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The northern quahog, Mercenaria mercenaria (= hard clam) is an important aquaculture species on the U.S. east coast and shares a partially sympatric distribution with a sister species Mercenaria campechiensis which is endemic to the mid-Atlantic coast from the Chesapeake Bay to Florida and the Gulf of Mexico. These two species are morphologically similar, and their identification is laborious and challenging. To support aquaculture breeding and restoration activities, it is essential to develop an accurate and easy method to identify the two Mercenaria species. In the present study, high-melting resolution analysis was applied to identify these two Mercenaria species and their hybrids using three genes of cytochrome oxidase subunit 1 (COJ), mitochondrial large ribosomal subunit (I6S r RNA), and internal transcribed spacer 1 (ITSI). The temperature melting points (TJ of COl, 16S rRNA, and ITSI were significantly different between the two Mercenaria species and could be used to distinguish M. mercenaria and M. campechiensis. By use of the melting T of COl, 16S r RNA, and ITSI, a discriminant function equation was established to effectively eliminate the impacts of intraspecific sequence variations on species identification. Compared with their true species classification, the accuracy of the predicted classification of each sample was 100% based on the discriminant function equation. Furthermore, a linear discriminant analysis model was used for cross-validation and the mean classification success was 100% with no observed erroneous classification. Moreover, the interspecific hybrids of M. mercenaria and M. campechiensis were verified by the melting curve of nuclear DNA marker ITSI, and their maternity was further clarified by mitochondrial DNA markers COl and 16S rRNA. The methodology developed in this study would be useful as a rapid and accurate tool to support Mercenaria aquaculture, breeding, and restoration. KEY WORDS: high-resolution melt analysis, Mercenaria mercenaria, Mercenaria campechiensis, species identification, hybrid, discriminant analysis, INTRODUCTION The northern quahog, Mercenaria mercenaria (also named hard clam) is an intertidal benthic infaunal species along the western Atlantic coast from the Gulf of St. Lawrence to Florida (Harte [...]

We conducted a systematic review to assess the current state of molecular-based research of aquatic macrophytes based on articles searched in SCOPUS and WoS databases. We found that the interest in molecular applications increased over time more rapidly than other approaches in aquatic macrophyte studies. The Neotropics, Indo-Malaysian, Australasia, and Afrotropical regions have a low publication rate on macrophytes' studied by molecular methods compared to the Palearctic and Nearctic regions. The gene regions of cpDNA and nrDNA were the most prominent, with the ITS being the most used. However, unusual markers for plants, such as mtDNA, were also detected. We found that 636 species of macrophytes received some study employing molecular techniques, representing 18% of the known aquatic macrophyte species on the planet. Therefore, there is still much to be explored about the genetic diversity of the world's aquatic flora, especially in the Neotropics, which has the highest diversity of macrophytes, and whose molecular techniques can help identify more species and elucidate the evolutionary history of this taxonomic group. [ABSTRACT FROM AUTHOR]

Diabetic retinopathy (DR) is a major complication of diabetes worldwide, significantly causing vision loss and blindness in working-age adults, and imposing a substantial socioeconomic burden globally. This review examines the crucial role of genetic factors in the development of DR and highlights the shift toward personalized treatment approaches. Advances in genetic research have identified specific genes and variations involved in angiogenesis, inflammation, and oxidative stress that increase DR susceptibility. Understanding these genetic markers enables early identification of at-risk individuals and the creation of personalized treatment plans. Incorporating these genetic insights, healthcare providers can develop early intervention strategies and tailored treatment plans to improve patient outcomes and minimize side effects. This review emphasizes the transformative potential of integrating genetic information into clinical practice, marking a paradigm shift in DR management and advancing toward a more personalized and effective healthcare model. [ABSTRACT FROM AUTHOR]

Introduction: Wheat awns are crucial determinants of wheat yield due to their capacity to photosynthesize and exchange gas. Understanding the genetic basis of awn length (AL) is essential for improving wheat yield in molecular breeding programs. Methods: In this study, quantitative trait loci (QTLs) of AL were analyzed using recombinant inbred line (RIL) mapping population referred to as YY-RILs, which was derived from a cross between Yannong 15 (YN15) and Yannong 1212 (YN1212). Results and discussion: Seven putative additive QTLs and 30 pairwise epistatic QTLs for AL were identified. Among them, five novel additive QTLs (except qAl- 2A and qAl-5A.2) and 30 novel pairwise epistatic QTLs were identified. qAl-5A.1 was repeatedly identified in all five environment datasets, which was considered to be one novel stable QTL for AL with minor additive effects. eqAl-2B.2-2 significantly interacted with eight loci and could be of great importance in regulating awn development. The genes associated with the major stable QTL of qAl-5A.2 and the minor stable QTL of qAl-2A were B1 and WFZP-A, respectively. Awn lengths exhibited significant genetic correlations with kernel weight and kernels per spike, which could affect grain protein content to a lesser extent. This study enhances our understanding of the genetic basis of awn development and identifies novel genes as well as markers for future genetic improvement of wheat yield. [ABSTRACT FROM AUTHOR]

Mutating replication-dependent (RD) histone genes is an important tool for understanding chromatin-based epigenetic regulation. Deploying this tool in metazoans is particularly challenging because RD histones in these organisms are typically encoded by many genes, often located at multiple loci. Such gene arrangements make the ability to generate homogenous histone mutant genotypes by site-specific gene editing quite difficult. Drosophila melanogaster provides a solution to this problem because the RD histone genes are organized into a single large tandem array that can be deleted and replaced with transgenes containing mutant histone genes. In the last ∼15 years several different RD histone gene replacement platforms were developed using this simple strategy. However, each platform contains weaknesses that preclude full use of the powerful developmental genetic capabilities available to Drosophila researchers. Here we describe the development of a newly engineered platform that rectifies many of these weaknesses. We used CRISPR to precisely delete the RD histone gene array (HisC), replacing it with a multifunctional cassette that permits site-specific insertion of either one or two synthetic gene arrays using selectable markers. We designed this cassette with the ability to selectively delete each of the integrated gene arrays in specific tissues using site-specific recombinases. We also present a method for rapidly synthesizing histone gene arrays of any genotype using Golden Gate cloning technologies. These improvements facilitate the generation of histone mutant cells in various tissues at different stages of Drosophila development and provide an opportunity to apply forward genetic strategies to interrogate chromatin structure and gene regulation. [ABSTRACT FROM AUTHOR]

Objectives Anti-IL-6 receptor antibodies are clinically efficacious in the management of RA with an associated increase in Tregs; however, the role of functional Treg subsets has yet to be clarified. This study aimed to evaluate how functional Treg subsets are altered by IL-6 receptor blockade and to analyse the relationship between these Treg subsets and the clinical outcome of RA. Methods We collected frozen peripheral blood mononuclear cells (PBMCs) from 40 patients with RA who started tocilizumab (TCZ) with or without MTX and 11 healthy controls (HCs). We fractionated Tregs with flow cytometry based on markers of phenotype and function and measured the proportions of detailed Treg subsets sequentially from baseline to week 52. Results The proportions of resting Tregs (rTregs) and rTregs+activated Tregs (aTregs) were significantly lower in RA patients at baseline than in HCs. The proportions of all those CD127low Tregs, rTregs, aTregs and rTregs+aTregs were significantly increased with TCZ treatment. In patients treated with TCZ without MTX, rTreg were increased. Patients with an increase in the proportion of rTregs at week 12 had significantly less arthritis flares during the observation period. Conclusions Blocking the IL-6 receptor with TCZ increased the proportion of rTregs, a functional Treg subpopulation. Patients with an early increase in rTregs showed a favourable treatment course and this increase in rTregs may reflect molecular remission induced by IL-6 signal inhibition. [ABSTRACT FROM AUTHOR]

Food falsification is a pressing issue in today's food industry, with fraudulent substitution of costly ingredients with cheaper alternatives occurring globally. Consequently, developing straightforward and efficient diagnostic systems to detect such fraud is a top priority in scientific research. The aim of the work was to develop a test system and protocol for polymerase chain reaction (PCR) to detect in food products of animal origin the substitution of expensive meat raw materials for by-products of poultry processing. For this, real-time polymerase chain reaction (RT-PCR) was used, which allows determining the qualitative and quantitative substitution in raw and technologically prepared products. Other methods for detecting falsification – enzyme immunoassay (ELISA/ELISA) or express methods in the form of a lateral flow immunoassay are less informative. The extraction of nucleic acids for real-time polymerase chain reaction depends on the source matrix, with higher concentrations obtained from germ cells and parenchymal organs. Extraction from muscle and plant tissues is more challenging, but thorough grinding of these samples improves nucleic acid concentration by 1.5 times using DNA extraction kits. The selection of primers and fluorescent probes through GenBank and PCR Primer Design/DNASTAR software enables efficient amplification and identification of target chicken DNA fragments in various matrices. [ABSTRACT FROM AUTHOR]

The use of medicinal plants for managing diabetes and related conditions has been an integral part of traditional healthcare systems throughout the world including Nagaland, India. Authentic identification of these medicinal plants is crucial for their safe and effective use. A study was aimed for authentic identification of some anti-diabetic potential ethnomedicinal plants from Nagaland, India using DNA sequence based molecular characterization by amplifying and sequencing of ITS, rbcL and matK barcode regions. DNA barcode loci from the nuclear and chloroplast genomes from 15 different ethnomedicinal anti-diabetic plants of Nagaland, India, were studied for molecular characterisation. Based on the ITS, rbcL and matK region sequences, three main discrimination methods, i.e., BLAST, Phylogenetic tree and genetic distance, were adopted to identify the species. Utilising DNA markers for identification is both highly advantageous and efficient due to its reliability and rapidity. Successful amplification across species and high blast hits (100 % identity) highlighted their potential for molecular characterisation. Phylogenetic trees constructed using various models showed distinct clades and subclades, with matK revealing hypervariability and rbcL demonstrating consistent matches. Genetic distances revealed varying levels of similarity, with certain species establishing close relationships based on pairwise comparisons. GC% variations were detected, potentially indicating nucleotide composition differences and functional constraints among species genomes. The findings of this study highlight that the ITS, rbcL , and matK regions serve as effective markers for verifying the authenticity of anti-diabetic medicinal plants indigenous to Nagaland, India. [Display omitted] • DNA markers based species identification of 15 antidiabetic plants from Nagaland. • ITS, matK and rbcL based identification complemented with phonological identification. • Consistency in rbcL and matK regions showing reliability as DNA barcode markers. • Sequence length variations attributed to genomic differences among plants. [ABSTRACT FROM AUTHOR]

This work demonstrates for the first time using molecular markers alongside chromosomes and the intermediate phenotype that a specimen of Dorcadion is an accidental first‐generation hybrid. The analyses were based on two mitochondrial and five nuclear molecular markers. While analysing the putative parental taxa of the hybrid, it was revealed that even Dorcadion lugubre lugubre Kraatz is likely a hybridogenic taxon. Coincidentally, a new lead was discovered concerning the parental taxa of Dorcadion aethiops (Scopoli), already known as a hybridogenic species. This new evidence of hybridisation adds to the recent publications to strengthen the hypothesis that, in Dorcadionini, this phenomenon is relatively frequent, and speciation is often reticulate: New taxa can appear through introgressive hybridisation, explaining in part the extreme species richness of the group. [ABSTRACT FROM AUTHOR]

The primary objective of this research is to isolate and distinguish indigenous fungal strains capable of breaking down hydrocarbons from soils contaminated with oil. This study encompasses various geographical sites within the oilfields of the Kurdistan Region of Iraq (KRI). The extracted DNA from the hypha was used for polymerase chain reaction (PCR) amplification using a universal primer (ITS1/ITS2). PCR product sequencing analyses were compared with the other related sequences in GenBank (NCBI) for molecular evolutionary analyses. Results showed that, out of 68 screened fungal strains, only two genera (i.e., Aspergillus spp. and Penicillium sp.) were identified as the most potent hydrocarbon degrading fungi. This was consistent with the highest hydrocarbon degradation percentage values (91.76% and 81.87%) calculated for Aspergillus spp. and Penicillium sp., respectively, after two months of bioremediation. DNA sequence analysis confirmed the validity of the species as A. fumigatus-KU321562.1, A. flavus-MH270609.1, A. niger-K452260.1, and P. chrysogenum-MK696383.1. In conclusion, molecular techniques employed in fungal taxonomy provide a high degree of accuracy and enable identification that doesn't depend on cultivation, relying on stable genetic markers. These markers furnish reliable and uniform data, granting researchers the ability to fine-tune the level of detail, thus proving indispensable for comprehending fungal diversity and a wide array of practical uses. [ABSTRACT FROM AUTHOR]

Context.--There have been exceedingly few reports of epidermodysplasia verruciformis (EV) or EV-like lesions in the vulva. We describe the first observation of vulvar lesions displaying synchronous EV-like histology and conventional high-grade squamous intraepithelial lesion (HSIL), a finding hitherto unreported in medical literature. Objectives.--To describe this novel vulvar lesion with hybrid features of HSIL and EV, attempt to confirm the hypothesis of coinfection with a and b human papillomavirus (a-HPV and b-HPV) genotypes, and describe relevant underlying genetic mutations. Design.--Cases were retrospectively selected from our institutional archive. Detailed review of clinical information, histologic examination, and whole genome sequencing (WGS) were performed. Results.--Five samples from 4 different patients were included. Three of 4 patients had a history of either iatrogenic immune suppression or prior immune deficiency, and all 3 featured classic HSIL and EV changes within the same lesion. One patient had no history of immune disorders, presented with EV-like changes and multinucleated atypia of the vulva, and was the sole patient without conventional HSIL. By WGS, several uniquely mappable reads pointed toward infection with multiple HPV genotypes, including both a-HPVs and b-HPVs. Mutations in genes implicated in cell-mediated immunity, such as DOCK8, CARMIL2, MST1, and others, were also found. Conclusions.--We provide the first description of vulvar lesions harboring simultaneous HSIL and EV features in the English-language literature, a phenomenon explained by coinfection with a-HPV and b-HPV genotypes. The finding of EV-like changes in a vulvar specimen should prompt assessment of the patient's immune status. [ABSTRACT FROM AUTHOR]

Carbon ion radiotherapy (CIRT) for pediatric cancer is currently limited because of the unknown risk of induction of secondary cancers. Medulloblastoma of Ptch1+/– mice offers a unique experimental system for radiation-induced carcinogenesis, in which tumors are classified into spontaneous and radiation-induced subtypes based on their features of loss of heterozygosity (LOH) that affect the wild-type Ptch1 allele. The present study aims to investigate in young Ptch1+/– mice the carcinogenic effect, and its age dependence, of the low-linear energy transfer (LET, ∼13 keV/µm) carbon ions, to which normal tissues in front of the tumor are exposed during therapy. We irradiated Ptch1+/– mice at postnatal day (P) 1, 4, or 10 with 290 MeV/u carbon ions (0.05–0.5 Gy; LET, 13 keV/µm) and monitored them for medulloblastoma development. Loss of heterozygosity of seven genetic markers on chromosome 13 (where Ptch1 resides) was studied to classify the tumors. Carbon ion exposure induced medulloblastoma most effectively at P1. The LOH patterns of tumors were either telomeric or interstitial, the latter occurring almost exclusively in the irradiated groups, allowing the use of interstitial LOH as a biomarker of radiation-induced tumors. Radiation-induced tumors developed during a narrow age window (most strongly at P1 and only moderately at P4, with suppressed tumorigenesis at P10). Calculated using previous results using 137Cs gamma rays, the values for relative biological effectiveness (RBE) regarding radiation-induced tumors were 4.1 (3.4, 4.8) and 4.3 (3.3, 5.2) (mean and 95% confidence interval) for exposure at P1 and 4, respectively. Thus, the RBE of carbon ions for medulloblastoma induction in Ptch1+/– mice was higher than the generally recognized RBE of 1–2 for cell killing, chromosome aberrations, and skin reactions. [ABSTRACT FROM AUTHOR]

Background The ganglionic eminences (GE) are fetal-specific structures that give rise to gamma-aminobutyric acid (GABA)- and acetylcholine-releasing neurons of the forebrain. Given the evidence for GABAergic, cholinergic, and neurodevelopmental disturbances in schizophrenia, we tested the potential involvement of GE neuron development in mediating genetic risk for the condition. Study Design We combined data from a recent large-scale genome-wide association study of schizophrenia with single-cell RNA sequencing data from the human GE to test the enrichment of schizophrenia risk variation in genes with high expression specificity for developing GE cell populations. We additionally performed the single nuclei Assay for Transposase-Accessible Chromatin with Sequencing (snATAC-Seq) to map potential regulatory genomic regions operating in individual cell populations of the human GE, using these to test for enrichment of schizophrenia common genetic variant liability and to functionally annotate non-coding variants-associated with the disorder. Study Results Schizophrenia common variant liability was enriched in genes with high expression specificity for developing neuron populations that are predicted to form dopamine D1 and D2 receptor-expressing GABAergic medium spiny neurons of the striatum, cortical somatostatin-positive GABAergic interneurons, calretinin-positive GABAergic neurons, and cholinergic neurons. Consistent with these findings, schizophrenia genetic risk was concentrated in predicted regulatory genomic sequence mapped in developing neuronal populations of the GE. Conclusions Our study implicates prenatal development of specific populations of GABAergic and cholinergic neurons in later susceptibility to schizophrenia, and provides a map of predicted regulatory genomic elements operating in cells of the GE. [ABSTRACT FROM AUTHOR]

Heat stress poses a significant environmental challenge that profoundly impacts wheat productivity. It disrupts vital physiological processes such as photosynthesis, by impeding the functionality of the photosynthetic apparatus and compromising plasma membrane stability, thereby detrimentally affecting grain development in wheat. The scarcity of identified marker trait associations pertinent to thermotolerance presents a formidable obstacle in the development of marker-assisted selection strategies against heat stress. To address this, wheat accessions were systematically exposed to both normal and heat stress conditions and phenotypic data were collected on physiological traits including proline content, canopy temperature depression, cell membrane injury, photosynthetic rate, transpiration rate (at vegetative and reproductive stage and 'stay-green'. Principal component analysis elucidated the most significant contributors being proline content, transpiration rate, and canopy temperature depression, which exhibited a synergistic relationship with grain yield. Remarkably, cluster analysis delineated the wheat accessions into four discrete groups based on physiological attributes. Moreover, to explore the relationship between physiological traits and DNA markers, 158 wheat accessions were genotyped with 186 SSRs. Allelic frequency and polymorphic information content value were found to be highest on genome A (4.94 and 0.688), chromosome 1A (5.00 and 0.712), and marker Xgwm44 (13.0 and 0.916). Population structure, principal coordinate analysis and cluster analysis also partitioned the wheat accessions into four subpopulations based on genotypic data, highlighting their genetic homogeneity. Population diversity and presence of linkage disequilibrium established the suitability of population for association mapping. Additionally, linkage disequilibrium decay was most pronounced within a 15–20 cM region on chromosome 1A. Association mapping revealed highly significant marker trait associations at Bonferroni correction P < 0.00027. Markers Xwmc418 (located on chromosome 3D) and Xgwm233 (chromosome 7A) demonstrated associations with transpiration rate, while marker Xgwm494 (chromosome 3A) exhibited an association with photosynthetic rates at both vegetative and reproductive stages under heat stress conditions. Additionally, markers Xwmc201 (chromosome 6A) and Xcfa2129 (chromosome 1A) displayed robust associations with canopy temperature depression, while markers Xbarc163 (chromosome 4B) and Xbarc49 (chromosome 5A) were strongly associated with cell membrane injury at both stages. Notably, marker Xbarc49 (chromosome 5A) exhibited a significant association with the 'stay-green' trait under heat stress conditions. These results offers the potential utility in marker-assisted selection, gene pyramiding and genomic selection models to predict performance of wheat accession under heat stress conditions. [ABSTRACT FROM AUTHOR]

Background Objective Methods Results Conclusions Emerging research implicates tau protein dysregulation in the pathophysiology of Huntington's disease.This study investigated skin tau quantification as a potential biomarker for Huntington's disease and its correlation with disease burden outcomes.In this cross‐sectional study, we measured skin tau levels using enzyme‐linked immunosorbent assay in 23 Huntington's disease mutations carriers and eight control subjects, examining group discrimination, correlations with genetic markers, clinical assessments, and neuroimaging data. Brain atrophy was quantified by both volumetric measurements from brain segmentation and a voxel‐based morphometry approach.Our findings showed elevated skin tau levels in manifest Huntington's disease compared with premanifest and healthy controls. These levels correlated with CAG repeat length, CAG‐Age‐Product score, composite Unified Huntington's Disease Rating Scale Total Motor Score, cognitive assessments, and disease‐related cortical and subcortical volumes, all independent of age and gender. Using skin tau levels in cluster analysis along with genetic and clinical measures led to improved subject stratification, providing enhanced distinction and validity of clusters.This study not only confirms the feasibility of skin tau quantification in Huntington's disease but also establishes its potential as a biomarker for enhancing group classification and assessing disease severity across the Huntington's disease spectrum, opening new directions in biomarker research. © 2024 International Parkinson and Movement Disorder Society. [ABSTRACT FROM AUTHOR]

Background: Amblyomma spp. ticks, known for their long mouthparts, bright ornate appearance and aggressive hunting behaviour, are vectors of a number of important pathogens. In southern Africa, 17 Amblyomma spp. are currently documented. Of these species, Amblyomma hebraeum and Amblyomma variegatum have been well studied due to their wide geographical range and their status as competent vectors of pathogens that are of veterinary and medical importance. Studies on other Amblyomma spp. in southern Africa have been neglected, fostering ongoing debates on the validity of certain species such as Amblyomma pomposum. This study investigated the inter- and intra-species variation of Amblyomma ticks collected in southern Africa, focusing on resolving the dispute about A. pomposum and A. variegatum being distinct species. Methods: Four Amblyomma tick species were collected from Angola, Mozambique, South Africa, Zambia and Zimbabwe, and were identified morphologically as Amblyomma eburneum (208), A. hebraeum (4758), A. pomposum (191) and A. variegatum (2577) using identification keys. Gene amplification targeting the 12S and 16S rRNA, cytochrome oxidase I, cytochrome B and internal transcribed spacer-2 genes was conducted for 204 ticks, for which varying success was achieved during amplification for each of the markers. Maximum likelihood analyses were performed in IQ-TREE. Results: The phylogenetic topologies and ABGD analyses of each individual gene clustered A. pomposum within the A. variegatum clade, while clearly separating A. eburneum and A. hebraeum from all other species. None of the genetic markers indicated intraspecific structuring on the basis of geographical origin, despite great distances between sampling sites. Conclusion: Our study concludes that there is insufficient molecular evidence to differentiate A. pomposum and A. variegatum from each other. We highlight the need for whole mitochondrial genome sequencing of these two species to resolve the ongoing controversies. Furthermore, we propose mating and hybrid viability studies between the two species to confirm their reproductive isolation. [ABSTRACT FROM AUTHOR]

Background: By 2020, obstructive sleep apnea (OSA), a prevalent respiratory disorder, had affected 26.6–43.2% of males and 8.7–27.8% of females worldwide. OSA is associated with conditions such as hypertension, diabetes, and tumor progression; however, the precise underlying pathways remain elusive. This study aims to identify genetic markers and molecular mechanisms of OSA to improve understanding and treatment strategies. Methods: The GSE135917 dataset related to OSA was obtained from the GEO database. Differentially expressed genes (DEGs) were subsequently identified. Weighted gene co-expression network analysis (WGCNA) was conducted to pinpoint disease-associated genes. The intersection of these data enabled the identification of potential diagnostic DEGs. Further analyses included Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment studies, exploration of protein–protein interactions based on these genes, and an examination of immune infiltration. Mendelian randomization was employed to validate core genes against the Genome-Wide Association Study database. Results: A total of 194 DEGs were identified in this study. WGCNA network analysis highlighted 2,502 DEGs associated with OSA. By intersecting these datasets, 53 diagnostic DEGs primarily involved in metabolic pathways were identified. Significant alterations were observed in immune cell populations, including memory B cells, plasma cells, naive CD4 T cells, M0 macrophages, and activated dendritic cells. CETN3, EEF1E1, PMM2, GTF2A2, and RRM2 emerged as hub genes implicated in the pathogenesis. A line graph model provides diagnostic insights. Mendelian randomization analysis confirmed a causal link between CETN3 and GTF2A2 with OSA. Conclusion: Through WGCNA, this analysis uncovered significant genetic foundations of OSA, identifying 2,502 DEGs and 194 genes associated with the disorder. Among these, CETN3 and GTF2A2 were found to have causal relationships with OSA. [ABSTRACT FROM AUTHOR]

The objective of this study was to assess the relative contributions of genetic and environmental factors to variation in palatal parameters in twins with completed maxillary growth. The subjects of this study comprised digital dental casts of 50 monozygotic and 35 dizygotic twin pairs. The subjects' average age was 17.95 ± 2.83 years. Zygosity determination was carried out using 15 specific DNA markers and an amel fragment of the amelogenin gene. The interdental distances were measured between selected dental landmarks at the occlusal and gingival planes. The palatal height, surface area and volume were measured between the gingival plane and the midpalate suture. High heritability estimates were observed for all transverse intra-arch measurements. The palate height (a2 = 0.8), dental arch width in the molar area (a2 = 0.86), palatal surface area (a2 = 0.61) and palate volume (a2 = 0.69) were under strong additive genetic control. Moderate genetic dominance was observed for dental arch widths at the gingival line in the canine (d2 = 0.5) and premolar regions (d2 = 0.78–0.81). Sexual dimorphism was shown, with males exhibiting a greater arch width, palate surface area and volume than females (p < 0.01). The majority of palate parameters variation in twins was controlled by genetic effects, and most were highly heritable. [ABSTRACT FROM AUTHOR]

Access to safe drinking water sources and appropriate sanitation facilities remains a dream in low and middle-income countries including South Africa. This study identified the origin of faecal pollution by using quantitative polymerase chain reaction (qPCR) targeting host-specific Bacteroidales genetic markers to track the distribution of human-specific (BacHum) and animal-specific (cattle—BacCow, chicken—Cytb, pig—Pig-2-Bac, dog—BacCan) markers in water sources used by rural communities of the Vhembe District Municipality (VDM). Results revealed the prevalence of BacHum, BacCow, and BacCan in all surface water sources in Thulamela Local Municipality (TLM) and Collins Chabane Local Municipality (CLM) during wet (100%) and dry seasons (50–75%). Cytb was not detected in untreated spring water in TLM and CLM, and Pig-2-Bac was not detected in untreated hand-dug well water in TLM during both seasons. Household-level analysis detected Cytb (28.8% wet, 17.5% dry), BacHum (34.4% wet, 25% dry for Pig-2-Bac) in stored untreated spring water in CLM, and Cytb (42.9% wet, 28.5% dry) in untreated hand-dug well water in TLM. Despite differences in detection frequencies of host-specific Bacteroidales, the study highlights the public health concern of faecal pollution in rural VDM households. [ABSTRACT FROM AUTHOR]

Since European settlement of Australia, substantial areas of subtropical rainforest have been cleared. More recently, effort is being made to restore areas of this ecological community. The financial investment and increasing reliance on ecological restoration in biodiversity conservation justifies a need for better understanding of how to improve success at the genetic level. This research measures genetic diversity (allelic richness [Rs], expected heterozygosity [He], and inbreeding using Wright's coefficient [FIS]) for expected neutral DNA markers in three Australian subtropical rainforest trees—White booyong (Argyrodendron trifoliolatum), Watkin's fig (Ficus watkinsiana), and Native tamarind (Diploglottis australis). Wild and restored populations of these species were compared in two neighboring regions in Northeast New South Wales (the Tweed Caldera and the Big Scrub). There were no statistically significant differences in Rs or He between wild and restored populations for any of the target species. Inbreeding was significantly higher in one of the restored versus wild population comparisons: F. watkinsiana in the Tweed (restored F = 0.20; wild F = −0.02; p = 0.01). The comparable levels of genetic diversity observed in restored and wild populations targeted in this study are likely due to informed practitioner perspectives and practices, staged plantings over several years, and high genetic diversity and low genetic differentiation within source populations. [ABSTRACT FROM AUTHOR]

Next‐generation sequencing (NGS) technologies have expanded the spectrum of forensic DNA analysis by facilitating efficient and precise genotyping of a large number of genetic markers. Yet, challenges persist regarding complex sample processing and assurance of equal molar concentrations across pooled samples. Since optimal cluster density is crucial for sequencing performance, the determination of both quantity and quality is indispensable for library preparation. In this study, we investigated the application of the Agilent 2100 Bioanalyzer for library quality control, as studies for forensic approaches, particularly for highly degraded postmortem samples, are rare. Our analysis encompassed assessing total DNA concentrations, fluorescence unit (FU) values, and adapter dimer concentrations in purified DNA libraries derived from buccal swabs and tissue samples of decomposed corpses. The sensitivity study tested a serial dilution derived from buccal swabs and revealed a decrease in FU values and an increase in adapter dimers with declining DNA input concentrations. Deviations in total DNA concentrations and average peak heights between the Agilent 2100 Bioanalyzer runs indicated a lack of repeatability in data and presented challenges in accurate quantification, which was also observed in previous studies. Yet, the analysis of degraded samples from decomposed human remains has shown the ability to detect adapter dimer concentrations, which can be crucial for the quality of subsequent NGS library preparation and sequencing success. Therefore, the Agilent 2100 Bioanalyzer proves to be a valuable tool for NGS quality control. [ABSTRACT FROM AUTHOR]

We consider random sample splitting for estimation and inference in high‐dimensional generalized linear models (GLMs), where we first apply the lasso to select a submodel using one subsample and then apply the debiased lasso to fit the selected model using the remaining subsample. We show that a sample splitting procedure based on the debiased lasso yields asymptotically normal estimates under mild conditions and that multiple splitting can address the loss of efficiency. Our simulation results indicate that using the debiased lasso instead of the standard maximum likelihood method in the estimation stage can vastly reduce the bias and variance of the resulting estimates. Furthermore, our multiple splitting debiased lasso method has better numerical performance than some existing methods for high‐dimensional GLMs proposed in the recent literature. We illustrate the proposed multiple splitting method with an analysis of the smoking data of the Mid‐South Tobacco Case–Control Study. [ABSTRACT FROM AUTHOR]

Background: Porcine Reproductive and Respiratory Syndrome (PRRS) is one of the most challenging viral diseases that cause substantial economic losses in the pig industry worldwide. The clinical signs of PRRS depend on, among others, the immunomodulatory properties of the PRRS virus strain, farm health status, herd immunity, and host genetics. The high virulence and mutation rate of PRRS virus limit the efficacy of vaccination programs. In recent years, several candidate genetic markers associated with PRRS resilience have been identified, and selective breeding was suggested as an additional approach to control PRRS under field conditions. Even so, it is essential to investigate the effects of these genetic markers on pigs' productivity. Our study aimed to assess the association between seven previously reported candidate genetic markers for host response to PRRS (rs80800372 in GBP1, rs340943904 in GBP5, rs322187731 in GBP6, rs1107556229 in CD163, rs338508371 in SGK1, rs80928141 in TAP1, and a 275-bp insertion in the promoter of MX1) and production traits in pigs under non-challenging conditions. Results: About 600 high-health Duroc pigs were genotyped for the selected genetic markers and their effects on production traits (live body weight, carcass weight, backfat thickness, intramuscular fat content and composition) were assessed using a linear model. The genetic markers GBP5_rs340943904, GBP6_rs322187731, CD163_rs1107556229, and the 275-bp insertion at the promoter of MX1 showed no relevant associations with growth and carcass traits at slaughter. Regarding GBP1_rs80800372 (WUR1000125), the favourable G allele for PRRS resilience displayed significant additive effects on backfat thickness (+ 1.18 ± 0.42 mm; p = 0.005) and lean content (-1.72 ± 0.56%; p ≤ 0.01) at slaughter. In addition, the genetic markers SGK1_rs338508371 and TAP1_rs8092814 were associated with the palmitoleic content in gluteus medius, without affecting the total of the monounsaturated fatty acids. Conclusions: Our results indicate that genetic markers for PRRS resilience have no relevant effects on growth and carcass traits in pigs reared under non-challenging conditions, except for GBP1_rs80800372 where the favourable allele for PRRS response has a negative impact on lean content. Therefore, since the effects of GBP1_rs80800372 were attributed to the causal variant GBP5_rs340943904, it seems beneficial to select pigs for the genetic marker at GBP5 instead of GBP1. Overall, pigs might be selected for enhanced PRRS resilience without compromising their overall productivity. [ABSTRACT FROM AUTHOR]

Epilepsy can be caused by a variety of causes, such as inborn errors of metabolism, organic acid disorders are the most significant type of metabolic disorders that cause seizures. The clinical manifestations of these diseases are generally nonspecific, and the types of seizures are different. Screening for multisystem clinical symptoms and identifying the underlying etiology are crucial for early treatment of epileptic seizures. This article provides a comprehensive summary of the pathogenesis, clinical features, diagnosis and treatment of epilepsy associated with organic acid metabolism disorders. Furthermore, relevant literature has also been reviewed to assist clinicians in the diagnosis of cases characterized by the coexistence of multisystemic symptoms and epileptic manifestations. [ABSTRACT FROM AUTHOR]

Purpose: Alzheimer's disease (AD) is a common neurodegenerative disease, which can lead to cognitive impairment and dementia. Since AD is tightly associated with aging and cellular senescence, objective of this study was to investigate the association between senescence-related genes and proteins (SRGs and SRPs) and the development of AD. Design: The whole study was based on transcriptomic analysis of control and AD brain tissues and Mendelian randomization (MR) analysis. Methods: For transcriptomic analysis, GSE5281 dataset from GEO database contains the transcriptomic data of human brain tissues (n = 161) from control group and AD patients. The expression of SRGs in control and AD brain tissues were compared by Student's t test. For MR analysis, the instrumental singlenucleotide polymorphisms (SNPs) associated with 110 SRPs were filtered and selected from a large genome-wide association study (GWAS) for plasma proteome. The causality between plasma levels of SRPs and AD was explored using GWAS data of AD from Lambert et al. (17,008 cases and 37,154 controls) and further validated by using data from FinnGen consortium (6,489 patients and 170,489 controls). MR estimate was performed using the inversevariance weighted (IVW) method and the heterogeneity and pleiotropy of results were tested. Results: Transcriptomic analysis identified 36 up-regulated (including PLAUR) and 8 down-regulated SRGs in AD brain tissues. In addition, the MR results at both discovery and validation stages supported the causality between plasma levels of PLAUR (IVW-p = 3.04E-2, odds ratio [OR]= 1.15), CD55 (IVW-p = 1.56E-3, OR= 0.86), and SERPINE2 (IVW-p = 2.74E-2, OR= 0.91) and the risk of AD. Conclusion: Our findings identified that PLAUR, as an SRG, may take part in the development of AD and found that high plasma levels of PLAUR was associated with increased risk of AD, indicating that this gene was a risk factor for this disease and providing the rationale of existing drugs or new preventative and therapeutic strategies. [ABSTRACT FROM AUTHOR]

Background: The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed. Results: Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species. Conclusions: Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus. [ABSTRACT FROM AUTHOR]

Simple Summary: This article explores the impact of chemotherapy on ovarian function in female cancer survivors, emphasizing the importance of preserving fertility alongside cancer treatment. Chemotherapy-induced ovarian failure (CIOF) poses a significant concern, affecting patients' quality of life. The study aims to identify genetic markers predictive of CIOF through a systematic review of existing literature. The review identifies four relevant studies focusing on genetic factors associated with CIOF. Findings suggest potential associations between genetic variations, like CYP3A4*1B and GSTA1, and CIOF risk. Moreover, BRCA mutations may influence ovarian reserve recovery post-chemotherapy. While current assessment methods rely on biochemical tests and ultrasound imaging, genetic testing holds promise for personalized fertility preservation strategies. Integrating genetic markers into clinical practice could revolutionize decision making in fertility preservation for female cancer survivors, enhancing reproductive potential preservation. Background: Recent advances in cancer diagnosis and treatment have significantly improved survival rates among women of reproductive age facing cancer. However, the potential iatrogenic loss of fertility caused by chemotherapeutic agents underscores the need to understand and predict chemotherapy-induced ovarian damage. This study addresses this gap by systematically reviewing the literature to investigate genetic markers associated with chemotherapy-induced ovarian failure (CIOF). Objective: The primary objective is to identify genetic markers linked to CIOF, contributing to a comprehensive understanding of the factors influencing fertility preservation in female cancer survivors. Methods: A systematic review was conducted using PubMed, EMBASE, Web of Science, Scopus, and OVID electronic databases from inception through December 2023. Studies were included if they featured genomic assessments of genes or polymorphisms related to CIOF in women with histologically confirmed tumors. Exclusion criteria comprised in vitro and animal studies, reviews, and pilot studies. The resulting four human-based studies were scrutinized for insights into genetic influences on CIOF. Results: Of the 5179 articles initially identified, four studies met the inclusion criteria, focusing on alkylating agents, particularly cyclophosphamide, and anthracyclines. Su et al. explored CYP3A41B variants, revealing modified associations with CIOF based on age. Charo et al. investigated GSTA1 and CYP2C19 polymorphisms, emphasizing the need to consider age and tamoxifen therapy in assessing associations. Oktay et al. delved into the impact of BRCA mutations on anti-Müllerian hormone (AMH) levels post-chemotherapy, supported by in vitro assays. Van der Perk et al. focused on childhood cancer survivors and revealed significant associations of CYP3A43 and CYP2B6*2 SNPs with AMH levels. Conclusions: This systematic review analyzes evidence regarding genetic markers influencing CIOF, emphasizing the complex interplay of age, specific genetic variants, and chemotherapy regimens. The findings underscore the need for a personalized approach in assessing CIOF risk, integrating genetic markers with traditional ovarian reserve testing. The implications of this study extend to potential advancements in fertility preservation strategies, offering clinicians a comprehensive baseline assessment for tailored interventions based on each patient's unique genetic profile. Further research is essential to validate these findings and establish a robust framework for integrating genetic markers into clinical practice. [ABSTRACT FROM AUTHOR]

Simple Summary: The current investigation identifies differentially expressed genes that specifically influence the serous subtype of ovarian cancer. This subtype accounts for around three-quarters of ovarian cancer cases. To identify these genes, transcriptomic profiles of serous ovarian cancer and non-cancerous tissue samples were extracted from the Gene Expression Omnibus. Differentially expressed genes were derived using GEO2R tool analyses; genes consistently found among upregulated genes in these profiles were considered to be a serous gene set. Next, the serous gene set was examined for its ontological function using the Molecular Signatures Database and its mutational impact on the gene expression profile of high-grade serous ovarian (HGSO) adenocarcinoma. Results showed that 26 genes are amplified in over 5% of HGSO cancer patients, and many of these amplified genes are related to the cell cycle. These cell cycle-related genes were also identified as being involved in the recurrence of serous ovarian cancer. Overall, this study identifies genes that are potential prognostic markers for serous ovarian cancer. The objective of this study was to identify differentially expressed genes and their potential influence on the carcinogenesis of serous-type ovarian cancer tumors. Serous cancer is an epithelial ovarian cancer subtype and is the most common type of ovarian cancer. Transcriptomic profiles of serous cancer and non-cancerous datasets were obtained from the Gene Expression Omnibus (GEO-NCBI). Differentially expressed genes were then derived from those profiles; the identified genes were consistently upregulated in three or more transcriptomic profiles. These genes were considered as the serous ovarian cancer gene set for further study. The serous gene set derived from the transcriptomic profiles was then evaluated for ontological functional analysis using the Molecular Signatures Database. Next, we examined the mutational impact of this serous gene set on the transcriptomic profile of high-grade serous ovarian (HGSO) adenocarcinoma using the cBioPortal database. Results from OncoPrint revealed that 26 genes were amplified in more than 5% of HGSO cancer patients. Interestingly, several of these genes are involved in cell cycle processes, including genes ATPase family AAA domain containing 2 (ATAD2), recQ-like helicase 4 (RECQL4), cyclin E1 (CCNE1), anti-silencing function 1B histone chaperone (ASF1B), ribonuclease H2 subunit A (RNASEH2A), structural maintenance of chromosome 4 (SMC4), cell division cycle associated 20 (CDC20), and cell division cycle associated 8 (CDCA8). The receiver operating characteristic (ROC) curve results also revealed higher specificity and sensitivity for this subtype of tumors. Furthermore, these genes may affect the recurrence of serous ovarian carcinogenesis. Overall, our analytical study identifies cell cycle-related genes that can potentially be targeted as diagnostic and prognostic markers for serous ovarian cancer. [ABSTRACT FROM AUTHOR]

Simple Summary: As global meat production is rapidly increasing, it is important to find sustainable sources of meat. Horsemeat is a viable alternative due to its lower environmental impact and high nutritional value. In this study, bioinformatics was used to determine genetic markers (SNPs) that could improve horsemeat production by focusing on orthologous genes related to meat yield in cattle and in QTLs for body weight and body size. Out of 268 markers, 27 SNPs in key genes such as LCORL, LASP1, IGF1R, and MSTN were prioritized. These findings can help small-scale farmers to breed horses with better meat yield. In addition, this information will be valuable for large-scale genetic studies to further evaluate these markers and improve breeding programs. This work lays the foundation for a better understanding of horse genetics and the advancement of horse breeding. In view of the predicted significant increase in global meat production, alternative sources such as horsemeat are becoming increasingly important due to their lower environmental impact and high nutritional value. This study aimed to identify SNP markers on the GeneSeek® Genomic Profiler™ Equine (Neogen, Lansing, MI, USA) that are important for horsemeat production traits. First, orthologous genes related to meat yield in cattle and common genes between horses and cattle within QTLs for body size and weight were identified. Markers for these genes were then evaluated based on predicted variant consequences, GERP scores, and positions within constrained elements and orthologous regulatory regions in pigs. A total of 268 markers in 57 genes related to meat production were analyzed. This resulted in 27 prioritized SNP markers in 22 genes, including notable markers in LCORL, LASP1, IGF1R, and MSTN. These results will benefit smallholder farmers by providing genetic insights for selective breeding that could improve meat yield. This study also supports future large-scale genetic analyses such as GWAS and Genomic Best Linear Unbiased Prediction (GBLUP). The results of this study may be helpful in improving the accuracy of genomic breeding values. However, limitations include reliance on bioinformatics without experimental validation. Future research can validate these markers and consider a wider range of traits to ensure accuracy in equine breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: The body size of ducks reflects their skeletal development and growth status. However, the rapid growth and early large body size of meat ducks negatively affect subsequent slaughter and processing. Therefore, it is necessary to identify candidate genetic markers and genes involved in body size regulation. In this study, we conducted genome-wide association studies (GWASs) on the body length (BL), keel bone length (KBL), neck length (NL), and breast width (BrW) of 42-day-old Pekin ducks (Anas platyrhynchos domestica). The results showed that BL and KBL had similar GWAS signals. Based on these results, we further identified causal haplotypes and candidate genes affecting BL and KBL. This research provides new genetic insights into the growth and development of Pekin ducks and has important implications for their breeding improvement. Body size is an important growth indicator in ducks and is a primary selection criterion for physical improvement. An excessively rapid growth rate in meat ducks can result in excessive body size, which may hinder subsequent processing and slaughter operations. However, only a few molecular markers related to body size have been studied in meat ducks. In this study, we performed a genome-wide association study (GWAS) to identify candidate genes and QTLs affecting body length (BL), keel bone length (KBL), neck length (NL), and breast width (BrW) in Pekin ducks (Anas platyrhynchos domestica). Our results indicate the significant SNP for NL is located within a pseudogene, whereas the significant SNP for BrW is located in an intergenic region. More importantly, our analysis identified a haplotype that was significantly associated with both BL and KBL. This haplotype, containing 48 single-nucleotide polymorphisms (SNPs), is localized within the XKR4 gene. The identification of this haplotype suggests that XKR4 may be a key candidate gene influencing BL and KBL in Pekin ducks. These findings have important implications for the breeding and genetic improvement of Pekin ducks, and provide valuable insights into the genetic architecture of body size traits in this species. [ABSTRACT FROM AUTHOR]

Environmental variations initiate chromatin modifications, leading to the exchange of histone subunits or the repositioning of nucleosomes. The phosphorylated histone variant H2A.X (γH2A.X) is recognized for the formation of foci that serve as established markers of DNA double-strand breaks (DSBs). Nevertheless, the precise roles of H2A.X in the cellular response to genotoxic stress and the impact of the plant hormone abscisic acid (ABA) remain incompletely understood. In this investigation, we implemented CRISPR/Cas9 technology to produce loss-of-function mutants of AtHTA3 and AtHTA5 in Arabidopsis. The phenotypes of the athta3 and athta5 single mutants were nearly identical to those of the wild-type Col-0. Nevertheless, the athta3 athta5 double mutants exhibited aberrant embryonic development, increased sensitivity to DNA damage, and higher sensitivity to ABA. The RT-qPCR analysis indicates that AtHTA3 and AtHTA5 negatively regulate the expression of AtABI3, a fundamental regulator in the ABA signaling pathway. Subsequent investigation demonstrated that AtABI3 participates in the genotoxic stress response by influencing the expression of DNA damage response genes, such as AtBRCA1, AtRAD51, and AtWEE1. Our research offers new insights into the role of H2A.X in the genotoxic and ABA responses of Arabidopsis. [ABSTRACT FROM AUTHOR]

The global challenge of feeding an ever-increasing population to maintain food security requires novel approaches to increase crop yields. Photosynthesis, the fundamental energy and material basis for plant life on Earth, is highly responsive to environmental conditions. Evaluating the operational status of the photosynthetic mechanism provides insights into plants' capacity to adapt to their surroundings. Despite immense effort, photosynthesis still falls short of its theoretical maximum efficiency, indicating significant potential for improvement. In this review, we provide background information on the various genetic aspects of photosynthesis, explain its complexity, and survey relevant genetic engineering approaches employed to improve the efficiency of photosynthesis. We discuss the latest success stories of gene-editing tools like CRISPR-Cas9 and synthetic biology in achieving precise refinements in targeted photosynthesis pathways, such as the Calvin-Benson cycle, electron transport chain, and photorespiration. We also discuss the genetic markers crucial for mitigating the impact of rapidly changing environmental conditions, such as extreme temperatures or drought, on photosynthesis and growth. This review aims to pinpoint optimization opportunities for photosynthesis, discuss recent advancements, and address the challenges in improving this critical process, fostering a globally food-secure future through sustainable food crop production. [ABSTRACT FROM AUTHOR]

The study of the state of Baikal endemic sponge populations is of great interest because of the occurrence of mass mortalities and disease in recent decades. To identify possible signs of species vulnerability to extinction, it is crucial to develop appropriate genetic markers that help developing measures for conservation. In this paper, we describe the population genetic structure of the Baikal endemic sponge Lubomirskia baikalensis examined with the set of microsatellite markers we developed. We analysed 251 samples from eight locations that cover all three basins of Lake Baikal. A genetic subdivision into three clusters was revealed. Such a structure can be explained mainly by the low ability of larvae to disperse. Despite the presence of dead and diseased individuals in all studied locations, all populations were in Hardy–Weinberg equilibrium and no bottleneck effect was found at all. This is the first time that a genetic connectivity study has been performed for L. baikalensis, a species endemic of Lake Baikal. Reconstruction of the changes in the effective population size agrees with the results obtained during drill sample analysis and it demonstrates that the effective population size was 55.5 times lower about 24,000 years ago, which indicates that apparently there is no threat of extinction of the Baikal endemic sponges at present. [ABSTRACT FROM AUTHOR]

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a devastating fungal disease that affects wheat globally. The planting of resistant cultivars is the most cost-effective strategy for controlling this disease. The Huanghuai region, as a major wheat-growing area, plays a crucial role in the spread and prevalence of wheat stem rust in China. In this study, 64 wheat accessions from this region were tested at the adult stage against two major Pgt races, 34MKGQM and 21C3CTHQM. DNA markers associated with the known resistance genes Sr31, Sr24, Sr25, Sr26, and Sr38 were measured to determine their presence in the tested accessions. In the 2023 field tests, 5 (7.8%) accessions were immune to 21C3CTHQM and 34MKGQM, while 35 (54.7%) and 39 (60.9%) were moderately resistant and resistant, respectively. The remaining 20 (30.7%) accessions were moderately susceptible and susceptible. In the 2024 tests, 12 (18.8%) and 14 (21.9%) entries were immune to both races; 29 (45.3%) and 30 (46.9%) were moderately resistant and resistant, respectively. Only two cultivars, Xinong 816 and Yimai 211, were immune in both years, and three entries showed some degrees of resistance in both years. Seven cultivars, including Zhongzhimai 23, Longxing 1, Yunong 937, Huaguan 301, Wanke 800, Shaanhe 285, and Yunong 612, showed increased susceptibility. DNA markers showed that 30 entries carried Sr31, while 6 entries carried Sr38. Genes Sr24, Sr25, and Sr26, which confer good resistance to the globally prevalent cultivars TKTTF and TTTRF, were absent from the set of tested entries. While this study surveyed the resistance levels of a cross-section of wheat from the southern part of the Huanghuai region and confirmed the presence of two known resistance genes, the basis of immunity or high levels of resistance in several lines remains obscure. [ABSTRACT FROM AUTHOR]

Simple Summary: This study genetically characterizes the Cape Verde palm tree, Phoenix atlantica, exploring its genetic differentiation and recent divergence from its relative, Phoenix dactylifera, while also examining its significance for conservation efforts and enhancing our understanding of the historical trajectories of African palm trees. The Cape Verde palm tree, Phoenix atlantica, holds significant ecological and cultural importance within the Cape Verde archipelago. However, its genetic distinctiveness has been questioned due to its close relationship and morphological similarity to the date palm (Phoenix dactylifera). In this study, we used an expanded sample set, 18 simple sequence repeat (SSR) markers, and a plastid minisatellite to characterize P. atlantica in Cape Verde and investigate its relationship with other Phoenix species. Our findings identify genetic markers that differentiate the P. atlantica genetic pool, including a unique fixed allele. We also provide evidence of the recent divergence of P. atlantica from Northern African date palm populations, suggesting a relatively recent colonization of Cape Verde by palm trees. Additionally, we characterized the genetic composition of palm tree populations across three Cape Verde islands, concluding that wild samples from certain populations in Boavista and Sal are best suited for establishing a seed and/or germplasm bank for replantation efforts, representing a crucial step for the conservation of Cape Verde's natural heritage. Overall, our results enhance the understanding of the historical trajectories and genetic characterization of palm trees in Africa, offering valuable insights for conservation strategies. [ABSTRACT FROM AUTHOR]

Introduction: Predicting the performance (yield or other integrative traits) of cultivated plants is complex because it involves not only estimating the genetic value of the candidates to selection, the interactions between the genotype and the environment (GxE) but also the epistatic interactions between genomic regions for a given trait, and the interactions between the traits contributing to the integrative trait. Classical Genomic Prediction (GP) models mostly account for additive effects and are not suitable to estimate non-additive effects such as epistasis. Therefore, the use of machine learning and deep learning methods has been previously proposed to model those non-linear effects. Methods: In this study, we propose a type of Artificial Neural Network (ANN) called Convolutional Neural Network (CNN) and compare it to two classical GP regression methods for their ability to predict an integrative trait of sorghum: aboveground fresh weight accumulation. We also suggest that the use of a crop growth model (CGM) can enhance predictions of integrative traits by decomposing them into more heritable intermediate traits. Results: The results show that CNN outperformed both LASSO and Bayes C methods in accuracy, suggesting that CNN are better suited to predict integrative traits. Furthermore, the predictive ability of the combined CGM-GP approach surpassed that of GP without the CGM integration, irrespective of the regression method used. Discussion: These results are consistent with recent works aiming to develop Genome-to-Phenotype models and advocate for the use of non-linear prediction methods, and the use of combined CGM-GP to enhance the prediction of crop performances. [ABSTRACT FROM AUTHOR]

Background: Selection markers are useful in genetic modification of yeast Pichia pastoris. However, the leakage of the promoter caused undesired expression of selection markers especially those toxic proteins like MazF, halting the cell growth and hampering the genetic manipulation in procaryotic system. In this study, a new counter-selectable marker-based strategy has been established for seamless modification with high efficiency and low toxicity. Results: At first, the leaky expression of the enhanced green fluorescent protein (EGFP) as a reporter gene under the control of six inducible promoters of P. pastoris was investigated in two hosts Escherichia coli and P. pastoris, respectively. The results demonstrated that the DAS1 and FDH1 promoters (PDAS1 and PFDH1) had the highest leakage expression activities in procaryotes and eukaryotes, and the DAS2 promoter (PDAS2) was inducible with medium strength but low leakage expression activity, all of which were selected for further investigation. Next, Mirabilis antiviral proteins (MAPs) c21873-1, c21873-1T (truncated form of c21873-1) and c23467 were mined as the new counter-selectable markers, and hygromycin B (Hyg B) resistance gene was used as the positive-selectable marker, respectively. Then, modular plasmids with MAP-target gene-Hyg B cassettes were constructed and used to transform into P. pastoris cells after linearization, and the target genes were integrated into its genome at the BmT1 locus through single-crossover homologous recombination (HR). After counter-selection induced by methanol medium, the markers c21873-1 and c21873-1T were recycled efficiently. But c23467 failed to be recycled due to its toxic effect on the P. pastoris cells. At last, the counter-selectable marker c21873-1 under the tightly regulated PDAS2 enabled the encoding genes of reporter EGFP and tested proteins to be integrated into the target locus and expressed successfully. Conclusions: We have developed MAP c21873-1 as a novel counter-selectable marker which could perform efficient gene knock-in by site-directed HR. Upon counter-selection, the marker could be recycled for repeated use, and no undesirable sequences were introduced except for the target gene. This unmarked genetic modification strategy may be extended to other genetic modification including but not limited to gene knock-out and site-directed mutagenesis in future. [ABSTRACT FROM AUTHOR]

Background: Giardiasis, caused by the protozoan parasite Giardia intestinalis, often presents a treatment challenge, particularly in terms of resistance to metronidazole. Despite extensive research, markers for metronidazole resistance have not yet been identified. Methods: This study analysed 28 clinical samples of G. intestinalis from sub-assemblage AII, characterised by varying responses to metronidazole treatment. We focussed on copy number variation (CNV) of the multi-copy flavohemoprotein gene, analysed using digital polymerase chain reaction (dPCR) and next generation sequencing (NGS). Additionally, chromosomal ploidy was tested in 18 of these samples. Flavohemoprotein CNV was also assessed in 17 samples from other sub-assemblages. Results: Analyses revealed variable CNVs of the flavohemoprotein gene among the isolates, with no correlation to clinical metronidazole resistance. Discrepancies in CNVs detected from NGS data were attributed to biases linked to the whole genome amplification. However, dPCR helped to clarify these discrepancies by providing more consistent CNV data. Significant differences in flavohemoprotein CNVs were observed across different G. intestinalis sub-assemblages. Notably, Giardia exhibits a propensity for aneuploidy, contributing to genomic variability within and between sub-assemblages. Conclusions: The complexity of the clinical metronidazole resistance in Giardia is influenced by multiple genetic factors, including CNVs and aneuploidy. No significant differences in the CNV of the flavohemoprotein gene between isolates from metronidazole-resistant and metronidazole-sensitive cases of giardiasis were found, underscoring the need for further research to identify reliable genetic markers for resistance. We demonstrate that dPCR and NGS are robust methods for analysing CNVs and provide cross-validating results, highlighting their utility in the genetic analyses of this parasite. [ABSTRACT FROM AUTHOR]

This comprehensive review explores the pivotal role of radiotherapy in cancer treatment, emphasizing the diverse applications of genetic profiling. The review highlights genetic markers for predicting radiation toxicity, enabling personalized treatment planning. It delves into the impact of genetic profiling on radiotherapy strategies across various cancer types, discussing research findings related to treatment response, prognosis, and therapeutic resistance. The integration of genetic profiling is shown to transform cancer treatment paradigms, offering insights into personalized radiotherapy regimens and guiding decisions in cases where standard protocols may fall short. Ultimately, the review underscores the potential of genetic profiling to enhance patient outcomes and advance precision medicine in oncology. [ABSTRACT FROM AUTHOR]

Background: Microbial robustness is crucial for developing cell factories that maintain consistent performance in a challenging environment such as large-scale bioreactors. Although tools exist to assess and understand robustness at a phenotypic level, the underlying metabolic and genetic mechanisms are not well defined, which limits our ability to engineer more strains with robust functions. Results: This study encompassed four steps. (I) Fitness and robustness were analyzed from a published dataset of yeast mutants grown in multiple environments. (II) Genes and metabolic processes affecting robustness or fitness were identified, and 14 of these genes were deleted in Saccharomyces cerevisiae CEN.PK113-7D. (III) The mutants bearing gene deletions were cultivated in three perturbation spaces mimicking typical industrial processes. (IV) Fitness and robustness were determined for each mutant in each perturbation space. We report that robustness varied according to the perturbation space. We identified genes associated with increased robustness such as MET28, linked to sulfur metabolism; as well as genes associated with decreased robustness, including TIR3 and WWM1, both involved in stress response and apoptosis. Conclusion: The present study demonstrates how phenomics datasets can be analyzed to reveal the relationship between phenotypic response and associated genes. Specifically, robustness analysis makes it possible to study the influence of single genes and metabolic processes on stable microbial performance in different perturbation spaces. Ultimately, this information can be used to enhance robustness in targeted strains. [ABSTRACT FROM AUTHOR]

Amomum villosum Lour. (A. villosum) is a valuable herbaceous plant that produces the famous traditional Chinese medicine Amori Fructus. Identifying molecular markers associated with the growth of A. villosum can facilitate molecular marker-assisted breeding of the plant. This study employed 75 A. villosum accessions as the test material and utilized 71 pairs of polymorphic simple sequence repeat (SSR) molecular markers to genotype the population. The study analyzed the association between SSR markers and phenotypic traits through the linkage imbalance and population structure analysis. Candidate genes associated with the molecular markers were also identified. The results showed that the phenotypic diversity index range of the 12 agronomic traits was 4.081–4.312 and conformed to a normal distribution. Moreover, 293 allelic variations were detected in the 75 accessions, with an average of 5.32 amplified alleles per loci, ranging from 3 to 8. The maximum number of amplified alleles for AVL12 was 8. The population structure and cluster analysis indicated that the accessions could be divided into two subgroups. Using the mixed linear model (MLM) model of population structure (Q)+kinship matrix (K) for association analysis, three SSR molecular markers significantly associated with the agronomic traits were detected. Fluorescence quantification was used to analyze the expression levels of six candidate genes, and it was found that three of the genes were differentially expressed in phenotypically different accessions. This study is the first to use SSR markers for genome-wide association study (GWAS) mapping and identification of the associated agronomic traits in A. villosum. The results of this study provide a basis for identifying genetic markers for growth traits for marker-assisted breeding in A. villosum. [ABSTRACT FROM AUTHOR]

In a wheat breeding line XQ-0508 showing consistent resistance to powdery mildew disease, a recessive gene, designated PmXQ-0508, was identified and mapped to a distal region on chromosome arm 2BS. Of three resistance-associated genes in this region, one encoding a protein kinase was selected as the primary candidate for PmXQ-0508. Ten closely linked DNA markers developed in the study could be used for marker-assisted selection for powdery-mildew resistance in breeding programs. [ABSTRACT FROM AUTHOR]

Tracking climatic conditions throughout the year is often assumed to be an adaptive behaviour underlying seasonal migration patterns in animal populations. We investigate this hypothesis using genetic markers data to map migratory connectivity for 27 genetically distinct bird populations from 7 species. We found that the variation in seasonal climate tracking across our suite of populations at a continental scale is more likely a consequence, rather than a direct driver, of migratory connectivity, which is primarily shaped by energy efficiency—i.e., optimizing the balance between accessing available resources and movement costs. However, our results also suggest that regional‐scale seasonal precipitation tracking affects population migration destinations, thus revealing a potential scale dependency of ecological processes driving migration. Our results have implications for the conservation of these migratory species under climate change, as populations tracking climate seasonally are potentially at higher risk if they adapt to a narrow range of climatic conditions. [ABSTRACT FROM AUTHOR]

The conservation biology field underscores the importance of understanding genetic diversity and gene flow within plant populations and the factors that influence them. This study employs Simple Sequence Repeat (SSR) molecular markers to investigate the genetic diversity of the endangered plant species Saussurea involucrata, offering a theoretical foundation for its conservation efforts. Utilizing sequencing results to screen SSR loci, we designed and scrutinized 18 polymorphic microsatellite primers across 112 samples from 11 populations in the Bayinbuluke region. Our findings reveal high genetic diversity (I = 0.837, He = 0.470) and substantial gene flow (Nm = 1.390) among S. involucrata populations (China, Xinjiang), potentially attributed to efficient pollen and seed dispersal mechanisms. Principal Coordinate Analysis (PCoA) indicates a lack of distinct genetic structuring within the Bayinbuluke populations. The cluster analysis using STRUCTURE reflected the genetic structure of S. involucrata to a certain extent compared with PCoA. The results showed that all samples were divided into four groups. To safeguard this species, we advocate for the in situ conservation of all S. involucrata populations in the area. The SSR markers developed in this study provide a valuable resource for future genetic research on S. involucrata. [ABSTRACT FROM AUTHOR]

The present study aimed to evaluate whether epigenetic markers are expressed in the dental follicles surrounding ectopically erupting teeth. Twenty‐one dental follicles were collected in 20 adolescent children through surgical exposure of ectopic teeth. The epigenetic modifications of DNA methylation and histone acetylation were evaluated by immunohistochemistry. The results showed cells positive for DNA‐methyltransferase 1 (DNMT1), DNA methyltransferase 3 beta (DNMT3B), ten‐eleven translocation‐2 (TET2), acetyl‐histone H3 (AcH3), acetyl‐histone H4 (AcH4), 5‐methylcytosine (5mC), and 5‐hydroxymethylcytosine (5hmC) were present in all the samples. The levels of epigenetic markers representing active chromatin (5hmC, AcH3, AcH4, and TET2) were statistically significantly higher than those of markers representing inactive chromatin (5mC, DNMT3B, DNMT1). In conclusion, follicles in ectopic teeth display major epigenetic modifications. In the follicles, epigenetic markers associated with the activation of bone‐related genes are more abundant than markers associated with the inactivation of bone‐related genes. [ABSTRACT FROM AUTHOR]

Colorectal cancer (CRC) is a complex malignancy with poorly understood molecular mechanisms, necessitating the identification of genetic markers. Although Ubiquitin domain-containing protein 1 (UBTD1) has received significant attention in the study of human cancers, its specific role in CRC is yet to be fully clarified. This study sought to examine how UBTD1 expression was associated with various clinical and pathological characteristics of CRC, and to determine its prognostic significance and biological function, utilizing data from clinical samples and large-scale databases. Notably, UBTD1 expression was found to be upregulated in CRC, resulting in decreased survival rates and unfavorable clinical characteristics such as advanced T, N, and pathological stages. The findings of the multivariate Cox regression analysis illustrated that UBTD1 expression upregulation is a significant independent marker of unfavorable outcomes in CRC patients. An examination of the functional enrichment of UBTD1 and the genes it co-expresses indicated that it could serve as an oncogene by modulating the expression of genes implicated in crucial tumorigenesis pathways and functions. Additionally, immune cell infiltration analysis suggested a link between UBTD1 levels and various immune cells, particularly macrophages. In conclusion, the use of UBTD1 as a biomarker for both the prognosis and diagnosis of CRC has promising prospects for further investigation and therapeutic approaches. [ABSTRACT FROM AUTHOR]

African swine fever virus (ASFV) is the causative agent of African swine fever (ASF), a highly infectious and lethal disease of domesticated swine. Outbreaks of ASF have been mostly restricted to the continent of Africa. The outbreaks that have occurred outside of Africa were controlled by extensive depopulation of the domesticated pig population. However, in 2007, an outbreak occurred in the country of Georgia, where ASFV infected wild pigs and quickly spread across eastern Europe. Since the reintroduction of ASF into Europe, variants of the current pandemic strain, ASFV Georgia 2007/01 (ASFV-G), which is classified as Genotype 2 based on p72 sequencing, have been reported in countries within western Europe, Asia, and the island of Hispaniola. Additionally, isolates collected in 2020 confirmed the presence of variants of ASFV-G in Nigeria. Recently, we reported similar variants of ASFV-G collected from domestic pigs suspected of dying of ASF in Ghana in 2022. Here, we retroactively report, based on full-length sequencing, that similar variants were present in Ghana in 2021. The SNP analysis revealed derivatives of ASFV with distinct genetic markers. Furthermore, we identified three full-length ASFV genomes as Genotype 1, indicating that there were two genotypes circulating in proximity during the 2021 ASF outbreaks in Ghana. [ABSTRACT FROM AUTHOR]

High-throughput genomic technologies are enabling the identification of thousands or even millions of single-nucleotide polymorphisms (SNPs). SNP markers are frequently used to analyze crop varieties, with the marker data summarized in a common VCF file. At present, it is difficult to identify the minimal SNP set, the smallest sets that can distinguish between all crop varieties listed in a VCF file, due to the absence of available ready-to-use tools capable of such characterization. Here, we describe the development of the ready-to-use open-source tool MDSearch (Minimal Discriminatory SNP Set Search) based on the identification of the MDS (minimal discriminatory set) of SNPs using random walking staring from the maximal discriminatory set. MDSearch can be used for disploid as well as poliploid species and both phased and unphased VCF files. MDSearch has been validated using a publicly available dataset of barley SNPs obtained by genotyping-by-sequencing. As a result, we have successfully identified a discriminating set of 19 SNP markers capable of distinguishing all 254 barley varieties included in our study. We expect that this program will prove useful to genomics researchers to support a variety of certifications. [ABSTRACT FROM AUTHOR]

The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype–environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net‐pens and RAS. After an 8‐week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re‐ranking for whole‐body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented. [ABSTRACT FROM AUTHOR]