bluuebunny/crossref_metadata_2025 huggingface dataset:
Pseudomonas kirkiae sp. nov., a novel species isolated from oak in the United Kingdom, and phylogenetic considerations of the genera Pseudomonas, Azotobacter and Azomonas
Authors: Bueno-Gonzalez Victoria , Brady Carrie , Denman Sandra , Allainguillaume Joël , Arnold Dawn
Published: February 2020

As the current episode of Acute Oak Decline (AOD) continues to affect native British oak in the United Kingdom, ongoing isolations from symptomatic and healthy oak have yielded a largePseudomonasspecies population. These strains could be divided into taxa representing three potential novel species. Recently, two of these taxa were described as novelPseudomonasspecies in thePseudomonas fluorescenslineage. Here, we demonstrate using a polyphasic approach that the third taxon represents another novelPseudomonasspecies. The 16S rRNA gene sequencing assigned the strains to thePseudomonas aeruginosalineage, while multilocus sequence analysis (based on partialgyrB,rpoBandrpoDsequences) placed the 13 strains in a single cluster on the border of thePseudomonas stutzerigroup. Whole genome intra-species comparisons (based on average nucleotide identity andin silicoDNA–DNA hybridization) confirmed that the strains belong to a single taxon, while the inter-species comparisons with closest phylogenetic relatives yielded similarity values below the accepted species threshold. Therefore, we propose these strains as a novel species, namelyPseudomonas kirkiaesp. nov., with the type strain FRB 229T(P4CT=LMG 31089T=NCPPB 4674T). The phylogenetic analyses performed in this study highlighted the difficulties in assigning novel species to the genusPseudomonasdue to its polyphyletic nature and close relationship to the genusAzotobacter. We further propose that a thorough taxonomic re-evaluation of the genusPseudomonasis essential and should be performed in the near future.
Candida albicans increases the pathogenicity of Staphylococcus aureus during polymicrobial infection of Galleria mellonella larvae
Authors: Sheehan Gerard , Tully Laura , Kavanagh Kevin A.
Published: February 2020

This study detailed the responses of Galleria mellonella larvae to disseminated infection caused by co-infection with Candida albicans and

Staphylococcus aureus

. Doses of C. albicans (1×105 larva−1) and

S. aureus

(1×104 larva−1) were non-lethal in mono-infection but when combined significantly (P<0.05) reduced larval survival at 24, 48 and 72 h relative to larvae receiving

S. aureus

(2×104 larva−1) alone. Co-infected larvae displayed a significantly higher density of

S. aureus

larva−1 compared to larvae infected solely with

S. aureus

. Co-infection resulted in dissemination throughout the host and the appearance of large nodules. Co-infection of larvae with C. albicans and

S. aureus

(2×104 larva−1) resulted in an increase in the density of circulating haemocytes compared to that in larvae infected with only

S. aureus

. Proteomic analysis of co-infected larval haemolymph revealed increased abundance of proteins associated with immune responses to bacterial and fungal infection such as cecropin-A (+45.4-fold), recognition proteins [e.g. peptidoglycan-recognition protein LB (+14-fold)] and proteins associated with nodule formation [e.g. Hdd11 (+33.3-fold)]. A range of proteins were also decreased in abundance following co-infection, including apolipophorin (−62.4-fold), alpha-esterase 45 (−7.7-fold) and serine proteinase (−6.2-fold). Co-infection of larvae resulted in enhanced proliferation of

S. aureus

compared to mono-infection and an immune response showing many similarities to the innate immune response of mammals to infection. The utility of G. mellonella larvae for studying polymicrobial infection is highlighted.
Rethinking success, integrity, and culture in research (Part 2) — A multi-actor qualitative study on problems of science
Authors: Bonn Noémie Aubert , Pinxten Wim
Published: February 2020

Background

Research misconduct and questionable research practices have been the subject of increasing attention in the past few years. But despite the rich body of research available, few empirical works provide the perspectives of non-researcher stakeholders.

Methods

To capture some of the forgotten voices, we conducted semi-structured interviews and focus groups with policy makers, funders, institution leaders, editors or publishers, research integrity office members, research integrity community members, laboratory technicians, researchers, research students, and former-researchers who changed career to inquire on the topics of success, integrity, and responsibilities in science. We used the Flemish biomedical landscape as a baseline to be able to grasp the views of interacting and complementary actors in a system setting.

Results

Given the breadth of our results, we divided our findings in a two-paper series with the current paper focusing on the problems that affect the quality and integrity of science. We first discovered that perspectives on misconduct, including the core reasons for condemning misconduct, differed between individuals and actor groups. Beyond misconduct, interviewees also identified numerous problems which affect the integrity of research. Issues related to personalities and attitudes, lack of knowledge of good practices, and research climate were mentioned. Elements that were described as essential for success (in the associate paper) were often thought to accentuate the problems of research climates by disrupting research cultures and research environments. Even though everyone agreed that current research climates need to be addressed, no one felt responsible nor capable of initiating change. Instead, respondents revealed a circle of blame and mistrust between actor groups.

Conclusions

Our findings resonate with recent debates, and extrapolate a few action points which might help advance the discussion. First, we must tackle how research is assessed. Second, approaches to promote better science should be revisited: not only should they directly address the impact of climates on research practices, but they should also redefine their objective to empower and support researchers rather than to capitalize on their compliance. Finally, inter-actor dialogues and shared decision making are crucial to building joint objectives for change.

Trial registration

osf.io/33v3m
Estimating and Testing an Index of Bias Attributable to Composite Outcomes in Comparative Studies
Authors: Diaz-Quijano Fredi Alexander
Published: February 2020

Objective

To develop an index to evaluate the bias attributable to composite outcomes (BACO) in comparative clinical studies.

Study design and Setting

I defined the BACO index as the ratio of the logarithm of the association measure (e.g., relative risk) of the composite outcome to that of its most relevant component endpoint (e.g., mortality). Methods to calculate the confidence intervals and test the null hypotheses (BACO index = 1) were described and applied in systematically selected clinical trials. Two other preselected trials were included as “positive controls” for being examples of primary composite outcomes disregarded due to inconsistency with the treatment effect on mortality.

Results

The BACO index values different from one were classified according to whether the use of composite outcomes overestimated (BACO index >1), underestimated (BACO index between zero and <1), or inverted (BACO index <0) the association between exposure and prognosis. In three of 23 systematically selected trials and the two positive controls, the BACO indices were significantly lower than one (p <0.005).

Conclusion

BACO index can warn that the composite outcome association is stronger, weaker, or even opposite than that of its most critical component.

What is new?

BACO index is the ratio of the logarithm of the association measure (e.g., RR) of the composite outcome to the logarithm of the association measure of the component endpoint that represents the study target (e.g., mortality).

In comparative studies, the BACO index can be used to evaluate the correspondence between the effect on a composite outcome and that on its most critical component.

This index could help to preset rules to make decisions for interpretation of clinical studies.

A significant BACO should lead to the caution that the association of the composite is stronger (BACO index >1), weaker (BACO index between zero and <1), or even opposite (BACO index <0) than that of its most critical component.
Transdiagnostic neurocognitive endophenotypes in major psychiatric illness
Authors: Holla Bharath , Dayal Pavithra , Das Aswathy , Bhattacharya Mahashweta , Manjula V , Ithal Dhruva , Balachander Srinivas , Mahadevan Jayant , Nadella Ravi Kumar , Sreeraj Vanteemar S , Benegal Vivek , Reddy Janardhan Y. C. , Mehta Urvakhsh Meherwan ,   ADBS Consortium, Viswanath Biju
Published: February 2020

We aimed to characterize potential transdiagnostic neurocognitive endophenotypes in a large cohort of multiplex families affected with two or more individuals having a major psychiatric illness(MPI) i.e., schizophrenia(SCZ), bipolar disorder(BPAD), substance use disorders(SUD) and obsessive-compulsive disorder(OCD). We recruited 640 individuals that included 256 affected individuals with MPI, 227 of their unaffected first-degree relatives(FDR) and 157 population healthy-controls(PHC). Neurocognitive battery included assessments of executive function, working memory, social cognition, verbal learning and recall. Linear mixed effects models were applied to the neurocognitive components to examine their transdiagnostic and endophenotype status after accounting for demographic and family variables. We also examined the relationship of cognitive domains with diagnosis-specific Family History Density score(FHD).

The deficits in cognitive flexibility, working memory and social cognition were transdiagnostic; processing speed was impaired in SCZ and BPAD groups while verbal learning and recall in SCZ, BPAD and SUD groups. These deficits with the exception of social cognition, worsened with age and parental education had protective effect. The unaffected FDRs had deficits in all the domains except processing speed in comparison to PHC; social cognition deficits were comparable to affected individuals. The diagnosis-specific FHD analysis showed that deficits in cognitive flexibility, working memory and social cognition were endophenotypes across disorders.

Evaluation of neurocognitive functions across multiple affected individuals in a large multiplex family-based cross-disorder cohort, has the potential to elucidate transdiagnostic as well as endophenotype vulnerabilities to psychiatric illness. This study adds to the emerging conceptualization of psychiatric illness as a combination of both diagnosis-specific and transdiagnostic markers.
Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (COVID-19)
Authors: Li Ruiyun , Pei Sen , Chen Bin , Song Yimeng , Zhang Tao , Yang Wan , Shaman Jeffrey
Published: February 2020

Background

Estimation of the fraction and contagiousness of undocumented novel coronavirus (COVID-19) infections is critical for understanding the overall prevalence and pandemic potential of this disease. Many mild infections are typically not reported and, depending on their contagiousness, may support stealth transmission and the spread of documented infection.

Methods

Here we use observations of reported infection and spread within China in conjunction with mobility data, a networked dynamic metapopulation model and Bayesian inference, to infer critical epidemiological characteristics associated with the emerging coronavirus, including the fraction of undocumented infections and their contagiousness.

Results

We estimate 86% of all infections were undocumented (95% CI: [82%-90%]) prior to the Wuhan travel shutdown (January 23, 2020). Per person, these undocumented infections were 52% as contagious as documented infections ([44%-69%]) and were the source of infection for two-thirds of documented cases. Our estimate of the reproductive number (2.23; [1.77-3.00]) aligns with earlier findings; however, after travel restrictions and control measures were imposed this number falls considerably.

Conclusions

A majority of COVID-19 infections were undocumented prior to implementation of control measures on January 23, and these undocumented infections substantially contributed to virus transmission. These findings explain the rapid geographic spread of COVID-19 and indicate containment of this virus will be particularly challenging. Our findings also indicate that heightened awareness of the outbreak, increased use of personal protective measures, and travel restriction have been associated with reductions of the overall force of infection; however, it is unclear whether this reduction will be sufficient to stem the virus spread.
A model simulation study on effects of intervention measures in Wuhan COVID-19 epidemic
Authors: Zhou Guopeng , Chi Chunhua
Published: February 2020

Background

In the beginning of January 2020, new unknown virus pneumonia cases started to emerge in local hospitals in Wuhan, China. This virus epidemic quickly became a public health emergency of international concern by the WHO. Enormous amount of medical supplies as well as healthcare personals from other provinces were mobilized to support Wuhan. This current work tent to help people understanding how infectious disease spread and the purpose and consequences of various efforts based on simulation model.

Method

a simulation model was created using known parameters. R0 set to 3 and mean incubation time to be 7.5days. the epidemic was divided to 3 periods. Simulation would run 50 times to mimic different patient0 status. Personal activity index was used to mimic different level of control measures. 141427709 simulated patients were created. Cumulation number of patients at the end of period 1 (day50) is 2868.7±1739.0. Total infected patients could be 913396.5 ± 559099.9 by the end of period 2 (day70) in free transmission state. And at day90, total patients number is 913396.5 ± 559099.9.

Conclusion

COVID-19 is a novel severe respiratory disease. This will put great burden on the shoulder of healthcare workers as well as on medical hardware and supplements. Current strict control measures help to contain disease from spreading. An early detecting, reporting and fast reacting system needs to be setup to prevent future unknown infectious disease.
Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary, CTCF-mediated chromatin looping and a long-range intergenic enhancer
Authors: Cheng Jessica , Clayton Joshua S. , Acemel Rafael D. , Zheng Ye , Taylor Rhonda L. , Keleş Sündüz , Franke Martin , Boackle Susan A. , Harley John B. , Quail Elizabeth , Gómez-Skarmeta José L. , Ulgiati Daniela
Published: February 2020

The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanisms underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression ofCR2and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topologically associated domains (TADs). Interestingly, an inter-TAD boundary was located within theCR1gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2andCD55) in B cells. We have uncovered novel, long-range mechanisms whereby autoimmune disease susceptibility may be influenced by genetic variants, thus highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease.

SIGNIFICANCE

The complement system is a complex network of protein effectors and regulators that play a key role in immunity. Several regulators of complement response are clustered within Regulators of Complement Activation (RCA) gene family. Its members are all functionally, structurally, and genetically related. However, the functional relevance of this close gene organisation is unknown. We show that the clustering of the RCA members is due to shared long-range regulatory elements and physical chromatin looping. We also reveal that the RCA genes are divided into two adjacent chromatin domains and a domain boundary falls within the body of an expressed gene (CR1). Overall, our findings in the RCA cluster offer insights into their evolution, biology and roles in disease.
Coral reef restoration efforts in Latin American countries and territories
Authors: Bayraktarov Elisa , Banaszak Anastazia T. , Montoya Maya Phanor , Kleypas Joanie , Arias-González Jesús E. , Blanco Macarena , Calle Triviño Johanna , Charuvi Nufar , Cortés Useche Camilo , Galván Victor , García Salgado Miguel A. , Gnecco Mariana , Guendulain García Sergio D. , Hernández Delgado Edwin A. , Marín Moraga José A. , Maya María Fernanda , Mendoza Quiroz Sandra , Cervantes Samantha Mercado , Morikawa Megan , Nava Gabriela , Pizarro Valeria , Sellares-Blasco Rita I. , Suleimán Ramos Samuel E. , Villalobos Cubero Tatiana , Villalpando María , Frías-Torres Sarah
Published: February 2020

Coral reefs worldwide are degrading due to climate change, overfishing, pollution, coastal development, bleaching and diseases. In areas where natural recovery is negligible or protection through management interventions insufficient, active restoration becomes critical. The Reef Futures symposium in 2018 brought together over 400 reef restoration experts, businesses, and civil organizations, and galvanized them to save coral reefs through restoration or identify alternative solutions. The symposium highlighted that solutions and discoveries from long-term and ongoing coral reef restoration projects in Spanish-speaking countries in the Caribbean and Eastern Tropical Pacific were not well known internationally. Therefore, a meeting of scientists and practitioners working in these locations was held to compile the data on the extent of coral reef restoration efforts, advances and challenges. Here, we present unpublished data from 12 coral reef restoration case studies from five Latin American countries, describe their motivations and techniques used, and provide estimates on total annual project cost per unit area of reef intervened, spatial extent as well as project duration. We found that most projects used direct transplantation, the coral gardening method, micro-fragmentation or larval propagation, and aimed to optimize or scale-up restoration approaches (51%) or provide alternative, sustainable livelihood opportunities (15%) followed by promoting coral reef conservation stewardship and re-establishing a self-sustaining, functioning reef ecosystem (both 13%). Reasons for restoring coral reefs were mainly biotic and experimental (both 42%), followed by idealistic and pragmatic motivations (both 8%). The median annual total cost from all projects was $93,000 USD (range: $10,000 USD - $331,802 USD) (2018 dollars) and intervened a median spatial area of 1 ha (range: 0.06 ha - 8.39 ha). The median project duration was 3 years; however, projects have lasted up to 17 years. Project feasibility was high with a median of 0.7 (range: 0.5 - 0.8). This study closes the knowledge gap between academia and practitioners and overcomes the language barrier by providing the first comprehensive compilation of data from ongoing coral reef restoration efforts in Latin America.
MouseCircuits.org: An online repository to guide the circuit era of disordered affect
Authors: Anderson Kristin R. , Dumitriu Dani
Published: February 2020

Affective disorders rank amongst the most disruptive and prevalent psychiatric diseases, resulting in enormous societal and economic burden, and immeasurable personal costs. Novel therapies are urgently needed but have remained elusive. The era of circuit-mapping in rodent models of disordered affect, ushered in by recent technological advancements allowing for precise and specific neural control, has reenergized the hope for precision psychiatry. Here, we present a novel whole-brain cumulative network and critically access the progress made to-date on circuits mediating affective-like behaviors in rodents to seek unifying principles of this cumulative data. We identified 106 original manuscripts in which optogenetics or chemogenetics were used to dissect behaviors related to fear-like, depressive-like or anxiety-like behaviors in rodents. Focusing on the 60 manuscripts that investigated pathways rather than regions, we identified emergent themes. We found that while a few pathways have been validated across similar behaviors and multiple labs, the data is mostly disjointed, with evidence of bidirectional effects of several pathways. Additionally, there is a need for analysis informed by observation prior to perturbation. Given the complex nature of brain connectivity, we argue that the compartmentalized viewpoint that develops as a consequence of fragmented pathway-specific manipulations does not readily lend itself to an integrative picture. To address this, we launched an interactive online consortium,MouseCircuits.org, an open-source platform for consolidated circuit data. This tool aims to support the shared vision of informed circuit dissection that ultimately leads to prevention and treatment of human disorders.
APA-Scan: Detection and Visualization of 3’-UTR Alternative Polyadenylation with RNA-seq and 3’-end-seq Data
Authors: Fahmi Naima Ahmed , Ahmed Khandakar Tanvir , Chang Jae-Woong , Nassereddeen Heba , Fan Deliang , Yong Jeongsik , Zhang Wei
Published: February 2020

Background

The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3’-untranslated region (3’-UTR) of mRNA produces transcripts with shorter or longer 3’-UTR. Often, 3’-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3’-UTR APA is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. Current bioinformatics pipelines have limited capability in profiling 3’-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3’-UTR APA only using RNA-seq read coverage, causing false positive identifications. To overcome these limitations, we developed APA-Scan, a robust program that identifies 3’-UTR APA events and visualizes the RNA-seq short-read coverage with gene annotations.

Methods

APA-Scan utilizes either predicted or experimentally validated actionable polyadenylation signals as a reference for polyadenylation sites and calculates the quantity of long and short 3’-UTR transcripts in the RNA-seq data. APA-Scan works in three major steps: (i) calculate the read coverage of the 3’-UTR regions of genes; (ii) identify the potential APA sites and evaluate the significance of the events among two biological conditions; (iii) graphical representation of user specific event with 3’-UTR annotation and read coverage on the 3’-UTR regions. APA-Scan is implemented in Python3. Source code and a comprehensive user’s manual are freely available athttps://github.com/compbiolabucf/APA-Scan.

Result

APA-Scan was applied to both simulated and real RNA-seq datasets and compared with two widely used baselines DaPars and APAtrap. In simulation APA-Scan significantly improved the accuracy of 3’-UTR APA identification compared to the other baselines. The performance of APA-Scan was also validated by 3’-end-seq data and qPCR on mouse embryonic fibroblast cells. The experiments confirm that APA-Scan can detect unannotated 3’ -UTR APA events and improve genome annotation.

Conclusion

APA-Scan is a comprehensive computational pipeline to detect transcriptome-wide 3’-UTR APA events. The pipeline integrates both RNA-seq and 3’-end-seq data information and can efficiently identify the significant events with a high-resolution short reads coverage plots.
The Structures of Secretory and Dimeric Immunoglobulin A
Authors: Bharathkar Sonya Kumar , Parker Benjamin W. , Malyutin Andrey G. , Haloi Nandan , Huey-Tubman Kathryn E. , Tajkhorshid Emad , Stadtmueller Beth M.
Published: February 2020

Secretory (S) Immunoglobulin (I) A is the predominant mucosal antibody, which binds pathogens and commensal microbes. SIgA is a polymeric antibody, typically containing two copies of IgA that assemble with one joining-chain (JC) to form dimeric (d) IgA that is bound by the polymeric Ig-receptor ectodomain, called secretory component (SC). Here we report the cryo-electron microscopy structures of murine SIgA and dIgA. Structures reveal two IgAs conjoined through four heavy-chain tailpieces and the JC that together form a β-sandwich-like fold. The two IgAs are bent and tilted with respect to each other, forming distinct concave and convex surfaces. In SIgA, SC is bound to one face, asymmetrically contacting both IgAs and JC. The bent and tilted arrangement of complex components limits the possible positions of both sets of antigen binding fragments (Fabs) and preserves steric accessibility to receptor binding sites, likely influencing antigen binding and effector functions.
The tRNA pseudouridine synthase TruB1 regulates the maturation and function of let-7 miRNA
Authors: Kurimoto Ryota , Chiba Tomoki , Ito Yoshiaki , Matsushima Takahide , Yano Yuki , Miyata Kohei , Suzuki Tsutomu , Tomita Kozo , Asahara Hiroshi
Published: February 2020

Let-7 is an evolutionary conserved microRNA that mediates post-transcriptional gene silencing to regulate a wide range of biological processes, including development, differentiation, and tumor suppression. Let-7 biogenesis is tightly regulated by several RNA-binding proteins, including Lin28A/B, which represses let-7 maturation. To identify new regulators of let-7, we devised a cell-based functional screen of RNA-binding proteins using a let-7 sensor luciferase reporter, and identified the tRNA pseudouridine synthase, TruB1. TruB1 enhanced maturation specifically of let-7 family members. Rather than inducing pseudouridylation of the miRNAs, HITS-CLIP (High throughput sequencing crosslinking immunoprecipitation) and biochemical analyses revealed direct binding between endogenous TruB1 and the stem-loop structure of pri-let-7, which also binds Lin28A/B. TruB1 selectively enhanced the interaction between pri-let-7 and the microprocessor DGCR-8, which mediates miRNA maturation. Finally, TruB1 suppressed cell proliferation, which was mediated in part by let-7. Altogether, we reveal an unexpected function for TruB1 in promoting let-7 maturation and function.
Semiautomated detection ofPseudomonas aeruginosafrom diverse water samples using highly selective Z-broth and a redox potential monitor
Authors: Szita Géza , Katalin Szakmár , Bernáth Sándor , Sövényi József , Fülöp Gábor , Janaki Hadjiev , Csikó György , Solymosi Norbert , Makrai László
Published: February 2020

Pseudomonas aeruginosais a facultative bacterial pathogen with increasing public health risk potential. Contaminated water in hospital environments is a growing cause of multidrug-resistentP. aeruginosanosocomial infections that are life-threatening and are costly to treat.P. aeruginosais common in natural water bodies, but it is not unusual in drinking water and has been detected in bottled water, also. Suppliers in Europe must eliminate live forms of the bacterium in drinking water to meet human consumption requirements. Laboratory testing for the presence of viableP. aeruginosais mostly done manually using culture media but conductance/impedimetry measurements for detection are also available. In order to improve expedience and cost efficiency as well as to automate the detection and the data registration, we applied the highly selective Z-broth culture media and redox potential monitoring to detectP. aeruginosafrom water. The Z-broth is based on only a few, stable chemicals that provide consistency of quality and long shelf life. It limits growth toP. aeruginosaand, thus, eliminates the need for subsequent microbiological identification steps of the European Standard procedure defined in ISO 16 266:2006 (2018). A redox potential monitor was used in this work, that simultaneously recorded 64 sample curves and automatically marked positive samples reliably within 24 hours after sample initialization. In comparison, the standard method requires additional tests that prolongs identification to some days. Practical applicability and reliability of the method in this paper was demonstrated by testing a total of 739 water samples of which 222 were tap water, 342 well water and 145 had been taken from swimming pools.

It is considered this method is well suited to process large numbers of samples for purposes of detectingP. aeruginosacontamination with relative ease, little cost in shortened time. Using Z-broth in combination with redox potential monitoring can be recommended for central laboratories for routine testing of drinking water for liveP. aeruginosapresence. As well, using this method for testing of fluids and surfaces forP. aeruginosacontamination would be advantageous in such environments as the hospital industry, swimming pools and spas, where cleaning routines andP. aeruginosatransmission prevention protocols could be made much more resultful and cost-effective due to ease and speed of processing both spot check and water samples.

Highlights

A method was applied for detection of viablePseudomonas aeruginosain 739 water samples.

Redox potential monitoring of Z-broth cultures exclusively registered growth ofP. aeruginosa.

The method is highly selective, reliable and partly automated, with lower labor costs.

The method is suited for testing of water and hospital environments forP. aeruginosa.
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation
Authors: Kamimoto Kenji , Hoffmann Christy M. , Morris Samantha A.
Published: February 2020

Here, we present CellOracle, a computational tool that integrates single-cell transcriptome and epigenome profiles to infer gene regulatory networks (GRNs), critical regulators of cell identity. Leveraging inferred GRNs, we simulate gene expression changes in response to transcription factor (TF) perturbation, enabling network configurations to be interrogatedin silico, facilitating their interpretation. We validate the efficacy of CellOracle to recapitulate known regulatory changes across hematopoiesis, correctly predicting the outcomes of well-characterized TF perturbations. Integrating CellOracle analysis with lineage tracing of direct reprogramming reveals distinct network configurations underlying different reprogramming failure modes. Furthermore, analysis of GRN reconfiguration along successful reprogramming trajectories identifies new factors to enhance target cell yield, uncovering a role for the AP-1 subunit Fos, with the hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations, at high-resolution, promoting new mechanistic insights into the regulation and reprogramming of cell identity.
Induction Of Chronic Stress Reveals An Interplay Of Stress Granules And TDP-43 Pathological Aggregates In Human ALS Fibroblasts And iPSC-Neurons
Authors: Ratti Antonia , Gumina Valentina , Lenzi Paola , Bossolasco Patrizia , Fulceri Federica , Volpe Clara , Bardelli Donatella , Pregnolato Francesca , Maraschi AnnaMaria , Fornai Francesco , Silani Vincenzo , Colombrita Claudia
Published: February 2020

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative diseases characterized by the presence of neuropathological aggregates of phosphorylated TDP-43 (P-TDP-43). The RNA-binding protein TDP-43 is also a component of stress granules (SG), cytoplasmic foci forming to arrest translation under sub-lethal stress conditions. Although commonly considered as distinct structures, a link between SG and pathological TDP-43 inclusions may occur despite evidence that TDP-43 pathology directly arises from SG is still under debate. Primary fibroblasts and iPSC-derived neurons (iPSC-N) from ALS patients carrying mutations inTARDBP(n=3) andC9ORF72(n=3) genes and from healthy controls (n=3) were exposed to oxidative stress by sodium arsenite. SG formation and cell response to stress was evaluated and quantified by immunofluorescence and electron microscopy analyses. We found that, not only an acute, but also a chronic oxidative insult, better mimicking a persistent condition of stress as in neurodegeneration, is able to induce SG formation in primary fibroblasts and iPSC-N. Importantly, only upon chronic stress, we observed TDP-43 recruitment into SG and the formation of distinct P-TDP-43 aggregates, very similar to the abnormal inclusions observed in ALS/FTD autoptic brains. Moreover, in fibroblasts, cell response to stress was different in control compared with mutant ALS cells, probably due to their different vulnerability. A quantitative analysis revealed also differences in terms of number of SG-forming cells and SG size, suggesting a different composition of foci in acute and chronic stress. In condition of prolonged stress, SG and P-TDP-43 aggregate formation was concomitant with p62 increase and autophagy dysregulation in both ALS fibroblasts and iPSC-N, as confirmed by immunofluorescence and ultrastructural analyses. We found that exposure to a chronic oxidative insult promotes the formation of both SG and P-TDP-43 aggregates in patient-derived cells, reinforcing the idea that SG fail to properly disassemble, interfering with the protein quality control system. Moreover, we obtained a disease cell model recapitulating ALS/FTD P-TDP-43 aggregates, which represents an invaluable bioassay to study TDP-43 pathology and develop therapeutic strategies aimed at disaggregating or preventing the formation of pathological inclusions.
Whole genome assembly ofCulex tarsalis
Authors: Main Bradley J. , Marcantonio Matteo , Johnston J. Spencer , Rasgon Jason L. , Brown C. Titus , Barker Christopher M.
Published: February 2020

The mosquito,Culex tarsalis, is a key vector in the western United States due to its role in transmission of zoonotic arboviruses that affect human health. Extensive research has been conducted onCx. tarsalisecology, feeding behavior, vector competence, autogeny, diapause, genetics, and insecticide resistance. Population genetic analyses in the western U.S. have identified at least three genetic clusters that are geographically distinct. Salivary gland-specific gene expression has also revealed genes involved in blood feeding. However, genetic studies of this mosquito have been hindered by the lack of a reference genome. To facilitate genomic studies inCx. tarsalis, we have assembled and annotated a reference genome (CtarK1) based on PacBio HiFi reads from a single male. Using theCx. tarsalistranscriptome and protein sequences fromCulex quinquefasciatus, approximately 17,456 protein-coding genes, including theparainsecticide resistance gene, were annotated in the CtarK1 genome. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 84.8% of the 2799 Dipteran BUSCO genes. The CtarK1 assembly is 790Mb with an N50 of 58kb. Using full mitochondrial genome alignments with other sequenced mosquito genomes we present a Bayesian phylogeny, which estimates that the divergence ofCx. tarsalisfromCulex quinquefasciatus, the most closely related mosquito species with a genome, occurred 15.8-22.2 million years ago.
A transcriptome for the early-branching fernBotrychium lunariaenables fine-grained resolution of population structure
Authors: Mossion Vinciane , Dauphin Benjamin , Grant Jason , Zemp Niklaus , Croll Daniel
Published: February 2020

Ferns are the second most dominant group of land plants after angiosperms. Extant species occupy an extensive range of habitats and contribute significantly to ecosystem functioning. Despite the importance of ferns, most taxa are poorly covered by genomic resources. The genusBotrychiumbelongs to the family Ophioglossaceae, one of the earliest divergent lineages of vascular plants, and has a cosmopolitan distribution with 35 species, half of which are polyploids. Here, we establish a transcriptome forBotrychium lunaria, a diploid species with an extremely large genome with a 1C value of 12.10 pg. We assembled 25,701 high-quality transcripts with an average length of 1,332 bp based on deep RNA-sequencing of a single individual. We sequenced an additional 11 transcriptomes of individuals from two populations in Switzerland, including the population of the reference individual. Based on read mapping to reference transcript sequences, we identified 374,510 single nucleotide polymorphisms (SNPs) segregating among individuals for an average density of 14 SNPs per kb. The transcriptome-wide markers provided unprecedented resolution of the population genetic structure revealing substantial variation in heterozygosity among individuals. We also constructed a phylogenomic tree of 90 taxa representing all fern orders to ascertain the placement of the genusBotrychium. The high-quality transcriptomic resources enable powerful population and phylogenomic studies in an important group of ferns.

Significance statement

Ferns pose substantial puzzles in terms of lifestyles, genome organization and population structure. Progress has been significantly hampered by the lack of genomic resources. Here, we present a transcriptome forBotrychium lunaria, a phylogenetically early-branching fern with an extremely large genome. We show that the new transcriptome improves phylogenetic resolution among early-branching ferns. Based on an additional 11 transcriptomes of the same species, we identify unexpected variation in population-level heterozygosity.
Vaccinia Virus Infection Inhibits Skin Dendritic Cell Migration to Draining Lymph Node
Authors: Aggio Juliana Bernardi , Krmeská Veronika , Ferguson Brian J. , Wowk Pryscilla Fanini , Rothfuchs Antonio Gigliotti
Published: February 2020

Despite the success of Vaccinia virus (VACV) against smallpox there remains a paucity of information on Dendritic cell (DC) responses to the virus, especially on the traffic of DCs and VACV to draining LN (dLN). Herein we studied skin DC migration in response to VACV and compared it to the tuberculosis vaccineMycobacterium bovisBacille Calmette-Guérin (BCG), another live-attenuated vaccine administered via the skin. In stark contrast to BCG, skin DCs did not relocate to dLN in response to VACV. This happened in spite of virus-induced accumulation of several other innate-immune cell populations in the dLN. UV inactivation of VACV or use of the Modified Vaccinia virus Ankara (MVA) strain promoted DC movement to dLN, indicating that the virus actively interferes with skin DC migration. This active immune suppression by VACV was potent enough to ablate the mobilization of skin DCs in response to BCG, and to reduce the transport of BCG to dLN. Expression of inflammatory mediators associated with BCG-triggered DC migration were absent from virus-injected skin, suggesting that other pathways provoke DC movement in response to replication-deficient VACV. Despite viral suppression of DC migration, VACV was detected in dLN much earlier than BCG, indicating a rapid, alternative route of viral traffic to dLN despite marked blockade of skin DC mobilization from the site of infection.
Contribution of CTCF binding to transcriptional activity at theHOXAlocus inNPM1-mutant AML cells
Authors: Ghasemi Reza , Struthers Heidi , Wilson Elisabeth R. , Spencer David H.
Published: February 2020

Transcriptional regulation of theHOXAgenes is thought to involve CTCF-mediated chromatin loops and the opposing actions of the COMPASS and Polycomb epigenetic complexes. We investigated the role of these mechanisms at theHOXAcluster in AML cells with the common NPM1c mutation, which express bothHOXAandHOXBgenes. CTCF binding at theHOXAlocus is conserved across primary AML samples, regardless ofHOXAgene expression, and defines a continuous chromatin domain marked by COMPASS-associated histone H3 trimethylation inNPM1-mutant primary AML samples. Profiling of the three-dimensional chromatin architecture ofNPM1-mutant OCI-AML3 cells identified chromatin loops between the activeHOXA9-HOXA11genes and loci in theSNX10gene and an intergenic region located 1.4Mbp upstream of theHOXAlocus. Deletion of CTCF binding sites in OCI-AML3 cells reduced these interactions, but resulted in new, CTCF-independent loops with regions in theSKAP2gene that were marked by enhancer-associated histone modifications in primary AML samples.HOXAgene expression was maintained in the CTCF deletion mutants, indicating that transcriptional activity at theHOXAlocus inNPM1-mutant AML cells does not require long-range CTCF-mediated chromatin interactions, and instead may be driven by intrinsic factors within theHOXAgene cluster.
TGF-β inhibitor accelerates BMP4-induced cochlear gap junction formation duringin vitrodifferentiation of embryonic stem cells
Authors: Fukunaga Ichiro , Chen Cheng , Oe Yoko , Danzaki Keiko , Ohta Sayaka , Koike Akito , Fujimoto Ayumi , Ikeda Katsuhisa , Kamiya Kazusaku
Published: February 2020

Mutations in the connexin 26 (CX26)/gap junction beta-2 (GJB2) gene are the most frequent cause of hereditary deafness worldwide. Using mouse induced pluripotent stem cells (iPSCs) and a BMP4 signal-based floating and adherent culture system, we recently producedin vitroresponsible forGJB2-related deafness (CX26-gap junction plaque-forming cells, CX26GJCs). However, to use these cells as a disease model platform for high-throughput drug screening or regenerative therapy, cell yields must be substantially increased. In addition to BMP4, presently uncharacterized factors may also induce CX26 gap junction (GJ) formation. A floating culture with embryonic stem cell (ESC) treatment and BMP4/TGF-β inhibitor (SB431542:SB) has been shown to result in greater production of isolatable CX26-positive small vesicles (CX26+ vesicles) and higherGjb2mRNA levels than BMP4 treatment alone, suggesting that SB may promote BMP4-mediated production of CX26+ vesicles in a dose-dependent manner, thereby increasing the yield of highly purified CX26GJCs.

In the present study, we first demonstrated that SB accelerates BMP4 induced GJ formation during stem cell differentiation. By controlling the concentration and timing of SB supplementation with CX26+ vesicle purification, large-scale production of highly purified CX26GJCs suitable for high-throughput drug screening or regenerative therapy forGJB2-related deafness may be possible.
Generation of multi-transgenic pigs using PiggyBac transposons co-expressing pectinase, xylanase, cellulase, β-1.3-1.4-glucanase and phytase
Authors: Wang Haoqiang , Li Guoling , Zhong Cuili , Mo Jianxin , Sun Yue , Shi Junsong , Zhou Rong , Li Zicong , Yang Huaqiang , Wu Zhenfang , Liu Dewu , Zhang Xianwei
Published: February 2020

The current challenges facing the pork industry are to maximize feed efficiency and minimize fecal emissions. Unlike ruminants, pigs lack a number of digestive enzymes like pectinase, xylanase, cellulase, β-1.3-1.4-glucanase and phytase to hydrolyze the cell walls of grains to release endocellular nutrients into their digestive tracts. Herein, we synthesized multiple cellulase and pectinase genes derived from lower organisms and then codon optimized these genes to be expressed in pigs. These genes were then cloned into our previously optimizedXynB(xylanase)-EsAPPA(phytase) bicistronic construct. We then successfully generated transgenic pigs that expressed four enzymes (Pg7fn(pectinase),XynB(xylanase),EsAPPA(phytase) andTeEGI(cellulase and β-glucanase)) using somatic cell cloning. Expression of these genes was parotid gland specific. Enzymatic assays using the saliva of these founders demonstrated high levels of phytase (2.0~3.4 U/mL) and xylanase (0.25~0.42 U/mL) activity, but low levels of pectinase (0.06~0.08 U/mL) activity. These multi-transgenic pigs are expected to contribute to enhance feed utilization and reduce environmental impact.
BARTweb: a web server for transcription factor association analysis
Authors: Ma Wenjing , Wang Zhenjia , Zhang Yifan , Magee Neal E. , Chen Yang , Zang Chongzhi
Published: February 2020

Identifying active transcription factors (TFs) that bind to cis-regulatory regions in the genome to regulate differential gene expression is a key task in gene regulation research. TF binding profiles from numerous existing ChIP-seq data can be utilized for association analysis with query data for TF identification, as alternative to DNA sequence motif analysis. Here, we present BARTweb, an interactive webserver for identifying TFs whose genomic binding patterns associate with input genomic features, by leveraging over 13,000 public ChIP-seq datasets for human and mouse. Using an updated Binding Analysis for Regulation of Transcription (BART) algorithm, BARTweb can identify functional TFs that regulate a gene set, or have a binding profile correlated with a ChIP-seq profile or enriched in a genomic region set, without a priori information of the cell type. Compared with the original BART package, BARTweb substantially reduces the execution time of a typical job by two orders of magnitude. We also show that BARTweb outperforms other existing tools in identifying true TFs from collected experimental data. BARTweb is a useful webserver for performing functional analysis of gene regulation. BARTweb is freely available athttp://bartweb.org.
Cell substrate patterns driven by curvature-sensitive actin polymerization: waves and podosomes
Authors: Naoz Moshe , Gov Nir S.
Published: February 2020

Cells adhered to an external solid substrate are observed to exhibit rich dynamics of actin structures on the basal membrane, which are distinct from those observed on the dorsal (free) membrane. Here we explore the dynamics of curved membrane proteins, or protein complexes, that recruit actin polymerization when the membrane is confined by the solid substrate. Such curved proteins can induce the spontaneous formation of membrane protrusions on the dorsal side of cells. However, on the basal side of the cells, such protrusions can only extend as far as the solid substrate and this constraint can convert such protrusions into propagating wave-like structures. We also demonstrate that adhesion molecules can stabilize localized protrusions, that resemble some features of podosomes. This coupling of curvature and actin forces may underlie the differences in the observed actin-membrane dynamics between the basal and dorsal sides of adhered cells.