bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile
Authors: Bravo Veronica , Katz Assaf , Porte Lorena , Weitzel Thomas , Varela Carmen , Gonzalez-Escalona Narjol , Blondel Carlos J. 
Published: July 2020

ABSTRACTCampylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n=81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for over a third of the genome sequences available of clinical strains from South America. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.AUTHOR SUMMARYCampylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. In this study, we performed an in-depth analysis of the genome sequences of 69 C. jejuni and 12 C. coli clinical strains isolated from Chile, which account for over a third of the sequences from clinical strains available from South America. We identified a high genetic diversity among C. jejuni strains and the unexpected identification of clade 3 C. coli strains, which are infrequently isolated from humans in other regions of the world. Most strains harbored the virulence factors described for Campylobacter. While ∼40% of strains harbored mutation in the gyrA gene described to confer fluoroquinolone resistance, very few strains encoded the determinants linked to macrolide resistance, currently used for the treatment of campylobacteriosis. Our study contributes to our knowledge of this important foodborne pathogen providing valuable data from South America.
Nucleosomal association and altered interactome underlie the mechanism of cataract caused by the R54C mutation of αA-crystallin
Authors: Ahsan Saad M. , Raman Bakthisaran , Ramakrishna Tangirala , Rao Ch. Mohan 
Published: July 2020

AbstractThe small heat shock protein (sHSP), αA-crystallin, plays an important role in eye lens development. It has three distinct domainsviz. the N-terminal domain, α-crystallin domain and the C-terminal extension. While the α-crystallin domain is conserved across the sHSP family, the N-terminal domain and the C-terminal extension are comparatively less conserved. Nevertheless, certain arginine residues in the N-terminal region of αA-crystallin are conserved across the sHSP family. Interestingly, most of the cataractcausing mutations in αA-crystallin occur in the conserved arginine residues. In order to understand the molecular basis of cataract caused by the R54C mutation in human αA-crystallin, we have compared the structure, chaperone activity, intracellular localization, effect on cell viability and “interactome” of wild-type and mutant αA-crystallin. Although R54CαA-crystallin exhibited slight changes in quaternary structure, its chaperone activity was comparable to that of the wild-type. When expressed in lens epithelial cells, R54CαA-crystallin triggered a stress-like response, resulting in nuclear translocation of αB-crystallin, disassembly of cytoskeletal elements and activation of Caspase 3, leading to apoptosis. Comparison of the “interactome” of the wild-type and mutant proteins revealed a striking increase in the interaction of the mutant protein with nucleosomal histones (H2A, H2B, H3 and H4). Using purified chromatin fractions, we show an increased association of R54CαA-crystallin with these nucleosomal histones, suggesting the potential role of the mutant in transcriptional modulation. Thus, the present study shows that alteration of “interactome” and its nucleosomal association, rather than loss of chaperone activity, is the molecular basis of cataract caused by the R54C mutation in αA-crystallin.
The Linear Element is a Stable Structure Along the Chromosome Axis in Fission Yeast
Authors: Ding Da-Qiao , Matsuda Atsushi , Okamasa Kasumi , Hiraoka Yasushi 
Published: July 2020

AbstractChromosomes structure changes dramatically upon entering meiosis to ensure the successful progression of meiosis-specific events. During this process, a multilayer proteinaceous structure called synaptonemal complex (SC) is formed in many eukaryotes. Instead, in the fission yeastSchizosaccharomyces pombe, linear elements (LinEs), which are structures related to an axial element of SC, form on the meiotic cohesin-based chromosome axis and are required for the formation of DNA double-strand breaks. In contrast to the well-organized SC structure, LinE structure had been observed only by silver-stained electron micrographs or in immuno-fluorescence stained spread nuclei. Thus, their fine structure and dynamics in intact living cells remain to be elucidated. In this study, we performed live cell imaging with wide-field fluorescence microscopy as well as 3D structured illumination microscopy (3D-SIM) for the four components of LinE, the Rec10, Rec25, Rec27 and Mug20. We found that LinEs consist of threads formed along the chromosome axes during the meiotic prophase. Rec10 binds to the chromosome itself and shapes into LinEs only in the presence of all the other LinE components. Rec25, Rec27, and Mug20 attach to the chromosome in the presence of Rec10. LinEs are stable in a short-time treatment with 1,6-hexanediol; and fluorescence recovery after photobleaching (FRAP) experiment reveals slow recovery from photobleaching, indicating a stable property of LinEs.
The role of CLV signalling in the negative regulation of mycorrhizal colonisation and nitrogen response of tomato
Authors: Wang Chenglei , Velandia Karen , Kwon Choon-Tak , Wulf Kate E. , Nichols David S. , Reid James B. , Foo Eloise 
Published: July 2020

AbstractPlants form mutualistic nutrient acquiring symbioses with microbes, including arbuscular mycorrhizal fungi. The formation of these symbioses is costly and plants employ a negative feedback loop termed autoregulation of mycorrhizae (AOM) to limit arbuscular mycorrhizae (AM) formation. We provide evidence for the role of one leucine-rich-repeat receptor like kinase (FAB), a hydroxyprolineO-arabinosyltransferase enzyme (FIN) and additional evidence for one receptor like protein (SlCLV2) in the negative regulation of AM formation in tomato. Reciprocal grafting experiments suggest that theFABgene acts locally in the root, while theSlCLV2gene may act in both the root and the shoot. External nutrients including phosphate and nitrate can also strongly suppress AM formation. We found that FAB and FIN are required for nitrate suppression of AM but are not required for the powerful suppression of AM colonisation by phosphate. This parallels some of the roles of legume homologs in the autoregulation of the more recently evolved symbioses with nitrogen-fixing bacteria leading to nodulation. This deep homology in the symbiotic role of these genes suggests that in addition to the early signalling events that lead to the establishment of AM and nodulation, the autoregulation pathway might also be considered part of the common symbiotic toolkit that enabled plants to form beneficial symbioses.HighlightWe describe the role of CLV signalling elements in the negative regulation of arbuscular mycorrhizal symbioses of tomato, including influencing nitrate but not phosphate suppression of mycorrhizal colonisation.
Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures
Authors: Polovinkin Vitaly , Khakurel Krishna , Babiak Michal , Angelov Borislav , Schneider Bohdan , Dohnalek Jan , Andreasson Jakob , Hajdu Janos 
Published: July 2020

AbstractElectron crystallography of sub-micron sized 3D protein crystals has emerged recently as a valuable field of structural biology.In mesocrystallization methods, utilizing lipidic mesophases, particularly lipidic cubic phases (LCPs), can produce high-quality 3D crystals of membrane proteins (MPs). A major step towards realising 3D electron crystallography of MP crystals, grownin meso, is to demonstrate electron diffraction from such crystals. The first task is to remove the viscous and sticky lipidic matrix, surrounding the crystals without damaging the crystals. Additionally, the crystals have to be thin enough to let electrons traverse them without significant multiple scattering. In the present work, we experimentally verified the concept that focused ion beam milling at cryogenic temperatures (cryo-FIB) can be used to remove excess host lipidic mesophase matrix, and then thin the crystals to a thickness suitable for electron diffraction. In this study, bacteriorhodopsin (BR) crystals grown in a lipidic mesophase of monoolein were used as a model system. LCP from a part of a 50-μm thick crystal, which was flash-frozen in liquid nitrogen, was milled away with a gallium FIB under cryogenic conditions, and a part of the crystal itself was thinned into a ∼210-nm thick lamella with the ion beam. The frozen sample was then transferred into an electron cryo-microscope (cryo-EM), and a nanovolume of ∼1400×1400×210 nm3of the BR lamella was exposed to 200-kV electrons at a fluence of ∼0.06 e−/Å2. The resulting electron diffraction peaks were detected beyond 2.7-Å resolution (with mean signal-to-noise ratio <I/σ(I)> of >7) by a CMOS-based Ceta 16M camera. The results demonstrate, that cryo-FIB milling produces high quality lamellae from crystals grown in lipidic mesophases, and pave the way for 3D electron crystallography on crystals grown or embedded in highly viscous media.SynopsisElectron diffraction experiments on crystals of membrane proteins grown in lipidic mesophases have not been possible due to a thick layer of viscous crystallisation medium around the crystals. Here we show that focused ion beam milling at cryogenic temperatures (cryo-FIB milling) can remove the viscous layer, and demonstrate high-quality electron diffraction on a FIB-milled lamella of a bacteriorhodopsin 3D crystal.
Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine co-varies with risk factors for Parkinson’s
Authors: Brimblecombe Katherine R. , Connor-Robson Natalie , Bataille Carole J. R. , Roberts Bradley M. , Gracie Caitlin , O’Connor Bethan , te Water Naude Rebecca , Karthik Gayathri , Russell Angela J. , Wade-Martins Richard , Cragg Stephanie J. 
Published: July 2020

AbstractCa2+entry into nigrostriatal dopamine (DA) neurons and axons via L-type voltage-gated Ca2+channels (LTCCs) contributes respectively to pacemaker activity and DA release, and has long been thought to contribute to vulnerability to degeneration in Parkinson’s disease. LTCC function is greater in DA axons and neurons from substantia nigra pars compacta than from ventral tegmental area, but this is not explained by channel expression level. We tested the hypothesis that LTCC-control of DA release is governed rather by local mechanisms, focussing on candidate biological factors known to operate differently between types of DA neurons and/or be associated with their differing vulnerability to parkinsonism, including biological sex, α-synuclein, DA transporters (DATs), and calbindin-D28k (Calb1). We detected evoked DA releaseex vivoin mouse striatal slices using fast-scan cyclic voltammetry, and assessed LTCC support of DA release by detecting the inhibition of DA release by the LTCC inhibitors isradipine or CP8. Using genetic knockouts or pharmacological manipulations we identified that striatal LTCC support of DA release depended on multiple intersecting factors, in a regionally and sexually divergent manner. LTCC function was promoted by factors associated with Parkinsonian risk, including male sex, α-synuclein, DAT, and a dorsolateral co-ordinate, but limited by factors associated with protection i.e. female sex, glucocerebrosidase activity, Calb1, and ventromedial co-ordinate. Together, these data show that LTCC function in DA axons, and isradipine effect, are locally governed and suggest they vary in a manner that in turn might impact on, or reflect, the cellular stress that leads to parkinsonian degeneration.Abstract Figure
Detecting oncogenic selection through biased allele retention in The Cancer Genome Atlas
Authors: Luft Juliet , Young Robert S. , Meynert Alison M. , Taylor Martin S. 
Published: July 2020

AbstractBackgroundThe loss of genetic diversity in segments over a genome (loss-of-heterozygosity, LOH) is a common occurrence in many types of cancer. By analysing patterns of preferential allelic retention during LOH in approximately 10,000 cancer samples from The Cancer Genome Atlas (TCGA), we sought to systematically identify genetic polymorphisms currently segregating in the human population that are preferentially selected for, or against during cancer development.ResultsExperimental batch effects and cross-sample contamination were found to be substantial confounders in this widely used and well studied dataset. To mitigate these we developed a generally applicable classifier (GenomeArtiFinder) to quantify contamination and other abnormalities. We provide these results as a resource to aid further analysis of TCGA whole exome sequencing data. In total, 1,678 pairs of samples (14.7%) were found to be contaminated or affected by systematic experimental error. After filtering, our analysis of LOH revealed an overall trend for biased retention of cancer-associated risk alleles previously identified by genome wide association studies. Analysis of predicted damaging germline variants identified highly significant oncogenic selection for recessive tumour suppressor alleles. These are enriched for biological pathways involved in genome maintenance and stability.ConclusionsOur results identified predicted damaging germline variants in genes responsible for the repair of DNA strand breaks and homologous repair as the most common targets of allele biased LOH. This suggests a ratchet-like process where heterozygous germline mutations in these genes reduce the efficacy of DNA double-strand break repair, increasing the likelihood of a second hit at the locus removing the wild-type allele and triggering an oncogenic mutator phenotype.
RNAxplorer: Harnessing the Power of Guiding Potentials to Sample RNA Landscapes
Authors: Entzian Gregor , Hofacker Ivo , Ponty Yann , Lorenz Ronny , Tanzer Andrea 
Published: July 2020

AbstractMotivationPredicting the folding dynamics of RNAs is a computationally difficult problem, first and foremost due to the combinatorial explosion of alternative structures in the folding space. Abstractions are therefore needed to simplify downstream analyses, and thus make them computationally tractable. This can be achieved by various structure sampling algorithms. However, current sampling methods are still time consuming and frequently fail to represent key elements of the folding space.MethodWe introduceRNAxplorer, a novel adaptive sampling method to efficiently explore the structure space of RNAs.RNAxploreruses dynamic programming to perform an efficient Boltzmann sampling in the presence of guiding potentials, which are accumulated into pseudo-energy terms and reflect similarity to already well-sampled structures. This way, we effectively steer sampling towards underrepresented or unexplored regions of the structure space.ResultsWe developed and applied different measures to benchmark our sampling methods against its competitors. Most of the measures show thatRNAxplorerproduces more diverse structure samples, yields rare conformations that may be inaccessible to other sampling methods and is better at finding the most relevant kinetic traps in the landscape. Thus, it produces a more representative coarse graining of the landscape, which is well suited to subsequently compute better approximations of RNA folding kinetics.Availabilityhttps://github.com/ViennaRNA/RNAxplorer/Contactandrea.tanzer@meduniwien.ac.at,ronny@tbi.univie.ac.at
Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks
Authors: Balzer Connor J. , James Michael L. , Helgeson Luke A. , Sirotkin Vladimir , Nolen Brad J. 
Published: July 2020

AbstractThe actin filament nucleator Arp2/3 complex is activated at cortical sites inS. pombeto assemble branched actin networks that drive endocytosis. Arp2/3 complex activators Wsp1 and Dip1 are required for proper actin assembly at endocytic sites, but how they coordinately control Arp2/3-mediated actin assembly is unknown. Alone, Dip1 activates Arp2/3 complex without preexisting actin filaments to nucleate “seed” filaments that activate Wsp1-bound Arp2/3 complex, thereby initiating branched actin network assembly. In contrast, because Wsp1 requires pre-existing filaments to activate, it has been assumed to function exclusively in propagating actin networks by stimulating branching from pre-existing filaments. Here we show that Wsp1 is important not only for propagation, but also for initiation of endocytic actin networks. Using single molecule TIRF microscopy we show that Wsp1 synergizes with Dip1 to co-activate Arp2/3 complex. Synergistic coactivation does not require pre-existing actin filaments, explaining how Wsp1 contributes to actin network initiation in cells.
Comparison of two commercial platforms and a laboratory developed test for detection of SARS-CoV-2 RNA
Authors: Mannonen Laura , Kallio-Kokko Hannimari , Loginov Raisa , Jääskeläinen Anu , Jokela Pia , Antikainen Jenni , Väre Paula , Kekäläinen Eliisa , Kurkela Satu , Jarva Hanna , Lappalainen Maija 
Published: July 2020

ABSTRACTMitigation of the ongoing COVID-19 pandemic requires reliable and accessible laboratory diagnostic services. We evaluated the performance of one LDT and two commercial tests, cobas® SARS-CoV-2 (Roche) and Amplidiag® COVID-19 (Mobidiag), for the detection of SARS-CoV-2 RNA in respiratory specimens. 183 specimens collected from suspected COVID-19 patients were studied with all three methods to compare their performance. In relation to the reference standard, which was established as the result obtained by two of the three studied methods, the positive percent agreement (PPA) was highest for cobas® test (100%), followed by Amplidiag® test and the LDT (98.9%). The negative percent agreement (NPA) was lowest for cobas® test (89.4%), followed by Amplidiag® test (98.8%) and the highest value was obtained for LDT (100%). The dilution series conducted for specimens, however, suggests significantly higher sensitivity for the cobas® assay in comparison with the other two assays and the low NPA value may be due to the same reason. In general, all tested assays performed adequately. Both the time from sample to result and hands-on time per sample were shortest for cobas® test. Clinical laboratories need to be prepared for uninterrupted high-throughput testing during the coming months in mitigation of the pandemic. To secure that, it is of critical importance for clinical laboratories to maintain several simultaneous platforms in their SARS-CoV-2 nucleic acid testing.
Identifying regions for enhanced control of gambiense sleeping sickness in the Democratic Republic of Congo
Authors: Huang Ching-I , Crump Ronald E , Brown Paul E , Spencer Simon E F , Miaka Erick Mwamba , Shampa Chansy , Keeling Matt J , Rock Kat S 
Published: July 2020

ABSTRACTGambiense human African trypanosomiasis (sleeping sickness, gHAT) is a disease targeted for elimination of transmission (EOT) by 2030. Despite the number of new cases reported annually being at a historical minimum, the likelihood of achieving EOT is unknown. We utilised modelling to study the impact of four strategies comprised of currently-available intervention methods including active and passive screening and vector control (VC) on transmission across 168 health zones in the Democratic Republic of the Congo. By estimating the median year of EOT and the probability of EOT by 2030 under each strategy, the model predicts only 81 health zones are on track to achieve the EOT target using medical-only strategies and this number drops to 52 when uncertainty is considered (> 90% probability). Although all health zones are predicted to meet EOT by 2030 under strategies with VC, blanket coverage is impractical so this analysis provides a priority list of health zones for consideration for supplementary VC implementation in conjunction with medical interventions.
Structural Barriers to Green and Blue Spaces: A Scoping Review Protocol
Authors: Nejade Rachel M. , Grace Daniel M. , Bowman Leigh R. 
Published: July 2020

AbstractBackgroundEmerging evidence has demonstrated that nature-based interventions (NBIs) can improve mental and physical health. Considering that the global burden of poor mental health continues to rise, such interventions could be a cost-effective means to improve mental health, as well as reconnect individuals with the natural world, and thus aid efforts. However, the effectiveness of NBIs as a prescriptive intervention is, in part, a function of access to blue and green spaces. Accordingly, this scoping review will explore how structural inequalities influence the effectiveness of nature-based interventions as treatment options for mental and physical ill health.MethodsA scoping review will be conducted to identify the barriers and facilitators associated with the utilisation of green and blue spaces. The review will follow the PRISMA-ScR guidelines, in addition to the associated Cochrane guidelines for scoping reviews. A literature search will be performed across five databases, and articles will be selected based on key inclusion/ exclusion criteria. All data will be extracted to a pre-defined charting table. The primary and secondary outcomes will be mental and physical health respectively.DiscussionThis review will better inform relevant stakeholders of the potential enablers and barriers of nature-based interventions, and thereby improve provision and implementation of NBIs as public health initiatives.Ethics and DisseminationAll data rely on secondary, publicly available data sources; therefore no ethical clearance is required.Upon completion, the results of this study will be disseminated via the Imperial College London Community and published in an open access, peer-reviewed journal.Article SummaryStrengths and Limitations of this StudyThis scoping review protocol is the first to focus on the accessibility to green and blue spaces in the context of mental and physical health.This protocol and subsequent review benefit from increased transparency, a systematised strategy (PRISMA-ScR), and a reduction in the risk of bias, through publication in an open access journal.This review will also capture grey literature - studies published outside peer-reviewed journals.Due to the broad nature of the review, the research may unearth more questions than solutions.Registration NumberOpen Science Framework: 10.17605/OSF.IO/8J5Q3