bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network analysis reveals how lipids and other cofactors influence membrane protein allostery
Authors: Westerlund Annie M. , Fleetwood Oliver , Perez-Conesa Sergio , Delemotte Lucie 
Published: July 2020

AbstractMany membrane proteins are modulated by external stimuli, such as small molecule binding or change in pH, transmembrane voltage or temperature. This modulation typically occurs at sites that are structurally distant from the functional site. Revealing the communication, known as allostery, between these two sites is key to understanding the mechanistic details of these proteins. Residue interaction networks of isolated proteins are commonly used to this end. Membrane proteins, however, are embedded in a lipid bilayer which may contribute to allosteric communication. The fast diffusion of lipids hinders direct use of standard residue interaction networks. Here, we present an extension which includes cofactors such as lipids and small molecules in the network. The novel framework is applied to three membrane proteins: a voltage-gated ion channel (KCNQ1), a G-protein coupled receptor (GPCR -β2 adrenergic receptor) and a pH-gated ion channel (KcsA). Through systematic analysis of the obtained networks and their components, we demonstrate the importance of lipids for membrane protein allostery. Finally, we reveal how small molecules may stabilize different protein states by allosterically coupling and decoupling the protein from the membrane.
The role of icIL-1RA type 1 in oral keratinocyte senescence and the development of the senescence associated secretory phenotype
Authors: Niklander Sven E , Crane Hannah L , Darda Lav , Lambert Daniel W , Hunter Keith D 
Published: July 2020

AbstractThere is compelling evidence that senescent cells, through the senescence-associated secretory phenotype (SASP), can promote malignant transformation and invasion. IL-1 is a key mediator of this cytokine network, but the control of its activity in the senescence program has not been elucidated. IL-1 signalling is regulated by IL-1RA, which has four variants. Here, we show that expression of intracellular IL-1RA type 1 (icIL-1RA1), which competitively inhibits binding of IL-1 to its receptor, is progressively lost during oral carcinogenesisex vivoand that the pattern of expression is associated with keratinocyte replicative fatein vitro. We demonstrate icIL-1RA1 is an important regulator of the SASP in mortal cells, as CRISPR-CAS9 mediated icIL-1RA1 knockdown in normal and mortal dysplastic oral keratinocytes is followed by increased IL-6 and IL-8 secretion, and rapid senescence following release from ROCK inhibition. Thus, we suggest that downregulation of icIL-1RA1 in early stages of the carcinogenesis process can enable the development of a premature and de-regulated SASP, creating a pro-inflammatory state in which cancer is more likely to arise.
De novo formation of an early endosome during Rab5 to Rab7 transition
Authors: Skjeldal Frode Miltzow , Haugen Linda Hofstad , Mateus Duarte , Frei Dominik , Bakke Oddmund 
Published: July 2020

AbstractRab5 and Rab7a are the main determinants of early and late endosomes and are important regulators of endosomal progression. The transport from early endosomes to late endosome seems to be regulated through an endosomal maturation switch where Rab5 is exchanged with Rab7a on the same endosome. Here we provide new insight into the mechanism of endosomal maturation where we have discovered a stepwise Rab5 detachment, sequentially regulated by Rab7a. The initial detachment of Rab5 is Rab7a independent and demonstrate a diffusion-like exchange between cytosol and endosomal membrane, and the second phase is slower where Rab5 converges into a specific domain that specifically detaches as a Rab5 indigenous endosome. Consequently, we show that early endosomal maturation regulated through the Rab5 to Rab7a switch induce the formation of a new fully functional early endosome. Progression through a stepwise early endosomal maturation regulates the direction of the transport and concomitantly regulates the homeostasis of early endosomes.
Strategic stakeholders’ typology and mapping using stakeholder network analyses on integrated crops-livestock farming systems in West New Guinea
Authors: Iyai Deny Anjelus , Widayati Isti , Fatem Hendrik , Nurhayati Dwi , Arim Maria , Monim Hanike , Ronsumbre Adolof , Baaka Alnita , Orisu Lily , Saragih Desni T.R. , Syufi Yafet , Nuhuyanan Lambertus E. , Woran Djonly , Mofu Wolfram , Randa Sangle Y. , Sonbait Lukas Y. , Arizona Rizki , Baransano Michael , Seseray Daniel , Pattiselanno Freddy , Yaku Alexander , Koibur Johan 
Published: July 2020

AbstractStakeholders and its network play prominent roles in development particularly agriculture sector. The involvement of many stakeholders and other parties shaped how farms can sustain in terms of economic, social and environment indicators. Exploring the importance and roles of actors become strategic and vital to recognize. Study was done in Manokwari using focus group discussion towards twenty various represented individuals, groups and mass institutions. The queries discussed concerning background, resources delivery, interconnectivity amongst actors, intervention and innovation. The finding is that the stakeholders in mixed crop-livestock are dominated by individuals’ actors who privately manage the farms officially has laws. These actors are commonly act like stakeholders who are positively important ruled the farms. The threats are real and exist and should be lowering as much as possible to mitigate the turn-back effect. The top five shared resources are access, satisfaction, power, knowledge and time allocation. Those resources will stay longer to sustain strong needs of the farms. The relationship of actors is dominated by positive similarity and the ranges of correlation are varying in between negative, neutral to positive. This is due to actors reluctant to deliver the intervention and innovation. Actors with low interest and low power should then be promote to high interest and power by using aids, guidance and services from each actor in mixed crop-livestock farms business.
Toxoplasma gondiiPPM3C, a secreted protein phosphatase, affects parasitophorous vacuole effector export
Authors: Mayoral Joshua A. , Tomita Tadakimi , Tu Vincent , Aguilan Jennifer T. , Sidoli Simone , Weiss Louis M. 
Published: July 2020

ABSTRACTToxoplasma gondiiis a highly successful parasite that infects a significant portion of the human population. As an intracellular parasite,T. gondiithrives within many different cell types due to its residence in the parasitophorous vacuole, a specialized and heavily modified compartment in which parasites divide. Within this vacuole, numerous secreted proteins facilitate functions that optimize intracellular survival. We characterized one such protein, TgPPM3C, which is predicted to contain a domain belonging to the PP2C class of serine/threonine phosphatases and is secreted by both tachyzoites and differentiating bradyzoites into the vacuolar lumen. Genetic deletion of TgPPM3C established that parasites lacking this predicted phosphatase exhibit a minor growth defectin vitro, are avirulent during acute infection in mice, and form fewer cysts in mouse brain during chronic infection. A label-free phosphoproteomic approach was utilized to identify putative TgPPM3C substrates and demonstrated several secreted proteins with altered phosphorylation status in the absence of TgPPM3C. Altered phosphorylation status was seen in MYR1, a protein essential to the process of protein effector export from the parasitophorous vacuole into the host cell, and in GRA16 and GRA28, two exported effector proteins. Defects were seen in the export of GRA16 and GRA28, but not the effector TgIST, in the TgPPM3C knockout strain. Parasites lacking TgPPM3C also exhibited defects in host c-Myc induction, a process influenced by effector export. Phosphomimetic mutations of GRA16 serine residues recapitulated export defects, implicating de-phosphorylation as an important process in facilitating the export of GRA16. These findings provide an example of the emerging critical role that phosphatases play in regulating the complex environment of theT. gondiiparasitophorous vacuole.
Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses
Authors: Flatt Justin W. , Domanska Aušra , Seppälä Alma L. , Butcher Sarah J. 
Published: July 2020

AbstractMajor efforts have been underway to develop broad-spectrum high potency capsid binders that inhibit the life cycle of enteroviruses, a large group (familyPicornaviridae) whose members include poliovirus, coxsackieviruses, echoviruses, numbered enteroviruses, and rhinoviruses. These diverse viruses cause a wide variety of illnesses, ranging from the mild common cold to hand-foot-and-mouth disease, myocarditis, pancreatitis, aseptic meningitis, and encephalitis. So-called classical capsid binders target a surface exposed hydrophobic pocket in one of the viral coat proteins (VP1) to prevent the genome uncoating process. However, efficacy, toxicity, emergence of drug-resistant viruses, and existence of certain enteroviral species that lack the VP1 pocket limit their clinical benefit. Recently, we identified a new druggable site at a conserved interface formed by multiple capsid proteins, the VP1-VP3 interprotomer pocket. To further study the properties that confer druggability at this site, we have determined high-resolution cryo-electron microscopy structures of two enteroviruses, coxsackieviruses B3 and B4, complexed with interprotomer-targeting compounds, CP17 and CP48 respectively. Until now, there has been no structure available for Coxsackievirus B4 despite the fact that the virus has long been implicated in the development of insulin-dependent diabetes mellitus. At better than 3 Å resolution, we could identify the detailed interactions that facilitate ligand binding. Both compounds target the same three conserved residues, each from a different polypeptide chain, to form a virion-stabilizing network inside the pocket. We measured the in silico binding energy for both inhibitors when anchored to the network and found a global stabilizing effect on the order of thousands of kcal/mol under saturating conditions (60 total sites per virion). Intriguingly, a recent X-ray structure has revealed that glutathione targets the same network within the interprotomer site of bovine enterovirus F3, where it is thought to facilitate virus assembly. In summary, our findings provide the structural basis for how a newly designed class of capsid binders target and stabilize enteroviruses. Future efforts to chemically optimize drugs for enhanced targeting to the interprotomer pocket is a promising endeavor in the fight against enteroviruses, especially given the possibility of synergistic effects when used in combination with classical VP1 binders like pleconaril.
Identification of VIMP as a gene inhibiting cytokine production in human CD4+ effector T cells
Authors: Capelle Christophe , Zeng Ni , Danileviciute Egle , Rodrigues Sabrina Freitas , Ollert Markus , Balling Rudi , He Feng Q. 
Published: July 2020

AbstractMany players regulating the CD4+T cell-mediated inflammatory response have already been identified. However, the critical nodes that constitute the regulatory and signalling networks underlying CD4 T cell responses are still missing. Using a correlation network-guided strategy based on time-series transcriptome data of human CD4+CD25-effector T cells (Teffs), here we identifiedVIMP(VCP-interacting membrane protein), one of the 25 genes encoding selenocysteine in humans, as a gene regulating the effector functions of human CD4 T cells. Knocking-downVIMPin Teffs enhanced their proliferation and expression of several cytokines, including IL-2 and CSF2. We identified VIMP as an endogenous inhibitor of cytokine production in Teffs via both, the E2F5 transcription regulatory pathway and the Ca2+/NFATC2 signalling pathway. Our work not only indicates that VIMP might be a promising therapeutic target for various diseases involving CD4 T cells, but also shows that our network-guided approach might be generally applicable to different types of cells and can significantly aid in predicting new functions of the genes of interest.One-sentence summaryUsing a network-guided approach, we identified that Selenoprotein S (SELS or VIMP) negatively regulates cytokine expression of human CD4+ effector T cells via the E2F5 and calcium Ca2+/NFATC2 pathways.
Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0)
Authors: Salavati Mazdak , Caulton Alex , Clark Richard , Gazova Iveta , Smith Timothy P. L. , Worley Kim C. , Cockett Noelle E. , Archibald Alan L. , Clarke Shannon M. , Murdoch Brenda M. , Clark Emily L. ,   on behalf of The Ovine FAANG Project Consortium
Published: July 2020

AbstractThe overall aim of the Ovine FAANG project is to provide a comprehensive annotation of the new highly contiguous sheep reference genome sequence (Oar rambouillet v1.0). Mapping of transcription start sites (TSS) is a key first step in understanding transcript regulation and diversity. Using 56 tissue samples collected from the reference ewe Benz2616 we have performed a global analysis of TSS and TSS- Enhancer clusters using Cap Analysis Gene Expression (CAGE) sequencing. CAGE measures RNA expression by 5’ cap-trapping and has been specifically designed to allow the characterization of TSS within promoters to single-nucleotide resolution. We have adapted an analysis pipeline that uses TagDust2 for clean-up and trimming, Bowtie2 for mapping, CAGEfightR for clustering and the Integrative Genomics Viewer (IGV) for visualization. Mapping of CAGE tags indicated that the expression levels of CAGE tag clusters varied across tissues. Expression profiles across tissues were validated using corresponding polyA+ mRNA-Seq data from the same samples. After removal of CAGE tags with < 10 read counts, 39.3% of TSS overlapped with 5’ ends of 31,113 transcripts that had been previously annotated by NCBI (out of a total of 56,308 from the NCBI annotation). For 25,195 of the transcripts, previously annotated by NCBI, no TSS meeting stringent criteria were identified. A further 14.7% of TSS mapped to within 50bp of annotated promoter regions. Intersecting these predicted TSS regions with annotated promoter regions (±50bp) revealed 46% of the predicted TSS were ‘novel’ and previously un-annotated. Using whole genome bisulphite sequencing data from the same tissues we were able to determine that a proportion of these ‘novel’ TSS were hypo-methylated (32.2%) indicating that they are likely to be reproducible rather than ‘noise’. This global analysis of TSS in sheep will significantly enhance the annotation of gene models in the new ovine reference assembly. Our analyses provide one of the highest resolution annotations of transcript regulation and diversity in a livestock species to date.
Single cell analysis of FOXP3 deficiencies in humans and mice unmasks intrinsic and extrinsic CD4+T cell perturbations
Authors: Zemmour David , Charbonnier Louis-Marie , Leon Juliette , Six Emmanuelle , Keles Sevgi , Delville Marianne , Baris Safa , Zuber Julien , Chen Karin , Neven Benedicte , Garcia-Lloret Maria I , Ruemmele Franck , Brugnara Carlo , Cerf-Bensussan Nadine , Rieux-Laucat Frederic , Cavazzana Marina , André Isabelle , Chatila Talal A. , Mathis Diane , Benoist Christophe 
Published: July 2020

ABSTRACTFOXP3deficiency in humans with IPEX syndrome and mice results in fatal systemic autoimmunity by altering regulatory T cell (Treg) physiology, but actual cellular and molecular mechanisms of disease are unclear, part because Treg surface markers may be unreliable in disease states. We used deep profiling by flow cytometry, population and single-cell RNAseq to analyze Tregs and conventional (Tconv) CD4+ T lymphocytes in cohorts of IPEX patients with a range of genetic lesions, and inFoxp3-deficient mice. In all patients and mice, heterogeneous Treg-like cells with an activeFOXP3locus were observed, some differing very little from normal Tregs, others more distant. Tconv showed no widespread activation or Th bias. The dominant mark was a monomorphic signature equally affecting all CD4+T cells, unexpectedly dampening tumor-Treg and cytokine-signaling modules. In mixed bone marrow chimeras, WT Tregs exerted dominant suppression, normalizing the states of mutant Treg and Tconv, extinguishing the disease signature, and revealing a small gene cluster truly regulated, cell-intrinsically, by FOXP3. These results suggest a two-step pathogenesis model, with therapeutic implications: limited downregulation of a few core Treg genes de-represses a systemic mediator(s), which imprints the disease signature on all T cells, and further dampens Treg function.
Can the occipital alpha-phase speed up visual detection through a real-time EEG-based brain-computer interface (BCI)?
Authors: Vigué-Guix Irene , Fernández Luis Morís , Cuello Mireia Torralba , Ruzzoli Manuela , Soto-Faraco Salvador 
Published: July 2020

ABSTRACTElectrical brain oscillations reflect fluctuations in neural excitability. Fluctuations in the alpha band (α, 8-12 Hz) in the occipito-parietal cortex are thought to regulate sensory responses, leading to cyclic variations in visual perception. Inspired by this theory, some past and recent studies have addressed the relationship between α-phase from extra-cranial EEG and behavioural responses to visual stimuli in humans. The latest studies have usedofflineapproaches to confirm α-gated cyclic patterns. However, a particularly relevant implication is the possibility to use this principleonlinefor real-time neurotechnology, whereby stimuli are time-locked to specific α-phases leading to predictable outcomes in performance. Here we aimed at providing a proof-of-concept for such real-time neurotechnology. Participants performed a speeded response task to visual targets that were presented upon a real-time estimation of the α-phase via an EEG closed-loop brain-computer interface (BCI). We predicted, according to the theory, a modulation of reaction times (RTs) along the α-cycle. Our BCI system achieved reliable trial-to-trial phase-locking of stimuli to the phase of individual occipito-parietal α-oscillations. Yet, the behavioural results did not support a consistent relation between RTs and the phase of the α-cycle neither at group nor single participant levels. We must conclude that although the α-phase might play a role in perceptual decisions from a theoretical perspective, its impact on EEG-based BCI application appears negligible.
Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model Archaeon
Authors: Makkay Andrea M. , Louyakis Artemis S. , Ram-Mohan Nikhil , Gophna Uri , Gogarten J. Peter , Papke R. Thane 
Published: July 2020

AbstractHorizontal gene transfer is a means by which bacteria, archaea, and eukaryotes are able to trade DNA within and between species. While there are a variety of mechanisms through which this genetic exchange can take place, one means prevalent in the archaeonHaloferax volcaniiinvolves the transient formation of cytoplasmic bridges between cells and is referred to as mating. This process can result in the exchange of very large fragments of DNA between the participating cells. Genes governing the process of mating, including triggers to initiate mating, mechanisms of cell fusion, and DNA exchange, have yet to be characterized. We used a transcriptomic approach to gain a more detailed knowledge of how mating might transpire. By examining the differential expression of genes expressed in cells harvested from mating conditions on a filter over time and comparing them to those expressed in a shaking culture, we were able to identify genes and pathways potentially associated with mating. These analyses provide new insights into both the mechanisms and barriers of mating inHfx. volcanii.
Comparison of three TaqMan Real-Time Reverse Transcription-PCR assays in detecting SARS-CoV-2
Authors: Xiao Yan , Li Zhen , Wang Xinming , Wang Yingying , Wang Ying , Wang Geng , Ren Lili , Li Jianguo 
Published: July 2020

AbstractQuick and accurate detection of SARS-CoV-2 is critical for COVID-19 control. Dozens of real-time reverse transcription PCR (qRT-PCR) assays have been developed to meet the urgent need of COVID-19 control. However, methodological comparisons among the developed qRT-PCR assays are limited. In the present study, we evaluated the sensitivity, specificity, amplification efficiency, and linear detection ranges of three qRT-PCR assays, including the assays developed by our group (IPBCAMS), and the assays recommended by WHO and China CDC (CCDC). The three qRT-PCR assays exhibited similar sensitivities, with the limit of detection (LOD) at about 10 copies per reaction (except the ORF 1b gene assay in CCDC assays with a LOD at about 100 copies per reaction). No cross reaction with other respiratory viruses were observed in all of the three qRT-PCR assays. Wide linear detection ranges from 106to 101copies per reaction and acceptable reproducibility were obtained. By using 25 clinical specimens, the N gene assay of IPBCAMS assays and CCDC assays performed better (with detection rates of 92% and 100%, respectively) than that of the WHO assays (with a detection rate of 60%), and the ORF 1b gene assay in IPBCAMS assays performed better (with a detection rate of 64%) than those of the WHO assays and the CCDC assays (with detection rates of 48% and 20%, respectively). In conclusion, the N gene assays of CCDC assays and IPBCAMS assays and the ORF 1b gene assay of IPBCAMS assays were recommended for qRT-PCR screening of SARS-CoV-2.