bluuebunny/crossref_metadata_2025 huggingface dataset:
The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly
Authors: Dincă Vlad , Lee Kyung Min , Vila Roger , Mutanen Marko
Published: September 2019

The Palaearctic butterflyMelitaea didymastands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens ofM. didymaranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected byWolbachiainfection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwiseFSTvalues, but some were also estimated to display various levels of gene flow.Melitaea didymarepresents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.
Evolution of ageing as a tangle of trade-offs: energy versus function
Authors: Maklakov Alexei A. , Chapman Tracey
Published: September 2019

Despite tremendous progress in recent years, our understanding of the evolution of ageing is still incomplete. A dominant paradigm maintains that ageing evolves due to the competing energy demands of reproduction and somatic maintenance leading to slow accumulation of unrepaired cellular damage with age. However, the centrality of energy trade-offs in ageing has been increasingly challenged as studies in different organisms have uncoupled the trade-off between reproduction and longevity. An emerging theory is that ageing instead is caused by biological processes that are optimized for early-life function but become harmful when they continue to run-on unabated in late life. This idea builds on the realization that early-life regulation of gene expression can break down in late life because natural selection is too weak to optimize it. Empirical evidence increasingly supports the hypothesis that suboptimal gene expression in adulthood can result in physiological malfunction leading to organismal senescence. We argue that the current state of the art in the study of ageing contradicts the widely held view that energy trade-offs between growth, reproduction, and longevity are the universal underpinning of senescence. Future research should focus on understanding the relative contribution of energy and function trade-offs to the evolution and expression of ageing.
Predicting individual clinical trajectories of depression with generative embedding
Authors: Frässle Stefan , Marquand Andre F. , Schmaal Lianne , Dinga Richard , Veltman Dick J. , van der Wee Nic J.A. , van Tol Marie-José , Schöbi Dario , Penninx Brenda W.J.H. , Stephan Klaas E.
Published: September 2019

Patients with major depressive disorder (MDD) show heterogeneous treatment response and highly variable clinical trajectories: while some patients experience swift and enduring recovery, others show relapsing-remitting or chronic disease course. Predicting individual clinical trajectories at an early disease stage is a key challenge for psychiatry and might facilitate individually tailored interventions. So far, however, reliable predictors at the single-patient level are absent.

Here, we evaluated the utility of a machine learning strategy – generative embedding – which combines an interpretable generative model with a discriminative classifier. Specifically, we used functional magnetic resonance imaging (fMRI) data of emotional face perception in 85 MDD patients from the multi-site longitudinal NEtherlands Study of Depression and Anxiety (NESDA) who had been followed up over two years and classified into three subgroups with distinct clinical trajectories. Combining a generative model of effective (directed) connectivity with support vector machines (SVMs), it was possible to predict whether a given patient will experience chronic depression vs. fast remission with a balanced accuracy of 79%. Gradual improvement vs. fast remission could still be predicted above-chance, but less convincingly, with a balanced accuracy of 61%. Importantly, generative embedding outperformed conventional (descriptive) measures such as functional connectivity or local BOLD activity, which did not predict clinical trajectories with above-chance accuracy. Furthermore, the predictive performance of generative embedding could be assigned to a specific network property: the dynamic modulation of connections by the emotional content of the trial-by-trial stimuli. Our findings suggest that a mechanistically informed generative model of a neuronal circuit underlying emotional face perception may have predictive utility for distinguishing disease courses in MDD patients.
Using Hierarchical Clustering to Explore Patterns of Deprivation Among English Local Authorities
Authors: Senior Steven L.
Published: September 2019

Background

The English Indices of Multiple Deprivation (IMD) is widely used as a measure of deprivation of geographic areas in analyses of health inequalities between places. However, similarly ranked areas can differ substantially in the underlying domains and indicators that are used to calculate the IMD score. These domains and indicators contain a richer set of data that might be useful for classifying local authorities. Clustering methods offer a set of techniques to identify groups of areas with similar patterns of deprivation. This could offer insights into areas that face similar challenges.

Methods

Hierarchical agglomerative (i.e. bottom-up) clustering methods were applied to sub-domain scores for 152 upper-tier local authorities. Recent advances in statistical testing allow clusters to be identified that are unlikely to have arisen from random partitioning of a homogeneous group. The resulting clusters are described in terms of their subdomain scores and basic geographic and demographic characteristics.

Results

Five statistically significant clusters of local authorities were identified. These clusters represented local authorities that were:

Most deprived, predominantly urban;

Least deprived, predominantly rural;

Less deprived, rural;

Deprived, high crime, high barriers to housing; and

Deprived, low education, poor employment, poor health.

Conclusion

Hierarchical clustering methods identify five distinct clusters that do not correspond closely to quintiles of deprivation. These methods can be used to draw on the richer set of information contained in the IMD domains and may help to identify places that face similar challenges, and places that appear similar in terms of IMD scores, but that face different challenges.
Genome-wide Selection Scan in an Arabian Peninsula Population Identifies aTNKShaplotype Linked to Metabolic Traits and Hypertension
Authors: Eaaswarkhanth Muthukrishnan , dos Santos Andre Luiz Campelo , Gokcumen Omer , Al-Mulla Fahd , Thanaraj Thangavel Alphonse
Published: September 2019

Despite the extreme and varying environmental conditions prevalent in the Arabian Peninsula, it has experienced several waves of human migrations following the out-of-Africa diaspora. Eventually, the inhabitants of the peninsula region adapted to the hot and dry environment. The adaptation and natural selection that shaped the extant human populations of the Arabian Peninsula region have been scarcely studied. In an attempt to explore natural selection in the region, we analyzed 662,750 variants in 583 Kuwaiti individuals. We searched for regions in the genome that display signatures of positive selection in the Kuwaiti population using an integrative approach in a conservative manner. We highlight a haplotype overlappingTNKSthat showed strong signals of positive selection based on the results of the multiple selection tests conducted (integrated Haplotype Score, Cross Population Extended Haplotype Homozygosity, Population Branch Statistics, and log-likelihood ratio scores). Notably, theTNKShaplotype under selection potentially conferred a fitness advantage to the Kuwaiti ancestors for surviving in the harsh environment while posing a major health risk to present-day Kuwaitis.
sRNAanno --- a database repository of uniformly-annotated small RNAs in plants
Authors: Chen Chengjie , Feng Junting , Liu Bo , Li Jiawei , Feng Lei , Yu Xiaoling , Zhai Jixian , Meyers Blake C. , Xia Rui
Published: September 2019

Small RNAs (sRNAs) are essential regulatory molecules, including three mayor classes in plants, microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Except miRNAs, the other two classes are not well-annotated and collected in public databases for most sequenced plant genomes. We performed comprehensive sRNA annotation for 138 plant species, which have fully sequenced genomes and public next-generation-sequencing (NGS) sRNA data available. The results are available via an online repository called sRNAanno (www.plantsRNAs.org). Compared to plant miRNAs deposited in miRBase, we obtained much more miRNAs, which are more complete and reliable because of consistent and high-stringent criteria used in our miRNA annotation. sRNAanno also provides free access to genomic information for >16,000 PHAS loci and >21,000,000 hc-siRNA loci annotated from these 138 plants. On the basis of Integrative Genomics Viewer (IGV), we developed a visualization tool for browsing NGS sRNA data (IGV-sRNA), which have been integrated a series of new functions compatible to specific sRNA features. To make sRNA annotation an easy task, sRNAanno also provides free service of sRNA annotation to the community. In summary, sRNAanno and IGV-sRNA are great resources to facilitate the genomic and genetic research of plant small RNAs.
Evolutionary origins of epidemic potential among human RNA viruses
Authors: Lu Lu , Brierley Liam , Robertson Gail , Zhang Feifei , Lycett Samantha , Smith Donald , Chase-Topping Margo , Simmonds Peter , Woolhouse Mark
Published: September 2019

To have epidemic potential, a pathogen must be able to spread in human populations, but of human-infective RNA viruses only a minority can do so. We investigated the evolution of human transmissibility through parallel analyses of 1755 virus genome sequences from 39 RNA virus genera. We identified 57 lineages containing human-transmissible species and estimated that at least 74% of these lineages have evolved directly from non-human viruses in other mammals or birds, a public health threat recently designated “Disease X”. Human-transmissible viruses rarely evolve from virus lineages that can infect but not transmit between humans. This result cautions against focussing surveillance and mitigation efforts narrowly on currently known human-infective virus lineages and supports calls for a better understanding of RNA virus diversity in non-human hosts.
Hydrodynamic regime drives flow reversals in suction feeding larval fishes during early ontogeny
Authors: Krishnan Krishnamoorthy , Nafi Asif Shahriar , Gurka Roi , Holzman Roi
Published: September 2019

Fish larvae are the smallest self-sustaining vertebrates. As such, they face multiple challenge that stem from their minute size, and from the hydrodynamic regime in which they dwell. This regime of intermediate Reynolds numbers (Re) was shown to affect the swimming of larval fish and impede their ability to capture prey. Numerical simulations indicate that the flow fields external to the mouth in younger larvae result in shallower spatial gradients, limiting the force exerted on the prey. However, observations on feeding larvae suggest that failures in prey capture can also occur during prey transport, although the mechanism causing these failures is unclear. We combine high-speed videography and numerical simulations to investigate the hydrodynamic mechanisms that impede prey transport in larval fishes. Detailed kinematics of the expanding mouth during prey capture by larvalSparus auratawere used to parameterize age-specific numerical models of the flows inside the mouth. These models reveal that, for small larvae that slowly expand their mouth, not all the fluid that enters the mouth cavity is expelled through the gills, resulting in flow reversal at the mouth orifice. This efflux at the mouth orifice was highest in the younger ages, but was also high (>8%) in slow strikes produced by larger fish. Our modeling explains the observations of “in-and-out” events in larval fish, where prey enters the mouth but is not swallowed. It further highlights the importance of prey transport as an integral part in determining suction feeding success.
Purification of native CCL7 and its functional interaction with selected chemokine receptors
Authors: Goncharuk Marina V. , Roy Debarati , Dubinnyi Maxim A. , Nadezhdin Kirill D. , Srivastava Ashish , Baidya Mithu , Dwivedi-Agnihotri Hemlata , Arseniev Alexander S. , Shukla Arun K.
Published: September 2019

Chemokine receptors form a major sub-family of G protein-coupled receptors (GPCRs) and they are involved in a number of cellular and physiological processes related to our immune response and regulation. A better structural understanding of ligand-binding, activation, signaling and regulation of chemokine receptors is very important to design potentially therapeutic interventions for human disorders arising from aberrant chemokine signaling. One of the key limitations in probing the structural details of chemokine receptors is the availability of large amounts of purified, homogenous and fully functional chemokine ligands, and the commercially available products, are not affordable for in-depth structural studies. Moreover, production of uniformly isotope-labeled chemokines, for example, suitable for NMR-based structural investigation, also remains challenging. Here, we have designed a streamlined approach to express and purify the human chemokine CCL7 as well as its15N-,15N/13C-,2H/15N/13C-isotope-labeled derivatives, at milligram levels usingE. coliexpression system. Purified CCL7 not only maintains a well-folded three-dimensional structure as analyzed using circular dichroism and1H/15N NMR but it also induces coupling of heterotrimeric G-proteins and β-arrestins for selected chemokine receptors in cellular system. Our strategy presented here may be applicable to other chemokines and therefore, provide a potentially generic and cost-effective approach to produce chemokines in large amounts for functional and structural studies.
Active transport of brilliant blue FCF across theDrosophilamidgut and Malpighian tubule epithelia
Authors: Livingston Dawson B.H. , Patel Hirva , Donini Andrew , MacMillan Heath A.
Published: September 2019

Under conditions of stress, many animals suffer from epithelial barrier disruption that can cause molecules to leak down their concentration gradients, potentially causing a loss of organismal homeostasis, further injury or death.Drosophilais a common insect model, used to study barrier disruption related to aging, traumatic injury, or environmental stress. Net leak of a non-toxic dye (Brilliant blue FCF) from the gut lumen to the hemolymph is often used to identify barrier failure under these conditions, butDrosophilaare capable of actively transporting structurally-similar compounds. Here, we examined whether cold stress (like other stresses) causes Brilliant blue FCF (BB-FCF) to appear in the hemolymph of flies fed the dye, and if so whetherDrosophilaare capable of clearing this dye from their body following chilling. Usingin situmidgut leak and transport assays as well as Ramsay assays of Malpighian tubule transport, we tested whether these ionoregulatory epithelia can actively transport BB-FCF. In doing so, we found that theDrosophilamidgut and Malpighian tubules can mobilize BB-FCF via an active transcellular pathway, suggesting that elevated concentrations of the dye in the hemolymph may occur from increased paracellular permeability, reduced transcellular clearance, or both.

Summary Statement

Drosophilaare able to actively secrete Brilliant blue FCF, a commonly used marker of barrier dysfunction
Lysenin toxin insertion mechanism is Calcium-dependent
Authors: Munguira Ignacio L.B.
Published: September 2019

Pore Forming Toxins (PFTs), formed mainly by virulence factors of bacteria, belongs to Pore Forming Protein (PFP) family. Secreted as soluble monomers, they bind specific targets in membranes where their oligomerization and insertion place. Lysenin, a member of the PFTs, forms and oligomer after sphingomyelin binding, the so-called prepore, which become inserted forming a pore after a conformational change triggered by a pH decrease. In crowded conditions, oligomers tends to stay in prepore form because the prepore-to-pore transition is sterically blocked. In this study, we investigate the effect of calcium ions in those crowded conditions, finding that calcium act as a trigger for lysenin insertion. We localize the residues responsible for calcium sensitivity in a small α-helix. Our results are not only one of the few complete structural descriptions of prepore-to-pore transitions but the very first that involves a calcium triggering mechanism. The presence of glutamic or aspartic acids in the insertion domains could be an indication that calcium may be a general trigger for PFTs and more generally PFP.
An atypical DYRK kinase connects quorum-sensing with posttranscriptional gene regulation inTrypanosoma brucei
Authors: Cayla Mathieu , McDonald Lindsay , MacGregor Paula , Matthews Keith R.
Published: September 2019

The sleeping sickness parasite,Trypanosoma brucei, uses quorum sensing (QS) to balance proliferation and transmission potential in the mammal bloodstream. A signal transduction cascade regulates this process, a component of which is a divergent member of the DYRK family of protein kinases, TbDYRK. Phylogenetic and mutational analysis in combination with activity and phenotypic assays revealed that TbDYRK exhibits a pre-activated confirmation and an atypical HxY activation loop motif, unlike DYRK kinases in other eukaryotes. Phosphoproteomic comparison of TbDYRK null mutants with wild type parasites identified molecules that operate on both the inhibitory ‘slender retainer’ and activatory ‘stumpy inducer’ arms of the QS control pathway. One of these molecules, the RNA-regulator TbZC3H20, regulates parasite QS, this being dependent on the integrity of its TbDYRK phosphorylation site. This analysis reveals fundamental differences to conventional DYRK family regulation and links trypanosome environmental sensing, signal transduction and developmental gene expression in a coherent pathway.
Inter-Species Differences in the Response of Sinus Node Cellular Pacemaking to Changes of Extracellular Calcium
Authors: Loewe Axel , Lutz Yannick , Nagy Norbert , Fabbri Alan , Schweda Christoph , Varró András , Severi Stefano
Published: September 2019

Changes of serum and extracellular ion concentrations occur regularly in patients with chronic kidney disease (CKD). Recently, hypocalcemia, i.e. a decrease of the extra-cellular calcium concentration [Ca2+]o, has been suggested as potential pathomechanism contributing to the unexplained high rate of sudden cardiac death (SCD) in CKD patients. In particular, there is a hypothesis that hypocalcaemia could slow down natural pacemaking in the human sinus node to fatal degrees. Here, we address the question whether there are inter-species differences in the response of cellular sinus node pacemaking to changes of [Ca2+]o. Towards this end, we employ computational models of mouse, rabbit and human sinus node cells. The Fabbri et al. human model was updated to consider changes of intracellular ion concentrations. We identified crucial inter-species differences in the response of cellular pacemaking in the sinus node to changes of [Ca2+]o with little changes of cycle length in mouse and rabbit models (<83 ms) in contrast to a pronounced bradycardic effect in the human model (up to > 1000 ms). Our results suggest that experiments with human sinus node cells are required to investigate the potential mechanism of hypocalcaemia-induced bradycardic SCD in CKD patients and small animal models are not well suited.
Establishing the phenotypic basis of adherent-invasiveEscherichia coli(AIEC) pathogenicity in intestinal inflammation
Authors: Kittana Hatem , Gomes-Neto João C. , Heck Kari , Sughroue Jason , Xian Yibo , Mantz Sara , Muñoz Rafael R. Segura , Cody Liz A. , Schmaltz Robert J. , Anderson Christopher L. , Moxley Rodney A. , Hostetter Jesse M. , Fernando Samodha C. , Clarke Jennifer , Kachman Stephen D. , Cressler Clayton E. , Benson Andrew K. , Walter Jens , Ramer-Tait Amanda E.
Published: September 2019

Background & Aims

Adherent-invasiveEscherichia coli(AIEC) are enriched in ileal Crohn’s disease patients and implicated in disease etiology. However, AIEC pathogenesis is poorly understood, and it is unclear if the expansion of these organisms contributes to inflammatory bowel disease (IBD). Questions also remain as to what extent the variousin vitrophenotypes used to classify AIEC are pathologically relevant.

Methods

We utilized a combination ofin vitrophenotyping and a murine model of intestinal inflammation to systematically relate AIEC phenotypes to pathogenicity for 30 mucosa-associated human-derivedE. colistrains.In vitroassays used included survival/replication in and TNF-α production by J774 macrophages as well as invasion/replication in Caco2 intestinal epithelial cells.

Results

AIEC do not form a phenotypic group that is clearly separated from non-AIEC. However,E. colistrains displayingin vitroAIEC phenotypes caused, on average, more severe intestinal inflammation. Survival/replication of strains in J774 and Caco2 cells were positively correlated with diseasein vivo, while adherence to Caco2 cells and TNF-α production by J774 cells were not. Importantly, co-colonization with adherent non-AIEC strains ameliorated AIEC-mediated disease.

Conclusion

Our findings do not support the existence of an AIEC pathovar that can be clearly separated from commensalE. coli. However, intracellular survival/replication phenotypes do contribute to murine intestinal inflammation, suggesting that the AIEC overgrowth observed in human IBD makes a causal contribution to disease. The ability to differentiate pathologically-relevant AIEC phenotypes from those that are not provides an important foundation for developing strategies to predict, diagnose and treat human IBD through characterizing and modulating patientE. colipopulations.
Withdrawal from Chronic Ethanol Exposure Increases Postsynaptic Glutamate Function of Insular Cortex Projections to the Rat Basolateral Amygdala
Authors: McGinnis Molly M. , Parrish Brian C. , McCool Brian A.
Published: September 2019

A key feature of alcohol use disorder (AUD) is negative affect during withdrawal, which often contributes to relapse and is thought to be caused by altered brain function, especially in circuits that are important mediators of emotional behaviors. Both the agranular insular cortex (AIC) and the basolateral amygdala (BLA) regulate emotions and are sensitive to ethanol-induced changes in synaptic plasticity. The AIC and BLA are reciprocally connected, however, and the effects of chronic ethanol exposure on this circuit have yet to be explored. Here, we use a combination of optogenetics and electrophysiology to examine the pre- and postsynaptic changes that occur to AIC – BLA synapses following withdrawal from 7- or 10-days of chronic intermittent ethanol (CIE) exposure. While CIE/withdrawal did not alter presynaptic glutamate release probably from AIC inputs, withdrawal from 10, but not 7, days of CIE increased AMPA receptor-mediated postsynaptic function at these synapses. Additionally, NMDA receptor-mediated currents evoked by electrical stimulation of the external capsule, which contains AIC afferents, were also increased during withdrawal. Notably, a single subanesthetic dose of ketamine administered at the onset of withdrawal prevented the withdrawal-induced increases in both AMPAR and NMDAR postsynaptic function. Ketamine also prevented the withdrawal-induced increases in anxiety-like behavior measured using the elevated zero maze. Together, these findings suggest that chronic ethanol exposure increases postsynaptic function within the AIC – BLA circuit and that ketamine can prevent ethanol withdrawal-induced alterations in synaptic plasticity and negative affect.
DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition
Authors: Chantarachot Thanin , Sorenson Reed S. , Hummel Maureen , Ke Haiyan , Kettenburg Alek T. , Chen Daniel , Aiyetiwa Karen , Dehesh Katayoon , Eulgem Thomas , Sieburth Leslie E. , Bailey-Serres Julia
Published: September 2019

Gene transcription is counterbalanced by mRNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA HELICASEs ofArabidopsis thalianacontrol the ephemerality of a subset of cellular mRNAs. These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. These RHs function to limit the precocious accumulation and translation of stress-responsive mRNAs associated with autoimmunity and growth inhibition under non-stress conditions. Given the conservation of this RH subfamily, they may control basal levels of conditionally-regulated mRNAs in diverse eukaryotes, accelerating responses without penalty.
Direct, sensitive and specific detection of individual single- or double-strand DNA breaks by fluorescence microscopy
Authors: Kordon Magdalena , Zarębski Mirosław , Solarczyk Kamil , Ma Hanhui , Pederson Thoru , Dobrucki Jurek
Published: September 2019

We here describe a technique termed STRIDE (SensiTive Recognition of Individual DNA Ends), which enables highly sensitive, specific, direct in situ detection of single- or double-strand DNA breaks (sSTRIDE or dSTRIDE), in nuclei of single cells, using fluorescence microscopy. Sensitivity of STRIDE was tested using specially developed CRISPR/Cas9 DNA damage induction system, capable of inducing small clusters or individual single- or double-strand breaks. STRIDE exhibits significantly higher sensitivity and specificity of detection of DNA breaks than the commonly used TUNEL assay or methods based on monitoring of recruitment of repair proteins or histone modifications at the damage site (e.g. γH2AX). Even individual genome site-specific DNA double-strand cuts induced by CRISPR/Cas9, as well as individual single-strand DNA scissions induced by the nickase version of Cas9, can be detected by STRIDE and precisely localized within the cell nucleus. We further show that STRIDE can detect low-level spontaneous DNA damage, including age-related DNA lesions, DNA breaks induced by several agents (bleomycin, doxorubicin, topotecan, hydrogen peroxide, UV, photosensitized reactions), and fragmentation of DNA in human spermatozoa. STRIDE methods are potentially useful in studies of mechanisms of DNA damage induction and repair in cell lines and primary cultures, including cells with impaired repair mechanisms.
Atlas of the Neuromuscular System in the TrachymedusaAglantha digitale: Insights from the advanced hydrozoan
Authors: Norekian Tigran P. , Moroz Leonid L.
Published: September 2019

Cnidaria is the sister taxon to bilaterian animals, and therefore, represents a key reference lineage to understand early origins and evolution of the neural systems. The hydromedusaAglantha digitaleis arguably the best electrophysiologically studied jellyfish because of its system of giant axons and unique fast swimming/escape behaviors. Here, using a combination of scanning electron microscopy and immunohistochemistry together with phalloidin labeling, we systematically characterize both neural and muscular systems inAglantha, summarizing and expanding further the previous knowledge on the microscopic neuroanatomy of this crucial reference species. We found that the majority, if not all (∼2500) neurons, that are labeled by FMRFamide antibody are different from those revealed by anti-α-tubulin immunostaining, making these two neuronal markers complementary to each other and, therefore, expanding the diversity of neural elements inAglanthawith two distinct neural subsystems. Our data uncovered the complex organization of neural networks forming a functional ‘annulus-type’ central nervous system with three subsets of giant axons, dozen subtypes of neurons, muscles and a variety of receptors fully integrated with epithelial conductive pathways supporting swimming, escape and feeding behaviors. The observed unique adaptations within theAglanthalineage (including giant axons innervating striated muscles) strongly support an extensive and wide-spread parallel evolution of integrative and effector systems across Metazoa.
Whole Cell Phenotypic Screening Of MMV Pathogen Box identifies Specific Inhibitors of Plasmodium falciparum merozoite maturation and egress
Authors: Patra Alok Tanala , Hingmire Tejashri Bhimashankar , Belekar Meenakshi , Xiong Aoli , Subramanian Gowtham , Bozdech Zbynek , Preiser Peter , Shanmugam Dhanasekaran , Chandramohanadas Rajesh
Published: September 2019

We report a systematic, cellular phenotype-based antimalarial screening of the MMV Pathogen Box collection, which facilitated the identification of specific blockers of late stage intraerythrocytic Plasmodium falciparum maturation. First, from standard growth inhibition asays, we discovered 62 additional antimalarials (EC50 ≤ 10μM) over previously known antimalarial candidates from Pathogen Box. A total of 90 potent molecules (EC50 ≤ 1μM) were selected for evaluating their stage-specific effects during the intra-erythrocytic development of P. falciparum. None of these molecules had significant effect on ring-trophozoite transition, 10 molecules inhibited trophozoite-schizont transition, and 21 molecules inhibited schizont-ring transition at 1μM. These compounds were further validated in secondary assays by flow cytometry and microscopic imaging of treated cells to prioritize 12 molecules as potent and selective blockers of schizont-ring transition. Seven of these were found to strongly inhibit calcium ionophore induced egress of Toxoplasma gondii, a related apicomplexan parasite, suggesting that the inhibitors may be acting via similar mechanism in the two parasites, which can be further exploited for target identification studies. Two of these molecules, with previously unknown mechanism of action, MMV020670 and MMV026356, were found to induce fragmentation of DNA in developing merozoites. Further mechanistic studies would facilitate therapeutic exploitation of these molecules as broadly active inhibitors targeting development and egress of apicomplexan parasites relevant to human health.
Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community
Authors: Bono Lisa M. , Orton Richard J. , Peredo Elena L. , Morrison Hilary G. , Sistrom Mark , Simmons Sheri , Turner Paul E.
Published: September 2019

Although metagenomics reveals that natural virus communities harbor vast genetic diversity, the spatiotemporal dynamics of viral diversity in the wild are seldom tested, especially across small geographic scales. This problem is usefully examined in the above-ground phyllosphere, because terrestrial plants are frequently infected by taxonomically-diverse RNA viruses, whose elevated mutation rates generate abundant allele diversity. Here, we studied the problem by comparative analysis of RNA virus samples over time from three spatially-separated patches of a common perennial legume, white clover (Trifolium repens L.), growing in a grassy lawn in Woods Hole Village (Falmouth, MA, USA). We predicted that clover samples would show similarly high levels of virus species (alpha) diversity across space, but differing among-patch diversity of non-dominant virus taxa over time (4 samples spanning 6 weeks). Results showed that recognizable alpha diversity in clover patches was consistently dominated by RNA virus family Alphaflexiviridae across space, but that all patches showed inconsistent spatiotemporal presence of a diversity of minority virus families. Also, we observed that white clover mosaic virus (WClMV) dominated all patches across space and time. The high coverage of WClMV fostered an haplotype analysis, which revealed that two strains of the virus consistently infected clover plants during the 6-week period.
NLRP3- and AIM2-autonomy in a mouse model of MSU crystal-induced acute inflammation in vivo suggests imiquimod-dependent targeting of Il-1[beta] expression as relevant therapy for gout patients.
Authors: Mariotte Alexandre , Decauwer Aurore , Po Chrystelle , Abou-Faycal Cherine , Pichot Angelique , Paul Nicodeme , Aouadi Ismael , Carapito Raphael , Frisch Benoit , Macquin Cecile , Chatelus Emmanuel , Sibilia Jean , Armspach Jean-Paul , Bahram Seiamak , Georgel Philippe
Published: September 2019

The role of Monosodium Urate (MSU) crystals in gout pathophysiology is well described, as is the major impact of IL-1b in the inflammatory reaction that constitutes the hallmark of the disease. However, despite the discovery of the NLRP3 inflammasome and its role as a Pattern Recognition Receptor linking the detection of a danger signal (MSU) to IL-1b; secretion in vitro, the precise mechanisms leading to joint inflammation in gout patients are still poorly understood. Here, we provide an extensive clinical, biological and molecular characterization of the acute uratic inflammation mouse model induced by subcutaneous injection of MSU crystals, which accurately mimics human gout. Our work reveals several key features of MSU-dependent inflammation and identifies novel therapeutic opportunities, among which the use of topical application of imiquimod to promote interferon-dependent anti-inflammatory action maybe relevant.
The wide distribution and horizontal transfers of beta satellite DNA in eukaryotes
Authors: Yang Jiawen , Yuan Bin , Wu Yu , Li Meiyu , Li Jian , Xu Donglin , Gao Zeng-hong , Ma Guangwei , Zhou Yiting , Zuo Yachao , Wang Jin , Guo Yabin
Published: September 2019

Beta satellite DNA (satDNA), also known as Sau3A sequences, are repeated DNA sequences reported in human and primate genomes. It is previously thought that beta satDNAs originated in old world monkeys and bursted in great apes. In this study, we searched 7,821 genome assemblies of 3,767 eukaryotic species and found that beta satDNAs are widely distributed across eukaryotes. The four major branches of eukaryotes, animals, fungi, plants and Harosa/SAR, all have multiple clades containing beta satDNAs. These results were also confirmed by searching whole genome sequencing data (SRA) and PCR assay. Beta satDNA sequences were found in all the primate clades, as well as in Dermoptera and Scandentia, indicating that the beta satDNAs in primates might originate in the common ancestor of Primatomorpha or Euarchonta. In contrast, the widely patchy distribution of beta satDNAs across eukaryotes presents a typical scenario of multiple horizontal transfers.

One-sentence summary

Beta satDNAs in Opimoda could be result of HT from Diaphoretickes and those in primates might have originated in common ancestor of Primatomorpha.
Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types
Authors: Bao Riyue , Luke Jason J.
Published: September 2019

The T cell-inflamed tumor microenvironment, characterized by CD8 T cells and type I/II interferon transcripts, is an important cancer immunotherapy biomarker. Tumor mutational profile may also dictate response with some oncogenes (i.e. WNT/β-catenin) known to mediate immuno-suppression. Building on these observations we performed a multi-omic analysis of human cancer correlating the T cell-inflamed gene expression signature with the somatic mutanome and transcriptome for different immune phenotypes, by tumor type and across cancers. Strong correlations were noted between mutations in oncogenes and non-T cell-inflamed tumors with examples including IDH1 and GNAQ as well as less well-known genes including KDM6A, CD11c and genes with unknown functions. Conversely, we observe many genes associating with the T cell-inflamed phenotype including VHL and PBRM1, among others. Analyzing gene expression patterns, we identify oncogenic mediators of immune exclusion broadly active across cancer types including HIF1A and MYC. Novel examples from specific tumors include sonic hedgehog signaling in ovarian cancer or hormone signaling and novel transcription factors across multiple tumors. Using network analysis, somatic and transcriptomic events were integrated, demonstrating that most non-T cell-inflamed tumors are influenced by multiple pathways. Validating these analyses, we observe significant inverse relationships between protein levels and the T cell-inflamed gene signature with examples including NRF2 in lung, ERBB2 in urothelial and choriogonadotropin in cervical cancer. Finally, we integrate available databases for drugs that might overcome or augment the identified mechanisms. These results nominate molecular targets and drugs potentially available for immediate translation into clinical trials for patients with cancer.
Loss of CHCHD2 and CHCHD10 activates OMA1 peptidase to disrupt mitochondrial cristae phenocopying patient mutations in vivo
Authors: Liu Yi-Ting , Huang Xiaoping , Nguyen Diana , Dombi Eszter , Springer Danielle A , Poulton Joanna , Sekine Shiori , Narendra Derek P
Published: September 2019

Dominant mutations in the mitochondrial paralogs CHCHD2 (C2) and CHCHD10 (C10) were recently identified as causing Parkinson’s disease and ALS/FTD/myopathy, respectively. Disruption of mitochondrial cristae has been observed in mutant C10 patient tissues and animal models, but the mechanism for this disruption remains controversial. Additionally, C10 patient mutant knock-in (KI) mice were recently reported to activate a mitochondrial integrated stress response (mt-ISR) and develop cardiomyopathy not seen in C10 knockout (KO) mice, calling into question whether mutant C10 pathogenesis is related to C2/C10 normal function or purely toxic gain of function. Here, using the first C2/10 double knockout (DKO) mice, we report that C10 pathogenesis and the normal function of C2/10 are intimately linked. Similar to patients with C10 mutations, we found that C2/10 DKO mice (but not either single KO mice) have disrupted mitochondrial cristae, due to cleavage of the mitochondrial shaping protein L-OPA1 by the stress-induced peptidase OMA1. OMA1 was found to be activated similarly in affected tissues of mutant C10 KI mice, demonstrating that L-OPA1 cleavage is a novel mechanism for cristae abnormalities due to both C10 mutation and C2/C10 loss, and that OMA1, a driver of neurodegeneration in other contexts, may be a therapeutic target. Finally, C2/10 DKO mice partially phenocopied mutant C10 KI mice with the development of cardiomyopathy and activation of the mt-ISR in affected tissues, tying mutant C10 pathogenesis to C2/C10 function.
The Hrq1 helicase stimulates Pso2 translesion nuclease activity to promote DNA inter-strand crosslink repair
Authors: Rogers Cody M. , Lee Chun-Ying , Parkins Samuel , Buehler Nicholas J. , Wenzel Sabine , Martínez-Márquez Francisco , Takagi Yuichiro , Myong Sua , Bochman Matthew L.
Published: September 2019

DNA inter-strand crosslink (ICL) repair requires a complicated network of DNA damage response pathways. Removal of these lesions is vital as they are physical barriers to essential DNA processes that require the separation of duplex DNA, such as replication and transcription. The Fanconi anemia (FA) pathway is the principle mechanism for ICL repair in metazoans and is coupled to replication. InSaccharomyces cerevisiae, a degenerate FA pathway is present, but ICLs are predominantly repaired by a pathway involving the Pso2 nuclease that is hypothesized to digest through the lesion to provide access for translesion polymerases. However, Pso2 lacks translesion nuclease activityin vitro, and mechanistic details of this pathway are lacking, especially relative to FA. We recently identified the Hrq1 helicase, a homolog of the disease-linked RECQL4, as a novel component of Pso2- mediated ICL repair. Here, we show that Hrq1 stimulates the Pso2 nuclease in a mechanism that requires Hrq1 catalytic activity. Importantly, Hrq1 also stimulates Pso2 translesion nuclease activity through a site- specific ICLin vitro. Stimulation of Pso2 nuclease activity is specific to eukaryotic RecQ4 subfamily helicases, and Hrq1 likely interacts with Pso2 through their N-terminal domains. These results advance our understanding of FA-independent ICL repair and establish a role for the RecQ4 helicases in the repair of these dangerous lesions.
Structural organization of the C1a-e-c supercomplex within the ciliary central apparatus
Authors: Fu Gang , Zhao Lei , Dymek Erin , Hou Yuqing , Song Kangkang , Phan Nhan , Shang Zhiguo , Smith Elizabeth F. , Witman George B. , Nicastro Daniela
Published: September 2019

Nearly all motile cilia contain a central apparatus (CA) composed of two connected singlet-microtubules with attached projections that play crucial roles in regulating ciliary motility. Defects in CA assembly usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of the CA projections are largely unknown. Here, we integrated biochemical and genetic approaches with cryo-electron tomography to compare the CA of wild typeChlamydomonaswith CA mutants. We identified a large (>2 MDa) complex, the C1a-e-c supercomplex, that requires the PF16 protein for assembly and contains the CA components FAP76, FAP81, FAP92, and FAP216. We localized these subunits within the supercomplex using nanogold-labeling and show that loss of any one of them results in impaired ciliary motility. These data provide insight into the subunit organization and three-dimensional (3D) structure of the CA, which is a prerequisite for understanding the molecular mechanisms by which the CA regulates ciliary beating.

Fu et al. use a wild-type vs. mutant comparison and cryo-electron tomography ofChlamydomonasflagella to identify central apparatus (CA) subunits and visualize their location in the native 3D CA structure. The study provides a better understanding of the CA and how it regulates ciliary motility.
A framework for testing different imputation methods for tabular datasets
Authors: Kossen Tabea , Livne Michelle , Madai Vince I , Galinovic Ivana , Frey Dietmar , Fiebach Jochen B
Published: September 2019

Background and purpose

Handling missing values is a prevalent challenge in the analysis of clinical data. The rise of data-driven models demands an efficient use of the available data. Methods to impute missing values are thus crucial. Here, we developed a publicly available framework to test different imputation methods and compared their impact in a typical stroke clinical dataset as a use case.

Methods

A clinical dataset based on the 1000Plus stroke study with 380 completed-entries patients was used. 13 common clinical parameters including numerical and categorical values were selected. Missing values in a missing-at-random (MAR) and missing-completely-at-random (MCAR) fashion from 0% to 60% were simulated and consequently imputed using the mean, hot-deck, multiple imputation by chained equations, expectation maximization method and listwise deletion. The performance was assessed by the root mean squared error, the absolute bias and the performance of a linear model for discharge mRS prediction.

Results

Listwise deletion was the worst performing method and started to be significantly worse than any imputation method from 2% (MAR) and 3% (MCAR) missing values on. The underlying missing value mechanism seemed to have a crucial influence on the identified best performing imputation method. Consequently no single imputation method outperformed all others. A significant performance drop of the linear model started from 11% (MAR+MCAR) and 18% (MCAR) missing values.

Conclusions

In the presented case study of a typical clinical stroke dataset we confirmed that listwise deletion should be avoided for dealing with missing values. Our findings indicate that the underlying missing value mechanism and other dataset characteristics strongly influence the best choice of imputation method. For future studies with similar data structure, we thus suggest to use the developed framework in this study to select the most suitable imputation method for a given dataset prior to analysis.
A CLN6-CLN8 complex recruits lysosomal enzymes at the ER for Golgi transfer
Authors: Bajaj Lakshya , di Ronza Alberto , Zheng Pengcheng , Eblimit Aiden , Pal Rituraj , Sharma Jaiprakash , Roman Dany , Collette John R. , Sifers Richard N. , Jung Sung Y. , Chen Rui , Schekman Randy W. , Sardiello Marco
Published: September 2019

Lysosomal enzymes are synthesized in the endoplasmic reticulum (ER) and transferred to the Golgi complex by interaction with the Batten disease protein CLN8. Here we investigated the relationship of this pathway with CLN6, an ER-associated protein of unknown function that is defective in a different Batten disease subtype. Experiments focused on protein interaction and trafficking identified CLN6 as an obligate component of a CLN6-CLN8 complex (herein referred to as EGRESS:ER-to-Golgi relaying ofenzymes of the lysosomalsystem) which recruits lysosomal enzymes at the ER to promote their Golgi transfer. Simultaneous deficiency of CLN6 and CLN8 did not aggravate mouse pathology compared to the single deficiencies, indicating that the EGRESS complex works as a functional unit. Mutagenesis experiments showed that the second luminal loop of CLN6 is required for the interaction of CLN6 with the enzymes but dispensable for interaction with CLN8, and in vitro and in vivo studies showed that CLN6 deficiency results in inefficient ER export of lysosomal enzymes and diminished levels of the enzymes at the lysosome. These results identify CLN6 and the EGRESS complex as key players in lysosome biogenesis and shed light on the molecular etiology of Batten disease caused by defects in CLN6.
Deep Mutational Scan of a cardiac sodium channel voltage sensor
Authors: Glazer Andrew M. , Kroncke Brett M. , Matreyek Kenneth A. , Yang Tao , Wada Yuko , Shields Tiffany , Salem Joe-Elie , Fowler Douglas M. , Roden Dan M.
Published: September 2019

Variants in ion channel genes have classically been studied in low-throughput by patch clamping. Deep Mutational Scanning (DMS) is a complementary approach that can simultaneously assess function of thousands of variants. We have developed and validated a method to perform a DMS of variants in SCN5A, which encodes the major voltage-gated sodium channel in the heart. We created a library of nearly all possible variants in a 36 base region of SCN5A in the S4 voltage sensor of domain IV and stably integrated the library into HEK293T cells. In preliminary experiments, challenge with three drugs (veratridine, brevetoxin, and ouabain) could discriminate wildtype channels from gain and loss of function pathogenic variants. High-throughput sequencing of the pre- and post-drug challenge pools was used to count the prevalence of each variant and identify variants with abnormal function. The DMS scores identified 40 putative gain of function and 33 putative loss of function variants. For 8/9 variants, patch clamping data was consistent with the scores. These experiments demonstrate the accuracy of a high-throughput in vitro scan of SCN5A variant function, which can be used to identify deleterious variants in SCN5A and other ion channel genes.