Macronutrient balance determines the human gut microbiome eubiosis: insights from in vitro gastrointestinal digestion and fermentation of eight pulse species by Da Bin Lee, In Seon Hwang

“…The interactions between macronutrients, the human gut microbiome, and their metabolites (short-chain fatty acids) were comprehensively investigated via an in vitro digestion and fermentation model subjected to eight pulse species. 16S rRNA sequencing and taxonomic analysis of pulse digesta fermented for up to 24 h revealed an increase in the relative abundance of gut health-detrimental genera represented by Escherichia-Shigella in kidney bean, soybean, cowpea, chickpea, and black bean samples. …”
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Support Vector Machine – Recursive Feature Elimination for Feature Selection on Multi-omics Lung Cancer Data by Nuraina Syaza Azman, Azurah A Samah, Ji Tong Lin, Hairudin Abdul Majid, Zuraini Ali Shah, Nies Hui Wen, Chan Weng Howe

“…Biological data obtained from sequencing technologies is growing exponentially. Multi-omics data is one of the biological data that exhibits high dimensionality, or more commonly known as the curse of dimensionality. …”
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Maternal obesity increases hypothalamic miR-505-5p expression in mouse offspring leading to altered fatty acid sensing and increased intake of high-fat food. by Laura Dearden, Isadora C Furigo, Lucas C Pantaleão, L W P Wong, Denise S Fernandez-Twinn, Juliana de Almeida-Faria, Katherine A Kentistou, Maria V Carreira, Guillaume Bidault, Antonio Vidal-Puig, Ken K Ong, John R B Perry, Jose Donato, Susan E Ozanne

“…Using a mouse model of maternal obesity, we observed increased intake of a high-fat diet (HFD) in offspring of obese mothers that precedes the development of obesity. Through small RNA sequencing, we identified programmed overexpression of hypothalamic miR-505-5p that is established in the fetus, lasts to adulthood and is maintained in hypothalamic neural progenitor cells cultured in vitro. …”
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Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024. by Andrew D Marques, Matthew Hogenauer, Natalie Bauer, Michelle Gibison, Beatrice DeMarco, Scott Sherrill-Mix, Carter Merenstein, Ronald G Collman, Roderick B Gagne, Frederic D Bushman

“…From the 165 SARS-CoV-2 positive WTD, we recovered 25 whole genome sequences and an additional 17 spike-targeted amplicon sequences. …”
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Clinical Report of a 17q12 Microdeletion with Additionally Unreported Clinical Features by Jennifer L. Roberts, Stephanie K. Gandomi, Melissa Parra, Ira Lu, Chia-Ling Gau, Majed Dasouki, Merlin G. Butler

“…Since syndrome-specific DNA sequencing studies failed to provide an explanation for this patient’s unusual habitus, we postulate that this case represents an expansion of the 17q12 microdeletion phenotype. …”
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Wharton’s Jelly-Derived Mesenchymal Stem Cells with High Aurora Kinase A Expression Show Improved Proliferation, Migration, and Therapeutic Potential by Sun Jeong Kim, Sang Eon Park, Jang Bin Jeong, Shin Ji Oh, Alee Choi, Yun Hee Kim, Suk-joo Choi, Soo-young Oh, Gyu Ha Ryu, Hong Bae Jeon, Jong Wook Chang

“…This study is aimed at identifying the upregulated genes in human Wharton’s jelly-derived MSCs (WJ-MSCs) with high proliferation potential using mRNA sequencing. Aurora kinase A (AURKA) and dedicator of cytokinesis 2 (DOCK2) were selected as the upregulated genes, and their effects on proliferation, migration, and colony formation of the WJ-MSCs were verified using small interfering RNA (siRNA) techniques. mRNA expression levels of both the genes were positively correlated with the proliferation capacity of WJ-MSCs. …”
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Genetic Analysis Reveals A Missense Mutation In Reactivation Gene-2 Causing Severe Combined Immunodeficiency Disease In A Pakistani Family by Shahida Awais, Lubna Siddique, Nida Shafi, Sobia Humerah, Summyah Niazi, Wafa Omer

“…Estimation of serum immunoglobulin’s were performed. DNA Sanger sequencing of RAG2 gene was performed to identify gene mutation. …”
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Molecular identification and genetic diversity analysis of Cryptosporidium spp. infecting dogs from central and northern Jordan: Detection of zoonotic genotype IId. by Rami M Mukbel, Eman M Etoom, Haifa B Hammad, Heidi L Enemark, Marwan M Abu Halaweh

“…Among the successfully sequenced samples, 25 (58.1%) were Cryptosporidium canis, 15 (34.9%) were Cryptosporidium parvum, and three (7.0%) were Cryptosporidium baileyi. …”
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Pain in Parkinson's Disease Associated with COMT Gene Polymorphisms by Wanjun Li, Yongqian Chen, Bowen Yin, Limei Zhang

“…Polymorphisms rs4633 and rs6267 were detected by PCR and direct sequencing. Results. Fifty-seven percent of PD patients experienced pain, consisting of PD-related pain (64.91%) (the majority was dystonia pain) and non-PD-related pain (35.09%) (psychogenic pain was most frequent). …”
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Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations by Carmen Molina-Pardines, Jose M. Haro-Moreno, Francisco Rodriguez-Valera, Mario López-Pérez

“…Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract…”
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A machine learning decision support tool optimizes WGS utilization in a neonatal intensive care unit by Edwin F. Juarez, Bennet Peterson, Erica Sanford Kobayashi, Sheldon Gilmer, Laura E. Tobin, Brandan Schultz, Jerica Lenberg, Jeanne Carroll, Shiyu Bai-Tong, Nathaly M. Sweeney, Curtis Beebe, Lawrence Stewart, Lauren Olsen, Julie Reinke, Elizabeth A. Kiernan, Rebecca Reimers, Kristen Wigby, Chris Tackaberry, Mark Yandell, Charlotte Hobbs, Matthew N. Bainbridge

“…Abstract The Mendelian Phenotype Search Engine (MPSE), a clinical decision support tool using Natural Language Processing and Machine Learning, helped neonatologists expedite decisions to whole genome sequencing (WGS) to diagnose patients in the neonatal intensive care unit. …”
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Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer’s disease by Michael H. Guo, Wan-Ping Lee, Badri Vardarajan, Gerard D. Schellenberg, Jennifer E. Phillips-Cremins

“…Here, we genotype 312,731 polymorphic STR tracts genome-wide using PCR-free whole genome sequencing data from 2981 individuals (1489 AD case and 1492 control individuals). …”
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Ensemble Methods with Voting Protocols Exhibit Superior Performance for Predicting Cancer Clinical Endpoints and Providing More Complete Coverage of Disease-Related Genes by Runyu Jing, Yu Liang, Yi Ran, Shengzhong Feng, Yanjie Wei, Li He

“…In genetic data modeling, the use of a limited number of samples for modeling and predicting, especially well below the attribute number, is difficult due to the enormous number of genes detected by a sequencing platform. In addition, many studies commonly use machine learning methods to evaluate genetic datasets to identify potential disease-related genes and drug targets, but to the best of our knowledge, the information associated with the selected gene set was not thoroughly elucidated in previous studies. …”
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Construction and Antiapoptosis Activities of Recombinant Adenoviral Expression Vector Carrying EBV Latent Membrane Protein 2A by Xishuang Liu, Yu Gao, Bing Luo, Youan Zhao

“…The vAd-2A was successfully constructed and identified by PCR, restriction digestion, and sequencing. LMP2A expression in SGC was identified by strong green fluorescence expression with fluorescence microscopic photograph and Southern blotting. …”
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Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome by Thi Kim Lien Nguyen, Van Dem Pham, Thu Huong Nguyen, Trung Kien Pham, Thi Quynh Huong Nguyen, Huy Hoang Nguyen

“…All 29 exons and exon-intron boundaries of NPHS1 were analyzed by PCR and DNA sequencing. Genetic analysis of the NPHS1 gene revealed one compound heterozygous variant p.Glu117Lys, one heterozygous missense mutation p.Asp310Asn, and one heterozygous frame-shifting mutation (c.3250_3251insG causing p.Val1084Glyfs⁎12) in patient 1. …”
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A Novel Mutation of the Calcium-Sensing Receptor Gene Causing Familial Hypocalciuric Hypercalcemia Complicates Medical Followup after Roux-en-Y Gastric Bypass: A Case Report and a... by Elin Rebecka Carlsson, Mai-Britt Toft Nielsen, Anne Mette Høgh, Rikke Veggerby Grønlund, Mogens Fenger, Louise Ambye

“…We describe a case of a 36-year-old woman with hypercalcemia and elevated PTH, initially suspected of having PHPT. Sequencing of the CaSR-gene revealed a mutation in nucleotide 437, changing the amino acid in position 146 from Glycine to Aspartate. …”
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KRAS and BRAF Mutation Detection: Is Immunohistochemistry a Possible Alternative to Molecular Biology in Colorectal Cancer? by Nicolas Piton, Francesco Borrini, Antonio Bolognese, Aude Lamy, Jean-Christophe Sabourin

“…Currently, KRAS and BRAF evaluation is based on molecular biology techniques such as SNaPshot or Sanger sequencing. As molecular testing is performed on formalin-fixed paraffin-embedded (FFPE) samples, immunodetection would appear to be an attractive alternative for detecting mutations. …”
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The TRPV1-PKM2-SREBP1 axis maintains microglial lipid homeostasis in Alzheimer’s disease by Xudong Sha, Jiayuan Lin, Kexin Wu, Jia Lu, Zhihua Yu

“…PKM2 dimerization was necessary for SREBP1 activation and lipogenesis of lipid droplet-accumulating microglia. RNA sequencing analysis of microglia isolated from 3xTg mice exhibited transcriptomic changes in lipid metabolism, innate inflammation, and phagocytosis dysfunction; these changes were improved with capsaicin-mediated pharmacological activation of TRPV1 via inhibition of PKM2 dimerization and reduction of SREBP1 activation. …”
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A glimpse into the biogeography, seasonality, and ecological functions of arctic marine Oomycota by Brandon T. Hassett, Marco Thines, Anthony Buaya, Sebastian Ploch, R. Gradinger

“…Thus, it was our aim to conduct a first screening, using a functional gene assay and high-throughput sequencing of two gene regions within the 18S rRNA locus to examine the diversity, richness, and phylogeny of marine Oomycota within Arctic sediment, seawater, and sea ice. …”
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Hepatocyte Nuclear Factor 1 Beta Mutation-associated Newborn Onset of Glomerulocystic Kidney Disease: A Case Presentation by Nilüfer Göknar, Melda Ekici Avcı, Diana Üçkardeş, Emre Keleşoğlu, Kübra Tekkuş Ermiş, Cengiz Candan

“…A 10-year-old boy who was evaluated for bilateral cystic kidneys and chronic kidney disease from the newborn period was diagnosed with HNF1B-related glomerulocystic disease by DNA sequencing. The differential diagnosis of autosomal dominant polycystic kidney disease was a diagnostic pitfall. …”
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