bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osa-miR820 regulatory node primes rice plants to tolerate salt stress in an agronomically advantageous manner
Authors: Sharma Neha , Kumar Sudhir , Sanan-Mishra Neeti 
Published: January 2021

AbstractPlant microRNAs (miRs) play an important role in regulating gene expression under normal and stressful environments. Here we report the functional implications on the role of Osa-miR820, which can be grouped as a young, rice-specific miR. It is a member of the class II transposon-derived small RNA family and is processed as 21-nt and 24-nt length variants, respectively. Size of the miR820 family varies from 1 to 16 across the Oryza AA genomes. The 21–nt Osa-miR820 negatively regulates ade novomethylase, OsDRM2 (domains rearranged methyl transferase) that prevents methylation of the CACTA transposon loci in the rice genome. In an earlier report we have detailed the expression profiles of Osa-miR820 and its target in abiotic stress responses using rice varieties exhibiting varying response to salt stress. In this study, artificial miR based approach was employed to specifically overexpress 21-nt Osa-miR820 in rice plants (OX-820). These plants exhibited enhanced vigour, ~25-30% increase in the number of spikelets per panicle and increased grain filling, under normal and salt stress conditions. The OX-820 lines showed a better water use efficiency and higher proline accumulation under salt stress. These plants can serve as a useful source for dissecting the molecular machinery governed by Osa-miR820:DRM2 node to prime tolerance to salt stress in an agronomically advantageous manner.
Targeted sensors for glutamatergic neurotransmission
Authors: Hao Yuchen , Toulmé Estelle , König Benjamin , Rosenmund Christian , Plested Andrew J.R. 
Published: January 2021

AbstractOptical report of neurotransmitter release allows visualization of excitatory synaptic transmission. Sensitive genetically-encoded glutamate reporters operating with a range of affinities and emission wavelengths are available. However, without targeting to synapses, the specificity of the fluorescent signal is uncertain, compared to sensors directed at vesicles or other synaptic markers. We fused the state-of-the-art reporter iGluSnFR to glutamate receptor auxiliary proteins in order to target it to postsynaptic sites. Chimeras of Stargazin and gamma-8 that we named SnFR-γ2 and SnFR-γ8, retained function and reported spontaneous glutamate release in hippocampal cells, with apparently diffraction-limited spatial precision. In autaptic neurons on micro island cultures, evoked release could be quantitatively detected at tens of synapses in a field of view whilst evoked currents were recorded simultaneously. These experiments revealed a specific postsynaptic deficit from Stargazin overexpression, resulting in synapses with normal release but without postsynaptic responses. This defect was reverted by delaying overexpression. By working at different calcium concentrations, we determined that SnFR-γ2 is a linear reporter of the global quantal parameters and short term synaptic plasticity, whereas iGluSnFR is not. On average, half of iGluSnFR regions of interest showing evoked fluorescence changes had intense rundown, whereas less than 5% of SnFR-γ2 ROIs did. We provide an open-source analysis suite for extracting quantal parameters including release probability from fluorescence time series of individual and grouped synaptic responses. Taken together, postsynaptic targeting improves several properties of iGluSnFR and further demonstrates the importance of subcellular targeting for optogenetic actuators and reporters.
Gradual opening of Smc arms in prokaryotic condensin
Authors: Nunez Roberto Vazquez , Polyhach Yevhen , Soh Young-Min , Jeschke Gunnar , Gruber Stephan 
Published: January 2021

SummaryMulti-subunit SMC ATPases control chromosome superstructure apparently by catalyzing a DNA-loop-extrusion reaction. SMC proteins harbor an ABC-type ATPase ‘head’ and a ‘hinge’ dimerization domain connected by a coiled coil ‘arm’. Two arms in a SMC dimer can co-align, thereby forming a rod-shaped particle. Upon ATP binding, SMC heads engage, and arms are thought to separate. Here, we studied the shape ofB. subtilisSmc-ScpAB by electron-spin resonance spectroscopy. Arm separation was readily detected proximal to the heads in the absence of ligands, while separation near the hinge largely depended on ATP and DNA. Artificial blockage of arm opening eliminated DNA stimulation of ATP hydrolysis, but did not prevent basal ATPase activity. We identified an arm-to-arm contact as being important for controlling the molecular transformations. Point mutations at this arm interface eliminate Smc function. We propose that partially open, intermediary conformations provide directionality to SMC DNA translocation by binding suitable DNA substrates.
DAP5 enables translation re-initiation on structured messenger RNAs
Authors: Weber Ramona , Kleemann Leon , Hirschberg Insa , Chung Min-Yi , Valkov Eugene , Igreja Cátia 
Published: January 2021

SummaryHalf of mammalian transcripts contain short upstream open reading frames (uORFs) that potentially regulate translation of the downstream coding sequence (CDS). The molecular mechanisms governing these events remain poorly understood. Here we find that the non-canonical initiation factor Death-associated protein 5 (DAP5 or eIF4G2) is selectively required for re-initiation at the main CDS following uORF translation. Using ribosome profiling and luciferase-based reporters coupled with mutational analysis we show that DAP5-mediated re-initiation occurs on messenger RNAs (mRNAs) with long, structure-prone 5′ leader sequences and persistent uORF translation. These mRNAs preferentially code for signalling factors such as kinases and phosphatases. We also report that cap/eIF4F- and eIF4A-dependent recruitment of DAP5 to the mRNA facilitates re-initiation by unrecycled post-termination 40S subunits. Our study reveals important mechanistic insights into how a non-canonical translation initiation factor involved in stem cell fate shapes the synthesis of specific signalling factors.
Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients
Authors: Desai Sanket , Rane Aishwarya , Joshi Asim , Dutt Amit 
Published: January 2021

AbstractWe present an updated version of our automated computational pipeline, Infection Pathogen Detector IPD 2.0 with a SARS-CoV-2 module, to perform genomic analysis to understand the pathogenesis and virulence of the virus. Analysing the currently available 208911 SARS-CoV2 genome sequences (as accessed on 28 Dec 2020), we generate an extensive database of sample- wise variants and clade annotation, which forms the core of the SARS-CoV-2 analysis module of the analysis pipeline. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil along with data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. Thus, the persistence of pandemic may lead to the emergence of newer regional strains with improved fitness. IPD 2.0 also adopts the recent dynamic clade nomenclature and shows improvement in accuracy of clade assignment, processing time and portability, to its predecessor and thus could be a vital tool to help facilitate genomic surveillance in a population to identify variants involved in breakthrough infections.
Optimum growth temperature declines with body size within fish species
Authors: Lindmark Max , Ohlberger Jan , Gårdmark Anna 
Published: January 2021

AbstractAccording to the temperature-size rule, warming of aquatic ecosystems is generally predicted to increase individual growth rates but reduce asymptotic body sizes of ectotherms. However, we lack a comprehensive understanding of how growth and key processes affecting it, such as consumption and metabolism, depend on both temperature and body mass within species. This limits our ability to inform growth models, link experimental data to observed growth patterns, and advance mechanistic food web models. To examine the combined effects of body size and temperature on individual growth, as well as the link between maximum consumption, metabolism and body growth, we conducted a systematic review and compiled experimental data on fishes from 52 studies that combined body mass and temperature treatments. By fitting hierarchical models accounting for variation between species, we estimated how maximum consumption and metabolic rate scale jointly with temperature and body mass within species. We found that whole-organism maximum consumption increases more slowly with body mass than metabolism, and is unimodal over the full temperature range, which leads to the prediction that optimum growth temperatures decline with body size. Using an independent dataset, we confirmed this negative relationship between optimum growth temperature and body size. Small individuals of a given population may therefore exhibit increased growth with initial warming, whereas larger conspecifics could be the first to experience negative impacts of warming on growth. These findings help advance mechanistic models of individual growth and food web dynamics and improve our understanding of how climate warming affects the growth and size structure of aquatic ectotherms.
Loss of the DYRK1A protein kinase results in reduction of ribosomal protein genes expression, ribosome mass and translation defects
Authors: Vona Chiara Di , Barba Laura , Ferrari Roberto , de la Luna Susana 
Published: January 2021

ABSTRACTRibosomal proteins (RPs) are evolutionary conserved proteins that are essential for protein translation. RP expression must be tightly regulated to ensure the appropriate assembly of ribosomes and to respond to the growth demands of cells. The elements regulating the transcription of RP genes (RPGs) have been characterized in yeast andDrosophila, yet how cells regulate the production of RPs in mammals is less well understood. Here, we show that a subset of RPG promoters is characterized by the presence of the palindromic TCTCGCGAGA motif and marked by the recruitment of the protein kinase DYRK1A. The presence of DYRK1A at these promoters is associated with enhanced binding of the TATA-binding protein, TBP, and it is negatively correlated with the binding of the GABP transcription factor, establishing at least two clusters of RPGs that could be coordinately regulated. However, DYRK1A silencing leads to a global reduction of RPGs, mRNA pointing at DYRK1A activities beyond those dependent on its chromatin association. Significantly, cells in which DYRK1A is depleted have reduced RP levels, fewer ribosomes, reduced global protein synthesis and smaller size. We therefore propose a novel role for DYRK1A in coordinating the expression of genes encoding RPs, thereby controlling cell growth in mammals.
Purification and partial characterization of a high hemagglutinating chitin-binding lectin fromAponogeton natanstubers
Authors: Dara Shashikanth , Lavudi Harikrishna Naik , Rao Venkateswara , Badithi Nanibabu , Kottapalli Seshagirirao 
Published: January 2021

AbstractA novel chitin-binding lectin was isolated from the tubers of a plantAponogeton natansfrom the monocot family Aponogetonaceae, designated as ANTL (Aponogeton natanstuber lectin). The lectin agglutinated both untreated and trypsin-treated rabbit erythrocytes, as well as human blood cells of groups A, B and O with different specificities. Lectin activity is inhibited by the oligomers ofN-acetylglucosamine. ANTL is a dimeric glycoprotein with molecular weight of ∼66 KDa and has two identical sub-units of 33 KDa. The carbohydrate percent is 8.2% of the total lectin. The lectin was thermo stable up to 50°C with broad pH optima (pH 4–10). ANTL is found to be potent mitogen for normal murine and human lymphocytes at the concentration as low as 1 µg/ml. Cytotoxic studies of the lectin on human U 266 cell lines has revealed that there is 50% decrease in the proliferation. The confirmation of both the hemagglutination and mitogenic proliferation activity suggests that ANTL is a Chitin-binding lectin with diverse functions. The pharmacological relevance of ANTL as a potent mitogen with some cytotoxic effect in certain cell lines are reported for the first time.HighlightsA novel chitin-binding lectin was purified from the tuber extracts ofAponogeton natans(ANTL) in a single step on chitin column by affinity chromatography.ANTL is a dimeric glycoprotein with a molecular weight of ∼66 KDa with high hemagglutination activity towards rabbit erythrocytes.The cytotoxic effect of ATNL on human cell lines U266 has shown 50 % inhibition of their proliferation.ANTL displayed potent mitogenic response towards murine and human peripheral blood mononuclear cells.
Growth and reproduction trade‐offs can estimate previous reproductive history in alpine ungulates
Authors: Larue Benjamin , Pelletier Fanie , Côté Steeve D. , Hamel Sandra , Festa‐Bianchet Marco 
Published: January 2021

Abstract

Life‐history theory predicts energy allocation trade‐offs between traits when resources are limited. If females reduce allocation to growth when they reproduce, annual growth could reveal past reproductive effort, which would be useful to assess population dynamics and harvest sustainability. The potential and accuracy of growth measures for predicting reproductive success have rarely been evaluated with individuals with known reproductive history.

We used long‐term monitoring of annual growth and reproduction of marked female bighorn sheep and mountain goats, two species in which primiparity normally occurs well before growth completion, to evaluate growth versus reproduction trade‐offs and their potential for predicting reproductive history of young females using mixed models and 10‐fold block cross‐validation.

We documented a significant reduction in mass gain and horn growth in young reproducing females of both species. This trade‐off was affected by individual differences in energy acquisition and allocation because population density and previous allocation to growth affected the trade‐off. We then parameterized models to predict individual reproductive history of young females based on the growth traits subjected to a reproductive trade‐off.

The accuracy of predictive models ranged from 85.2% to 91.0% across species and traits, indicating that growth is a good predictor of reproductive history. This method is especially useful for population management of species with traits that form permanent visible yearly annuli because they retain a record of annual growth that allows retrospective estimation of reproductive history over multiple years.

Synthesis and applications. We show that because growth significantly decreased in years of allocation to reproduction, annual growth increments provide insights on reproductive history of young females. Population or temporal differences in reproduction of young females affect demographic rates and sustainable harvest. Growth measures of traits that form yearly annuli, such as teeth and horns, could be easily obtained at a low cost from animals harvested or found dead in multiple species. Thus, predictive models of reproductive history based on annual growth could assist conservation and management in a broad range of species.
FOUR MODES OF NEIGHBOURHOOD GOVERNANCE: The View from Nanjing, China
Authors: Wang Ying , Clarke Nick 
Published: January 2021

AbstractIn a context of global moves towards decentralization and neighbourhood governance, this article focuses on neighbourhood governance in Nanjing, China. We draw on interviews and observations in 32 neighbourhoods to examine how neighbourhood governance plays out in different neighbourhoods. We identify and describe four modes of governance—collective consumption, service privatization, civic provision and state‐sponsored—to argue that neighbourhood governance develops on the ground in diverse and complex ways, necessitating scholars to be cautious when seeking to generalize about it at the scale of the city, let alone that of the nation‐state or the globe. We argue that relationships between actors are important units of analysis when considering how effective governance is achieved in different neighbourhoods; diversity and complexity in neighbourhood governance partly reflect the role of the state in these relationships. In turn the role of the state partly reflects processes of policy evolution in particular neighbourhoods.
The Asymmetric Effect of Reporting Flexibility on Priced Risk
Authors: BLOOMFIELD MATTHEW J. 
Published: January 2021

AbstractMost firms covary more positively with downmarkets than upmarkets—a phenomenon I refer to as “risk asymmetry.” I predict and find that risk asymmetry is caused, at least in part, by a firm's ability to selectively obfuscate poor performance. Risk asymmetry decreases significantly when firms are required to adhere to the more stringent auditing standards mandated under Section 404 of the Sarbanes‐Oxley Act, however this decrease is more muted for firms with weak internal controls. Consistent with my predictions, these patterns are stronger for more market‐sensitive firms and weaker for firms that include relative performance evaluation in their CEOs' pay packages. Taken together with prior literature (which documents that risk asymmetry is priced), my results suggest that a firm can lower its cost of capital by credibly reducing its ability to obfuscate value‐relevant information.
Comparative transcriptome analysis of thiamethoxam susceptible and resistant Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae), using RNA‐sequencing
Authors: Chen Xue Dong , Neupane Surendra , Gill Torrence A. , Gossett Hunter , Pelz‐Stelinski Kirsten S. , Stelinski Lukasz L. 
Published: January 2021

AbstractAsian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), transmits the causal pathogen of huanglongbing and is a global pest of citrus. D. citri populations exhibit resistance to multiple insecticide modes of action in areas where these chemicals have been overused. We performed genome‐wide transcriptional analysis for two field populations of D. citri (Wauchula and Lake Alfred, Florida, USA) that exhibit 1300‐fold resistance to the neonicotinoid insecticide, thiamethoxam, and compared it to that of susceptible psyllids collected from the same area and without imposed selection. The Lake Alfred population responded to insecticide resistance by up‐regulation of 240 genes and down‐regulation of 148 others. The Wauchula population exhibited similar patterns to the Lake Alfred population with up‐regulation of 253 genes and down‐regulation of 115 others. Gene Ontology annotation associated with cellular processes, cell, and catalytic activity were assigned to differentially expressed genes (DEGs). The DEGs from Lake Alfred and Wauchula populations were mapped to Kyoto Encyclopedia of Gene and Genomes pathways and implicated enrichment of metabolic pathways, oxidative phosphorylation, extracellular matrix‐receptor interaction, terpenoid backbone biosynthesis, and insect hormone biosynthesis in the resistant populations. Up‐regulation of 60s ribosomal proteins, UDP‐gluscoyltransferases, cytochrome c oxidases, and CYP and ABC transporters among thiamethoxam‐resistant D. citri implicates a broad array of novel and conventionally understood resistance mechanisms.
Immune checkpoint inhibitors‐induced eosinophilic pneumonia: A case report
Authors: Hara Kanako , Yamasaki Kei , Tahara Masahiro , Kimuro Rieko , Yamaguchi Yudai , Suzuki Yu , Kawabata Hiroki , Kawanami Toshinori , Fujimoto Naohiro , Yatera Kazuhiro 
Published: January 2021

AbstractA 78‐year‐old male with renal cell carcinoma was treated with combined immunotherapy of nivolumab and ipilimumab. After four courses of the treatment, a chest computed tomography (CT) revealed newly formed ground‐glass opacities (GGOs) in both the lower lung lobes; drug‐induced pneumonia was speculated. Eosinophil counts were elevated in both peripheral blood and bronchoalveolar lavage fluid. Both the immune checkpoint inhibitors (ICIs) were discontinued, following which the chest CT findings improved. Based on these findings, a diagnosis of ICI‐induced eosinophilic pneumonia was made. Hence, clinicians should be wary of the risk of eosinophilic pneumonia during ICI‐anticancer therapy.
Identifying prostate cancer in men with non‐suspicious multi‐parametric magnetic resonance imaging of the prostate
Authors: Doan Paul , Lahoud John , Kim Lawrence , Patel Manish I. 
Published: January 2021

AbstractBackgroundTo formulate clinical pathways for identifying clinically significant prostate cancer (csPC) and avoiding insignificant prostate cancer (isPC) in those without suspicious regions of interest on multi‐parametric magnetic resonance imaging (mpMRI) of the prostate.MethodsA retrospective review identified patients with negative mpMRI who underwent subsequent transperineal prostate biopsy across two centres. Patient characteristics and association with biopsy results were evaluated using univariate and multivariate regression analyses.ResultsA total of 144 patients were identified as having negative mpMRI and undergoing subsequent transperineal prostate biopsy; 18% (25/144) of the cohort were found to have csPC. Logistic regression analysis failed to identify statistically significant predictive factors. In this cohort, if all patients with prostate‐specific antigen > 3.0 were biopsied the least amount of csPC is missed, at 20% (5/25) however all isPC would be diagnosed. The least amount of isPC is diagnosed with a biopsy threshold of >15% from the European Randomized Study of Screening for Prostate Cancer calculator with 20% (5/25) of isPC diagnoses made however only 10.5% (2/19) csPC would be diagnosed. A biopsy threshold of >5% risk reduces the number of csPC missed to 37% (7/19) however increases isPC diagnoses to 54% (13/24) of the population.ConclusionFalse‐negative rates of prostate MRI for csPC are significant within our cohort at 18%. The decision to biopsy should be made in conjunction with a risk profile acceptable by the patient and clinician. The current study demonstrates that there is a need to balance the risk of missing csPC and harm of diagnosing isPC.
Abdominal wall heterotopic ossification following damage control laparotomy: an unusual bone to pick
Authors: Jacob Mathew O. , Reddipogu Jonathan , Jacob Jacob 
Published: January 2021

AbstractBackgroundHeterotopic ossification (HO) refers to the development of extra‐skeletal bone in muscle and soft tissues, following tissue insult secondary to surgery or trauma. This pathological process is considered as the result of severe inflammatory cell cascade initiated after local trauma and subsequent attempt at tissue repair involving resident mesenchymal cells. We present a series of 12 cases of abdominal HO (AHO), over 8 years, following damage control laparotomies (DCLs).MethodsMedical records of 50 patients who underwent DCLs at Alice Springs Hospital between 2010 and 2018 were retrospectively reviewed for AHO. Demographic data were extracted. Abdominal X‐rays and computed tomography scans of 47 patients were reviewed for AHO.ResultsTwelve patients (25%) developed AHO of varying diversity ranging from small insignificant lesions to clinically palpable lesions in the abdominal wall. Data revealed relatively younger male preponderance. DCL for severe acute pancreatitis (SAP) was associated with AHO (P < 0.1, 90% CI). Longer periods of ventilation, intensive care unit stay and admission to hospital were strongly associated with AHO (P < 0.01, 95% CI). Occurrence of AHO with SAP was significantly higher compared to patients without SAP (relative risk 3.54, P < 0.001). Only two patients required surgical excision of HO prior to definitive closure of the abdomen.ConclusionThe authors conclude that AHO occurred more frequently in younger males. DCL for SAP was a significant risk factor. Extended periods of ventilation, intensive care unit stay and hospital admission were strongly associated with the development of AHO. Preoperative detection of HO is essential prior to planning definitive closure of the abdomen.