EVALUATION OF ASSISTANCE TOOLS FOR DIAGNOSIS OF DISEASES BY APPROACHING TO PERSONALIZED MEDICINE ON METAGENOMIC DATA by Phan Tấn Tài, Tạ Đặng Vĩnh Phúc, Phan Nguyễn Minh Thảo, Nguyễn Thị Ngọc Chăm, Đào Công Tính, Phạm Huỳnh Ngọc, Nguyễn Thanh Hải

“…In recent years, Metagenomic data, or “multi-genome” data, has been increasingly used for research in “personalized medicine” approaches with the purpose of improving and enhancing effectiveness in human health care. …”
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HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data. by Evan Gorstein, Rosa Aghdam, Claudia Solís-Lemus

“…Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm's behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. …”
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Screen of propionate-producing probiotic strains in attenuating murine colitis by modulating immune response and restoring the intestinal barrier by Ting Shu, Xizi Song, Silu Zhang, Xiaoli Zhou, Zhizhu Zhang, Pengfei Wang, Hu Canying, Jie Pan, Xiaoshuang Dai, Yan Tan, Wu Xiyang, Huicui Meng, Guoxun Xiao, Huaijie Hao

“…Probiotics produce propionate, a short-chain fatty acid that restores intestinal balance and reduces inflammation.Comparative genomic analysis of propionate pathway integrity was performed to nominate 41 candidate strains. …”
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A Protein with Unknown Function, Ps495620, Is Critical for the Sporulation and Oospore Production of <i>Phytophthora sojae</i> by Xiaoran Du, Yan Zeng, Yiying Li, Qin Peng, Jianqiang Miao, Xili Liu

“…An analysis of the <i>Phytophthora sojae</i> genome database identified the protein Ps495620, which has no domain annotations and functional predictions in <i>Phytophthora</i>. …”
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INTESTINAL MICROBIOME - A LEADING FACTOR IN HUMAN HEALTH AND DISEASES by E. Blum Hubert

“…Based on modern molecular, genetic, epigenetic microbiologic and biochemical studies it is, on the one hand, possible to identify disease-related point mutations and single nucleotide polymorphisms within genome-wide association analyses (GWAS). On the other hand, high throughput array and other technologies made it possible to simultaneously analyze thousands of genes (DNA) or gene products (RNA and proteins), resulting in an individual gene or gene expression profile (‘signature’) or to characterize the individual microbiome and its pathogenetic potential. …”
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Decoding the mechanisms behind second primary cancers by Meiyuan Zeng, Anqi Lin, Aimin Jiang, Zhengang Qiu, Hongman Zhang, Shifu Chen, Mingyan Xu, Zaoqu Liu, Quan Cheng, Jian Zhang, Peng Luo

“…This review summarizes recent studies on the mechanisms of SPCs, including the roles of genomic changes after first primary cancer (FPC) treatments, stromal cell phenotypic and metabolic changes, hormone levels and receptor expression, immunosuppression, aberrant gene methylation, EGFR signaling, and cell-free DNA in SPC development. …”
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Relationship between Periodontitis and Glaucoma: A Cross-Sectional Study by Soo Hwan Byun, Dae Myoung Yoo, Minwook Chang, Hyo Geun Choi, Seok Jin Hong

“…This prospective cohort study used epidemiological data from the Korean Genome and Epidemiology Study performed between 2004 and 2016. …”
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The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. by Patrick A Carroll, Brian W Freie, Pei Feng Cheng, Sivakanthan Kasinathan, Haiwei Gu, Theresa Hedrich, James A Dowdle, Vivek Venkataramani, Vijay Ramani, Xiaoying Wu, Daniel Raftery, Jay Shendure, Donald E Ayer, Charles H Muller, Robert N Eisenman

“…This is concomitant with dysregulation of the expression of male-specific GC transcripts and proteins. Our genomic and functional analyses identify loci directly bound by MLX involved in these processes, including metabolic targets, obligate components of male-specific GC development, and apoptotic effectors. …”
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Classifications of triple-negative breast cancer: insights and current therapeutic approaches by Ziqi Chen, Yumeng Liu, Minchuan Lyu, Chi Ho Chan, Meiheng Sun, Xin Yang, Shuangying Qiao, Zheng Chen, Sifan Yu, Meishen Ren, Aiping Lu, Ge Zhang, Fangfei Li, Yuanyuan Yu

“…Additionally, TNBC exhibits significant heterogeneity at histopathological, proteomic, transcriptomic, and genomic levels, further complicating the development of effective treatments. …”
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Psychrophilic Enzymes: From Folding to Function and Biotechnology by Georges Feller

“…Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. …”
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Dynamic changes of peptidome and release of polysaccharide in sea cucumber (Apostichopus japonicus) hydrolysates depending on enzymatic hydrolysis approaches by Yanchao Wang, Yan Song, Yaoguang Chang, Yanyan Liu, Guangning Chen, Changhu Xue

“…Here, inspired by the clarification of Apostichopus japonicus genome, we investigated the enzymatic hydrolysis of sea cucumber body wall by using the omics strategy. …”
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High Prevalence of Candida Yeast in Milk Samples from Cows Suffering from Mastitis in Poland by Bozena Dworecka-Kaszak, Alicja Krutkiewicz, Daniel Szopa, Miroslaw Kleczkowski, Malgorzata Biegańska

“…Seven different species classified as Candida were identified basing on phenotypic properties, and the dominating species was C. parapsilosis. Genomic DNA was isolated and amplified in PCR with ITS1 and NL2 primers. …”
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Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM by Matthew Cook, Christian Freniere, Chunxiang Wu, Faith Lozano, Yong Xiong

“…Summary: One of the striking features of human immunodeficiency virus (HIV) is the capsid, a fullerene cone comprised of pleomorphic capsid protein (CA) that shields the viral genome and recruits cofactors. Despite significant advances in understanding the mechanisms of HIV-1 CA assembly and host factor interactions, HIV-2 CA assembly remains poorly understood. …”
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Microbial methane production from calcium carbonate at moderately alkaline pH by Nicole A. Fiore, Anthony J. Kohtz, Daniel N. Miller, Sanjay Antony-Babu, Donald Pan, Caitlin Lahey, Xi Huang, Yongfeng Lu, Nicole R. Buan, Karrie A. Weber

“…Cells were observed in association with the carbonate mineral matrix via coherent anti-Stokes Raman scattering and two-photon excitation fluorescence microscopy. Genome-resolved metagenomics of the enrichment community confirmed the presence of a methanogen (Methanobacterium sp.) with the metabolic potential for hydrogenotrophic methanogenesis in addition to five bacterial community members. …”
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Antifungal Resistance and New Strategies to Control Fungal Infections by Patrick Vandeputte, Selene Ferrari, Alix T. Coste

“…Discovery of new putative antifungal targets is performed through genome-wide approaches for a better understanding of the human pathogenic fungi biology.…”
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Hypermutability bypasses genetic constraints in SCV phenotypic switching in Pseudomonas aeruginosa biofilms by Romina A. Tobares, Román A. Martino, Claudia A. Colque, Gaston L. Castillo Moro, Alejandro J. Moyano, Andrea G. Albarracín Orio, Andrea M. Smania

“…Through experimental evolution and whole-genome sequencing, we show that both wild-type and mutator strains undergo parallel evolution by accumulating compensatory mutations in factors regulating intracellular c-di-GMP levels, particularly in the Wsp and Yfi systems. …”
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Modelling the Effect of SPION Size in a Stent Assisted Magnetic Drug Targeting System with Interparticle Interactions by Adil Mardinoglu, P. J. Cregg

“…Cancer is a leading cause of death worldwide and it is caused by the interaction of genomic, environmental, and lifestyle factors. Although chemotherapy is one way of treating cancers, it also damages healthy cells and may cause severe side effects. …”
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The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children by Zeni Wu, Mingyue Jiang, Mengmeng Jia, Jian Sang, Qing Wang, Yunshao Xu, Li Qi, Weizhong Yang, Luzhao Feng

“…This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. …”
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Species-Specific Gene, spt5, in the Qualitative and Quantitative Detection of Boletus reticulatus by Zhan Lei, Chen Zhang, Yinjiao Li, Lunzhao Yi, Ying Shang

“…Meanwhile, SYBR Green I based quantitative PCR results were highly sensitive, and the limit of detection was 0.04 ng of genomic DNA. These experiments illustrated that spt5 is an ideal species-specific gene for the quantitative and qualitative detection of B. reticulatus. …”
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Primary Ovarian Choriocarcinoma: Rare Entity by Mequanent Tariku Adow, Shimelis Fantu Gebresilasie, Natnael Alemayehu Abebe

“…In patients with adnexal mass presenting with nonspecific symptoms especially with high Doppler blood flow of the mass on ultrasound evaluation, serum beta-human chorionic gonadotropin determination is recommended before laparotomy. In setups where the genomic test is not available, histological and clinical effort to differentiate gestational versus nongestational choriocarcinoma is useful for specific management decision.…”
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