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arXiv 2019年

作者： Burke, Paulo E.P. Costa, Luciano da F. Bioinformatics Graduate Program University of São Paulo São CarlosSP Brazil São Carlos Institute of Physics University of São Paulo PO Box 369 São CarlosSP13560-970 Brazil

Several interdisciplinary areas have appeared at the interface between biological and physical sciences. In this work, we suggest a complex network-based methodology for analyzing the interrelationships between some of these interdisciplinary areas, including bioinformatics, Computational Biology, Biochemistry, among others. This approach has been applied over respective data derived from Wikipedia. Related reviews from the scientific literature are also considered as a reference, yielding a respective bipartite hypergraph which can be used to gain insights about the interrelationships underlying the considered interdisciplinary areas. Several interesting results are obtained, including greater interconnection between the considered interdisciplinary areas with biological than with physical sciences. A good agreement was also found between the network obtained from Wikipedia and the interrelationships revealed by the literature reviews. At the same time, the former network was found to exhibit more intricate relationships than in the hypergraph derived from the literature review. Copyright © 2019, The Authors. All rights reserved.

关键词： Complex networks

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Mutations in protein kinase Cγ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition

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Science Signaling 2022年第753期15卷 eabk1147页

作者： Pilo, Caila A. Baffi, Timothy R. Kornev, Alexandr P. Kunkel, Maya T. Malfavon, Mario Chen, Dong-Hui Rossitto, Leigh-Ana Chen, Daniel X. Huang, Liang-Chin Longman, Cheryl Kannan, Natarajan Raskind, Wendy H. Gonzalez, David J. Taylor, Susan S. Gorrie, George Newton, Alexandra C. Department of Pharmacology University of California La Jolla San Diego 92037 CA United States Biomedical Sciences Graduate Program University of California La Jolla San Diego 92037 CA United States Department of Neurology University of Washington Seattle 98195 WA United States Institute of Bioinformatics University of Georgia Athens 30602 GA United States Queen Elizabeth University Hospital Glasgow G51 4TF United Kingdom Department of Biochemistry and Molecular Biology University of Georgia Athens 30602 GA United States Department of Medicine/Medical Genetics University of Washington Seattle 98195 WA United States Department of Psychiatry and Behavioral Sciences University of Washington Seattle 98195 WA United States Mental Illness Research Education and Clinical Center Department of Veterans Affairs Seattle 98108 WA United States

Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca2+-regulated protein kinase Cγ (PKCγ), leading to Purkinje cell degeneration and progre...

Spinocerebellar ataxia type 14 (SCA14) is a neurodegenerative disease caused by germline variants in the diacylglycerol (DAG)/Ca²⁺-regulated protein kinase Cγ (PKCγ), leading to Purkinje cell degeneration and progressive cerebellar dysfunction. Most of the identified mutations cluster in the DAG-sensing C1 domains. Here, we found with a FRET-based activity reporter that SCA14-associated PKCγ mutations, including a previously undescribed variant, D115Y, enhanced the basal activity of the kinase by compromising its autoinhibition. Unlike other mutations in PKC that impair its autoinhibition but lead to its degradation, the C1 domain mutations protected PKCγ from such down-regulation. This enhanced basal signaling rewired the brain phosphoproteome, as revealed by phosphoproteomic analysis of cerebella from mice expressing a human SCA14-associated H101Y mutant PKCγ transgene. Mutations that induced a high basal activity in vitro were associated with earlier average age of onset in patients. Furthermore, the extent of disrupted autoinhibition, but not agonist-stimulated activity, correlated with disease severity. Molecular modeling indicated that almost all SCA14 variants not within the C1 domain were located at interfaces with the C1B domain, suggesting that mutations in and proximal to the C1B domain are a susceptibility for SCA14 because they uniquely enhance PKCγ basal activity while protecting the enzyme from down-regulation. These results provide insight into how PKCγ activation is modulated and how deregulation of the cerebellar phosphoproteome by SCA14-associated mutations affects disease progression. Copyright © 2022 The Authors, some rights reserved.

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eIF3 Associates with 80S Ribosomes to Promote Translation Elongation, Mitochondrial Homeostasis, and Muscle Health

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Journal of Cleaner Production 2020年第4期79卷 575-587.e7页

作者： Lin, Yingying Li, Fajin Huang, Linlu Polte, Christine Duan, Haoran Fang, Jianhuo Sun, Li Xing, Xudong Tian, Guiyou Cheng, Yabin Ignatova, Zoya Yang, Xuerui Wolf, Dieter A. School of Pharmaceutical Sciences Fujian Provincial Key Laboratory of Innovative Drug Target Research Xiamen University Xiamen Fujian361102 China MOE Key Laboratory of Bioinformatics Center for Synthetic & Systems Biology School of Life Sciences Tsinghua University Beijing100084 China Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science Tsinghua University Beijing100084 China Biochemistry and Molecular Biology University of Hamburg Hamburg20146 Germany State Key Laboratory of Cellular Stress Biology Xiamen University Xiamen Fujian361102 China

eIF3, a multi-subunit complex with numerous functions in canonical translation initiation, is known to interact with 40S and 60S ribosomal proteins and translation elongation factors, but a direct involvement in translation elongation has never been demonstrated. We found that eIF3 deficiency reduced early ribosomal elongation speed between codons 25 and 75 on a set of ∼2,700 mRNAs encoding proteins associated with mitochondrial and membrane functions, resulting in defective synthesis of their encoded proteins. To promote elongation, eIF3 interacts with 80S ribosomes translating the first ∼60 codons and serves to recruit protein quality-control factors, functions required for normal mitochondrial physiology. Accordingly, eIF3e+/− mice accumulate defective mitochondria in skeletal muscle and show a progressive decline in muscle strength. Hence, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for mitochondrial physiology and muscle health. © 2020 Elsevier Inc.

关键词： Elongation

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A phase vocoder without requiring phase unwrapping

IEEJ Transactions on Electronics, Information and Systems

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IEEJ Transactions on Electronics, Information and Systems 2018年第4期138卷 352-359页

作者： Yoneguchi, Ryoichi Murakami, Takahiro Electrical Engineering Program Graduate School of Science and Technology Meiji University 1-1-1 Higashi-mita Tama-ku Kawasaki Kanagawa214-8571 Japan Department of Electronics and Bioinformatics School of Science and Technology Meiji University 1-1-1 Higashi-mita Tama-ku Kawasaki Kanagawa214-8571 Japan

In recent years, a number of algorithms for controlling parameters of an acoustic signal have been realized according as hardware technologies have been developed. A phase vocoder is one of the widely known methods for time scale modification (TSM) and pitch scale modification (PSM). The phase vocoder converts the length and the pitch of the acoustic signal by increasing or decreasing an instantaneous angular frequency. However, due to the phase unwrapping problem that occurs when the instantaneous angular frequency is estimated, the phase vocoder distorts the waveform of the modified signal. In order to alleviate this problem, we present a new algorithm for the phase vocoder. Our method does not encounter the phase unwrapping problem since we directly use the difference of phases between adjacent analysis frames to avoid estimating the instantaneous angular frequency. Moreover, our approach is effective even when the characteristics of the acoustic signal, e.g., a frequency and amplitude, change rapidly. © 2018 The Institute of Electrical Engineers of Japan.

关键词： Acoustic waves

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Genetic drift in range expansions is very sensitive to density feedback in dispersal and growth

arXiv

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arXiv 2019年

作者： Birzu, Gabriel Matin, Sakib Hallatschek, Oskar Korolev, Kirill S. Department of Physics Boston University BostonMA02215 United States Departments of Physics and Integrative Biology University of California BerkeleyCA94720 United States Department of Physics and Graduate Program in Bioinformatics Boston University BostonMA02215 United States

Theory predicts rapid genetic drift in expanding populations due to the serial founder effect at the expansion front. Yet, many natural populations maintain high genetic diversity in the newly colonized regions. Here, we investigate whether density-dependent dispersal could provide a resolution of this paradox. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because many more migrants from the diverse, high-density regions arrive at the expansion edge. When density-dependence is weak or negative, the effective population size of the front scales only logarithmically with the carrying capacity. The dependence, however, switches to a sublinear power law and then to a linear increase as the density-dependence becomes strongly positive. To understand these results, we introduce a unified framework that predicts how the strength of genetic drift depends on the density-dependence in both dispersal and growth. This theory reveals that the transitions between different regimes of diversity loss are controlled by a single, universal parameter: the ratio of the expansion velocity to the geometric mean of dispersal and growth rates at expansion edge. Importantly, our results suggest that positive density-dependence could dramatically alter evolution in expanding populations even when its contributions to the expansion velocity is small. Copyright © 2019, The Authors. All rights reserved.

关键词： Expansion

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Fast and Effective Clustering Method for Ancestry Estimation

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Procedia Computer Science 2019年 157卷 306-312页

作者： Arif Budiarto Bharuno Mahesworo James Baurley Teddy Suparyanto Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 BioRealm LLC USA Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia

Ancestry estimation which provides family history information is one of the most popular services in direct-to-consumer genomic testing. It is also an important task which aimed to reduce the confounding by ancestry on the relationship of genotypes and disease risk in assocation studies. Several methods have been developed to generate the best ancestry estimated scores even though some of them are still facing inefficient computation time. In this paper, a combination method between KMeans clustering and PCA is proposed estimate ancestry estimation from SNP genotyping data. This method was compared with baseline model, called fastSTRUCTURE, in term of the quality of clustering and computation time. Public data from 1000 Genome project is used to train and evaluate the proposed model and the baseline model. The proposed model can successfully generate clusters with better accuracy than fastSTRUCTURE (91.02% over 90.39%). More importantly, it can boost the computation time until 100 times faster than fastSTRUCTURE (from 490 seconds to 4.86 seconds).

关键词： Ancestry Estimation Population Stratification Clustering bioinformatics Genomics

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Author Correction: A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH

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Nature biotechnology 2023年第7期41卷 1027页

作者： Bojing Blair Jia Adam Jussila Colin Kern Quan Zhu Bing Ren Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Medical Scientist Training Program University of California San Diego La Jolla CA USA. Department of Cellular and Molecular Medicine Center for Epigenomics University of California San Diego La Jolla CA USA. Department of Cellular and Molecular Medicine Center for Epigenomics University of California San Diego La Jolla CA USA. biren@health.ucsd.edu. Ludwig Institute for Cancer Research La Jolla CA USA. biren@health.ucsd.edu. Institute of Genomic Medicine Moores Cancer Center School of Medicine University of California San Diego La Jolla CA USA. biren@health.ucsd.edu.

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Comparing the Accuracy of Multiple Commercial Wearable Devices: A Method

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Procedia Computer Science 2019年 157卷 567-572页

作者： Bens Pardamean Haryono Soeparno Bharuno Mahesworo Arif Budiarto James Baurley Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 BioRealm LLC USA

To maintain a good fitness level, performing a minimum daily physical activity is important. Many people think that they have already met the suggested guidelines. However, most of them were wrong when they quantify their activity level using a personal activity tracker device. This problem indicates the need for personal physical activity tracker or wearable device to maintain the fitness level. However, as wide-range wearable devices available today, it is difficult to find the most suitable one regarding the price and quality. This paper proposes a study to explore the association between the quality and the price of the devices. The quality is evaluated by comparing the accuracy of the heart rate sensor and step counter of several wearable devices with the ground truth measurements. The test result is then analyzed using a series of statistical methods including, a paired t-test, Pearson’s correlation test, and Bland-Altman plot. Both t-test and correlation coefficient is used to plot the association between quality and price.

关键词： Wearable Device Fitness Tracker Correlation Heart Rate Step Counting Bland-Altman

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A large-scale binding and functional map of human RNA-binding proteins (vol 583, pg 711, 2020)

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NATURE 2021年第7842期589卷 E5-E5页

作者： Van Nostrand, Eric L. Freese, Peter Pratt, Gabriel A. Wang, Xiaofeng Wei, Xintao Xiao, Rui Blue, Steven M. Chen, Jia-Yu Cody, Neal A. L. Dominguez, Daniel Olson, Sara Sundararaman, Balaji Zhan, Lijun Bazile, Cassandra Bouvrette, Louis Philip Benoit Bergalet, Julie Duff, Michael O. Garcia, Keri E. Gelboin-Burkhart, Chelsea Hochman, Myles Lambert, Nicole J. Li, Hairi McGurk, Michael P. Nguyen, Thai B. Palden, Tsultrim Rabano, Ines Sathe, Shashank Stanton, Rebecca Su, Amanda Wang, Ruth Yee, Brian A. Zhou, Bing Louie, Ashley L. Aigner, Stefan Fu, Xiang-Dong Lecuyer, Eric Burge, Christopher B. Graveley, Brenton R. Yeo, Gene W. Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA Institute for Genomic Medicine University of California San Diego La Jolla CA USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Medical Research Institute Wuhan University Wuhan China Program in Computational and Systems Biology Massachusetts Institute of Technology Cambridge MA USA Department of Biology Massachusetts Institute of Technology Cambridge MA USA Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA USA Institut de Recherches Cliniques de Montréal (IRCM) Montreal Quebec Canada Department of Biochemistry and Molecular Medicine Université de Montréal Montreal Quebec Canada Division of Experimental Medicine McGill University Montreal Quebec Canada Department of Genetics and Genome Sciences Institute for Systems Genomics UConn Health Farmington CT USA

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An integrated system of mobile application and IoT solution for pond monitoring

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IOP Conference Series: Earth and Environmental Science 2021年第1期794卷

作者： Ferdinan Darmalim Alam Ahmad Hidayat Tjeng Wawan Cenggoro Kartika Purwandari Sutristo Darmalim Bens Pardamean NusaNet Jakarta Indonesia 12710 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The current progress of information and communication technology has been critical to the development of the Internet of Things (IoT) in a aquaculture system. IoT solution in this system utilizes interconnectivity between devices to obtain fish pond monitoring data from sensing devices and then transmit the data to a remote server to be analyzed for decision-making in pond management. In this paper, we propose a smart pond IoT solution that provides a continuous and real-time pond monitoring. The system principally embeds five sensors that measure critical environmental parameters to determine water quality: temperature, pH, dissolved oxygen (DO), total dissolved solids (TDS), and salinity. The IoT solution also integrates the development of a mobile application on the android platform that allows remote monitoring capabilities for users to maintain efficient pond management. The application is designed with a friendly-user interface that helps the farmer to monitor sensor measurements, manage fish production cycle, record fish feeding schedule, and also monitor the health status of fish from multiple ponds.

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