bluuebunny/crossref_metadata_2025_split huggingface dataset:
Composite mutations give an extra insight into epistasis
Authors: Zorin Evgenii M. , Erazo Carolina M. , Ivankov Dmitry N. 
Published: June 2022

AbstractThe intricate genotype-phenotype relationship has been a long-standing issue in biology, important both from the fundamental and applied points of view. One of the major irregularities hindering progress in establishing these links is epistasis – the complex and elusive interaction between mutations. Despite the vast accumulated genetic data and progress in this area, epistasis is still far from being completely understood. Epistasis can be studied quantitatively in combinatorially complete datasets, which form hypercubes in protein sequence space, where connected sequences are one mutation away from each other. However, this might be insufficient to portray the full picture of epistatic interactions. To extend the repertoire of the methods for exploring epistasis, we propose here to consider hyperrectangles, where some edges connect sequences being two or more mutations away from each other. The present work formalizes the theoretical knowledge about these novel structures and compares the amount of epistasis identified in hypercubes and hyperrectangles constructed from experimental datasets. A new algorithm, CuboidME, was developed for calculating hyperrectangles, which were then compared to hypercubes. In the experimental datasets, there were four orders of magnitude more hyperrectangles than hypercubes for the same sample size. Subsequently, we showed that for the studied datasets there is an increase in epistasis measured by epistatic coefficients in hyperrectangles compared to hypercubes. For the same datasets, hyperrectangles could find more sign epistasis than using hypercubes alone. We also show that there is a trend for increase in epistasis with increasing number of mutations being considered in a hyperrectangle. The results indicate that hyperrectangles can be used to reveal more information on epistasis in a fitness landscape, especially if it is combinatorially incomplete.
Epithelial protein lost in neoplasm (EPLIN)-β is a novel substrate of ornithine decarboxylase antizyme 1, mediating cellular migration
Authors: Li Dan , Neo Suat Peng , Gunaratne Jayantha , Sabapathy Kanaga 
Published: June 2022

AbstractPolyamines promote cellular proliferation, and their levels are controlled by ornithine decarboxylase antizyme 1 (Az1), through the proteasome-mediated, ubiquitin-independent degradation of ornithine decarboxylase (ODC), the rate-limiting enzyme of polyamine biosynthesis. Az1-mediated degradation of other substrates such as cyclin D1, DNp73 and Mps1 also regulate cellular migration and centrosome amplification, and collectively, the currently known six Az1-substrates are all linked with tumorigenesis. To understand if Az1-mediated protein degradation might play a key role in regulating cellular process associated with tumorigenesis, we employed quantitative proteomics to identify novel Az1 substrates. In this report, we describe the identification of LIM domain and Actin-binding protein 1 (LIMA1), also known as epithelial protein lost in neoplasm (EPLIN), as a new target of Az1. Interestingly, between the two isoforms of EPLIN (α and β), only EPLIN-β is the substrate of Az1, degraded in a proteasome-dependent and ubiquitination-independent manner. Absence of Az1 led to elevated EPLIN-β levels, which is causal to enhanced cellular migration of Az1-/- cells. Consistently, higher levels of LIMA1 expression correlated with poorer overall survival of colorectal cancer patients. Taken together, this study identifies EPLIN-β as a novel Az1 substrate that regulates cellular migration.
Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald’s rule of stages
Authors: Chakraborty Debayan , Straub John E. , Thirumalai D 
Published: June 2022

AbstractThe transition from a disordered to an assembly-competent and sparsely populated monomeric state (N*) in amyloidogenic sequences is a crucial event in the aggregation cascade. Using a well-calibrated model for Intrinsically Disordered Proteins (IDPs), we show that the N* states, which bear considerable resemblance to distinct polymorphic fibril structures found in experiments, not only appear as excitations on the monomer free energy landscapes of Aβ40 and Aβ42 but also initiate the aggregation cascade. Interestingly, for Aβ42, the transitions to the different N* states are in accord with Ostwald’s rule of stages, with the least stable structures forming ahead of thermodynamically favored structures, which appear only on longer time-scales. Despite having similar topographies, the Aβ40 and Aβ42 monomer landscapes exhibit different extent of ruggedness, particularly in the vicinity of N* states, which we show have profound implications in dictating the intramolecular diffusion rates, and subsequent self-assembly into higher order structures. The network of connected kinetic states, which for Aβ42 is considerably more complex than for Aβ40, shows that the most favored dimerization routes proceed via the N* states. Direct transition between the disordered ground states within the monomer and dimer basins is less likely. The Ostwald’s rule of stages holds widely, qualitatively explaining the unusual features in other fibril forming IDPs, such as Fused in Sarcoma (FUS). Similarly, the N* theory accounts for dimer formation in small disordered polyglutamine peptides, implicated in the Huntington disease.Graphical TOC Entry
Oligomerisation of a plant helper NLR requires cell-surface and intracellular immune receptor activation
Authors: Feehan Joanna M. , Wang Junli , Sun Xinhua , Choi Jihyeon , Ahn Hee-Kyung , Ngou Bruno Pok Man , Parker Jane E. , Jones Jonathan D. G. 
Published: June 2022

AbstractPlant disease resistance involves both detection of microbial molecular patterns by cell-surface pattern recognition receptors and detection of pathogen effectors by intracellular NLR immune receptors. NLRs are classified as sensor NLRs, involved in effector detection, or helper NLRs required for sensor NLR signalling. TIR-domain-containing sensor NLRs (TNLs) require helper NLRs NRG1 and ADR1 for resistance, and their activation of defense also requires the lipase-domain proteins EDS1, SAG101 and PAD4. We investigated how the helper NLR NRG1 supports TNL-initiated immunity with EDS1 and SAG101. We find that NRG1 associates with EDS1 and SAG101 at the plasma membrane and in the nucleus, but only self-associates at the plasma membrane. Activation of TNLs is sufficient to trigger NRG1-EDS1-SAG101 interaction, but cell-surface receptor-initiated defense is also required to form an oligomeric Resistosome. The data point to formation of NRG1-EDS1-SAG101 heterotrimers in the nucleus upon intracellular receptor activation alone and indicate formation of NRG1-EDS1-SAG101 Resistosomes at the plasma membrane upon co-activation of intracellular and cell surface-receptor pathways.
Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction
Authors: Mueth Nicholas A. , Hulbert Scot H. 
Published: June 2022

AbstractThe wheat stripe rust fungus (Puccinia striiformis f.sp tritici) poses a significant challenge to global wheat production. Plant defense induction against pathogens is partly modulated by small RNA (sRNA) molecules that downregulate complementary protein-coding transcripts. Additionally, the two-way RNA exchange between host and microbe involves cross-kingdom gene silencing that impacts pathogen virulence, yet few examples are known among rust fungi. The purpose of this study was to discover small RNA-target pairs on each side of this interaction. We performed sRNA sequencing and parallel analysis of RNA ends (PARE) in infected and uninfected wheat seedlings and combined these data with gene expression information. Wheat 24 nt heterochromatic siRNA (hc-siRNA) sequences were suppressed upon infection, while specific 35 nt tRNA and rRNA fragments were strongly induced. Target transcripts were identified by the observation of high mRNA slicing frequency at the precise position of sRNA binding sites. Wheat small RNAs showed evidence of cleaving several fungal transcripts including a ribosomal protein-coding gene and a glycosyl hydrolase effector gene. In P. striiformis, we confirmed and expanded previous findings that sRNAs feature microRNA-like sequences and siRNAs originating from long inverted repeats near protein-coding genes. Long inverted repeat regions produced sets of phased sRNAs at 21 nt intervals. Fungal sRNAs were identified that target native transcripts coding for transposons and protein kinases. Cross-kingdom gene targets of pathogen sRNAs included wheat nucleotide-binding domain leucine-rich repeat receptors (NLRs) and multiple families of defense-related transcription factors. The identified target genes shed light on an intricately co-evolved interaction and provide useful prospects for the development of pathogen control biotechnology.
Calcineurin associates with centrosomes and regulates cilia length maintenance
Authors: Tsekitsidou Eirini , Wang Jennifer T. , Wong Cassandra J. , Ulengin-Talkish Idil , Stearns Tim , Gingras Anne-Claude , Cyert Martha S. 
Published: June 2022

AbstractCalcineurin, or PP2B, the Ca2+ and calmodulin-activated phosphatase and target of immunosuppressants, has many substrates and functions that remain undiscovered. By combining rapid proximity-dependent labeling with cell cycle synchronization, we mapped calcineurin’s spatial distribution in different cell cycle stages. While calcineurin-proximal proteins did not vary significantly between interphase and mitosis, calcineurin consistently associated with multiple centrosomal/ciliary proteins. These include POC5, which binds centrin in a Ca2+-dependent manner and is a component of the luminal scaffold that stabilizes centrioles. We show that POC5 contains a calcineurin substrate motif (PxIxIT-type) that mediates calcineurin binding in vivo and in vitro. Using indirect immunofluorescence and expansion microscopy, we demonstrate that calcineurin co-localizes with POC5 at the centrosome, and further show that calcineurin inhibitors alter POC5 distribution within the centriole lumen. Our discovery that calcineurin directly associates with centrosomal proteins highlights a role for Ca2+ and calcineurin signaling at these organelles. Calcineurin inhibition promotes primary cilia elongation without affecting ciliogenesis. Thus, Ca2+ signaling within cilia includes previously unknown functions for calcineurin in cilia length maintenance, a process frequently disrupted in ciliopathies.Summary statementCalcineurin phosphatase participates in centrosome and cilia regulation. Calcineurin localizes to centrosomes, where it interacts with partner POC5, and its inhibition promotes cilia elongation.
Cytokine and phenotypic cell profiles in human cutaneous leishmaniasis caused byLeishmania donovani
Authors: Wijesooriya Hiruni , Samaranayake Nilakshi , Karunaweera Nadira D. 
Published: June 2022

AbstractBackgroundThe innate immune mediators are likely to influence the clinical phenotype of leishmaniasis by primary responses which limit or facilitate the spread of the parasite, as well as by modulating adaptive immunity. This study investigated the response of key innate immune cells in a focus which regularly reports localised cutaneous leishmaniasis (LCL) caused byLeishmania donovani, a species which typically causes visceral disease.MethodsPeripheral blood mononuclear cell (PBMC) derived macrophage and dendritic cell responses to solubleLeishmaniaantigen (SLA) were compared between patients with LCL and healthy controls from endemic and non-endemic areas. Inflammatory mediators produced by macrophages (TNF-α, NO, TGF-β and IL-10) and dendritic cells (IL-12p70, IL-10) and cell surface markers of macrophage polarization, activation and maturation were determined at 24h, 48h and 72h by Enzyme-linked immunosorbent assay (ELISA) and flowcytometry.ResultsPatient derived macrophages and dendritic cells produced higher levels of both pro and anti-inflammatory mediators compared to controls (p<0.05) with the best discrimination for active disease observed at 72h. Data demonstrated an early activation of macrophages and a subsequent pro-inflammatory bias, as indicated by temporal profiles of TNF-α/TGF-β and TNF-α/IL-10 ratios and higher proportions of classical (M1) macrophages. Higher TGF-β levels were observed in cells from patients with ulcerated or persistent lesions. Immune responses by cells derived from controls in endemic and non-endemic regions did not differ significantly from each other.ConclusionsThe overall immunophenotypic profile suggests that LCL observed in the country is the result of a balancing immune response between pro-inflammatory and regulatory mediators. The mediators which showed distinct profiles in patients warrant further investigation as potential candidates for immunotherapeutic approaches. A comparison with visceral leishmaniasis caused by the same species, would provide further evidence on the differential role of these mediators in the resulting clinical phenotype.
KLF7 Promotes Preadipocyte Proliferation via Activation of the Akt Signaling Pathway by Cis-regulating CDKN3
Authors: Jia Ziqiu , Jin Zhao , Shao Shuli , Xu Hu , Li Wen , Khan Mahmood , Wang Weiyu , Zhang Weiwei , Sun Yingning 
Published: June 2022

AbstractKrüppel-like transcription factor 7 (KLF7) promotes preadipocyte proliferation; however, its target gene in this process has not yet been identified. Using KLF7 ChIP-seq analysis, we previously showed that a KLF7-binding peak is present upstream of the cyclin-dependent kinase inhibitor 3 gene (CDKN3) in chicken preadipocytes. In the current study, we identified CDKN3 as a target gene of KLF7 that mediates the effects of KLF7 on preadipocyte proliferation. Furthermore, 5′-truncating mutation analysis showed that the minimal promoter was located between CDKN3 nt −160 and nt −7 (relative to the translation initiation codon ATG). KLF7 overexpression increased CDKN3 promoter activity in the DF-1 and immortalized chicken preadipocyte (ICP1) cell lines. Deletion of the putative binding site of KLF7 abolished the promotive effect of KLF7 overexpression on CDKN3 promoter activity. Moreover, CDKN3-knockdown and -overexpression assays revealed that CDKN3 enhanced ICP1 cell proliferation. Flow cytometry analysis showed that CDKN3 accelerated the G1/S transition. Further, we found that KLF7 promoted ICP1 cell proliferation via Akt phosphorylation by regulating CDKN3. Taken together, these results suggest that KLF7 promotes preadipocyte proliferation via activating the Akt signaling pathway by cis-regulating CDKN3, thus driving the G1/S transition.
MIDAS2: Metagenomic Intra-species Diversity Analysis System
Authors: Zhao Chunyu , Dimitrov Boris , Goldman Miriam , Nayfach Stephen , Pollard Katherine S. 
Published: June 2022

AbstractSummaryThe Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants (CNVs) in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.Availability and ImplementationThe source code is available at https://github.com/czbiohub/MIDAS2. The documentation is available at https://midas2.readthedocs.io/en/latest/.Supplementary InformationSupplementary data are available at Bioinformatics online.
The virtualome: a computational framework to evaluate microbiome analyses
Authors: Serrano-Antón Belén , Rodríguez-Ventura Francisco , Colomer-Vidal Pere , Cigliano Riccardo Aiese , Arias Clemente F. , Bertocchini Federica 
Published: June 2022

ABSTRACTMicrobiomes have been the focus of a substantial research effort in the last decades. The composition of microbial populations is normally determined by comparing DNA sequences sampled from those populations with the sequences stored in genomic databases. Therefore, the amount of information available in databanks should be expected to constrain the accuracy of microbiome analyses. Albeit normally ignored in microbiome studies, this constraint could severely compromise the reliability of microbiome data. To test this hypothesis, we generated virtualomes, virtual bacterial populations that exhibit the ecological structure of real-world microbiomes. Confronting the analyses of virtualomes with their original composition revealed critical issues in the current approach to characterizing microbiomes, issues that were empirically confirmed by analyzing the microbiome of Galleria mellonella larvae. To reduce the uncertainty of microbiome data, the effort in the field must be channeled towards significantly increasing the amount of available genomic information.
Mutagenesis and structural modeling implicate RME-8 IWN domains as conformational control points
Authors: Norris Anne , McManus Collin , Wang Simon , Ying Rachel , Grant Barth D. 
Published: June 2022

AbstractAfter endocytosis, transmembrane cargo is differentially sorted into degradative or recycling pathways. This process is facilitated by recruitment into physically distinct degradative or recycling microdomains on the limiting membrane of individual endosomes. Endosomal sorting complexes required for transport (ESCRT) mark the degradative microdomain, while the recycling domain is marked by the retromer complex and associated proteins RME-8 and SNX-1. The separation of endosomal microdomains is also controlled by RME-8 and SNX-1, at least in part via removal of degradative component HRS/HGRS-1 from the recycling microdomain. This activity is likely due to recruitment and activation of chaperone Hsc70 to the recycling microdomain by the RME-8 DNAJ domain. To better understand the mechanism of RME-8 function we performed a new phylogenetic analysis of RME-8 and identified new conserved sequence features. In a complementary approach, we performed structure-function analysis that identified the C-terminus as important for microdomain localization and likely substrate binding, while N-terminal sequences beyond the known single N-terminal PH-like domain are important for endosome recruitment. Random mutagenesis identified IWN4, and by analogy IWN3, to be important for the inhibitory DNAJ domain binding. Combining AlphaFold structural predictions with in vivo truncation and point mutation analysis of RME-8, we propose a model whereby SNX-1 and the IWN domains control the conformation of RME-8 and hence the productive exposure of the DNAJ domain. Furthermore, we propose that the activation of RME-8 is cyclical, with SNX-1 acting as an activator and a target of RME-8 uncoating activity.
Inhibition of the TRIM24 bromodomain reactivates latent HIV-1
Authors: Horvath Riley M. , Brumme Zabrina L. , Sadowski Ivan 
Published: June 2022

AbstractExpression of the HIV-1 genome by RNA Polymerase II is regulated at multiple steps, as are most cellular genes, including recruitment of general transcription factors and control of transcriptional elongation from the core promoter. We recently discovered that tripartite motif protein TRIM24 is recruited to the HIV-1 Long Terminal Repeat (LTR) by interaction with TFII-I and causes transcriptional elongation by stimulating association of PTEF-b/ CDK9. Because TRIM24 is required for stimulation of transcription from the HIV-1 LTR, we were surprised to find that IACS-9571, a specific inhibitor of the TRIM24 C-terminal bromodomain, induces HIV-1 provirus expression in otherwise untreated cells. IACS-9571 reactivates HIV-1 in T cell lines bearing multiple different provirus models of HIV-1 latency. Additionally, treatment with this TRIM24 bromodomain inhibitor encourages productive HIV-1 expression in newly infected cells and inhibits formation of immediate latent transcriptionally repressed provirus. IACS-9571 synergizes with PMA, ionomycin, TNF-α and PEP005 to activate HIV-1 expression. Furthermore, co-treatment of CD4+ T cells from individuals with HIV-1 on antiretroviral therapy (ART) with PEP005 and IACS-9571 caused robust provirus expression. Notably, IACS-9571 did not cause global activation of T cells; rather, it inhibited induction of IL2 and CD69 expression in human PBMCs and Jurkat T cells treated with PEP005 or PMA. These observations indicate the TRIM24 bromodomain inhibitor IACS-9571 represents a novel HIV-1 latency reversing agent (LRA), and unlike other compounds with this activity, causes partial suppression of T cell activation while inducing expression of latent provirus.
Sequential antibiotic therapy in the lab and in the patient
Authors: Nyhoegen Christin , Uecker Hildegard 
Published: June 2022

AbstractLaboratory experiments suggest that rapid cycling of antibiotics during the course of treatment could successfully counter resistance evolution. Drugs involving collateral sensitivity could be particularly suitable for such therapies. However, the environmental conditionsin-vivodiffer from thosein-vitro. One key difference is that drugs can be switched abruptly in the lab, while in the patient, pharmacokinetic processes lead to changing antibiotic concentrations including periods of dose overlaps from consecutive administrations. During such overlap phases, drug-drug interactions may affect the evolutionary dynamics. To address the gap between the lab and potential clinical applications, we set up two models for comparison - a ‘lab model’ and a pharmacokinetic-pharmacodynamic ‘patient model’. The analysis shows that in the lab, the most rapid cycling suppresses the bacterial population always at least as well as other regimens. For patient treatment, however, a little slower cycling can sometimes be preferable if the pharmacodynamic curve is steep or if drugs interact antagonistically. When resistance is absent prior to treatment, collateral sensitivity brings no substantial benefit unless the cell division rate is low and drug cycling slow. By contrast, drug-drug interactions strongly influence the treatment efficiency of rapid regimens, demonstrating their importance for the optimal choice of drug pairs.