bluuebunny/crossref_metadata_2025 huggingface dataset:
Sex differences in predictors and regional patterns of brain-age-gap estimates
Authors: Sanford N , Ge R , Antoniades M , Modabbernia A , Haas SS , Whalley HC , Galea L , Popescu SG , Cole JH , Frangou S
Published: January 2022

Background

The brain-age-gap estimate (brainAGE) quantifies the difference between chronological age and age predicted by applying machine-learning models to neuroimaging data, and is considered a biomarker of brain health. Understanding sex-differences in brainAGE is a significant step toward precision medicine.

Methods

Global and local brainAGE (G-brainAGE and L-brainAGE, respectively) were computed by applying machine learning algorithms to brain structural magnetic resonance imaging data from 1113 healthy young adults (54.45% females; age range: 22-37 years) participating in the Human Connectome Project. Sex-differences were determined in G-brainAGE and L-brainAGE. Random forest regression was used to determine sex-specific associations between G-brainAGE and non-imaging measures pertaining to sociodemographic characteristics and mental, physical, and cognitive functions.

Results

L-brainAGE showed sex-specific differences in brain ageing. In females, compared to males, L-brainAGE was higher in the cerebellum and brainstem and lower in the prefrontal cortex and insula. Although sex-differences in G-brainAGE were minimal, associations between G-brainAGE and non-imaging measures differed between sexes with the exception for poor sleep quality, which was common to both. The most important predictor of higher G-brainAGE was non-white race in males and systolic blood pressure in females.

Conclusions

The results demonstrate the value of applying sex-specific analyses and machine learning methods to advance our understanding of sex-related differences in factors that influence the rate of brain ageing and provide a foundation for targeted interventions.
RET activation controlled by MAB21L4-CacyBP interaction drives squamous cell carcinoma
Authors: Srivastava Ankit , Tommasi Cristina , Sessions Dane , Mah Angela , Bencomo Tomas , Garcia Jasmine M. , Jiang Tiffany , Lee Michael , Shen Joseph Y. , Seow Lek Wei , Nguyen Audrey , Rajapakshe Kimal , Coarfa Cristian , Tsai Kenneth Y. , Lopez-Pajares Vanessa , Lee Carolyn S.
Published: January 2022

Epithelial squamous cell carcinomas (SCC) most commonly originate in the skin, where they display disruptions in the normally tightly regulated homeostatic balance between keratinocyte proliferation and terminal differentiation. We performed a transcriptome-wide screen for genes of unknown function that possess inverse expression patterns in differentiating keratinocytes compared to cutaneous SCC (cSCC) and identified MAB21L4 (C2ORF54) as an enforcer of terminal differentiation that suppresses carcinogenesis. Loss of MAB21L4 in human cSCC organoids enabled malignant transformation through increased expression of the receptor tyrosine kinase rearranged during transfection (RET). In addition to transcriptional upregulation of RET, MAB21L4 deletion preempted recruitment of the CacyBP-Siah1 E3 ligase complex to RET and reduced its ubiquitylation. Both genetic disruption of RET or selective RET inhibition with BLU-667 (pralsetinib) suppressed tumorigenesis in SCC organoids and in vivo tumors while inducing concomitant differentiation. Our results suggest that targeting RET activation is a potential therapeutic strategy for treating SCC.

Statement of Significance

Few targeted therapies are available to individuals with cSCC who seek or require non-surgical management. Our study demonstrates that downregulation of RET is required for epithelial differentiation and opposes carcinogenesis in cSCC as well as SCC arising from other epithelial tissues.
Environment constrains fitness advantages of division of labor in microbial consortia engineered for metabolite push or pull interactions
Authors: Beck Ashley E. , Pintar Kathryn , Schepens Diana , Schrammeck Ashley , Johnson Timothy , Bleem Alissa , Du Martina , Harcombe William R. , Bernstein Hans C. , Heys Jeffrey J. , Gedeon Tomas , Carlson Ross P.
Published: January 2022

Fitness benefits from division of labor in microbial consortia are well documented, but the dependency of the benefits on environmental context is poorly understood. Two synthetic Escherichia coli consortia were built to test the relationships between exchanged organic acid, local environment, and opportunity costs of different metabolic strategies. Opportunity costs quantify benefits not realized due to selecting one phenotype over another. The consortia catabolized glucose and exchanged either acetic or lactic acid to create producer-consumer food webs. The organic acids had different inhibitory properties and different opportunity costs associated with their positions in central metabolism. The exchanged metabolites modulated different consortial dynamics. The acetic acid-exchanging (AAE) consortium had a ‘push’ interaction motif where acetic acid was secreted faster by the producer than the consumer imported it, while the lactic acid-exchanging (LAE) consortium had a ‘pull’ interaction motif where the consumer imported lactic acid at a comparable rate to its production. The LAE consortium outperformed wild type (WT) batch cultures under the environmental context of weakly buffered conditions, achieving a 55% increase in biomass titer, a 51% increase in biomass per proton yield, an 86% increase in substrate conversion, and the complete elimination of byproduct accumulation all relative to the WT. However, the LAE consortium had the tradeoff of a 42% lower specific growth rate. The AAE consortium did not outperform the WT in any considered fitness metric. Fitness advantages of the LAE consortium were sensitive to environment; increasing the medium buffering capacity negated the fitness advantages compared to WT.

IMPORTANCE

Most naturally occurring microorganisms persist in consortia where metabolic interactions are common and often essential to ecosystem function. This study uses synthetic ecology to test how different cellular interaction motifs influence fitness properties of consortia. Environmental context ultimately controlled the division of labor fitness as shifts from weakly buffered to highly buffered conditions negated the benefits of the strategy. Understanding the limits of division of labor advances our understanding of natural community functioning which is central to nutrient cycling and provides design rules for assembling consortia used in applied bioprocessing.
Antigenic determinants of SARS-CoV-2-specific CD4+ T cell lines reveals M protein-driven dysregulation of interferon signaling
Authors: Gazzinelli-Guimaraes Pedro Henrique , Sanku Gayatri , Sette Alessandro , Weiskopf Daniela , Schaughency Paul , Lack Justin , Nutman Thomas B.
Published: January 2022

We generated CD4+ T cell lines (TCLs) reactive to either SARSCoV-2 spike (S) or membrane (M) proteins from unexposed naïve T cells from six healthy donor volunteers to understand in fine detail whether the S and M structural proteins have intrinsic differences in driving antigen-specific CD4+ T cell responses. Having shown that each of the TCLs were antigen-specific and antigen-reactive, single cell mRNA analyses demonstrated that SARS-CoV-2 S and M proteins drive strikingly distinct molecular signatures. Whereas the S-specific responses are virtually indistinguishable from those responses induced by other viral antigens (e.g. CMV), the M protein-specific CD4+ TCLs have a transcriptomic signature that indicate a marked suppression of interferon signaling, characterized by a downregulation of the genes encoding ISG15, IFITM1, IFI6, MX1, STAT1, OAS1, IFI35, IFIT3 and IRF7 (a molecular signature which is not dissimilar to that found in severe COVID-19). Our study suggests a potential link between the antigen specificity of the SARS-CoV-2-reactive CD4+ T cells and the development of specific sets of adaptive immune responses. Moreover, the balance between T cells of significantly different specificities may be the key to understand how CD4+ T cell dysregulation can determine the clinical outcomes of COVID-19.
Graph Theoretical Measures of Fast Ripples Support the Epileptic Network Hypothesis.
Authors: Weiss Shennan Aibel , Pastore Tomas , Orosz Iren , Rubinstein Daniel , Gorniak Richard , Waldman Zachary , Fried Itzhak , Wu Chengyuan , Sharan Ashwini , Slezak Diego , Worrell Greg , Engel Jerome , Sperling Michael , Staba Richard
Published: January 2022

The epileptic network hypothesis and epileptogenic zone (EZ) hypothesis are two theories of ictogenesis. The network hypothesis posits that coordinated activity among interconnected nodes produces seizures. The EZ hypothesis posits that distinct regions are necessary and sufficient for seizure generation. High-frequency oscillations (HFOs), and particularly fast ripples (FR), are thought to be biomarkers of the EZ. We sought to test these theories by comparing HFO rates and networks in surgical responders and non-responders, with no appreciable change in seizure frequency or severity, within a retrospective cohort of 48 patients implanted with stereo-EEG electrodes. We recorded inter-ictal activity during non-rapid eye movement sleep and semi-automatically detected and quantified HFOs. Each electrode contact was localized in normalized coordinates. We found that the accuracy of seizure-onset zone (SOZ) electrode contact classification using HFO rates (ripples 80-250 Hz, and FR 250-600 Hz) was not significantly different in surgical responders and non-responders, suggesting that in non-responders the EZ partially encompassed the SOZ(s) (p>0.05). We also found that in the responders, FR on oscillations exhibited a higher spectral content in the SOZ compared to the non-SOZ (p<1e-5). In contrast, in the non-responders the FR had a lower spectral content in the SOZ (p<1e-5). We constructed two different networks of FR with a spectral content > 350 Hz. The first was a rate-distance network that multiplied the Euclidian distance between FR generating contacts by the average rate of FR in the two contacts. The radius of the rate-distance network, which excluded SOZ nodes, discriminated non-responders, including patients not offered resection or responsive neurostimulation (RNS) due to diffuse multi-focal onsets, with an accuracy of 0.77 [95% confidence interval (CI) 0.56-0.98]. The second FR network was constructed using the mutual information (MI) between the timing of the events to measure functional connectivity. For most non-responders, this network had a longer characteristic path length, lower mean local efficiency in the non-SOZ, and a higher nodal strength among non-SOZ nodes relative to SOZ nodes. The graphical theoretical measures from the rate-distance and MI networks of 22 non-RNS treated patients was used to train a support vector machine, which when tested on 13 distinct patients classified non-responders with an accuracy of 0.92 [95% CI 0.75-1]. These results support the epileptic network hypothesis, refute the EZ hypothesis, and suggest that surgical non-responders, and patients not selected for resection or RNS, exhibit a decentralized FR network consisting of widely distributed, hyperexcitable FR generating nodes.
Transmission dynamics and vaccination strategies for Crimean-Congo haemorrhagic fever virus in Afghanistan: a modelling study
Authors: Vesga Juan F , Clark Madeleine H A , Ayazi Edris , Apolloni Andrea , Leslie Toby , Edmunds W John , Métras Raphaëlle
Published: January 2022

Background

Crimean-Congo haemorrhagic fever virus (CCHFV) is a highly pathogenic virus for which a safe and effective vaccine is not yet available, despite being considered a priority emerging pathogen. Understanding transmission patterns and the use of potential effective vaccines are central elements of the future plan against this infection.

Methods

We developed a series of models of transmission amongst livestock, and spillover infection into humans. We use real-world human and animal data from a CCHFV endemic area in Afghanistan (Herat) to calibrate our models. We assess the value of environmental drivers as proxy indicators of vector activity, and select the best model using deviance information criteria. Finally we assess the impact of vaccination by simulating campaigns targeted to humans or livestock, and to high-risk subpopulations (i.e, farmers).

Findings

Saturation deficit is the indicator that better explains tick activity trends in Herat. Recent increments in reported CCHFV cases in this area are more likely explained by increased surveillance capacity instead of changes in the background transmission dynamics. Modelling suggests that clinical cases only represent 31% (95% CrI 28%-33%) of total infections in this area. Vaccination campaigns targeting humans would result in a much larger impact than livestock vaccination (266 vs 31 clinical cases averted respectively) and a more efficient option when assessed in courses per case averted (35 vs 431 respectively). Targeted vaccination to farmers is impactful and more efficient, resulting in 19 courses per case averted (95% CrI 7-62) compared to targeting the general population (35 95% CrI 16-107)

Interpretation

CCHFV is endemic in Herat, and transmission cycles are well predicted by environmental drivers like saturation deficit. Vaccinating humans is likely to be more efficient and impactful than animals, and importantly targeted interventions to high risk groups like farmers can offer a more efficient approach to vaccine roll-out.

Funding

W.J.E., JFV and MHAC were funded by the Department of Health and Social Care using UK Aid funding managed by the National Institute for Health Research (Vaccine Efficacy Evaluation for Priority Emerging Diseases: PR-OD-1017-20002). The views expressed in this publication are those of the authors and not necessarily those of the Department of Health and Social Care.
Causal associations between body fat accumulation and COVID-19 severity: A Mendelian randomization study
Authors: Yoshiji Satoshi , Tanaka Daisuke , Minamino Hiroto , Murakami Takaaki , Fujita Yoshihito , Richards J. Brent , Inagaki Nobuya
Published: January 2022

Purpose

The causal effects of body fat mass and body fat-free mass on coronavirus disease 2019 (COVID-19) severity remain unclear. Here, we used Mendelian randomization (MR) to evaluate the causal relationships between body fat-related traits and COVID-19 severity.

Material and Methods

We identified single nucleotide polymorphisms associated with body mass index (BMI) and direct measures of body fat (i.e., body fat percentage, body fat mass, and body fat-free mass) in 461,460, 454,633, 454,137, and 454,850 individuals of European ancestry from the UK Biobank, respectively. We then performed two-sample MR to ascertain their effects on severe COVID-19 (cases: 4,792; controls: 1,054,664) from the COVID-19 Host Genetics Initiative.

Results

We found that an increase in BMI, body fat percentage, and body fat mass by one standard deviation were each associated with severe COVID-19 (odds ratio (OR)BMI = 1.49, 95%CI: 1.19–1.87, P = 5.57×10−4; ORbody fat percentage = 1.94, 95%CI: 1.41–2.67, P = 5.07×10−5; and ORbody fat mass = 1.61, 95%CI: 1.28–2.04, P = 5.51×10−5). Further, we evaluated independent causal effects of body fat mass and body fat-free mass using multivariable MR and revealed that only body fat mass was independently associated with severe COVID-19 (ORbody fat mass = 2.91, 95%CI: 1.71–4.96, P = 8.85×10−5 and ORbody fat-free mass = 1.02, 95%CI: 0.61–1.67, P = 0.945).

Conclusions

This study demonstrates the causal effects of body fat accumulation on COVID-19 severity and indicates that the biological pathways influencing the relationship between COVID-19 and obesity are likely mediated through body fat mass.
Coupling a Live Cell Directed Evolution Assay with Coevolutionary Landscapes to Engineer an Improved Fluorescent Rhodopsin Chloride Sensor
Authors: Chi Hsichuan , Zhou Qin , Tutol Jasmine N. , Phelps Shelby M. , Lee Jessica , Kapadia Paarth , Morcos Faruck , Dodani Sheel C.
Published: January 2022

Our understanding of chloride in biology can be accelerated through the application of fluorescent protein-based sensors in living cells. Laboratory-guided evolution can be used to diversify and identify sensors with specific properties. Recently, we established that the fluorescent proton-pumping rhodopsinwtGR fromGloeobacter violaceuscan be converted into a fluorescent sensor for chloride. To unlock this non-natural function, a single point mutation at the Schiff counterion position from D121V was introduced intowtGR fused with cyan fluorescent protein (CFP) resulting in GR1-CFP. Here, we have integrated coevolutionary analysis with directed evolution to understand how the rhodopsin sequence space can be explored and engineered to improve this starting point. We first show how evolutionary couplings are predictive of functional sites in the rhodopsin family and how a fitness metric based on sequence can be used to quantify known proton-pumping activities of GR-CFP variants. Then, we couple this ability to predict potential functional outcomes with a screening and selection assay in liveEscherichia colito reduce the mutational search space of five residues along the proton-pumping pathway in GR1-CFP. This iterative selection process results in GR2-CFP with four additional mutations, E132K, A84K, T125C, and V245I. Finally, bulk, and single fluorescence measurements in liveE. colireveal that GR2-CFP is a reversible, ratiometric fluorescent sensor for extracellular chloride with an improved dynamic range. We anticipate that our framework will be applicable to other systems, providing a more efficient methodology to engineer fluorescent-protein based sensors with desired properties.

Abstract Figure
Poison frog dietary preference depends on prey type and alkaloid load
Authors: Moskowitz Nora A. , D’Agui Rachel , Alvarez-Buylla Aurora , Fiocca Katherine , O’Connell Lauren A.
Published: January 2022

The ability to acquire chemical defenses through the diet has evolved across several major taxa. Chemically defended organisms may need to balance chemical defense acquisition and nutritional quality of prey items. However, these dietary preferences and potential trade-offs are rarely considered in the framework of diet-derived defenses. Poison frogs (Family Dendrobatidae) acquire defensive alkaloids from their arthropod diet of ants and mites, although their dietary preferences have never been investigated. We conducted prey preference assays with the Dyeing Poison frog (Dendrobates tinctorius) to test the hypothesis that alkaloid load and prey traits influence frog dietary preferences. We tested size preferences (big versus small) within each of four prey groups (ants, beetles, flies, and fly larvae) and found that frogs preferred interacting with smaller prey items of the fly and beetle groups. Frog taxonomic prey preferences were also tested as we experimentally increased their chemical defense load by feeding frogs decahydroquinoline, an alkaloid compound similar to those naturally found in their diet. Contrary to our expectations, overall preferences did not change during alkaloid consumption, as frogs across groups preferred fly larvae over other prey. Finally, we assessed the protein and lipid content of prey items and found that small ants have the highest lipid content while large fly larvae have the highest protein content. Our results suggest that consideration of toxicity and prey nutritional value are important factors in understanding the evolution of acquired chemical defenses and niche partitioning as a whole.
Dopamine and ALK4 signaling synergize to induce PCBP1-mediated alternative splicing of FosB and sustained behavioral sensitization to cocaine
Authors: Krapacher Favio A. , Fernández-Suárez Diana , Andersson Annika , Carrier-Ruiz Alvaro , Ibáñez Carlos F.
Published: January 2022

ΔFosB, an alternative spliced product of FosB, is an essential component of dopamine-induced reward pathways and a master switch for addiction. However, the molecular mechanisms of its generation and regulation by dopamine signaling are unknown. Here we report that dopamine D1 receptor signaling synergizes with the activin/ALK4/Smad3 pathway to potentiate the generation of ΔFosB mRNA in medium spiny neurons (MSNs) of the nucleus-accumbens (NAc) through activation of the RNA binding protein PCBP1, a regulator of mRNA splicing. Concurrent activation of PCBP1 and Smad3 by D1 and ALK4 signaling induced their interaction, nuclear translocation, and binding to sequences in exon-4 and intron-4 of FosB mRNA. Ablation of either ALK4 or PCBP1 in MSNs impaired ΔFosB mRNA induction and nuclear translocation of ΔFosB protein in response to repeated co-stimulation of D1 and ALK4 receptors. Importantly, ALK4 was required in NAc MSNs of adult mice for behavioral sensitization to cocaine. These findings uncover an unexpected mechanism for ΔFosB generation and drug-induced sensitization through convergent dopamine and ALK4 signaling.
Genetic variation of human myokine signaling is dominated by biologic sex and sex hormones
Authors: Velez Leandro M. , Van Cassandra , Moore Timothy M. , Zhou Zhenqi , Johnson Casey , Hevener Andrea L. , Seldin Marcus M.
Published: January 2022

Abstract/Introduction

Proteins secreted from skeletal muscle, termed myokines, allow muscle to impact systemic physiology and disease. Myokines play critical roles in a variety of processes, including metabolic homeostasis, exercise improvements, inflammation, cancer and cognitive functions1–6. Despite the clear relevance of these factors in mediating a multitude of physiological outcomes, the genetic architecture, regulation and functions of myokines, as well as degree of conservation of these communication circuits remains inadequately understood. Given that biologic sex controls critical aspects of nearly every physiologic outcome, it is essential to consider when relating specific mechanisms to complex genetic and metabolic interactions. Specifically, many metabolic traits impacted by myokines show striking sex differences arising from hormonal7–10, genetic7,11 or gene-by-sex interactions12,13. In this study, we performed a genetic survey of myokine gene regulation and cross-tissue signaling in humans where sex as a biological variable was emphasized. While expression levels of a majority of myokines and cell proportions within skeletal muscle showed little differences between males and females, nearly all significant cross-tissue enrichments operated in a sex-specific or hormone-dependent fashion; in particular, with estrogens. These sex- and hormone-specific effects were consistent across key metabolic tissues: liver, pancreas, hypothalamus, intestine, heart, visceral and subcutaneous adipose tissue. Skeletal muscle estrogen receptor enrichments across metabolic tissues appeared stronger than androgen receptor and, surprisingly, ~3-fold higher in males compared to females. To define the causal roles of estrogen signaling on myokine gene expression and functions, we generated male and female mice which lack estrogen receptor α (Esr1) specifically in skeletal muscle and integrated global RNA-Sequencing with human data. These analyses highlighted mechanisms of sex-dependent myokine signaling conserved between species, such as myostatin enriched for divergent substrate utilization pathways between sexes. Several other sex-dependent mechanisms of myokine signaling were uncovered, such as muscle-derived TNFα exerting stronger inflammatory signaling in females compared to males and GPX3 as a male-specific link between glycolytic fiber abundance and hepatic inflammation. Collectively, we provide the first genetic survey of human myokines and highlight sex and estrogen receptor signaling as critical variables when assaying myokine functions and how changes in cell composition impact other metabolic organs.
Elucidating Collective Translocation of Nanoparticles Across the Skin Lipid Barrier: A Molecular Dynamics Study
Authors: Badhe Yogesh , Sharma Pradyumn , Gupta Rakesh , Rai Beena
Published: January 2022

The top layer of skin, the stratum corneum, provides a formidable barrier to the skin. Nanoparticles are utilized and further explored for personal and health care applications related to the skin. In past years several researchers have studied the translocation and permeation of nanoparticles of various shapes, sizes, and surface chemistry through the cell membranes. Most of these studies focused on a single nanoparticle and a simple bilayer system, whereas skin has a highly complex lipid membrane architecture. Moreover, it is highly unlikely that a nanoparticle formulation applied on the skin will not have multiple nanoparticle-nanoparticle and skin-nanoparticle interactions. In this study, we have utilized coarse-grained MARTINI molecular dynamics simulations to assess the interactions of two types (bare and dodecane-thiol coated) of nanoparticles with two models (single bilayer and double bilayer) of skin lipid membranes. The nanoparticles were found to be partitioned from the water layer to the lipid membrane as an individual entity as well as in the cluster form. It was discovered that each nanoparticle reached the interior of both single bilayer and double bilayer membrane irrespective of nanoparticle type and concentration, though coated particles were observed to efficiently traverse across bilayer when compared with bare particles. The coated nanoparticles also created a single large cluster inside the membrane, whereas bare nanoparticles were found in small clusters. Both the nanoparticles exhibited preferential interactions with cholesterol molecules present in the lipid membrane as compared to other lipid components of the membrane. We have also observed that the single membrane model exhibited unrealistic instability at moderate to the higher concentration of nanoparticles, and hence for translocation study, at minimum double bilayer model should be employed.
Network architecture producing swing to stance transitions in an insect walking system
Authors: Strohmer Beck , Mantziaris Charalampos , Kynigopoulos Demos , Manoonpong Poramate , Larsen Leon Bonde , Büschges Ansgar
Published: January 2022

The walking system of the stick insect is one of the most thoroughly described invertebrate systems. We know a lot about the role of sensory input in the control of stepping of a single leg. However, the neuronal organization and connectivity of the central neural networks underlying the rhythmic activation and coordination of leg muscles still remain elusive. It is assumed that these networks can couple in the absence of phasic sensory input due to the observation of spontaneous recurrent patterns (SRPs) of coordinated motor activity equivalent to fictive stepping-phase transitions. Here we sought to quantify the phase of motor activity within SRPs in the isolated and interconnected meso- and metathoracic ganglia. We show that SRPs occur not only in the meso-, but also in the metathoracic ganglia of the stick insect, discovering a qualitative difference between them. We construct a network based on neurophysiological data capable of reproducing the measured SRP phases to investigate this difference. By comparing network output to the biological measurements we confirm the plausibility of the architecture and provide a hypothesis to account for these qualitative differences. The neural architecture we present couples individual central pattern generators to reproduce the fictive stepping-phase transitions observed in deafferented stick insect preparations after pharmacological activation, providing insights into the neural architecture underlying coordinated locomotion.
Automatically tracking feeding behavior in populations of foraging C. elegans
Authors: Bonnard Elsa , Liu Jun , Zjacic Nicolina , Alvarez Luis , Scholz Monika
Published: January 2022

C. elegans feeds on bacteria and other small microorganisms which it ingests using its pharynx, a neuromuscular pump. Currently, measuring feeding behavior requires tracking a single animal, indirectly estimating food intake from population-level metrics, or using restrained animals. To enable large throughput feeding measurements of unrestrained, crawling worms on agarose plates at a single worm resolution, we developed an imaging protocol and a complementary image analysis tool called PharaGlow. We image up to 50 unrestrained crawling worms simultaneously and extract locomotion and feeding behaviors. We demonstrate the tool’s robustness and high-throughput capabilities by measuring feeding in different use-case scenarios, such as through development, with genetic and chemical perturbations that result in faster and slower pumping, and in the presence or absence of food. Finally, we demonstrate that our tool is capable of long-term imaging by showing behavioral dynamics of mating animals over an hour. The low-resolution fluorescence microscopes required are readily available in C. elegans laboratories, and in combination with our python-based analysis workflow makes this methodology easily accessible. PharaGlow therefore enables the observation and analysis of the temporal dynamics of food intake and locomotory behaviors with high-throughput and precision in a user-friendly system.
rrQNet: protein contact map quality estimation by deep evolutionary reconciliation
Authors: Roche Rahmatullah , Bhattacharya Sutanu , Shuvo Md Hossain , Bhattacharya Debswapna
Published: January 2022

Protein contact maps have proven to be a valuable tool in the deep learning revolution of protein structure prediction, ushering in the recent breakthrough by AlphaFold2. However, self-assessment of the quality of predicted structures are typically performed at the granularity of 3D coordinates as opposed to directly exploiting the rotation- and translation-invariant 2D contact maps. Here we present rrQNet, a deep learning method for self-assessment in 2D by contact map quality estimation. Our approach is based on the intuition that for a contact map to be of high quality, the residue pairs predicted to be in contact should be mutually consistent with the evolutionary context of the protein. The deep neural network architecture of rrQNet implements this intuition by cascading two deep modules—one encoding the evolutionary context and the other performing evolutionary reconciliation. The penultimate stage of rrQNet estimates the quality scores at the interacting residue-pair level, which are then aggregated for estimating the quality of a contact map. This design choice offers versatility at varied resolutions from individual residue pairs to full-fledged contact maps. Trained on multiple complementary sources of contact predictors, rrQNet facilitates generalizability across various contact maps. By rigorously testing using publicly available datasets and comparing against several in-house baseline approaches, we show that rrQNet accurately reproduces the true quality score of a predicted contact map and successfully distinguishes between accurate and inaccurate contact maps predicted by a wide variety of contact predictors. The open-source rrQNet software package is freely available at https://github.com/Bhattacharya-Lab/rrQNet.
Pairwise and higher-order epistatic effects among somatic cancer mutations across oncogenesis
Authors: Alfaro-Murillo Jorge A. , Townsend Jeffrey P.
Published: January 2022

Cancer occurs as a consequence of multiple somatic mutations that lead to uncontrolled cell growth. Mutual exclusivity and co-occurrence of mutations imply—but do not prove—that they can exert synergistic or antagonistic epistatic effects on oncogenesis. Knowledge of these interactions, and the consequent trajectories of mutation and selection that lead to cancer has been a longstanding goal within the cancer research community. Recent research has revealed mutation rates and scaled selection coefficients for specific recurrent variants across many cancer types. However, estimation of pairwise and higher-order effects—essential to estimation of the trajectory of likely cancer genotoypes—has been a challenge. Therefore, we have developed a continuous-time Markov chain model that enables the estimation of mutation origination and fixation (flux), dependent on somatic cancer genotype. Coupling the continuous-time Markov chain model with a deconvolution approach provides estimates of underlying mutation rates and selection across the trajectory of oncogenesis. We demonstrate computation of fluxes and selection coefficients in a somatic evolutionary model for the four most frequently variant driver genes (TP53, LRP1B, KRASandSTK11) from 565 cases of lung adenocarcinoma. Our analysis reveals multiple antagonistic epistatic effects that reduce the possible routes of oncogenesis, and inform cancer research regarding viable trajectories of somatic evolution whose progression could be forestalled by precision medicine. Synergistic epistatic effects are also identified, most notably in the somatic genotypeTP53+LRP1Bfor mutations in theKRASgene, and in somatic genotypes containingKRASorTP53mutations for mutations in theSTK11gene. Large positive fluxes ofKRASvariants were driven by large selection coefficients, whereas the flux towardLRP1Bmutations was substantially aided by a large mutation rate for this gene. The approach enables inference of the most likely routes of site-specific variant evolution and estimation of the strength of selection operating on each step along the route, a key component of what we need to know to develop and implement personalized cancer therapies.
Quantitative proteomics of the CDK9 interactome reveals a novel function of the HSP90-CDC37-P-TEFb complex for BETi-induced HIV-1 latency reactivation
Authors: Wang Cong , Pan Zhenrui , He Yaohui , Zhang Zhanming , Liu Rongdiao , Xue Yuhua , Zhou Qiang , Gao Xiang
Published: January 2022

Brd4 has been intensively investigated as a promising drug target because of its implicated functions in oncogenesis, inflammation and HIV-1 transcription. The formation of the Brd4-P-TEFb (CDK9/Cyclin T1) complex and its regulation of transcriptional elongation is critical for HIV latency reactivation and expression of many oncogenes. To further investigate the mechanism of the Brd4-P-TEFb complex in controlling elongation, mass spectrometry-based quantitative proteomics of the CDK9 interactome was performed. Upon treatment with the selective BET bromodomain inhibitor (BETi) JQ1, 535 proteins were successfully identified with high confidence as CDK9-interacting proteins. Among them, that increased bindings of HSP90 and CDC37 to CDK9 were particularly striking, and our data suggest that the HSP90-CDC37-P-TEFb complex is involved in controlling P-TEFb’s dynamic equilibrium during BETi-induced HIV-1 latency reactivation. Furthermore, the HSP90-CDC37-P-TEFb complex directly regulates HIV-1 transcription and relies on the recruitment by heat shock factor 1 (HSF1) for binding to the HIV-1 promoter. These results advance the understanding of HSP90-CDC37-P-TEFb in HIV-1 latency reversal and enlighten the development of potential strategies to eradicate HIV-1 using a combination of targeted drugs.
Combination of Spironolactone and Sitagliptin Improves Clinical Outcomes of Outpatients with COVID-19: A Prospective Cohort Study
Authors: Davarpanah Mohammad Ali , Adatorwovor Reuben , Mansoori Yasaman , Ramsheh Fatemeh Sadat Rajaie , Parsa Amir , Hajiani Mehdi , Faramarzi Hossein , Kavuluru Ramakanth , Asadipooya Kamyar
Published: January 2022

Rationale

Coronavirus disease 2019 (COVID-19) leads to hospitalization and death, especially in elderly and those with comorbidities. There are evidences showing that sitagliptin and spironolactone can potentially improve the clinical outcomes of COVID-19 cases.

Objective

In this observational study on acutely symptomatic outpatient COVID-19 cases, we investigated the effects of spironolactone and sitagliptin on the outcomes of the disease.

Methods

This prospective cohort study was conducted at Shiraz University of Medical Sciences Clinics during the fifth wave of the COVID-19 pandemic between July 2021 and September 2021. We followed mild to moderate symptomatic COVID-19 patients, who were treated with either combination (spironolactone 100 mg daily and sitagliptin 100 mg daily) or standard (steroid, antiviral and/or supportive care) therapy up to 30 days. Our primary outcome was hospitalization rate. The secondary outcomes included ER visit, duration of disease, and complications, such as hypoglycemia, low blood pressure or altered mental status.

Results

Of the 206 patients referred to clinics, 103 received standard therapy and 103 treated with combination therapy. There were no significant differences in baseline characteristics, except for slightly higher clinical score in control group (6.92 ± 4.01 control, 4.87 ± 2.92 combination; P <0.0001). Treatment with combination therapy was associated with lower admission rate (5.8% combination, 22.3% control; P = 0.0011), ER visits (7.8% combination, 23.3% control; P = 0.0021) and average duration of symptoms (6.67 ± 2.30 days combination, 18.71 ± 6.49 days control; P =<0.0001).

Conclusion

In this prospective cohort study of acutely ill outpatients with COVID-19, the combination of sitagliptin and spironolactone reduced duration of COVID infection and hospital visits better than standard therapeutic approaches. The effects of combination of sitagliptin and spironolactone in COVID-19 patients should be further verified in a double blind, randomized, placebo-controlled trial.

Iranian Registry of Clinical Trials

IRCT registration number: IRCT20201003048904N2, Registration date: December 10, 2020.
Quantifying the direct and indirect protection provided by insecticide treated bed nets against malaria
Authors: Unwin H. Juliette T. , Smith Ellie Sherrard , Churcher Thomas S. , Ghani Azra C.
Published: January 2022

Long lasting insecticide treated mosquito nets (LLINs) provide both direct and indirect protection against bites from mosquitoes potentially transmitting malaria. Direct personal protection is provided to net users given both the net’s physical barrier and its insecticidal action. Indirect mass protection for the community is afforded through reduced infectious bites per person annually (entomological inoculation rate, EIR). Quantifying these protective effects can help strategize options for net interventions, particularly as insecticide-resistant mosquitoes spread.

These types of protection are inherently linked, rendering it impossible to empirically quantify the contribution of each to the overall ‘community effect’, instead we investigate this with a modelling framework and compare model predictions to trends with Demographic Health Survey (DHS) data.

Our modelling exercise predicts that in a situation with an EIR of 100, the reduction in EIR from an untreated net used by 80% of the population is 52% [95% CI: 12% - 84%] for users and 21% [95% CI: 0% - 57%] for non-users. Due to the impact of the insecticide, the reduction in EIR for LLINs is 89% [95% CI: 67% - 98%] for users and 74% [95% CI: 48% - 92%] for non-users, but this protection reduces as insecticide resistance in mosquitoes increases. Modelled trends in the difference in protection between users and non-users across endemicity and net usage levels are consistent with DHS data (2000-2018).

This study supports the concept of a community effect from LLINs, highlights the value of blocking and killing mosquitoes for community protection. Achieving high LLIN usage is always preferential, but there remains protection to non-users as the number of people using nets increases.
Claspin is required for growth recovery from serum starvation through regulating the PI3K-PDK1-mTOR pathway
Authors: Yang Chi-Chun , Masai Hisao
Published: January 2022

Growth recovery from serum starvation requires the activation of PI3 kinase (PI3K)-PDK1-Akt-mTOR pathways. Claspin plays multiple important roles in regulation of DNA replication as a mediator for the cellular response to replication stress, an integral replication fork factor that facilitates replication fork progression and a factor that promotes initiation by recruiting Cdc7 kinase. Here, we report a novel role of Claspin in growth recovery from serum starvation. In the absence of Claspin, cells do not proceed into S phase and eventually die. Claspin interacts with PI3K and mTOR, and is required for activation of PI3K-PDK1-mTOR and for that of mTOR downstream factors, p70S6K and 4E-BP1, but not for p38 MAPK cascade during the recovery from serum starvation. PDK1 interacts with Claspin, notably with CKBD, in a manner dependent on phosphorylation of the latter protein, and is required for interaction of mTOR with Claspin. p53 and ROS (Reactive Oxygen Species) inhibitors increased survival of Claspin-deficient cells released from serum starvation. Thus, Claspin plays a novel role as a mediator/protein platform for nutrition-induced proliferation/survival signaling by activating the mTOR pathway.
Molecular and connectomic vulnerability shape cross-disorder cortical abnormalities
Authors: Hansen Justine Y. , Shafiei Golia , Vogel Jacob W. , Smart Kelly , Bearden Carrie E. , Hoogman Martine , Franke Barbara , van Rooij Daan , Buitelaar Jan , McDonald Carrie R. , Sisodiya Sanjay M. , Schmaal Lianne , Veltman Dick J. , van den Heuvel Odile A. , Stein Dan J. , van Erp Theo G. M. , Ching Christopher R. K. , Andreassen Ole A. , Hajek Tomas , Opel Nils , Modinos Gemma , Aleman André , van der Werf Ysbrand , Jahanshad Neda , Thomopoulos Sophia I. , Thompson Paul M. , Carson Richard E. , Dagher Alain , Misic Bratislav
Published: January 2022

Numerous brain disorders demonstrate structural brain abnormalities, which are thought to arise from molecular perturbations or connectome miswiring. The unique and shared contributions of these molecular and connectomic vulnerabilities to brain disorders remain unknown, and has yet to be studied in a single multi-disorder framework. Using MRI morphometry from the ENIGMA consortium, we construct maps of cortical abnormalities for thirteen neurodevelopmental, neurological, and psychiatric disorders from N = 21 000 patients and N = 26 000 controls, collected using a harmonized processing protocol. We systematically compare cortical maps to multiple micro-architectural measures, including gene expression, neurotransmitter density, metabolism, and myelination (molecular vulnerability), as well as global connectomic measures including number of connections, centrality, and connection diversity (connectomic vulnerability). We find that regional molecular vulnerability and macroscale brain network architecture interact to drive the spatial patterning of cortical abnormalities in multiple disorders. Local attributes, particularly neurotransmitter receptor profiles, constitute the best predictors of both disorder-specific cortical morphology and cross-disorder similarity. Finally, we find that cross-disorder abnormalities are consistently subtended by a small subset of network epicentres in bilateral sensory-motor, medial temporal lobe, precuneus, and superior parietal cortex. Collectively, our results highlight how local biological attributes and global connectivity jointly shape cross-disorder cortical abnormalities.
An atlas of plant full-length RNA reveals tissue-specific and evolutionarily-conserved regulation of poly(A) tail length
Authors: Jia Jinbu , Lu Wenqin , Liu Bo , Yu Yiming , Jin Xianhao , Shu Yi , Long Yanping , Zhai Jixian
Published: January 2022

Introductory paragraph

Poly(A) tail is a hallmark of eukaryotic mRNA and its length plays an essential role in regulating mRNA metabolism1–3. However, a comprehensive resource for plant poly(A) tail length has yet to be established. Here, we applied a poly(A)-enrichment-free, Nanopore-based method4,5 to profile full-length RNA with poly(A) tail information in plants. Our atlas contains over 120 million polyadenylated mRNA molecules from seven different tissues of Arabidopsis, as well as the shoot tissue of maize, soybean and rice. In most tissues, the size of plant poly(A) tails shows peaks at approximately 20 and 45 nt, presumably the sizes protected by one and two poly(A) binding proteins (PABP), respectively2,6, while the poly(A) tails in pollen exhibit a distinct pattern with strong peaks centered at 55 and 80 nt. Moreover, poly(A) tail length is regulated in a gene-specific manner — mRNAs with short half-lives in general have long poly(A) tails, while mRNAs with long half-lives are featured with relatively short poly(A) tails that peak at ~45 nt, suggesting that protection of poly(A) tail in this size by PABP is essential for mRNA stability. Across species, poly(A) tails in the nucleus are almost twice as long as in the cytoplasm, implying a conserved rapid shortening process of poly(A) tail occurs before the mRNA is stabilized in cytoplasm. Our comprehensive dataset lays the groundwork for future functional and evolutionary studies on poly(A) tail length regulation in plants.
VCF2Prot: An Efficient and Parallel Tool for Generating Personalized Proteomes from VCF Files
Authors: ElAbd Hesham , Degenhardt Frauke , Lenz Tobias L. , Franke Andre , Wendorff Mareike
Published: January 2022

Motivation

The ability to generate sample-specific protein sequences is a crucial step in neo-antigen discovery, cancer vaccine development, and proteogenomics. The revolutionary increase in the throughput of sequencers has fueled large-scale genomic and transcriptomic studies, holding great promises for the emerging field of personalized medicine. However, most sequencing projects store their sequencing data in an abbreviated variant calling format (VCF) that is not immediately amenable to subsequent proteomic and peptidomic analyses. Furthermore, data processing of such increasingly massive genome-scale datasets calls for parallel and concurrent programming, and consequently refactoring of existing algorithms and/or the development of new parallel algorithms.

Results

Here, we introduce sequence intermediate representation (SIR), a novel and generic algorithm for generating personalized or sample-specific protein sequences from a consequence-called VCF file and the corresponding reference proteome. An implementation of SIR, named VCF2Prot, was developed to aid personalized medicine and proteogenomics by generating personalized proteomes in FASTA format from a collection of consequence-called genomic alterations stored in a VCF file. Benchmarking VCF2Prot against the recently published PrecisionProDB showed an ~1000-fold improvement in runtime (depending on the input size). Furthermore, in a scale-up study VCF2Prot processed a VCF file containing 99,254 variants observed across 8,192 patients in ~ 11 minutes, demonstrating the massive improvement in the execution speed and the utility of SIR and VCF2prot in bridging large-scale genomic and proteomic studies.

Availability and Implementation

VCF2Prot comes with a permissive MIT-license, enabling the commercial and non-commercial utilization of the tool. The source code along with precompiled versions for Linux/Mac OS are available at https://github.com/ikmb/vcf2prot. The modular units used for building VCF2Prot are available as a Rust crate at https://crates.io/crates/ppgg with documentations and examples at https://docs.rs/ppgg/0.1.4/ppgg/ under the same MIT-license.