bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel copper-sensing two-component system for activating Dsb genes in bacteria
Authors: Yu Liang , Cao Qiao , Chen Weizhong , Yang Nana , Yang Cai-Guang , Ji Quanjiang , Wu Min , Bae Taeok , Lan Lefu
Published: August 2020

Copper is an essential element for biological systems but becomes toxic when present in excess. InPseudomonas aeruginosa, an important human pathogen, the resistance to copper requires the induction ofdsbDEGoperon encoding proteins involved in disulfide-bond formation (Dsb). However, it is unknown how the copper stress induces the transcription of the operon. Here, we report that the exogenous copper induces the transcription of thedsbDEGoperon through a new copper-sensing two-component system named DsbRS. ThedsbRSis divergently transcribed from thedsbDEGoperon, and the response regulator DsbR binds to the intergenic region between the operons. In the absence of copper, the sensor kinase DsbS acts as a phosphatase toward DsbR and thus blocks the transcription of the operons. However, in the presence of copper, the metal ion directly binds to the sensor domain of DsbS, for which the Cys82 residue plays a critical role. The copper-binding appears to inhibit the phosphatase activity of DsbS, leading to activation of DsbR. The copper resistance of thedsbRSknock-out mutant was restored by ectopic expression of thedsbDEGoperon, confirming the critical role of the operon in the resistance to copper. Strikingly, cognates ofdsbRS-dsbDEGpair are widely distributed across eubacteria. Also, a DsbR-binding site, which contains the consensus sequence 5’-TAA-N7-TTAAT-3’, is detected in the promoter region ofdsbDEGhomologs in those species. Thus, regulation of Dsb genes by DsbRS represents a novel mechanism by which bacterial cells cope with copper stress.

Importance

Copper is an essential redox active cofactor that becomes highly cytotoxic when present in excess. Therefore, in order to evade copper toxicity, bacteria must perceive copper stress and tightly regulate genes expression. In the present study, we identify a new copper-sensing two-component system (designated DsbRS) inPseudomonas aeruginosa, an important human pathogen. We provide multiple lines of evidence that upon copper binding to the periplasmic domain of DsbS, its phosphatase activity is blocked, and the phosphorylated DsbR directly activates the transcription of a number of copper-induced genes including those involved in protein disulfide-bond formation (Dsb). This study suggests that regulation of Dsb genes by DsbRS may be an underappreciated regulatory mechanism by which bacteria sense and respond to copper.
Unique roles of vaginalMegasphaeraphylotypes in reproductive health
Authors: Glascock Abigail L. , Jimenez Nicole R. , Boundy Sam , Koparde Vishal N. , Brooks J. Paul , Edwards David J. , Strauss Jerome F. , Jefferson Kimberly K. , Serrano Myrna G. , Buck Gregory A. ,   Vaginal Microbiome Consortium, Fettweis Jennifer M.
Published: August 2020

The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual taxa and their contributions to negative health outcomes have yet to be well characterized. Here, we examine two vaginal bacterial taxa grouped within the genusMegasphaerathat have been previously associated with bacterial vaginosis (BV) and pregnancy complications. Phylogenetic analyses support the classification of these taxa as two distinct species. These two phylotypes,Megasphaeraphylotype 1 (MP1) andMegasphaeraphylotype 2 (MP2), differ in genomic structure and metabolic potential, suggestive of differential roles within the vaginal environment. Further, these vaginal taxa show evidence of genome reduction and changes in DNA base composition, which may be common features of host dependence and/or adaptation to the vaginal environment. In a cohort of 3,870 women, we observed that MP1 has a stronger positive association with bacterial vaginosis whereas MP2 was positively associated with trichomoniasis. MP1, in contrast to MP2 and other common BV-associated organisms, was not significantly excluded in pregnancy. In a cohort of 52 pregnant women, MP1 was both present and transcriptionally active in 75.4% of vaginal samples. Conversely, MP2 was largely absent in the pregnant cohort. This study provides insight into the evolutionary history, genomic potential and predicted functional role of two clinically relevant vaginal microbial taxa.
An automated framework for efficiently designing deep convolutional neural networks in genomics
Authors: Zhang Zijun , Park Christopher Y. , Theesfeld Chandra L. , Troyanskaya Olga G.
Published: August 2020

Convolutional neural networks (CNNs) have become a standard for analysis of biological sequences. Tuning of network architectures is essential for CNN’s performance, yet it requires substantial knowledge of machine learning and commitment of time and effort. This process thus imposes a major barrier to broad and effective application of modern deep learning in genomics. Here, we present AMBER, a fully automated framework to efficiently design and apply CNNs for genomic sequences. AMBER designs optimal models for user-specified biological questions through the state-of-the-art Neural Architecture Search (NAS). We applied AMBER to the task of modelling genomic regulatory features and demonstrated that the predictions of the AMBER-designed model are significantly more accurate than the equivalent baseline non-NAS models and match or even exceed published expert-designed models. Interpretation of AMBER architecture search revealed its design principles of utilizing the full space of computational operations for accurately modelling genomic sequences. Furthermore, we illustrated the use of AMBER to accurately discover functional genomic variants in allele-specific binding and disease heritability enrichment. AMBER provides an efficient automated method for designing accurate deep learning models in genomics.
Cnr2 is important for Ribbon Synapse Maturation and Function in Hair Cells and Photoreceptors
Authors: Colon-Cruz Luis , Rodriguez-Morales Roberto , Santana-Cruz Alexis , Cantres-Velez Juan , Torrado-Tapias Aranza , Yudowski Guillermo , Kensler Robert , Marie Bruno , Burgess Shawn M , Renaud Olivier , Varshney Gaurav K , Behra Martine
Published: August 2020

The role of the cannabinoid receptor 2 (CNR2) is still poorly described in sensory epithelia. We found strong cnr2 expression in hair cells (HCs) of the inner ear and the lateral line (LL), a superficial sensory structure in fish. Next, we demonstrated that sensory synapses in HCs were severely perturbed in larvae lacking cnr2. Appearance and distribution of presynaptic ribbons and calcium channels (Cav1.3) were profoundly altered in mutant animals. Clustering of membrane-associated guanylate kinase (MAGUK) in post-synaptic densities (PSDs) was also heavily affected, suggesting a role for cnr2 for maintaining the sensory synapse. Furthermore, vesicular trafficking in HCs was strongly perturbed suggesting a retrograde action of the endocannabinoid system (ECs) via cnr2 that was modulating HC mechanotransduction. We found similar perturbations in retinal ribbon synapses. Finally, we showed that larval swimming behaviors after sound and light stimulations were significantly different in mutant animals. Thus, we propose that cnr2 is critical for the processing of sensory information in the developing larva
Atypical genomic patterning of the cerebral cortex in autism with poor early language outcome
Authors: Lombardo Michael V. , Eyler Lisa , Pramparo Tiziano , Gazestani Vahid H. , Hagler Donald J. , Chen Chi-Hua , Dale Anders M. , Seidlitz Jakob , Bethlehem Richard A. I. , Bertelsen Natasha , Barnes Cynthia Carter , Lopez Linda , Campbell Kathleen , Lewis Nathan E. , Pierce Karen , Courchesne Eric
Published: August 2020

Cortical regional identities develop through anterior-posterior (A-P) and dorsal-ventral (D-V) prenatal genomic patterning gradients. Here we find that A-P and D-V genomic patterning of cortical surface area (SA) and thickness (CT) is intact in typically developing and autistic toddlers with good language outcome, but is absent in autistic toddlers with poor early language outcome. Genes driving this effect are prominent in midgestational A-P and D-V gene expression gradients and prenatal cell types driving SA and CT variation (e.g., progenitor cells versus excitatory neurons). These genes are also important for vocal learning, human-specific evolution, and prenatal co-expression networks enriched for high-penetrance autism risk genes. Autism with poor early language outcome may be linked to atypical genomic cortical patterning starting in prenatal periods and which impacts later development of regional functional specialization and circuit formation.

One Sentence Summary

Genomic patterning of the cortex is atypical in autistic toddlers with poor early language outcome.
Reactive or transgenic increase in microglial TYROBP reveals a TREM2-independent TYROBP-APOE link in wild-type and Alzheimer’s-related mice
Authors: Audrain Mickael , Haure-Mirande Jean-Vianney , Mleczko Justyna , Wang Minghui , Griffin Jennifer K. , Fraser Paul , Zhang Bin , Gandy Sam , Ehrlich Michelle E.
Published: August 2020

Microglial TYROBP (also known as DAP12) has been identified by computational transcriptomics as a network hub and driver in late-onset sporadic Alzheimer’s disease (AD) and as an important regulator of the microglial environmental sensing function. TYROBP is the transmembrane adaptor of AD-related receptors TREM2 and CR3, but importantly, TYROBP interacts with many other receptors, and little is known about its roles in microglial action and/or in the pathogenesis of AD. Herein, using dual RNAin situhybridization and immunohistochemistry, we demonstrate that endogenousTyrobptranscription is increased specifically in recruited microglia in the brains of wild-type and AD-related mouse models. To determine whether chronically elevated TYROBP might modify microglial phenotype and/or progression of AD pathogenesis, we generated a novel transgenic mouse overexpressing TYROBP in microglia. TYROBP-overexpressing mice were crossed with eitherAPP/PSEN1orMAPTP301Smice, resulting in a decrease of the amyloid burden in the former and an increase of TAU phosphorylation in the latter. Apolipoprotein E (Apoe) transcription was upregulated inMAPTP301Smice overexpressing TYROBP and transcription of genes previously associated withApoe, includingAxl,Ccl2,TgfβandIl6, was altered in bothAPP/PSEN1andMAPTP301Smice overexpressing TYROBP. Lastly,TyrobpandApoemRNAs were clearly increased inTrem2-null mice in microglia recruited around a cortical stab injury or amyloid-β (Aβ) deposits. Conversely, microglialApoetranscription was dramatically diminished whenTyrobpwas absent. Our results provide compelling evidence that TYROBP-APOE signaling in the microglial sensome does not require TREM2. We propose that activation of a TREM2-independent TYROBP-APOE signaling could be an early or even initiating step in the transformation of microglia from the homeostatic phenotype to the Disease-Associated Microglia (DAM) phenotype.
Agonist and antagonist diverted twisting motions of single TRPV1 channel
Authors: Fujimura Shoko , Mio Kazuhiro , Kuramochi Masahiro , Sekiguchi Hiroshi , Ikezaki Keigo , Mio Muneyo , Hengphasatporn Kowit , Shigeta Yasuteru , Kubo Tai , Sasaki Yuji C.
Published: August 2020

Transient receptor potential vanilloid type 1 (TRPV1) channels are activated by heat, vanilloids, and extracellular protons. Cryo-EM has revealed various conformations of TRPV1, and these structures suggest an intramolecular twisting motion in response to ligand binding. However, limited experimental data support this observation. Here we analyzed the intramolecular motion of TRPV1 using diffracted X-ray tracking (DXT). DXT analyzes trajectories of Laue spots generated from attached gold nanocrystals, and provides picometer spatial and microsecond time scale information about intramolecular motion. We observed that both an agonist and a competitive antagonist evoked rotating bias in TRPV1, though these biases were in opposing directions. Furthermore, the rotational bias generated by capsaicin was reversed between the wild type and the capsaicin-insensitive Y511A mutant. Our findings bolster the understanding of the mechanisms used activation and modulation of TRP channels, and this knowledge can be exploited for pharmacological usage such as inhibitor design.
Intracellular accumulation and secretion of hydrophobin-enriched vesicles aid the rapid sporulation of molds
Authors: Cai Feng , Zhao Zheng , Gao Renwei , Ding Mingyue , Jiang Siqi , Gao Qi , Chenthamara Komal , Grujic Marica , Fu Zhifei , Zhang Jian , Przylucka Agnes , Xu Pingyong , Akcapinar Günseli Bayram , Shen Qirong , Druzhinina Irina S.
Published: August 2020

Fungi can rapidly produce large amounts of spores suitable for aerial dispersal. The hydrophobicity of spores is provided by the unique amphiphilic and superior surface-active proteins – hydrophobins (HFBs) – that self-assemble at hydrophobic/hydrophilic interfaces and thus change surface properties. Using the HFB-enriched moldTrichodermaand the HFB-free yeastPichia pastoris, we revealed a distinctive HFB secretory pathway that includes an intracellular accumulation of HFBs in lipid bodies (LBs) that can internalize in vacuoles. The resulting vacuolar multicisternal structures (VMS) are stabilized by HFB layers that line up on their surfaces. These HFB-enriched VMSs can move to the periplasm for secretion or become fused in large tonoplast-like organelles. The latter contributes to the maintenance of turgor pressure required for the erection of sporogenic structures and rapid HFB secretion by squeezing out periplasmic VMSs through the cell wall. Thus, HFBs are essential accessory proteins for the development of aerial hyphae and colony architecture.
Genetic ablation of serotonin receptor 2B improves aortic valve hemodynamics in a high-cholesterol diet mouse model
Authors: Joll J. Ethan , Clark Cynthia R. , Peters Christine S. , Raddatz Michael A. , Bersi Matthew R. , Merryman W. David
Published: August 2020

Calcific aortic valve disease (CAVD) is a deadly disease that is rising in prevalence due to population aging. While the disease is complex and poorly understood, one well-documented driver of valvulopathy is serotonin agonism. Both serotonin overexpression, as seen with carcinoid tumors and drug-related agonism, such as with Fenfluramine use, are linked with various diseases of the valves. Thus, the objective of this study was to determine if genetic ablation or pharmacological antagonism of the 5-HT2Bserotonin receptor (gene:Htr2b) could improve the hemodynamic and histological progression of calcific aortic valve disease.Htr2bmutant mice were crossed withNotch1+/-mice, an established small animal model of CAVD, to determine if genetic ablation affects CAVD progression. To assess the effect of pharmacological inhibition on CAVD progression,Notch1+/-mice were treated with the 5-HT2Breceptor antagonist SB204741. Mice were analyzed using echocardiography, histology, immunofluorescence, and real-time quantitative polymerase chain reaction.Htr2bmutant mice showed lower aortic valve peak velocity and mean pressure gradient – classical hemodynamic indicators of aortic valve stenosis – without concurrent left ventricle change. 5-HT2Breceptor antagonism, however, did not affect hemodynamic progression. Leaflet thickness, collagen density, and CAVD-associated transcriptional markers were not significantly different in any group. This study reveals that genetic ablation ofHtr2battenuates hemodynamic development of CAVD in theNotch1+/-mice, but pharmacological antagonism may require high doses or long-term treatment to slow progression.
Bacterial behavior in human blood reveals complement evaders with persister-like features
Authors: Pont Stéphane , Fraikin Nathan , Caspar Yvan , Van Melderen Laurence , Attrée Ina , Cretin François
Published: August 2020

Abstracts

Bacterial bloodstream infections (BSI) are a major health concern and can cause up to 40% mortality.Pseudomonas aeruginosaBSI is often of nosocomial origin and is associated with a particularly poor prognosis. The mechanism of bacterial persistence in blood is still largely unknown. Here, we analyzed the behavior of a cohort of clinical and laboratoryPseudomonas aeruginosastrains in human blood. In this specific environment, complement was the main defensive mechanism, acting either by direct bacterial lysis or by opsonophagocytosis, which required recognition by immune cells. We found highly variable survival rates for different strains in blood, whatever their origin, serotype, or the nature of their secreted toxins and despite their detection by immune cells. We identified and characterized a complement-tolerant subpopulation of bacterial cells that we named “evaders”. Evaders represented 0.1-0.001% of the initial bacterial load and displayed transient tolerance. Although evaders shared some features with bacterial persisters, which tolerate antibiotic treatment, they appear to have evolved distinct strategies to escape complement. We detected the evaders for five other major human pathogens:Acinetobacter baumannii, Burkholderia multivorans, enteroaggregativeEscherichia coli, Klebsiella pneumoniae, andYersinia enterocolitica. Thus, the evaders could allow the pathogen to persist within the bloodstream, and may be the cause of fatal bacteremia or dissemination, notably in the absence of effective antibiotic treatments.

Author summary for “Complement evaders”

Blood infections by antibiotic resistant bacteria, notablyPseudomonas aeruginosa, are major concerns in hospital settings. The complex interplay betweenP.aeruginosaand the innate immune system in the context of human blood is still poorly understood. By studying the behavior of variousP.aeruginosastrains in human whole blood and plasma, we showed that bacterial strains display different rate of tolerance to the complement system. Despite the complement microbicide activity, most bacteria withstand elimination through phenotypic heterogeneity creating a tiny (<0.1%) subpopulation of transiently tolerant evaders. While genetically identical to the rest of the complement-sensitive population, evaders allow the bacteria to persist in plasma. This phenotypic heterogeneity thus prevents total elimination of the pathogen from the circulation, and represent a new strategy to disseminate within the organism.
Spike protein mutational landscape in India: Could Muller’s ratchet be a future game-changer for COVID-19?
Authors: Banerjee Rachana , Basak Kausik , Ghosh Anamika , Rajachandran Vyshakh , Sureka Kamakshi , Ganguly Debabani , Chattopadhyay Sujay
Published: August 2020

The dire need of effective preventive measures and treatment approaches against SARS-CoV-2 virus, causing COVID-19 pandemic, calls for an in-depth understanding of its evolutionary dynamics with attention to specific geographic locations, since lockdown and social distancing to prevent the virus spread could lead to distinct localized dynamics of virus evolution within and between countries owing to different environmental and host-specific selection pressures. To decipher any correlation between SARS-CoV-2 evolution and its epidemiology in India, we studied the mutational diversity of spike glycoprotein, the key player for the attachment, fusion and entry of virus to the host cell. For this, we analyzed the sequences of 630 Indian isolates as available in GISAID database till June 07, 2020, and detected the spike protein variants to emerge from two major ancestors – Wuhan-Hu-1/2019 and its D614G variant. Average stability of the docked spike protein – host receptor (S-R) complexes for these variants correlated strongly (R2=0.96) with the fatality rates across Indian states. However, while more than half of the variants were found unique to India, 67% of all variants showed lower stability of S-R complex than the respective ancestral variants, indicating a possible fitness loss in recently emerged variants, despite a continuous increase in mutation rate. These results conform to the sharply declining fatality rate countrywide (>7-fold during April 11 – June 28, 2020). Altogether, while we propose the potential of S-R complex stability to track disease severity, we urge an immediate need to explore if SARS-CoV-2 is approaching mutational meltdown in India.

Author summary

Epidemiological features are intricately linked to evolutionary diversity of rapidly evolving pathogens, and SARS-CoV-2 is no exception. Our work suggests the potential of average stability of complexes formed by the circulating spike mutational variants and the human host receptor to track the severity of SARS-CoV-2 infection in a given region. In India, the stability of these complexes for recent variants tend to decrease relative to their ancestral ones, following countrywide declining fatality rate, in contrast to an increasing mutation rate. We hypothesize such a scenario as nascent footprints of Muller’s ratchet, proposing large-scale population genomics study for its validation, since this understanding could lead to therapeutic approaches for facilitating mutational meltdown of SARS-CoV-2, as experienced earlier for influenza A virus.
First report of antiviral activity of carbon nanofibers: Enhancement of the viral inhibition capacity of calcium alginate films
Authors: Sanmartín-Santos Isaías , Gandía-Llop Sofía , Serrano-Aroca Ángel
Published: August 2020

The World Health Organization has called for new effective and affordable alternative antiviral materials for the prevention and treatment of viral infections. In this regard, calcium alginate has previously shown to possesses antiviral activity against the enveloped double-stranded DNA herpes simplex virus type 1. However, non-enveloped viruses are more resistant to inactivation than enveloped ones. Thus, the viral inhibition capacity of calcium alginate and the effect of adding a minuscule amount of carbon nanomaterials (0.1%w/w) have been explored here against a non-enveloped double-stranded DNA virus model for the first time. The results of this study showed that neat calcium alginate films are able to inactivate this type of non-enveloped virus and that including that extremely low percentage of carbon nanofibers significantly enhanced its viral inhibition from ~55.6% to 96.33%. This is the first published study to demonstrate CNFs’ antiviral activity. However, adding this small percentage of graphene oxide did not improve the antiviral activity of calcium alginate, although both composite biomaterials possess antiviral and other outstanding properties very promising for biomedical applications.
Infection and transmission of SARS-CoV-2 depends on heparan sulfate proteoglycans
Authors: Bermejo-Jambrina Marta , Eder Julia , Kaptein Tanja M. , van Hamme John L. , Helgers Leanne C. , Vlaming Killian E. , Brouwer Philip J.M. , Vlaar Alexander P.J. , van Baarle Frank E.H.P. , Spaargaren Marcel , de Bree Godelieve J. , Nijmeijer Bernadien M. , Kootstra Neeltje A. , van Gils Marit J. , Sanders Rogier W. , Geijtenbeek Teunis B. H.
Published: August 2020

The current pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and outbreaks of new variants highlight the need for preventive treatments. Here we identified heparan sulfate proteoglycans as attachment receptors for SARS-CoV-2. Notably, neutralizing antibodies against SARS-CoV-2 isolated from COVID-19 patients interfered with SARS-CoV-2 binding to heparan sulfate proteoglycans, which might be an additional mechanism of antibodies to neutralize infection. SARS-CoV-2 binding to and infection of epithelial cells was blocked by low molecular weight heparins (LMWH). Although dendritic cells (DCs) and mucosal Langerhans cells (LCs) were not infected by SARS-CoV-2, both DC subsets efficiently captured SARS-CoV-2 via heparan sulfate proteoglycans, and transmitted the virus to ACE2-positive cells. Moreover, human primary nasal cells were infected by SARS-CoV-2 and infection was blocked by pre-treatment with LMWH. These data strongly suggest that heparan sulfate proteoglycans are important attachment receptors facilitating infection and transmission, and support the use of LMWH as prophylaxis against SARS-CoV-2 infection.
Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2
Authors: Chen Catherine Z. , Shinn Paul , Itkin Zina , Eastman Richard T. , Bostwick Robert , Rasmussen Lynn , Huang Ruili , Shen Min , Hu Xin , Wilson Kelli M. , Brooks Brianna , Guo Hui , Zhao Tongan , Klump-Thomas Carleen , Simeonov Anton , Michael Samuel G. , Lo Donald C. , Hall Matthew D. , Zheng Wei
Published: August 2020

Drug repurposing is a rapid approach to identifying therapeutics for the treatment of emerging infectious diseases such as COVID-19. To address the urgent need for treatment options, we carried out a quantitative high-throughput screen using a SARS-CoV-2 cytopathic assay with a compound collection of 8,810 approved and investigational drugs, mechanism-based bioactive compounds, and natural products. Three hundred and nineteen compounds with anti-SARS-CoV-2 activities were identified and confirmed, including 91 approved drug and 49 investigational drugs. Among these confirmed compounds, the anti-SARS-CoV-2 activities of 230 compounds, including 38 approved drugs, have not been previously reported. Chlorprothixene, methotrimeprazine, and piperacetazine were the three most potent FDA approved drugs with anti-SARS-CoV-2 activities. These three compounds have not been previously reported to have anti-SARS-CoV-2 activities, although their antiviral activities against SARS-CoV and Ebola virus have been reported. These results demonstrate that this comprehensive data set of drug repurposing screen for SARS-CoV-2 is useful for drug repurposing efforts including design of new drug combinations for clinical trials.
IFITM proteins promote SARS-CoV-2 infection and are targets for virus inhibition
Authors: Bozzo Caterina Prelli , Nchioua Rayhane , Volcic Meta , Krüger Jana , Heller Sandra , Stürzel Christina M. , Kmiec Dorota , Conzelmann Carina , Müller Janis , Zech Fabian , Schütz Desiree , Koepke Lennart , Braun Elisabeth , Groß Rüdiger , Wettstein Lukas , Weil Tatjana , Weiß Johanna , Sauter Daniel , Münch Jan , Diofano Federica , Goffinet Christine , Catanese Alberto , Schön Michael , Böckers Tobias , Stenger Steffen , Sato Kei , Just Steffen , Kleger Alexander , Sparrer Konstantin M.J. , Kirchhoff Frank
Published: August 2020

Interferon-induced transmembrane proteins (IFITMs 1, 2 and 3) are thought to restrict numerous viral pathogens including severe acute respiratory syndrome coronaviruses (SARS-CoVs). However, most evidence comes from single-round pseudovirus infection studies of cells that overexpress IFITMs. Here, we verified that artificial overexpression of IFITMs blocks SARS-CoV-2 infection. Strikingly, however, endogenous IFITM expression was essential for efficient infection of genuine SARS-CoV-2 in human lung cells. Our results indicate that the SARS-CoV-2 Spike protein interacts with IFITMs and hijacks them for efficient viral entry. IFITM proteins were expressed and further induced by interferons in human lung, gut, heart and brain cells. Intriguingly, IFITM-derived peptides and targeting antibodies inhibited SARS-CoV-2 entry and replication in human lung cells, cardiomyocytes and gut organoids. Our results show that IFITM proteins are important cofactors for SARS-CoV-2 infection of human cell types representing in vivo targets for viral transmission, dissemination and pathogenesis and suitable targets for therapeutic approaches.
Enhanced reinstatement of naturalistic event memories due to hippocampal-network-targeted stimulation
Authors: Hebscher Melissa , Kragel James E. , Kahnt Thorsten , Voss Joel L.
Published: August 2020

Episodic memory involves the reinstatement of distributed patterns of brain activity present when events were initially experienced. The hippocampus is thought to coordinate reinstatement via its interactions with a network of brain regions, but this hypothesis has not been causally tested in humans. The current study directly tested the involvement of the hippocampal network in reinstatement using network-targeted noninvasive stimulation. We measured reinstatement of multi-voxel patterns of fMRI activity during encoding and retrieval of naturalistic video clips depicting everyday activities. Reinstatement of video-specific activity patterns was robust in posterior-parietal and occipital areas previously implicated in event reinstatement. Theta-burst stimulation targeting the hippocampal network increased videospecific reinstatement of fMRI activity patterns in occipital cortex and improved memory accuracy relative to stimulation of a control out-of-network location. Furthermore, stimulation targeting the hippocampal network influenced the trial-by-trial relationship between hippocampal activity during encoding and later reinstatement in occipital cortex. These findings implicate the hippocampal network in the reinstatement of spatially distributed patterns of event-specific activity, and identify a role for the hippocampus in encoding complex naturalistic events that later undergo cortical reinstatement.
Fitting side-chain NMR relaxation data using molecular simulations
Authors: Kümmerer Felix , Orioli Simone , Harding-Larsen David , Hoffmann Falk , Gavrilov Yulian , Teilum Kaare , Lindorff-Larsen Kresten
Published: August 2020

Proteins display a wealth of dynamical motions that can be probed using both experiments and simulations. We present an approach to integrate side chain NMR relaxation measurements with molecular dynamics simulations to study the structure and dynamics of these motions. The approach, which we term ABSURDer (Average Block Selection Using Relaxation Data with Entropy Restraints) can be used to find a set of trajectories that are in agreement with relaxation measurements. We apply the method to deuterium relaxation measurements in T4 lysozyme, and show how it can be used to integrate the accuracy of the NMR measurements with the molecular models of protein dynamics afforded by the simulations. We show how fitting of dynamic quantities leads to improved agreement with static properties, and highlight areas needed for further improvements of the approach.
Activation of VTA GABA Neurons Disrupts Reward Seeking by Altering Temporal Processing
Authors: Shields Andrea K. , Suarez Mauricio , Wakabayashi Ken T. , Bass Caroline E.
Published: August 2020

The role of ventral tegmental area (VTA) dopamine in reward, cue processing, and interval timing is well characterized. Using a combinatorial viral approach to target activating DREADDs (DesignerReceptorsExclusivelyActivated byDesignerDrugs, hM3D) to GABAergic neurons in the VTA of male rats, we previously showed that activation disrupts responding to reward-predictive cues. Here we explored how VTA GABA neurons influence the perception of time in two fixed interval (FI) tasks, one where the reward or interval is not paired with predictive cues (Non-Cued FI), and another where the start of the FI is signaled by a constant tone that continues until the rewarded response is emitted (Cued FI). Under vehicle conditions in both tasks, responding was characterized by “scalloping” over the 30s FI, in which responding increased towards the end of the FI. However, when VTA GABA neurons were activated in the Non-Cued FI, the time between the end of the 30s interval and when the rats made a reinforced response increased. Additionally, post-reinforcement pauses and overall session length increased. In the Cued FI task, VTA GABA activation produced erratic responding, with a decrease in earned rewards. Thus, while both tasks were disrupted by VTA GABA activation, responding that is constrained by a cue was more sensitive to this manipulation, possibly due to convergent effects on timing and cue processing. Together these results demonstrate that VTA GABA activity disrupts the perception of interval timing, particularly when the timing is set by cues.
Machine learning optimization of peptides for presentation by class II MHCs
Authors: Dai Zheng , Huisman Brooke D. , Zeng Haoyang , Carter Brandon , Jain Siddhartha , Birnbaum Michael E. , Gifford David K.
Published: August 2020

T cells play a critical role in normal immune responses to pathogens and cancer and can be targeted to MHC-presented antigens via interventions such as peptide vaccines. Here, we present a machine learning method to optimize the presentation of peptides by class II MHCs by modifying the peptide’s anchor residues. Our method first learns a model of peptide affinity for a class II MHC using an ensemble of deep residual networks, and then uses the model to propose anchor residue changes to improve peptide affinity. We use a high throughput yeast display assay to show that anchor residue optimization successfully improved peptide binding.
Human essentiality genes and targeted oncology therapies
Authors: Harper Andrew R. , McDermott Ultan , Petrovski Slavé
Published: August 2020

Human essentiality genes are significantly enriched in targeted therapies successfully used in oncology. Embedding human essentiality metrics into discovery pipelines could optimise the delivery of highly effective targeted therapies among clinical development strategies.
Links between mouse and vole social networks and their gut microbiomes support predictions from metacommunity theory
Authors: Jameson Joël W. , Kembel Steven W. , Réale Denis
Published: August 2020

Metacommunity theory predicts that strongly connected individuals will harbour similar gut microbiomes (GMs) and affiliating with more individuals should increase GM diversity. Additionally, cross-species bacterial transmission may play a role in how interspecific interactions affect host community dynamics. We tracked sympatric mice (Peromyscus maniculatus) and voles (Myodes gapperi) and constructed social networks for each species and both species together. We tested whether: 1) similarity in GM composition between individuals correlates with their social proximity within and across species; 2) GM diversity correlates with a host’s number of conspecific or heterospecific neighbours. We could not differentiate associations between GM composition and mouse social proximity or habitat. In voles, social proximity explained part of the GM composition. GM composition associated with interspecific social proximity, and mouse GM diversity correlated with number of vole neighbours. Contributions of host-host bacterial transmission to the GM partly follow metacommunity theory but depend on host species.
ICA-based Denoising Strategies in Breath-Hold Induced Cerebrovascular Reactivity Mapping with Multi Echo BOLD fMRI
Authors: Moia Stefano , Termenon Maite , Uruñuela Eneko , Chen Gang , Stickland Rachael C. , Bright Molly G. , Caballero-Gaudes César
Published: August 2020

Performing a BOLD functional MRI (fMRI) acquisition during breath-hold (BH) tasks is a non-invasive, robust method to estimate cerebrovascular reactivity (CVR). However, movement and breathing-related artefacts caused by the BH can substantially hinder CVR estimates due to their high temporal collinearity with the effect of interest, and attention has to be paid when choosing which analysis model should be applied to the data. In this study, we evaluate the performance of multiple analysis strategies based on lagged general linear models applied on multi-echo BOLD fMRI data, acquired in ten subjects performing a BH task during ten sessions, to obtain subjectspecific CVR and haemodynamic lag estimates. The evaluated approaches range from conventional regression models including drifts and motion timecourses as nuisance regressors applied on singleecho or optimally-combined data, to more complex models including regressors obtained from multi-echo independent component analysis with different grades of orthogonalization in order to preserve the effect of interest, i.e. the CVR. We compare these models in terms of their ability to make signal intensity changes independent from motion, as well as the reliability as measured by voxelwise intraclass correlation coefficients of both CVR and lag maps over time. Our results reveal that a conservative independent component analysis model applied on the optimally-combined multi-echo fMRI signal offers the largest reduction of motion-related effects in the signal, while yielding reliable CVR amplitude and lag estimates, although a conventional regression model applied on the optimally-combined data results in similar estimates. This work demonstrate the usefulness of multi-echo based fMRI acquisitions and independent component analysis denoising for precision mapping of CVR in single subjects based on BH paradigms, fostering its potential as a clinically-viable neuroimaging tool for individual patients. It also proves that the way in which data-driven regressors should be incorporated in the analysis model is not straight-forward due to their complex interaction with the BH-induced BOLD response.
A distinct growth physiology enhances bacterial growth under rapid nutrient fluctuations
Authors: Nguyen Jen , Fernandez Vicente , Pontrelli Sammy , Sauer Uwe , Ackermann Martin , Stocker Roman
Published: August 2020

It has been long known that bacteria coordinate their physiology with environmental nutrient, yet our current understanding offers little intuition for how bacteria respond to the second-to-minute scale fluctuations in nutrient concentration characteristic of many microbial habitats. To investigate the effects of rapid nutrient fluctuations on bacterial growth, we coupled custom microfluidics with single-cell microscopy to quantify the growth rate ofE. coliexperiencing 30 s to 60 min nutrient fluctuations. Compared to steady environments of equal average concentration, fluctuating environments reduced growth rate by up to 50%. However, measured reductions in growth rate were only 38% of the growth loss predicted from single nutrient shifts — an enhancement produced by the distinct growth response of cells grown in environments that fluctuate rather than shift once. We report an unexpected physiology adapted for growth in nutrient fluctuations and implicate nutrient timescale as a critical environmental parameter beyond nutrient concentration and source.
An inexpensive semi-automated sample processing pipeline for cell-free RNA
Authors: Moufarrej Mira N. , Quake Stephen R.
Published: August 2020

Despite advances in automated liquid handling and microfluidics, preparing samples for RNA sequencing at scale generally requires expensive equipment, which is beyond the reach of many academic labs. Manual sample preparation remains a slow, expensive, and error-prone process. Here, we describe a low-cost, semi-automated pipeline to extract cell-free RNA (cfRNA) that like many RNA isolation protocols, can be decomposed into three subparts – RNA extraction, DNA digestion, and RNA cleaning and concentration. RT-qPCR data using a synthetic spike-in confirms comparable RNA quality as compared to manual sample processing, the gold-standard used in our prior work. The semi-automated pipeline also shows striking improvement in sample throughput (+12x), time spent (−11x), cost (−3x), and biohazardous waste produced (−4x) as compared to its manual counterpart. In total, this protocol enables cfRNA extraction from 96 samples simultaneously in 4.5 hours; in practice, this dramatically improves time to results as demonstrated in our recent work [1] where it was used to process 404 samples in 27 hours. Importantly, any lab already has most of the parts required (manual pipette, corresponding tips and kits) to build a semi-automated sample processing pipeline of their own and would only need to purchase or 3D-print a few extra parts ($5.5K total). This pipeline is also generalizable for many nucleic acid extraction applications, thereby increasing the scale of studies, which can be performed in small research labs.
Boosting photosynthetic machinery and defense priming with chitosan application on tomato plants infected withFusarium oxysporumf. sp.lycopersici
Authors: Carmona Sandra L. , del Pilar Villarreal-Navarrete Andrea , Burbano-David Diana , Gómez-Marroquín Magda , Torres-Rojas Esperanza , Soto-Suárez Mauricio
Published: August 2020

Physiological processes of plants infected by vascular pathogens are mainly affected by vascular bundle obstruction, decreasing the absorption of water and nutrients and gas exchange by stomatal closure, and inducing oxidative cascades and PSII alterations. Chitosan, a derivative of chitin present in the cell wall of some organisms including fungi, induces plant defense responses, activating systemic resistance. In this study, the effect of chitosan on the physiological and molecular responses of tomato plants infected withFusarium oxysporumf. sp.lycopersici(Fol) was studied, evaluating the maximum potential quantum efficiency of PSII photochemistry (Fv/Fm), photochemical efficiency of PSII (Y(II)), photochemical quenching (qP), stomatal conductance (gs), relative water content (RWC), proline content, photosynthetic pigments, dry mass, and differential gene expression (PAL, LOXA, ERF1,andPR1) of defense markers. A reduction of 70% in the incidence and 91% in the severity of the disease was achieved in plants treated with chitosan, mitigating the damage caused byFolon Fv/Fm, Y(II), and chlorophyll contents by 23%, 36%, and 47%, respectively. Less impact was observed on qP, gs, RWC, and dry mass (16%, 11%, and 26%, respectively). Chitosan-treated andFol-infected plants over-expressedPR1agene suggesting a priming-associated response. These results demonstrate the high potential of chitosan to protect tomato plants againstFolby regulating physiological and molecular responses in tomato plants.
Color compensation in anomalous trichromats assessed with fMRI
Authors: Tregillus Katherine E.M. , Isherwood Zoey J. , Vanston John E. , Engel Stephen A. , MacLeod Donald I.A. , Kuriki Ichiro , Webster Michael A.
Published: August 2020

Anomalous trichromacy is a common form of congenital color-deficiency resulting from a genetic alteration in the photopigments of the eye’s light receptors. The changes reduce sensitivity to reddish and greenish hues, yet previous work suggests that these observers may experience the world to be more colorful than their altered receptor sensitivities would predict, potentially indicating an amplification of post-receptoral signals. However, past evidence suggesting such a gain adjustment rests on subjective measures of color appearance or salience. We directly tested for neural amplification by using fMRI to measure cortical responses in color-anomalous and normal control observers. Color contrast response functions were measured in two experiments with different tasks to control for attentional factors. Both experiments showed a predictable reduction in chromatic responses for anomalous trichromats in primary visual cortex. However, in later areas V2v and V3v, chromatic responses in the two groups were indistinguishable. Our results provide direct evidence for neural plasticity that compensates for the deficiency in the initial receptor color signals and suggest that the site of this compensation is in early visual cortex.
Epigenetic memory as a time integral over prior history of Polycomb phase separation
Authors: Eeftens Jorine M. , Kapoor Manya , Brangwynne Clifford P.
Published: August 2020

Structural organization of the genome into transcriptionally active euchromatin and silenced heterochromatin is essential for eukaryotic cell function. Heterochromatin is a more compact form of chromatin, and is associated with characteristic post-translational histone modifications and chromatin binding proteins. Phase-separation has recently been suggested as a mechanism for heterochromatin formation, through condensation of heterochromatin associated proteins. However, it is unclear how phase-separated condensates can contribute to stable and robust repression, particularly for heritable epigenetic changes. The Polycomb complex PRC1 is known to be key for heterochromatin formation, but the multitude of Polycomb proteins has hindered our understanding of their collective contribution to chromatin repression. Here, we take a quantitative live cell imaging approach to show that PRC1 proteins form multicomponent condensates through hetero-oligomerization. They preferentially seed at H3K27me3 marks, and subsequently write H2AK119Ub marks. Using optogenetics to nucleate local Polycomb condensates, we show that Polycomb phase separation can induce chromatin compaction, but phase separation is dispensable for maintenance of the compacted state. Our data are consistent with a model in which the time integral of historical Polycomb phase separation is progressively recorded in repressive histone marks, which subsequently drive chromatin compaction. These findings link the equilibrium thermodynamics of phase separation with the fundamentally non-equilibrium concept of epigenetic memory.
Probabilistic Framework for Integration of Mass Spectrum and Retention Time Information in Small Molecule Identification
Authors: Bach Eric , Rogers Simon , Williamson John , Rousu Juho
Published: August 2020

Motivation

Identification of small molecules in a biological sample remains a major bottleneck in molecular biology, despite a decade of rapid development of computational approaches for predicting molecular structures using mass spectrometry (MS) data. Recently, there has been increasing interest in utilizing other information sources, such as liquid chromatography (LC) retention time (RT), to improve the MS based identifications.

Results

We put forward a probabilistic modelling framework to integrate MS and RT data of multiple features in an LC-MS experiment. We model the MS measurements and all pairwise retention order information as a Markov random field and use efficient approximate inference for scoring and ranking potential molecular structures. Our experiments show improved identification accuracy by combining tandem mass spectrometry data (MS2) and retention orders using our approach, thereby outperforming state-of-the-art methods. Furthermore, we demonstrate the benefit of our model when only a subset of LC-MS features have MS2measurements available besides MS1.

Availability and implementation

Software and data is freely available athttps://github.com/aalto-ics-kepaco/msms_rt_score_integration.

Contact

eric.bach@aalto.fi