bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eco-evolutionary dynamics of prior selfing rate promotes the coexistence without niche partitioning under reproductive interference
Authors: Katsuhara Koki R. , Tachiki Yuuya , Iritani Ryosuke , Ushimaru Atushi 
Published: April 2020

AbstractWhen the two or more plants species share the same pollinators, pollinator-mediated reproductive interference make coexistence difficult. Recent studies suggested prior autonomous selfing mitigate reproductive interference, could enabling coexistence without pollination niche partitioning (pre-emptive selfing hypothesis). However, there are no studies to test whether evolution of prior selfing promote the coexistence, considering eco-evolutionary dynamics of population size, selfing rate and inbreeding depression.To examine conditions that the evolution of prior selfing promote coexistence under mutual reproductive interference especially in the point of view for pollinator availability and dynamics of inbreeding depression, we constructed individual-based model in which two plant species compete against each other in the form of mutual reproductive interference and can evolve prior autonomous selfing rate. We expected that purging of deleterious mutations could cause evolutionary rescue because inferior species could rescue population density through the evolution of prior selfing if the strength of inbreeding depression decreases with an increase of population’s selfing rate.Our simulation demonstrated that the evolution of prior selfing could promote the coexistence while reproductive interference caused competitive exclusion without evolution. We found that lower pollinator availability tended to prefer rapid evolutionary shift to higher prior selfing rate, it neutralizes the negative effect of reproductive interference, and population dynamics exhibit neutral random walk in both species. When the strength of inbreeding depression decreased with an increase in population’s selfing rate, moderate pollinator availability resulted in long-term coexistence in which relative-abundance-dependent selection on the prior selfing rate rescue population density of inferior species intermittently.Synthesis. We showed that the evolution of prior selfing could increase population growth rate of inferior species and consequently enable the long-term coexistence with evolutionary rescue. This is the new mechanisms explaining co-evolutionary coexistence of closely related plant species without niche partitioning and consistent with recent studies reported that closely related mixed-mating species are sympatrically growing even under the mutual reproductive interference.
Development of a simple and accurate molecular tool forSpodoptera frugiperdaspecies identification using LAMP
Authors: Kim Juil , Nam Hwa Yeun , Kwon Min , Kim Hyun Ju , Yi Hwi-Jong , Haenniger Sabine , Unbehend Melanie , Heckel David G. 
Published: April 2020

ABSTRACTThe fall armyworm,Spodoptera frugiperdais a native species in the Americas. However, nowadays it is one of the most serious invasive lepidopteran pests in African and Asian countries.S. frugiperdahas been spread very quickly after the first outbreak was reported in many countries. Based on mt genome sequence alignment,S. frugiperdaspecific sequence region was identified in tRNAs coding region between NADH dehydrogenase, ND3 and ND5. By using this unique region, species diagnostic primers were designed and applied in LAMP (lamp loop mediated isothermal amplification) assay as well as conventional PCR to identify the field-collected samples ofS. frugiperda. Optimal incubation condition of LAMP assay was 61°C for 90 minutes with 4 LAMP primers, and additional loop primer increased the amplification efficiency. Also, wide range of DNA concentration responded in LAMP assay and minimum detectable DNA concentration was 10 pg. This LAMP assay was also applied in DNA releasing technique from larval and adult sample, without DNA extraction, 95°C incubation for five minutes of the tissue sample. This new molecular diagnostic method is easy to use and accurate. It possibly applied in intensive field monitoring ofS. frugiperdaand its ecological studies.
Comparison of SARS-CoV-2 infections among 3 species of non-human primates
Authors: Lu Shuaiyao , Zhao Yuan , Yu Wenhai , Yang Yun , Gao Jiahong , Wang Junbin , Kuang Dexuan , Yang Mengli , Yang Jing , Ma Chunxia , Xu Jingwen , Qian Xingli , Li Haiyan , Zhao Siwen , Li Jingmei , Wang Haixuan , Long Haiting , Zhou Jingxian , Luo Fangyu , Ding Kaiyun , Wu Daoju , Zhang Yong , Dong Yinliang , Liu Yuqin , Zheng Yingqiu , Lin Xiaochen , Jiao Li , Zheng Huanying , Dai Qing , Sun Qiangmin , Hu Yunzhang , Ke Changwen , Liu Hongqi , Peng Xiaozhong 
Published: April 2020

AbstractCOVID-19, caused by SARS-CoV-2 infection, has recently been announced as a pandemic all over the world. Plenty of diagnostic, preventive and therapeutic knowledges have been enriched from clinical studies since December 2019. However, animal models, particularly non-human primate models, are urgently needed for critical questions that could not be answered in clinical patients, evaluations of anti-viral drugs and vaccines. In this study, two families of non-human primates, Old world monkeys (12Macaca mulatta, 6Macaca fascicularis) and New world monkeys (6Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Clinical signs were recorded. Samples were collected for analysis of viral shedding, viremia and histopathological examination. Increased body temperature was observed in 100% (12/12)M. mulatta, 33.3% (2/6)M. fascicularisand none (0/6) ofC. jacchuspost inoculation of SARS-CoV-2. All ofM. mulattaandM. fascicularisshowed chest radiographic abnormality. Viral genomes were detected in nasal swabs, throat swabs, anal swabs and blood from all 3 species of monkeys. Viral shedding from upper respiratory samples reached the peak between day 6 and day 8 post inoculation. From necropsiedM. mulattaandM. fascicularis, the tissues showing virus positive were mainly lung, weasand, bronchus and spleen. No viral genome was seen in any of tissues from 2 necropsiedC. jacchus.Severe gross lesions and histopathological changes were observed in lung, heart and stomach of SARS-CoV-2 infected animals. In summary, we have established a NHP model for COVID-19, which could be used to evaluate drugs and vaccines, and investigate viral pathogenesis.M. mulattais the most susceptible to SARS-CoV-2 infection, followed byM. fascicularisandC. jacchus.One Sentence SummaryM. mulattais the most susceptible to SARS-CoV-2 infection as compared toM. fascicularisandC. jacchus.
Symptom-level genetic modelling identifies novel risk loci and unravels the shared genetic architecture of anxiety and depression
Authors: Thorp Jackson G. , Campos Adrian I. , Grotzinger Andrew D. , Gerring Zachary , An Jiyuan , Ong Jue-Sheng , Wang Wei ,   23andMe Research Team, Shringarpure Suyash , Byrne Enda M. , MacGregor Stuart , Martin Nicholas G. , Medland Sarah E. , Middeldorp Christel M. , Derks Eske M. 
Published: April 2020

AbstractDepression and anxiety are highly prevalent and comorbid psychiatric traits that cause considerable burden worldwide. Previous studies have revealed substantial genetic overlap between depression, anxiety, and a closely related personality trait – neuroticism. Here, we use factor analysis and genomic structural equation modelling (Genomic SEM) to investigate the genetic factor structure underlying 28 items assessing depression, anxiety and neuroticism. Symptoms of depression and anxiety loaded on two distinct, although genetically correlated factors, while neuroticism items were partitioned between them. We leveraged this factor structure to conduct multivariate genome-wide association analyses on latent factors of anxiety symptoms and depressive symptoms, using data from over 400,000 individuals in the UK Biobank. We identified 89 independent variants for the depressive factor (61 genomic loci, 29 novel) and 102 independent variants for the anxiety factor (73 loci, 71 novels). Of these variants, 72% and 78%, respectively, replicated in an independent 23andMe cohort of ∼1.9 million individuals with self-reported diagnosis of depression (634,037 cases) and anxiety (624,615 cases). A pairwise GWAS analysis revealed substantial genetic overlap between anxiety and depression but also showed trait-specific genetic influences; e.g. genomic regions specific to depressive symptoms were associated with hypertriglyceridemia, while regions specific to anxiety symptoms were linked to blood pressure phenotypes. The substantial genetic overlap between the two traits was further evidenced by a lack of trait-specificity in polygenic prediction of depressive and anxiety symptoms. Our results provide novel insight into the genetic architecture of depression and anxiety and comorbidity between them.
Effect of protein structure on evolution of cotranslational folding
Authors: Zhao V. , Jacobs W. M. , Shakhnovich E. I. 
Published: April 2020

AbstractCotranslational folding is expected to occur when the folding speed of the nascent chain is faster than the translation speed of the ribosome, but it is difficult to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how native structure influences evolution of cotranslational folding. We developed a model that connects protein folding during and after translation to cellular fitness. Model proteins evolved improved folding speed and stability, with proteins adopting one of two strategies for folding quickly. Low contact order proteins evolve to fold cotranslationally. Such proteins adopt native conformations early on during the translation process, with each subsequently translated residue establishing additional native contacts. On the other hand, high contact order proteins tend not to be stable in their native conformations until the full chain is nearly extruded. We also simulated evolution of slowly translating codons, finding that slowing translation at certain positions enhances cotranslational folding. Finally, we investigated real protein structures using a previously published dataset that identified evolutionarily conserved rare codons inE. coligenes and associated such codons with cotranslational folding intermediates. We found that protein substructures preceding conserved rare codons tend to have lower contact orders, in line with our finding that lower contact order proteins are more likely to fold cotranslationally. Our work shows how evolutionary selection pressure can cause proteins with local contact topologies to evolve cotranslational folding.Statement of significanceSubstantial evidence exists for proteins folding as they are translated by the ribosome. Here we developed a biologically intuitive evolutionary model to show that avoiding premature protein degradation can be a sufficient evolutionary force to drive evolution of cotranslational folding. Furthermore, we find that whether a protein’s native fold consists of more local or more nonlocal contacts affects whether cotranslational folding evolves. Proteins with local contact topologies are more likely to evolve cotranslational folding through nonsynonymous mutations that strengthen native contacts as well as through synonymous mutations that provide sufficient time for cotranslational folding intermediates to form.
Acoustic analysis and playback experiments do not support the taxonomic revision of the Central and Western Canary Islands subspecies of the Eurasian Stone-curlew (Burhinus o. distinctus)
Authors: Dragonetti Marco , Caprara Massimo , Rodríguez-Godoy Felipe , Barone Rubén , Cerdeña V. Rubén , Giunchi Dimitri 
Published: April 2020

AbstractCapsuleAcoustic analysis does not support the elevation ofB. o. distinctusto full species.AimsTo verify whether the vocal repertoires ofB. o. oedicnemusandB. o. distinctusshow biologically significant quantitative and qualitative differences.MethodsIntegration of acoustic analysis of some of the most frequently uttered call types recorded in Italy and in Canary Islands with playback experiments.ResultsThe vocal repertoires of the individuals belonging to the two subspecies were rather similar, but the quantitative analysis of acoustic parameters evidenced some differences between the considered populations. In particular, the three most used call types showed higher frequency and higher utterance rhythm forB. o. distinctusthan forB. o. eodicnemus. Playback experiments indicated that individuals from the nominate subspecies responded in the same way to the playback of calls of individuals belonging to both subspecies.ConclusionAcoustic analysis supports the distinctiveness of Stone-curlew populations from Central and Western Canary Islands, thus confirming the available morphological and genetic data. These results, however, do not suggest the elevation ofB. o. distinctusto full species.
In vitroandin silicoanalyses of the angiotensin-I converting enzyme inhibitory activity of peptides identified fromBellamya bengalensisprotein hydrolysates
Authors: Dey Tanmoy Kumar , Chatterjee Roshni , Roychoudhury Anadi , Paul Debjyoti , Mandal Rahul Shubhra , Roy Souvik , Dhar Pubali 
Published: April 2020

AbstractThe study focuses on identification of ACE-inhibitory peptides from the proteolytic digests of muscle protein ofBellamya bengalensisand its underlying mechanism. 120 min Alcalase-hydrolysates were ultrafiltered to isolate the small peptide fraction (<3kDa) andin vitroACE-inhibitory activity was analyzed. The IC50value of the 120 min hydrolysate ultafiltered fraction was found to be 86.74 ± 0.575 µg/mL, while the IC50of Lisinopril is 0.31 ± 0.07 µg/mL. This fraction was assessed in MALDI-ToF mass-spectrometer and five peptides were sequenced viade novosequencing. The ACE-inhibitory potential of the peptides have a positive correlation with the hydrophobicity of the amino acids. Synthetic analogue of the peptide (IC50value 8.52 ± 0.779 µg/mL) was used to understand the thermodynamics of the inhibition by checking the binding affinity of the peptide to ACE by Isothermal titration calorimetry compared with lisinopril, and further substantiated byin silicosite specific molecular docking study.
Estimation of cellularity in tumours treated with Neoadjuvant therapy: A comparison of Machine Learning algorithms
Authors: Ortega-Ruíz Mauricio Alberto , Karabağ Cefa , Garduño Victor García , Reyes-Aldasoro Constantino Carlos 
Published: April 2020

AbstractThis paper describes a method for residual tumour cellularity (TC) estimation in Neoadjuvant treatment (NAT) of advanced breast cancer. This is determined manually by visual inspection by a radiologist, then an automated computation will contribute to reduce time workload and increase precision and accuracy. TC is estimated as the ratio of tumour area by total image area estimated after the NAT. The method proposed computes TC by using machine learning techniques trained with information on morphological parameters of segmented nuclei in order to classify regions of the image as tumour or normal. The data is provided by the 2019 SPIE Breast challenge, which was proposed to develop automated TC computation algorithms. Three algorithms were implemented: Support Vector Machines, Nearest K-means and Adaptive Boosting (AdaBoost) decision trees. Performance based on accuracy is compared and evaluated and the best result was obtained with Support Vector Machines. Results obtained by the methods implemented were submitted during ongoing challenge with a maximum of 0.76 of prediction probability of success.
Isolated Nuclei Stiffen in Response to Low Intensity Vibration
Authors: Newberg J , Schimpf J , Woods K , Loisate S , Davis P H , Uzer G 
Published: April 2020

ABSTRACTThe nucleus, central to all cellular activity, relies on both direct mechanical input and its molecular transducers to sense and respond to external stimuli. While it has been shown that isolated nuclei can adapt to applied forceex vivo, the mechanisms governing nuclear mechanoadaptation in response to physiologic forcesin vivoremain unclear. To investigate nuclear mechanoadaptation in cells, we developed an atomic force microscopy (AFM) based procedure to probe live nuclei isolated from mesenchymal stem cells (MSCs) following the application of low intensity vibration (LIV) to determine whether nuclear stiffness increases as a result of LIV. Results indicated that isolated nuclei were, on average, 30% softer than nuclei tested within intact MSCs prior to LIV. When the nucleus was isolated following LIV (0.7g, 90Hz, 20min) applied four times (4x) separated by 1h intervals, stiffness of isolated nuclei increased 75% compared to non-LIV controls. LIV-induced nuclear stiffening required functional Linker of Nucleoskeleton and Cytoskeleton (LINC) complex, but was not accompanied by increased levels of the nuclear envelope proteins LaminA/C or Sun-2. While depleting LaminA/C or Sun-1&2 resulted in either a 47% or 39%increasedheterochromatin to nuclear area ratio in isolated nuclei, the heterochromatin to nuclear area ratio wasdecreasedby 25% in LIV-treated nuclei compared to controls, indicating LIV-induced changes in the chromatin structure. Overall, our findings indicate that increased apparent cell stiffness in response to exogenous mechanical challenge of MSCs in the form of LIV is in part retained by increased nuclear stiffness and changes in chromatin structure.
Evaluation of Neuropharmacological Effects of Different Chemical Extracts ofFlemingia Stricta(Roxb.) Leaves
Authors: Biozid Md. Shahrear , Alam Mohammad Nazmul , Abeden Md. Jainul , Rahman Md. Masudur , Islam Md. Rafikul 
Published: April 2020

AbstractBackgroundTraditional preparation of the leaf ofFlemingia stricta(Fabaceae) Roxb., a medicinal plant of the Indian subcontinent, has been used for treatment of different diseases as herbal preparation. Our purpose was to analyze Neuropharmacological effects of different chemical extracts ofFlemingia strictaRoxb. as particular form of behavioral inhibition that occurs in response to novel environmental events.MethodsIn present study, the anxiogenic activity of crude extracts ofFlemingia strictaleaves was determined using standard animal behavioral models, such as hole cross and open field; Sedative property and anxiolytic potential were assessed by conducting thiopental sodium induced sleeping times tests and elevated plus maze test respectively.ResultsThe crude extracts at both dose (200 and 400mg/kg) exhibited a significant (P<0.05, P<0.01) dose-dependent suppression of motor activity and exploratory activity of mice in both open field and hole cross test. In anxiolytic study, extracts displayed increased percentage of entry into open arm at the dose of 200 and 400mg/kg. Extracts produced a significant (P<0.05, P<0.01) increase in sleeping duration and reduction of onset of sleep compared to sodium thiopental at both doses (200 and 400mg/kg).ConclusionThis study demonstrates that the treated extracts have significant central nervous system depressant effect. Further studies on the active constituent of the extract can provide approaches for therapeutic intervention.
Comparative morphological and transcriptomic analyses reveal novel chemosensory genes in the poultry red mite,Dermanyssus gallinaeand knockdown by RNA interference
Authors: Bhowmick Biswajit , Tang Yu , Lin Fang , Øines Øivind , Zhao Jianguo , Liao Chenghong , Ignell Rickard , Hansson Bill S. , Han Qian 
Published: April 2020

AbstractDetection of chemical cues via chemosensory receptor proteins are essential for most animals, and underlies critical behaviors, including location and discrimination of food resources, identification of sexual partners and avoidance of predators. The current knowledge of how chemical cues are detected is based primarily on data acquired from studies on insects, while our understanding of the molecular basis for chemoreception in acari, mites in particular, remains limited. The poultry red mite (PRM),Dermanyssus gallinae, is one of the most important blood-feeding ectoparasites of poultry. Unlike other ectoparasites on animals, PRM feeds mainly at night. During daytime, these animals hide themselves in crevices around the poultry house. The diversity in habitat usage, as well as the demonstrated host finding and avoidance behaviors suggest that PRM relies on their sense of smell to orchestrate complex behavioral decisions. Comparative transcriptome analyses revealed the presence of candidate variant ionotropic receptors (IRs), odorant binding proteins (OBPs), niemann-pick proteins type C2 (NPC2) and sensory neuron membrane proteins (SNMPs). Some of these proteins were highly and differentially expressed in the forelegs of PRM. Rhodopsin-like G protein-coupled receptors (GPCRs) were also identified, while insect-specific odorant receptors (ORs) and odorant co-receptors (ORcos) were not detected. Furthermore, using scanning electron microscopy (SEM), the tarsomeres of all legs pairs were shown to be equipped with sensilla chaetica with or without tip pores, while wall-pored olfactory sensilla chaetica were restricted to the distal-most tarsomeres of the forelegs. Further, using the conserved odorant binding protein (OBP) as a test case, the results showed that RNA interference (RNAi) can be induced inD. gallinaechemosensory tissues. This study is the first to describe the presence of chemosensory genes in anyDermanyssidaefamily. It is also the first report of chemosensory gene knockdown by RNAi in any mite species and demonstrate that their diminutive size, less than 1 mm, is not a major impediment when applying gene knockdown approaches. Our findings make a significant step forward in understanding the chemosensory abilities ofD. gallinae.
Pen-strep influence macrophage mechanical property and mechano-response to microenvironment
Authors: Zhao Weikang , Hu Buwei , Zhang Xuexiang , Wang Pingping 
Published: April 2020

AbstractPenicillin-streptomycin (Pen-strep) is a common antibiotic used to prevent bacterial infection in cell culture and clinical treatment. Current research found pen-strep increased macrophage modulus but limited influence on cell adhesion. Phalloidin statin image indicates pen-strep mediate cell morphology on different extracellular matrix coated surface. The roundness analyzes further illustrated pen-strep promote cell spread on PDMS rubber, type I collagen, laminin, poly amino acid, poly-RGD peptides. Finally, YAP-1 and TAZ upregulation and β1 integrin downregulation may be the causes of cell elasticity and mechano-response to extracellular matrix (ECM) change.
Water as a reactant in the differential expression of proteins in cancer
Authors: Dick Jeffrey M. 
Published: April 2020

AbstractHow the abundances of proteins are shaped by tumor microenvironments, such as hypoxic conditions and higher water content compared to normal tissues, is an important question for cancer biochemistry. Compositional analysis of more than 250 datasets for differentially expressed proteins compiled from the literature reveals a higher stoichiometric hydration state in multiple cancer types compared to normal tissue; this trend is also evident in pan-cancer transcriptomic and proteomic datasets from The Cancer Genome Atlas and Human Protein Atlas. These findings support the notion of a basic physicochemical link between increased water content in tumors and the patterns of gene and protein expression in cancer. The generally increased hydration state is juxtaposed with a wide spectrum of carbon oxidation states of differentially expressed proteins, which may be associated with different gene ages, host tissue properties and metabolic features of specific cancer types.