bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs
Authors: Zhang Meng , Gui Miao , Wang Zi-Fu , Gorgulla Christoph , Yu James J , Wu Hao , Sun Zhen-yu , Klenk Christoph , Merklinger Lisa , Morstein Lena , Hagn Franz , Plückthun Andreas , Brown Alan , Nasr Mahmoud L , Wagner Gerhard
Published: June 2020

G protein coupled receptors (GPCRs) are the largest superfamily of transmembrane proteins and the targets of over 30% of currently marketed pharmaceuticals1,2. Although several structures have been solved for GPCR-G protein complexes3–17, structural studies of the complex in a physiological lipid membrane environment are lacking. Additionally, most previous studies required additional antibodies/nanobodies and/or engineered G proteins for complex stabilization. In the absence of a native complex structure, the underlying mechanism of G protein activation leading to GDP/GTP exchange remains unclear. Here, we report cryo-EM structures of lipid bilayer-bound complexes of neurotensin, neurotensin receptor 1, and Gαi1β1γ1 protein in two conformational states, resolved to 4.1 and 4.2 Å resolution. The structures were determined without any stabilizing antibodies/nanobodies, and thus provide a native-like platform for understanding the structural basis of GPCR-G protein complex formation. Our structures reveal an extended network of protein-protein interactions at the GPCR-G protein interface compared to in detergent micelles, defining roles for the lipid membrane in modulating the structure and dynamics of complex formation, and providing a molecular explanation for the stronger interaction between GPCR and G protein in lipid bilayers. We propose a detailed allosteric mechanism for GDP release, providing new insights into the activation of G proteins for downstream signaling under near native conditions.
Not quite human, not quite machine: Electrophysiological responses to robot faces
Authors: Geiger Allie R. , Balas Benjamin
Published: June 2020

Face recognition is supported by selective neural mechanisms that are sensitive to various aspects of facial appearance. These include ERP components like the P100, N170, and P200 which exhibit different patterns of selectivity for various aspects of facial appearance. Examining the boundary between faces and non-faces using these responses is one way to develop a more robust understanding of the representation of faces in visual cortex and determine what critical properties an image must possess to be considered face-like. Here, we probe this boundary by examining how face-sensitive ERP components respond to robot faces. Robot faces are an interesting stimulus class because they can differ markedly from human faces in terms of shape, surface properties, and the configuration of facial features, but are also interpreted as social agents in a range of settings. In two experiments, we examined how the P100 and N170 responded to human faces, robot faces, and non-face objects (clocks). We found that robot faces elicit intermediate responses from face-sensitive components relative to non-face objects and both real and artificial human faces (Exp. 1), and also that the face inversion effect was only partly evident in robot faces (Exp. 2). We conclude that robot faces are an intermediate stimulus class that offers insight into the perceptual and cognitive factors that affect how social agents are identified and categorized.
Molecular Dynamics Simulations of Bacterial Outer Membrane Lipid Extraction: Adequate Sampling?
Authors: Shearer Jonathan , Marzinek Jan K. , Bond Peter J. , Khalid Syma
Published: June 2020

The outer membrane of Gram-negative bacteria is almost exclusively composed of lipopolysaccharide in its outer leaflet, whereas the inner leaflet contains a mixture of phospholipids. Lipopolysaccharide diffuses at least an order of magnitude slower than phospholipids, which can cause issues for molecular dynamics simulations in terms of adequate sampling. Here we test a number of simulation protocols for their ability to achieve convergence with reasonable computational effort using the MARTINI coarse-grained force-field. This is tested in the context both of potential of mean force (PMF) calculations for lipid extraction from membranes, and of lateral mixing within the membrane phase. We find that decoupling the cations that cross-link the lipopolysaccharide headgroups from the extracted lipid during PMF calculations is the best approach to achieve convergence comparable to that for phospholipid extraction. We also show that lateral lipopolysaccharide mixing/sorting is very slow and not readily addressable even with Hamiltonian replica exchange. We discuss why more sorting may be unrealistic for the short (microseconds) timescales we simulate and provide an outlook for future studies of lipopolysaccharide-containing membranes.
An ABA Synthesis Enzyme AlleleOsNCED2Promotes the Aerobic Adaption in Upland Rice
Authors: Huang Liyu , Bao Yachong , Qin Shiwen , Ning Min , Lyu Jun , Zhang Shilai , Huang Guangfu , Zhang Jing , Wang Wensheng , Fu Binying , Hu Fengyi
Published: June 2020

There are two ecotypes, upland rice and irrigate rice, during its evolution in rice. Upland rice exhibits aerobic adaptive phenotype via its stronger root system and more rapid drought responses compared with its counterpart, irrigated rice. We assessed the functional variation and applications of the aerobic adaptive alleleOsNCED2Tcloned from IRAT104 which is a cultivar of upland rice.OsNCED2-overexpressing transgenic rice andOsNCED2T-NILs exhibited significantly higher ABA contents at the seedling and reproductive stages, which can improve root development (RD) and drought tolerance (DT) to promote aerobic adaptation in upland rice. RNA-Seq-based expression profiling of transgenic versus wild-type rice identifiedOsNCED2-mediated pathways that regulate RD and DT. Meanwhile,OsNCED2-overexpressing rice exhibited significantly increased reactive oxygen species (ROS)-scavenging abilities and transcription levels of many stress- and development-related genes, which regulate RD and DT. A SNP mutation (C to T) from irrigated rice to upland rice, caused the functional variation ofOsNCED2, and the enhanced RD and DT mediated by this site under aerobic conditions could promote higher yield of upland rice. These results show thatOsNCED2T, through ABA synthesis, positively modulates RD and DT which confers aerobic adaptation in upland rice and might serve as a novel gene for breeding aerobic adaptive or water-saving rice.
Phytohormone production by the arbuscular mycorrhizal fungusRhizophagus irregularis
Authors: Pons Simon , Fournier Sylvie , Chervin Christian , Bécard Guillaume , Rochange Soizic , Frey Nicolas Frei Dit , Pagès Virginie Puech
Published: June 2020

Arbuscular mycorrhizal symbiosis is a mutualistic interaction between most land plants and fungi of the glomeromycotina subphylum. The initiation, development and regulation of this symbiosis involve numerous signalling events between and within the symbiotic partners. Among other signals, phytohormones are known to play important roles at various stages of the interaction. During presymbiotic steps, plant roots exude strigolactones which stimulate the fungus, and favour the initiation of symbiosis. At later stages, different plant hormone classes can act as positive or negative regulators of the interaction. Although the fungus is known to reciprocally emit regulatory signals, its potential contribution to the phytohormonal pool has received little attention, and has so far only been addressed by indirect assays. In this study, using mass spectrometry, we analyzed phytohormones released into the medium by germinated spores of the arbuscular mycorrhizal fungusRhizophagus irregularis. We detected the presence of a cytokinin (isopentenyl-adenosine) and an auxin (indole-acetic acid). In addition, we identified a gibberellin (gibberellic acid 4) in spore extracts. We also used gas chromatography to show thatR. irregularisproduces ethylene from methionine and the α-keto γ-methylthiobutyric acid pathway. These results highlight the possibility for AM fungi to use phytohormones to interact with their host plants, or to regulate their own development.
A split methyl halide transferase AND gate that reports by synthesizing an indicator gas
Authors: Fulk Emily M. , Huh Dongkuk , Atkinson Joshua T. , Lie Margaret , Masiello Caroline A. , Silberg Jonathan J.
Published: June 2020

It is challenging to detect microbial reactions in highly opaque or autofluorescent environments like soils, seawater, and wastewater. To develop a simple approach for monitoring post-translational reactions within microbes situated in environmental matrices, we designed a methyl halide transferase (MHT) fragment complementation assay that reports by synthesizing an indicator gas. We show that backbone fission within regions of high sequence variability in the Rossmann-fold domain yields split MHT (sMHT) AND gates whose fragments cooperatively associate to synthesize CH3Br. Additionally, we identify a sMHT whose fragments require fusion to pairs of interacting partner proteins for maximal activity. We also show that sMHT fragments fused to FKBP12 and the FKBP-rapamycin binding domain of mTOR display significantly enhanced CH3Br production in the presence of rapamycin. This gas production is reversed in the presence of the competitive inhibitor of FKBP12/FKPB dimerization, indicating that sMHT is a reversible reporter of post-translational reactions. This sMHT represents the first genetic AND gate that can report on protein-protein interactions via an indicator gas. Because indicator gases can be measured in the headspaces of complex environmental samples, this protein fragment complementation assay should be useful for monitoring the dynamics of diverse molecular interactions within microbes situated in hard-to-image marine and terrestrial matrices.
Campaign-Based Citizen Science for Environmental Mycology: the “Science Solstice” and “Summer Soil-stice” Projects to Assess Drug Resistance in Air and SoilborneAspergillus fumigatus
Authors: Shelton Jennifer M. G. , Fisher Matthew C. , Singer Andrew C.
Published: June 2020

Citizen science projects are often undertaken for ecological and environmental research purposes but also have great potential for use in microbiology research to track the emergence and spread of pathogens in the environment. ‘Science Solstice’ and ‘Summer Soil-stice’ are mycology citizen science projects aimed at assessing drug resistance inAspergillus fumigatusfungal spores found in air and soil, respectively, in the United Kingdom (UK).A. fumigatusplays an important role in the environment as a decomposer of plant material, but is also an opportunistic human lung pathogen. Infection with drug-resistant spores can lead to a worse clinical outcome for the patient.

On the first four solstice and equinox days between June 2018 and June 2019, volunteers were asked to collect air samples from their homes and workplaces and return them to our lab in Freepost envelopes. An additional round of samples was requested from volunteer’s gardens and/or compost on the June 2019 solstice. In total, 787 volunteers returned 2,132 air samples and 509 soil samples, which grew a total of 7,991A. fumigatuscolonies. The estimated total cost of the study was £2,650; the equivalent of 33 pence perA. fumigatuscolony grown.

Incorporating citizen science into the environmental surveillance of drug-resistantA. fumigatusallowed for the simultaneous collection of hundreds of environmental samples across the entire UK on the same day. The insights generated from this study would not be practical in the absence of public participation and offers opportunities to ask scientific questions that were previously unaskable.
Task Related Neural Activity Following Primary Motor Cortical Ischemic Injury in Rats
Authors: Pack Andrea R. , Murphy Max D. , Barbay Scott , Nudo Randolph J. , Guggenmos David J.
Published: June 2020

Acquired injuries to primary motor cortex (M1) contribute to motor impairment and disability. Functional recovery is predicated on the reorganization of spared areas, which has been demonstrated through cortical motor map representations and neuroanatomical projection and termination patterns. The purpose of this study was to understand how neurophysiological outputs of spared motor areas relate to motor recovery of a skilled reach task following an ischemic infarct to M1. We examined changes in single unit activity within ipsilesional pre-motor (PM) and contralesional M1 cortices of rats during a behavioral task after a unilateral ischemic injury to ipsilesional M1. The data show a shift in neuronal firing patterns in the contralateral PM and ipsilateral M1 during behavioral recovery in lesion rats compared to a non-lesion control group, suggesting that spike-timing properties are altered in specific phases of the task, and that this altered activity may support spontaneous restoration of motor behavior.

SIGNIFICANCE STATEMENT

Following ischemic stroke to primary motor cortex (M1), motor recovery is associated with reorganization of spared cortical motor areas in injured and spared hemispheres. Currently, it is unclear how cortical plasticity within spared motor areas relates to motor recovery. This study examines how task-related neural activity within spared motor areas in rats correlates with motor restoration of a skilled reach task following an ischemic infarct to M1. The data suggest contralateral pre-motor and ipsilateral M1 alter their neural response profiles with respect to the timing of a motor task during recovery. To our knowledge, this is the first demonstration of a compensatory single-spike neurophysiological mechanism that may explain how remote, spared cortical areas contribute to functional recovery after M1 injury.
The impact of interactions on invasion and colonization resistance in microbial communities
Authors: Kurkjian Helen , Akbari M. Javad , Momeni Babak
Published: June 2020

In human microbiota, the prevention or promotion of invasions can be crucial to human health. Invasion outcomes, in turn, are impacted by the composition of resident communities and interactions among resident microbes. Microbial communities differ from communities composed of other types of organisms in that many microbial interactions are mediated by chemicals that are released into or consumed from the environment. We ask what determines invasion outcomes in such microbial communities. Here, we use a model based on chemical-mediated interactions among microbial species to assess the impact of positive and negative interactions on invasion outcomes. We classified invasion outcomes as resistance, augmentation, displacement, or disruption depending on whether the richness of the resident community was maintained or dropped and whether the invader was maintained in the community or went extinct. We found that as the number of invaders increased relative to size of the resident community, resident communities were increasingly disrupted. As facilitation of the invader by the resident community increased, resistance outcomes were replaced by displacement and augmentation. By contrast, as facilitation increased among residents, displacement outcomes shifted to resistance. When facilitation of the resident community by the invader was eliminated, augmentation outcomes were replaced by displacement outcomes, while when inhibition of residents by invaders was eliminated, there was little change in the frequency of invasion outcomes. These results suggest that a better understanding of the chemical-mediated interactions within resident communities and between residents and invaders is crucial to predicting the success of invasions into microbial communities.
Effects of a Contusive Spinal Cord Injury on Spinal Motor Neuron Activity and Conduction Time in Rats
Authors: Borrell Jordan A. , Krizsan-Agbas Dora , Nudo Randolph J. , Frost Shawn B.
Published: June 2020

Objective

The purpose of this study was to determine the effects of spinal cord injury (SCI) on spike activity evoked in the hindlimb spinal cord of the rat from cortical electrical stimulation.

Approach

Adult, male, Sprague Dawley rats were randomly assigned to a Healthy or SCI group. SCI rats were given a 175 kDyn dorsal midline contusion injury at the level of the T8 vertebrae. At four weeks post-SCI, intracortical microstimulation (ICMS) was delivered at several sites in the hindlimb motor cortex of anesthetized rats, and evoked neural activity was recorded from corresponding sites throughout the dorsoventral depths of the spinal cord and EMG activity from hindlimb muscles.

Main results

In healthy rats, post-ICMS spike histograms showed reliable, evoked spike activity during a short-latency epoch 10-12 ms after the initiation of the ICMS pulse train (short). Longer latency spikes occurred between ~20-60 ms, generally following a Gaussian distribution, rising above baseline at time LON, followed by a peak response (Lp), and then falling below baseline at time LOFF. EMG responses occurred between LONand Lp(25-27 ms). In SCI rats, short-latency responses were still present, long-latency responses were disrupted or eliminated, and EMG responses were never evoked. The retention of the short-latency responses indicates that spared descending spinal fibers, most likely via the cortico-reticulospinal pathway, can still depolarize spinal cord motor neurons after a dorsal midline contusion injury.

Significance

This study provides novel insights into the role of alternate pathways for voluntary control of hindlimb movements after SCI that disrupts the corticospinal tract in the rat.
Enhanced analgesic cholinergic tone after neuropathy
Authors: Dhanasobhon Dhanasak , Medrano Maria-Carmen , Moreno-Lopez Yunuen , Kavraal Sehrazat , Bichara Charlotte , Schlichter Rémy , Inquimbert Perrine , Yalcin Ipek , Cordero-Erausquin Matilde
Published: June 2020

At the spinal cord level, a tone of endogenous acetylcholine (ACh) modulates nociceptive sensory processing. Increasing the level of spinal ACh induces analgesia in naïve animals or in situation of acute pain in the clinics, but whether this is still the case in situations or models of chronic pain is controversial. Here, we demonstrate the persistence, and even increased impact of the analgesic cholinergic tone acting through nicotinic receptors in neuropathic mice. The neuropathy does not affect the number and properties of dorsal horn cholinergic neurons, proposed to be the source of spinal ACh. Subthreshold doses of acetylcholinesterase (AChE) inhibitors in sham animals become anti-allodynic in cuff mice suggesting that the alterations occur in the cholino-receptive neurons. Thus endogenous cholinergic signaling can be manipulated with low doses of drugs to relieve mechanical allodynia in animal neuropathy models. This opens new avenues with potentially fewer side effects for neuropathic pain treatment.
Confronting pitfalls of AI-augmented molecular dynamics using statistical physics
Authors: Pant Shashank , Smith Zachary , Wang Yihang , Tajkhorshid Emad , Tiwary Pratyush
Published: June 2020

Artificial intelligence (AI)-based approaches have had indubitable impact across the sciences through the ability to extract relevant information from raw data. Recently AI has also seen use for enhancing the efficiency of molecular simulations, wherein AI derived slow modes are used to accelerate the simulation in targeted ways. However, while typical fields where AI is used are characterized by a plethora of data, molecular simulations per-construction suffer from limited sampling and thus limited data. As such the use of AI in molecular simulations can suffer from a dangerous situation where the AI-optimization could get stuck in spurious regimes, leading to incorrect characterization of the reaction coordinate (RC) for the problem at hand. When such an incorrect RC is then used to perform additional simulations, one could start to deviate progressively from the ground truth. To deal with this problem of spurious AI-solutions, here we report a novel and automated algorithm using ideas from statistical mechanics. It is based on the notion that a more reliable AI-solution will be one that maximizes the time-scale separation between slow and fast processes. To learn this time-scale separation even from limited data, we use a maximum caliber-based framework. We show the applicability of this automatic protocol for 3 classic benchmark problems, namely the conformational dynamics of a model peptide, ligand-unbinding from a protein, and folding/unfolding energy landscape of the C-terminal domain of protein G. We believe our work will lead to increased and robust use of trustworthy AI in molecular simulations of complex systems.
Synthetic observations from deep generative models and binary omics data with limited sample size
Authors: Nußberger Jens , Boesel Frederic , Lenz Stefan , Binder Harald , Hess Moritz
Published: June 2020

Deep generative models can be trained to represent the joint distribution of data, such as measurements of single nucleotide polymorphisms (SNPs) from several individuals. Subsequently, synthetic observations are obtained by drawing from this distribution. This has been shown to be useful for several tasks, such as removal of noise, imputation, for better understanding underlying patterns, or even exchanging data under privacy constraints. Yet, it is still unclear how well these approaches work with limited sample size. We investigate such settings specifically for binary data, e.g., as relevant when considering SNP measurements, and evaluate three frequently employed generative modeling approaches, variational autoencoders (VAEs), deep Boltzmann machines (DBMs) and generative adversarial networks (GANs). This includes conditional approaches, such as when considering gene expression conditional on SNPs. Recovery of pair-wise odds ratios is considered as a primary performance criterion. For simulated as well as real SNP data, we observe that DBMs generally can recover structure for up to 100 variables with as little as 500 observations, with a tendency of over-estimating odds ratios when not carefully tuned. VAEs generally get the direction and relative strength of pairwise relations right, yet with considerable under-estimation of odds ratios. GANs provide stable results only with larger sample sizes and strong pair-wise relations in the data. Taken together, DBMs and VAEs (in contrast to GANs) appear to be well suited for binary omics data, even at rather small sample sizes. This opens the way for many potential applications where synthetic observations from omics data might be useful.
A hybrid Embden–Meyerhof–Parnas pathway provides a synthetic link between sugar and phosphate metabolism
Authors: Lee Yoojin , Cho Hye Jeong , Woo Han Min
Published: June 2020

The fundamental Embden–Meyerhoff–Paranas (EMP) pathway for sugar catabolism, anabolism, and energy metabolism has been reconstituted with non-oxidative glycolysis (NOG). Although carbon conservation was achieved via NOG, the energy metabolism was significantly limited. Herein, we showed the construction of a hybrid EMP that replaced the first phase of the EMP inCorynebacterium glutamicumwith NOG and revealed a metabolic link of carbon and phosphorus metabolism. In accordance with synthetic glucose kinase activity and phosphoketolase on the hybrid EMP, cell growth was completely recovered in theC. glutamicum pfkAmutant strain where the first phase of EMP was eliminated. Notably, we have revealed a phosphate-replenishing pathway that involved trehalose biosynthesis for the generation of inorganic phosphate (Pi) sources in the hybrid EMP when external Pisupply was limited. Thus, the re-designed hybrid EMP pathway with balanced carbon and phosphorus states provides an efficient microbial platform for biochemical production.
Unilateral and Bilateral Subthalamic stimulation differently promote apathy: a translational approach
Authors: Vachez Yvan , Bahout Marie , Magnard Robin , David Pierre-Maxime , Carcenac Carole , Robert Gabriel , Savasta Marc , Carnicella Sebastien , Vérin Marc , Boulet Sabrina
Published: June 2020

Apathy, depression, and anxiety represent the main neuropsychiatric symptoms of Parkinson’s disease (PD). How subthalamic nucleus deep brain stimulation (STN-DBS) influences these symptoms, especially apathy, is a controversial topic. The present translational study investigates and compares the effect of bilateral or unilateral STN-DBS on this neuropsychiatric triad, combining a pre-clinical approach in rodents and a clinical follow-up of patients with PD. While depression and anxiety related behaviors remain unchanged, bilateral but not unilateral STN-DBS consistently induces apathy in patients and a reward seeking deficit in rodents. Together, these data substantiate the claim that STN-DBS may induce apathy by itself and suggest that bilateral but not the unilateral stimulation might be a critical factor.
Localized cell-surface sampling of a secreted factor using cell-targeting beads
Authors: van Neel Tammi L. , Berry Samuel B. , Berthier Erwin , Theberge Ashleigh B.
Published: June 2020

Intercellular communication through the secretion of soluble factors plays a vital role in a wide range of biological processes (e.g., homeostasis, immune response), yet identification and quantification of many of these factors can be challenging due to their degradation or sequestration in cell culture media prior to analysis. Here, we present a customizable bead-based system capable of simultaneously binding to live cells (through antibody-mediated cell-tethering) and capturing cell-secreted molecules. Our functionalized beads capture secreted molecules (e.g., hepatocyte growth factor secreted by fibroblasts) that are diminished when sampledviatraditional supernatant analysis techniques (p < 0.05), effectively rescuing reduced signal in the presence of neutralizing components in the cell culture media. Our system enables capture and analysis of molecules integral to chemical communication that would otherwise be markedly decreased prior to analysis.

For Table of Contents Only
Defining the impact of deep brain stimulation contact size and shape on neural selectivity
Authors: Anderson Daria Nesterovich , Dorval Alan D. , Rolston John D. , Pulst Stefan M. , Anderson Collin J
Published: June 2020

Background

Understanding neural selectivity is essential for optimizing medical applications of deep brain stimulation (DBS). We previously showed that modulation of the DBS waveform can induce changes in orientation-based selectivity, and that lengthening of DBS pulses or directional segmentation can reduce preferential selectivity for large axons. In this work, we sought to answer a simple, but important question: how do the size and shape of the contact influence neural selectivity?

Methods

We created multicompartment neuron models for several axon diameters and used finite element modeling with standard-sized cylindrical leads to determine the effects on changing contact size and shape on axon activation profiles and volumes of tissue activated. Contacts ranged in size from 0.04 to 16 mm2, compared with a standard size of 6 mm2.

Results

We found that changes in contact size induce substantial changes in orientation-based selectivity in the context of a cylindrical lead, and rectangular shaping of the contact can alter this selectivity. Smaller contact sizes were more effective in constraining neural activation to small, nearby axons representative of grey matter. However, micro-scale contacts enable only limited spread of neural activation before exceeding standard charge density limitations; further, energetic efficiency is optimized by somewhat larger contacts.

Interpretations

Small-scale contacts are optimal for constraining stimulation in nearby grey matter and avoiding orientation-selective activation. However, given charge density limitations and energy inefficiency of micro-scale contacts, our results suggest that contacts about half the size of those on segmented clinical leads may optimize efficiency and charge density limitation avoidance.
Co-Occurrence of Enzyme Domains Guides the Discovery of an Oxazolone Synthetase
Authors: de Rond Tristan , Asay Julia E. , Moore Bradley S.
Published: June 2020

Multidomain enzymes are cellular machines that orchestrate two or more catalytic activities to carry out metabolic transformations with increased control and speed. Our understanding of these enzymes’ capabilities drives progress in fundamental metabolic research, biocatalysis, and human health. Here, we report the development of a new genome mining approach for the targeted discovery of novel biochemical transformations through the analysis of co-occurring enzyme domains (CO-ED) in a single protein. CO-ED was designed to identify unannotated multifunctional enzymes for functional characterization and discovery based on the premise that linked enzyme domains have evolved to function collaboratively. Guided by CO-ED, we targeted an unannotated predicted ThiF-nitroreductase di-domain enzyme found in more than 50 proteobacteria. Through heterologous expression and biochemical reconstitution, we discovered a series of new natural products containing the rare oxazolone (azlactone) heterocycle and characterized the di-domain enzyme as the first reported oxazolone synthetase in biology. This enzyme has the potential to become a valuable biocatalyst for the production of versatile oxazolone synthetic intermediates. This proof-of-principle experiment validates CO-ED-guided genome mining as a new method with potential broad utility for both the discovery of novel enzymatic transformations and the functional gene annotation of multidomain enzymes.

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Direct RNA sequencing reveals structural differences between transcript isoforms
Authors: Ashley Aw Jong Ghut , Lim Shaun W. , Wang Jia Xu , Shen Yang , Kaewsapsak Pornchai , Louis Kok Eng Piew , Li Chenhao , Ng Boon Hsi , Vardy Leah A. , Tan Meng How , Nagarajan Niranjan , Wan Yue
Published: June 2020

The ability to correctly assign structure information to an individual transcript in a continuous and phased manner is critical to understanding RNA function. RNA structure play important roles in every step of an RNA’s lifecycle, however current short-read high throughput RNA structure mapping strategies are long, complex and cannot assign unique structures to individual gene-linked isoforms in shared sequences. To address these limitations, we present an approach that combines structure probing with SHAPE-like compound NAI-N3, nanopore direct RNA sequencing, and one-class support vector machines to detect secondary structures on near full-length RNAs (PORE-cupine).PORE-cupineprovides rapid, direct, accurate and robust structure information along known RNAs and recapitulates global structural features in human embryonic stem cells. The majority of gene-linked isoforms showed structural differences in shared sequences both local and distal to the alternative splice site, highlighting the importance of long-read sequencing for phasing of structures. Structural differences between gene-linked isoforms are associated with differential translation efficiencies globally, highlighting the role of structure as a pervasive mechanism for regulating isoform-specific gene expression inside cells.
scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks
Authors: Jin Ting , Rehani Peter , Ying Mufang , Huang Jiawei , Liu Shuang , Roussos Panagiotis , Wang Daifeng
Published: June 2020

Understanding cell-type-specific gene regulatory mechanisms from genetic variants to diseases remains challenging. To address this, we developed an open-source computational pipeline, scGRNom, to predict the cell-type disease genes and regulatory networks from multi-omics data, including cell-type chromatin interactions, epigenomics, and single-cell transcriptomics. With applications to Schizophrenia and Alzheimer’s Disease, our predicted cell-type regulatory networks link transcription factors and enhancers to disease genes for excitatory and inhibitory neurons, microglia, and oligodendrocytes. The enrichments of cell-type disease genes reveal cross-disease and disease-specific functions and pathways. Finally, machine learning analysis found that cell-type disease genes shared by diseases have improved clinical phenotype predictions.
Whole blood immunophenotyping uncovers immature neutrophil-to-VD2 T-cell ratio as an early prognostic marker for severe COVID-19
Authors: Carissimo Guillaume , Xu Weili , Kwok Immanuel , Abdad Mohammad Yazid , Chan Yi-Hao , Fong Siew-Wai , Puan Kia Joo , Lee Cheryl Yi-Pin , Yeo Nicholas Kim-Wah , Amrun Siti Naqiah , Chee Rhonda Sin-Ling , How Wilson , Chan Stephrene , Fan Eugene Bingwen , Andiappan Anand Kumar , Lee Bernett , Rötzschke Olaf , Young Barnaby Edward , Leo Yee-Sin , Lye David C. , Renia Laurent , Ng Lai Guan , Larbi Anis , Ng Lisa F.P.
Published: June 2020

SARS-CoV-2 is the novel coronavirus responsible for the current COVID-19 pandemic. Severe complications are observed only in a small proportion of infected patients but the cellular mechanisms underlying this progression are still unknown. Comprehensive flow cytometry of whole blood samples from 54 COVID-19 patients revealed a dramatic increase in the number of immature neutrophils. This increase strongly correlated with disease severity and was associated with elevated IL-6 and IP-10 levels, two key players in the cytokine storm. The most pronounced decrease in cell counts was observed for CD8 T-cells and VD2 γδ T-cells, which both exhibited increased differentiation and activation. ROC analysis revealed that the count ratio of immature neutrophils to CD8 or VD2 T-cells predicts pneumonia onset (0.9071) as well as hypoxia onset (0.8908) with high sensitivity and specificity. It would thus be a useful prognostic marker for preventive patient management and improved healthcare resource management.
Model-based learning deficits in compulsivity are linked to faulty representations of task structure
Authors: Seow Tricia X.F. , O’Connell Redmond , Gillan Claire M.
Published: June 2020

Individuals with higher levels of compulsivity exhibit poorer performance on tasks that require model-based planning but the underlying causes have yet to be established. Here, we sought to determine whether these deficits stem from impoverished action-outcome relational knowledge (i.e. issues building an accurate model of the world) and/or an inability to translate models into action. 192 participants performed a two-step reinforcement learning task with concurrent EEG recordings. We found that representations of task-relevant action-outcome associations reflected in reaction time and parietal-occipital alpha-band power were stronger in individuals whose decisions were more model-based, and critically, were weaker in those high in compulsivity. At the time of choice, mid-frontal theta power, a general marker of cognitive control, was also negatively associated with compulsivity, but not model-based planning. These data suggest that model-based planning deficits in compulsive individuals may arise from failures in building an accurate model of the world.
DNA glycosylase NEIL2 preventsFusobacterium-mediated inflammation and DNA damage in colonic epithelial cells
Authors: Sayed Ibrahim M , Chakraborty Anirban , Ali Amer , Sharma Aditi , Sahan Ayse Z. , Sahoo Debashis , Ghosh Pradipta , Hazra Tapas K , Das Soumita
Published: June 2020

Colorectal cancer (CRC) is the third most prevalent and deadly cancer. Approximately, 15-20 % of CRCs display microsatellite instability (MSI); however, the majority (80–85%) of cases are sporadic and known as microsatellite stable (MSS). Several recent studies indicated that infection and uncontrolled inflammation initiate DNA damage and lead to cancer progression. One of the major microbes,Fusobacterium nucleatum(Fn) is highly associated with CRC, but the role of DNA repair in microbe-associated CRC has been largely unknown. Here we show that NEIL2, an oxidized base-specific DNA glycosylase, is significantly downregulated among all the key DNA repair proteins involved in various DNA repair pathways, after infection ofFnwith stem-cell-based enteroid-derived monolayers (EDMs) of murine and human healthy subjects. Furthermore, followingFninfection, NEIL2-null mouse-derived EDMs showed significantly higher level of DNA damage, including double strand breaks, and inflammatory cytokines.. Murine CRC model also showed downregulation of the NEIL2 transcript and accumulation of DNA damage. Importantly, analysis of publicly available transcriptomic data showed that the downregulation of NEIL2 is specific for MSS compared to MSI CRCs. We thus conclude that the pathogenic bacterial infection-induced downregulation of NEIL2, and consequent accumulation of DNA damage, play critical roles in the progression of CRC.
Simple Assay, Kinetics, and Biochemical Trends for Soil Microbial Catalases
Authors: Chabot Michael , Morales Ernesto , Cummings Jacob , Rios Nicholas , Giatpaiboon Scott , Mogul Rakesh
Published: June 2020

In this report, we expand upon the enzymology and biochemical ecology of soil catalases through development and application of a simple kinetic model and assay based upon volume displacement. Through this approach, we (A) directly relate apparent Michaelis-Menten terms to the catalase reaction mechanism, (B) obtain upper estimates of the intrinsic rate constants for the catalase communityand moles of catalase per 16S rRNA gene copy number, (C) utilize catalase specific activities (SAs) to obtain biomass estimates of soil and permafrost communities (LOD, ~104copy number gdw−1), and (D) relate kinetic trends to changes in bacterial community structure. This model represents a novel approach to the kinetic treatment of soil catalases, while simultaneously incorporating barometric adjustments to afford comparisons across field measurements. As per our model, and when compared to garden soils, biological soil crusts exhibited ~2-fold lower values for, ≥105-fold higher catalase moles per biomass (250-1200 zmol copy number−1), and ~104-fold higher SAs per biomass (74-230 fkat copy number−1). However, the highest SAs were obtained from permafrost and high-elevation soil communities (5900-6700 fkat copy number−1). In sum, these total trends suggest that microbial communities which experience higher degrees of native oxidative stress possess higher basal intracellular catalase concentrations and SAs per biomass, and that differing kinetic profiles across catalase communities are indicative of phylum and/or genus-level changes in community structure. For microbial ecology, therefore, these measures effectively serve as markers for microbial activity and abundance, and additionally provide insights into the community responses to exogenous stress.

Importance

The efficient management of oxidative stresses arising from environmental pressures are central to the homeostasis of soil microbial communities. Among the enzymes that manage oxidative stress are catalases, which degrade hydrogen peroxide into oxygen gas and water. In this report, we detail the development and application of a simple kinetic model and assay to measure catalase reaction rates and estimate soil biomass. Our assay is based upon volume displacement, and is low-cost, field-amenable, and suitable for scientists and educators from all disciplines. Our results suggest that microbial communities that experience higher degrees of native oxidative stress possess higher basal intracellular catalase concentrations and specific activities when expressed per biomass. For microbial ecology, therefore, these measures serve as biochemical markers for microbial activity and abundance, and provide insights into the community responses to exogenous stress; thereby providing a novel means to study active microbial communities in soils and permafrost.
A pan-genome method to determine core regions of theBacillus subtilisandEscherichia coligenomes
Authors: Sutton Granger , Fogel Gary B. , Abramson Bradley , Brinkac Lauren , Michael Todd , Liu Enoch S. , Thomas Sterling
Published: June 2020

Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. We show that these core regions are very likely to contain all or almost all essential genes. We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.

Importance

The pan-genome approach presented in this paper can be used to determine core regions of a genome and has many possible applications. Synthetic engineering design can be informed by which genes/regions are more conserved (core) versus less conserved. The level of conservation of adjacent non-core genes tends to define cassettes of genes which may be part of a pathway or system that can inform researchers about possible functional significance. The pattern of gene presence across the different genomes of a species can inform the understanding of evolution and horizontal gene acquisition. The approach saves considerable time and effort relative to laboratory methods used to identify essential genes in species.
Electromechanics of lipid-modulated gating of Kv channels
Authors: Thomas Nidhin , Mandadapu Kranthi K. , Agrawal Ashutosh
Published: June 2020

Experimental studies reveal that anionic lipid POPA and non-phospholipid cholesterol inhibit the gating of voltage-sensitive potassium (Kv) channels at 5–10% molar concentrations. Intriguingly, other anionic lipids similar to POPA, like POPG, have minimal impact on the gating of the same channels for reasons that remain obscure. Our long-timescale atomistic simulations show that POPA preferentially solvates the voltage sensor domains of Kv channels by direct electrostatic interactions between the positively charged arginine and negatively charged phosphate groups. Cholesterol solvates the voltage sensor domains through CH-πinteractions between the cholesterol rings and the aromatic side chains of phenylalanine and tyrosine residues. A continuum electromechanical model predicts that POPA lipids may restrict the vertical motion of voltage-sensor domain through direct electrostatic interactions, while cholesterol may oppose the radial motion of the pore domain of the channel by increasing the mechanical rigidity of the membrane. The electromechanical model predictions are consistent with measurements of the activation curves of Kv channels for various lipids. The atomistic simulations also suggest that the solvation due to POPG is much weaker likely due to its bigger head-group size. Thus the channel activity appears to be tied to the local lipid environment, allowing lipids to regulate channel gating in low concentrations.
MHC class I and II genes in Serpentes
Authors: Olivieri D.N. , Mirete-Bachiller S. , Gambón-Deza F.
Published: June 2020

Genes of the major class I and II histocompatibility complex have been extensively studied in mammals. Studies of these antigens in reptiles are very scarce. Here we describe the characteristics of these genes in the suborder Serpentes. We identified the presence of a much larger number of molecules of class I and beta chains of class II than found in mammals. Snakes only have one gene for the class II alpha chain. In these species, class I genes can be classified into two types. Approximately half of the genes lack 10 amino acids in theα1 domain, producing a structural alteration in the interaction region with the T lymphocyte receptor. In the genome ofThamnophis elegans, two haplotypes of an individual were studied revealing a different number and location of class I genes between these haplotypes. The results indicate that in these species, the diversity in the MHC is generated by the presence or absence of genes, independent of the presence of alleles.
Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community
Authors: Becker Daniel J. , Speer Kelly A. , Korstian Jennifer M. , Volokhov Dmitriy V. , Droke Hannah F. , Brown Alexis M. , Baijnauth Catherene L. , Padgett-Stewart Ticha , Broders Hugh G. , Plowright Raina K. , Rainwater Thomas R. , Fenton M. Brock , Simmons Nancy B. , Chumchal Matthew M.
Published: June 2020

Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare.

We capitalized on extreme mercury variation in a diverse bat community in Belize to test association among contaminants, immunity, and infection. By comparing a previous dataset of bats sampled in 2014 with new data from 2017, representing a period of rapid agricultural land conversion, we first confirmed bat species more reliant on aquatic prey had higher fur mercury. Bats in the agricultural habitat also had higher mercury in recent years. We then tested covariation between mercury and cellular immunity and determined if such relationships mediated associations between mercury and common bacterial pathogens. As bat ecology can dictate exposure to mercury and pathogens, we also assessed species-specific patterns in mercury–infection relationships.

Across the bat community, individuals with higher mercury had fewer neutrophils but not lymphocytes, suggesting stronger associations with innate immunity. However, the odds of infection for hemoplasmas andBartonellaspp. were generally lowest in bats with high mercury, and relationships between mercury and immunity did not mediate infection patterns. Mercury also showed species- and clade-specific relationships with infection, being associated with especially low odds for hemoplasmas inPteronotus mesoamericanusandDermanura phaeotis.ForBartonellaspp., mercury was associated with particularly low odds in the genusPteronotusbut high odds in the Stenodermatinae.

Synthesis and application:Lower general infection risk in bats with high mercury despite weaker innate defense suggests contaminant-driven loss of pathogen habitat (i.e., anemia) or vector mortality as possible causes. Greater attention to these potential pathways could help disentangle relationships among contaminants, immunity, and infection in anthropogenic habitats and help forecast disease risks. Our results also suggest contaminants may increase infection risk in some taxa but not others, emphasizing the importance of considering surveillance and management at different phylogenetic scales.