bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuronal hyperexcitability is a DLK-dependent trigger of HSV-1 reactivation that can be induced by IL-1
Authors: Cuddy Sean R. , Schinlever Austin R. , Dochnal Sara , Suzich Jon , Kundu Parijat , Downs Taylor K. , Farah Mina , Desai Bimal , Boutell Chris , Cliffe Anna R.
Published: April 2020

Herpes Simplex Virus (HSV) establishes a latent infection in neurons and periodically reactivates to cause disease. The neuronal stimuli that trigger HSV reactivation have not been fully elucidated. Here we demonstrate that HSV reactivation can be induced by neuronal hyperexcitability. Neuronal stimulation-induced reactivation was dependent on voltage-gated ion and hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, demonstrating that neuronal activity is required for reactivation. Hyperexcitability-induced reactivation was dependent on the neuronal pathway of DLK/JNK activation and progressed via an initial wave of viral gene expression that was independent of histone demethylase activity and linked to histone phosphorylation. IL-1β induces neuronal hyperexcitability and is released under conditions of stress and fever; both known triggers of clinical HSV reactivation. IL-1β induced histone phosphorylation in sympathetic neurons, and importantly HSV reactivation, which was dependent on DLK and neuronal excitability. Thus, HSV co-opts an innate immune pathway resulting from IL-1 stimulation of neurons to induce reactivation.
Unexpected sounds non-selectively inhibit active visual stimulus representations
Authors: Soh Cheol , Wessel Jan R.
Published: April 2020

The brain’s capacity to process unexpected events is key to cognitive flexibility. The most well-known effect of unexpected events is the interruption of attentional engagement (distraction). We tested whether unexpected events interrupt attentional representations by activating a neural mechanism for inhibitory control. This mechanism is most well-characterized within the motor system. However, recent work showed that it is automatically activated by unexpected events and can explain some of their non-motor effects (e.g., on working memory representations). Here, human participants attended to lateralized flickering visual stimuli, producing steady-state visual evoked potentials (SSVEP) in the scalp-electroencephalogram. After unexpected sounds, the SSVEP was rapidly suppressed. Using a functional localizer (stop-signal) task and independent component analysis, we then identified a fronto-central EEG source whose activity indexes inhibitory motor control. Unexpected sounds in the SSVEP task also activated this source. Using single-trial analyses, we found that sub-components of this source differentially relate to sound-related SSVEP changes: while its N2 component predicted the subsequent suppression of the attended-stimulus SSVEP, the P3 component predicted the suppression of the SSVEP to the unattended stimulus. These results shed new light on the processes underlying fronto-central control signals and have implications for phenomena such as distraction and the attentional blink.
Membrane receptor MerTK is a newly identified transcriptional regulator that associates to chromatin as nanoclusters during human DC differentiation
Authors: Borgman Kyra. J.E. , Flórez-Grau Georgina , Ricci Maria A. , Manzo Carlo , Lakadamyali Melike , Cambi Alessandra , Benítez-Ribas Daniel , Campelo Felix , Garcia-Parajo Maria. F.
Published: April 2020

MerTK is a transmembrane receptor tyrosine kinase (RTK) mainly expressed in dendritic cells (DCs) and macrophages where it plays an important role in immunotolerance, but also in activating oncogenic signalling pathways. Albeit MerTK is exploited as clinical target in cancer and auto-immune disorders, the mechanisms that regulate its diverse functions are poorly understood. Here, we identified a remarkably high pool of the full receptor in the nucleus of human DCs. Nuclear translocation was ligand-dependent. Importantly, MerTK nuclear levels correlated to DC differentiation and were spatiotemporally regulated by the transmembrane receptor LRP-1. Using dual-colour super-resolution nanoscopy we discovered that nuclear MerTK forms nanoclusters, whose strength strongly depends on chromatin accessibility during DC differentiation. We finally revealed high transcription capacity of MerTK. Overall, our work indicates that nuclear MerTK acts as a transcription factor regulating DC differentiation, thus implicating for the first time a physiological function for RTK nuclear translocation in immunity.
Taxonomy of neural oscillation events in primate auditory cortex
Authors: Neymotin Samuel A , Tal Idan , Barczak Annamaria , O’Connell Monica N. , McGinnis Tammy , Markowitz Noah , Espinal Elizabeth , Griffith Erica , Anwar Haroon , Dura-Bernal Salvador , Schroeder Charles E , Lytton William W , Jones Stephanie R , Bickel Stephan , Lakatos Peter
Published: April 2020

Electrophysiological oscillations in the brain have been shown to occur as multi-cycle events, with onset and offset dependent on behavioral and cognitive state. To provide a baseline for state-related and task-related events, we quantified oscillation features in resting-state recordings. We used two invasively-recorded electrophysiology datasets: one from human, and one from non-human primate auditory system. After removing incidentally occuring event related potentials, we used a wavelet transform based method to quantify oscillation features. We identified about 2 million oscillation events, classified within traditional frequency bands: delta, theta, alpha, beta, low gamma, gamma, high gamma. Oscillation events of 1-44 cycles were present in at least one frequency band in 90% of the time in human and non-human primate recordings. Individual oscillation events were characterized by non-constant frequency and amplitude. This result naturally contrasts with prior studies which assumed such constancy, but is consistent with evidence from event-associated oscillations. We measured oscillation event duration, frequency span, and waveform shape. Oscillations tended to exhibit multiple cycles per event, verifiable by comparing filtered to unfiltered waveforms. In addition to the clearintra-event rhythmicity, there was also evidence ofinter-event rhythmicity within bands, demonstrated by finding that coefficient of variation of interval distributions and Fano Factor measures differed significantly from a Poisson distribution assumption. Overall, our study demonstrates that rhythmic, multi-cycle oscillation events dominate auditory cortical dynamics.
Molecular architecture and domain arrangement of the placental malaria protein VAR2CSA suggests a model for receptor binding
Authors: Bewley Maria C. , Gautam Lovely , Gowda D. Channe , Flanagan John M.
Published: April 2020

VAR2CSA is the placental-malaria specific member of the antigenically variantPlasmodium falciparumerythrocyte membrane protein 1 (PfEMP1) family. It is expressed on the surface ofPlasmodium falciparuminfected host red blood cells and binds to specific chondroitin-4-sulfate (CSA) chains of the placental proteoglycan receptor. The functional ~310 kDa ectodomain of VAR2CSA is a multi-domain protein that requires a minimum 12-mer CSA molecule for specific, high affinity receptor binding. However, how these domains interact to create the receptor binding surface is not known, limiting efforts to exploit its potential as an effective vaccine or drug target. Using small angle X-ray scattering and single particle reconstruction from negative stained electron micrographs of the ectodomain and multidomain constructs, we have determined the structural architecture of VAR2CSA. The relative location of the domains creates two distinct pores that can each accommodate the 12-mer of CSA, suggesting a model for receptor binding. This model has important implications for understanding cytoadherence of IRBCs and potentially provides a starting point for developing novel strategies to prevent and/or treat placental malaria.
Thermal Control of T-cell Immunotherapy
Authors: Abedi Mohamad H. , Lee Justin , Piraner Dan I. , Shapiro Mikhail G.
Published: April 2020

Genetically engineered T-cells are being developed to perform a variety of therapeutic functions. However, no robust mechanisms exist to externally control the activity of T-cells at specific locations within the body. Such spatiotemporal control could help mitigate potential off-target toxicity due to incomplete molecular specificity in applications such as T-cell immunotherapy against solid tumors. Temperature is a versatile external control signal that can be delivered to target tissuesin vivousing techniques such as focused ultrasound and magnetic hyperthermia. Here, we test the ability of heat shock promoters to mediate thermal actuation of genetic circuits in primary human T-cells in the well-tolerated temperature range of 37–42°C, and introduce genetic architectures enabling the tuning of the amplitude and duration of thermal activation. We demonstrate the use of these circuits to control the expression of chimeric antigen receptors and cytokines, and the killing of target tumor cells. This technology provides a critical tool to direct the activity of T-cells after they are deployed inside the body.
Two spaced training trials induce associative ERK-dependent long-term memory inNeohelice granulata
Authors: Ramos Santiago Ojea , Andina Matías , Romano Arturo , Feld Mariana
Published: April 2020

Memory formation depends upon several parametric training conditions. Among them, trial number and inter-trial interval (ITI) are key factors to induce long-term retention. However, it is still unclear how individual training trials contribute to mechanisms underlying memory formation and stabilization. Contextual conditioning inNeohelice granulatahas traditionally elicited associative long-term memory (LTM) after 15 spaced (ITI = 3 min) trials. Here, we show that LTM in crabs can be induced after only two training trials by increasing the ITI to 45 min (2t-LTM) and maintaining the same training duration as in traditional protocols. This new LTM observed was preserved for at least 96 h, exhibited protein synthesis dependence during consolidation and reconsolidation as well as context-specificity. Moreover, we demonstrate that 2t-LTM depends on inter-trial and post-training ERK activation showing a faster phosphorylation after the second trial compared to the first one. In summary, we present a new training protocol in crabs with reduced number of trials that shows associative features similar to traditional spaced training. This novel protocol allows intra-training manipulation and the assessment of individual trial contribution to LTM formation.
Repairing neural damage in aC. eleganschemosensory circuit using genetically engineered synapses
Authors: Rabinowitch Ithai , Upadhyaya Bishal , Pant Aaradhya , Bai Jihong
Published: April 2020

Neuronal loss can considerably diminish neural circuit function, impairing normal behavior by disrupting information flow in the circuit. We reasoned that by rerouting the flow of information in the damaged circuit it may be possible to offset these negative outcomes. We examined this possibility using the well-characterized chemosensory circuit of the nematode wormC. elegans. In this circuit, a main sensory neuron class sends parallel outputs to several interneuron classes. We found that the removal of one of these interneuron classes impairs chemotaxis to attractive odors, revealing a prominent path for information flow in the circuit. To alleviate these deficiencies, we sought to reinforce a remaining neural pathway. We used genetically engineered electrical synapses for this purpose, and observed the successful recovery of chemotaxis performance. However, we were surprised to find that the recovery was largely mediated by inadvertently formed left-right lateral electrical connections within individual neuron classes. Our analysis suggests that these additional electrical synapses help restore circuit function by amplifying weakened neuronal signals in the damaged circuit. These results demonstrate the power of genetically engineered synapses to regulate information flow and signal intensity in damaged neural circuits.
Tuning trophoblast invasion in a gelatin hydrogel via soluble cues from the maternal-fetal interface
Authors: Zambuto Samantha G. , Clancy Kathryn B.H. , Harley Brendan A.C.
Published: April 2020

Trophoblast cells play multiple critical roles in pregnancy, notably modulating blastocyst attachment to the endometrium as well as invading into and actively remodeling the endometrium to facilitate biotransport needs of the growing embryo. Despite the importance of trophoblast invasion for processes essential at early stages of pregnancy, much remains unknown regarding the balance of signaling molecules that may influence trophoblast invasion into the endometrium. The goal of this study was to use a three-dimensional trophoblast spheroid invasion assays to examine the effect of cues from the maternal-fetal interface on trophoblast invasion. We report use of a methacrylamide-functionalized gelatin (GelMA) hydrogel to support quantitative analysis of trophoblast outgrowth area and cell viability. We show this multidimensional model of trophoblast invasion can resolve quantifiable differences in outgrowth area and viability in the presence of a known invasion promoter, epidermal growth factor, and a known invasion inhibitor, transforming growth factor β1. We then investigate the sensitivity of trophoblast invasion to cortisol, a hormone associated with exogenous stressors. Together, this approach provides a toolset to investigate the coordinated action of physiological and pathophysiological processes on early stages of trophoblast invasion.

IMPACT STATEMENT

Trophoblast cells from the invading blastocyst play crucial roles in pregnancy, including remodeling endometrial structure to support embryonic biotransport needs; however, much remains unknown regarding the balance of signaling molecules that may influence trophoblast invasion. We show this multidimensional model of invasion can resolve quantifiable differences in outgrowth area and viability in the presence of known invasion promoters and inhibitors and then investigate invasion sensitivity to cortisol, a hormone associated with exogenous stressors. This approach provides a toolset to investigate the coordinated action of molecules from the maternal-fetal interface on trophoblast invasion that may be challenging to study in humans.
Single-cell analysis of human lung epithelia reveals concomitant expression of the SARS-CoV-2 receptor ACE2 with multiple virus receptors and scavengers in alveolar type II cells
Authors: Han Guangchun , Sinjab Ansam , Treekitkarnmongkol Warapen , Brennan Patrick , Hara Kieko , Chang Kyle , Bogatenkova Elena , Sanchez-Espiridion Beatriz , Behrens Carmen , Gao Boning , Girard Luc , Zhang Jianjun , Sepesi Boris , Cascone Tina , Byers Lauren , Gibbons Don L. , Chen Jichao , Moghaddam Seyed Javad , Ostrin Edwin J. , Fujimoto Junya , Shay Jerry , Heymach John V. , Minna John D. , Dubinett Steven , Scheet Paul A. , Wistuba Ignacio I. , Hill Edward , Telesco Shannon , Stevenson Christopher , Spira Avrum E. , Wang Linghua , Kadara Humam
Published: April 2020

The novel coronavirus SARS-CoV-2 was identified as the causative agent of the ongoing pandemic COVID 19. COVID-19-associated deaths are mainly attributed to severe pneumonia and respiratory failure. Recent work demonstrated that SARS-CoV-2 binds to angiotensin converting enzyme 2 (ACE2) in the lung. To better understandACE2abundance and expression patterns in the lung we interrogated our in-house single-cell RNA-sequencing dataset containing 70,085 EPCAM+ lung epithelial cells from paired normal and lung adenocarcinoma tissues. Transcriptomic analysis revealed a diverse repertoire of airway lineages that included alveolar type I and II, bronchioalveolar, club/secretory, quiescent and proliferating basal, ciliated and malignant cells as well as rare populations such as ionocytes. While the fraction of lung epithelial cells expressingACE2was low (1.7% overall), alveolar type II (AT2, 2.2%ACE2+) cells exhibited highest levels ofACE2expression among all cell subsets. Further analysis of the AT2 compartment (n = 27,235 cells) revealed a number of genes co-expressed withACE2that are important for lung pathobiology including those associated with chronic obstructive pulmonary disease (COPD;HHIP), pneumonia and infection (FGGandC4BPA) as well as malarial/bacterial (CD36) and viral (DMBT1) scavenging which, for the most part, were increased in smoker versus light or non-smoker cells. Notably,DMBT1was highly expressed in AT2 cells relative to other lung epithelial subsets and its expression positively correlated withACE2. We describe a population ofACE2-positive AT2 cells that co-express pathogen (including viral) receptors (e.g.DMBT1) with crucial roles in host defense thus comprising plausible phenotypic targets for treatment of COVID-19.
Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a
Authors: Tang Dan , Sheng Jingwen , Xu Liangting , Zhan Xiechao , Liu Jiaming , Hui Jiang , Shu Xiaoling , Liu Xiaoyu , Zhang Tizhong , Jiang Lan , Zhou Cuiyan , Li Wenqi , Cheng Wei , Li Zhonghan , Wang Kunjie , Lu Kefeng , Yan Chuangye , Qi Shiqian
Published: April 2020

A massive intronic hexanucleotide repeat (GGGGCC) expansion inC9ORF72is a genetic origin of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recently, C9ORF72, together with SMCR8 and WDR41, has been shown to regulate autophagy and function as Rab GEF. However, the precise function of C9ORF72 remains unclear. Here, we report the cryo-EM structure of the human C9ORF72-SMCR8-WDR41 complex at a resolution of 3.2 Å. The structure reveals the dimeric assembly of a heterotrimer of C9ORF72-SMCR8-WDR41. Notably, the C-terminal tail of C9ORF72 and the DENN domain of SMCR8 play critical roles in the dimerization of the two protomers of the C9ORF72-SMCR8-WDR41 complex. In the protomer, C9ORF72 and WDR41 are joined by SMCR8 without direct interaction. WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix. Interestingly, the prominent structural feature of C9ORF72-SMCR8 resembles that of the FLNC-FNIP2 complex, the GTPase activating protein (GAP) of RagC/D. Structural comparison and sequence alignment revealed that Arg147 of SMCR8 is conserved and corresponds to the arginine finger of FLCN, and biochemical analysis indicated that the Arg147 of SMCR8 is critical to the stimulatory effect of the C9ORF72-SMCR8 complex on Rab8a and Rab11a. Our study not only illustrates the basis of C9ORF72-SMCR8-WDR41 complex assembly but also reveals the GAP activity of the C9ORF72-SMCR8 complex.

Significance Statement

C9ORF72, together with SMCR8 and WDR41, has been shown to form a stable complex that participates in the regulation of membrane trafficking. We report the cryo-EM structure of the C9ORF72-SMCR8-WDR41 complex at atomic resolution. Notably, the stoichiometry of the three subunits in the C9ORF72-SMCR8-WDR41 complex is 2:2:2. Interestingly, the C-termini of C9ORF72 and the DENN domain of SMCR8 mediate the dimerization of the two C9ORF72-SMCR8-WDR41 protomers in the complex. Moreover, WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix without direct contact with C9ORF72. Most importantly, the C9ORF72-SMCR8 complex works as a GAP for Rab8a and Rab11ain vitro,and the Arg147 of SMCR8 is the arginine finger.
Extending the spacing between the Shine-Dalgarno sequence and P-site codon reduces the rate of mRNA translocation
Authors: Wakabayashi Hironao , Warnasooriya Chandani , Ermolenko Dmitri N.
Published: April 2020

By forming basepairing interactions with the 3’ end of 16S rRNA, mRNA Shine-Dalgarno (SD) sequences positioned upstream of Open Reading Frames (ORFs) facilitate translation initiation. During the elongation phase of protein synthesis, intragenic SD-like sequences stimulate ribosome frameshifting and may also slow down ribosome movement along mRNA. Here, we show that the length of the spacer between the SD sequence and P-site codon strongly affects the rate of ribosome translocation. Increasing the spacer length beyond six nucleotides destabilizes mRNA-ribosome interactions and results in a 5-10 fold reduction of the translocation rate. These observations suggest that during translation, the spacer between the SD sequence and P-site codon undergoes structural rearrangements, which slow down mRNA translocation and promote mRNA frameshifting.
In situ impedance measurements on postmortem porcine brain
Authors: Poßner Lucas , Laukner Matthias , Wilhelmy Florian , Lindner Dirk , Pliquett Uwe , Petkovic Bojana , Ziolkowski Marek , Knösche Thomas R. , Weise Konstantin
Published: April 2020

The paper presents an experimental study where the distinctness of grey and white matter of an in situ postmortem porcine brain by impedance measurements is investigated. Experimental conditions that would allow to conduct the same experiment on in vivo human brain tissue are replicated.

https://doi.org/10.1515/cdbme-2019-XXXX
Molecular rationale for hantavirus neutralization by a reservoir host-derived monoclonal antibody
Authors: Rissanen Ilona , Stass Robert , Krumm Stefanie A. , Seow Jeffrey , Hulswit Ruben J.G. , Paesen Guido C. , Hepojoki Jussi , Vapalahti Olli , Lundkvist Åke , Reynard Olivier , Volchkov Viktor , Doores Katie J. , Huiskonen Juha T. , Bowden Thomas A.
Published: April 2020

The intricate lattice of Gn and Gc glycoprotein spike complexes at the surface of hantaviruses facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Here, through study of a neutralizing monoclonal antibody (mAb 4G2) generated in a bank vole reservoir host following infection with Puumala virus (PUUV), we provide molecular-level insights into how antibody-mediated targeting of the hantaviral glycoprotein lattice effectively neutralizes the virus. Crystallographic analysis reveals that mAb 4G2 binds to a multi-domain site on Gc in the pre-fusion state, and that Fab binding is incompatible with the conformational changes of the Gc that are required for host cell entry. Cryo-electron microscopy of PUUV-like particles treated with Fab 4G2 demonstrates that the antibody binds to monomeric Gc at breaks in the Gn-Gc lattice, highlighting the immunological accessibility of Gc monomers on the mature hantavirus surface and the plastic nature of the higher-order lattice assembly. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of hantaviruses.
Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes
Authors: Mármol-Sanchez Emilio , Luigi-Sierra María Gracia , Castelló Anna , Guan Dailu , Quintanilla Raquel , Tonda Raul , Amills Marcel
Published: April 2020

Background

Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The variability of miRNA genes and their corresponding 3’UTR binding sites might disrupt canonical conserved miRNA-mRNA pairing, thus modifying gene expression patterns. The presence of polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits has been poorly characterized in pigs so far.

Results

By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we have identified 285 single nucleotide polymorphisms (SNPs) mapping to miRNA loci, as well as 109,724 SNPs located in predicted 7mer-m8 miRNA binding sites within porcine 3’UTRs. Porcine miRNA genes show a reduced SNP density compared with their flanking non-miRNA regions. By sequencing the genomes of 5 Duroc boars, we have identified 12 miRNA SNPs that have been subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses between miRNA SNPs and 38 lipid-related traits as well as hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were carried out. The most relevant association detected was the one between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor andPPP1CCmRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits.

Conclusions

Porcine miRNA genes show a reduced variability consistent with strong purifying selection, particularly in the seed region, which plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are the ones with the strongest consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with the hepatic mRNA levels of thePPP1CCgene, one of its predicted targets. Although experimental confirmation of such interaction has been obtained in humans but not in pigs, this result highlights the need of further investigating the functional effects of miRNA polymorphisms located outside the seed region on gene expression in pigs.
Organ-on-a-chip model of vascularized human bone marrow niches
Authors: Glaser Drew E. , Curtis Matthew B. , Sariano Peter A. , Rollins Zachary A. , Shergill Bhupinder S. , Anand Aravind , Deely Alyssa M. , Shirure Venktesh S. , Anderson Leif , Lowen Jeremy M. , Ng Natalie R. , Weilbaecher Katherine , Link Daniel C. , George Steven C.
Published: April 2020

Animal models of bone marrow have limited spatial and temporal resolution to observe biological events (intravasation and cellular egress) and are inadequate to dissect dynamic events at the niche level (100 microns). Utilizing microfluidic and stem cell technology, we present a 3Din vitromodel of human bone marrow that contains perivascular and endosteal niches complete with dynamic, perfusable vascular networks. We demonstrate that our model can performin vivofunctions including maintenance and differentiation of CD34+hematopoietic stem/progenitor cells (HSPC) for up to fourteen days, egress of myeloid progenitors, and expression of markers consistent within vivohuman bone marrow. The platform design enables the addition of tissue niches at a later timepoint to probe mechanisms such as tumor cell migration. Overall, we present a novel organ-on-a-chip platform that is capable of recapitulating the human bone marrow microenvironment to observe hematopoietic phenomena at high spatial and temporal resolution.
Microbial communities in an ultra-oligotrophic sea are more affected by season than by distance from shore
Authors: Haber Markus , Rosenberg Dalit Roth , Lalzar Maya , Burgsdorf Ilia , Saurav Kumar , Lionheart Regina , Lehahn Yoav , Aharonovich Dikla , Sher Daniel , Krom Michael D. , Steindler Laura
Published: April 2020

Marine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. We studied temporal and spatial patterns of the microbial community structure and activity along a coast to offshore transect from the Israeli coast of the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of two consecutive years. The ultra-oligotrophic status of the South Eastern Mediterranean Sea was reflected in the microbial community composition that was dominated by oligotrophic microbial groups such as SAR11 throughout the year, even at the most coastal station sampled. Seasons affected microbial communities much more than distance from shore explaining about half of the observed variability in the microbial community, compared to only about 6% that was explained by station. However, the most coastal site differed significantly in community structure and activity from the three further offshore stations in early winter and summer, but not in spring. Our data on the microbial community composition and its seasonality from a transect into the South Eastern Levantine basin support the notion that the EMS behaves similar to open gyres rather than an inland sea.
Cyclical Regression Covariates remove the major confounding effect of cyclical developmental gene expression with strain-specific drug response in the malaria parasitePlasmodium falciparum
Authors: Foster Gabriel J. , Button-Simons Katrina , Vendrely Katelyn , Romero-Severson Jeanne , Ferdig Michael T.
Published: April 2020

Background

The cyclical nature of parasite gene expression in the intraerythrocytic development cycle (IDC) in human blood confounds the accurate detection of specific transcriptional differences due to drug resistance inPlasmodium falciparum. Here, we propose the use of cyclical regression covariates to eliminate the major confounding of developmentally driven transcriptional changes with changes due to drug response. We show that elimination of this confounding can reduce both Type I and Type II errors, and demonstrate the effect of approach on real data.

Results

We apply this method to two publicly available datasets, and demonstrate its ability to reduce the potential confounding of differences in expression due the species-specific intraerythrocytic development cycle from strain-specific differences in drug response. We show that the application of cyclical regression covariates has minimal impact on the pool of transcripts identified as significantly different in a dataset generated from single timepoint clinical blood samples with low variance for developmental stage and a profound impact on another clinical data set with more variance among the samples for developmental stage.

Conclusions

Cyclical regression covariates have immediate application to studies wherein-vitrosynchronization of all samples to the same developmental timepoint is not feasible, primarily parasite transcriptome sequencing direct from clinical blood samples, a widely used approach to frontline detection of emerging drug resistance.
Tensorpac : an open-source Python toolbox for tensor-based Phase-Amplitude Coupling measurement in electrophysiological brain signals
Authors: Combrisson Etienne , Nest Timothy , Brovelli Andrea , Ince Robin A.A. , Soto Juan LP , Guillot Aymeric , Jerbi Karim
Published: April 2020

Despite being the focus of a thriving field of research, the biological mechanisms that underlie information integration in the brain are not yet fully understood. A theory that has gained a lot of traction in recent years suggests that multi-scale integration is regulated by a hierarchy of mutually interacting neural oscillations. In particular, there is accumulating evidence that phase-amplitude coupling (PAC), a specific form of cross-frequency interaction, plays a key role in numerous cognitive processes. Current research in the field is not only hampered by the absence of a gold standard for PAC analysis, but also by the computational costs of running exhaustive computations on large and high-dimensional electrophysiological brain signals. In addition, various signal properties and analyses parameters can lead to spurious PAC. Here, we present Tensorpac, an open-source Python toolbox dedicated to PAC analysis of neurophysiological data. The advantages of Tensorpac include (1) higher computational efficiency thanks to software design that combines tensor computations and parallel computing, (2) the implementation of all most widely used PAC methods in one package, (3) the statistical analysis of PAC measures, and (4) extended PAC visualization capabilities. Tensorpac is distributed under a BSD-3-Clause license and can be launched on any operating system (Linux, OSX and Windows). It can be installed directly via pip or downloaded from Github (https://github.com/EtienneCmb/tensorpac). By making Tensorpac available, we aim to enhance the reproducibility and quality of PAC research, and provide open tools that will accelerate future method development in neuroscience.
Role of TRPV1 in colonic mucin production and gut microbiota profile
Authors: Kumar Vijay , Mahajan Neha , Khare Pragyanshu , Kondepudi Kanthi Kiran , Bishnoi Mahendra
Published: April 2020

PURPOSE

This study focuses on exploring the role of sensory cation channel Transient Receptor Potential channel subfamily Vanilloid 1 (TRPV1) in gut health, specifically mucus secretion and microflora profile in gut.

METHODS AND RESULTS

We employed resiniferatoxin (ultrapotent TRPV1 agonist) induced chemo-denervation model in rats and studied the effects of TRPV1 ablation on gut mucus secretion patterns. Histological and transcriptional analysis showed substantial decrease in mucus production as well as in expression of genes involved in goblet cells differentiation, mucin production and glycosylation. 16S metagenome analysis revealed changes in abundance of various gut bacteria, including decrease in beneficial bacteria likeLactobacillus sppandClostridia spp.Also, TRPV1 ablation significantly decreased the levels of short chain fatty acids,i.e.acetate and butyrate.

CONCLUSION

The present study provides first evidence that systemic TRPV1 ablation leads to impairment in mucus secretion and causes dysbiosis in gut. Further, it suggests to address mucin production and gut microbiota related adverse effects during the development of TRPV1 antagonism/ablation-based therapeutic and preventive strategies.
A Zinc-dependent metalloproteinase in the intracellular adaptation ofBrucella abortusin macrophages
Authors: Gómez Leonardo A. , Alvarez Francisco I. , Molina Raúl , Soto Rodrigo , Daza-Castro Carla , Flores Manuel , León Yrvin , Oñate Angel A.
Published: April 2020

Brucella abortusis a pathogen that survives in macrophages. Several virulence factors participate in this process, including the open reading frame (ORF) BAB1_0270 codifying of a Zinc-dependent metalloproteinase. Here, its contribution in the process of intracellular adaptation was analyzed by infecting RAW264.7 macrophages with the mutantB. abortus Δ270 strain. Results showed that this Zinc-dependent metalloproteinase is a cytoplasmic protein that conforms an operon with a transcriptional regulator, which may constitute a type II toxin-antitoxin system. Functionally, this Zinc-dependent metalloproteinase participated neither in the adherence nor the initial intracellular traffic ofB. abortusin macrophages. Nevertheless, its deletion significantly increased the co-localization ofB. abortus Δ270 with phagolysosomal cathepsin D, reducing both its co-localization with calnexin, present in endoplasmic reticulum derived vesicles, and its intracellular replication within macrophages. Besides,B. abortus Δ270-infected macrophages produced significantly higher levels of TNF-α, IL-6, CD80 and CD86 thanB. abortus2308, even when several genes involved in virulence (vjbR,hutC,bvrR,virB1) were up-regulated in this mutant. Finally, its deletion significantly reduced the capacity ofB. abortus Δ270 to adapt, grow and express several virulence factors under acidic conditions. Based on these results, we discuss the role of this Zinc-dependent metalloproteinase in the regulation of the virulence of this pathogen, concluding that it contributes significantly to the intracellular adaptation ofB. abortus2308 during the infection of macrophages.

Author summary

Brucella abortusis the causative agent of the brucellosis, a highly contagious diseases. A Zinc-dependent metalloproteinase contributes significantly in the intracellular survival. Here, we demonstrate that this metalloproteinase has homology with ImmA/IrrE proteases, which are involved in the bacterial resistance to hostile environment. Furthermore, it conforms a gene pair with a transcriptional regulator, being required byB. abortusto escape from phagolysosomes, to achieve the endoplasmic reticulum and replicate within macrophages. Its deletion fromB. abortusstimulated the macrophages, which produced higher levels of pro-inflammatory cytokines and co-stimulatory proteins. This pathogen showed a reduced ability to adapt and grow under acidic conditions, which would negatively affect its escape from phagolysosomes and consequently, stimulating macrophages. Therefore, this work describes how this Zinc-dependent metalloproteinase significantly contributes in the intracellular adaptation ofB. abortus2308 in macrophages.
Development and validation of a real-time RT-PCR test for screening pepper and tomato seed lots for the presence of pospiviroids
Authors: Botermans Marleen , Roenhorst Johanna W. , Hooftman Marinus , Verhoeven Jacobus Th.J. , Metz Eveline , van Veen Esther J. , Geraats Bart P.J. , Kemper Mark , Beugelsdijk Debora C.M. , Koenraadt Harrie , Jodlowska Agata , Westenberg Marcel
Published: April 2020

Potato spindle tuber viroid and other pospiviroids can cause serious diseases in potato and tomato crops. Consequently, pospiviroids are regulated in several countries. Since seed transmission is considered as a pathway for the introduction and spread of pospiviroids, some countries demand for the testing of seed lots of solanaceous crops for the presence of pospiviroids. A real-time RT-PCR test, named PospiSense, was developed for testing pepper (Capsicum annuum) and tomato (Solanum lycopersicum) seeds for seven pospiviroid species known to occur naturally in these crops. The test consists of two multiplex reactions running in parallel, PospiSense 1 and PospiSense 2, that target Citrus exocortis viroid (CEVd), Columnea latent viroid (CLVd), pepper chat fruit viroid (PCFVd), potato spindle tuber viroid (PSTVd), tomato apical stunt viroid (TASVd), tomato chlorotic dwarf viroid (TCDVd) and tomato planta macho viroid (TPMVd, including the former Mexican papita viroid). Dahlia latent viroid (DLVd) is used as an internal isolation control. Validation of the test showed that for both pepper and tomato seeds the current requirements of a routine screening test are fulfilled, i.e. the ability to detect one infested seed in a sample of c.1000 seeds for each of these seven pospiviroids. Additionally, the Pospisense test performed well in an inter-laboratory comparison, which included two routine seed-testing laboratories, and as such provides a relatively easy alternative to the currently used tests.
Murine cytomegaloviruses m139 targets DDX3 to curtail interferon production and promote viral replication
Authors: Puhach Olha , Ostermann Eleonore , Krisp Christoph , Frascaroli Giada , Schlüter Hartmut , Brinkmann Melanie M. , Brune Wolfram
Published: April 2020

Cytomegaloviruses (CMV) infect many different cell types and tissues in their respective hosts. Monocytes and macrophages play an important role in CMV dissemination from the site of infection to target organs. Moreover, macrophages are specialized in pathogen sensing and respond to infection by secreting cytokines and interferons. In murine cytomegalovirus (MCMV), a model for human cytomegalovirus, several genes required for efficient replication in macrophages have been identified, but their specific functions remain poorly understood. Here we show that MCMV m139, a gene of the conserved US22 gene family, encodes a protein that interacts with the DEAD box helicase DDX3, a protein involved in pathogen sensing and interferon (IFN) induction, and the E3 ubiquitin ligase UBR5. DDX3 and UBR5 also participate in the transcription, processing, and translation of a subset of cellular mRNAs. We show that m139 inhibits DDX3-mediated IFN-β induction and is necessary for efficient viral replication in bone-marrow derived macrophages. In vivo, m139 is crucial for viral dissemination to local lymph nodes and to the salivary glands. An m139-deficient MCMV also replicated to lower titers in SVEC4-10 endothelial cells. This replication defect was not accompanied by increased IFN-β transcription, but was rescued by knockout of either DDX3 or UBR5. Moreover, m139 co-localized with DDX3 and UBR5 in viral replication compartments in the cell nucleus. These results suggest that m139 inhibits DDX3-mediated IFN-β production in macrophages and antagonizes DDX3 and UBR5-dependent functions related to RNA metabolism in endothelial cells.

Author Summary

Human cytomegalovirus is an opportunistic pathogen that causes severe infections in immunocompromised individuals. The virus infects certain types, such as macrophages and endothelial cells, to ensure its dissemination within the body. Little is known about the viral factors that promote a productive infection of these cell types. The identification of critical viral factors and the molecular pathways they target can lead to the development of novel antiviral treatment strategies. Using the mouse cytomegalovirus as a model, we studied the viral m139 gene, which is important for virus replication in macrophages and endothelial cells and for dissemination in the mouse. This gene encodes a protein that interacts with the host proteins DDX3 and UBR5. Both proteins are involved in gene expression, and the RNA helicase DDX3 also participates in mounting an innate antiviral response. By interacting with DDX3 and UBR5, m139 ensures efficient viral replication in endothelial cells. Importantly, we identify m139 as a new viral DDX3 inhibitor, which curtails the production of interferon in macrophages.
The aggregate effect of implementation strength of family planning programs on modern contraceptive use at the health systems level in rural Malawi
Authors: Pattnaik Anooj , Mohan Diwakar , Tsui Amy , Chipokosa Sam , Katengeza Hans , Ndawala Jameson , Marx Melissa A.
Published: April 2020

Background

To explore the association between the strength of implementation of family planning (FP) programs on the use of modern contraceptives. Specifically, how strongly these programs are being implemented across a health facility’s catchment area in Malawi and the odds of a woman in that catchment area is using modern contraceptives. This information can be used to assess whether the combined impact of multiple large-scale FP programs is leading to change in the health outcomes they aim to improve.

Methods and findings

We used data from the 2017 Implementation Strength Assessment (ISA) that quantified how much of family planning programs at the health facility and community health worker levels were being implemented across every district of Malawi. We used a summary measure developed in a previous study that employs quantitative methods to combine data across FP domains and health system levels. We tested the association of this summary measure for implementation strength with household data from the 2015 Malawi Demographic Health Survey (DHS). We found that areas with stronger implementation of FP programs had higher odds of women using modern contraceptives compared with areas with weaker implementation. The association of ISA with use of modern contraception was different by education, marital status, and geography. After controlling for these factors, we found that the adjusted odds of using a modern contraceptive was three times higher in catchment areas with high implementation strength compared to those with lower strength.

Conclusion

Metrics that summarize how strongly FP programs are being implemented were used to show a statistically significantly positive relationship between increasing implementation strength and higher rates of modern contraceptive use. Decisionmakers at the various levels of health authority can use this type of summary measure to better understand the combined impact of their diverse FP programming and inform future programmatic and policy decisions. The findings also reinforce the idea that having a well-supported and supplied cadre of community health workers supplementing FP provision at the health facility can be an important health systems mechanism, especially in rural settings and to target youth populations.
A flexible repertoire of transcription factor binding sites and diversity threshold determines enhancer activity in embryonic stem cells
Authors: Singh Gurdeep , Mullany Shanelle , Moorthy Sakthi D , Zhang Richard , Mehdi Tahmid , Tian Ruxiao , Moses Alan M , Mitchell Jennifer A
Published: April 2020

Transcriptional enhancers are critical for development, phenotype evolution and often mutated in disease contexts; however, even in well-studied cell types, the sequence code conferring enhancer activity remains unknown. We found genomic regions with conserved binding of multiple transcription factors in mouse and human embryonic stem cells (ESCs) contain on average 12.6 conserved transcription factor binding sites (TFBS). These TFBS are a diverse repertoire of 70 different sequences representing the binding sites of both known and novel ESC regulators. Remarkably, using a diverse set of TFBS from this repertoire was sufficient to construct short synthetic enhancers with activity comparable to native enhancers. Site directed mutagenesis of conserved TFBS in endogenous enhancers or TFBS deletion from synthetic sequences revealed a requirement for more than ten different TFBS. Furthermore, specific TFBS, including the OCT4:SOX2 co-motif, are dispensable, despite co-binding the OCT4, SOX2 and NANOG master regulators of pluripotency. These findings reveal a TFBS diversity threshold overrides the need for optimized regulatory grammar and individual TFBS that bind specific master regulators.
Immune-challenged vampire bats produce fewer contact calls
Authors: Stockmaier Sebastian , Bolnick Daniel. I. , Page Rachel. A. , Josic Darija , Carter Gerald G.
Published: April 2020

Infections can affect how animals vocalize and, hence, interact with conspecifics. While this effect has been shown for mate-attraction calls, other vocalizations that facilitate social contact have received less attention. When isolated, vampire bats produce contact calls which attract highly associated groupmates. Here, we test the effect of an immune challenge on contact calling rates of individually isolated vampire bats. Sickness behavior did not appear to change call structure, but it decreased the number of contact calls produced. This effect could decrease contact with groupmates and augment other established mechanisms by which sickness reduces social encounters (e.g. mortality, lethargy, and social withdrawal or disinterest).
Structure of the TFIIIC subcomplex τA provides insights into RNA polymerase III pre-initiation complex formation
Authors: Vorländer Matthias K. , Jungblut Anna , Karius Kai , Baudin Florence , Grötsch Helga , Kosinski Jan , Müller Christoph W.
Published: April 2020

Transcription factor (TF) IIIC is a conserved eukaryotic six-subunit protein complex with dual function. It serves as a general TF for most RNA polymerase (Pol) III genes by recruiting TFIIIB, but it is also involved in chromatin organization and regulation of Pol II genes through interaction with CTCF and condensin II. Here, we report the structure of theS. cerevisiaeTFIIIC subcomplex τA, which contains the most conserved subunits of TFIIIC and is responsible for recruitment of TFIIIB and transcription start site (TSS) selection at Pol III genes. We show that τA binding to its promoter is auto-inhibited by a disordered acidic tail of subunit τ95. We further provide a negative stain reconstruction of τA bound to the TFIIIB subunits Brf1 and TBP with an unexpected location of Brf1 and TBP. This shows that a ruler element in τA achieves positioning of TFIIIB upstream of the TSS, and suggests remodeling of the complex during assembly of TFIIIB by TFIIIC.