bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Speed AFM directly visualizes conformational dynamics of the HIV-Vif protein complex
Authors: Pan Yangang , Shlyakhtenko Luda S. , Lyubchenko Yuri L. 
Published: May 2020

AbstractViral infectivity factor (Vif) is a protein that is essential for the replication of the HIV-1 virus. The key function of Vif is to disrupt the antiviral activity of APOBEC3 proteins, which mutate viral nucleic acids. Inside the cell, Vif binds to the host cell proteins Elongin-C, Elongin-B, and CBF-β, forming a four-protein complex called VCBC. The structure of VCBC in complex with the Cullin5 (Cul5) protein has been solved by X-ray crystallography, and recently, using molecular dynamic (MD) simulations, the dynamics of VCBC and VCBC-Cul5 complexes were characterized. Here, we applied time-lapse high-speed atomic force microscopy (HS-AFM) to visualize the conformational changes of the VCBC complex. We determined the three most favorable conformations of the VCBC complex, which we identified as triangle, dumbbell, and globular structures. In addition, we characterized the dynamics of each of these structures. While our data show a very dynamic behavior for all these structures, we found the triangle and dumbbell structures to be the most dynamic. These findings provide insight into the structure and dynamics of the VCBC complex and support further research into the improvement of HIV treatment, as Vif is essential for virus survival in the cell.
Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Kidney Disease-Related Genes in Patients with Diabetic Kidney Disease
Authors: Lazaro-Guevara Jose , Morales Julio Fierro , Wright A. Hunter , Gunville River , Frodsham Scott G. , Pezzolesi Melissa H. , Zaffino Courtney A. , Al-Rabadi Laith , Ramkumar Nirupama , Pezzolesi Marcus G. 
Published: May 2020

AbstractDiabetes is the most common cause of chronic kidney disease (CKD). For patients with diabetes and CKD, the underlying cause of their kidney disease is often assumed to be a consequence of their diabetes. Without histopathological confirmation, however, the underlying cause of their kidney disease is unclear. Recent studies have shown that next-generation sequencing (NGS) provides a promising avenue toward uncovering and establishing precise genetic diagnoses in various forms of kidney disease. Here, we set out to investigate the genetic basis of disease in non-diabetic kidney disease (NDKD) and diabetic kidney disease (DKD) patients by performing targeted NGS using a custom panel comprised of 345 kidney disease-related genes. Our analysis identified rare diagnostic variants that were consistent with the clinical diagnosis of 19% of the NDKD patients included in this study. Similarly, 22% of DKD patients were found to carry rare pathogenic/likely pathogenic variants in kidney disease-related genes included on our panel. Genetic variants suggestive of NDKD were detected in 3% of the diabetic patients included in this study. Our findings suggest that rare variants in kidney disease-related genes in the context of diabetic pathophysiology may play a role in the pathogenesis of kidney disease in patients with diabetes.Key MessagesWhat is already known about this subject?For patients with diabetes and chronic kidney disease, the underlying cause of their kidney disease is often assumed to be a consequence of their diabetes; without histopathological confirmation, however, the underlying cause of their kidney disease is unclear.Next-generation sequencing (NGS) provides a promising avenue toward uncovering and establishing precise genetic diagnoses in various forms of kidney disease.What are the new findings?Using targeted NGS and a custom panel comprised of 345 kidney disease-related genes, we found that 22% of diabetic kidney disease patients were found to carry rare pathogenic/likely pathogenic variants in kidney disease-related genes included on our panel.Genetic variants suggestive of non-diabetic kidney disease were detected in 3% of the diabetic patients included in this study.How might these results change the focus of research or clinical practice?Our findings suggest that rare variants in kidney disease-related genes in the context of diabetic pathophysiology may play a role in the pathogenesis of kidney disease in patients with diabetes.Importantly, improved understanding of the underlying disease process in diabetic kidney disease could have major implications in terms of patient care and monitoring as well as for research studies in this field.
ASYMMETRIC EXPRESSION OF ARGONAUTES IN ARABIDOPSIS REPRODUCTIVE TISSUES
Authors: Jullien PE , Bonnet DMV , Pumplin N , Schröder JA , Voinnet O 
Published: May 2020

AbstractDuring sexual reproduction, development of a totipotent zygote from the fusion of highly differentiated gametes is accompanied by dynamic regulation of gene expression. This notably involves RNA silencing operated by Argonautes (AGO) effector proteins. While AGOs’ roles duringArabidopsissomatic life have been extensively investigated, less is known about their expression during reproduction, which proceeds via double-fertilization of an egg and a central cell, leading respectively to the embryo and a supportive tissue known as endosperm. Using full-locus translational reporters for all tenArabidopsisAGOs, we uncover cell-specific expression patterns and AGO-intrinsic subcellular localizations in reproductive tissues. However, while someArabidopsisAGOs are enriched in both male and female gametes,i.e. sperm and egg cells, they are comparably low-expressed in accessory,i.e. vegetative and central cells. Likewise, following fertilization, several AGOs are expressed in the early embryo, yet below detection in the early endosperm. Thus, there is pre- and post-fertilization asymmetry between the embryo and endosperm lineages. Later during embryo development, AGO9, AGO5 and AGO7 are restricted to the apical embryonic meristem in contrast to AGO1, AGO4, AGO6 and AGO10. Beside shedding light onto potential roles for RNA silencing duringArabidopsisreproduction, the plant material generated here should constitute a valuable asset enabling functional AGOs studies in many tissues beyond those involved in reproduction.Summary statementArabidopsis genome encodes ten Argonautes proteins showing distinct expression pattern as well as intracellular localisation during sexual reproduction.
Early endocytosis as a key to understanding mechanisms of plasmalemma tension regulation in filamentous fungi
Authors: Mazheika Igor , Voronko Oxana , Kamzolkina Olga 
Published: May 2020

ABSTRACTTwo main systems regulate the plasmalemma tension and provide a close connection of the protoplast with the cell wall in fungi: turgor pressure and actin cytoskeleton. These systems work together with the plasmalemma focal adhesion to the cell wall and their contribution to fungal cell organization has been partially studied, but remains controversial in model filamentous ascomycetes and oomycetes, and even less investigated in filamentous basidiomycetes. Early endocytosis, in which F-actin is actively involved, can be used to research of mechanisms regulating the plasmalemma tension, since the latter influences on the primary endocytic vesicles formation. This study examined the effects of actin polymerization inhibitors and hyperosmotic shock on early endocytosis and cell morphology in two filamentous basidiomycetes. The main obtained results: (i) depolymerization of F-actin leads to the fast formation of primary endocytic vesicles but to inhibition of their scission; (ii) moderate hyperosmotic shock does not affect the dynamics of early endocytosis. These and a number of other results allowed offering a curtain model of regulation the plasmalemma tension in basidiomycetes. According to this model, the plasmalemma tension in many nonapical cells of hyphae is more often regulated not by turgor pressure, but by a system of actin driver cables that are associated with the proteins of focal adhesion sites. The change in the plasmalemma tension occurs similar to the movement of the curtain along the curtain rod using the curtain drivers. This model addresses the fundamental properties of the fungal structure and physiology and requires confirmation, including through the yet technically unavailable high quality labeling of the actin cytoskeleton of basidiomycetes.
Seesaw Conformations of Npl4 in the Human p97 Complex and the Inhibitory Mechanism of a Disulfiram Derivative
Authors: Pan Man , Zheng Qingyun , Yu Yuanyuan , Ai Huasong , Xie Yuan , Zeng Xin , Wang Chu , Liu Lei , Zhao Minglei 
Published: May 2020

ABSTRACTp97, also known as valosin-containing protein (VCP) or Cdc48, plays a central role in cellular protein homeostasis1. Human p97 mutations are associated with several neurodegenerative diseases2,3. Targeting p97 and its cofactors is a strategy for cancer drug development4. Despite significant structural insights into the fungal homolog Cdc485–7, little is known about how human p97 interacts with its cofactors. Recently, the anti-alcohol abuse drug disulfiram was found to target cancer through Npl4, a cofactor of p978, but the molecular mechanism remains elusive. Here, using single-particle cryo-electron microscopy (cryo-EM), we uncovered three Npl4 conformational states in complex with human p97 before ATP hydrolysis. The motion of Npl4 results from its zinc finger motifs interacting with the N domain of p97, which is essential for the unfolding activity of p97. In vitro and cell-based assays showed that under oxidative conditions, the disulfiram derivative bis-(diethyldithiocarbamate)-copper (CuET) inhibits p97 function by releasing cupric ions, which disrupt the zinc finger motifs of Npl4, locking the essential conformational switch of the complex.
Hyperpyrexia leading to death in a patient with severe COVID-19 disease
Authors: Singhal Tanu , Phadtare Sourabh , Pai Sunil , Raodeo Amit 
Published: May 2020

AbstractWe describe here the clinical course of a 42 year old male with severe COVID 19 disease treated at a private hospital in Mumbai, India. This patient with very high inflammatory markers at admission was treated with supportive care, mechanical ventilation, anticoagulation, hydroxychloroquine, corticosteroids, tocilizumab, intravenous insulin, antibiotics, sedation and paralysis. There was sustained improvement in his respiratory status and decline in ventilator settings with decline and normalization of CRP, D dimer and PCT. However high fever persisted that did not respond to paracetamol and NSAIDS. On day 8 of admission his axillary temperature touched 107F followed by rapid clinical deterioration and death within the next 12 hours, Blood cultures were consistently sterile. While death was related to hyperpyrexia, the cause of this hyperpyrexia is uncertain.
Improved Reference Genome forCyclotella CrypticaCCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)
Authors: Roberts Wade R. , Downey Kala M. , Ruck Elizabeth C. , Traller Jesse C. , Alverson Andrew J. 
Published: May 2020

ABSTRACTThe diatom,Cyclotella cryptica, is a well-established experimental model for physiological studies and, more recently, biotechnology applications of diatoms. To further facilitate its use as a model diatom species, we report an improved reference genome assembly and annotation forC. crypticastrain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of theC. crypticagenome. The high-qualityC. crypticagenome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.Data available fromNCBI BioProjects PRJNA628076 and PRJNA589195
Talin Rod Domain Containing Protein 1 (TLNRD1) is a novel actin-bundling protein which promotes filopodia formation
Authors: Cowell Alana R , Jacquemet Guillaume , Singh Abhimanyu K , Ammon York-Christoph , Brown David G , Akhmanova Anna , Ivaska Johanna , Goult Benjamin T. 
Published: May 2020

AbstractTalin is a mechanosensitive adapter protein which couples integrins to the cytoskeleton and regulates integrin-mediated adhesion. Talin rod domain-containing protein-1 (TLNRD1) shares 22% homology with the R7R8 domains of talin, and is highly conserved throughout vertebrate evolution, however little is known about its function. Here we show that TLNRD1 is an α-helical protein which shares the same atypical topology as talin R7R8, but forms a novel antiparallel dimer arrangement. Actin co-sedimentation assays and electron microscopy reveal TLNRD1 is an actin-bundling protein that forms tight actin bundles. In addition, TLNRD1 binds to the same LD-motif containing proteins, RIAM and KANK, as talin, and thus may act in competition with talin. Filopodia are cell protrusions supported by tightly bundled actin filaments and TLNRD1 localises to filopodia tips, increases filopodia number and promotes cell migration in 2D. Together our results suggest that TLNRD1 has similar functionality to talin R7R8, serving as a nexus between the actin and microtubule cytoskeletons independent of adhesion complexes.
Agro-morphological and phenotypic variability of sweet basil (Ocimum basilicumL.) genotypes for breeding purposes
Authors: Yaldiz Gulsum , Camlica Mahmut 
Published: May 2020

AbstractThe genus Ocimum is very complicated due to the presence of huge morphological variability along with genetic diversity. Basil (Ocimum basilicum L.) has pharmacological properties like headaches, coughs, diarrhea, constipation, warts, worms, kidney malfunction, and its potential as a therapeutic agent in treating various age-related diseases. The present investigation comprised of sixty-one genotypes of basil was undertaken to characterize the genotypes based on morphological and phenological features, herbs and essential oil yield of genotypes. A wide range of variations for traits like days to first cutting (56.92-101.6), plant height (13.67-71.90 cm), branch number (3.28-19.43 number/plant), fresh herb yields (12.94-274.11 g/plant), and essential oil yield (0.04-1.71%) were observed and can be useful for breeding purposes. PI 652070 and PI 296391 genotypes were found superior in case of the highest herbs yield as compared with other genotypes. Overall, in PI 358469 and Ames 32309 genotypes exhibited the highest essential oil content. The constellation analysis was conducted to investigate the genetic diversity of basil genotypes. According to the constellation plot analysis, leaf shape and color were evaluated in 2017 and most of the basil genotypes located in the same main group. In 2018, moonlight and dino cultivars located in the same cluster 1 (C1) with PI 141198 (US/Maryland) genotype and Georgia genotypes located in the same main group and they also took place in the sub-main group except Ames 32314 genotype depending on UPOV criteria. Each two years, Bolu genotype and midnight were found in the same main group.
Identification of differential gene expression pattern in lens epithelial cells derived from cataractous and non-cataractous lenses of Shumiya cataract rat
Authors: Ishida Hidetoshi , Shibata Teppei , Nakamura Yuka , Ishigaki Yasuhito , Singh Dhirendra P , Sasaki Hiroshi , Kubo Eri 
Published: May 2020

AbstractThe Shumiya cataract rat (SCR) is a model for hereditary cataract. Two-third of these rats develop lens opacity within 10-11-weeks. Onset of cataract is attributed to the synergetic effect of lanosterol synthase (Lss) and farnesyl-diphosphate farnesyltransferase 1 (Fdft1) mutant alleles that lead to cholesterol deficiency in the lenses, which in turn adversely affects lens biology including the growth and differentiation of lens epithelial cells (LECs). Nevertheless, the molecular events and changes in gene expression associated with the onset of lens opacity in SCR is poorly understood. In the present study, a microarray-based approach was employed to analyze comparative gene expression changes in LECs isolated from the pre-cataractous and cataractous stages of lenses of 5-, 8- and 10-week-old SCRs. The changes in gene expression observed in microarray results in the LECs were further validated using real-time PCR and western blot analyses. Lens opacity was not observed in 5-week-old rats. However, histological analysis revealed mild dysplasia in the anterior suture and poorly differentiated fiber cells at the bow region. Expression of approximately 100 genes, including major intrinsic protein of lens fiber (MIPand Aquaporin0), deoxyribonuclease II beta (Dnase2b), heat shock protein B1 (Hspb1), and crystallin γ (γCry) B, C, and F were found to be significantly downregulated (0.07-0.5 fold) in rat LECs derived from cataract lenses compared to that in noncataractous lenses (control). Thus, our study aimed to identify the gene expression patterns during cataract formation in SCRs, which may be responsible for cataractogenesis in SCR. We proposed that mutation in lanosterol synthase was responsible for the downregulation of genes associated with lens fiber differentiation, which in turn leads to the formation of cataract in these rats. Our findings may have wider implications in understanding the effect of cholesterol deficiency and the role of cholesterol-lowering therapeutics on cataractogenesis.
High Throughput Designing and Mutational Mapping of RBD-ACE2 Interface Guide Non-Conventional Therapeutic Strategies for COVID-19
Authors: Padhi Aditya K. , Kalita Parismita , Zhang Kam Y. J. , Tripathi Timir 
Published: May 2020

ABSTRACTConsidering the current status of the SARS-CoV-2 pandemic, sequence variations and possibly structural changes in the rapidly evolving SARS-CoV-2 is highly expected in the coming months. The SARS-CoV-2 spike (S) protein is responsible for mediating viral attachment and fusion with cell membranes. Mutations in the receptor-binding domain (RBD) of the S-protein occur at the most variable part of the SARS-CoV-2 genome, and specific sites of S-protein have undergone positive selection impacting the viral pathogenicity. In the present work, we used high-throughput computation to design 100,000 mutants in RBD interfacial residues and identify novel affinity-enhancing and affinity-weakening mutations. Our data suggest that SARS-CoV-2 can establish a higher rate of infectivity and pathogenesis when it acquires combinatorial mutations at the interfacial residues in RBD. Mapping of the mutational landscape of the interaction site suggests that a few of these residues are the hot-spot residues with a very high tendency to undergo positive selection. Knowledge of the affinity-enhancing mutations may guide the identification of potential cold-spots for this mutation as targets for developing a possible therapeutic strategy instead of hot-spots, and vice versa. Understanding of the molecular interactions between the virus and host protein presents a detailed systems view of viral infection mechanisms. The applications of the present research can be explored in multiple antiviral strategies, including monoclonal antibody therapy, vaccine design, and importantly in understanding the clinical pathogenesis of the virus itself. Our work presents research directions for the exploitation of non-conventional solutions for COVID-19.
K-fiber bundles in the mitotic spindle are mechanically reinforced by Kif15
Authors: Begley Marcus A , Solon April L , Davis Elizabeth Mae , Sherrill Michael Grant , Ohi Ryoma , Elting Mary Williard 
Published: May 2020

AbstractThe mitotic spindle, a self-constructed microtubule-based machine, segregates chromosomes into two eventual daughter nuclei. In mammalian cells, microtubule bundles called kinetochore-fibers (k-fibers) anchor chromosomes within the spindle. Chromosome segregation thus depends on the mechanical integrity of k-fibers. Here, we investigate the physical and molecular basis of k-fiber bundle cohesion. We sever k-fibers using laser ablation, thereby detaching them from poles and testing the contribution of pole-localized force generation to k-fiber cohesion. We then measure the physical response of the remaining kinetochore-bound segments of the k-fibers. We observe that microtubules within ablated k-fibers often, but not always, splay apart from their minus-ends. Furthermore, we find that minus-end clustering forces induced in response to ablation seem at least partially responsible for k-fiber splaying. We also investigate the role of the putative k-fiber-binding kinesin-12 Kif15. We find that pharmacological inhibition of Kif15 microtubule binding reduces k-fiber mechanical integrity. In contrast, inhibition of its motor activity but not its microtubule binding does not greatly affect splaying. Altogether, the data suggest that forces holding k-fibers together are of similar magnitude to other spindle forces, and that Kif15, acting as a microtubule crosslinker, helps fortify and repair k-fibers. This feature of Kif15 may help support robust k-fiber function and prevent chromosome segregation errors.
UBTD1 regulates ceramide balance and endolysosomal positioning to coordinate EGFR signaling
Authors: Torrino S , Tiroille V , Dolfi B , Dufies M , Hinault C , Bonesso L , Dagnino S , Uhler JP , Irondelle M , Gay AS , Fleuriot L , Debayle D , Lacas-Gervais S , Cormont M , Bertero T , Bost F , Gilleron J , Clavel S 
Published: May 2020

AbstractTo adapt in an ever-changing environment, cells must integrate physical and chemical signals and translate them into biological meaningful information through complex signaling pathways. By combining lipidomic and proteomic approaches with functional analysis, we have shown that UBTD1 (Ubiquitin domain-containing protein 1) plays a crucial role in both the EGFR (Epidermal Growth Factor Receptor) self-phosphorylation and its lysosomal degradation. On the one hand, by modulating the cellular level of ceramides through ASAH1 (N-Acylsphingosine Amidohydrolase 1) ubiquitination, UBTD1 controls the ligand-independent phosphorylation of EGFR. On the other hand, UBTD1,viathe ubiquitination of SQSTM1/p62 (Sequestosome 1) and endolysosome positioning, participates in the lysosomal degradation of EGFR. The coordination of these two ubiquitin-dependent processes contributes to the control of the duration of the EGFR signal. Moreover, we showed that UBTD1 depletion exacerbates EGFR signaling and induces cell proliferation emphasizing ahithertounknown function of UBTD1 in EGF-driven cell proliferation.