bluuebunny/crossref_metadata_2025 huggingface dataset:
GABAAα Subunit Control of Hyperactive Behavior in Developing Zebrafish
Authors: Barnaby Wayne , Barclay Hanna E. Dorman , Nagarkar Akanksha , Perkins Matthew , Teicher Gregory , Trapani Josef G. , Downes Gerald B.
Published: July 2021

GABAAreceptors mediate rapid responses to the neurotransmitter GABA and are robust regulators of the brain and spinal cord neural networks that control locomotor behaviors, such as walking and swimming. In developing zebrafish, gross pharmacological blockade of these receptors causes hyperactive swimming, which has been embraced as an epilepsy model. Although GABAAreceptors are important to control locomotor behavior, the large number of subunits and homeostatic compensatory mechanisms have challenged efforts to determine subunit-selective roles. To address this issue, we mutated each of the eight zebrafish GABAAα subunit genes individually and in pairs using a CRISPR-Cas9 somatic inactivation approach, then we examined the swimming behavior of the mutants at two developmental stages. We found that disrupting the expression of specific pairs of subunits resulted in different abnormalities in swimming behavior at the first development stage. Mutation of α4 and α5 selectively resulted in longer duration swimming episodes, mutations in α3 and α4 selectively caused excess, large-amplitude body flexions (C-bends), and mutation of α3 and α5 resulted in increases in both of these measures of hyperactivity. At the later stage of development, hyperactive phenotypes were nearly absent, suggesting that homeostatic compensation was able to overcome the disruption of even multiple subunits. Taken together, our results identify subunit-selective roles for GABAAα3, α4, and α5 in regulating locomotion. Given that these subunits exhibit spatially restricted expression patterns, these results provide a foundation to identify neurons and GABAergic networks that control discrete aspects of locomotor behavior.
Network analysis after epigenome wide methylation study revealed JUP as a regulator of co-methylated risk-module for T2DM
Authors: Giri Anil K , Prasad Gauri , Parekkat Vaisak , Rajashekar Donaka , Tandon Nikhil , Bharadwaj Dwaipayan
Published: July 2021

Controlling the global Type 2 diabetes mellitus (T2DM) pandemic requires a better understanding of its risk factors across different populations, and needs markers that can precisely predict the individual risk to the disease. DNA methylation due to environmental factors is a known mechanism for conferring risk to T2DM. To identify such methylation signatures and associated risk to the disease, we performed an epigenome-wide-association study (EWAS) in 844 individuals of Indo-European origin. Within the Indian population, we identified and validated 6 novel differentially methylated CpG sites in PDCD6IP, MIR1287, 5S_rRNA, HDAC9, KCNK16, and RTN1 genes associated with T2DM risk at the epigenome-wide-significance-level (p<1.2×10-7). Further, we also replicated the association of 3 known CpG sites in TXNIP, SREBF1 and CPT1A in the Indian population. Using methylation-based-network analysis, we identified 4 co-methylated modules, which we named as turquoise, yellow, brown, and blue, among differentially methylated CpG sites in discovery phase samples. We observed that methylation of the brown module with 28 CpG sites, associated with T2DM risk factors (e.g., BMI, insulin, C-peptide). Upon further analysis, we noted that these methylation signatures at 14 of the brown module’s CpG can be used as marker to segregate T2DM patients with good glycemic control (e.g., low HbA1c) but poor lipid profile (low HDL and high TG) from the other patients. Additionally, we discovered that rs6503650 in the JUP gene regulates methylation at all the 14 hub CpG sites of the brown modules as methQTL. Our network-assisted epigenome-wide association study is the first to systematically explore DNA methylations conferring risks to T2DM. In addition, the study shows the potential use of identified risk CpG sites for patient segregation with different clinical outcomes. These findings can be useful for better stratification of patient in order to improve the clinical management and treatment outcomes.
Parallel genetic changes underlie integrated craniofacial traits in an adaptive radiation of trophic specialist pupfishes
Authors: St. John Michelle E. , Dunker Julia C. , Richards Emilie J. , Romero Stephanie , Martin Christopher H.
Published: July 2021

Many factors such as divergence time, shared standing genetic variation, frequency of introgression, and mutation rates can influence the likelihood of whether populations adapt to similar environments via parallel or non-parallel genetic changes. However, the frequency of parallel vs non-parallel genetic changes resulting in parallel phenotypic evolution is still unknown. In this study, we used a QTL mapping approach to investigate the genetic basis of highly divergent craniofacial traits between scale- and snail-eating trophic specialist species across similar hypersaline lake environments in an adaptive radiation of pupfishes endemic to San Salvador Island, Bahamas. We raised F2 intercrosses of scale- and snail-eaters from two different lake populations of sympatric specialists, estimated linkage maps, scanned for significant QTL for 30 skeletal and craniofacial traits, and compared the location of QTL between lakes to quantify parallel and non-parallel genetic changes. We found strong support for parallel genetic changes in both lakes for five traits in which we detected a significant QTL in at least one lake. However, many of these shared QTL affected different, but highly correlated craniofacial traits in each lake, suggesting that pleiotropy and trait integration should not be neglected when estimating rates of parallel evolution. We further observed a 23-52% increase in adaptive introgression within shared QTL, suggesting that introgression may be important for parallel evolution. Overall, our results suggest that the same genomic regions contribute to parallel integrated craniofacial phenotypes across lakes. We also highlight the need for more expansive searches for shared QTL when testing for parallel evolution.
Neutralization of Delta variant with sera of Covishield vaccinees and COVID-19 recovered vaccinated individuals
Authors: Sapkal Gajanan N. , Yadav Pragya D. , Sahay Rima R. , Deshpande Gururaj , Gupta Nivedita , Nyayanit Dimpal A , Patil Deepak Y. , Kumar Sanjay , Abraham Priya , Panda Samiran , Bhargava Balram
Published: July 2021

The recent emergence of B.1.617 lineage has created grave public health problem in India. The lineage further mutated to generate sub-lineages B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.617.3. Apparently, the Delta variant has slowly dominated the other variants including B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.617.3. With this, World Health Organization has described this sub-lineage as variant of concern. The high transmissibility associated with Delta variant has led to second wave of pandemic in India which affected millions of people. Besides this, variant of concerns has been reported to show lower neutralization to several approved vaccines. This has led to breakthrough infections after completion of vaccination regimen. There is limited information available on the duration of protective immune response post-infection, vaccination or breakthrough infection with SARS-CoV-2. In this study, we have evaluated immune response in sera of the Covishield vaccinated individuals belonging to category: I. one dose vaccinated, II. two doses vaccinated, III. COVID-19 recovered plus one dose vaccinated, IV. COVID-19 recovered plus two doses vaccinated and V. breakthrough COVID-19 cases. The findings of the study demonstrated that the breakthrough cases and the COVID-19 recovered individuals with one or two dose of vaccine had relatively higher protection against Delta variant in comparison to the participants who were administered either one or two doses of Covishield™. Prior vaccination results in less severe disease against subsequent infection provide evidence that both humoral and cellular immune response play an important role in protection.
Knowledge-based antibody repertoire simulation, a novel allele detection tool evaluation and application
Authors: Yang Xiujia , Zhu Yan , Zeng Huikun , Chen Sen , Guan Junjie , Wang Qilong , Lan Chunhong , Sun Deqiang , Yu Xueqing , Zhang Zhenhai
Published: July 2021

Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data via multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel alleles using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the novel alleles detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies via Ig-seq.
Tetrapod diversity facets in jeopardy during the Anthropocene
Authors: Tordoni Enrico , Toussaint Aurèle , Pärtel Meelis , Nogues-Bravo David , Theodoridis Spyros , Carmona Carlos Pérez
Published: July 2021

Human activities have eroded biodiversity, yet the varying influence of past versus recent impacts across the distinct facets of biodiversity is still poorly understood. Weighting taxonomic information by phylogenetic and functional diversity in a novel multifaceted index (μ-Diversity) across more than 17,000 tetrapod species, we show the geography of multifaceted tetrapod diversity, and the role of climate stability and water-energy dynamics coupled with the timing of inception of agriculture in explaining broad-scale patterns of tetrapod diversity. In particular, the varying geography of the timing of agriculture expansion since the Neolithic affected μ-Diversity at least as much as recent human impacts, especially in birds, mammals, and reptiles, suggesting that human imprints may have shaped tetrapod diversity for millennia through legacy effects of past land use modifications. The long-lasting effect of humans will only accelerate, as the most diverse areas for μ-Diversity (tropical Africa, South East Asia and Central and South America) are disproportionally exposed to both future climate and land-use change.
Strategies for the site-specific decoration of DNA origami nanostructures with functionally intact proteins
Authors: Hellmeier Joschka , Platzer René , Mühlgrabner Vanessa , Schneider Magdalena C. , Kurz Elke , Schütz Gerhard J. , Huppa Johannes B. , Sevcsik Eva
Published: July 2021

DNA origami structures provide flexible scaffolds for the organization of single biomolecules with nanometer precision. While they find increasing use for a variety of biological applications, the functionalization with proteins at defined stoichiometry, high yield, and under preservation of protein function remains challenging. In this study, we applied single molecule fluorescence microscopy in combination with a cell biological functional assay to systematically evaluate different strategies for the site-specific decoration of DNA origami structures, focusing on efficiency, stoichiometry and protein functionality. Using an activating ligand of the T-cell receptor (TCR) as protein of interest, we found that two commonly used methodologies underperformed with regard to stoichiometry and protein functionality. While strategies employing tetravalent wildtype streptavidin for coupling of a biotinylated TCR-ligand yielded mixed populations of DNA origami structures featuring up to 3 proteins, the use of divalent (dSAv) or DNA-conjugated monovalent streptavidin (mSAv) allowed for site-specific attachment of a single biotinylated TCR-ligand. The most straightforward decoration strategy, via covalent DNA conjugation, resulted in a 3-fold decrease in ligand potency, likely due to charge-mediated impairment of protein function. Replacing DNA with charge-neutral PNA in a ligand conjugate emerged as the coupling strategy with the best overall performance in our study, as it produced the highest yield with no multivalent DNA origami structures and fully retained protein functionality. With our study we aim to provide guidelines for the stoichiometrically defined, site-specific functionalization of DNA origami structures with proteins of choice serving a wide range of biological applications.
Improved Metabolite Prediction Using Microbiome Data-Based Elastic Net Models
Authors: Xie Jialiu , Cho Hunyong , Lin Bridget M. , Pillai Malvika , Heimisdottir Lara H. , Bandyopadhyay Dipankar , Zou Fei , Roach Jeffrey , Divaris Kimon , Wu Di
Published: July 2021

Microbiome data are becoming increasingly available in large health cohorts yet metabolomics data are still scant. While many studies generate microbiome data, they lack matched metabolomics data or have considerable missing proportions of metabolites. Since metabolomics is key to understanding microbial and general biological activities, the possibility of imputing individual metabolites or inferring metabolomics pathways from microbial taxonomy or metagenomics is intriguing. Importantly, current metabolomics profiling methods such as the HMP Unified Metabolic Analysis Network (HUMAnN) have unknown accuracy and are limited in their ability to predict individual metabolites. To address this gap, we developed a novel metabolite prediction method, and we present its application and evaluation in an oral microbiome study. We developed ENVIM based on the Elastic Net Model (ENM) to predict metabolites using micorbiome data. ENVIM introduces an extra step to ENM to consider variable importance scores and thus achieve better prediction power. We investigate the metabolite prediction performance of ENVIM using metagenomic and metatranscriptomic data in a supragingival biofilm multi-omics dataset of 297 children ages 3-5 who were participants of a community-based study of early childhood oral health (ZOE 2.0) in North Carolina, United States. We further validate ENVIM in two additional publicly available multi-omics datasets generated from studies of gut health and vagina health. We select gene-family sets based on variable importance scores and modify the existing ENM strategy used in the MelonnPan prediction software to accommodate the unique features of microbiome and metabolome data. We evaluate metagenomic and metatranscriptomic predictors and compare the prediction performance of ENVIM to the standard ENM employed in MelonnPan. The newly-developed ENVIM method showed superior metabolite predictive accuracy than MelonnPan using metatranscriptomics data only, metagenomics data only, or both of these two. Both methods perform better prediction using gut or vagina microbiome data than using oral microbiome data for the samples’ corresponding metabolites. The top predictable compounds have been reported in all these three datasets from three different body sites. Enrichment of prediction some contributing species has been detected.
Physics-based inverse design of cholesterol attracting transmembrane helices reveals a paradoxical role of hydrophobic length
Authors: Methorst Jeroen , Verwei Nino , Hoffmann Christian , Chodnicki Paweł , Sansevrino Roberto , Wang Han , van Hilten Niek , Aschmann Dennis , Kros Alexander , Andreas Loren , Czub Jacek , Milovanovic Dragomir , Risselada Herre Jelger
Published: July 2021

The occurrence of linear cholesterol-recognition motifs in alpha-helical transmembrane domains has long been debated. Here, we demonstrate the ability of a genetic algorithm guided by coarse-grained molecular dynamics simulations—a method coined evolutionary molecular dynamics (Evo-MD)—to directly resolve the sequence which maximally attracts cholesterol for single-pass alpha-helical transmembrane domains (TMDs). We illustrate that the evolutionary landscape of cholesterol attraction in membrane proteins is characterized by a sharp, well-defined global optimum. Surprisingly, this optimal solution features an unusual short, slender hydrophobic block surrounded by three successive lysines. Owing to the membrane thickening effect of cholesterol, cholesterol-enriched ordered phases favor TMDs characterized by a long rather than a too short hydrophobic length (a negative hydrophobic mismatch). However, this short hydrophobic pattern evidently offers a pronounced net advantage for the attraction of free cholesterol in both coarse-grained and atomistic simulations. We illustrate that optimal cholesterol attraction is in fact based on the superposition of two distinct structural features: (i) slenderness and (ii) hydrophobic mismatch. In addition, we explore the evolutionary occurrence and feasibility of the two features by analyzing existing databases of membrane proteins and through the direct expression of analogous short hydrophobic sequences in live cell assays. The puzzling sequence variability of proposed linear cholesterol-recognition motifs is indicative of a sub-optimal membrane-mediated attraction of cholesterol which markedly differs from ligand binding based on shape compatibility.

Significance Statement

Our work demonstrates how a synergy between evolutionary algorithms and high-throughput coarse-grained molecular dynamics can yield fundamentally new insights into the evolutionary fingerprints of protein-mediated lipid sorting. We illustrate that the evolutionary landscape of cholesterol attraction in isolated transmembrane domains is characterized by a well-defined global optimum. In contrast, sub-optimal attraction of cholesterol is associated with a diverse solution space and features a high sequence variability despite acting on the same unique molecule. The contrasting physicochemical nature of the resolved attraction optimum suggests that cholesterol attraction via linear motifs does not pose a dominant pressure on the evolution of transmembrane proteins.
Hypervariable-Locus Melting Typing (HLMT): a novel, fast and inexpensive sequencing-free approach to pathogen typing based on High Resolution Melting (HRM) analysis
Authors: Perini Matteo , Piazza Aurora , Panelli Simona , Papaleo Stella , Alvaro Alessandro , Vailati Francesca , Corbella Marta , Saluzzo Francesca , Gona Floriana , Castelli Daniele , Farina Claudio , Marone Piero , Cirillo Daniela Maria , Cavallero Annalisa , Zuccotti Gian Vincenzo , Comandatore Francesco
Published: July 2021

Objectives

Subspecies pathogen typing is a pivotal tool to detect the emergence of high-risk clones in hospital settings and to limit their spreading among patients. Unfortunately, the most used subspecies typing methods (i.e. Pulsed-field Gel Electrophoresis - PFGE, Multi-Locus Sequence Typing - MLST and Whole Genome Sequencing - WGS) are too expensive and time consuming to be suitable for real-time surveillance. Here we present Hypervariable-Locus Melting Typing (HLMT), a novel subspecies typing approach based on High Resolution Melting (HRM) analysis, which allows pathogen typing in a few hours and with ∼5 euros per sample.

Methods

HLMT types the strains by clustering them using melting temperatures (HLMT-clustering) and/or by assigning them to Melting Types (MTs) on the basis of a reference dataset (HLMT-assignment). We applied HLMT (clustering and typing) to 134 Klebsiella pneumoniae strains collected during outbreaks or surveillance programs in four hospitals. Then, we compared HLMT typing results to PFGE, MLST and WGS.

Results

HLMT-clustering distinguishes most of the K. pneumoniae high-risk clones with a sensitivity comparable to PFGE and MLST. It also drawed surveillance epidemiological curves comparable to those obtained by MLST, PFGE and WGS typing. Furthermore, the results obtained by HLMT-assignment were coherent to MLST for 96% of the typed strains with a Jaccard index of 0.912.

Conclusions

HLMT is a fast and scalable method for pathogen typing, suitable for real-time hospital microbiological surveillance. HLMT is also inexpensive and thus it is applicable to infection control programs in low-middle income countries.
Programmable Cleavage of Double-stranded DNA by Combined Action of Argonaute CbAgo from Clostridium butyricum and Nuclease Deficient RecBC Helicase from E.coli
Authors: Vaiskunaite Rita , Vainauskas Jogirdas , Morris Janna , Potapov Vladimir , Bitinaite Jurate
Published: July 2021

Prokaryotic Argonautes (pAgos) use small nucleic acids as specificity guides to cleave single-stranded DNA at complementary sequences. DNA targeting function of pAgos creates attractive opportunities for DNA manipulations that require programmable DNA cleavage. Discovery of mesophilic Argonautes active at physiological temperature places pAgos closer to their possible application for genome editing as a simpler alternative to CRISPR/Cas nucleases. Currently, the use of mesophilic pAgos as programmable DNA endonucleases is hampered by their poor action on double-stranded DNA (dsDNA), mainly due to their inability to invade the DNA duplex. The present study demonstrates that efficient in vitro cleavage of double-stranded DNA by mesophilic Argonaute CbAgo from Clostridium butyricum can be activated via the DNA strand unwinding activity of nuclease deficient mutant of RecBC DNA helicase from Escherichia coli (referred to as RecBexo-C). Properties of CbAgo and characteristics of simultaneous cleavage of complementary DNA strands in concurrence with DNA strand unwinding by RecBexo-C were thoroughly explored using 0.3-25 kb DNA substrates. When combined with RecBexo-C helicase, CbAgo was capable of cleaving target sequences located 11-12.5 kb from the ends of linear dsDNA at 37ºC. Our study demonstrates that CbAgo with RecBexo-C can be programmed to generate dsDNA fragments flanked with custom-designed single-stranded overhangs suitable for ligation with compatible DNA fragments. At present, the combination of CbAgo and RecBexo-C represents the most efficient mesophilic DNA-guided DNA-cleaving programmable endonuclease for use in diagnostic and synthetic biology methods that require sequence-specific nicking/cleavage of dsDNA at any desired location.
Fungal community composition along a gradient of permafrost thaw
Authors: Kluge Mariana , Wurzbacher Christian , Wauthy Maxime , Clemmensen Karina Engelbrecht , Hawkes Jeffrey , Einarsdottir Karolina , Stenlid Jan , Peura Sari
Published: July 2021

Thermokarst activity at permafrost sites releases considerable amount of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi growing in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing a gradient of permafrost integrity. Samples were taken from the ponds surface water, the detritus and the sediment at the bottom of the ponds. These samples were extracted for total DNA, which was then amplified using primers targeting the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Surface water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.
PEPSDI: Scalable and flexible inference framework for stochastic dynamic single-cell models
Authors: Persson Sebastian , Welkenhuysen Niek , Shashkova Sviatlana , Wiqvist Samuel , Reith Patrick , Schmidt Gregor W. , Picchini Umberto , Cvijovic Marija
Published: July 2021

Mathematical modelling is an invaluable tool to describe dynamic cellular processes and to rationalise cell-to-cell variability within the population. This requires statistical methods to infer unknown model parameters from dynamic, multi-individual data accounting for heterogeneity caused by both intrinsic and extrinsic noise. Here we present PEPSDI, a scalable and flexible framework for Bayesian inference in state-space mixed-effects stochastic dynamic single-cell models. Unlike previous frameworks, PEPSDI imposes a few modelling assumptions when inferring unknown model parameters from time-lapse data. Specifically, it can infer model parameters when intrinsic noise is modelled by either exact or approximate stochastic simulators, and when extrinsic noise is modelled by either time-varying, or time-constant parameters that vary between cells. This allowed us to identify hexokinase activity as a source of extrinsic noise, and to deduce that sugar availability dictates cell-to-cell variability in the budding yeastSaccharomyces cerevisiaeSNF1 nutrient sensing pathway.
miR-155 exerts posttranscriptional control of autoimmune regulator (Aire) and tissue-restricted antigen genes in medullary thymic epithelial cells
Authors: Tanaka Pedro Paranhos , Oliveira Ernna Hérida , Vieira-Machado Mayara Cristina , Duarte Max Jordan , Assis Amanda Freire , Bombonato-Prado Karina Fittipaldi , Passos Geraldo Aleixo
Published: July 2021

Background

The autoimmune regulator (Aire) gene is critical for the appropriate establishment of central immune tolerance. As one of the main controllers of promiscuous gene expression in the thymus, Aire promotes the expression of thousands of downstream tissue-restricted antigen (TRA) genes, cell adhesion genes and transcription factor genes in medullary thymic epithelial cells (mTECs). Despite the increasing knowledge about the role of Aire as an upstream transcriptional controller, little is known about the mechanisms by which this gene could be regulated.

Results

Here, we assessed the posttranscriptional control of Aire by miRNAs. The in silico miRNA-mRNA interaction analysis predicted thermodynamically stable hybridization between the 3′ UTR of Aire mRNA and miR-155, which was confirmed to occur within the cellular milieu through a luciferase reporter assay. This finding enabled us to hypothesize that miR-155 might play a role as an intracellular posttranscriptional regulator of Aire mRNA. To test this hypothesis, we transfected a murine mTEC cell line with a miR-155 mimic in vitro, which reduced the mRNA and protein levels of Aire. Moreover, large-scale transcriptome analysis showed the modulation of 311 downstream mRNAs, which included 58 TRA mRNAs. Moreover, miR-155 mimic-transfected cells exhibited a decrease in their chemotaxis property compared with control thymocytes.

Conclusion

Overall, the results indicate that miR-155 may posttranscriptionally control Aire mRNA as well as a crucial process by which mTECs allow migration of thymocytes through chemotaxis.
Fungal effector SIB1 of Colletotrichum orbiculare has unique structural features and can suppress plant immunity in Nicotiana benthamiana
Authors: Zhang Ru , Isozumi Noriyoshi , Mori Masashi , Okuta Ryuta , Singkaravanit-Ogawa Suthitar , Imamura Tomohiro , Gan Pamela , Shirasu Ken , Ohki Shinya , Takano Yoshitaka
Published: July 2021

Functional screening of effector candidates using a transient expression assay in Nicotiana benthamiana identified two virulence-related effectors, named SIB1 and SIB2 (Suppression of Immunity in N. benthamiana), of an anthracnose fungus Colletotrichum orbiculare, which infects both cucurbits and N. benthamiana. Agrobacterium-mediated transient expression of SIB1 or SIB2 increased the susceptibility of N. benthamiana to C. orbiculare, which suggested these effectors can suppress immune responses in N. benthamiana. The presence of SIB1 and SIB2 homologs was found to be limited to the genus Colletotrichum. SIB1 suppressed both the generation of reactive oxygen species (ROS) triggered by the bacterial pathogen-associated molecular pattern (PAMP), flg22, and the cell death response triggered by the Phytophthora infestans INF1 elicitin in N. benthamiana. We determined the NMR-based structure of SIB1 to obtain its structural insights. The three-dimensional structure of SIB1 comprises five β-strands, each containing three disulfide bonds. The overall conformation was found to be a cylindrical shape, such as the well-known antiparallel β-barrel structure. However, the β-strands were found to display a unique topology, one pair of these β-strands formed a parallel β-sheet. These results suggest that the effector SIB1 present in Colletotrichum fungi has unique structural features and can suppress PAMP-triggered immunity (PTI) in N. benthamiana.
Co-deletion of ATAD1 with PTEN primes cells for BIM-mediated apoptosis
Authors: Winter Jacob M. , Fresenius Heidi L. , Keys Heather R. , Cunningham Corey N. , Ryan Jeremy , Sirohi Deepika , Berg Jordan A. , Tripp Sheryl R. , Barta Paige , Agarwal Neeraj , Letai Anthony , Sabatini David M. , Wohlever Matthew L. , Rutter Jared
Published: July 2021

PTEN is a potent tumor suppressor gene that is frequently mutated or deleted in human cancers. Such deletions often include portions of the 10q23 locus beyond the bounds of PTEN itself, in many cases resulting in the disruption of additional genes. Coincidental loss of PTEN-adjacent genes might impose vulnerabilities that could either affect patient outcome basally or be exploited therapeutically. Here we describe how the loss of ATAD1, which is adjacent to and frequently co-deleted with PTEN, predisposes cancer cells to apoptosis and correlates with improved survival in cancer patients. ATAD1 directly and specifically extracts the pro-apoptotic BIM protein from mitochondria to inactivate it. Cells lacking ATAD1 are hypersensitive to clinically used proteasome inhibitors, which increase BIM and trigger apoptosis. Thus, we demonstrate that mitochondrial protein quality control interfaces with cell death in a clinically actionable manner.
Localization of signaling receptors maximizes cellular information acquisition in spatially-structured natural environments
Authors: Wang Zitong Jerry , Thomson Matt
Published: July 2021

Cells in natural environments like tissue or soil sense and respond to extracellular ligands with intricately structured and non-monotonic spatial distributions, sculpted by processes such as fluid flow and substrate adhesion. In this work, we show that spatial sensing and navigation can be optimized by adapting the spatial organization of signaling pathways to the spatial structure of the environment. We develop an information-theoretic framework for computing the optimal spatial organization of a sensing system for a given signaling environment. We find that receptor localization maximizes information acquisition in simulated natural contexts, including tissue and soil. Receptor localization extends naturally to produce a dynamic protocol for continuously redistributing signaling receptors, which when implemented using simple feedback, boosts cell navigation efficiency by 30-fold. Broadly, our work shows how cells can maximize the fidelity of information transfer by adapting the spatial organization of signaling molecules to the spatial structure of the environment.
In vivo proximity biotin ligation identifies the interactome of Egalitarian, a Dynein cargo adaptor
Authors: Baker Frederick C. , Neiswender Hannah , Veeranan-Karmegam Rajalakshmi , Gonsalvez Graydon B.
Published: July 2021

Numerous motors of the Kinesin family contribute to plus-end directed microtubule transport. However, almost all transport towards the minus-end of microtubules involves Dynein. Understanding the mechanism by which Dynein transports this vast diversity of cargo is the focus of intense research. In select cases, adaptors that link a particular cargo with Dynein have been identified. However, the sheer diversity of cargo suggests that additional adaptors must exist. We used the Drosophila egg chamber as a model to address this issue. Within egg chambers, Egalitarian is required for linking mRNA with Dynein. However, in the absence of Egalitarian, Dynein transport into the oocyte is severely compromised. This suggests that additional cargoes might be liked to Dynein in an Egalitarian-dependent manner. We therefore used proximity biotin ligation to define the interactome of Egalitarian. This approach yielded several novel interacting partners, including P body components and proteins that associate with Dynein in mammalian cells. We also devised and validated a nanobody based proximity biotinylation strategy which can be used to define the interactome of any GFP-tagged protein.
Erythroid differentiation in mouse erythroleukemia cells is driven via actin filament-tropomodulin3-tropomyosin networks
Authors: Ghosh Arit , Coffin Megan , West Richard , Fowler Velia
Published: July 2021

Erythroid differentiation (ED) is a complex cellular process entailing morphologically distinct maturation stages of erythroblasts during terminal differentiation. Studies of actin filament assembly and organization during terminal ED have revealed essential roles for the pointed-end actin filament capping proteins, tropomodulins (Tmod1 and Tmod3). Additionally, tropomyosin (Tpm) binding to Tmods is a key feature promoting Tmod-mediated actin filament capping. Global deletion ofTmod3leads to embryonic lethality in mice with impaired ED. To test a cell autonomous function for Tmod3 and further decipher its biochemical function during ED, we generated aTmod3knockout in a mouse erythroleukemia cell line (Mel ds19).Tmod3knockout cells appeared normal prior to ED, but showed defects during progression of ED, characterized by a marked failure to reduce cell and nuclear size, reduced viability and increased apoptosis. In Mel ds19 cells, both Tpms and actin were preferentially associated with the Triton-X 100 insoluble cytoskeleton during ED, indicating Tpm-coated actin filament assembly during ED. While loss of Tmod3 did not lead to a change in total actin levels, it led to a severe reduction in the proportion of Tpms and actin associated with the Triton-X 100 insoluble cytoskeleton during ED. We conclude that Tmod3-regulation of actin cytoskeleton assembly via Tpms is integral to morphological maturation and cell survival during normal erythroid terminal differentiation.
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Authors: Cartney Ann M. Mc , Shafin Kishwar , Alonge Michael , Bzikadze Andrey V. , Formenti Giulio , Fungtammasan Arkarachai , Howe Kerstin , Jain Chirag , Koren Sergey , Logsdon Glennis A. , Miga Karen H. , Mikheenko Alla , Paten Benedict , Shumate Alaina , Soto Daniela C. , Sović Ivan , Wood Jonathan MD , Zook Justin M. , Phillippy Adam M. , Rhie Arang
Published: July 2021

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Though derived from highly accurate sequencing, evaluation revealed that the initial T2T draft assembly had evidence of small errors and structural misassemblies. To correct these errors, we designed a novel repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly QV to 73.9. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both PacBio HiFi and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies
Blockade of pro-fibrotic response mediated by the miR-143/-145 cluster prevents targeted therapy-induced phenotypic plasticity and resistance in melanoma
Authors: Diazzi S. , Baeri A. , Fassy J. , Lecacheur M. , Marin-Bejar O. , Girard C.A. , Lefevre L. , Lacoux C. , Irondelle M. , Mounier C. , Truchi M. , Couralet M. , Carminati A. , Berestjuk I. , Larbret F. , Vassaux G. , Marine J.-C. , Deckert M. , Mari B. , Tartare-Deckert S.
Published: July 2021

Lineage dedifferentiation towards a mesenchymal-like state is a common mechanism of adaptive response and resistance to targeted therapy in melanoma. Yet, the transcriptional network driving this phenotypic plasticity remains elusive. Remarkably, this cellular state displays myofibroblast and fibrotic features and escapes MAPK inhibitors (MAPKi) through extracellular matrix (ECM) remodeling activities. Here we show that the anti-fibrotic drug Nintedanib/BIBF1120 is active to normalize the fibrous ECM network, enhance the efficacy of MAPK-targeted therapy and delay tumor relapse in a pre-clinical model of melanoma. We also uncovered the molecular networks that regulate the acquisition of this resistant phenotype and its reversion by Nintedanib, pointing the miR-143/-145 pro-fibrotic cluster as a driver of the therapy-resistant mesenchymal-like phenotype. Upregulation of the miR-143/-145 cluster under BRAFi/MAPKi therapy was observed in melanoma cells in vitro and in vivo and was associated with an invasive/undifferentiated profile of resistant cells. The 2 mature miRNAs generated from this cluster, miR-143-3p and miR-145-5p collaborated to mediate phenotypic transition towards a drug resistant undifferentiated mesenchymal-like state by targeting Fascin actin-bundling protein 1 (FSCN1), modulating the dynamic crosstalk between the actin cytoskeleton and the ECM through the regulation of focal adhesion dynamics as well as contributing to a fine-tuning of mechanotransduction pathways. Our study brings insights into a novel miRNA-mediated regulatory network that contributes to non-genetic adaptive drug resistance and provides proof-of-principle that preventing MAPKi-induced pro-fibrotic stromal response is a viable therapeutic opportunity for patients on targeted therapy.
Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes
Authors: Maatouk Mohamad , Ibrahim Ahmad , Rolain Jean-Marc , Merhej Vicky , Bittar Fadi
Published: July 2021

Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new unique branch, thanks to the intensive application of metagenomics and advances of sequencing technologies. Despite their ultra-small size, reduced genome and metabolic pathways which mainly depend on symbiotic/exo-parasitic relationship with their bacterial host, CPR microbes are abundant and ubiquitous in almost all environments and are consequently survivors in highly competitive circumstances within microbial communities. They have been eventually identified by 16S rRNA analysis and represent more than 26% of microbial diversity. CPR microbes were able to survive in this context, although their defence mechanisms and phenotypic characteristic remain, however, poorly explored. Here, we conducted a thorough in-silico analysis on 4,062 CPR genomes to test whether these ultrasmall microorganisms might encode for antibiotic resistance (AR)-like enzymes. We used an adapted AR screening criteria with an exhaustive consensus database and complementary steps conferring their resistance functions. We conclude by reporting the surprising discovery of rich reservoir of divergent AR-like genes (n= 30,545 HITs, mean=7.5 HITs/genome [0-41] encoding for 89 AR enzymes, distributed across the 13 CPR phyla, and associated with 14 different chemical classes of antimicrobials. However, most HITs found (93.6%) were linked to glycopeptide, beta-lactams, macrolide-lincosamide-streptogramin, tetracycline and aminoglycoside resistance. Moreover, a distinct AR profile was discerned between the microgenomates group and Candidatus Parcubacteria, and between each of them and other CPR phyla. CPR cells seem to be active players during microbial competitive interactions and are well-equipped for the microbial combat in different habitats, supporting their natural survival/persistence and continued existence.
Between two walls: Modeling the adsorption behavior of β-glucosidase A on bare and SAM-functionalised gold surfaces
Authors: Bourassin Nicolas , Barbault Florent , Baaden Marc , Sacquin-Mora Sophie
Published: July 2021

The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multi-scale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and SAM-functionalized gold surfaces. We monitored the enzyme position and orientation during the MD trajectories, and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but also less specific, and more likely to disrupt the enzyme’s function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a keypoint when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.

TOC image
Implications of Spike-glycoprotein processing at S1/S2 by Furin, at S2’ by Furin and/or TMPRSS2 and shedding of ACE2: cell-to-cell fusion, cell entry and infectivity of SARS-CoV-2
Authors: Essalmani Rachid , Jain Jaspreet , Susan-Resiga Delia , Andréo Ursula , Evagelidis Alexandra , Derbali Rabeb Mouna , Huynh David N. , Dallaire Frédéric , Laporte Mélanie , Delpal Adrien , Sutto-Ortiz Priscila , Coutard Bruno , Mapa Claudine , Wilcoxen Keith , Decroly Étienne , Pham Tram NQ , Cohen Éric A. , Seidah Nabil G.
Published: July 2021

Disclaimer Statement

The author has withdrawn this manuscript due to a duplicate posting of manuscript number 423106. Therefore, the author does not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (Nabil G. Seidah at seidahn@ircm.qc.ca.
Betacoronavirus-specific alternate splicing
Authors: Karlebach Guy , Aronow Bruce , Baylin Stephen B. , Butler Daniel , Foox Jonathan , Levy Shawn , Meydan Cem , Mozsary Christopher , Saravia-Butler Amanda M , Taylor Deanne M , Wurtele Eve , Mason Christopher E , Beheshti Afshin , Robinson Peter N
Published: July 2021

Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection as well as datasets from the betacoronaviruses SARS-CoV and MERS as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification and a smaller number of exons than differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by DAS and DGE in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS, potentially modifying a broad range of cellular functions and affecting a diverse set of genes and biological functions.
Synthesis, crystal structure and thermal properties of poly[bis[μ-3-(aminomethyl)pyridine-κ2
N:N′]bis(thiocyanato-κN)manganese(II)]
Authors: Krebs Christoph , Jess Inke , Näther Christian
Published: July 2021

The reaction of Mn(NCS)2 with a stoichiometric amount of 3-(aminomethyl)pyridine in ethanol led to the formation of the title compound, [Mn(NCS)2(C6H8N2)2]
n
, which is isotypic to its Zn, Co and Cd analogues. The manganese cation is located on a centre of inversion and is octahedrally coordinated in an all-trans configuration by two terminal N-bonded thiocyanate anions as well as four 3-(aminomethyl)pyridine co-ligands, of which two coordinate with the pyridine N atom and two with the amino N atom. The 3-(aminomethyl)pyridine co-ligands connect the MnII cations into layers extending parallel to (10\overline{1}). These layers are further connected into a three-dimensional network by relatively strong intermolecular N—H...S hydrogen bonding. Comparison of the experimental X-ray powder diffraction pattern with the calculated pattern on the basis of single-crystal data proves the formation of a pure crystalline phase. IR measurements showed the CN stretching vibration of the thiocyanate anions at 2067 cm−1, which is in agreement with the presence of terminally N-bonded anionic ligands. TG–DTA measurements revealed that the title compound decomposes at about 500 K.
The Chicago Riverwalk: urban sustainability lessons
Authors: Al-Kodmany Kheir M.
Published: July 2021

Purpose

This paper reviews, summarizes and pieces together scattered information on the newly completed Chicago Riverwalk in Chicago, Illinois. It explains the design process that transformed an outmoded infrastructure and disused river banks into an attractive gathering civic space, a linear urban park and a functional transportation corridor.

Design/methodology/approach

Literature review.

Findings

Overall, the paper reports on one of the latest projects in Chicago that symbolizes the city's long history and earnest commitment to urban sustainability.

Research limitations/implications

The paper identifies key urban sustainability lessons that are transferable to other cities.

Originality/value

It is the first paper that stitches together scattered information on the topic.
Access control of human resource records: case of the University of Cape Coast, Ghana
Authors: Andoh Raphael Papa Kweku , Attafuah Alfred
Published: July 2021

Purpose

Security of human resource records is important because of their nature but they are not adequately managed. This study aims to investigate access control issues affecting the security and confidentiality of human resource records at the University of Cape Coast.

Design/methodology/approach

A qualitative approach was used to conduct the study. Purposive sampling was used to select staff at the Directorate of Human Resource, University of Cape Coast. A textual analysis was used in analysing responses to open-ended questions leading to the identification of patterns and their subsequent categorisation. An interview was also conducted.

Findings

It was found that effective strategies were implemented in controlling access to human resource information and records making them secure. The challenges identified were in two categories: existing and anticipated challenges. Suggestions to resolve the challenges were also enumerated.

Originality/value

This study highlights the need to ensure access to human resource records is controlled so that they are secured and kept confidential. This study contributes to knowledge in the broader context of information and records management and specifically, human resource information and records management. It also adds to the dearth of empirical studies that focus on the security and confidentiality of human resource records.