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JOURNAL ARTICLE
Qianying Hu, Jianhua Chen, Jingjing Ma, Yuting Li, Yifeng Xu, Chaoyan Yue, Enzhao Cong
PURPOSE: Postpartum depression (PPD) brings adverse and serious consequences to both new parents and newborns. Neuroticism affects PPD, which remains controversial for confounding factors and reverse causality in cross-sectional research. Therefore, mendelian randomization (MR) study has been adopted to investigate their causal relationship. METHODS: This study utilized large-scale genome-wide association study genetic pooled data from three major databases: the United Kingdom Biobank, the European Bioinformatics Institute, and the FinnGen databases...
April 18, 2024: Archives of Women's Mental Health
#22
JOURNAL ARTICLE
Hyo-Jin Lee, Kyung-Sook Whang
Three Gram-stain-negative, aerobic, non-motile and coccobacilli-shaped bacterial strains, designated as NPKOSM-4T , NPKOSM-8 and MO-31T , were isolated from rice paddy soil. They had 96.5-100 % 16S rRNA gene sequence similarity to each other, and strains NPKOSM-4T and NPKOSM-8 showed 100 % 16S rRNA gene sequence similarity, confirming that they were the same species. Comparative analysis of 16S rRNA genes with closely related type strains showed that three isolates were most closely related to Falsiroseomonas terricola EM0302T (96...
April 2024: International Journal of Systematic and Evolutionary Microbiology
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JOURNAL ARTICLE
Wei-Ling Zhang, Mei-Chin Lai, Saulwood Lin, Wen-Chieh Chen, Yu-Chen Deng, Shu-Jung Lai, Sue-Yao Wu, Chuan-Chuan Hung, Jiun-Yan Ding, Sheng-Chung Chen
A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T , was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04T utilized formate, H2 /CO2 , 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0...
April 2024: International Journal of Systematic and Evolutionary Microbiology
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JOURNAL ARTICLE
Mohammad A Anwar, Ammar H Keshteli, Haiyan Yang, Windy Wang, Xukun Li, Helen M Messier, Pieter R Cullis, Christoph H Borchers, Robert Fraser, David S Wishart
Over a decade ago, longitudinal multiomics analysis was pioneered for early disease detection and individually tailored precision health interventions. However, high sample processing costs, expansive multiomics measurements along with complex data analysis have made this approach to precision/personalized medicine impractical. Here we describe in a case report, a more practical approach that uses fewer measurements, annual sampling, and faster decision making. We also show how this approach offers promise to detect an exceedingly rare and potentially fatal condition before it fully manifests...
April 17, 2024: Omics: a Journal of Integrative Biology
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JOURNAL ARTICLE
Bowei Chen, Min Wang, Yile Guo, Zihui Zhang, Wei Zhou, Lesheng Cao, Tianxu Zhang, Shahid Ali, Linan Xie, Yuhua Li, Gaurav Zinta, Shanwen Sun, Qingzhu Zhang
DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs...
April 18, 2024: Molecular Ecology
#26
JOURNAL ARTICLE
Ningning Wu, Yan Wu, Le Liu, Qi Zhang, Yu Lv, Ye Yuan, Jian He, Qirong Shen
A Gram-stain-negative bacterium, designated XZ-24T , was isolated from sediment of a river in Mianyang city, Sichuan province, PR China. Cells (1.0-2.0 µm long and 0.4-0.5 µm in width) were strictly aerobic, non-spore-forming, rod shaped, prosthecate and motile by means of a polar flagellum. Growth occurred at 10-37 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum pH 7.0) and with 0-3.0 % (w/v) NaCl (optimum 1.0 % NaCl). The results of phylogenetic analysis based on genomes and 16S rRNA gene sequences indicated that XZ-24T formed a distinct phyletic branch within the family Caulobacteraceae and was most closely related to members of the genera Brevundimonas , Caulobacter and Phenylobacterium with 95...
April 2024: International Journal of Systematic and Evolutionary Microbiology
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JOURNAL ARTICLE
Ruwani L Wimalasekara, Ellen M E Sykes, Dawn White, Chris Rathgeber, Ayush Kumar
We report the whole-genome sequence and antibiotic-resistance gene profile of an Acinetobacter calcoaceticus isolate, designated AC001_UM, taken from soil along the Red River in Winnipeg, Manitoba, Canada. The genome comprised 3,916,544 nucleotides (GC content: 38.7%). Antibiotic-resistance gene analysis revealed a class D β-lactamase and three efflux pump families.
April 18, 2024: Microbiology Resource Announcements
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JOURNAL ARTICLE
Azeez Alade, Tabitha Peter, Tamara Busch, Waheed Awotoye, Deepti Anand, Oladayo Abimbola, Emmanuel Aladenika, Mojisola Olujitan, Oscar Rysavy, Phuong Fawng Nguyen, Thirona Naicker, Peter A Mossey, Lord J J Gowans, Mekonen A Eshete, Wasiu L Adeyemo, Erliang Zeng, Eric Van Otterloo, Michael O'Rorke, Adebowale Adeyemo, Jeffrey C Murray, Salil A Lachke, Paul A Romitti, Azeez Butali
Nonsyndromic orofacial clefts (NSOFCs) represent a large proportion (70%-80%) of all OFCs. They can be broadly categorized into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO). Although NSCL/P and NSCPO are considered etiologically distinct, recent evidence suggests the presence of shared genetic risks. Thus, we investigated the genetic overlap between NSCL/P and NSCPO using African genome-wide association study (GWAS) data on NSOFCs. These data consist of 814 NSCL/P, 205 NSCPO cases, and 2159 unrelated controls...
April 18, 2024: Genetic Epidemiology
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JOURNAL ARTICLE
Kriti Roopendra, Priyanka, Amaresh Chandra, Yusuf Akhter, Sangeeta Saxena
In the present study, we analyzed GA3 (gibberellin)-treated sugarcane samples at the transcriptomic level to elucidate the differential expression of genes that influence sucrose accumulation. Previous research has suggested that GA3 application can potentially delay sink saturation by enhancing sink strength and demand, enabling the accommodation of more sucrose. To investigate the potential role of GA-induced modification of sink capacity in promoting higher sucrose accumulation, we sought to unravel the differential expression of transcripts and analyze their functional annotation...
2024: Physiologia Plantarum
#30
JOURNAL ARTICLE
Tengyu Weng, Xiaoning Zhang, Juan He, Yi Yang, Chengxin Li
BACKGROUND: Ultraviolet radiation causes skin photoaging by producing a variety of enzymes, which impact both skin health and hinder beauty. Currently, the early diagnosis and treatment of photoaging remain a challenge. Bioinformatics analysis has strong advantages in exploring core genes and the biological pathways of photoaging. AIMS: To screen and validate key risk genes associated with plasminogen in photoaging and to identify potential target genes for photoaging...
April 17, 2024: Journal of Cosmetic Dermatology
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JOURNAL ARTICLE
Kuntal Sen, Rima Izem, Yuelin Long, Jiji Jiang, Laura L Konczal, Robert J McCarter, Andrea L Gropman, Jirair K Bedoyan
BACKGROUND: Ornithine transcarbamylase deficiency (OTCD) due to an X-linked OTC mutation, is responsible for moderate to severe hyperammonemia (HA) with substantial morbidity and mortality. About 80% of females with OTCD remain apparently "asymptomatic" with limited studies of their clinical characteristics and long-term health vulnerabilities. Multimodal neuroimaging studies and executive function testing have shown that asymptomatic females exhibit limitations when stressed to perform at higher cognitive load and had reduced activation of the prefrontal cortex...
April 2024: Molecular Genetics & Genomic Medicine
#32
JOURNAL ARTICLE
Malihe Aghasizadeh, Asieh Ahmadi Hoseini, Reza Sahebi, Tooba Kazemi, Parisa Asadiyan-Sohan, Habibollah Esmaily, Sara Samadi, Amir Avan, Gordon A Ferns, Saeede Khosravi, Hamideh Ghazizadeh, Ebrahim Miri-Moghaddam, Majid Ghayour-Mobarhan
BACKGROUND: Loss-of-function (LOF) variants of the angiopoietin-like 3 (ANGPTL3) gene are reported to be associated with serum triglyceride (TG) and high-density lipoprotein cholesterol (HDL-C) concentrations and thereby affect the risk of cardiovascular disease (CVD). OBJECTIVE: In the present study, we examined the association of rs10789117 in the ANGPTL 3 gene locus and the risk of CVD in the group of people who were part of the Mashhad-Stroke and Heart-Atherosclerotic-Disorders (MASHAD) cohort...
April 2024: Molecular Genetics & Genomic Medicine
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JOURNAL ARTICLE
Lin-Lin Wang, Ping-Shan Pan, Hui Ma, Chun He, Zai-Long Qin, Wei He, Jing Huang, Shu-Yin Tan, Da-Hua Meng, Hong-Wei Wei, Ai-Hua Yin
BACKGROUND: Malformations of cortical development (MCD) are a group of congenital disorders characterized by structural abnormalities in the brain cortex. The clinical manifestations include refractory epilepsy, mental retardation, and cognitive impairment. Genetic factors play a key role in the etiology of MCD. Currently, there is no curative treatment for MCD. Phenotypes such as epilepsy and cerebral palsy cannot be observed in the fetus. Therefore, the diagnosis of MCD is typically based on fetal brain magnetic resonance imaging (MRI), ultrasound, or genetic testing...
April 2024: Molecular Genetics & Genomic Medicine
#34
JOURNAL ARTICLE
J Sebastian Garcia-Medina, Karolina Sienkiewicz, S Anand Narayanan, Eliah G Overbey, Kirill Grigorev, Krista A Ryon, Marissa Burke, Jacqueline Proszynski, Braden Tierney, Caleb M Schmidt, Nuria Mencia-Trinchant, Remi Klotz, Veronica Ortiz, Jonathan Foox, Christopher Chin, Deena Najjar, Irina Matei, Irenaeus Chan, Carlos Cruchaga, Ashley Kleinman, JangKeun Kim, Alexander Lucaci, Conor Loy, Omary Mzava, Iwijn De Vlaminck, Anvita Singaraju, Lynn E Taylor, Julian C Schmidt, Michael A Schmidt, Kelly Blease, Juan Moreno, Andrew Boddicker, Junhua Zhao, Bryan Lajoie, Andrew Altomare, Semyon Kruglyak, Shawn Levy, Min Yu, Duane C Hassane, Susan M Bailey, Kelly Bolton, Jaime Mateus, Christopher E Mason
BACKGROUND: The Inspiration4 (I4) mission, the first all-civilian orbital flight mission, investigated the physiological effects of short-duration spaceflight through a multi-omic approach. Despite advances, there remains much to learn about human adaptation to spaceflight's unique challenges, including microgravity, immune system perturbations, and radiation exposure. METHODS: To provide a detailed genetics analysis of the mission, we collected dried blood spots pre-, during, and post-flight for DNA extraction...
March 2024: Precision Clinical Medicine
#35
JOURNAL ARTICLE
Aida Jlassi, Rim Rejaibi, Maroua Manai, Ghada Sahraoui, Fatma Zahra Guerfali, Lamia Charfi, Amel Mezlini, Mohamed Manai, Karima Mrad, Raoudha Doghri
INTRODUCTION: Immunotherapy by blocking immune checkpoints programmed death/ligand (PD1/PDL1) and cytotoxic T-lymphocyte-associated protein 4(CTLA4) has emerged as new therapeutic targets in cancer. However, their efficacy has been limited due to resistance. A new- checkpoint V-domain Ig-containing suppressor of T cell activation (VISTA) has appeared, but the use of its inhibition effect in combination with antibodies targeting PDL1/PD1and CTLA4 has not been reported in ovarian cancer...
2024: Frontiers in Oncology
#36
JOURNAL ARTICLE
Joaquin Garcia-Solorio, Juan Carlos Núñez-Enriquez, Marco Jiménez-Olivares, Janet Flores-Lujano, Fernanda Flores-Espino, Carolina Molina-Garay, Alejandra Cervera, Diana Casique-Aguirre, José Gabriel Peñaloza-Gonzalez, Ma Del Rocío Baños-Lara, Ángel García-Soto, César Alejandro Galván-Díaz, Alberto Olaya-Vargas, Hilario Flores Aguilar, Minerva Mata-Rocha, Miguel Ángel Garrido-Hernández, Juan Carlos Solís-Poblano, Nuria Citlalli Luna-Silva, Lena Sarahi Cano-Cuapio, Pierre Mitchel Aristil-Chery, Fernando Herrera-Quezada, Karol Carrillo-Sanchez, Anallely Muñoz-Rivas, Luis Leonardo Flores-Lagunes, Elvia Cristina Mendoza-Caamal, Beatriz Eugenia Villegas-Torres, Vincent González-Osnaya, Elva Jiménez-Hernández, José Refugio Torres-Nava, Jorge Alfonso Martín-Trejo, María de Lourdes Gutiérrez-Rivera, Rosa Martha Espinosa-Elizondo, Laura Elizabeth Merino-Pasaye, María Luisa Pérez-Saldívar, Silvia Jiménez-Morales, Everardo Curiel-Quesada, Haydeé Rosas-Vargas, Juan Manuel Mejía-Arangure, Carmen Alaez-Verson
BACKGROUND: Recurrent genetic alterations contributing to leukemogenesis have been identified in pediatric B-cell Acute Lymphoblastic Leukemia (B-ALL), and some are useful for refining classification, prognosis, and treatment selection. IKZF1plus is a complex biomarker associated with a poor prognosis. It is characterized by IKZF1 deletion coexisting with PAX5 , CDKN2A/2B , or PAR1 region deletions. The mutational spectrum and clinical impact of these alterations have scarcely been explored in Mexican pediatric patients with B-ALL...
2024: Frontiers in Oncology
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JOURNAL ARTICLE
Yong Gao, Si Yin
The mountainous region of southern China has been characterized by its complicated environment and topography. Amorphophallus kiusianus Makino 1913 is a representative species of extreme habitat preference that resides mainly in this region. To help study the genetic differentiation mechanisms of A. kiusianus populations, we sequenced the first chloroplast genome of this species using next-generation sequencing. The chloroplast genome was 166,269 bp in length with an average GC content of 36% (GenBank accession number: PP072243)...
2024: Mitochondrial DNA. Part B. Resources
#38
JOURNAL ARTICLE
Shen Ma, Ran Hao, Yi-Wei Lu, Hui-Po Wang, Jie Hu, Yi-Xin Qi
BACKGROUND: Distant metastasis remains the leading cause of death among patients with breast cancer (BRCA). The process of cancer metastasis involves multiple mechanisms, including compromised immune system. However, not all genes involved in immune function have been comprehensively identified. METHODS: Firstly 1623 BRCA samples, including transcriptome sequencing and clinical information, were acquired from Gene Expression Omnibus (GSE102818, GSE45255, GSE86166) and The Cancer Genome Atlas-BRCA (TCGA-BRCA) dataset...
2024: Breast Cancer: Targets and Therapy
#39
JOURNAL ARTICLE
Adrián César-Razquin, Josep Casacuberta, Tamas Dalmay, Silvia Federici, Sara Jacchia, Dafni Maria Kagkli, Simon Moxon, Nikoletta Papadopoulou
As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. This Technical Note to the applicants puts together requirements and recommendations for the quality assessment of the methodology, analysis and reporting when DNA sequencing is used for the molecular characterisation of GM plants...
April 2024: EFSA journal
#40
JOURNAL ARTICLE
Asha Anand, Shailja Chauhan, Aparna Chodon, Kavitha Velayudha Vimala Kumar, S Saravanakumar, Gopal Pandi
The microRNAs are endogenous, regulating gene expression either at the DNA or RNA level. Despite the availability of extensive studies on microRNA generation in plants, reports on their abundance, biogenesis, and consequent gene regulation in plant organelles remain naVve. Building on previous studies involving pre-miRNA sequencing in Abelmoschus esculentus , we demonstrated that three putative microRNAs were raised from the chloroplast genome. In the current study, we have characterized the genesis of these three microRNAs through a combination of bioinformatics and experimental approaches...
2024: Biotechnologia
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