Genes, Vol. 14, Pages 403: Variable Selection for Sparse Data with Applications to Vaginal Microbiome and Gene Expression Data
irawi Sparse data with a high portion of zeros arise in various disciplines. Modeling sparse high-dimensional data is a challenging and growing research area. In this paper, we provide statistical methods and tools for analyzing sparse data in a fairly general and complex context. We utilize two real scientific applications as illustrations, including a longitudinal vaginal microbiome data and a high dimensional gene expression data. We recommend zero-inflated model selections and significance tests to identify the time intervals when the pregnant and non-pregnant groups of women are significantly different in terms of...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Niloufar Dousti Mousavi Jie Yang Hani Aldirawi Tags: Article Source Type: research

Genes, Vol. 14, Pages 404: Delineating the Spectrum of Genetic Variants Associated with Bardet-Biedl Syndrome in Consanguineous Pakistani Pedigrees
This study aimed to find the molecular basis of Bardet-Biedl syndrome (BBS) in Pakistani consanguineous families. A total of 12 affected families were enrolled. Clinical investigations were performed to access the BBS-associated phenotypes. Whole exome sequencing was conducted on one affected individual from each family. The computational functional analysis predicted the variants’ pathogenic effects and modeled the mutated proteins. Whole-exome sequencing revealed 9 pathogenic variants in six genes associated with BBS in 12 families. The BBS6/MKS was the most common BBS causative gene identified in five fami...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Ali Raza Rao Aamir Nazir Samina Imtiaz Sohail Aziz Paracha Yar Muhammad Waryah Ikram Din Ujjan Ijaz Anwar Afia Iqbal Federico A. Santoni Inayat Shah Khitab Gul Hafiz Muhammad Azhar Baig Ali Muhammad Waryah Stylianos E. Antonarakis Muhammad Ansar Tags: Article Source Type: research

Genes, Vol. 14, Pages 405: The Genetics of Primary Biliary Cholangitis: A GWAS and Post-GWAS Update
This study provides an overview of current data regarding the genetic factors of PBC as well as post-GWAS approaches to identifying primary functional variants and effector genes in disease-susceptibility loci. Possible mechanisms of these genetic factors in the development of PBC are also discussed, focusing on four major disease pathways identified by in silico gene set analyses, namely, (1) antigen presentation by human leukocyte antigens, (2) interleukin-12-related pathways, (3) cellular responses to tumor necrosis factor, and (4) B cell activation, maturation, and differentiation pathways. (Source: Genes)
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Yuki Hitomi Minoru Nakamura Tags: Review Source Type: research

Genes, Vol. 14, Pages 396: Fusion Gene-Based Classification of Variant Cytogenetic Rearrangements in Acute Myeloid Leukemia
We report here the identification of four variant t(8;V;21) translocations in newly diagnosed AML patients. Two patients showed a t(8;14) and a t(8;10) variation, respectively, with a morphologically normal-appearing chromosome 21 in each initial karyotype. Subsequent fluorescence in situ hybridization (FISH) on metaphase cells revealed cryptic three-way translocations t(8;14;21) and t(8;10;21). Each resulted in RUNX1::RUNX1T1 fusion. The other two patients showed karyotypically visible three-way translocations t(8;16;21) and t(8;20;21), respectively. Each resulted in RUNX1::RUNX1T1 fusion. Our findings demonstrate the imp...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Mary Gudipati Melody Butler Rima Koka Maria R. Baer Yi Ning Tags: Communication Source Type: research

Genes, Vol. 14, Pages 397: Tandem Repeat DNA Provides Many Cytological Markers for Hybrid Zone Analysis in Two Subspecies of the Grasshopper Chorthippus parallelus
M. Camacho Recent advances in next generation sequencing (NGS) have greatly increased our understanding of non-coding tandem repeat (TR) DNA. Here we show how TR DNA can be useful for the study of hybrid zones (HZ), as it serves as a marker to identify introgression in areas where two biological entities come in contact. We used Illumina libraries to analyse two subspecies of the grasshopper Chorthippus parallelus, which currently form a HZ in the Pyrenees. We retrieved a total of 152 TR sequences, and used fluorescent in situ hybridization (FISH) to map 77 families in purebred individuals from both subspecies. Our ana...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Beatriz Navarro-Dom ínguez Josefa Cabrero Mar ía Dolores López-León Francisco J. Ruiz-Ruano Miguel Pita Jos é L. Bella Juan Pedro M. Camacho Tags: Article Source Type: research

Genes, Vol. 14, Pages 398: Suppressors of Break-Induced Replication in Human Cells
Michael Leffak Short tandem DNA repeats are drivers of genome instability. To identify suppressors of break-induced mutagenesis human cells, unbiased genetic screens were conducted using a lentiviral shRNA library. The recipient cells possessed fragile non-B DNA that could induce DNA double-strand breaks (DSBs), integrated at an ectopic chromosomal site adjacent to a thymidine kinase marker gene. Mutagenesis of the thymidine kinase gene rendered cells resistant to the nucleoside analog ganciclovir (GCV). The screen identified genes that have established roles in DNA replication and repair, chromatin modification, re...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Stanley Dean Rider French J. Damewood Rujuta Yashodhan Gadgil David C. Hitch Venicia Alhawach Resha Shrestha Matilyn Shanahan Nathen Zavada Michael Leffak Tags: Article Source Type: research

Genes, Vol. 14, Pages 399: Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment
oise Wonkam The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI....
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Elvis Twumasi Aboagye Samuel Mawuli Adadey Edmond Wonkam-Tingang Lucas Amenga-Etego Gordon A. Awandare Ambroise Wonkam Tags: Systematic Review Source Type: research

Genes, Vol. 14, Pages 400: Concomitant Calcium Channelopathies Involving CACNA1A and CACNA1F: A Case Report and Review of the Literature
This study describes the clinical and genetic features of a unique 12-year-old boy harboring two congenital calcium channelopathies, involving the CACNA1A and CACNA1F genes, and provides an unadulterated view of the natural history of sporadic hemiplegic migraine type 1 (SHM1) due to the patient’s inability to tolerate any preventative medication. The patient presents with episodes of vomiting, hemiplegia, cerebral edema, seizure, fever, transient blindness, and encephalopathy. He is nonverbal, nonambulatory, and forced to have a very limited diet due to abnormal immune responses. The SHM1 manifestations appa...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Donna Schaare Sara M. Sarasua Laina Lusk Shridhar Parthasarathy Liangjiang Wang Ingo Helbig Luigi Boccuto Tags: Case Report Source Type: research

Genes, Vol. 14, Pages 401: Increased On-Target Rate and Risk of Concatemerization after CRISPR-Enhanced Targeting in ES Cells
hristine Birling The French mouse clinic (Institut Clinique de la Souris; ICS) has produced more than 2000 targeting vectors for ‘à la carte’ mutagenesis in C57BL/6N mice. Although most of the vectors were used successfully for homologous recombination in murine embryonic stem cells (ESCs), a few have failed to target a specific locus after several attempts. We show here that co-electroporation of a CRISPR plasmid with the same targeting construct as the one that failed previously allows the systematic achievement of positive clones. A careful validation of these clones is, ho...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Val érie Erbs Romain Lorentz Benjamin Eisenman Laurence Schaeffer Laurence Luppi Loic Lindner Yann H érault Guillaume Pavlovic Marie Wattenhofer-Donz é Marie-Christine Birling Tags: Article Source Type: research

Genes, Vol. 14, Pages 402: CD99 and the Chicken Alloantigen D Blood System
L. Taylor The chicken D blood system is one of 13 alloantigen systems found on chicken red blood cells. Classical recombinant studies located the D blood system on chicken chromosome 1, but the candidate gene was unknown. Multiple resources were utilized to identify the chicken D system candidate gene, including genome sequence information from both research and elite egg production lines for which D system alloantigen alleles were reported, and DNA from both pedigree and non-pedigree samples with known D alleles. Genome-wide association analyses using a 600 K or a 54 K SNP chip plus DNA from independent samples identi...
Source: Genes - February 3, 2023 Category: Genetics & Stem Cells Authors: Janet E. Fulton Wiola Drobik-Czwarno Ashlee R. Lund Carl J. Schmidt Robert L. Taylor Tags: Article Source Type: research

Genes, Vol. 14, Pages 391: A Role for the Interactions between Pol & delta; and PCNA Revealed by Analysis of pol3-01 Yeast Mutants
Genes, Vol. 14, Pages 391: A Role for the Interactions between Polδ and PCNA Revealed by Analysis of pol3-01 Yeast Mutants Genes doi: 10.3390/genes14020391 Authors: Shaked Nir Heyman Mika Golan Batia Liefshitz Martin Kupiec Several DNA polymerases participate in DNA synthesis during genome replication and DNA repair. PCNA, a homotrimeric ring, acts as a processivity factor for DNA polymerases. PCNA also acts as a “landing pad” for proteins that interact with chromatin and DNA at the moving fork. The interaction between PCNA and polymerase delta (Polδ) is med...
Source: Genes - February 2, 2023 Category: Genetics & Stem Cells Authors: Shaked Nir Heyman Mika Golan Batia Liefshitz Martin Kupiec Tags: Article Source Type: research

Genes, Vol. 14, Pages 392: Genomic Insights and Functional Analysis Reveal Plant Growth Promotion Traits of Paenibacillus mucilaginosus G78
In this study, the genome of P. mucilaginosus G78 was sequenced using Illumina NovaSeq PE150. It contains 8,576,872 bp with a GC content of 58.5%, and was taxonomically characterized. Additionally, a total of 7338 genes with 143 tRNAs, 41 rRNAs, and 5 ncRNAs were identified. This strain can prohibit the growth of the plant pathogen, but also has the capability to form biofilm, solubilize phosphate, and produce IAA. Twenty-six gene clusters encoding secondary metabolites were identified, and the genotypic characterization indirectly proved its resistant ability to ampicillin, bacitracin, polymyxin and chloramphenicol. The p...
Source: Genes - February 2, 2023 Category: Genetics & Stem Cells Authors: Dan Wang Verena Poinsot Wangxi Li Yusheng Lu Chong Liu Yaying Li Kaizhi Xie Lili Sun Chaohong Shi Huanlong Peng Wanling Li Changmin Zhou Wenjie Gu Tags: Article Source Type: research

Genes, Vol. 14, Pages 390: Proteomic and Transcriptomic Responses of the Desiccation-Tolerant Moss Racomitrium canescens in the Rapid Rehydration Processes
i Sha Jing Li The moss Racomitrium canescens (R. canescens) has strong desiccation tolerance. It can remain desiccated for years and yet recover within minutes of rehydration. Understanding the responses and mechanisms underlying this rapid rehydration capacity in bryophytes could identify candidate genes that improve crop drought tolerance. We explored these responses using physiology, proteomics, and transcriptomics. Label-free quantitative proteomics comparing desiccated plants and samples rehydrated for 1 min or 6 h suggesting that damage to chromatin and the cytoskeleton had occurred during desiccation, and poin...
Source: Genes - February 2, 2023 Category: Genetics & Stem Cells Authors: Yifang Peng Tianyi Ma Xin Wang Meijuan Zhang Yingxu Xu Jie Wei Wei Sha Jing Li Tags: Article Source Type: research

Genes, Vol. 14, Pages 393: Deregulated E2F Activity as a Cancer-Cell Specific Therapeutic Tool
Warita Kiyoshi Ohtani The transcription factor E2F, the principal target of the tumor suppressor pRB, plays crucial roles in cell proliferation and tumor suppression. In almost all cancers, pRB function is disabled, and E2F activity is enhanced. To specifically target cancer cells, trials have been undertaken to suppress enhanced E2F activity to restrain cell proliferation or selectively kill cancer cells, utilizing enhanced E2F activity. However, these approaches may also impact normal growing cells, since growth stimulation also inactivates pRB and enhances E2F activity. E2F activated upon the loss of pRB control (...
Source: Genes - February 2, 2023 Category: Genetics & Stem Cells Authors: Rinka Nakajima Lin Zhao Yaxuan Zhou Mashiro Shirasawa Ayato Uchida Hikaru Murakawa Mariana Fikriyanti Ritsuko Iwanaga Andrew P. Bradford Keigo Araki Tomoko Warita Kiyoshi Ohtani Tags: Review Source Type: research

Genes, Vol. 14, Pages 394: Detecting Melanocortin 1 Receptor Gene & rsquo;s SNPs by CRISPR/enAsCas12a
Genes, Vol. 14, Pages 394: Detecting Melanocortin 1 Receptor Gene’s SNPs by CRISPR/enAsCas12a Genes doi: 10.3390/genes14020394 Authors: Wei Yang Dagang Tao Bingrong Xu Yueting Zheng Shuhong Zhao Beyond its powerful genome-editing capabilities, the CRISPR/Cas system has opened up a new era of molecular diagnostics due to its highly specific base recognition and trans-cleavage activity. However, most CRISPR/Cas detection systems are mainly used to detect nucleic acids of bacteria or viruses, while the application of single nucleotide polymorphism (SNP) detection is limited. The MC1R SNPs were invest...
Source: Genes - February 2, 2023 Category: Genetics & Stem Cells Authors: Wei Yang Dagang Tao Bingrong Xu Yueting Zheng Shuhong Zhao Tags: Article Source Type: research