bluuebunny/crossref_metadata_2025 huggingface dataset:
Grapevine microbiota reflect diversity among compartments and complex interactions within and among root and shoot systems
Authors: Swift Joel F. , Hall Megan E. , Harris Zachary N. , Kwasniewski Misha T. , Miller Allison J.
Published: November 2020

Background

Within an individual plant, different compartments (e.g. roots, leaves, fruits) host distinct communities of microorganisms due to variation in structural characteristics and resource availability. Grafting, which joins the root system of one individual with the shoot system of a second genetically distinct individual, has the potential to bring the microbial communities of different genotypes together. An important question is the extent to which unique root system and shoot system genotypes, when grafted together, influence the microbiota of the graft partner. Our study sought to answer this question by utilizing an experimental vineyard composed of ‘Chambourcin’ vines growing ungrafted and grafted to three different rootstocks, replicated across three irrigation treatments. We characterized bacterial and fungal communities in roots, leaves, and berries, as well as surrounding soil. Our objectives were to (1) characterize the microbiota of compartments within the root system (roots and adjacent soil) and the shoot system (leaves and berries), (2) determine the influence of rootstock genotypes, irrigation, and their interaction on the microbiota of aboveground and belowground compartments, and (3) investigate the distribution of microorganisms implicated in the late-season grapevine bunch rot disease sour rot (Acetobacterales and Saccharomycetes).

Results

Compartments were significantly differentiated in bacterial and fungal richness and composition. Abundance-based machine learning accurately predicted the compartment and differential abundance analysis showed a large portion of taxa differed significantly across compartments. Rootstock genotypes did not differ significantly in microbial community richness or composition; however, individual microbial taxa exhibited significant differences in abundance based on rootstock and irrigation treatment. The relative abundance of Acetobacterales and Saccharomycetes in the berry was influenced by complex interactions among rootstock genotype and irrigation.

Conclusion

Our results indicate that grapevine compartments retain distinct core microbiota regardless of the rootstock to which they are grafted. While rootstock genotype generally had a subtle impact on global patterns of microbial diversity, we found associations between rootstock genotypes and specific groups of microorganisms. Further experimental validation is needed in order to understand how associations with these microorganisms impacts a vine’s susceptibility to sour rot upon damage and whether the characteristics of wine are impacted.
COVID-19 genetic risk and Neanderthals: A case study highlighting the importance of scrutinizing diversity
Authors: Wohlers Inken , Calonga-Solís Verónica , Jobst Jan-Niklas , Busch Hauke
Published: November 2020

Recent genome wide association studies (GWAS) have identified genetic risk factors for developing severe COVID-19 symptoms. The first published study reported a 1bp insertion rs11385942 on chromosome 3 (1) and subsequent studies single nucleotide variants (SNVs) such as rs35044562, rs67959919 (2) and rs13078854 (3), all highly correlated with each other. Zeberg and Pääbo (4) subsequently traced them back to Neanderthal origin. They found that a 49.4 kb genomic region including the risk allele of rs35044562 is inherited from Neanderthals of Vindija in Croatia. Here we add a differently focused evaluation of this major genetic risk factor to these recent analyses. We show that (i) COVID-19-related genetic factors of three previously assessed Neanderthals deviate from those of modern humans and that (ii) they differ among world-wide human populations, which compromises risk prediction in non-Europeans. Currently, caution is thus advised in the genetic risk assessment of non-Europeans during this world-wide COVID-19 pandemic.
Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4
Authors: Hoeksema Marten A. , Shen Zeyang , Holtman Inge R. , Zheng An , Spann Nathan , Cobo Isidoro , Gymrek Melissa , Glass Christopher K.
Published: November 2020

Mechanisms by which non-coding genetic variation influences gene expression remain only partially understood but are considered to be major determinants of phenotypic diversity and disease risk. Here, we evaluated effects of >50 million SNPs and InDels provided by five inbred strains of mice on the responses of macrophages to interleukin 4 (IL-4), a cytokine that plays pleiotropic roles in immunity and tissue homeostasis. Remarkably, of >600 genes induced >2-fold by IL-4 across the five strains, only 26 genes reached this threshold in all strains. By applying deep learning and motif mutation analyses to epigenetic data for macrophages from each strain, we identified the dominant combinations of lineage determining and signal-dependent transcription factors driving late enhancer activation. These studies further revealed mechanisms by which non-coding genetic variation influences absolute levels of enhancer activity and their dynamic responses to IL-4, thereby contributing to strain-differential patterns of gene expression and phenotypic diversity.
Relationships between the Bone Expression of Alzheimer Disease-Related Genes, Bone Remodelling Genes and Cortical Bone Structure in Neck of Femur Fracture
Authors: Stapledon Catherine J.M. , Stamenkov Roumen , Cappai Roberto , Clark Jillian M. , Bourke Alice , Solomon L. Bogdan , Atkins Gerald J.
Published: November 2020

Neck of femur (NOF) fracture is a prevalent fracture type amongst the ageing and osteoporotic populations, commonly requiring total hip replacement (THR) surgery. Increased fracture risk has also been associated with Alzheimer disease (AD) in the aged. Here, we sought to identify possible relationships between the pathologies of osteoporosis and dementia by analysing bone expression of neurotropic or dementia-related genes in patients undergoing THR surgery for NOF fracture. Femoral bone samples from 66 NOF patients were examined for expression of the neurotropic genes amyloid precursor protein (APP), APP-like protein-2 (APLP2), Beta Secretase Cleaving Enzyme-1 (BACE1) and nerve growth factor (NGF). Relationships were examined between the expression of these and of bone regulatory genes, systemic factors and bone structural parameters ascertained from plain radiographs. We found strong relative levels of expression and positive correlations betweenAPP, APLP2, BACE1andNGFlevels in NOF bone. Significant correlations were found betweenAPP, APLP2, BACE1mRNA levels and bone remodelling genesTRAP, RANKL, and theRANKL:OPGmRNA ratio, indicative of potential functional relationships at the time of fracture. Analysis of the whole cohort, as well as non-dementia and dementia sub-groups, revealed structural relationships betweenAPPandAPLP2mRNA expression and lateral femoral cortical thickness. These findings suggest that osteoporosis and AD may share common molecular pathways of disease progression, perhaps explaining the common risk factors associated with these diseases. The observation of a potential pathologic role for AD-related genes in bone may also provide alternative treatment strategies for osteoporosis and fracture prevention.
Paraspeckles are constructed as block copolymer micelles through microphase separation
Authors: Yamazaki Tomohiro , Yamamoto Tetsuya , Yoshino Hyura , Souquere Sylvie , Nakagawa Shinichi , Pierron Gerard , Hirose Tetsuro
Published: November 2020

Paraspeckles are constructed by NEAT1_2 architectural long noncoding RNAs and possess characteristic cylindrical shapes with highly ordered internal organization, distinct from typical liquid–liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. We then applied a theoretical framework using soft matter physics to understand the principles that determine the NEAT1_2 organization, shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through microphase separation. This work provides an experimentally-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding microphase-separated condensates in cells.
The mental health of staff working in intensive care during COVID-19
Authors: Greenberg Neil , Weston Dale , Hall Charlotte , Caulfield Tristan , Williamson Victoria , Fong Kevin
Published: November 2020

Background

Intensive Care Unit (ICU), anaesthetic and theatres staff have faced significant challenges during the COVID-19 pandemic which have the potential to adversely affect their mental health

Aims

To identify the rates of probable mental health disorder in ICU and anaesthetic staff in six English hospitals during June and July 2020

Methods

An anonymised brief web-based survey comprising standardised questionnaires examining depression, anxiety symptoms, symptoms of Post Traumatic Stress Disorder (PTSD), wellbeing and alcohol use was administered to staff.

Results

709 participants completed the surveys comprising 291 (41%) doctors, 344 (48.5%) nurses, and 74 (10.4%) other healthcare staff. Over half (58.8%) reported good wellbeing, however 45.4% met the threshold for probable clinical significance on at least one of the following measures: severe depression (6.3%), PTSD (39.5%), severe anxiety (11.3%) or problem drinking (7.2%). 13.4% of respondents reported frequent thoughts of being better off dead, or of hurting themselves in the past two weeks. We found that doctors consistently reported better mental health than nurses.

Conclusions

We found substantial rates of probable mental health disorders, and thoughts of self-harm, amongst ICU staff; these difficulties were especially prevalent in nurses. These results indicate the need for a national strategy to protect the mental health, and decrease the risk of functional impairment, of ICU staff whilst they carry out their essential work during COVID-19.

Occ Med Statements: article should contain 3 statements (each max of 3 bullets of max 50 words each)

What is already known about this subject

Intensive care unit (ICU) staff are regularly exposed to traumatic situations as part of their job

Previous studies have shown them to be at risk of psychological and moral distress

Little is known about the mental health of ICU staff during the current pandemic

What this study adds

Almost half of ICU staff report symptoms consistent with a probable diagnosis of post traumatic stress disorder, severe depression or anxiety or problem drinking

Around 1 in 7 ICU staff report recent thoughts of self-harm or of wanting to be better off dead

Nursing staff are more likely to report higher levels of distress than doctors or other clinical staff

What impact this may have on practice or policy

Healthcare managers need to prioritise staff mental health support and timely access to evidence based treatments for ICU staff

Supervisors and managers should be aware that a substantial proportion of ICU staff may perform less well because of their current poor state of mental health

More work is needed to understand whether the high levels of mental health symptoms identified in this study are truly indicative of high levels of clinical need for mental healthcare
SARS-CoV-2 antibody prevalence and symptoms in a local Austrian population
Authors: Ladage Dennis , Höglinger Yana , Ladage Dorothee , Adler Christoph , Yalcin Israfil , Braun Ralf J.
Published: November 2020

Background

Since December 2019 the novel coronavirus (SARS-CoV-2) is the center of global attention due to its rapid transmission and toll on health care systems and global economy. Population-based serosurveys measuring antibodies for SARS-CoV-2 provide one method for estimating infection rates and monitoring the progression of the epidemic.

Methods

In June 2020 we succeeded in testing almost half of the population of an Austrian township (n=835 of 1359 inhabitants) with a reported higher incidence for COVID-19 infections. We determined the level of prevalence for SARS-CoV-2 in this population, factors affecting, and symptoms correlated with prior infection.

Results

We found a high prevalence of 9% positive antibodies among the town population in comparison to 6% of the neighboring villages. Only 20% of SARS-CoV-2 cases self-declared being asymptomatic. In contrast, we identified six single major symptoms, including anosmia/ageusia, weight loss, anorexia, general debility, dyspnea, and fever, and especially their combination to be of high prognostic value for predicting SARS-CoV-2 infection in a patient. Our comparison of the gold standard lab-based ELISA test and the on-site antibody test demonstrated a lack of accuracy for the latter test form.

Conclusions

This population study demonstrated a high prevalence of antibodies to SARS-CoV-2 as a marker of both active and past infections in an Austrian township. Several symptoms revealed a diagnostic value especially in combination. Results from self-administered antibody tests should be considered with caution.
A Digital CRISPR-based Method for the Rapid Detection and Absolute Quantification of Viral Nucleic Acids
Authors: Wu Xiaolin , Chan Cheryl , Lee Yie Hou , Springs Stacy L. , Lu Timothy K. , Yu Hanry
Published: November 2020

Quantitative real-time PCR and CRISPR-based methods detect SARS-CoV-2 in 1 hour but do not allow for the absolute quantification of virus particles, which could reduce inter-lab variability and accelerate research. The 4-hour reaction time of the existing digital PCR-based method for absolute virus quantification is too long for widespread application. We report a RApid DIgital Crispr Approach (RADICA) for the absolute quantification of SARS-CoV-2 DNA and Epstein–Barr virus DNA in human samples that yields results within 1 hour. For validation, we compared RADICA to digital PCR for quantifying synthetic SARS-CoV-2 DNA and Epstein–Barr viral DNA. RADICA allows absolute quantification of DNA with a dynamic range from 0.6 to 2027 copies/µL (R2 value > 0.98), without cross-reactivity on similar virus or human background DNA. Thus, RADICA can accurately detect and quantify nucleic acid in 1h without thermal cycling, providing a 4-fold faster alternative to digital PCR-based virus detection.
Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients
Authors: Wyres Kelly L. , Hawkey Jane , Mirčeta Mirianne , Judd Louise M. , Wick Ryan R. , Gorrie Claire L. , Pratt Nigel F. , Garlick Jill S. , Watson Kerrie M. , Pilcher David V. , McGloughlin Steve A. , Abbott Iain J. , Macesic Nenad , Spelman Denis W. , Jenney Adam W. J. , Holt Kathryn E.
Published: November 2020

Background

Third-generation cephalosporin-resistant Gram-negatives (3GCR-GN) and vancomycin-resistant Enterococci (VRE) are common causes of multi-drug resistant healthcare-associated infections, for which gut colonisation is considered a prerequisite. However, there remains a key knowledge gap about colonisation and infection dynamics in high-risk settings such as the intensive care unit (ICU), thus hampering infection prevention efforts.

Methods

We performed a three-month prospective genomic survey of infection and gut-colonisation with 3GCR-GN and VRE among patients admitted to an Australian ICU.

Results

Among 287 patients screened on admission, 17.4% and 8.4% were colonised by 3GCR-GN and VRE, respectively. Escherichia coli was the most common species (n=36 episodes, 58.1%) and the most common cause of 3GCR-GN infection. Only two VRE infections were identified. The rate of infection among patients colonised with E. coli was low, but higher than those who were not colonised on admission (6% vs 2% E. coli, p=0.3). While few patients were colonised with 3GCR-Klebsiella pneumoniae or Pseudomonas aeruginosa on admission (n=4), all such patients developed infections with the colonising strain. Genomic analyses revealed 10 putative nosocomial transmission clusters: four VRE, six 3GCR-GN, with epidemiologically linked clusters accounting for 21% and 6% of episodes, respectively (OR 4.3, p=0.02).

Conclusions

3GCR-E. coli and VRE were the most common gut colonisers. E. coli was the most common cause of 3GCR-GN infection, but other 3GCR-GN species showed greater risk for infection in colonised patients. Larger studies are warranted to elucidate the relative risks of different colonisers and guide the use of screening in ICU infection control.

Key points

Surveillance for VRE or ESBL Gram-negative bacteria in ICU showed distinct species-specific clinical risk profiles. VRE and ESBL-Escherichia coli were the most common colonisers, but were associated with lower attack rate and transmission rate, compared with rarer coloniser Klebsiella pneumoniae.
Using convolutional neural network to predict remission of diabetes after gastric bypass surgery: a machine learning study from the Scandinavian Obesity Surgery Register
Authors: Cao Yang , Näslund Ingmar , Näslund Erik , Ottosson Johan , Montgomery Scott , Stenberg Erik
Published: November 2020

Background

Prediction of diabetes remission is an important topic in the evaluation of patients with type-2 diabetes (T2D) before bariatric surgery. While several high-quality predictive indices are available, artificial intelligence (AI) algorithms offer the potential for higher predictive capability. The objective was to construct and validate an AI prediction model for diabetes remission after Roux-en-Y gastric bypass surgery.

Methods

Patients who underwent surgery from 2007 until 2017 were included in the study, with collection of individual data from the Scandinavian Obesity Surgery Registry (SOReg), the Swedish National Patients Register, the Swedish Prescribed Drugs Register, and Statistics Sweden. A 7-layer convolution neural network (CNN) model was developed using 80% of patients randomly selected from SOReg and 20% of patients for external testing. The predictive capability of the CNN model and currently used scores (DiaRem, Ad-DiaRem, DiaBetter and IMS) were compared.

Results

In total, 8057 patients with T2D were included in the study. At 2 years after surgery 77.1% achieved pharmacological remission, while 62.2% achieved complete remission. The area under the receiver operating curve (AUC) for the CNN-model for pharmacological remission was 0.85 [95% confidence interval (CI): 0.83-0.86] during validation, and 0.83 for the final test, which was 9-12% better than the traditional predictive indices. AUC for complete remission was 0.83 (95% CI: 0.81-0.85) during validation, and 0.82 for the final test, which was 9-11% better than the traditional predictive indices.

Conclusion

The CNN method had better predictive capability compared to traditional indices for diabetes remission. However, further validation is needed in other countries to evaluate its external generalizability.
Social innovation research checklist: A crowdsourcing open call and digital hackathon to develop a checklist for research to advance social innovation in health
Authors: Kpokiri Eneyi , Chen Elizabeth , Li Jingjing , Payne Sarah , Shrestha Priyanka , Afsana Kaosar , Amazigo Uche , Awor Phyllis , de Lavison Jean-Francois , Khan Saqif , Mier-Alpaño Jana D. , Ong Alberto , Subhedar Shivani , Wachmuth Isabelle , Mehta Kala M. , Halpaap Beatrice , Tucker Joseph D.
Published: November 2020

While social innovations in health have shown promise in closing the healthcare delivery gap, especially in low- and middle-income countries (LMICs), more research is needed to evaluate, scale up, and sustain social innovations. Research checklists can standardize and improve reporting of research findings, promote transparency, and increase replicability of study results and findings. This article describes the development of a 17-item social innovation in health research checklist to assess and report social innovation projects and provides examples of good reporting. The checklist is adapted from the TIDieR checklist and will facilitate more complete and transparent reporting and increase end user engagement.

Summary points

While many social innovations have been developed and shown promise in closing the healthcare delivery gap, more research is needed to evaluate social innovation

The Social Innovation in Health Research Checklist, the first of its kind, is a 17-item checklist to improve reporting completeness and promote transparency in the development, implementation, and evaluation of social innovations in health

The research checklist was developed through a three-step process, including a global open call for ideas, a scoping review, and a three-round modified Delphi process

Use of this research checklist will enable researchers, innovators and partners to learn more about the process and results of social innovation in health research
Experiences of living with mental health problems during the COVID-19 pandemic in the UK: a coproduced, participatory qualitative interview study
Authors: Gillard Steven , Dare Ceri , Hardy Jackie , Nyikavaranda Patrick , Olive Rachel Rowan , Shah Prisha , Birken Mary , Foye Una , Ocloo Josephine , Pearce Ellie , Stefanidou Theodora , Pitman Alexandra , Simpson Alan , Johnson Sonia , Lloyd-Evans Brynmor
Published: November 2020

Purpose

Research is beginning to quantify the impact of COVID-19 on people with pre-existing mental health conditions. Our paper addresses a lack of in-depth qualitative research exploring their experiences and perceptions of how life has changed at this time.

Methods

We used qualitative interviews (N=49) to explore experiences of the pandemic for people with pre-existing mental health conditions. In a participatory, coproduced approach, researchers with lived experiences of mental health conditions conducted interviews and analysed data as part of a multi-disciplinary research team.

Results

Existing mental health difficulties were exacerbated for many people. People experienced specific psychological impacts of the pandemic, struggles with social connectedness, and inadequate access to mental health services, while some found new ways to cope and connect to community. New remote ways to access mental health care, including digital solutions, provided continuity of care for some but presented substantial barriers for others. People from black and ethnic minority (BAME) communities experienced heightened anxiety, stigma and racism associated with the pandemic, further impacting their mental health.

Conclusion

There is a need for evidence-based solutions to achieve accessible and effective mental health care in response to the pandemic, especially remote approaches to care. Further research should explore the long-term impacts of COVID-19 on people with pre-existing mental health conditions. Particular attention should be paid to understanding inequalities of impact on mental health, especially for people from BAME communities.
Infection patterns of endemic human coronaviruses in rural households in coastal Kenya
Authors: Nyaguthii Dickson Machira , Otieno Grieven P. , Kombe Ivy K. , Koech Dorothy , Mutunga Martin , Medley Graham F. , Nokes D. James , Munywoki Patrick K.
Published: November 2020

Introduction

The natural history and transmission patterns of endemic human coronaviruses are of increased interest following the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).

Methods

In rural Kenya 483 individuals from 47 households were followed for six months (2009-10) with nasopharyngeal swabs collected twice weekly regardless of symptoms. A total of 16,918 swabs were tested for human coronavirus (hCoV) OC43, NL63 and 229E and other respiratory viruses using polymerase chain reaction.

Results

From 346 (71.6%) household members 629 hCoV infection episodes were defined with 36.3% being symptomatic: varying by hCoV type and decreasing with age. Symptomatic episodes (aHR=0.6 (95% CI:0.5-0.8) or those with elevated peak viral load (medium aHR=0.4 (0.3-0.6); high aHR=0.31 (0.2-0.4)) had longer viral shedding compared to their respective counterparts. Homologous reinfections were observed in 99 (19.9%) of 497 first infections. School-age children (55%) were the most common index cases with those having medium (aOR=5.3 (2.3 – 12.0)) or high (8.1 (2.9 - 22.5)) peak viral load most often generating secondary cases.

Conclusion

Household coronavirus infection was common, frequently asymptomatic and mostly introduced by school-age children. Secondary transmission was influenced by viral load of index cases. Homologous-type reinfection was common. These data may be insightful for SARS-CoV-2.
Metabolic characterization of plasma and cyst fluid from cystic precursors to pancreatic cancer patients reveal metabolic signatures of bacterial infection
Authors: Morgell Ann , Reisz Julie A. , Ateeb Zeeshan , Davanian Haleh , Reinsbach Susanne E. , Halimi Asif , Gaiser Rogier , Valente Roberto , Arnelo Urban , Chiaro Marco Del , Sällberg Chen Margaret , D’Alessandro Angelo
Published: November 2020

Pancreatic cancer is the seventh leading cause of cancer-related death worldwide, with a 5-year survival rate as low as 9%. One factor complicating the management of pancreatic cancer is the lack of reliable tools for early diagnosis. While up to 50% of the adult population has been shown to develop precancerous pancreatic cysts, limited and insufficient approaches are currently available to determine whether a cyst is going to progress into pancreatic cancer. Recently, we used metabolomics approaches to identify candidate markers of disease progression in patients diagnosed with intraductal papillary mucinous neoplasms (IPMNs) undergoing pancreatic resection. Here we enrolled an independent cohort to verify the candidate markers from our previous study with orthogonal quantitative methods in plasma and cyst fluid from serous cystic neoplasm and IPMN (either low- or high-grade dysplasia or pancreatic ductal adenocarcinoma). We thus validated these markers with absolute quantitative methods through the auxilium of stable isotope-labelled internal standards in a new independent cohort. Finally, we identified novel markers of IPMN status and disease progression – including amino acids, carboxylic acids, conjugated bile acids, free and carnitine-conjugated fatty acids, purine oxidation products and TMAO. We show that the levels of these metabolites of potential bacterial origin correlated with the degree of bacterial enrichment in the cyst, as determined by 16S RNA. Overall, our findings are interesting per se, owing to the validation of previous markers and identification of novel small molecule signatures of IPMN and disease progression. In addition, our findings further fuel the provoking debate as to whether bacterial infections may represent an etiological contributor to the development and severity of the disease in pancreatic cancer, in like fashion to other cancers (e.g.,Helicobacter pyloriand gastric cancer).

Key points

We identified and quantified novel markers of IPMN cyst status and pancreatic cancer disease progression – including amino acids, carboxylic acids, conjugated bile acids, free and carnitine-conjugated fatty acids, purine oxidation products and TMAO.

We show that the levels of these metabolites of potential bacterial origin correlated with the degree of bacterial enrichment in the cyst, as determined by 16S RNA.
Whole-genome sequencing reveals new Alzheimer’s disease-associated rare variants in loci related to synaptic function and neuronal development
Authors: Prokopenko Dmitry , Morgan Sarah L. , Mullin Kristina , Hofmann Oliver , Chapman Brad , Kirchner Rory , Amberkar Sandeep , Wohlers Inken , Lange Christoph , Hide Winston , Bertram Lars , Tanzi Rudolph E.
Published: November 2020

INTRODUCTION

Genome-wide association studies have led to numerous genetic loci associated with Alzheimer’s disease (AD). Whole-genome sequencing (WGS) now permit genome-wide analyses to identify rare variants contributing to AD risk.

METHODS

We performed single-variant and spatial clustering-based testing on rare variants (minor allele frequency ≤1%) in a family-based WGS-based association study of 2,247 subjects from 605 multiplex AD families, followed by replication in 1,669 unrelated individuals.

RESULTS

We identified 13 new AD candidate loci that yielded consistent rare-variant signals in discovery and replication cohorts (4 from single-variant, 9 from spatial-clustering), implicating these genes: FNBP1L, SEL1L, LINC00298, PRKCH, C15ORF41, C2CD3, KIF2A, APC, LHX9, NALCN, CTNNA2, SYTL3, CLSTN2.

DISCUSSION

Downstream analyses of these novel loci highlight synaptic function, in contrast to common AD-associated variants, which implicate innate immunity. These loci have not been previously associated with AD, emphasizing the ability of WGS to identify AD-associated rare variants, particularly outside of coding regions.
Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches
Authors: Kothe Caroline Isabel , Bolotin Alexander , Kraïem Bochra-Farah , Dridi Bedis , Team FoodMicrobiome , Renault Pierre
Published: November 2020

Halophilic and halotolerant bacteria are generally assumed to live in natural environments, although they may also be found in foods such as cheese and seafood. These salt-loving bacteria have only been occasionally characterized in cheese, and studies on their ecological and technological functions are still scarce. We therefore selected 13 traditional cheeses in order to systematically characterize these microorganisms in their rinds via cultural, genomic and metagenomic methods. Using different salt-based media, we identified 35 strains with unique 16S rRNA andrpoBgene sequences, whose whole genome was sequenced. The most frequently isolated species are the halotolerant Gram-positive bacteriaBrevibacterium aurantiacum(6) andStaphylococcus equorum(3), which are also frequently added as starters. Their genomic analyses confirm the high genetic diversity ofB. aurantiacumand reveal the presence of two subspecies inS. equorum, as well as the genetic proximity of several cheese strains to bovine isolates. Additionally, we isolated 15 Gram-negative strains, potentially defining ten new species of halophilic cheese bacteria, in particular for the generaHalomonasandPsychrobacter. The use of these genomes as a reference to complement those existing in the databases allowed us to study the representativeness of 66 species of halophilic and halotolerant bacteria in 74 cheese rind metagenomes. The Gram-negative species are particularly abundant in a wide variety of cheeses with high moisture, such as washed-rind cheeses. Finally, analyses of co-occurrences reveal assemblies, including the frequent coexistence of several species of the same genus, forming moderately complex ecosystems with functional redundancies that probably ensure stable cheese development.

IMPORTANCE

Salt is commonly added to food to avoid the growth of pathogens by lowering water activity, resulting in profound changes in the medium that lead to the development of particular ecosystems dominated by halophilic and halotolerant bacteria, communities that probably originate in the natural environment. In order to explore these communities that have been poorly studied in food up until now, we developed a combined approach that includes cultures, genomics and metagenomics to deconstruct these ecosystems in cheese rinds. This approach allowed us to isolate 26 different species, ten of which belong to still undescribed species that could be used as references to promote advances in functional studies of this particular world. The metagenomic scan of 74 cheese rind samples for the assembly of 66 halophilic and halotolerant species showed that these bacteria are widely distributed and form moderately complex ecosystems where related species coexist and probably jointly contribute to safe and efficient cheese development.
Endometrium-on-a-chip reveals the endometrial transcriptome, and protein content of secretome are altered by changes in circulating concentrations of insulin and glucosein vitro
Authors: De Bem Tiago H. C. , Tinning Haidee , Vasconcelos Elton J. R. , Wang Dapeng , Forde Niamh
Published: November 2020

The molecular interactions between the maternal environment and developing embryo that are key for early pregnancy success are known to be influenced by factors such as the metabolic status. We are, however, limited in our understanding of the mechanism by which these individual nutritional stressors alter endometrial function and thein uteroenvironment for early pregnancy success. Here we report for the first time the use of endometrium-on-a-chip microfluidics approach to produce a multi-cellular endometriumin vitro, that is exposed to glucose and insulin concentrations associated with maternal metabolic stressors. Following isolation of endometrial cells (epithelial and stromal) from the uteri of non-pregnant cows in early-luteal phase (Day 4-7 approximately) epithelial cells were seeded into the upper chamber (4-6 104cells/mL) and stromal cells seeded in the lower chamber (1.5-2 104cells/mL). Three different concentration of glucose 1) 0.5 mM 2) 5.0 mM or 3) 50 mM or insulin 1) Vehicle, 2) 1 ng/mL or 3) 10 ng/mL were performed in the endometrial cells at a flow rate of 1µL/min for 72 hr to mimic the rate of secretionin vivo. Quantitative differences in the transcriptomic response of the cells and the secreted proteome ofin vitro-derived uterine luminal fluid (ULF) were determined by RNA-sequencing andTMTrespectively. Changes in maternal glucose altered 21 and 191 protein coding genes in epithelial and stromal cells respectively (p<0.05). While there was a dose-dependent quantitative change in protein secretome (1 and 23 proteins). Insulin resulted in limited transcriptional changes including insulin-like binding proteins that were cell specific (5, 12, and 20) but altered the quantitative secretion of 196 proteins including those involved in extracellular matrix-receptor interaction and proteoglycan signaling in cancer. Collectively, these highlight the potential mechanism by which changes to maternal glucose and insulin alter uterine function.
Baculovirus actin-rearrangement-inducing factor ARIF-1 induces the formation of dynamic clusters of invadosome-like structures
Authors: Lauko Domokos I. , Ohkawa Taro , Mares Sergio E. , Welch Matthew D.
Published: November 2020

The baculovirusAutographa californicamultiple nucleopolyhedrovirus (AcMNPV), a pathogen of lepidopteran insects, has a striking dependence on the host cell actin cytoskeleton. During the delayed-early stage of infection, AcMNPV was shown to induce the accumulation of actin at the cortex of infected cells. However, the dynamics and molecular mechanism of cortical actin assembly remained unknown. Here, we show that AcMNPV induces dynamic cortical clusters of dot-like actin structures that resemble clusters of invadosomes in mammalian cells. Furthermore, we find that the AcMNPV protein actin-rearrangement-inducing factor-1 (ARIF-1), which was previously shown to be necessary and sufficient for cortical actin assembly and efficient viral infection in insect hosts, is both necessary and sufficient for invadosome-like structure formation. We mapped the sequences within the C-terminal cytoplasmic region of ARIF-1 that are required for invadosome-like structure formation and identified individual tyrosine and proline residues that are required for organizing these structures. Additionally, we found that ARIF-1 and the invadosome-associated proteins cortactin and the Arp2/3 complex localize to invadosome-like structures, and Arp2/3 complex is required for their formation. These ARIF-1-induced invadosome-like structures may be important for the function of ARIF-1 in systemic virus spread.
Overcoming Resistance to BRAFV600EInhibition in Melanoma by Deciphering and Targeting Personalized Protein Network Alterations
Authors: Vasudevan S. , Flashner-Abramson E. , Adejumobi I. Adesoji , Vilencki D. , Stefansky S. , Rubinstein A.M. , Kravchenko-Balasha N.
Published: November 2020

BRAFV600Emelanoma patients, despite initially responding to the clinically prescribed anti-BRAFV600Etherapy, often relapse and their tumors develop drug resistance. While it is widely accepted that these tumors are originally driven by the BRAFV600Emutation, they often eventually diverge and become supported by various signaling networks. Therefore, patient-specific altered signaling signatures should be deciphered and treated individually.

In this study, we design individualized melanoma combination treatments based on personalized network alterations. Using an information-theoretic approach, we compute high-resolution patient-specific altered signaling signatures. These altered signaling signatures each consist of several co-expressed subnetworks, which should all be targeted to optimally inhibit the entire altered signaling flux. Based on these data, we design smart, personalized drug combinations, often consisting of FDA-approved drugs. We validate our approach in vitro and in vivo showing that individualized drug combinations that are rationally based on patient-specific altered signaling signatures are more efficient than the clinically used anti-BRAFV600Eor BRAFV600E/MEK targeted therapy. Furthermore, these drug combinations are highly selective, as a drug combination efficient for one BRAFV600Etumor is significantly less efficient for another, and vice versa. The approach presented herein can be broadly applicable to aid clinicians to rationally design patient-specific anti-melanoma drug combinations.
Shock and Detonation Waves at an Interface and the Collision of Action Potentials
Authors: Shrivastava Shamit
Published: November 2020

Action potentials in neurons are known to annihilate each other upon collision, while there are cases where they might penetrate each other. Compression waves that travel within the plasma membrane of a neuron have previously been proposed as a thermodynamic basis for the propagation of action potentials. In this context, it was recently shown that two-dimensional compressive shock waves in the model system of lipid monolayers can nearly annihilate each other upon head-on collision when excited close to a phase transition. However, weaker shock waves showed penetration. In general, once the approximation of small perturbation is not valid, compression waves do not interact linearly anymore. While experiments in lipid monolayers demonstrated this principle, a mechanism remained unclear. In this article, we summarise the fundamentals of shock physics as applied to an interface and how it previously explained the observation of threshold and saturation of shockwaves in the lipid monolayer (all – or – none). While the theory has the same fundamental premise as the soliton model, i.e. the conservation laws and thermodynamics, we elaborate on how the two approaches make different predictions with regards to collisions and the detailed structure of the wave-front. As a case study and a new result, we show that previously unexplained annihilation of shock waves in the lipid monolayer is a direct consequence of the nature of state changes, i.e. jump conditions, within these shockwaves, and elaborate on the consequence of these results for the general understanding of the excitation waves in a thermo-fluids framework.
Antibiotic resistance amongEscherichia coliandSalmonellaisolated from dairy cattle feces in Texas
Authors: Manishimwe Rosine , Moncada Paola M. , Bugarel Marie , Scott H. Morgan , Loneragan Guy H.
Published: November 2020

This study was conducted to develop and field-test a low cost protocol to estimate the isolate- and sample-level prevalence of resistance to critically important antibiotic drugs amongEscherichia coliandSalmonellaisolated from dairy cattle feces.E. coliandSalmonellawere isolated from and screened on selective media, with and without antibiotics respectively. Bacterial isolates were further tested for susceptibility to a suite of antibiotics using disk diffusion. Molecular methods were performed on select bacterial isolates to identify and distinguish genetic determinants associated with the observed phenotypes. Among 85 non-type-specificE. colirandomly isolated from MacConkey agar without antibiotics, the isolate-level prevalence of resistance to tetracycline was the highest (8.2%), there was no isolate resistant to third-generation cephalosporin (0.0%) and one isolate was resistant to nalidixic acid (1.2%). Among 37E. colirecovered from MacConkey agar with cefotaxime at 1.0µg/ml, 100% were resistant to ampicillin and 56.8% were resistant to a third-generation cephalosporin (ceftriaxone). Among 22E. coliisolates recovered from MacConkey agar with ciprofloxacin at 0.5µg/ml, 90.9% were resistant to tetracycline whereas 77.3% and 54.5% were resistant to nalidixic acid and ciprofloxacin respectively. SixteenSalmonellawere isolated and only one demonstrated any resistance (i.e., single resistance to streptomycin). AmongE. coliisolates that were either resistant or intermediate to ceftriaxone, an AmpC phenotype was more common than an extended spectrum beta-lactamase (ESBL) phenotype (29 versus 10 isolates, respectively). Among 24E. coliisolates that were whole genome sequenced, phenotypic profiles of antibiotic resistance detected were generally substantiated by genotypic profiles. For instance, all isolates with an AmpC phenotype carried ablaCMY2gene. The protocol used in this study is suited to detecting and estimating prevalence of antimicrobial resistance in bacteria isolated from food animal feces in resource-limited laboratories in the developing world.
Cryopreservation ofHydractinia symbiolongicarpussperm to support community-based repository development for preservation of genetic resources
Authors: Huene Aidan L. , Nicotra Matthew L. , Weis Virginia M. , Tiersch Terrence R.
Published: November 2020

Hydractinia symbiolongicarpusis an emerging model organism in which cutting-edge genomic tools and resources are being developed for use in a growing number of research fields. However, one limitation of this model system is the lack of long-term storage for genetic resources. Our goal in this study was to establish a generalizable approach to sperm cryopreservation that would support future repository development and could be applied to many species according to available resources. Our approach was to: 1) Assess sperm characteristics and standardize collection and processing; 2) Assess acute toxicity to cryoprotectants, and 3) Evaluate and refine freezing conditions to permit post-thaw fertilization and produce viable offspring. By following this approach, we found thatHydractiniasperm incubated in 5% DMSO, equilibrated at 4°C for 20 min, and cooled at a rate of 20°C/min to - 80°C at a cell concentration of 108-109/mL in 0.25-mL aliquots were able to fertilize 150-300 eggs which yielded offspring that could metamorphose into juvenile polyps. In addition, improvements were made for processing sperm using a customized 3-D printed collection system. Other opportunities for improvement include optimizing the volumetric sperm-to-egg ratio for fertilization. Establishing repository capabilities for theHydractiniaresearch community will be essential for future development, maintenance, protection, and distribution of genetic resources. More broadly, this application-based approach highlights the long-term value of establishing repository-level resources that can be expanded to fit community needs.
Multiplex detection of “CandidatusLiberibacter asiaticus” andSpiroplasma citriby qPCR and droplet digital PCR
Authors: Maheshwari Yogita , Selvaraj Vijayanandraj , Godfrey Kristine , Hajeri Subhas , Yokomi Raymond
Published: November 2020

“CandidatusLiberibacter asiaticus” (CLas) andSpiroplasma citriare phloem-limited bacteria that infect citrus and are transmitted by insect vectors.S. citricauses citrus stubborn disease (CSD) and is vectored by the beet leafhopper in California.CLas is associated with the devastating citrus disease, Huanglongbing (HLB), and is vectored by the Asian citrus psyllid.CLas is a regulatory pathogen spreading in citrus on residential properties in southern California and is an imminent threat to spread to commercial citrus plantings. CSD is endemic in California and has symptoms in citrus that can be easily confused with HLB. Consequently, a multiplex qPCR and duplex droplet digital PCR (ddPCR) were developed for simultaneous detection ofCLas andS. citri. The multiplex qPCR assay was designed to detect multicopy genes ofCLas - RNR (5 copies) andS. citri– SPV1 ORF1 (13 copies), respectively, and citrus cytochrome oxidase (COX) as internal positive control. Absolute quantitation of these pathogens was achieved by duplex ddPCR as a supplement for marginal qPCR results. Duplex ddPCR allowed higher sensitivity than qPCR for detection ofCLas andS. citri. ddPCR showed higher resilience to inhibitors and yielded highly reproducible results. The multiplex qPCR assay has the benefit of testing both pathogens at reduced cost and can serve to augment the official regulatory protocol forCLas detection in California. Moreover, the ddPCR provided unambiguous absolute detection ofCLas andS. citriat very low concentrations without any standards for pathogen titer.
Signalling Network of Breast Cancer Cells in Response to Progesterone
Authors: Wright Roni H. G. , Vastolo Viviana , Oliete Javier Quilez , Carbonell-Caballero José , Beato Miguel
Published: November 2020

Breast cancer cells enter into the cell cycle following progestin exposure by the activation of signalling cascades involving a plethora of enzymes, transcription factors and co-factors that transmit the external signal from the cell membrane to chromatin, ultimately leading to a change of the gene expression program. Although many of the events within the signalling network have been described in isolation, how they globally team up to generate the final cell response is unclear. In this study we use antibody microarrays and phosphoproteomics to provide a dynamic global signalling map that reveals new key regulated proteins and links between previously known and novel pathways. Detailed analysis of the data revealed intriguing changes in protein complexes involved in nuclear structure, EMT, cell adhesion, as well as transcription factors previously not associated with breast cancer proliferation. As different post-translational modifications can mediate complex crosstalk mechanisms and massive PARylation is also rapidly induced by progestins, we provide details of important chromatin regulatory complexes containing both phosphorylated and PARylated proteins. This study contributes an important resource for the scientific community, as it identifies novel players and connections meaningful for breast cancer cell biology and potentially relevant for cancer management. (197 w)