bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRIM5α restriction of HIV-1-N74D viruses in lymphocytes is caused by a loss of cyclophilin A protection
Authors: Selyutina Anastasia , Simons Lacy M. , Bulnes-Ramos Angel , Hultquist Judd F. , Diaz-Griffero Felipe 
Published: September 2020

ABSTRACTThe core of HIV-1 viruses bearing the capsid change N74D (HIV-1-N74D) do not bind the human protein cleavage and polyadenylation specificity factor subunit 6 (CPSF6). In addition, HIV-1-N74D viruses have altered patterns of integration site preference in human cell lines. In primary human CD4+ T cells, HIV-1-N74D viruses exhibit infectivity defects when compared to wild type. The reason for this loss of infectivity in primary cells is unknown. We first investigated whether loss of CPSF6 binding accounts for the loss of infectivity. Depletion of CPSF6 in human CD4+T cells did not affect the early stages of wild-type HIV-1 replication, suggesting that defective infectivity in the case of HIV-1-N74D is not due to the loss of CPSF6 binding. Based on our previous result that cyclophilin A (Cyp A) protected HIV-1 from human tripartite motif-containing protein 5α (TRIM5αhu) restriction in CD4+T cells, we tested whether TRIM5αhuwas involved in the decreased infectivity observed for HIV-1-N74D. Depletion of TRIM5αhuin CD4+T cells rescued the infectivity of HIV-1-N74D, suggesting that HIV-1-N74D cores interacted with TRIM5αhu. Accordingly, TRIM5αhubinding to HIV-1-N74D cores was increased compared with that of wild-type cores, and consistently, HIV-1-N74D cores lost their ability to bind Cyp A. In conclusion, we showed that the decreased infectivity of HIV-1-N74D in CD4+T cells is due to a loss of Cyp A protection from TRIM5αhurestriction activity.
Lifestyle-specificS-nitrosylation of protein cysteine thiols regulatesEscherichia colibiofilm formation and resistance to oxidative stress
Authors: Barraud Nicolas , Létoffé Sylvie , Beloin Christophe , Vinh Joelle , Chiappetta Giovanni , Ghigo Jean-Marc 
Published: September 2020

SUMMARYCommunities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteineS-nitrosylation in aerobic and anaerobic biofilm and planktonicEscherichia colicultures and we identified proteins with biofilm-specificS-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairingS-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG and GltD altered important biofilm properties, including motility, biofilm maturation or resistance to oxidative stress. Our study therefore revealed thatS-nitrosylation constitutes a physiological basis underlying functions critical forE. coliadaptation to the biofilm environment.
Design, expression, purification and characterization of a YFP-tagged 2019-nCoV spike receptor-binding domain construct
Authors: Bierig Tobias , Collu Gabriella , Blanc Alain , Poghosyan Emiliya , Benoit Roger. M. 
Published: September 2020

Abstract2019-nCoV is the causative agent of the serious, still ongoing, worldwide COVID-19 pandemic. High quality recombinant virus proteins are required for research related to the development of vaccines and improved assays, and to the general understanding of virus action. The receptor-binding domain (RBD) of the 2019-nCoV spike (S) protein contains disulfide bonds and N-linked glycosylations, therefore, it is typically produced by secretion. Here, we describe a construct and protocol for the expression and purification of yellow fluorescent protein (YFP) labeled 2019-nCoV spike RBD. The fusion protein, in the vector pcDNA 4/TO, comprises an N-terminal interferon alpha 2 (IFNα2) signal peptide, an eYFP, a FLAG-tag, a human rhinovirus 3C protease cleavage site, the RBD of the 2019-nCoV spike protein and a C-terminal 8x His-tag. We stably transfected HEK 293 cells. Following expansion of the cells, the fusion protein was secreted from adherent cells into serum-free medium. Ni-NTA IMAC purification resulted in very high protein purity, based on analysis by SDS-PAGE. The fusion protein was soluble and monodisperse, as confirmed by size-exclusion chromatography (SEC) and negative staining electron microscopy. Deglycosylation experiments confirmed the presence of N-linked glycosylations in the secreted protein. Complex formation with the peptidase domain of human angiotensin-converting enzyme 2 (ACE2), the receptor for the 2019-nCoV spike RBD, was confirmed by SEC, both for the YFP-fused spike RBD and for spike RBD alone, after removal of YFP by proteolytic cleavage. Possible applications for the fusion protein include binding studies on cells orin vitro, fluorescent labeling of potential virus-binding sites on cells, the use as an antigen for immunization studies or as a tool for the development of novel virus- or antibody-detection assays.
The antimicrobial peptide TAT-RasGAP317-326inhibits the formation and the expansion of bacterial biofilmsin vitro
Authors: Heinonen Tytti , Hargraves Simone , Georgieva Maria , Widmann Christian , Jacquier Nicolas 
Published: September 2020

AbstractBiofilms are structured aggregates of bacteria embedded in a self-produced matrix. Pathogenic bacteria can form biofilms on surfaces and in tissues leading to nosocomial and chronic infections. While antibiotics are largely inefficient in limiting biofilm formation and expansion, antimicrobial peptides (AMPs) are emerging as alternative anti-biofilm treatments. In this study, we explore the effect of the newly described AMP TAT-RasGAP317-326onAcinetobacter baumannii, Pseudomonas aeruginosaandStaphylococcus aureusbiofilms. We observe that TAT-RasGAP317-326inhibits the formation of biofilms at concentrations equivalent or two times superior to the minimal inhibitory concentration (MIC) of the corresponding planktonic bacteria. Moreover, TAT-RasGAP317-326limits the expansion ofA. baumanniiandP. aeruginosaestablished biofilms at concentrations 2-4 times superior to the MIC. These results further confirm the potential of AMPs against biofilms, expand the antimicrobial potential of TAT-RasGAP317-326and support further development of this peptide as an alternative antimicrobial treatment.
Chromosome-level genome assemblies of the malaria vectorsAnopheles coluzziiandAnopheles arabiensis
Authors: Zamyatin Anton , Avdeyev Pavel , Liang Jiangtao , Sharma Atashi , Chen Chujia , Lukyanchikova Varvara , Alexeev Nikita , Tu Zhijian , Alekseyev Max A. , Sharakhov Igor V. 
Published: September 2020

AbstractBackgroundAnopheles coluzziiandAn. arabiensisbelong to theAn. gambiaecomplex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species.FindingsIn this study, we producedde novochromosome-level genome assemblies forAn. coluzziiandAn. arabiensisusing the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 Mbp and 256.8 Mbp of the total assemblies forAn. coluzziiandAn. arabiensis, respectively. Each assembly consists of three chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomiccoordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions inAn. coluzziiandAn. arabiensis.ConclusionThe new chromosome-level assemblies will facilitate functional and population genomic studies inAn. coluzziiandAn. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.
The roseoloviruses downregulate the protein tyrosine phosphatase PTPRC (CD45)
Authors: Whyte Melissa L. , Smith Kelsey , Buchberger Amanda , Luecke Linda Berg , Tjan Lidya Handayani , Mori Yasuko , Gundry Rebekah L , Hudson Amy W. 
Published: September 2020

AbstractLike all herpesviruses, the roseoloviruses (HHV6A, -6B, and -7) establish lifelong infection within their host, requiring these viruses to evade host anti-viral responses. One common host-evasion strategy is the downregulation of host-encoded, surface-expressed glycoproteins. Roseoloviruses have been shown to evade host the host immune response by downregulating NK-activating ligands, MHC class I, and the TCR/CD3 complex. To more globally identify glycoproteins that are differentially expressed on the surface of HHV6A-infected cells, we performed cell surface capture of N-linked glycoproteins present on the surface of T cells infected with HHV6A, and compared these to proteins present on the surface of uninfected T cells. We found that the protein tyrosine phosphatase CD45 is downregulated in T cells infected with HHV6A. We also demonstrated that CD45 is similarly downregulated in cells infected with HHV-7. CD45 is essential for signaling through the T cell receptor and as such, is necessary for developing a fully functional immune response. Interestingly, the closely related β-herpesviruses human cytomegalovirus (HCMV) and murine cytomegalovirus (MCMV) have also separately evolved unique mechanisms to target CD45. While HCMV and MCMV target CD45 signaling and trafficking, HHV6A acts to downregulate CD45 transcripts.ImportanceHuman herpesviruses-6 and -7 infect essentially 100% of the world’s population before the age of 5 and then remain latent or persistent in their host throughout life. As such, these viruses are among the most pervasive and stealthy of all viruses. Host immune cells rely on the presence of surface-expressed proteins to identify and target virus-infected cells. Here, we investigated the changes that occur to proteins expressed on the cell surface of T cells after infection with human herpesvirus-6A. We discovered that HHV-6A infection results in a reduction of CD45 on the surface of infected cells. Targeting of CD45 may prevent activation of these virus-infected T cells, possibly lengthening the life of the infected T cell so that it can harbor latent virus.
Cell type specific labeling and partial connectomes of dopaminergic circuits reveal non-synaptic communication and large-scale axonal remodeling after exposure to cocaine
Authors: Wildenberg G.A. , Sorokina A.M. , Koranda J.L. , Monical A. , Heer C. , Sheffield M.E. , Zhuang X. , McGehee DS , Kasthuri N. 
Published: September 2020

SummaryDopaminergic (DA) neurons exert profound influences on behavior including addiction. However, how DA axons communicate with target neurons and how those communications change, for example, with drug exposure, remains poorly understood. We combine recent advances in cell type specific labeling for electron microscopy with large volume three-dimensional serial electron microscopy – ‘connectomics’- to detail DA connections in the Nucleus Accumbens (NAc) across multiple animals and after exposure to cocaine. We find that DA axonal varicosities are of four general types: 38% are empty, 25% contain few small (∼50 nm diameter) vesicles, 19% contain few large (∼133 nm diameter) vesicles, and 18% have mixed small and large vesicles, suggesting that DA axons may use multiple types of neurotransmitters. Individual DA axons were significantly more likely to contain multiple varicosities of the same type relative to chance, suggesting a new method of DA axon classification. Across all categories, we find only rare examples (<2%, 6/410) of varicosities making specific synapses with any neighboring neuron with the few examples being made exclusively on the shafts and soma of resident NAc neurons. Instead, we find much more frequently (15%) that DA varicosities form spinule-like structures: physical membrane interdigitations with nearby dendrites or excitatory and inhibitory axons. Days after a brief exposure to cocaine, DA axons were extensively branched relative to controls but with similar densities of varicosities and spinules. Additionally, cocaine exposure results in the formation of blind-ended “bulbs” in DA axons, filled with mitochondria, and reminiscent of axonal retraction in the developing and damaged brain. Every bulb was surrounded by elaborated glia further suggestive of active remodeling. Finally, mitochondrial lengths increased by ∼2.2 times relative to control throughout DA axons and NAc spiny dendrites after cocaine exposure but not in DA soma or DA dendrites. We conclude that DA axonal transmission is unlikely to be mediated via classical synapses in the NAc and that the major locus of anatomical plasticity of DA circuits after exposure to cocaine are large scale axonal rearrangements with correlated changes in mitochondria.
Structural and Functional Characterization of Host FHL1 Protein Interaction with Hypervariable Domain of Chikungunya Virus nsP3 Protein
Authors: Lukash Tetyana , Agback Tatiana , Dominguez Francisco , Shiliaev Nikita , Meshram Chetan , Frolova Elena I. , Agback Peter , Frolov Ilya 
Published: September 2020

ABSTRACTDecades of insufficient control resulted in unprecedented spread of chikungunya virus (CHIKV) around the globe and millions already suffered from the highly debilitating disease. Nevertheless, the current understanding of CHIKV-host interactions and adaptability of the virus to replication in mosquitoes and mammalian hosts is still elusive. Our new study shows that four-and-a-half LIM domain protein (FHL1) is one of the host factors that interact with hypervariable domain (HVD) of CHIKV nsP3. Unlike G3BPs, FHL1 is not a pre-requisite of CHIKV replication, and many commonly used cell lines do not express FHL1. However, its expression has detectable stimulatory effect(s) on CHIKV replication, and theFhl1KO cell lines demonstrate slower infection spread. The NMR-based studies revealed that the binding site of FHL1 in CHIKV nsP3 HVD overlaps with that of another pro-viral host factor, CD2AP. The structural data also demonstrated that FHL1-HVD interaction is mostly determined by LIM1 domain of FHL1. However, it does not mirror binding of the entire protein, suggesting that other LIM domains are involved. In agreement with previously published data, our biological experiments showed that interactions of CHIKV HVD with CD2AP and FHL1 have additive positive effects on the efficiency of CHIKV replication. This study shows that CHIKV mutants with extensive modifications of FHL1- or both FHL1- and CD2AP- binding sites remain viable and develop spreading infection in multiple cell types. Thus, such modifications of HVD may improve live CHIKV vaccine candidates in terms of their safety and stability of the attenuated phenotype.IMPORTANCEReplication of chikungunya virus (CHIKV) is determined by a wide range of host factors. Previously, we have demonstrated that the hypervariable domain (HVD) of CHIKV nsP3 protein contains linear motifs that recruit defined families of host proteins into formation of functional viral replication complexes. Now, using NMR-based structural and biological approaches, we have characterized the binding site of cellular FHL1 protein in CHIKV HVD and defined the biological significance of this interaction. In contrast to previously described binding of G3BP to CHIKV HVD, the FHL1-HVD interaction was found to not be a prerequisite of viral replication. However, the presence of FHL1 has a stimulatory effect on CHIKV infectivity and subsequently, the infection spread. FHL1 and CD2AP proteins were found to have overlapping binding sites in CHIKV HVD and additive pro-viral functions. Elimination of FHL1-binding site in nsP3 HVD can be used for the development of stable, live attenuated vaccine candidates.
A real-time, transient kinetic study ofDrosophila melanogasterDicer-2 elucidates mechanism of termini-dependent cleavage of dsRNA
Authors: Singh Raushan K. , Jonely McKenzie , Leslie Evan , Rejali Nick A. , Noriega Rodrigo , Bass Brenda L. 
Published: September 2020

SUMMARYDrosophila melanogasterDicer-2 (dmDcr-2) differentially processes dsRNA with blunt or 2 nucleotide 3’-overhanging termini. We investigated the transient kinetic mechanism of these reactions using a rapid reaction stopped-flow technique and time-resolved fluorescence spectroscopy. We found that ATP binding to dmDcr-2’s helicase domain impacts the kinetics of dsRNA binding and dissociation in a termini-dependent manner, emphasizing the termini-dependent discrimination of dsRNA on a biologically-relevant time-scale. ATP-hydrolysis mediates local unwinding of dsRNA, and directional translocation on unwound single-stranded RNA, which is concurrent with a slow rewinding prior to dsRNA cleavage. Time-resolved fluorescence anisotropy reveals a nucleotide-dependent change in conformational dynamics of the helicase and Platform•PAZ domains in the nanosecond timescale that is correlated with termini-dependent dsRNA cleavage. Our study delineates kinetic events and transient intermediates for a Dicer-catalyzed reaction, thus establishing a framework for understanding other Dicers and how accessory factors modulate the reaction.
A small-molecule oral agonist of the human glucagon-like peptide-1 receptor
Authors: Griffith David A. , Edmonds David J. , Fortin Jean-Phillipe , Kalgutkar Amit S. , Kuzmiski J. Brent , Loria Paula M. , Saxena Aditi R. , Bagley Scott W. , Buckeridge Clare , Curto John M. , Derksen David R. , Dias João M. , Griffor Matthew C. , Han Seungil , Jackson V. Margaret , Landis Margaret S. , Lettiere Daniel J. , Limberakis Chris , Liu Yuhang , Mathiowetz Alan M. , Piotrowski David W. , Price David A. , Ruggeri Roger B. , Tess David A. 
Published: September 2020

AbstractPeptide agonists of the glucagon-like peptide-1 receptor (GLP-1R) have revolutionized diabetes therapy, but their use has been limited by the requirement for injection. Here we describe the first effective, orally bioavailable small molecule GLP-1R agonists. A sensitized high-throughput screen identified a series of small molecule GLP-1R agonists that were optimized to promote endogenous GLP-1R signaling with nM potency. These small molecule agonists increased insulin levels in primates but not rodents, which is explained by a cryo-EM structure that revealed a binding pocket requiring primate-specific tryptophan 33. Importantly, oral administration of agonist PF-06882961 to healthy humans produced dose-dependent declines in serum glucose (NCT03309241). This opens the door to a new era of oral small molecule therapies that target the well-validated GLP-1R pathway for metabolic health.One Sentence SummaryPF-06882961 is an orally administered small molecule that activates the GLP-1 receptor to lower blood glucose in humans.
Humanistic leadership in the UAE context
Authors: Anadol Yaprak , Behery Mohamed 
Published: September 2020

PurposeThe main intention of this paper is to understand humanistic leadership through an eminent leader representing the United Arab Emirates (UAE) culture. The authors identified a prominent humanistic leader of a well-known private university in Dubai as an example, analyzing his leadership approach from a humanistic lens and demonstrating humanistic leadership characteristics linked to the cultural roots.Design/methodology/approachThis paper is designed as a single case to examine how humanistic leadership behaviors and practices are applied in an organization and how they are connected to the UAE culture. The leader and his seven followers are interviewed by using semi-structured forms, and inductive conventional content analysis was utilized to identify common themes and concepts related to humanistic leadership traits in the UAE.FindingsThe paper highlights ten themes named humility, respect, care, fairness, transparency, well-being orientation, generosity, family focus and will with humanistic determination. These themes coincide with the various well-accepted humanistic literature theories and are also aligned with salient Islamic values and the existing humanistic leadership theories. A humanistic leadership description is provided to show the implications to the UAE context.Research limitations/implicationsThis study only focuses on a single higher education institution, and further studies need to be conducted to reach a generalization.Practical implicationsThe paper offers an alternative humanistic leadership for government departments, semi private and private companies to create an organizational culture where those values are flourished and creating an awareness in youth leadership programs to include humanistic leadership principles that will eventually increase social welfare.Originality/valueThis study provides an insight into humanistic leadership phenomenon by giving a contextual example from the UAE. As there has been no attempt to link humanistic leadership to the UAE culture, the findings of this paper will contribute to cross-cultural leadership research.
Manninen’s mixture model for conjugate conduction and mixed convection heat transfer of a nanofluid in a rotational/stationary circular enclosure
Authors: Hoseininejad Faraz , Dinarvand Saeed , Yazdi Mohammad Eftekhari 
Published: September 2020

Purpose
This study aims to investigate numerically the problem of conjugate conduction and mixed convection heat transfer of a nanofluid in a rotational/stationary circular enclosure using a two-phase mixture model.

Design/methodology/approach
Hot and cold surfaces on the wall or inside the enclosure (heater and cooler) are maintained at constant temperature of Th and Tc, respectively, whereas other parts are thermally insulated. To examine the effects of various parameters such as Richardson number (0.01 = Ri =100), thermal conductivity ratio of solid to base fluid (1 = Kr = 100), volume fraction of nanoparticle (0 = φ = 0.05), insertion of conductive covers (C.Cs) around the heater in a different shape (triangular, circular or square), segmentation and arrangement of the conductive blocks (C.Bs) and rotation direction of the enclosure on the flow structure and heat transfer rate, two-dimensional equations of mass, momentum and energy conservation, as well as volume fraction, are solved using finite volume method and Semi-Implicit Method for Pressure Linked Equations (SIMPLE) algorithm.

Findings
The results show that inserting C.C around heater can increase or decrease heat transfer rate, and it depends on thermal conductivity ratio of solid to pure fluid. Also, it is found that by the division of C.B and location of its portions in a horizontal configuration, heat transfer rate reduces. Moreover, it is observed that external heating and cooling of the enclosure causes enhancement of heat transfer relative to that of internal heating and cooling. Finally, results illustrate that under the condition that cylinders rotate in the same direction, the heat transfer rate increases as compared to those that rotate in the opposite direction. Hence rotation direction of cylinders can be used as a desired parameter for controlling heat transfer rate.

Originality/value
A comprehensive report of results for the problem of conjugate conduction and mixed convection heat transfer in a circular cylinder containing different shapes of C.C, conducting obstacle and heater and cooler has been presented. An efficient numerical technique has been developed to solve this problem. The achievements of this paper are purely original, and the numerical results were never published by any researcher.