bluuebunny/crossref_metadata_2025 huggingface dataset:
Bioinformatics of Potential Biomarkers in Patients with Repeated Implantation Failure
Authors: Gao Mingxia , Kang Yue , Li Bin , Fan Shuang , Zhang Xuehong
Published: April 2020

Objective

This study applied the public genetic databases high-throughput gene expression omnibus (GEO) database to compare the difference of gene screening between the repeated implantation failure (RIF) patients and women with normal endometrium. This study aims to provide additional information for the diagnosis and treatment in RIF patients through the gene set enrichment analysis and the construction of protein–protein interactions (PPIs) network.

Method

The human endometrial microarray data of RIF and normal control group were obtained from the GEO database provided by the National Center for Biotechnology Information (NCBI). The analysis and the review of differential gene screening, gene ontology (GO) pathway analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and PPIs network construction were carried out.

Result

273 genes with differential expression, 87 up-regulated and 186 down-regulated genes, were obtained through differential gene analysis. 50 genes with the most significant differential expression fold change were screened for subsequent analysis. KEGG results indicated that the top three related pathways were cancer pathway, MAPK signaling pathway, and homologous recombination pathway when the relevant pathways were sequenced according to the correlation size. GO analysis showed that differentially expressed genes were involved in protein phosphorylation, complement activation, and other biological processes. PPIs analysis demonstrated that targeted genes show high correlation to the endometrial receptivity, including PAEP, CXCL14, HOXB3, CD55, and VEGFA, all were down-regulated in RIF endometrial tissues compared to the control group, and these genes also influenced and regulated each other.

Conclusion

Through public databases and bioinformatics, several factors in endometrial receptivity that affect RIF directly and indirectly were found. In particular, the immune and angiogenesis factors stood out the most. The different genes which regulate the immune response and angiogenesis response may become new targeted treatment for RIF.
Potent neutralizing antibodies in the sera of convalescent COVID-19 patients are directed against conserved linear epitopes on the SARS-CoV-2 spike protein
Authors: Poh Chek Meng , Carissimo Guillaume , Wang Bei , Amrun Siti Naqiah , Lee Cheryl Yi-Pin , Chee Rhonda Sin-Ling , Yeo Nicholas Kim-Wah , Lee Wen-Hsin , Leo Yee-Sin , Chen Mark I-Cheng , Tan Seow-Yen , Ann Chai Louis Yi , Kalimuddin Shirin , Thien Siew-Yee , Young Barnaby Edward , Lye David C. , Wang Cheng-I , Renia Laurent , Ng Lisa F.P.
Published: April 2020

The ongoing SARS-CoV-2 pandemic demands rapid identification of immunogenic targets for the design of efficient vaccines and serological detection tools. In this report, using pools of overlapping linear peptides and functional assays, we present two immunodominant regions on the spike glycoprotein that were highly recognized by neutralizing antibodies in the sera of COVID-19 convalescent patients. One is highly specific to SARS-CoV-2, and the other is a potential pan-coronavirus target.
Atlas of ACE2 gene expression in mammals reveals novel insights in transmisson of SARS-Cov-2
Authors: Sun Kun , Gu Liuqi , Ma Li , Duan Yunfeng
Published: April 2020

Background

COVID-19 has become a worldwide pandemic. It is caused by a novel coronavirus named SARS-CoV-2 with elusive origin. SARS-CoV-2 infects mammalian cells by binding to ACE2, a transmembrane protein. Therefore, the conservation of ACE2 and its expression pattern across mammalian species, which are yet to be comprehensively investigated, may provide valuable insights into tracing potential hosts of SARS-CoV-2.

Methods

We analyzed gene conservation of ACE2 across mammals and collected more than 140 transcriptome datasets from human and common mammalian species, including presumed hosts of SARS-CoV-2 and other animals in close contact with humans. In order to enable comparisons across species and tissues, we used a unified pipeline to quantify and normalize ACE2 expression levels.

Results

We first found high conservation of ACE2 genes among common mammals at both DNA and peptide levels, suggesting that a broad range of mammalian species can potentially be the hosts of SARS-CoV-2. Next, we showed that high level of ACE2 expression in certain human tissues is consistent with clinical symptoms of COVID-19 patients. Furthermore, we observed that ACE2 expressed in a species-specific manner in the mammals examined. Notably, high expression in skin and eyes in cat and dog suggested that these animals may play roles in transmitting SARS-CoV-2 to humans.

Conclusions

Through building the first atlas of ACE2 expression in pets and livestock, we identified species and tissues susceptible to SARS-CoV-2 infection, yielding novel insights into the viral transmission.
Increases in canopy mortality and their impact on the demographic structure of Europe’s forests
Authors: Senf Cornelius , Sebald Julius , Seidl Rupert
Published: April 2020

Pulses of tree mortality have been reported for many ecosystems across the globe recently. Yet, large-scale trends in tree mortality remain poorly quantified. Manually analyzing more than 680,000 satellite image chips at 19,896 plot locations, we here show that forest canopy mortality in Europe has continuously increased since 1985 (+1.5 ± 0.28 % yr-1), with the highest canopy mortality rate of the past 34 years observed in 2018 (1.14 ± 0.16 %). Using simulations, we demonstrate that a continued increase in canopy mortality will strongly alter forest demography, with the median forest age falling below 30 years in more than 50% of Europe’s countries by 2050. These demographic changes can have substantial cascading effects on forest regeneration, biodiversity, and carbon storage. The current trend of increasing canopy mortality is thus challenging the future of Europe’s forests, and should be a key priority of forest policy and management.
Different responses to cell crowding determine the clonal fitness of p53 and Notch inhibiting mutations in squamous epithelia
Authors: Kostiou Vasiliki , Hall Michael WJ , Jones Philip H , Hall Benjamin A
Published: April 2020

The growth and competition of cells in epithelial tissues plays an important role in both tissue homeostasis and the robustness of normal tissues to pre-cancer mutation. Whilst wild-type cells compete neutrally for dominance in the un-mutated tissue, naturally occurring mutations in individual cells may lend them a fitness advantage that can allow tissue colonisation. In mouse oesophageal epithelia, the growth of p53 mutants and a dominant negative mutant of the Notch downstream target Maml1 (DN_Maml1) have been shown to have different colonisation properties despite strong quantitative similarities in the growth of individual clones. Here we show that in order to recapitulate these behaviours whilst maintaining tissue turnover models need to take account of the response of cells to increased areal density in the tissue colonised by mutant cells. We demonstrate that p53 mutant clone growth approximates a logistic curve, but that without including limitations on mutation induced expansion the overall proliferation rate of the tissue drops due to space restrictions. In contrast, the ability of DN_Maml1 mutations to displace the wild-type population reflects a feedback that effects both mutant and wild-type cells equally. We go on to show how these distinct feedbacks are consistent with the distribution of mutations observed in human datasets.
Plumage convergence resulting from social mimicry in birds? A tetrachromatic view
Authors: Meneses-Giorgi María Alejandra , Cadena Carlos Daniel
Published: April 2020

Social mimicry may lead to convergent evolution when interactions with conspecific and heterospecific individuals drive evolution towards similar phenotypes in different species. Several hypotheses accounting for convergence in communication signals based on mechanisms of social mimicry exist, but evaluations of how similar species are given the visual system of receptors of such signals have been ostensibly missing from tests of such hypotheses. We used plumage reflectance measurements and models of avian color discrimination to evaluate the efficacy of visual deception and therefore the plausibility of mimicry hypotheses accounting for plumage convergence among six species of passerine birds in the flycatcher family (Tyrannidae) with strikingly similar plumage. We rejected interspecific social mimicry hypotheses as an explanation for the similarity between one putative model species and putative mimics because deception seems unlikely given the visual system of passerines. However, plumage similarity was consistent with a role for selective pressures exerted by predators because dorsal coloration of putative model and mimic species was indistinguishable by visually oriented raptors. Experiments and behavioral observations are necessary to better characterize social interactions and to test predictions of alternative mimicry hypotheses proposed to account for convergence.
Learning excitatory-inhibitory neuronal assemblies in recurrent networks
Authors: Mackwood Owen , Naumann Laura B. , Sprekeler Henning
Published: April 2020

In sensory circuits with poor feature topography, stimulus-specific feedback inhibition necessitates carefully tuned synaptic circuitry. Recent experimental data from mouse primary visual cortex (V1) show that synapses between pyramidal neurons and parvalbumin-expressing (PV) inhibitory interneurons tend to be stronger for neurons that respond to similar stimulus features. The mechanism that underlies the formation of such excitatory-inhibitory (E/I) assemblies is unresolved. Here, we show that activity-dependent synaptic plasticity on input and output synapses of PV interneurons generates a circuit structure that is consistent with mouse V1. Using a computational model, we show that both forms of plasticity must act synergistically to form the observed E/I assemblies. Once established, these assemblies produce a stimulus-specific competition between pyramidal neurons. Our model suggests that activity-dependent plasticity can enable inhibitory circuits to actively shape cortical computations.
Sex-segregated range use by black-and-white ruffed lemurs (Varecia variegata) in Ranomafana National Park, Madagascar
Authors: Baden Andrea L. , Gerber Brian D.
Published: April 2020

Ranging behavior is one important strategy by which nonhuman primates obtain access to resources critical to their biological maintenance and reproductive success. As most primates live in permanent social groups, their members must balance the benefits of group living with the costs of intragroup competition for resources. However, some taxa live in more spatiotemporally flexible social groups, whose members modify patterns of association and range use as a method to mitigate these costs. Here, we describe the range use of black-and-white ruffed lemurs (Varecia variegata) at Mangevo, an undisturbed primary rainforest site in Ranomafana National Park, Madagascar and characterize sex-differences in annual home range area, overlap, and daily distances traveled. Moreover, we characterized seasonal variability in range use and ask whether ranging behaviors can be explained by either climatic or reproductive seasonality. We found that females used significantly larger home ranges than males, though sexes shared equal and moderate levels of home range overlap. Overall, range use did not vary across seasons; though within sexes, male range use varied significantly with climatic variation. Moreover, daily path length was best predicted by day length, female reproductive state, and sex. While the patterns of range use and spatial association presented here share some similarities with ‘bisexually bonded’ community models described for chimpanzees, we argue that ruffed lemurs represent yet another community model wherein ‘neighborhoods’ of overlapping males and females affiliate with each other moreso than with other, more distantly located community members, and to the exclusion of members from adjacent communities.
Abundance and localization of human UBE3A protein isoforms
Authors: Sirois Carissa L. , Bloom Judy E. , Fink James J. , Gorka Dea , Keller Steffen , Germain Noelle D. , Levine Eric S. , Chamberlain Stormy J.
Published: April 2020

Loss ofUBE3A expression,a gene regulated by genomic imprinting, causes Angelman Syndrome (AS), a rare neurodevelopmental disorder. TheUBE3Agene encodes an E3 ubiquitin ligase with three known protein isoforms in humans. Studies in mouse suggest that the human isoforms may have differences in localization and neuronal function. A recent case study reported mild AS phenotypes in individuals lacking one specific isoform. Here we have used CRISPR/Cas9 to generate isogenic human embryonic stem cells (hESCs) that lack the individual protein isoforms. We demonstrate that isoform 1 accounts for the majority of UBE3A protein in hESCs and neurons. We also show that UBE3A predominantly localizes to the cytoplasm in both wild type and isoform-null cells. Finally, we show that neurons lacking isoform 1 display a less severe electrophysiological AS phenotype.
Systematic Chemogenetic Library Assembly
Authors: Canham Stephen M. , Wang Yuan , Cornett Allen , Auld Douglas S. , Baeschlin Daniel K. , Patoor Maude , Skaanderup Philip R. , Honda Ayako , Llamas Luis , Wendel Greg , Mapa Felipa A. , Aspesi Peter , Labbe-Giguere Nancy , Gamber Gabriel G. , Palacios Daniel S. , Schuffenhauer Ansgar , Deng Zhan , Nigsch Florian , Frederiksen Mathias , Bushell Simon M. , Rothman Deborah , Jain Rishi K. , Hemmerle Horst , Briner Karin , Porter Jeffery A. , Tallarico John A. , Jenkins Jeremy L.
Published: April 2020

The assembly of chemogenetic libraries composed of chemical probes provides tremendous value to biomedical research, but requires substantial effort to ensure diversity as well as quality of the contents. We are assembling a chemogenetic library by data mining and crowdsourcing institutional expertise. We are sharing our methodology, lessons learned, and disclosing our current collection of 4186 compounds with their primary annotated gene targets.
Understanding COVID-19 spreading through simulation modeling and scenarios comparison: preliminary results
Authors: Bordehore Cesar , Herrador Zaida , Fonfría Eva S. , Navarro Miriam
Published: April 2020

Since late 2019 the world is facing the rapid spreading of a novel viral disease (SARS-CoV-2) provoked by the coronavirus 2 infection (COVID-19), declared pandemic last 12 March 2020. As of 27 March 2020, there were more than 500,000 confirmed cases and 23,335 deaths worldwide. In those places with a rapid growth in numbers of sick people in need of hospitalization and intensive care, this demand has over-saturate the medical facilities and, in turn, rise the mortality rate.

In the absence of a vaccine, classical epidemiological measures such as testing, quarantine and physical distancing are ways to reduce the growing speed of new infections. Thus, these measures should be a priority for all governments in order to minimize the morbidity and mortality associated to this disease.

System dynamics is widely used in many fields of the biological sciences to study and explain changing systems. The system dynamics approach can help us understand the rapid spread of an infectious disease such as COVID-19 and also generate scenarios to test the effect of different control measures.

The aim of this study is to provide an open model (using STELLA® from Iseesystems) that can be customized to any area/region and by any user, allowing them to evaluate the different behavior of the COVID-19 dynamics under different scenarios. Thus, our intention is not to generate a model to accurately predict the evolution of the disease nor to supplant others more robust -official and non-official-from governments and renowned institutions. We believe that scenarios comparison can be an effective tool to convince the society of the need of a colossal and unprecedented effort to reduce new infections and ultimately, fatalities.
Patterns of the COVID19 pandemic spread around the world: exponential vs power laws
Authors: Komarova Natalia L. , Schang Luis M. , Wodarz Dominik
Published: April 2020

We have analyzed the COVID19 epidemic data of more than 174 countries (excluding China) in the period between January 22 and March 28, 2020. We found that some countries (such as the US, the UK, and Canada) follow an exponential epidemic growth, while others (like Italy and several other European countries) show a power law like growth. Regardless of the best fitting law, many countries can be shown to follow a common trajectory that is similar to Italy (the epicenter at the time of analysis), but with varying degrees of delay. We found that countries with “younger” epidemics, i.e. countries where the epidemic started more recently, tend to exhibit more exponential like behavior, while countries that were closer behind Italy tend to follow a power law growth. We hypothesize that there is a universal growth pattern of this infection that starts off as exponential and subsequently becomes more power law like. Although it cannot be excluded that this growth pattern is a consequence of social distancing measures, an alternative explanation is that it is an intrinsic epidemic growth law, dictated by a spatially distributed community structure, where the growth in individual highly mixed communities is exponential but the longer term, local geographical spread (in the absence of global mixing) results in a power-law. This is supported by computer simulations of a metapopulation model that gives rise to predictions about the growth dynamics that are consistent with correlations found in the epidemiological data. Therefore, seeing a deviation from straight exponential growth may be a natural progression of the epidemic in each country. On the practical side, this indicates that (i) even in the absence of strict social distancing interventions, exponential growth is not an accurate predictor of longer term infection spread, and (ii) a deviation from exponential spread and a reduction of estimated doubling times do not necessarily indicate successful interventions, which are instead indicated by a transition to a reduced power or by a deviation from power law behavior.
Risk factors for severe corona virus disease 2019 (COVID-19) patients : a systematic review and meta analysis
Authors: Xu Lizhen , Mao Yaqian , Chen Gang
Published: April 2020

Importance

With the increasing number of infections for COVID-19, the global health resources are deficient. At present, we don’t have specific medicines or vaccines against novel coronavirus pneumonia (NCP) and our assessment of risk factors for patients with severe pneumonia was limited. In order to maximize the use of limited medical resources, we should distinguish between mild and severe patients as early as possible.

Objective

To systematically review the evidence of risk factors for severe corona virus disease 2019 (COVID-19) patients.

Evidence Review

We conducted a comprehensive search for primary literature in both Chinese and English electronic bibliographic data bases including China National Knowledge Infrastructure (CNKI), Wanfang, Weipu, Chinese Biomedicine Literature Database (CBM-SinoMed), MEDLINE (via PubMed), EMBASE, Cochrane Central Register, and Web of science. The American agency for health research and quality (AHRQ) tool were used for assessing risk of bias. Mata-analysis was undertaken using STATA version 15.0.

Results

20 articles (N=4062 participants) were eligible for this systematic review and meta-analysis. First in this review and meta-analysis, we found that elderly male patients with a high body mass index, high breathing rate and a combination of underlying diseases (such as hypertension, diabetes, cardiovascular disease, and chronic obstructive pulmonary disease) were more likely to develop into critically ill patients. second, compared with ordinary patients, severe patients had more significant symptom such as fever and dyspnea. Besides, the laboratory test results of severe patients had more abnormal than non-severe patients, such as the elevated levels of white-cell counts, liver enzymes, lactate dehydrogenase, creatine kinase, c-reactive protein and procalcitonin, etc, while the decreased levels of lymphocytes and albumin, etc.

Interpretation

This is the first systematic review investigating the risk factors for severe corona virus disease 2019 (COVID-19) patients. The findings are presented and discussed by different clinical characteristics. Therefore, our review may provide guidance for clinical decision-making and optimizes resource allocation.

Key Points

Question

What are the risk factors for severe patients with corona virus disease 2019 (COVID-19)?

Findings

First in this review and meta-analysis, we found that elderly male patients with a high body mass index, high breathing rate and a combination of underlying diseases were more likely to develop into critically ill patients. second, compared with ordinary patients, severe patients had more significant symptom such as fever and dyspnea. Last, we also found that the laboratory test results of severe patients had more abnormal than non-severe patients.

Meaning

This review summaried the risk factors of severe COVID-19 patients and aim to provide a basis for early identification of severe patients by clinicians.
COVID-19 Epidemic in Switzerland: Growth Prediction and Containment Strategy Using Artificial Intelligence and Big Data
Authors: Marini Marcello , Chokani Ndaona , Abhari Reza S.
Published: April 2020

Using a previously developed agent-based artificial intelligence simulation platform (EnerPol) coupled with ‘Big Data,’ the evolution and containment of COVID-19 in Switzerland is examined. The EnerPol platform has been used in a broad range of case studies in different sectors in all of Europe, USA, Japan, South Korea and sub Saharan Africa over the last 10 years. In the present study, the entire Swiss population (8.57 million people), including cross-border commuters, and the entire Swiss public and private transport network that is simulated to assess transmission of the COVID-19 virus. The individual contacts within the population, and possible transmission pathways, are established from a simulation of daily activities that are calibrated with micro-census data. Various governmental interventions with regards to closures and social distancing are also implemented. The epidemiology of the COVID-19 virus is based on publicly available statistical data and adapted to Swiss demographics. The predictions estimate that between 22 February and 11 April 2020, there will be 720 deaths from 83’300 COVID-19 cases, and 73’300 will have recovered; our preliminary variability in these estimates is about 21% over the aforementioned period. In the absence of governmental intervention, 42.7% of the Swiss population would have been infected by 25 April 2020 compared to our prediction of a 1% infection over this time period, saving thousands of lives. It is argued that future scenarios regarding relaxation of the lockdown should be carefully simulated, as by 19 April 2020, there will still remain a substantial number of infected individuals, who could retrigger a second spread of COVID-19. Through the use of a digital tool, such as Enerpol, to evaluate in a data-driven manner the impacts of various policy scenarios, the most effective measures to mitigate a spread of COVID-19 can be devised while we await the deployment of large-scale vaccination for the population globally. By tailoring the spatio-temporal characteristics of the spread to match the capacity of local healthcare facilities, appropriate logistic needs can be determined, in order not to overwhelm the health care services across the country.
How will this continue? Modelling interactions between the COVID-19 pandemic and policy responses
Authors: Rossberg Axel G. , Knell Robert J.
Published: April 2020

Much of the uncertainty about the progression of the COVID-19 pandemic stems from questions about when and how non-pharmaceutical interventions (NPI) by governments, in particular social distancing measures, are implemented, to what extent the population complies with these measures, and how compliance changes through time. Further uncertainty comes from a lack of knowledge of the potential effects of removing interventions once the epidemic is declining. By combining an epidemiological model of COVID-19 for the United Kingdom with simple sub-models for these societal processes, this study aims to shed light on the conceivable trajectories that the pandemic might follow over the next 1.5 years. We show strong improvements in outcomes if governments review NPI more frequently whereas, in comparison, the stability of compliance has surprisingly small effects on cumulative mortality. Assuming that mortality does considerably increase once a country’s hospital capacity is breached, we show that the inherent randomness of societal processes can lead to a wide range of possible outcomes, both in terms of disease dynamics and mortality, even when the principles according to which policy and population operate are identical.. Our model is easily modified to take other aspects of the socio-pandemic interaction into account.
Exploring Ruthenium-based organometallic inhibitors against Plasmodium Calcium Dependent Kinase 2 (PfCDPK2): a combined ensemble docking, QM paramterization and molecular dynamics study
Authors: Patel Dhaval , Athar Mohd , Jha Prakash C.
Published: April 2020

Recent advances in the metal-organic framework (MOF) have accelerated the discovery of novel metal-based anticancer, antibacterial and antimalarial compounds. This is substantiated by many serendipitously discovered metals (Ru, Rh, and Ir) based inhibitors that established the importance of metal inserted into the known organic scaffold. Conversely, it is possible to design novel bioactive compounds by mimicking hypervalent carbon atoms by transition metals. This process can be facilitated by computational drug discovery by treating metal center using optimized parameters that can be used for molecular docking and molecular dynamics simulations. Further, the method can be plugged with high computational power and refined algorithms to interpret chemical phenomena with atomic-level insights. In the present work, we have demonstrated an approach for parameterizing three organometallic ligands (FLL, E52, and staurosporine) using MCPB.py. In particular, we report that E52 and FLL have a better shape complimentary and affinity compared to staurosporine identified inhibitor (staurosporine) against Calcium-dependent protein kinases 2 (CDPK2). This study also revealed that a flexible approach (ensemble) outperforms for the given target with dynamic movements. The calculated MMPBSA energies for staurosporine, FLL and E52 were −66.461 ± 2.192, −67.182 ± 1.971 and −91.339 ± 2.745 kcal/mol respectively.
Purifying selection can reduce intraspecific mitochondrial gene variation to that of nuclear rRNA
Authors: Matumba Tshifhiwa G. , Oliver Jody , Barker Nigel P. , McQuaid Christopher D. , Teske Peter R.
Published: April 2020

Mitochondrial DNA (mtDNA) has long been used to date the divergence between species, and to explore the time when species’ effective population sizes changed. The idea that mitochondrial DNA is useful for molecular dating rests on the premise that its evolution is neutral. This premise was questionable to begin with, and even though it has long been challenged, the evidence against clock-like evolution of mtDNA is usually ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related and widely distributed rocky shore snails whose geographical ranges are defined by different thermal preferences. To our knowledge, this is the first study to use nuclear rRNA sequence for studying species-level genealogies instead of phylogenetics, presumably because this marker is considered to be uninformative at this taxonomic level. Even though the COI gene evolves at least an order of magnitude faster, which was reflected in high inter-specific divergence, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions were completely different for the two markers. Assuming that 28S evolves effectively clock-like, these findings likely illustrate variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by divergent selection between the two species. Although these two selective forces together make mtDNA suitable as a DNA barcoding marker because they create a ‘barcoding gap’, estimates of demographic change can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA beyond DNA barcoding is limited.
Changes amid constancy: flower and leaf microbiomes along land use gradients and between bioregions
Authors: Gaube Paul , Junker Robert R. , Keller Alexander
Published: April 2020

Microbial communities inhabiting above-ground parts of plants affect their host’s development, fitness and function. Although studies on plant-associated microbes are of growing interest, environmental drivers of flower microbiomes in particular are poorly characterized. In this study, we investigated flower and leaf epiphytic bacterial microbiomes ofRanunculus acrisandTrifolium pratenseusing metabarcoding of 16S ribosomal DNA in three German bioregions and along land-use intensity gradients. Our data suggests that the structures of bacterial communities clearly differed between plant species and tissue types. Also, floral bacterial communities ofR. acrisshowed higher variability in comparison toT. pratense. Bacteria usually associated with pollinators were found solely in flower samples, while such usually associated with the rhizosphere were only present in high abundances on leaves. We identified Pseudomonadaceae, Enterobacteriaceae and Sphingomonadaceae as the most abundant taxa on flowers, while Sphingomonadaceae, Methylobacteriaceae and Cytophagaceae dominated bacterial communities on leaves. We found strong bacterial turnover already for short geographic distances, which however did not increase with the long distances between bioregions. High land use intensity caused phylogenetically less diverse and more homogenous bacterial communities. This was associated with a loss of rare bacterial families. Intensification of mowing and fertilization affected almost all plant associated bacterial communities, while grazing had only minor effects on bacterial structures ofT. pratenseflowers. However, dominant taxa were mostly resilient to mowing, grazing and fertilization. Despite that, we identified indicator taxa for regularly disturbed environments in flower microbiomes.
Comparative study of contact repulsion in control and mutant macrophages using a novel interaction detection
Authors: Solís-Lemus JA , Sánchez-Sánchez BJ , Marcotti S , Burki M , Stramer B , Reyes-Aldasoro CC
Published: April 2020

This paper compares the contact-repulsion movement of mutant and wild-type macrophages using a novel interaction detection mechanism. The migrating macrophages are observed inDrosophilaembryos. The study is carried out by a framework calledmacrosight, which analyses the movement and interaction of migrating macrophages. The framework incorporates a segmentation and tracking algorithm into analysing motion characteristics of cells after contact. In this particular study, the interactions between cells is characterised in the case of control embryos and Shot3mutants, where the cells have been altered to suppress a specific protein, looking to understand what drives the movement. Statistical significance between control and mutant cells was found when comparing the direction of motion after contact in specific conditions. Such discoveries provide insights for future developments in combining biological experiments to computational analysis. Cell Segmentation, Cell Tracking, Macrophages, Cell Shape, Contact Analysis
ULTRASOUND-ASSISTED MAGNETIC NANOPARTICLE-BASED GENE DELIVERY
Authors: Zhang Wei , Abdelrasoul Gaser N. , Savchenko Oleksandra , Abdrabou Abdalla , Wang Zhixiang , Chen Jie
Published: April 2020

Low-intensity pulsed ultrasound (LIPUS), a special type of ultrasonic stimulation, is attracting a lot of attention for both clinical and scientific research. In this paper, we report a concept of a new method using magnetic nanoparticles (MNPs) for LIPUS-assisted gene delivery. The MNPs are iron oxide superparamagnetic nanoparticles, coated with polyethyleneimine (PEI), which introduces a high positive surface charge, favorable for the binding of genetic material. Due to the paramagnetic properties of the MNPs, the application of an external magnetic field increases transfection efficiency; meanwhile, LIPUS stimulation enhances cell permeability. We found out that stimulation at the intensity of 30 mW/cm2for 10 minutes yields optimal results with a minimal adverse effect on the cells. Combining the effect of the external magnetic field and LIPUS, the genetic material (GFP or Cherry Red plasmid in our case) can enter the cells. The flow cytometry results showed that by using just a magnetic field to direct the genetic material, the transfection efficiency of HEK 293 cells that were treated with our MNPs was 56.1%. Coupled with LIPUS stimulation, it increased to 61.5% or 19% higher than the positive control (Lipofectamine 2000). In addition, compared with the positive control, our method showed less toxicity. Cell viability after transfection was 63.61%, 19% higher than with the standard transfection technique. In conclusion, we designed a new gene-delivery technique that is affordable, targeted, shows low-toxicity, yet high transfection efficiency, compared to other conventional approaches.

The Graphical Abstract
Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales
Authors: De León Luis F. , Cornejo Aydeé , Gavilán Ronnie G. , Aguilar Celestino
Published: April 2020

Aquatic macroinvertebrates play a crucial role in freshwater ecosystems, but their diversity remains poorly known, particularly in the tropics. This “taxonomic void” represents limits our understanding of biodiversity patterns and processes in freshwater ecosystems, and the scale at which they operate. We used DNA barcoding to estimate lineage diversity (and the diversity of unique haplotypes) in 224 specimens of freshwater macroinvertebrates at a small spatial scale within the Panama Canal Watershed (PCW). In addition, we compiled available barcoding data to assess macroinvertebrate diversity at a broader spatial scale spanning the Isthmus of Panama. Consistently across two species delimitation algorithms (i.e., ABGD and GMYC), we found high lineage diversity within the PCW, with ~ 100-106 molecular operational taxonomic units (MOTUs at 2% sequence divergence) across 168 unique haplotypes. We also found a high lineage diversity along the Isthmus of Panama, but this diversity peaked within the PCW. However, our rarefaction/extrapolation approach showed that this diversity remains under sampled. As expected, these results indicate that the diversity of Neotropical freshwater macroinvertebrates is higher than previously thought, with the possibility of high endemicity even at narrow spatial scales. Geographic isolation is likely a main factor shaping these patterns of diversity. However, local disturbances such as the rupture of the continental divide due to the construction of the Panama Canal might be reshaping these patterns of diversity at a local scale. Although further work is needed to better understand the processes driving diversification in freshwater macroinvertebrates, we suggest that Neotropical streams represent continental islands of diversity. Understanding these islands of diversity is crucial in the face of increasing human disturbance.
Borrelia afzeliidoes not suppress the development of anti-tick immunity in bank voles
Authors: Gomez-Chamorro Andrea , Li Yating , Herrera Adrian , Rais Olivier , Dautel Hans , Voordouw Maarten J.
Published: April 2020

Vector-borne pathogens manipulate their vertebrate hosts to enhance their transmission to arthropod vectors. The ability of vertebrate hosts to develop acquired immunity against arthropod vectors represents an existential threat for both the vector and the pathogen. The purpose of the study was to test whether the tick-borne spirochete bacteriumBorrelia afzeliicould suppress the development of acquired immunity to its tick vectorIxodes ricinusin the bank voleMyodes glareolus, which is an important host for both the tick and the pathogen. We created a group ofB. afzelii-infected bank voles and an uninfected control group by exposing lab-reared animals to infected or uninfected ticks. At 1, 2, and 3 months post-infection, all bank voles were infested with larvalI. ricinusticks. The bank voles developed a strong antibody response against tick salivary gland extract proteins. This anti-tick immunity had negative effects on tick fitness traits including engorged larval weight, unfed nymphal weight, larva-to-nymph molting time and larva-to-nymph molting success. Infection withB. afzeliidid not suppress the development of acquired immunity againstI. ricinusticks. The development of anti-tick immunity was strongly correlated with a dramatic temporal decline in both the bacterial abundance in the host ear tissues and the host-tick transmission success ofB. afzelii. Our study suggests that the development of anti-tick immunity in bank voles has important consequences for the density of infected ticks and the risk of Lyme borreliosis.

Importance

Many pathogens enhance their persistence and transmission by suppressing the immune system of their host. We used an experimental infection approach to test whether the Lyme disease pathogen,Borrelia afzelii, could suppress the development of acquired immunity against its tick vector (Ixodes ricinus) in the bank vole (Myodes glareolus), but found no evidence for this phenomenon. Uninfected andB. afzelii-infected bank voles both developed a strong IgG antibody response against tick salivary gland extract following repeated infestations withI. ricinusticks. The development of anti-tick immunity was negatively correlated with the abundance ofB. afzeliiin ear tissue biopsies and with host-to-tick transmission toI. ricinusticks. Our study suggests that anti-tick immunity in the bank vole reduces the prevalence of this important tick-borne pathogen.
A combined RNA-Seq and comparative genomics approach identifies 1,085 candidate structured RNAs expressed in human microbiomes
Authors: Fremin Brayon J. , Bhatt Ami S.
Published: April 2020

Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches by searching for motif structures in genomic sequence data. However, only a subset of these candidate structured RNAs, those from culturable, well-studied microbes, have been shown to be transcribed. As the human microbiome contains thousands of species and strains of microbes, we sought to apply both informatic and experimental approaches to these organisms to identify novel transcribed structured RNAs. We combine an experimental approach, RNA-Seq, with an informatic approach, comparative genomics across the human microbiome project, to discover 1,085 candidate, conserved structured RNAs that are actively transcribed in human fecal microbiomes. These predictions include novel tracrRNAs that associate withCas9and RNA structures encoded in overlapping regions of the genome that are in opposing orientations. In summary, this combined experimental and computational approach enables the discovery of thousands of novel candidate structured RNAs.
Contemporary Enterovirus D68 strains show enhanced replication and translation at 37°C
Authors: Smith Brendan D. , Pekosz Andrew
Published: April 2020

Enterovirus D68 (EV-D68) emerged in 2014 as an important pathogen linked to severe lower respiratory disease and acute flaccid myelitis outbreaks. Historically associated with mild common-cold-like symptoms, clusters of severe disease attributed to EV-D68 appeared during a series of outbreaks in 2014, 2016, and 2018. Previous studies of historic EV-D68 strains demonstrated attenuated replication at temperatures of the lower respiratory tract (37°C), when compared to the upper respiratory tract (32°C). By testing a panel of historic and contemporary EV-D68 strains at 32°C and 37°C, we demonstrate that contemporary strains of EV-D68 undergo little to no attenuation at increased temperatures. Contemporary strains produced higher levels of viral proteins at 32°C and 37°C than historic strains, although both strains infected similar numbers of cells and had comparable amounts of replication complexes. IRES activity assays with dual-luciferase reporter plasmids demonstrated enhanced translation in recent EV-D68 strains mapped to regions of variability in the 5’ UTR found only in contemporary strains. Using an infectious clone system, we demonstrate that the translation advantage dictated by the 5’ UTR does not solely mediate temperature sensitivity. The strain-dependent effects of temperature on the EV-D68 life cycle gives insight into the susceptibility of the lower respiratory system to contemporary strains.

IMPORTANCE

Enterovirus-D68 (EV-D68) emerged in 2014 as a causative agent of biannual severe pediatric respiratory disease and acute flaccid myelitis (AFM). We show that recent EV-D68 viruses have gained the ability to replicate at 37°C. Enhanced virus protein translation seemed to correlate with enhanced virus replication at 37°C but other genetic factors are also contributing to this phenotype. An enhanced ability to replicate at core body temperature may have allowed EV-D68 to penetrate both lower in the respiratory tract and into the central nervous system, explaining the recent surge in severe disease associated with virus infection.
The diagnostic challenges and clinical course of a myeloid/lymphoid neoplasm with eosinophilia and ZBTB20-JAK2 gene fusion presenting as B-lymphoblastic leukemia
Authors: Lee Winston Y. , Pfau Ruthann B. , Choi Sarah M. , Yang Jiong , Xiao Hong , Putnam Eileen M. , Ryan Russell JH. , Bixby Dale L. , Shao Lina
Published: April 2020

We report the diagnostic challenges and the clinical course of a patient with an extraordinary presentation of B-lymphoblastic leukemia (B-ALL) with eosinophilia. We identified a novel ZBTB20-JAK2 gene fusion as a chimeric RNA transcript using the Archer platform. This gene fusion from the same patient was recently identified by Peterson et al. (2019) at the genomic level using a different sequencing technology platform. The configuration of this gene fusion predicts the production of a kinase-activating JAK2 fusion protein, which would normally lead to a diagnosis of Philadelphia chromosome–like B-ALL (Ph-like B-ALL). However, the unusual presentation of eosinophilia led us to demonstrate the presence of this gene fusion in nonlymphoid hematopoietic cells by fluorescence in situ hybridization (FISH) studies with morphologic correlation. Therefore, we believe this disease, in fact, represents blast crisis arising from an underlying myeloid neoplasm with JAK2 rearrangements. This case illustrates the difficulty in differentiating Ph-like B-ALL and myeloid/lymphoid neoplasm with eosinophilia and gene rearrangements (MLN-EGR) in blast crisis. As currently defined, the diagnosis of MLN-EGR relies on the hematologic presentations and the identification of marker gene fusions (including PCM1-JAK2, ETV6-JAK2, and BCR-JAK2). However, these same gene fusions, when limited to B-lymphoblasts, also define Ph-like B-ALL. Yet, our case does not conform to either condition. Therefore, the assessment for lineage restriction of gene rearrangements to reflect the pathophysiologic difference between B-ALL and MLN-EGR in blast crisis is likely a more robust diagnostic approach and allows the inclusion of MLN-EGR with novel gene fusions.
Two-Step Bacterial Artificial Chromosome (BAC) Engineering: Preparation and Verification of the Recombinant Shuttle Vector
Authors: Heintz Nathaniel , Gong Shiaoching
Published: April 2020

Plasmid DNA is prepared from the recombinant shuttle vector pLD53.SCAB/A-B created by cloning of the A and B homology arms for two-step bacterial artificial chromosome (BAC) engineering. To confirm that the A-box and B-box arms have been successfully incorporated into pLD53.SCAB, the pattern of enzyme digestion of the modified plasmid is compared with that of the unmodified pLD53.SCAB. Once the shuttle vector is shown to carry the proper sequences, it is ready for transfer into the BAC host.
Using the Xenopus Oocyte Toolbox
Authors: Mowry Kimberly L.
Published: April 2020

The Xenopus oocyte is a unique model system, allowing both the study of complex biological processes within a cellular context through expression of exogenous mRNAs and proteins, and the study of the cell, molecular, and developmental biology of the oocyte itself. During oogenesis, Xenopus oocytes grow dramatically in size, with a mature oocyte having a diameter of ∼1.3 mm, and become highly polarized, localizing many mRNAs and proteins. Thus, the mature oocyte is a repository of maternal mRNAs and proteins that will direct early embryogenesis prior to zygotic genome transcription. Importantly, the Xenopus oocyte also has the capacity to translate exogenous microinjected RNAs, which has enabled breakthroughs in a wide range of areas including cell biology, developmental biology, molecular biology, and physiology. This introduction outlines how Xenopus oocytes can be used to study a variety of important biological questions.
Methods for Measuring the Concentrations of Proteins
Authors: Kielkopf Clara L. , Bauer William , Urbatsch Ina L.
Published: April 2020

Determining the concentration of protein samples generally is accomplished either by measuring the UV absorbance at 280 nm or by reacting the protein quantitatively with dyes and/or metal ions (Bradford, Lowry, or BCA assays). For purified proteins, UV absorbance remains the most popular method because it is fast, convenient, and reproducible; it does not consume the protein; and it requires no additional reagents, standards, or incubations. No method of protein concentration determination is perfect because each is subject to a different set of constraints such as interference of buffer components and contaminating proteins in direct UV determination (A280) or reactivity of individual proteins and buffer components with the detecting reagents in colorimetric assays. In cases in which protein concentration is critical (e.g., determination of catalytic rate constants for an enzyme), it may be advisable to compare the results of several assays.