bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multiregional assessment of transnational pathways of introduction
Authors: McGrannachan Chris M. , Pagad Shyama , McGeoch Melodie A. 
Published: November 2020

AbstractInformation on the pathways by which alien taxa are introduced to new regions is vital for prioritising policy and management responses to invasions. However, available datasets are often compiled using disparate methods, making comparison and collation of pathway data difficult. Using a standardised framework for recording and categorising pathway data can help to rectify this problem and provide the information necessary to develop indicators for reporting on alien introductions. We combine the Convention on Biological Diversity’s Pathways Categorisation Scheme (CPC) with data compiled by the Invasive Species Specialist Group (ISSG) to report on multiregional trends on alien introduction pathways over the past 200+ years. We found a significant increase in the documented number of multiregional alien introduction events across all pathways of the CPC’s three hierarchical levels. The ‘escape’ pathway is the most common documented pathway used by alien taxa. Transport stowaways via shipping-related vectors are a rapidly increasing contribution to alien introductions. Most alien introduction events were of unknown pathway origin, highlighting the challenge of information gaps in pathway data and reiterating the need for standardised information-gathering practices. Combining the CPC framework with alien introduction pathways data will standardise pathway information and facilitate the development of global indicators of trends in alien introductions and the pathways they use. These indicators have the potential to inform policy and management strategies for preventing future biological invasions and can be downscaled to national and regional levels that are applicable across taxa and ecosystems.
Moderate and intensive mechanical loading differentially modulate the phenotype of tendon stem/progenitor cellsin vivo
Authors: Zhang Jianying , Nie Daibang , Williamson Kelly , McDowell Arthur , Hogan MaCalus V. , Wang James H-C. 
Published: November 2020

ABSTRACTTo examine the differential mechanobiological responses of specific resident tendon cells, we developed anin vivomodel of whole-body irradiation followed by injection of either tendon stem/progenitor cells (TSCs) expressing green fluorescent protein (GFP-TSCs) or mature tenocytes expressing GFP (GFP-TNCs) into the patellar tendons of wild type C57 mice. Injected mice were subjected to moderate treadmill running (MTR) and intensive treadmill running (ITR). In MTR mice, both GFP-TSC and GFP-TNC injected tendons maintained normal cell morphology with elevated expression of tendon related markers collagen I and tenomodulin. In ITR mice injected with GFP-TNCs, cells also maintained an elongated shape similar to the shape found in normal/untreated control mice, as well as elevated expression of tendon related markers. However, ITR mice injected with GFP-TSCs showed typical tendinopathic changes, such as cell morphology transitioning to a round shape, elevated chondrogenic differentiation, and increased gene expression of non-tenocyte related genes LPL, Runx-2, and SOX-9. Increased gene expression data was supported by immunostaining showing elevated expression of SOX-9, Runx-2, and PPARγ. This study provides evidence that while MTR maintains tendon homeostasis by promoting the differentiation of TSCs into tenocytes, ITR may cause the development of tendinopathy by inducing non-tenocyte differentiation of TSCs, thus leading to the presence of non-tendinous tissues in tendon.
Influence of tropical pastures on grazing behavior parameters of young lambs
Authors: Fabíola Tontini Jalise , Poli Cesar Henrique Espírito Candal , da Silva Hampel Viviane , de Souza Farias Mariana , Fajardo Neuza Maria , da Silva Joseane Anjos , Farinatti Luís Henrique Ebling , Muir James Pierre 
Published: November 2020

AbstractTropical sward characteristics can alter lamb ingestive behavior. Our study evaluated the ingestive behavior of young lambs in different tropical pastures to identify which variables interfere in their grazing activity. Two years of study were carried out with 54 weaned lambs distributed in three different swards: 1) monoculture of a upright grass, guinea grass (Panicum maximum; GG); 2) monoculture of a shrubby legume pigeon pea (Cajanus cajan; PP) and 3) contiguous areas with half the paddock with GG and half with PP (GP). The experiment was set out in a randomized complete block design. Lamb ingestive behavior was observed from sunrise to sunset with records every 5 minutes. To identify the main variables that affected with the lamb grazing activity, a multivariate analysis of the Decision Tree was performed. Our results showed that there was no difference in the ingestive behavior parameters of young lambs in different swards (P> 0.05). There was interaction among the swards and the experimental periods for the variables idleness time and biting rate (P≤ 0.05). Grazing time of the animals increased 40% with experimental period progression. The Decision Tree identified leaf:stem ratio as the variable that most influenced lamb grazing time in GG and GP swards while in the PP sward grazing time was directly related to the pasture height. The behavior of young lambs on tropical pasture is variable as there is a change in the behavioral response over time. In addition, the grazing time of these animals can be estimated by means of variables related to pasture structural characteristics (leaf:stem ratio and height) together with chemical variables.
Towards Targeting the Disordered SARS-CoV-2 Nsp2 C-terminal Region: Partial Structure and Dampened Mobility Revealed by NMR Spectroscopy
Authors: Mompeán Miguel , Treviño Miguel Á. , Laurents Douglas V. 
Published: November 2020

AbstractIntrinsically disordered proteins (IDPs) play essential roles in regulating physiological processes in eukaryotic cells. Many virus use their own IDPs to “hack” these processes to disactive host defenses and promote viral growth. Thus, viral IDPs are attractive drug targets. While IDPs are hard to study by X-ray crystallography or cryo-EM, atomic level information on their conformational perferences and dynamics can be obtained using NMR spectroscopy. SARS-CoV-2 Nsp2 interacts with human proteins that regulate translation initiation and endosome vesicle sorting, and the C-terminal region of this protein is predicted to be disordered. Molecules that block these interactions could be valuable leads for drug development. To enable inhibitor screening and to uncover conformational preferences and dynamics, we have expressed and purified the13C,15N-labeled C-terminal region of Nsp2. The13Cβ and backbone13CO,1HN,13Cα and15N nuclei were assigned by analysis of a series of 2D1H-15N HSQC and13C-15N CON as well as 3D HNCO, HNCA, CBCAcoNH and HncocaNH spectra. Overall, the chemical shift data confirm that this region is chiefly disordered, but contains two five-residue segments that adopt a small population of β-strand structure. Whereas the region is flexible on ms/ms timescales as gauged by T1ρmeasurements, the {1H}-15N NOEs reveal a flexibility on ns/ps timescales that is midway between a fully flexible and a completely rigid chain.
Towards Semantic fMRI Neurofeedback: Navigating among Mental States using Real-time Representational Similarity Analysis
Authors: Russo Andrea G. , Lührs Michael , Di Salle Francesco , Esposito Fabrizio , Goebel Rainer 
Published: November 2020

AbstractObjectiveReal-time functional magnetic resonance imaging neurofeedback (rt-fMRI-NF) is a non-invasive MRI procedure allowing examined participants to learn to self-regulate brain activity by performing mental tasks. A novel two-step rt-fMRI-NF procedure is proposed whereby the feedback display is updated in real-time based on high level (semantic) representations of experimental stimuli via real-time representational similarity analysis of multi-voxel patterns of brain activity.ApproachIn a localizer session, the stimuli become associated with anchored points on a two-dimensional representational space where distances approximate between-pattern (dis)similarities. In the NF session, participants modulate their brain response, displayed as a movable point, to engage in a specific neural representation. The developed method pipeline is verified in a proof-of-concept rt-fMRI-NF study at 7 Tesla using imagery of concrete objects. The dependence on noise is more systematically assessed on artificial fMRI data with similar (simulated) spatio-temporal structure and variable (injected) signal and noise. A series of brain activity patterns from the ventral visual cortex is evaluated via on-line and off-line analyses and the performances of the method are reported under different noise conditions.Main resultsThe participant in the proof-of-concept study exhibited robust activation patterns in the localizer session and managed to control the neural representation of a stimulus towards the selected target, in the NF session. The offline analyses validated the rt-fMRI-NF results, showing that the rapid convergence to the target representation is noise-dependent.SignificanceOur proof-of-concept study demonstrates the potential of semantic NF designs where the participant navigates among different mental states. Compared to traditional NF designs (e.g. using a thermometer display to set the level of the neural signal), the proposed approach provides content-specific feedback to the participant and extra degrees of freedom to the experimenter enabling real-time control of the neural activity towards a target brain state without suggesting a specific mental strategy to the subject.
Canonical Wnt signalling is activated during BEC-to-hepatocyte conversionin vivoand modulates liver epithelial cell plasticity in hepatic organoids
Authors: Valle-Encinas Eider , Aleksieva Niya , Velasco Martinez Carmen , Dawes Michael , Zverev Matthew , Müller Miryam , Offergeld Anika , Smalley Matthew J , Hogan Catherine , Forbes Stuart J , Bird Tom G , Dale Trevor C 
Published: November 2020

SummaryWhile it is recognized that the Wnt/ß-catenin pathway orchestrates hepatocyte proliferation in both homeostasis and injury, little is known about the importance of β-catenin in biliary epithelial cell (BEC) plasticity. In this study, the dynamics of activation of the canonical Wnt pathway were investigated during BEC-to-hepatocyte conversion using as a model methionine/choline deficient (MCD)-injured livers where hepatocyte proliferation was compromised by the overexpression of p21. In this model, activation of β-catenin was found an event associated with BEC reprogramming. Using ductal organoids to model BECs transitioning into hepatocytes, we found that activation of the Wnt/ß-catenin pathway in these cells promoted partial escape from a biliary fate and triggered the acquisition of progenitor cell features. Our data furthermore support that BECs are source of Wnt ligands and that Rspo proteins potentially act as the limiting factor controlling the activation of β-catenin activation and BEC reprogramming during severe liver damage.
Importin α7 deficiency causes infertility in male mice by disrupting spermatogenesis
Authors: Liu Na , Qadri Fatimunnisa , Busch Hauke , Huegel Stefanie , Sihn Gabin , Chuykin Ilya , Hartmann Enno , Bader Michael , Rother Franziska 
Published: November 2020

AbstractSpermatogenesis is driven by an ordered series of events, which rely on trafficking of specific proteins between nucleus and cytoplasm. The importin α family of proteins mediates movement of specific cargo proteins when bound to importin β. Importin α genes have distinct expression patterns in mouse testis, implying they may have unique roles during mammalian spermatogenesis. Here we use a loss-of-function approach to specifically determine the role of importin α7 in spermatogenesis and male fertility. We show that ablation of importin α7 in male mice leads to infertility and has multiple cumulative effects on both germ cells and Sertoli cells. Importin α7-deficient mice exhibit an impaired Sertoli cell function, including loss of Sertoli cells and a compromised nuclear transport of the androgen receptor. Furthermore, our data demonstrate devastating defects in spermiogenesis that are accompanied by disturbed histone-protamine-exchange, absence of the transcriptional regulator Brwd1 and altered expression of Rfx2 target genes, resulting in incomplete sperm maturation and massive loss of sperms. Our work uncovers the essential role of importin α7 in spermatogenesis and hence in male fertility.
Plant-specific histone deacetylases are essential for early as well as late stages of Medicago nodule development
Authors: Li Huchen , Schilderink Stefan , Cao Qingqin , Kulikova Olga , Bisseling Ton 
Published: November 2020

ABSTRACTLegume and rhizobium can establish a nitrogen-fixing nodule symbiosis. Previous studies have shown that several transcription factors that play a role in (lateral) root development are also involved in nodule development. Chromatin remodelling factors, like transcription factors, are key players in regulating gene expression. However, it has not been studied whether chromatin remodelling genes that are essential for root development get involved in nodule development. Here we studied the role of Medicago histone deacetylases (MtHDTs) in nodule development. Their Arabidopsis orthologs have been shown to play a role in root development. The expression ofMtHDTsis induced in nodule primordia and is maintained in nodule meristem and infection zone. Conditional knock-down of their expression in a nodule-specific way by RNAi blocks nodule primordium development. A few nodules still can be formed but their nodule meristems are smaller and rhizobial colonization of the cells derived from the meristem is markedly reduced. Although the HDTs are expressed during nodule and root development, transcriptome analyses indicate that HDTs control the development of these organs in a different manner. During nodule development the MtHDTs positively regulate3-hydroxy-3-methylglutaryl coenzyme a reductase 1(MtHMGR1). The decreased expression ofMtHMGR1is sufficient to explain the block of primordium formation.ONE SENTENCE SUMMARYPlant-specific histone deacetylases regulate the expression of3-hydroxy-3-methylglutaryl-coenzyme A reductasesto control root nodule development.
The role of XPB/Ssl2 dsDNA translocation processivity in transcription-start-site scanning
Authors: Tomko Eric J. , Luyties Olivia , Rimel Jenna K. , Tsai Chi-Lin , Fuss Jill O. , Fishburn James , Hahn Steven , Tsutakawa Susan E. , Taatjes Dylan J. , Galburt Eric A. 
Published: November 2020

AbstractThe general transcription factor TFIIH contains three ATP-dependent catalytic activities. TFIIH functions in nucleotide excision repair primarily as a DNA helicase and in Pol II transcription initiation as a dsDNA translocase and protein kinase. During initiation, the XPB/Ssl2 subunit of TFIIH couples ATP hydrolysis to dsDNA translocation facilitating promoter opening and the kinase module phosphorylates the C-terminal domain to facilitate the transition to elongation. These functions are conserved between metazoans and yeast; however, yeast TFIIH also drives transcription start-site scanning in which Pol II scans downstream DNA to locate productive start-sites. The ten-subunit holo-TFIIH fromS. cerevisiaehas a processive dsDNA translocase activity required for scanning and a structural role in scanning has been ascribed to the three-subunit TFIIH kinase module. Here, we assess the dsDNA translocase activity of ten-subunit holo- and core-TFIIH complexes (i.e. seven subunits, lacking the kinase module) from bothS. cerevisiaeandH. sapiens. We find that neither holo nor core human TFIIH exhibit processive translocation, consistent with the lack of start-site scanning in humans. Furthermore, in contrast to holo-TFIIH, theS. cerevisiaecore-TFIIH also lacks processive translocation and its dsDNA-stimulated ATPase activity was reduced ~5-fold to a level comparable to the human complexes, potentially explaining the reported upstream shift in start-site observed in the absence of theS. cerevisiaekinase module. These results suggest that neither human norS. cerevisiaecore-TFIIH can translocate efficiently, and that theS. cerevisiaekinase module functions as a processivity factor to allow for robust transcription start-site scanning.
Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states
Authors: Chen Xueqing , Emerson Mark M. 
Published: November 2020

AbstractNotch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized inhibition of Notch signaling in restricted progenitor cells does not alter the number of cones derived from these cells. Cell cycle promotion is not a primary effect of Notch signaling but an indirect effect on progenitor cell state transitions that leads to depletion of the multipotent progenitor cell population. Taken together, this suggests that the role of Notch signaling in cone photoreceptor formation and proliferation are both mediated by a localized function of Notch in multipotent retinal progenitor cells to repress the formation of restricted progenitor cells.
PCMD-1 bridges the centrioles and the PCM scaffold inC. elegans
Authors: Stenzel Lisa , Mehler Judith , Schreiner Alina , Üstüner Sim , Zuccoli Elisa , Zanin Esther , Mikeladze-Dvali Tamara 
Published: November 2020

ABSTRACTCorrect cell division relies on the formation of a bipolar spindle. In animal cells, microtubule nucleation at the spindle poles is facilitated by the pericentriolar material (PCM), which assembles around a pair of centrioles. Although centrioles are essential for PCM assembly, proteins that anchor the PCM to the centrioles are less known. Here we investigate the molecular function of PCMD-1 in bridging the PCM and the centrioles inCaenorhabditis elegans.We demonstrate that centrosomal recruitment of PCMD-1 is dependent on the outer centriolar protein SAS-7. While the most C-terminal part of PCMD-1 is sufficient to target it to the centrosome, the coiled-coil domain promotes its accumulation by facilitating self-interaction. We reveal that PCMD-1 is bridging the centrioles and PCM scaffold through protein-protein interactions with the PCM scaffold protein SPD-5, the mitotic kinase PLK-1 and the centriolar protein SAS-4. Using an ectopic translocation assay, we show that PCMD-1 is able to selectively recruit downstream PCM scaffold components to an ectopic location in the cell, indicating that PCMD-1 is sufficient to anchor the PCM scaffold proteins to the centrioles. Our work suggests that PCMD-1 is an essential functional bridge between the centrioles and the PCM.
A Tn-seq screen ofStreptococcus pneumoniaeuncovers DNA repair as the major pathway for desiccation tolerance and transmission
Authors: Matthews Allison J. , Rowe Hannah M. , Rosch Jason W. , Camilli Andrew 
Published: November 2020

ABSTRACTStreptococcus pneumoniaeis an opportunistic pathogen that is a common cause of serious invasive diseases such as pneumonia, bacteremia, meningitis, and otitis media. Transmission of this bacterium has classically been thought to occur through inhalation of respiratory droplets and direct contact with nasal secretions. However, the demonstration thatS. pneumoniaeis desiccation tolerant, and therefore environmentally stable for extended periods of time, opens up the possibility that this pathogen is also transmitted via contaminated surfaces (fomites). To better understand the molecular mechanisms that enableS. pneumoniaeto survive periods of desiccation, we performed a high throughput transposon sequencing (Tn-seq) screen in search of genetic determinants of desiccation tolerance. We identified 42 genes whose disruption reduced desiccation tolerance, and 45 genes that enhanced desiccation tolerance. The nucleotide excision repair pathway was the most enriched category in our Tn-seq results, and we found that additional DNA repair pathways are required for desiccation tolerance, demonstrating the importance of maintaining genome integrity after desiccation. Deletion of the nucleotide excision repair geneuvrAresulted in decreased transmission efficiency between infant mice, indicating a correlation between desiccation tolerance and pneumococcal transmission. Understanding the molecular mechanisms that enable pneumococcal persistence in the environment may enable targeting of these pathways to prevent fomite transmission, thereby preventing the establishment of new colonization and any resulting invasive disease.