease progression.

Weightlifters could do less and get stronger by changing the amount they lift each session, according to new research.

Sports scientists from the University of Lincoln, UK, compared the average weights lifted by two groups over six weeks: one using a traditional training method of a "one rep max" - the maximum weight an athlete could lift - and one using a load velocity profile, where the weights were tailored so they lift either more or less at each session.

All who used the load velocity profile became stronger despite lifting less overall during the six week period.

Traditionally, the one rep max would be used to dictate the weight load for all sessions.

Researchers established the one rep max in the two groups. They then used a linear positional transducer - essentially a specialised stopwatch and tape measure - to record the length of time it took to lift the weight, and the distance the weight was moved to establish a "velocity measurement" in one of the groups. That coupled with the one rep max established the load velocity profile for the athlete.

At each session, the load velocity group completed a warm-up consisting of a series of repetitions where the weight load was gradually increased and their velocity measurement taken. Each rep was recorded and compared with their pre-established load-velocity profile.

This comparison enabled the participants' training load to be adjusted based on their performance that day: if the athlete was moving the same load at a faster velocity, the weight was increased, but if they were lifting slower, the weight load would be reduced.

The findings can be used to improve muscular strength and power, and have positive implications for the management of fatigue during resistance training.

Dr Harry Dorrell from the University of Lincoln's School of Sport and Exercise Science led the study. He said: "There are a lot of factors which can contribute to an athletes' performance on a particular day, such as how much sleep they have had, nutrition, or motivational factors, but with traditional percentage-based methods we would have no insight into how this effects their strength.

"The velocity-based training enabled us to see if they were up or down on their normal performance and thus adjust the load accordingly. It's about making sure the athlete is lifting the optimal load for them, on that particular day. If you lift too little then you won't stimulate the body as you intend to; but if you lift too much you'll be fatigued, which increases the risk of injury.

"This fatigue won't necessarily happen immediately, either. You could lift too much regularly, and three weeks down the line this will catch up with you and you'll find that the muscles are too fatigued to manage what you believe should be in your ability."

Sixteen men aged between 18 to 29 years, with body masses ranging from 70kg to 120kg with at least two years' weight training experience, took part in the trial which included two training sessions a week over a course of six weeks.

They performed a back squat, bench press, strict overhead press, and a conventional deadlift, and the results at the start and end of the six weeks training were recorded.

Researchers also recorded the athlete's countermovement jump, a term used to describe the explosive lower-body power, and found that only the velocity group's had improved.

Following the trial, those using the velocity based training method could lift an average of 15kg more on the back squat than when they started, rising from 147kg to 162kg, despite their training loads being an average of nine per cent less at each session; they lifted six per cent less on the bench press per session but could take on an extra 8kg by the final session; the overhead press saw a 4kg increase in the one rep max despite lifting six per cent less during training; and the deadlift rose from 176kg to 188kg even with an average decrease of two per cent on their training loads.

Dr Dorrell added: "While some of these changes could be considered as only "small improvements" and were similar to the group using the traditional training method, the velocity group lifted significantly less in order to see the gains they made. The idea of velocity based training has been around for a while, but until now there hasn't been any science to prove that it actually works; the science has finally caught up."

Commercially available kinetic measuring devices, including apps, now mean that anyone could easily carry out the same training method at home or in the gym.

31 January 2020, Cambridge - Researchers at EMBL's European Bioinformatics Institute (EMBL-EBI) and Queen Mary University of London have led a study to categorise which genes are essential for supporting life. The results from this study could be a useful new resource to help researchers identify mutations responsible for rare childhood diseases.

Identifying which genes are linked to a rare disease is one of the most difficult challenges geneticists face. The low prevalence of these diseases within the population makes it difficult to research and fully understand their causes. However, huge advances in the diagnosis of rare diseases are now being made thanks to innovations in sequencing technology.

This research, published in Nature Communications, compares knockout mice viability and phenotyping data from the International Mouse Phenotyping Consortium (IMPC) with human cell lines provided by the Broad Institute's Project Achilles to create categories indicating how crucial a gene is to producing viable life.

The researchers also identified new mutations likely responsible for rare childhood diseases by comparing their data with unsolved cases of genetic disorders identified in the 100,000 Genomes Project and the Deciphering Developmental Disorders (DDD) datasets.

Defining genes essential for life

"Loss of gene function is often referred to as a binary concept; lethal or viable," says Violeta Muñoz-Fuentes, Biologist, Mouse Informatics at EMBL-EBI. "In this study we show that gene essentiality is more of a spectrum ranging from cellular lethal, developmental lethal, subviable, viable with a visible phenotype, and viable without a visible phenotype."

The scientists define these categories for 3819 genes to create an open access database that can be used to benefit other researchers and provide insight for clinical applications.

"When you sequence a person's genome it's not always one mutation that stands out as altering a gene's function," says Terry Meehan, Coordinator of Mouse Informatics at EMBL-EBI. "We currently don't have a handle on which genes are important for development and which have a minor impact."

Loss of function gene categories

Cellular lethal: genes essential for cell viability

Developmental lethal: genes essential for organism development

Viable: organisms fully develop

Subviable: organism survival is less than expected

Diagnosing rare disorders

"This study combines multiple sources of data from large scale projects to identify new candidate genes that, when mutated, are likely to have a causal relationship with rare human disorders," says Pilar Cacheiro, Research Fellow at Queen Mary University of London. "Nearly 6% of the population are affected by these diseases during their lives."

Advances in whole genome sequencing (WGS) are changing the way we research and diagnose rare genetic diseases. However, the majority of rare disease patients remain undiagnosed due to a lack of detection or because a previously unknown gene is disrupted. This study furthers our understanding of rare disease genes by providing clinicians and researchers with an open access resource, which can be used to identify high-quality candidates for rare disease mutations.

"Of particular interest for application to healthcare, we demonstrate that the set of genes that are essential for organism development is particularly associated with known human developmental disorders," says Damian Smedley, Reader in Computational Genomics at Queen Mary University of London. "This provides candidates for undiscovered causative genes for these conditions."

Several high-scoring candidates from this study have been added to the open access resource GeneMatcher, used by researchers and clinicians all over the globe to share gene information. You can also freely access the study data in EMBL-EBI's Biostudies and at the International Mouse Phenotyping Consortium.

CHAMPAIGN, Ill. -- Artificial sweeteners such as sucralose provide the seductive taste of sweetness without the calories contained in sugar - a seeming win-win for people who need to control their blood sugar and insulin levels or weight.

However, simply tasting or consuming sucralose may affect blood glucose and insulin levels on glucose tolerance tests, scientists at the University of Illinois found in a new study.

The findings suggest that despite having no calories, sucralose may have metabolic effects in some users, said M. Yanina Pepino, a professor of food science and human nutrition at the U. of I., who led the research.

"The most important take-home message is that sweet taste in itself may have an impact on carbohydrate metabolism and glucose control," Pepino said. "Even though the sample population in our study was small, the findings add to a body of evidence that suggests sweetness should be consumed in moderation, regardless of the calories."

The study included 10 people of healthy weight and 11 people with obesity; none of the participants had diabetes or were regular users of artificial sweeteners.

The participants underwent three oral glucose tolerance tests on separate days spaced about a week apart. Prior to one test they consumed distilled water; prior to another, sucralose; and prior to a third test they tasted but did not swallow sucralose.

They performed one of these actions 10 minutes before drinking a solution containing 75 grams of glucose.

The amount of sucralose - 48 milligrams - that the study participants ingested provides a level of sweetness equivalent to that in a typical diet soda, Pepino said.

At each visit, a catheter was inserted into a radial artery to obtain blood samples at regular intervals during the hour before and five hours after the participants drank the glucose. The scientists measured participants' blood concentrations of sucralose, insulin, glucose and other hormones.

Sucralose had differing effects depending on whether participants ingested it or only tasted it and whether they had obesity, the researchers found.

When people of healthy weight swallowed the sucralose, their blood insulin levels decreased modestly during the first hour, and their insulin sensitivity increased by about 50%, said graduate student Clara Salame, who co-wrote the study.

However, when people with obesity swallowed the sucralose, their insulin levels increased significantly more than when they drank water or when they tasted the sucralose but spit it out.

"While insulin responses to either tasting or swallowing the sucralose were similar in those of normal weight, those responses were very different in people with obesity," Pepino said. "Therefore, we hypothesize that some post-ingestive effects of sucralose may occur only in people with obesity.

"However, our study included people who were not habitual consumers of artificial sweeteners, and further studies are needed to explore what happens with this acute effect of sucralose after long-term use."

Pepino cautioned that since the various artificial sweeteners have very different chemical structures and the body may handle them differently - some are broken down in the stomach while others remain unabsorbed in the intestine - the findings on post-ingestive effects may be unique to sucralose.

However, since all artificial sweeteners activate the sweet taste receptors in the mouth, the metabolic effects associated with sweetness may be more generalizable, she said.

Pepino said she had expected that tasting sucralose and spitting it out would have similar effects to consuming water; thus, she was surprised to discover that participants' insulin levels were affected by taste alone.

"Interestingly, we found that in both groups of people - those with obesity and those of normal weight - there was a reduction in insulin response to the glucose tolerance test when they just tasted sweetness before drinking the glucose solution. It was the most surprising finding, and we are following up on that in a new study," Pepino said.

"What our data suggest is that there are mechanisms that we don't understand clearly about how the human body regulates glucose and the potential metabolic effects of tasting something sweet beyond providing a sense of pleasure," Pepino said.

On January 24, 2020, the French Ministry of Health confirmed the first three cases of patients affected by the Wuhan coronavirus. On January 29, 2020, the Institut Pasteur, which is responsible for monitoring respiratory viruses in France, sequenced the whole genome of the coronavirus known as "2019-nCoV", becoming the first institution in Europe to sequence the virus since the start of the outbreak. The virus was sequenced at the Institut Pasteur's Mutualized Platform for Microbiology (P2M), which performs genome sequencing on bacterial, viral, fungal and parasite strains received by National Reference Centers and World Health Organization Collaborating Centers for the purpose of infectious disease surveillance.

In December 2019, an outbreak of apparently viral pneumonia of unknown etiology emerged in the city of Wuhan, in the Chinese province of Hubei.

On January 9, 2020, the Chinese health authorities and the World Health Organization (WHO) announced the discovery of a novel coronavirus, known as 2019-nCoV, which was confirmed as the agent responsible for the pneumonia cases (see the Institut Pasteur's fact sheet on the "Wuhan coronavirus" - page in French).

Over the weekend of January 11-12, the Chinese authorities shared the full sequence of the coronavirus genome, as detected in samples taken from the first patients. "Sequencing the genome of pathogens is crucial for the development of specific diagnostic tests and the identification of potential treatment options," explains Sylvie van der Werf, Director of the National Reference Center (CNR) for Respiratory Viruses at the Institut Pasteur.

Friday January 24, 2020. Detection of the virus confirmed in France

On Friday January 24, late in the morning, the Institut Pasteur received samples of three suspected cases (two patients in Paris and one in Bordeaux). "Using the samples taken from these patients, we detected the novel coronavirus," says Sylvie Behillil, Deputy Director of the CNR at the Institut Pasteur.

From Friday January 24, 2020. Viral genome sequenced at the Institut Pasteur

That same Friday evening, scientists launched the process of sequencing the viral genome based on the samples. The CNR prepared the material for sequencing, ready for P2M to begin work immediately the following Monday. The sequencing run was completed by early evening on the Tuesday, and the scientists used data analysis to obtain the sequence of the whole genome in two of the first three confirmed cases in France. "This proves the efficacy of the CNR's process of analysis based on viral sequencing," continues Vincent Enouf.

Thursday January 30, 2020. The Institut Pasteur obtains and shares the whole sequence of the virus

The P2M platform (see inset below) currently performs at an extremely high level; the average time taken to produce sequences ranges from three days (for emergencies) to a maximum of ten days. In this case, it took just three days for the whole sequence to be determined: "We performed data analysis during the night from Tuesday to Wednesday, then corroborated the results on Wednesday with counter analysis," explains Vincent Enouf. "The whole sequence was confirmed in just three days."

What can we learn from it? "The sequences were identical in all our samples. One member of the couple must have contaminated the other, as the virus is the same." The two full sequences of the virus isolated in two of the first French cases were submitted to the Global Initiative on Sharing All Influenza Data (GISAID) platform,1 which was initially developed to share sequences and monitor the genetic evolution of influenza viruses, a process that is vital to determine the composition of the influenza vaccine. A special "coronavirus" tab has been created so that the scientific community can work together and advance at a quicker pace.

"Around twenty other sequences of the novel coronavirus genome have been obtained worldwide, and if we compare them with ours, we can see that they are all very close; there is not much diversity in the viruses analyzed, which suggests that coronavirus 2019-nCoV did not need to mutate in order to adapt and spread," continues Vincent Enouf.

The National Reference Center (CNR) for Respiratory Viruses at the Institut Pasteur in Paris is one of WHO's reference laboratories for coronavirus 2019-nCoV.

A total of eight people from the CNR and two from the P2M sequencing platform have been working on the virus this week and will continue to monitor the outbreak in France.

P2M, a state-of-the-art mutualized platform for microbiology also open to external CNRs

P2M is also available to external CNRs for sequencing. In 2019 it worked with four CNRs based outside the Institut Pasteur. The platform sequences bacteria, viruses, parasites and fungi. Thanks to experience gained over the past five years (since 2015), P2M today offers a highly efficient service, as shown by a first-pass success rate (i.e. a high-quality sequence providing comprehensive information on the entire genome) of more than 95% in 2019. Sequence production takes between three days (for emergencies) and ten days at most.

In 2019, P2M sequenced around 25,000 pathogens. Genome sequencing increases the sensitivity threshold for outbreak detection. Early identification of outbreaks by the Institut Pasteur's scientists (clustered cases in a short space of time caused by the same pathogen) enables epidemiologists to get to work immediately to determine the origins of the outbreak, and the authorities to coordinate the public health response.

Simple sequence repeats (SSRs) are regions of DNA with high diversity, and they have long been a mainstay for botanists examining the genetic structure of plant populations. However, as the cost of sequencing DNA continues to plummet and genetic technologies advance, newer techniques for mapping genetic diversity such as genotyping-by-sequencing (GBS) or RAD-seq have begun to rival the traditional use of SSRs. In research presented in a recent issue of Applications in Plant Sciences, Dr. Mark Chapman optimized the process of identifying SSRs from genomic and transcriptomic data, helping to assure the continued use and relevance of SSRs in the age of high-throughput sequencing (HTS).

Sequence data generated using HTS can be used to identify candidate SSRs, for which researchers can design primers to examine genetic structure in a species. However, little work has been done to calibrate or optimize this process, both in terms of guidelines for reasonable parameters to specify, or what kind or depth of sequencing may be sufficient and appropriate to identify a workable set of SSRs.

"I've used transcriptome data for over a decade to generate molecular markers and have often wondered whether using genomes or transcriptomes would be preferable," said Dr. Chapman, Associate Professor in Ecology and Evolutionary Biology at the University of Southampton. This study found that each data source had its benefits; genomic data may be preferable in species with low polymorphism, but transcriptomic data usually assembles into longer sequences more amenable to designing primers, and these primers may be more transferable across species.

"In addition, I always generate thousands of markers and only use a dozen or so, so I've always wondered what depth of sequencing would one have to generate to be sure of identifying a small number of markers for a basic population genetic study," said Dr. Chapman.

Researchers on a budget may look to generate the minimum necessary sequence data for SSR identification. Now these researchers have some guidance as to how many reads are sufficient: this study found that small assemblies of two million read pairs could generate about 200-2000 potential markers from the genome assemblies and about 600-3650 from the transcriptome assemblies.

As the cost of sequencing falls below the cost of labor for sample preparation, researchers are increasingly using newer techniques such as GBS and RAD-seq to map genetic diversity in populations. However, Dr. Chapman still sees a place for SSRs in the future of population genetics research. "SSRs have advantages over those other technologies that are unlikely to change even if costs go down, for example, the SSRs can be designed from specific genes of interest," said Dr. Chapman. "Also GBS and RAD-seq aren't really being explored for polyploids, whereas SSR scoring in polyploids can be done, with a bit of background information or careful design of primers. The untailored approach of GBS and RAD-seq is likely to resolve a lot of unscorable alleles in polyploids."

SSRs are a relatively inexpensive and efficient way to map genetic diversity in populations. The deluge of genetic data available from HTS can help to efficiently identify sets of SSRs, but until now there have not been clear guidelines for researchers seeking to do this work. In optimizing protocols and laying out major considerations in generating SSRs from genomic and transcriptomic data, Dr. Chapman has helped to bring SSR studies up to date.

As well as sequencing the whole genome of coronavirus 2019-nCoV, the Institut Pasteur continued to work on the samples taken from the first confirmed cases. The quality of these initial samples enabled rapid cell-culture isolation of the new virus. The Institut Pasteur's scientists now have access to the virus responsible for the infection. The isolation of the virus paves the way for new diagnostic, therapeutic and prophylactic approaches.

With the whole viral genome of coronavirus 2019-nCoV having recently been sequenced at the Institut Pasteur, the isolation of strains of coronavirus 2019-nCoV detected in France has now been successfully finalized, in a very short space of time, using the samples taken from the first confirmed French cases.

Coronavirus 2019-nCoV, responsible for the cases of pneumonia that emerged in China (see the Institut Pasteur's fact sheet on the Wuhan coronavirus - page in French), differs from two other viruses that are well known for causing respiratory outbreaks in recent years: the SARS-CoV virus, responsible for the SARS outbreak in 2003, and MERS-CoV, responsible for an outbreak that has been under way since 2012 in the Middle East.

The Institut Pasteur was actively involved in tackling these previous outbreaks, which yielded valuable lessons for the current situation. "For both SARS-CoV and MERS-CoV, cells known as Vero E6 were identified to culture the two coronaviruses," explains Sylvie van der Werf, Director of the National Reference Center (CNR) for Respiratory Viruses at the Institut Pasteur. "In January 2020, we brought them out of our collection, which is kept under strictly controlled conditions, so that we would be ready as soon as we detected a positive sample for coronavirus 2019-nCoV."

Extremely rapid growth of the virus in culture

The Institut Pasteur was therefore well prepared, and on Friday January 24, 2020, the very day that the first cases were confirmed, it began the process of culturing the samples that had tested positive for the virus on Vero E6 cells. "Using detection methods, we had observed a high viral load in the samples taken from the patients in hospital in Paris. This enabled us to identify which samples should be cultured first," says Sylvie Behillil, Deputy Director of the CNR at the Institut Pasteur.

The viruses continued to be cultured over the weekend of January 25-26, 2020. By the morning of Monday January 27, the culture had already grown! "We didn't think that it would grow so quickly," continues Sylvie Behillil. The rapid growth of the culture may be explained by "the high viral load in the samples," but also by "the quality of the samples," adds Vincent Enouf, Deputy Director of the CNR at the Institut Pasteur.

"We could see the cells becoming damaged and then grouping together, which can indicate that they have been infected. But we did not observe this cytopathic effect for all the inoculated samples; that reassured us that we had managed to isolate the strains, and this was then confirmed by additional analyses."

Virus 2019-nCoV now available for research

Now that the Institut Pasteur's scientists have access to coronavirus 2019-nCoV, they can set out to improve scientific knowledge about the virus.

Research will focus on four main areas.

Serology. Analyzing antigen-antibody reactions based on the antibodies found in patients' blood serum, and developing an effective serology test to screen for the infection among the population.NB: This is not a rapid diagnostic test for hospital use; it is a test to identify seroconversion in the population.

Development of specific treatments. Testing known antiviral molecules that act on the replication cycle of some viruses to assess their therapeutic or even prophylactic potential, and looking for antibodies that may have therapeutic applications.

Vaccination. Based on the virus, developing vaccine approaches that have already been explored for other viruses – Ebola, MERS-CoV and SARS-CoV –, with the aim of proposing a vaccine candidate.

Viral pathogenesis. Understanding how the virus works, how it replicates and interacts with the cell and the host organism, to gain a clearer picture of its pathogenic nature and identify biomarkers for infection or new targets for the development of treatments.

Studies have shown a rapid increase in new cases of type 1 diabetes worldwide. However, scientists and researchers have struggled to identify a direct cause. Many have questioned if changes in the environment or lifestyle have impacted the disease. In a newly released review paper published in The Lancet Diabetes & Endocrinology, faculty from the Colorado School of Public Health at the Anschutz Medical Campus examined whether any environmental exposures can explain why type 1 diabetes is on the rise.

"The incidence of type 1 diabetes has increased 3 percent per year over the past three decades. This increase is too rapid to be due to genetic factors, suggesting that environmental factors may play a role," said Jill Norris, MPH, PhD, professor and chair of epidemiology at the Colorado School of Public Health and lead author of the paper.

Identifying environmental factors associated with type 1 diabetes that influence its incidence can inform future preventive trials and searches for other environmental risk factors. In this paper, researchers reviewed the literature on environmental factors like air pollution, diet, childhood obesity, the duration of breastfeeding, the introduction of cow's milk, infections, and many others that showcase an impact on type 1 diabetes.

The researchers then looked at prevalence of an exposure over time while varying its annual increase under simulated scenarios. Using the simulated data, the research showed that if a single factor were to explain the changes in the incidence of type 1 diabetes over the past few decades, it would have to be very strongly associated with the risk of type 1 diabetes.

The simulated scenarios showed that an environmental factor that increased at a constant rate from nearly absent in the population to nearly ubiquitous would have to confer a relative risk of 5 to explain an approximately 3 percent annual increase in the incidence of type 1 diabetes. However, most of the environmental factors reviewed had a relative risk of less than 2.

"While several factors have been associated with type 1 diabetes, none of the associations are of a magnitude that can explain the rapid increase in incidence alone," Norris said. "Moreover, evidence of the changing prevalence of these same exposures over time is not convincing nor consistent."

The paper explains that more research is required, and it is possible that multiple factors simultaneously may account for the increase in type 1 diabetes cases. Other factors are that the magnitude of observed associations may have been underestimated due to exposure measurement error or mismodeling of complex exposure-time-response relationships.

The study concludes that the identification of environmental factors influencing type 1 diabetes risk and increased understanding of the etiology at the individual level, regardless of the ability to explain the changing incidence at the population level, is important because of the implications for prevention.

Therapeutic horseback riding combined with brain-building exercises can improve the dexterity, coordination and strength of children with neurodevelopmental disorders, shows a study in Frontiers in Veterinary Science.

Neurodevelopmental disorders - such as attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) - affect as many as one in six American children. Physical activity is known to benefit these patients in a variety of ways, but this is the first study showing the short and long-term effects of a program combining horseback riding and cognitive training.

"We wanted to investigate how a combination of equine-assisted activities and various brain-building tasks, administered by a speech therapist, would affect motor skills in children with disorders including autism spectrum disorder and attention deficit hyperactivity," says Dr. Brandon Rigby, of the Texas Woman's University in the United States.

"Our findings should be helpful to therapists and other healthcare professionals who are tasked with implementing strategies and interventions to improve motor skill proficiency in children and youth with ADHD and ASD, which were the most common diagnoses in our study."

For their study, Rigby and his collaborators recruited 25 children with neurodevelopmental disorders between the ages of 5 and 16. Each child completed one of several different programs ranging in length from eight weeks to one year. The programs included weekly introductory horseback riding, as well as sessions with a speech therapist two to three times per week.

During the horseback riding, the children learned about horse anatomy, riding equipment, and the basics of riding. The brain-building activities focused on exercises that train the brain to process sensory information such as sound, sight, balance and spatial orientation. These sessions included music therapy, eye tracking exercises and hand-eye coordination tasks. The children and their parents were also given daily exercises that they could perform at home.

After eight weeks of the program, the children showed improved motor skills, although there was sometimes a delay before the changes became apparent. For the participants that continued the program for one year, these benefits continued for the duration of the study. These participants also showed improvements in their behavior and academic performance, including social and communication skills. Additionally, anecdotal responses from parents and caregivers suggested that the children were more positive, focused and calm both in and outside of the program.

Given the small size of the study, larger-scale research is still needed to better understand the potential benefits to the range of neurodevelopmental disorders. Some limitations include the varying diagnoses of the participants (as opposed to looking at benefits per ADHD or autism specifically), and the allowance to continue prescribed medications or therapies outside the scope of this program. Despite this, the program's results are promising, and the researchers hope that this will inspire further interest in cross-disciplinary programs.

"These findings may allow for a greater demand for these programs, ultimately making them more accessible and affordable," says Rigby.

Unlike what we commonly refer to as 'genes', these phantom genes or 'Long noncoding RNA' (LncRNAs) do not lead to the production of proteins that our cells, and thus our entire bodies are made of.

Previously, it was believed that LncRNAs served no major purpose in cells, but new research now shows that one of these LncRNAs termed 'LincIRS2' is important for safeguarding our metabolism as LincIRS2 loss favors development of metabolic complications in mice.

In my estimate, only the function of less than 100 of the nearly 60,000 LncRNAs encoded in our genomes has been truly understood says Jan-Wilhelm Kornfeld, Danish Diabetes Academy (DDA) professor for Molecular Biology of Metabolic Diseases at University of Southern Denmark.

In clear comparison, researchers have largely understood the function of the 20,344 genes that encode proteins.

That's why it's so exciting that we were able to identify the key role of this particular LncRNA using mice as a model organism, he says.

In addition, we were able to delineate a new, exciting mechanisms for how LncRNAs themselves are controlled.

Editing mice with CRISPR

Using the 'molecular scissor' CRISPR/Cas9, Jan-Wilhelm Kornfelds research team succeeded in cutting out LincIRS2 from the mouse's genome. Next, the researchers observed that mice lacking LincIRS2 developed metabolic complications like elevated blood sugar levels when the LncRNA had been deactivated. Conversely, when performing treatments that activate LincIRS2, mice maintained healthy blood sugar levels even when becoming obese.

It is difficult to predict exactly how this new knowledge can be used, but it is intriguing to speculate that restoring or inhibiting specific LncRNAs could be used to treat diabetic patients or other metabolic disorders one day, says Jan-Wilhelm Kornfeld.

His research team just published these new findings in the prestigious journal Nature Communications. The lead author of the article is Dr. Marta Pradas-Juni, who is a postdoc in Jan-Wilhelm Kornfelds' research team.

Fact: What is a Long noncoding RNA?

DNA serves as blueprint for producing proteins that constitute the essential building blocks all cells are made of. The molecular intermediary that converts DNA information into proteins is called RNA. Thus, RNA's primary purpose is to translate the 'genes' DNA into protein.

In our bodies, 20,344 different genes are specifically designed to create the many different proteins that our bodies require. The majority of these so-called protein-coding RNAs have been mapped by scientists. That is why, we today largely understand exactly which proteins these RNAs give rise to.

However, nearly 60,000 RNAs called 'Long noncoding RNAs' are written into our genomes that never contribute to the formation of a protein. How they function, and how they are involved in disease development is largely unknown.

PITTSBURGH (Jan. 31, 2020) ... Let's talk about slime.

Mucus is a protective, slimy secretion produced by goblet cells and which lines organs of the respiratory, digestive, and reproductive systems. Slime production is essential to health, and an imbalance can be life-threatening. Patients with diseases such as asthma, chronic obstructive pulmonary disease (COPD), and ulcerative colitis produce too much mucus, often after growing too many goblet cells. Loss of goblet cells can be equally devastating - for instance during cancer, after infection, or injury. The balance of slime creation, amount, and transport is critical, so doctors and medical researchers have long sought the origins of goblet cells and have been eager to control processes that regenerate them and maintain balanced populations.

Recently, a group of bioengineers at the University of Pittsburgh discovered a case of goblet cell regeneration that is both easily accessible and happens incredibly fast on cells isolated from early developing frog embryos. Their findings were published this week in the journal Nature Communications (DOI: 10.1038/s41467-020-14385-y).

Lance Davidson, William Kepler Whiteford Professor of Bioengineering at Pitt, leads the MechMorpho Lab in the Swanson School of Engineering where his researchers study the role of mechanics in human cells as well as the Xenopus embryo - an aquatic frog native to South Africa.

"The Xenopus tadpole, like many frogs, has a respiratory skin that can exchange oxygen and perform tasks similar to a human lung," explained Davidson. "Like the human lung, the surface of the Xenopus respiratory skin is a mucociliated epithelium, which is a tissue formed from goblet cells and ciliated cells that also protects the larva against pathogens. Because of these evolutionary similarities, our group uses frog embryonic organoids to examine how tissue mechanics impact cell growth and tissue formation."

Studying this species is a rapid and cost-effective way to explore the genetic origins of biomechanics and how mechanical cues are sensed, not just in the frog embryo, but universally. When clinicians study cancer in patients, such changes can take weeks, months, or even years, but in a frog embryo, changes happen within hours.

"In this project, we took a group of mesenchymal cells out of the early embryo and formed them into a spherical aggregate, and within five hours, they began to change," Davidson said. "These cells are known to differentiate into a variety of types, but in this scenario, we discovered that they changed very dramatically into a type of cell that they would not have changed into had they been in the embryo."

The lab surprisingly uncovered a case of regeneration that restores a mucociliated epithelium from mesenchymal cells. They performed the experiment multiple times to confirm the unexpected findings and began to look closely at what microenvironmental cues could drive cells into an entirely new type.

"We have tools to modulate the mechanical microenvironment that houses the cells, and to our surprise, we found that if we made the environment stiffer, the aggregates changed into these epithelial cells," explained Davidson. "If we made it softer, we were able to block them from changing. This finding shows that mechanics alone can cause important changes in the cells, and that is a remarkable thing."

Davidson's group is interested in how cells, influenced by mechanics, may affect disease states. The results detailed in this article may drive new questions in cancer biology, prompting researchers to consider whether certain kinds of invasive cancer cells might revert to a resting cell type based on the stiffness or softness of their surroundings.

"When applying these results to cancer biology, one might ask, 'If tumors are surrounded by soft tissues, would they become dormant and basically non-invasive?' Or, 'If you have them in stiff tissues, would they invade and become deadly?'" said Davidson. "These are major questions in the field that biomechanics may be able to help answer. Many researchers focus solely on the chemical pathways, but we are also finding mechanical influencers of disease."

Hye Young Kim, research fellow at the Korea Advanced Institute of Science and Technology (KAIST) and former member of the MechMorpho Lab, will continue this work at the Center for Vascular Research at KAIST's Institute for Basic Science. She will study how cell motility changes during regeneration and how epithelial cells assemble a new epithelium. Davidson and his lab will explore how this novel case of mechanical cues are sensed by mesenchymal cells and how these mechanical induction pathways are integrated with known pathways that control cell fate choices.

"Frog embryos and organoids give us unparalleled access to study these processes, far more access than is possible with human organs," he said. "The old ideas that regeneration is controlled exclusively by diffusing growth factors and hormones is giving way to the recognition that the physical mechanics of the environment - such as how rubbery or fluid the environment - play just as critical a role."

The circadian clock system (from Latin "circa diem", about a day) allows the organisms to anticipate periodical changes of geophysical time, and to adjust to these changes. Nearly all the cells in our body comprise molecular clocks that regulate and synchronize metabolic functions to a 24-hour cycle of day-night changes. Today, increasing evidence show that disturbances in our internal clocks stemming from frequent time zone changes, irregular working schedules or ageing, have a significant impact on the development of metabolic diseases in human beings, including type-2 diabetes. Such disturbances seem to prevent the proper functioning of the cells in the pancreatic islet that secrete insulin and glucagon, the hormones that regulate blood sugar levels. By comparing the pancreatic cells of type 2 diabetic human donors with those of healthy people, researchers at the University of Geneva (UNIGE) and at the University Hospitals of Geneva (HUG), Switzerland, were able to demonstrate, for the first time, that the pancreatic islet cells derived from the Type 2 Diabetic human donors bear compromised circadian oscillators. The disruption of the circadian clocks was concomitant with the perturbation of hormone secretion. Moreover, using clock modulator molecule dubbed Nobiletin, extracted from lemon peel, the researchers succeeded in "repairing" the disrupted cellular clocks and in partial restoring of the islet cell function. These results, published in the Proceedings of the National Academy of Sciences of the United States, provide a first insight into innovative approach for diabetes care.

Two years ago, the team led by Charna Dibner, Principle Investigator in the Departments of Medicine and of Cell Physiology and Metabolism, and Diabetes Centre at UNIGE Faculty of Medicine, and at HUG, has already shown that in rodents the perturbation of pancreatic cellular clocks led to disrupted insulin and glucagon secretion, thus promoting the onset of diabetes. But what is the situation in human beings? "We had also previously observed that if the clocks of human pancreatic cells were artificially disrupted in the cellular culture in vitro, secretion of the key islet hormones - insulin and glucagon - was compromised,» says Volodymyr Petrenko, a researcher in Dr. Dibner's lab and the first author of these publications. Hence our next step, that we report here, was to unravel whether the circadian rhythms were perturbed in human pancreatic islets in type 2 diabetes, and, if so, how would this perturbation affect the islet function."

Using combined bioluminescence-fluorescence time-lapse microscopy, a technology that allows tracking the molecular clock activity in living cells very precisely over time, the scientists compared the behaviour of pancreatic cell of type-2 diabetic donors and those of healthy subjects throughout the day. "The verdict is indisputable", says Charna Dibner. The biological rhythms of the islet cells in type-2 diabetes exhibit both reduced amplitudes of circadian oscillations and poor synchronization capacity. &laquoAs a result, hormone secretion is no longer coordinated. Moreover, the defects in temporal coordination of insulin and glucagon secretion observed in patients with type-2 diabetes were comparable to those measured in healthy islet cells with artificially-disrupted circadian clock."

It's all in the timing!

Circadian clocks represent the daily cycles governing the various cellular functions. There are several interlocking levels of synchronization of these clocks, the main one being light, which in particular regulates the central clock located in the cerebral hypothalamus. Like a conductor in the orchestra, it regulates peripheral clocks present in organs and cells. The latter are therefore partly centrally regulated, but function differently in each organ, and even in each cell, depending on their functions. "Pancreatic cells are also subject to the rhythm of fasting and food intake, and to a tight hormonal regulation", says Charna Dibner. "Coordinating all levels of regulation therefore allows the optimization of metabolic functions. Clocks deregulation in pancreatic islet leads to a compromised function: they are not anymore anticipating food-derived signals. Indeed, if you eat the same food but at night rather than during the day, you may gain weight much faster, due to a suboptimal response of your metabolism."

Setting the right time again

Step two of their research: the Geneva scientists used Nobiletin, a small clock modulator molecule - a natural ingredient of lemon peel whose impact on circadian clocks has been recently discovered - in order to resynchronize the clocks. "By acting on one of the core-clock components, it resets efficiently the amplitude of the oscillations in the human islets" says Volodymyr Petrenko. "And as soon as we got the clocks back in sync, we also observed an improvement in insulin secretion."

"This is the first proof of principle that repairing compromised circadian clocks may help improving the function of the pancreatic islet hormone secretion", says Charna Dibner. "We will continue by exploring this repair mechanism in vivo, first in animal models. Our society experiences epidemic growth in metabolic diseases, concomitant with shifted working and eating schedules, and lack of sleep. By re-synchronizing the perturbed molecular clocks, either by personalized eating and exercise schedules or with the help of clock modulator molecules, we hope to ultimately be able to provide an innovative solution to an epidemical metabolic problem affecting an ever-increasing proportion of the world's population. ."

Physicists believe that in the Universe's first ten microseconds free quarks and gluons filled all of spacetime, forming a new phase of matter named 'quark-gluon plasma' (QGP). Experimental and theoretical work at CERN was instrumental in the discovery of this hot soup of primordial matter, which is recreated today in accelerator-based lab experiments. To discover QGP in such experiments, the observation of exotic 'strange' quarks is very important. If QGP is created, strangeness is readily produced through collisions between gluons. In analysis published in EPJ ST, Dr Johann Rafelski from The University of Arizona, United States, also working at CERN, presents how our understanding of this characteristic strangeness production signature has evolved over the span of his long career.

Using the style of a 'personal diary', Rafelski firstly reviews and summarises decades of work. Describing leading experimental and theoretical contributions, he recounts how and why strange quarks are produced so efficiently in QGP, and how this behaviour has been exploited for QGP discovery. He also explores strangeness as a tool in the search and discovery of this primordial phase of matter; existent at unimaginably high temperatures and pressures. He then follows the line of research through to the ongoing experimental ultra-high-energy experiments involving head-on collisions between both heavy nuclei and lighter protons, carried out at CERN's Large Hadron Collider (LHC).

Secondly, Rafelski follows the narrative with a commented set of his own unpublished work, focusing on pioneering theories and QGP discovery. He also includes a selection from the comments of referees offering both criticism and praise for these studies; along with his own present-day perspectives. This review highlights the numerous successes enjoyed by theorists, through decades of tireless effort to explain and understand the primordial QGP. All the same, it shows that many pressing questions remain to be answered. Rafelski continues to contribute to the field through his rich research experience and will undoubtedly inspire new generations of physicists to continue the study of exotic quarks in the primordial Universe.

Effortless learning during sleep is the dream of many people. The supportive effect of smells on learning success when presented both during learning and sleep was first proven in an extensive sleep laboratory study. Researchers at the University of Freiburg - Medical Center, the Freiburg Institute for Frontier Areas of Psychology and Mental Health (IGPP) and the Faculty of Biology at the University of Freiburg have now shown that this effect can be also achieved very easily outside the lab. For the study, pupils in two school classes learned English vocabulary - with and without scent sticks during the learning period and also at night. The students remembered the vocabulary much better with a scent. The study was published in the Nature Group's Open Access journal Scientific Reports on 27 January 2020.

"We showed that the supportive effect of fragrances works very reliably in everyday life and can be used in a targeted way," said study leader PD Dr. Jürgen Kornmeier, head of the Perception and Cognition Research Group at the Freiburg-based IGPP and scientist at the Department of Psychiatry and Psychotherapy at the University of Freiburg - Medical Center in Germany.

The smell of roses when learning and sleeping

For the study, first author and student teacher Franziska Neumann conducted several experiments with 54 students from two 6th grade classes of a school in southern Germany. The young participants from the test group were asked to place rose-scented incense sticks on their desks at home while learning English vocabulary and on the bedside table next to the bed at night. In another experiment, they also placed the incense sticks on the table next to them during a vocabulary test at school during an English test. The results were compared with test results in which no incense sticks were used during one or more phases.

"The students showed a significant increase in learning success by about 30 percent if the incense sticks were used during both the learning and sleeping phases," says Neumann. The results also suggest that the additional use of the incense sticks during the vocabulary test promotes memory.

Findings are suitable for everyday use

"One particular finding beyond the seminal initial study was, that the fragrance also works when it is present all night," says Kornmeier. "This makes the findings suitable for everyday use." Previous studies had assumed that the fragrance needs to be only present during a particularly sensitive sleeping phase. However, since this sleep phase needs to be determined by an effortful measurement of brain activity by means of an electroencephalogram (EEG) in the sleep laboratory, this finding was not suitable for everyday use. "Our study shows that we can make learning during sleep easier. And who would have thought that our nose could help considerably in this," says Kornmeier.

Rat spermatozoa are two to four times larger than that of other animal species and are easily damaged by changes in pH, osmotic pressure, and temperature. Because these animals are very frequently used in medical research, a cryopreservation method was developed nearly 20 years ago. However, rat spermatozoa motility after thawing is extremely poor, and unless artificial insemination is performed at night (10:00-11:00 pm) no offspring will be produced. Furthermore, the number of offspring produced after successful artificial insemination is often lower than normal so the cryopreservation of rat sperm is not typically considered practical.

To improve cryopreservation methods, Professor Nakagata and Dr. Takeo of the Center for Animal Resources and Development (CARD) at Kumamoto University, Japan have been searching for methods to retain sperm mobility after thawing. They knew that the freezing process significantly reduced sperm motility, so they attempted to chill the sperm first to reduce movement as much as possible before freezing.

They tested their cryopreservation method on a type of genetically modified rat (EGFP rat) sperm that emits green fluorescence and then used it for in vitro fertilization. Surprisingly, the fertilization rate exceeded 80% and the experiment successfully produced over 300 offspring from the sperm of one male rat.

Sperm cryopreservation is easier than the cryopreservation of fertilized eggs, and many cells (50 - 100 million) can be obtained from a single male rat. In recent years, genetically modified rats useful for human disease research have been produced using genome editing technology. This indicates that there is a need for an efficient technique to preserve genetically modified rat strains. The cryopreservation technology developed here can provide an efficient storage method of genetically modified rats and could accelerate the development of treatments for intractable diseases.
"Compared to mice, rats are about ten times the size, require a larger housing space, and simply cost more to keep. There is a need to reduce the amount of space they take up and their cost for research labs," said Professor Nakagata. "Our cryopreservation technique is likely to be very useful in the preservation of genetically modified rat strains. We believe that it could become a new global standard for research resources."