Single-cell RNA-seq analysis reveals microenvironmental infiltration of myeloid cells and pancreatic prognostic markers in PDAC by Yanying Fan, Lili Wu, Xinyu Qiu, Han Shi, Longhang Wu, Juan Lin, Jie Lin, Tianhong Teng

“…Methods Single-cell RNA sequencing (scRNA-seq) data were downloaded from t the Tumor Immune Single-cell Hub and gene expression data were retrieved from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. …”
Get full text

Quantitative proteomic analysis unveils a critical role of VARS1 in hepatocellular carcinoma aggressiveness through the modulation of MAGI1 expression by Natalia Hermán-Sánchez, Mercedes del Rio-Moreno, Rubén Ciria, Marina E. Sánchez-Frias, Maite G. Fernández-Barrena, Iker Uriarte, Eduardo Chicano-Galvez, Ignacio Ortea, Ángela Peralbo-Molina, Javier Briceño, Matías A. Avila, Manuel Rodríguez-Perálvarez, Raúl M. Luque, Juan L. López-Cánovas, Manuel D. Gahete

“…Patients with ARSs upregulation had genomic/transcriptomic characteristics of the proliferative HCC. …”
Get full text

<i>Ex Vivo</i> Regional Gene Therapy Compared to Recombinant BMP-2 for the Treatment of Critical-Size Bone Defects: An In Vivo Single-Cell RNA-Sequencing Study by Arijita Sarkar, Matthew C. Gallo, Jennifer A. Bell, Cory K. Mayfield, Jacob R. Ball, Mina Ayad, Elizabeth Lechtholz-Zey, Stephanie W. Chang, Osamu Sugiyama, Denis Evseenko, Jay R. Lieberman

“…Here, for the first time, we performed single-cell RNA sequencing (10x Genomics) of hematoma tissue in six rats with critical-sized femoral defects that were treated with either regional gene therapy or rhBMP-2. …”
Get full text

The frequency of distribution of the genotypes of the IL4 polymorphism (rs 2243250) in psoriasis and psoriatic arthritis by A. A. Barilo, M. V. Smolnikova, S. V. Smirnova

“…Genotyping allelic variants was carried out by the method of restriction analysis of amplification products (RFLP-analysis) of specific regions of the genome. In PS carriers of the C/С IL4 (rs2243250), the value of the PASI index is statistically significantly lower relative to the carriers of the C/T and T/T genotypes. …”
Get full text

Domestication of different varieties in the cheese-making fungus Geotrichum candidum by Bennetot, Bastien, Vernadet, Jean-Philippe, Perkins, Vincent, Hautefeuille, Sophie, Rodríguez de la Vega, Ricardo C., O’Donnell, Samuel, Snirc, Alodie, Grondin, Cécile, Lessard, Marie-Hélène, Peron, Anne-Claire, Labrie, Steve, Landaud, Sophie, Giraud, Tatiana, Ropars, Jeanne

“…Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. …”
Get full text

Eucalyptus grandis WRKY genes provide insight into the role of arbuscular mycorrhizal symbiosis in defense against Ralstonia solanacearum by Jianlang Zhang, Xinzhu Yang, Chunyu Huo, Xinyi Fan, Qiutong Liu, Zhihong Liu, Yu Su, Zujing Chen, Zujing Chen

“…IntroductionWRKY transcription factors are essential for plant growth, health, and responses to biotic and abiotic stress.MethodsIn this study, we performed a deep in silico characterization of the WRKY gene family in the genome of Eucalyptus grandis. We also analyzed the expression profiles of these genes upon colonization by the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis (Ri) and infection with the bacterial pathogen Ralstonia solanacearum (Rs).ResultsA total of 117 EgWRKYs were identified. …”
Get full text

Causal linkage between adult height and kidney function: An integrated population-scale observational analysis and Mendelian randomization study. by Sehoon Park, Soojin Lee, Yaerim Kim, Yeonhee Lee, Min Woo Kang, Kwangsoo Kim, Yong Chul Kim, Seung Seok Han, Hajeong Lee, Jung Pyo Lee, Kwon Wook Joo, Chun Soo Lim, Yon Su Kim, Dong Ki Kim

“…Second, the genetic instrument for adult height, as reported by the GIANT consortium, was implemented, and summary-level MR of eGFRcreatinine and CKDcreatinine in a CKDGen genome-wide association study was performed (N = 567,460), with multivariable MR being adjusted for the effects of genetic predisposition on body mass index. …”
Get full text

Investigating the miRNA-mRNA interactome of human trabecular meshwork cells treated with TGF-β1 provides insights into the pathogenesis of pseudoexfoliation glaucoma. by Anton W Roodnat, Chelsey Doyle, Breedge Callaghan, Karen Lester, Megan Henry, Carl Sheridan, Declan J McKenna, Colin E Willoughby, Sarah D Atkinson

“…This is the first study to present a genome-wide microRNA-mRNA regulatory network for human trabecular meshwork cells treated with TGF-β1 and may serve to generate unbiased hypotheses about regulatory functions and mRNA targets of miRNAs in pseudoexfoliation glaucoma and may help to develop miRNA-based therapeutics.…”
Get full text

Kidney damage on fertility and pregnancy: A Mendelian randomization. by Jin Ren, Qiuyan Huang, Xiaowei Lie, Xingli Tong, Qi Yao, Ge Zhou

“…The genetic instruments and outcome data were derived from various large genome-wide association studies.<h4>Results</h4>Adverse pregnancy outcomes: Our analyses supported a suggestive causal effect of CKD and estimated glomerular filtration rate (eGFR) rapid on stillbirth, with CKD having an odds ratio (OR) of 1.020 [95% confidence interval (CI) 1.002 to 1.038] and eGFR rapid having an OR of 1.026 (95% CI 1.004-1.048). …”
Get full text

Lipid Metabolism-Related Gene Signature Predicts Prognosis and Indicates Immune Microenvironment Infiltration in Advanced Gastric Cancer by Lijian He, Qiange Ye, Yanmei Zhu, Wenqi Zhong, Guifang Xu, Lei Wang, Zhangding Wang, Xiaoping Zou

“…We obtained gene expression profiles from The Cancer Genome Atlas (TCGA) database for early and advanced gastric cancer samples and performed differential expression analysis to identify specific lipid metabolism-related genes in AGC. …”
Get full text

Causal Associations Between Sarcopenia and Gestational Diabetes Mellitus by Huang Y, Zhao S, Hong J, Shen L, Wang Z, Wang D

“…In this study, we used a bi-directional Mendelian randomization (MR) approach to explore this intricate relationship.Methods: This study utilized data from FinnGen datasets and genome-wide association studies. A bi-directional MR study was conducted. …”
Get full text

Analysis of strawberry genetic collection (Fragaria L.) for Rca2 and Rpfl genes with molecular markers by I. V. Luk’yanchuk, A. S. Lyzhin, I. I. Kozlova

“…The use of molecular markers allows to determine with high reliability the presence of the necessary genes in the genome and to identify promising forms. Some of the common strawberry's diseases, causing significant damage to strawberry plantations, are anthracnose (Colletotrichum acutatum Simmonds) and red stele root rot (Phytophthora fragariae var. fragariae Hickman). …”
Get full text

Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers by R. B. Aitnazarov, T. M. Mishakova, N. S. Yudin

“…Identification of the genetic variations controlling the adaptation of local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great relevance. …”
Get full text

Molecular Epidemiology of Escherichia coli Resistant to Carbapenems, Fluoroquinolones, and Aminoglycosides Isolated from One of the Largest Hospitals in Vietnam in 2014–2019 by Tohru Miyoshi-Akiyama, Do Van Thanh, Truong Thai Phuong, Nguyen Quang Huy, Pham Thi Phuong Thuy, Teruo Kirikae, Pham Hong Nhung, Norio Ohmagari

“…This study was designed to clarify the molecular epidemiology of Escherichia coli isolates resistant to carbapenems, fluoroquinolones, and aminoglycosides isolated from patients admitted to one of the largest hospitals in Vietnam in 2014–2019 based on both whole-genome sequencing (WGS) and phenotypic data. Methodology. …”
Get full text

Genetic gain of grain yield and quality in bread wheat cultivars representing 40 years of breeding in Morocco by S. Bennani, M. Taghouti, F. Gaboun

“…Adopting advanced technologies, like genomic selection, adequate agronomic practices, and more efficient selection criteria are essential steps to further increase simultaneously grain yield and quality traits.…”
Get full text

Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology by Matteo P. Ferla, Rubén Sánchez-García, Rachael E. Skyner, Stefan Gahbauer, Jenny C. Taylor, Frank von Delft, Brian D. Marsden, Charlotte M. Deane

Get full text

Adiponectin Gene Polymorphisms and Possible Susceptibility to Metabolic Syndrome among the Sudanese Population: A Case-Control Study by Altaf S. Mosad, Ghada A. Elfadil, Alsadig Gassoum, Khanssa M. Elamin, Nazik Elmalaika Obaid Seid Ahmed Husain

“…The guanidine extraction procedure was used to extract genomic DNA from EDTA whole blood by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP); samples were genotyped for the polymorphisms (rs266729), (rs2241766), and (rs1501299). …”
Get full text

Assessing Microbial Diversity in Páramo Soils (Multistrategy Analysis): Effects of Potato Farming and Livestock Grazing in Nevados National Natural Park, Colombia by Lizeth Manuela Avellaneda-Torres, Tomás León Sicard, Edlin Guerra Castro, Esperanza Torres-Rojas

Get full text

Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention by Ashley A Hibberd, Anna Lyra, Arthur C Ouwehand, Peter Rolny, Helena Lindegren, Lennart Cedgård, Yvonne Wettergren

Get full text

Influence of different types of sterile cytoplasms (A3, A4, 9E) on the combining ability of CMS lines of sorghum by O. P. Kibalnik, L. A. Elkonin

“…In order to investigate the effect of different types of sterile cytoplasm (A3, A4, 9E) on CA in sorghum, we studied the manifestation of a number of biological and agronomic traits in 54 F1 hybrid combinations obtained using iso-nuclear CMS lines with the nuclear genome of the line Zheltozernoye 10, differing only in the types of sterile cytoplasm (A3, A4 and 9E). …”
Get full text