bluuebunny/crossref_metadata_2025 huggingface dataset:
Topological Data Analysis of Human Brain Networks Through Order Statistics
Authors: Das Soumya , Anand D. Vijay , Chung Moo K.
Published: April 2022

Understanding the topological characteristics of the brain network across a population is central to understanding brain functions. The abstraction of human connectome as a graph has been pivotal in gaining insights on the topological features of the brain network. The development of group-level statistical inference procedures in brain graphs while accounting for the heterogeneity and randomness still remains a difficult task. In this study, we develop a robust statistical framework based on persistent homology using the order statistics for analyzing brain networks. The use of order statistics greatly simplifies the computation of the persistent barcodes. We validate the proposed methods using comprehensive simulation studies and subsequently apply to the resting-state functional magnetic resonance images. We conclude a statistically significant topological difference between the male and female brain networks.

Author summary

We fit a random graph model to the brain network and compute the expected persistent barcodes using order statistics. This novel approach significantly simplifies the computation of expected persistent barcodes, which otherwise requires complex theoretical constructs. Subsequently, the proposed statistical framework is used to discriminate if two groups of brain networks are topologically different. The method is applied in determining the sexual dimorphism in the shape of resting-state functional magnetic resonance images.
D27-LIKE1 carotenoid isomerase has a preference towards trans/cis and cis/cis conversions in Arabidopsis
Authors: Gulyás Zsolt , Moncsek Blanka , Áron Hamow Kamirán , Stráner Pál , Badics Eszter , Incze Norbert , Darkó Éva , Nagy Valéria , Perczel András , Kovács László , Soós Vilmos
Published: April 2022

Carotenoids are colourful isoprenoids that contribute to a variety of physiological processes in plants. They also function as biosynthesis precursors of abscisic acid (ABA) and strigolactones (SLs). SL biosynthesis starts with the enzymatic conversion of all-trans-β-carotene to 9-cis-β-carotene by the DWARF27 (D27) isomerase. In Arabidopsis, D27 has two closely related paralogs, D27-LIKE1 and D27-LIKE2 which were predicted to be β-carotene-isomerases. Here we characterised D27-LIKE1 and identified some key aspects of its function. Arabidopsis d27-like1-1 mutant does not display any SL or karrikin-deficient traits, however, it exhibits a substantially higher 9-cis-violaxanthin content. In vitro feeding assays with recombinant D27-LIKE1 revealed that the protein exhibits affinity to all β-carotene isoforms but with an exclusive preference towards trans/cis conversions and the interconversion between 9-cis, 13-cis and 15-cis-β-carotene forms. Feeding experiments with zeaxanthin and violaxanthin isomers revealed that D27-LIKE1 accepts these xanthophylls as substrates. The remarkably higher 9-cis-violaxanthin content of the mutant is accompanied by a slightly higher ABA level. Finally, we presented evidence that D27-LIKE1 mRNA is phloem mobile and D27-LIKE1 is an ancient isomerase with long evolutionary history. In summary, we demonstrated that D27-LIKE1 is a carotenoid isomerase with multi-substrate specificity and has a characteristic preference towards the catalysation of cis/cis interconversion of carotenoids. Therefore, D27-LIKE1 is a potential regulator of carotenoid cis pools and eventually, SL and ABA biosynthesis pathways.
Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy
Authors: Guo Binjie , Zheng Hanyu , Jiang Haohan , Li Xiaodan , Guan Naiyu , Zuo Yanming , Zhang Yicheng , Yang Hengfu , Wang Xuhua
Published: April 2022

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying machine learning methods. To overcome this limitation, in a novel end-to-end architecture (named FeatNN), we develop a coevolutionary strategy to jointly represent the structure and sequence features of proteins and ultimately optimize the mathematical models for predicting CPA. Furthermore, from the perspective of data-driven approach, we proposed a rational method that can utilize both high- and low-quality databases to optimize the accuracy and generalization ability of FeatNN in CPA prediction tasks. Notably, we visually interpret the feature interaction process between sequence and structure in the rationally designed architecture. As a result, FeatNN considerably outperforms the state-of-the-art (SOTA) baseline in virtual drug screening tasks, indicating the feasibility of this approach for practical use. FeatNN provides an outstanding method for higher CPA prediction accuracy and better generalization ability by efficiently representing multimodal information of proteins via a coevolutionary strategy.
Isometric Spiracular Scaling in Scarab Beetles: Implications for Diffusive and Advective Oxygen Transport
Authors: Wagner Julian M. , Klok C. Jaco , Duell Meghan E. , Socha John J. , Cao Guohua , Gong Hao , Harrison Jon F.
Published: April 2022

The scaling of respiratory structures has been hypothesized to be a major driving factor in the evolution of many aspects of animal physiology. Here we provide the first assessment of the scaling of the spiracles in insects using ten scarab beetle species differing 180x in mass, including some of the most massive extant insect species. Using X-ray microtomography, we measured the cross-sectional area and depth of all eight spiracles, enabling the calculation of their diffusive and advective capacities. Each of these metrics scaled with geometric isometry.Because diffusive capacities scale with lower slopes than metabolic rates, the largest beetles measured require 10-fold higher PO2gradients across the spiracles to sustain metabolism by diffusion compared to the smallest species. Large beetles can exchange sufficient oxygen for resting metabolism by diffusion across the spiracles, but not during flight. In contrast, spiracular advective capacities scale similarly or more steeply than metabolic rates, so spiracular advective capacities should match or exceed respiratory demands in the largest beetles. These data illustrate a general principle of gas exchange: scaling of respiratory transport structures with geometric isometry diminishes the potential for diffusive gas exchange but enhances advective capacities; combining such structural scaling with muscle-driven ventilation allows larger animals to achieve high metabolic rates when active.
A snapshot of statistical methods used in experimental immunoblotting: A scoping review
Authors: Gosselin Romain-Daniel
Published: April 2022

Among the many avenues considered to make life science more reproducible, the improvement of the quality and openness of statistical methods has taken centre stage. However, although disparities across research fields and techniques are not unknown, they remain largely unexplored. The present scoping review aims to provide a first overview of statistical methods used in biochemical research involving immunoblotting (also referred to as western blotting), a technique frequently used to quantify proteins of interest. A reverse chronological systematic sampling was implemented to explore the PubMed online browser and analyse 2932 experimental conditions (i.e., experimental groups) in quantitative immunoblots from 64 articles published at the end of 2021. The statistical test (actual study size n = 67) and software (actual study size n = 61) used for each article and the sample size for each experimental condition were documented. The results indicate an omnipresence of parametric tests, mostly one-way analysis of variance (ANOVA, 15/67) and Student’s t-test (13/67), but for many articles the statistical procedure was not clearly divulged (23/67). GraphPad Prism was the most commonly used statistical package (36/61), but many (14/61) articles did not reveal the package used. Finally, the sample size was clearly disclosed in only 1054/2932 conditions in which its median value was 3 (IQR = [3 - 6]). This study suggests that the transparency of reporting might be suboptimal in immunoblotting research and prompts more comprehensive systematic reviews in future.
Learning to Express Reward Prediction Error-like Dopaminergic Activity Requires Plastic Representations of Time
Authors: Cone Ian , Clopath Claudia , Shouval Harel Z.
Published: April 2022

The dominant theoretical framework to account for reinforcement learning in the brain is temporal difference (TD) reinforcement learning. The normative motivation for TD theory is that the brain needs to learn about expected future rewards in order to learn how to maximize these rewards. The TD framework predicts that some neuronal elements should represent the reward prediction error (RPE), which means they signal the difference between the expected future rewards and the actual rewards. What makes the TD learning theory so prominent is that the firing properties of dopaminergic neurons in the ventral tegmental area (VTA) appear similar to those of RPE model-neurons in TD learning. Biologically plausible implementations of TD learning assume a fixed temporal basis for each stimulus that might eventually predict a reward. Here we show on the basis of first principles that such a fixed temporal basis is implausible. We also show that certain predictions of TD learning are inconsistent with experimental data. We propose instead an alternative theoretical framework, coined FLEX (FlexiblyLearnedErrors in Expected Reward). In FLEX, feature specific representations of time are learned, allowing for neural representations of stimuli to adjust their timing and relation to rewards in an online manner. As an indirect consequence, dopamine in FLEX resembles, but is not equivalent to RPE. In FLEX dopamine acts as an instructive signal which helps build temporal models of the environment. FLEX is a general theoretical framework that has many possible biophysical implementations. In order to show that FLEX is a feasible approach, we present a specific biophysically plausible model which implements the principles of FLEX. We show that this implementation can account for various reinforcement learning paradigms, and that its results and predictions are consistent with a preponderance of both existing and reanalyzed experimental data.
Gαq modulates the energy metabolism of osteoclasts
Authors: Chakraborty S. , Handrick B. , Yu D. , Bode K. , Hafner A. , Schenz J. , Schaack D. , Uhle F. , Tachibana T. , Kamitani S. , Vogl T. , Kubatzky K.F.
Published: April 2022

The bacterial protein toxin Pasteurella multocida toxin (PMT) mediates RANKL-independent osteoclast differentiation. Although these osteoclasts are small, their resorptive activity is high and destroys the nasal turbinate bones of pigs. Analysis of the proteome of classical and toxin-derived osteoclasts showed that PMT induces the upregulation of metabolic pathways. This includes strong glycolytic activity, increased expression of GLUT1 and upregulation of the mTOR pathway. As OxPhos components are also expressed more efficiently, cells display increased mitochondrial respiration. We found that the heterotrimeric G protein Gαq plays a central role in this hypermetabolic cell activation. Gαq triggers mitochondrial relocalisation of pSerSTAT3 and an increase in OPA1 expression. Overexpression of Gαq in Hoxb8 cells mimicked this hypermetabolic phenotype and resulted in higher glycolytic and mitochondrial activity as well as increased bone resorptive activity. Rheumatoid arthritis patients show an increase in Gnaq expression especially in the synovial fluid, suggesting that Gαq is a target of pathophysiological relevance.
Different factors drive community assembly of rare and common ectomycorrhizal fungi
Authors: van Galen Laura G. , Orlovich David A. , Lord Janice M. , Bohorquez Julia , Nilsen Andy R. , Summerfield Tina C. , Larcombe Matthew J.
Published: April 2022

1.

Understanding what drives community assembly processes and how communities respond to environmental gradients are fundamental goals in community ecology. Ectomycorrhizal fungi support major forest systems across the globe, but the diversity, distribution and environmental controls affecting ectomycorrhizal community composition are unknown in many regions, particularly in the southern hemisphere. Here we investigate the assembly of ectomycorrhizal fungal communities based on eDNA samples from 81 Nothofagus forests across New Zealand’s South Island. We apply zeta diversity analysis and multi-site generalised dissimilarity modelling (MS-GDM) to investigate assembly patterns and quantify the effects of 43 biotic and environmental variables on community turnover. The zeta diversity MS-GDM framework differentiates between the environmental factors driving turnover of rare and common species, so provides a more complete picture of community dynamics than traditional beta diversity analyses. Results showed that community assembly was dominated by deterministic rather than stochastic processes. Soil variables were important drivers across the full range of rare, intermediate and common species. Ground cover variables, forest patch size and rainfall had greater effects on turnover of rare species, whereas temperature variables and host tree size had greater effects on common species turnover. Applying these methods for the first time to fungi demonstrates that there are distinct differences in the ecological processes affecting different aspects of the ectomycorrhizal community, which has important implications for understanding the functional effects of community responses to environmental change.
Multiple lines of evidence indicate survival of the Ivory-billed Woodpecker in Louisiana
Authors: Latta Steven C. , Michaels Mark A. , Scheifler Don , Michot Thomas C. , Shrum Peggy L. , Johnson Patricia , Tischendorf Jay , Weeks Michael , Trochet John , Ford Bob
Published: April 2022

The history of decline of the Ivory-billed Woodpecker is long, complex, and controversial. The last widely accepted sighting of this species in continental North America was 1944. Reports of Ivory-billed Woodpeckers have continued, yet in 2021 the U.S. Fish and Wildlife Service proposed declaring the species extinct. We draw on 10 years of search effort, and provide trail camera photos and drone videos suggesting the consistent presence of Ivory-billed Woodpeckers at our study site. Data indicate repeated re-use of foraging sites and core habitat. We offer insights into behaviors of the Ivory-billed Woodpecker that contribute to difficulty in finding this species. We discuss results with regard to the value of accumulated evidence, and what repeated observations may indicate for continued survival of this iconic species.
Transcription factors organize into functional groups on the linear genome and in 3D chromatin
Authors: Vadnala Rakesh Netha , Hannenhalli Sridhar , Narlikar Leelavati , Siddharthan Rahul
Published: April 2022

Transcription factors (TFs) and their binding sites have evolved to interact cooperatively or competitively with each other. Here we examine in detail, across multiple cell lines, such cooperation or competition among TFs both in sequential and spatial proximity (using chromatin conformation capture assays) on one hand, and based on both in vivo binding as well as TF binding motifs on the other. We ascertain significantly co-occurring (“attractive”) or avoiding (“repulsive”) TF pairs using robust randomized models that retain the essential characteristics of the experimental data. Across human cell lines TFs organize into two groups, with intra-group attraction and inter-group repulsion. This is true for both sequential and spatial proximity, as well as for both in vivo binding and motifs. Attractive TF pairs exhibit significantly more physical interactions suggesting an underlying mechanism. The two TF groups differ significantly in their genomic and network properties, as well in their function—while one group regulates housekeeping function, the other potentially regulates lineage-specific functions, that are disrupted in cancer. We also show that weaker binding sites tend to occur in spatially interacting regions of the genome. Our results suggest a complex pattern of spatial cooperativity of TFs that has evolved along with the genome to support housekeeping and lineage-specific functions.
The Delta variant SARS-CoV-2 spike protein uniquely promotes aggregation of pseudotyped viral particles
Authors: Petersen Jennifer D. , Lu Jianming , Fitzgerald Wendy , Zhou Fei , Blank Paul S. , Matthies Doreen , Zimmerberg Joshua
Published: April 2022

Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudotyped with other SARS-CoV-2 spike variants do not show aggregation by any of these criteria. The contribution to infection kinetics of the Delta spike’s unique property to aggregate is discussed with respect to recent evidence for collective infection by other viruses. Irrespective of this intriguing possibility, spike-dependent aggregation is a new functional parameter of spike-expressing viral particles to evaluate in future spike protein variants.
TLR2 axis on peripheral blood mononuclear cells regulates inflammatory responses to circulating, non-infectious immature dengue virus particles
Authors: Aguilar-Briseño José A. , Pereira Lennon Ramos , van der Laan Marleen , Pauzuolis Mindaugas , ter Ellen Bram M. , Upasani Vinit , Moser Jill , de Souza Ferreira Luís Carlos , Smit Jolanda M. , Rodenhuis-Zybert Izabela A.
Published: April 2022

Severe dengue virus (DENV) infection is characterized by exacerbated inflammatory responses that lead to endothelial dysfunction and plasma leakage. We have recently demonstrated that Toll-like receptor 2 (TLR2) on blood monocytes senses DENV infection leading to endothelial activation. Here, we report that non-infectious immature DENV particles, which are released in large numbers by DENV-infected cells, drive endothelial activation via the TLR2 axis. We show that fully immature DENV particles induce a rapid, within 6 hours post-infection, inflammatory response in PBMCs. Furthermore, pharmacological blocking of TLR2/TLR6/CD14 and/or NF-kB prior to exposure of PBMCs to immature DENV reduces the initial production of inter alia TNF-α and IL-1β by monocytes and prevents endothelial activation. However, prolonged TLR2 block induces TNF-α production and leads to exacerbated endothelial activation, indicating that TLR2-mediated responses play an important role not only in the initiation but also the resolution of inflammation. Altogether, these data indicate that the maturation status of the virus has the potential to influence the kinetics and extent of inflammatory responses during DENV infection.

Author Summary

Severe dengue virus (DENV) infection is characterized by endothelial dysfunction leading to vascular permeability and plasma leakage. This is thought to be mediated by the exacerbated production of inflammatory mediators from cells of the innate immune system. We have previously demonstrated that Toll-like receptor 2 (TLR2), a pattern recognition receptor present on the surface of human monocytes, can sense DENV infection leading to the activation of the endothelium. Importantly, a large proportion of DENV particles is immature and are not readily infectious. Here we aimed to elucidate if and how these non-infectious immature DENV particles contribute to systemic inflammation. We evaluated if monocytes sense immature DENV and found that sensing of immature DENV induced early inflammatory responses in PBMCs. Pharmacological inhibition of TLR2/TLR6/CD14 and/or NF-κB prior to exposure to immature DENV demonstrates that this is the pathway leading to the early production inflammatory mediators and endothelial activation. However, prolonged inhibition of TLR2 induced the production of TNF-α and the subsequent activation of the endothelium, suggesting that TLR2-mediated responses play an important tole during both, initiation and resolution of inflammation. We propose that the maturation status of DENV in the human host can influence the extent and kinetics of the inflammatory responses during DENV infection.
Tissue-Specific Transcriptome Responses to Fusarium Head Blight and Fusarium Root Rot
Authors: Haidoulis J F. , Nicholson P.
Published: April 2022

Fusarium head blight (FHB) and Fusarium root rot (FRR) are important diseases of small-grained cereals caused by Fusarium species. While host response to FHB has been subject to extensive study, very little is known about response to FRR and the transcriptome responses of FHB and FRR have not been thoroughly compared. Brachypodium distachyon (Bd) is an effective model for investigating host responses to both FHB and FRR. In this study the transcriptome response of Bd to F. graminearum (Fg) infection of heads and roots was investigated. An RNA-seq analysis was performed on both Bd FHB and FRR during the early infection. Additionally, an RNA-seq analysis was performed on in vitro samples of Fg for comparison with Fg gene expression in planta. Differential gene expression and gene-list enrichment analyses were used to compare FHB and FRR transcriptome responses in both Bd and Fg. Differential expression of selected genes was confirmed using RT-qPCR. Most genes associated with receptor signalling, cell-wall modification, oxidative stress metabolism, and cytokinin and auxin biosynthesis and signalling genes were generally upregulated in FHB or were downregulated in FRR. In contrast, Bd genes involved in jasmonic acid and ethylene biosynthesis and signalling, and antimicrobial production were similarly differentially expressed in both tissues in response to infection. A transcriptome analysis of predicted Fg effectors with the same infected material revealed elevated expression of both core tissue- independent genes including cell-wall degradation enzymes and the gene cluster for DON production but also several tissue-dependent genes including those for aurofusarin production and cutin degradation. This evidence suggests that Fg modulates its transcriptome to different tissues of the same host.
Restoration of high-sensitivity patterned vision in motion with an engineered light-gated G protein-coupled receptor
Authors: Holt Amy , Berry Michael H. , Lo Jamie , Donthamsetti Prashant , Visel Meike , Broichhagen Johannes , Flannery John G. , Isacoff Ehud Y.
Published: April 2022

Inherited retinal degenerations (IRDs) result in blindness due to apoptotic cell death of rods and cones, but spare other retinal neurons, providing a potential that delivery of a light-activated signaling protein to surviving neurons may restore vision. We previously demonstrated that aspects of vision could be restored by introduction into surviving cells of a G protein-coupled receptor for glutamate (mGluR) bearing a tethered photoswitchable agonist. However, this system, containing one photoswitchable agonist per glutamate binding site, yielded low sensitivity, responding only to visual stimuli at the intensity of bright outdoor light, similar to channelrhodopsins. To increase sensitivity, we designed a multi-branched photoswitch, bearing four light-activatable glutamates for each glutamate binding site. When tethered to a modified mGluR2 expressed in retinal ganglion cells via intravitreal AAV gene delivery, this photoswitch boosted sensitivity by ~100-fold compared to the unbranched (single photo-ligand) photoswitch. This improvement in sensitivity enabled an IRD mouse model (rd1) to perform visually-guided object recognition under incidental room light and pattern recognition using standard LCD computer displays. The restored line pattern differentiation approached the acuity reported for normal mouse vision. Pattern recognition functioned as well as wildtype vision with line patterns moving at speeds of up to 36°/s. In summary, this two-component chemical-optogenetic approach combines high sensitivity and high acuity with superior motion vision, and, unlike optogenetic gene therapy, can be adjusted for dose, upgraded, as new photoswitches are developed, and discontinued at will.
SARS-CoV-2 and its variants, but not Omicron, induces thymic atrophy and impaired T cell development
Authors: Rizvi Zaigham Abbas , Sadhu Srikanth , Dandotiya Jyotsna , Binyka Akshay , Sharma Puja , Singh Virendra , Das Vinayaka , Khatri Ritika , Kumar Rajesh , Samal Sweety , Kalia Manjula , Awasthi Amit
Published: April 2022

Pathogenic infections cause thymic atrophy, perturb thymic-T cell development and alter immunological response. Previous studies reported dysregulated T cell function and lymphopenia in coronavirus disease-19 (COVID-19) patients. However, immune-pathological changes, in the thymus, post severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection have not been elucidated. Here, we report SARS-CoV-2 infects thymocytes, depletes CD4+CD8+ (double positive; DP) T cell population associated with an increased apoptosis of thymocytes, which leads to severe thymic atrophy in K18-hACE2-Tg mice. CD44+CD25-T cells were found to be enriched in infected thymus, indicating an early arrest in the T cell developmental pathway. Further, Interferon gamma (IFN-γ) was crucial for thymic atrophy, as anti-IFN-γ antibody neutralization rescued the loss of thymic involution. Therapeutic use of remdesivir (prototype anti-viral drug) was also able to rescue thymic atrophy. While Omicron variant of SARS-CoV2 caused marginal thymic atrophy, delta variant of SARS-CoV-2 exhibited most profound thymic atrophy characterized by severely depleted DP T cells. Recently characterized broadly SARS-CoV-2 neutralizing monoclonal antibody P4A2 was able to rescue thymic atrophy and restore thymic developmental pathway of T cells. Together, we provide the first report of SARS-CoV-2 associated thymic atrophy resulting from impaired T cell developmental pathway and also explains dysregulated T cell function in COVID-19.
Organisation of gene programs revealed by unsupervised analysis of diverse gene-trait associations
Authors: Mizikovsky Dalia , Sanchez Marina Naval , Nefzger Christian M. , Partida Gabriel Cuellar , Palpant Nathan J.
Published: April 2022

Genome wide association studies provide statistical measures of gene-trait associations that reveal how genetic variation influences phenotypes. This study develops an unsupervised dimensionality reduction method called UnTANGLeD (Unsupervised Trait Analysis of Networks from Gene Level Data) which organises 16,849 genes into discrete gene programs by measuring the statistical association between genetic variants and 1,393 diverse complex traits. UnTANGLeD reveals 173 gene clusters enriched for protein-protein interactions and highly distinct biological processes governing development, signalling, disease, and homeostasis. We identify diverse gene networks with robust interactions but not associated with known biological processes. Analysis of independent disease traits shows that UnTANGLeD gene clusters are conserved across all complex traits, providing a simple and powerful framework to predict novel gene candidates and programs influencing orthogonal disease phenotypes. Collectively, this study demonstrates that gene programs co-ordinately orchestrating cell functions can be identified without reliance on prior knowledge, providing a method for use in functional annotation, hypothesis generation, machine learning and prediction algorithms, and the interpretation of diverse genomic data.
Expression Analysis, Molecular Characterization and Prognostic Evaluation on TMED4 and TMED9 Gene Expression in Glioma
Authors: Ullah Md. Asad , Tabassum Tahani , Farzana Maisha , Moin Abu Tayab , Zohora Umme Salma , Rahman Mohammad Shahedur
Published: April 2022

Here, we utilized a database mining approach to unfold the prognostic and therapeutic potentials of Transmembrane EmP24 Trafficking Protein 4 (TMED4) and 9 (TMED) coding gene expressions in glioma. Both the genes were found to be overexpressed at the mRNA and protein level in low grade glioma (LGG) and glioblastoma multiforme (GBM) tissues including different glioma cell lines. Significant increase in the expression level of these genes with advancing glioma patients’ age, glioma grades and histological subtypes was observed. Differential and distinct promoter and coding sequence methylation pattern of TMED4 and TMED9 was observed in LGG and GBM tissues that may aid in methylation-sensitive diagnosis of glioma patients. The presence of multiple heterozygous genetic alterations (frequency: 0.4-1.1%) in those genes unveiled their potentials in high-throughput screening of glioma patients. The overexpression of TMED4 and TMED9 genes was associated with poor overall survival (OS) of LGG and GBM patients (HR:>1.6). Association of the expression levels of these genes with different immune cell infiltration levels i.e., B cell and T cell and modulators like CD274 and IL10RB was observed providing assurance in TMED-based diagnostic measure and therapeutic intervention discovery. Furthermore, functional enrichment analysis of the neighbor genes of TMED4 and TMED9 revealed that they are involved in metal ion binding, focal adhesion of cells and protein processing, and the deregulation of these activities are associated with gliomagenesis. Altogether, this study suggests that TMED4 and TMED9 are potential prognostic and therapeutic targets for glioma. However, further laboratory research is warranted.
Ultra-high-throughput microbial single-cell whole genome sequencing for genome-resolved metagenomics
Authors: Li Jie , Zhang Rong , Li Ting , Shi Qingyuan , Song Zhangyue , Jiang Lichun , Shi Yunfeng , Ma Conghui , Liang Xue , Zhang Jingwei , Liu Yifan
Published: April 2022

Microbes exist widely in nature. However, less than 1% of the species of microorganisms have been discovered so far, and more than 99% of microorganisms still remain unknown, which is called microbial dark matter. Unravelling microbial dark matter is not only helpful for exploring the unknown microbial world, but also of great significance for human health research. Ever since a long time ago, due to technical limitations, the microbiome, to a great extent, is still a black box. The traditional population-based metagenomic analysis tools are without single microbial resolution and they are stretched when studying rare and unknown microbial species. Here, we use high-throughput microdroplet technology to achieve the whole genome amplification of microbial single-cell genomes in pico-litter sized microdroplets, and develop subsequent library preparation steps such as indexing of the genome, to achieve the development of ultra-high-throughput microbial single-cell whole genome sequencing for genome-resolved metagenomics, aiming to provide a powerful new weapon for exploring microbial dark matter and other microbiological studies.
Oncogenic metabolic rewiring independent of proliferative control in human mammary epithelial cells
Authors: Dong Wentao , Keibler Mark A. , Moon Sun Jin , Cho Patricia , Liu Nian , Berrios Christian J. , Kelleher Joanne K. , Sikes Hadley D. , Iliopoulos Othon , Coloff Jonathan L. , Vander Heiden Matthew G. , Stephanopoulos Gregory
Published: April 2022

The use of isotopic tracers and metabolic flux analysis (MFA) has unveiled a number of metabolic pathways differentially activated in cancer cells. To support efforts to design effective metabolic therapies for cancer, we sought to distinguish metabolic behavior in cancer versus normal cells growing at the same rate. To this end, we performed13C-isotope tracing and MFA in human mammary epithelial cells (HMECs) harboring different combinations of oncogenes. By introducing a new quantity termed metabolic flux intensity, defined as pathway flux divided by specific growth rate, we showed that metabolism is dually controlled by proliferation and oncogenotypes.13C-MFA further revealed that oxidative pentose phosphate pathway (oxPPP), malate dehydrogenase (MDH) and isocitrate dehydrogenase (IDH) were most enhanced in cancerous HMECs. Drug targeting of these pathways selectively reduced growth in the tumorigenic HMEC line. Our study provides direct evidence that metabolism of cancer cells is different than that of normal proliferating cells.
Distal-less homeobox genes Dlx5/6 regulate Müllerian duct regression
Authors: Mullen Rachel D. , Bellessort Brice , Levi Giovanni , Behringer Richard R.
Published: April 2022

Dlx5 and Dlx6 encode distal-less homeodomain transcription factors that are present in the genome as a linked pair at a single locus. Dlx5 and Dlx6 have redundant roles in craniofacial, skeletal, and uterine development. Previously, we performed a transcriptome comparison for anti-Müllerian hormone (AMH)-induced genes expressed in the Müllerian duct mesenchyme of male and female mouse embryos. In that study, we found that Dlx5 transcripts were nearly seven-fold higher in males compared to females and Dlx6 transcripts were found only in males, suggesting they may be AMH-induced genes. Therefore, we investigated the role of Dlx5 and Dlx6 during AMH-induced Müllerian duct regression. We found that Dlx5 was detected in the male Müllerian duct mesenchyme from E14.5 to E16.5. In contrast, in female embryos Dlx5 was detected in the Müllerian duct epithelium. Dlx6 expression in Müllerian duct mesenchyme was restricted to males. Dlx6 expression was not detected in female Müllerian duct mesenchyme or epithelium. Genetic experiments showed that AMH signaling is necessary for Dlx5 and Dlx6 expression. Müllerian duct regression was variable in Dlx5 homozygous mutant males at E16.5, ranging from regression like controls to a block in Müllerian duct regression. In E16.5 Dlx6 homozygous mutants, Müllerian duct tissue persisted primarily in the region adjacent to the testes. In Dlx5-6 double homozygous mutant males Müllerian duct regression was also found to be incomplete but more severe than either single mutant. These studies suggest that Dlx5 and Dlx6 act redundantly to mediate AMH-induced Müllerian duct regression during male differentiation.
Machine learning improves global models of plant diversity
Authors: Cai Lirong , Kreft Holger , Taylor Amanda , Denelle Pierre , Schrader Julian , Essl Franz , van Kleunen Mark , Pergl Jan , Pyšek Petr , Stein Anke , Winter Marten , Barcelona Julie F. , Fuentes Nicol , Inderjit  , Karger Dirk Nikolaus , Kartesz John , Kuprijanov Andreij , Nishino Misako , Nickrent Daniel , Nowak Arkadiusz , Patzelt Annette , Pelser Pieter B. , Singh Paramjit , Wieringa Jan J. , Weigelt Patrick
Published: April 2022

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, neural networks) and conventional statistical methods (generalised linear models, generalised additive models) to model species richness and phylogenetic richness of vascular plants worldwide based on 830 regional plant inventories including c. 300,000 species and predictors of past and present environmental conditions. Machine learning showed an outstanding performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modelling techniques (ensemble predictions) to reveal global patterns and centres of plant diversity at multiple resolutions down to 7,774 km2. Our predictive maps provide the most accurate estimates of global plant diversity available to date at grain sizes relevant for conservation and macroecology.
The Neural Response at the Fundamental Frequency of Speech is Modulated by Word-level Acoustic and Linguistic Information
Authors: Kegler Mikolaj , Weissbart Hugo , Reichenbach Tobias
Published: April 2022

Spoken language comprehension requires rapid and continuous integration of information, from lower-level acoustic to higher-level linguistic features. Much of this processing occurs in the cerebral cortex. Its neural activity exhibits, for instance, correlates of predictive processing, emerging at delays of a few hundred milliseconds. However, the auditory pathways are also characterized by extensive feedback loops from higher-level cortical areas to lower-level ones as well as to subcortical structures. Early neural activity can therefore be influenced by higher-level cognitive processes, but it remains unclear whether such feedback contributes to linguistic processing. Here, we investigated early speech-evoked neural activity that emerges at the fundamental frequency. We analyzed EEG recordings obtained when subjects listened to a story read by a single speaker. We identified a response tracking the speaker’s fundamental frequency that occurred at a delay of 11 ms, while another response elicited by the high-frequency modulation of the envelope of higher harmonics exhibited a larger magnitude and longer latency of about 18 ms. Subsequently, we determined the magnitude of these early neural responses for each individual word in the story. We then quantified the context-independent frequency of each word and used a language model to compute context-dependent word surprisal and precision. The word surprisal represented how predictable a word is, given the previous context, and the word precision reflected the confidence about predicting the next word from the past context. We found that the word-level neural responses at the fundamental frequency were predominantly influenced by the acoustic features: the average fundamental frequency and its variability. Amongst the linguistic features, only context-independent word frequency showed a weak but significant modulation of the neural response to the high-frequency envelope modulation. Our results show that the early neural response at the fundamental frequency is already influenced by acoustic as well as linguistic information, suggesting top-down modulation of this neural response.
SARS-CoV-2 mutations affect proteasome processing to alter CD8+T cell responses
Authors: Wellington Dannielle , Yin Zixi , Yu Zhanru , Heilig Raphael , Davis Simon , Fischer Roman , Felce Suet Ling , Hublitz Philip , Beveridge Ryan , Dong Danning , Liu Guihai , Yao Xuan , Peng Yanchun , Kessler Benedikt M , Dong Tao
Published: April 2022

Viral CD8+epitopes are generated by the cellular turnover of viral proteins, predominantly by the proteasome. Mutations located within viral epitopes can result in escape from memory T cells but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two of the most dominant SARS-CoV-2 nucleoprotein CD8+epitopes, we identified mutations in epitope flanking regions and investigated the contribution of these mutations to antigen processing and T cell activation using SARS-CoV-2 nucleoprotein transduced B cell lines andin vitroproteasomal processing of peptides. We found that decreased NP9-17-B*27:05 CD8+T cell responses to the NP-Q7K mutation correlated with lower epitope surface expression, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on antigen processing and presentation, thereby contributing to escape from immunodominant T cell responses. Alternatively, mutations could enhance antigen processing and efficacy of T cell recognition, opening new avenues for improving future vaccine designs.

One Sentence Summary

Natural mutations in the flanking regions of known immunodominant SARS-CoV-2 nucleoprotein epitopes can decrease CD8+T cell responses leading to partial escape.
Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis
Authors: Nagaratnam Nirupa , Martin-Garcia Jose M. , Yang Jay-How , Goode Matthew R. , Ketawala Gihan , Craciunescu Felicia M. , Zook James D. , Grant Thomas D. , Fromme Raimund , Hansen Debra T. , Fromme Petra
Published: April 2022

Francisella tularensis is an extremely infectious pathogen and a category A bioterrorism agent. It causes the highly contagious zoonosis, Tularemia. Currently, FDA approved vaccines against tularemia are unavailable. F. tularensis outer membrane protein A (FopA) is a well-studied virulence determinant and protective antigen against tularemia. It is a major outer membrane protein (Omp) of F. tularensis. However, FopA-based therapeutic intervention is hindered due to lack of complete structural information for membrane localized mature FopA. In our study, we established recombinant expression, monodisperse purification, crystallization and X-ray diffraction (∼6.5 Å) of membrane localized mature FopA. Further, we performed bioinformatics and biophysical experiments to unveil its structural organization in the outer membrane. FopA consists of 393 amino acids and has less than 40% sequence identity to known bacterial Omps. Using comprehensive sequence alignments and structure predictions together with existing partial structural information, we propose a two-domain organization for FopA. Circular dichroism spectroscopy and heat modifiability assay confirmed FopA has a β-barrel domain consistent with alphafold2’s prediction of an eight stranded β-barrel at the N-terminus. Small angle X-ray scattering (SAXS) and native-polyacrylamide gel electrophoresis revealed FopA purified in detergent micelles is predominantly dimeric. Molecular density derived from SAXS at 31 Å shows putative dimeric N-terminal β-barrels surrounded by detergent corona and connected to C-terminal domains via flexible linker. Disorder analysis predicts N- and C-terminal domains are interspersed by a long intrinsically disordered region and alphafold2 predicts this region to be largely unstructured. Taken together, we propose a dimeric, two-domain organization of FopA in the outer membrane: the N-terminal β-barrel is membrane embedded, provides dimerization interface and tethers to membrane extrinsic C-terminal domain via long flexible linker. Structure determination of membrane localized mature FopA is essential to understand its role in pathogenesis and develop anti-tularemia therapeutics. Our results pave the way towards it.
Molecular Architecture of the Chikungunya Virus Replication Complex
Authors: Tan Yaw Bia , Chmielewski David , Yien Law Michelle Cheok , Zhang Kuo , He Yu , Chen Muyuan , Jin Jing , Luo Dahai , Chiu Wah
Published: April 2022

All positive-strand (+) RNA viruses assemble membrane-associated replication complexes (RCs) for viral RNA synthesis in virus-infected cells. However, how these multi-component RCs assemble and function in synthesizing, processing, and transporting viral RNAs to the cytosol remains poorly defined. Here, we determined both the structure of the core RNA replicase of chikungunya virus (family Togaviridae) at a near-atomic level and the native RC architecture in its cellular context at the subnanometer resolution, using in vitro reconstitution and in situ electron cryotomography, respectively. Within the core RNA replicase (nsP1+2+4), the viral RNA-dependent RNA polymerase nsP4, in complex with nsP2 helicase-protease, was found to co-fold with the membrane-anchored nsP1 RNA-capping dodecameric ring and is located asymmetrically within nsP1 central pore. This complex forms the minimal core RNA replicase, while the addition of a large cytoplasmic ring next to the C-terminus of nsP1 forms the holo-RNA-RC as observed at the neck of spherules formed in virus-infected cells. These results represent a major conceptual advance in elucidating the molecular mechanisms of RNA virus replication and the principles underlying the molecular architecture of RCs, likely to be shared with many pathogenic (+) RNA viruses. At last, our study will direct the needed development of antiviral therapies targeting RCs of pathogenic viruses.

CryoEM structure of the chikungunya virus replication complex reveals a multicomponent RNA synthesis nanomachine embedded in the plasma membrane of the host cell.
Development of a monoclonal antibody to a vibriophage as a proxy forVibrio choleraedetection
Authors: Sayeed Md. Abu , Paisie Taylor , Alam Meer Taifur , Ali Afsar , Camilli Andrew , Wrammert Jens , Khan Ashraful Islam , Qadri Firdausi , Salemi Marco , Morris J. Glenn , Nelson Eric J.
Published: April 2022

Cholera is an acute watery diarrheal disease that causes high rates of morbidity and mortality without treatment. Early detection of the etiologic agent of toxigenicVibrio choleraeis important to mobilize treatment and mitigate outbreaks. Monoclonal antibody (mAb) based rapid diagnostic tests (RDTs) enable early detection in settings without laboratory capacity. However, the odds of an RDT testing positive are reduced by nearly 90% when the common virulent bacteriophage ICP1 is present. We hypothesize that adding a mAb for the common, and specific, virulent bacteriophage ICP1 as a proxy forV. choleraeto an RDT will increase diagnostic sensitivity when virulent ICP1 phage are present. In this study, we used anin-silicoapproach to identify immunogenic ICP1 protein targets that were conserved across disparate time periods and locations. Specificity of targets to cholera patients with known ICP1 was determined, and specific targets were used to produce mAbs in a murine model. Candidate mAbs to the head protein demonstrated specificity to ICP1 by ELISA and an ICP1 phage neutralization assay. The limit of detection of the final mAb candidate for ICP1 phage particles spiked into cholera stool matrix was 8 × 105plaque forming units by Western blot analysis. This mAb will be incorporated into a RDT prototype for evaluation in a future diagnostic study to test the guiding hypothesis behind this study.
Structure of Importin-4 bound to the H3-H4·ASF1 histone·histone chaperone complex
Authors: Bernardes Natalia Elisa , Fung Ho Yee Joyce , Li Yang , Chen Zhe , Chook Yuh Min
Published: April 2022

Importin-4 is the primary nuclear import receptor of core histones H3 and H4. Importin-4 binds the H3-H4 dimer and histone-chaperone ASF1 prior to nuclear import, but available structures of Importin-4·histone tail complexes do not explain how Importin-4 recognizes the biologically relevant heterotrimeric H3-H4·ASF1 cargo. Our 3.5 Å Importin-4·H3-H4·ASF1 cryo-electron microscopy structure revealed interactions with H3-H4·ASF1 different those suggested by previous Importin-H3 tail peptide structures. The N-terminal half of Importin-4 clamps the globular histone domain and the H3 αN helix while its C-terminal half binds the H3 N-terminal tail weakly, with negligible tail contribution to binding energy; ASF1 binds H3-H4 without contacting Importin-4. Together, ASF1 and Importin-4 shield nucleosomal interfaces of H3-H4 to chaperone and import it into the nucleus, where Importin-4 undergoes large conformational changes as RanGTP binds to release H3-H4·ASF1. This work explains the mechanisms of nuclear import of full-length H3-H4.