bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and genetic analysis of infectious spleen and kidney necrosis virus (ISKNV) in ornamental fish from non-clinical cases: First report from India
Authors: Pattanayak Sabyasachi , Paul Anirban , Sahoo Pramoda Kumar 
Published: August 2020

AbstractInfectious spleen and kidney necrosis virus (ISKNV), a type species of the genusMegalocytivirus, poses a threat to ornamental fish trade as most cases show nonspecific symptoms, thus making timely diagnosis challenging. Apparently health molly (Poecilia sphenops) and angelfish (Pterophyllum scalare) collected from two distinct geographic localities of India were screened for four genera underIridoviridae,Megalocytivirusi.e, ISKNV, turbot reddish body iridovirus (TRBIV) and red seabream iridovirus (RSIV); ranaviruses and Singapore grouper iridovirus; and Lymphocystivirus through molecular approach. In total seven numbers out of 35 samples (20%), ISKNV genome fragments were detected. A PCR assay using major capsid protein (MCP) gene was standardised to detect and differentiate infections within theMegalocytivirusgenus, even without aid of sequencing. This forms the first report of ISKNV infection in ornamental fish from India. Moreover, the ISKNV infection was confirmed by PCR and sequence analysis of MCP and ATPase genes. The sequence of these genes showed that Indian isolate being 99-100% similar to the complete genome or reference strain of ISKNV. Phylogenetic reconstruction demonstrated the present strain belonging to ISKNV genotype I. Furthermore, structural stability of the MCP revealed this strain was more stable than ISKNV genotype II, RSIV and TRBIV at 25°C and pH 7.0. Thus, strong pan-India surveillance is recommended to reduce trade risk.
Genetic diversity and population structure analyses in the Alpine plum (Prunus brigantinaVill.) confirm its affiliation to the Armeniaca section
Authors: Shuo Liu , Stephane Decroocq , Elodie Harte , David Tricon , Aurelie Chague , Gulnara Balakishiyeva , Tatiana Kostritsyna , Timur Turdiev , Marion Fisher-Le Saux , Sylvie Dallot , Tatiana Giraud , Veronique Decroocq 
Published: August 2020

AbstractIn-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briançon apricot)Prunus brigantinaVill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wildP. brigantinasamples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to informin situconservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships ofP. brigantinawith other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity inP. brigantinaand a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important forin situconservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected forex-situconservation in a core collection that encompasses the whole detectedP. brigantinaallelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with EuropeanP. armeniacacultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placedP. brigantinacloser to Armeniaca species than to Prunus species. Our results thus confirm the classification ofP. brigantinawithin the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies.
The biophysical basis underlying the maintenance of early phase long-term potentiation
Authors: Becker Moritz F. P. , Tetzlaff Christian 
Published: August 2020

AbstractThe maintenance of synaptic changes resulting from long-term potentiation (LTP) is essential for brain function such as memory and learning. Different LTP phases have been associated with diverse molecular processes and pathways, and the molecular underpinnings of LTP on the short, as well as long time scales, are well established. However, the principles on the intermediate time scale of 1-6 hours that mediate the early phase of LTP (E-LTP) remain elusive. We hypothesize that the interplay between specific features of postsynaptic receptor trafficking is responsible for sustaining synaptic changes during this LTP phase. We test this hypothesis by formalizing a biophysical model that integrates several experimentally-motivated mechanisms. The model captures a wide range of experimental findings and predicts that synaptic changes are preserved for hours when the receptor dynamics are shaped by the interplay of structural changes of the spine in conjunction with increased trafficking from recycling endosomes and the cooperative binding of receptors. Furthermore, our model provides several predictions to verify our findings experimentally.Author summaryThe cognitive ability of learning is associated with plasticity-induced changes in synaptic transmission efficacy mediated by AMPA receptors. Synaptic changes depend on a multitude of molecular and physiological mechanisms, building complex interaction networks. By formalizing and employing a biophysical model of AMPAR trafficking, we unravel and evaluate the interplay between key mechanisms such as receptor binding, exocytosis, morphological changes, and cooperative receptor binding. Our findings indicate that cooperative receptor binding in conjunction with morphological changes of the spine and increased trafficking from recycling endosomes leads to the maintenance of synaptic changes on behaviorally relevant time spans. Characterizing the principles underlying synaptic changes will provide insight into the role of synaptic dynamics in neurodegenerative diseases.
Visualization of Phase-Amplitude Coupling Using Rhythmic High-Frequency Activity
Authors: Hashimoto Hiroaki , Khoo Hui Ming , Yanagisawa Takufumi , Tani Naoki , Oshino Satoru , Kishima Haruhiko , Hirata Masayuki 
Published: August 2020

AbstractObjectiveHigh-frequency activities (HFAs) and phase-amplitude coupling (PAC) are gaining attention as key neurophysiological biomarkers for studying human epilepsy. We aimed to clarify and visualize how HFAs are modulated by the phase of low-frequency bands during seizures.MethodsWe used intracranial electrodes to record seizures of symptomatic focal epilepsy (15 seizures in seven patients). Ripples (80–250 Hz), as representative of HFAs, were evaluated along with PAC. The synchronization index (SI), representing PAC, was used to analyze the coupling between the amplitude of ripples and the phase of lower frequencies. We created a video in which the intracranial electrode contacts were represented by circles that were scaled linearly to the power changes of ripple.ResultsThe main low frequency band modulating ictal-ripple activities was the θ band (4–8 Hz), and after completion of ictal-ripple burst, δ (1–4 Hz)-ripple PAC occurred. The video showed that fluctuation of the diameter of these circles indicated the rhythmic changes during significant high values of θ-ripple PAC.ConclusionsWe inferred that ripple activities occurring during seizure evolution were modulated by θ rhythm. In addition, we concluded that rhythmic circles’ fluctuation presented in the video represents the PAC phenomenon. Our video is thus a useful tool for understanding how ripple activity is modulated by the low-frequency phase in relation with PAC.
Functional diagnostics using fresh uncultured lung tumor cells to guide personalized treatments
Authors: Talwelkar Sarang S. , Mäyränpää Mikko I. , Søraas Lars , Potdar Swapnil , Bao Jie , Hemmes Annabrita , Linnavirta Nora , Lømo Jon , Räsänen Jari , Knuuttila Aija , Wennerberg Krister , Verschuren Emmy W. 
Published: August 2020

SUMMARYFunctional profiling of a cancer patient’s tumor cells holds potential to tailor personalized cancer treatment. Here we report the utility of Fresh Uncultured Tumor-derived EpCAM+ epithelial Cells (FUTC) forex vivodrug response interrogation. Analysis of murineKrasmutant FUTCs demonstrated pharmacological and adaptive signaling profiles comparable to subtype-matched cultured cells. Applying FUTC profiling on non-small cell lung cancer patient samples, we generated robust drug response data in 18 of 19 cases, where the cells exhibited targeted drug sensitivities corresponding to their oncogenic drivers. In one of these cases, anEGFRmutant lung adenocarcinoma patient refractory to osimertinib, FUTC profiling was used to guide compassionate treatment. FUTC profiling identified selective sensitivity to disulfiram and the combination of carboplatin plus etoposide and the patient received substantial clinical benefit from the treatment with these agents. We conclude that FUTC profiling provides a robust, rapid, and actionable assessment of personalized cancer treatment options.
Quantitative yeast-yeast two hybrid for discovery and binding affinity estimation of protein-protein interactions
Authors: Bacon Kaitlyn , Blain Abigail , Bowen John , Burroughs Matthew , McArthur Nikki , Menegatti Stefano , Rao Balaji M. 
Published: August 2020

AbstractQuantifying the binding affinity of protein-protein interactions is important for elucidating connections within biochemical signaling pathways, as well as characterization of binding proteins isolated from combinatorial libraries. We describe a quantitative yeast-yeast two hybrid (qYY2H) system that not only enables discovery of specific protein-protein interactions, but also efficient, quantitative estimation of their binding affinities (KD). In qYY2H, the bait and prey proteins are expressed as yeast cell surface fusions using yeast surface display. We developed a semi-empirical framework for estimating theKDof monovalent bait-prey interactions, using measurements of the apparentKDof yeast-yeast binding, which is mediated by multivalent interactions between yeast-displayed bait and prey. Using qYY2H, we identified interaction partners of SMAD3 and the tandem WW domains of YAP from a cDNA library and characterized their binding affinities. Finally, we showed that qYY2H could also quantitatively evaluate binding interactions mediated by post-translational modifications on the bait protein.
Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis
Authors: Hall Chelsea , Camilli Sara , Dwaah Henry , Kornegay Benjamin , Lacy Christine A. , Hill Malcolm S. , Hill April L. 
Published: August 2020

AbstractIn many freshwater habitats, green algae form intracellular symbioses with a variety of heterotrophic host taxa including several species of freshwater sponge. These sponges perform important ecological roles in their habitats, and the poriferan:green algae partnerships offers unique opportunities to study the evolutionary origins and ecological persistence of endosymbioses. We examined the association betweenEphydatia muelleriand its chlorophyte partner to identify features of host cellular and genetic responses to the presence of intracellular algal partners.Chlorella-likegreen algal symbionts were isolated from field-collected adultE. muelleritissue harboring algae. The sponge-derived algae were successfully cultured and subsequently used to reinfect aposymbioticE. muelleritissue. We used confocal microscopy to follow the fate of the sponge-derived algae after inoculating algae-freeE. muellerigrown from gemmules to show temporal patterns of symbiont location within host tissue. We also infected aposymbioticE. muelleriwith sponge-derived algae, and performed RNASeq to study differential expression patterns in the host relative to symbiotic states. We compare and contrast our findings with work in other systems (e.g., endosymbioticHydra) to explore possible conserved evolutionary pathways that may lead to stable mutualistic endosymbioses. Our work demonstrates that freshwater sponges offer many tractable qualities to study features of intracellular occupancy and thus meet criteria desired for a model system.
Rational engineering ofKluyveromyces marxianusto create a chassis for the production of aromatic products
Authors: Rajkumar Arun S. , Morrissey John P. 
Published: August 2020

AbstractThe yeastKluyveromyces marxianusoffers unique potential for industrial biotechnology because of useful features like rapid growth, thermotolerance and a wide substrate range. As an emerging alternative platform,K. marxianusrequires the development and validation of metabolic engineering strategies to best utilize its metabolism as a basis for bio-based production. To illustrate the synthetic biology strategies to be followed and showcase its potential, we describe a comprehensive approach to rationally engineer a metabolic pathway inK. marxianus. We use the phenylalanine biosynthetic pathway both as a prototype and because phenylalanine is a precursor for commercially valuable secondary metabolites. First, we modify and overexpress the pathway to be resistant to feedback inhibition so as to overproduce phenylalaninede novofrom synthetic minimal medium. Second, we assess native and heterologous means to increase precursor supply to the biosynthetic pathway. Finally, we eliminate branch points and competing reactions in the pathway and rebalance precursors to redirect metabolic flux to a specific product, 2-phenylethanol (2-PE). As a result, we are able to construct robust strains capable of producing over 800 mg L−12-PE from minimal medium. The strains we constructed are a promising platform for the production of aromatic amino acid-based biochemicals, and our results illustrate challenges with attempting to combine individually beneficial modifications in an integrated platform.
Construction of a complete set ofNeisseria meningitidisdefined mutants – the NeMeSys 2.0 collection – and its use for the phenotypic profiling of the genome of an important human pathogen
Authors: Muir Alastair , Gurung Ishwori , Cehovin Ana , Bazin Adelme , Vallenet David , Pelicic Vladimir 
Published: August 2020

AbstractOne of the great challenges in biology is to determine the function of millions of genes of unknown function. Even in model bacterial species, there is a sizeable proportion of such genes, which has fundamental and practical consequences. Here, we constructed a complete collection of defined mutants in protein-coding genes – named NeMeSys 2.0 – in the human pathogenNeisseria meningitidis, consisting of individual mutants in 1,584 non-essential genes. This effort identified 391 essential genes – broadly conserved in other bacteria – leading to a full overview of the essential meningococcal genome, associated with just four underlying basic biological functions: 1) expression of genome information, 2) preservation of genome information, 3) cell membrane structure/function, and 4) cytosolic metabolism. Subsequently, we illustrated the utility of the NeMeSys 2.0 collection for determining gene function by identifying 1) a novel and conserved family of histidinol-phosphatase, 2) 20 genes, including three new ones, involved in the biology of type IV pili, a widespread virulence factor, and 3) several conditionally essential genes found in regions of genome plasticity encoding antitoxins and/or immunity proteins, which become dispensable when the gene encoding the cognate toxin is deleted. These findings have implications beyond the meningococcus. The NeMeSys 2.0 collection is an invaluable resource paving the way for a global phenotypic landscape in a major human bacterial pathogen.
Influence of multi-axial dynamic constraint on cell alignment and contractility in engineered tissues
Authors: Reynolds Noel H. , McEvoy Eoin , Panadero Pérez Juan Alberto , Coleman Ryan J. , McGarry Patrick 
Published: August 2020

AbstractIn this study an experimental rig is developed to investigate the influence of tissue constraint and cyclic loading on cell alignment and active cell force generation in uniaxial and biaxial engineered tissues constructs. Addition of contractile cells to collagen hydrogels dramatically increases the measured forces in uniaxial and biaxial constructs under dynamic loading. This increase in measured force is due to active cell contractility, as is evident from the decreased force after treatment with cytochalasin-D. Prior to dynamic loading, cells are highly aligned in uniaxially constrained tissues but are uniformly distributed in biaxially constrained tissues, demonstrating the importance of tissue constraints on cell alignment. Dynamic uniaxial stretching resulted in a slight increase in cell alignment in the centre of the tissue, whereas dynamic biaxial stretching had no significant effect on cell alignment. Our active modelling framework accurately predicts our experimental trends and suggests that a slightly higher (3%) total SF formation occurs at the centre of a biaxial tissue compared to the uniaxial tissue. However, high alignment of SFs and lateral compaction in the case of the uniaxially constrained tissue results in a significantly higher (75%) actively generated cell contractile stress, compared to the biaxially constrained tissue. These findings have significant implications for engineering of contractile tissue constructs.
Bimodal evolution of Src and Abl kinase substrate specificity revealed using mammalian cell extract as substrate pool
Authors: Finneran Patrick , Soucheray Margaret , Wilson Christopher , Otten Renee , Buosi Vanessa , Krogan Nevan J. , Swaney Danielle L. , Theobald Douglas L. , Kern Dorothee 
Published: August 2020

AbstractThe specificity of phosphorylation by protein kinases is essential to the integrity of biological signal transduction. While peptide sequence specificity for individual kinases has been examined previously, here we explore the evolutionary progression that has led to the modern substrate specificity of two non-receptor tyrosine kinases, Abl and Src. To efficiently determine the substrate specificity of modern and reconstructed ancestral kinases, we developed a method using mammalian cell lysate as the substrate pool, thereby representing the naturally occurring substrate proteins. We find that the oldest tyrosine kinase ancestor was a promiscuous enzyme that evolved through a more specific last common ancestor into a specific human Abl. In contrast, the parallel pathway to human Src involved a loss of substrate specificity, leading to general promiscuity. These results add a new facet to our understanding of the evolution of signaling pathways, with both subfunctionalization and neofunctionalization along the evolutionary trajectories.
Deletion of the voltage-gated calcium channel, CaV1.3, causes deficits in motor performance and associative learning
Authors: Lauffer Marisol , Wen Hsiang , Myers Bryn , Plumb Ashley , Parker Krystal , Williams Aislinn 
Published: August 2020

AbstractL-type voltage-gated calcium channels are important regulators of neuronal activity and are widely expressed throughout the brain. One of the major L-type voltage-gated calcium channel isoforms in the brain is CaV1.3. Mice lacking CaV1.3 are reported to have impairments in fear conditioning and depressive-like behaviors, which have been linked to CaV1.3 function in the hippocampus and amygdala. Genetic variation in CaV1.3 has been linked to a variety of psychiatric disorders, including autism and schizophrenia, which are associated with altered motor learning, associative learning, and social function. Here, we explored whether CaV1.3 plays a role in these behaviors. We found that CaV1.3 knockout mice have deficits in rotarod learning despite normal locomotor function. Deletion of CaV1.3 is also associated with impaired gait adaptation and associative learning on the Erasmus Ladder. We did not observe any impairments in CaV1.3 knockout mice on assays of anxiety-like, depression-like, or social preference behaviors. Our results suggest an important role for CaV1.3 in neural circuits involved in motor learning and concur with previous data showing its involvement in associative learning.
The Posterior Insular Cortex is Necessary for the Consolidation of Tone Fear Conditioning
Authors: de Paiva J.P.Q. , Bueno A.P.A. , Dos Santos Corrêa M. , Oliveira M.G.M. , Ferreira T.L , Fornari R.V. 
Published: August 2020

ABSTRACTThe insular cortex (IC) is notably implicated in emotional and cognitive processing; however, little is known regarding to what extent its two main subregions play functionally distinct roles on memory consolidation of conditioned fear tasks. Here we verified the effects of temporary functional inactivation of the anterior (aIC) and posterior IC (pIC) on contextual and tone fear memory. Rats received post-training bilateral infusions of the GABAAreceptor agonist muscimol into either the aIC or pIC and were tested 48 and 72 hours after the conditioning session to assess contextual (CFC) and tone (TFC) fear conditioning, respectively. Inactivation of the aIC during memory consolidation did not affect fear memory for CFC or TFC. On the other hand, post-training inactivation of the pIC impaired TFC but not CFC. Our findings indicate that the pIC is a necessary part of the neural circuitry related to the consolidation of cued-fear memories.HighlightsWe studied the role of the anterior (aIC) and posterior (pIC) insula in fear memoryPost-training inactivation of aIC and pIC did not impact contextual fear conditioningThe pIC but not aIC is necessary for the consolidation of tone fear conditioning
Murine GFP-Mx1 forms phase-separated nuclear condensates and associates with cytoplasmic intermediate filaments: novel antiviral activity against vesicular stomatitis virus
Authors: Sehgal Pravin B. , Yuan Hujuan , Scott Mia F. , Deng Yan , Liang Feng-Xia , Mackiewicz Andrzej 
Published: August 2020

AbstractType I and III interferons (IFNs) induce expression of the “myxovirus resistance proteins” MxA in human cells and its ortholog Mx1 in murine cells. Human MxA formscytoplasmicstructures, some tethered to intermediate filaments. In contrast, murine Mx1 mainly formsnuclearbodies. Both HuMxA and MuMx1 are antiviral towards influenza A virus (FLUAV) (an orthomyxovirus). However, it has long been considered that HuMxA, butnotMuMx1, was antiviral towards vesicular stomatitis virus (VSV) (a rhabdovirus). We previously reported that the cytoplasmic human GFP-MxA structures in Huh7 hepatoma cells were phase-separated membraneless organelles (MLOs) (“biomolecular condensates”). In the present study we investigated whether nuclear murine Mx1 structures might also represent phase-separated biomolecular condensates. The transient expression of murine GFP-Mx1 in Huh7 hepatoma and Mich-2H6 melanoma cells led to the appearance of Mx1 nuclear bodies. These GFP-MuMx1 nuclear bodies were rapidly disassembled by exposing cells to 1, 6-hexanediol (5% w/v), or to hypotonic buffer (40-50 mosM), consistent with properties of membraneless phase-separated condensates. FRAP assays revealed that the GFP-MuMx1 nuclear bodies upon photobleaching showed a slow partial recovery (mobile fraction: ∼18%) suggestive of a gel-like consistency. Surprisingly, expression of GFP-MuMx1 in Huh7 cells also led to the appearance of MuMx1 in a novel cytoplasmic giantin-based intermediate filament meshwork and in cytoplasmic structures in 20-30% of transiently transfected Huh7 cells. Remarkably, Huh7 cells with cytoplasmic murine GFP-MuMx1 filaments, but not those with only nuclear bodies, showed antiviral activity towards VSV. Thus, murine GFP-Mx1 nuclear bodies comprised phase-separated condensates. Unexpectedly, GFP-MuMx1 associated with cytoplasmic giantin-based intermediate filaments in a subset of Huh7 cells, and, such cells showed antiviral activity towards VSV.