bluuebunny/crossref_metadata_2025 huggingface dataset:
The impacts of body mass on immune cell concentrations in birds
Authors: Ruhs Emily Cornelius , Martin Lynn B. , Downs Cynthia J.
Published: April 2020

Body mass affects many biological traits, but its impacts on immune defenses are fairly unknown. Recent research on mammals found that neutrophil concentrations scaled hypermetrically with body mass, a result not predicted by any existing theory. Although this mammalian model might predict how leukocyte concentrations scale with body mass in other vertebrates, vertebrate classes are distinct in many ways that might affect their current and historic interactions with parasites and hence the evolution of their immune systems. Subsequently, here, we asked which existing scaling hypothesis best-predicted relationships between body mass and lymphocyte, eosinophil, and heterophil concentrations—the avian functional equivalent of neutrophils—among >100 species of birds. We then examined the predictive power of body mass relative to life-history variation, as an extensive literature indicates that the scheduling of key life events has influenced immune system variation among species. Finally, we ask whether these scaling patterns differ from the patterns we observed in mammals. We found that an intercept-only model best-explained lymphocyte and eosinophil concentrations among birds; body mass minimally influenced these two cell types. For heterophils, however, body mass explained over 30% of the variation in concentrations among species, much more than life-history variation (~8%). As with mammalian neutrophils, avian heterophils scaled hypermetrically (b=0.19 ± 0.05), but significantly steeper than mammals (~1.5x). As such, we discuss why birds might require more broadly-protective cells compared to mammals of the same body size. Body mass appears to have strong influences on the architecture of immune systems, which could impact host-parasite coevolution and even zoonotic disease risk for humans.
Multimodal memory T cell profiling identifies a reduction in a polyfunctional Th17 state associated with tuberculosis progression
Authors: Nathan Aparna , Beynor Jessica I. , Baglaenko Yuriy , Suliman Sara , Ishigaki Kazuyoshi , Asgari Samira , Huang Chuan-Chin , Luo Yang , Zhang Zibiao , Tamara Kattya Lopez , Jimenez Judith , Calderón Roger I. , Lecca Leonid , van Rhijn Ildiko , Moody D. Branch , Murray Megan B. , Raychaudhuri Soumya
Published: April 2020

Mycobacterium tuberculosis(M.tb) results in 10 million active tuberculosis (TB) cases and 1.5 million deaths each year1, making it the world’s leading infectious cause of death2. Infection leads to either an asymptomatic latent state or TB disease. Memory T cells have been implicated in TB disease progression, but the specific cell states involved have not yet been delineated because of the limited scope of traditional profiling strategies. Furthermore, immune activation during infection confounds underlying differences in T cell state distributions that influence risk of progression. Here, we used a multimodal single-cell approach to integrate measurements of transcripts and 30 functionally relevant surface proteins to comprehensively define the memory T cell landscape at steady state (i.e., outside of active infection). We profiled 500,000 memory T cells from 259 Peruvians > 4.7 years after they had either latentM.tbinfection or active disease and defined 31 distinct memory T cell states, including a CD4+CD26+CD161+CCR6+ effector memory state that was significantly reduced in patients who had developed active TB (OR = 0.80, 95% CI: 0.73–0.87, p = 1.21 × 10−6). This state was also polyfunctional; inex vivostimulation, it was enriched for IL-17 and IL-22 production, consistent with a Th17-skewed phenotype, but also had more capacity to produce IFNγ than other CD161+CCR6+ Th17 cells. Additionally, in progressors, IL-17 and IL-22 production in this cell state was significantly lower than in non-progressors. Reduced abundance and function of this state may be an important factor in failure to controlM.tbinfection.
A mathematical investigation of chemotherapy-induced peripheral neuropathy
Authors: Verma Parul , Eaton Muriel , Kienle Achim , Flockerzi Dietrich , Yang Yang , Ramkrishna Doraiswami
Published: April 2020

Chemotherapy-induced peripheral neuropathy (CIPN) is a prevalent, painful side effect which arises due to a number of chemotherapy agents. CIPN can have a prolonged effect on quality of life. Chemotherapy treatment is often reduced or stopped altogether because of the severe pain. Currently, there are no FDA-approved treatments for CIPN partially due to its complex pathogenesis in multiple pathways involving a variety of channels, specifically, voltage-gated ion channels. A surrogate of neuropathic pain in anin vitrosetting is hyperexcitability in dorsal root ganglia (DRG) peripheral sensory neurons. Our study employs bifurcation theory to investigate the role of voltage-gated ion channels in inducing hyperexcitability as a consequence of spontaneous firing, due to the common chemotherapy agent paclitaxel. Our mathematical investigation suggests that the sodium channel Nav1.8 and the delayed rectifier potassium channel conductances are the most critical for hyperexcitability in normal firing small DRG neurons. Introducing paclitaxel into the model, our bifurcation analysis predicts that hyperexcitability is extreme for a medium dose of paclitaxel, which is validated by multi-electrode array recordings. Our findings using multi-electrode array experiments reveal that the Nav1.8 blocker A-803467 and the delayed rectifier potassium enhancer L-alpha-phosphatidyl-D-myo-inositol 4,5-diphosphate, dioctanoyl (PIP2) have a protective effect on the firing rate of DRG when administered separately together with paclitaxel as suggested by our bifurcation analysis.
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses
Authors: Dugourd Aurelien , Kuppe Christoph , Sciacovelli Marco , Gjerga Enio , Emdal Kristina B. , Bekker-Jensen Dorte B. , Kranz Jennifer , Bindels Eric. M. J. , Costa Ana S. H. , Olsen Jesper V. , Frezza Christian , Kramann Rafael , Saez-Rodriguez Julio
Published: April 2020

Multi-omics datasets can provide molecular insights beyond the sum of individual omics. Diverse tools have been recently developed to integrate such datasets, but there are limited strategies to systematically extract mechanistic hypotheses from them. Here, we present COSMOS (Causal Oriented Search of Multi-Omics Space), a method that integrates phosphoproteomics, transcriptomics, and metabolics datasets. COSMOS combines extensive prior knowledge of signaling, metabolic, and gene regulatory networks with computational methods to estimate activities of transcription factors and kinases as well as network-level causal reasoning. COSMOS provides mechanistic hypotheses for experimental observations across multi-omics datasets. We applied COSMOS to a dataset comprising transcriptomics, phosphoproteomics, and metabolomics data from healthy and cancerous tissue from nine renal cell carcinoma patients. We used COSMOS to generate novel hypotheses such as the impact of Androgen Receptor on nucleoside metabolism and the influence of the JAK-STAT pathway on propionyl coenzyme A production. We expect that our freely available method will be broadly useful to extract mechanistic insights from multi-omics studies.

Abstract Figure
Computation in the human cerebral cortex uses less than 0.2 watts yet this great expense is optimal when considering communication costs
Authors: Levy William B , Calvert Victoria G.
Published: April 2020

Darwinian evolution tends to produce energy-efficient outcomes. On the other hand, energy limits computation, be it neural and probabilistic or digital and logical. After establishing an energy-efficient viewpoint, we define computation and construct an energy-constrained, computational function that can be optimized. This function implies a specific distinction between ATP-consuming processes, especially computationper sevs action potentials and other costs of communication. As a result, the partitioning of ATP-consumption here differs from earlier work. A bits/J optimization of computation requires an energy audit of the human brain. Instead of using the oft-quoted 20 watts of glucose available to the brain (1, 2), the partitioning and audit reveals that cortical computation consumes 0.2 watts of ATP while long-distance communication costs are over 20-fold greater. The bits/joule computational optimization implies a transient information rate of more than 7 bits/sec/neuron.

Significance Statement

Engineers hold up the human brain as a low energy form of computation. However from the simplest physical viewpoint, a neuron’s computation cost is remarkably larger than the best possible bits/joule – off by a factor of 108. Here we explicate, in the context of energy consumption, a definition of neural computation that is optimal given explicit constraints. The plausibility of this definition as Nature’s perspective is supported by an energy-audit of the human brain. The audit itself requires certain novel perspectives and calculations revealing that communication costs are 20-fold computational costs.
Directional biases in whole hand motion perception revealed by mid-air tactile stimulation
Authors: Perquin Marlou N , Taylor Mason , Lorusso Jarred , Kolasinski James
Published: April 2020

Human machine interfaces are increasingly designed to reduce our reliance on the dominantly used senses of vision and audition. Many emerging technologies are attempting to convey complex spatiotemporal information via tactile percepts shown to be effective in the visual domain, such as shape and motion. Despite the intuitive appeal of touch as a method of feedback, we do not know to what extent the hand can substitute for the retina in this way. Here we ask whether the tactile system can be used to perceive complex whole hand motion stimuli, and whether it exhibits the same kind of established perceptual biases as reported in the visual domain. Using ultrasound stimulation, we were able to project complex moving dot percepts onto the palm in mid-air, over 30cm above an emitter device. We generated dot kinetogram stimuli involving motion in three different directional axes (‘Horizontal’, ‘Vertical’, and ‘Oblique’) on the ventral surface of the hand. We found clear evidence that participants were able to discriminate tactile motion direction. Furthermore, there was a marked directional bias in motion perception: participants were better and more confident at discriminating motion in the vertical and horizontal axes of the hand, compared to those stimuli moving obliquely. This pattern directly mirrors the perceptional biases that have been robustly reported in the visual field, termed the ‘Oblique Effect’. These data show the existence of biases in motion perception that transcend sensory modality. Furthermore, we extend the Oblique Effect to a whole hand scale, using motion stimuli presented on the broad and relatively low acuity surface of the palm, away from the densely innervated and much studied fingertips. These findings also highlight targeted ultrasound stimulation as a versatile means by which to convey potentially complex spatial and temporal information without the need for a user to wear or touch a device. This ability is particularly attractive as a potential feedback mechanism for application in contact-free human machine interfaces.
GRNUlar: Gene Regulatory Network reconstruction using Unrolled algorithm from Single Cell RNA-Sequencing data
Authors: Shrivastava Harsh , Zhang Xiuwei , Aluru Srinivas , Song Le
Published: April 2020

Motivation

Gene regulatory networks (GRNs) are graphs that specify the interactions between transcription factors (TFs) and their target genes. Understanding these interactions is crucial for studying the mechanisms in cell differentiation, growth and development. Computational methods are needed to infer these networks from measured data. Although the availability of single cell RNA-Sequencing (scRNA-Seq) data provides unprecedented scale and resolution of gene-expression data, the inference of GRNs remains a challenge, mainly due to the complexity of the regulatory relationships and the noise in the data.

Results

We proposeGRNUlar, a novel deep learning architecture based on the unrolled algorithms idea for GRN inference from scRNA-Seq data. Like some existing methods which use prior information of which genes are TFs,GRNUlaralso incorporates this TF information using a sparse multi-task deep learning architecture. We also demonstrate the application of a recently developed unrolled architectureGLADto recover undirected GRNs in the absence of TF information. These unrolled architectures require supervision to train, for which we leverage the existing synthetic data simulators which generate scRNA-Seq data guided by a GRN. We show that unrolled algorithms outperform the state-of-the-art methods on synthetic data as well as real datasets in both the settings of TF information being absent or available.

Availability

Github link toGRNUlar-https://github.com/Harshs27/GRNUlar

Contact

hshrivastava3@gatech.edu
Identification and Removal of Doublets with DoubletDecon
Authors: DePasquale Erica A. K. , Schnell Daniel , Chetal Kashish , Salomonisi Nathan
Published: April 2020

Retention of multiplet captures in single-cell RNA-sequencing (scRNA-seq) data can hinder identification of discrete or transitional cell populations and associated marker genes. To overcome this challenge, we created DoubletDecon to identify and remove doublets, multiplets of two cells, by using a combination of deconvolution to identify putative doublets and analyses of unique gene expression. Here we provide the protocol for running DoubletDecon on scRNA-seq data.

For complete details on the use of this protocol, please see DePasquale et al. (2019) (https://doi.org/10.1016/j.celrep.2019.09.082).

GRAPHICAL ABSTRACT
Computationally-guided exchange of substrate selectivity motifs in a modular polyketide synthase acyltransferase
Authors: Kalkreuter Edward , Bingham Kyle S , Keeler Aaron M , Lowell Andrew N , Schmidt Jennifer J. , Sherman David H , Williams Gavin J
Published: April 2020

Acyltransferases (ATs) of modular polyketide synthases catalyze the installation of malonyl-CoA extenders into polyketide scaffolds. Subsequently, AT domains have been targeted extensively to site-selectively introduce various extenders into polyketides. Yet, a complete inventory of AT residues responsible for substrate selection has not been established, critically limiting the efficiency and scope of AT engineering. Here, molecular dynamics simulations were used to prioritize ~50 mutations in the active site of EryAT6 from erythromycin biosynthesis. Following detailedin vitrostudies, 13 mutations across 10 residues were identified to significantly impact extender unit selectivity, including nine residues that were previously unassociated with AT specificity. Unique insights gained from the MD studies and the novel EryAT6 mutations led to identification of two previously unexplored structural motifs within the AT active site. Remarkably, exchanging both motifs in EryAT6 with those from ATs with unusual extender specificities provided chimeric PKS modules with expanded and inverted substrate specificity. Our enhanced understanding of AT substrate selectivity and application of this motif-swapping strategy is expected to advance our ability to engineer PKSs towards designer polyketides.
Integrated genomics and comprehensive validation reveal novel drivers of genomic evolution in esophageal adenocarcinoma
Authors: Kumar Subodh , Buon Leutz , Talluri Srikanth , Roncador Marco , Liao Chengcheng , Zhao Jiangning , Shi Jialan , Chakraborty Chandraditya , Gonzalez Gabriel B. , Tai Yu-Tzu , Prabhala Rao , Samur Mehmet K. , Munshi Nikhil C. , Shammas Masood A.
Published: April 2020

Identification of genes driving genomic evolution can provide novel targets for cancer treatment and prevention. Here we show identification of a genomic instability gene signature, using an integrated genomics approach. Elevated expression of this signature correlated with poor survival in esophageal adenocarcinoma (EAC) as well as three other human cancers. Knockout and overexpression screens confirmed the relevance of this signature to genomic instability. Indepth evaluation of TTK (a kinase), TPX2 (spindle assembly factor) and RAD54B (recombination protein) further confirmed their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrated that DNA damage and homologous recombination were common mechanisms of genomic instability induced by these genes. Consistently, a TTK inhibitor impaired EAC cell growth in vivo, and increased chemotherapy-induced cytotoxicity while inhibiting genomic instability in surviving cells. Thus inhibitors of TTK and other genes identified in this study have potential to inhibit/delay genomic evolution and tumor growth. Such inhibitors also have potential to increase chemotherapy-induced cytotoxicity while reducing its harmful genomic impact in EAC and possibly other cancers.
The anti-lipidemic drug simvastatin modulates Epigenetic Biomarkers in the AmphipodGammarus locusta
Authors: Alves Nélson , Neuparth Teresa , Barros Susana , Santos Miguel M.
Published: April 2020

The adverse effects of certain environmental chemicals have been recently associated with epigenome’s modulation. Although the changes in the epigenetic signature are still not integrated into hazard and risk assessment, they are interesting candidates for linking environmental exposures to altered phenotypes given that these changes may be passed across multiple non-exposed generations. Here, we addressed the effects of simvastatin (SIM), one of the most prescribed human pharmaceuticals, in epigenetic regulators of the amphipodGammarus locusta, as a proxy to support its integration in hazard and environmental risk assessment. SIM is a known modulator of epigenome in mammalian cell lines, and has been reported to impactG. locustaecological endpoints at environmentally relevant levels.G. locustajuveniles were exposed to three SIM concentrations (0.32, 1.6 and 8 µg.L-1), for 15 days. The basal expression of selected epigenetic regulators was determined, along with the quantification of DNA methylation levels and the assessment of key ecological endpoints. Exposure to 0.32 and 8 µg.L-1SIM induced significant downregulation of DNA methyltransferase1 (dnmt1), concomitantly with Global DNA hypomethylation and impact on growth. Overall, this work is the first to validate the basal expression of key epigenetic regulators in a keystone marine crustacean, supporting the integration of epigenetic biomarkers into hazard assessment frameworks.
Big trees drive forest structure patterns across a lowland Amazon regrowth gradient
Authors: Fontoura Caron Tassiana Maylla , Rodriguez Chuma Victor Juan Ulises , Arévalo Sandi Alexander , Norris Darren
Published: April 2020

Degraded Amazonian forests can take decades to recover and the ecological results of natural regeneration are still uncertain. Here we use field data collected across 15 lowland Amazon smallholder properties to examine the relationships between forest structure, mammal diversity, regrowth type, regrowth age, topography and hydrography. Forest structure was quantified together with mammal diversity in 30 paired regrowth-control plots. Forest regrowth stage was classified into three groups: late second-regrowth, early second-regrowth and abandoned pasture. Basal area in regrowth plots remained less than half that recorded in control plots even after 20-25 years. Although basal area did increase in sequence from pasture, early to late-regrowth plots, there was a significant decline in basal area of late-regrowth control plots associated with a decline in the proportion of large trees. There was also contrasting support for different non-mutually exclusive hypotheses, with proportion of small trees (DBH <20cm) most strongly supported by topography (altitude and slope) whereas the proportion of large trees (DBH >60cm) supported by plot type and regrowth class. These findings support calls for increased efforts to actively conserve large trees to avoid retrogressive succession around edges of degraded Amazon forests.
Circuits for integrating learnt and innate valences in the fly brain
Authors: Eschbach Claire , Fushiki Akira , Winding Michael , Afonso Bruno , Andrade Ingrid V , Cocanougher Benjamin T , Eichler Katharina , Gepner Ruben , Si Guangwei , Valdes-Aleman Javier , Gershow Marc , Jefferis Gregory SXE , Truman James W , Fetter Richard D , Samuel Aravinthan , Cardona Albert , Zlatic Marta
Published: April 2020

Animal behavior is shaped both by evolution and by individual experience. In many species parallel brain pathways are thought to encode innate and learnt behavior drives and as a result may link the same sensory cue to different actions if innate and learnt drives are in opposition. How these opposing drives are integrated into a single coherent action is not well understood. In insects, the Mushroom Body Output Neurons (MBONs) and the Lateral Horn Neurons (LHNs) are thought to provide the learnt and innate drives, respectively. However their patterns of convergence and the mechanisms by which their outputs are used to select actions are not well understood. We used electron microscopy reconstruction to comprehensively map the downstream targets of all MBONs inDrosophilalarva and characterise their patterns of convergence with LHNs. We discovered convergence neurons that receive direct input from MBONs and LHNs and compare opposite behaviour drives. Functional imaging and optogenetic manipulation suggest these convergence neurons compute the overall predicted value of approaching or avoiding an odor and mediate action selection. Our study describes the circuit mechanisms allowing integration of opposing drives from parallel olfactory pathways.
ITPK1-Dependent Inositol Polyphosphates Regulate Auxin Responses inArabidopsis thaliana
Authors: Laha Nargis Parvin , Dhir Yashika Walia , Giehl Ricardo F.H. , Schäfer Eva Maria , Gaugler Philipp , Shishavan Zhaleh Haghighat , Gulabani Hitika , Mao Haibin , Zheng Ning , von Wirén Nicolaus , Jessen Henning J. , Saiardi Adolfo , Bhattacharjee Saikat , Laha Debabrata , Schaaf Gabriel
Published: April 2020

The combinatorial phosphorylation ofmyo-inositolresults in the generation of different inositol phosphates (InsP), of which phytic acid (InsP6) is the most abundant species in eukaryotes. InsP6is also the precursor of higher phosphorylated forms called inositol pyrophosphates (PP-InsPs), such as InsP7and InsP8, which are characterized by a diphosphate moiety and are also ubiquitously found in eukaryotic cells. While PP-InsPs regulate various cellular processes in animals and yeast, their biosynthesis and functions in plants has remained largely elusive because plant genomes do not encode canonical InsP6kinases. Recently, it was shown that Arabidopsis ITPK1 catalyzes the phosphorylation of InsP6to the natural 5-InsP7isomerin vitro. Here, we demonstrate that Arabidopsis ITPK1 contributes to the synthesis of InsP7in planta. We further find a critical role of ITPK1 in auxin-related processes including primary root elongation, leaf venation, thermomorphogenic and gravitropic responses, and sensitivity towards exogenously applied auxin. Notably, 5-InsP7binds to recombinant auxin receptor complex, consisting of the F-Box protein TIR1, ASK1 and the transcriptional repressor IAA7, with high affinity. Furthermore, a specific increase in 5-InsP7in a heterologous yeast expression system results in elevated interaction of the TIR1 homologs AFB1 and AFB2 with various AUX/IAA-type transcriptional repressors. We also identified a physical interaction between ITPK1 and TIR1, suggesting a dedicated channeling of an activating factor, such as 5-InsP7, to the auxin receptor complex. Our findings expand the mechanistic understanding of auxin perception and lay the biochemical and genetic basis to uncover physiological processes regulated by 5-InsP7.
Socioeconomic variation across multiple cities predicts avian life-history strategies
Authors: Kinnunen Riikka P , Fraser Kevin , Schmidt Chloé , Garroway Colin J
Published: April 2020

Cities are the planet’s newest ecosystem and thus provide the opportunity to study community formation directly following major permanent environmental change. The human social and built components of environments can vary widely across different cities, yet it is largely unknown how these features of a city covary with the traits of colonizing species. We constructed a new dataset from open-source data with 44,670 observations of 160 Passerine species observed 1,908 urban areas across the United States. We found that as a city’s housing density and median income increased it tended to support more migratory species and species with smaller body sizes and shorter lifespans. This suggests that differential survival and reproduction at the species-level can quickly generate geographical patterns of species trait variation across urban environments similar to those found in natural settings without the need for evolutionary change.
Representational pattern similarity of electrical brain activity reveals rapid and specific prediction during language comprehension
Authors: Hubbard Ryan J. , Federmeier Kara D.
Published: April 2020

Predicting upcoming stimuli and events is a critical function of the brain, and understanding the mechanisms of prediction has thus become a central topic in neuroscientific research. Language provides a fertile testing ground for examining predictive mechanisms, as comprehenders use context to predict different features of upcoming words. Although there is a substantive body of research on prediction in language, many aspects of the mechanisms of prediction remain elusive, in part due to a lack of methodological tools to probe prediction formation in the moment. To elucidate what features are neurally pre-activated and when, we used representational similarity analysis (RSA) on data from a sentence reading task (Federmeier et al., 2007). We compared EEG activity patterns elicited by expected and unexpected sentence final words to patterns from the preceding words of the sentence, in both strongly and weakly constraining sentences. Pattern similarity with the final word was increased in an early time window (suggestive of visual feature activation) following the presentation of the pre-final word, and this increase was modulated by both expectancy and constraint (greatest for strongly constrained expected words). This was not seen at earlier words, suggesting that predictions are precisely timed. Additionally, pre-final word activity – the predicted representation - had negative similarity with later final word activity, but only for strongly expected words. Together, these findings shed light on the mechanisms of prediction in the brain: features of upcoming stimuli are rapidly pre-activated following related cues, but the predicted information may receive reduced subsequent processing upon confirmation.
pDriver: A novel method for unravelling personalised coding and miRNA cancer drivers
Authors: Pham Vu VH , Liu Lin , Bracken Cameron P , Nguyen Thin , Goodall Gregory J , Li Jiuyong , Le Thuc D
Published: April 2020

Motivation

Unravelling cancer driver genes is important in cancer research. Although computational methods have been developed to identify cancer drivers, most of them detect cancer drivers at population level. However, two patients who have the same cancer type and receive the same treatment may have different outcomes because each patient has a different genome and their disease might be driven by different driver genes. Therefore new methods are being developed for discovering cancer drivers at individual level, but existing personalised methods only focus on coding drivers while microRNAs (miRNAs) have been shown to drive cancer progression as well. Thus, novel methods are required to discover both coding and miRNA cancer drivers at individual level.

Results

We propose the novel method,pDriver, to discover personalised cancer drivers.pDriverincludes two stages: (1) Constructing gene networks for each cancer patient and (2) Discovering cancer drivers for each patient based on the constructed gene networks. To demonstrate the effectiveness ofpDriver, we have applied it to five TCGA cancer datasets and compared it with the state-of-the-art methods. The result indicates thatpDriveris more effective than other methods. Furthermore,pDrivercan also detect miRNA cancer drivers and most of them have been confirmed to be associated with cancer by literature. We further analyse the predicted personalised drivers for breast cancer patients and the result shows that they are significantly enriched in many GO processes and KEGG pathways involved in breast cancer.

Availability and implementation

pDriveris available athttps://github.com/pvvhoang/pDriver

Contact

Thuc.Le@unisa.edu.au

Supplementary information

Supplementary data are available atBioinformaticsonline.
The trajectory of discrete gating charges in a voltage-gated potassium channel
Authors: Priest Michael F. , Lee Elizabeth E.L. , Bezanilla Francisco
Published: April 2020

Positively-charged amino acids respond to membrane potential changes to drive voltage sensor movement in voltage-gated ion channels, but determining the trajectory of voltage sensor gating charges has proven difficult. We optically tracked the movement of the two most extracellular charged residues (R1, R2) in the Shaker potassium channel voltage sensor using a fluorescent positively-charged bimane derivative (qBBr) that is strongly quenched by tryptophan. By individually mutating residues to tryptophan within the putative trajectory of gating charges, we observed that the charge pathway during activation is a rotation and a tilted translation that differs between R1 and R2 and is distinct from their deactivation pathway. Tryptophan-induced quenching of qBBr also indicates that a crucial residue of the hydrophobic plug is linked to the Cole-Moore shift through its interaction with R1. Finally, we show that this approach extends to additional voltage-sensing membrane proteins using theCiona intestinalisvoltage sensitive phosphatase (CiVSP).
Auranofin resistance inToxoplasma gondiidecreases the accumulation of reactive oxygen species but does not target parasite thioredoxin reductase
Authors: Ma Christopher I. , Tirtorahardjo James A. , Jan Sharon , Schweizer Sakura S. , Rosario Shawn A. C. , Du Yanmiao , Zhang Jerry J. , Morrissette Naomi S. , Andrade Rosa M.
Published: April 2020

Auranofin, a reprofiled FDA-approved drug originally designed to treat rheumatoid arthritis, has emerged as a promising anti-parasitic drug. It induces the accumulation of reactive oxygen species (ROS) in parasites, includingToxoplasma gondii. We generated auranofin resistantT. gondiilines through chemical mutagenesis in order to identify the molecular target of this drug. Resistant clones were confirmed with a competition assay using wild-typeT. gondiiexpressing yellow fluorescence protein (YFP) as a reference strain. The predicted auranofin target, thioredoxin reductase, was not mutated in any of our resistantlines. Subsequent whole genomic sequencing analysis (WGS) did not reveal a consensus resistance locus, although many have point mutations in genes encoding redox-relevant proteins such as superoxide dismutase (TgSOD2) and ribonucleotide reductase. We investigated the SOD2 L201P mutation and found that it was not sufficient to confer resistance when introduced into wild-type parasites. Resistant clones accumulated less ROS than their wild type counterparts. Our results demonstrate that resistance to auranofin inT. gondiienhances its ability to abate oxidative stress through diverse mechanisms. This evidence supports a hypothesized mechanism of auranofin anti-parasitic activity as disruption of redox homeostasis.
Lower complexity of motor primitives ensures robust control of high-speed human locomotion
Authors: Santuz Alessandro , Ekizos Antonis , Kunimasa Yoko , Kijima Kota , Ishikawa Masaki , Arampatzis Adamantios
Published: April 2020

Walking and running are mechanically and energetically different locomotion modes. For selecting one or another, speed is a parameter of paramount importance. Yet, both are likely controlled by similar low-dimensional neuronal networks that reflect in patterned muscle activations called muscle synergies. Here, we investigated how humans synergistically activate muscles during locomotion at different submaximal and maximal speeds. We analysed the duration and complexity (or irregularity) over time of motor primitives, the temporal components of muscle synergies. We found that the challenge imposed by controlling high-speed locomotion forces the central nervous system to produce muscle activation patterns that are wider and less complex relative to the duration of the gait cycle. The motor modules, or time-independent coefficients, were redistributed as locomotion speed changed. These outcomes show that robust locomotion control at challenging speeds is achieved by modulating the relative contribution of muscle activations and producing less complex and wider control signals, whereas slow speeds allow for more irregular control.
Ligand-independent EGFR oligomers do not rely on the active state asymmetric kinase dimer
Authors: Byrne Patrick O. , Hristova Kalina , Leahy Daniel J.
Published: April 2020

The human Epidermal Growth Factor Receptor (EGFR/ERBB1) is a Receptor Tyrosine Kinase (RTK) that forms active oligomers in response to ligand. Much evidence indicates that EGFR/ERBB1 forms oligomers in the absence of ligand, but the structure and physiological role of these ligand-independent dimers remain unclear. We use fluorescence microscopy to measure the oligomer stability and FRET efficiency for homo- and hetero-oligomers of fluorescent-protein labeled forms of EGFR and its paralog, Human Epidermal Growth Factor Receptor 2 (HER2/ERBB2) in vesicles derived from native cell membranes. Both receptors form ligand-independent oligomers at physiological plasma membrane concentrations. Mutations introduced in the EGFR kinase region at a key interface within the active state dimer alter the FRET efficiency within ligand-independent EGFR oligomers but do not affect their stability. These results indicate that ligand-independent EGFR oligomers do not require this interface and that the inactive state ensemble is distinct from the EGFR active state ensemble.
Expression ofACE2, the SARS-CoV-2 receptor, andTMPRSS2in prostate epithelial cells
Authors: Song Hanbing , Seddighzadeh Bobak , Cooperberg Matthew R. , Huang Franklin W.
Published: April 2020

The COVID-19 pandemic has spread across more than 200 countries and resulted in over 170,000 deaths. For unclear reasons, higher mortality rates from COVID-19 have been reported in men compared to women. While the SARS-CoV-2 receptorACE2and serine proteaseTMPRSS2have been detected in lung and other tissues, it is not clear what sex differences may exist. We analyzed a publicly-available normal human prostate single-cell RNA sequencing dataset and foundTMPRSS2andACE2co-expressing cells in epithelial cells, with a higher proportion in club and hillock cells. Then we investigated datasets of lung epithelial cells and also found club cells co-expressingTMPRSS2andACE2. A comparison ofACE2expression in lung tissue between males and females showed higher expression in males and a larger proportion ofACE2+ cells in male type II pneumocytes, with preliminary evidence that type II pneumocytes of all lung epithelial cell types showed the highest expression ofACE2. These results raise the possibility that sex differences inACE2expression and the presence of double-positive cells in the prostate may contribute to the observed disparities of COVID-19.
Subnanometer-resolution structure determinationin situby a hybrid subtomogram averaging – single particle cryoEM – workflow
Authors: Sanchez Ricardo , Zhang Yingyi , Chen Wenbo , Dietrich Lea , Kudryashev Misha
Published: April 2020

Cryo electron tomography (cryo-ET) combined with subtomogram averaging (StA) enables structural determination of macromolecules in their native context. A few structures were reported by StA at resolution higher than 4.5 Å, however all of these are from viral structural proteins or vesicle coats. Reaching high resolution for a broader range of samples is uncommon due to beam-induced sample drift, poor signal-to-noise ratio (SNR) of images, challenges in CTF correction, limited number of particles. Here we propose a strategy to address these issues, which consists of a tomographic data collection scheme and a processing workflow. Tilt series are collected with higher electron dose at zero-degree tilt in order to increase SNR. Next, after performing StA conventionally, we extract 2D projections of the particles of interest from the higher SNR images and use the single particle analysis tools to refine the particle alignment and generate a reconstruction. We benchmarked our proposedhybrid StA (hStA)workflow and improved the resolution for tobacco mosaic virus from 7.2 to 5.2 Å and the resolution for the ion channel RyR1 in crowded native membranes from 12.9 to 9.1 Å. We demonstrate thathStAcan improve the resolution obtained by conventional StA and promises to be a useful tool for StA projects aiming at subnanometer resolution or higher.
Validation of a SARS-CoV-2 spike protein ELISA for use in contact investigations and sero-surveillance
Authors: Freeman Brandi , Lester Sandra , Mills Lisa , Rasheed Mohammad Ata Ur , Moye Stefany , Abiona Olubukola , Hutchinson Geoffrey B. , Morales-Betoulle Maria , Krapinunaya Inna , Gibbons Ardith , Chiang Cheng-Feng , Cannon Deborah , Klena John , Johnson Jeffrey A. , Owen Sherry Michele , Graham Barney S. , Corbett Kizzmekia S. , Thornburg Natalie J.
Published: April 2020

Since emergence of SARS-CoV-2 in late 2019, there has been a critical need to understand prevalence, transmission patterns, to calculate the burden of disease and case fatality rates. Molecular diagnostics, the gold standard for identifying viremic cases, are not ideal for determining true case counts and rates of asymptomatic infection. Serological detection of SARS-CoV-2 specific antibodies can contribute to filling these knowledge gaps. In this study, we describe optimization and validation of a SARS-CoV-2-specific-enzyme linked immunosorbent assay (ELISA) using the prefusion-stabilized form of the spike protein [1]. We performed receiver operator characteristic (ROC) analyses to define the specificities and sensitivities of the optimized assay and examined cross reactivity with immune sera from persons confirmed to have had infections with other coronaviruses. These assays will be used to perform contact investigations and to conduct large-scale, cross sectional surveillance to define disease burden in the population.
Anxiety enhances pain in a model of osteoarthritis and is associated with altered endogenous opioid function and reduced opioid analgesia
Authors: Lillywhite Amanda , Woodhams Stephen G. , Watson David J. G. , Li Li , Burston James J. , Gowler Peter R. W. , Canals Meritxell , Walsh David A. , Hathway Gareth J. , Chapman Victoria
Published: April 2020

Chronic pain states such as osteoarthritis (OA) are often associated with negative affect, including anxiety and depression. This is, in turn, associated with greater opioid analgesic use, potentially contributing to current and future opioid crises. We utilise an animal model to investigate the neurobiological mechanisms underlying increased opioid use associated with high anxiety and chronic pain.

Combining a genetic model of negative affect, the Wistar Kyoto (WKY) rat, and intra-articular injection of monosodium iodoacetate (MIA; 1mg), our model of high anxiety and augmented OA-like pain behaviour mirrors the clinical problem. Effects of morphine (0.5-6mg.kg-1) on pain behaviour and spinal nociceptive neuronal activity were determined in WKY rats, and normo-anxiety Wistar rats, 3 weeks after MIA injection. WKY rats developed augmented OA-like pain, and had blunted inhibitory responses to morphine, when compared to Wistar rats. Potential alterations in endogenous opioid function were probed via systemic blockade of opioid receptors with naloxone (0.1-1mg.kg-1), quantification of circulating levels of β-endorphin, and determination of spinal expression of the mu-opioid receptor (MOR). These studies revealed increased opioidergic tone, and increased spinal desensitization of MORs via the master phosphorylation site at serine residue 375, in this model.

We demonstrate attenuated MOR function in the absence of previous exogenous opioid ligand exposure in our model of high anxiety and OA-like pain, which may account for reduced analgesic effect of morphine and provide a potential explanation for increased opioid analgesic intake in high anxiety chronic pain patients.

Significance Statement

Chronic pain affects large numbers of people, and pain management often relies on poorly effective opioid analgesics, the iatrogenic effects of which are increasingly recognised. The endogenous opioid system - the target for exogenous opioid analgesics - plays key roles in emotional affective states and pain control, but the complex interplay between anxiety, chronic pain, and endogenous opioid system function is challenging to study in people. Here, we have addressed this using a clinically-relevant experimental model. Anxiety-like behaviour was associated with increased chronic arthritis-like pain behaviour, altered opioid receptor function, and reduced efficacy of opioid analgesics. We provide new evidence, which may explain why chronic pain patients with comorbid high anxiety have higher opioid analgesic use.
Investigation of a night soil compost psychrotrophic bacteriumGlutamicibacter arilaitensisLJH19 for its safety, efficient hydrolytic and plant growth-promoting potential
Authors: Borker Shruti Sinai , Thakur Aman , Kumar Sanjeet , Kumari Sareeka , Kumar Rakshak , Kumar Sanjay
Published: April 2020

Night soil compost (NSC) has traditionally been a source of organic manure in north-western Himalaya. Lately, this traditional method is declining due to modernization, its unhygienic conditions and social apprehensions. Reduction in the age-old traditional practice has led to excessive usage of chemical fertilizers and shortage of water in the eco-sensitive region. Microbiological intervention was attempted to obtain bacterial consortia for accelerated degradation of human faeces in cold climate to improvise this traditional knowledge.Glutamicibacter arilaitensisLJH19, a psychrotrophic bacteria was identified as one such potential candidate for the proposed consortia. The bacterium was isolated from NSC of Lahaul valley and exhibited potential hydrolytic activities, the specific activities of amylase, cellulase and xylanase was observed as 186.76 U/mg, 21.85 U/mg and 11.31 U/mg respectively. Additionally, the strain possessed multiple plant growth-promoting (PGP) traits. The bacterium produced 166.11 µg/ml indole acetic acid and 85.72 % siderophore units, and solubilized 44.76 µg/ml phosphate. Whole genome sequence (3,602,821 bps) endorsed the cold adaptation, polysaccharide metabolism, PGP potential of the bacterium. Genome mining revealed biosynthetic gene clusters for type III polyketide synthase (PKS), terpene, and siderophore in agreement with its potential PGP traits. Comparative genomics within the genus revealed 217 unique genes specific to hydrolytic and PGP activity. Negative haemolysis and biofilm production and susceptibility towards all 12 tested antibiotics indicated the bacterium to be a safe bioinoculant. Genomic investigation supported the bacterium safety with absence of any virulence and antibiotic resistance genes. We propose the strain LJH19 to be a potentially safe bioinoculant candidate for efficient degradation of night soil owing to its survivability in cold and its efficient hydrolytic and PGP potential.
Mapping the neural circuitry of predator fear in the nonhuman primate
Authors: Montardy Quentin , Kwan William C. , Mundinano Inaki C. , Fox Dylan M. , Wang Liping , Gross Cornelius T. , Bourne James A.
Published: April 2020

In rodents, innate and learned fear of predators depends on the medial hypothalamic defensive system, a conserved brain network that lies downstream of the amygdala. However, it remains unknown whether this network is involved in primate fear. Here we demonstrate that visually evoked predator fear recruits a homologous medial hypothalamic defense system in the nonhuman primate
Regulation of Neural Circuit Development by Cadherin-11 Provides Implications for Autism
Authors: Frei Jeannine A. , Niescier Robert F. , Bridi Morgan S. , Durens Madel , Nestor Jonathan E. , Kilander Michaela B. C. , Yuan Xiaobing , Dykxhoorn Derek M. , Nestor Michael W. , Huang Shiyong , Blatt Gene J. , Lin Yu-Chih
Published: April 2020

Autism spectrum disorder (ASD) is a neurological condition characterized by alterations in social interaction and communication, and restricted and/or repetitive behaviors. The classical type II cadherins cadherin-8 (Cdh8, CDH8) and cadherin-11 (Cdh11, CDH11) have been implicated as autism risk gene candidates. To explore the role of cadherins in the etiology of autism, we investigated their expression patterns during mouse brain development and in autism-specific human tissue. In mice, expression of cadherin-8 and cadherin-11 was developmentally regulated and enriched in the cortex, hippocampus, and thalamus/striatum during the peak of dendrite formation and synaptogenesis. Both cadherins were expressed in synaptic compartments but only cadherin-8 associated with the excitatory synaptic marker neuroligin-1. Induced pluripotent stem cell (iPSC)-derived cortical neural precursor cells (NPCs) and cortical organoids generated from individuals with autism showed upregulated CDH8 expression levels while CDH11 expression levels were downregulated. We usedCdh11knockout mice of both sexes to analyze the function of cadherin-11, which could help explain phenotypes observed in autism.Cdh11-/-hippocampal neurons exhibited increased dendritic complexity along with altered neuronal and synaptic activity. Similar to the expression profiles in human tissue, levels of cadherin-8 were significantly elevated inCdh11knockout brains. Additionally, excitatory synaptic markers neuroligin-1 and PSD-95 were both increased. Together, these results strongly suggest that cadherin-11 is involved in regulating the development of neuronal circuitry and that alterations in the expression levels of cadherin-11 may contribute to the etiology of autism.

Significance Statement

Autism is a neurodevelopmental condition with high genetic and phenotypic heterogeneity. Multiple genes have been implicated in autism, including the cadherin superfamily of adhesion molecules, cadherin-8 and cadherin-11. This study first characterizes the expression profiles of cadherin-8 and cadherin-11 to understand the potential roles they play in the development of neurons. The study further describes novel contributions of cadherin-11 in neural circuit formation. Loss of cadherin-11 in mice results in altered levels of several synaptic proteins, including PSD-95, neuroligin-1, and cadherin-8, and changes the morphology and activity of excitatory neurons. The levels of cadherin-8 and cadherin-11 in human cells of autistic individuals are both altered, strengthening the hypothesis that these two cadherins may involve in aspects of autism etiology.