bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioinformatics analysis and collection of protein post-translational modification sites in human viruses
Authors: Xiang Yujia , Zou Quan , Zhao Lilin 
Published: April 2020

AbstractIn viruses, post-translational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for better understanding the mechanism of viral infections and finding potential drug targets. However, few studies have investigated the roles of viral PTMs in virus-human interactions using comprehensive viral PTM datasets. To fill this gap, firstly, we developed a viral post-translational modification database (VPTMdb) for collecting systematic information of viral PTM data. The VPTMdb contains 912 PTM sites that integrate 414 experimental-confirmed PTM sites with 98 proteins in 45 human viruses manually extracted from 162 publications and 498 PTMs extracted from UniProtKB/Swiss-Prot. Secondly, we investigated the viral PTM sequence motifs, the function of target human proteins, and characteristics of PTM protein domains. The results showed that (i) viral PTMs have the consensus motifs with human proteins in phosphorylation, SUMOylation and N-glycosylation. (ii) The function of human proteins that targeted by viral PTM proteins are related to protein targeting, translation, and localization. (iii) Viral PTMs are more likely to be enriched in protein domains. The findings should make an important contribution to the field of virus-human interaction. Moreover, we created a novel sequence-based classifier named VPTMpre to help users predict viral protein phosphorylation sites. Finally, an online web server was implemented for users to download viral protein PTM data and predict phosphorylation sites of interest.Author summaryPost-translational modifications (PTMs) plays an important role in the regulation of viral proteins; However, due to the limitation of data sets, there has been no detailed investigation of viral protein PTMs characteristics. In this manuscript, we collected experimentally verified viral protein post-translational modification sites and analysed viral PTMs data from a bioinformatics perspective. Besides, we constructed a novel feature-based machine learning model for predicting phosphorylation site. This is the first study to explore the roles of viral protein modification in virus infection using computational methods. The valuable viral protein PTM data resource will provide new insights into virus-host interaction.
Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders
Authors: Sun Yan , Liu Fengxia , Fan Chunna , Wang Yaoshen , Song Lijie , Fang Zhonghai , Han Rui , Wang Zhonghua , Wang Xiaodan , Yang Ziying , Xu Zhenpeng , Peng Jiguang , Shi Chaonan , Zhang Hongyun , Dong Wei , Huang Hui , Li Yun , Le Yanqun , Sun Jun , Peng Zhiyu 
Published: April 2020

AbstractBackgroundWith the reduce of cost and incomparable advantages, WGS is likely to change the way of clinical diagnosis of rare and undiagnosed diseases. However, the sensitivity and breadth of coverage of clinical WGS as a diagnostic test for genetic disorders has not been fully evaluated, especially for CNV detection.MethodsAll the samples underwent WGS using MGISEQ-2000. The performance of NA12878, YH cell line, and the Chinese trios were measured for sensitivity, PPV, depth and breadth of coverage. We also compared the performance of WES and WGS using NA12878. The sensitivity and PPV were tested using family-based trio design in the Chinese trios. We also developed a systematic WGS pipeline for the analysis of 8 clinical cases with known disease-causing variants.ResultsIn general, the sensitivity and PPV for SNV/indel detection increased with mean depth, and reached a plateau at a ~40X mean depth using down-sampling samples of NA12878. With a mean depth of 40X, the sensitivity of homozyous and heterozygous SNPs of NA12878 was >99.25% and >99.50% respectively, and PPVs were 99.97% and 98.96%. Homozygous and heterozygous indels showed lower sensitivity and PPV. The sensitivity and PPV is still not 100% even with a mean depth of ~150X. We also observed a substantial variation in the sensitivity of CNV detection across different tools, especially in CNVs with a size of less than 1kb. In general, the breadth of coverage for disease-associated genes and CNVs increased with mean depth. The sensitivity and coverage of WGS (~40X) is better than WES (~120X). Among the Chinese trios with ~40X mean depth, the sensitivity in the offspring was >99.48% and >96.36% for SNP and indel detection, and PPVs were 99.86% and 97.93%. All the 12 previously validated variants in the 8 clinical cases were successfully detected by our WGS pipeline.ConclusionsThe current standard of a mean depth of 40X may be sufficient for SNV/indel detection and identification of most CNVs. Clinical scientists should know the range of sensitivity and PPV for different classes of variants for a particular WGS pipeline, which would be useful when interpreting and delivering clinical reports.
Cellular senescence and quiescence are associated with altered ribosomal RNA methylation and processing
Authors: Yang Guohuan , Heisenberger Clemens , Kos-Braun Isabelle C. , Polacek Norbert , Grillari Johannes , Schosserer Markus , Koš Martin 
Published: April 2020

AbstractThe 2’-O-methylation (2’-O-Me) of ribosomal RNA (rRNA) shows plasticity potentially associated with specific cell phenotypes. We used RiboMeth-seq profiling to reveal 2’-O-Me patterns specific to stress induced premature senescent (SIPS), quiescent and proliferating human dermal fibroblasts. The altered methylation levels in SIPS and quiescence partially correlated with the expression of specific snoRNAs but not fibrillarin. Senescence and quiescence were accompanied by a trend towards preferred usage of one of the two alternative ribosome biogenesis pathways.
Resources for genome editing in livestock: Cas9-expressing chickens and pigs
Authors: Bartsch Denise , Sid Hicham , Rieblinger Beate , Hellmich Romina , Schlickenrieder Antonina , Lengyel Kamila , Flisikowski Krzysztof , Flisikowska Tatiana , Simm Nina , Grodziecki Alessandro , Perleberg Carolin , Kupatt Christian , Wolf Eckhard , Kessler Barbara , Kettler Lutz , Luksch Harald , Hagag Ibrahim T. , Wise Daniel , Kaufman Jim , Kaufer Benedikt B. , Schnieke Angelika , Schusser Benjamin 
Published: April 2020

AbstractGenetically modified animals continue to provide important insights in biomedical sciences. Research has focused mostly on genetically modified mice so far, but other species like pigs resemble more closely the human physiology. In addition, cross-species comparisons with phylogenetically distant species such as chickens provide powerful insights into fundamental biological and biomedical processes. One of the most versatile genetic methods applicable across species is CRISPR/Cas9. Here, we report for the first time the generation of Cas9 transgenic chickens and pigs that allowin vivogenome editing in these two important agricultural species. We demonstrated that Cas9 is constitutively expressed in all organs of both species and that the animals are healthy and fertile. In addition, we confirmed the functionality of Cas9 for a number of different target genes and for a variety of cell types. Taken together, these transgenic animal species expressing Cas9 provide an unprecedented tool for agricultural and biomedical research, and will facilitate organ specific reverse genetics as well as cross-species comparisons.Significance statementGenome engineering of animals is crucial for translational medicine and the study of genetic traits. Here, we generated transgenic chickens and pigs that ubiquitously express the Cas9 endonuclease, providing the basis forin vivogenome editing. We demonstrated the functionality of this system by successful genome editing in chicken and porcine cells and tissues. These animals facilitate organ specificin vivogenome editing in both species without laborious germ line modifications, which will reduce the number of animals needed for genetic studies. They also provide a new tool for functional genomics, developmental biology and numerous other applications in biomedical and agricultural science.
Large domains of heterochromatin direct the formation of short mitotic chromosome loops
Authors: Fitz-James Maximilian H. , Tong Pin , Pidoux Alison L. , Ozadam Hakan , Yang Liyan , White Sharon A. , Dekker Job , Allshire Robin C. 
Published: April 2020

AbstractDuring mitosis chromosomes reorganise into highly compact, rod-shaped forms, thought to consist of consecutive chromatin loops around a central protein scaffold. Condensin complexes are involved in chromatin compaction, but the contribution of other chromatin proteins, DNA sequence and histone modifications is less understood. A large region of fission yeast DNA inserted into a mouse chromosome was previously observed to adopt a mitotic organisation distinct from that of surrounding mouse DNA. Here we show that a similar distinct structure is common to a large subset of insertion events in both mouse and human cells and is coincident with the presence of high levels of heterochromatic H3 lysine 9 trimethylation (H3K9me3). Hi-C and microscopy indicate that the heterochromatinised fission yeast DNA is organised into smaller chromatin loops than flanking euchromatic mouse chromatin. We conclude that heterochromatin alters chromatin loop size, thus contributing to the distinct appearance of heterochromatin on mitotic chromosomes, such as at centromeres.
Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation
Authors: Carlsen A. T. , Tabard Cossa V. 
Published: April 2020

ABSTRACTSolid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.STATEMENT OF SIGNIFICANCENanopore sensing allows investigation of biomolecular structure in aqueous solution, including electricfield-induced changes in protein conformation. This nanopore-based study probes: (1) the tetramerdimer transition of streptavidin, observing the effects of increasing voltage with varying salt type and concentration; (2) the possible conformational states of DNA-streptavidin complexes when confined inside a pore. We describe a broadly applicable geometric approach that maps stepwise changes in the nanopore signal to real-time conformational transitions. These results represent progress toward accurate interpretation of nanopore signals generated by molecular complexes.
Evolution-based design of chorismate mutase enzymes
Authors: Russ William P. , Figliuzzi Matteo , Stocker Christian , Barrat-Charlaix Pierre , Socolich Michael , Kast Peter , Hilvert Donald , Monasson Remi , Cocco Simona , Weigt Martin , Ranganathan Rama 
Published: April 2020

The rational design of enzymes is an important goal for both fundamental and practical reasons. Here, we describe a design process in which we learn the constraints for specifying proteins purely from evolutionary sequence data, build libraries of synthetic genes, and test them for activityin vivousing a quantitative complementation assay. For chorismate mutase, a key enzyme in the biosynthesis of aromatic amino acids, we demonstrate the design of natural-like catalytic function with substantial sequence diversity. Further optimization focuses the generative model towards function in a specific genomic context. The data show that sequence-based statistical models suffice to specify proteins and provide access to an enormous space of synthetic functional sequences. This result provides a foundation for a general process for evolution-based design of artificial proteins.One-sentence summaryAn evolution-based, data-driven engineering process can build synthetic functional enzymes.
Cross-talk between individual phenol soluble modulins inS. aureusbiofilm formation
Authors: Zaman Masihuz , Andreasen Maria 
Published: April 2020

ABSTRACTThe infective ability of the opportunistic pathogenStaphylococcus aureusis associated with biofilm mediated resistance to host immune response and even disinfectants and indeedS. aureusis recognized as the most frequent cause of biofilm associated infections. Phenol-soluble modulin (PSM) peptides serve various roles in pathogenicity while also comprising the structural scaffold ofS. aureusbiofilms through self-assembly into functional amyloids, but the role of the individual PSMs during biofilm formation remains poorly understood and the molecular pathways of PSM self-assembly have proved challenging to identify. Here, we show a high degree of cooperation between individual PSMs during the formation of functional amyloids in biofilm formation. The fast aggregating PSMα3 initiates the aggregation by forming unstable aggregates capable of seeding the formation of aggregates by other PSM peptides into the formation of stable amyloid structures. Using chemical kinetics along with spectroscopic techniques we dissect the molecular mechanism of aggregation of the individual peptides to show that PSMα1, PSMα3 and PSMβ1 display secondary nucleation whereas βPSM2 aggregates through primary nucleation and elongation. Our findings suggest that the various PSMs have evolved to ensure fast and efficient biofilm formation through cooperation between individual peptides.
Ecology and molecular targets of hypermutation in the global microbiome
Authors: Roux Simon , Paul Blair G. , Bagby Sarah C. , Allen Michelle A. , Attwood Graeme , Cavicchioli Ricardo , Chistoserdova Ludmila , Hallam Steven J. , Hernandez Maria E. , Hess Matthias , Liu Wen-Tso , O’Malley Michelle A. , Peng Xuefeng , Rich Virginia I. , Saleska Scott , Eloe-Fadrosh Emiley A. 
Published: April 2020

AbstractChanges in the sequence of an organism’s genome, i.e. mutations, are the raw material of evolution1. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as Diversity-generating retroelements (DGRs)2–4. DGRs introduce mutations in specific target genes, and were characterized from several cultivated bacteria and bacteriophages2. Whilst a larger diversity of DGR loci has been identified in genomic data from environmental samples, i.e. metagenomes, the ecological role of these DGRs and their associated evolutionary drivers remain poorly understood5–7. Here we built and analyzed an extensive dataset of >30,000 metagenome-derived DGRs, and determine that DGRs have a single evolutionary origin and a universal bias towards adenine mutations. We further identified six major lineages of DGRs, each associated with a specific ecological niche defined as a genome type, i.e. whether the DGR is encoded on a viral or cellular genome, a limited set of taxa and environments, and a distinct type of target. Finally, we leverage read mapping and metagenomic time series to demonstrate that DGRs are consistently and broadly active, and responsible for >10% of all amino acid changes in some organisms at a conservative estimate. Overall, these results highlight the strong constraints under which DGRs diversify and expand, and elucidate several distinct roles these elements play in natural communities and in shaping microbial community structure and function in our environment.
Transcriptome Analysis in Yeast Reveals the Externality of Position Effect
Authors: Gui Qian , Deng Shuyun , Shi Wenjun , Cai Xiujuan , Zhou Zhen-Zhen , Yang Jian-Rong , Chen Xiaoshu 
Published: April 2020

ABSTRACTWhen a gene is integrated into the chromosome, its activity depends on the genomic context. Although this phenomenon of “position effect” was widely reported, how the integration event affects the local environment, or the “externality” of position effect, remained largely unexplored, let alone the mechanism or phenotypic consequence of such externality. Here, we examined the transcriptome profiles of ∼250Saccharomyces cerevisiaestrains, each withGFPinserted into a different locus of the wild-type strain. We found that the GFP expression level and the change of expression of genes near the integration site decreases in genomic regions with high density of essential genes. This observation was found associated with H3K4me2 by further joint-analysis with public genome-wide histone modification profiles. More importantly, we found that the expression changes of neighboring genes, but not the GFP expression, exerted a significant impact on cellular growth rate. As a result, genomic loci that grant higher GFP expression immediately after the integration will have lower total yield of GFP in the long run. Our results, which were consistent with the competition for transcriptional resources among neighboring genes, revealed a previously unappreciated facet of the position effect, and highlighted its impact on the fate of genomic integration of exogenous genes, which has profound implications for biological engineering and pathology of virus integrative to host genome.
Systematic Chromatin Architecture Analysis inXenopus tropicalisReveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes
Authors: Niu Longjian , Shen Wei , Shi Zhaoying , He Na , Wan Jing , Sun Jialei , Zhang Yuedong , Huang Yingzhang , Wang Wenjing , Fang Chao , Li Jiashuo , Zheng Piaopiao , Cheung Edwin , Chen Yonglong , Li Li , Hou Chunhui 
Published: April 2020

ABSTRACTMetazoan genomes are folded into 3D structures in interphase nuclei. However, the molecular mechanism remains unknown. Here, we show that topologically associating domains (TADs) form in two waves duringXenopus tropicalisembryogenesis, first at zygotic genome activation and then as the expression of CTCF and Rad21 is elevated. We also found TAD structures continually change for at least three times during development. Surprisingly, the directionality index is preferentially stronger on one side of TADs where orientation-biased CTCF and Rad21 binding are observed, a conserved pattern that is found in human cells as well. Depletion analysis revealed CTCF, Rad21, and RPB1, a component of RNAPII, are required for the establishment of TADs. Overall, our work shows thatXenopusis a powerful model for chromosome architecture analysis. Furthermore, our findings indicate that cohesin-mediated extrusion may anchor at orientation-biased CTCF binding sites, supporting a CTCF-anchored extrusion model as the mechanism for TAD establishment.
Glycan analysis of human neutrophil granules implicates a maturation-dependent glycosylation machinery
Authors: Venkatakrishnan Vignesh , Dieckmann Regis , Loke Ian , Tjondro Harry , Chatterjee Sayantani , Bylund Johan , Thaysen-Andersen Morten , Karlsson Niclas G. , Karlsson-Bengtsson Anna 
Published: April 2020

AbstractProtein glycosylation is essential to trafficking and immune functions of human neutrophils. During granulopoeisis in the bone marrow, distinct neutrophil granules are successively formed. Distinct receptors and effector proteins, many of which are glycosylated, are targeted to each type of granule according to their time of expression, a process called ‘targeting-by-timing’. Therefore, these granules are time capsules reflecting different times of maturation that can be used to understand how glycosylation evolves during granulopoiesis. Herein, neutrophil subcellular granules were fractionated by Percoll density gradient centrifugation andN- andO-glycans present in each compartment were analyzed by liquid chromatography and tandem mass spectrometry. We found abundant paucimannosidicN-glycans and lack ofO-glycans in early-formed azurophil granules (AG), whereas later-formed specific and gelatinase granules (SG and GG) contained complexN- andO-glycans with remarkably elongatedN-acetyllactosamine repeats with Lewis-x and sialyl-Lewis-x epitopes. Many glycans identified are unique to neutrophils and their complexity increased progressively from AG to SG and then to GG, suggesting temporal changes in the glycosylation machinery indicative of ‘glycosylation-by-timing’ during granulopoiesis. In summary, this comprehensive neutrophil granule glycome map, the first of its kind, highlights novel granule-specific glycosylation features and is a crucial first step towards a better understanding of the mechanisms regulating protein glycosylation during neutrophil granulopoiesis and a more detailed understanding of neutrophil biology and function.
The mediating role of human capital and management accounting information system in the relationship between innovation strategy and internal process performance and the impact on corporate financial performance
Authors: Hutahayan Benny 
Published: April 2020

PurposeAnalyze the importance of sustainable innovation strategy applied in manufacturing companies in Indonesia which affects the company's financial performance through several mediating variables.Design/methodology/approachThe population in this research was medium and large manufacturing company business units in East Java. Business units are part of a company considered as the profit center. The business unit as the unit of analysis in this research is part of the organization that: (1) is responsible for the production and marketing of a product or set of products; (2) is formed by product type; (3) has its own competitors which are different from competitors of other business units or divisions within a parent company; (4) has a manager who is responsible and has authority over the planning and implementation of strategies to achieve the specified profit target.FindingsInnovation strategy has a significant effect on financial performance. Human capital does not significantly mediate the relationship between innovation strategy and financial performance. Capital performance and internal performance do not mediate the relationship between innovation strategy and financial performance. Management accounting information system does not mediate the relationship between innovation strategy and financial performance. Internal process performance mediates the relationship between innovation strategy and financial performance. Management accounting information system and internal process performance mediate the relationship between innovation strategy and financial performance.Originality/valueThe difference in findings confirms that this research needs to be conducted. On the other hand, there is no research that has comprehensively tested the mediating effects of Human Capital and Management Accounting Information System in the relationship between Innovation Strategy and Internal Process Performance and the Impact on Corporate Financial Performance. The originality of this research can be seen in the use of contingency theory which narrows the gap between the industrial organization (I/O) paradigm and the resource-based view (RBV) regarding competitive advantage and performance. Specifically, this research introduces innovation strategy, human capital, management accounting information system, and internal business process performance as the contingency factors that affect financial performance. Second, empirically, this research tries to reduce the gap in empirical research by offering new research model and new research establishment at the level of strategic business units (SBU) in manufacturing companies in East Java. This research is expected to be useful for policy decision making, especially for managers who want to improve strategic business unit's financial performance.