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Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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10 pages, 2062 KiB  
Communication
Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat
by Shengyu Guan, Weining Li, Hai Jin, Lu Zhang and Guoshi Liu
Genes 2023, 14(5), 1122; https://doi.org/10.3390/genes14051122 - 22 May 2023
Cited by 14 | Viewed by 3802
Abstract
As an important genotyping platform, SNP chips are essential for implementing genomic selection. In this article, we introduced the development of a liquid SNP chip panel for dairy goats. This panel contains 54,188 SNPs based on genotyping by targeted sequencing (GBTS) technology. The [...] Read more.
As an important genotyping platform, SNP chips are essential for implementing genomic selection. In this article, we introduced the development of a liquid SNP chip panel for dairy goats. This panel contains 54,188 SNPs based on genotyping by targeted sequencing (GBTS) technology. The source of SNPs in the panel were from the whole-genome resequencing of 110 dairy goats from three European and two Chinese indigenous dairy goat breeds. The performance of this liquid SNP chip panel was evaluated by genotyping 200 additional goats. Fifteen of them were randomly selected for whole-genome resequencing. The average capture ratio of the panel design loci was 98.41%, and the genotype concordance with resequencing reached 98.02%. We further used this chip panel to conduct genome-wide association studies (GWAS) to detect genetic loci that affect coat color in dairy goats. A single significant association signal for hair color was found on chromosome 8 at 31.52–35.02 Mb. The TYRP1 gene, which is associated with coat color in goats, was identified to be located at this genomic region (chromosome 8: 31,500,048-31,519,064). The emergence of high-precision and low-cost liquid microarrays will improve the analysis of genomics and breeding efficiency of dairy goats. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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18 pages, 2300 KiB  
Article
Biallelic Variants in Seven Different Genes Associated with Clinically Suspected Bardet–Biedl Syndrome
by Hamed Nawaz, Mujahid, Sher Alam Khan, Farhana Bibi, Ahmed Waqas, Abdul Bari, Fardous, Niamatullah Khan, Nazif Muhammad, Amjad Khan, Sohail Aziz Paracha, Qamre Alam, Mohammad Azhar Kamal, Misbahuddin M. Rafeeq, Noor Muhammad, Fayaz Ul Haq, Shazia Khan, Arif Mahmood, Saadullah Khan and Muhammad Umair
Genes 2023, 14(5), 1113; https://doi.org/10.3390/genes14051113 - 19 May 2023
Cited by 9 | Viewed by 3652
Abstract
Bardet–Biedl syndrome (BBS) is a rare clinically and genetically heterogeneous autosomal recessive multi-systemic disorder with 22 known genes. The primary clinical and diagnostic features include six different hallmarks, such as rod–cone dystrophy, learning difficulties, renal abnormalities, male hypogonadism, post-axial polydactyly, and obesity. Here, [...] Read more.
Bardet–Biedl syndrome (BBS) is a rare clinically and genetically heterogeneous autosomal recessive multi-systemic disorder with 22 known genes. The primary clinical and diagnostic features include six different hallmarks, such as rod–cone dystrophy, learning difficulties, renal abnormalities, male hypogonadism, post-axial polydactyly, and obesity. Here, we report nine consanguineous families and a non-consanguineous family with several affected individuals presenting typical clinical features of BBS. In the present study, 10 BBS Pakistani families were subjected to whole exome sequencing (WES), which revealed novel/recurrent gene variants, including a homozygous nonsense mutation (c.94C>T; p.Gln32Ter) in the IFT27 (NM_006860.5) gene in family A, a homozygous nonsense mutation (c.160A>T; p.Lys54Ter) in the BBIP1 (NM_001195306.1) gene in family B, a homozygous nonsense variant (c.720C>A; p.Cys240Ter) in the WDPCP (NM_015910.7) in family C, a homozygous nonsense variant (c.505A>T; p.Lys169Ter) in the LZTFL1 (NM_020347.4) in family D, pathogenic homozygous 1 bp deletion (c.775delA; p.Thr259Leufs*21) in the MKKS/BBS5 (NM_170784.3) gene in family E, a pathogenic homozygous missense variant (c.1339G>A; p.Ala447Thr) in BBS1 (NM_024649.4) in families F and G, a pathogenic homozygous donor splice site variant (c.951+1G>A; p?) in BBS1 (NM_024649.4) in family H, a pathogenic bi-allelic nonsense variant in MKKS (NM_170784.3) (c.119C>G; p.Ser40*) in family I, and homozygous pathogenic frameshift variants (c.196delA; p.Arg66Glufs*12) in BBS5 (NM_152384.3) in family J. Our findings extend the mutation and phenotypic spectrum of four different types of ciliopathies causing BBS and also support the importance of these genes in the development of multi-systemic human genetic disorders. Full article
(This article belongs to the Special Issue Functional Studies of Genetic Variants Involved in Human Genetic Diseases)
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11 pages, 865 KiB  
Article
Polymorphisms Analysis of BMP15, GDF9 and BMPR1B in Tibetan Cashmere Goat (Capra hircus)
by Tianzeng Song, Yacheng Liu, Renqing Cuomu, Yao Tan, Cuoji A. Wang, Ji De, Xiaohan Cao and Xianyin Zeng
Genes 2023, 14(5), 1102; https://doi.org/10.3390/genes14051102 - 18 May 2023
Cited by 7 | Viewed by 2639
Abstract
The Tibetan cashmere goat is a prolific goat breed in China. In sheep breeds, natural mutations have demonstrated that the transforming growth factor beta (TGF-β) super family ligands, such as growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15 [...] Read more.
The Tibetan cashmere goat is a prolific goat breed in China. In sheep breeds, natural mutations have demonstrated that the transforming growth factor beta (TGF-β) super family ligands, such as growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15) and their type I receptor (bone morphogenetic protein receptor (BMPR1B), are essential for ovulation and increasing litter size. In this study, 216 female Tibetan cashmere goats were sampled, and candidate genes with fecundity traits were detected via restriction fragment length polymorphism (RFLP) and sequenced. Four polymorphic loci were found in specific amplification fragments of BMP15 and GDF9. Two SNP sites of the BMP15 gene were discovered, namely G732A and C805G. The G732A mutation did not cause the change in amino acids, and the frequencies of each genotype were 0.695 for the GG type, 0.282 for the GA type and 0.023 for the AA type. The C805G mutation caused amino acids to change from glutamine to glutamate. The genotype frequencies were 0.620 for the CC type, 0.320 for the CG type and 0.320 for the CG type. For the GG type 0.060, the G3 and G4 mutations of the GDF9 gene were all homozygous mutations. Two known SNP sites, C719T and G1189A, were detected in the Tibetan cashmere goat GDF9 gene, of which the C719T mutation caused a change of alanine to valine, with a genotype frequency of 0.944 for the CC type and 0.056 for the CT type, whereas no TT type was found. The G1189A mutation caused valine to become isoleucine, and the frequencies of each genotype were 0.579 for the GG type, 0.305 for the GA type and 0.116 for the AA type; G1, B2, B3, B4, FecXH, FecXI, FecXL, G2, G5, G6, G7, G8, FecGE, FecTT and FecB mutations were not found in Tibetan cashmere goats. The results of this study provide a data basis for future studies of BMP15, GDF9 and BMPR1B gene mutations in goats. Full article
(This article belongs to the Special Issue Evolution, Molecular Ecology, Phylogeography, and Phylogenetics of Mammals)
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24 pages, 752 KiB  
Review
Genomic Dynamics and Functional Insights under Salt Stress in Gossypium hirsutum L.
by Zunaira Anwar, Aqsa Ijaz, Allah Ditta, Baohua Wang, Fang Liu, Sana Muhy-Ud-Din Khan, Sajjad Haidar, Hafiz Mumtaz Hassan and Muhammad Kashif Riaz Khan
Genes 2023, 14(5), 1103; https://doi.org/10.3390/genes14051103 - 18 May 2023
Cited by 17 | Viewed by 3266
Abstract
The changing climate is intensifying salt stress globally. Salt stress is a menace to cotton crop quality and yield. The seedling, germination, and emergence phases are more prone to the effects of salt stress than other stages. Higher levels of salt can lead [...] Read more.
The changing climate is intensifying salt stress globally. Salt stress is a menace to cotton crop quality and yield. The seedling, germination, and emergence phases are more prone to the effects of salt stress than other stages. Higher levels of salt can lead to delayed flowering, a reduced number of fruiting positions, shedding of fruits, decreased boll weight, and yellowing of fiber, all of which have an adverse effect on the yield and quality of the seed cotton. However, sensitivity toward salt stress is dependent on the salt type, cotton growth phase, and genotype. As the threat of salt stress continues to grow, it is crucial to gain a comprehensive understanding of the mechanisms underlying salt tolerance in plants and to identify potential avenues for enhancing the salt tolerance of cotton. The emergence of marker-assisted selection, in conjunction with next-generation sequencing technologies, has streamlined cotton breeding efforts. This review begins by providing an overview of the causes of salt stress in cotton, as well as the underlying theory of salt tolerance. Subsequently, it summarizes the breeding methods that utilize marker-assisted selection, genomic selection, and techniques for identifying elite salt-tolerant markers in wild species or mutated materials. Finally, novel cotton breeding possibilities based on the approaches stated above are presented and debated. Full article
(This article belongs to the Special Issue Advances in Cotton Breeding and Genetics)
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20 pages, 7378 KiB  
Article
EDLM: Ensemble Deep Learning Model to Detect Mutation for the Early Detection of Cholangiocarcinoma
by Asghar Ali Shah, Fahad Alturise, Tamim Alkhalifah, Amna Faisal and Yaser Daanial Khan
Genes 2023, 14(5), 1104; https://doi.org/10.3390/genes14051104 - 18 May 2023
Cited by 7 | Viewed by 3007
Abstract
The most common cause of mortality and disability globally right now is cholangiocarcinoma, one of the worst forms of cancer that may affect people. When cholangiocarcinoma develops, the DNA of the bile duct cells is altered. Cholangiocarcinoma claims the lives of about 7000 [...] Read more.
The most common cause of mortality and disability globally right now is cholangiocarcinoma, one of the worst forms of cancer that may affect people. When cholangiocarcinoma develops, the DNA of the bile duct cells is altered. Cholangiocarcinoma claims the lives of about 7000 individuals annually. Women pass away less often than men. Asians have the greatest fatality rate. Following Whites (20%) and Asians (22%), African Americans (45%) saw the greatest increase in cholangiocarcinoma mortality between 2021 and 2022. For instance, 60–70% of cholangiocarcinoma patients have local infiltration or distant metastases, which makes them unable to receive a curative surgical procedure. Across the board, the median survival time is less than a year. Many researchers work hard to detect cholangiocarcinoma, but this is after the appearance of symptoms, which is late detection. If cholangiocarcinoma progression is detected at an earlier stage, then it will help doctors and patients in treatment. Therefore, an ensemble deep learning model (EDLM), which consists of three deep learning algorithms—long short-term model (LSTM), gated recurrent units (GRUs), and bi-directional LSTM (BLSTM)—is developed for the early identification of cholangiocarcinoma. Several tests are presented, such as a 10-fold cross-validation test (10-FCVT), an independent set test (IST), and a self-consistency test (SCT). Several statistical techniques are used to evaluate the proposed model, such as accuracy (Acc), sensitivity (Sn), specificity (Sp), and Matthew’s correlation coefficient (MCC). There are 672 mutations in 45 distinct cholangiocarcinoma genes among the 516 human samples included in the proposed study. The IST has the highest Acc at 98%, outperforming all other validation approaches. Full article
(This article belongs to the Special Issue Bioinformatics of Sequencing Data: A Machine Learning Approach)
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8 pages, 551 KiB  
Brief Report
ITGAM rs1143679 Variant in Systemic Lupus Erythematosus Is Associated with Increased Serum Calcification Propensity
by Matthieu Halfon, Li Zhang, Driss Ehirchiou, Vishnuprabu Durairaj Pandian, Suzan Dahdal, Uyen Huynh-Do, Andreas Pasch, Camillo Ribi and Nathalie Busso
Genes 2023, 14(5), 1105; https://doi.org/10.3390/genes14051105 - 18 May 2023
Cited by 1 | Viewed by 2500
Abstract
Objectives: CD11B/ITGAM (Integrin Subunit α M) mediates the adhesion of monocytes, macrophages, and granulocytes and promotes the phagocytosis of complement-coated particles. Variants of the ITGAM gene are candidates for genetic susceptibility to systemic lupus erythematosus (SLE). SNP rs1143679 (R77H) of CD11B particularly increases [...] Read more.
Objectives: CD11B/ITGAM (Integrin Subunit α M) mediates the adhesion of monocytes, macrophages, and granulocytes and promotes the phagocytosis of complement-coated particles. Variants of the ITGAM gene are candidates for genetic susceptibility to systemic lupus erythematosus (SLE). SNP rs1143679 (R77H) of CD11B particularly increases the risk of developing SLE. Deficiency of CD11B is linked to premature extra-osseous calcification, as seen in the cartilage of animals with osteoarthritis. Serum calcification propensity measured by the T50 test is a surrogate marker for systemic calcification and reflects increased cardiovascular (CV) risk. We aimed to assess whether the CD11B R77H gene variant is associated with a higher serum calcification propensity (i.e., a lower T50 value) in SLE patients compared to the wild-type allele (WT). Methods: Cross-sectional study incorporating adults with SLE genotyped for the CD11B variant R77H and assessed for serum calcification propensity with the T50 method. Participants were included in a multicenter trans-disciplinary cohort and fulfilled the 1997 revised American College of Rheumatology (ACR) criteria for SLE. We used descriptive statistics for comparing baseline characteristics and sequential T50 measurements in subjects with the R77H variant vs. WT CD11B. Results: Of the 167 patients, 108 (65%) were G/G (WT), 53 (32%) were G/A heterozygous, and 6 (3%) were A/A homozygous for the R77H variant. A/A patients cumulated more ACR criteria upon inclusion (7 ± 2 vs. 5 ± 1 in G/G and G/A; p = 0.02). There were no differences between the groups in terms of global disease activity, kidney involvement, and chronic renal failure. Complement C3 levels were lower in A/A individuals compared to others (0.6 ± 0.08 vs. 0.9 ± 0.25 g/L; p = 0.02). Baseline T50 did not differ between the groups (A/A 278 ± 42′ vs. 297 ± 50′ in G/G and G/A; p = 0.28). Considering all sequential T50 test results, serum calcification propensity was significantly increased in A/A individuals compared to others (253 ± 50 vs. 290 ± 54; p = 0.008). Conclusions: SLE patients with homozygosity for the R77H variant and repeated T50 assessment displayed an increased serum calcification propensity (i.e., a lower T50) and lower C3 levels compared to heterozygous and WT CD11B, without differing with respect to global disease activity and kidney involvement. This suggests an increased CV risk in SLE patients homozygous for the R77H variant of CD11B. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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13 pages, 835 KiB  
Article
Social, Genetics and Histopathological Factors Related to Titin (TTN) Gene Mutation and Survival in Women with Ovarian Serous Cystadenocarcinoma: Bioinformatics Analysis
by Fabiana de Campos Gomes, Eric Renato Lima Figueiredo, Ediane Nunes De Araújo, Edila Monteiro De Andrade, Carlos Diego Lisbôa Carneiro, Gabriel Mácola De Almeida, Helana Augusta Andrade Leal Dias, Lucélia Inoue Bispo Teixeira, Manuela Trindade Almeida, Mariusa Fernandes De Farias, Natália Albim Linhares, Natasha Lima Da Fonseca, Yago Dos Santos Pereira and João Simão de Melo-Neto
Genes 2023, 14(5), 1092; https://doi.org/10.3390/genes14051092 - 16 May 2023
Cited by 9 | Viewed by 2772
Abstract
Several factors may increase the risk of development of ovarian cancer. In this study, we investigated the relationship between social, genetic, and histopathologic factors in women with ovarian serous cystadenocarcinoma and titin (TTN) mutations, whether the TTN gene mutation may be [...] Read more.
Several factors may increase the risk of development of ovarian cancer. In this study, we investigated the relationship between social, genetic, and histopathologic factors in women with ovarian serous cystadenocarcinoma and titin (TTN) mutations, whether the TTN gene mutation may be a predictor, and its impact on mortality and survival in these patients. A total of 585 samples from patients with ovarian serous cystadenocarcinoma were collected from The Cancer Genome Atlas and PanCancer Atlas through the cBioPortal for analysis of social, genetic, and histopathological factors. Logistic regression was used to investigate whether TTN mutation could be a predictor, and the Kaplan–Meier method was applied to analyze survival time. TTN mutation frequency did not differ between age at diagnosis, tumor stage, and race, and was related to increased Buffa hypoxia score (p = 0.004), mutation count (p < 0.0001), Winter hypoxia Score (p = 0.030), nonsynonymous tumor mutation burden (TMB) (p < 0.0001), and reduced microsatellite instability sensor score (p = 0.010). The number of mutations (p < 0.0001) and winter hypoxia score (p = 0.008) were positively associated with TTN mutations, and nonsynonymous TMB (p < 0.0001) proved to be a predictor. Mutated TTN affects the score of genetic variables involved in cancer cell metabolism in ovarian cystadenocarcinoma. Full article
(This article belongs to the Section Bioinformatics)
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22 pages, 4106 KiB  
Article
Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves
by Jie Wang, Huimei Fan, Mianying Li, Kaisen Zhao, Siqi Xia, Yang Chen, Jiahao Shao, Tao Tang, Xue Bai, Zheliang Liu, Yusheng Lu, Xiangrui Chen, Wenqiang Sun, Xianbo Jia and Songjia Lai
Genes 2023, 14(5), 1093; https://doi.org/10.3390/genes14051093 - 16 May 2023
Cited by 8 | Viewed by 2214
Abstract
Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed [...] Read more.
Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM–receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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23 pages, 1399 KiB  
Review
The Role of Pharmacogenetics in Personalizing the Antidepressant and Anxiolytic Therapy
by Milica Radosavljevic, Dubravka Svob Strac, Jasna Jancic and Janko Samardzic
Genes 2023, 14(5), 1095; https://doi.org/10.3390/genes14051095 - 16 May 2023
Cited by 25 | Viewed by 9732
Abstract
Pharmacotherapy for neuropsychiatric disorders, such as anxiety and depression, has been characterized by significant inter-individual variability in drug response and the development of side effects. Pharmacogenetics, as a key part of personalized medicine, aims to optimize therapy according to a patient’s individual genetic [...] Read more.
Pharmacotherapy for neuropsychiatric disorders, such as anxiety and depression, has been characterized by significant inter-individual variability in drug response and the development of side effects. Pharmacogenetics, as a key part of personalized medicine, aims to optimize therapy according to a patient’s individual genetic signature by targeting genetic variations involved in pharmacokinetic or pharmacodynamic processes. Pharmacokinetic variability refers to variations in a drug’s absorption, distribution, metabolism, and elimination, whereas pharmacodynamic variability results from variable interactions of an active drug with its target molecules. Pharmacogenetic research on depression and anxiety has focused on genetic polymorphisms affecting metabolizing cytochrome P450 (CYP) and uridine 5’-diphospho-glucuronosyltransferase (UGT) enzymes, P-glycoprotein ATP-binding cassette (ABC) transporters, and monoamine and γ-aminobutyric acid (GABA) metabolic enzymes, transporters, and receptors. Recent pharmacogenetic studies have revealed that more efficient and safer treatments with antidepressants and anxiolytics could be achieved through genotype-guided decisions. However, because pharmacogenetics cannot explain all observed heritable variations in drug response, an emerging field of pharmacoepigenetics investigates how epigenetic mechanisms, which modify gene expression without altering the genetic code, might influence individual responses to drugs. By understanding the epi(genetic) variability of a patient’s response to pharmacotherapy, clinicians could select more effective drugs while minimizing the likelihood of adverse reactions and therefore improve the quality of treatment. Full article
(This article belongs to the Special Issue Genetic Basis of Stress-Related Neuropsychiatric Disorders)
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20 pages, 1569 KiB  
Review
Genetic Predictors of Antipsychotic Efflux Impairment via Blood-Brain Barrier: Role of Transport Proteins
by Regina F. Nasyrova, Natalia A. Shnayder, Sofia M. Osipova, Aiperi K. Khasanova, Ilya S. Efremov, Mustafa Al-Zamil, Marina M. Petrova, Ekaterina A. Narodova, Natalia P. Garganeeva and German A. Shipulin
Genes 2023, 14(5), 1085; https://doi.org/10.3390/genes14051085 - 15 May 2023
Cited by 8 | Viewed by 3129
Abstract
Antipsychotic (AP)—induced adverse drug reactions (ADRs) are a current problem of biological and clinical psychiatry. Despite the development of new generations of APs, the problem of AP-induced ADRs has not been solved and continues to be actively studied. One of the important mechanisms [...] Read more.
Antipsychotic (AP)—induced adverse drug reactions (ADRs) are a current problem of biological and clinical psychiatry. Despite the development of new generations of APs, the problem of AP-induced ADRs has not been solved and continues to be actively studied. One of the important mechanisms for the development of AP-induced ADRs is a genetically-determined impairment of AP efflux across the blood-brain barrier (BBB). We present a narrative review of publications in databases (PubMed, Springer, Scopus, Web of Science E-Library) and online resources: The Human Protein Atlas; GeneCards: The Human Gene Database; US National Library of Medicine; SNPedia; OMIM Online Mendelian Inheritance in Man; The PharmGKB. The role of 15 transport proteins involved in the efflux of drugs and other xenobiotics across cell membranes (P-gp, TAP1, TAP2, MDR3, BSEP, MRP1, MRP2, MRP3, MRP4, MRP5, MRP6, MRP7, MRP8, MRP9, BCRP) was analyzed. The important role of three transporter proteins (P-gp, BCRP, MRP1) in the efflux of APs through the BBB was shown, as well as the association of the functional activity and expression of these transport proteins with low-functional and non-functional single nucleotide variants (SNVs)/polymorphisms of the ABCB1, ABCG2, ABCC1 genes, encoding these transport proteins, respectively, in patients with schizophrenia spectrum disorders (SSDs). The authors propose a new pharmacogenetic panel “Transporter protein (PT)—Antipsychotic (AP) Pharmacogenetic test (PGx)” (PTAP-PGx), which allows the evaluation of the cumulative contribution of the studied genetic biomarkers of the impairment of AP efflux through the BBB. The authors also propose a riskometer for PTAP-PGx and a decision-making algorithm for psychiatrists. Conclusions: Understanding the role of the transportation of impaired APs across the BBB and the use of genetic biomarkers for its disruption may make it possible to reduce the frequency and severity of AP-induced ADRs, since this risk can be partially modified by the personalized selection of APs and their dosing rates, taking into account the genetic predisposition of the patient with SSD. Full article
(This article belongs to the Special Issue Single-Nucleotide Polymorphisms: Association, Molecular Function, Application, and Progress)
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11 pages, 1620 KiB  
Article
phox2ba: The Potential Genetic Link behind the Overlap in the Symptomatology between CHARGE and Central Congenital Hypoventilation Syndromes
by Jessica E. MacLean, Jaime N. Wertman, Sergey V. Prykhozhij, Emily Chedrawe, Stewart Langley, Shelby L. Steele, Kevin Ban, Kim Blake and Jason N. Berman
Genes 2023, 14(5), 1086; https://doi.org/10.3390/genes14051086 - 15 May 2023
Cited by 1 | Viewed by 2073
Abstract
CHARGE syndrome typically results from mutations in the gene encoding chromodomain helicase DNA-binding protein 7 (CHD7). CHD7 is involved in regulating neural crest development, which gives rise to tissues of the skull/face and the autonomic nervous system (ANS). Individuals with CHARGE [...] Read more.
CHARGE syndrome typically results from mutations in the gene encoding chromodomain helicase DNA-binding protein 7 (CHD7). CHD7 is involved in regulating neural crest development, which gives rise to tissues of the skull/face and the autonomic nervous system (ANS). Individuals with CHARGE syndrome are frequently born with anomalies requiring multiple surgeries and often experience adverse events post-anesthesia, including oxygen desaturations, decreased respiratory rates, and heart rate abnormalities. Central congenital hypoventilation syndrome (CCHS) affects ANS components that regulate breathing. Its hallmark feature is hypoventilation during sleep, clinically resembling observations in anesthetized CHARGE patients. Loss of PHOX2B (paired-like homeobox 2b) underlies CCHS. Employing a chd7-null zebrafish model, we investigated physiologic responses to anesthesia and compared these to loss of phox2b. Heart rates were lower in chd7 mutants compared to the wild-type. Exposure to tricaine, a zebrafish anesthetic/muscle relaxant, revealed that chd7 mutants took longer to become anesthetized, with higher respiratory rates during recovery. chd7 mutant larvae demonstrated unique phox2ba expression patterns. The knockdown of phox2ba reduced larval heart rates similar to chd7 mutants. chd7 mutant fish are a valuable preclinical model to investigate anesthesia in CHARGE syndrome and reveal a novel functional link between CHARGE syndrome and CCHS. Full article
(This article belongs to the Special Issue Zebrafish Models for Human Genetic Disease Studies)
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20 pages, 3229 KiB  
Article
An Improved Machine Learning-Based Approach to Assess the Microbial Diversity in Major North Indian River Ecosystems
by Nalinikanta Choudhury, Tanmaya Kumar Sahu, Atmakuri Ramakrishna Rao, Ajaya Kumar Rout and Bijay Kumar Behera
Genes 2023, 14(5), 1082; https://doi.org/10.3390/genes14051082 - 14 May 2023
Cited by 8 | Viewed by 2601
Abstract
The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence [...] Read more.
The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics). Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants and Animals)
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16 pages, 2386 KiB  
Review
G-Quadruplexes in Nuclear Biomolecular Condensates
by Iuliia Pavlova, Mikhail Iudin, Anastasiya Surdina, Vjacheslav Severov and Anna Varizhuk
Genes 2023, 14(5), 1076; https://doi.org/10.3390/genes14051076 - 13 May 2023
Cited by 10 | Viewed by 3999
Abstract
G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, [...] Read more.
G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleoli, speckles, and paraspeckles. The limitations of the underlying assays and the remaining open questions are outlined. We also discuss the molecular basis for the apparent permissive role of G4s in the in vitro condensate assembly based on the interactome data. To highlight the prospects and risks of G4-targeting therapies with respect to the phase transitions, we also touch upon the reported effects of G4-stabilizing small molecules on nuclear biomolecular condensates. Full article
(This article belongs to the Special Issue Investigation of the Importance of Non-B DNA Structures at the Interface between Chemistry and Biology)
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15 pages, 6409 KiB  
Article
Stacking Multiple Genes Improves Resistance to Chilo suppressalis, Magnaporthe oryzae, and Nilaparvata lugens in Transgenic Rice
by Bai Li, Zhongkai Chen, Huizhen Chen, Chunlei Wang, Liyan Song, Yue Sun, Yicong Cai, Dahu Zhou, Linjuan Ouyang, Changlan Zhu, Haohua He and Xiaosong Peng
Genes 2023, 14(5), 1070; https://doi.org/10.3390/genes14051070 - 12 May 2023
Cited by 3 | Viewed by 2471
Abstract
The ability of various pests and diseases to adapt to a single plant resistance gene over time leads to loss of resistance in transgenic rice. Therefore, introduction of different pest and disease resistance genes is critical for successful cultivation of transgenic rice strains [...] Read more.
The ability of various pests and diseases to adapt to a single plant resistance gene over time leads to loss of resistance in transgenic rice. Therefore, introduction of different pest and disease resistance genes is critical for successful cultivation of transgenic rice strains with broad-spectrum resistance to multiple pathogens. Here, we produced resistance rice lines with multiple, stacked resistance genes by stacking breeding and comprehensively evaluated their resistance to Chilo suppressalis (striped rice stemborer), Magnaporthe oryzae (rice blast), and Nilaparvata lugens (brown planthopper) in a pesticide-free environment. CRY1C and CRY2A are exogenous genes from Bacillus thuringiensis. Pib, Pikm, and Bph29 are natural genes in rice. CH121TJH was introduced into CRY 1C, Pib, Pikm, and Bph29. CH891TJH and R205XTJH were introduced into CRY 2A, Pib, Pikm, and Bph29. Compared with those observed in their recurrent parents, CH121TJH significantly increased the mortality of borers. The other two lines CH891TJH and R205XTJH are the same result. Three lines introduction of Pib and Pikm significantly reduced the area of rice blast lesions, and introduction of Bph29 significantly reduced seedling mortality from N. lugens. Introduction of the exogenous genes had relatively few effects on agronomic and yield traits of the original parents. These findings suggest that stacking of rice resistance genes through molecular marker-assisted backcross breeding can confer broad spectrum and multiple resistance in differently genetic backgrounds. Full article
(This article belongs to the Topic Genetic Engineering in Agriculture)
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10 pages, 4200 KiB  
Article
US Population Data for 94 Identity-Informative SNP Loci
by Kevin M. Kiesler, Lisa A. Borsuk, Carolyn R. Steffen, Peter M. Vallone and Katherine B. Gettings
Genes 2023, 14(5), 1071; https://doi.org/10.3390/genes14051071 - 12 May 2023
Cited by 9 | Viewed by 2457
Abstract
The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of [...] Read more.
The US National Institute of Standards and Technology (NIST) analyzed a set of 1036 samples representing four major US population groups (African American, Asian American, Caucasian, and Hispanic) with 94 single nucleotide polymorphisms (SNPs) used for individual identification (iiSNPs). The compact size of iiSNP amplicons compared to short tandem repeat (STR) markers increases the likelihood of successful amplification with degraded DNA samples. Allele frequencies and relevant forensic statistics were calculated for each population group as well as the aggregate population sample. Examination of sequence data in the regions flanking the targeted SNPs identified additional variants, which can be combined with the target SNPs to form microhaplotypes (multiple phased SNPs within a short-read sequence). Comparison of iiSNP performance with and without flanking SNP variation identified four amplicons containing microhaplotypes with observed heterozygosity increases of greater than 15% over the targeted SNP alone. For this set of 1036 samples, comparison of average match probabilities from iiSNPs with the 20 CODIS core STR markers yielded an estimate of 1.7 × 10−38 for iiSNPs (assuming independence between all 94 SNPs), which was four orders of magnitude lower (more discriminating) than STRs where internal sequence variation was considered, and 10 orders of magnitude lower than STRs using established capillary electrophoresis length-based genotypes. Full article
(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics)
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31 pages, 1326 KiB  
Review
Crosstalk between miRNAs and DNA Methylation in Cancer
by Michela Saviana, Patricia Le, Lavender Micalo, Daniel Del Valle-Morales, Giulia Romano, Mario Acunzo, Howard Li and Patrick Nana-Sinkam
Genes 2023, 14(5), 1075; https://doi.org/10.3390/genes14051075 - 12 May 2023
Cited by 34 | Viewed by 6149
Abstract
miRNAs are some of the most well-characterized regulators of gene expression. Integral to several physiological processes, their aberrant expression often drives the pathogenesis of both benign and malignant diseases. Similarly, DNA methylation represents an epigenetic modification influencing transcription and playing a critical role [...] Read more.
miRNAs are some of the most well-characterized regulators of gene expression. Integral to several physiological processes, their aberrant expression often drives the pathogenesis of both benign and malignant diseases. Similarly, DNA methylation represents an epigenetic modification influencing transcription and playing a critical role in silencing numerous genes. The silencing of tumor suppressor genes through DNA methylation has been reported in many types of cancer and is associated with tumor development and progression. A growing body of literature has described the crosstalk between DNA methylation and miRNAs as an additional layer in the regulation of gene expression. Methylation in miRNA promoter regions inhibits its transcription, while miRNAs can target transcripts and subsequently regulate the proteins responsible for DNA methylation. Such relationships between miRNA and DNA methylation serve an important regulatory role in several tumor types and highlight a novel avenue for potential therapeutic targets. In this review, we discuss the crosstalk between DNA methylation and miRNA expression in the pathogenesis of cancer and describe how miRNAs influence DNA methylation and, conversely, how methylation impacts the expression of miRNAs. Finally, we address how these epigenetic modifications may be leveraged as biomarkers in cancer. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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13 pages, 7351 KiB  
Article
Melatonin Protects the Apoptosis of Sheep Granulosa Cells by Suppressing Oxidative Stress via MAP3K8 and FOS Pathway
by Bo Zhai, Xu Li, Zhongli Zhao, Yang Cao, Xinxin Liu, Zheng Liu, Huihai Ma and Wenfa Lu
Genes 2023, 14(5), 1067; https://doi.org/10.3390/genes14051067 - 11 May 2023
Cited by 9 | Viewed by 2601
Abstract
Melatonin is not only a highly effective active oxygen scavenger but also an important reproductive hormone. Melatonin has a regulatory effect on animal reproduction, especially on the ovaries. It can affect the proliferation and apoptosis of cells in follicles. However, the mechanisms of [...] Read more.
Melatonin is not only a highly effective active oxygen scavenger but also an important reproductive hormone. Melatonin has a regulatory effect on animal reproduction, especially on the ovaries. It can affect the proliferation and apoptosis of cells in follicles. However, the mechanisms of the dual antioxidation and anti-apoptosis effects of melatonin on granulosa cells are still not clear, especially in sheep. Therefore, we investigated the mechanisms of the protective effect of melatonin against oxidative damage in granulosa cells. At a concentration of 250 µmol/L, H2O2 promoted granulosa cell apoptosis; however, 10 ng/mL melatonin effectively alleviated the pro-apoptotic effect of H2O2. Furthermore, through the application of high-throughput sequencing technology, we identified 109 significantly differentially expressed genes (35 upregulated and 74 downregulated genes) involved in the protective effect of melatonin against apoptosis. The expression levels of nine related genes, i.e., ATF3, FIBIN, FOS, HSPA6, MAP3K8, FOSB, PET117, DLX2, and TRIB1, changed significantly. MAP3K8 and FOS gene overexpression impacted the protective effect of melatonin in granulosa cells; the two genes exhibited an upstream and downstream regulatory relationship. Our findings indicated that melatonin alleviated H2O2-induced apoptosis in sheep granulosa cells through the MAP3K8-FOS pathway. Full article
(This article belongs to the Special Issue Genetic Regulation of Animal Reproduction)
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12 pages, 4052 KiB  
Article
The Complete Chloroplast Genomes of Blepharoglossum elegans and B. grossum and Comparative Analysis with Related Species (Orchidaceae, Malaxideae)
by Wenting Yang, Kunlin Wu, Lin Fang, Songjun Zeng and Lin Li
Genes 2023, 14(5), 1069; https://doi.org/10.3390/genes14051069 - 11 May 2023
Cited by 2 | Viewed by 2388
Abstract
Blepharoglossum is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of Blepharoglossum has been challenged, and the phylogenetic relationships among its allied [...] Read more.
Blepharoglossum is a rare orchid genus of the Malaxidinae primarily distributed in tropical Pacific islands, with several species occurring in the Taiwan and Hainan Islands of China. Currently, the monophyletic status of Blepharoglossum has been challenged, and the phylogenetic relationships among its allied groups have remained unresolved with traditional DNA markers. In this study, we initially sequenced and annotated the chloroplast (cp) genomes of two Blepharoglossum species, Blepharoglossum elegans (Lindl.) L. Li and Blepharoglossum grossum (Rchb.f.) L. Li. These cp genomes of Blepharoglossum share the typical quadripartite and circular structure. Each of the genomes encodes a total of 133 functional genes, including 87 protein-coding genes (CDS), 38 tRNA genes and 8 rRNA genes. By comparing the sequence differences between these two cp genomes, it was found that they are relatively conserved in terms of overall gene content and gene arrangement. However, a total of 684 SNPs and 2664 indels were still identified, with ycf1, clpP, and trnK-UUU protein-coding genes having the highest number of SNPs and indels. In further comparative analyses among the six cp genomes in Malaxidinae, significant sequence divergences were identified in the intergenic regions, namely rps16–trnQ-UUG, trnS-GCU–trnG-GCC, rpoB–trnC-GCA, trnE-UUC–trnT-GGU, trnF-GAA–trnV-UAC, atpB–rbcL, petA–psbJ, psbE–petL, psbB–psbT, trnN-GUU–rpl32, trnV-GAC–rps7, and rps7–trnL-CAA, and five coding regions, including matK, and rpoC2, ycf1, and two ycf2 genes. Phylogenetic analysis indicated that Blepharoglossum and Oberonia form a highly supported sister group relationship. Our results are consistent with previous studies and present increased resolution among major clades. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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9 pages, 901 KiB  
Brief Report
Expression of Transposable Elements in the Brain of the Drosophila melanogaster Model for Fragile X Syndrome
by Maria Dolores De Donno, Antonietta Puricella, Simona D’Attis, Valeria Specchia and Maria Pia Bozzetti
Genes 2023, 14(5), 1060; https://doi.org/10.3390/genes14051060 - 9 May 2023
Cited by 1 | Viewed by 2549
Abstract
Fragile X syndrome is a neuro-developmental disease affecting intellectual abilities and social interactions. Drosophila melanogaster represents a consolidated model to study neuronal pathways underlying this syndrome, especially because the model recapitulates complex behavioural phenotypes. Drosophila Fragile X protein, or FMRP, is required for [...] Read more.
Fragile X syndrome is a neuro-developmental disease affecting intellectual abilities and social interactions. Drosophila melanogaster represents a consolidated model to study neuronal pathways underlying this syndrome, especially because the model recapitulates complex behavioural phenotypes. Drosophila Fragile X protein, or FMRP, is required for a normal neuronal structure and for correct synaptic differentiation in both the peripheral and central nervous systems, as well as for synaptic connectivity during development of the neuronal circuits. At the molecular level, FMRP has a crucial role in RNA homeostasis, including a role in transposon RNA regulation in the gonads of D. m. Transposons are repetitive sequences regulated at both the transcriptional and post-transcriptional levels to avoid genomic instability. De-regulation of transposons in the brain in response to chromatin relaxation has previously been related to neurodegenerative events in Drosophila models. Here, we demonstrate for the first time that FMRP is required for transposon silencing in larval and adult brains of Drosophila “loss of function” dFmr1 mutants. This study highlights that flies kept in isolation, defined as asocial conditions, experience activation of transposable elements. In all, these results suggest a role for transposons in the pathogenesis of certain neurological alterations in Fragile X as well as in abnormal social behaviors. Full article
(This article belongs to the Special Issue Epigenetics of Fragile X and Other Neurodevelopmental Disorders)
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12 pages, 1850 KiB  
Article
Ribonuclease D Processes a Small RNA Regulator of Multicellular Development in Myxobacteria
by Sarah M. Cossey, Gregory J. Velicer and Yuen-Tsu Nicco Yu
Genes 2023, 14(5), 1061; https://doi.org/10.3390/genes14051061 - 9 May 2023
Cited by 2 | Viewed by 2278
Abstract
By targeting mRNA transcripts, non-coding small RNAs (sRNAs) regulate the expression of genes governing a wide range of bacterial functions. In the social myxobacterium Myxococcus xanthus, the sRNA Pxr serves as a gatekeeper of the regulatory pathway controlling the life-cycle transition from [...] Read more.
By targeting mRNA transcripts, non-coding small RNAs (sRNAs) regulate the expression of genes governing a wide range of bacterial functions. In the social myxobacterium Myxococcus xanthus, the sRNA Pxr serves as a gatekeeper of the regulatory pathway controlling the life-cycle transition from vegetative growth to multicellular fruiting body development. When nutrients are abundant, Pxr prevents the initiation of the developmental program, but Pxr-mediated inhibition is alleviated when cells starve. To identify genes essential for Pxr function, a developmentally defective strain in which Pxr-mediated blockage of development is constitutively active (strain “OC”) was transposon-mutagenized to identify suppressor mutations that inactivate or bypass Pxr inhibition and thereby restore development. One of the four loci in which a transposon insertion restored development is rnd, encoding the Ribonuclease D protein (RNase D). RNase D is an exonuclease important for tRNA maturation. Here, we show that disruption of rnd abolishes the accumulation of Pxr-S, the product of Pxr processing from a longer precursor form (Pxr-L) and the active inhibitor of development. Additionally, the decrease in Pxr-S caused by rnd disruption was associated with increased accumulation primarily of a longer novel Pxr-specific transcript (Pxr-XL) rather than of Pxr-L. The introduction of a plasmid expressing rnd reverted cells back to OC-like phenotypes in development and Pxr accumulation, indicating that a lack of RNase D alone suppresses the developmental defect of OC. Moreover, an in vitro Pxr-processing assay demonstrated that RNase D processes Pxr-XL into Pxr-L; this implies that overall, Pxr sRNA maturation requires a sequential two-step processing. Collectively, our results indicate that a housekeeping ribonuclease plays a central role in a model form of microbial aggregative development. To our knowledge, this is the first evidence implicating RNase D in sRNA processing. Full article
(This article belongs to the Special Issue The Genetic Basis of Microbial Sociality)
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14 pages, 4699 KiB  
Article
Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs
by Sui Liufu, Qun Lan, Xiaolin Liu, Bohe Chen, Xueli Xu, Nini Ai, Xintong Li, Zonggang Yu and Haiming Ma
Genes 2023, 14(5), 1050; https://doi.org/10.3390/genes14051050 - 8 May 2023
Cited by 9 | Viewed by 3454
Abstract
The growth and development of the Longissimus Dorsi muscle are complex, playing an important role in the determination of pork quality. The study of the Longissimus Dorsi muscle at the mRNA level is particularly crucial for finding molecular approaches to improving meat quality [...] Read more.
The growth and development of the Longissimus Dorsi muscle are complex, playing an important role in the determination of pork quality. The study of the Longissimus Dorsi muscle at the mRNA level is particularly crucial for finding molecular approaches to improving meat quality in pig breeding. The current study utilized transcriptome technology to explore the regulatory mechanisms of muscle growth and intramuscular fat (IMF) deposition in the Longissimus Dorsi muscle at three core developmental stages (natal stage on day 1, growing stage on day 60, and finishing stage on day 210) in Ningxiang pigs. Our results revealed 441 differentially expressed genes (DEGs) in common for day 1 vs. day 60 and day 60 vs. day 210, and GO (Gene Ontology) analysis showed that candidate genes RIPOR2, MEGF10, KLHL40, PLEC, TBX3, FBP2, and HOMER1 may be closely related to muscle growth and development, while KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that DEGs (UBC, SLC27A5, RXRG, PRKCQ, PRKAG2, PPARGC1A, PLIN5, PLIN4, IRS2, and CPT1B) involved the PPAR (Peroxisome Proliferator-Activated Receptor) signaling pathway and adipocytokine signaling pathway, which might play a pivotal role in the regulation of IMF deposition. PPI (Protein-Protein Interaction Networks) analysis found that the STAT1 gene was the top hub gene. Taken together, our results provide evidence for the molecular mechanisms of growth and development and IMF deposition in Longissimus Dorsi muscle to optimize carcass mass. Full article
(This article belongs to the Special Issue Genetics and Genomics of Pig Breeding)
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15 pages, 8411 KiB  
Article
Developing CuS for Predicting Aggressiveness and Prognosis in Lung Adenocarcinoma
by Honghao Liu, Haijun Che, Mengyan Zhang, Jinyue Lv, Chengjie Pu, Jiawei Wu, Yan Zhang and Yue Gu
Genes 2023, 14(5), 1055; https://doi.org/10.3390/genes14051055 - 8 May 2023
Cited by 1 | Viewed by 2303
Abstract
Cuproptosis is a newfound cell death form that depends on copper (Cu) ionophores to transport Cu into cancer cells. Studies on the relationship have covered most common cancer types and analyzed the links between cuproptosis-related genes (CRGs) and various aspects of tumor characteristics. [...] Read more.
Cuproptosis is a newfound cell death form that depends on copper (Cu) ionophores to transport Cu into cancer cells. Studies on the relationship have covered most common cancer types and analyzed the links between cuproptosis-related genes (CRGs) and various aspects of tumor characteristics. In this study, we evaluated the role of cuproptosis in lung adenocarcinoma (LUAD) and constructed the cuproptosis-related score (CuS) to predict aggressiveness and prognosis in LUAD, so as to achieve precise treatment for patients. CuS had a better predictive performance than cuproptosis genes, possibly due to the synergy of SLC family genes, and patients with a high CuS had a poor prognosis. Functional enrichment analysis revealed the correlation between CuS and immune and mitochondrial pathways in multiple datasets. Furthermore, we predicted six potential drugs targeting high-CuS patients, including AZD3759, which is a targeted drug for LUAD. In conclusion, cuproptosis is involved in LUAD aggressiveness, and CuS can accurately predict the prognosis of patients. These findings provide a basis for precise treatment of patients with high CuS in LUAD. Full article
(This article belongs to the Special Issue DNA and RNA Epigenetics and Transcriptomics Research, 2nd Edition)
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15 pages, 4153 KiB  
Article
Comparative Transcriptome Analyses of Leg Muscle during Early Growth between Geese (Anser cygnoides) Breeds Differing in Body Size Characteristics
by Jun Tang, Hongjia Ouyang, Xiaomei Chen, Danli Jiang, Yunbo Tian, Yunmao Huang and Xu Shen
Genes 2023, 14(5), 1048; https://doi.org/10.3390/genes14051048 - 7 May 2023
Cited by 12 | Viewed by 2341
Abstract
Goose is an important poultry commonly raised for meat. The early growth performance of geese significantly influences their market weight and slaughter weight, affecting the poultry industry’s economic benefits. To identify the growth surge between the Shitou goose and the Wuzong goose, we [...] Read more.
Goose is an important poultry commonly raised for meat. The early growth performance of geese significantly influences their market weight and slaughter weight, affecting the poultry industry’s economic benefits. To identify the growth surge between the Shitou goose and the Wuzong goose, we collected the early growth body traits from 0 to 12 weeks. In addition, we investigated the transcriptomic changes in leg muscles at the high growth speed period to reveal the difference between the two geese breeds. We also estimated the growth curve parameters under three models, including the logistic, von Bertalanffy, and Gompertz models. The results showed that except for body length and keel length, the best-fitting model between the body weight and body size of the Shitou and Wuzong was the logistic model. The growth turning points of Shitou and Wuzong were 5.954 and 4.944 weeks, respectively, and the turning point of their body weight was 1459.01 g and 478.54 g, respectively. Growth surge occurred at 2–9 weeks in Shitou goose and at 1–7 weeks in Wuzong goose. The body size traits of the Shitou goose and Wuzong goose showed a trend of rapid growth in the early stage and slow growth in the later stage, and the Shitou goose growth was higher than the Wuzong goose. For transcriptome sequencing, a total of 87 differentially expressed genes (DEGs) were identified with a fold change ≥ 2 and a false discovery rate < 0.05. Many DEGs have a potential function for growth, such as CXCL12, SSTR4, FABP5, SLC2A1, MYLK4, and EIF4E3. KEGG pathway analysis identified that some DEGs were significantly enriched in the calcium signaling pathway, which may promote muscle growth. The gene–gene interaction network of DEGs was mainly related to the transmission of cell signals and substances, hematological system development, and functions. This study can provide theoretical guidance for the production and breeding management of the Shitou goose and Wuzong goose and help reveal the genetic mechanisms underlying diverse body sizes between two goose breeds. Full article
(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)
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18 pages, 4443 KiB  
Article
Preliminary Study: DNA Transfer and Persistence on Non-Porous Surfaces Submerged in Spring Water
by Morgan L. Korzik, Josep De Alcaraz-Fossoul, Michael S. Adamowicz and David San Pietro
Genes 2023, 14(5), 1045; https://doi.org/10.3390/genes14051045 - 6 May 2023
Cited by 2 | Viewed by 3602
Abstract
Submerged items are often thought to lack evidentiary value. However, previous studies have shown the ability to recover DNA from submerged porous items for upwards of six weeks. The crevices or interweaving fibers in porous items are thought to protect DNA from being [...] Read more.
Submerged items are often thought to lack evidentiary value. However, previous studies have shown the ability to recover DNA from submerged porous items for upwards of six weeks. The crevices or interweaving fibers in porous items are thought to protect DNA from being washed away. It is hypothesized that, because non-porous surfaces do not have the same traits that might aid in DNA retention, then DNA quantities and the number of donor alleles recovered would decrease over longer submersion periods. Additionally, it is hypothesized that DNA quantity and the number of alleles would be negatively affected by flow conditions. Neat saliva of known DNA quantity was applied to glass slides and exposed to stagnant and flowing spring water to observe the effects on both DNA quantity and STR detection. Results supported that DNA deposited onto glass and subsequently submerged in water experienced a decrease in DNA quantity over time, yet submersion did not have as strong of a negative effect on the detected amplification product. Additionally, an increase in DNA quantity and detected amplification product from designated blank slides (no initial DNA added) could indicate the possibility of DNA transfer. Full article
(This article belongs to the Special Issue Advances in Forensic Molecular Genetics)
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13 pages, 640 KiB  
Review
A Glimpse into Chromatin Organization and Nuclear Lamina Contribution in Neuronal Differentiation
by Salvatore Martino, Pietro Salvatore Carollo and Viviana Barra
Genes 2023, 14(5), 1046; https://doi.org/10.3390/genes14051046 - 6 May 2023
Cited by 4 | Viewed by 3254
Abstract
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through [...] Read more.
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through the formation of specific regions of active as well as inactive chromatin, allow the coordinated regulation of the genes for each cell fate. In this mini-review, we discuss the current knowledge regarding the regulation of three-dimensional chromatin structure during neuronal differentiation. We also focus on the role the nuclear lamina plays in neurogenesis to ensure the tethering of the chromatin to the nuclear envelope. Full article
(This article belongs to the Special Issue Chromatin Organization in Cell Differentiation)
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15 pages, 1662 KiB  
Article
Freezing Does Not Alter Sperm Telomere Length despite Increasing DNA Oxidation and Fragmentation
by Charlène Gouhier, Hanae Pons-Rejraji, Sandra Dollet, Laure Chaput, Céline Bourgne, Marc Berger, Bruno Pereira, Andrei Tchirkov and Florence Brugnon
Genes 2023, 14(5), 1039; https://doi.org/10.3390/genes14051039 - 3 May 2023
Cited by 5 | Viewed by 2464
Abstract
Correlations were reported between sperm telomere length (STL) and male fertility, sperm DNA fragmentation, and oxidation. Sperm freezing is widely used for assisted reproductive techniques, fertility preservation, and sperm donation. However, its impact on STL remains unknown. For this study, semen surplus from [...] Read more.
Correlations were reported between sperm telomere length (STL) and male fertility, sperm DNA fragmentation, and oxidation. Sperm freezing is widely used for assisted reproductive techniques, fertility preservation, and sperm donation. However, its impact on STL remains unknown. For this study, semen surplus from patients who underwent routine semen analysis were used. The impact of slow freezing on STL was analyzed by performing qPCR before and after freezing. Sperm populations with different STL were evaluated using Q-FISH. The relationship between sperm DNA oxidation, DNA fragmentation, and STL was assessed in fresh and frozen sperm samples. No significant impact of slow freezing on STL was observed, neither measured by qPCR nor Q-FISH. However, Q-FISH allowed for the distinguishing of sperm populations with different STLs within individual sperm samples. Slow freezing induced different STL distributions for some of the analyzed sperm samples, but no correlation was found between STL and sperm DNA fragmentation or oxidation. Slow freezing does not alter STL despite increasing sperm DNA oxidation and fragmentation. As STL alterations could be transmitted to offspring, the lack of impact of the slow freezing method on STL ensures the safety of this procedure. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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20 pages, 33493 KiB  
Article
Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis
by Suchanda Dey, Mahendra Gaur, Ellen M. E. Sykes, Monica Prusty, Selvakumar Elangovan, Sangita Dixit, Sanghamitra Pati, Ayush Kumar and Enketeswara Subudhi
Genes 2023, 14(5), 1037; https://doi.org/10.3390/genes14051037 - 2 May 2023
Cited by 11 | Viewed by 4311
Abstract
Background: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. Methods: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships [...] Read more.
Background: The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. Methods: A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis. Results: The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147’s initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621. Conclusions: Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions. Full article
(This article belongs to the Special Issue Omics and Bioinformatics)
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17 pages, 4066 KiB  
Article
Donkey Oil-Based Ketogenic Diet Prevents Tumor Progression by Regulating Intratumor Inflammation, Metastasis and Angiogenesis in CT26 Tumor-Bearing Mice
by Huachen Zhang, Lan Xie, Ning Zhang, Xingzhen Qi, Ting Lu, Jingya Xing, Muhammad Faheem Akhtar, Lanjie Li and Guiqin Liu
Genes 2023, 14(5), 1024; https://doi.org/10.3390/genes14051024 - 30 Apr 2023
Cited by 7 | Viewed by 10498
Abstract
Colon cancer is one of the typical malignant tumors, and its prevalence has increased yearly. The ketogenic diet (KD) is a low-carbohydrate and high-fat dietary regimen that inhibits tumor growth. Donkey oil (DO) is a product with a high nutrient content and a [...] Read more.
Colon cancer is one of the typical malignant tumors, and its prevalence has increased yearly. The ketogenic diet (KD) is a low-carbohydrate and high-fat dietary regimen that inhibits tumor growth. Donkey oil (DO) is a product with a high nutrient content and a high bioavailability of unsaturated fatty acids. Current research investigated the impact of the DO-based KD (DOKD) on CT26 colon cancer in vivo. Our findings revealed that DOKD administration significantly lowered CT26+ tumor cell growth in mice, and the blood β-hydroxybutyrate levels in the DOKD group was significantly higher than those in the natural diet group. Western blot results showed that DOKD significantly down-regulated Src, hypoxia inducible factor-1α (HIF-1α), extracellular signal-related kinases 1 and 2 (Erk1/2), snail, neural cadherin (N-cadherin), vimentin, matrix metallopeptidase 9 (MMP9), signal transducer and activator of transcription 3 (STAT3), and vascular endothelial growth factor A (VEGFA), and it significantly up-regulated the expressions of Sirt3, S100a9, interleukin (IL)-17, nuclear factor-kappaB (NF-κB) p65, Toll-like receptor 4 (TLR4), MyD88, and tumor necrosis factor-α. Meanwhile, in vitro validation results showed that LW6 (a HIF-1α inhibitor) significantly down-regulated the expressions of HIF-1α, N-cadherin, vimentin, MMP9, and VEGFA, which supported those of the in vivo findings. Furthermore, we found that DOKD inhibited CT26+ tumor cell growth by regulating inflammation, metastasis, and angiogenesis by activating the IL-17/TLR4/NF-κB p65 pathway and inhibiting the activation of the Src/HIF-1α/Erk1/2/Snail/N-cadherin/Vimentin/MMP9 and Erk1/2/HIF-1α/STAT3/VEGFA pathways. Our findings suggest that DOKD may suppress colon cancer progression and help prevent colon cancer cachexia. Full article
(This article belongs to the Special Issue Equine Genetics and Genomics)
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16 pages, 658 KiB  
Article
Comparison of Genetic Susceptibility to Coronary Heart Disease in the Hungarian Populations: Risk Prediction Models for Coronary Heart Disease
by Nayla Nasr, Beáta Soltész, János Sándor, Róza Ádány and Szilvia Fiatal
Genes 2023, 14(5), 1033; https://doi.org/10.3390/genes14051033 - 30 Apr 2023
Cited by 2 | Viewed by 2539
Abstract
Background and Aim: It was evaluated whether the integration of genetic risk scores (GRS-unweighted, wGRS-weighted) into conventional risk factor (CRF) models for coronary heart disease or acute myocardial infarction (CHD/AMI) could improve the predictive ability of the models. Methods: Subjects and [...] Read more.
Background and Aim: It was evaluated whether the integration of genetic risk scores (GRS-unweighted, wGRS-weighted) into conventional risk factor (CRF) models for coronary heart disease or acute myocardial infarction (CHD/AMI) could improve the predictive ability of the models. Methods: Subjects and data collected in a previous survey were used to perform regression and ROC curve analyses as well as to examine the role of genetic components. Thirty SNPs were selected, and genotype and phenotype data were available for 558 participants (general: N = 279 and Roma: N = 279). Results: The mean GRS (27.27 ± 3.43 vs. 26.68 ± 3.51, p = 0.046) and wGRS (3.52 ± 0.68 vs. 3.33 ± 0.62, p = 0.001) were significantly higher in the general population. The addition of the wGRS to the CRF model yielded the strongest improvement in discrimination among Roma (from 0.8616 to 0.8674), while the addition of GRS to the CRF model yielded the strongest improvement in discrimination in the general population (from 0.8149 to 0.8160). In addition to that, the Roma individuals were likely to develop CHD/AMI at a younger age than subjects in the general population. Conclusions: The combination of the CRFs and genetic components improved the model’s performance and predicted AMI/CHD better than CRFs alone. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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21 pages, 2405 KiB  
Review
Lagging Strand Initiation Processes in DNA Replication of Eukaryotes—Strings of Highly Coordinated Reactions Governed by Multiprotein Complexes
by Heinz Peter Nasheuer and Nichodemus O. Onwubiko
Genes 2023, 14(5), 1012; https://doi.org/10.3390/genes14051012 - 29 Apr 2023
Cited by 5 | Viewed by 3655
Abstract
In their influential reviews, Hanahan and Weinberg coined the term ‘Hallmarks of Cancer’ and described genome instability as a property of cells enabling cancer development. Accurate DNA replication of genomes is central to diminishing genome instability. Here, the understanding of the initiation of [...] Read more.
In their influential reviews, Hanahan and Weinberg coined the term ‘Hallmarks of Cancer’ and described genome instability as a property of cells enabling cancer development. Accurate DNA replication of genomes is central to diminishing genome instability. Here, the understanding of the initiation of DNA synthesis in origins of DNA replication to start leading strand synthesis and the initiation of Okazaki fragment on the lagging strand are crucial to control genome instability. Recent findings have provided new insights into the mechanism of the remodelling of the prime initiation enzyme, DNA polymerase α-primase (Pol-prim), during primer synthesis, how the enzyme complex achieves lagging strand synthesis, and how it is linked to replication forks to achieve optimal initiation of Okazaki fragments. Moreover, the central roles of RNA primer synthesis by Pol-prim in multiple genome stability pathways such as replication fork restart and protection of DNA against degradation by exonucleases during double-strand break repair are discussed. Full article
(This article belongs to the Special Issue DNA Replication/Repair, and the DNA Damage Response in Human Disease 2023)
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20 pages, 4771 KiB  
Article
Genome-Wide Association Study Identified Novel SNPs Associated with Chlorophyll Content in Maize
by Yueting Jin, Dan Li, Meiling Liu, Zhenhai Cui, Daqiu Sun, Cong Li, Ao Zhang, Huiying Cao and Yanye Ruan
Genes 2023, 14(5), 1010; https://doi.org/10.3390/genes14051010 - 29 Apr 2023
Cited by 9 | Viewed by 2497
Abstract
Chlorophyll is an essential component that captures light energy to drive photosynthesis. Chlorophyll content can affect photosynthetic activity and thus yield. Therefore, mining candidate genes of chlorophyll content will help increase maize production. Here, we performed a genome-wide association study (GWAS) on chlorophyll [...] Read more.
Chlorophyll is an essential component that captures light energy to drive photosynthesis. Chlorophyll content can affect photosynthetic activity and thus yield. Therefore, mining candidate genes of chlorophyll content will help increase maize production. Here, we performed a genome-wide association study (GWAS) on chlorophyll content and its dynamic changes in 378 maize inbred lines with extensive natural variation. Our phenotypic assessment showed that chlorophyll content and its dynamic changes were natural variations with a moderate genetic level of 0.66/0.67. A total of 19 single-nucleotide polymorphisms (SNPs) were found associated with 76 candidate genes, of which one SNP, 2376873-7-G, co-localized in chlorophyll content and area under the chlorophyll content curve (AUCCC). Zm00001d026568 and Zm00001d026569 were highly associated with SNP 2376873-7-G and encoded pentatricopeptide repeat-containing protein and chloroplastic palmitoyl-acyl carrier protein thioesterase, respectively. As expected, higher expression levels of these two genes are associated with higher chlorophyll contents. These results provide a certain experimental basis for discovering the candidate genes of chlorophyll content and finally provide new insights for cultivating high-yield and excellent maize suitable for planting environment. Full article
(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics)
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17 pages, 990 KiB  
Review
Exploring the Diet-Gut Microbiota-Epigenetics Crosstalk Relevant to Neonatal Diabetes
by Naser A. Alsharairi
Genes 2023, 14(5), 1017; https://doi.org/10.3390/genes14051017 - 29 Apr 2023
Cited by 9 | Viewed by 3908
Abstract
Neonatal diabetes (NDM) is a rare monogenic disorder that presents as hyperglycemia during the first six months of life. The link between early-life gut microbiota dysbiosis and susceptibility to NDM remains uncertain. Experimental studies have demonstrated that gestational diabetes mellitus (GDM) could develop [...] Read more.
Neonatal diabetes (NDM) is a rare monogenic disorder that presents as hyperglycemia during the first six months of life. The link between early-life gut microbiota dysbiosis and susceptibility to NDM remains uncertain. Experimental studies have demonstrated that gestational diabetes mellitus (GDM) could develop into meconium/gut microbiota dysbiosis in newborns, and thus, it is thought to be a mediator in the pathogenesis of NDM. Epigenetic modifications have been considered as potential mechanisms by which the gut microbiota and susceptibility genes interact with the neonatal immune system. Several epigenome-wide association studies have revealed that GDM is associated with neonatal cord blood and/or placental DNA methylation alterations. However, the mechanisms linking diet in GDM with gut microbiota alterations, which may in turn induce the expression of genes linked to NDM, are yet to be unraveled. Therefore, the focus of this review is to highlight the impacts of diet, gut microbiota, and epigenetic crosstalk on altered gene expression in NDM. Full article
(This article belongs to the Special Issue Human Microbiota: Current Updates on Pathogenetic Mechanisms and Methodological Advances)
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21 pages, 4991 KiB  
Article
Metabarcoding of Antarctic Lichens from Areas with Different Deglaciation Times Reveals a High Diversity of Lichen-Associated Communities
by Andreas Beck, Angélica Casanova-Katny and Julia Gerasimova
Genes 2023, 14(5), 1019; https://doi.org/10.3390/genes14051019 - 29 Apr 2023
Cited by 5 | Viewed by 3128
Abstract
Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of [...] Read more.
Lichens have developed numerous adaptations to optimise their survival under harsh abiotic stress, colonise different substrates, and reach substantial population sizes and high coverage in ice-free Antarctic areas, benefiting from a symbiotic lifestyle. As lichen thalli represent consortia with an unknown number of participants, it is important to know about the accessory organisms and their relationships with various environmental conditions. To this end, we analysed lichen-associated communities from Himantormia lugubris, Placopsis antarctica, P. contortuplicata, and Ramalina terebrata, collected from soils with differing deglaciation times, using a metabarcoding approach. In general, many more Ascomycete taxa are associated with the investigated lichens compared to Basidiomycota. Given our sampling, a consistently higher number of lichen-associated eukaryotes are estimated to be present in areas with deglaciation times of longer than 5000 years compared to more recently deglaciated areas. Thus far, members of Dothideomycetes, Leotiomycetes, and Arthoniomycetes have been restricted to the Placopsis specimens from areas with deglaciation times longer than 5000 years. Striking differences between the associated organisms of R. terebrata and H. lugubris have also been discovered. Thus, a species-specific basidiomycete, Tremella, was revealed for R. terebrata, as was a member of Capnodiales for H. lugubris. Our study provides further understanding of the complex terricolous lichen-associated mycobiome using the metabarcoding approach. It also illustrates the necessity to extend our knowledge of complex lichen symbiosis and further improve the coverage of microbial eukaryotes in DNA barcode libraries, including more extended sampling. Full article
(This article belongs to the Special Issue Polar Genomics)
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14 pages, 344 KiB  
Review
The Genomic Landscape of Melanoma and Its Therapeutic Implications
by Ting-Ting Yang, Sebastian Yu, Chiao-Li Khale Ke and Shih-Tsung Cheng
Genes 2023, 14(5), 1021; https://doi.org/10.3390/genes14051021 - 29 Apr 2023
Cited by 15 | Viewed by 4004
Abstract
Melanoma is one of the most aggressive malignancies of the skin. The genetic composition of melanoma is complex and varies among different subtypes. With the aid of recent technologies such as next generation sequencing and single-cell sequencing, our understanding of the genomic landscape [...] Read more.
Melanoma is one of the most aggressive malignancies of the skin. The genetic composition of melanoma is complex and varies among different subtypes. With the aid of recent technologies such as next generation sequencing and single-cell sequencing, our understanding of the genomic landscape of melanoma and its tumor microenvironment has become increasingly clear. These advances may provide explanation to the heterogenic treatment outcomes of melanoma patients under current therapeutic guidelines and provide further insights to the development of potential new therapeutic targets. Here, we provide a comprehensive review on the genetics related to melanoma tumorigenesis, metastasis, and prognosis. We also review the genetics affecting the melanoma tumor microenvironment and its relation to tumor progression and treatment. Full article
(This article belongs to the Special Issue Genetics of Complex Cutaneous Disorders)
21 pages, 5593 KiB  
Article
The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum
by Tena Gržan, Mira Dombi, Evelin Despot-Slade, Damira Veseljak, Marin Volarić, Nevenka Meštrović, Miroslav Plohl and Brankica Mravinac
Genes 2023, 14(5), 999; https://doi.org/10.3390/genes14050999 - 28 Apr 2023
Cited by 11 | Viewed by 2220
Abstract
The red flour beetle Tribolium castaneum is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderate-copy-number satellite DNAs (satDNAs) have been described in the assembled part of its genome. In [...] Read more.
The red flour beetle Tribolium castaneum is an important pest of stored agricultural products and the first beetle whose genome was sequenced. So far, one high-copy-number and ten moderate-copy-number satellite DNAs (satDNAs) have been described in the assembled part of its genome. In this work, we aimed to catalog the entire collection of T. castaneum satDNAs. We resequenced the genome using Illumina technology and predicted potential satDNAs via graph-based sequence clustering. In this way, we discovered 46 novel satDNAs that occupied a total of 2.1% of the genome and were, therefore, considered low-copy-number satellites. Their repeat units, preferentially 140–180 bp and 300–340 bp long, showed a high A + T composition ranging from 59.2 to 80.1%. In the current assembly, we annotated the majority of the low-copy-number satDNAs on one or a few chromosomes, discovering mainly transposable elements in their vicinity. The current assembly also revealed that many of the in silico predicted satDNAs were organized into short arrays not much longer than five consecutive repeats, and some of them also had numerous repeat units scattered throughout the genome. Although 20% of the unassembled genome sequence masked the genuine state, the predominance of scattered repeats for some low-copy satDNAs raises the question of whether these are essentially interspersed repeats that occur in tandem only sporadically, with the potential to be satDNA “seeds”. Full article
(This article belongs to the Special Issue Satellite DNA Genomics)
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14 pages, 2157 KiB  
Article
Differential Brain Expression Patterns of microRNAs Related to Olfactory Performance in Honey Bees (Apis mellifera)
by Jingnan Huang, Tianbao Wang, Yuanmei Qiu, Aqai Kalan Hassanyar, Zhaonan Zhang, Qiaoling Sun, Xiaomin Ni, Kejun Yu, Yongkang Guo, Changsheng Yang, Yang Lü, Hongyi Nie, Yan Lin, Zhiguo Li and Songkun Su
Genes 2023, 14(5), 1000; https://doi.org/10.3390/genes14051000 - 28 Apr 2023
Cited by 7 | Viewed by 2896
Abstract
MicroRNAs (miRNAs) play a vital role in the nerve regulation of honey bees (Apis mellifera). This study aims to investigate the differences in expression of miRNAs in a honey bee’s brain for olfactory learning tasks and to explore their potential role [...] Read more.
MicroRNAs (miRNAs) play a vital role in the nerve regulation of honey bees (Apis mellifera). This study aims to investigate the differences in expression of miRNAs in a honey bee’s brain for olfactory learning tasks and to explore their potential role in a honey bee’s olfactory learning and memory. In this study, 12 day old honey bees with strong and weak olfactory performances were utilized to investigate the influence of miRNAs on olfactory learning behavior. The honey bee brains were dissected, and a small RNA-seq technique was used for high-throughput sequencing. The data analysis of the miRNA sequences revealed that 14 differentially expressed miRNAs (DEmiRNAs) between the two groups, strong (S) and weak (W), for olfactory performance in honey bees were identified, which included seven up-regulated and seven down-regulated. The qPCR verification results of the 14 miRNAs showed that four miRNAs (miR-184-3p, miR-276-3p, miR-87-3p, and miR-124-3p) were significantly associated with olfactory learning and memory. The target genes of these DEmiRNAs were subjected to the GO database annotation and KEGG pathway enrichment analyses. The functional annotation and pathway analysis showed that the neuroactive ligand-receptor interaction pathway, oxidative phosphorylation, biosynthesis of amino acids, pentose phosphate pathway, carbon metabolism, and terpenoid backbone biosynthesis may be a great important pathway related to olfactory learning and memory in honey bees. Our findings together further explained the relationship between olfactory performance and the brain function of honey bees at the molecular level and provides a basis for further study on miRNAs related to olfactory learning and memory in honey bees. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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15 pages, 2205 KiB  
Review
Recent Advances in Genetics and Genomics of Snub-Nosed Monkeys (Rhinopithecus) and Their Implications for Phylogeny, Conservation, and Adaptation
by Weimin Kuang, Dietmar Zinner, Yuan Li, Xueqin Yao, Christian Roos and Li Yu
Genes 2023, 14(5), 985; https://doi.org/10.3390/genes14050985 - 27 Apr 2023
Cited by 10 | Viewed by 4021
Abstract
The snub-nosed monkey genus Rhinopithecus (Colobinae) comprises five species (Rhinopithecus roxellana, Rhinopithecus brelichi, Rhinopithecus bieti, Rhinopithecus strykeri, and Rhinopithecus avunculus). They are range-restricted species occurring only in small areas in China, Vietnam, and Myanmar. All extant species [...] Read more.
The snub-nosed monkey genus Rhinopithecus (Colobinae) comprises five species (Rhinopithecus roxellana, Rhinopithecus brelichi, Rhinopithecus bieti, Rhinopithecus strykeri, and Rhinopithecus avunculus). They are range-restricted species occurring only in small areas in China, Vietnam, and Myanmar. All extant species are listed as endangered or critically endangered by the International Union for Conservation of Nature (IUCN) Red List, all with decreasing populations. With the development of molecular genetics and the improvement and cost reduction in whole-genome sequencing, knowledge about evolutionary processes has improved largely in recent years. Here, we review recent major advances in snub-nosed monkey genetics and genomics and their impact on our understanding of the phylogeny, phylogeography, population genetic structure, landscape genetics, demographic history, and molecular mechanisms of adaptation to folivory and high altitudes in this primate genus. We further discuss future directions in this research field, in particular how genomic information can contribute to the conservation of snub-nosed monkeys. Full article
(This article belongs to the Special Issue Primate Phylogeny and Genetics)
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15 pages, 4636 KiB  
Article
Transcriptome Signatures of Atlantic Salmon—Resistant Phenotypes against Sea Lice Infestation Are Associated with Tissue Repair
by Valentina Valenzuela-Muñoz, Cristian Gallardo-Escárate, Diego Valenzuela-Miranda, Gustavo Nuñez-Acuña, Bárbara P. Benavente, Alejandro Alert and Marta Arevalo
Genes 2023, 14(5), 986; https://doi.org/10.3390/genes14050986 - 27 Apr 2023
Cited by 4 | Viewed by 2661
Abstract
Salmon aquaculture is constantly threatened by pathogens that impact fish health, welfare, and productivity, including the sea louse Caligus rogercresseyi. This marine ectoparasite is mainly controlled through delousing drug treatments that have lost efficacy. Therein, strategies such as salmon breeding selection represent [...] Read more.
Salmon aquaculture is constantly threatened by pathogens that impact fish health, welfare, and productivity, including the sea louse Caligus rogercresseyi. This marine ectoparasite is mainly controlled through delousing drug treatments that have lost efficacy. Therein, strategies such as salmon breeding selection represent a sustainable alternative to produce fish with resistance to sea lice. This study explored the whole-transcriptome changes in Atlantic salmon families with contrasting resistance phenotypes against lice infestation. In total, 121 Atlantic salmon families were challenged with 35 copepodites per fish and ranked after 14 infestation days. Skin and head kidney tissue from the top two lowest (R) and highest (S) infested families were sequenced by the Illumina platform. Genome-scale transcriptome analysis showed different expression profiles between the phenotypes. Significant differences in chromosome modulation between the R and S families were observed in skin tissue. Notably, the upregulation of genes associated with tissue repairs, such as collagen and myosin, was found in R families. Furthermore, skin tissue of resistant families showed the highest number of genes associated with molecular functions such as ion binding, transferase, and cytokine activity, compared with the susceptible. Interestingly, lncRNAs differentially modulated in the R/S families are located near genes associated with immune response, which are upregulated in the R family. Finally, SNPs variations were identified in both salmon families, where the resistant ones showed the highest number of SNPs variations. Remarkably, among the genes with SPNs, genes associated with the tissue repair process were identified. This study reported Atlantic salmon chromosome regions exclusively expressed in R or S Atlantic salmon families’ phenotypes. Furthermore, due to the presence of SNPs and high expression of tissue repair genes in the resistant families, it is possible to suggest mucosal immune activation associated with the Atlantic salmon resistance to sea louse infestation. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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12 pages, 2725 KiB  
Article
The YBR056W-A and Its Ortholog YDR034W-B of S. cerevisiae Belonging to CYSTM Family Participate in Manganese Stress Overcoming
by Anton Zvonarev, Larisa Ledova, Lubov Ryazanova, Airat Valiakhmetov, Vasilina Farofonova and Tatiana Kulakovskaya
Genes 2023, 14(5), 987; https://doi.org/10.3390/genes14050987 - 27 Apr 2023
Cited by 4 | Viewed by 1923
Abstract
The CYSTM (cysteine-rich transmembrane module) protein family comprises small molecular cysteine-rich tail-anchored membrane proteins found in many eukaryotes. The Saccharomyces cerevisiae strains carrying the CYSTM genes YDRO34W-B and YBR056W-A (MNC1) fused with GFP were used to test the expression of these [...] Read more.
The CYSTM (cysteine-rich transmembrane module) protein family comprises small molecular cysteine-rich tail-anchored membrane proteins found in many eukaryotes. The Saccharomyces cerevisiae strains carrying the CYSTM genes YDRO34W-B and YBR056W-A (MNC1) fused with GFP were used to test the expression of these genes under different stresses. The YBR056W-A (MNC1) and YDR034W-B genes are expressed under stress conditions caused by the toxic concentrations of heavy metal ions, such as manganese, cobalt, nickel, zinc, cuprum, and 2.4-dinitrophenol uncoupler. The expression level of YDR034W-B was higher than that of YBR056W-A under alkali and cadmium stresses. The Ydr034w-b-GFP and Ybr056w-a-GFP proteins differ in the cellular localization: Ydr034w-b-GFP was mainly observed in the plasma membrane and vacuolar membrane, while Ybr056w-a-GFP was observed in the cytoplasm, probably in intracellular membranes. The null-mutants in both genes demonstrated decreased cell concentration and lytic phenotype when cultivated in the presence of excess manganese. This allows for speculations about the involvement of Mnc1 and Ydr034w-b proteins in manganese stress overcoming. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2023)
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14 pages, 1682 KiB  
Article
Association between HLA Class II Alleles/Haplotypes and Genomic Ancestry in Brazilian Patients with Type 1 Diabetes: A Nationwide Exploratory Study
by Marília Brito Gomes, Vandilson Rodrigues, Deborah Conte Santos, Paulo Ricardo Villas Bôas, Dayse A. Silva, Rossana Santiago de Sousa Azulay, Sergio Atala Dib, Elizabeth João Pavin, Virgínia Oliveira Fernandes, Renan Magalhães Montenegro Junior, João Soares Felicio, Rosangela Réa, Carlos Antonio Negrato and Luís Cristóvão Porto
Genes 2023, 14(5), 991; https://doi.org/10.3390/genes14050991 - 27 Apr 2023
Cited by 7 | Viewed by 3667
Abstract
We aimed to identify HLA-DRB1, -DQA1, and -DQB1 alleles/haplotypes associated with European, African, or Native American genomic ancestry (GA) in admixed Brazilian patients with type 1 diabetes (T1D). This exploratory nationwide study enrolled 1599 participants. GA percentage was inferred using a [...] Read more.
We aimed to identify HLA-DRB1, -DQA1, and -DQB1 alleles/haplotypes associated with European, African, or Native American genomic ancestry (GA) in admixed Brazilian patients with type 1 diabetes (T1D). This exploratory nationwide study enrolled 1599 participants. GA percentage was inferred using a panel of 46 ancestry informative marker-insertion/deletion. Receiver operating characteristic curve analysis (ROC) was applied to identify HLA class II alleles related to European, African, or Native American GA, and showed significant (p < 0.05) accuracy for identifying HLA risk alleles related to European GA: for DRB1*03:01, the area under the curve was (AUC) 0.533; for DRB1*04:01 AUC = 0.558, for DRB1*04:02 AUC = 0.545. A better accuracy for identifying African GA was observed for the risk allele DRB1*09:01AUC = 0.679 and for the protective alleles DRB1*03:02 AUC = 0.649, DRB1*11:02 AUC = 0.636, and DRB1*15:03 AUC = 0.690. Higher percentage of European GA was observed in patients with risk haplotypes (p < 0.05). African GA percentage was higher in patients with protective haplotypes (p < 0.05). Risk alleles and haplotypes were related to European GA and protective alleles/haplotypes to African GA. Future studies with other ancestry markers are warranted to fill the gap in knowledge regarding the genetic origin of T1D in highly admixed populations such as that found in Brazil. Full article
(This article belongs to the Special Issue Genetics of Autoimmune Diseases)
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17 pages, 7261 KiB  
Article
Coronin 1C, Regulated by Multiple microRNAs, Facilitates Cancer Cell Aggressiveness in Pancreatic Ductal Adenocarcinoma
by Kosuke Fukuda, Naohiko Seki, Ryutaro Yasudome, Reiko Mitsueda, Shunichi Asai, Mayuko Kato, Tetsuya Idichi, Hiroshi Kurahara and Takao Ohtsuka
Genes 2023, 14(5), 995; https://doi.org/10.3390/genes14050995 - 27 Apr 2023
Cited by 3 | Viewed by 2777
Abstract
Coronin proteins are actin-related proteins containing WD repeat domains encoded by seven genes (CORO1A, CORO1B, CORO1C, CORO2A, CORO2B, CORO6, and CORO7) in the human genome. Analysis of large cohort data from The Cancer Genome Atlas [...] Read more.
Coronin proteins are actin-related proteins containing WD repeat domains encoded by seven genes (CORO1A, CORO1B, CORO1C, CORO2A, CORO2B, CORO6, and CORO7) in the human genome. Analysis of large cohort data from The Cancer Genome Atlas revealed that expression of CORO1A, CORO1B, CORO1C, CORO2A, and CORO7 was significantly upregulated in pancreatic ductal adenocarcinoma (PDAC) tissues (p < 0.05). Moreover, high expression of CORO1C and CORO2A significantly predicted the 5 year survival rate of patients with PDAC (p = 0.0071 and p = 0.0389, respectively). In this study, we focused on CORO1C and investigated its functional significance and epigenetic regulation in PDAC cells. Knockdown assays using siRNAs targeting CORO1C were performed in PDAC cells. Aggressive cancer cell phenotypes, especially cancer cell migration and invasion, were inhibited by CORO1C knockdown. The involvement of microRNAs (miRNAs) is a molecular mechanism underlying the aberrant expression of cancer-related genes in cancer cells. Our in silico analysis revealed that five miRNAs (miR-26a-5p, miR-29c-3p, miR-130b-5p, miR-148a-5p, and miR-217) are putative candidate miRNAs regulating CORO1C expression in PDAC cells. Importantly, all five miRNAs exhibited tumor-suppressive functions and four miRNAs except miR-130b-5p negatively regulated CORO1C expression in PDAC cells. CORO1C and its downstream signaling molecules are potential therapeutic targets in PDAC. Full article
(This article belongs to the Special Issue Genomics and Epigenomics of Gastrointestinal Disorders)
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20 pages, 7878 KiB  
Article
Direct and Secondary Transfer of Touch DNA on a Credit Card: Evidence Evaluation Given Activity Level Propositions and Application of Bayesian Networks
by Martina Onofri, Cristina Altomare, Simona Severini, Federica Tommolini, Massimo Lancia, Luigi Carlini, Cristiana Gambelunghe and Eugenia Carnevali
Genes 2023, 14(5), 996; https://doi.org/10.3390/genes14050996 - 27 Apr 2023
Cited by 11 | Viewed by 3605
Abstract
In a judiciary setting, questions regarding the mechanisms of transfer, persistence, and recovery of DNA are increasingly more common. The forensic expert is now asked to evaluate the strength of DNA trace evidence at activity level, thus assessing if a trace, given its [...] Read more.
In a judiciary setting, questions regarding the mechanisms of transfer, persistence, and recovery of DNA are increasingly more common. The forensic expert is now asked to evaluate the strength of DNA trace evidence at activity level, thus assessing if a trace, given its qualitative and quantitative features, could be the result of an alleged activity. The present study is the reproduction of a real-life casework scenario of illicit credit card use by a co-worker (POI) of its owner (O). After assessing the shedding propensity of the participants, differences in DNA traces’ qualitative and quantitative characteristics, given scenarios of primary and secondary transfer of touch DNA on a credit card, a non-porous plastic support, were investigated. A case-specific Bayesian Network to aid statistical evaluation was created and discrete observations, meaning the presence/absence of POI as a major contributor in both traces from direct and secondary transfer, were used to inform the probabilities of disputed activity events. Likelihood Ratios at activity level (LRα) were calculated for each possible outcome resulting from the DNA analysis. In instances where only POI and POI plus an unknown individual are retrieved, the values obtained show moderate to low support in favour of the prosecution proposition. Full article
(This article belongs to the Special Issue Improved Methods in Forensic DNA Analysis)
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14 pages, 3897 KiB  
Article
Contribution of Genetic Test to Early Diagnosis of Methylenetetrahydrofolate Reductase (MTHFR) Deficiency: The Experience of a Reference Center in Southern Italy
by Ferdinando Barretta, Fabiana Uomo, Simona Fecarotta, Lucia Albano, Daniela Crisci, Alessandra Verde, Maria Grazia Fisco, Giovanna Gallo, Daniela Dottore Stagna, Maria Rosaria Pricolo, Marianna Alagia, Gaetano Terrone, Alessandro Rossi, Giancarlo Parenti, Margherita Ruoppolo, Cristina Mazzaccara and Giulia Frisso
Genes 2023, 14(5), 980; https://doi.org/10.3390/genes14050980 - 26 Apr 2023
Cited by 4 | Viewed by 5425
Abstract
Background: the deficiency of 5,10-Methylenetetrahydrofolate reductase (MTHFR) constitutes a rare and severe metabolic disease and is included in most expanded newborn screening (NBS) programs worldwide. Patients with severe MTHFR deficiency develop neurological disorders and premature vascular disease. Timely diagnosis through NBS allows early [...] Read more.
Background: the deficiency of 5,10-Methylenetetrahydrofolate reductase (MTHFR) constitutes a rare and severe metabolic disease and is included in most expanded newborn screening (NBS) programs worldwide. Patients with severe MTHFR deficiency develop neurological disorders and premature vascular disease. Timely diagnosis through NBS allows early treatment, resulting in improved outcomes. Methods: we report the diagnostic yield of genetic testing for MTHFR deficiency diagnosis, in a reference Centre of Southern Italy between 2017 and 2022. MTHFR deficiency was suspected in four newborns showing hypomethioninemia and hyperhomocysteinemia; otherwise, one patient born in pre-screening era showed clinical symptoms and laboratory signs that prompted to perform genetic testing for MTHFR deficiency. Results: molecular analysis of the MTHFR gene revealed a genotype compatible with MTHFR deficiency in two NBS-positive newborns and in the symptomatic patient. This allowed for promptly beginning the adequate metabolic therapy. Conclusions: our results strongly support the need for genetic testing to quickly support the definitive diagnosis of MTHFR deficiency and start therapy. Furthermore, our study extends knowledge of the molecular epidemiology of MTHFR deficiency by identifying a novel mutation in the MTHFR gene. Full article
(This article belongs to the Special Issue Newborn Genetic Screening)
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12 pages, 1175 KiB  
Article
Evaluation and Verification of a microRNA Panel Using Quadratic Discriminant Analysis for the Classification of Human Body Fluids in DNA Extracts
by Ciara Rhodes, Carolyn Lewis, Kelsey Price, Anaya Valentine, Mary-Randall A. Creighton, Edward Boone and Sarah Seashols-Williams
Genes 2023, 14(5), 968; https://doi.org/10.3390/genes14050968 - 25 Apr 2023
Cited by 1 | Viewed by 4501
Abstract
There is significant interest in the use of miRNA analysis for forensic body fluid identification. Demonstrated co-extraction and detection in DNA extracts could make the use of miRNAs a more streamlined molecular body fluid identification method than other RNA-based methods. We previously reported [...] Read more.
There is significant interest in the use of miRNA analysis for forensic body fluid identification. Demonstrated co-extraction and detection in DNA extracts could make the use of miRNAs a more streamlined molecular body fluid identification method than other RNA-based methods. We previously reported a reverse transcription-quantitative PCR (RT-qPCR) panel of eight miRNAs that classified venous and menstrual blood, feces, urine, saliva, semen, and vaginal secretions using a quadratic discriminant analysis (QDA) model with 93% accuracy in RNA extracts. Herein, miRNA expression in DNA extracts from 50 donors of each body fluid were tested using the model. Initially, a classification rate of 87% was obtained, which increased to 92% when three additional miRNAs were added. Body fluid identification was found to be reliable across population samples of mixed ages, ethnicities, and sex, with 72–98% of the unknown samples classifying correctly. The model was then tested against compromised samples and over biological cycles, where classification accuracy varied, depending on the body fluid. In conclusion, we demonstrated the ability to classify body fluids using miRNA expression from DNA extracts, eliminating the need for RNA extraction, greatly reducing evidentiary sample consumption and processing time in forensic laboratories, but acknowledge that compromised semen and saliva samples can fail to classify properly, and mixed sample classification remains untested and may have limitations. Full article
(This article belongs to the Special Issue Advances in Forensic Molecular Genetics)
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12 pages, 734 KiB  
Article
LncRNA-SNPs in a Brazilian Breast Cancer Cohort: A Case-Control Study
by Carolina Mathias, Anelis Maria Marin, Ana Flávia Kohler, Heloisa Bruna Soligo Sanchuki, Natalie Sukow, Marcia Holsbach Beltrame, Suelen Cristina Soares Baal, Ana Paula Martins Sebastião, Enilze Maria de Souza Fonseca Ribeiro, Daniela Fiori Gradia, Mateus Nóbrega Aoki and Jaqueline Carvalho de Oliveira
Genes 2023, 14(5), 971; https://doi.org/10.3390/genes14050971 - 25 Apr 2023
Cited by 2 | Viewed by 2239
Abstract
Long noncoding RNAs (lncRNAs) are a class of non-coding RNAs that contain more than 200 nucleotides and exhibit a versatile regulatory capacity. Genomic alterations in lncRNAs have already been investigated in several complex diseases, including breast cancer (BC). BC is a highly heterogeneous [...] Read more.
Long noncoding RNAs (lncRNAs) are a class of non-coding RNAs that contain more than 200 nucleotides and exhibit a versatile regulatory capacity. Genomic alterations in lncRNAs have already been investigated in several complex diseases, including breast cancer (BC). BC is a highly heterogeneous disease and is the most prevalent cancer type among women worldwide. Single nucleotide polymorphisms (SNPs) in lncRNA regions appear to have an important role in BC susceptibility; however, little is known about lncRNA-SNPs in the Brazilian population. This study used Brazilian tumor samples to identify lncRNA-SNPs with a biological role in BC development. We applied a bioinformatic approach intersecting lncRNAs that are differentially expressed in BC tumor samples using The Cancer Genome Atlas (TCGA) cohort data and looked for lncRNAs with SNPs associated with BC in the Genome Wide Association Studies (GWAS) catalog. We highlight four lncRNA-SNPs—rs3803662, rs4415084, rs4784227, and rs7716600—which were genotyped in Brazilian BC samples in a case-control study. The SNPs rs4415084 and rs7716600 were associated with BC development at higher risk. These SNPs were also associated with progesterone status and lymph node status, respectively. The rs3803662/rs4784227 haplotype GT was associated with BC risk. These genomic alterations were also evaluated in light of the lncRNA’s secondary structure and gain/loss of miRNA binding sites to better understand its biological functions. We emphasize that our bioinformatics approach could find lncRNA-SNPs with a potential biological role in BC development and that lncRNA-SNPs should be more deeply investigated in a highly heterogeneous disease population. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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14 pages, 2161 KiB  
Article
Identification of LncRNAs and Functional Analysis of ceRNA Related to Fatty Acid Synthesis during Flax Seed Development
by Xinsen Yang, Caiyue Liu, Qiaoling Tang, Tianbao Zhang, Limin Wang, Lida Han, Jianping Zhang and Xinwu Pei
Genes 2023, 14(5), 967; https://doi.org/10.3390/genes14050967 - 24 Apr 2023
Cited by 3 | Viewed by 1873
Abstract
Flax is a flowering plant cultivated for its oil and contains various unsaturated fatty acids. Linseed oil is known as the “deep-sea fish oil” of plants, and is beneficial to brain and blood lipids, among other positive effects. Long non-coding RNAs (lncRNAs) play [...] Read more.
Flax is a flowering plant cultivated for its oil and contains various unsaturated fatty acids. Linseed oil is known as the “deep-sea fish oil” of plants, and is beneficial to brain and blood lipids, among other positive effects. Long non-coding RNAs (lncRNAs) play an important role in plant growth and development. There are not many studies assessing how lncRNAs are related to the fatty acid synthesis of flax. The relative oil contents of the seeds of the variety Heiya NO.14 (for fiber) and the variety Macbeth (for oil) were determined at 5 day, 10 day, 20 day, and 30 day after flowering. We found that 10–20 day is an important period for ALA accumulation in the Macbeth variety. The strand-specific transcriptome data were analyzed at these four time points, and a series of lncRNAs related to flax seed development were screened. A competing endogenous RNA (ceRNA) network was constructed and the accuracy of the network was verified using qRT-PCR. MSTRG.20631.1 could act with miR156 on the same target, squamosa promoter-binding-like protein (SPL), to influence fatty acid biosynthesis through a gluconeogenesis-related pathway during flax seed development. This study provides a theoretical basis for future studies assessing the potential functions of lncRNAs during seed development. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 1025 KiB  
Review
Neuroprotective Peptides and New Strategies for Ischemic Stroke Drug Discoveries
by Lyudmila V. Dergunova, Ivan B. Filippenkov, Svetlana A. Limborska and Nikolay F. Myasoedov
Genes 2023, 14(5), 953; https://doi.org/10.3390/genes14050953 - 22 Apr 2023
Cited by 18 | Viewed by 7092
Abstract
Ischemic stroke continues to be one of the leading causes of death and disability in the adult population worldwide. The currently used pharmacological methods for the treatment of ischemic stroke are not effective enough and require the search for new tools and approaches [...] Read more.
Ischemic stroke continues to be one of the leading causes of death and disability in the adult population worldwide. The currently used pharmacological methods for the treatment of ischemic stroke are not effective enough and require the search for new tools and approaches to identify therapeutic targets and potential neuroprotectors. Today, in the development of neuroprotective drugs for the treatment of stroke, special attention is paid to peptides. Namely, peptide action is aimed at blocking the cascade of pathological processes caused by a decrease in blood flow to the brain tissues. Different groups of peptides have therapeutic potential in ischemia. Among them are small interfering peptides that block protein–protein interactions, cationic arginine-rich peptides with a combination of various neuroprotective properties, shuttle peptides that ensure the permeability of neuroprotectors through the blood–brain barrier, and synthetic peptides that mimic natural regulatory peptides and hormones. In this review, we consider the latest achievements and trends in the development of new biologically active peptides, as well as the role of transcriptomic analysis in identifying the molecular mechanisms of action of potential drugs aimed at the treatment of ischemic stroke. Full article
(This article belongs to the Special Issue Genomics of Stroke)
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25 pages, 1912 KiB  
Review
Metabolic Myopathies in the Era of Next-Generation Sequencing
by Jon Andoni Urtizberea, Gianmarco Severa and Edoardo Malfatti
Genes 2023, 14(5), 954; https://doi.org/10.3390/genes14050954 - 22 Apr 2023
Cited by 11 | Viewed by 6668
Abstract
Metabolic myopathies are rare inherited disorders that deserve more attention from neurologists and pediatricians. Pompe disease and McArdle disease represent some of the most common diseases in clinical practice; however, other less common diseases are now better-known. In general the pathophysiology of metabolic [...] Read more.
Metabolic myopathies are rare inherited disorders that deserve more attention from neurologists and pediatricians. Pompe disease and McArdle disease represent some of the most common diseases in clinical practice; however, other less common diseases are now better-known. In general the pathophysiology of metabolic myopathies needs to be better understood. Thanks to the advent of next-generation sequencing (NGS), genetic testing has replaced more invasive investigations and sophisticated enzymatic assays to reach a final diagnosis in many cases. The current diagnostic algorithms for metabolic myopathies have integrated this paradigm shift and restrict invasive investigations for complicated cases. Moreover, NGS contributes to the discovery of novel genes and proteins, providing new insights into muscle metabolism and pathophysiology. More importantly, a growing number of these conditions are amenable to therapeutic approaches such as diets of different kinds, exercise training protocols, and enzyme replacement therapy or gene therapy. Prevention and management—notably of rhabdomyolysis—are key to avoiding serious and potentially life-threatening complications and improving patients’ quality of life. Although not devoid of limitations, the newborn screening programs that are currently mushrooming across the globe show that early intervention in metabolic myopathies is a key factor for better therapeutic efficacy and long-term prognosis. As a whole NGS has largely increased the diagnostic yield of metabolic myopathies, but more invasive but classical investigations are still critical when the genetic diagnosis is unclear or when it comes to optimizing the follow-up and care of these muscular disorders. Full article
(This article belongs to the Special Issue Neuromuscular Disorders: Clinical Treatment and Molecular Genetics)
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24 pages, 1555 KiB  
Review
On the Future Perspectives of Some Medicinal Plants within Lamiaceae Botanic Family Regarding Their Comprehensive Properties and Resistance against Biotic and Abiotic Stresses
by Dan Ioan Avasiloaiei, Mariana Calara, Petre Marian Brezeanu, Otilia Cristina Murariu and Creola Brezeanu
Genes 2023, 14(5), 955; https://doi.org/10.3390/genes14050955 - 22 Apr 2023
Cited by 21 | Viewed by 4188
Abstract
Lamiaceae is one of the largest botanical families, encompassing over 6000 species that include a variety of aromatic and medicinal spices. The current study is focused on three plants within this botanical family: basil (Ocimum basilicum L.), thyme (Thymus vulgaris L.), [...] Read more.
Lamiaceae is one of the largest botanical families, encompassing over 6000 species that include a variety of aromatic and medicinal spices. The current study is focused on three plants within this botanical family: basil (Ocimum basilicum L.), thyme (Thymus vulgaris L.), and summer savory (Satureja hortensis L.). These three species contain primary and secondary metabolites such as phenolic and flavonoid compounds, fatty acids, antioxidants, and essential oils and have traditionally been used for flavoring, food preservation, and medicinal purposes. The goal of this study is to provide an overview of the nutraceutical, therapeutic, antioxidant, and antibacterial key features of these three aromatics to explore new breeding challenges and opportunities for varietal development. In this context, a literature search has been performed to describe the phytochemical profile of both primary and secondary metabolites and their pharmacological uses, as well as to further explore accession availability in the medicine industry and also to emphasize their bioactive roles in plant ecology and biotic and abiotic stress adaptability. The aim of this review is to explore future perspectives on the development of new, highly valuable basil, summer savory, and thyme cultivars. The findings of the current review emphasize the importance of identifying the key compounds and genes involved in stress resistance that can also provide valuable insights for further improvement of these important medicinal plants. Full article
(This article belongs to the Special Issue Phylogenetics, Genetics, and Breeding of Medicinal Plants)
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12 pages, 1531 KiB  
Article
Japanese Flounder pol-miR-155 Is Involved in Edwardsiella tarda Infection via ATG3
by Zhanwei Zhang and Xiaolu Guan
Genes 2023, 14(5), 958; https://doi.org/10.3390/genes14050958 - 22 Apr 2023
Cited by 5 | Viewed by 2026
Abstract
MicroRNAs (miRNAs) are small RNA molecules that function in the post-transcriptionally regulation of the expression of diverse genes, including those involved in immune defense. Edwardsiella tarda can infect a broad range of hosts and cause severe disease in aquatic species, including Japanese flounder [...] Read more.
MicroRNAs (miRNAs) are small RNA molecules that function in the post-transcriptionally regulation of the expression of diverse genes, including those involved in immune defense. Edwardsiella tarda can infect a broad range of hosts and cause severe disease in aquatic species, including Japanese flounder (Paralichthys olivaceus). In this study, we examined the regulation mechanism of a flounder miRNA, pol-miR-155, during the infection of E. tarda. Pol-miR-155 was identified to target flounder ATG3. Overexpression of pol-miR-155 or knockdown of ATG3 expression suppressed autophagy and promoted the intracellular replication of E. tarda in flounder cells. Overexpression of pol-miR-155 activated the NF-κB signaling pathway and further promoted the expression of downstream immune related genes of interleukin (IL)-6 and IL-8. These results unraveled the regulatory effect of pol-miR-155 in autophagy and in E. tarda infection. Full article
(This article belongs to the Special Issue Advances in Genes and Genomics of Aquatic Animals and Pathogens)
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