bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glutathione synthetase overexpression in Acidithiobacillus ferrooxidans improves halotolerance of iron oxidation
Authors: Inaba Yuta , West Alan C. , Banta Scott 
Published: July 2021

AbstractAcidithiobacillus ferrooxidans are well-studied iron- and sulfur-oxidizing acidophilic chemolithoautotrophs that are exploited for their ability to participate in the bioleaching of metal sulfides. Here, we overexpressed the endogenous glutamate--cysteine ligase and glutathione synthetase genes in separate strains and found that glutathione synthetase overexpression increased intracellular glutathione levels. We explored the impact of pH on the halotolerance of iron oxidation in wild type and engineered cultures. The increase in glutathione allowed the modified cells to grow under salt concentrations and pH conditions that are fully inhibitory to wild type cells. These results indicate that glutathione overexpression can be used to increase halotolerance in A. ferrooxidans and would likely be a useful strategy on other acidophilic bacteria.ImportanceThe use of acidophilic bacteria in the hydrometallurgical processing of sulfide ores can enable many benefits including the potential reduction of environmental impacts. The cells involved in bioleaching tend to have limited halotolerance, and increased halotolerance could enable several benefits, including a reduction in the need for fresh water resources. We show that the genetic modification of A. ferrooxidans for the overproduction of glutathione is a promising strategy to enable cells to resist the oxidative stress that can occur during growth in the presence of salt.
Simultaneousin vivoPharmacokinetics and Pharmacodynamics of TDF Intravaginal Ring during High-dose Vaginal SHIV Challenge in Pigtail Macaques
Authors: Halavaty Katarina Kotnik , Ott Adina K. , Maric Danijela , Su Jonathan T. , Matias Edgar , Allen Edward J. , Martin Amy , Pereira Lara , Deyounks Frank , Smith James M. , Kiser Patrick F. , Hope Thomas J. 
Published: July 2021

AbstractThe demonstration of complete protection of macaques in a repeated low dose virus challenge by a tenofovir disoproxil fumarate (TDF) intravaginal ring (IVR) and the success of the dapivirine IVR in clinical trials highlighted the potential of IVRs as pre- exposure prophylaxis against HIV. Efficacy of TDF ring was not investigated in sexually active women. Our understanding of the mechanisms of protection is limited. To address this knowledge gap, we performed simultaneous pharmacokinetic and pharmacodynamic analysis of a TDF-IVR at the site of SIV challenge in pigtail macaques at the anatomical and cellular level. Specifically, we challenged TDF-IVR administered pigtail macaques with a single high dose of a non-replicative SIV-based vector containing a dual reporter system that helped us to identify the earliest targets of SIV infection within the mucosa. Two and three days after challenge, the macaques were euthanized and tenofovir (TFV) concentrations were measured in the female reproductive tract (FRT) by HPLC-MS/MS to correlate drug concentrations and SIV-vector transduction efficiency. TFV formed a gradient through the mucosal tissue, with the highest concentrations near the ring, in the upper vagina and endocervix. Despite this, several transduction events were identified with the most common sites being in the ovaries. Moreover, proviral DNA was detected in the cervix and vagina. Thus, our studies demonstrate an uneven distribution of TFV in the FRT of macaques after release from a TDF-IVR that leads to incomplete FRT protection from high viral dose challenge.
Co-localization of different neurotransmitter transporters on synaptic vesicles is sparse except of VGLUT1 and ZnT3
Authors: Upmanyu Neha , Jin Jialin , von der Emde Henrik , Ganzella Marcelo , Bösche Leon , Malviya Viveka Nand , Zhuleku Evi , Politi Antonio , Ninov Momchil , Silbern Ivan , Leutenegger Marcel , Urlaub Henning , Riedel Dietmar , Preobraschenski Julia , Milosevic Ira , Hell Stefan W , Jahn Reinhard , Sambandan Sivakumar 
Published: July 2021

SUMMARYVesicular transporters (VTs) define the type of neurotransmitter that synaptic vesicles (SVs) store and release. While certain neurons in mammalian brain release multiple transmitters, the prevalence, physiology of such pluralism and if the release occurs from same or distinct vesicle pools is not clear. Using quantitative single vesicle imaging, we show that a small population of neuronal SVs indeed contain different VTs to accomplish corelease. Surprisingly, this population is highly diverse (27 types), expressing distinct dual transporters suggesting corelease of various combinations of neurotransmitters. Using glutamatergic vesicles as an example, we demonstrate that transporter colocalization not only determine the transmitter type but also influences the SV content and synaptic quantal size. Thus, presence of diverse transporters on the same vesicle is bona-fide and, depending on the VT types, this may act as one mechanism to regulate neurotransmitter type, content and release in space and time.
Structural Insights into the Venus flytrap Mechanosensitive Ion Channel Flycatcher1
Authors: Jojoa-Cruz Sebastian , Saotome Kei , Tsui Che Chun (Alex) , Lee Wen-Hsin , Sansom Mark S. P. , Murthy Swetha E. , Patapoutian Ardem , Ward Andrew B. 
Published: July 2021

AbstractFlycatcher1 (FLYC1), a MscS homolog, has recently been identified as a candidate mechanosensitive (MS) ion channel involved in Venus flytrap prey recognition. FLYC1 is larger and its sequence diverges from previously studied MscS homologs, suggesting it has unique structural features that contribute to its function. Here, we characterized FLYC1 by cryo-electron microscopy, molecular dynamics simulations, and electrophysiology. Akin to bacterial MscS and plant MSL1 channels, we find that FLYC1 central core includes side portals in the cytoplasmic cage that regulate ion conduction, by identifying critical residues that modulate channel conductance. Topologically unique cytoplasmic flanking regions can adopt ‘up’ or ‘down’ conformations, making the channel asymmetric. Disruption of an up conformation-specific interaction severely delays channel deactivation by 40-fold likely due to stabilization of the channel open state. Our results illustrate novel structural features and likely conformational transitions that regulate mechano-gating of FLYC1.
Reliability of Decision-Making and Reinforcement Learning Computational Parameters
Authors: Mkrtchian Anahit , Valton Vincent , Roiser Jonathan P. 
Published: July 2021

AbstractComputational models can offer mechanistic insight into cognition and therefore have the potential to transform our understanding of psychiatric disorders and their treatment. For translational efforts to be successful, it is imperative that computational measures capture individual characteristics reliably. Here we examine the reliability of reinforcement learning and economic models derived from two commonly used tasks. Healthy individuals (N=50) completed a restless four-armed bandit and a calibrated gambling task twice, two weeks apart. Reward and punishment learning rates from the reinforcement learning model showed good reliability and reward and punishment sensitivity from the same model had fair reliability; while risk aversion and loss aversion parameters from a prospect theory model exhibited good and excellent reliability, respectively. Both models were further able to predict future behaviour above chance within individuals. This prediction was better when based on participants’ own model parameters than other participants’ parameter estimates. These results suggest that reinforcement learning, and particularly prospect theory parameters, as derived from a restless four-armed bandit and a calibrated gambling task, can be measured reliably to assess learning and decision-making mechanisms. Overall, these findings indicate the translational potential of clinically-relevant computational parameters for precision psychiatry.
Designed architectural proteins that tune DNA looping in bacteria
Authors: Tse David , Becker Nicole A. , Young Robert T. , Olson Wilma K. , Peters Justin P. , Schwab Tanya L. , Clark Karl J. , Maher L. James 
Published: July 2021

AbstractArchitectural proteins alter the shape of DNA, often by distorting the double helix and introducing sharp kinks that relieve strain in tightly-bent DNA structures. Here we design and test artificial architectural proteins based on a sequence-specific Transcription Activator-like Effector (TALE) protein, either alone or fused to a eukaryotic high mobility group B (HMGB) DNA-bending domain. We hypothesized that TALE protein binding would stiffen DNA to bending and twisting, acting as an architectural protein that antagonizes the formation of small DNA loops. In contrast, fusion to an HMGB domain was hypothesized to generate a targeted DNA-bending architectural protein that facilitates DNA looping. We provide evidence fromE. coliLac repressor gene regulatory loops supporting these hypotheses in living bacteria. Both data fitting to a thermodynamic DNA looping model and sophisticated molecular modeling support the interpretation of these results. We find that TALE protein binding inhibits looping by stiffening DNA to bending and twisting, while the Nhp6A domain enhances looping by bending DNA without introducing twisting flexibility. Our work illustrates artificial approaches to sculpt DNA geometry with functional consequences. Similar approaches may be applicable to tune the stability of small DNA loops in eukaryotes.
Pathology and immunity after SARS-CoV-2 infection in male ferrets is affected by age and inoculation route
Authors: van de Ven Koen , van Dijken Harry , Wijsman Lisa , Gomersbach Angéla , Schouten Tanja , Kool Jolanda , Lenz Stefanie , Roholl Paul , Meijer Adam , van Kasteren Puck , de Jonge Jørgen 
Published: July 2021

AbstractImproving COVID-19 intervention strategies partly relies on animal models to study SARS-CoV-2 disease and immunity. In our pursuit to establish a model for severe COVID-19, we inoculated young and adult male ferrets intranasally or intratracheally with SARS-CoV-2. Intranasal inoculation established an infection in all ferrets, with viral dissemination into the brain and gut. Upon intratracheal inoculation only adult ferrets became infected. However, neither inoculation route induced observable COVID-19 symptoms. Despite this, a persistent inflammation in the nose was prominent in especially young ferrets and follicular hyperplasia in the bronchi developed 21 days post infection. These effects -if sustained- might resemble long-COVID. Respiratory and systemic cellular responses and antibody responses were induced only in animals with an established infection. We conclude that intranasally-infected ferrets resemble asymptomatic COVID-19 and possibly aspects of long-COVID. Combined with the increasing portfolio to measure adaptive immunity, ferrets are a relevant model for SARS-CoV-2 vaccine research.
A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
Authors: Neumann Manuel , Xu Xiaocai , Smaczniak Cezary , Schumacher Julia , Yan Wenhao , Blüthgen Nils , Greb Thomas , Jönsson Henrik , Traas Jan , Kaufmann Kerstin , Muino Jose M 
Published: July 2021

ABSTRACTIdentity and functions of plant cells are influenced by their precise cellular location within the plant body. Cellular heterogeneity in growth and differentiation trajectories results in organ patterning. Therefore, assessing this heterogeneity at molecular scale is a major question in developmental biology. Single-cell transcriptomics (scRNA-seq) allows to characterize and quantify gene expression heterogeneity in developing organs at unprecedented resolution. However, the original physical location of the cell is lost during the scRNA-seq procedure. To recover the original location of cells is essential to link gene activity with cellular function and morphology. Here, we reconstruct genome-wide gene expression patterns of individual cells in a floral meristem by combining single-nuclei RNA-seq with 3D spatial reconstruction. By this, gene expression differences among meristematic domains giving rise to different tissue and organ types can be determined. As a proof of principle, the data are used to trace the initiation of vascular identity within the floral meristem. Our work demonstrates the power of spatially reconstructed single cell transcriptome atlases to understand plant morphogenesis. The floral meristem 3D gene expression atlas can be accessed at http://threed-flower-meristem.herokuapp.com
A novel post-translational proteomics platform identifies neurite outgrowth impairments in Parkinson’s diseaseGBA-N370Sdopamine neurons
Authors: Bogetofte Helle , Ryan Brent J. , Jensen Pia , Vergoossen Dana L.E. , Barnkob Mike B. , Kiani Lisa , Chughtai Uroosa , Brandes Janine , Vowles Jane , Bunn Fiona , Kilfeather Peter , Fernandes Hugo J.R. , Caffrey Tara , Meyer Morten , Cowley Sally A. , Larsen Martin R. , Wade-Martins Richard 
Published: July 2021

AbstractThe causes of Parkinson’s disease (PD) likely involve complex interactions between environmental factors and susceptibility genes with variants at theGBAlocus encoding the glucocerebrosidase (GCase) enzyme being the strongest common genetic risk factor for PD. To understandGBA-related disease mechanisms, we used a novel multipart-enrichment proteomics and post-translational modification workflow to simultaneously identify peptides with phosphorylation, reversible cysteine-modifications or sialylated N-linked glycosylation, alongside unmodified proteins.We identified large numbers of dysregulated proteins and post-translational modifications (PTMs) in heterozygousGBA-N370SPD patient induced pluripotent stem cells (iPSC)-derived dopamine neurons. Alterations in glycosylation status of lysosomal proteins identified disturbances in the autophagy-lysosomal pathway, concurrent with upstream perturbations in mTOR phosphorylation and activity inGBA-N370SiPSC-dopamine neurons. In addition, the strategy revealed several native and modified proteins encoded by PD-associated genes to be dysregulated inGBA-N370Sneurons, enhancing our understanding of the wider role ofGBAmutations on the neuronal proteome. Integrated pathway analysis of all datasets revealed impaired neuritogenesis inGBA-N370SPD iPSC-dopamine neurons and identified tau (MAPT) as a key mediator of this process. Using a functional assay, we confirmed neurite outgrowth deficits inGBA-N370SPD neurons and a central role for tau in this process. Furthermore, pharmacological restoration of GCase activity inGBA-N370SPD patient neurons rescued the neurite outgrowth deficit. Overall, this study demonstrates the potential of PTMomics to elucidate novel neurodegeneration-associated pathways and identify phenotypes and potential drug targets in complex disease models.
In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography
Authors: Tashman Joshua W. , Shiwarski Daniel J. , Ruesch Alexander , Lanni Frederick , Kainerstorfer Jana M. , Feinberg Adam W. 
Published: July 2021

AbstractAs 3D bioprinting has grown as a fabrication technology, so too has the need for improved analytical methods to characterize these engineered constructs. This is especially challenging for soft tissues composed of hydrogels and cells as these materials readily deform, posing a barrier when trying to assess print fidelity and other properties non- destructively. Indeed, given the importance of structure-function relationships in most tissue types, establishing that the 3D architecture of the bioprinted construct matches its intended anatomic design is critical. Here we report development of a multimaterial bioprinting platform with integrated optical coherence tomography (OCT) for in situ volumetric imaging, error detection, and 3D reconstruction. While generally applicable to extrusion-based 3D bioprinting, we also report improvements to the Freeform Reversible Embedding of Suspended Hydrogels (FRESH) bioprinting process through new collagen bioink compositions, support bath optical clearing, and machine pathing. This enables high-fidelity 3D volumetric imaging with micron scale resolution over centimeter length scales, the ability to detect a range of print defect types within a 3D volume, and real-time imaging of the printing process at each print layer. These advances provide FRESH and other extrusion-based 3D bioprinting approaches with a comprehensive methodology for quality assessment that has been absent in the field to date, paving the way for translation of these engineered tissues to the clinic and ultimately to achieving regulatory approval.TeaserTransparent FRESH support bath enables in situ 3D volumetric imaging and validation of patient-derived tissue constructs.
CellProfiler 4: Improvements in Speed, Utility and Usability
Authors: Stirling David R. , Swain-Bowden Madison J. , Lucas Alice M. , Carpenter Anne E. , Cimini Beth A. , Goodman Allen 
Published: July 2021

AbstractBackgroundImaging data contains a substantial amount of information which can be difficult to evaluate by eye. With the expansion of high throughput microscopy methodologies producing increasingly large datasets, automated and objective analysis of the resulting images is essential to effectively extract biological information from this data. CellProfiler is a free, open source image analysis program which enables researchers to generate modular pipelines with which to process microscopy images into interpretable measurements.ResultsHerein we describe CellProfiler 4, a new version of this software with expanded functionality. Based on user feedback, we have made several user interface refinements to improve the usability of the software. We introduced new modules to expand the capabilities of the software. We also evaluated performance and made targeted optimizations to reduce the time and cost associated with running common large-scale analysis pipelines.ConclusionsCellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions. This release will ensure that researchers will have continued access to CellProfiler’s powerful computational tools in the coming years.
Trends and Gaps on Philippine Scombrid Research: A bibliometric analysis
Authors: Gadut Jay-Ar L. , Deocaris Custer C. , Alinsug Malona V. 
Published: July 2021

ABSTRACTPhilippine scombrids have been among the top priorities in fisheries research due primarily to their economic value worldwide. Assessment of the number of studies under general themes (diversity, ecology, taxonomy and systematics, diseases and parasites, and conservation) provides essential information to evaluate trends and gaps of research. This study presents a bibliometric evaluation of the temporal trends from 2000-2019 on Philippine scombrid research. Seven out of nine tuna species have SREA values equal to or higher than 1 with Thunnus albacares being the most researched tuna species. Twelve out of thirteen non-tuna species have SREA values less than one, thus indicating low research effort. It was apparent that there were significant differences in the number of studies in each thematic area except in ‘chemical analysis’ and ‘diseases and parasites’ between scombrid groups where there was low research effort observed. The research points at the uneven research distributions between scombrid groups in each thematic area. As locally published research are significantly behind foreign publications in terms of citation index, international collaborations by Filipino researchers have shown an increase research impact. Our study hopes to influence the local and international R&D agenda on Philippine scombrids and promote solidarity among nations towards its conservation and management.
miRNAFinder: A Comprehensive Web Resource for Plant Pre-microRNA Classification
Authors: Lokuge Sandali , Jayasundara Shyaman , Ihalagedara Puwasuru , Kahanda Indika , Herath Damayanthi 
Published: July 2021

AbstractmicroRNAs (miRNAs) are known as one of the small non-coding RNA molecules that control the expression of genes at the RNA level, while some operate at the DNA level. They typically range from 20–24 nucleotides in length and can be found in the plant and animal kingdoms as well as in some viruses. Computational approaches have overcome the limitations of the experimental methods and have performed well in identifying miRNAs. Compared to mature miRNAs, precursor miRNAs (pre-miRNAs) are long and have a hairpin loop structure with structural features. Therefore, most in-silico tools are implemented for pre-miRNA identification. This study presents a multilayer perceptron (MLP) based classifier implemented using 180 features under sequential, structural, and thermodynamic feature categories for plant pre-miRNA identification. This classifier has a 92% accuracy, a 94% specificity, and a 90% sensitivity. We have further tested this model with other small non-coding RNA types and obtained 78% accuracy. Furthermore, we introduce a novel dataset to train and test machine learning models, addressing the overlapping data issue in the positive training and testing datasets presented in PlantMiRNAPred for the classification of real and pseudo-plant pre-miRNAs. The new dataset and the classifier that can be used with any plant species are deployed on a web server freely accessible at http://mirnafinder.shyaman.me/.
Bacterial community composition of the sea grape Caulerpa lentillifera: a comparison between healthy and diseased states
Authors: Kopprio Germán A. , Luyen Nguyen Dinh , Cuong Le Huu , Fricke Anna , Kunzmann Andreas , Huong Le Mai , Gärdes Astrid 
Published: July 2021

SummaryThe bacterial communities of the sea grape Caulerpa lentillifera were studied during a disease outbreak in Vietnam. The Rhodobacteraceae and Rhodovulum dominated the composition of healthy C. lentillifera. Clear differences between healthy and diseased cases were observed at order, genus and Operational Taxonomic Unit (OTU) level. Bacterial diversity was lower in healthy C. lentillifera, probably because of antimicrobial compounds from the macroalgae and/or from Clostridium, Cutibacterium or Micrococcus bacteria. The likely beneficial role of Bradyrhizobium, Paracoccus and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The white coloration of diseased C. lentillifera may not only be associated with pathogens but also with an oxidative response. Aquibacter, Winogradskyella and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Moreover, Thalassobius OTU 2935 and 1635 may represent detrimental Rhodobacteraceae. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further metagenomic and biotechnological approaches are needed to confirm functions of some microbes on this macroalgae to enhance food security in the tropics.