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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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13 pages, 3956 KiB  
Article
Peanut AhmTERF1 Regulates Root Growth by Modulating Mitochondrial Abundance
by Limei Li, Xiaoyun Li, Chen Yang and Ling Li
Genes 2023, 14(1), 209; https://doi.org/10.3390/genes14010209 - 13 Jan 2023
Cited by 3 | Viewed by 2077
Abstract
Mitochondria are responsible for energy generation, as well as key metabolic and signaling pathways, and thus affect the entire developmental process of plants as well as their responses to stress. In metazoans, mitochondrial transcription termination factors (mTERFs) are known to regulate mitochondrial transcription. [...] Read more.
Mitochondria are responsible for energy generation, as well as key metabolic and signaling pathways, and thus affect the entire developmental process of plants as well as their responses to stress. In metazoans, mitochondrial transcription termination factors (mTERFs) are known to regulate mitochondrial transcription. mTERFs have also been discovered in plants, but only a few of these proteins have been explored for their biological functions. Here, we report a role in root growth for mitochondria-associated protein AhmTERF1 in peanut (Arachis hypogaea L.). Overexpressing AhmTERF1 significantly stimulated the growth of peanut hairy roots and transgenic Arabidopsis. Surprisingly, AhmTERF1 is predominantly expressed in the root meristem where it increases mitochondrial abundance. AhmTERF1 binding to mtDNA was enriched in the RRN18 and RRN26 regions, suggesting it is related to the accumulation of mitochondrial ribosomes. Peanut is one of the main oil crops and the important source of edible oil and AhmTERF1 likely affects agronomic traits related to root growth in different peanut cultivars. We propose that peanut AhmTERF1 is an important protein for root growth due to its role in regulating mitochondrial abundance. Full article
(This article belongs to the Special Issue Genomics and Breeding of Oil Crops)
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12 pages, 3623 KiB  
Article
The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei
by Tianzhe Zhang, Yunan Wang and Hao Song
Genes 2023, 14(1), 210; https://doi.org/10.3390/genes14010210 - 13 Jan 2023
Cited by 1 | Viewed by 2906
Abstract
The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial [...] Read more.
The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs. Full article
(This article belongs to the Special Issue Genetic Evolution of Marine Shellfish)
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12 pages, 373 KiB  
Article
Support Interval for Two-Sample Summary Data-Based Mendelian Randomization
by Kai Wang
Genes 2023, 14(1), 211; https://doi.org/10.3390/genes14010211 - 13 Jan 2023
Cited by 3 | Viewed by 2741
Abstract
The summary-data-based Mendelian randomization (SMR) method is gaining popularity in estimating the causal effect of an exposure on an outcome. In practice, the instrument SNP is often selected from the genome-wide association study (GWAS) on the exposure but no correction is made for [...] Read more.
The summary-data-based Mendelian randomization (SMR) method is gaining popularity in estimating the causal effect of an exposure on an outcome. In practice, the instrument SNP is often selected from the genome-wide association study (GWAS) on the exposure but no correction is made for such selection in downstream analysis, leading to a biased estimate of the effect size and invalid inference. We address this issue by using the likelihood derived from the sampling distribution of the estimated SNP effects in the exposure GWAS and the outcome GWAS. This likelihood takes into account how the instrument SNPs are selected. Since the effective sample size is 1, the asymptotic theory does not apply. We use a support for a profile likelihood as an interval estimate of the causal effect. Simulation studies indicate that this support has robust coverage while the confidence interval implied by the SMR method has lower-than-nominal coverage. Furthermore, the variance of the two-stage least squares estimate of the causal effect is shown to be the same as the variance used for SMR for one-sample data when there is no selection. Full article
(This article belongs to the Topic Big Data in Healthcare, Bioinformatics and Precision Medicine)
(This article belongs to the Section Bioinformatics)
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13 pages, 250 KiB  
Review
Genetic Influences on Fetal Alcohol Spectrum Disorder
by Danielle Sambo and David Goldman
Genes 2023, 14(1), 195; https://doi.org/10.3390/genes14010195 - 12 Jan 2023
Cited by 21 | Viewed by 9605
Abstract
Fetal alcohol spectrum disorder (FASD) encompasses the range of deleterious outcomes of prenatal alcohol exposure (PAE) in the affected offspring, including developmental delay, intellectual disability, attention deficits, and conduct disorders. Several factors contribute to the risk for and severity of FASD, including the [...] Read more.
Fetal alcohol spectrum disorder (FASD) encompasses the range of deleterious outcomes of prenatal alcohol exposure (PAE) in the affected offspring, including developmental delay, intellectual disability, attention deficits, and conduct disorders. Several factors contribute to the risk for and severity of FASD, including the timing, dose, and duration of PAE and maternal factors such as age and nutrition. Although poorly understood, genetic factors also contribute to the expression of FASD, with studies in both humans and animal models revealing genetic influences on susceptibility. In this article, we review the literature related to the genetics of FASD in humans, including twin studies, candidate gene studies in different populations, and genetic testing identifying copy number variants. Overall, these studies suggest different genetic factors, both in the mother and in the offspring, influence the phenotypic outcomes of PAE. While further work is needed, understanding how genetic factors influence FASD will provide insight into the mechanisms contributing to alcohol teratogenicity and FASD risk and ultimately may lead to means for early detection and intervention. Full article
(This article belongs to the Special Issue Genetics and Genomics of Addiction)
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22 pages, 4274 KiB  
Article
Changes in Hox Gene Chromatin Organization during Odontogenic Lineage Specification
by Gokul Gopinathan, Xinmin Zhang, Xianghong Luan and Thomas G. H. Diekwisch
Genes 2023, 14(1), 198; https://doi.org/10.3390/genes14010198 - 12 Jan 2023
Cited by 2 | Viewed by 2610
Abstract
Craniofacial tissues comprise highly evolved organs characterized by a relative lack of expression in the HOX family transcription factors. In the present study, we sought to define the epigenetic events that limit HOX gene expression from undifferentiated neural crest cells to semi-differentiated odontogenic [...] Read more.
Craniofacial tissues comprise highly evolved organs characterized by a relative lack of expression in the HOX family transcription factors. In the present study, we sought to define the epigenetic events that limit HOX gene expression from undifferentiated neural crest cells to semi-differentiated odontogenic progenitors and to explore the effects of elevated levels of HOX. The ChIP-chip data demonstrated high levels of repressive H3K27me3 marks on the HOX gene promoters in ES and cranial neural crest cells when compared to the H3K4me3 marks, while the K4/K27 ratio was less repressive in the odontogenic progenitors, dental follicle, dental pulp, periodontal ligament fibroblasts, alveolar bone osteoblasts, and cementoblasts. The gene expression of multiple HOX genes, especially those from the HOXA and HOXB clusters, was significantly elevated and many times higher in alveolar bone cells than in the dental follicle cells. In addition, the HOX levels in the skeletal osteoblasts were many times higher in the trunk osteoblasts compared to the alveolar bone osteoblasts, and the repressive mark H3K27me3 promoter occupancy was substantially and significantly elevated in the alveolar bone osteoblasts when compared to the trunk osteoblasts. To explore the effect of elevated HOX levels in craniofacial neural crest cells, HOX expression was induced by transfecting cells with the Cdx4 transcription factor, resulting in a significant decrease in the mineralization markers, RUNX2, OSX, and OCN upon HOX elevation. Promoting HOX gene expression in developing teeth using the small molecule EZH2 inhibitor GSK126 resulted in an increased number of patterning events, supernumerary cusp formation, and increased Hoxa4 and Hoxb6 gene expression when compared to the controls. Together, these studies illustrate the profound effects of epigenetic regulatory events at all stages of the differentiation of craniofacial peripheral tissues from the neural crest, including lineage specification, tissue differentiation, and patterning. Full article
(This article belongs to the Special Issue Chromatin Organization in Cell Differentiation)
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15 pages, 7218 KiB  
Article
Genome-Wide Analysis of Aquaporin Gene Family in Triticum turgidum and Its Expression Profile in Response to Salt Stress
by Mahnaz Yaghobi and Parviz Heidari
Genes 2023, 14(1), 202; https://doi.org/10.3390/genes14010202 - 12 Jan 2023
Cited by 43 | Viewed by 3496
Abstract
During the response of plants to water stresses, aquaporin (AQP) plays a prominent role in membrane water transport based on the received upstream signals. Due to the importance of the AQP gene family, studies have been conducted that investigate the function and regulatory [...] Read more.
During the response of plants to water stresses, aquaporin (AQP) plays a prominent role in membrane water transport based on the received upstream signals. Due to the importance of the AQP gene family, studies have been conducted that investigate the function and regulatory system of these genes. However, many of their molecular aspects are still unknown. This study aims to carry out a genome-wide investigation of the AQP gene family in Triticum turgidum using bioinformatics tools and to investigate the expression patterns of some members in response to salt stress. Our results show that there are 80 TtAQP genes in T. turgidum, which are classified into four main groups based on phylogenetic analysis. Several duplications were observed between the members of the TtAQP gene family, and high diversity in response to post-translational modifications was observed between TtAQP family members. The expression pattern of TtAQP genes disclosed that these genes are primarily upregulated in response to salt stress. Additionally, the qPCR data revealed that TtAQPs are more induced in delayed responses to salinity stress. Overall, our findings illustrate that TtAQP members are diverse in terms of their structure, regulatory systems, and expression levels. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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10 pages, 1476 KiB  
Hypothesis
How Can CpG Methylations, and Pair-to-Pair Correlations between the Main (Gene) and the Opposite Strands, Suggest a Bending DNA Loop: Insights into the 5′-UTR of DAT1
by Vincenza Di Paola, Martina Morrone, Valentina Poli, Andrea Fuso, Esterina Pascale and Walter Adriani
Genes 2023, 14(1), 190; https://doi.org/10.3390/genes14010190 - 11 Jan 2023
Cited by 1 | Viewed by 1884
Abstract
A working hypothesis issues from patterns of methylation in the 5′-UTR of the DAT1 gene. We considered relationships between pairs of CpGs, of which one on the main-gene strand and another on the complementary opposite strand (COS). We elaborated on data from ADHD [...] Read more.
A working hypothesis issues from patterns of methylation in the 5′-UTR of the DAT1 gene. We considered relationships between pairs of CpGs, of which one on the main-gene strand and another on the complementary opposite strand (COS). We elaborated on data from ADHD children: we calculated all possible combinations of probabilities (estimated by multiplying two raw values of methylation) in pairs of CpGs from either strand. We analyzed all correlations between any given pair and all other pairs. For pairs correlating with M6-M6COS, some pairs had cytosines positioning to the reciprocal right (e.g., M3-M2COS and M6-M5COS), other pairs had cytosines positioning to the reciprocal left (e.g., M2-M3COS; M5-M6COS). Significant pair-to-pair correlations emerged between main-strand and COS CpG pairs. Through graphic representations, we hypothesized that DNA folded to looping conformations: the C1GG C2GG C3GG and C5G C6G motifs would become close enough to allow cytosines 1-2-3 to interact with cytosines 5-6 (on both strands). Data further suggest a sliding, with left- and right-ward oscillations of DNA strands. While thorough empirical verification is needed, we hypothesize simultaneous methylation of main-strand and COS DNA (“methylation dynamics”) to serve as a promising biomarker. Full article
(This article belongs to the Special Issue Genetic Basis of Stress-Related Neuropsychiatric Disorders)
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12 pages, 2225 KiB  
Article
Small Body, Large Chromosomes: Centric Fusions Shaped the Karyotype of the Amazonian Miniature Fish Nannostomus anduzei (Characiformes, Lebiasinidae)
by Renata Luiza Rosa de Moraes, Francisco de Menezes Cavalcante Sassi, Manoela Maria Ferreira Marinho, Petr Ráb, Jorge Ivan Rebelo Porto, Eliana Feldberg and Marcelo de Bello Cioffi
Genes 2023, 14(1), 192; https://doi.org/10.3390/genes14010192 - 11 Jan 2023
Cited by 1 | Viewed by 2333
Abstract
Miniature refers to species with extraordinarily small adult body size when adult and can be found within all major metazoan groups. It is considered that miniature species have experienced severe alteration of numerous morphological traits during evolution. For a variety of reasons, including [...] Read more.
Miniature refers to species with extraordinarily small adult body size when adult and can be found within all major metazoan groups. It is considered that miniature species have experienced severe alteration of numerous morphological traits during evolution. For a variety of reasons, including severe labor concerns during collecting, chromosomal acquisition, and taxonomic issues, miniature fishes are neglected and understudied. Since some available studies indicate possible relationship between diploid chromosome number (2n) and body size in fishes, we aimed to study one of the smallest Neotropical fish Nannostomus anduzei (Teleostei, Characiformes, Lebiasinidae), using both conventional (Giemsa staining, C-banding) and molecular cytogenetic methods (FISH mapping of rDNAs, microsatellites, and telomeric sequences). Our research revealed that N. anduzei possesses one of the lowest diploid chromosome numbers (2n = 22) among teleost fishes, and its karyotype is entirely composed of large metacentric chromosomes. All chromosomes, except for pair number 11, showed an 18S rDNA signal in the pericentromeric region. 5S rDNA signals were detected in the pericentromeric regions of chromosome pair number 1 and 6, displaying synteny to 18S rDNA signals. Interstitial telomeric sites (ITS) were identified in the centromeric region of pairs 6 and 8, indicating that centric fusions played a significant role in karyotype evolution of studied species. Our study provides further evidence supporting the trend of diploid chromosome number reduction along with miniaturization of adult body size in fishes. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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18 pages, 341 KiB  
Article
Vitamin D Receptor Gene Polymorphisms Affect Osteoporosis-Related Traits and Response to Antiresorptive Therapy
by Vladimira Mondockova, Veronika Kovacova, Nina Zemanova, Martina Babikova, Monika Martiniakova, Drahomir Galbavy and Radoslav Omelka
Genes 2023, 14(1), 193; https://doi.org/10.3390/genes14010193 - 11 Jan 2023
Cited by 13 | Viewed by 2902
Abstract
The present study analyzed the effect of vitamin D receptor (VDR) gene polymorphisms (ApaI, TaqI, BsmI, FokI, and Cdx2) on bone mineral density (BMD), biochemical parameters and bone turnover markers, fracture prevalence, and response to three types of antiresorptive therapy (estrogen-progesterone, [...] Read more.
The present study analyzed the effect of vitamin D receptor (VDR) gene polymorphisms (ApaI, TaqI, BsmI, FokI, and Cdx2) on bone mineral density (BMD), biochemical parameters and bone turnover markers, fracture prevalence, and response to three types of antiresorptive therapy (estrogen-progesterone, raloxifene, and ibandronate) in 356 postmenopausal women from Slovakia. Association analysis revealed a significant effect of BsmI polymorphism on lumbar spine BMD, serum osteocalcin (OC), and β-CrossLaps levels. While ApaI and Cdx2 polymorphisms were associated with OC and alkaline phosphatase, TaqI polymorphism affected all turnover markers. ApaI, TaqI, and BsmI genotypes increased the risk of spinal, radial, or total fractures with odds ratios ranging from 2.03 to 3.17. Each of therapy types evaluated had a beneficial effect on all osteoporosis-related traits; however, the VDR gene affected only ibandronate and raloxifene treatment. ApaI/aa, TaqI/TT, and BsmI/bb genotypes showed a weaker or no response to ibandronate therapy in femoral and spinal BMD. The impact of aforementioned polymorphisms on turnover markers was also genotype dependent. On the contrary, only TaqI and BsmI polymorphisms influenced raloxifene therapy, even only in lumbar spine BMD. These results point to the potential of using the VDR gene in personalized pharmacotherapy of osteoporosis. Full article
(This article belongs to the Special Issue Genetics of Complex Human Disease)
18 pages, 5344 KiB  
Article
Wide-Range Portrayal of AP2/ERF Transcription Factor Family in Maize (Zea mays L.) Development and Stress Responses
by Cheng Cheng, Likun An, Fangzhe Li, Wahaj Ahmad, Muhammad Aslam, Muhammad Zia Ul Haq, Yuanxin Yan and Ramala Masood Ahmad
Genes 2023, 14(1), 194; https://doi.org/10.3390/genes14010194 - 11 Jan 2023
Cited by 24 | Viewed by 4275
Abstract
The APETALA2/Ethylene-Responsive Transcriptional Factors containing conservative AP2/ERF domains constituted a plant-specific transcription factor (TF) superfamily, called AP2/ERF. The configuration of the AP2/ERF superfamily in maize has remained unresolved. In this study, we identified the 229 AP2/ERF genes in the [...] Read more.
The APETALA2/Ethylene-Responsive Transcriptional Factors containing conservative AP2/ERF domains constituted a plant-specific transcription factor (TF) superfamily, called AP2/ERF. The configuration of the AP2/ERF superfamily in maize has remained unresolved. In this study, we identified the 229 AP2/ERF genes in the latest (B73 RefGen_v5) maize reference genome. Phylogenetic classification of the ZmAP2/ERF family members categorized it into five clades, including 27 AP2 (APETALA2), 5 RAV (Related to ABI3/VP), 89 DREB (dehydration responsive element binding), 105 ERF (ethylene responsive factors), and a soloist. The duplication events of the paralogous genes occurred from 1.724–25.855 MYA, a key route to maize evolution. Structural analysis reveals that they have more introns and few exons. The results showed that 32 ZmAP2/ERFs regulate biotic stresses, and 24 ZmAP2/ERFs are involved in responses towards abiotic stresses. Additionally, the expression analysis showed that DREB family members are involved in plant sex determination. The real-time quantitative expression profiling of ZmAP2/ERFs in the leaves of the maize inbred line B73 under ABA, JA, salt, drought, heat, and wounding stress revealed their specific expression patterns. Conclusively, this study unveiled the evolutionary pathway of ZmAP2/ERFs and its essential role in stress and developmental processes. The generated information will be useful for stress resilience maize breeding programs. Full article
(This article belongs to the Special Issue Genome-Wide Identifications: Recent Trends in Genomic Studies)
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11 pages, 298 KiB  
Article
Generating Minimal Models of H1N1 NS1 Gene Sequences Using Alignment-Based and Alignment-Free Algorithms
by Meng Fang, Jiawei Xu, Nan Sun and Stephen S.-T. Yau
Genes 2023, 14(1), 186; https://doi.org/10.3390/genes14010186 - 10 Jan 2023
Cited by 1 | Viewed by 1587
Abstract
For virus classification and tracing, one idea is to generate minimal models from the gene sequences of each virus group for comparative analysis within and between classes, as well as classification and tracing of new sequences. The starting point of defining a minimal [...] Read more.
For virus classification and tracing, one idea is to generate minimal models from the gene sequences of each virus group for comparative analysis within and between classes, as well as classification and tracing of new sequences. The starting point of defining a minimal model for a group of gene sequences is to find their longest common sequence (LCS), but this is a non-deterministic polynomial-time hard (NP-hard) problem. Therefore, we applied some heuristic approaches of finding LCS, as well as some of the newer methods of treating gene sequences, including multiple sequence alignment (MSA) and k-mer natural vector (NV) encoding. To evaluate our algorithms, a five-fold cross validation classification scheme on a dataset of H1N1 virus non-structural protein 1 (NS1) gene was analyzed. The results indicate that the MSA-based algorithm has the best performance measured by classification accuracy, while the NV-based algorithm exhibits advantages in the time complexity of generating minimal models. Full article
(This article belongs to the Special Issue Statistical Methods for Genetic Epidemiology)
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20 pages, 980 KiB  
Review
Genetic Diversity, Conservation, and Utilization of Plant Genetic Resources
by Romesh Kumar Salgotra and Bhagirath Singh Chauhan
Genes 2023, 14(1), 174; https://doi.org/10.3390/genes14010174 - 9 Jan 2023
Cited by 240 | Viewed by 36142
Abstract
Plant genetic resources (PGRs) are the total hereditary material, which includes all the alleles of various genes, present in a crop species and its wild relatives. They are a major resource that humans depend on to increase farming resilience and profit. Hence, the [...] Read more.
Plant genetic resources (PGRs) are the total hereditary material, which includes all the alleles of various genes, present in a crop species and its wild relatives. They are a major resource that humans depend on to increase farming resilience and profit. Hence, the demand for genetic resources will increase as the world population increases. There is a need to conserve and maintain the genetic diversity of these valuable resources for sustainable food security. Due to environmental changes and genetic erosion, some valuable genetic resources have already become extinct. The landraces, wild relatives, wild species, genetic stock, advanced breeding material, and modern varieties are some of the important plant genetic resources. These diverse resources have contributed to maintaining sustainable biodiversity. New crop varieties with desirable traits have been developed using these resources. Novel genes/alleles linked to the trait of interest are transferred into the commercially cultivated varieties using biotechnological tools. Diversity should be maintained as a genetic resource for the sustainable development of new crop varieties. Additionally, advances in biotechnological tools, such as next-generation sequencing, molecular markers, in vitro culture technology, cryopreservation, and gene banks, help in the precise characterization and conservation of rare and endangered species. Genomic tools help in the identification of quantitative trait loci (QTLs) and novel genes in plants that can be transferred through marker-assisted selection and marker-assisted backcrossing breeding approaches. This article focuses on the recent development in maintaining the diversity of genetic resources, their conservation, and their sustainable utilization to secure global food security. Full article
(This article belongs to the Special Issue Genetic Diversity, Conservation and Utilization of Plant Genetic Resources)
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13 pages, 294 KiB  
Article
Association between Genetic Variants and Peripheral Neuropathy in Patients with NSCLC Treated with First-Line Platinum-Based Therapy
by Corine de Jong, Gerarda J. M. Herder, Simone W. A. van Haarlem, Femke S. van der Meer, Anne S. R. van Lindert, Alexandra ten Heuvel, Jan Brouwer, Toine C. G. Egberts and Vera H. M. Deneer
Genes 2023, 14(1), 170; https://doi.org/10.3390/genes14010170 - 7 Jan 2023
Cited by 5 | Viewed by 2491
Abstract
Background: Chemotherapy-induced peripheral neuropathy (CIPN) is a common, disabling side effect in non-small cell lung cancer (NSCLC) patients treated with platinum-based therapy. There is increasing evidence for associations between genetic variants and susceptibility to CIPN. The aim of this study was to further [...] Read more.
Background: Chemotherapy-induced peripheral neuropathy (CIPN) is a common, disabling side effect in non-small cell lung cancer (NSCLC) patients treated with platinum-based therapy. There is increasing evidence for associations between genetic variants and susceptibility to CIPN. The aim of this study was to further explore genetic risk factors for CIPN by investigating previously reported genetic associations. Methods: A multicenter prospective follow-up study (PGxLUNG, NTR NL5373610015) in NSCLC patients (stage II-IV) treated with first-line platinum-based (cisplatin or carboplatin) chemotherapy was conducted. Clinical evaluation of neuropathy (CTCAE v4.03) was performed at baseline and before each cycle (four cycles, every three weeks) of chemotherapy and at three and six months after treatment initiation. The relationship between 34 single nucleotide polymorphisms (SNPs) in 26 genes and any grade (grade ≥ 1) and severe (grade ≥ 2) CIPN was assessed by using univariate and multivariate logistic regression modelling. Results: In total, 320 patients were included of which 26.3% (n = 84) and 8.1% (n = 26) experienced any grade and severe CIPN, respectively. The GG-genotype (rs879207, A > G) of TRPV1, a gene expressed in peripheral sensory neurons, was observed in 11.3% (n = 36) of the patients and associated with an increased risk of severe neuropathy (OR 5.2, 95%CI 2.1–12.8, adjusted p-value 0.012). A quarter (25%, n = 9/36) of the patients with the GG-genotype developed severe neuropathy compared to 6% (n = 17/282) of the patients with the AG- or AA-genotype. Multivariate logistic regression analysis showed statistically significant associations between the GG-genotype (ORadj 4.7, 95%CI 1.8–12.3) and between concomitant use of paclitaxel (ORadj 7.2, 95%CI 2.5–21.1) and severe CIPN. Conclusions: Patients with the GG-genotype (rs879207) of TRPV1 have an almost 5-fold higher risk of developing severe neuropathy when treated with platinum-based therapy. Future studies should aim to validate these findings in an independent cohort and to further investigated the individualization of platinum-based chemotherapy in clinical practice. Full article
(This article belongs to the Section Pharmacogenetics)
13 pages, 2503 KiB  
Article
Gathering the Stakeholder’s Perspective: Experiences and Opportunities in Rare Genetic Disease Research
by Lauren K. White, T. Blaine Crowley, Brenda Finucane, Emily J. McClellan, Sarah Donoghue, Sixto Garcia-Minaur, Gabriela M. Repetto, Matthias Fischer, Sebastien Jacquemont, Raquel E. Gur, Anne M. Maillard, Kirsten A. Donald, Anne S. Bassett, Ann Swillen and Donna M. McDonald-McGinn
Genes 2023, 14(1), 169; https://doi.org/10.3390/genes14010169 - 7 Jan 2023
Cited by 2 | Viewed by 2338
Abstract
Background: Research participant feedback is rarely collected; therefore, investigators have limited understanding regarding stakeholders’ (affected individuals/caregivers) motivation to participate. Members of the Genes to Mental Health Network (G2MH) surveyed stakeholders affected by copy number variants (CNVs) regarding perceived incentives for study participation, opinions [...] Read more.
Background: Research participant feedback is rarely collected; therefore, investigators have limited understanding regarding stakeholders’ (affected individuals/caregivers) motivation to participate. Members of the Genes to Mental Health Network (G2MH) surveyed stakeholders affected by copy number variants (CNVs) regarding perceived incentives for study participation, opinions concerning research priorities, and the necessity for future funding. Respondents were also asked about feelings of preparedness, research burden, and satisfaction with research study participation. Methods: Modified validated surveys were used to assess stakeholders´ views across three domains: (1) Research Study Enrollment, Retainment, Withdrawal, and Future Participation; (2) Overall Research Experience, Burden, and Preparedness; (3) Research Priorities and Obstacles. Top box score analyses were performed. Results: A total of 704 stakeholders´ responded from 29 countries representing 55 CNVs. The top reasons for initial participation in the research included reasons related to education and altruism. The top reasons for leaving a research study included treatment risks and side effects. The importance of sharing research findings and laboratory results with stakeholders was underscored by participants. Most stakeholders reported positive research experiences. Conclusions: This study provides important insight into how individuals and families affected with a rare CNV feel toward research participation and their overall experience in rare disease research. There are clear targets for areas of improvement for study teams, although many stakeholders reported positive research experiences. Key findings from this international survey may help advance collaborative research and improve the experience of participants, investigators, and other stakeholders moving forward. Full article
(This article belongs to the Special Issue 22q11.2 Deletion Syndrome)
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20 pages, 2309 KiB  
Article
Prenatal Screening and Diagnostic Considerations for 22q11.2 Microdeletions
by Natalie Blagowidow, Beata Nowakowska, Erica Schindewolf, Francesca Romana Grati, Carolina Putotto, Jeroen Breckpot, Ann Swillen, Terrence Blaine Crowley, Joanne C. Y. Loo, Lauren A. Lairson, Sólveig Óskarsdóttir, Erik Boot, Sixto Garcia-Minaur, Maria Cristina Digilio, Bruno Marino, Beverly Coleman, Julie S. Moldenhauer, Anne S. Bassett and Donna M. McDonald-McGinn
Genes 2023, 14(1), 160; https://doi.org/10.3390/genes14010160 - 6 Jan 2023
Cited by 19 | Viewed by 10155
Abstract
Diagnosis of a chromosome 22q11.2 microdeletion and its associated deletion syndrome (22q11.2DS) is optimally made early. We reviewed the available literature to provide contemporary guidance and recommendations related to the prenatal period. Indications for prenatal diagnostic testing include a parent or child with [...] Read more.
Diagnosis of a chromosome 22q11.2 microdeletion and its associated deletion syndrome (22q11.2DS) is optimally made early. We reviewed the available literature to provide contemporary guidance and recommendations related to the prenatal period. Indications for prenatal diagnostic testing include a parent or child with the 22q11.2 microdeletion or suggestive prenatal screening results. Definitive diagnosis by genetic testing of chorionic villi or amniocytes using a chromosomal microarray will detect clinically relevant microdeletions. Screening options include noninvasive prenatal screening (NIPS) and imaging. The potential benefits and limitations of each screening method should be clearly conveyed. NIPS, a genetic option available from 10 weeks gestational age, has a 70–83% detection rate and a 40–50% PPV for most associated 22q11.2 microdeletions. Prenatal imaging, usually by ultrasound, can detect several physical features associated with 22q11.2DS. Findings vary, related to detection methods, gestational age, and relative specificity. Conotruncal cardiac anomalies are more strongly associated than skeletal, urinary tract, or other congenital anomalies such as thymic hypoplasia or cavum septi pellucidi dilatation. Among others, intrauterine growth restriction and polyhydramnios are additional associated, prenatally detectable signs. Preconception genetic counselling should be offered to males and females with 22q11.2DS, as there is a 50% risk of transmission in each pregnancy. A previous history of a de novo 22q11.2 microdeletion conveys a low risk of recurrence. Prenatal genetic counselling includes an offer of screening or diagnostic testing and discussion of results. The goal is to facilitate optimal perinatal care. Full article
(This article belongs to the Special Issue 22q11.2 Deletion Syndrome)
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13 pages, 14918 KiB  
Article
Do Noncoding and Coding Sites in Angiosperm Chloroplast DNA Have Different Mutation Processes?
by Brian R. Morton
Genes 2023, 14(1), 148; https://doi.org/10.3390/genes14010148 - 5 Jan 2023
Cited by 1 | Viewed by 1967
Abstract
Fourfold degenerate sites within coding regions and intergenic sites have both been used as estimates of neutral evolution. In chloroplast DNA, the pattern of substitution at intergenic sites is strongly dependent on the composition of the surrounding hexanucleotide composed of the three base [...] Read more.
Fourfold degenerate sites within coding regions and intergenic sites have both been used as estimates of neutral evolution. In chloroplast DNA, the pattern of substitution at intergenic sites is strongly dependent on the composition of the surrounding hexanucleotide composed of the three base pairs on each side, which suggests that the mutation process is highly context-dependent in this genome. This study examines the context-dependency of substitutions at fourfold degenerate sites in protein-coding regions and compares the pattern to what has been observed at intergenic sites. Overall, there is strong similarity between the two types of sites, but there are some intriguing differences. One of these is that substitutions of G and C are significantly higher at fourfold degenerate sites across a range of contexts. In fact, A → T and T → A substitutions are the only substitution types that occur at a lower rate at fourfold degenerate sites. The data are not consistent with selective constraints being responsible for the difference in substitution patterns between intergenic and fourfold degenerate sites. Rather, it is suggested that the difference may be a result of different epigenetic modifications that result in slightly different mutation patterns in coding and intergenic DNA. Full article
(This article belongs to the Special Issue Plant Plastid Genome)
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14 pages, 2776 KiB  
Article
Analysis of CAT Gene Family and Functional Identification of OsCAT3 in Rice
by Wenxiang Jiang, Qing Ye, Zheng Wu, Qiuyun Zhang, Lianhong Wang, Jialin Liu, Xiafei Hu, Dandan Guo, Xiaoqing Wang, Zelin Zhang, Haohua He and Lifang Hu
Genes 2023, 14(1), 138; https://doi.org/10.3390/genes14010138 - 4 Jan 2023
Cited by 20 | Viewed by 4443
Abstract
Catalase (CAT) is an important antioxidant enzyme in plants that plays a key role in plant growth and stress responses. CAT is usually encoded by a small gene family that has been cloned and functionally studied in some species, such as Arabidopsis, [...] Read more.
Catalase (CAT) is an important antioxidant enzyme in plants that plays a key role in plant growth and stress responses. CAT is usually encoded by a small gene family that has been cloned and functionally studied in some species, such as Arabidopsis, wheat and cucumber, but its specific roles in rice are not clear at present. In this study, we identified three CAT family genes (OsCAT1, OsCAT2 and OsCAT3) in the rice genome and performed a systematic bioinformatics analysis. RT−PCR analysis revealed that OsCAT1–OsCAT3 was primarily expressed in vegetative tissues such as roots, stems and leaves. Since OsCAT3 showed the highest expression level among the three OsCAT genes, we then focused on its related functions. OsCAT3 prokaryotic expression protein has an obvious ability to remove H2O2. The OsCAT3crispr plant was short and had a low survival rate, the leaves were small with brown lesions, and the activities of the CAT, POD and SOD enzymes were significantly reduced. A microarray analysis showed that differentially expressed genes were primarily enriched in toxin metabolism and photosynthesis. This study laid a foundation for further understanding the function of the rice OsCAT gene. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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20 pages, 1622 KiB  
Review
Interacting Networks of the Hypothalamic–Pituitary–Ovarian Axis Regulate Layer Hens Performance
by Jinbo Zhao, Hongbin Pan, Yong Liu, Yang He, Hongmei Shi and Changrong Ge
Genes 2023, 14(1), 141; https://doi.org/10.3390/genes14010141 - 4 Jan 2023
Cited by 21 | Viewed by 4390
Abstract
Egg production is a vital biological and economic trait for poultry breeding. The ‘hypothalamic–pituitary–ovarian (HPO) axis’ determines the egg production, which affects the layer hens industry income. At the organism level, the HPO axis is influenced by the factors related to metabolic and [...] Read more.
Egg production is a vital biological and economic trait for poultry breeding. The ‘hypothalamic–pituitary–ovarian (HPO) axis’ determines the egg production, which affects the layer hens industry income. At the organism level, the HPO axis is influenced by the factors related to metabolic and nutritional status, environment, and genetics, whereas at the cellular and molecular levels, the HPO axis is influenced by the factors related to endocrine and metabolic regulation, cytokines, key genes, signaling pathways, post-transcriptional processing, and epigenetic modifications. MiRNAs and lncRNAs play a critical role in follicle selection and development, atresia, and ovulation in layer hens; in particular, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells. The current review elaborates on the regulation of the HPO axis and its role in the laying performance of hens at the organism, cellular, and molecular levels. In addition, this review provides an overview of the interactive network regulation mechanism of the HPO axis in layer hens, as well as comprehensive knowledge for successfully utilizing their genetic resources. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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12 pages, 304 KiB  
Review
Interaction between Boron and Other Elements in Plants
by Ying Long and Jiashi Peng
Genes 2023, 14(1), 130; https://doi.org/10.3390/genes14010130 - 3 Jan 2023
Cited by 41 | Viewed by 7733
Abstract
Boron (B) is an essential mineral nutrient for growth of plants, and B deficiency is now a worldwide problem that limits production of B deficiency-sensitive crops, such as rape and cotton. Agronomic practice has told that balanced B and other mineral nutrient fertilizer [...] Read more.
Boron (B) is an essential mineral nutrient for growth of plants, and B deficiency is now a worldwide problem that limits production of B deficiency-sensitive crops, such as rape and cotton. Agronomic practice has told that balanced B and other mineral nutrient fertilizer applications is helpful to promote crop yield. In recent years, much research has reported that applying B can also reduce the accumulation of toxic elements such as cadmium and aluminum in plants and alleviate their toxicity symptoms. Therefore, the relation between B and other elements has become an interesting issue for plant nutritionists. Here we summarize the research progress of the interaction between B and macronutrients such as nitrogen, phosphorus, calcium, potassium, magnesium, and sulfur, essential micronutrients such as iron, manganese, zinc, copper, and molybdenum, and beneficial elements such as sodium, selenium, and silicon. Moreover, the interaction between B and toxic elements such as cadmium and aluminum, which pose a serious threat to agriculture, is also discussed in this paper. Finally, the possible physiological mechanisms of the interaction between B and other elements in plants is reviewed. We propose that the cell wall is an important intermediary between interaction of B and other elements, and competitive inhibition of elements and related signal transduction pathways also play a role. Currently, research on the physiological role of B in plants mainly focuses on its involvement in the structure and function of cell walls, and our understanding of the details for interactions between B and other elements also tend to relate to the cell wall. However, we know little about the metabolic process of B inside cells, including its interactions with other elements. More research is needed to address the aforementioned research questions in future. Full article
(This article belongs to the Special Issue Signal Transduction Pathway in Plants)
13 pages, 3023 KiB  
Article
Transcriptomic Profiling Reveals an Enhancer RNA Signature for Recurrence Prediction in Colorectal Cancer
by Divya Sahu, Chen-Ching Lin and Ajay Goel
Genes 2023, 14(1), 137; https://doi.org/10.3390/genes14010137 - 3 Jan 2023
Cited by 1 | Viewed by 2497
Abstract
Background: Colorectal cancer (CRC) is one of the most fatal malignancies worldwide, and this is in part due to high rates of tumor recurrence in these patients. Currently, TNM staging remains the gold standard for predicting prognosis and recurrence in CRC patients; however, [...] Read more.
Background: Colorectal cancer (CRC) is one of the most fatal malignancies worldwide, and this is in part due to high rates of tumor recurrence in these patients. Currently, TNM staging remains the gold standard for predicting prognosis and recurrence in CRC patients; however, this approach is inadequate for identifying high-risk patients with the highest likelihood of disease recurrence. Recent evidence has revealed that enhancer RNAs (eRNAs) represent a higher level of cellular regulation, and their expression is frequently dysregulated in several cancers, including CRC. However, the clinical significance of eRNAs as recurrence predictor biomarkers in CRC remains unexplored, which is the primary aim of this study. Results: We performed a systematic analysis of eRNA expression profiles in colon cancer (CC) and rectal cancer (RC) patients from the TCGA dataset. By using rigorous biomarker discovery approaches by splitting the entire dataset into a training and testing cohort, we identified a 22-eRNA panel in CC and a 19-eRNA panel in RC for predicting tumor recurrence. The Kaplan–Meier analysis showed that biomarker panels robustly stratified low and high-risk CC (p = 7.29 × 10−5) and RC (p = 6.81 × 10−3) patients with recurrence. Multivariate and LASSO Cox regression models indicated that both biomarker panels were independent predictors of recurrence and significantly superior to TNM staging in CC (HR = 11.89, p = 9.54 × 10−4) and RC (HR = 3.91, p = 3.52 × 10−2). Notably, the ROC curves demonstrated that both panels exhibited excellent recurrence prediction accuracy in CC (AUC = 0.833; 95% CI: 0.74–0.93) and RC (AUC = 0.834; 95% CI: 0.72–0.92) patients. Subsequently, a combination signature that included the eRNA panels and TNM staging achieved an even greater predictive accuracy in patients with CC (AUC = 0.85). Conclusions: Herein, we report a novel eRNA signature for predicting recurrence in patients with CRC. Further experimental validation in independent clinical cohorts, these biomarkers can potentially improve current risk stratification approaches for guiding precision oncology treatments in patients suffering from this lethal malignancy. Full article
(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2023)
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21 pages, 6313 KiB  
Article
An Aggrephagy-Related LncRNA Signature for the Prognosis of Pancreatic Adenocarcinoma
by Xueyuan Huang, Hao Chi, Siqi Gou, Xiyuan Guo, Lin Li, Gaoge Peng, Jinhao Zhang, Jiayu Xu, Siji Nian and Qing Yuan
Genes 2023, 14(1), 124; https://doi.org/10.3390/genes14010124 - 2 Jan 2023
Cited by 37 | Viewed by 3450
Abstract
Pancreatic adenocarcinoma (PAAD) is a common, highly malignant, and aggressive gastrointestinal tumor. The conventional treatment of PAAD shows poor results, and patients have poor prognosis. The synthesis and degradation of proteins are essential for the occurrence and development of tumors. Aggrephagy is a [...] Read more.
Pancreatic adenocarcinoma (PAAD) is a common, highly malignant, and aggressive gastrointestinal tumor. The conventional treatment of PAAD shows poor results, and patients have poor prognosis. The synthesis and degradation of proteins are essential for the occurrence and development of tumors. Aggrephagy is a type of autophagy that selectively degrades aggregated proteins. It decreases the formation of aggregates by degrading proteins, thus reducing the harm to cells. By breaking down proteins, it decreases the formation of aggregates; thus, minimizing damage to cells. For evaluating the response to immunotherapy and prognosis in PAAD patients, in this study, we developed a reliable signature based on aggrephagy-related genes (ARGs). We obtained 298 AGGLncRNAs. Based on the results of one-way Cox and LASSO analyses, the lncRNA signature was constructed. In the risk model, the prognosis of patients in the low-risk group was noticeably better than that of the patients in the high-risk group. Additionally, the ROC curves and nomograms validated the capacity of the risk model to predict the prognosis of PAAD. The patients in the low-risk and high-risk groups showed considerable variations in functional enrichment and immunological analysis. Regarding drug sensitivity, the low-risk and high-risk groups had different half-maximal inhibitory concentrations (IC50). Full article
(This article belongs to the Special Issue Bioinformatics and Genetics of Human Diseases)
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19 pages, 1506 KiB  
Review
Recent Advances in Genome-Engineering Strategies
by Michaela A. Boti, Konstantina Athanasopoulou, Panagiotis G. Adamopoulos, Diamantis C. Sideris and Andreas Scorilas
Genes 2023, 14(1), 129; https://doi.org/10.3390/genes14010129 - 2 Jan 2023
Cited by 23 | Viewed by 6446
Abstract
In October 2020, the chemistry Nobel Prize was awarded to Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of a new promising genome-editing tool: the genetic scissors of CRISPR-Cas9. The identification of CRISPR arrays and the subsequent identification of cas genes, which [...] Read more.
In October 2020, the chemistry Nobel Prize was awarded to Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of a new promising genome-editing tool: the genetic scissors of CRISPR-Cas9. The identification of CRISPR arrays and the subsequent identification of cas genes, which together represent an adaptive immunological system that exists not only in bacteria but also in archaea, led to the development of diverse strategies used for precise DNA editing, providing new insights in basic research and in clinical practice. Due to their advantageous features, the CRISPR-Cas systems are already employed in several biological and medical research fields as the most suitable technique for genome engineering. In this review, we aim to describe the CRISPR-Cas systems that have been identified among prokaryotic organisms and engineered for genome manipulation studies. Furthermore, a comprehensive comparison between the innovative CRISPR-Cas methodology and the previously utilized ZFN and TALEN editing nucleases is also discussed. Ultimately, we highlight the contribution of CRISPR-Cas methodology in modern biomedicine and the current plethora of available applications for gene KO, repression and/or overexpression, as well as their potential implementation in therapeutical strategies that aim to improve patients’ quality of life. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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20 pages, 1685 KiB  
Review
Transgenerational Epigenetic Inheritance of Traumatic Experience in Mammals
by Jana Švorcová
Genes 2023, 14(1), 120; https://doi.org/10.3390/genes14010120 - 1 Jan 2023
Cited by 21 | Viewed by 16889
Abstract
In recent years, we have seen an increasing amount of evidence pointing to the existence of a non-genetic heredity of the effects of events such as separation from parents, threat to life, or other traumatising experiences such as famine. This heredity is often [...] Read more.
In recent years, we have seen an increasing amount of evidence pointing to the existence of a non-genetic heredity of the effects of events such as separation from parents, threat to life, or other traumatising experiences such as famine. This heredity is often mediated by epigenetic regulations of gene expression and may be transferred even across several generations. In this review, we focus on studies which involve transgenerational epigenetic inheritance (TEI), with a short detour to intergenerational studies focused on the inheritance of trauma or stressful experiences. The reviewed studies show a plethora of universal changes which stress exposure initiates on multiple levels of organisation ranging from hormonal production and the hypothalamic-pituitary-adrenal (HPA) axis modulation all the way to cognition, behaviour, or propensity to certain psychiatric or metabolic disorders. This review will also provide an overview of relevant methodology and difficulties linked to implementation of epigenetic studies. A better understanding of these processes may help us elucidate the evolutionary pathways which are at work in the course of emergence of the diseases and disorders associated with exposure to trauma, either direct or in a previous generation. Full article
(This article belongs to the Special Issue Mechanisms of Transgenerational Epigenetic Inheritance)
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10 pages, 854 KiB  
Article
ITS1 Barcode and Phytochemical Analysis by Gas Chromatography–Mass Spectrometry of Corynaea crassa Hook. f (Balanophoraceae) from Ecuador and Peru
by Alexandra López-Barrera, Efrén Santos-Ordóñez, Ricardo Pacheco-Coello, Liliana Villao-Uzho, Migdalia Miranda, Yamilet Gutiérrez, Iván Chóez-Guaranda and Segundo Guillermo Ruiz-Reyes
Genes 2023, 14(1), 88; https://doi.org/10.3390/genes14010088 - 28 Dec 2022
Cited by 1 | Viewed by 2564
Abstract
The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be [...] Read more.
The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be found in some regions of America, from Costa Rica to Bolivia. Phytochemical and genetic characterization of medicinal plants is needed for proper identification of metabolites responsible for medicinal properties and for genotyping, respectively. Moreover, characterization of medicinal plants through the use of DNA barcodes is an important tool for phylogenetic analysis and identification of species; furthermore, complemented with phytochemical analysis, both are useful for identification of plant species and quality control of medicinal products. The objective of this study was to analyze the species of C. crassa collected in Ecuador and Peru from the phylogenetic and phytochemical point of view. Polymerase chain reaction (PCR) was performed for amplification of the internal transcribed spacer 1 (ITS1) region after DNA extraction of samples of C. crassa. Blast analysis was performed in the GenBank database with the ITS1 sequences obtained from two accessions of C. crassa from Ecuador (GenBank accession numbers OM471920 and OM471919 for isolates CIBE-17 and CIBE-18, respectively) and three from Peru (GenBank accession numbers OM471921, OM471922, and OM471923 for isolates CIBE-13, CIBE-14, and CIBE-15, respectively). The accessions available in the GenBank were used for phylogenetic analysis. For the phytochemical analysis, hydroalcoholic extracts were obtained by maceration using 80% ethanol as solvent, followed by a derivatization process and analysis by gas chromatography–mass spectrometry. Based on the phylogenetic analysis of the C. crassa samples, the ITS1 sequence could be used to differentiate C. crassa of different locations. The samples of C. crassa from Ecuador and Peru are more similar between them than with other clades including Helosis spp. The phytochemical study revealed differences in the presence and relative abundance of some metabolites; mainly eugenol, 1,4-lactone arabinonic acid, dimethoxyrabelomycin and azelaic acid, which are reported for the first time for the species under study and the genus Corynaea. These results are the first findings on the combined analysis using genetic and phytochemical analysis for C. crassa, which could be used as a useful tool for quality control of the C. crassa species in medicinal products. Full article
(This article belongs to the Special Issue Molecular Markers in Plant Genetics and Breeding)
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16 pages, 2613 KiB  
Article
Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?—A Case Study of Pulsatilla patens (L.) Mill
by Kamil Szandar, Sawicki Jakub, Łukasz Paukszto, Katarzyna Krawczyk and Monika Szczecińska
Genes 2023, 14(1), 67; https://doi.org/10.3390/genes14010067 - 25 Dec 2022
Cited by 2 | Viewed by 2457
Abstract
Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the [...] Read more.
Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD—ccsA, rps4—rps16, and trnL(UAG)—ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes—11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset. Full article
(This article belongs to the Topic Plant Chloroplast Genome and Evolution)
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4 pages, 194 KiB  
Editorial
Special Issue “Feature Papers in Population and Evolutionary Genetics and Genomics”
by Maria-Anna Kyrgiafini and Zissis Mamuris
Genes 2023, 14(1), 38; https://doi.org/10.3390/genes14010038 - 23 Dec 2022
Viewed by 1311
Abstract
Theodosius Dobzhansky famously wrote in 1973 that “nothing in biology makes sense except in the light of evolution” [...] Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
10 pages, 876 KiB  
Communication
Genotype Distribution of the ACTN3 p.R577X Polymorphism in Elite Badminton Players: A Preliminary Study
by Javier Abián-Vicén, Pablo Abián, Alfredo Bravo-Sánchez, Inés Piñas-Bonilla, Beatriz Lara and Juan Del Coso
Genes 2023, 14(1), 50; https://doi.org/10.3390/genes14010050 - 23 Dec 2022
Cited by 2 | Viewed by 3542
Abstract
α-Actinin-3 is a protein with a structural role at the sarcomeric Z-line in skeletal muscle. As it is only present in fast-type muscle fibers, α-actinin-3 is considered a key mechanical component to produce high-intensity muscle contractions and to withstand external tension applied to [...] Read more.
α-Actinin-3 is a protein with a structural role at the sarcomeric Z-line in skeletal muscle. As it is only present in fast-type muscle fibers, α-actinin-3 is considered a key mechanical component to produce high-intensity muscle contractions and to withstand external tension applied to the skeletal muscle. α-Actinin-3 is encoded by the gene ACTN3, which has a single-nucleotide polymorphism (p.R577X; rs1815739) that affects the expression of α-actinin-3 due to the presence of a stop codon. Individuals homozygous for the 577R allele (i.e., RR genotype) and RX heterozygotes express functional α-actinin-3, while those homozygous for the 577X (i.e., XX genotype) express a non-functional protein. There is ample evidence to support the associations between the ACTN3 genotype and athletic performance, with higher frequencies of the 577R allele in elite and professional sprint and power athletes than in control populations. This suggests a beneficial influence of possessing functional α-actinin-3 to become an elite athlete in power-based disciplines. However, no previous investigation has determined the frequency of the ACTN3 genotypes in elite badminton players, despite this sport being characterized by high-intensity actions of intermittent nature such as changes of direction, accelerations, jumps and smashes. The purpose of this study was to analyze ACTN3 R577X genotype frequencies in professional badminton players to establish whether this polymorphism is associated with elite athlete status. A total of 53 European Caucasian professional badminton players competing in the 2018 European Badminton Championships volunteered to participate in the study. Thirty-one were men (26.2 ± 4.4 years) and twenty-two were women (23.4 ± 4.5 years). Chi-squared tests were used to analyze the differences in the distribution of ACTN3 genotypes (RR, RX and XX) between categories and sexes. The ACTN3 RR genotype was the most frequent in the sample of professional badminton players (RR = 49.1%, RX = 22.6% and XX = 28.3%). None of the badminton players ranked in the world’s top ten possessed the XX genotype (RX = 60%, RR = 40%). The distribution of the ACTN3 genotypes was similar between male and female professional badminton players (men: RR = 45.2%, RX = 25.8% and XX = 29.0%; women: RR = 54.5%, RX = 18.2% and XX = 27.3%; χ2 = 0.58; p = 0.750). The distribution of the ACTN3 genotypes in badminton players was different from the 1000 genome database for the European population (χ2 = 15.5; p < 0.001), with an overrepresentation of the RR genotype (p < 0.05) and an underrepresentation of the RX genotype (p < 0.01). In conclusion, the expression of functional α-actinin-3, associated with RR and RX genotypes in the ACTN3 gene may confer an advantage for reaching the status of elite athlete in badminton, and especially the world’s top-ten ranking. Large-scale studies with different ethnic backgrounds are needed to confirm the association of the R allele of ACTN3 with badminton performance. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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12 pages, 1523 KiB  
Article
Predictors of Smoking in Older Adults and an Epigenetic Validation of Self-Report
by Jeffrey D. Long, Michael P. Gehlsen, Joanna Moody, Gracie Weeks and Robert Philibert
Genes 2023, 14(1), 25; https://doi.org/10.3390/genes14010025 - 22 Dec 2022
Cited by 1 | Viewed by 2046
Abstract
There are several established predictors of smoking, but it is unknown if these predictors operate similarly for young and old smokers. We examined clinical data from the National Lung Screening Trial (NLST) to determine the predictive ability of gender, body mass index (BMI), [...] Read more.
There are several established predictors of smoking, but it is unknown if these predictors operate similarly for young and old smokers. We examined clinical data from the National Lung Screening Trial (NLST) to determine the predictive ability of gender, body mass index (BMI), marital status, and race on smoking behavior, with emphasis on gender interactions. In addition, we validated the self-report of smoking behaviors for a subgroup that had available epigenetic data in the form of cg05575921 methylation. Participants were N=9572 current or former smokers from the NLST biofluids database, age 55–74, minimum of 30 pack years, and mostly White. A subgroup of N=3084 who had DNA were used for the self-report validation analysis. The predictor analysis was based on the larger group and used penalized logistic regression to predict the self-report of being a former or current smoker at baseline. Cg05575921 methylation showed a moderate ability to discriminate among former and current smokers, AUC = 0.85 (95% confidence interval = [0.83, 0.86]). The final selected variables for the prediction model were BMI, gender, BMI by gender, age, divorced (vs. married), education, and race. The gender by BMI interaction was such that males had a higher probability of current smoking for lower BMI, but this switched to females having higher current smoking for overweight to obese. There is evidence that the self-reported smoking behavior in NLST is moderately accurate. The results of the primary analysis are consistent with the general smoking literature, and our results provide additional specificity regarding the gender by BMI interaction. Body weight issues might play a role in smoking cessation for older established smokers in a similar manner as younger smokers. It could be that women have less success with cessation when their BMI increases. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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15 pages, 2062 KiB  
Article
Sex Differences in Response to Marek’s Disease: Mapping Quantitative Trait Loci Regions (QTLRs) to the Z Chromosome
by Ehud Lipkin, Jacqueline Smith, Morris Soller, David W. Burt and Janet E. Fulton
Genes 2023, 14(1), 20; https://doi.org/10.3390/genes14010020 - 21 Dec 2022
Cited by 3 | Viewed by 2421
Abstract
Marek’s Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome [...] Read more.
Marek’s Disease (MD) has a significant impact on both the global poultry economy and animal welfare. The disease pathology can include neurological damage and tumour formation. Sexual dimorphism in immunity and known higher susceptibility of females to MD makes the chicken Z chromosome (GGZ) a particularly attractive target to study the chicken MD response. Previously, we used a Hy-Line F6 population from a full-sib advanced intercross line to map MD QTL regions (QTLRs) on all chicken autosomes. Here, we mapped MD QTLRs on GGZ in the previously utilized F6 population with individual genotypes and phenotypes, and in eight elite commercial egg production lines with daughter-tested sires and selective DNA pooling (SDP). Four MD QTLRs were found from each analysis. Some of these QTLRs overlap regions from previous reports. All QTLRs were tested by individuals from the same eight lines used in the SDP and genotyped with markers located within and around the QTLRs. All QTLRs were confirmed. The results exemplify the complexity of MD resistance in chickens and the complex distribution of p-values and Linkage Disequilibrium (LD) pattern and their effect on localization of the causative elements. Considering the fragments and interdigitated LD blocks while using LD to aid localization of causative elements, one must look beyond the non-significant markers, for possible distant markers and blocks in high LD with the significant block. The QTLRs found here may explain at least part of the gender differences in MD tolerance, and provide targets for mitigating the effects of MD. Full article
(This article belongs to the Collection Feature Papers in ‘Animal Genetics and Genomics’)
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15 pages, 2019 KiB  
Review
Roles of Polycomb Complexes in the Reconstruction of 3D Genome Architecture during Preimplantation Embryonic Development
by Longtao Yu, Hengxiang Shen and Xiaowen Lyu
Genes 2022, 13(12), 2382; https://doi.org/10.3390/genes13122382 - 16 Dec 2022
Cited by 1 | Viewed by 2813
Abstract
The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP [...] Read more.
The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP reveal that regulatory elements (Res), such as enhancers and promoters, may participate in the precise regulation of expression of tissue-specific genes important for both embryogenesis and organogenesis by recruiting Polycomb Group (PcG) complexes. PcG complexes usually poise the transcription of developmental genes by forming Polycomb bodies to compact poised enhancers and promoters marked by H3K27me3 in the 3D space. Additionally, recent studies have also uncovered their roles in transcriptional activation. To better understand the full complexities in the mechanisms of how PcG complexes regulate transcription and long-range 3D contacts of enhancers and promoters during developmental programs, we outline novel insights regarding PcG-associated dramatic changes in the 3D chromatin conformation in developmental programs of early embryos and naïve-ground-state transitions of pluripotent embryonic stem cells (ESCs), and highlight the distinct roles of unique and common subunits of canonical and non-canonical PcG complexes in shaping genome architectures and transcriptional programs. Full article
(This article belongs to the Special Issue Dynamics of 3D Genome Organization)
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12 pages, 2444 KiB  
Article
PCYT1A Missense Variant in Vizslas with Disproportionate Dwarfism
by Odette Ludwig-Peisker, Emily Ansel, Daniela Schweizer, Vidhya Jagannathan, Robert Loechel and Tosso Leeb
Genes 2022, 13(12), 2354; https://doi.org/10.3390/genes13122354 - 13 Dec 2022
Cited by 1 | Viewed by 3773
Abstract
Disproportionate dwarfism phenotypes represent a heterogeneous subset of skeletal dysplasias and have been described in many species including humans and dogs. In this study, we investigated Vizsla dogs that were affected by disproportionate dwarfism that we propose to designate as skeletal dysplasia 3 [...] Read more.
Disproportionate dwarfism phenotypes represent a heterogeneous subset of skeletal dysplasias and have been described in many species including humans and dogs. In this study, we investigated Vizsla dogs that were affected by disproportionate dwarfism that we propose to designate as skeletal dysplasia 3 (SD3). The most striking skeletal changes comprised a marked shortening and deformation of the humerus and femur. An extended pedigree with six affected dogs suggested autosomal recessive inheritance. Combined linkage and homozygosity mapping localized a potential genetic defect to a ~4 Mb interval on chromosome 33. We sequenced the genome of an affected dog, and comparison with 926 control genomes revealed a single, private protein-changing variant in the critical interval, PCYT1A:XM_038583131.1:c.673T>C, predicted to cause an exchange of a highly conserved amino acid, XP_038439059.1:p.(Y225H). We observed perfect co-segregation of the genotypes with the phenotype in the studied family. When genotyping additional Vizslas, we encountered a single dog with disproportionate dwarfism that did not carry the mutant PCYT1A allele, which we hypothesize was due to heterogeneity. In the remaining 130 dogs, we observed perfect genotype–phenotype association, and none of the unaffected dogs were homozygous for the mutant PCYT1A allele. PCYT1A loss-of-function variants cause spondylometaphyseal dysplasia with cone–rod dystrophy (SMD-CRD) in humans. The skeletal changes in Vizslas were comparable to human patients. So far, no ocular phenotype has been recognized in dwarf Vizslas. We propose the PCYT1A missense variant as a candidate causative variant for SD3. Our data facilitate genetic testing of Vizslas to prevent the unintentional breeding of further affected puppies. Full article
(This article belongs to the Special Issue Advances in Canine Genetics)
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19 pages, 4239 KiB  
Article
Evolutionary Relationships and Divergence of Filamin Gene Family Involved in Development and Stress in Cotton (Gossypium hirsutum L.)
by Mingyang Wang, Lanxin Wu, Shouhong Zhu, Wei Chen, Jinbo Yao, Yan Li, Tengyu Li, Haihong Shang and Yongshan Zhang
Genes 2022, 13(12), 2313; https://doi.org/10.3390/genes13122313 - 8 Dec 2022
Viewed by 1835
Abstract
Filamin protein is characterized by an N-terminal actin-binding domain that is followed by 24 Ig (immunoglobulin)-like repeats, which act as hubs for interactions with a variety of proteins. In humans, this family has been found to be involved in cancer cell invasion and [...] Read more.
Filamin protein is characterized by an N-terminal actin-binding domain that is followed by 24 Ig (immunoglobulin)-like repeats, which act as hubs for interactions with a variety of proteins. In humans, this family has been found to be involved in cancer cell invasion and metastasis and can be involved in a variety of growth signal transduction processes, but it is less studied in plants. Therefore, in this study, 54 Filamin gene family members from 23 plant species were investigated and divided into two subfamilies: FLMN and GEX2. Subcellular localization showed that most of the Filamin gene family members were located in the cell membrane. A total of 47 Filamin gene pairs were identified, most of which were whole-genome copies. Through the analyses of cis-acting elements, expression patterns and quantitative fluorescence, it was found that GH_ A02G0519 and GH_ D02G0539 are mainly expressed in the reproductive organs of upland cotton, and their interacting proteins are also related to the fertilization process, whereas GH_A02G0216 and GH_D02G0235 were related to stress. Thus, it is speculated that two genes of the GEX2 subfamily (GH_A02G0519 and GH_D02G0539) may be involved in the reproductive development of cotton and may affect the fertilization process of cotton. This study provides a theoretical basis for the further study of the cotton Filamin gene family. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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14 pages, 1762 KiB  
Article
Unaffected Li-Fraumeni Syndrome Carrier Parent Demonstrates Allele-Specific mRNA Stabilization of Wild-Type TP53 Compared to Affected Offspring
by Jeffrey S. Buzby, Shirley A. Williams and Diane J. Nugent
Genes 2022, 13(12), 2302; https://doi.org/10.3390/genes13122302 - 7 Dec 2022
Viewed by 2124
Abstract
Li-Fraumeni Syndrome (LFS) is an autosomal dominant disorder where an oncogenic TP53 germline mutation is inherited by offspring of a carrier parent. p53 is a key tumor suppressor regulating cell cycle arrest in response to DNA damage. Unexpectedly, some mutant TP53 carriers remain [...] Read more.
Li-Fraumeni Syndrome (LFS) is an autosomal dominant disorder where an oncogenic TP53 germline mutation is inherited by offspring of a carrier parent. p53 is a key tumor suppressor regulating cell cycle arrest in response to DNA damage. Unexpectedly, some mutant TP53 carriers remain unaffected, while their children develop cancer early in life. To begin unravelling this paradox, the response of dermal fibroblasts (dFb) isolated from a child with LFS was compared to those from her unaffected father after UV exposure. Phospho-Chk1[S345], a key activator of cell cycle arrest, was increased by UV induction in the LFS patient compared to their unaffected parent dFb. This result, along with previous findings of reduced CDKN1A/p21 UV induction in affected dFb, suggest that cell cycle dysregulation may contribute to cancer onset in the affected LFS subject but not the unaffected parent. Mutant p53 protein and its promoter binding affinity were also higher in dFb from the LFS patient compared to their unaffected parent. These results were as predicted based on decreased mutant TP53 allele-specific mRNA expression previously found in unaffected dFb. Investigation of the potential mechanism regulating this TP53 allele-specific expression found that, while epigenetic promoter methylation was not detectable, TP53 wild-type mRNA was specifically stabilized in the unaffected dFb. Hence, the allele-specific stabilization of wild-type TP53 mRNA may allow an unaffected parent to counteract genotoxic stress by means more characteristic of homozygous wild-type TP53 individuals than their affected offspring, providing protection from the oncogenesis associated with LFS. Full article
(This article belongs to the Special Issue Carcinogenesis as an Evolutionary Process)
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15 pages, 1628 KiB  
Article
Characterizing Macrophages Diversity in COVID-19 Patients Using Deep Learning
by Mario A. Flores, Karla Paniagua, Wenjian Huang, Ricardo Ramirez, Leonardo Falcon, Andy Liu, Yidong Chen, Yufei Huang and Yufang Jin
Genes 2022, 13(12), 2264; https://doi.org/10.3390/genes13122264 - 1 Dec 2022
Cited by 2 | Viewed by 2918
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent responsible for coronavirus disease 2019 (COVID-19), has affected the lives of billions and killed millions of infected people. This virus has been demonstrated to have different outcomes among individuals, with some of [...] Read more.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent responsible for coronavirus disease 2019 (COVID-19), has affected the lives of billions and killed millions of infected people. This virus has been demonstrated to have different outcomes among individuals, with some of them presenting a mild infection, while others present severe symptoms or even death. The identification of the molecular states related to the severity of a COVID-19 infection has become of the utmost importance to understanding the differences in critical immune response. In this study, we computationally processed a set of publicly available single-cell RNA-Seq (scRNA-Seq) data of 12 Bronchoalveolar Lavage Fluid (BALF) samples diagnosed as having a mild, severe, or no infection, and generated a high-quality dataset that consists of 63,734 cells, each with 23,916 genes. We extended the cell-type and sub-type composition identification and our analysis showed significant differences in cell-type composition in mild and severe groups compared to the normal. Importantly, inflammatory responses were dramatically elevated in the severe group, which was evidenced by the significant increase in macrophages, from 10.56% in the normal group to 20.97% in the mild group and 34.15% in the severe group. As an indicator of immune defense, populations of T cells accounted for 24.76% in the mild group and decreased to 7.35% in the severe group. To verify these findings, we developed several artificial neural networks (ANNs) and graph convolutional neural network (GCNN) models. We showed that the GCNN models reach a prediction accuracy of the infection of 91.16% using data from subtypes of macrophages. Overall, our study indicates significant differences in the gene expression profiles of inflammatory response and immune cells of severely infected patients. Full article
(This article belongs to the Special Issue Selected Papers from the International Conference on Intelligent Biology and Medicine (ICIBM 2022))
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12 pages, 1243 KiB  
Article
Assessment of Rare Genetic Variants to Identify Candidate Modifier Genes Underlying Neurological Manifestations in Neurofibromatosis 1 Patients
by Jie Tang, Niu Li, Guoqiang Li, Jian Wang, Tingting Yu and Ruen Yao
Genes 2022, 13(12), 2218; https://doi.org/10.3390/genes13122218 - 26 Nov 2022
Viewed by 1943
Abstract
Neurological phenotypes such as intellectual disability occur in almost half of patients with neurofibromatosis 1 (NF1). Current genotype–phenotype studies have failed to reveal the mechanism underlying this clinical variability. Despite the presence of pathogenic variants of NF1, modifier genes likely determine the occurrence [...] Read more.
Neurological phenotypes such as intellectual disability occur in almost half of patients with neurofibromatosis 1 (NF1). Current genotype–phenotype studies have failed to reveal the mechanism underlying this clinical variability. Despite the presence of pathogenic variants of NF1, modifier genes likely determine the occurrence and severity of neurological phenotypes. Exome sequencing data were used to identify genetic variants in 13 NF1 patients and 457 healthy controls, and this information was used to identify candidate modifier genes underlying neurological phenotypes based on an optimal sequence kernel association test. Thirty-six genes were identified as significant modifying factors in patients with neurological phenotypes and all are highly expressed in the nervous system. A review of the literature confirmed that 19 genes including CUL7, DPH1, and BCO1 are clearly associated with the alteration of neurological functioning and development. Our study revealed the enrichment of rare variants of 19 genes closely related to neurological development and functioning in NF1 patients with neurological phenotypes, indicating possible modifier genes and variants affecting neurodevelopment. Further studies on rare genetic variants of candidate modifier genes may help explain the clinical heterogeneity of NF1. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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14 pages, 4564 KiB  
Article
Dbf4 Zn-Finger Motif Is Specifically Required for Stimulation of Ctf19-Activated Origins in Saccharomyces cerevisiae
by Meghan V. Petrie, Haiyang Zhang, Emily M. Arnold, Yan Gan and Oscar M. Aparicio
Genes 2022, 13(12), 2202; https://doi.org/10.3390/genes13122202 - 24 Nov 2022
Viewed by 2086
Abstract
Eukaryotic genomes are replicated in spatiotemporal patterns that are stereotypical for individual genomes and developmental profiles. In the model system Saccharomyces cerevisiae, two primary mechanisms determine the preferential activation of replication origins during early S phase, thereby largely defining the consequent replication [...] Read more.
Eukaryotic genomes are replicated in spatiotemporal patterns that are stereotypical for individual genomes and developmental profiles. In the model system Saccharomyces cerevisiae, two primary mechanisms determine the preferential activation of replication origins during early S phase, thereby largely defining the consequent replication profiles of these cells. Both mechanisms are thought to act through specific recruitment of a rate-limiting initiation factor, Dbf4-dependent kinase (DDK), to a subset of licensed replication origins. Fkh1/2 is responsible for stimulation of most early-firing origins, except for centromere (CEN)-proximal origins that recruit DDK via the kinetochore protein Ctf19, which is required for their early firing. The C-terminus of Dbf4 has been implicated in its recruitment to origins via both the Fkh1/2 and Ctf19 mechanisms. Here, we show that the Zn-finger motif within the C-terminus is specifically required for Dbf4 recruitment to CENs to stimulate CEN-proximal/Ctf19-dependent origins, whereas stimulation of origins via the Fkh1/2 pathway remains largely intact. These findings re-open the question of exactly how Fkh1/2 and DDK act together to stimulate replication origin initiation. Full article
(This article belongs to the Special Issue DNA Replication Kinetics)
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15 pages, 6420 KiB  
Technical Note
A Multigraph-Based Representation of Hi-C Data
by Diána Makai, András Cseh, Adél Sepsi and Szabolcs Makai
Genes 2022, 13(12), 2189; https://doi.org/10.3390/genes13122189 - 23 Nov 2022
Viewed by 2996
Abstract
Chromatin–chromatin interactions and three-dimensional (3D) spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts to [...] Read more.
Chromatin–chromatin interactions and three-dimensional (3D) spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts to environmental stimuli, the linear sequence information needs to be interpreted in three-dimensional space, which is still a challenging task. Here, we propose a novel, heuristic approach to represent Hi-C datasets by a whole-genomic pseudo-structure in 3D space. The baseline of our approach is the construction of a multigraph from genomic-sequence data and Hi-C interaction data, then applying a modified force-directed layout algorithm. The resulting layout is a pseudo-structure. While pseudo-structures are not based on direct observation and their details are inherent to settings, surprisingly, they demonstrate interesting, overall similarities of known genome structures of both barley and rice, namely, the Rabl and Rosette-like conformation. It has an exciting potential to be extended by additional omics data (RNA-seq, Chip-seq, etc.), allowing to visualize the dynamics of the pseudo-structures across various tissues or developmental stages. Furthermore, this novel method would make it possible to revisit most Hi-C data accumulated in the public domain in the last decade. Full article
(This article belongs to the Special Issue Application of Bioinformatics in Plants)
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14 pages, 2547 KiB  
Article
Anticipating the Next Chess Move: Blocking SARS-CoV-2 Replication and Simultaneously Disarming Viral Escape Mechanisms
by Samir Mansour Moraes Casseb, André Salim Khayat, Jorge Estefano Santana de Souza, Edivaldo Herculano Correa de Oliveira, Sidney Emanuel Batista Dos Santos, Pedro Fernando da Costa Vasconcelos and Paulo Pimentel de Assumpção
Genes 2022, 13(11), 2147; https://doi.org/10.3390/genes13112147 - 18 Nov 2022
Cited by 2 | Viewed by 2441
Abstract
The COVID-19 pandemic initiated a race to determine the best measures to control the disease and to save as many people as possible. Efforts to implement social distancing, the use of masks, and massive vaccination programs turned out to be essential in reducing [...] Read more.
The COVID-19 pandemic initiated a race to determine the best measures to control the disease and to save as many people as possible. Efforts to implement social distancing, the use of masks, and massive vaccination programs turned out to be essential in reducing the devastating effects of the pandemic. Nevertheless, the high mutation rates of SARS-CoV-2 challenge the vaccination strategy and maintain the threat of new outbreaks due to the risk of infection surges and even lethal variations able to resist the effects of vaccines and upset the balance. Most of the new therapies tested against SARS-CoV-2 came from already available formulations developed to treat other diseases, so they were not specifically developed for SARS-CoV-2. In parallel, the knowledge produced regarding the molecular mechanisms involved in this disease was vast due to massive efforts worldwide. Taking advantage of such a vast molecular understanding of virus genomes and disease mechanisms, a targeted molecular therapy based on siRNA specifically developed to reach exclusive SARS-CoV-2 genomic sequences was tested in a non-transformed human cell model. Since coronavirus can escape from siRNA by producing siRNA inhibitors, a complex strategy to simultaneously strike both the viral infectious mechanism and the capability of evading siRNA therapy was developed. The combined administration of the chosen produced siRNA proved to be highly effective in successfully reducing viral load and keeping virus replication under control, even after many days of treatment, unlike the combinations of siRNAs lacking this anti-anti-siRNA capability. Additionally, the developed therapy did not harm the normal cells, which was demonstrated because, instead of testing the siRNA in nonhuman cells or in transformed human cells, a non-transformed human thyroid cell was specifically chosen for the experiment. The proposed siRNA combination could reduce the viral load and allow the cellular recovery, presenting a potential innovation for consideration as an additional strategy to counter or cope COVID-19. Full article
(This article belongs to the Section Viral Genomics)
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8 pages, 1944 KiB  
Article
Congenital Nail Disorders among Children with Suspected Ectodermal Dysplasias
by Sigrun Maier-Wohlfart, Carmen Aicher, Ines Willershausen, Nicolai Peschel, Udo Meißner, Lina Gölz and Holm Schneider
Genes 2022, 13(11), 2119; https://doi.org/10.3390/genes13112119 - 15 Nov 2022
Cited by 2 | Viewed by 6012
Abstract
We report on a cohort of 204 children referred between January 2017 and January 2022 to the German Center for Ectodermal Dysplasias, Erlangen. The most frequent reasons for referral were tooth malformations and lack of multiple teeth leading to the suspicion of an [...] Read more.
We report on a cohort of 204 children referred between January 2017 and January 2022 to the German Center for Ectodermal Dysplasias, Erlangen. The most frequent reasons for referral were tooth malformations and lack of multiple teeth leading to the suspicion of an ectodermal dysplasia. Many patients also suffered from being unable to perspire. Nail abnormalities, in contrast, represented a much rarer finding, albeit the impact on some individuals was large. As ectodermal dysplasias are congenital genetic conditions affecting the development and/or homeostasis of two or more ectodermal derivatives, including hair, teeth, nails, and certain glands, we analyzed congenital nail disorders detected in these patients. Dystrophic or otherwise abnormal nails were evident in 17 of 18 subjects with pathogenic WNT10A or GJB6 variants but in none of 161 children with EDA variants underlying X-linked hypohidrotic ectodermal dysplasia. However, 2 of 17 children who carry mutations in EDAR or EDARADD, two other genes involved in the ectodysplasin A signaling pathway, showed nail abnormalities, such as brittle or hypoplastic nails. TP63 variants were regularly associated with nail disorders. In one girl, anonychia congenita caused by a compound heterozygous variant of the R-spondin-4 gene (RSPO4) was diagnosed. Thus, nail dysplasia is rarer among patients with ectodermal dysplasia than commonly thought. Full article
(This article belongs to the Special Issue Molecular Biology and Treatment of Genodermatoses)
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9 pages, 1642 KiB  
Communication
Targeted Panel Sequencing Identifies an Intronic c.5225-3C>G Variant of the FBN1 Gene Causing Sporadic Marfan Syndrome with Annuloaortic Ectasia
by Kyung Hwa Kim, Tae Yun Kim, Soon Jin Kim, Yong Gon Cho, Joonhong Park and Woori Jang
Genes 2022, 13(11), 2108; https://doi.org/10.3390/genes13112108 - 13 Nov 2022
Cited by 1 | Viewed by 2318
Abstract
Marfan syndrome (MFS) is a hereditary connective tissue disease whose clinical severity varies widely. Mutations of the FBN1 gene encoding fibrillin-1 are the most common genetic cause of Marfanoid habitus; however, about 10% of MFS patients are unaware of their genetic defects. Herein, [...] Read more.
Marfan syndrome (MFS) is a hereditary connective tissue disease whose clinical severity varies widely. Mutations of the FBN1 gene encoding fibrillin-1 are the most common genetic cause of Marfanoid habitus; however, about 10% of MFS patients are unaware of their genetic defects. Herein, we report a Korean patient with MFS and annuloaortic ectasia caused by an intronic c.5225-3C>G variant of the FBN1 gene identified by targeted panel sequencing. The reverse transcription analysis of FBN1 revealed that the intron 43 sequence from positions c.5297-1516 to c.5297-1 was retained at the coding sequence as a consequence of the c.5225-3C>G variant enhancing a cryptic splice acceptor site (c.5297-1518_5297-1517AG) in intron 43. The retained sequence of the part of intron 43 caused the same effect as insertion mutation (NM_000138.5:c.5297_c.5298ins5297-1516_5297-1), resulting in a frameshift mutation resulting in p.Ile1767Trpfs*3. The patient underwent an urgent modified Bentall operation with a 29 mm mechanical valve for annuloaortic ectasia and severe aortic valve regurgitation. This report emphasizes the need for functional investigations into the diagnostic workflows of certain diseases or gene panels with suspected high rates of intronic variants and potential pathogenic effects. Hence, further descriptions of individuals with intronic variants causing alternative splicing expected to have pathogenic effects at different transcript levels are crucial for improving our understanding. Full article
(This article belongs to the Special Issue Next Generation Sequencing in Clinical Diagnostics)
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3 pages, 185 KiB  
Editorial
Special Issue: Genetics of Psychiatric Disease and the Basics of Neurobiology
by Laia Rodriguez-Revenga and Maria Isabel Alvarez-Mora
Genes 2022, 13(11), 2008; https://doi.org/10.3390/genes13112008 - 2 Nov 2022
Viewed by 1455
Abstract
A psychiatric disorder is a mental illness involving significant disturbances in thinking, emotional regulation or behavior [...] Full article
(This article belongs to the Special Issue Genetics of Psychiatric Disease and the Basics of Neurobiology)
16 pages, 1270 KiB  
Article
Genetic Hearing Loss Affects Cochlear Processing
by Cris Lanting, Ad Snik, Joop Leijendeckers, Arjan Bosman and Ronald Pennings
Genes 2022, 13(11), 1923; https://doi.org/10.3390/genes13111923 - 22 Oct 2022
Viewed by 1638
Abstract
The relationship between speech recognition and hereditary hearing loss is not straightforward. Underlying genetic defects might determine an impaired cochlear processing of sound. We obtained data from nine groups of patients with a specific type of genetic hearing loss. For each group, the [...] Read more.
The relationship between speech recognition and hereditary hearing loss is not straightforward. Underlying genetic defects might determine an impaired cochlear processing of sound. We obtained data from nine groups of patients with a specific type of genetic hearing loss. For each group, the affected cochlear site-of-lesion was determined based on previously published animal studies. Retrospectively obtained speech recognition scores in noise were related to several aspects of supra-threshold cochlear processing as assessed by psychophysical measurements. The differences in speech perception in noise between these patient groups could be explained by these factors and partially by the hypothesized affected structure of the cochlea, suggesting that speech recognition in noise was associated with a genetics-related malfunctioning of the cochlea. In particular, regression models indicate that loudness growth and spectral resolution best describe the cochlear distortions and are thus a good biomarker for speech understanding in noise. Full article
(This article belongs to the Special Issue Functional Otogenetics)
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10 pages, 273 KiB  
Article
Posttransplant Complications and Genetic Loci Involved in Telomere Maintenance in Heart Transplant Patients
by Dana Dlouha, Jevgenija Vymetalova, Sarka Novakova, Pavlina Huckova, Vera Lanska and Jaroslav Alois Hubacek
Genes 2022, 13(10), 1855; https://doi.org/10.3390/genes13101855 - 14 Oct 2022
Cited by 1 | Viewed by 1624
Abstract
Reaching critically short telomeres induces cellular senescence and ultimately cell death. Cellular senescence contributes to the loss of tissue function. We aimed to determine the association between variants within genes involved in telomere length maintenance, posttransplant events, and aortic telomere length in heart [...] Read more.
Reaching critically short telomeres induces cellular senescence and ultimately cell death. Cellular senescence contributes to the loss of tissue function. We aimed to determine the association between variants within genes involved in telomere length maintenance, posttransplant events, and aortic telomere length in heart transplant patients. DNA was isolated from paired aortic samples of 383 heart recipients (age 50.7 ± 11.9 years) and corresponding donors (age 38.7 ± 12.0 years). Variants within the TERC (rs12696304), TERF2IP (rs3784929 and rs8053257), and OBCF1 (rs4387287) genes were genotyped, and telomere length was measured using qPCR. We identified similar frequencies of genotypes in heart donors and recipients. Antibody-mediated rejection (AMR) was more common (p < 0.05) in carriers of at least one G allele within the TERF2IP locus (rs3784929). Chronic graft dysfunction (CGD) was associated with the TERC (rs12696304) GG donor genotype (p = 0.05). The genetic risk score did not determine posttransplant complication risk prediction. No associations between the analyzed polymorphisms and telomere length were detected in either donor or recipient DNA. In conclusion, possible associations between donor TERF2IP (rs3784929) and AMR and between TERC (rs12696304) and CGD were found. SNPs within the examined genes were not associated with telomere length in transplanted patients. Full article
(This article belongs to the Special Issue Single-Nucleotide Polymorphisms: Association, Molecular Function, Application, and Progress)
11 pages, 2226 KiB  
Article
Spatial and Temporal Expression Characteristics of the HBB Gene Family in Six Different Pig Breeds
by Xin Guo, Zhiguo Liu, Yulian Mu, Lei Huang, Kui Li and Jing Zhang
Genes 2022, 13(10), 1822; https://doi.org/10.3390/genes13101822 - 9 Oct 2022
Viewed by 3293
Abstract
β-Thalassemia induces hemolytic anemia caused by mutations in the β-chain gene locus. As humans progress from embryo to adulthood, hemoglobin recombines twice. To test whether similar hemoglobin reassembly occurs in pigs, bioinformatics tools were used to predict the pig hemoglobin-encoding gene. We then [...] Read more.
β-Thalassemia induces hemolytic anemia caused by mutations in the β-chain gene locus. As humans progress from embryo to adulthood, hemoglobin recombines twice. To test whether similar hemoglobin reassembly occurs in pigs, bioinformatics tools were used to predict the pig hemoglobin-encoding gene. We then systematically analyzed the expression patterns of the HBB gene family in three developmental stages (weaning, sexual maturity and physical maturity) of six different pig breeds (Landrace, Yorkshire, Wuzhishan, Songliao black, Meishan and Tibetan). The results showed that the new hemoglobin coding gene ‘HBB-like’ was found in pigs, while the HBG gene did not exist in pigs, indicating that human-like reassembly might not exist in pigs. The HBB and HBB-like genes shared highly similar amino acid sequences and gene sequences. The genes on the β-chain were highly similar between humans and pigs and the amino acid sequences of human and pig HBB genes at position 26 and positions 41–42 were identical. qPCR results showed that there were significant differences in the spatiotemporal expression patterns of the four genes (HBA, HBB, HBB-like and HBE) across breeds. Our results provide a foundation for follow-up studies assessing the relationship between the gene-encoding hemoglobin and β-thalassemia disease, as well as the construction of a gene-edited β-thalassemia miniature pig model to assess β-thalassemia treatments. Full article
(This article belongs to the Topic Animal Models of Human Disease)
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12 pages, 1477 KiB  
Article
Expression Activity of Artificial Promoters for Disease Resistance in Transgenic Eucalyptus urophylla
by Zhenchi Huang, Qingchun Xu, Xiaolan Fang and Zhihua Wu
Genes 2022, 13(10), 1813; https://doi.org/10.3390/genes13101813 - 7 Oct 2022
Cited by 2 | Viewed by 2165
Abstract
The transcriptional properties of artificial promoters are closely related to the type and arrangement position of cis-elements. GWSF (374-bp) was an effective SPIP with four cis-element dimers. There were four pathogen-inducible cis-elements in the GWSF promoter (GST1-boxes, W-boxes, S-boxes, and F-boxes) and a [...] Read more.
The transcriptional properties of artificial promoters are closely related to the type and arrangement position of cis-elements. GWSF (374-bp) was an effective SPIP with four cis-element dimers. There were four pathogen-inducible cis-elements in the GWSF promoter (GST1-boxes, W-boxes, S-boxes, and F-boxes) and a minimal cauliflower mosaic virus 35S promoter. V-element dimers were inserted into the upstream (VGWSF), midstream (GWVSF), and downstream (GWSFV) regions of the original GWSF promoter sequence to examine their affect on the position. The expression activity of promoters was analyzed and estimated using the histochemical staining of leaf discs of eucalyptus with transient expression, an image digitization method to extract the color features, and the induction treatment by a plant pathogenic microorganism/inducer and qPCR assays. The histochemical staining results of the adventitious buds indicated that the promoters had been successfully integrated into the E. urophylla genome and that they drove the expression of the gus gene. There was a noticeable difference in the intensity of color between the adventitious buds on the same callus block, as well as the intensity of color within the same adventitious bud. According to the established two-factor model of blue value, there was a greater difference between the levels of the genotype factor than the promoter factor in eucalyptus leaf discs. Further, the basal and inducible transcriptional levels of the three improved promoters were investigated by qPCR. With the basal transcriptional level of the GWSF promoter normalized to one, the relative basal levels of VGWSF, GWVSF, and GWSFV were 1.40, 1.45, and 4.15, respectively. The qPCR results were consistent with the staining results of GUS histochemical staining. The three improved promoters all had the properties of being induced by salicylic acid, Ralstonia solanacearum, and Phytophthora capsici. The three improved promoters demonstrated a significantly higher TMV induction activity: their induction activity from high to low was GWSFV > GWVSF > VGWSF. The findings will be beneficial to the construction and optimization of artificial promoters for transgenic plants. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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15 pages, 6066 KiB  
Article
The Identification and Characterization of the KNOX Gene Family as an Active Regulator of Leaf Development in Trifolium repens
by Jinwan Fan, Gang Nie, Jieyu Ma, Ruchang Hu, Jie He, Feifei Wu, Zhongfu Yang, Sainan Ma, Xin Zhang and Xinquan Zhang
Genes 2022, 13(10), 1778; https://doi.org/10.3390/genes13101778 - 1 Oct 2022
Viewed by 2898
Abstract
Leaves are the primary and critical feed for herbivores. They directly determine the yield and quality of legume forage. Trifolium repens (T. repens) is an indispensable legume species, widely cultivated in temperate pastures due to its nutritional value and nitrogen fixation. [...] Read more.
Leaves are the primary and critical feed for herbivores. They directly determine the yield and quality of legume forage. Trifolium repens (T. repens) is an indispensable legume species, widely cultivated in temperate pastures due to its nutritional value and nitrogen fixation. Although the leaves of T. repens are typical trifoliate, they have unusual patterns to adapt to herbivore feeding. The number of leaflets in T. repens affects its production and utilization. The KNOX gene family encodes transcriptional regulators that are vital in regulating and developing leaves. Identification and characterization of TrKNOX gene family as an active regulator of leaf development in T. repens were studied. A total of 21 TrKNOX genes were identified from the T. repens genome database and classified into three subgroups (Class I, Class II, and Class M) based on phylogenetic analysis. Nineteen of the genes identified had four conserved domains, except for KNOX5 and KNOX9, which belong to Class M. Varying expression levels of TrKNOX genes were observed at different developmental stages and complexities of leaves. KNOX9 was observed to upregulate the leaf complexity of T. repens. Research on TrKNOX genes could be novel and further assist in exploring their functions and cultivating high-quality T. repens varieties. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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6 pages, 989 KiB  
Essay
The Crazy Biology
by Philippe Monget
Genes 2022, 13(10), 1769; https://doi.org/10.3390/genes13101769 - 30 Sep 2022
Viewed by 1953
Abstract
Since the end of the 1980s and the advent of molecular biology, then the beginning of the 2000s with the sequencing of whole genomes, modern tools have never ceased to amaze us and provide answers to questions that we didn’t even dare ask [...] Read more.
Since the end of the 1980s and the advent of molecular biology, then the beginning of the 2000s with the sequencing of whole genomes, modern tools have never ceased to amaze us and provide answers to questions that we didn’t even dare ask ourselves before: Why do elephants have fewer cancers than humans? Why do humans have such big brains? How does a eukaryotic cell recognize a “foreign” DNA sequence? Are there molecular crossroads of incompatible functions? Can cells count each other? These fascinating questions have made biology in recent years almost crazy. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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13 pages, 1560 KiB  
Article
TWEAK and TNFα, Both TNF Ligand Family Members and Multiple Sclerosis-Related Cytokines, Induce Distinct Gene Response in Human Brain Microvascular Endothelial Cells
by Delphine Stephan, Anais Roger, Jehanne Aghzadi, Sylvie Carmona, Christophe Picard, Jean-Philippe Dales and Sophie Desplat-Jégo
Genes 2022, 13(10), 1714; https://doi.org/10.3390/genes13101714 - 24 Sep 2022
Cited by 4 | Viewed by 2380
Abstract
Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is a member of the TNF ligand family involved in various diseases including brain inflammatory pathologies such as multiple sclerosis. It has been demonstrated that TWEAK can induce cerebrovascular permeability in an in vitro model [...] Read more.
Tumor necrosis factor-like weak inducer of apoptosis (TWEAK) is a member of the TNF ligand family involved in various diseases including brain inflammatory pathologies such as multiple sclerosis. It has been demonstrated that TWEAK can induce cerebrovascular permeability in an in vitro model of the blood–brain barrier. The molecular mechanisms playing a role in TWEAK versus TNFα signaling on cerebral microvascular endothelial cells are not well defined. Therefore, we aimed to identify gene expression changes in cultures of human brain microvascular endothelial cells (hCMEC/D3) to address changes initiated by TWEAK exposure. Taken together, our studies highlighted that gene involved in leukocyte extravasation, notably claudin-5, were differentially modulated by TWEAK and TNFα. We identified differential gene expression of hCMEC/D3 cells at three timepoints following TWEAK versus TNFα stimulation and also found distinct modulations of several canonical pathways including the actin cytoskeleton, vascular endothelial growth factor (VEGF), Rho family GTPases, and phosphatase and tensin homolog (PTEN) pathways. To our knowledge, this is the first study to interrogate and compare the effects of TWEAK versus TNFα on gene expression in brain microvascular endothelial cells. Full article
(This article belongs to the Special Issue Genetic and Molecular Mechanisms in Multiple Sclerosis)
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13 pages, 1808 KiB  
Article
Differentially Methylated DNA Regions and Left Ventricular Hypertrophy in African Americans: A HyperGEN Study
by Alana C. Jones, Amit Patki, Steven A. Claas, Hemant K. Tiwari, Ninad S. Chaudhary, Devin M. Absher, Leslie A. Lange, Ethan M. Lange, Wei Zhao, Scott M. Ratliff, Sharon L. R. Kardia, Jennifer A. Smith, Marguerite R. Irvin and Donna K. Arnett
Genes 2022, 13(10), 1700; https://doi.org/10.3390/genes13101700 - 22 Sep 2022
Cited by 1 | Viewed by 2657
Abstract
Left ventricular (LV) hypertrophy (LVH) is an independent risk factor for cardiovascular disease, and African Americans experience a disparate high risk of LVH. Genetic studies have identified potential candidate genes and variants related to the condition. Epigenetic modifications may continue to help unravel [...] Read more.
Left ventricular (LV) hypertrophy (LVH) is an independent risk factor for cardiovascular disease, and African Americans experience a disparate high risk of LVH. Genetic studies have identified potential candidate genes and variants related to the condition. Epigenetic modifications may continue to help unravel disease mechanisms. We used methylation and echocardiography data from 636 African Americans selected from the Hypertension Genetic Epidemiology Network (HyperGEN) to identify differentially methylated regions (DMRs) associated with LVH. DNA extracted from whole blood was assayed on Illumina Methyl450 arrays. We fit linear mixed models to examine associations between co-methylated regions and LV traits, and we then conducted single CpG analyses within significant DMRs. We identified associations between DMRs and ejection fraction (XKR6), LV internal diastolic dimension (TRAK1), LV mass index (GSE1, RPS15 A, PSMD7), and relative wall thickness (DNHD1). In single CpG analysis, CpG sites annotated to TRAK1 and DNHD1 were significant. These CpGs were not associated with LV traits in replication cohorts but the direction of effect for DNHD1 was consistent across cohorts. Of note, DNHD1, GSE1, and PSMD7 may contribute to cardiac structural function. Future studies should evaluate relationships between regional DNA methylation patterns and the development of LVH. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Contributions to Hypertension and Blood Pressure Response to Interventions)
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8 pages, 602 KiB  
Article
Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population
by Monica Abreu-Glowacka, Witold Pepinski, Eliza Michalak, Magdalena Konarzewska, Krzysztof Zak, Malgorzata Skawronska, Anna Niemcunowicz-Janica, Ireneusz Soltyszewski, Pawel Krajewski and Czeslaw Zaba
Genes 2022, 13(10), 1683; https://doi.org/10.3390/genes13101683 - 20 Sep 2022
Cited by 1 | Viewed by 1997
Abstract
(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included [...] Read more.
(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included in the Investigator DIPplex kit (Qiagen) were obtained in a sample of 631 unrelated Polish individuals. Allelic frequency data were compared with those reported for selected populations (3) Results: All the loci conformed with Hardy-Weinberg equilibrium after applying a Bonferroni correction and no pair-wise significant linkage disequilibrium was detected. (4) Conclusions: DIPplex Kit differences were high among populations worldwide. The InDel markers are highly discriminating for human identification purposes in the Polish population. Full article
(This article belongs to the Special Issue Genetic Structure of Human Populations)
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