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Large-Scale Analyses of Glycosylation in Cellulases

Genomics, Proteomics & bioinformatics 2009年第4期7卷 194-199页

作者： Fengfeng Zhou Victor Olman Ying Xu Computational Systems Biology Laboratory Department of Biochemistry and Molecular Biology/Institute of Bioinformatics University of Georgia Athens GA 30602-7229 USA BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge TN 37830-8050 USA.

Cellulases are important glycosyl hydrolases （GHs） that hydrolyze cellulose polymers into smaller oligosaccharides by breaking the cellulose β （1→4） bonds, and they are widely used to produce cellulosic ethanol from the plant biomass. N-linked and O-linked glycosylations were proposed to impact the catalytic efficiency, cellulose binding affinity and the stability of cellulases based on observations of individual cellulases. As far as we know, there has not been any systematic analysis of the distributions of N-linked and O-linked glycosylated residues in cellulases, mainly due to the limited annotations of the relevant functional domains and the glycosylated residues. We have computationally annotated the functional domains and glycosylated residues in cellulases, and conducted a systematic analysis of the distributions of the N-linked and O-linked glycosylated residues in these enzymes. Many N-linked glycosylated residues were known to be in the GH domains of cellulases, but they are there probably just by chance, since the GH domain usually occupies more than half of the sequence length of a cellulase. Our analysis indicates that the O-linked glycosylated residues are significantly enriched in the linker re- gions between the carbohydrate binding module （CBM） domains and GH domains of cellulases. Possible mechanisms are discussed.

关键词： glycosylation cellulase large-scale analyses

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Unveiling the multifaceted domain polymorphism of the Menshen antiphage system

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Nucleic acids research 2025年第9期53卷 gkaf357页

作者： Huan Li Yongjun Tan Dwaipayan Basu Kevin D Corbett Dapeng Zhang Department of Biology College of Arts and Sciences Saint Louis University Saint Louis MO 63103 United States. Department of Chemistry and Biochemistry University of California San Diego La Jolla CA 92093 United States. Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA 92093 United States. Department of Molecular Biology University of California San Diego La Jolla CA 92093 United States. Program of Bioinformatics and Computational Biology School of Science and Engineering Saint Louis University Saint Louis MO 63103 United States.

Recent advances have significantly enriched our understanding of complex bacteria-phage interactions. To date, over one hundred bacterial antiphage systems have been identified, yet the mechanisms of many, including the recently discovered Menshen system, remain elusive. We employed comparative genomics and protein bioinformatics for a systematic investigation of the Menshen system, focusing on its organization, structure, function, and evolution. By delineating six primary domain determinants and predicting their functions, we propose that the three components (NsnA-B-C) of Menshen likely act as sensor, transducer, and effector modules, respectively. Notably, we unveil remarkable polymorphism in domain composition within both NsnA and NsnC. NsnA proteins universally share ParB-DUF262 and DNA-binding ParBDB domains, and often include additional DNA-binding modules at their N-termini. NsnC effectors exhibit diverse inactive PIN (inPIN)-like domains for target recognition in their N-termini, and multiple nuclease domains for toxicity in their C-termini. We demonstrate that this multifaceted polymorphism results from the independent integration of various sensor domains into NsnA, alongside constant shuffling and diversification of the inPIN and effector domains in NsnC. These findings not only elucidate the functional diversity and inter-subunit interactions of the Menshen system, but also underscore its exceptional capacity for adaptability and versatility in the ongoing arms race between bacteria and phages.

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Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

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Chinese Chemical Letters 2021年第4期32卷 1515-1518页

作者： Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional *** NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE *** this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related *** order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB *** rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

关键词： Negative thermal expansion Conformational change Polyarylamides Density-functional theory Dibenzocyclooctadiene

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Neutral Theory and the Somatic Evolution of Cancer (vol 35, pg 1308, 2018)

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MOLECULAR biology AND EVOLUTION 2018年第6期35卷 1561-1561页

作者： Cannataro, Vincent L. Townsend, Jeffrey P. Department of Biostatistics Yale University New Haven CT Department of Biostatistics Yale University New Haven CT Program in Computational Biology and Bioinformatics Department of Ecology and Evolutionary Biology Yale University New Haven CT Corresponding author: E-mail: jeffrey.townsend@yale.edu. Associate editor

Kimura’s neutral theory argued that positive selection was not responsible for an appreciable fraction of molecular substitutions. Correspondingly, quantitative analysis reveals that the vast majority of substitutions in cancer genomes are not detectably under selection. Insights from the somatic evolution of cancer reveal that beneficial substitutions in cancer constitute a small but important fraction of the molecular variants. The molecular evolution of cancer community will benefit by incorporating the neutral theory of molecular evolution into their understanding and analysis of cancer evolution—and accepting the use of tractable, predictive models, even when there is some evidence that they are not perfect.

关键词： molecular evolution neutral theory cancer tumor genetics distribution of fitness effects somatic mutation

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Designing metabolic engineering strategies with genome-scale metabolic flux modeling

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Advances in Genomics and Genetics 2015年 5卷 93页

作者： Yen, Jiun Y Tanniche, Imen Fisher, Amanda K Gillaspy, Glenda E Bevan, David R Senger, Ryan S Department of Biological Systems Engineering Virginia Tech Department of Biochemistry Virginia Tech Genomics Bioinformatics and Computational Biology Interdisciplinary Program Virginia Tech

New in silico tools that make use of genome-scale metabolic flux modeling are improving the design of metabolic engineering strategies. This review highlights the latest developments in this area, explains the interface between these in silico tools and the experimental implementation tools of metabolic engineers, and provides a way forward so that in silico predictions can better mimic reality and more experimental methods can be considered in simulation studies. The several methodologies for solving genome-scale models (eg, flux balance analysis [FBA], parsimonious FBA, flux variability analysis, and minimization of metabolic adjustment) all have unique advantages and applications. There are two basic approaches to designing metabolic engineering strategies in silico, and both have demonstrated success in the literature. The first involves: 1) making a genetic manipulation in a model; 2) testing for improved performance through simulation; and 3) iterating the process. The second approach has been used in more recently designed in silico tools and involves: 1) comparing metabolic flux profiles of a wild-type and ideally engineered state and 2) designing engineering strategies based on the differences in these flux profiles. Improvements in genome-scale modeling are anticipated in areas such as the inclusion of all relevant cellular machinery, the ability to understand and anticipate the results of combinatorial enrichment experiments, and constructing dynamic and flexible biomass equations that can respond to environmental and genetic manipulations.

关键词： genome-scale modeling flux balance analysis flux variability analysis minimization of metabolic adjustment metabolic bottleneck pathway optimization

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A Comparison of Lossless Compression Methods in Microscopy Data Storage Applications: Microscopy compression comparison 23

A Comparison of Lossless Compression Methods in Microscopy D...

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6th International Conference on Software Engineering and Information Management, ICSIM 2023

作者： Walker, Logan Alexander Li, Ye McGlothlin, Maggie Cai, Dawen University of Michigan Biophysics Program Department of Computational Medicine and Bioinformatics United States University of Michigan Cell and Developmental Biology United States University of Michigan Cell and Developmental Biology Biophysics Program Neuroscience United States

ISBN: (纸本)9781450398237

Modern high-throughput microscopy methods such as light-sheet imaging and electron microscopy can produce petabytes of data inside of a single experiment. Storage of these large images, however, is challenging because of the difficulty of moving, storing, and analyzing such vast amounts of data, which is often collected at very high data rates (>1GBps). In this report, we provide a comparison of the performance of several compression algorithms using a collection of published and unpublished datasets including confocal, fMOST, and pathology images. We also use simulated data to demonstrate the efficiency of each algorithm as image content or entropy increases. As a result of this work, we recommend the use of the BLOSC algorithm combined with ZSTD for various microscopy applications, as it produces the best compression ratio over a collection of conditions. © 2023 ACM.

关键词： Information management

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Investigation of RNA-RNA Interactions Using the RISE Database

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Current Protocols in bioinformatics 2018年第1期64卷 e58/1-e58/1页

作者： Ju, Yanyan Gong, Jing Yang, Yucheng T. Zhang, Qiangfeng Cliff MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology Center for Synthetic and Systems Biology Tsinghua-Peking Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing China Department of Molecular Biophysics and Biochemistry Yale University New Haven CT United States Program in Computational Biology and Bioinformatics Yale University New Haven CT United States

RNA-RNA interactions (RRIs) are essential to understanding the regulatory mechanisms of RNAs. Mapping RRIs in vivo in a transcriptome-wide manner remained challenging until the recent development of several sequencing-based technologies. However, RRIs generated from large-scale studies had not been systematically collected and analyzed before. This article introduces RISE, a database of the RNA Interactome from Sequencing Experiments. RISE provides a comprehensive collection of RRIs in human, mouse, and yeast, derived from transcriptome-wide sequencing experiments, as well as targeted sequencing studies and other public databases/datasets. To facilitate better understanding of the biological roles of these RRIs, RISE also offers rich functional annotations involving RNAs, and an interactive interface to explore the analysis results. Here, we provide a brief description of the RISE website and a step-by-step protocol for using RISE to study RRIs. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

关键词： interaction RISE RNA RNA structure RNA-RNA sequencing experiments

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Refinement of under-determined loops of human prion protein by database-derived distance constraints

Refinement of under-determined loops of human prion protein ...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Feng Cui Kriti Mukhopadhyay Won-Bin Young Robert L. Jernigan Zhijun Wu Program on Bioinformatics and Computational Biology Department of Mathematics USA University Research Park Ames IA USA Department of Biochemistry Biophysics and Molecular Biology Iowa State University USA Program on Bioinformatics and Computational Biology USA

computational simulations of the conversion from the normal cellular prion (PrP c ) to the scrapie prion (PrP Sc ) are usually based on the structures determined by NMR because of the difficulties in crystallizing prion protein. Due to insufficient experimental restraints, a biologically critical loop region in PrP c (residues 167-171), which is a potential binding site for Protein X, is under-determined in most mammalian species. Here, we show that by adding information about distance constraints derived from a database of high-resolution protein structures, this under-determined loop as well as other secondary structural elements of the E200K variant of human prion protein (hPrP c ), a disease-related isoform, can be refined into more realistic structures in the structural ensemble with improved quality and increased accuracy. In particular, the ensemble becomes more compact after the refinement and the percentage of residues in the most favourable region of the Ramachandran diagram is increased to about 90% in the refined structures from the 80 to 85% range in the previously reported structures. Our results not only provide significantly improved structures of the prion protein and hence would facilitate insights into its conversion in the spongiform encephalopathies, but also demonstrate the strong potential for using databases of known protein structures for structure determination and refinement.

关键词： Humans Proteins Databases Diseases Nuclear magnetic resonance Genetic mutations computational biology Brain Pathogens Amino acids

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Optimization and Practical Use of Composition Based Approaches Towards Identification and Collection of Genomic Islands and Their Ontology in Prokaryotes

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Procedia Computer Science 2015年 51卷 670-679页

作者： Rian Pierneef Oliver Bezuidt Oleg N. Reva The University of Pretoria Department Biochemistry Bioinformatics and Computational Biology Unit Pretoria 0002 South Africa

Motivation Horizontally transferred genomic islands (islands, GIs) have been referred to as important factors which contribute towards bacterial evolution in general and particularly towards the emergences of pathogens and outbreak instances. The development of tools for identification of such elements and retracing their distribution will help to understand how such cases arise. Sequence composition has been used to identify GIs, infer their phylogeny; and determine their relative time of insertion. Collection of metadata on known GIs will enhance insight into horizontal gene transfer ontology and flow. Results This paper introduces the merger of SeqWord Genomic Islands Sniffer (SWGIS), which utilizes composition based approaches for identification of GIs in bacterial genomic sequences, and the Predicted Genomic Islands (Pre_GI) database, which houses 26,744 islands found in 2,407 bacterial plasmids and chromosomes. SWGIS is a standalone program that detects GIs using a set of optimized parametric measures with estimates of acceptable false positive and false negative rates. Pre_GI is a novel repository that includes island ontology and flux. This study furthermore illustrates the need for parametric optimization towards the prediction of GIs to minimize false negative and false positive predictions. In addition Pre_GI emphasizes the practicality of the compounded knowledge that the database affords in detection and visualization of ontological links between GIs. Availability SWGIS is freely available on the web at http://***/SeqWord/sniffer/*** , and Pre_GI is freely accessible at http://***/***.

关键词： Genomic island Horizontal gene transfer Database Ontology

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Uncertainty abounds, what now?

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Science 2025年第6740期387卷 1261页

作者： Dov Greenbaum Mark Gerstein The reviewer is at the Zvi Meitar Institute for Legal Implications of Emerging Technologies The reviewer is at the Harry Radzyner Law School The reviewer is at the Dina Recanati School of Medicine Reichman University Herzliya Israel The reviewer is at the Department of Biomedical Informatics and Data Science The reviewer is at the Program in Computational Biology and Bioinformatics The reviewer is at the Department of Computer Science Yale University New Haven CT USA.

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