Genes

14 pages, 1222 KiB

Open AccessEditor’s ChoiceArticle

Genotype and Phenotype Analyses of a Novel WFS1 Variant (c.2512C>T p.(Pro838Ser)) Associated with DFNA6/14/38

by Hedwig M. Velde, Xanne J. J. Huizenga, Helger G. Yntema, Lonneke Haer-Wigman, Andy J. Beynon, Jaap Oostrik, Sjoert A. H. Pegge, Hannie Kremer, Cris P. Lanting and Ronald J. E. Pennings

Genes 2023, 14(2), 457; https://doi.org/10.3390/genes14020457 - 10 Feb 2023

Cited by 8 | Viewed by 2604

Abstract

The aim of this study is to contribute to a better description of the genotypic and phenotypic spectrum of DFNA6/14/38 and aid in counseling future patients identified with this variant. Therefore, we describe the genotype and phenotype in a large Dutch–German family (W21-1472) [...] Read more.

The aim of this study is to contribute to a better description of the genotypic and phenotypic spectrum of DFNA6/14/38 and aid in counseling future patients identified with this variant. Therefore, we describe the genotype and phenotype in a large Dutch–German family (W21-1472) with autosomal dominant non-syndromic, low-frequency sensorineural hearing loss (LFSNHL). Exome sequencing and targeted analysis of a hearing impairment gene panel were used to genetically screen the proband. Co-segregation of the identified variant with hearing loss was assessed by Sanger sequencing. The phenotypic evaluation consisted of anamnesis, clinical questionnaires, physical examination and examination of audiovestibular function. A novel likely pathogenic WFS1 variant (NM_006005.3:c.2512C>T p.(Pro838Ser)) was identified in the proband and found to co-segregate with LFSNHL, characteristic of DFNA6/14/38, in this family. The self-reported age of onset of hearing loss (HL) ranged from congenital to 50 years of age. In the young subjects, HL was demonstrated in early childhood. At all ages, an LFSNHL (0.25–2 kHz) of about 50–60 decibel hearing level (dB HL) was observed. HL in the higher frequencies showed inter-individual variability. The dizziness handicap inventory (DHI) was completed by eight affected subjects and indicated a moderate handicap in two of them (aged 77 and 70). Vestibular examinations (n = 4) showed abnormalities, particularly in otolith function. In conclusion, we identified a novel WFS1 variant that co-segregates with DFNA6/14/38 in this family. We found indications of mild vestibular dysfunction, although it is uncertain whether this is related to the identified WFS1 variant or is an incidental finding. We would like to emphasize that conventional neonatal hearing screening programs are not sensitive to HL in DFNA6/14/38 patients, because high-frequency hearing thresholds are initially preserved. Therefore, we suggest screening newborns in DFNA6/14/38 families with more frequency-specific methods. Full article

(This article belongs to the Special Issue Functional Otogenetics)

► Show Figures

Figure 1

14 pages, 3613 KiB

Open AccessEditor’s ChoiceArticle

Complete Chloroplast Genome Sequence of the Long Blooming Cultivar Camellia ‘Xiari Qixin’: Genome Features, Comparative and Phylogenetic Analysis

by Yufen Xu, Yanju Liu, Zhaoyan Yu and Xiaocheng Jia

Genes 2023, 14(2), 460; https://doi.org/10.3390/genes14020460 - 10 Feb 2023

Cited by 4 | Viewed by 2303

Abstract

The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia ‘Xiari Qixin’ belongs to one of the typical cultivars in the [...] Read more.

The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia ‘Xiari Qixin’ belongs to one of the typical cultivars in the four seasons camellia hybrids series. Due to its long flowering period, this kind of cultivar is identified as a precious resource of camellia flowers. In this study, the complete chloroplast genome sequence of C. ‘Xiari Qixin’ was first reported. Its whole chloroplast genome is 157,039 bp in length with an overall GC content of 37.30%, composed of a large single copy region (LSC, 86,674 bp), a small single copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,042 bp each). A total of 134 genes were predicted in this genome, including 8 ribosomal RNA genes, 37 transfer RNA genes, and 89 protein-coding genes. In addition, 50 simple sequence repeats (SSRs) and 36 long repeat sequences were detected. By comparing C. ‘Xiari Qixin’ and seven Camellia species on the chloroplast genome, seven mutation hotspot regions were identified, including psbK, trnS (GCU)-trnG(GCC), trnG(GCC), petN-psbM, trnF(GAA)-ndhJ, trnP(UGG)-psaJ, and ycf1. Phylogenetic analysis of 30 chloroplast genomes showed that the genetic relationship between C. ‘Xiari Qixin’ and Camellia azalea is quite close in evolution. These results could not only provide a valuable database for determining the maternal origin of Camellia cultivars, but also contribute to the exploration of the phylogenetic relationship and utilization of germplasm resources for Camellia. Full article

(This article belongs to the Special Issue Plant Plastid Genome)

► Show Figures

Figure 1

15 pages, 4889 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

ThrRS-Mediated Translation Regulation of the RNA Polymerase III Subunit RPC10 Occurs through an Element with Similarity to Cognate tRNA ASL and Affects tRNA Levels

by Ofri Levi, Monalisha Mallik and Yoav S. Arava

Genes 2023, 14(2), 462; https://doi.org/10.3390/genes14020462 - 10 Feb 2023

Cited by 3 | Viewed by 2481

Abstract

Aminoacyl tRNA synthetases (aaRSs) are a well-studied family of enzymes with a canonical role in charging tRNAs with a specific amino acid. These proteins appear to also have non-canonical roles, including post-transcriptional regulation of mRNA expression. Many aaRSs were found to bind mRNAs [...] Read more.

Aminoacyl tRNA synthetases (aaRSs) are a well-studied family of enzymes with a canonical role in charging tRNAs with a specific amino acid. These proteins appear to also have non-canonical roles, including post-transcriptional regulation of mRNA expression. Many aaRSs were found to bind mRNAs and regulate their translation into proteins. However, the mRNA targets, mechanism of interaction, and regulatory consequences of this binding are not fully resolved. Here, we focused on yeast cytosolic threonine tRNA synthetase (ThrRS) to decipher its impact on mRNA binding. Affinity purification of ThrRS with its associated mRNAs followed by transcriptome analysis revealed a preference for mRNAs encoding RNA polymerase subunits. An mRNA that was significantly bound compared to all others was the mRNA encoding RPC10, a small subunit of RNA polymerase III. Structural modeling suggested that this mRNA includes a stem-loop element that is similar to the anti-codon stem loop (ASL) structure of ThrRS cognate tRNA (tRNA^Thr). We introduced random mutations within this element and found that almost every change from the normal sequence leads to reduced binding by ThrRS. Furthermore, point mutations at six key positions that abolish the predicted ASL-like structure showed a significant decrease in ThrRS binding with a decrease in RPC10 protein levels. Concomitantly, tRNA^Thr levels were reduced in the mutated strain. These data suggest a novel regulatory mechanism in which cellular tRNA levels are regulated through a mimicking element within an RNA polymerase III subunit in a manner that involves the tRNA cognate aaRS. Full article

(This article belongs to the Special Issue Emerging Roles of tRNAs in Health and Disease)

► Show Figures

Figure 1

16 pages, 3147 KiB

Open AccessEditor’s ChoiceArticle

Comparative Hypothalamic Transcriptome Analysis Reveals Crucial mRNAs, lncRNAs, and circRNAs Affecting Litter Size in Goats

by Shucan Dong, Biwei Hou, Chuang Yang, Yaokun Li, Baoli Sun, Yongqing Guo, Ming Deng, Dewu Liu and Guangbin Liu

Genes 2023, 14(2), 444; https://doi.org/10.3390/genes14020444 - 9 Feb 2023

Cited by 9 | Viewed by 2205

Abstract

Litter size is an important indicator to measure the reproductive performance of goats, which is affected by the reproductive function of animals. The hypothalamus, as the regulatory center of the endocrine system, plays an important role in the reproduction of female animals. Here, [...] Read more.

Litter size is an important indicator to measure the reproductive performance of goats, which is affected by the reproductive function of animals. The hypothalamus, as the regulatory center of the endocrine system, plays an important role in the reproduction of female animals. Here, we performed high-throughput RNA sequencing using hypothalamic tissue from high-fecundity and low-fecundity Leizhou goats to explore critical functional genes associated with litter size. Differentially expressed mRNA, lncRNA, and circRNAs were screened using DESeq and were enriched, and then analyzed by Gene Ontology and Kyoto Encyclopedia of Gene and Genome. Results showed that some of these differentially expressed mRNAs could be enriched in reproductive processes, jak-STAT, prolactin signaling pathway, and other signaling pathways related to reproduction, such as SOCS3. Furthermore, the central proteins POSTN, MFAP5, and DCN from protein–protein interaction may regulate animal reproductive activity by affecting cell proliferation and apoptosis. lncRNA MSTRG.33887.2 as well as circRNAs chicirc_098002, chicirc_072583, and chicirc_053531 may be able to influence animal reproduction by participating in folate metabolism and energy metabolism homeostasis through their respective target genes. Our results expand the molecular mechanism of hypothalamic regulation on animal reproduction. Full article

(This article belongs to the Section Animal Genetics and Genomics)

► Show Figures

Figure 1

10 pages, 2570 KiB

Open AccessEditor’s ChoiceTechnical Note

DraculR: A Web-Based Application for In Silico Haemolysis Detection in High-Throughput microRNA Sequencing Data

by Melanie D. Smith, Shalem Y. Leemaqz, Tanja Jankovic-Karasoulos, Dylan McCullough, Dale McAninch, Anya L. Arthurs, James Breen, Claire T. Roberts and Katherine A. Pillman

Genes 2023, 14(2), 448; https://doi.org/10.3390/genes14020448 - 9 Feb 2023

Cited by 2 | Viewed by 2082

Abstract

The search for novel microRNA (miRNA) biomarkers in plasma is hampered by haemolysis, the lysis and subsequent release of red blood cell contents, including miRNAs, into surrounding fluid. The biomarker potential of miRNAs comes in part from their multicompartment origin and the long-lived [...] Read more.

The search for novel microRNA (miRNA) biomarkers in plasma is hampered by haemolysis, the lysis and subsequent release of red blood cell contents, including miRNAs, into surrounding fluid. The biomarker potential of miRNAs comes in part from their multicompartment origin and the long-lived nature of miRNA transcripts in plasma, giving researchers a functional window for tissues that are otherwise difficult or disadvantageous to sample. The inclusion of red-blood-cell-derived miRNA transcripts in downstream analysis introduces a source of error that is difficult to identify posthoc and may lead to spurious results. Where access to a physical specimen is not possible, our tool will provide an in silico approach to haemolysis prediction. We present DraculR, an interactive Shiny/R application that enables a user to upload miRNA expression data from a short-read sequencing of human plasma as a raw read counts table and interactively calculate a metric that indicates the degree of haemolysis contamination. The code, DraculR web tool and its tutorial are freely available as detailed herein. Full article

(This article belongs to the Collection Feature Papers in Bioinformatics)

► Show Figures

Figure 1

14 pages, 949 KiB

Open AccessEditor’s ChoiceArticle

Study on Sperm-Cell Detection Using YOLOv5 Architecture with Labaled Dataset

by Michal Dobrovolny, Jakub Benes, Jaroslav Langer, Ondrej Krejcar and Ali Selamat

Genes 2023, 14(2), 451; https://doi.org/10.3390/genes14020451 - 9 Feb 2023

Cited by 14 | Viewed by 5643

Abstract

Infertility has recently emerged as a severe medical problem. The essential elements in male infertility are sperm morphology, sperm motility, and sperm density. In order to analyze sperm motility, density, and morphology, laboratory experts do a semen analysis. However, it is simple to [...] Read more.

Infertility has recently emerged as a severe medical problem. The essential elements in male infertility are sperm morphology, sperm motility, and sperm density. In order to analyze sperm motility, density, and morphology, laboratory experts do a semen analysis. However, it is simple to err when using a subjective interpretation based on laboratory observation. In this work, a computer-aided sperm count estimation approach is suggested to lessen the impact of experts in semen analysis. Object detection techniques concentrating on sperm motility estimate the number of active sperm in the semen. This study provides an overview of other techniques that we can compare. The Visem dataset from the Association for Computing Machinery was used to test the proposed strategy. We created a labelled dataset to prove that our network can detect sperms in images. The best not-super tuned result is mAP

72.15

. Full article

(This article belongs to the Special Issue Selected Papers from the 9th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2022))

► Show Figures

Figure 1

8 pages, 268 KiB

Open AccessEditor’s ChoiceCommunication

Impact of pri-let-7a-1 rs10739971 for Gastric Cancer Predisposition in an Amazon Region

by Roberta Borges Andrade, Amanda de Nazaré Cohen-Paes, Diana Feio da Veiga Borges Leal, Karla Beatriz Cardias Cereja Pantoja, Laura Patrícia Albarello Gellen, Darlen Cardoso de Carvalho, Tatiane Piedade de Souza, Marianne Rodrigues Fernandes, Paulo Pimentel de Assumpcão, Rommel Mario Rodríguez Burbano, Sidney Emanuel Batista dos Santos and Ney Pereira Carneiro dos Santos

Genes 2023, 14(2), 453; https://doi.org/10.3390/genes14020453 - 9 Feb 2023

Cited by 1 | Viewed by 1644

Abstract

Gastric cancer (GC) is the fifth most common type of cancer and the fourth leading cause of cancer death. In Brazil, GC has a high incidence and mortality rates, and it is highly variable by region. The Amazon region has significant rising rates [...] Read more.

Gastric cancer (GC) is the fifth most common type of cancer and the fourth leading cause of cancer death. In Brazil, GC has a high incidence and mortality rates, and it is highly variable by region. The Amazon region has significant rising rates among all Brazil regions. Only very few studies have evaluated the association between genetic variants and the risk of gastric cancer in the Brazilian Amazon population. Therefore, this study aimed to investigate associations between single nucleotide polymorphisms of miRNA processing genes and the risk for GC in this population. Potentially functional single nucleotide polymorphisms from miRNA processing genes were genotyped in 159 cases and 193 healthy controls by QuantStudio Real Time PCR. According to our findings, the genotype GG of the variant rs10739971 presents a lower risk to the development of GC in comparison to the remaining genotypes (p = 0.000016; OR = 0.055; 95% CI = 0.015–0.206). This is the first study to report the association of pri-let-7a-1 rs10739971 with GC in the Brazilian Amazon population, which is a highly mixed population with a unique genetic constitution that is different from other populations that are studied in the vast majority of scientific research. Full article

(This article belongs to the Special Issue Molecular Biomarkers of Solid Tumors)

13 pages, 1578 KiB

Open AccessEditor’s ChoiceArticle

The Impact of Variation in the Toll-like Receptor 3 Gene on Epizootic Hemorrhagic Disease in Illinois Wild White-Tailed Deer (Odocoileus virginianus)

by Jacob E. Wessels, Yasuko Ishida, Nelda A. Rivera, Spencer L. Stirewalt, William M. Brown, Jan E. Novakofski, Alfred L. Roca and Nohra E. Mateus-Pinilla

Genes 2023, 14(2), 426; https://doi.org/10.3390/genes14020426 - 8 Feb 2023

Cited by 3 | Viewed by 3599

Abstract

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined [...] Read more.

Epizootic hemorrhagic disease (EHD) leads to high mortality in white-tailed deer (Odocoileus virginianus) and is caused by a double-stranded RNA (dsRNA) virus. Toll-like receptor 3 (TLR3) plays a role in host immune detection and response to dsRNA viruses. We, therefore, examined the role of genetic variation within the TLR3 gene in EHD among 84 Illinois wild white-tailed deer (26 EHD-positive deer and 58 EHD-negative controls). The entire coding region of the TLR3 gene was sequenced: 2715 base pairs encoding 904 amino acids. We identified 85 haplotypes with 77 single nucleotide polymorphisms (SNPs), of which 45 were synonymous mutations and 32 were non-synonymous. Two non-synonymous SNPs differed significantly in frequency between EHD-positive and EHD-negative deer. In the EHD-positive deer, phenylalanine was relatively less likely to be encoded at codon positions 59 and 116, whereas leucine and serine (respectively) were detected less frequently in EHD-negative deer. Both amino acid substitutions were predicted to impact protein structure or function. Understanding associations between TLR3 polymorphisms and EHD provides insights into the role of host genetics in outbreaks of EHD in deer, which may allow wildlife agencies to better understand the severity of outbreaks. Full article

(This article belongs to the Section Animal Genetics and Genomics)

► Show Figures

Figure 1

13 pages, 1981 KiB

Open AccessEditor’s ChoiceArticle

A Novel DLG1 Variant in a Family with Brugada Syndrome: Clinical Characteristics and In Silico Analysis

by Maria d’Apolito, Francesco Santoro, Rosa Santacroce, Giorgia Cordisco, Ilaria Ragnatela, Girolamo D’Arienzo, Pier Luigi Pellegrino, Natale Daniele Brunetti and Maurizio Margaglione

Genes 2023, 14(2), 427; https://doi.org/10.3390/genes14020427 - 8 Feb 2023

Cited by 7 | Viewed by 3645

Abstract

Background: Brugada syndrome (BrS) is an inherited primary channelopathy syndrome associated to sudden cardiac death. Overall, variants have been identified in eighteen genes encoding for ion channel subunits and seven genes for regulatory proteins. Recently, a missense variant in DLG1 has been found [...] Read more.

Background: Brugada syndrome (BrS) is an inherited primary channelopathy syndrome associated to sudden cardiac death. Overall, variants have been identified in eighteen genes encoding for ion channel subunits and seven genes for regulatory proteins. Recently, a missense variant in DLG1 has been found within a BrS phenotype-positive patient. DLG1 encodes for synapse associated protein 97 (SAP97), a protein characterized by the presence of multiple domains for protein–protein interactions including PDZ domains. In cardiomyocytes, SAP97 interacts with Nav1.5, a PDZ binding motif of SCN5A and others potassium channel subunits. Aim of the Study: To characterize the phenotype of an Italian family with BrS syndrome carrying a DLG1 variant. Methods: Clinical and genetic investigations were performed. Genetic testing was performed with whole-exome sequencing (WES) using the Illumina platform. According to the standard protocol, a variant found by WES was confirmed in all members of the family by bi-directional capillary Sanger resequencing. The effect of the variant was investigated by using in silico prediction of pathogenicity. Results: The index case was a 74-year-old man with spontaneous type 1 BrS ECG pattern that experienced syncope and underwent ICD implantation. WES of the index case, performed assuming a dominant mode of inheritance, identified a heterozygous variant, c.1556G>A (p.R519H), in the exon 15 of the DLG1 gene. In the pedigree investigation, 6 out of 12 family members had the variant. Carriers of the gene variant all had BrS ECG type 1 drug induced and showed heterogeneous cardiac phenotypes with two patients experiencing syncope during exercise and fever, respectively. The amino acid residue #519 lies near a PDZ domain and in silico analysis suggested a causal role for the variant. Modelling of the resulting protein structure predicted that the variant disrupts an H-bond and a likelihood of being pathogenic. As a consequence, it is likely that a conformational change affects protein functionality and the modulating role on ion channels. Conclusions: A DLG1 gene variant identified was associated with BrS. The variant could modify the formation of multichannel protein complexes, affecting ion channels to specific compartments in cardiomyocytes. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

► Show Figures

Figure 1

8 pages, 1112 KiB

Open AccessEditor’s ChoiceCase Report

Hereditary Cancer Syndrome in a Family with Double Mutation in BRIP1 and MUTYH Genes

by Giovanna D’Elia, Gemma Caliendo, Luana Passariello, Luisa Albanese, Jasmine Makker, Anna Maria Molinari and Maria Teresa Vietri

Genes 2023, 14(2), 428; https://doi.org/10.3390/genes14020428 - 8 Feb 2023

Cited by 3 | Viewed by 3278

Abstract

Hereditary cancer syndromes predispose to several types of cancer due to inherited pathogenic variants in susceptibility genes. We describe the case of a 57-year-old woman, diagnosed with breast cancer, and her family. The proband belongs to a family with a suspected tumor syndrome, [...] Read more.

Hereditary cancer syndromes predispose to several types of cancer due to inherited pathogenic variants in susceptibility genes. We describe the case of a 57-year-old woman, diagnosed with breast cancer, and her family. The proband belongs to a family with a suspected tumor syndrome, due to other cancer cases in her family from the paternal and maternal sides. After oncogenetic counseling, she was subjected to mutational analysis with an NGS panel analyzing 27 genes. The genetic analysis showed two monoallelic mutations in low penetrance genes, c.1187G>A (p.G396D) in MUTYH and c.55dup (p.Tyr19Leufs*2) in BRIP1. One of the mutations was inherited from the maternal side and the other from the paternal side, suggesting two different cancer syndrome types in the family. MUTYH mutation was related to the onset of cancers on the paternal side, as confirmed by the occurrence of the same mutation in the proband’s cousin. BRIP1 mutation was found in the proband’s mother, indicating that it was related to the cancer cases observed on the maternal side, including breast cancer and sarcoma. Advances in NGS technologies have allowed the identification of mutations in families with hereditary cancers in genes other than those related to a specific suspected syndrome. A complete oncogenetic counseling, together with molecular tests that enable a simultaneous analysis of multiple genes, is essential for the identification of a correct tumor syndrome and for clinical decision-making in a patient and his/her family. The detection of mutations in multiple susceptibility genes allows the initiation of early risk-reducing measures for identified mutation carriers among family members and to include them in a proper surveillance program for specific syndromes. Moreover, it may enable an adapted treatment for the affected patient, permitting personalized therapeutic options. Full article

(This article belongs to the Collection Genotype-Phenotype Study in Disease)

► Show Figures

Figure 1

16 pages, 2138 KiB

Open AccessEditor’s ChoiceCase Report

Tuberous Sclerosis, Type II Diabetes Mellitus and the PI3K/AKT/mTOR Signaling Pathways—Case Report and Literature Review

by Claudia Maria Jurca, Kinga Kozma, Codruta Diana Petchesi, Dana Carmen Zaha, Ioan Magyar, Mihai Munteanu, Lucian Faur, Aurora Jurca, Dan Bembea, Emilia Severin and Alexandru Daniel Jurca

Genes 2023, 14(2), 433; https://doi.org/10.3390/genes14020433 - 8 Feb 2023

Cited by 13 | Viewed by 4184

Abstract

Tuberous sclerosis complex (TSC) is a rare autosomal dominant neurocutaneous syndrome. It is manifested mainly in cutaneous lesions, epilepsy and the emergence of hamartomas in several tissues and organs. The disease sets in due to mutations in two tumor suppressor genes: TSC1 and [...] Read more.

Tuberous sclerosis complex (TSC) is a rare autosomal dominant neurocutaneous syndrome. It is manifested mainly in cutaneous lesions, epilepsy and the emergence of hamartomas in several tissues and organs. The disease sets in due to mutations in two tumor suppressor genes: TSC1 and TSC2. The authors present the case of a 33-year-old female patient registered with the Bihor County Regional Center of Medical Genetics (RCMG) since 2021 with a TSC diagnosis. She was diagnosed with epilepsy at eight months old. At 18 years old she was diagnosed with tuberous sclerosis and was referred to the neurology department. Since 2013 she has been registered with the department for diabetes and nutritional diseases with a type 2 diabetes mellitus (T2DM) diagnosis. The clinical examination revealed: growth delay, obesity, facial angiofibromas, sebaceous adenomas, depigmented macules, papillomatous tumorlets in the thorax (bilateral) and neck, periungual fibroma in both lower limbs, frequent convulsive seizures; on a biological level, high glycemia and glycated hemoglobin levels. Brain MRI displayed a distinctive TS aspect with five bilateral hamartomatous subependymal nodules associating cortical/subcortical tubers with the frontal, temporal and occipital distribution. Molecular diagnosis showed a pathogenic variant in the TSC1 gene, exon 13, c.1270A>T (p. Arg424*). Current treatment targets diabetes (Metformin, Gliclazide and the GLP-1 analog semaglutide) and epilepsy (Carbamazepine and Clonazepam). This case report presents a rare association between type 2 diabetes mellitus and Tuberous Sclerosis Complex. We suggest that the diabetes medication Metformin may have positive effects on both the progression of the tumor associated with TSC and the seizures specific to TSC and we assume that the association of TSC and T2DM in the presented cases is accidental, as there are no similar cases reported in the literature. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

► Show Figures

Figure 1

12 pages, 796 KiB

Open AccessEditor’s ChoiceArticle

by Ieva Golubickaite, Rasa Ugenskiene, Agne Bartnykaite, Lina Poskiene, Aurelija Vegiene, Evaldas Padervinskis, Viktoras Rudzianskas and Elona Juozaityte

Genes 2023, 14(2), 434; https://doi.org/10.3390/genes14020434 - 8 Feb 2023

Cited by 1 | Viewed by 2267

Abstract

In 2020, 878,348 newly reported cases and 444,347 deaths related to head and neck cancer were reported. These numbers suggest that there is still a need for molecular biomarkers for the diagnosis and prognosis of the disease. In this study, we aimed to [...] Read more.

In 2020, 878,348 newly reported cases and 444,347 deaths related to head and neck cancer were reported. These numbers suggest that there is still a need for molecular biomarkers for the diagnosis and prognosis of the disease. In this study, we aimed to analyze mitochondria-related mitochondrial transcription factor A (TFAM) and DNA polymerase γ (POLG) single-nucleotide polymorphisms (SNPs) in the head and neck cancer patient group and evaluate associations between SNPs, disease characteristics, and patient outcomes. Genotyping was performed using TaqMan probes with Real-Time polymerase chain reaction. We found associations between TFAM gene SNPs rs11006129 and rs3900887 and patient survival status. We found that patients with the TFAM rs11006129 CC genotype and non-carriers of the T allele had longer survival times than those with the CT genotype or T-allele carriers. Additionally, patients with the TFAM rs3900887 A allele tended to have shorter survival times than non-carriers of the A allele. Our findings suggest that variants in the TFAM gene may play an important role in head and neck cancer patient survival and could be considered and further evaluated as prognostic biomarkers. However, due to the limited sample size (n = 115), further studies in larger and more diverse cohorts are needed to confirm these findings. Full article

(This article belongs to the Special Issue Head and Neck Genetics)

► Show Figures

Figure 1

13 pages, 5716 KiB

Open AccessEditor’s ChoiceArticle

Whole-Genome Analysis Reveals the Dynamic Evolution of Holocentric Chromosomes in Satyrine Butterflies

by Elena A. Pazhenkova and Vladimir A. Lukhtanov

Genes 2023, 14(2), 437; https://doi.org/10.3390/genes14020437 - 8 Feb 2023

Cited by 7 | Viewed by 3372

Abstract

Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are [...] Read more.

Butterfly chromosomes are holocentric, i.e., lacking a localized centromere. Potentially, this can lead to rapid karyotypic evolution through chromosome fissions and fusions, since fragmented chromosomes retain kinetic activity, while fused chromosomes are not dicentric. However, the actual mechanisms of butterfly genome evolution are poorly understood. Here, we analyzed chromosome-scale genome assemblies to identify structural rearrangements between karyotypes of satyrine butterfly species. For the species pair Erebia ligea–Maniola jurtina, sharing the ancestral diploid karyotype 2n = 56 + ZW, we demonstrate a high level of chromosomal macrosynteny and nine inversions separating these species. We show that the formation of a karyotype with a low number of chromosomes (2n = 36 + ZW) in Erebia aethiops was based on ten fusions, including one autosome–sex chromosome fusion, resulting in a neo-Z chromosome. We also detected inversions on the Z sex chromosome that were differentially fixed between the species. We conclude that chromosomal evolution is dynamic in the satyrines, even in the lineage that preserves the ancestral chromosome number. We hypothesize that the exceptional role of Z chromosomes in speciation may be further enhanced by inversions and sex chromosome–autosome fusions. We argue that not only fusions/fissions but also inversions are drivers of the holocentromere-mediated mode of chromosomal speciation. Full article

(This article belongs to the Special Issue Chromosome Evolution and Karyotype Analysis)

► Show Figures

Figure 1

10 pages, 1971 KiB

Open AccessEditor’s ChoiceArticle

MCD Inhibits Lipid Deposition in Goat Intramuscular Preadipocytes

by Changheng Yang, Qi Li, Yaqiu Lin, Yong Wang, Hengbo Shi, Lian Huang, Wangsheng Zhao, Hua Xiang and Jiangjiang Zhu

Genes 2023, 14(2), 440; https://doi.org/10.3390/genes14020440 - 8 Feb 2023

Cited by 10 | Viewed by 2569

Abstract

Malonyl-CoA decarboxylase (MCD) is a major regulator of fatty acid oxidation catalyzing the decarboxylation of malonyl coenzyme A (malonyl-CoA). Although its involvement in human diseases has been well studied, its role in intramuscular fat (IMF) deposition remains unknown. In this present [...] Read more.

Malonyl-CoA decarboxylase (MCD) is a major regulator of fatty acid oxidation catalyzing the decarboxylation of malonyl coenzyme A (malonyl-CoA). Although its involvement in human diseases has been well studied, its role in intramuscular fat (IMF) deposition remains unknown. In this present study, 1726 bp of MCD cDNA was cloned (OM937122) from goat liver, including 5′UTR of 27 bp, 3′UTR of 199 bp, and CDS of 1500 bp, encoding 499 amino acids. In this present study, although the overexpression of MCD increased the mRNA expression of FASN and DGAT2, the expression of ATGL and ACOX1 was also activated significantly and resulted in a decrease in cellular lipid deposition in goat intramuscular preadipocytes. Meanwhile, the silencing of MCD increased the cellular lipid deposition and was accompanied by the expression activation of DGAT2 and the expression suppression of ATGL and HSL, despite the expression suppression of genes related to fatty acid synthesis, including ACC and FASN. However, the expression of DGAT1 was not affected significantly (p > 0.05) by the expression alteration of MCD in this present study. Furthermore, 2025 bp of MCD promoter was obtained and predicted to be regulated by C/EBPα, SP1, SREBP1, and PPARG. In summary, although different pathways may respond to the expression alteration of MCD, the expression of MCD was negatively correlated with the cellular lipid deposition in goat intramuscular preadipocytes. These data may be beneficial for enhancing our understanding of the regulation of IMF deposition in goats. Full article

(This article belongs to the Section Animal Genetics and Genomics)

► Show Figures

Figure 1

13 pages, 956 KiB

Open AccessEditor’s ChoiceSystematic Review

Telomere Length, a New Biomarker of Male (in)Fertility? A Systematic Review of the Literature

by Anne-Julie Fattet, Maxime Chaillot and Isabelle Koscinski

Genes 2023, 14(2), 425; https://doi.org/10.3390/genes14020425 - 7 Feb 2023

Cited by 12 | Viewed by 3983

Abstract

Male factors are suspected in around half cases of infertility, of which up to 40% are diagnosed as idiopathic. In the context of a continuously increased resort to ART and increased decline of semen parameters, it is of greatest interest to evaluate an [...] Read more.

Male factors are suspected in around half cases of infertility, of which up to 40% are diagnosed as idiopathic. In the context of a continuously increased resort to ART and increased decline of semen parameters, it is of greatest interest to evaluate an additional potential biomarker of sperm quality. According to PRISMA guidelines, this systematic review of the literature selected studies evaluating telomere length in sperm and/or in leukocytes as a potential male fertility biomarker. Twenty-two publications (3168 participants) were included in this review of experimental evidence. For each study, authors determined if there was a correlation between telomere length and semen parameters or fertility outcomes. Of the 13 studies concerning sperm telomere length (STL) and semen parameters, ten found an association between short STL and altered parameters. Concerning the impact of STL on ART results, the data are conflicting. However, eight of the 13 included studies about fertility found significantly longer sperm telomeres in fertile men than in infertile men. In leukocytes, the seven studies reported conflicting findings. Shorter sperm telomeres appear to be associated with altered semen parameters or male infertility. Telomere length may be considered as a new molecular marker of spermatogenesis and sperm quality, and thus is related to male fertility potential. However, additional studies are needed to define the place of the STL in the assessment of individual fertility. Full article

(This article belongs to the Special Issue Genetic Causes of Human Infertility)

► Show Figures

Figure 1

12 pages, 2717 KiB

Open AccessEditor’s ChoiceArticle

The Satellite DNAs Populating the Genome of Trigona hyalinata and the Sharing of a Highly Abundant satDNA in Trigona Genus

by Jaqueline A. Pereira, Diogo C. Cabral-de-Mello and Denilce M. Lopes

Genes 2023, 14(2), 418; https://doi.org/10.3390/genes14020418 - 6 Feb 2023

Cited by 7 | Viewed by 2264

Abstract

Among Meliponini species, c-heterochromatin can occupy large portions of chromosomes. This characteristic could be useful for understanding evolutionary patterns of satellite DNAs (satDNAs), although few sequences have been characterized in these bees. In Trigona, phylogenetically represented by clades A and B, [...] Read more.

Among Meliponini species, c-heterochromatin can occupy large portions of chromosomes. This characteristic could be useful for understanding evolutionary patterns of satellite DNAs (satDNAs), although few sequences have been characterized in these bees. In Trigona, phylogenetically represented by clades A and B, the c-heterochromatin is mostly located in one chromosome arm. Here we used different techniques, including restriction endonucleases and genome sequencing followed by chromosomal analysis, to identify satDNAs that may be contributing to the evolution of c-heterochromatin in Trigona. Our results revealed a highly abundant ThyaSat01-301 satDNA, corresponding to about 13.77% of the Trigona hyalinata genome. Another seven satDNAs were identified, one corresponding to 2.24%, and the other six corresponding to 0.545% of the genome. The satDNA ThyaSat01-301 was shown to be one of the main constituents of the c-heterochromatin of this species, as well as of other species belonging to clade B of Trigona. However, this satDNA was not observed on the chromosomes of species from clade A, demonstrating that the c-heterochromatin is evolving divergently between species of clade A and B, as a consequence of the evolution of repetitive DNA sequences. Finally, our data suggest the molecular diversification of the karyotypes, despite a conservated macrochromosomal structure on the genus. Full article

(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)

► Show Figures

Figure 1

18 pages, 816 KiB

Open AccessEditor’s ChoiceReview

Translational Bioinformatics Applied to the Study of Complex Diseases

by Matheus Correia Casotti, Débora Dummer Meira, Lyvia Neves Rebello Alves, Barbara Gomes de Oliveira Bessa, Camilly Victória Campanharo, Creuza Rachel Vicente, Carla Carvalho Aguiar, Daniel de Almeida Duque, Débora Gonçalves Barbosa, Eldamária de Vargas Wolfgramm dos Santos, Fernanda Mariano Garcia, Flávia de Paula, Gabriel Mendonça Santana, Isabele Pagani Pavan, Luana Santos Louro, Raquel Furlani Rocon Braga, Raquel Silva dos Reis Trabach, Thomas Santos Louro, Elizeu Fagundes de Carvalho and Iúri Drumond Louro

Genes 2023, 14(2), 419; https://doi.org/10.3390/genes14020419 - 6 Feb 2023

Cited by 9 | Viewed by 4618

Abstract

Translational Bioinformatics (TBI) is defined as the union of translational medicine and bioinformatics. It emerges as a major advance in science and technology by covering everything, from the most basic database discoveries, to the development of algorithms for molecular and cellular analysis, as [...] Read more.

Translational Bioinformatics (TBI) is defined as the union of translational medicine and bioinformatics. It emerges as a major advance in science and technology by covering everything, from the most basic database discoveries, to the development of algorithms for molecular and cellular analysis, as well as their clinical applications. This technology makes it possible to access the knowledge of scientific evidence and apply it to clinical practice. This manuscript aims to highlight the role of TBI in the study of complex diseases, as well as its application to the understanding and treatment of cancer. An integrative literature review was carried out, obtaining articles through several websites, among them: PUBMED, Science Direct, NCBI-PMC, Scientific Electronic Library Online (SciELO), and Google Academic, published in English, Spanish, and Portuguese, indexed in the referred databases and answering the following guiding question: “How does TBI provide a scientific understanding of complex diseases?” An additional effort is aimed at the dissemination, inclusion, and perpetuation of TBI knowledge from the academic environment to society, helping the study, understanding, and elucidating of complex disease mechanics and their treatment. Full article

(This article belongs to the Collection Feature Papers in Bioinformatics)

► Show Figures

Figure 1

11 pages, 1397 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

A Cell System-Assisted Strategy for Evaluating the Natural Antioxidant-Induced Double-Stranded DNA Break (DSB) Style

by Yuduki Someya, Sakine Kobayashi, Kazuya Toriumi, Shigeki Takeda, Noritaka Adachi and Aya Kurosawa

Genes 2023, 14(2), 420; https://doi.org/10.3390/genes14020420 - 6 Feb 2023

Cited by 3 | Viewed by 2726

Abstract

Natural antioxidants derived from plants exert various physiological effects, including antitumor effects. However, the molecular mechanisms of each natural antioxidant have not yet been fully elucidated. Identifying the targets of natural antioxidants with antitumor properties in vitro is costly and time-consuming, and the [...] Read more.

Natural antioxidants derived from plants exert various physiological effects, including antitumor effects. However, the molecular mechanisms of each natural antioxidant have not yet been fully elucidated. Identifying the targets of natural antioxidants with antitumor properties in vitro is costly and time-consuming, and the results thus obtained may not reliably reflect in vivo conditions. Therefore, to enhance understanding regarding the antitumor effects of natural antioxidants, we focused on DNA, one of the targets of anticancer drugs, and evaluated whether antioxidants, e.g., sulforaphane, resveratrol, quercetin, kaempferol, and genistein, which exert antitumor effects, induce DNA damage using gene-knockout cell lines derived from human Nalm-6 and HeLa cells pretreated with the DNA-dependent protein kinase inhibitor NU7026. Our results suggested that sulforaphane induces single-strand breaks or DNA strand crosslinks and that quercetin induces double-strand breaks. In contrast, resveratrol showed the ability to exert cytotoxic effects other than DNA damage. Our results also suggested that kaempferol and genistein induce DNA damage via unknown mechanisms. Taken together, the use of this evaluation system facilitates the analysis of the cytotoxic mechanisms of natural antioxidants. Full article

(This article belongs to the Special Issue DNA Damage Induced by Anti-cancer Agents)

► Show Figures

Graphical abstract

32 pages, 6848 KiB

Open AccessEditor’s ChoiceReview

Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review

by Francelly Martínez Sosa and Małgorzata Pilot

Genes 2023, 14(2), 416; https://doi.org/10.3390/genes14020416 - 5 Feb 2023

Cited by 9 | Viewed by 5955

Abstract

Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent [...] Read more.

Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution. Full article

(This article belongs to the Section Genes & Environments)

► Show Figures

Graphical abstract

12 pages, 256 KiB

Open AccessEditor’s ChoiceReview

Advances in Ophthalmic Epigenetics and Implications for Epigenetic Therapies: A Review

by Spencer M. Moore and John B. Christoforidis

Genes 2023, 14(2), 417; https://doi.org/10.3390/genes14020417 - 5 Feb 2023

Cited by 4 | Viewed by 3897

Abstract

The epigenome represents a vast molecular apparatus that writes, reads, and erases chemical modifications to the DNA and histone code without changing the DNA base-pair sequence itself. Recent advances in molecular sequencing technology have revealed that epigenetic chromatin marks directly mediate critical events [...] Read more.

The epigenome represents a vast molecular apparatus that writes, reads, and erases chemical modifications to the DNA and histone code without changing the DNA base-pair sequence itself. Recent advances in molecular sequencing technology have revealed that epigenetic chromatin marks directly mediate critical events in retinal development, aging, and degeneration. Epigenetic signaling regulates retinal progenitor (RPC) cell cycle exit during retinal laminar development, giving rise to retinal ganglion cells (RGCs), amacrine cells, horizontal cells, bipolar cells, photoreceptors, and Müller glia. Age-related epigenetic changes such as DNA methylation in the retina and optic nerve are accelerated in pathogenic conditions such as glaucoma and macular degeneration, but reversing these epigenetic marks may represent a novel therapeutic target. Epigenetic writers also integrate environmental signals such as hypoxia, inflammation, and hyperglycemia in complex retinal conditions such as diabetic retinopathy (DR) and choroidal neovascularization (CNV). Histone deacetylase (HDAC) inhibitors protect against apoptosis and photoreceptor degeneration in animal models of retinitis pigmentosa (RP). The epigenome represents an intriguing therapeutic target for age-, genetic-, and neovascular-related retinal diseases, though more work is needed before advancement to clinical trials. Full article

(This article belongs to the Special Issue Ophthalmic Genetics, Epigenetics, and Disease)

6 pages, 238 KiB

Open AccessEditor’s ChoiceCommunication

Effect of Different Anticoagulant Agents on Immune-Related Genes in Leukocytes Isolated from the Whole-Blood of Holstein Cows

by Viviana Floridia, Marta Sfulcini, Enrico D’Alessandro, Luca Cattaneo, Matteo Mezzetti, Luigi Liotta, Erminio Trevisi, Vincenzo Lopreiato and Andrea Minuti

Genes 2023, 14(2), 406; https://doi.org/10.3390/genes14020406 - 4 Feb 2023

Cited by 1 | Viewed by 2669

Abstract

Anticoagulants, such as ethylenediaminetetraacetic acid (EDTA), sodium citrate (Na-citrate), or heparin are normally used in hematological clinical tests to prevent coagulation. Although anticoagulants are fundamental for the correct application of clinical tests, they produce adverse effects in different fields, such as those involving [...] Read more.

Anticoagulants, such as ethylenediaminetetraacetic acid (EDTA), sodium citrate (Na-citrate), or heparin are normally used in hematological clinical tests to prevent coagulation. Although anticoagulants are fundamental for the correct application of clinical tests, they produce adverse effects in different fields, such as those involving specific molecular techniques; for instance, quantitative real time polymerase chain reactions (qPCR) and gene expression evaluation. For this reason, the aim of this study was to evaluate the expression of 14 genes in leukocytes that were isolated from the blood of Holstein cows, and which were collected in Li-heparin, K-EDTA, or Na-citrate tubes; then, they were analyzed using qPCR. Only the SDHA gene showed a significant dependence (p ≤ 0.05) on the anticoagulant that was used with the lowest expression; this was observed in Na-Citrate after being compared with Li-heparin and K-EDTA (p < 0.05). Although a variation in transcript abundance with the three anticoagulants was observed in almost all the investigated genes, the relative abundance levels were not statistically significant. In conclusion, the qPCR results were not influenced by the presence of the anticoagulant; thus, we had the opportunity to choose the test tube that was used in the experiment without interfering effects impacting the gene expression levels caused by the anticoagulant. Full article

(This article belongs to the Section Animal Genetics and Genomics)

17 pages, 1161 KiB

Open AccessEditor’s ChoiceReview

Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic

by Luis Daniel González-Vázquez and Miguel Arenas

Genes 2023, 14(2), 407; https://doi.org/10.3390/genes14020407 - 4 Feb 2023

Cited by 21 | Viewed by 5533

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order [...] Read more.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10⁻³–10⁻⁴ substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments. Full article

(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2023)

► Show Figures

Figure 1

14 pages, 1126 KiB

Open AccessEditor’s ChoiceReview

Chemokine Regulation in Temporomandibular Joint Disease: A Comprehensive Review

by Yusen Qiao, Jun Li, Catherine Yuh, Frank Ko, Louis G. Mercuri, Jad Alkhudari, Robin Pourzal and Chun-do Oh

Genes 2023, 14(2), 408; https://doi.org/10.3390/genes14020408 - 4 Feb 2023

Cited by 13 | Viewed by 3463

Abstract

Temporomandibular joint disorders (TMDs) are conditions that affect the muscles of mastication and joints that connect the mandible to the base of the skull. Although TMJ disorders are associated with symptoms, the causes are not well proven. Chemokines play an important role in [...] Read more.

Temporomandibular joint disorders (TMDs) are conditions that affect the muscles of mastication and joints that connect the mandible to the base of the skull. Although TMJ disorders are associated with symptoms, the causes are not well proven. Chemokines play an important role in the pathogenesis of TMJ disease by promoting chemotaxis inflammatory cells to destroy the joint synovium, cartilage, subchondral bone, and other structures. Therefore, enhancing our understanding of chemokines is critical for developing appropriate treatment of TMJ. In this review, we discuss chemokines including MCP-1, MIP-1α, MIP-3a, RANTES, IL-8, SDF-1, and fractalkine that are known to be involved in TMJ diseases. In addition, we present novel findings that CCL2 is involved in β-catenin-mediated TMJ osteoarthritis (OA) and potential molecular targets for the development of effective therapies. The effects of common inflammatory factors, IL-1β and TNF-α, on chemotaxis are also described. In conclusion, this review aims to provide a theoretical basis for future chemokine-targeted therapies for TMJ OA. Full article

(This article belongs to the Special Issue Genetic Risks and Molecular Epidemiology of Osteoarthritis)

► Show Figures

Figure 1

14 pages, 2165 KiB

Open AccessEditor’s ChoiceArticle

An Iterative Unsupervised Method for Gene Expression Differentiation

by Olga Georgieva

Genes 2023, 14(2), 412; https://doi.org/10.3390/genes14020412 - 4 Feb 2023

Cited by 1 | Viewed by 1876

Abstract

For several decades, intensive research for understanding gene activity and its role in organism’s lives is the research focus of scientists in different areas. A part of these investigations is the analysis of gene expression data for selecting differentially expressed genes. Methods that [...] Read more.

For several decades, intensive research for understanding gene activity and its role in organism’s lives is the research focus of scientists in different areas. A part of these investigations is the analysis of gene expression data for selecting differentially expressed genes. Methods that identify the interested genes have been proposed on statistical data analysis. The problem is that there is no good agreement among them, as different results are produced by distinct methods. By taking the advantage of the unsupervised data analysis, an iterative clustering procedure that finds differentially expressed genes shows promising results. In the present paper, a comparative study of the clustering methods applied for gene expression analysis is presented to explicate the choice of the clustering algorithm implemented in the method. An investigation of different distance measures is provided to reveal those that increase the efficiency of the method in finding the real data structure. Further, the method is improved by incorporating an additional aggregation measure based on the standard deviation of the expression levels. Its usage increases the gene distinction as a new amount of differentially expressed genes is found. The method is summarized in a detailed procedure. The significance of the method is proved by an analysis of two mice strain data sets. The differentially expressed genes defined by the proposed method are compared with those selected by the well-known statistical methods applied to the same data set. Full article

(This article belongs to the Special Issue Selected Papers from the 9th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2022))

► Show Figures

Figure 1

8 pages, 1029 KiB

Open AccessEditor’s ChoiceCommunication

Fusion Gene-Based Classification of Variant Cytogenetic Rearrangements in Acute Myeloid Leukemia

by Mary Gudipati, Melody Butler, Rima Koka, Maria R. Baer and Yi Ning

Genes 2023, 14(2), 396; https://doi.org/10.3390/genes14020396 - 3 Feb 2023

Cited by 1 | Viewed by 2667

Abstract

Acute myeloid leukemia (AML) represents a heterogeneous disease entity that is continuously moving to a more genetically defined classification. The classification of AML with recurrent chromosomal translocations, including those involving core binding factor subunits, plays a critical role in diagnosis, prognosis, treatment stratification, [...] Read more.

Acute myeloid leukemia (AML) represents a heterogeneous disease entity that is continuously moving to a more genetically defined classification. The classification of AML with recurrent chromosomal translocations, including those involving core binding factor subunits, plays a critical role in diagnosis, prognosis, treatment stratification, and residual disease evaluation. Accurate classification of variant cytogenetic rearrangements in AML contributes to effective clinical management. 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 importance of recognizing variant forms of t(8;21) translocations and emphasize the value of applying RUNX1::RUNX1T1 FISH for the detection of cryptic and complex rearrangements when abnormalities involving chromosome band 8q22 are observed in patients with AML. Full article

(This article belongs to the Special Issue Advances in Clinical Cytogenetics)

► Show Figures

Figure 1

18 pages, 4409 KiB

Open AccessEditor’s ChoiceArticle

Tandem Repeat DNA Provides Many Cytological Markers for Hybrid Zone Analysis in Two Subspecies of the Grasshopper Chorthippus parallelus

by Beatriz Navarro-Domínguez, Josefa Cabrero, María Dolores López-León, Francisco J. Ruiz-Ruano, Miguel Pita, José L. Bella and Juan Pedro M. Camacho

Genes 2023, 14(2), 397; https://doi.org/10.3390/genes14020397 - 3 Feb 2023

Cited by 7 | Viewed by 2715

Abstract

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 [...] Read more.

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 analysis revealed 50 TR families that could serve as markers for analysis of this HZ, using FISH. Differential TR bands were unevenly distributed between chromosomes and subspecies. Some of these TR families yielded FISH bands in only one of the subspecies, suggesting the amplification of these TR families after the geographic separation of the subspecies in the Pleistocene. Our cytological analysis of two TR markers along a transect of the Pyrenean hybrid zone showed asymmetrical introgression of one subspecies into the other, consistent with previous findings using other markers. These results demonstrate the reliability of TR-band markers for hybrid zone studies. Full article

(This article belongs to the Special Issue State-of-the-Art in Insect Cytogenetics)

► Show Figures

Figure 1

21 pages, 2333 KiB

Open AccessEditor’s ChoiceSystematic Review

Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment

by Elvis Twumasi Aboagye, Samuel Mawuli Adadey, Edmond Wonkam-Tingang, Lucas Amenga-Etego, Gordon A. Awandare and Ambroise Wonkam

Genes 2023, 14(2), 399; https://doi.org/10.3390/genes14020399 - 3 Feb 2023

Cited by 9 | Viewed by 3383

Abstract

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 [...] Read more.

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. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number “CRD42020198573”. Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants’ origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits. Full article

(This article belongs to the Special Issue New Advances in Genetic Research on Hearing Loss)

► Show Figures

Figure 1

15 pages, 1815 KiB

Open AccessEditor’s ChoiceArticle

Increased On-Target Rate and Risk of Concatemerization after CRISPR-Enhanced Targeting in ES Cells

by Valérie Erbs, Romain Lorentz, Benjamin Eisenman, Laurence Schaeffer, Laurence Luppi, Loic Lindner, Yann Hérault, Guillaume Pavlovic, Marie Wattenhofer-Donzé and Marie-Christine Birling

Genes 2023, 14(2), 401; https://doi.org/10.3390/genes14020401 - 3 Feb 2023

Cited by 5 | Viewed by 3135

Abstract

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 [...] Read more.

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, however, necessary as a significant number of clones (but not all) show a concatemerization of the targeting plasmid at the locus. A detailed Southern blot analysis permitted characterization of the nature of these events as standard long-range 5′ and 3′ PCRs were not able to distinguish between correct and incorrect alleles. We show that a simple and inexpensive PCR performed prior to ESC amplification allows detection and elimination of those clones with concatemers. Finally, although we only tested murine ESCs, our results highlight the risk of mis-validation of any genetically modified cell line (such as established lines, induced pluripotent stem cells or those used for ex vivo gene therapy) that combines the use of CRISPR/Cas9 and a circular double-stranded donor. We strongly advise the CRISPR community to perform a Southern blot with internal probes when using CRISPR to enhance homologous recombination in any cell type, including fertilized oocytes. Full article

(This article belongs to the Special Issue Transgenic Animal Models for Disease Research)

► Show Figures

Figure 1

17 pages, 5048 KiB

Open AccessEditor’s ChoiceReview

The Genetics of Primary Biliary Cholangitis: A GWAS and Post-GWAS Update

by Yuki Hitomi and Minoru Nakamura

Genes 2023, 14(2), 405; https://doi.org/10.3390/genes14020405 - 3 Feb 2023

Cited by 17 | Viewed by 3889

Abstract

Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which the small intrahepatic bile ducts are destroyed by autoimmune reactions. Among autoimmune diseases, which are polygenic complex traits caused by the combined contribution of genetic and environmental factors, PBC exhibits [...] Read more.

Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which the small intrahepatic bile ducts are destroyed by autoimmune reactions. Among autoimmune diseases, which are polygenic complex traits caused by the combined contribution of genetic and environmental factors, PBC exhibits the strongest involvement of genetic heritability in disease development. As at December 2022, genome-wide association studies (GWASs) and associated meta-analyses identified approximately 70 PBC susceptibility gene loci in various populations, including those of European and East Asian descent. However, the molecular mechanisms through which these susceptibility loci affect the pathogenesis of PBC are not fully understood. 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. Full article

(This article belongs to the Special Issue Genetics of Autoimmune Diseases)

► Show Figures

Figure 1

18 pages, 6320 KiB

Open AccessEditor’s ChoiceArticle

Genomic Insights and Functional Analysis Reveal Plant Growth Promotion Traits of Paenibacillus mucilaginosus G78

by Dan Wang, Verena Poinsot, Wangxi Li, Yusheng Lu, Chong Liu, Yaying Li, Kaizhi Xie, Lili Sun, Chaohong Shi, Huanlong Peng, Wanling Li, Changmin Zhou and Wenjie Gu

Genes 2023, 14(2), 392; https://doi.org/10.3390/genes14020392 - 2 Feb 2023

Cited by 8 | Viewed by 3234

Abstract

Paenibacillus mucilaginosus has widely been reported as a plant growth-promoting rhizobacteria (PGPR). However, the important genomic insights into plant growth promotion in this species remain undescribed. In this study, the genome of P. mucilaginosus G78 was sequenced using Illumina NovaSeq PE150. It contains [...] Read more.

Paenibacillus mucilaginosus has widely been reported as a plant growth-promoting rhizobacteria (PGPR). However, the important genomic insights into plant growth promotion in this species remain undescribed. 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 7337 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 putative exopolysaccharide biosynthesis and biofilm formation gene clusters were explored. According to the genetic features, the potential monosaccharides of its exopolysaccharides for P. mucilaginosus G78 may include glucose, mannose, galactose, fucose, that can probably be acetylated and pyruvated. Conservation of the pelADEFG compared with other 40 Paenibacillus species suggests that Pel may be specific biofilm matrix component in P. mucilaginosus. Several genes relevant to plant growth-promoting traits, i.e., IAA production and phosphate solubilization are well conserved compared with other 40 other Paenibacillus strains. The current study can benefit for understanding the plant growth-promoting traits of P. mucilaginosus as well as its potential application in agriculture as PGPR. Full article

(This article belongs to the Special Issue Molecular Research on Host-Microbe Interactions)

► Show Figures

Figure 1

18 pages, 1088 KiB

Open AccessEditor’s ChoiceReview

Deregulated E2F Activity as a Cancer-Cell Specific Therapeutic Tool

by Rinka Nakajima, Lin Zhao, Yaxuan Zhou, Mashiro Shirasawa, Ayato Uchida, Hikaru Murakawa, Mariana Fikriyanti, Ritsuko Iwanaga, Andrew P. Bradford, Keigo Araki, Tomoko Warita and Kiyoshi Ohtani

Genes 2023, 14(2), 393; https://doi.org/10.3390/genes14020393 - 2 Feb 2023

Cited by 15 | Viewed by 5060

Abstract

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 [...] Read more.

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 (deregulated E2F) activates tumor suppressor genes, which are not activated by E2F induced by growth stimulation, inducing cellular senescence or apoptosis to protect cells from tumorigenesis. Deregulated E2F activity is tolerated in cancer cells due to inactivation of the ARF-p53 pathway, thus representing a feature unique to cancer cells. Deregulated E2F activity, which activates tumor suppressor genes, is distinct from enhanced E2F activity, which activates growth-related genes, in that deregulated E2F activity does not depend on the heterodimeric partner DP. Indeed, the ARF promoter, which is specifically activated by deregulated E2F, showed higher cancer-cell specific activity, compared to the E2F1 promoter, which is also activated by E2F induced by growth stimulation. Thus, deregulated E2F activity is an attractive potential therapeutic tool to specifically target cancer cells. Full article

(This article belongs to the Special Issue Molecular Oncology—Unmasking the True Nature of Cancer 2023)

► Show Figures

Figure 1

11 pages, 1559 KiB

Open AccessEditor’s ChoiceArticle

Detecting Melanocortin 1 Receptor Gene’s SNPs by CRISPR/enAsCas12a

by Wei Yang, Dagang Tao, Bingrong Xu, Yueting Zheng and Shuhong Zhao

Genes 2023, 14(2), 394; https://doi.org/10.3390/genes14020394 - 2 Feb 2023

Cited by 5 | Viewed by 2346

Abstract

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, [...] Read more.

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 investigated by CRISPR/enAsCas12a and are not limited to the protospacer adjacent motif (PAM) sequence in vitro. Specifically, we optimized the reaction conditions, which proved that the enAsCas12a has a preference for divalent magnesium ion (Mg²⁺) and can effectively distinguish the genes with a single base difference in the presence of Mg²⁺, and the Melanocortin l receptor (MC1R) gene with three kinds of SNP sites (T305C, T363C, and G727A) was quantitatively detected. Since the enAsCas12a is not limited by PAM sequence in vitro, the method shown here can extend this extraordinary CRISPR/enAsCas12a detection system to other SNP targets, thus providing a general SNP detection toolbox. Full article

(This article belongs to the Special Issue CRISPR-Based Nucleic Acid Detection and Genome Editing in Animals)

► Show Figures

Figure 1

25 pages, 2038 KiB

Open AccessEditor’s ChoiceReview

Morphological and Molecular Bases of Male Infertility: A Closer Look at Sperm Flagellum

by Rute Pereira and Mário Sousa

Genes 2023, 14(2), 383; https://doi.org/10.3390/genes14020383 - 1 Feb 2023

Cited by 21 | Viewed by 11225

Abstract

Infertility is a major health problem worldwide without an effective therapy or cure. It is estimated to affect 8–12% of couples in the reproductive age group, equally affecting both genders. There is no single cause of infertility, and its knowledge is still far [...] Read more.

Infertility is a major health problem worldwide without an effective therapy or cure. It is estimated to affect 8–12% of couples in the reproductive age group, equally affecting both genders. There is no single cause of infertility, and its knowledge is still far from complete, with about 30% of infertile couples having no cause identified (named idiopathic infertility). Among male causes of infertility, asthenozoospermia (i.e., reduced sperm motility) is one of the most observed, being estimated that more than 20% of infertile men have this condition. In recent years, many researchers have focused on possible factors leading to asthenozoospermia, revealing the existence of many cellular and molecular players. So far, more than 4000 genes are thought to be involved in sperm production and as regulators of different aspects of sperm development, maturation, and function, and all can potentially cause male infertility if mutated. In this review, we aim to give a brief overview of the typical sperm flagellum morphology and compile some of the most relevant information regarding the genetic factors involved in male infertility, with a focus on sperm immotility and on genes related to sperm flagellum development, structure, or function. Full article

(This article belongs to the Special Issue Genetic Causes of Human Infertility)

► Show Figures

Figure 1

13 pages, 2139 KiB

Open AccessEditor’s ChoiceArticle

RNA-Seq Reveals the Roles of Long Non-Coding RNAs (lncRNAs) in Cashmere Fiber Production Performance of Cashmere Goats in China

by Xinmiao Wu, Yuanhua Gu, Shiqiang Li, Shiwei Guo, Jiqing Wang, Yuzhu Luo, Jiang Hu, Xiu Liu, Shaobin Li, Zhiyun Hao, Mingna Li and Bingang Shi

Genes 2023, 14(2), 384; https://doi.org/10.3390/genes14020384 - 1 Feb 2023

Cited by 7 | Viewed by 2159

Abstract

Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA being >200 nucleotides in length, and they are found to participate in hair follicle growth and development and wool fiber traits regulation. However, there are limited studies reporting the role of lncRNAs in [...] Read more.

Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA being >200 nucleotides in length, and they are found to participate in hair follicle growth and development and wool fiber traits regulation. However, there are limited studies reporting the role of lncRNAs in cashmere fiber production in cashmere goats. In this study, Liaoning cashmere (LC) goats (n = 6) and Ziwuling black (ZB) goats (n = 6) with remarkable divergences in cashmere yield, cashmere fiber diameter, and cashmere color were selected for the construction of expression profiles of lncRNAs in skin tissue using RNA sequencing (RNA-seq). According to our previous report about the expression profiles of mRNAs originated from the same skin tissue as those used in the study, the cis and trans target genes of differentially expressed lncRNAs between the two caprine breeds were screened, resulting in a lncRNA–mRNA network. A total of 129 lncRNAs were differentially expressed in caprine skin tissue samples between LC goats and ZB goats. The presence of 2 cis target genes and 48 trans target genes for the differentially expressed lncRNAs resulted in 2 lncRNA-cis target gene pairs and 93 lncRNA-trans target gene pairs. The target genes concentrated on signaling pathways that were related to fiber follicle development, cashmere fiber diameter, and cashmere fiber color, including PPAR signaling pathway, metabolic pathways, fatty acid metabolism, fatty acid biosynthesis, tyrosine metabolism, and melanogenesis. A lncRNA–mRNA network revealed 22 lncRNA-trans target gene pairs for seven differentially expressed lncRNAs selected, of which 13 trans target genes contributed to regulation of cashmere fiber diameter, while nine trans target genes were responsible for cashmere fiber color. This study brings a clear explanation about the influences of lncRNAs over cashmere fiber traits in cashmere goats. Full article

(This article belongs to the Special Issue Genetic Regulation and Molecular Phylogeny in Goat and Sheep Breeding)

► Show Figures

Figure 1

21 pages, 1401 KiB

Open AccessEditor’s ChoiceArticle

Assessing Outlier Probabilities in Transcriptomics Data When Evaluating a Classifier

by Magdalena Kircher, Josefin Säurich, Michael Selle and Klaus Jung

Genes 2023, 14(2), 387; https://doi.org/10.3390/genes14020387 - 1 Feb 2023

Viewed by 2978

Abstract

Outliers in the training or test set used to fit and evaluate a classifier on transcriptomics data can considerably change the estimated performance of the model. Hence, an either too weak or a too optimistic accuracy is then reported and the estimated model [...] Read more.

Outliers in the training or test set used to fit and evaluate a classifier on transcriptomics data can considerably change the estimated performance of the model. Hence, an either too weak or a too optimistic accuracy is then reported and the estimated model performance cannot be reproduced on independent data. It is then also doubtful whether a classifier qualifies for clinical usage. We estimate classifier performances in simulated gene expression data with artificial outliers and in two real-world datasets. As a new approach, we use two outlier detection methods within a bootstrap procedure to estimate the outlier probability for each sample and evaluate classifiers before and after outlier removal by means of cross-validation. We found that the removal of outliers changed the classification performance notably. For the most part, removing outliers improved the classification results. Taking into account the fact that there are various, sometimes unclear reasons for a sample to be an outlier, we strongly advocate to always report the performance of a transcriptomics classifier with and without outliers in training and test data. This provides a more diverse picture of a classifier’s performance and prevents reporting models that later turn out to be not applicable for clinical diagnoses. Full article

(This article belongs to the Collection Feature Papers in Bioinformatics)

► Show Figures

Figure 1

11 pages, 23042 KiB

Open AccessEditor’s ChoiceArticle

KEGG_Extractor: An Effective Extraction Tool for KEGG Orthologs

by Chao Zhang, Zhongwei Chen, Miming Zhang and Shulei Jia

Genes 2023, 14(2), 386; https://doi.org/10.3390/genes14020386 - 1 Feb 2023

Cited by 11 | Viewed by 5619

Abstract

The KEGG Orthology (KO) database is a widely used molecular function reference database which can be used to conduct functional annotation of most microorganisms. At present, there are many KEGG tools based on the KO entries for annotating functional orthologs. However, determining how [...] Read more.

The KEGG Orthology (KO) database is a widely used molecular function reference database which can be used to conduct functional annotation of most microorganisms. At present, there are many KEGG tools based on the KO entries for annotating functional orthologs. However, determining how to efficiently extract and sort the annotation results of KEGG still hinders the subsequent genome analysis. There is a lack of effective measures used to quickly extract and classify the gene sequences and species information of the KEGG annotations. Here, we present a supporting tool: KEGG_Extractor for species-specific genes extraction and classification, which can output the results through an iterative keyword matching algorithm. It can not only extract and classify the amino acid sequences, but also the nucleotide sequences, and it has proved to be fast and efficient for microbial analysis. Analysis of the ancient Wood Ljungdahl (WL) pathway through the KEGG_Extractor reveals that ~226 archaeal strains contained the WL pathway-related genes. Most of them were Methanococcus maripaludis, Methanosarcina mazei and members of the Methanobacterium, Thermococcus and Methanosarcina genus. Using the KEGG_Extractor, the ARWL database was constructed, which had a high accuracy and complement. This tool helps to link genes with the KEGG pathway and promote the reconstruction of molecular networks. Availability and implementation: KEGG_Extractor is freely available from the GitHub. Full article

(This article belongs to the Section Bioinformatics)

► Show Figures

Figure 1

10 pages, 2352 KiB

Open AccessEditor’s ChoiceCase Report

De Novo Variant in the KCNJ9 Gene as a Possible Cause of Neonatal Seizures

by Taisiya O. Kochetkova, Dmitry N. Maslennikov, Ekaterina R. Tolmacheva, Jekaterina Shubina, Anna S. Bolshakova, Dzhenneta I. Suvorova, Anna V. Degtyareva, Irina V. Orlovskaya, Maria V. Kuznetsova, Anastasia A. Rachkova, Gennady T. Sukhikh, Denis V. Rebrikov and Dmitriy Yu. Trofimov

Genes 2023, 14(2), 366; https://doi.org/10.3390/genes14020366 - 31 Jan 2023

Cited by 1 | Viewed by 2380

Abstract

Background: The reduction in next-generation sequencing (NGS) costs allows for using this method for newborn screening for monogenic diseases (MDs). In this report, we describe a clinical case of a newborn participating in the EXAMEN project (ClinicalTrials.gov Identifier: NCT05325749). Methods: The child presented [...] Read more.

Background: The reduction in next-generation sequencing (NGS) costs allows for using this method for newborn screening for monogenic diseases (MDs). In this report, we describe a clinical case of a newborn participating in the EXAMEN project (ClinicalTrials.gov Identifier: NCT05325749). Methods: The child presented with convulsive syndrome on the third day of life. Generalized convulsive seizures were accompanied by electroencephalographic patterns corresponding to epileptiform activity. Proband WES expanded to trio sequencing was performed. Results: A differential diagnosis was made between symptomatic (dysmetabolic, structural, infectious) neonatal seizures and benign neonatal seizures. There were no data in favor of the dysmetabolic, structural, or infectious nature of seizures. Molecular karyotyping and whole exome sequencing were not informative. Trio WES revealed a de novo variant in the KCNJ9 gene (1:160087612T > C, p.Phe326Ser, NM_004983), for which, according to the OMIM database, no association with the disease has been described to date. Three-dimensional modeling was used to predict the structure of the KCNJ9 protein using the known structure of its homologs. According to the predictions, Phe326Ser change possibly disrupts the hydrophobic contacts with the valine side chain. Destabilization of the neighboring structures may undermine the formation of GIRK2/GIRK3 tetramers necessary for their proper functioning. Conclusions: We believe that the identified variant may be the cause of the disease in this patient but further studies, including the search for other patients with the KCNJ9 variants, are needed. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

► Show Figures

Figure 1

19 pages, 7146 KiB

Open AccessEditor’s ChoiceArticle

Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean

by Nooral Amin, Naveed Ahmad, Mohamed A. S. Khalifa, Yeyao Du, Ajmal Mandozai, Aimal Nawaz Khattak and Wang Piwu

Genes 2023, 14(2), 369; https://doi.org/10.3390/genes14020369 - 31 Jan 2023

Cited by 9 | Viewed by 3281

Abstract

The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of [...] Read more.

The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of nodulation-specific NIN proteins during nodulation and rhizobial infection under nitrogen starvation in soybean still remain unclear. Here, we investigated the genome-wide identification of RWP-RK transcription factors and their essential role in nitrate-inducible and stress-responsive gene expression in soybean. In total, 28 RWP-RK genes were identified from the soybean genome, which were unevenly distributed on 20 chromosomes from 5 distinct groups during phylogeny classification. The conserved topology of RWP-RK protein motifs, cis-acting elements, and functional annotation has led to their potential as key regulators during plant growth, development, and diverse stress responses. The RNA-seq data revealed that the up-regulation of GmRWP-RK genes in the nodules indicated that these genes might play crucial roles during root nodulation in soybean. Furthermore, qRT-PCR analysis revealed that most GmRWP-RK genes under Phytophthora sojae infection and diverse environmental conditions (such as heat, nitrogen, and salt) were significantly induced, thus opening a new window of possibilities into their regulatory roles in adaptation mechanisms that allow soybean to tolerate biotic and abiotic stress. In addition, the dual luciferase assay indicated that GmRWP-RK1 and GmRWP-RK2 efficiently bind to the promoters of GmYUC2, GmSPL9, and GmNIN, highlighting their possible involvement in nodule formation. Together, our findings provide novel insights into the functional role of the RWP-RK family during defense responses and root nodulation in soybean. Full article

(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)

► Show Figures

Figure 1

14 pages, 10577 KiB

Open AccessEditor’s ChoiceReview

GDP-Mannose Pyrophosphorylase B (GMPPB)-Related Disorders

by Pitcha Chompoopong and Margherita Milone

Genes 2023, 14(2), 372; https://doi.org/10.3390/genes14020372 - 31 Jan 2023

Cited by 11 | Viewed by 4423

Abstract

GDP-mannose pyrophosphorylase B (GMPPB) is a cytoplasmic protein that catalyzes the formation of GDP-mannose. Impaired GMPPB function reduces the amount of GDP-mannose available for the O-mannosylation of α-dystroglycan (α-DG) and ultimately leads to disruptions of the link between α-DG and extracellular proteins, hence [...] Read more.

GDP-mannose pyrophosphorylase B (GMPPB) is a cytoplasmic protein that catalyzes the formation of GDP-mannose. Impaired GMPPB function reduces the amount of GDP-mannose available for the O-mannosylation of α-dystroglycan (α-DG) and ultimately leads to disruptions of the link between α-DG and extracellular proteins, hence dystroglycanopathy. GMPPB-related disorders are inherited in an autosomal recessive manner and caused by mutations in either a homozygous or compound heterozygous state. The clinical spectrum of GMPPB-related disorders spans from severe congenital muscular dystrophy (CMD) with brain and eye abnormalities to mild forms of limb-girdle muscular dystrophy (LGMD) to recurrent rhabdomyolysis without overt muscle weakness. GMPPB mutations can also lead to the defect of neuromuscular transmission and congenital myasthenic syndrome due to altered glycosylation of the acetylcholine receptor subunits and other synaptic proteins. Such impairment of neuromuscular transmission is a unique feature of GMPPB-related disorders among dystroglycanopathies. LGMD is the most common phenotypic presentation, characterized by predominant proximal weakness involving lower more than upper limbs. Facial, ocular, bulbar, and respiratory muscles are largely spared. Some patients demonstrate fluctuating fatigable weakness suggesting neuromuscular junction involvement. Patients with CMD phenotype often also have structural brain defects, intellectual disability, epilepsy, and ophthalmic abnormalities. Creatine kinase levels are typically elevated, ranging from 2 to >50 times the upper limit of normal. Involvement of the neuromuscular junction is demonstrated by the decrement in the compound muscle action potential amplitude on low-frequency (2–3 Hz) repetitive nerve stimulation in proximal muscles but not in facial muscles. Muscle biopsies typically show myopathic changes with variable degrees of reduced α-DG expression. Higher mobility of β-DG on Western blotting represents a specific feature of GMPPB-related disorders, distinguishing it from other α-dystroglycanopathies. Patients with clinical and electrophysiologic features of neuromuscular transmission defect can respond to acetylcholinesterase inhibitors alone or combined with 3,4 diaminopyridine or salbutamol. Full article

(This article belongs to the Special Issue Genetics of Muscular Dystrophies from Pathogenesis to Gene Therapy)

► Show Figures

Figure 1

16 pages, 3208 KiB

Open AccessEditor’s ChoiceReview

Rust (Uromyces viciae-fabae Pers. de-Bary) of Pea (Pisum sativum L.): Present Status and Future Resistance Breeding Opportunities

by Anil Kumar Singh, Chanda Kushwaha, Kumari Shikha, Ramesh Chand, Gyan P. Mishra, Harsh Kumar Dikshit, Jyoti Devi, Muraleedhar S. Aski, Shiv Kumar, Sanjeev Gupta and Ramakrishnan M. Nair

Genes 2023, 14(2), 374; https://doi.org/10.3390/genes14020374 - 31 Jan 2023

Cited by 11 | Viewed by 6058

Abstract

Uromyces viciae-fabae Pers. de-Bary is an important fungal pathogen causing rust in peas (Pisum sativum L.). It is reported in mild to severe forms from different parts of the world where the pea is grown. Host specificity has been indicated [...] Read more.

Uromyces viciae-fabae Pers. de-Bary is an important fungal pathogen causing rust in peas (Pisum sativum L.). It is reported in mild to severe forms from different parts of the world where the pea is grown. Host specificity has been indicated in this pathogen in the field but has not yet been established under controlled conditions. The uredinial states of U. viciae-fabae are infective under temperate and tropical conditions. Aeciospores are infective in the Indian subcontinent. The genetics of rust resistance was reported qualitatively. However, non-hypersensitive resistance responses and more recent studies emphasized the quantitative nature of pea rust resistance. Partial resistance/slow rusting had been described as a durable resistance in peas. Such resistance is of the pre-haustorial type and expressed as longer incubation and latent period, poor infection efficiency, a smaller number of aecial cups/pustules, and lower units of AUDPC (Area Under Disease Progress Curve). Screening techniques dealing with slow rusting should consider growth stages and environment, as both have a significant influence on the disease scores. Our knowledge about the genetics of rust resistance is increasing, and now molecular markers linked with gene/QTLs (Quantitative Trait Loci) of rust resistance have been identified in peas. The mapping efforts conducted in peas came out with some potent markers associated with rust resistance, but they must be validated under multi-location trails before use in the marker-assisted selection of rust resistance in pea breeding programs. Full article

(This article belongs to the Special Issue Molecular Mechanism of Plant Stress Resistance)

► Show Figures

Figure 1

17 pages, 602 KiB

Open AccessEditor’s ChoiceReview

The Genetic Side of the Mood: A Scientometric Review of the Genetic Basis of Mood Disorders

by Giovanni Bonacina, Alessandro Carollo and Gianluca Esposito

Genes 2023, 14(2), 352; https://doi.org/10.3390/genes14020352 - 30 Jan 2023

Cited by 11 | Viewed by 4551

Abstract

Mood disorders are highly heritable psychiatric disorders. Over the years, many genetic polymorphisms have been identified to pose a higher risk for the development of mood disorders. To overview the literature on the genetics of mood disorders, a scientometric analysis was performed on [...] Read more.

Mood disorders are highly heritable psychiatric disorders. Over the years, many genetic polymorphisms have been identified to pose a higher risk for the development of mood disorders. To overview the literature on the genetics of mood disorders, a scientometric analysis was performed on a sample of 5342 documents downloaded from Scopus. The most active countries and the most impactful documents in the field were identified. Furthermore, a total of 13 main thematic clusters emerged in the literature. From the qualitative inspection of clusters, it emerged that the research interest moved from a monogenic to a polygenic risk framework. Researchers have moved from the study of single genes in the early 1990s to conducting genome-wide association studies around 2015. In this way, genetic overlaps between mood disorders and other psychiatric conditions emerged too. Furthermore, around the 2010s, the interaction between genes and environmental factors emerged as pivotal in understanding the risk for mood disorders. The inspection of thematic clusters provides a valuable insight into the past and recent trends of research in the genetics of mood disorders and sheds light onto future lines of research. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Factors and Their Interactions in the Susceptibility to Multifactorial Diseases)

► Show Figures

Figure 1

20 pages, 1952 KiB

Open AccessEditor’s ChoiceReview

Common Genetic Factors and Pathways in Alzheimer’s Disease and Ischemic Stroke: Evidences from GWAS

by Wei Dong and Yue Huang

Genes 2023, 14(2), 353; https://doi.org/10.3390/genes14020353 - 30 Jan 2023

Cited by 6 | Viewed by 4252

Abstract

Alzheimer’s disease (AD) and ischemic stroke (IS) are common neurological disorders, and the comorbidity of these two brain diseases is often seen. Although AD and IS were regarded as two distinct disease entities, in terms of different etiologies and clinical presentation, recent genome-wide [...] Read more.

Alzheimer’s disease (AD) and ischemic stroke (IS) are common neurological disorders, and the comorbidity of these two brain diseases is often seen. Although AD and IS were regarded as two distinct disease entities, in terms of different etiologies and clinical presentation, recent genome-wide association studies (GWASs) revealed that there were common risk genes between AD and IS, indicating common molecular pathways and their common pathophysiology. In this review, we summarize AD and IS risk single nucleotide polymorphisms (SNPs) and their representative genes from the GWAS Catalog database, and find thirteen common risk genes, but no common risk SNPs. Furthermore, the common molecular pathways associated with these risk gene products are summarized from the GeneCards database and clustered into inflammation and immunity, G protein-coupled receptor, and signal transduction. At least seven of these thirteen genes can be regulated by 23 microRNAs identified from the TargetScan database. Taken together, the imbalance of these molecular pathways may give rise to these two common brain disorders. This review sheds light on the pathogenesis of comorbidity of AD and IS, and provides molecular targets for disease prevention, manipulation, and brain health maintenance. Full article

(This article belongs to the Special Issue Genetics of Complex Human Disease)

► Show Figures

Figure 1

16 pages, 2981 KiB

Open AccessEditor’s ChoiceArticle

Phylogenetic Position of Haemaphysalis kashmirensis and Haemaphysalis cornupunctata, with Notes on Rickettsia spp.

by Shah Masood Khan, Mehran Khan, Abdulaziz Alouffi, Mashal M. Almutairi, Muhmmad Numan, Shafi Ullah, Muhammad Kashif Obaid, Zia Ul Islam, Haroon Ahmed, Tetsuya Tanaka and Abid Ali

Genes 2023, 14(2), 360; https://doi.org/10.3390/genes14020360 - 30 Jan 2023

Cited by 15 | Viewed by 2310

Abstract

Despite high diversity in the Oriental region, ticks of the genus Haemaphysalis have been neglected regarding their genetic data and vector potential. This study aimed to genetically characterize three species of the genus Haemaphysalis: Haemaphysalis cornupunctata, Haemaphysalis kashmirensis, and Haemaphysalis montgomeryi [...] Read more.

Despite high diversity in the Oriental region, ticks of the genus Haemaphysalis have been neglected regarding their genetic data and vector potential. This study aimed to genetically characterize three species of the genus Haemaphysalis: Haemaphysalis cornupunctata, Haemaphysalis kashmirensis, and Haemaphysalis montgomeryi infesting goats and sheep, and Rickettsia spp. associated with these tick species in the Hindu Kush Himalayan range of Pakistan. Altogether, 834 ticks were collected by examining 120 hosts including goats (64/120, 53.3%) and sheep (56/120, 46.6%), in which 86 (71.6%) hosts were found to be tick-infested. The morphologically identified ticks were subjected to DNA extraction and PCR for the amplification of partial 16S rDNA and cox fragments. Rickettsia spp. associated with the collected ticks were detected through the amplification of gltA, ompA and ompB partial fragments. The 16S rDNA of H. cornupunctata and H. montgomeryi showed a maximum identity of 100% with the sequences of the same species, whereas the 16S rDNA of H. kashmirensis showed the highest identity of 93–95% with Haemaphysalis sulcata. The cox sequence of H. montgomeryi displayed 100% identity with the same species. In comparison, the cox sequences of H. cornupunctata and H. kashmirensis showed maximum identities of 87.65–89.22% with Haemaphysalis punctata and 89.34% with H. sulcata, respectively. The gltA sequence of Rickettsia sp. from H. kashmirensis showed the highest identity of 97.89% with Rickettsia conorii subsp. raoultii, while the ompA and ompB fragments from the same DNA samples revealed 100% and 98.16% identity with Rickettsia sp. and “Candidatus Rickettsia longicornii”, respectively. Another gltA sequence amplified from H. montgomeryi ticks showed 100% identity with Rickettsia hoogstraalii, while the attempts to amplify ompA and ompB for R. hoogstraalii were unsuccessful. In the phylogenetic tree, the 16S rDNA of H. cornupunctata clustered with the corresponding species while its cox clustered with H. punctata. Both 16S rDNA and cox sequences of H. kashmirensis clustered with H. sulcata. The gltA sequence of Rickettsia sp. was clustered individually in the spotted fever (SF) group of Rickettsia, while the gltA sequence of R. hoogstraalii was clustered with the same species in the transition group of Rickettsia. In the SF group, the rickettsial ompA and ompB sequence clustered with undetermined Rickettsia sp. and “Candidatus Rickettsia longicornii”, respectively. This is the earliest study regarding the genetic characterization of H. kashmirensis. This study indicated that ticks belong to the genus Haemaphysalis have the potential of harboring and/or transmitting Rickettsia spp. in the region. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

► Show Figures

Figure 1

20 pages, 6854 KiB

Open AccessEditor’s ChoiceArticle

Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean

by Johanna C. Winder, William Boulton, Asaf Salamov, Sarah Lena Eggers, Katja Metfies, Vincent Moulton and Thomas Mock

Genes 2023, 14(2), 363; https://doi.org/10.3390/genes14020363 - 30 Jan 2023

Cited by 10 | Viewed by 3616

Abstract

Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural [...] Read more.

Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean. Full article

(This article belongs to the Special Issue Polar Genomics)

► Show Figures

Figure 1

13 pages, 3113 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Comparative Proteomic Analysis of Glycolytic and Oxidative Muscle in Pigs

by Xiaofan Tan, Yu He, Yuqiao He, Zhiwei Yan, Jing Chen, Ruixue Zhao, Xin Sui, Lei Zhang, Xuehai Du, David M. Irwin, Shuyi Zhang and Bojiang Li

Genes 2023, 14(2), 361; https://doi.org/10.3390/genes14020361 - 30 Jan 2023

Cited by 12 | Viewed by 2591

Abstract

The quality of meat is highly correlated with muscle fiber type. However, the mechanisms via which proteins regulate muscle fiber types in pigs are not entirely understood. In the current study, we have performed proteomic profiling of fast/glycolytic biceps femoris (BF) and slow/oxidative [...] Read more.

The quality of meat is highly correlated with muscle fiber type. However, the mechanisms via which proteins regulate muscle fiber types in pigs are not entirely understood. In the current study, we have performed proteomic profiling of fast/glycolytic biceps femoris (BF) and slow/oxidative soleus (SOL) muscles and identified several candidate differential proteins among these. We performed proteomic analyses based on tandem mass tags (TMTs) and identified a total of 26,228 peptides corresponding to 2667 proteins among the BF and SOL muscle samples. Among these, we found 204 differentially expressed proteins (DEPs) between BF and SOL muscle, with 56 up-regulated and 148 down-regulated DEPs in SOL muscle samples. KEGG and GO enrichment analyses of the DEPs revealed that the DEPs are involved in some GO terms (e.g., actin cytoskeleton, myosin complex, and cytoskeletal parts) and signaling pathways (PI3K-Akt and NF-kappa B signaling pathways) that influence muscle fiber type. A regulatory network of protein–protein interaction (PPI) between these DEPs that regulates muscle fiber types was constructed, which demonstrates how three down-regulated DEPs, including PFKM, GAPDH, and PKM, interact with other proteins to potentially control the glycolytic process. This study offers a new understanding of the molecular mechanisms in glycolytic and oxidative muscles as well as a novel approach for enhancing meat quality by transforming the type of muscle fibers in pigs. Full article

(This article belongs to the Special Issue Recent Advances in Pig Molecular Genetics and Breeding)

► Show Figures

Figure 1

17 pages, 1254 KiB

Open AccessEditor’s ChoiceReview

Telomere Fragility and MiDAS: Managing the Gaps at the End of the Road

by Ryan P. Barnes, Sanjana A. Thosar and Patricia L. Opresko

Genes 2023, 14(2), 348; https://doi.org/10.3390/genes14020348 - 29 Jan 2023

Cited by 8 | Viewed by 5021

Abstract

Telomeres present inherent difficulties to the DNA replication machinery due to their repetitive sequence content, formation of non-B DNA secondary structures, and the presence of the nucleo-protein t-loop. Especially in cancer cells, telomeres are hot spots for replication stress, which can result in [...] Read more.

Telomeres present inherent difficulties to the DNA replication machinery due to their repetitive sequence content, formation of non-B DNA secondary structures, and the presence of the nucleo-protein t-loop. Especially in cancer cells, telomeres are hot spots for replication stress, which can result in a visible phenotype in metaphase cells termed “telomere fragility”. A mechanism cells employ to mitigate replication stress, including at telomeres, is DNA synthesis in mitosis (MiDAS). While these phenomena are both observed in mitotic cells, the relationship between them is poorly understood; however, a common link is DNA replication stress. In this review, we will summarize what is known to regulate telomere fragility and telomere MiDAS, paying special attention to the proteins which play a role in these telomere phenotypes. Full article

(This article belongs to the Special Issue DNA Replication/Repair, and the DNA Damage Response in Human Disease)

► Show Figures

Figure 1

11 pages, 1725 KiB

Open AccessEditor’s ChoiceArticle

Response Surface Methodology for Optimization of Multiplex-PCR Protocols for Detection of TYLCV, TSWV and Fol Molecular Markers: Analytical Performance Evaluation

by Richecarde Lafrance, José Benigno Valdez-Torres, Claudia Villicaña, Raymundo Saúl García-Estrada, Mayra Janeth Esparza-Araiza and Josefina León-Félix

Genes 2023, 14(2), 337; https://doi.org/10.3390/genes14020337 - 28 Jan 2023

Cited by 3 | Viewed by 3689

Abstract

Molecular markers linked to disease resistance genes which affect economically important crops are of great interest. In the case of tomato, a major focus on resistance breeding to multiple fungal and viral pathogens such as Tomato yellow leaf curl virus (TYLCV), Tomato spotted [...] Read more.

Molecular markers linked to disease resistance genes which affect economically important crops are of great interest. In the case of tomato, a major focus on resistance breeding to multiple fungal and viral pathogens such as Tomato yellow leaf curl virus (TYLCV), Tomato spotted wilt virus (TSWV) and Fusarium oxysporum f. sp. lycopersici (Fol), have led to the introgression of several resistance genes; therefore, molecular markers have become important in molecular-assisted selection (MAS) of tomato varieties resistant to those pathogens. However, assays that allow simultaneous evaluation of resistant genotypes, such as multiplex PCR, need to be optimized and evaluated to demonstrate their analytical performance, as many factors can affect them. This work aimed to generate multiplex PCR protocols for the joint detection of the molecular markers associated with pathogen resistance genes in tomato plants that are sensitive, specific and repeatable. For the optimization a central composite design of a response surface methodology (RSM-CCD) was used. For analytical performance evaluation, specificity/selectivity and sensibility (limit of detection and dynamic range) were analyzed. Two protocols were optimized: the first one with a desirability of 1.00, contained two markers (At-2 and P7-43) linked to I- and I-3-resistant genes. The second one with a desirability of 0.99, contained markers (SSR-67, SW5 and P6-25) linked to I-, Sw-5-, and Ty-3-resistant genes. For protocol 1, all the commercial hybrids (7/7) were resistant to Fol, and for protocol 2, two hybrids were resistant to Fol, one to TSWV and one to TYLCV with good analytical performance. In both protocols, the varieties considered susceptible to the pathogens, no-amplicon or susceptible amplicons, were observed. The optimized multiplex PCR protocols showed dynamic ranges from 5.97 up to 161.3 ng DNA. The limit of detection was 17.92 ng and 53.76 ng DNA for protocols 1 and 2, respectively, giving 100% positive results in the test replicates. This method allowed to develop optimized multiplex PCR protocols with few assays which translates into less time and resources, without sacrificing method performance. Full article

(This article belongs to the Section Genes & Environments)

► Show Figures

Figure 1

13 pages, 957 KiB

Open AccessEditor’s ChoiceArticle

The Genetic Background of Hearing Loss in Patients with EVA and Cochlear Malformation

by Natalia Bałdyga, Dominika Oziębło, Nina Gan, Mariusz Furmanek, Marcin L. Leja, Henryk Skarżyński and Monika Ołdak

Genes 2023, 14(2), 335; https://doi.org/10.3390/genes14020335 - 28 Jan 2023

Cited by 5 | Viewed by 2563

Abstract

The most frequently observed congenital inner ear malformation is enlarged vestibular aqueduct (EVA). It is often accompanied with incomplete partition type 2 (IP2) of the cochlea and a dilated vestibule, which together constitute Mondini malformation. Pathogenic SLC26A4 variants are considered the major cause [...] Read more.

The most frequently observed congenital inner ear malformation is enlarged vestibular aqueduct (EVA). It is often accompanied with incomplete partition type 2 (IP2) of the cochlea and a dilated vestibule, which together constitute Mondini malformation. Pathogenic SLC26A4 variants are considered the major cause of inner ear malformation but the genetics still needs clarification. The aim of this study was to identify the cause of EVA in patients with hearing loss (HL). Genomic DNA was isolated from HL patients with radiologically confirmed bilateral EVA (n = 23) and analyzed by next generation sequencing using a custom HL gene panel encompassing 237 HL-related genes or a clinical exome. The presence and segregation of selected variants and the CEVA haplotype (in the 5′ region of SLC26A4) was verified by Sanger sequencing. Minigene assay was used to evaluate the impact of novel synonymous variant on splicing. Genetic testing identified the cause of EVA in 17/23 individuals (74%). Two pathogenic variants in the SLC26A4 gene were identified as the cause of EVA in 8 of them (35%), and a CEVA haplotype was regarded as the cause of EVA in 6 of 7 patients (86%) who carried only one SLC26A4 genetic variant. In two individuals with a phenotype matching branchio-oto-renal (BOR) spectrum disorder, cochlear hypoplasia resulted from EYA1 pathogenic variants. In one patient, a novel variant in CHD7 was detected. Our study shows that SLC26A4, together with the CEVA haplotype, accounts for more than half of EVA cases. Syndromic forms of HL should also be considered in patients with EVA. We conclude that to better understand inner ear development and the pathogenesis of its malformations, there is a need to look for pathogenic variants in noncoding regions of known HL genes or to link them with novel candidate HL genes. Full article

(This article belongs to the Special Issue Genetics of Ear Development and Hearing Loss)

► Show Figures

Figure 1

11 pages, 752 KiB

Open AccessEditor’s ChoiceArticle

Identification of Germline Variants in Patients with Hereditary Cancer Syndromes in Northeast Mexico

by Diana Cristina Pérez-Ibave, María Lourdes Garza-Rodríguez, María Fernanda Noriega-Iriondo, Sonia María Flores-Moreno, Manuel Ismael González-Geroniz, Absalon Espinoza-Velazco, Ana Lilia Castruita-Ávila, Fernando Alcorta-Núñez, Omar Alejandro Zayas-Villanueva, Juan Francisco González-Guerrero, Adelina Alcorta-Garza, Oscar Vidal-Gutiérrez and Carlos Horacio Burciaga-Flores

Genes 2023, 14(2), 341; https://doi.org/10.3390/genes14020341 - 28 Jan 2023

Cited by 8 | Viewed by 2948

Abstract

Hereditary cancer syndromes (HCS) are genetic diseases with an increased risk of developing cancer. This research describes the implementation of a cancer prevention model, genetic counseling, and germline variants testing in an oncologic center in Mexico. A total of 315 patients received genetic [...] Read more.

Hereditary cancer syndromes (HCS) are genetic diseases with an increased risk of developing cancer. This research describes the implementation of a cancer prevention model, genetic counseling, and germline variants testing in an oncologic center in Mexico. A total of 315 patients received genetic counseling, genetic testing was offered, and 205 individuals were tested for HCS. In 6 years, 131 (63.90%) probands and 74 (36.09%) relatives were tested. Among the probands, we found that 85 (63.9%) had at least one germline variant. We identified founder mutations in BRCA1 and a novel variant in APC that led to the creation of an in-house detection process for the whole family. The most frequent syndrome was hereditary breast and ovarian cancer syndrome (HBOC) (41 cases with BRCA1 germline variants in most of the cases), followed by eight cases of hereditary non-polyposic cancer syndrome (HNPCC or Lynch syndrome) (with MLH1 as the primarily responsible gene), and other high cancer risk syndromes. Genetic counseling in HCS is still a global challenge. Multigene panels are an essential tool to detect the variants frequency. Our program has a high detection rate of probands with HCS and pathogenic variants (40%), compared with other reports that detect 10% in other populations. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

► Show Figures

Graphical abstract

14 pages, 2201 KiB

Open AccessEditor’s ChoiceArticle

High Levels of Diversity in Anopheles Subgenus Kerteszia Revealed by Species Delimitation Analyses

by Brian P. Bourke, Richard C. Wilkerson, Fredy Ruiz-Lopez, Silvia A. Justi, David B. Pecor, Martha L. Quinones, Juan-Carlos Navarro, Joubert Alarcón Ormaza, Joubert Alarcón Ormaza, Jr., Ranulfo González, Carmen Flores-Mendoza, Fanny Castro, Jesús E. Escovar and Yvonne-Marie Linton

Genes 2023, 14(2), 344; https://doi.org/10.3390/genes14020344 - 28 Jan 2023

Cited by 5 | Viewed by 2709

Abstract

The Anopheles subgenus Kerteszia is a poorly understood group of mosquitoes that includes several species of medical importance. Although there are currently twelve recognized species in the subgenus, previous studies have shown that this is likely to be an underestimate of species diversity. [...] Read more.

The Anopheles subgenus Kerteszia is a poorly understood group of mosquitoes that includes several species of medical importance. Although there are currently twelve recognized species in the subgenus, previous studies have shown that this is likely to be an underestimate of species diversity. Here, we undertake a baseline study of species delimitation using the barcode region of the mtDNA COI gene to explore species diversity among a geographically and taxonomically diverse range of Kerteszia specimens. Beginning with 10 of 12 morphologically identified Kerteszia species spanning eight countries, species delimitation analyses indicated a high degree of cryptic diversity. Overall, our analyses found support for at least 28 species clusters within the subgenus Kerteszia. The most diverse taxon was Anopheles neivai, a known malaria vector, with eight species clusters. Five other species taxa showed strong signatures of species complex structure, among them Anopheles bellator, which is also considered a malaria vector. There was some evidence for species structure within An. homunculus, although the results were equivocal across delimitation analyses. The current study, therefore, suggests that species diversity within the subgenus Kerteszia has been grossly underestimated. Further work will be required to build on this molecular characterization of species diversity and will rely on genomic level approaches and additional morphological data to test these species hypotheses. Full article

(This article belongs to the Special Issue Advances in Evolutionary Genetics and Phylogenetics of Mosquito Species)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Editor’s Choice Articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI