bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discrete virus factories form in the cytoplasm of cells co-infected with two strains of the segmented dsRNA virus, infectious bursal disease virus (IBDV), that subsequently coalesce
Authors: Campbell Elle A. , Gray Alice G. , Wells Joanna , Simpson Jennifer , Hawes Pippa C. , Broadbent Andrew J. 
Published: December 2019

AbstractTheBirnaviridaefamily, responsible for major economic losses to poultry and aquaculture, are non-enveloped viruses with a segmented double-stranded (ds)RNA genome that replicate in discrete cytoplasmic virus factories (VFs). Reassortment is common, however, the underlying mechanism remains unknown given that VFs may act as a barrier to genome mixing. In order to provide new information on VF trafficking during dsRNA virus co-infection, we rescued two recombinant infectious bursal disease viruses (IBDVs) of strain PBG98 containing either a split GFP11- or Tetracysteine (TC)- tag fused to the VP1 polymerase (PBG98-VP1-GFP11 and PBG98-VP1-TC). DF-1 cells transfected with GFP1-10 prior to PBG98-VP1-GFP11 infection, or stained with ReAsH following PBG98-VP1-TC infection, had green or red foci in the cytoplasm respectively that co-localised with VP3 and dsRNA, consistent with VFs. The average number of VFs decreased from a mean of 60 to 5 per cell between 10 and 24 hours post infection (hpi) (p<0.001), while the average area increased from 1.24 μm2to 45.01μm2(p<0.001), and live cell imaging revealed that the VFs were highly dynamic structures that coalesced in the cytoplasm. Small VFs moved faster than large (average 0.57μm/s at 16 hpi compared to 0.22 μm/s at 22 hpi), and VF coalescence was dependent on an intact microtubule network and actin cytoskeleton. During co-infection with PBG98-VP1-GFP11 and PBG98-VP1-TC viruses, discrete VFs initially formed from each input virus that subsequently coalesced 10-16 hours post-infection. We speculate that dsRNA virus reassortment requires VF coalescence, and the potential for reassortment increases at later time points in infection.ImportanceReassortment is common in viruses with segmented double stranded (ds)RNA genomes. However, these viruses typically replicate within discrete cytoplasmic virus factories (VFs) that may represent a barrier to genome mixing. We generated the first replication competent tagged reporter birnaviruses, infectious bursal disease viruses (IBDVs) containing a split GFP11 or tetracysteine (TC) tag and used the viruses to track the location and movement of IBDV VFs, in order to better understand the intracellular dynamics of VFs from two different strains of dsRNA virus during a co-infection. Discrete VFs initially formed from each virus that subsequently coalesced from 10 hours pi. We hypothesise that VF coalescence is required for the reassortment of dsRNA viruses and the potential for reassortment increases later in the replication cycle. This study provides new information that adds to our understanding of dsRNA virus VF trafficking.
The Glyco-enzyme adaptor GOLPH3 Links Intra-Golgi Transport Dynamics to Glycosylation Patterns and Cell Proliferation
Authors: Rizzo Riccardo , Russo Domenico , Kurokawa Kazuo , Sahu Pranoy , Lombardi Bernadette , Supino Domenico , Zhukovsky Mikhail , Vocat Anthony , Pothukuchi Prathyush , Kunnathully Vidya , Capolupo Laura , Boncompain Gaelle , Vitagliano Carlo , Marino Federica Zito , Aquino Gabriella , Montariello Daniela , Henklein Petra , Mandrich Luigi , Botti Gerardo , Clausen Henrik , Mandel Ulla , Yamaji Toshiyuki , Hanada Kentaro , Budillon Alfredo , Perez Franck , Parashuraman Seetharaman , Hannun Yusuf A , Nakano Akihiko , Corda Daniela , D’Angelo Giovanni , Luini Alberto 
Published: December 2019

AbstractGlycans are ubiquitous sugar polymers with major biological functions that are assembled by glyco-enzymes onto cargo molecules during their transport through the Golgi complex. How the Golgi determines glycan assembly is poorly understood. By relying on the Golgi cisternal maturation model and using the glyco-enzyme adaptor and oncoprotein GOLPH3 as a molecular tool, we define the first example of how the Golgi controls glycosylation and associated cell functions. GOLPH3, acting as a component of the cisternal maturation mechanism, selectively binds and recycles a subset of glyco-enzymes of the glycosphingolipid synthetic pathway, hinders their escape to the lysosomes and hence increases their levels through a novel lysosomal degradation-regulated mechanism. This enhances the production of specific growth-inducing glycosphingolipids and reprograms the glycosphingolipid pathway to potentiate mitogenic signaling and cell proliferation. These findings unravel unforeseen organizing principles of Golgi-dependent glycosylation and delineate a paradigm for glycan assembly by the Golgi transport mechanisms. Moreover, they indicate a new role of cisternal maturation as a regulator of glycosylation, and outline a novel mechanism of action for GOLPH3-induced proliferation.
Human Skeletal Muscle has Large Capacity to Increase Carnosine Content in Response to Beta-Alanine Supplementation. A Systematic Review with Bayesian Individual and Aggregate Data E-Max Model and Meta-Analysis
Authors: Rezende Nathalia Saffioti , Swinton Paul , de Oliveira Luana Farias , da Silva Rafa Pires , da Silva Vinicius Eira , Nemezio Kleiner , Yamaguchi Guilherme , Artioli Guilherme G , Gualano Bruno , Saunders Bryan , Dolan Eimear 
Published: December 2019

ABSTRACTBeta-alanine (BA) supplementation increases muscle carnosine content (MCarn), and is ergogenic in many situations. Currently, many questions on the nature of the Mcarn response to supplementation are open, and the response to these has considerable potential to enhance the efficacy and applications of this supplementation strategy.ObjectiveTo conduct a Bayesian analysis of available data on the Mcarn response to BA supplementation.MethodsA systematic review with meta-analysis of individual and published aggregate data using a dose response (Emax) model was conducted. The protocol was designed according to PRISMA guidelines. A three-step screening strategy was undertaken to identify studies that measured the Mcarn response to BA supplementation. In addition, individual data from 5 separate studies conducted in the authors’ laboratory were analysed. Data were extracted from all controlled and uncontrolled supplementation studies conducted on healthy humans. Meta-regression was used to consider the influence of potential moderators (including dose, sex, age, baseline Mcarn and analysis method used) on the primary outcome.Results and ConclusionThe Emax model indicated that human skeletal muscle has large capacity for non-linear Mcarn accumulation, and that commonly used BA supplementation protocols may not come close to saturating muscle carnosine content. Neither baseline values, nor sex, appear to influence subsequent response to supplementation. Analysis of individual data indicated that Mcarn is relatively stable in the absence of intervention, and effectually all participants respond to BA supplementation (99.3% response [95%CrI: 96.2 – 100]).
Natural scene statistics predict how humans pool information across space in the estimation of surface tilt
Authors: Kim Seha , Burge Johannes 
Published: December 2019

ABSTRACTVisual systems estimate the three-dimensional (3D) structure of scenes from information in two-dimensional (2D) retinal images. Visual systems use multiple sources of information to improve the accuracy of these estimates, including statistical knowledge of the probable spatial arrangements of natural scenes. Here, we examine how 3D surface tilts are spatially related in real-world scenes, and show that humans pool information across space when estimating surface tilt in accordance with these spatial relationships. We develop a hierarchical model of surface tilt estimation that is grounded in the statistics of tilt in natural scenes and images. The model computes a global tilt estimate by pooling local tilt estimates within an adaptive spatial neighborhood. The spatial neighborhood in which local estimates are pooled changes according to the value of the local estimate at a target location. The hierarchical model provides more accurate estimates of groundtruth tilt in natural scenes and provides a better account of human performance than the local model. Taken together, the results imply that the human visual system pools information about surface tilt across space in accordance with natural scene statistics.
Development and clinical validation of a targeted RNAseq panel (Fusion-STAMP) for diagnostic and predictive gene fusion detection in solid tumors
Authors: Nohr Erik , Kunder Christian A. , Jones Carol , Sutton Shirley , Fung Eula , Zhu Hongbo , Feng Sharon J. , Gojenola Linda , Bustamante Carlos D. , Zehnder James L. , Costa Helio A. 
Published: December 2019

AbstractRNA sequencing is emerging as a powerful technique to detect a diverse array of fusions in human neoplasia, but few clinically validated assays have been described to date. We designed and validated a hybrid-capture RNAseq assay for FFPE tissue (Fusion-STAMP). It fully targets the transcript isoforms of 43 genes selected for their known impact as actionable targets of existing and emerging anti-cancer therapies (especially in lung adenocarcinomas), prognostic features, and/or utility as diagnostic cancer biomarkers (especially in sarcomas). 57 fusion results across 34 samples were evaluated. Fusion-STAMP demonstrated high overall accuracy with 98% sensitivity and 94% specificity for fusion detection. There was high intra- and inter-run reproducibility. Detection was sensitive to approximately 10% tumor, though this is expected to be impacted by fusion transcript expression levels, hybrid capture efficiency, and RNA quality. Challenges of clinically validating RNA sequencing for fusion detection include a low average RNA quality in FFPE specimens, and variable RNA total content and expression profile per cell. These challenges contribute to highly variable on-target rates, total read pairs, and total mapped read pairs. False positive results may be caused by intergenic splicing, barcode hopping / index hopping, or misalignment. Despite this, Fusion-STAMP demonstrates high overall performance metrics for qualitative fusion detection and is expected to provide clinical utility in identifying actionable fusions.
Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms
Authors: McKnight Laura E , Crandall Johnathan G , Bailey Thomas B , Banks Orion GB , Orlandi Kona N , Truong Vi N , Waddell Grace L , Wiles Elizabeth T , Donovan Drake A , Hansen Scott D , Selker Eric U , McKnight Jeffrey N 
Published: December 2019

AbstractEukaryotic DNA is packaged into nucleosomes, the smallest repeating unit of chromatin. The positions of nucleosomes determine the relative accessibility of genomic DNA. Several protocols exist for mapping nucleosome positions in eukaryotic genomes in order to study the relationship between chromatin structure and DNA-dependent processes. These nucleosome mapping protocols can be laborious and, at minimum, require two to three days to isolate nucleosome-protected DNA fragments. We have developed a streamlined protocol for mapping nucleosomes from S. cerevisiae liquid culture or from patches on solid agar. This method isolates nucleosome-sized footprints in three hours using 1.5 ml tubes with minimal chemical waste. We validate that these footprints match those produced by previously published methods and we demonstrate that our protocol works for N. crassa and S. pombe. A slightly modified protocol can be used for isolation of nucleosome-protected DNA fragments from a variety of wild fungal specimens thereby providing a simple, easily multiplexed and unified strategy to map nucleosome positions in model and non-model fungi. Finally, we demonstrate recovery of nucleosome footprints from the diploid myeloid leukemia cell line PLB-985 in less than three hours using an abbreviated version of the same protocol. With reduced volume and incubation times and a streamlined workflow, the described method should be compatible with high-throughput, automated creation of MNase-seq libraries. We believe this simple validated method for rapidly producing sequencing-ready nucleosome footprints from a variety of organisms will make nucleosome mapping studies widely accessible to researchers globally.
Precise levels of Nectin-3 and an interaction with Afadin are required for proper synapse formation in postnatal visual cortex
Authors: Tomorsky Johanna , Parker Philip R. L. , Doe Chris Q. , Niell Cristopher M. 
Published: December 2019

AbstractBackgroundDeveloping cortical neurons express a tightly choreographed sequence of cytoskeletal and transmembrane proteins to form and strengthen specific synaptic connections during circuit formation. Nectin-3 is a cell-adhesion molecule with previously described roles in synapse formation and maintenance. This protein and its binding partner, Nectin-1, are selectively expressed in upper-layer neurons of mouse visual cortex, but their role in the development of cortical circuits is unknown.MethodsHere we block Nectin-3 expression (via shRNA) or overexpress Nectin-3 in developing layer 2/3 visual cortical neurons using in utero electroporation. We then assay dendritic spine densities at three developmental time points: eye opening (postnatal day (P)14), one week following eye opening after a period of heightened synaptogenesis (P21), and at the close of the critical period for ocular dominance plasticity (P35).ResultsKnockdown of Nectin-3 beginning at E15.5 or ∼P19 increased dendritic spine densities at P21 or P35, respectively. Conversely, overexpressing full length Nectin-3 at E15.5 led to decreased dendritic spine densities when all ages were considered together. Interestingly, an even greater decrease in dendritic spine densities, particularly at P21, was observed when we overexpressed Nectin-3 lacking its Afadin binding domain, indicating Afadin may facilitate spine morphogenesis after eye opening.ConclusionThese data collectively suggest that the proper levels of Nectin-3, as well as the interaction of Nectin-3 with Afadin, facilitate normal synapse formation after eye opening in layer 2/3 visual cortical neurons.
VIRAL DELIVERY OF GDNF PROMOTES FUNCTIONAL INTEGRATION OF HUMAN STEM CELL GRAFTS IN PARKINSON’S DISEASE
Authors: Gantner Carlos W , de Luzy Isabelle R , Kauhausen Jessica A , Moriarty Niamh , Niclis Jonathan C , Penna Vanessa , Hunt Cameron P. , Bye Christopher R , Ermine Charlotte M , Pouton Colin W , Kirik Deniz , Thompson Lachlan H , Parish Clare L 
Published: December 2019

AbstractThe derivation of neurotransmitter and region-specific neuronal populations from human pluripotent stem cells (PSC) provides impetus for advancing cell therapies into the clinic. At the forefront is our ability to generate ventral midbrain (VM) dopaminergic (DA) progenitors, suitable for transplantation in Parkinson’s disease (PD). Pre-clinical studies, however, have highlighted the low proportion of DA neurons within these grafts and their inferior plasticity by comparison to human fetal donor transplants. Here we sought to examine whether modification of the host environment, through viral delivery of a developmentally critical molecule, glial cell line-derived neurotrophic factor (GDNF), could improve graft survival, integration and function in Parkinsonian rodents. Utilising LMX1A- and PITX3-GFP hPSC reporter lines, we tracked the response of DA progenitors implanted into either a GDNF-rich environment, or in a second group, after a 3-week delay in onset of exposure. We found that early exposure of the graft to GDNF promoted survival of DA and non-DA cells, leading to enhanced motor recovery in PD rats. Delayed overexpression of intrastriatal GDNF also promoted motor recovery in transplanted rats, through alternate selective mechanisms including enhanced A9/A10 specification, increased DA graft plasticity, greater activation of striatal neurons and elevated DA metabolism. Lastly, transcriptional profiling of the grafts highlighted novel genes underpinning these changes. Collectively these results demonstrate the potential of targeted neurotrophic gene therapy strategies to improve human PSC graft outcomes.
Widespread interaction between ADAR1 and transcriptional byproducts
Authors: Wu Chan-Shuo , Tang Sze Jing , Tan Hong Kee , Hung Li-Yuan , Teo Wei Wen , Li Jia , An Omer , Tan Kar Tong , Zhou Qiling , Chen Leilei , Tenen Daniel G. , Yang Henry 
Published: December 2019

AbstractBackgroundADAR1, an adenosine-to-inosine (A-to-I) RNA editing enzyme, has an emerging role in cancer immunotherapy. ADAR1 presumably works by suppressing cellular innate immunity response to endogenously generated double-stranded RNAs through RNA editing. However, RNA species that are directly regulated by ADAR1 mediated RNA editing processes remain poorly defined.ResultsIn this study, we used a novel bioinformatics approach to track ADAR1-RNA interactions. By integrating DNA-seq, RNA-seq, and ADAR1 RNA immunoprecipitation sequencing (fRIP-seq) data of K562 cell line, we provided the first in-situ landscape profiling of ADAR1 RNA binding and editing activities. With long RNA fragments captured by ADAR1 immunoprecipitation, we were able to identify exon junctions and genomic boundaries used by ADAR1-associated RNAs and thus we could possibly trace pre-RNA processing steps that had been acting on them. Our methodology allowed us to acquire the knowledge of transcriptome-wide scenario of ADAR1 activities. Intriguingly, we found that ADAR1 had a tendency to interact with transcriptional byproducts originated from obscure regions such as introns and intergenic regions.ConclusionsOur observation might shed light on the dual role of ADAR1 proteins not only in diversifying the transcriptome, but also in reigning RNA debris from obscure regions. Moreover, as the functional potential of seemly transcriptional byproducts is just beginning to emerge, this study would bridge ADAR1 with other fields of RNA biology.
Microbial residents of the Atlantis Massif’s shallow serpentinite subsurface
Authors: Motamedi Shahrzad , Orcutt Beth N. , Früh-Green Gretchen L. , Twing Katrina I. , Pendleton H. Lizethe , Brazelton William J. 
Published: December 2019

AbstractThe Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth’s upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H2), methane (CH4), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous sequences of shallow (<16 meters below seafloor) marine serpentinites and mafic assemblages. Here, we report the first census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing. The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into consideration both presence/absence as well as relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobiia, and Chloroflexi.ImportanceInternational Ocean Discovery Program Expedition 357: “Serpentinization and Life” utilized seabed drills for the first time to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide the first window into the diversity of microbial communities inhabiting subseafloor serpentinites.
Time and mode of Culicidae evolutionary history
Authors: da Silva Alexandre Freitas , Machado Laís Ceschini , de Paula Marcia Bicudo , Vieira Carla Júlia da Silva Pessoa , Bronzoni Roberta Vieira de Morais , de Melo Santos Maria Alice Varjal , Wallau Gabriel Luz 
Published: December 2019

AbstractMosquitoes are insects of medical importance due their role as vectors of different pathogens to humans and other mammals. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquitoes species. Here we sequenced the mitogenomes of mosquitoes species through low-coverage sequencing and data mining. A total of 37 draft mitogenomes were assembled representing 11 genera and 16 of those were sequenced for the first time. The recovered mitogenomes showed a coverage breadth average of 81.24%. Most of the species were clustered in monophyletic clades with other members of their own genus with exception of the Aedini tribe which was paraphyletic corroborating other findings. We established for the first time the monophyletic status of eight species from the tribe Mansoniini including both Coquillettidia and Mansonia genus and established the basal positioning of Aedeomyiini and Uranotaeniini tribes regarding the Culicinae subfamily. Molecular clock dated the Culicidae family emergence around 273 MYA and the split between Anophelinae and Culicinae subfamily around 182 MYA in the Jurassic period. Low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge generating basic fundamental information to the understanding of the role of these species as pathogen vectors.
Genetic risk of dementia modifies the impact of obesity on limbic white matter and spatial navigation behavior in cognitively healthy adults
Authors: Mole Jilu P. , Fasano Fabrizio , Evans John , Sims Rebecca , Hamilton Derek A. , Kidd Emma , Metzler-Baddeley Claudia 
Published: December 2019

AbstractA family history (FH) of dementia,APOE-ε4 genotype, and obesity are major risk factors for developing Alzheimer’s disease but their combined effects on the brain and cognition remain elusive. We tested the hypothesis that these risk factors affect apparent white matter (WM) myelin and cognition including spatial navigation and processing speed in 166 asymptomatic individuals (38-71 years). Microstructure in temporal [fornix, parahippocampal cingulum, uncinate fasciculus], motor and whole-brain WM was assessed with myelin-sensitive indices from quantitative magnetization transfer [macromolecular proton fraction (MPF)] and axon density from diffusion imaging. Individuals with the highest genetic risk (FH+ andAPOE-ε4) compared to those with FH+ alone showed obesity-related reductions in MPF and axon density in the right parahippocampal cingulum. No effects were present for those without FH. Furthermore, FH modulated obesity-related effects on spatial navigation behaviour. In summary, an individual’s genetic dementia risk influenced the impact of obesity on WM myelin and cognition.