bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the regulatory role of miRNAs responsible for proanthocyanidin biosynthesis in the underutilized legume Psophocarpus tetragonolobus (L.) DC
Authors: Nayak Sagar Prasad , Prasad Priti , Singh Vinayak , Tripathi Abhinandan Mani , Bag Sumit Kumar , Mohanty Chandra Sekhar 
Published: July 2021

AbstractThe underutilized legume winged bean (Psophocarpus tetragonolobus (L.) DC.) is deposited with various degrees of proanathocyanidin (PA) or condensed tannin (CT) on its seed-coat. PA content of two different lines of P. tetragonolobus was estimated and accordingly they were denoted as high-proanthocyanidin containing winged bean (HPW) and low-proanthocyanidin containing winged bean (LPW). The level of PA-content varied as 59.23 mg/g in HPW and 8.68 mg/g in LPW when estimated through vanillin-HCl assay. The identification and quantification of catechin and epigallocatechin gallate were estimated in a range of 63.8 mg/g and 2.3mg/g respectively in HPW whereas only epigallocatechin gallate was reported in LPW line with a value of 3 mg/g. A comparative miRNA profiling of the leaf-tissues of these contrasting lines of P. tetragonolobus revealed a total of 139 mature miRNAs. Isoforms of known novel miRNAs were also identified in this study. Differentially expressed miRNAs e.g., miR156, miR396, miR4414b, miR4416c, miR894, miR2111 and miR5139 were validated through qRT-PCR analysis. Target prediction of the identified miRNAs especially miR156, miR396, miR4416b shows that they have a potential role in the proanthocyanidin biosynthesis of P. tetragonolobus. The study will provide the basis for understanding the role of miRNAs in regulating the biosynthesis of proanthocyanidin.
Important Docking study of Structure of Plasmodium falciparum thioredoxin reductase-thioredoxin complex: the case of potent drug Telatinib, a small molecule angiogenesis inhibitor
Authors: Ferrari Ivan Vito 
Published: July 2021

AbstractBackgroundOver the last decades, malaria parasites have been rapidly developing resistance against antimalarial drugs, which underlines the need for novel drug targets. Thioredoxin reductase (TrxR) is crucially involved in redox homeostasis and essential for Plasmodium falciparum. In this communication, we report first time important Docking study by in Silico approach, using AutoDock Vina. After a selective analysis of over 300 drugs, processed with Pyrx (a Virtual Screening software into the active site of protein (ID PDB 4J56 Thioredoxin reductase 2 Chain A), we noticed excellent value of Binding Energy of Telatinib estimated by Pyrx software. These results are comparable to the crystallized ligand FAD (FLAVIN-ADENINE DINUCLEOTIDE) completed in the above-mentioned protein. Indeed, from the results of Autodock Vina, Telatinib an inhibitor of tyrosine kinases, has excellent a Binding affinity value, ca. −12 kcal/mol.
High consistency of trophic niches in soil microarthropod species (Oribatida, Acari) across soil depth and forest type
Authors: Lu Jing-Zhong , Cordes Peter , Maraun Mark , Scheu Stefan 
Published: July 2021

AbstractIndividuals of species may differ in resource use within and between populations. High intraspecific variation in resource use may hamper the co-existence of species in natural communities. To better understand the intraspecific variation in trophic niches of oribatid mites (Oribatida, Acari), we quantified stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) of 40 Oribatida species that co-occurred in litter and soil of five forest types (European beech, Douglas fir, Norway spruce, two beech–conifer mixed forests) covering a range of environmental conditions. We found that although stable isotopes in litter and soil varied among forest types, δ13C and δ15N values of Oribatida and their trophic niches were remarkably stable between litter and soil, and also among forest types. We considered four trophic guilds of Oribatida representing the guild composition of the regional species pool; notably, trophic niches of Oribatida guilds also did not vary with soil depth. Furthermore, δ13C of Oribatida was more enriched (detrital shift) in European beech than in coniferous forests, but δ15N of Oribatida did not vary among forest types, indicating that basal resources of Oribatida are variable, but trophic positions are highly consistent across forest ecosystems. We conclude that trophic positions of Oribatida species and guilds are consistent across different forest types, and Oribatida species occupy virtually identical trophic niches irrespective of the soil depth they are colonizing. Overall, the results suggest that low intraspecific variability facilitates Oribatida niche differentiation and species coexistence.
Variability of pollen grains quality in oat amphiploids and their parental species
Authors: Tomaszewska Paulina , Kosina Romuald 
Published: July 2021

AbstractThe reproductive potential of oat species and their hybrid progeny (amphiploids) was evaluated during three vegetation seasons. Morphotypes and viability of pollen grains were described by means of correlations and regression, while relationships between taxa were analysed with the use of numerical taxonomy methods. Size of pollen grains varied between the growing seasons, but the relations between the taxa appeared to be stable. Viability of pollen grains was environmentally modified and showed no correlation with pollen length. In an ordination space, amphiploids were discriminated from parental species. In both group of plants, a positive correlation between the pollen size and the level of ploidy was maintained; however, along a regression line, amphiploids were located among species with a high level of ploidy and were extreme units deviating from the regression line. Developmental anomalies of pollen grains had a low frequency, with the formation of micrograins being the most common event. Such a pattern of development can prove that some pollen grains were chromosomally unbalanced. Anomalous morphotypes of pollen were more common in hybrid types than in species, including pollens with many poruses, which were found only in amphiploids. Frequencies of multiporate grains and micropollens were strongly correlated. In an ordination space, monoporate types (species) were discriminated from multiporate types (amphiploids). In general, the high level of pollen viability in amphiploids can prove their genomic stabilisation through many generations of their reproduction.
Modelling time evolution of in blood alcohol concentration
Authors: Gelabert Antoni Oliver 
Published: July 2021

AbstractA theoretical model based on mass conservation is proposed to predict blood alcohol concentration (BAC) over time. The proposed model takes as input the body parameters, the data timing for each drink, as well as his alcoholic strength and ingested amount. Three test cases with variations are presented and discussed. The results given are obtained by solving numerically the equation proposed. The solution predicts a well located alcohol peak and a reasonable time of alcohol body cleaning. This model represents a first order approach to a complex problem. Similar scenarios, like, for instance, drug concentrations can be modelled by using the same concept. The proposed model has been implemented on easy-to-use program COGORZA, which source code is available online at https://github.com/tonibois/Cogorza.
IRI-CCE: A Platform for Evaluating CRISPR-based Base Editing Tools and Its Components
Authors: Shelake Rahul Mahadev , Pramanik Dibyajyoti , Kim Jae-Yean 
Published: July 2021

AbstractRapid assessment of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated Cas protein)-based genome editing (GE) tools and their components are critical aspects for successful applications in different organisms. In many bacteria, double-stranded breaks (DSBs) generated by CRISPR/Cas tool generally cause cell death due to the lack of an efficient non-homologous end-joining pathway and restricts its use. CRISPR-based DSB-free base editors (BEs) have been applied for precise nucleotide editing in bacteria, which does not need to make DSBs. However, optimization of newer BE tools in bacteria is challenging owing to the toxic effects of BE reagents expressed using strong promoters. Improved variants of two main BEs capable of converting C-to-T (CBE) and A-to-G (ABE) have been recently developed but yet to be tested in bacteria. Here, we report a platform for in vivo rapid investigation of CRISPR-BE components in Escherichia coli (IRI-CCE) comprising different combinations of promoters/terminators. We demonstrate the use of IRI-CEE to characterize different variants of CBEs (PmCDA1, evoCDA1, APOBEC3A) and ABEs (ABE8e, ABE9e), exhibiting that each independent BE has its specific editing pattern for a given target site and promoter type. Additionally, the IRI-CCE platform offers a rapid way to screen functional gRNAs. In summary, CRISPR-BE components expressed by promoters of different strengths in the IRI-CCE allow an analysis of various BE tools, including cloned biopart modules and gRNAs.
A General Biphasic-Bodyweight Model for Scaling Basal Metabolic Rate, Glomerular Filtration Rate and Drug Clearance from Birth to Adulthood
Authors: Hu Teh-Min 
Published: July 2021

AbstractUnderstanding the maturation process of human physiology and metabolism has broad medical and pharmaceutical implications. Age and bodyweight are frequently considered as separate variables in modeling the dynamical changes of human organ functions and of drug clearance from birth to adulthood. The objective of this study is to propose a unified, continuous and bodyweight-only equation to quantify the changes of human basal metabolic rate (BMR), glomerular filtration rate (GFR) and drug clearance (CL) from infancy to adulthood. The BMR datasets were retrieved from a comprehensive historical database of male and female subjects (0.02 to 64 years). The CL datasets for 17 drugs and the GFR dataset were generated from age-incorporated maturation-and-growth models with reported parameter values. The model used in the simulation is independent of the proposed model. A statistical approach was used to simulate the model generated CL and GFR data for a hypothetical population with 26 age groups (ranging from 0 to 20 years). Besides, individual CL data for one drug, and sparse PBPK-modeled CL values for two drugs were also included for analysis. A 4-parameter, mixed-allometry equation with two power-law functions of bodyweight was proposed and evaluated as a general model using nonlinear regression and dimensionless analysis. All datasets universally reveal biphasic curves with two distinct linear segments on log-log plots. Compared with simple allometry, the biphasic model fits satisfactorily to all datasets (based on Akaike’s Information Criterion and residual plots). The biphasic equation consists of two reciprocal allometric terms that asymptotically determine the overall curvature. The fitting results show a superlinear scaling phase (slope >1; ca. 1.5 – 3.5) below the characteristic bodyweight at the phase transition; and above which, a sublinear scaling phase (slope <1; ca. 0.5 – 0.7) is evident. The phase-transition bodyweight is ranging from 5 to 20 kg (corresponding to 0.5 – 9 years) and the mean value is around 10 kg (∼2 years) for all data sets. The dimensionless analysis generalizes, and offers quantitative realization of, the maturation and growth process. In conclusion, the proposed mixed-allometry equation is a generic model that quantitatively describes the phase transition occurring in the human maturation process of BMR, GFR and drug CL.
MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities
Authors: Wang Ziye , Huang Pingqin , You Ronghui , Sun Fengzhu , Zhu Shanfeng 
Published: July 2021

AbstractBinning is an essential procedure during metagenomic data analysis. However, the available individual binning methods usually do not simultaneously fully use different features or biological information. Furthermore, it is challenging to integrate multiple binning results efficiently and effectively. Therefore, we developed an ensemble binner, MetaBinner, which generates component results with multiple types of features and utilizes single-copy gene (SCG) information for k-means initialization. It then utilizes a two-step ensemble strategy based on SCGs to integrate the component results. Extensive experimental results over three large-scale simulated datasets and one real-world dataset demonstrate that MetaBinner outperforms other state-of-the-art individual binners and ensemble binners. MetaBinner is freely available athttps://github.com/ziyewang/MetaBinner.
The northern gene flow into southeastern East Asians inferred from genome-wide array genotyping
Authors: He Guanglin , Li Yingxiang , Zou Xing , Yeh Hui-Yuan , Tang Renkuan , Wang Peixin , Bai Jingya , Yang Xiaomin , Wang Zheng , Guo Jianxin , Chen Jinwen , Chen Jing , Yang Meiqing , Zhao Jing , Sun Jin , Zhu Kongyang , Ma Hao , Wang Rui , Yang Wenjiao , Hu Rong , Wei Lan-Hai , Hou Yiping , Wang Mengge , Chen Gang , Wang Chuan-Chao 
Published: July 2021

ABSTRACTThe population history of Southeast China remains poorly understood due to the sparse sampling of present-day populations and far less modeling with ancient genomic data. We here newly reported genome-wide genotyping data from 207 present-day Han Chinese and Hmong-Mien-speaking She people from Fujian and Taiwan, southeast China. We co-analyzed with 66 early-Neolithic to Iron-Age ancient Fujian and Taiwan individuals obtained from literature to explore the genetic continuity and admixture based on the genetic variations of high-resolution time transect. We found the genetic differentiation between northern and southern East Asians defined by a north-south East Asian genetic cline and the studied southern East Asians were clustered in the southern end of this cline. We also found that southeastern coastal continental modern East Asians harbored the genetic differentiation with other southern Tai-Kadai, Hmong-Mien, Austronesian and Austroasiatic speakers, as well as geographically close Neolithic-to-Iron Age populations, but relatedly close to post-Neolithic Yellow River ancients, which suggested the influence of southward gene flow on the modern southern coastal gene pool. Besides, we also identified one new Hmong-Mien genetic cline in East Asia with the coastal Fujian She localizing at the intersection position between Hmong-Mien and Han clines in the principal component analysis. She people show stronger genetic affinity with southern East Asian indigenous populations with the main ancestry deriving from Hanben-related populations. The southeastern Han Chinese could be modeled with the primary ancestry deriving from the group related to the Yellow River Basin millet farmers and the remaining from groups related to southeastern ancient indigenous rice farmers, which was consistent with the northern China origin of modern southeastern Han Chinese and in line with the historically and archaeologically attested southward migrations of Han people and their ancestors. Interestingly, f4-statistics and three-way admixture model results showed both coastal ancient sources related to Austronesian speakers and inland ancient sources related to Austroasiatic speakers complexed the modern observed fine-scale genetic structure here. Our estimated north-south admixture time ranges based on the decay of the linkage disequilibrium spanned from the Bronze age to historic periods, suggesting the recent large-scale population migrations and subsequent admixture participated in the formation of modern Han in Southeast Asia.
Functional asymmetry and chemical reactivity of CsoR family persulfide sensors
Authors: Fakhoury Joseph N. , Zhang Yifan , Edmonds Katherine A. , Bringas Mauro , Luebke Justin L. , Gonzalez-Gutierrez Giovanni , Capdevila Daiana A. , Giedroc David P. 
Published: July 2021

AbstractCstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily that regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens. A cysteine thiol pair on CstR reacts with RSS to form a mixture of interprotomer di-, tri- and tetrasulfide crosslinks, which drives transcriptional derepression of CstR-regulated genes. In some bacteria, notably methicillin-resistant Staphylococcus aureus (MRSA), CstR and CsoR, a Cu(I)-sensor, exhibit no regulatory crosstalk in cells, despite maintaining an identical pair of cysteines. We report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, together with the first crystallographic structure of a CstR protein and mass spectrometry-based kinetic profiling experiments to obtain new insights into the molecular basis of RSS specificity in CstRs. The more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. This cysteine, C30 in SpCstR, is separated from the resolving thiol, C59’, by an Asn55’ wedge. Chemical reactivity experiments reveal a striking asymmetry of reactivity, preserved in all CstRs and with all oxidants tested; however, the distribution of crosslinked products varies markedly among CstRs. Substitution of N55 with Ala in SpCstR significantly impacts the distribution of species, despite adopting the same structure as the parent repressor. We show that CstRs react with hydrogen peroxide, a finding that contrasts sharply with other structurally distinct persulfide sensors from Gram-negative bacteria. This suggests that other factors may enhance the specificity and repressor activity of CstRs in cells.
Towards an integrative multi-omics workflow
Authors: Jeanneret Florian , Gazut Stéphane 
Published: July 2021

AbstractThe advent of high-throughput techniques has greatly enhanced biological discovery. Last years, analysis of multi-omics data has taken the front seat to improve physiological understanding. Handling functional enrichment results from various biological data raises practical questions.We propose an integrative workflow to better interpret biological process insights in a multi-omics approach applied to breast cancer data from The Cancer Genome Atlas (TCGA) related to Invasive Ductal Carcinoma (IDC) and Invasive Lobular Carcinoma (ILC). Pathway enrichment by Over Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) has been conducted with both features information from differential expression analysis or selected features from multi-block sPLS-DA methods. Then, comprehensive comparisons of enrichment results have been carried out by looking at classical enrichment analysis, probabilities pooling by Stouffer’s Z scores method and pathways clustering in biological themes.Our work shows that ORA enrichment with selected sPLS-DA features and pathways probabilities pooling by Stouffer’s method lead to enrichment maps highly associated to physiological knowledge of IDC or ILC phenotypes, better than ORA and GSEA with differential expression driven features.
Connectivity between the hippocampus and default mode network during the relief – but not elicitation – of curiosity supports curiosity-enhanced memory enhancements
Authors: Murphy Charlotte , Ranganath Charan , Gruber Matthias J. 
Published: July 2021

AbstractConsistent with the idea that curiosity enhances information seeking, it has been shown that activity within both the dopaminergic circuit and hippocampus supports curiosity-enhanced learning. However, the role of whole-brain mechanisms involved in cognitive control (fronto-parietal network; FPN) and memory integration (default mode network; DMN) that might underpin curiosity states and their effects on memory remain elusive. We hypothesised that the FPN and DMN should distinguish between high- and low-curiosity conditions and be recruited more heavily for later remembered information associated with high-curiosity. Here, we used functional magnetic resonance imaging whilst participants completed a trivia paradigm, in which we presented trivia questions associated with high- and low-curiosity, followed by the associated answer. After a short delay, we tested memory for trivia answers. We adopted a network-based parcellation of the brain into subnetworks of the FPN and DMN to examine how neural activity within, and functional connectivity between, each subnetwork predicts curiosity-enhanced memory. Across elicitation and relief of curiosity, we found focal recruitment of FPNA and widespread recruitment of DMN subnetworks in support of curiosity and curiosity-enhanced memory. Most importantly, during the elicitation of curiosity, functional subcortical connectivity and across cortical networks, but not subcortical-cortical coupling, correlated with curiosity-enhanced memory. However, during the relief of curiosity, coupling between subcortical regions and DMNA emerged in support of curiosity-enhanced memory. Taken together, our results provide the first evidence about how neuromodulatory mechanisms via the hippocampal-dopaminergic circuit trigger states of curiosity and thereby communicate to higher-order cortical regions to facilitate curiosity-enhanced memory.Significant statementDoes neural activity within, and functional connectivity between, the dopaminergic-hippocampal network, fronto-parietal network (FPN), and default mode network (DMN) underpin curiosity states and their effects on memory? Here, we show how the dopaminergic system together with the hippocampus interact specifically with subnetwork DMNA potentially reflecting how subcortical regions support the enhancement of memory intergration of semantic information associated with curiosity. As DMNA (the core DMN subnetwork) was also functionally coupled with the whole DMN network and the semantic control network (FPNA), these findings provide a plausible neuromodulatory mechanism through which hippocampal-dopaminergic input triggers curiosity and then communicates to higher-order brain regions via DMNA to facilitate curiosity-enhanced memory.
The cryo-EM structure of the chloroplast ClpP complex reveals an interaction with the co-chaperonin complex that inhibits ClpP proteolytic activity
Authors: Wang Ning , Wang Yifan , Zhao Qian , Zhang Xiang , Peng Chao , Zhang Wenjuan , Liu Yanan , Vallon Olivier , Schroda Michael , Cong Yao , Liu Cuimin 
Published: July 2021

AbstractProtein homeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. We determined the structure of the chloroplast ClpP complex from Chlamydomonas reinhardtiiby cryo-EM. ClpP contains two heptameric catalytic rings without any symmetry. The top ring contains one ClpR6, three ClpP4 and three ClpP5 subunits while the bottom ring is composed of three ClpP1C subunits and one each of the ClpR1-4 subunits. ClpR3, ClpR4 and ClpT4 subunits connect the two rings and stabilize the complex. The chloroplast Cpn11/20/23 co-chaperonin, a co-factor of Cpn60, forms a cap on the top of ClpP by protruding mobile loops into hydrophobic clefts at the surface of the top ring. The co-chaperonin repressed ClpP proteolytic activity in vitro. By regulating Cpn60 chaperone and ClpP protease activity, the co-chaperonin may play a role in coordinating protein folding and degradation in the chloroplast.