bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pest control strategies after first signs of invasive black rat: case study in the Community of Madrid
Authors: Bermejo-Nogales Azucena , Navas José M. 
Published: January 2021

AbstractRodents are animals that provoke special concern in the rural and urban areas as may cause potential damage in facilities and infrastructures as well as social alarm. The control of rodent populations is based on prevention and on what it has been called an “Integrated Pest Management” strategy. The most important species affected by this strategy are brown rat (Rattus norvegicus), black rat (Rattus rattus L.) and mouse (Mus musculus). In the present work, our original objective was to monitor changes in status or range of rodent species in the Community of Madrid (Spain). We conducted in coordination with the professional organization of Pest Control Operators “ANECPLA” a procedure designed to obtain faecal samples in locations with rodenticide treatment. Determination of pest specie was based on cytochrome b (cytb) sequences and phylogenetic analysis. We received samples from a variety of locations in which a rodenticide treatment was applied due to infestation or to citizen notice. While we recorded a number of data about the distribution of brown rat the presence of black rat was unexpectedly discovered. The detection of this species implies changes in pest control strategies to improve the results in the application of rodenticides available in the market.Key MessageRodent pest control is a key issue but little is known about Spanish populations. We aimed to know how many rat species there are in Central Spain, specifically in the Community of Madrid. We found for the first time the presence of black rat and a new wild strain of brown rat in this area. These findings have change the strategies of rodent treatment and stresses the importance of population studies for a better control.
Transcripts switched off at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripeningV. viniferafruit
Authors: Savoi Stefania , Torregrosa Laurent , Romieu Charles 
Published: January 2021

AbstractTranscriptomic changes at the cessation of sugar accumulation in the pericarp ofVitis viniferawere addressed on single berries re-synchronized according to their individual growth patterns. The net rates of water, sugars and K+accumulation inferred from individual growth and solute concentration confirmed that these inflows stopped simultaneously in the ripe berry, while the small amount of malic acid remaining at this stage was still being oxidized at low rate. Re-synchronized individual berries displayed negligible variations in gene expression among triplicates. RNA-Seq studies revealed sharp reprogramming of cell wall enzymes and structural proteins at the stop of phloem unloading, associated with an 80% repression of multiple sugar transporters and aquaporins on the plasma or tonoplast membranes, with the noticeable exception of H+/sugar symporters, that were rather weakly and constitutively expressed. This was verified in three genotypes placed in contrasted thermo-hydric conditions. The prevalence of SWEET suggests that electrogenic transporters would play a minor role on the plasma membranes of SE/CC complex and the one of the flesh, while sucrose/H+exchangers dominate on its tonoplast.Cis-regulatory elements present in their promoters allowed to sort these transporters in different groups, also including specific TIPs and PIPs paralogs, and cohorts of cell wall related genes. Together with simple thermodynamic considerations, these results lead to propose that H+/sugar exchangers at the tonoplast, associated with a considerably acidic vacuolar pH, may exhaust cytosolic sugars in the flesh and alleviate the need for supplementary energization of sugar transport at the plasma membrane.
Piriformospora indica employs host’s putrescine for growth promotion in plants
Authors: Kundu Anish , Jogawat Abhimanyu , Mishra Shruti , Kundu Pritha , Vadassery Jyothilakshmi 
Published: January 2021

AbstractGrowth promotion by endosymbiont Piriformospora indica has been observed in various plants; however, specific functional metabolites involved in P. indica mediated growth promotion are unknown. A GC-MS based untargeted metabolite analysis was used to identify Solanum lycopersicum metabolites altered during P. indica mediated growth promotion. Metabolomic analysis showed primary metabolites altered and specifically putrescine to be maximally induced in roots during the interaction. P. indica induced putrescine biosynthetic gene SlADC1 in S. lycopersicum and acts via arginine decarboxylase (ADC) mediated pathway. P. indica did not promote growth in Sladc-VIGS (virus induced gene silencing of SlADC gene) lines of S. lycopersicum and when the ADC enzyme was inhibited with an inhibitor, DL-α-(Difluoromethyl) arginine. In Arabidopsis adc knock-out mutants, P. indica do not promote growth and this response was rescued upon exogenous application of putrescine. Putrescine promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4, GA7) levels in S. lycopersicum. Putrescine is also important for P. indica hyphal growth indicating that it is co-adapted by both host and microbe. Hence, we conclude that putrescine is an essential metabolite and its biosynthesis in plants is crucial for P. indica mediated growth promotion and fungal growth.
Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions
Authors: Hosni Nicole Dittrich , Anauate Ana Carolina , Boim Mirian Aparecida 
Published: January 2021

ABSTRACTBackgroundReal-time PCR remains currently the gold standard method for gene expression studies. Identification of the best reference gene is a key point in performing high quality qPCR, providing strong support for results, as well as performing as a source of bias when inappropriately chosen. Mesangial cells and podocytes, as essential cell lines to study diabetic kidney disease (DKD) physiopathology, demand accurate analysis of the reference genes used so far to enhance validity of gene expression studies, especially regarding high glucose (HG) and DKD treatments, with angiotensin II receptor blockers (e.g. Losartan) being the most commonly used. This study aimed to evaluate the suitability and define the most stable reference gene for mesangial cells and podocytes studies of anin vitroDKD model of disease and its treatment.MethodsFive software packages (RefFinder, NormFinder, GeNorm, Bestkeeper, and DataAssist) and the comparative ΔCt method were selected to analyze six different candidate genes:HPRT, ACTB, PGAM-1, GAPDH, PPIA,andB2M.RNA was extracted and cDNA was synthesized from immortalized mouse mesangial cells and podocytes cultured in 4 groups: control (n=5; 5mM glucose), mannitol (n=5; 30mM, as osmotic control), HG (n=5; 30mM glucose), and HG + losartan (n=5; 30mM glucose and 10-4mM of losartan). Real-time PCR was performed according to MIQE guidelines.ResultsWe identified that the use of 2 genes is the best combination for qPCR normalization for both mesangial cell and podocytes. For mesangial cells, the combination ofHPRTandACTBpresented higher stability values. For podocytes,HPRTandGAPDHshowed the best results.ConclusionThis analysis provides support for the use ofHPRTandACTBas reference genes in mouse mesangial cell studies of gene expression via real-time PCR technique, while for podocytes,HPRTandGAPDHshould be chosen.
Integration of spatial transcriptomic and single cell sequencing identifies expression patterns underlying immune and epithelial cell cross-talk in acute kidney injury
Authors: Ferreira Ricardo Melo , Sabo Angela R. , Winfree Seth , Collins Kimberly S. , Janosevic Danielle , Gulbronson Connor , Cheng Ying-Hua , Casbon Lauren , Barwinska Daria , Ferkowicz Michael J. , Xuei Xiaoling , Zhang Chi , Dunn Kenneth W. , Kelly Katherine J. , Sutton Timothy A. , Hato Takashi , Dagher Pierre C. , El-Achkar Tarek M. , Eadon Michael T. 
Published: January 2021

AbstractDespite important advances in studying experimental and clinical acute kidney injury (AKI), the pathogenesis of this disease remains incompletely understood. Single cell sequencing studies have closed this knowledge gap by characterizing the transcriptomic signature of different cell types within the kidney. However, the spatial distribution of injury can be regional and affect cells heterogeneously. We first optimized coordination of spatial transcriptomics and single nuclear sequencing datasets, mapping 30 dominant cell types to a human nephrectomy sample. The predicted cell type spots corresponded with the underlying hematoxylin and eosin histopathology. To study the implications of acute kidney injury on the distribution of transcript expression, we then characterized the spatial transcriptomic signature of two murine AKI models: ischemia reperfusion injury (IRI) and cecal ligation puncture (CLP). Localized regions of reduced overall expression were found associated with tissue injury pathways. Using single cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. As expected, neutrophils infiltrated the renal medullary outer stripe in the ischemia model. Atf3 was identified as a chemotactic factor in S3 proximal tubule cells. In the CLP model, infiltrating macrophages dominated the outer cortical signature and Mdk was identified as a corresponding chemotactic factor. The regional distribution of these immune cells was validated with multiplexed CO-Detection by inDEXing (CODEX) immunofluorescence. Spatial transcriptomic sequencing can aid in uncovering the mechanisms driving immune cell infiltration and allow detection of relevant subpopulations in single cell sequencing. The complementarity of these technologies facilitates the development of a transcriptomic kidney atlas in health and disease.
The intrinsic chaperone network of Arabidopsis stem cells confers protection against proteotoxic stress
Authors: Llamas Ernesto , Torres-Montilla Salvador , Lee Hyun Ju , Barja María Victoria , Schlimgen Elena , Dunken Nick , Wagle Prerana , Werr Wolfgang , Zuccaro Alga , Rodríguez-Concepción Manuel , Vilchez David 
Published: January 2021

AbstractThe biological purpose of plant stem cells is to maintain themselves while providing new pools of differentiated cells that form organs and rejuvenate or replace damaged tissues1-3. Protein homeostasis, or proteostasis, is required for cell function and viability4-7. However, the link between proteostasis and plant stem cell identity remains unknown. In contrast to their differentiated counterparts, we find that root stem cells can prevent the accumulation of aggregated proteins even under proteotoxic stress conditions such as heat stress or proteasome inhibition. Notably, root stem cells exhibit enhanced expression of distinct chaperones that maintain proteome integrity. Particularly, intrinsic high levels of the TRiC/CCT chaperonin determine stem cell maintenance and their remarkable ability to suppress protein aggregation. Overexpression of CCT8, a key activator of TRiC/CCT assembly8, is sufficient to ameliorate protein aggregation in differentiated cells and confer resistance to proteotoxic stress in plants. Taken together, our results indicate that enhanced proteostasis mechanisms in stem cells could be an important requirement for plants to persist under extreme environmental conditions and reach extreme long ages. Thus, proteostasis of stem cells could provide insights to design and breed plants tolerant to environmental challenges caused by the climate change.
Oncogenic RAS instructs morphological transformation of human epithelia via differential tissue mechanics
Authors: Nyga A. , Muñoz J. , Dercksen S. , Fornabaio G. , Uroz M. , Trepat X. , Baum B. , Matthews H. , Conte V. 
Published: January 2021

AbstractThe RAS proto-oncogene is a critical regulator of cell state, morphology and mechanics, and plays a key role in cancer progression. Here, by using a human epithelial model in vitro, we ask how morpho-mechanical changes driven by oncogenic RAS activation at the level of individual cells are collectively integrated to drive changes in tissue behaviour. We found that the uniform oncogenic expression of HRAS.V12 in confined epithelial monolayers causes reproducible changes in the structure and organization of the tissue, which acquires a transitory bilayered morphology. RAS-driven bilayering associates with reproducible layer-specific differences in cell-cell contractility and cell-matrix forces. These drive the initially flat tissues to form three-dimensional structures mimicking some of the behaviours seen in human cancers. Our findings establish a physical mechanism of cellular collectives through which uniform expression of RAS can be interpreted differently in different places of the same tissue to regulate its physiological and pathological morphology.
Txikispora philomaiosn. sp., n. g., a Micro-Eukaryotic Pathogen of Amphipods, Reveals Parasitism and Hidden Diversity in Class Filasterea
Authors: Urrutia Ander , Mitsi Konstantina , Foster Rachel , Ross Stuart , Carr Martin , Marigomez Ionan , Leger Michelle M. , Ruiz-Trillo Iñaki , Feist Stephen W. , Bass David 
Published: January 2021

ABSTRACTThis study provides a morphological, ultrastructural, and phylogenetic characterization of a novel micro-eukaryotic parasite (2.3-2.6 µm) infecting generaEchinogammarusandOrchestia. Longitudinal studies across two years revealed that infection prevalence peaked in late April and May, reaching 64% inEchinogammarussp. and 15% inOrchestiasp., but was seldom detected during the rest of the year. The parasite infected predominantly haemolymph, connective tissue, tegument, and gonad, although hepatopancreas and nervous tissue were affected in heavier infections, eliciting melanization and granuloma formation. Cell division occurred inside walled parasitic cysts, often within host haemocytes, resulting in haemolymph congestion. Small subunit (18S) rRNA gene phylogenies including related environmental sequences placed the novel parasite as a highly divergent lineage within Class Filasterea, which together with Choanoflagellatea represent the closest protistan relatives of Metazoa. We describe the new parasite asTxikispora philomaiosn. sp. n. g., the first confirmed parasitic filasterean lineage, which otherwise comprises four free-living flagellates and a rarely observed endosymbiont of snails. Lineage-specific PCR probing of other hosts and surrounding environments only detectedT. philomaiosin the platyhelminthProcerodessp. We expand the known diversity of Filasterea by targeted searches of metagenomic datasets, resulting in 13 previously unknown lineages from environmental samples.
Antifungal activity of Propranolol againstFusariumkeratitis isolates from the Mycotic Ulcer Treatment Trial (MUTT) and the United States
Authors: Bao Ruina , Ross Brandon S. , Perez Cecilia G. , Poimenidou Galini , Prajna N. Venkatesh , Cramer Robert A. , Zegans Michael E. 
Published: January 2021

SYNOPSISBackgroundFusariumkeratitis is an infection of the cornea that often results in corneal perforation requiring corneal transplantation even with topical ocular antifungal therapy. The polyene natamycin remains the current antifungal of choice forFusariumkeratitis, but prompt sterilization of the cornea is often not achieved with contemporary therapy. Recently, natamycin synergy with the beta-adrenergic antagonist timolol againstFusariumspecies was reported.ObjectiveOur objective in this study was to characterize thein vitroantifungal effects of additional beta-adrenergic antagonists alone or in combination with natamycin onFusariumkeratitis isolates from the Mycotic Ulcer Treatment Trial (MUTT) and USA.MethodsMicrobroth dilution assays were used to determine the minimal inhibitory concentration (MIC) of beta-adrenergic antagonists against 18Fusarium spp. keratitis (10 from MUTT, 8 from USA) and 3Aspergillus fumigatusisolates. The fractional inhibitory concentration index (FICI) was calculated to assess interactions with natamycin.ResultsMost beta-blockers did not show antifungal activity or synergy with natamycin with the exception of propranolol. A racemic mix of propranolol had fungicidal activity with MIC between 31 and 83 μg/mL for theFusariumisolates. The MIC of the less cardioactive R enantiomer was lower (27-83 μg/mL) than the MIC of the S enantiomer (42-104 μg/mL). The MICs of both propranolol and natamycin were lower in combination but were not synergistic. The MIC of propranolol was 156 μg/mL for theA. fumigatusisolates.ConclusionsPropranolol has intrinsicin vitrofungicidal activity and lowers the MIC of natamycin. Both the R and S enantiomers of propranolol had antifungal activity with the MIC modestly but significantly lower for R-propranolol. These findings have relevance both for the treatment of fungal keratitis and of glaucoma in the setting of fungal keratitis. Further study of propranolol’s antifungal activity may lead to a novel treatment for fungal keratitis and possibly other fungal infections.Trial RegistrationClinicalTrials.gov Identifier:NCT00997035(MUTT Trial)
Global analysis of cell behavior and protein localization dynamics reveals region-specific functions for Shroom3 and N-cadherin during neural tube closure
Authors: Baldwin Austin T. , Kim Juliana , Wallingford John B. 
Published: January 2021

AbstractFailures of neural tube closure are common and serious birth defects, yet we have a poor understanding of the interaction of genetics and cell biology during neural tube closure. Additionally, mutations that cause neural tube defects (NTDs) tend to affect anterior or posterior regions of the neural tube but rarely both, indicating a regional specificity to NTD genetics. To better understand the regional specificity of cell behaviors during neural tube closure, we analyzed the dynamic localization of actin and N-cadherin via high-resolution tissue-level time-lapse microscopy duringXenopusneural tube closure. To investigate the regionality of gene function, we generated mosaic mutations inshroom3, a key regulator or neural tube closure This approach elucidates new differences between cell behaviors during cranial/anterior and spinal/posterior neural tube closure, provides mechanistic insight into the function ofshroom3and demonstrates the ability of tissue-level imaging and analysis to generate cell-biological mechanistic insights into neural tube closure.
Coevolutionary Analysis and Perturbation-Based Network Modeling of the SARS-CoV-2 Spike Protein Complexes with Antibodies: Binding-Induced Control of Dynamics, Allosteric Interactions and Signaling
Authors: Verkhivker Gennady M. , Di Paola Luisa 
Published: January 2021

AbstractThe structural and biochemical studies of the SARS-CoV-2 spike glycoproteins and complexes with highly potent antibodies have revealed multiple conformation-dependent epitopes highlighting the link between conformational plasticity of spike proteins and capacity for eliciting specific binding and broad neutralization responses. In this study, we used coevolutionary analysis, molecular simulations, and perturbation-based hierarchical network modeling of the SARS-CoV-2 S complexes with H014, S309, S2M11 and S2E12 antibodies targeting distinct epitopes to explore molecular mechanisms underlying binding-induced modulation of dynamics, stability and allosteric signaling in the spike protein trimers. The results of this study revealed key regulatory centers that can govern allosteric interactions and communications in the SARS-CoV-2 spike proteins. Through coevolutionary analysis of the SARS-CoV-2 spike proteins, we identified highly coevolving hotspots and functional clusters forming coevolutionary networks. The results revealed significant coevolutionary couplings between functional regions separated by the medium-range distances which may help to facilitate a functional cross-talk between distant allosteric regions in the SARS-CoV-2 spike complexes with antibodies. We also discovered a potential mechanism by which antibody-specific targeting of coevolutionary centers can allow for efficient modulation of allosteric interactions and signal propagation between remote functional regions. Using a hierarchical network modeling and perturbation-response scanning analysis, we demonstrated that binding of antibodies could leverage direct contacts with coevolutionary hotspots to allosterically restore and enhance couplings between spatially separated functional regions, thereby protecting the spike apparatus from membrane fusion. The results of this study also suggested that antibody binding can induce a switch from a moderately cooperative population-shift mechanism, governing structural changes of the ligand-free SARS-CoV-2 spike protein, to antibody-induced highly cooperative mechanism that can better withstand mutations in the functional regions without significant deleterious consequences for protein function. This study provides a novel insight into allosteric regulatory mechanisms of SARS-CoV-2 S proteins, showing that antibodies can modulate allosteric interactions and signaling of spike proteins, providing a plausible strategy for therapeutic intervention by targeting specific hotspots of allosteric interactions in the SARS-CoV-2 proteins.
Deep Learning Achieves Neuroradiologist-Level Performance in Detecting Hydrocephalus Requiring Treatment
Authors: Huang Yu , Moreno Raquel , Malani Rachna , Meng Alicia , Swinburne Nathaniel , Holodny Andrei I , Choi Ye , Rusinek Henry , Golomb James B , George Ajax , Parra Lucas C , Young Robert J 
Published: January 2021

AbstractPurposeIn large clinical centers a small subset of patients present with hydrocephalus that requires surgical treatment. We aimed to develop a screening tool to detect such cases from the head MRI with performance comparable to neuroradiologists.MethodsWe leveraged 496 clinical MRI exams collected retrospectively at a single clinical site from patients referred for any reason. This diagnostic dataset was enriched to have 259 hydrocephalus cases. A 3D convolutional neural network was trained on 16 manually segmented exams (ten hydrocephalus) and subsequently used to automatically segment the remaining 480 exams and extract volumetric anatomical features. A linear classifier of these features was trained on 240 exams to detect cases of hydrocephalus that required treatment with surgical intervention. Performance was compared to four neuroradiologists on the remaining 240 exams. Performance was also evaluated on a separate screening dataset of 451 exams collected from a routine clinical population to predict the consensus reading from four neuroradiologists using images alone. The pipeline was also tested on an external dataset of 31 exams from a 2nd clinical site.ResultsThe most discriminant features were the Magnetic Resonance Hydrocephalic Index (MRHI), ventricle volume, and the ratio between ventricle and brain volume. At matching sensitivity, the specificity of the machine and the neuroradiologists did not show significant differences for detection of hydrocephalus on either dataset (proportions test, p > 0.05). ROC performance compared favorably with the state-of-the-art (AUC 0.90–0.96), and replicated in the external validation.ConclusionHydrocephalus cases requiring treatment can be detected automatically from MRI in a heterogeneous patient population based on quantitative characterization of brain anatomy with performance comparable to that of neuroradiologists.