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Transcriptomic Data Integration Inferring the Dominance of Starch Biosynthesis in Carbon Utilization of Developing Cassava Roots

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Procedia Computer Science 2012年 11卷 96-106页

作者： Wanatsanan Siriwat Saowalak Kalapanulak Malinee Suksangpanomrung Supatcharee Netrphan Asawin Meechai Treenut Saithong Bioinformatics and Systems Biology Program School of Bioresources and Technology and School of Information Technology King Mongkut's University of Technology Thonburi (Bang Khun Thian campus) Bangkok 10150 Thailand School of Bioresources and Technology King Mongkut's University of Technology Thonburi (Bang Khun Thian campus) Bangkok 10150 Thailand Systems Biology and Bioinformatics Research Group Pilot Plant Development and Training Institute King Mongkut's University of Technology Thonburi Bangkok 10150 Thailand National Center for Genetic Engineering and Biotechnology (BIOTEC) Pathumthani 12120 Thailand Department of Chemical Engineering King Mongkut's University of Technology Thonburi Bangkok 10140 Thailand

Carbon metabolism, which is an important process underlying the plant development, has been extensively studied in model plant Arabidopsis, however the understanding in this process for cassava root crop is very little. To enhance our understanding into the process, we studied carbon partitioning during cassava root development at the transcriptional level via transciptomic data integration into the metabolic pathways. The transcriptome data of three different developmental stages of cassava roots—fibrous root (FR), developing storage root (DR), and mature storage root (MR) from Yang et al. [1] —was integrated into the key carbon metabolism pathways reconstructed following the protocol of Rongsirikul et al. [2] . According to the 43 differentially expressed genes (56 proteins IDs) mapped into the pathways, we found that the genes involved in starch biosynthesis are more up-regulated, in contrast to the expression of genes in the cell wall biosynthesis and respiration. The results may imply the significance of starch biosynthesis among the carbon utilization processes in the developing cassava roots. In other words, the carbon source from α-D-glucose-1-phosphate (G1P) might be mostly used for starch biosynthesis rather than cell wall biosynthesis and respiration pathways during cassava root development.

关键词： carbon partitioning carbon metabolism pathway starch biosynthesis cassava root development data integration

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Study of enhancer-promoter interactome during mouse embryonic development with H3K4me3 PLAC-seq

Study of enhancer-promoter interactome during mouse embryoni...

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第十八次中国暨国际生物物理大会

作者： Miao Yu Rongxin Fang Ivan Juric Nathan Zemke Armen Abnousi Rong Hu Ming Hu Bing Ren School of Life Sciences Fudan University Ludwig Institute for Cancer Research Bioinformatics and Systems Biology Graduate Program University of California Department of Quantitative Health Sciences Lerner Research Institute Cleveland Clinic Foundation Center for Epigenomics Department of Cellular and Molecular Medicine University of California

Formation of long-range chromatin loops is a crucial step in transcriptional activation of target genes by distal enhancers. Mapping such structural features can help define target genes for enhancers and annotate non-coding sequence variants linked to human ***, we developed Proximity Ligation-Assisted ChIP-seq (PLAC-seq), which detects high-resolution long-range chromatin interactions at selected genomic regions through combination of in situ Hi-C and chromatin IP. We also developed a computational method, MAPS (Model-based Analysis of PLAC-seq and HiChIP) to process the data from such experiments and identify long-range chromatin interactions with high reproducibility and precision. By application of H3K4me3 PLAC-seq in mouse fetal tissues we identify182,403 long-range chromatin interactions at 10kb resolution. Through integrative analysis with RNA-seq, ATAC-seq and ChIP-seq data, we are able to link the genes with their potential regulatory enhancers.

关键词： Study of enhancer-promoter interactome during mouse embryonic development with H3K4me3 PLAC-seq

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Evolution at the edge of expanding populations

arXiv

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arXiv 2017年

作者： Deforet, Maxime Carmona-Fontaine, Carlos Korolev, Kirill S. Xavier, Joao B. Sorbonne Université Centre National de la Recherche Rcientifique Laboratoire Jean Perrin LJP Paris75005 France Center for Genomics and Systems Biology Department of Biology New York University New York CityNY10003 United States Department of Physics Graduate Program in Bioinformatics Boston University BostonMA02215 Program in Computational Biology Memorial Sloan-Kettering Cancer Center New York CityNY10065 United States

Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of evolution where organisms pay a reproductive cost to disperse faster. When does selection favor this 'survival of the fastest?' We searched for a simple rule, motivated by evolution experiments where swarming bacteria evolved into an hyperswarmer mutant which disperses ∼ 100% faster but pays a growth cost of ∼ 10% to make many copies of its flagellum. We analyzed a two-species model based on the Fisher equation to explain this observation: the population expansion rate (v) results from an interplay of growth (r) and dispersal (D) and is independent of the carrying capacity: v = 2 √rD. A mutant can take over the edge only if its expansion rate (v2) exceeds the expansion rate of the established species' (v1);this simple condition (v2> v1) determines the maximum cost in slower growth that a faster mutant can pay and still be able to take over. Numerical simulations and time-course experiments where we tracked evolution by imaging bacteria suggest that our findings are general: less favorable conditions delay but do not entirely prevent the success of the fastest. Thus, the expansion rate defines a traveling wave fitness, which could be combined with trade-offs to predict evolution of expanding populations. Copyright © 2017, The Authors. All rights reserved.

关键词： Bacteria

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The mTORC1 complex in pre-osteoblasts regulates whole-body energy metabolism independently of osteocalcin

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Bone Research 2021年第1期9卷 109-125页

作者： Pawanrat Tangseefa Sally K.Martin Peck Yin Chin James Breen Chui Yan Mah Paul A.Baldock Gary A.Wittert Amanda J.Page Christopher G.Proud Stephen Fitter Andrew C.W.Zannettino Adelaide Medical School Faculty of Health and Medical ScienceUniversity of AdelaideAdelaide5005 SAAustralia Cancer Program Precision Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaide5000 SAAustralia Research Centre for Reproductive Health School of Paediatrics and Reproductive HealthUniversity of AdelaideAdelaide5005 SAAustralia Computational&Systems Biology program Precision Medicine ThemeSouth Australian Health and Medical Research InstituteAdelaide5000 SAAustralia Robinson Research Institute University of AdelaideAdelaideSA 5005Australia Bioinformatics Hub University of AdelaideAdelaideSA 5005Australia Freemasons Foundation Centre for Men’s Health University of AdelaideAdelaide5005 SAAustralia Skeletal Metabolism Group Garvan Institute of Medical ResearchSydney2010 NSWAustralia Nutrition Diabetes&Metabolism ProgramLifelong Health ThemeSouth Australian Health and Medical Research InstituteAdelaide5000 SAAustralia School of Biological Sciences University of AdelaideAdelaide5005 SAAustralia Central Adelaide Local Health Network AdelaideSAAustralia

Overnutrition causes hyperactivation of mTORC1-dependent negative feedback loops leading to the downregulation of insulin signaling and development of insulin *** osteoblasts(OBs),insulin signaling plays a crucial role in the control of systemic glucose *** utilized mice with conditional deletion of Rptor to investigate how the loss of mTORC1 function in OB affects glucose metabolism under normal and overnutrition dietary *** to the controls,chow-fed Rptorob−/−mice had substantially less fat mass and exhibited adipocyte ***,upon feeding with high-fat diet,mice with pre-and post-natal deletion of Rptor in OBs were protected from diet-induced obesity and exhibited improved glucose metabolism with lower fasting glucose and insulin levels,increased glucose tolerance and insulin *** leanness and resistance to weight gain was not attributable to changes in food intake,physical activity or lipid absorption but instead was due to increased energy expenditure and greater whole-body substrate ***-seq revealed an increase in glycolysis and skeletal insulin signaling pathways,which correlated with the potentiation of insulin signaling and increased insulin-dependent glucose uptake in Rptorknockout ***,these findings point to a critical role for the mTORC1 complex in the skeletal regulation of wholebody glucose metabolism and the skeletal development of insulin resistance.

关键词： metabolism mTORC1 homeostasis

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HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

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Nature Communications 2021年第1期12卷 3366页

作者： Sahin, Merve Wong, Wilfred Zhan, Yingqian Van Deynze, Kinsey Koche, Richard Leslie, Christina S. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY United States Tri-Institutional Training Program in Computational Biology and Medicine New York NY United States Center for Epigenetics Research Memorial Sloan Kettering Cancer Center New York NY United States Bioinformatics Program University of California at San Diego San Diego CA United States

Recent genome-wide chromosome conformation capture assays such as Hi-C and HiChIP have vastly expanded the resolution and throughput with which we can study 3D genomic architecture and function. Here, we present HiC-DC+, a software tool for Hi-C/HiChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework. HiC-DC+ integrates with popular preprocessing and visualization tools and includes topologically associating domain (TAD) and A/B compartment callers. We found that HiC-DC+ can more accurately identify enhancer-promoter interactions in H3K27ac HiChIP, as validated by CRISPRi-FlowFISH experiments, compared to existing methods. Differential HiC-DC+ analyses of published HiChIP and Hi-C data sets in settings of cellular differentiation and cohesin perturbation systematically and quantitatively recovers biological findings, including enhancer hubs, TAD aggregation, and the relationship between promoter-enhancer loop dynamics and gene expression changes. HiC-DC+ therefore provides a principled statistical analysis tool to empower genome-wide studies of 3D chromatin architecture and function. © 2021, The Author(s).

关键词： Chromosomes Software Statistical methods

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Dental Disease Detection based on CNN for Panoramic Dental Radiographs 11

Dental Disease Detection based on CNN for Panoramic Dental R...

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11th IEEE International Conference on Intelligent Computing and Information systems, ICICIS 2023

作者： El Bagoury, Manar Al-Shetairy, Mirna Ahmed, Omar Mehanny, Samah S Hamdy, Tassneem Omar, Gihan Akram, Marwan Mohamed, Rana Amr, Hebatullah Gad, Walaa Ain Shams University Faculty of Computer and Information Sciences Bioinformatics Program Cairo Egypt Ain Shams University Faculty of Computer and Information Sciences Computer Science Department Cairo Egypt Faculty of Dentistry Cairo and Galala Universities Oral Biology Department Cairo Egypt Cairo University Faculty of Dentistry Oral and Maxillofacial Radiology Department Cairo Egypt Future University in Egypt Faculty of Oral and Dental Medicine Oral Radiology Department Cairo Egypt Ain Shams University Faculty of Computer and Information Sciences Information Systems Department Cairo Egypt

ISBN: (纸本)9798350322101

Panoramic dental radiography is one of the examination tools frequently performed in dental clinics and hospitals as it captures a wide range of the dental region and its surroundings, but due to the complex structure of the dental area and lack of time, dentists focus on tiny parts of the images. With the help of Machine Learning, dentists can detect dental defects and anomalies faster and more accurately. In this study, a data set of 733 panoramic radiographs of adult patients was collected from the faculty of Oral and Dental Medicine, Future University, Egypt. Using a combination of pre-trained CNN architecture and a finetuned network, the collected panoramic radiographs were used to determine the optimal architecture. The purpose of this research was to develop a computer-aided detection system based on a finetuned CNN algorithm, and to evaluate the accuracy and usefulness of this system for the detection of proximal and occlusal caries, interdental and inter radicular alveolar bone loss, periapical lesions, and impacted teeth in panoramic radiographs. Different object detection models were tested to detect selected dental diseases that were found in the panoramic radiographs, and after a few experiments, the YOLOv5 architecture was proved to be the most optimal after achieving 0.61 mAP@0.5 and 0.28 mAP@ [0.5-0.95] for the total six classes. This is the best-achieved results to our knowledge. © 2023 IEEE.

关键词： Object detection

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Structural insights into the role of N-terminal integrity in PhoSL for core-fucosylated N-glycan recognition

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International Journal of Biological Macromolecules 2024年 255卷 128309页

作者： Lou, Yuan-Chao Tu, Cheng-Fen Chou, Chun-Chi Yeh, Hsin-Hong Chien, Chia-Yu Sadotra, Sushant Chen, Chinpan Yang, Ruey-Bing Hsu, Chun-Hua Institute of Biomedical Sciences Academia Sinica Taipei115 Taiwan Department of Agricultural Chemistry National Taiwan University Taipei106 Taiwan Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300 Taiwan Biomedical Translation Research Center Academia Sinica Taipei115 Taiwan Ph.D. Program in Drug Discovery and Development Industry College of Pharmacy Taipei Medical University Taipei110 Taiwan Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei106 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei106 Taiwan Center for Computational and Systems Biology National Taiwan University Taipei106 Taiwan

PhoSL (Pholiota squarrosa Lectin) has an exceptional binding affinity for biomolecules with core-fucosylated N-glycans. This modification involves the addition of fucose to the inner N-acetylglucosamine within the N-glycan structure and is known to influence many physiological processes. Nevertheless, the molecular interactions underlying high-affinity binding of native PhoSL to core-fucosylated N-glycans remain largely unknown. In this study, we devised a strategy to produce PhoSL with the essential structural characteristics of the native protein (n-PhoSL). To do so, a fusion protein was expressed in E. coli and purified. Then, enzymatic cleavage and incubation with glutathione were utilized to recapitulate the native primary structure and disulfide bonding pattern. Subsequently, we identified the residues crucial for n-PhoSL binding to core-fucosylated chitobiose (N2F) via NMR spectroscopy. Additionally, crystal structures were solved for both apo n-PhoSL and its N2F complex. These analyses suggested a pivotal role of the N-terminal amine in maintaining the integrity of the binding pocket and actively contributing to core-fucose recognition. In support of this idea, the inclusion of additional residues at the N-terminus considerably reduced binding affinity and PhoSL cytotoxicity toward breast cancer cells. Taken together, these findings can facilitate the utilization of PhoSL in basic research, diagnostics and therapeutic strategies. © 2023 Elsevier B.V.

关键词： Proteins

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Comparative Genomics of Human Adenovirus Types 7,14 and 55 Emergent and Re-emergent in China:New Epidemic Threats

Comparative Genomics of Human Adenovirus Types 7,14 and 55 E...

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第五届武汉现代病毒学国际研讨会

作者： Qiwei Zhang Donald Seto Suhui Zhao Bin Cao Changbing Wang Bing Zhu Yi Chen Changwen Ke Lirong Zou Jie Zhou Shuping Jing Zetao Cheng Chengsong Wan School of Public Health and Tropical Medicine Southern Medical University Bioinformatics and Computational Biology Program School of Systems BiologyGeorge Mason UniversityManassasVAUSA Department of Infectious Diseases and Clinical Microbiology Beijing Chao-Yang Hospital Central Laboratory Guangzhou Women and Children's Medical Center Guangdong Provincial Center for Diseases Control and Prevention

Human adenovirus types 7,14 and 55(HAdV-B7,-B14 and -B55) caused several acute respiratory disease(ARD) outbreaks in America,Europe and Asia recently,including in *** genome of HAdV-B14 firstly isolated in China by us in 2010,is highly similar with those causing ARD outbreaks in US during 2006-2009,with 15 mismatches,3 deletions, 7 insertions and 99.92%identity,all belonging to the same genotype HAdV-B14p1 by

关键词： Comparative Genomics of Human Adenovirus Types 7,14 and 55 Emergent and Re-emergent in China:New Epidemic Threats

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Diversity and Suitability of the State-of-the-Art Wearable and Wireless EEG systems Review

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IEEE Journal of Biomedical and Health Informatics 2023年第8期27卷 3830-3843页

作者： He, Congying Chen, Yu-Yi Phang, Chun-Ren Stevenson, Cory Chen, I-Ping Jung, Tzyy-Ping Ko, Li-Wei Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Institute of Applied Arts National Yang Ming Chiao Tung University Hsinchu30010 Taiwan International Ph.D. Program in Interdisciplinary Neuroscience National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Institute for Neural Computation and Institute of Engineering in Medicine University of California San DiegoCA90093 United States National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Institute of Electrical and Control Engineering Department of Electronics and Electrical Engineering Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu30010 Taiwan Department of Biomedical Science and Environment Biology Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung80708 Taiwan

Wireless electroencephalography (EEG) systems have been attracting increasing attention in recent times. Both the number of articles discussing wireless EEG and their proportion relative to general EEG publications have increased over years. These trends indicate that wireless EEG systems could be more accessible to researchers and the research community has recognized the potential of wireless EEG systems. To explore the development and diverse applications of wireless EEG systems, this review highlights the trends in wearable and wireless EEG systems over the past decade and compares the specifications and research applications of the major wireless systems marketed by 16 companies. For each product, five parameters (number of channels, sampling rate, cost, battery life, and resolution) were assessed for comparison. Currently, these wearable and portable wireless EEG systems have three main application areas: consumer, clinical, and research. To address this multitude of options, the article also discussed the thought process to find a suitable device that meets personalization and use cases specificities. These investigations suggest that low-price and convenience are key factors for consumer applications, wireless EEG systems with FDA or CE-certification may be more suitable for clinical settings, and devices that provide raw EEG data with high-density channels are important for laboratory research. This article presents an overview of the current state of the wireless EEG systems specifications and possible applications and serves as a guide point as it is expected that more influential and novel research will cyclically promote the development of such EEG systems. © 2023 IEEE.

关键词： Electroencephalography

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An Investigation of the Required MR Bone Attenuation Correction for Quantitative Whole-Body PET/MR Imaging Using Clinical NaF PET/CT Studies

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International Journal of Medical Physics, Clinical Engineering and Radiation Oncology 2018年第3期7卷 273-295页

作者： Hua A. Ai Osama Mawlawi R. Jason Stafford Jim Bankson Yiping Shao Michele Guindani Richard E. Wendt III Department of Imaging Physics The University of Texas MD Anderson Cancer Center Houston USA Medical Physics Program The University of Texas Graduate School of Biomedical Sciences at Houston Houston USA Department of Radiation Oncology UT Southwest Medical Center Dallas USA Department of Biostatistics The University of Texas MD Anderson Cancer Center Houston USA Biostatistics Bioinformatics and Systems Biology Program The University of Texas Graduate School of Biomedical Sciences at Houston Houston USA

Tissue-classification-based attenuation correction strategies have been previously proposed to correct for bone attenuation in PET/MR imaging and simulated using computed tomography. However, the complication of voxel averaging uniquely associated with bone has not been considered explicitly in the past. This study investigated the effect of voxel averaging between bone and soft tissue in attenuation images and determined how accurately bone must be detected in MR images in order to perform acceptable attenuation correction of PET data by using CT-simulated attenuation correction. We found out that treating bone as soft tissue caused a mean quantification difference of -9.9% ± 5.5% in all 119 bone lesions. There were no significant differences between lesions in the pelvis and the vertebrae. The nominal difference in lesions in the ribs was significantly lower, likely due to the spatial misregistration between the emission and attenuation images. Interestingly, a non-monotonic relationship between the bone imaging ability and the absolute PET quantification accuracy was observed, with the minimal quantification difference achieved at a BVF around 40% for skull lesions (2.6% ± 2.1%), and 30% for non-skull lesions (1.4% ± 1.1%) and all lesions (1.5% ± 1.3%). This study established that a bone classification sensitivity of approximately 30% BVF is required in order for MR-based attenuation correction methods to achieve optimal quantification in whole-body PET/MR studies. For this purpose, higher bone imaging ability of MR may not be necessary.

关键词： PET/MR Attenuation Correction MR-Based Attenuation Correction

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