bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of High-Grain Diet with Buffering Agent on the Milk Protein Synthesis in Lactating Goats
Authors: He Meilin , Nie Xintian , Wang Huanhuan , Yan Shuping , Zhang Yuanshu 
Published: May 2020

AbstractFeeding of straw as main roughage with numerous high-grain diets improves the performance of ruminants but it can easily lead to subacute ruminal acidosis. In recent years, buffering agent is applied to prevent the acid poisoning of ruminants and improve the production performance of ruminants in animal husbandry. it is necessary to understand feeding high-grain diet with buffering agent which transport carriers amino acids mainly take amino acids into the mammary gland and the signal mechanism of amino acids in the mammary gland synthesize milk proteins. To gain insight on the effects of a high-grain diet with buffering agent on the amino acids in the jugular blood, and the effects of amino acids on the synthesis of milk protein, commercial kit and high performance liquid chromatography (HPLC) were applied to determine the concentration of amino acids of jugular blood samples, quantitative real-time PCR, comparative proteomic approach and western blot were employed to investigate proteins differentially expressed in mammary tissues and the mechanism of amino acids on the synthesis of milk protein in mammary gland of lactating dairy goats fed high-grain diet with buffering agent or only high-grain diet.Results showed that feeding high-grain diet with buffering agent to lactating dairy goats could outstanding increase amino acid content of jugular blood (p<0.05), and mRNA transcriptional level of amino acid transporters in the mammary gland were also increased; the CSN2 and LF protein expression level were significant higher by 2-DE technique, MALDI-TOF/TOF proteomics analyzer and western blot analysis further validated in mammary of lactating dairy goats compared with high-grain group; the research on the mechanism of milk protein synthesis increasing suggested that it was related to the activation of mTOR pathway signaling.Feeding of high-grain diet with buffering agent promoted the jugular vein blood of amino acids concentration, and more amino acids flowed into the mammary. In addition, milk protein synthesis was increased and the increase of milk protein synthesis was related to the activation of mTOR pathway signalling.
A novel tool for standardizing clinical data in a realism-based common data model
Authors: Freedman Hayden G. , Williams Heather , Miller Mark A. , Birtwell David , Mowery Danielle L. , Stoeckert Christian J. 
Published: May 2020

AbstractStandardizing clinical information in a common data model is important for promoting interoperability and facilitating high quality research. Semantic Web technologies such as Resource Description Framework can be utilized to their full potential when a clinical data model accurately reflects the reality of the clinical situation it describes. To this end, the Open Biomedical Ontologies Foundry provides a set of ontologies that conform to the principles of realism and can be used to create a realism-based clinical data model. However, the challenge of programmatically defining such a model and loading data from disparate sources into the model has not been addressed by pre-existing software solutions. The PennTURBO Semantic Engine is a tool developed at the University of Pennsylvania that works in conjunction with data aggregation software to transform source-specific RDF data into a source-independent, realism-based data model. This system sources classes from an application ontology and specifically defines how instances of those classes may relate to each other. Additionally, the system defines and executes RDF data transformations by launching dynamically generated SPARQL update statements. The Semantic Engine was designed as a generalizable RDF data standardization tool, and is able to work with various data models and incoming data sources. Its human-readable configuration files can easily be shared between institutions, providing the basis for collaboration on a standard realism-based clinical data model.
Cobalt(III) Schiff Base complexes stabilize non-fibrillar amyloid-β aggregates with reduced toxicity
Authors: Roberts K. F. , Brue C. R. , Preston A. , Baxter D. , Herzog E. , Varelas E. , Meade T. J. 
Published: May 2020

AbstractThe aggregation of Aβ is believed to be foundational to the pathogenesis of Alzheimer’s disease (AD).In vitroaggregation kinetics have been shown to correlate with rates of disease progression in both AD patients and animal models, thus proving to be a useful metric for testing Aβ-targeted therapeutics. Here we present evidence of Cobalt(III) Schiff base complex (Co(III)-sb) modulation of Aβ aggregation kinetics by a variety of complementary techniques. These include Thioflavin T (ThT) fluorescence, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). Our data was fitted to kinetic rate laws using a mathematical model developed by Knowles et al. in order to extract mechanistic information about the effect of Co(III)-sb on aggregation kinetics. Our analysis revealed that Co(III)-sb significantly decreases the kinetic parameter k+,and significantly increases the polymerization rate kn, suggesting that Co(III)-sb causes Aβ to rapidly form stable oligomeric species that are unable to elongate into mature fibrils. This result was corroborated by TEM and AFM of Aβ aggregatesin vitro. We also demonstrate that Aβ aggregate mixtures produced in the presence of Co(III)-sb exhibit decreased cytotoxicity compared to untreated samples.Statement of SignificanceAmyloid-β is thought to be a key mediator in the pathology of Alzheimer’s disease, yet its precise mechanisms of toxicity are poorly understood. The interaction of Aβ with endogenous metal ions via its N terminal Histidine residues has been shown to alter the peptide’s aggregation and toxicity. As such, metal-based complexes have been developed both as therapeutic agents as well as tools for investigating the role of metal binding in the pathogenesis of AD. This work expands on our previous studies developing Cobalt(III) Schiff base complexes as amyloid inhibitors. Here we demonstrate effective inhibition of aggregation by various complementary modalities. Additionally we show that Co(III)-sb reduces the toxicity of Aβ aggregates to cells in culture.
Are mice born normally with an egg-only diet?
Authors: Isobe Ken-ichi , Sato Natsumi , Ono Karin , Fujita Haruka , kawamura Marin , Sasaki Harumi , Yamamoto Saori , Nishio Naomi 
Published: May 2020

AbstractChicken eggs (egg) contain high amounts of important proteins and fat with a very low amount of carbohydrates, and also contain all vitamins and minerals needed for the chick to develop. We mated 8-week-old mice consuming an egg-only diet, and examined whether mice got pregnant and mice gave birth. Then we continued to raise newborn mice only consuming an egg-only diet compared to normal chew diet. We found that the rate of pregnancy of the mice consuming an egg-only diet was not different from that of the mice consuming normal chew diet. Further, we found that the number of pupus born from the mother consuming only eggs was not different from that of the mother consuming normal chew diet. However, the newborn mice from the mother fed only eggs did not grow healthy when they consume egg-only diet. Only few mice were alive at one month after birth. Then we change the diet just before or just after birth from egg only diet to normal chew diet and we found that both group grew healthy more than one month. These results indicate that mice are born healthy only with egg only diet.
Effect of different derivatization protocols on the calculation of trophic position using amino acids compound-specific stable isotopes
Authors: Martinez Stephane , Lalzer Maya , Shemesh Eli , Einbinder Shai , Tchernov Beverly Goodman , Tchernov Dan 
Published: May 2020

AbstractAmino acids compound-specific nitrogen stable isotope (AA-CSIA) is an emerging tool in ecology for understanding trophic system dynamics. While it has been successfully used for several independent studies across a range of environments and study locations, researchers have encountered calculation issues for determining trophic position values. Most studies introduce modifications to the constants of trophic position equation calculations, but then fail to account for the equation variations when comparing the results of separate research studies. The acceptance of this approach is related to the underlying presumption that no addition of the exogenous nitrogen atom occurs in the different methods and, therefore, such variations should not affect the outcome. In this paper, we evaluate the use of the EZfaast amino acid derivatization kit (chloroformate) and compare it to the isotopic results of two other derivatization methods. We highlight new considerations for working with AA-CSIA that might account for some of the variations in the results and lead researchers to modify constants in the equation. This likely requires developing the unique constants per derivatization method in order to be able to compare the trophic position results across different studies.
Thrombin-free polymerization leads to pure fibrin(ogen) materials with extended processing capacity
Authors: Rieu Clément , Mosser Gervaise , Haye Bernard , Sanson Nicolas , Coradin Thibaud , Trichet Léa 
Published: May 2020

AbstractFibrin is a key protein for various clinical applications such as tissue reconstruction. However, in contrast to type I collagen, fibrin shaping has so far faced major limitations related to the necessity to add thrombin enzyme to fibrinogen precursors to induce fibrin self-assembly. Here we report a thrombin-free gelation pathway of fibrinogen solutions by incubation at 37°C in mild acidic conditions. We unravel the biochemical mechanisms underlying the gelation process and draw comparison between fibrinogen and fibrin at both molecular and supramolecular levels in these conditions. The protocol enables to control the viscosity of fibrin(ogen) solutions, and to induce fibrin(ogen) gel formation by simple 37°C incubation, with a reinforcement effect at neutralization. It facilitates processing of fibrin(ogen) materials, for coating, molding and extrusion, and offers new possibilities such as 3D printing. This approach is further compatible with type I collagen processing and can provide advanced tissue engineering scaffolds with high bioactivity.
Seizures are a druggable mechanistic link between TBI and subsequent tauopathy
Authors: Alyenbaawi Hadeel , Kanyo Richard , Locskai Laszlo F. , Kamali-Jamil Razieh , DuVal Michèle G. , Bai Qing , Wille Holger , Burton Edward A. , Allison W. Ted 
Published: May 2020

SummaryTraumatic brain injury (TBI) is a prominent risk factor for neurodegenerative diseases and dementias including chronic traumatic encephalopathy (CTE). TBI and CTE, like all tauopathies, are characterized by accumulation of Tau into aggregates that progressively spread to other brain regions in a prion-like manner. The mechanisms that promote spreading and cellular uptake of tau seeds after TBI are not fully understood, in part due to lack of tractable animal models. Here, we test the putative roles for excess neuronal activity and dynamin-dependent endocytosis in promoting thein vivospread of tauopathy. We introduce ‘tauopathy reporter’ zebrafish expressing a genetically-encoded fluorescent Tau biosensor that reliably reports accumulation of human tau species when seededviaintra-ventricular brain injections. Subjecting zebrafish larvae to a novel TBI paradigm produced various TBI symptoms including cell death, hemorrhage, blood flow abnormalities, post–traumatic seizures, and Tau inclusions. Bath application of anticonvulsant drugs rescued TBI-induced tauopathy and cell death; these benefits were attributable to inhibition of post-traumatic seizures because co-application of convulsants reversed these beneficial effects. However, one convulsant drug, 4-Aminopyridine, unexpectedly abrogated TBI-induced tauopathy - this was due to its inhibitory action on endocytosis as confirmed via additional dynamin inhibitors. These data suggest a role for seizure activity and dynamin-dependent endocytosis in the prion-like seeding and spreading of tauopathy following TBI. Further work is warranted regarding anti-convulsants that dampen post-traumatic seizures as a route to moderating subsequent tauopathy. Moreover, the data highlight the utility of deployingin vivoTau biosensor and TBI methods in larval zebrafish, especially regarding drug screening and intervention.Graphical AbstractHighlightsIntroduces first Traumatic Brain Injury (TBI) model in larval zebrafish, and its easyTBI induces clinically relevant cell death, haemorrhage & post-traumatic seizuresCa2+imagingduringTBI reveals spike in brain activity concomitant with seizuresTau-GFP Biosensor allows repeatedin vivomeasures of prion-like tau aggregationpost-TBI, anticonvulsants stop tauopathies akin to Chronic Traumatic Encephalopathy
Identification ofFusarium solanif. sp.pisi(Fsp) responsive genes inPisum sativum
Authors: Williamson-Benavides Bruce A. , Sharpe Richard , Nelson Grant , Bodah Eliane T. , Porter Lyndon D. , Dhingra Amit 
Published: May 2020

AbstractPisum sativum(pea) is rapidly emerging as an inexpensive and major contributor to the plant-derived protein market. Due to its nitrogen-fixation capability, short life cycle, and low water usage, pea is a useful cover-and-break crop that requires minimal external inputs. It is critical for sustainable agriculture and indispensable for future food security. Root rot in pea, caused by the fungal pathogenFusarium solanif. sp.pisi(Fsp), can result in a 15-60% reduction in yield. It is urgent to understand the molecular basis ofFspinteraction in pea to develop root rot tolerant cultivars. A complementary genetics and gene expression approach was undertaken in this study to identifyFsp-responsive genes in four tolerant and four susceptible pea genotypes. Time course RNAseq was performed on both sets of genotypes afterFspchallenge. Analysis of the transcriptome data resulted in the identification of 42,905 differentially expressed contigs (DECs). Interestingly, the vast majority of DECs were overexpressed in the susceptible genotypes at all sampling time points, rather than in the tolerant genotypes. Gene expression and GO enrichment analyses revealed genes coding for receptor-mediated endocytosis, sugar transporters, salicylic acid synthesis and signaling, and cell death were overexpressed in the susceptible genotypes. In the tolerant genotypes, genes involved in exocytosis, and secretion by cell, the anthocyanin synthesis pathway, as well as the DRR230 gene, a pathogenesis-related (PR) gene, were overexpressed. The complementary genetic and RNAseq approach has yielded a set of potential genes that could be targeted for improved tolerance against root rot inP. sativum. Fspchallenge produced a futile transcriptomic response in the susceptible genotypes. This type of response is hypothesized to be related to the speed at which the pathogen infestation advances in the susceptible genotypes, and the preexisting level of disease-preparedness in the tolerant genotypes.
A systematic dissection of human primary osteoblastsin vivoat single-cell resolution
Authors: Gong Yun , Yang Junxiao , Li Xiaohua , Zhou Cui , Chen Yu , Wang Zun , Qiu Xiang , Liu Ying , Zhang Huixi , Greenbaum Jonathan , Cheng Liang , Hu Yihe , Xie Jie , Yang Xuecheng , Li Yusheng , Bai Yuntong , Wang Yu-Ping , Chen Yiping , Tan Li-Jun , Shen Hui , Xiao Hong-Mei , Deng Hong-Wen 
Published: May 2020

AbstractOsteoblasts are multifunctional bone cells, which play essential roles in bone formation, angiogenesis regulation, as well as maintenance of hematopoiesis. Although bothin vivoandin vitrostudies on mice have identified several potential osteoblast subtypes based on their different transition stages or biological responses to external stimuli, the categorization of primary osteoblast subtypesin vivoin humans has not yet been achieved. Here, we used single-cell RNA sequencing (scRNA-seq) to perform a systematic cellular taxonomy dissection of freshly isolated human osteoblasts. Based on the gene expression patterns and cell lineage reconstruction, we identified three distinct cell clusters including preosteoblasts, mature osteoblasts, and an undetermined rare osteoblast subpopulation. This novel subtype was mainly characterized by the nuclear receptor subfamily 4 group A member 1 and 2 (NR4A1 and NR4A2), and its existence was confirmed by immunofluorescence staining. Trajectory inference analysis suggested that the undetermined cluster, together with the preosteoblasts, are involved in the regulation of osteoblastogenesis and also give rise to mature osteoblasts. Investigation of the biological processes and signaling pathways enriched in each subpopulation revealed that in addition to bone formation, preosteoblasts and undetermined osteoblasts may also regulate both angiogenesis and hemopoiesis. Finally, we demonstrated that there are systematic differences between the transcriptional profiles of human osteoblastsin vivoand mouse osteoblasts bothin vivoandin vitro, highlighting the necessity for studying bone physiological processes in humans rather than solely relying on mouse models. Our findings provide novel insights into the cellular heterogeneity and potential biological functions of human primary osteoblasts at the single-cell level, which is an important and necessary step to further dissect the biological roles of osteoblasts in bone metabolism under various (patho-) physiological conditions.
De NovoAssembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration
Authors: Wa Sin Simon Yung , Lu Lily , Edwards Scott V. 
Published: May 2020

AbstractNorthern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype–phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly contiguous assembly forC. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene inC. cardinalis. Transcription factor binding motifs discovered in the unique insertion region inC. cardinalissuggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000–250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome ofC. cardinalisprovides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.
Chromosome-level genome construction of a Japanese stickleback species using ultra-dense linkage analysis using single-cell sequencing of sperms
Authors: Yoshitake Kazutoshi , Ishikawa Asano , Yonezawa Ryo , Kinoshita Shigeharu , Kitano Jun , Asakawa Shuichi 
Published: May 2020

AbstractThe presence of high quality genomes at the chromosome level is very useful in the search for the causal genes of mutants and in genetic breeding. The advent of next-generation sequencers has made it easier to decode genomes, but it is still difficult to construct the genomes of higher organisms. In order to construct the genome of a higher organism, the genome sequence of the organism is extended to the length of the chromosome by linkage analysis after assembly and scaffolding. However, in the past linkage analysis, it was difficult to make a high-density linkage map, and it was not possible to analyze organisms without an established breeding system. As an innovative alternative to conventional linkage analysis, we devised a method for genotyping sperm using 10x single-cell genome (CNV) sequencing libraries to generate a linkage map without interbreeding individuals. The genome was constructed using sperm fromGasterosteus nipponicus, and single-cell genotyping yielded 1,864,430 very dense hetero-SNPs. The average coverage per sperm cell is 0.13x. The number of sperm used is 1,738, which is an order of magnitude higher than the number of sperm used for conventional linkage analysis. We have improved the linkage analysis tool SELDLA (Scaffold Extender with Low Depth Linkage Analysis) so that we can analyze the data in accordance with the characteristics of single-cell genotyping data. Finally, we were able to determine the location and orientation on the chromosome for 85.6% of the contigs in the 456 Mbase genome ofGasterosteus nipponicussequenced in nanopores. A total of 95.6% of the contigs in which a cross-reaction was detected within the contigs.