bluuebunny/crossref_metadata_2025 huggingface dataset:
C53 interacting with UFM1-protein ligase 1 regulates microtubule nucleation in response to ER stress
Authors: Klebanovych Anastasiya , Vinopal Stanislav , Dráberová Eduarda , Sládková Vladimíra , Sulimenko Tetyana , Sulimenko Vadym , Vosecká Věra , Macůrek Libor , Legido Agustin , Dráber Pavel
Published: December 2020

ER distribution depends on microtubules, and ER homeostasis disturbance activates the unfolded protein response resulting in ER remodeling. CDK5RAP3 (C53) implicated in various signaling pathways interacts with UFM1-protein ligase 1 (UFL1), which mediates the ufmylation of proteins in response to ER stress. Here we find that UFL1 and C53 associate with γ-tubulin ring complex proteins. Knockout ofUFL1orC53in human osteosarcoma cells induces ER stress, centrosomal microtubule nucleation accompanied by γ-tubulin accumulation and ER expansion. C53, whose protein level is modulated by UFL1, associates with the centrosome and rescues microtubule nucleation in cells lacking UFL1. Pharmacological induction of ER stress by tunicamycin also leads to increased microtubule nucleation and ER expansion. Furthermore, tunicamycin suppresses the association of C53 with the centrosome. These findings point to a novel mechanism for the relief of ER stress by stimulation of centrosomal microtubule nucleation.
Infrared spectral markers for the nephroprotective effects ofFicus deltoideain streptozotocin-induced diabetic rats
Authors: Samsulrizal Nurdiana , Yong-Meng Goh , Ahmad Hafandi , Syimal’ain Azmi Nur , Mohamad Zin Noor Syaffinaz Noor , Mahdi Ebrahimi
Published: December 2020

Fourier Transform Infrared (FTIR) is an established analytical technique to elucidate new discriminatory biomarkers. Our previous study showed thatFicus deltoidea(Ficus: Moraceae) is capable of increasing insulin secretion and improving tissue regeneration by reducing oxidative stress in diabetic rats. However, the assessment of treatment response is limited by the paucity of biomarkers. We aimed to evaluate the potential use of FTIR for assessing the nephroprotective effects ofFicus deltoidea(Ficus: Moraceae) in diabetic rats. A rat model of diabetes was induced using a single intraperitoneal injection of streptozotocin (STZ) (60 mg/kg body weight). Methanolic extract ofF. deltoideawas administered orally at a dose of 1000 mg/kg body weight for eight weeks. Fasting blood glucose, serum insulin and kidney function parameters were examined. The kidneys were subsequently subjected to FTIR and histological analyses. Enzyme-linked immunosorbent assays (ELISA) assessed the levels of oxidative stress, antioxidant, and apoptosis-related proteins in the kidney tissue. The results show, for the first time, that there is a good agreement between changes in kidney and FTIR peaks. The IR peaks (1545 cm−1and 1511 cm-1) corresponding to amide II were restored by treatment withF. deltoidea. Multivariate analysis demonstrated that the diabetic rats treated withF. deltoideahad similar clustering pattern that of the normal animals. Biochemical and histological examination further confirmed the nephroprotective effect ofF. deltoidea. Thus, demonstrating how FTIR spectroscopy could be used for the diagnosis of diabetes kidney disease.
KATK: fast genotyping of rare variants directly from unmapped sequencing reads
Authors: Kaplinski Lauris , Möls Märt , Puurand Tarmo , Pajuste Fanny-Dhelia , Remm Maido
Published: December 2020

Motivation

KATK is a fast and accurate software tool for calling variants directly from raw NGS reads. It uses predefined k-mers to retrieve only the reads of interest from the FASTQ file and calls genotypes by aligning retrieved reads locally. KATK does not use data about known polymorphisms and has NC (No Call) as default genotype. The reference or variant allele is called only if there is sufficient evidence for their presence in data. Thus it is not biased against rare variants orde novomutations.

Results

With simulated datasets, we achieved a false negative rate of 0.23% (sensitivity 99.77%) and a false discovery rate of 0.19%. Calling all human exonic regions with KATK requires 1-2 h, depending on sequencing coverage.

Availability

KATK is distributed under the terms of GNU GPL v3. The k-mer databases are distributed under the Creative Commons CC BY-NC-SA license. The source code is available at GitHub as part of Genometester4 package (https://github.com/bioinfo-ut/GenomeTester4/). The binaries of KATK package and k-mer databases described in the current paper are available onhttp://bioinfo.ut.ee/KATK/.
Are indigenous territories effective natural climate solutions? A neotropical analysis using matching methods and geographic discontinuity designs
Authors: Alejo Camilo , Meyer Chris , Walker Wayne S. , Gorelik Seth R. , Josse Carmen , Aragon-Osejo Jose Luis , Rios Sandra , Augusto Cicero , Llanos Andres , Coomes Oliver T. , Potvin Catherine
Published: December 2020

Indigenous Territories (ITs) with less centralized forest governance than Protected Areas (PAs) may represent cost-effective natural climate solutions to meet the Paris agreement. However, the literature has been limited to examining the effect of ITs on deforestation, despite the influence of anthropogenic degradation. Thus, little is known about the temporal and spatial effect of allocating ITs on carbon stocks dynamics that account for losses from deforestation and degradation. Using Amazon Basin countries and Panama, this study aims to estimate the temporal and spatial effects of ITs and PAs on carbon stocks. To estimate the temporal effects, we use annual carbon density maps, matching analysis, and linear mixed models. Furthermore, we explore the spatial heterogeneity of these estimates through geographic discontinuity designs, allowing us to assess the spatial effect of ITs and PAs boundaries on carbon stocks. The temporal effects highlight that allocating ITs preserves carbon stocks and buffer losses as PAs in Panama and Amazon Basin countries. The geographic discontinuity designs reveal that ITs’ boundaries secure more extensive carbon stocks than their surroundings, and this difference tends to increase towards the least accessible areas, suggesting that indigenous land use in neotropical forests may have a temporarily and spatially stable impact on carbon stocks. Our findings imply that ITs in neotropical forests support Nationally Determined Contributions (NDCs) under the Paris Agreement. Thus, Indigenous peoples must become recipients of countries’ results-based payments.
DeterminingAspergillus fumigatustranscription factor expression and function during invasion of the mammalian lung
Authors: Liu Hong , Xu Wenjie , Bruno Vincent M. , Phan Quynh T. , Solis Norma V. , Woolford Carol A. , Ehrlich Rachel , Shetty Amol C. , McCraken Carie , Lin Jianfeng , Mitchell Aaron P. , Filler Scott G.
Published: December 2020

To gain a better understanding of the transcriptional response ofAspergillus fumigatusduring invasive pulmonary infection, we used a NanoString nCounter to assess the transcript levels of 467A. fumigatusgenes during growth in the lungs of immunosuppressed mice. These genes included ones known to respond to diverse environmental conditions and those encoding most transcription factors in theA. fumigatusgenome. We found that invasive growthin vivoinduces a unique transcriptional profile as the organism responds to nutrient limitation and attack by host phagocytes. Thisin vivotranscriptional response is largely mimicked byin vitrogrowth inAspergillusminimal medium that is deficient in nitrogen, iron, and/or zinc. From the transcriptional profiling data, we selected 9 transcription factor genes that were either highly expressed or strongly up-regulated duringin vivogrowth. Deletion mutants were constructed for each of these genes and assessed for virulence in mice. Two transcription factor genes were found to be required for maximal virulence. One wasrlmA,which governs the ability of the organism to proliferate in the lung. The other wasace1, which regulates of the expression of multiple secondary metabolite gene clusters and mycotoxin genes independently oflaeA. Using deletion and overexpression mutants, we determined that the attenuated virulence of the Δace1mutant is due to decreased expressionaspf1,which specifies a ribotoxin, but is not mediated by reduced expression of the fumigaclavine gene cluster or the fumagillin-pseruotin supercluster. Thus,in vivotranscriptional profiling focused on transcription factors genes provides a facile approach to identifying novel virulence regulators.

Author summary

AlthoughA. fumigatuscauses the majority of cases of invasive aspergillosis, the function of most of the genes in its genome remains unknown. To identify genes encoding transcription factors that may be important for virulence, we used a NanoString nCounter to measure the mRNA levels ofA. fumigatustranscription factor genes in the lungs of mice with invasive aspergillosis. The transcriptional profiling data indicate that the organism is exposed to nutrient limitation and stress during growth in the lungs, and that it responds by up-regulating genes that encode mycotoxins and secondary metabolites.In vitro,this response was most closely mimicked by growth in medium that was deficient in nitrogen, iron and/or zinc. Using the transcriptional profiling data, we identified two transcription factors that governA. fumigatusvirulence. These were RlmA, which is governs proliferation in the lung and Ace1, which controls the production of mycotoxins and secondary metabolites.
Shared population-level dynamics in monkey premotor cortex during solo action, joint action and action observation
Authors: Pezzulo Giovanni , Donnarumma Francesco , Ferrari-Toniolo Simone , Cisek Paul , Battaglia-Mayer Alexandra
Published: December 2020

Studies of neural population dynamics of cell activity from monkey motor areas during reaching show that it mostly represents the generation and timing of motor behavior. We compared neural dynamics in dorsal premotor cortex (PMd) during the performance of a visuomotor task executed individually or cooperatively and during an observation task. In the visuomotor conditions, monkeys applied isometric forces on a joystick to guide a visual cursor in different directions, either alone or jointly with a conspecific. In the observation condition, they observed the cursor’s motion guided by the partner. We found that in PMd neural dynamics were widely shared across action execution and observation, with cursor motion directions more accurately discriminated than task types. This suggests that PMd encodes spatial aspects irrespective of specific behavioral demands. Furthermore, our results suggest that largest components of premotor population dynamics, which have previously been suggested to reflect a transformation from planning to movement execution, may rather reflect higher cognitive-motor processes, such as the covert representation of actions and goals shared across tasks that require movement and those that do not.

HIGHLIGHTS

In PMd neural dynamics is shared across action execution and mere observation

Task directional features are more accurately discriminated than action types

Spatial aspects are encoded in PMd independently from specific behavioral demands

PMd dynamics largely reflect higher cognitive-motor processes rather than strictly motor-related functions
Optogenetic Amplification Circuits for Light-Induced Metabolic Control
Authors: Zhao Evan M. , Lalwani Makoto A. , Chen Jhong-Min , Orillac Paulina , Toettcher Jared E. , Avalos José L.
Published: December 2020

Dynamic control of microbial metabolism is an effective strategy to improve chemical production in fermentations. While dynamic control is most often implemented using chemical inducers, optogenetics offers an attractive alternative due to the high tunability and reversibility afforded by light. However, a major concern of applying optogenetics in metabolic engineering is the risk of insufficient light penetration at high cell densities, especially in large bioreactors. Here, we present a new series of optogenetic circuits we call OptoAMP, which amplify the transcriptional response to blue light by as much as 21.8-fold compared to the basal circuit (OptoEXP). These circuits show as much as a 41-fold induction between dark and light conditions, efficient activation at light doses as low as ~1%, and strong homogeneous light-induction in bioreactors of at least 5L, with limited illumination at cell densities above 40 OD600. We demonstrate the ability of OptoAMP circuits to control engineered metabolic pathways in novel three-phase fermentations using different light schedules to control enzyme expression and improve production of lactic acid, isobutanol, and naringenin. These circuits expand the applicability of optogenetics to metabolic engineering.
Prenatal THC does not affect female mesolimbic dopaminergic system in preadolescent rats
Authors: Traccis Francesco , Serra Valeria , Sagheddu Claudia , Congiu Mauro , Saba Pierluigi , Giua Gabriele , Devoto Paola , Frau Roberto , Cheer Joseph Francois , Melis Miriam
Published: December 2020

Cannabis use among pregnant women is increasing worldwide along with permissive sociocultural attitudes towards it. Prenatal cannabis exposure (PCE), however, is associated with adverse outcome among offspring ranging from reduced birth weight to child psychopathology. We have previously shown that male rat offspring prenatally exposed to Δ9-tetrahydrocannabinol (THC), a rat model of PCE, exhibit extensive molecular, cellular and synaptic changes in dopamine neurons of the ventral tegmental area (VTA), resulting in a susceptible mesolimbic dopamine system associated with a psychotic-like endophenotype. This phenotype only reveals itself upon a single exposure to THC in males but not females. Here, we characterized the impact of PCE on female behaviors and mesolimbic dopamine system function by combining in vivo single-unit extracellular recordings in anesthetized animals and ex vivo patch clamp recordings, along with neurochemical and behavioral analyses. We find that PCE female offspring do not show any spontaneous or THC-induced behavioral disease-relevant phenotypes. The THC-induced increase of dopamine levels in nucleus accumbens was reduced in PCE female offspring, even when VTA dopamine activity in vivo and ex vivo did not differ compared to control. These findings indicate that PCE impacts mesolimbic dopamine function and its related-behavioral domains in a sex-dependent manner and warrant further investigations to decipher the mechanisms determining this sex-related protective effect from intrauterine THC exposure.

Highlights

PCE female offspring do not manifest a disease-relevant phenotype

Prenatal THC does not affect female dopaminergic neurons

PCE female mesolimbic dopamine function is less responsive to acute THC
Herpes Simplex Virus Co-Infection Facilitates Rolling Circle Replication of the Adeno-Associated Virus Genome
Authors: Meier Anita F. , Tobler Kurt , Leisi Remo , Lkharrazi Anouk , Ros Carlos , Fraefel Cornel
Published: December 2020

Adeno-associated virus (AAV) genome replication only occurs in the presence of a co-infecting helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1). AdV5-supported replication of the AAV genome has been described to occur in a strand-displacement rolling hairpin replication (RHR) mechanism initiated at the AAV 3’ inverted terminal repeat (ITR) end. It has been assumed that the same mechanism applies to HSV-1-supported AAV genome replication. Using nanopore sequencing as a novel, high-throughput approach to study viral genome replication we demonstrate the formation of double-stranded head-to-tail concatemers of AAV genomes in the presence of HSV-1, thus providing evidence for an unequivocal rolling circle replication (RCR) mechanism. This stands in contrast to the textbook model of AAV genome replication when HSV-1 is the helper virus.

SIGNIFICANCE

Efficient adeno-associated virus (AAV) replication requires the presence of helper factors, which can be provided by co-infecting helper viruses such as adenoviruses or herpesviruses. AAV replication has been described to occur as a rolling hairpin replication mechanism. However, we show that during a herpes simplex virus type 1 (HSV-1) supported replication, AAV rolling circle-like replication intermediates are formed. Thus, this study stands in contrast to the textbook model of AAV genome replication. Additionally, we introduce nanopore sequencing as a novel, high-throughput approach to study viral genome replication in unprecedented detail.
Drosophila glue protects from predation
Authors: Borne Flora , Prigent Stéphane R. , Molet Mathieu , Courtier-Orgogozo Virginie
Published: December 2020

Animals can be permanently attached to a substrate in terrestrial environments at certain stages of their development. Pupa adhesion has evolved multiple times in insects and is thought to maintain the animal in a place where it is not detectable by predators. Here, we investigate whether pupa adhesion in Drosophila can also protect the animal by preventing potential predators from detaching the pupa. We measured the adhesion of Drosophila species sampled from the same area and found that pupa adhesion varies among species, which can be explained by different glue production strategies. Then, we compared attached and manually detached pupae in both field and laboratory assays to investigate the role of pupa adhesion to prevent predation. First, we found that attached pupae remain on site 30 % more than detached pupae in the field after three days, probably because they are less predated. Second, we observed that attached pupae are less efficiently predated by ants in the laboratory: they are not carried back to the ant nest and more ants are needed to consume them onsite. Our results show that pupa adhesion can prevent the animal from being taken away by predators and is crucial for Drosophila fly survival.
Time Perception through the Processing of Verb Tenses: An ERP study regarding Mental Time Travel
Authors: Papageorgiou Charalabos , Giannopoulos Anastasios E. , Fokas Athanasios S. , Thompson Paul M. , Kapsalis Nikolaos C. , Papageorgiou Panos , Stachtea Xanthi , Capsalis Christos N.
Published: December 2020

Humans are equipped with the so-called Mental Time Travel (MTT) ability, which allows them to consciously construct and elaborate past or future scenes. The mechanisms underlying MTT remain elusive. This study focused on the late positive potential (LPP) and alpha oscillations, considering that LPP covaries with the temporal continuity whereas the alpha oscillations index the temporal organization of perception. To that end, subjects were asked to focus on performing two mental functions engaging working memory, which involved mental self-projection into either the present-past (PP) border or the present-future (PF) border. To evaluate underlying mechanisms, the evoked frontal late positive potentials (LPP) as well as their cortical sources were analyzed via the standardized low-resolution brain electromagnetic tomography (sLORETA) technique. The LPP amplitudes - in the left lateral prefrontal areas that were elicited during PF tasks - were significantly higher than those associated with PP, whereas opposite patterns were observed in the central and right prefrontal areas. Crucially, the LPP activations of both the PP and PF self-projections overlapped with the brain’s default mode network and related interacting areas. Finally, we found enhanced alpha-related activation with respect to PP in comparison to PF, predominantly over the right hemisphere central brain regions (specifically, the precentral gyrus). These findings confirm that the two types of self-projection, as reflected by the frontally-distributed LPP, share common cortical resources that recruit different brain regions in a balanced way. This balanced distribution of brain activation might signify that biological time tends to behave in a homeostatic way.
Identification of key genes and associated pathways in neuroendocrine tumors through bioinformatics analysis and predictions of small drug molecules
Authors: Devarbhavi Praveenkumar , Vastrad Basavaraj , Tengli Anandkumar , Vastrad Chanabasayya , Kotturshetti Iranna
Published: December 2020

Neuroendocrine tumor (NET) is one of malignant cancer and is identified with high morbidity and mortality rates around the world. With indigent clinical outcomes, potential biomarkers for diagnosis, prognosis and drug target are crucial to explore. The aim of this study is to examine the gene expression module of NET and to identify potential diagnostic and prognostic biomarkers as well as to find out new drug target. The differentially expressed genes (DEGs) identified from GSE65286 dataset was used for pathway enrichment analyses and gene ontology (GO) enrichment analyses and protein - protein interaction (PPI) analysis and module analysis. Moreover, miRNAs and transcription factors (TFs) that regulated the up and down regulated genes were predicted. Furthermore, validation of hub genes was performed. Finally, molecular docking studies were performed. DEGs were identified, including 453 down regulated and 459 up regulated genes. Pathway and GO enrichment analysis revealed that DEGs were enriched in sucrose degradation, creatine biosynthesis, anion transport and modulation of chemical synaptic transmission. Important hub genes and target genes were identified through PPI network, modules, target gene - miRNA network and target gene - TF network. Finally, survival analyses, receiver operating characteristic (ROC) curve and RT-PCR validated the significant difference of ATP1A1, LGALS3, LDHA, SYK, VDR, OBSL1, KRT40, WWOX, NINL and PPP2R2B between metastatic NET and normal controls. In conclusion, the DEGs and hub genes with their regulatory elements identified in this study will help us understand the molecular mechanisms underlying NET and provide candidate targets for future research.
Multiplexed experimental strategies for fragment library screening using SPR biosensors
Authors: FitzGerald Edward A. , Vagrys Darius , Opassi Giulia , Klein Hanna F. , Hamilton David J. , Boronat Pierre , Cederfelt Daniela , Talibov Vladimir O. , Abramsson Mia , Moberg Anna , Lindgren Maria T. , Holmgren Claes , Dobritzsch Doreen , Davis Ben , O’Brien Peter , Wijtmans Maikel , van Muijlwijk-Koezen Jacqueline E. , Hubbard Roderick E. , de Esch Iwan J.P , Danielson U. Helena
Published: December 2020

Surface plasmon resonance biosensor technology (SPR) is ideally suited for fragment-based lead discovery. However, generally suitable experimental procedures or detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are lacking. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. By adopting a multiplexed strategy, the range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded. We here illustrate innovative strategies using five challenging targets and variants thereof. Two libraries of 90 and 1056 fragments were screened using two different flow-based SPR biosensor systems, allowing different experimental approaches. Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted.
Neoantigen driven B cell and CD4+T follicular helper cell collaboration promotes robust anti-tumor CD8+T cell responses
Authors: Cui Can , Wang Jiawei , Chen Ping-Min , Connolly Kelli A. , Damo Martina , Fagerberg Eric , Chen Shuting , Eisenbarth Stephanie C. , Zhao Hongyu , Craft Joseph , Joshi Nikhil S.
Published: December 2020

CD4+T follicular helper (TFH) cells provide help to B cells, which is critical for germinal center (GC) formation, but the importance of TFH-B cell interactions in cancer is unclear. We found TFH cells correlated with GC B cells and with prolonged survival of lung adenocarcinoma (LUAD) patients. To investigate further, we developed an LUAD model, in which tumor cells expressed B-cell- and T-cell-recognized neoantigens. Interactions between tumor-specific TFH and GC B cells were necessary for tumor control, as were effector CD8+T cells. The latter were reduced in the absence of T cell-B cell interactions or the IL-21 receptor. IL-21 was produced primarily by TFH cells, development of which required B cells. Moreover, development of tumor-specific TFH cell-responses was also reliant upon tumors that expressed B-cell-recognized neoantigens. Thus, tumor-neoantigens themselves can control the fate decisions of tumor-specific CD4+T cells by facilitating interactions with tumor-specific B cells.

Abstract Figure
SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation
Authors: Thorne Lucy G , Reuschl Ann-Kathrin , Zuliani-Alvarez Lorena , Whelan Matthew V.X. , Noursadeghi Mahdad , Jolly Clare , Towers Greg J
Published: December 2020

SARS-CoV-2 infection causes broad-spectrum immunopathological disease, exacerbated by inflammatory co-morbidities. A better understanding of mechanisms underpinning virus-associated inflammation is required to develop effective therapeutics. Here we discover that SARS-CoV-2 replicates rapidly in lung epithelial cells despite triggering a robust innate immune response through activation of cytoplasmic RNA-ensors RIG-I and MDA5. The inflammatory mediators produced during epithelial cell infection can stimulate primary human macrophages to enhance cytokine production and drive cellular activation. Critically, this can be limited by abrogating RNA sensing, or by inhibiting downstream signalling pathways. SARS-CoV-2 further exacerbates the local inflammatory environment when macrophages or epithelial cells are primed with exogenous inflammatory stimuli. We propose that RNA sensing of SARS-CoV-2 in lung epithelium is a key driver of inflammation, the extent of which is influenced by the inflammatory state of the local environment, and that specific inhibition of innate immune pathways may beneficially mitigate inflammation-associated COVID-19.

Highlights

SARS-CoV-2 activates RNA sensors and consequent inflammatory responses in lung epithelial cells

Epithelial RNA sensing responses drive pro-inflammatory macrophage activation

Exogenous inflammatory stimuli exacerbate responses to SARS-CoV-2 in both eplithelial cells and macrophages

Immunomodulators inhibit RNA sensing responses and consequent macrophage inflammation

Graphical Abstract
A cognitive state transformation model for task-general and task-specific subsystems of the brain connectome
Authors: Yoo Kwangsun , Rosenberg Monica D , Kwon Young Hye , Scheinost Dustin , Constable R Todd , Chun Marvin M
Published: December 2020

The human brain flexibly controls different cognitive behaviors, such as memory and attention, to satisfy contextual demands. Much progress has been made to reveal task-induced modulations in the whole-brain functional connectome, but we still lack a way to model changes in the brain’s functional organization. Here, we present a novel connectome-to-connectome (C2C) state transformation framework that enables us to model the brain’s functional reorganization in response to specific task goals. Using functional magnetic resonance imaging data from the Human Connectome Project, we demonstrate that the C2C model accurately generates an individual’s task-specific connectomes from their task-free connectome with a high degree of specificity across seven different cognitive states. Moreover, the C2C model amplifies behaviorally relevant individual differences in the task-free connectome, thereby improving behavioral predictions. Finally, the C2C model reveals how the connectome reorganizes between cognitive states. Previous studies have reported that task-induced modulation of the brain connectome is domain-specific as well as domain-general, but did not specify how brain systems reconfigure to specific cognitive states. Our observations support the existence of reliable state-specific systems in the brain and indicate that we can quantitatively describe patterns of brain reorganization, common across individuals, in a computational model.
Identification of COVID-19-relevant transcriptional regulatory networks and associated kinases as potential therapeutic targets
Authors: Su Chen , Rousseau Simon , Emad Amin
Published: December 2020

Identification of transcriptional regulatory mechanisms and signaling networks involved in the response of host to infection by SARS-CoV-2 is a powerful approach that provides a systems biology view of gene expression programs involved in COVID-19 and may enable identification of novel therapeutic targets and strategies to mitigate the impact of this disease. In this study, we combined a series of recently developed computational tools to identify transcriptional regulatory networks involved in the response of epithelial cells to infection by SARS-CoV-2, and particularly regulatory mechanisms that are specific to this virus. In addition, using network-guided analyses, we identified signaling pathways that are associated with these networks and kinases that may regulate them. The results identified classical antiviral response pathways including Interferon response factors (IRFs), interferons (IFNs), and JAK-STAT signaling as key elements upregulated by SARS-CoV-2 in comparison to mock-treated cells. In addition, comparing SARS-Cov-2 infection of airway epithelial cells to other respiratory viruses identified pathways associated with regulation of inflammation (MAPK14) and immunity (BTK, MBX) that may contribute to exacerbate organ damage linked with complications of COVID-19. The regulatory networks identified herein reflect a combination of experimentally validated hits and novel pathways supporting the computational pipeline to quickly narrow down promising avenue of investigations when facing an emerging and novel disease such as COVID-19.
Diffusion of metabolites across gap junctions mediates metabolic coordination of β-islet cells
Authors: Rao Vishnu P. , Rizzo Megan A.
Published: December 2020

Loss of oscillatory insulin secretion is an early marker of type II diabetes. In an individual beta-cell, insulin secretion is triggered by glucose metabolism, which leads to membrane depolarization and calcium influx. Islet β-cells display coordinated secretion; however, it is unclear how the heterogeneous population of insulin-secreting beta cells coordinate their response to glucose. The mechanisms underlying both electrical and calcium synchronicity are well explored. Even so, the mechanism governing metabolic coordination is unclear given key glycolytic enzymes’ heterogeneous expression. To understand how islet cells coordinate their metabolic activity, a microfluidic applicator delivered glucose stimulation to spatially defined areas of isolated mouse islets. We measured metabolic responses using NADH/NADPH (or NAD(P)H) autofluorescence and calcium changes using Fluo-4 fluorescence. Glucose stimulated a rise in NAD(P)H even in islet areas unexposed to the treatment, suggesting metabolic coordination. A gap junction inhibitor blocked the coordinated NAD(P)H rise in the low-glucose areas. Additionally, metabolic communication did not occur in immortalized β-cell clusters known to lack gap junctions, demonstrating their importance for metabolic coupling. Metabolic communication also preceded glucose-stimulated rises in intracellular calcium. Further, pharmacological blockade of calcium influx did not disrupt NAD(P)H rises in untreated regions. These data suggest that metabolic coordination between islet beta-cells relies on gap-junctional activity and precedes synchronous electrical and calcium activity.
Massive colonization of protein-coding exons by selfish genetic elements inParameciumgermline genomes
Authors: Sellis Diamantis , Guérin Frédéric , Arnaiz Olivier , Pett Walker , Lerat Emmanuelle , Boggetto Nicole , Krenek Sascha , Berendonk Thomas , Couloux Arnaud , Aury Jean-Marc , Labadie Karine , Malinsky Sophie , Bhullar Simran , Meyer Eric , Sperling Linda , Duret Laurent , Duharcourt Sandra
Published: December 2020

Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome ofParamecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences, called Internal Eliminated Sequences (IESs), that have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of nineParameciumspecies (from ∼100 Mb inP. aureliaspecies to > 1.5 Gb inP. caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single-copy in present-day genomes, we identified several families of mobile IESs, including non-autonomous elements acquired via horizontal transfer, that generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs inParamecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across theaureliaclade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution ofParameciumIESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.
MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline
Authors:   A collaboration between the U.S. Department of Energy and TRACK-TBI, Moon Joseph , Bremer Peer-Timo , Mukherjee Pratik , Markowitz Amy J. , Palacios Eva M. , Cai Lanya T. , Rodriguez Alexis , Xiao Yukai , Manley Geoffrey T. , Madduri Ravi K.
Published: December 2020

Large-scale diffusion MRI tractography remains a significant challenge. Users must orchestrate a complex sequence of instructions that requires many software packages with complex dependencies and high computational cost. We developed MaPPeRTrac, a probabilistic tractography pipeline that simplifies and vastly accelerates this process on a wide range of high performance computing (HPC) environments. It fully automates the entire tractography pipeline, from management of raw MRI machine data to edge density imaging (EDI) of the structural connectome. Dependencies are containerized withDockerorSingularityand de-coupled from code to enable rapid proto-typing and modification. Data artifacts are strictly organized with theBrain Imaging Data Structure(BIDS) to ensure that they are findable, accessible, interoperable, and reusable following FAIR principles. The pipeline takes full advantage of HPC resources using theParslparallel programming frame-work, resulting in the creation of connectome datasets of unprecedented size. MaPPeRTrac is publicly available and tested on commercial and scientific hardware, so that it may accelerate brain connectome research for a broader user community.
Genome evolution in a putatively asexual wasp
Authors: Tvedte Eric S. , Ward Austin C. , Trendle Benjamin , Forbes Andrew A. , Logsdon John M.
Published: December 2020

Asexual lineages are destined for extinction—a result predicted by theory and revealed in practice. Short-term benefits of asexuality are eventually outstripped by their fitness costs: losses of sex and recombination are together expected to reduce efficacy of selection, increase mutation load, and thus, lower fitness. We characterized genomic patterns of accumulating mutations inDiachasma muliebre, a parasitic wasp that has apparently lost sex, an inference supported by many decades of field collections of 1000s of individuals in which only females were found. The split betweenD. muliebreand its closest sexual relative,Diachasma ferrugineum, is quite recent, allowing us to observe initial events in the evolution of this putative asexual species. First, we find a faster rate of molecular evolution across theD. muliebregenome. In addition, we observed a marked excess of replacement nucleotide substitutions in orthologous genes in the putatively asexualD. muliebrewhen compared toD. ferrugineum. This pattern directly indicates genome-wide relaxed selection in this young, putatively asexual species, the resulting mutational load from which is expected to ultimately lead to extinction. However, these genomic effects occur in the presence of genomic recombination initially detected by a previous study and also supported by analyses of genome-wide substitution rates within codons. In addition, following completion of the genome sequence and its analysis, we discovered twoD. muliebremales, suggesting the possibility of rare sex in this species. Haplodiploid animals, including the sexual ancestors ofD. muliebre, bear small genetic loads, likely making their initial transitions to asexuality relatively benign. Paradoxically, an elevated rate of mutation accumulation resulting from asexuality, when accompanied by retention of recombination and/or rare sex, could actually be beneficial: we hypothesize that the novel variation introduced by mutation along with limited shuffling of genes may facilitate initial adaptation and extend persistence of such lineages.
Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope remodeling and function in stomatal complex development and pollen viability
Authors: McKenna JF , Gumber HK , Turpin ZM , Jalovec AM , Kartick AC , Graumann K , Bass HW
Published: December 2020

In eukaryotes, the nuclear envelope (NE) encloses chromatin and separates it from the rest of the cell. The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex physically bridges across the NE, linking nuclear and cytoplasmic components. In plants, these LINC complexes are beginning to be ascribed roles in cellular and nuclear functions, including chromatin organization, regulation of nuclei shape and movement, and cell division. Homologs of core LINC components, KASH and SUN proteins, have previously been identified in maize. Here, we characterized the presumed LINC-associated maize nucleoskeletal proteins NCH1 and NCH2, homologs of members of the plant NMCP/CRWN family, and MKAKU41, homologous to AtKAKU4. All three proteins localized to the nuclear periphery when transiently and heterologously expressed as fluorescent protein fusions inNicotiana benthamiana. Overexpression of MKAKU41 caused dramatic changes in the organization of the nuclear periphery, including nuclear invaginations that stained positive for non-nucleoplasmic markers of the inner and outer NE, and the ER. The severity of these invaginations was altered by changes in LINC connections and the actin cytoskeleton. In maize, MKAKU41 appeared to share genetic functions with other LINC components, including control of nuclei shape, stomatal complex development, and pollen viability. Overall, our data show that NCH1, NCH2, and MKAKU41 have characteristic properties of LINC-associated plant nucleoskeletal proteins, including interactions with NE components suggestive of functions at the nuclear periphery that impact the overall nuclear architecture.
A test of the hypothesis that variable mutation rates create signals that have previously been interpreted as evidence of archaic introgression into humans
Authors: Amos William
Published: December 2020

It is widely accepted that non-African humans carry 1-2% Neanderthal DNA due to historical inter-breeding. However, inferences about introgression rely on a critical assumption that mutation rate is constant and that back-mutations are too rare to be important. Both these assumptions have been challenged, and recent evidence points towards an alternative model where signals interpreted as introgression are driven mainly by higher mutation rates in Africa. In this model, non-Africans appear closer to archaics not because they harbour introgressed fragments but because Africans have diverged more. Here I test this idea by using the density of rare, human-specific variants (RHSVs) as a proxy for recent mutation rate. I find that sites that contribute most to the signal interpreted as introgression tend to occur in tightly defined regions spanning only a few hundred bases in which mutation rate differs greatly between the two human populations being compared. Mutation rate is invariably higher in the population into which introgression isnotinferred. I confirmed that RHSV density reflects mutation rate by conducting a parallel analysis looking at the density of RHSVs around sites with three alleles, an independent class of site that also requires recurrent mutations to form. Near-identical peaks in RHSV density are found, suggesting a common cause. Similarly, coalescent simulations confirm that, with constant mutation rate, introgressed fragments do not occur preferentially in regions with a high density of rare, human-specific variants. Together, these observations are difficult to reconcile with a model where excess base-sharing is driven by archaic legacies but instead provide support for a higher mutation rate inside Africa driving increased divergence from the ancestral human state.
Motor guidance by long-range communication through the microtubule highway
Authors: Wijeratne Sithara S. , Fiorenza Shane A. , Subramanian Radhika , Betterton Meredith D.
Published: December 2020

Coupling of motor proteins within arrays drives muscle contraction, flagellar beating, chromosome segregation, and other biological processes. Current models of motor coupling invoke either direct mechanical linkage or protein crowding, which rely on short-range motor-motor interactions. In contrast, coupling mechanisms that act at longer length scales remain largely unexplored. Here we report that microtubules can physically couple motor movement in the absence of short-range interactions. The human kinesin-4 Kif4A changes the run-length and velocity of other motors on the same microtubule in the dilute binding limit, when 10-nm-sized motors are separated by microns. This effect does not depend on specific motor-motor interactions because similar changes in Kif4A motility are induced by kinesin-1 motors. A micron-scale attractive interaction potential between motors is sufficient to recreate the experimental results in a computational model. Unexpectedly, our theory suggests that long-range microtubule-mediated coupling not only affects binding kinetics but also motor mechanochemistry. Therefore, motors can sense and respond to motors bound several microns away on a microtubule. These results suggest a paradigm in which the microtubule lattice, rather than being merely a passive track, is a dynamic medium responsive to binding proteins to enable new forms of collective motor behavior.
Genetic architecture of transmission stage production and virulence in schistosome parasites
Authors: CLEC’H Winka LE , Chevalier Frédéric D. , McDew-White Marina , Menon Vinay , Arya Grace-Ann , Anderson Timothy J.C.
Published: December 2020

Both theory and experimental data from pathogens suggest that the production of transmission stages should be strongly associated with virulence, but the genetic bases of parasite transmission/virulence traits are poorly understood. The blood flukeSchistosoma mansonishows extensive variation in numbers of cercariae larvae shed and in their virulence to infected snail hosts, consistent with expected trade-offs between parasite transmission and virulence. We crossed schistosomes from two populations that differ 8-fold in cercarial shedding and in their virulence toBiomphalaria glabratasnail hosts, and determined four-week cercarial shedding profiles in F0, F1 and 376 F2 progeny from two independent crosses in inbred snails. Sequencing and linkage analysis revealed that cercarial production is polygenic and controlled by five QTLs. These QTLs act additively, explaining 28.56% of the phenotypic variation. These results demonstrate that the genetic architecture of key traits relevant to schistosome ecology can be dissected using classical linkage mapping approaches.
A novel deep-sea bacterial threonine dehydratase drives cysteine desulfuration and hydrogen sulfide production
Authors: Ma Ning , Sun Yufan , Zhang Wen , Sun Chaomin
Published: December 2020

Cysteine desulfuration is one of the main ways for hydrogen sulfide (H2S) generation in cells and is usually conducted by cystathionine γ-lyase. Herein, we describe a newly discovered deep-sea bacterial threonine dehydratase (psTD), which is surprisingly discovered to drive L-cysteine desulfuration. The mechanisms of psTD catalyzing cysteine desulfuration towards H2S production are first clarifiedin vitroandin vivothrough a combination of genetic and biochemical methods. Furthermore, based on the solved structures of psTD and its various mutants, two or three pockets are found in the active site of psTD, and switch states between inward and outward orientation of a key amino acid R77 determine the open or close status of Pocket III for small molecule exchanges, which further facilitates cysteine desulfuration. Our results reveal the functional diversity and structural specificity of psTD towards L-cysteine desulfuration and H2S formation. Given the broad distribution of psTD homologs in different bacteria, we speculate that some threonine dehydratases have evolved a novel function towards cysteine desulfuration, which benefits the producer to utilize cysteine as a sulfur source for better adapting external environments.
Functional Characterization of a Lassa Virus Fusion Inhibitors Adaptive Mutant
Authors: Guo Jiao , Zhang Guangshun , Liu Yang , Cao Junyuan , Zhang Mengmeng , Lan Xiaohao , Zhang Yueli , Liu Chenchen , Xiao Gengfu , Wang Wei
Published: December 2020

Lassa virus (LASV) glycoprotein complex (GPC) contains retained stable-signal peptide (SSP), GP1, and GP2. SSP interacts with GP2 and provides an interface targeted by numerous fusion inhibitors. Serially passaging of LASV with inhibitors allowed some adaptive mutants to be obtained of which most had mutations located in the transmembrane (TM) domain of GP2. In the current study, we focused on the F446L mutant, which is reported to confer resistance to ST-series inhibitors. We found that F446L conferred cross-resistance to structurally distinct inhibitors. Furthermore, F446L increased the fusion activities of LASV and Mopeia virus GPC, elevating the pH threshold for fusion of LASV and promoting fusion of MOPV at neutral pH. F446L exerted little effect on the pseudotype viral growth profile or thermostability. By introducing other residues to the conserved F446 locus, it was found that this site was less compatible with a similar tyrosine residue and was intolerable to charged residues. These results help characterize the fusion inhibitor target located in the TM domain of GP2, which should be useful for drug and vaccine design.

IMPORTANCE

The LASV SSP-GP2 interface provides an Achilles heel that is targeted by numerous inhibitors. However, the emergence of resistant viruses is a major concern for direct antiviral drugs. In this study, we investigated the F446L mutant located in the GPC TM domain to determine the relationship between drug resistance, membrane fusion activity, viral growth kinetics, and thermostability. These results will be helpful in monitoring drug-resistant variants, as well as the advancement of drug and vaccine design.