Genes, Vol. 15, Pages 276: Genetic Risk Factors and Clinical Outcomes in Childhood Eye Cancers: A Review
orgio Zauli Childhood eye cancers, although rare, present substantial health challenges, affecting the pediatric population with a remarkable impact on their lives and families. This comprehensive review provides insights into the various types of ocular tumors, primarily focusing on malignant eye tumors, their genetic predispositions, and advancements in managing these conditions. Understanding the genetic risk factors is crucial for early detection, risk assessment, and the development of targeted therapies. This review discusses genome-wide association (GWAS) and next-generation sequencing (NGS) studies to find comm...
Source: Genes - February 22, 2024 Category: Genetics & Stem Cells Authors: Syed Hameed Angeli Christy Yu Bashaer Almadani Shereen Abualkhair Khabir Ahmad Giorgio Zauli Tags: Review Source Type: research

Genes, Vol. 15, Pages 268: Cross-Omic Transcription Factor Analysis: An Insight on Transcription Factor Accessibility and Expression Correlation
i Carlo It is well known how sequencing technologies propelled cellular biology research in recent years, providing incredible insight into the basic mechanisms of cells. Single-cell RNA sequencing is at the front in this field, with single-cell ATAC sequencing supporting it and becoming more popular. In this regard, multi-modal technologies play a crucial role, allowing the possibility to simultaneously perform the mentioned sequencing modalities on the same cells. Yet, there still needs to be a clear and dedicated way to analyze these multi-modal data. One of the current methods is to calculate the Gene Activity Matr...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Lorenzo Martini Roberta Bardini Alessandro Savino Stefano Di Carlo Tags: Article Source Type: research

Genes, Vol. 15, Pages 269: Regulation of myo-miR-24-3p on the Myogenesis and Fiber Type Transformation of Skeletal Muscle
In this study, we observed a critical miRNA, miR-24-3p, which exhibited higher expression levels in Tongcheng (obese-type) pigs compared to Landrace (lean-type) pigs. Furthermore, we found that miR-24-3p was highly expressed in the dorsal muscle of pigs and the quadriceps muscle of mice. Functionally, miR-24-3p was found to inhibit proliferation and promote differentiation in muscle cells. Additionally, miR-24-3p was shown to facilitate the conversion of slow muscle fibers to fast muscle fibers and influence the expression of GLUT4, a glucose transporter. Moreover, in a mouse model of skeletal muscle injury, we demonstrate...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Danyang Fan Yilong Yao Yanwen Liu Chao Yan Fanqinyu Li Shilong Wang Mei Yu Bingkun Xie Zhonglin Tang Tags: Article Source Type: research

Genes, Vol. 15, Pages 270: Transcriptomic Insights and Cytochrome P450 Gene Analysis in Kadsura coccinea for Lignan Biosynthesis
Sen Wang Kadsura coccinea is a medicinal plant from the Schisandraceae family that is native to China and has great pharmacological potential due to its lignans. However, there are significant knowledge gaps regarding the genetic and molecular mechanisms of lignans. We used transcriptome sequencing technology to analyze root, stem, and leaf samples, focusing on the identification and phylogenetic analysis of Cytochrome P450 (CYP) genes. High-quality data containing 158,385 transcripts and 68,978 unigenes were obtained. In addition, 36,293 unigenes in at least one database, and 23,335 across five databases (Nr, KEGG,...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Hanyu Fu Chuan Guo Jiqing Peng Fengxia Shao Song Sheng Sen Wang Tags: Article Source Type: research

Genes, Vol. 15, Pages 271: Genome-Wide Identification and Analysis of APC E3 Ubiquitin Ligase Genes Family in Triticum aestivum
This study identified 14 members of the APC gene family in the wheat genome and divided them into three subgroups (CCS52B, CCS52A, and CDC20) to better understand their functions. Promoter sequence analysis revealed the presence of several cis-acting elements related to hormone and stress responses in the APC E3 ubiquitin ligases in wheat. All identified APC E3 ubiquitin ligase family members were highly expressed in the leaves, and the expression of most genes was induced by the application of methyl jasmonate (MeJA). In addition, the APC gene family in wheat may play a role in plant defense mechanisms. This study compreh...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Jinnan Wang Tianye Zhang Aizhu Tu Haoxin Xie Haichao Hu Jianping Chen Jian Yang Tags: Article Source Type: research

Genes, Vol. 15, Pages 272: Epigenetic Regulation in Schizophrenia: Focus on Methylation and Histone Modifications in Human Studies
rnandez Despite extensive research over the last few decades, the etiology of schizophrenia (SZ) remains unclear. SZ is a pathological disorder that is highly debilitating and deeply affects the lifestyle and minds of those affected. Several factors (one or in combination) have been reported as contributors to SZ pathogenesis, including neurodevelopmental, environmental, genetic and epigenetic factors. Deoxyribonucleic acid (DNA) methylation and post-translational modification (PTM) of histone proteins are potentially contributing epigenetic processes involved in transcriptional activity, chromatin folding, cell divisi...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Natasha Delphin Caitlin Aust Lyn Griffiths Francesca Fernandez Tags: Review Source Type: research

Genes, Vol. 15, Pages 265: Genome-Wide Characterization of the Phenylalanine Ammonia-Lyase Gene Family and Their Potential Roles in Response to Aspergillus flavus L. Infection in Cultivated Peanut (Arachis hypogaea L.)
ng Suoyi Han Xinyou Zhang Phenylalanine ammonia-lyase (PAL) is an essential enzyme in the phenylpropanoid pathway, in which numerous aromatic intermediate metabolites play significant roles in plant growth, adaptation, and disease resistance. Cultivated peanuts are highly susceptible to Aspergillus flavus L. infection. Although PAL genes have been characterized in various major crops, no systematic studies have been conducted in cultivated peanuts, especially in response to A. flavus infection. In the present study, a systematic genome-wide analysis was conducted to identify PAL genes in the Arachis hypogaea L. gen...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Pengpei Chai Mengjie Cui Qi Zhao Linjie Chen Tengda Guo Jingkun Guo Chendi Wu Pei Du Hua Liu Jing Xu Zheng Zheng Bingyan Huang Wenzhao Dong Suoyi Han Xinyou Zhang Tags: Article Source Type: research

Genes, Vol. 15, Pages 266: Genetic Advancements in Infantile Epileptic Spasms Syndrome and Opportunities for Precision Medicine
n Whitney Infantile epileptic spasms syndrome (IESS) is a devastating developmental epileptic encephalopathy (DEE) consisting of epileptic spasms, as well as one or both of developmental regression or stagnation and hypsarrhythmia on EEG. A myriad of aetiologies are associated with the development of IESS; broadly, 60% of cases are thought to be structural, metabolic or infectious in nature, with the remainder genetic or of unknown cause. Epilepsy genetics is a growing field, and over 28 copy number variants and 70 single gene pathogenic variants related to IESS have been discovered to date. While not exhaustive, some ...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Hannah E. Snyder Puneet Jain Rajesh RamachandranNair Kevin C. Jones Robyn Whitney Tags: Review Source Type: research

Genes, Vol. 15, Pages 267: Genome and Transcriptome Analysis of the Torreya grandis WRKY Gene Family during Seed Development
hui Shi Torreya grandis, an economically significant evergreen tree species exclusive to subtropical China, is highly valued for its seeds. However, the seed development process of T. grandis remains relatively unexplored. Given the pivotal role WRKY transcription factors (TFs) play in coordinating diverse cellular and biological activities, as well as crucial signaling pathways essential for plant growth and development, and the lack of comprehensive investigation into their specific functions in T. grandis, our study investigated its genome and successfully isolated 78 WRKY genes and categorized them into three disti...
Source: Genes - February 21, 2024 Category: Genetics & Stem Cells Authors: Ruiqian Zhu Ning Gao Jiali Luo Wenhui Shi Tags: Article Source Type: research

Genes, Vol. 15, Pages 262: Modeling within and between Sub-Genomes Epistasis of Synthetic Hexaploid Wheat for Genome-Enabled Prediction of Diseases
The objective of this study is to investigate whether there is a discernible influence pattern from the D sub-genome with epistasis in genomic models for wheat diseases. Four genomic statistical models were employed; two models considered the linear genomic relationship of the lines. The first model (G) utilized all molecular markers, while the second model (ABD) utilized three matrices representing the A, B, and D sub-genomes. The remaining two models incorporated epistasis, one (GI) using all markers and the other (ABDI) considering markers in sub-genomes A, B, and D, including inter- and intra-sub-genome interactions. T...
Source: Genes - February 20, 2024 Category: Genetics & Stem Cells Authors: Jaime Cuevas David Gonz ález-Diéguez Susanne Dreisigacker Johannes W. R. Martini Leo Crespo-Herrera Nerida Lozano-Ramirez Pawan K. Singh Xinyao He Julio Huerta Jose Crossa Tags: Article Source Type: research

Genes, Vol. 15, Pages 263: Comparative Analysis of Chloroplast Genomes of & ldquo;Tiantai Wu-Yao & rdquo; (Lindera aggregata) and Taxa of the Same Genus and Different Genera
In this study, we sequenced, assembled and annotated the chloroplast genome of L. aggregata and reannotated and corrected eight unverified annotations in the same genus. The chloroplast genomes taxa from Lindera and from different genera of Lauraceae were compared and analyzed, and their phylogenetic relationship and divergence time were speculated. All the 36 chloroplast genomes had typical quadripartite structures that ranged from 150,749 to 154,736 bp in total length. These genomes encoded 111–112 unique genes, including 78–79 protein-coding genes, 29–30 tRNA and 4 ...
Source: Genes - February 20, 2024 Category: Genetics & Stem Cells Authors: Yujie Shi Zhen Chen Jingyong Jiang Xiaobai Li Wei Zeng Tags: Article Source Type: research

Genes, Vol. 15, Pages 264: Discovery, Pathogenesis, and Complete Genome Characterization of Lates calcarifer Herpesvirus
er Hoek Ad de Groof In 2015 and 2016, two Barramundi (Lates calcarifer) farms in Singapore reported a disease outbreak characterized by lethargic behavior, pronounced inappetence, generalized skin lesions, erosions of the fins and tail, and ultimately high mortality in their fish. Next-generation sequencing and PCR confirmed presence of a novel virus belonging to the Alloherpesviridae family, Lates calcarifer herpesvirus (LCHV), which was subsequently isolated and cultured. We characterize, for the first time, the complete genome of two cultured LCHV isolates. The genome contains a long unique region of approximately...
Source: Genes - February 20, 2024 Category: Genetics & Stem Cells Authors: Bartjan Simmelink Jordy P. M. Coolen Wannes Vogels Martin Deijs Jessica L. M. van der Last-Kempkes Kah Sing Ng Siow Foong Chang Koen Gevers Liesbeth Harkema Lia van der Hoek Ad de Groof Tags: Article Source Type: research

Genes, Vol. 15, Pages 260: FecB Was Associated with Litter Size and Follows Mendel & rsquo;s Laws of Inheritance When It Transited to Next Generation in Suhu Meat Sheep Breeding Population
Genes, Vol. 15, Pages 260: FecB Was Associated with Litter Size and Follows Mendel’s Laws of Inheritance When It Transited to Next Generation in Suhu Meat Sheep Breeding Population Genes doi: 10.3390/genes15030260 Authors: Pengwei Su Yifei Gu Shanhe Wang Xiukai Cao Xiaoyang Lv Tesfaye Getachew Yutao Li Zhenghai Song Zehu Yuan Wei Sun In order to investigate the effect of FecB on litter size and growth and development traits of Suhu meat sheep and the inheritance patterns of FecB between parents and offspring in the population. In this experiment, 2241 sheep from the Suhu meat sheep popul...
Source: Genes - February 20, 2024 Category: Genetics & Stem Cells Authors: Pengwei Su Yifei Gu Shanhe Wang Xiukai Cao Xiaoyang Lv Tesfaye Getachew Yutao Li Zhenghai Song Zehu Yuan Wei Sun Tags: Article Source Type: research

Genes, Vol. 15, Pages 261: Antibiotic-Free Gene Vectors: A 25-Year Journey to Clinical Trials
man Until very recently, the major use, for gene therapy, specifically of linear or circular DNA, such as plasmids, was as ancillary products for viral vectors’ production or as a genetic template for mRNA production. Thanks to targeted and more efficient physical or chemical delivery techniques and to the refinement of their structure, non-viral plasmid DNA are now under intensive consideration as pharmaceutical drugs. Plasmids traditionally carry an antibiotic resistance gene for providing the selection pressure necessary for maintenance in a bacterial host. Nearly a dozen different antibiotic-free gene...
Source: Genes - February 20, 2024 Category: Genetics & Stem Cells Authors: Corinne Marie Daniel Scherman Tags: Review Source Type: research

Genes, Vol. 15, Pages 259: Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform
In this study, we used a Vela Sentosa kit (Vela Diagnostics, Kendall, Singapore), which is usually used for the Ion Torrent personal genome machine (PGM) platform, to sequence HIV using the Illumina Miseq platform. After RNA extraction and reverse transcriptase-polymerase chain reaction (RT-PCR), minor modifications were applied to the Vela Sentosa kit to adapt it to the Illumina Miseq platform. Analysis of the results showed the same mutations present in the samples using both sequencing platforms. The total number of reads varied from 185,069 to 752,343 and from 642,162 to 2,074,028 in the Ion Torrent PGM platform and th...
Source: Genes - February 19, 2024 Category: Genetics & Stem Cells Authors: Nasserdine Papa Mze C écile Fernand-Laurent Solen Daugabel Olfa Zanzouri St éphanie Marque Juillet Tags: Article Source Type: research