bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of anticoagulation therapy in older patients with chronic kidney disease and atrial fibrillation
Authors: He Wenfeng , Zhang Hao , Zhu Wengen , Xue Zhengbiao
Published: October 2019

Background:

The role of anticoagulation therapy for stroke prevention in older atrial fibrillation (AF) patients with chronic kidney disease (CKD) remains unclear. Therefore, we conducted a meta-analysis to explore the efficacy and safety of anticoagulation therapy in this population.

Methods:

The Cochrane Library, PubMed, and Embase databases were systematically searched for studies reporting the effect of anticoagulation therapy in older patients with AF and CKD. The risk ratios (RRs) and 95% confidence intervals (CIs) were regarded as the risk estimates. A random-effects model selected was to evaluate the treatment outcomes. The presentations were based on the Preferred Reporting Items for reporting systematic reviews and meta-analyses statement.

Results:

A total of 7 studies with 24,794 older patients with AF and CKD were included. The follow-up of the included studies ranged from 0.9 to 9.0 years. In older patients with no dialysis, compared with nonanticoagulants, anticoagulants reduced the risk of all-cause death (RR 0.66, 95% CI 0.54–0.79), but had comparable risks of ischemic stroke/transient ischemic attack (TIA, RR 0.91, 95% CI 0.46–1.79) and bleeding (RR 1.17, 95% CI 0.86–1.60). In older patients with dialysis, compared with nonanticoagulants, anticoagulants increased the risk of bleeding (RR 1.37, 95% CI 1.09–1.74), but had similar risks of ischemic stroke/TIA (RR 1.18, 95% CI 0.88–1.58) and death (RR 0.87, 95% CI 0.60–1.27).

Conclusion:

Compared with nonanticoagulation, anticoagulation therapy is associated with a reduced risk of death in older AF patients with nondialysis, but an increased risk of bleeding in older patients with dialysis.
An engineered CRISPR/Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells
Authors: Bowling Sarah , Sritharan Duluxan , Osorio Fernando G. , Nguyen Maximilian , Cheung Priscilla , Rodriguez-Fraticelli Alejo , Patel Sachin , Fujiwara Yuko , Li Bin E. , Orkin Stuart H. , Hormoz Sahand , Camargo Fernando D.
Published: October 2019

Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Particularly in the context of stem cell biology, analysis of single cell lineages in their native state has elucidated novel fates and highlighted heterogeneity of function. Coupling of such ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CARLIN (for CRISPR Array Repair LINeage tracing) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures based on in vivo stem cell function without a need for markers or cell sorting.
An elusive endosymbiont: DoesWolbachiaoccur naturally inAedes aegypti?
Authors: Ross Perran A. , Callahan Ashley G. , Yang Qiong , Jasper Moshe , Arif A. K. M. , Noor Afizah A. , Nazni W. A. , Hoffmann Ary A.
Published: October 2019

Wolbachiaare maternally-inherited endosymbiotic bacteria found within many insect species.Aedesmosquitoes experimentally infected withWolbachiaare being released into the field forAedes-borne disease control. TheseWolbachiainfections induce cytoplasmic incompatibility which is used to suppress populations through incompatible matings or replace populations through the reproductive advantage provided by this mechanism. However the presence of naturally-occurringWolbachiain target populations could interfere with both population replacement and suppression programs depending on the compatibility patterns between strains.Aedes aegyptiwere thought to not harborWolbachianaturally but several recent studies have detectedWolbachiain natural populations of this mosquito. We therefore review the evidence for naturalWolbachiainfections inAe. aegyptito date and discuss limitations of these studies. We draw on research from other mosquito species to outline the potential implications of naturalWolbachiainfections inAe. aegyptifor disease control. To validate previous reports, we obtained a laboratory population ofAe. aegyptifrom New Mexico, USA, that harbors a naturalWolbachiainfection, and we conducted field surveys in Kuala Lumpur, Malaysia where a naturalWolbachiainfection has also been reported. However, we were unable to detectWolbachiainfection in both the laboratory and field populations. Because the presence of naturally-occurringWolbachiainAe. aegypticould have profound implications forWolbachia-based disease control programs, it is important to continue to accurately assess theWolbachiastatus of targetAedespopulations.
DeepImageJ: A user-friendly environment to run deep learning models in ImageJ
Authors: Gómez-de-Mariscal Estibaliz , García-López-de-Haro Carlos , Ouyang Wei , Donati Laurène , Lundberg Emma , Unser Michael , Muñoz-Barrutia Arrate , Sage Daniel
Published: October 2019

DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learn ing (DL) models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained DL models (BioImage Model Zoo). Hence, non-experts can easily perform common image processing tasks in life-science research with DL-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state-of-the-art solutions and it is equipped with utility tools for developers to include new models. Very recently, several train ing frameworks have adopted the deepImageJ format to deploy their work in one of the most used software in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of DL models in life-sciences applications and bioimage informatics.
The evolution of competitive ability for essential resources
Authors: Bernhardt Joey R. , Kratina Pavel , Pereira Aaron , Tamminen Manu , Thomas Mridul K. , Narwani Anita
Published: October 2019

Competition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species’ minimum resource requirements, their R*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered - to what extent are species’ competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposedChlamydomonas reinhardtiifor approximately 285 generations to seven environments in chemostats which differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients.
An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses
Authors: Radhakrishnan Guru V. , Keller Jean , Rich Melanie K. , Vernié Tatiana , Mbadinga Mbaginda Duchesse L. , Vigneron Nicolas , Cottret Ludovic , San Clemente Hélène , Libourel Cyril , Cheema Jitender , Linde Anna-Malin , Eklund D. Magnus , Cheng Shifeng , Wong Gane KS , Lagercrantz Ulf , Li Fay-Wei , Oldroyd Giles E. D. , Delaux Pierre-Marc
Published: October 2019

Plants are the foundation of terrestrial ecosystems and their colonization of land was facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following that founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Through analysis of 271 transcriptomes and 122 plant genomes, we demonstrate that the common symbiosis signalling pathway controlling the association with arbuscular mycorrhizal fungi and with nitrogen-fixing bacteria specifically co-evolved with intracellular endosymbioses, including ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. In contrast, species forming exclusively extracellular symbioses like ectomycorrhizae or associations with cyanobacteria have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million years of plant diversification.
A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas
Authors: Siegle Joshua H. , Jia Xiaoxuan , Durand Séverine , Gale Sam , Bennett Corbett , Graddis Nile , Heller Greggory , Ramirez Tamina K. , Choi Hannah , Luviano Jennifer A. , Groblewski Peter A. , Ahmed Ruweida , Arkhipov Anton , Bernard Amy , Billeh Yazan N. , Brown Dillan , Buice Michael A. , Cain Nicolas , Caldejon Shiella , Casal Linzy , Cho Andrew , Chvilicek Maggie , Cox Timothy C. , Dai Kael , Denman Daniel J. , de Vries Saskia E. J. , Dietzman Roald , Esposito Luke , Farrell Colin , Feng David , Galbraith John , Garrett Marina , Gelfand Emily C. , Hancock Nicole , Harris Julie A. , Howard Robert , Hu Brian , Hytnen Ross , Iyer Ramakrishnan , Jessett Erika , Johnson Katelyn , Kato India , Kiggins Justin , Lambert Sophie , Lecoq Jerome , Ledochowitsch Peter , Lee Jung Hoon , Leon Arielle , Li Yang , Liang Elizabeth , Long Fuhui , Mace Kyla , Melchior Jose , Millman Daniel , Mollenkopf Tyler , Nayan Chelsea , Ng Lydia , Ngo Kiet , Nguyen Thuyahn , Nicovich Philip R. , North Kat , Ocker Gabriel Koch , Ollerenshaw Doug , Oliver Michael , Pachitariu Marius , Perkins Jed , Reding Melissa , Reid David , Robertson Miranda , Ronellenfitch Kara , Seid Sam , Slaughterbeck Cliff , Stoecklin Michelle , Sullivan David , Sutton Ben , Swapp Jackie , Thompson Carol , Turner Kristen , Wakeman Wayne , Whitesell Jennifer D. , Williams Derric , Williford Ali , Young Rob , Zeng Hongkui , Naylor Sarah , Phillips John W. , Reid R. Clay , Mihalas Stefan , Olsen Shawn R. , Koch Christof
Published: October 2019

The mammalian visual system, from retina to neocortex, has been extensively studied at both anatomical and functional levels. Anatomy indicates the cortico-thalamic system is hierarchical, but characterization of cellular-level functional interactions across multiple levels of this hierarchy is lacking, partially due to the challenge of simultaneously recording activity across numerous regions. Here, we describe a large, open dataset (part of theAllen Brain Observatory) that surveys spiking from units in six cortical and two thalamic regions responding to a battery of visual stimuli. Using spike cross-correlation analysis, we find that inter-area functional connectivity mirrors the anatomical hierarchy from theAllen Mouse Brain Connectivity Atlas. Classical functional measures of hierarchy, including visual response latency, receptive field size, phase-locking to a drifting grating stimulus, and autocorrelation timescale are all correlated with the anatomical hierarchy. Moreover, recordings during a visual task support the behavioral relevance of hierarchical processing. Overall, this dataset and the hierarchy we describe provide a foundation for understanding coding and dynamics in the mouse cortico-thalamic visual system.
Evaluation of nutraceuticals including vitamin B12and xenobiotic degradation capacity ofPleurotusspecies
Authors: Patel Yashvant , Vishwakarma Sanjay Kumar , Sunita Kumari
Published: October 2019

Diverse edaphic zone (namely: usar, wastelands, forest area, wetlands, flood prone area and fertile lands) were identified in the eastern part of Uttar Pradesh and collected species ofPleurotusfor present study. A total of 39 purified isolates were evaluated for the presence of neutraceuticals like proteins, carbohydrates, phenolic and vitamin B12along with xenobiotic dye degradation capacity for textile dyes (MG and BPB) and production of laccase enzyme simultaneously. Isolate no. 06, appeared most distant in dendrogram having two major clusters, which also showed highest MG degradation capacity, however, other isolates also showed excellent degradation of BPB; and the laccase activity was found in the range of 4.03 to 19.13 IU/ml of crude enzyme extract from mycelia. All the isolates used in the present study, were also mounted for their genetic diversity analysis through RAPD. Diversity study revealed gene frequency from 0.012 to 0.987 and the average gene diversity for all RAPD loci were 0.244. The Shannon Information Index was 0.397. The unbiased genetic similarity among all pairs of isolates was 0.36 to 0.93 with a mean of 0.64. Significant genetic diversity, nutraceuticals and laccase enzyme availability and dye degradation capacity within the studied genusPleurotuswas found, which makes necessary to carry out a selection process in each one for superior selection not only for human being but also many aquatic as well as other terrestrial flora and fauna. Present investigation suggest that due to wide range of variation within species, the adaptation of strains to different edaphic zones must be taken into account in selection processes.
SapTrap assembly ofC. elegansMosSCI transgene vectors
Authors: Fan Xintao , De Henau Sasha , Feinstein Julia , Miller Stephanie I. , Han Bingjie , Frøkjær-Jensen Christian , Griffin Erik E.
Published: October 2019

The Mos1-mediated Single-Copy Insertion (MosSCI) method is widely used to establish stableCaenorhabditis eleganstransgenic strains. Cloning MosSCI targeting plasmids can be cumbersome because it requires assembling multiple genetic elements including a promoter, a 3’UTR and gene fragments. Recently, Schwartz and Jorgensen developed the SapTrap method for the one-step assembly of plasmids containing components of the CRISPR/Cas9 system forC. elegans(Schwartz and Jorgensen 2016 Genetics, 202:1277-1288). Here, we report on the adaptation of the SapTrap method for the efficient and modular assembly of a promoter, 3’UTR and either 2 or 3 gene fragments in a MosSCI targeting vector in a single reaction. We generated a toolkit that includes several fluorescent tags, components of the ePDZ/LOV optogenetic system and regulatory elements that control gene expression in theC. elegansgermline. As a proof of principle, we generated a collection of strains that fluorescently label the endoplasmic reticulum and mitochondria in the hermaphrodite germline and that enable the light-stimulated recruitment of mitochondria to centrosomes in the one-cell worm embryo. The method described here offers a flexible and efficient method for assembly of custom MosSCI targeting vectors.
Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)
Authors: Wang Xi , Bernhardsson Carolina , Ingvarsson Pär K.
Published: October 2019

Under the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses inP. abiesin an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity ofP.abiesis low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe inP. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.
Physical activity and risk of lung cancer: a two-sample Mendelian randomization study
Authors: Baumeister Sebastian E , Leitzmann Michael F , Bahls Martin , Meisinger Christa , Amos Christopher I , Hung Rayjean J ,   Cancer in Lung of the International Lung Cancer Consortium (TRICL-ILCCO),   Lung Cancer Cohort Consortium (LC3), Teumer Alexander , Baurecht Hansjörg
Published: October 2019

Abstract

Observational studies have suggested that physical activity might lower the risk of lung cancer in former and current smokers but not in never smokers. Using genetic instruments for self-reported and accelerometer-measured physical activity traits implemented through two-sample Mendelian randomization (MR), we sought to strengthen the evidence for causality. We used 18 genome-wide significant (P < 5×10−8) single nucleotide polymorphisms (SNPs) for self-reported moderate-to-vigorous physical activity and seven SNPs for accelerometer-measured (‘average acceleration’) physical activity from up to 377,234 UK Biobank participants and evaluated these in relation to risk using 29,266 lung cancer cases (including 11,273 adenocarcinomas, 7,426 squamous cell and 2,664 small cell cases) and 56,450 controls. The MR analysis suggested no effect of self-reported physical activity (odds ratio (OR) [95% confidence interval (CI)] = 0.67 [0.42-1.05], P-value = 0.081, Q-value = 0.243) and accelerometer-measured activity (OR [95% CI] = 0.98 [0.93-1.03], P-value = 0.372,Q-value = 0.562) on lung cancer. There was no evidence for associations of physical activity with histologic types and lung cancer in ever and never smokers. Replication analysis using genetic instruments from a different genome-wide study and sensitivity analysis to address potential pleiotropic effects led to no substantive change in estimates. These findings do not support a protective relationship between physical activity and the risk of lung cancer.

Significance

The present study provides little evidence that recommending physical activity would help to prevent lung cancer.
Fluorescence photography of patterns and waves of bacterial adaptation at high antibiotic doses
Authors: Reding Carlos , Hewlett Mark , Bergmiller Tobias , Gudelj Ivana , Beardmore Robert
Published: October 2019

Fisher suggested advantageous genes would spread through populations as a wave so we sought genetic waves in evolving populations, as follows. By fusing a fluorescent marker to a drug efflux protein (AcrB) whose expression providesEscherichia coliwith resistance to some antibiotics, we quantified the evolution and spread of drug-resistantE. colithrough spacetime using image analysis and quantitative PCR. As is done in hospitals routinely, we exposed the bacterium to a gradient of antibiotic in a ‘disk diffusion’ drug susceptibility test that we videoed. The videos show complex spatio-genomic patterns redolent of, yet more complex than, Fisher’s predictions whereby a decelerating wave front of advantageous genes colonises towards the antibiotic source, forming bullseye patterns en route and leaving a wave back of bacterial sub-populations expressing AcrB at decreasing levels away from the drug source. qPCR data show thatE. colisited at rapidly-adapting spatial hotspots gain 2 additional copies ofacr, the operon that encodes AcrB, within 24h and imaging data show resistant sub-populations thrive most near the antibiotic source due to non-monotone relationships between inhibition due to antibiotic and distance from the source. In the spirit of Fisher, we provide an explicitly spatial nonlinear diffusion equation that exhibits these properties too. Finally, linear diffusion theory quantifies how the spatial extent of bacterial killing scales with increases in antibiotic dosage, predicting that microbes can survive chemotherapies that have been escalated to 250× the clinical dosage if the antibiotic is diffusion-limited.
Sick plants in grassland communities: a growth-defense trade-off is the main driver of fungal pathogen abundance and impact
Authors: Cappelli Seraina L. , Pichon Noémie A. , Kempel Anne , Allan Eric
Published: October 2019

Aboveground fungal pathogens can substantially reduce biomass production in grasslands. However, we lack a mechanistic understanding of the drivers of fungal infection and impact. Using a global change biodiversity experiment we show that the trade-off between plant growth and defense is the main determinant of fungal infection in grasslands. Nitrogen addition only indirectly increased infection via shifting plant communities towards more fast growing species. Plant diversity did not decrease infection, likely because the spillover of generalist pathogens or dominance of susceptible species counteracted dilution effects. There was also evidence that fungal pathogens reduced biomass more strongly in diverse communities. Further, fungicide altered plant-pathogen interactions beyond just removing pathogens, probably by removing certain fungi more efficiently than others. Our results show that fungal pathogens have large effects on plant functional composition and biomass production and highlight the importance of considering changes in pathogen community composition to understand their effects.
Succession of physiological stages hallmarks the transcriptomic response of fungusAspergillus nigerto lignocellulose
Authors: van Munster Jolanda M. , Daly Paul , Blythe Martin J. , Ibbett Roger , Kokolski Matt , Gaddipati Sanyasi , Lindquist Erika , Singan Vasanth R. , Barry Kerrie W. , Lipzen Anna , Ngan Chew Yee , Petzold Christopher J. , Chan Leanne Jade G. , Arvas Mikko , Raulo Roxane , Pullan Steven T. , Delmas Stéphane , Grigoriev Igor V. , Tucker Gregory A. , Simmons Blake A. , Archer David B.
Published: October 2019

Background

Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producerAspergilllus nigerover its life time to six substrates important for biofuel production.

Results

We analysed the response ofA. nigerto the feedstockMiscanthusand compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of theAspergillus nidulansfatty acid beta-oxidation transcriptional regulatorfarA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds.

Conclusion

In this study, which includes the first transcriptional response of Aspergilli toMiscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.
Studying POU2F1 to Unveil the Structural Facet for Pan-Cancer Analysis Considering the Functional Annotations and Sequence-Structure Space Paradigm
Authors: Dey A. , Sen S. , Maulik U.
Published: October 2019

POU domain class 2 homebox 1 (POU2F1) is largely known for its transcription factor(TF) activity. Due to its association with different types of malignancies, POU2F1 becomes one of the key factors in pan-cancer analysis. However, in spite of understanding it as a potential drug target, none of the drug has been designed till date due to its extreme dynamicity. In this article, we have proposed a three fold comprehensive framework for understanding the structural conservation and co-variation of POU2F1. Firstly, a gene regulatory network based non-pathogenic and pathogenic study have been performed to understand the strong association between cancers and POU2F1. After that, based on evolutionary sequence space study, the comparative sequential dynamicity of the protein members of POU domain family has been observed mostly between non-human and human samples. Subsequently, the reciprocity effect of the residual co-variation has been identified through direct coupling analysis. Along with that, the structure of POU2F1 has been analysed depending on quality assessment and normal mode based structure network. Comparing the sequence and structure space information, the most significant set of residue viz., 3, 9, 13, 17, 20, 21, 28, 35, 36 have been identified as structural facet for stable binding. It is observed that targeting these residues can help to prevent the monomeric aggregations. This study demonstrates-the observed malleability of POU2F1 is one of the prime reason behind its functional multiplicity in terms of protein moonlighting.

SIGNIFICANCE

POU2F1 is one of the important TFs associated with several malignancies. In spite of orderly stable structure in primitive family proteins, this protein is highly unstable at the monomeric stage. Previous studies show that POU2F1 has a clear association with 121 different diseases. Therefore, it becomes one of the important links in the pan-cancer study. Interestingly, TFs can be considered as a potential drug target. However, it is hardly possible to control the extreme dynamicity of TFs. In this regard, protein moonlighting plays an important role. We have tried to provide a theoretical frame to build understanding on POU2F1. The study provides pathogenic and non-pathogenic connections of the protein in terms of comprehensive and precise Gene Regulatory Network. Subsequently, the instability has been unveiled and the structural facet has been identified. Finally, the specified set of function for a suitable session to target the protein is analyzed based on protein moonlighting properties.
Association between DNA methylation and ADHD symptoms from birth to school age: A prospective meta-analysis
Authors: Neumann Alexander , Walton Esther , Alemany Silvia , Cecil Charlotte , González Juan Ramon , Jima Dereje D. , Lahti Jari , Tuominen Samuli T. , Barker Edward D. , Binder Elisabeth , Caramaschi Doretta , Carracedo Ángel , Czamara Darina , Evandt Jorunn , Felix Janine F. , Fuemmeler Bernard F. , Gutzkow Kristine B. , Hoyo Cathrine , Julvez Jordi , Kajantie Eero , Laivuori Hannele , Maguire Rachel , Maitre Léa , Murphy Susan K. , Murcia Mario , Villa Pia M. , Sharp Gemma , Sunyer Jordi , Raikkönen Katri , Bakermans-Kranenburg Marian , van IJzendoorn Marinus , Guxens Mònica , Relton Caroline L. , Tiemeier Henning
Published: October 2019

Attention-deficit and hyperactivity disorder (ADHD) is a common childhood disorder with a substantial genetic component. However, the extent to which epigenetic mechanisms play a role in the etiology of the disorder is not known. We performed epigenome-wide association studies (EWAS) within the Pregnancy And Childhood Epigenetics (PACE) Consortium to identify DNA methylation sites associated with ADHD symptoms at two methylation assessment periods: birth and school-age. We examined associations of DNA methylation in cord blood with repeatedly assessed ADHD symptoms (age range 4-15 years) in 2477 children from five cohorts and DNA methylation at school-age with concurrent ADHD symptoms (age 7-11 years) in 2374 children from ten cohorts. CpGs identified with nominal significance (p<0.05) in either of the EWAS were correlated between timepoints (ρ=0.30), suggesting overlap in associations, however, top signals were very different. At birth, we identified nine CpGs that were associated with later ADHD symptoms (P<1*10−7), including ERC2 and CREB5. Peripheral blood DNA methylation at one of these CpGs (cg01271805 located in the promotor region of ERC2, which regulates neurotransmitter release) was previously associated with brain methylation. Another (cg25520701) lies within the gene body of CREB5, which was associated with neurite outgrowth and an ADHD diagnosis in previous studies. In contrast, at school-age, no CpGs were associated with ADHD with P<1*10−7. In conclusion, we found evidence in this study that DNA methylation at birth is associated with ADHD. Future studies are needed to confirm the utility of methylation variation as biomarker and its involvement in causal pathways.
Presynaptic inhibition of cutaneous afferents prevents self-generated itch
Authors: Escalante Augusto , Klein Rüdiger
Published: October 2019

Chronic itch represents an incapacitating burden on patients suffering a wide spectrum of diseases. Despite recent advances in our understanding of the cells and circuits implicated in the processing of itch information, chronic itch often presents itself without apparent cause. Here, we identify a spinal subpopulation of inhibitory neurons defined by the expression of Ptf1a involved in gating mechanosensory information self-generated during movement. These neurons receive tactile and motor input and establish presynaptic inhibitory contacts on mechanosensory afferents. Loss of Ptf1a neurons leads to increased hairy skin sensitivity and chronic itch, at least partially mediated through the classic itch pathway involving gastrin releasing peptide receptor (GRPR) spinal neurons. Conversely, chemogenetic activation of GRPR neurons elicits itch which is suppressed by concomitant activation of Ptf1a neurons. These findings shed new light on the circuit mechanisms implicated in chronic itch and open novel targets for therapy developments.

Highlights

*

Ptf1a specifies adult spinal presynaptic neurons contacting cutaneous afferents

*

Loss of spinal Ptf1a+ neurons leads to self-generated itch and excessive grooming

*

Absence of Ptf1a+ neurons increases hairy skin sensitivity which triggers scratching

*

GRPR+ neurons act downstream of Ptf1a+ neurons in spontaneous itch
Deaminase associated single nucleotide variants in blood and saliva-derived exomes from healthy subjects
Authors: Hall Nathan E. , Mamrot Jared , Frampton Christopher M.A. , Read Prue , Steele Edward J. , Bischof Robert J. , Lindley Robyn A.
Published: October 2019

Background

Deaminases play an important role in shaping inherited and somatic variants. Disease related SNVs are associated with deaminase mutagenesis and genome instability. Here, we investigate the reproducibility and variance of whole exome SNV calls in blood and saliva of healthy subjects and analyze variants associated with AID, ADAR, APOBEC3G and APOBEC3B deaminase sequence motifs.

Methods

Samples from twenty-four healthy Caucasian volunteers, allocated into two groups, underwent whole exome sequencing. Group 1 (n=12) analysis involved one blood and four saliva replicates. A single saliva sample was sequenced for Group 2 subjects (n=12). Overall, a total of 72 whole exome datasets were analyzed. Biological (Group 1 & 2) and technical (Group 1) variance of SNV calls and deaminase metrics were calculated and analyzed using intraclass correlation coefficients. Candidate somatic SNVs were identified and evaluated.

Results

We report high blood-saliva concordance in germline SNVs from whole exome sequencing. Concordant SNVs, found in all subject replicates, accounted for 97% of SNVs located within the protein coding sequence of genes. Discordant SNVs have a 30% overlap with variants that fail gnomAD quality filters and are less likely to be found in dbSNP. SNV calls and deaminase-associated metrics were found to be reproducible and robust (intraclass correlation coefficients >0.95). No somatic SNVs were conclusively identified when comparing blood and saliva samples.

Conclusions

Saliva and blood both provide high quality sources of DNA for whole exome sequencing, with no difference in ability to resolve SNVs and deaminase-associated metrics. We did not identify somatic SNVs when comparing blood and saliva of healthy individuals, and we conclude that more specialized investigative methods are required to comprehensively assess the impact of deaminase activity on genome stability in healthy individuals.
Genetic design automation for autonomous formation of multicellular shapes from a single cell progenitor
Authors: Appleton Evan , Mehdipour Noushin , Daifuku Tristan , Briers Demarcus , Haghighi Iman , Moret Michael , Chao George , Wannier Timothy , Chiappino-Pepe Anush , Huang Jeremy , Belta Calin , Church George
Published: October 2019

Abstract

Multi-cellular organisms originate from a single cell, ultimately giving rise to mature organisms of heterogeneous cell type composition in complex structures. Recent work in the areas of stem cell biology and tissue engineering have laid major groundwork in the ability to convert certain types of cells into other types, but there has been limited progress in the ability to control the morphology of cellular masses as they grow. Contemporary approaches to this problem have included the use of artificial scaffolds, 3D bioprinting, and complex media formulations, however, there are no existing approaches to controlling this process purely through genetics and from a single-cell starting point. Here we describe a computer-aided design approach for designing recombinase-based genetic circuits for controlling the formation of multi-cellular masses into arbitrary shapes in human cells.
High throughput CRISPR screening identifies genes involved in macrophage viability and inflammatory pathways
Authors: Covarrubias Sergio , Vollmers Apple , Capili Allyson , Boettcher Michael , Robinson Elektra K. , O’Briain Laura , Vollmers Christopher , Blau James , McManus Michael , Carpenter Susan
Published: October 2019

Macrophages are critical cells of the innate immune system involved in the recognition and destruction of invading microbes in addition to the resolution of inflammation and maintenance of homeostasis. Understanding the genes involved in all aspects of macrophage biology is essential to gaining new insights into immune system dysregulation during diseases that range from autoinflammatory to cancer. Here we utilize high throughput clustered regularly interspaced short palindromic repeats (CRISPR) screening to generate a resource that identifies genes required for macrophage viability and function. First, we employ a pooled based CRISPR/Cas nuclease active screening approach to identify essential genes required for macrophage viability by targeting genes within coding exons. In addition, we also target 3’UTRs to gain insights into newcis-regulatory regions that control expression of these essential genes. Second, using our recently generated NF-κB reporter macrophage line, we perform a fluorescence-activated cell sorting (FACS)-based high-throughput genetic screen to identify regulators of inflammation. We identify a number of novel positive and negative regulators of the NF-κB pathway as well as unraveling complexities of the TNF signaling cascade showing it can function in an autocrine manner to negatively regulate the pathway. Utilizing a single complex library design we are capable of interrogating various aspects of macrophage biology, generating a resource for future studies.

Author Summary

Excess inflammation is associated with a variety of autoimmune diseases and cancers. Macrophages are important mediators of this inflammatory response. Defining the genes involved in their viability and effector function is needed to completely understand these two important aspects of macrophage biology. Here we screened over 21,000 genes and generated a resource guide of genes required for macrophage viability as well as novel positive and negative regulators of NF-κB signaling.
Using transcranial magnetic stimulation to map the cortical representation of lower-limb muscles
Authors: Davies Jennifer L
Published: October 2019

The aim of this study was to evaluate the extent to which transcranial magnetic stimulation (TMS) can identify discrete cortical representation of lower-limb muscles in healthy individuals. Data were obtained from 16 young healthy adults (12 women, four men; mean [SD] age 23.0 [2.6] years). Motor evoked potentials were recorded from the resting vastus medialis, rectus femoris, vastus lateralis, medial and lateral hamstring, and medial and lateral gastrocnemius muscles on the right side of the body using bipolar surface electrodes. TMS was delivered through a 110-mm double-cone coil at 63 sites over the left hemisphere. Location and size of the cortical representation and the number of discrete peaks were quantified for each muscle. Within the quadriceps muscle group there was a main effect of muscle on anterior-posterior centre of gravity (p = 0.010), but the magnitude of the difference was very small. Within the quadriceps there was a main effect of muscle on medial-lateral hotspot (p = 0.027) and map volume (p = 0.047), but no post-hoc tests were significant. The topography of each lower-limb muscle was complex, displaying multiple peaks that were present across the stimulation grid, and variable across individuals. The results of this study indicate that TMS delivered with a 110-mm double-cone coil could not reliably identify discrete cortical representations of resting lower-limb muscles when responses were measured using bipolar surface electromyography. The characteristics of the cortical representation of lower-limb muscles reported here provide a basis against which to evaluate cortical reorganisation in clinical populations.
LITESEC-T3SS - Light-controlled protein delivery into eukaryotic cells with high spatial and temporal resolution
Authors: Lindner Florian , Milne-Davies Bailey , Langenfeld Katja , Diepold Andreas
Published: October 2019

Many bacteria employ a type III secretion system (T3SS), also called injectisome, to translocate proteins into eukaryotic host cells through a hollow extracellular needle. The system can efficiently transport heterologous cargo, which makes it a uniquely suited tool for the translocation of proteins into eukaryotic cells. However, the injectisome indiscriminately injects proteins into any adjoining eukaryotic cell, and this lack of target specificity currently limits its application in biotechnology and healthcare. In this study, we exploit the dynamic nature of the T3SS to control protein secretion and translocation into eukaryotic cells by light. By combining optogenetic interaction switches with the dynamic cytosolic T3SS component SctQ, the cytosolic availability of SctQ and in consequence T3SS-dependent effector secretion can be regulated by external light. The resulting system, which we call LITESEC-T3SS (Light-inducedtranslocation ofeffectors throughsequestration ofendogenouscomponents of theT3SS), allows rapid, specific, and reversible activation or deactivation of the T3SS upon illumination. We demonstrate the application of the system for light-regulated translocation of a heterologous reporter protein into cultured eukaryotic cells. LITESEC-T3SS represents a new method to achieve unparalleled spatial and temporal resolution for the controlled protein translocation into eukaryotic host cells.
Functionally-informed fine-mapping and polygenic localization of complex trait heritability
Authors: Weissbrod Omer , Hormozdiari Farhad , Benner Christian , Cui Ran , Ulirsch Jacob , Gazal Steven , Schoech Armin P. , van de Geijn Bryce , Reshef Yakir , Márquez-Luna Carla , O’Connor Luke , Pirinen Matti , Finucane Hilary K. , Price Alkes L.
Published: October 2019

Fine-mapping aims to identify causal variants impacting complex traits. Several recent methods improve fine-mapping accuracy by prioritizing variants in enriched functional annotations. However, these methods can only use information at genome-wide significant loci (or a small number of functional annotations), severely limiting the benefit of functional data. We propose PolyFun, a computationally scalable framework to improve fine-mapping accuracy using genome-wide functional data for a broad set of coding, conserved, regulatory and LD-related annotations. PolyFun prioritizes variants in enriched functional annotations by specifying prior causal probabilities for fine-mapping methods such as SuSiE or FINEMAP, employing special procedures to ensure robustness to model misspecification and winner’s curse. In simulations with in-sample LD, PolyFun + SuSiE and PolyFun + FINEMAP were well-calibrated and identified >20% more variants with posterior causal probability >0.95 than their non-functionally informed counterparts (and >33% more fine-mapped variants than previous functionally-informed fine-mapping methods). In simulations with mismatched reference LD, PolyFun + SuSiE remained well-calibrated when reducing the maximum number of assumed causal SNPs per locus, which reduces absolute power but still produces large relative improvements. In analyses of 49 UK Biobank traits (average N=318K) with in-sample LD, PolyFun + SuSiE identified 3,025 fine-mapped variant-trait pairs with posterior causal probability >0.95, a >32% improvement vs. SuSiE; 223 variants were fine-mapped for multiple genetically uncorrelated traits, indicating pervasive pleiotropy. We used posterior mean per-SNP heritabilities from PolyFun + SuSiE to perform polygenic localization, constructing minimal sets of common SNPs causally explaining 50% of common SNP heritability; these sets ranged in size from 28 (hair color) to 3,400 (height) to 2 million (number of children). In conclusion, PolyFun prioritizes variants for functional follow-up and provides insights into complex trait architectures.
Pseudomonas two-partner secretion toxin Exolysin contributes to insect killing
Authors: Job Viviana , Bouillot Stéphanie , Gueguen Erwan , Robert-Genthon Mylène , Panchev Peter , Elsen Sylvie , Attrée Ina
Published: October 2019

Pseudomonas chlororaphis is a promising biocontrol agent promoting plant-growth and providing protection against pest insects and phytopathogenic fungi. We have identified in the genome of P. chlororaphis PA23 an operon encoding the toxin Exolysin (ExlA) and its outer-membrane transporter, ExlB. We found that P. chlororaphis producing ExlA (ExlAPch) is cytotoxic towards murine macrophages and human epithelial cells at 30 °C. P. chlororaphis PA23 provoked shrinkage of epithelial cell, leakage of cytoplasmic components and subsequent cell death. During infection, ExlAPch incorporated into epithelial cell membranes within detergent-resistant lipid rafts, suggesting the same mechanisms of cell destruction by pore-formation as reported for P. aeruginosa toxin. ExlAPch was not involved in the capacity of the strain to kill fungi, amoeba or other bacteria. The contribution of ExlA in insecticidal activity of P. chlororaphis was evaluated in the wax moth larvae Galleria mallonella and in Drosophila melanogaster flies. The impact of the deletion of a gene encoding exlA homologue was tested in the natural fly pathogen P. entonomophila. In both models, the ExlA absence delayed killing, suggesting the contribution of the toxin in bacteria-insect pathogenic interactions.
CLASP mediates microtubule repair by promoting tubulin incorporation into damaged lattices
Authors: Aher Amol , Rai Dipti , Schaedel Laura , Gaillard Jeremie , John Karin , Blanchoin Laurent , Thery Manuel , Akhmanova Anna
Published: October 2019

Microtubule network plays a key role in cell division, motility and intracellular trafficking. Microtubule lattices are generally regarded as stable structures that undergo turnover through dynamic instability of their ends [1]. However, recent evidence suggests that microtubules also exchange tubulin dimers at the sites of lattice defects, which can either be induced by mechanical stress or occur spontaneously during polymerization [2–4]. Tubulin incorporation can restore microtubule integrity; moreover, “islands” of freshly incorporated GTP-tubulin can inhibit microtubule disassembly and promote rescues [3–7]. Microtubule repair occurs in vitro in the presence of tubulin alone [2–4, 8]. However, in cells, it is likely to be regulated by specific factors, the nature of which is currently unknown. CLASP is an interesting candidate for microtubule repair, because it induces microtubule nucleation, stimulates rescue and suppresses catastrophes by stabilizing incomplete growing plus ends with lagging protofilaments and promoting their conversion into complete ones [9–16]. Here, we used in vitro reconstitution assays combined with laser microsurgery and microfluidics to show that CLASP2α indeed stimulates microtubule lattice repair. CLASP2α promoted tubulin incorporation into damaged lattice sites thereby restoring microtubule integrity. Furthermore, it induced the formation of complete tubes from partial protofilament assemblies and inhibited microtubule softening caused by hydrodynamic flow-induced bending. A single CLASP2α domain, TOG2, which suppresses catastrophes when tethered to microtubules, was sufficient to stimulate microtubule repair, indicating that catastrophe suppression and lattice repair are mechanistically similar. Our results suggest that the cellular machinery controlling microtubule nucleation and growth can also help to maintain microtubule integrity.