Genes, Vol. 15, Pages 319: Massive Parallel DNA Sequencing of Patients with Inherited Cardiomyopathies in Cyprus and Suggestion of Digenic or Oligogenic Inheritance
We report on variants in 25 families, where pathogenicity was predicted by different computational approaches, databases, and an in-house filtering analysis. All variants were validated using Sanger sequencing. Familial segregation was tested when possible. We identified 41 different variants in 26 genes. Analytically, we identified fifteen variants previously reported in the Human Gene Mutation Database: twelve mentioned as disease-causing mutations (DM) and three as probable disease-causing mutations (DM?). Additionally, we identified 26 novel variants. We classified the forty-one variants as follows: twenty-eight (68.3%...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Constantina Koutsofti Marios Ioannides Christiana Polydorou Gregory Papagregoriou Apostolos Malatras George Michael Irene Hadjiioannou Stylianos Pieri Eleni M. Loizidou Christos Eftychiou Elias Papasavvas Theodoros Christophides Anna Alkelai Manav Kapoor Tags: Article Source Type: research

Genes, Vol. 15, Pages 320: Population Structure and Genetic Diversity of the Toona ciliata (Meliaceae) Complex Assayed with Chloroplast DNA Markers
Xin-Sheng Hu Toona ciliata is a deciduous or semi-deciduous tree species and belongs to the Toona genus of the Meliaceae family. Owing to low natural regeneration and over-exploitation, the species is listed as an endangered species at level II in China and its conservation has received increasing concern. Here, we sampled 447 individuals from 29 populations across the range-wide distribution of the T. ciliata complex in China and assessed their genetic variation using two chloroplast DNA markers. The results showed that the overall haplotype diversity and nucleotide diversity per site were high at h = 0.9767 and &...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Zi-Yun Wang Ying Hu Yan-Wen Lv Yu Xiao Zi-Han He Chao Wu Xin-Sheng Hu Tags: Article Source Type: research

Genes, Vol. 15, Pages 310: Identification and Analysis of Axolotl Homologs for Proteins Implicated in Human Neurodegenerative Proteinopathies
Jada Lewis Neurodegenerative proteinopathies such as Alzheimer’s Disease are characterized by abnormal protein aggregation and neurodegeneration. Neuroresilience or regenerative strategies to prevent neurodegeneration, preserve function, or restore lost neurons may have the potential to combat human proteinopathies; however, the adult human brain possesses a limited capacity to replace lost neurons. In contrast, axolotls (Ambystoma mexicanum) show robust brain regeneration. To determine whether axolotls may help identify potential neuroresilience or regenerative strategies in humans, we first interrogate...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Lucas M. James Zachary Strickland Noah Lopez Jessica L. Whited Malcolm Maden Jada Lewis Tags: Article Source Type: research

Genes, Vol. 15, Pages 311: Clinical and Genetic Aspects of Juvenile Amyotrophic Lateral Sclerosis: A Promising Era Emerges
Antônio Troccoli Chieia Adriel Rêgo Barbosa Vinícius Lopes Braga Wladimir Bocca Vieira de Rezende Pinto Acary Souza Bulle Oliveira Juvenile Amyotrophic Lateral Sclerosis is a genetically heterogeneous neurodegenerative disorder, which is frequently misdiagnosed due to low clinical suspicion and little knowledge about disease characteristics. More than 20 different genetic loci have been associated with both sporadic and familial juvenile Amyotrophic Lateral Sclerosis. Currently, almost 40% of cases have an identifiable monogenic basis; type 6, associated with FUS gene variants, is the most prevalent globall...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Paulo Victor Sgobbi de Souza Paulo de Lima Serrano Igor Braga Farias Roberta Ismael Lacerda Machado Bruno de Mattos Lombardi Badia H élvia Bertoldo de Oliveira Alana Strucker Barbosa Camila Alves Pereira Vanessa de Freitas Moreira Marco Ant ônio Troccol Tags: Review Source Type: research

Genes, Vol. 15, Pages 309: Novel Pathogenic Variants Leading to Sporadic Amyotrophic Lateral Sclerosis in Greek Patients
This study aims to provide a comprehensive investigation of genetic variants found in SOD1, FUS and TARDBP genes in Greek sporadic ALS (sALS) cases. Our sequencing analysis of the coding regions of the abovementioned genes that include the majority of the variants that lead to ALS in 32 sALS patients and 3 healthy relatives revealed 6 variants in SOD1, 19 variants in FUS and 37 variants in TARDBP, of which the SOD1 p.D90A and the FUS c.*356G>A (rs886051940) variants have been previously associated with ALS, while two novel nonsense pathogenic variants were also identified, namely FUS p.R241* and TDP-43 p.Y214*. ...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Ouliana Ivantsik Anne John Kyriaki Kydonopoulou Konstantinos Mitropoulos Spyridon Gerou Bassam R. Ali George P. Patrinos Tags: Article Source Type: research

Genes, Vol. 15, Pages 312: Gene Expression Analysis for Uterine Cervix and Corpus Cancer Characterization
Ortuño The analysis of gene expression quantification data is a powerful and widely used approach in cancer research. This work provides new insights into the transcriptomic changes that occur in healthy uterine tissue compared to those in cancerous tissues and explores the differences associated with uterine cancer localizations and histological subtypes. To achieve this, RNA-Seq data from the TCGA database were preprocessed and analyzed using the KnowSeq package. Firstly, a kNN model was applied to classify uterine cervix cancer, uterine corpus cancer, and healthy uterine samples. Through variable selection, a three...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Luc ía Almorox Laura Antequera Ignacio Rojas Luis Javier Herrera Francisco M. Ortu ño Tags: Article Source Type: research

Genes, Vol. 15, Pages 314: Multiplex Real-Time PCR-Based Newborn Screening for Severe Primary Immunodeficiency and Spinal Muscular Atrophy in Osaka, Japan: Our Results after 3 Years
We describe our experience of optional NBS for severe PID and SMA in Osaka, Japan. A multiplex TaqMan qPCR assay was used for the optional NBS program. The assay was able to quantify the levels of T-cell receptor excision circles and kappa-deleting recombination excision circles, which is useful for severe combined immunodeficiency and B-cell deficiency screening, and can simultaneously detect the homozygous deletion of SMN1 exon 7, which is useful for NBS for SMA. In total, 105,419 newborns were eligible for the optional NBS program between 1 August 2020 and 31 August 2023. A case each of X-linked agammaglobulinemia and S...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Tomokazu Kimizu Masatoshi Nozaki Yousuke Okada Akihisa Sawada Misaki Morisaki Hiroshi Fujita Akemi Irie Keiko Matsuda Yuiko Hasegawa Eriko Nishi Nobuhiko Okamoto Masanobu Kawai Kohsuke Imai Yasuhiro Suzuki Kazuko Wada Nobuaki Mitsuda Shinobu Ida Tags: Article Source Type: research

Genes, Vol. 15, Pages 313: Runs of Homozygosity Detection and Selection Signature Analysis for Local Goat Breeds in Yunnan, China
This study uncovers genetic diversity and inbreeding levels within local goat breeds in Yunnan province, China. The identification of specific genes associated with economic traits and adaptability provides actionable insights for utilization and conservation efforts. (Source: Genes)
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Chang Huang Qian Zhao Qian Chen Yinxiao Su Yuehui Ma Shaohui Ye Qianjun Zhao Tags: Article Source Type: research

Genes, Vol. 15, Pages 315: Cloning and Analysis of Expression of Genes Related to Carotenoid Metabolism in Different Fruit Color Mutants of Pepper (Capsicum annuum L.)
In this study, red wild-type pepper XHB, SP01, PC01 and their corresponding mutants H0809 (orange), SP02 (yellow), and PC02 (orange) were used as research materials. The Ggps, Psy, Lcyb, Crtz, Zep, and Ccs genes involved in carotenoid biosynthesis were cloned, and bioinformatics and expression analyses were carried out. The results showed that the full lengths of the six genes were 1110 bp, 2844 bp, 1497 bp, 2025 bp, 510 bp, and 1497 bp, and they encoded 369, 419, 498, 315, 169, and 498 amino acids, respectively. Except for the full-length Ccs gene, which could not be amplified in the yellow mutant SP02 and the orange muta...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Penglong Feng Yayi Wang Junqin Wen Yanjing Ren Qiwen Zhong Quanhui Li Tags: Article Source Type: research

Genes, Vol. 15, Pages 316: Identification of Salt-Sensitive and Salt-Tolerant Genes through Weighted Gene Co-Expression Networks across Multiple Datasets: A Centralization and Differential Correlation Analysis
In this study, we propose an integration of multiple datasets to identify potential key transcription factors. This involves utilizing network analysis based on weighted co-expression networks, focusing on gene-centric measurement and differential co-expression relationships among genes. Consequently, our analysis reveals 86 genes located in markers from previous meta-QTL analysis. Moreover, six transcription factors, namely LOC_Os03g45410 (OsTBP2), LOC_Os07g42400 (OsGATA23), LOC_Os01g13030 (OsIAA3), LOC_Os05g34050 (OsbZIP39), LOC_Os09g29930 (OsBIM1), and LOC_Os10g10990 (transcription initiation factor IIF), exhibited sign...
Source: Genes - February 28, 2024 Category: Genetics & Stem Cells Authors: Pajaree Sonsungsan Apichat Suratanee Teerapong Buaboocha Supachitra Chadchawan Kitiporn Plaimas Tags: Article Source Type: research

Genes, Vol. 15, Pages 303: Autotetraploid Induction of Three A-Genome Wild Peanut Species, Arachis cardenasii, A. correntina, and A. diogoi
Hsuan Chen A-genome Arachis species (AA; 2n = 2x = 20) are commonly used as secondary germplasm sources in cultivated peanut breeding, Arachis hypogaea L. (AABB; 2n = 4x = 40), for the introgression of various biotic and abiotic stress resistance genes. Genome doubling is critical to overcoming the hybridization barrier of infertility that arises from ploidy-level differences between wild germplasm and cultivated peanuts. To develop improved genome doubling methods, four trials of various concentrations of the mitotic inhibitor treatments colchicine, oryzalin, and trifluralin were tested on the seedlings and seeds of ...
Source: Genes - February 27, 2024 Category: Genetics & Stem Cells Authors: Robert W. Suppa Ryan J. Andres Jeffrey C. Dunne Ramsey F. Arram Thomas B. Morgan Hsuan Chen Tags: Article Source Type: research

Genes, Vol. 15, Pages 306: UNC5C: Novel Gene Associated with Psychiatric Disorders Impacts Dysregulation of Axon Guidance Pathways
ne Francesco Calì The UNC-5 family of netrin receptor genes, predominantly expressed in brain tissues, plays a pivotal role in various neuronal processes. Mutations in genes involved in axon development contribute to a wide spectrum of human diseases, including developmental, neuropsychiatric, and neurodegenerative disorders. The NTN1/DCC signaling pathway, interacting with UNC5C, plays a crucial role in central nervous system axon guidance and has been associated with psychiatric disorders during adolescence in humans. Whole-exome sequencing analysis unveiled two compound heterozygous causative mutations within the...
Source: Genes - February 27, 2024 Category: Genetics & Stem Cells Authors: Simone Treccarichi Pinella Failla Mirella Vinci Antonino Musumeci Angelo Gloria Anna Vasta Giuseppe Calabrese Carla Papa Concetta Federico Salvatore Saccone Francesco Cal ì Tags: Article Source Type: research

Genes, Vol. 15, Pages 307: Genome-Wide Identification of Vascular Plant One-Zinc-Finger Gene Family in Six Cucurbitaceae Species and the Role of CmoVOZ2 in Salt and Drought Stress Tolerance
In this study, a total of 17 VOZ genes in the Cucurbitaceae family were investigated using various bioinformatics methods. The 17 VOZ genes in Cucurbitaceae are distributed across 16 chromosomes. Based on the affinity of VOZ proteins to AtVOZ proteins, these 17 proteins were categorized into two groups: group I encompassed eight VOZ members, while group II comprised nine VOZ members. The expression profiles of CmoVOZs under various hormonal and abiotic stresses indicated that these genes were induced differentially by JA, ABA, GA, salt, and drought stress. Subsequently, CmoVOZ1 and CmoVOZ2 were found to be transcriptionall...
Source: Genes - February 27, 2024 Category: Genetics & Stem Cells Authors: Xu Zhang Jiao Tu Zhang Tags: Article Source Type: research

Genes, Vol. 15, Pages 305: Developmental Changes in Genome Replication Progression in Pluripotent versus Differentiated Human Cells
stina Cardoso DNA replication is a fundamental process ensuring the maintenance of the genome each time cells divide. This is particularly relevant early in development when cells divide profusely, later giving rise to entire organs. Here, we analyze and compare the genome replication progression in human embryonic stem cells, induced pluripotent stem cells, and differentiated cells. Using single-cell microscopic approaches, we map the spatio-temporal genome replication as a function of chromatin marks/compaction level. Furthermore, we mapped the replication timing of subchromosomal tandem repeat regions and interspers...
Source: Genes - February 27, 2024 Category: Genetics & Stem Cells Authors: Sunil Kumar Pradhan Teresa Lozoya Paulina Prorok Yue Yuan Anne Lehmkuhl Peng Zhang M. Cristina Cardoso Tags: Article Source Type: research

Genes, Vol. 15, Pages 308: Mapping and Detection of Genes Related to Trichome Development in Black Gram (Vigna mungo (L.) Hepper)
In this study, a high-density map with 5734 bin markers using an F2 population derived from a trichome-bearing and a glabrous cultivar of black gram was constructed, and a major quantitative trait locus (QTL) related to trichomes was identified. Six candidate genes were located in the mapped interval region. Fourteen single-nucleotide polymorphisms (SNPs) or insertion/deletions (indels) were associated with those genes. One indel was located in the coding region of the gene designated as Scaffold_9372_HRSCAF_11447.164. Real-time quantitative PCR (qPCR) analysis demonstrated that only one candidate gene, Scaffold_9372_HRSCA...
Source: Genes - February 27, 2024 Category: Genetics & Stem Cells Authors: Dan Gong Jianling Li Suhua Wang Aihua Sha Lixia Wang Tags: Article Source Type: research