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Creatine and l-carnitine attenuate muscular laminopathy in the LMNA mutation transgenic zebrafish

Scientific Reports 2024年第1期14卷 1-19页

作者： Pan, Shao-Wei Wang, Horng-Dar Hsiao, He-Yun Hsu, Po-Jui Tseng, Yung-Che Liang, Wen-Chen Jong, Yuh-Jyh Yuh, Chiou-Hwa Institute of Molecular and Genomic Medicine National Health Research Institutes Miaoli Zhunan Taiwan Institute of Biotechnology National Tsing Hua University Hsinchu Taiwan Department of Laboratory Medicine Mackay Memorial Hospital Taipei Taiwan Department of Medical Laboratory Science and Biotechnology Yuanpei University of Medical Technology Hsinchu Taiwan Department of Nursing MacKay Medical College Taipei Taiwan Marine Research Station Institute of Cellular and Organism Biology Academia Sinica I-Lan Taiwan Department of Pediatrics School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Graduate Institute of Clinical Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Pediatrics Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Translational Research Center of Neuromuscular Diseases Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Laboratory Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Drug Development and Value Creation Research Center Kaohsiung Medical University Kaohsiung Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu Taiwan Ph.D. Program in Environmental and Occupational Medicine Kaohsiung Medical University Kaohsiung Taiwan

Lamin A/C gene (LMNA) mutations contribute to severe striated muscle laminopathies, affecting cardiac and skeletal muscles, with limited treatment options. In this study, we delve into the investigations of five distinct LMNA mutations, including three novel variants and two pathogenic variants identified in patients with muscular laminopathy. Our approach employs zebrafish models to comprehensively study these variants. Transgenic zebrafish expressing wild-type LMNA and each mutation undergo extensive morphological profiling, swimming behavior assessments, muscle endurance evaluations, heartbeat measurement, and histopathological analysis of skeletal muscles. Additionally, these models serve as platform for focused drug screening. We explore the transcriptomic landscape through qPCR and RNAseq to unveil altered gene expression profiles in muscle tissues. Larvae of LMNA(L35P), LMNA(E358K), and LMNA(R453W) transgenic fish exhibit reduced swim speed compared to LMNA(WT) measured by DanioVision. All LMNA transgenic adult fish exhibit reduced swim speed compared to LMNA(WT) in T-maze. Moreover, all LMNA transgenic adult fish, except LMNA(E358K), display weaker muscle endurance than LMNA(WT) measured by swimming tunnel. Histochemical staining reveals decreased fiber size in all LMNA mutations transgenic fish, excluding LMNA(WT) fish. Interestingly, LMNA(A539V) and LMNA(E358K) exhibited elevated heartbeats. We recognize potential limitations with transgene overexpression and conducted association calculations to explore its effects on zebrafish phenotypes. Our results suggest lamin A/C overexpression may not directly impact mutant phenotypes, such as impaired swim speed, increased heart rates, or decreased muscle fiber diameter. Utilizing LMNA zebrafish models for drug screening, we identify l-carnitine treatment rescuing muscle endurance in LMNA(L35P) and creatine treatment reversing muscle endurance in LMNA(R453W) zebrafish models. Creatine activates AMPK and mTOR pathw

关键词： Creatine l-Carnitine LMNA Striated muscle laminopathy Zebrafish

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Characterization and expression of the microtubule associated protein tau gene isoforms and their impact on clinical outcomes in glioma patients

Computational and Structural Biotechnology Reports

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Computational and Structural Biotechnology Reports 2024年 1卷

作者： Axel M. Hidalgo Vipin Singh Thenral Mangadu Deblina Guha Enrique I. Ramos Chandrima Das Shrikanth S. Gadad Bioinformatics Program The University of Texas at El Paso USA Center of Emphasis in Cancer Department of Molecular and Translational Medicine Texas Tech University Health Sciences Center El Paso 130 Rick Francis st. El Paso TX 79905 USA Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics 1/AF Bidhannagar Kolkata 700064 India Minority AIDS Research Center Department of Health Sciences The University of Texas at El Paso TX 79968 USA The University of Texas at El Paso TX 79968 USA HomiBhaba National Institute Mumbai 400094 India L. Frederick Francis Graduate School of Biomedical Sciences Texas Tech University Health Sciences Center El Paso 130 Rick Francis st. El Paso TX 79905 USA Mays Cancer Center UT Health San Antonio MD Anderson Cancer Center San Antonio TX 78229 USA

Gliomas are the most common tumors found in the central nervous system. They are classified based on their histopathological malignancy. Low-grade gliomas (LGG) can turn into glioblastomas (GBM), the most aggressive form of brain cancer with the worst prognosis. Previous studies have shown that microtubule-associated protein tau ( MAPT ) is increased in GBM and that reducing it can improve survival in animal models. On the other hand, elevated MAPT expression has been linked to increased survival in LGG, indicating its potential as a survival biomarker. However, previous studies have primarily focused on the canonical protein-coding transcripts and gene-level expression of MAPT , disregarding the diversity of its many isoforms. Many diseases in almost every tissue have been associated with a dysregulation of alternative splicing, either through an altered ratio of the expressed isoforms or by expressing aberrant transcripts with different alternative transcription start and termination sites. This study investigates the association of specific MAPT transcripts with survival in LGG and GBM using publicly available genomic datasets and performing statistical analyses. The results of the study indicated coding and several non-coding isoforms associated with overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). After including the relevant predictors as covariates, it was observed that among the protein-coding isoforms, MAPT-205 and MAPT-201 were significantly associated with clinical survival endpoints, but with opposite trends. These findings highlight the importance of studying the role of MAPT isoforms in glioma cellular phenotypes, aggressiveness, and patient survival.

关键词： Transcription Gene expression Differential exon usage Isoforms

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Comparing the Efficacy and Safety of Treating Chronic Hepatitis B Infection during Pregnancy with Lamivudine,Telbivudine,and Tenofovir:A Meta-analysis

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Journal of Clinical and Translational Hepatology 2019年第3期7卷 197-212页

作者： Shahnaz Sali Mohammad Darvishi Mojtaba GhasemiAdl Meisam Akhlaghdoust Azin Mirzazadeh Somayeh Elikaei Behjati Hossein Sheikh-Zeinolabedini Shervin Shokouhi Soheil Tavakolpour Infectious Diseases and Tropical Medicine Research Center Shahid Beheshti University of Medical SciencesTehranIran Department of Aerospace and Subaquatic Medicine Infectious Diseases and Tropical Medicine Research Center(IDTMRC)AJA University of Medical SciencesTehranIran Pharmaceutical Sciences Research Center Tehran University of Medical SciencesTehranIran Pars Advanced and Minimally Invasive Medical Manners Research Center Pars HospitalIran University of Medical SciencesTehranIran Joint Bioinformatics Graduate Program University of Arkansas Little Rock and University of Arkansas for Medical SciencesLittle RockARUSA The Genetics Department at Islamic Azad University Science and Research BranchTehranIran Infectious Diseases and Tropical Medicine Research Center Shahid Beheshti University of Medical SciencesTehran 198396-3113Iran

Background and Aims:The perinatal transmission of hepatitis B virus(HBV)remains an important global health ***,a systematic review and meta-analysis were conducted to evaluate the evidence regarding the efficacy and maternal/fetal safety of treating pregnant women with lamivudine,telbivudine(LdT),and tenofovir(TDF).Methods:A PubMed and Scopus search resulted in 1,076 records,which were reduced to 36,containing 7,717 pregnant women with chronic HBV infection and 7467 infants meeting the inclusion *** latest search was in August ***:Treatment with LdT,but not lamivudine and TDF,could significantly reduce the hepatitis B virus surface antigen-positive rate(odds ratio(OR)=0.37)in infants;it also led to higher rates of hepatitis B e antigen loss(OR=12.14),hepatitis B e antigen seroconversion(OR=8.93),and alanine aminotransferase normalization in mothers(OR=1.49).Each of these treatments was able to significantly reduce HBV DNA positivity at birth(total OR=0.19)and mother-to-child-transmission of HBV(total OR=0.15),and to cause higher rates of HBV DNA suppression in mothers(total OR=25.53).However,nucleos(t)ide analogues might also be involved in creatine kinase elevation(total OR=7.48).In contrast,no significant association was found between nucleos(t)ide analogue therapy and preterm/premature births,congenital malformation,low birth weight,and abortion or fetal/infant *** results suggested LdT's high capability of preventing ***,TDF failed to show significant associations to a reduced risk of mother-to-child-transmission,probably due to the low number of patients ***:Although using either lamivudine,LdT,orTDF could lead to more favorable maternal/fetal outcomes,LdT seemed to show more potential in resolving certain infant-and maternal-related *** studies on the safety profile of such treatments are required.

关键词： Hepatitis B virus Antiviral therapy Tenofovir Telbivudine Lamivudine Nucleos(t)ide analogues Pregnancy

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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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Analysis of Acoustic Features in Gender Identification Model for English and Bahasa Indonesia Telephone Speeches

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Procedia Computer Science 2019年 157卷 199-204页

作者： Muhamad Fitra Kacamarga Tjeng Wawan Cenggoro Arif Budiarto Reza Rahutomo Bens Pardamean Eureka.ai 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 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

One of the most interesting topics in auditory problem is determining gender of the speaker. In recent years, machine learning has gained significant attentions as a way to build a classifier from labeled data which also can be implemented to build a gender classifier. In this study we develop gender classifier using two different datasets with different languages, English and Bahasa Indonesia. Each data from both datasets is represented by 20 acoustic features. Multi Layer Perceptron (MLP) is used to build the classification model using all these features and trained only on English dataset. This model is evaluated in both dataset to get the performance matrices consist of accuracy, AUROC, precision and recall. Ultimately, using this model we also identify and compare important features from both dataset to see the different characteristics of English and Bahasa Indonesia speeches.

关键词： Gender Identification Acoustic Feature Speech Recognition

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Lockdown strategy worth lives: The SEIRD modelling in COVID-19 outbreak in Indonesia

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IOP Conference Series: Earth and Environmental Science 2021年第1期729卷

作者： I Nurlaila A A Hidayat B Pardamean Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta Indonesia 11480 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 Indonesia 11480

Lockdowns, despite their conflicting restrictions and consequences they might offer when enforced as a national strategy, are deemed to be suggestive for a prompt conquer to the Coronavirus Disease-19 (COVID-19) outbreak. There have been some success stories such as in China, South Korea and our ASEAN member fellow, Vietnam, which exhibited extremely fallen numbers of COVID-19 cases post the enforcement of lockdown. Indonesia, however, remains in the crux of dispute whether or not the lockdown is opted to force COVID-19 transmission down under control. We, in this respect, employ the most popular model which has been broadly applied in the field of epidemiology, referred to as SEIRD (Susceptible, Exposed, Infectious, Recovered, and Death), the extension form of an age-structured SEIR, where the Death (D) is included to provide more factual situation. We modify the I (Infectious) fraction as symp-tomatic (Is) and asymptomatic (Ia) infectives. There are three lockdown scenarios simulated in our modified SEIRD with the starting date are 26 April 2020 when the immediate lockdown was enacted-and a-week and two-week-gaps, respectively. We figured out that by stipulating the lockdown without delay (26 April 2020), the new cases could be kept below 10,000. A week delay escalates case number to 5,000 and delay for one more week results in beyond 20,000 new cases. Furthermore, when the intervention is delayed following the delayed lockdown, normalization would demand a longer period within which dealing with more critical and dying patients is unavoidable and should be more anticipated.

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PapSmear Image Recording System for Artificial Intelligence Data Collection

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

作者： Tjeng Wawan Cenggoro 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 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Cervical cancer is one of the most leading causes of death for women worldwide. To reduce the mortality caused by cervical cancer, early screening techniques such as pap smear need to be carried out more extensively. Forthat, the availability of an automatic screening system is essential. In this paper, we proposed a system that can collect the dataset needed to train an Artificial Intelligence (AI) system for the automatic pap smear screening system. The proposed system can be integrated seamlessly to the current pap smear result recording procedure; hence avoiding any possible complication.

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DNAku Consumers Profile: One of The First Direct to Customer Genetics Testing in Indonesia

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

作者： Deby Erina Parung Kians Azizatikarna Dian Amirulloh Erlin Listiyaningsih Bharuno Mahesworo Arif Budiarto Simon Bens Pardamean Genetics Indonesia Jakarta Indonesia 12940 Bioinformatics & 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 Program Bina Nusantara University Jakarta Indonesia 11480

DNAku test is one of the first direct to customer genetics testing in Indonesia. DNAku test came with a different approach as it gave their customer reports of their genetic predisposition to corresponding traits. Four months after launch, we create consumer report of this genetics testing based on DNAku questionnaire results. We applied three statistical methods, including descriptive statistics, multivariate normality test, and t-test to the demographic data of the DNAku customers. The result shows population clusters which may represent population groups that are interested in genetics testing. The questionnaire also has questions about the customer's lifestyle. The results of these questions were processed to find the lifestyle of DNAku customers.

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Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil (vol 13, 1004, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-11页

作者： Naslavsky, Michel S. Scliar, Marilia O. Yamamoto, Guilherme L. Wang, Jaqueline Yu Ting Zverinova, Stepanka Karp, Tatiana Nunes, Kelly Ceroni, Jose Ricardo Magliocco de Carvalho, Diego Lima da Silva Simoes, Carlos Eduardo Bozoklian, Daniel Nonaka, Ricardo dos Santos Brito Silva, Nayane da Silva Souza, Andreia de Souza Andrade, Heloisa Passos, Marilia Rodrigues Silva Castro, Camila Ferreira Bannwart Mendes-Junior, Celso T. Mercuri, Rafael L. V. Miller, Thiago L. A. Buzzo, Jose Leonel Rego, Fernanda O. Araujo, Nathalia M. Magalhaes, Wagner C. S. Mingroni-Netto, Regina Celia Borda, Victor Guio, Heinner Rojas, Carlos P. Sanchez, Cesar Caceres, Omar Dean, Michael Barreto, Mauricio L. Lima-Costa, Maria Fernanda Horta, Bernardo L. Tarazona-Santos, Eduardo Meyer, Diogo Galante, Pedro A. F. Guryev, Victor Castelli, Erick C. Duarte, Yeda A. O. Passos-Bueno, Maria Rita Zatz, Mayana Human Genome and Stem Cell Research Center University of São Paulo São Paulo SP Brazil Department of Genetics and Evolutionary Biology Biosciences Institute University of São Paulo São Paulo SP Brazil Hospital Israelita Albert Einstein São Paulo SP Brazil Instituto da Criança Faculdade de Medicina da Universidade de São Paulo São Paulo SP Brazil Orthopedic Research Labs Boston Children’s Hospital and Department of Genetics Harvard Medical School Boston MA USA Laboratório DASA São Paulo Brazil Laboratory of Genome Structure and Ageing European Research Institute for the Biology of Ageing University Medical Center Groningen Groningen Netherlands São Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory School of Medicine Botucatu State of São Paulo Brazil São Paulo State University (UNESP) Department of Pathology School of Medicine Botucatu State of São Paulo Brazil Departamento de Química Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto São Paulo Brazil Centro de Oncologia Molecular Hospital Sirio-Libanes São Paulo Brazil Department of Biochemistry Institute of Chemistry University of São Paulo São Paulo São Paulo Brazil Bioinformatics Graduate program University of São Paulo São Paulo Brazil Departamento de Genética Ecologia e Evolução Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte MG Brazil Núcleo de Ensino e Pesquisa Instituto Mário Penna Belo Horizonte MG Brazil Laboratorio de Biotecnologia y Biologia Molecular Instituto Nacional de Salud Lima Peru Universidad de Huánuco Huánuco Peru Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA Instituto de Saúde Coletiva Universidade Federal da Bahia Salvador BA 40110-040 Brazil Center for Data and Knowledge Integration for Health Institute Gonçalo Muniz Fundação Oswaldo Cruz Salvador BA Brazil Instituto de Pesquisas René Rachou Fundação Os

As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS.

关键词： Data publication and archiving Haplotypes Mobile elements Rare variants Structural variation

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A Design of Deep Learning Experimentation for Fruit Freshness Detection

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

作者： Febrian Valentino Tjeng Wawan Cenggoro Bens Pardamean Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480 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

Indonesia is a country with a tropical climate so that fruit and vegetable plants can grow easily in *** have many good nutrients such as vitamins, proteins and others. But the fruit also has a period where the fruit is said to be fresh *** this time there are still many fruit supplier companies that send fruit unfit for consumption due to lack of accuracy in the process of sorting the fruit when the fruit is taken from the plantation and the entry of other fruit into an improper packaging. Thus, it makes detecting food spoilage from the production stage to consumption is very important. We propose a design of computer vision-based technique usingdeep learning with the Convolutional Neural Network (CNN) model to detect fruit freshness. The specially designed CNN model is then evaluated with public datasets of fruits fresh and rotten for classification derived from Kaggle.

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