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Ketosis, evidenced by hyperketonemia with elevated blood β‐hydroxybutyrate (BHB) levels, is a significant metabolic disorder of dairy cattle, typically diagnosed within the first 6 weeks post‐calving when high energy levels are essential to milk production. Our study aimed to identify genetic markers linked to hyperketonemia (HYK) patterns in Holstein cows during early lactation and compare these to HYK‐negative cows. We screened 964 cows for HYK using a threshold of BHB ≥1.2 mmol/L during the first 2 weeks postpartum (screening period, SP). Cows that tested negative initially were retested the following week. Cows were deemed HYK‐negative (CON group) if BHB levels were below 1.2 mmol/L in both tests, while those with BHB levels exceeding this threshold at any test were treated and classified as HYK‐positive (HYK+). Post‐treatment, HYK+ cows were monitored for two‐week follow‐up period (FP) and classified based on their recovery: cured (CUR; consistently low BHB), recurrent (REC; fluctuating BHB levels), severe (SEV; high initial BHB that decreased), or chronic (CHR; persistently high BHB). Using 489 cows that were genotyped, a GWAS was conducted using GCTA software, revealing significant associations of several SNPs across different HYK patterns when compared to the CON group. These SNPs were primarily linked to genes affecting milk traits and were enriched in biological pathways relevant to protein glycosylation, inflammatory response, glucose homeostasis, and fatty acid synthesis. Our findings highlight genomic regions, potential candidate genes, and biological pathways related to ketosis, underscoring potential targets for improving health management in dairy cattle. These insights could lead to better strategies for managing ketosis through genetic selection, ultimately enhancing dairy cattle welfare and productivity. Further research with a larger number of cows is recommended to validate these findings and help confirm the implicated SNPs and genes. [ABSTRACT FROM AUTHOR]

Ascochyta blight (AB) disease, caused by the fungal pathogen Ascochyta rabiei, is a major production constraint in many chickpea‐growing regions worldwide, causing substantial reductions in grain yield and seed quality. The management of AB is challenging due to limited genetic resistance and the evolving aggressiveness of A. rabiei. Currently, there is a heavy reliance on visual assessment by expert pathologists for the detection and quantification of disease severity, and limited ability to impartially quantify pathogen growth and inoculum potential in the field. In this study, we address these gaps by developing a single‐copy genetic marker for the sensitive detection and quantification of A. rabiei mycelium and conidiospores. Using a droplet digital PCR (ddPCR) assay, our method provides a sensitive (≤5 × 10−2 pg DNA, 1 gene copy) approach to assess A. rabiei biomass throughout its lifecycle on living and dead plant tissues. The method (i) has specificity to A. rabiei in diseased plant samples; (ii) discriminates among chickpea cultivars with varying AB resistance prior to the onset of visible symptoms; (iii) detects differences in primary A. rabiei conidiospore inoculum load from field‐grown chickpea stubble; and (iv) has potential application to disease management, breeding and epidemiology. [ABSTRACT FROM AUTHOR]

ABSTRACT This study investigated the effects of different doses of vitamin E on oxidative stress, cognitive function, and gene expression in aged mice. A total of 32 male mice, aged 12 months, were divided into a control group and three treatment groups. These groups received varying daily doses of vitamin E for a period of 28 days. The results showed significant improvements in cognitive function, specifically in working memory and spatial learning, in the groups that received vitamin E (100, 200, or 400 mg/kg) compared to the control group. The markers of oxidative stress and antioxidant enzyme activities also demonstrated improvements, with higher doses of vitamin E showing greater effects. The analysis of gene expression revealed increased expression of SIRT1, Nrf2, and Calstabin2, particularly at higher doses of vitamin E. These findings suggest that vitamin E supplementation may help counteract age‐related cellular changes. The study concludes that vitamin E supplementation can reduce oxidative stress, enhance cognitive function, and affect genetic markers of aging in mice, which may have therapeutic benefits in addressing age‐related cognitive decline and oxidative damage. Further research is necessary to investigate the clinical implications of these findings in humans. [ABSTRACT FROM AUTHOR]

Objective Methods Results Significance Brain somatic variants in SLC35A2 were recently identified as a genetic marker for mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE). The role of SLC35A2 in cortical development and the contributions of abnormal neurons and oligodendrocytes to seizure activity in MOGHE remain largely unexplored.Here, we generated a novel Slc35a2 floxed allele, which we used to develop two Slc35a2 conditional knockout mouse lines targeting (1) the Emx1 dorsal telencephalic lineage (excitatory neurons and glia) and (2) the Olig2 lineage (oligodendrocytes). We examined brain structure, behavior, and seizure activity.Knockout of Slc35a2 from the Emx1 lineage, which targets both cortical neurons and oligodendrocytes, resulted in early lethality and caused abnormal cortical development, increased oligodendroglial cell density, early onset seizures, and developmental delays akin to what is observed in patients with MOGHE. By tracing neuronal development with 5‐Ethynyl‐2'‐deoxyuridine (EdU) birthdating experiments, we found that Slc35a2 deficiency disrupts corticogenesis by delaying radial migration of neurons from the subventricular zone. To discern the contributions of oligodendrocytes to these phenotypes, we knocked out Slc35a2 from the Olig2 lineage. This recapitulated the increased oligodendroglial cell density and resulted in abnormal electroencephalographic activity, but without a clear seizure phenotype, suggesting Slc35a2 deficiency in neurons is required for epileptogenesis.This study presents two novel Slc35a2 conditional knockout mouse models and characterizes the effects on brain development, behavior, and epileptogenesis. Together, these results demonstrate a direct causal role for SLC35A2 in MOGHE‐like phenotypes, including a critical role in neuronal migration during brain development, and identify neurons as key contributors to SLC35A2‐related epileptogenesis. [ABSTRACT FROM AUTHOR]

ABSTRACT Current rDNA reference sequence databases are tailored towards shorter DNA markers, such as parts of the 16/18S marker or the internally transcribed spacer (ITS) region. However, due to advances in long‐read DNA sequencing technologies, longer stretches of the rDNA operon are increasingly used in environmental sequencing studies to increase the phylogenetic resolution. There is, therefore, a growing need for longer rDNA reference sequences. Here, we present the ribosomal operon database (ROD), which includes eukaryotic full‐length rDNA operons fished from publicly available genome assemblies. Full‐length operons were detected in 34.1% of the 34,701 examined eukaryotic genome assemblies from NCBI. In most cases (53.1%), more than one operon variant was detected, which can be due to intragenomic operon copy variability, allelic variation in non‐haploid genomes, or technical errors from the sequencing and assembly process. The highest copy number found was 5947 in Zea mays. In total, 453,697 unique operons were detected, with 69,480 operon variant clusters remaining after intragenomic clustering at 99% sequence identity. The operon length varied extensively across eukaryotes, ranging from 4136 to 16,463 bp, which will lead to considerable polymerase chain reaction (PCR) bias during amplification of the entire operon. Clustering the full‐length operons revealed that the different parts (i.e., 18S, 28S, and the hypervariable regions V4 and V9 of 18S) provide divergent taxonomic resolution, with 18S, the V4 and V9 regions being the most conserved. The ROD will be updated regularly to provide an increasing number of full‐length rDNA operons to the scientific community. [ABSTRACT FROM AUTHOR]

The importance of genetic diversity has been recognised by the Convention on Biological Diversity but attempts at monitoring or improving the genetic diversity of populations have been minimal. Here, we investigate changes over time in the genetic diversity of a wild insect species, Maniola jurtina (Lepidoptera: Nymphalidae) and present a large‐scale investigation into contemporary spatial genetic diversity. Using microsatellite markers, we calculate multiple measures of genetic diversity and divergence for M. jurtina populations over 8 years in the UK and compare these findings with long‐term abundance trends. We also conduct a large‐scale spatial analysis into the genetic diversity and population structuring of M. jurtina across Europe. All UK populations sampled have high levels of gene flow and genetic diversity, with genetic diversity stable over time. Across Europe, we find some population structuring between populations in the UK and the European mainland, suggesting restricted geneflow between the two regions. The monitoring of a wild species' genetic diversity is an achievable aim, and one that could be carried out for many species, particularly Lepidoptera. Future approaches may aim to develop higher resolution genetic markers and cover a wider range of species. The use of abundance data offers additional insight, and we find that concurrent, dedicated genetic monitoring can provide effective tracking of biodiversity trends. [ABSTRACT FROM AUTHOR]

Subacute sclerosing panencephalitis (SSPE) is a progressive and catastrophic neurodegenerative disorder due to persistent infection with the aberrant measles virus in the brain. The exact etiology of SSPE is still unknown, and early diagnosis remains a challenge, especially with the atypical presentations. The pathogenesis of SSPE involves a complex interplay between viral factors and immunological response of the host. The presenting review demonstrates an extensive glimpse of the immuno‐genetics of SSPE, exploring the single‐nucleotide polymorphisms (SNPs), genetic risk factors and immune responses that influence susceptibility and disease progression. [ABSTRACT FROM AUTHOR]

ABSTRACT Objective Materials and Methods Results Conclusion Proliferative verrucous leukoplakia (PVL) is an oral potentially malignant disorder. Forms that affect only one tissue are poorly studied, especially the exclusively gingival PVL (gPVL), which may have a more increased malignant transformation potential. The aim of the present study was to characterise the gPVL and its risk of malignant transformation to better raise awareness of this specific disorder.The systematic review was performed on PubMed, Scopus, Web of Science and Google Scholar. Only articles reporting primary studies, case reports and case series were included. The meta‐analysis was performed for the cancer prevalence, proportion of smokers, age and sex ratio, recurrences of gPVL and mortality.A total of 1298 studies were assessed for eligibility by reading titles and abstracts. Fourteen original articles were included with a total of 58 patients. The malignant transformation rate of gPVL was 47.75%. The mortality was 5.84%. The mean follow‐up duration before malignant transformation was 3 years.gPVL seems to have a faster malignant transformation rate than the other forms of PVL. Finding anatomo‐pathological or genetic markers could be a line of research to predict gPVL malignant transformation and improve its diagnosis and treatment. [ABSTRACT FROM AUTHOR]

The orchid Dactylorhiza cantabrica H.A. Pedersen is a narrow endemic occurring in the western Cantabrian Mountains in northwest Spain. Previous allozyme and morphological studies suggest that it might have resulted from the hybridization of two widespread congeners: the triploid Dactylorhiza insularis and the diploid Dactylorhiza sambucina. However, this hypothesis has not been tested using multiple genetic markers necessary to analyze phylogenies in complex genera such as Dactylorhiza. In this study, the Hyb‐Seq technique is applied together with the universal Angiosperms353 probe kit to sequence multiple plastid and low‐copy nuclear genes. The phylogenetic relationships between the three species, estimated based on 269 and 266 nuclear genes under concatenation and coalescent‐based approaches, respectively, revealed highly supported clades containing each putative parent, D. insularis and D. sambucina. The position of D. cantabrica was not well resolved, suggesting the existence of mixed inheritance, where different genes come from each parent. Phylogenetic networks, used for visualizing the conflict between nuclear gene trees, placed D. cantabrica between the two parents and revealed high levels of reticulation. In addition, nuclear genetic variation within and among species was explored with allele frequency‐based tools further supporting the intermediate position of D. cantabrica and the hypothesis of a recent hybrid origin. Finally, 75 plastid genes revealed that D. insularis might have been the maternal donor. Altogether, our results point to the allopolyploid origin of D. cantabrica from D. insularis and D. sambucina, as well as to the clear genetic differentiation of the two parental species. [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]

The rapid advancement of biotechnology over the recent decades has amplified the importance of DNA detection and quantification assays. Many of these assays, such as gel electrophoresis, microscopy, flow cytometry, and the detection of amplification in quantitative polymerase chain reaction (qPCR), rely on the use of DNA‐binding fluorescent dyes. This article presents a comprehensive study of six Thiazole‐Orange‐based fluorescent DNA‐binding dyes: SYBR Safe, SYBR Green, Pico Green, SYTO‐16, SYTO‐9, and the benzothiazole‐based analogue (TOPhBu) of the latter. The selected DNA markers were synthesized at a 10‐milligram scale and characterised spectroscopically to quantify their fluorescence enhancement upon binding to double‐stranded DNA. The ability of the dyes to detect DNA at low concentrations was evaluated using two new metrics, absolute fluorescence enhancement (AFE) and relative fluorescence enhancement (RFE). Quantum chemical calculations shed new light on the mechanism of their fluorogenicity through modelling the excited state behaviour and DNA binding of the dyes. Their analytical performance was further tested in qPCR experiments. The experimental results of this work highlight some important differences in the sensitivity and qPCR efficiency of the studied DNA‐binding dyes which will facilitate the DNA marker selection for analytical purposes and the future development of novel DNA sensors. [ABSTRACT FROM AUTHOR]

The genus Urotrygon comprises small‐ to medium‐sized endemic round rays on the American continent and has undergone several synonymization processes. Here, we used an integrative taxonomic approach, including meristic, morphometric, and mtDNA analyses, to resolve the particularly intricate relationship among Urotrygon munda Gill, 1863, Urotrygon chilensis (Günther, 1872), and Urotrygon asterias (Jordan & Gilbert, 1883). The latter species is currently a synonym of U. munda but is also considered the U. chilensis "northern morphotype." These taxonomic entities have historically been confounded, mainly due to their phenotypical resemblance along their geographic distribution in the eastern Pacific. We assessed 78 specimens (43 "northern" and 30 "southern morphotypes" of U. chilensis, as well as 5 U. munda) using 19 external variables for taxonomic and morphometric analysis. Distinct meristic patterns, including pectoral and pelvic ceratotrichia, vertebrae number, and thorn distribution along the dorsal midline, were observed in the series‐type specimens of the three taxonomic entities. Our multivariate morphometric analyses consistently differentiated the three groups as distinct taxonomic entities, with an overall classification accuracy of 66.7%. The meristic results also provided reliable information distinguishing the three entities. Based on the nicotinamide adenine dinucleotide (NADH2) and cytochrome oxidase subunit I (COI) genes, our phylogenetic analysis were consistent with the morphometric and meristic data, supporting these three entities as distinct species having their own evolutionary lineages. Our comprehensive approach confidently demonstrated that the northern U. chilensis morphotype matched and corresponded to the description of the Starry round ray, U. asterias, confirming its taxonomic resurrection as a valid species distinct from U. chilensis and U. munda. The geographic distribution of U. asterias spans from the tropical west coast of Mexico (including the Gulf of California) to Costa Rica, revealing that microevolutionary processes have well‐defined population clades within this range. Furthermore, U. chilensis is unequivocally established as the sole Urotrygon species occurring south of the Guayaquil marine ecoregion. In addition, the public COI and NADH2 sequences available for Urotrygon hosted in the ad hoc online databases were found to be misidentified, emphasizing the need for rigorous taxonomic scrutiny in this group. Finally, our research underscores the significance of an integrative approach that combines morphometric, meristic, and molecular techniques with historical data to disentangle the complexities of closely related taxa. [ABSTRACT FROM AUTHOR]

Since the World Health Organization (WHO) 2016 revision, the number of molecular markers required for diffuse gliomas has increased, placing a burden on clinical practice. We have established an in‐house, molecular diagnostic platform using Senshin‐Iryo, a feature of Japan's unique healthcare system, and partially modified the analysis method in accordance with the WHO 2021 revision. Herein, we review over a total 5 years of achievements using this platform. Analyses of IDH, BRAF, and H3 point mutations, loss of heterozygosity (LOH) on 1p/19q and chromosomes 10 and 17, and MGMT methylation were combined into a set that was submitted to Senshin‐Iryo as "Drug resistance gene testing for anticancer chemotherapy" and was approved in August 2018. Subsequently, in October 2021, Sanger sequencing for the TERT promoter mutation was added to the set, and LOH analysis was replaced with multiplex ligation‐dependent probe amplification (MLPA) to analyze 1p/19q codeletion and newly required genetic markers, such as EGFR, PTEN, and CDKN2A from WHO 2021. Among the over 200 cases included, 54 were analyzed after the WHO 2021 revision. The laboratory has maintained a diagnostic platform where molecular diagnoses are confirmed within 2 weeks. Initial expenditures exceeded the income from patient copayments; however, it has gradually been reduced to running costs alone and is approaching profitability. After the WHO 2021 revision, diagnoses were confirmed using molecular markers obtained from Senshin‐Iryo in 38 of 54 cases (70.1%). Among the remaining 16 patients, only four (7.4%) were diagnosed with diffuse glioma, not elsewhere classified, which was excluded in 12 cases where glioblastoma was confirmed by histopathological diagnosis. Our Senshin‐Iryo trial functioned as a salvage system to overcome the transition period between continued revisions of WHO classification that has caused a clinical dilemma in the Japanese healthcare system. [ABSTRACT FROM AUTHOR]

Male infertility due to asthenozoospermia is quite frequent, but its etiology is poorly understood. We recruited two infertile brothers, born to first‐cousin parents from Pakistan, displaying idiopathic asthenozoospermia with mild stuttering disorder but no ciliary‐related symptoms. Whole‐exome sequencing identified a splicing variant (c.916+1G>A) in ARMC3, recessively co‐segregating with asthenozoospermia in the family. The ARMC3 protein is evolutionarily highly conserved and is mostly expressed in the brain and testicular tissue of human. The ARMC3 splicing mutation leads to the exclusion of exon 8, resulting in a predicted truncated protein (p.Glu245_Asp305delfs*16). Quantitative real‐time PCR revealed a significant decrease at mRNA level for ARMC3 and Western blot analysis did not detect ARMC3 protein in the patient's sperm. Individuals homozygous for the ARMC3 splicing variant displayed reduced sperm motility with frequent morphological abnormalities of sperm flagella. Transmission electron microscopy of the affected individual IV: 2 revealed vacuolation in sperm mitochondria at the midpiece and disrupted flagellar ultrastructure in the principal and end piece. Altogether, our results indicate that this novel homozygous ARMC3 splicing mutation destabilizes sperm flagella and leads to asthenozoospermia in our patients, providing a novel marker for genetic counseling and diagnosis of male infertility. [ABSTRACT FROM AUTHOR]

The provision of care to offspring is a costly endeavour that can be hijacked by others—known as brood parasitism. Females can choose to lay eggs in the nest of a conspecific female, resulting in extra‐pair maternity (EPM).Burying beetles of the genus Nicrophorus use small vertebrate carcasses for reproduction and provide biparental care to their offspring. Carcasses are a rare resource; thus, competition often occurs among adults of the same sex.A previous study examined the outcomes of competition and subsequent parental care of Nicrophorus vespilloides using laboratory experiments. Larvae of losing females were sometimes cared for by the winning females, which is generally an evidence of EPM.However, the presence of EPM in burying beetles under natural conditions has not yet been well established. Here, we focused on the reproduction of N. quadripunctatus in the field. To examine the presence of EPM, maternity analysis was performed on 149 offspring and their caring females in 10 broods, using 8 microsatellite DNA loci.Seven larvae originating from three broods were unrelated to their caring females. There were one to three unrelated larvae in each of the three broods. Thus, EPM occurs in N. quadripunctatus reproduction under natural conditions. [ABSTRACT FROM AUTHOR]

Many unique high‐altitude mountain ecosystems have been declining due to climate change, posing a threat to flora and fauna that have adapted to these ecosystems. This study explores the evolution of high‐altitude adaptations, focusing on female flightlessness and diel activity, in geometrid moths (Lepidoptera: Ennominae, Gnophini) within the European Alps. We constructed a phylogeny of Gnophini moths using a dataset of 157 taxa, with up to seven genetic markers and traced the evolutionary history of diel activity and wing length reduction in females. Analysis of divergence times suggested that female flightlessness has evolved at least three times independently between the early and late Miocene. The evolution of wing length reduction is likely correlated with elevation, indicating adaptations to cold and windy conditions in high altitude. The evolutionary events leading to shifts in adult diel activity, from ancestral nocturnality to diurnality, have occurred independently at least three times and may also be a consequence of adaptations at high elevations. Strikingly, among diurnal Sciadia, two species have evolved further to become nocturnal like their ancestors. Our findings highlight how phylogenies can provide new insights into evolutionary patterns in moths. We provided a robust basis for resolving taxonomic ambiguities in Alpine Gnophini, leading us to propose 10 changes to the current classification: Scrupodes Lee & Sihvonen gen. n., Elophos Boisduval (type species Geometra operaria Hübner) is considered a junior synonym of Sciadia Hübner syn. n., Yezognophos dilucidaria (Denis & Schiffermüller) and Y. sproengertsi (Püngeler) are transferred to Parietaria Leraut comb. n., Yezognophos serotinaria (Denis & Schiffermüller) is transferred to Scrupeus Lee & Sihvonen comb. n., Elophos caelibaria (Heydenreich), E. zirbitzensis (Pieszcek), E. operaria (Hübner) and E. andereggaria (De La Harpe) are transferred to Sciadia Hübner comb. n. and Dichrognophos Wehrli (type species Gnophos orthogonia Wehrli) is transferred from Ennominae: Cassymini to Ennominae: Gnophini. [ABSTRACT FROM AUTHOR]

Fish hybridization is common in aquaculture worldwide, including in Brazil, with cross‐breeding between species of the genera Piaractus and Colossoma taking the lead. However, little is known about the genetic damage caused by hybrids that escape into natural environments. In the upper Paraná River region, hybrid fishes are overproduced; therefore, the use of molecular techniques for their monitoring and identification is necessary. This study aimed to detect the presence of possible hybridization between Piaractus and Colossoma in the upper Paraná River using the molecular markers cytochrome c oxidase subunit 1 (COI) and α‐tropomyosin (TROP). Fragments from 53 fish samples were analysed, and 41 samples were considered hybrids, with 12 confirmed pure, six as Piaractus mesopotamicus (pacu) and six as Piaractus brachypomus (pirapitinga). This is the first record of P. brachypomus, which is an invasive species in this basin, while Colossoma macropomum has not been observed. Molecular markers efficiently detected hybrids in the Ivinhema and Paraná rivers. The results showed a predominance of hybrid specimens from P. mesopotamicus × P. brachypomus. Our study suggests that more restrictions on hybridization and better supervision of fish farms are needed to prevent the escape of hybrids and the consequent ecological and genetic damage to native populations. We warn of the risk of a decline in the population of P. mesopotamicus, as this species is of great importance for fishing and maintaining the ecosystem. [ABSTRACT FROM AUTHOR]

Summary Background Methods Results Conclusion Sickle cell disease (SCD) is a Mendelian disorder characterized by a point mutation in the β‐globin gene that leads to sickling of erythrocytes. Several studies have shown that absolute neutrophil count is strongly associated with clinical severity of SCD, suggesting an apparent role of white blood cells (WBC) in SCD pathology. However, the mechanism by which genetic variants lead to WBC count differences in SCD patients remains unclear.Genome‐wide association (GWA) analyses were carried out amongst a cohort of 2409 Brazil SCD participants. Association of WBC count and genetic markers were investigated in homozygous sickle cell anaemia participants and compound heterozygous sickle cell haemoglobin C participants.GWA analysis showed that variants in genes TERT, ACKR1, and FAM3C are associated with WBC count variation. The well‐studied association between WBC count and Duffy null phenotype (variant in ACKR1) in healthy populations was replicated, reinforcing the influence of the SNP rs2814778 (T>C) in WBC count.Genetics plays an important role in regulating WBC count in patients with SCD. Our results point to possible mechanisms involved in WBC count variation and as increased WBC count is associated with more severe SCD, these results could suggest potential therapeutic targets for individuals with SCD. [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]

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]

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]

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]

Nonobstructive azoospermia (NOA) is considered to be the most severe form of male infertility. Meiotic arrest is one of the major causes of NOA and can be caused by single gene mutations. Here, a novel homozygous missense mutation (c.131G>T) in the MEI1 gene was identified through whole exome sequencing in a Chinese men with NOA caused by meiotic arrest. Bioinformatics and genetic analysis predicted that this novel mutation may be deleterious. Our findings confirm that spermatogenesis is arrested at the primary spermatocyte stage, with defective programed DNA double‐strand breaks (DSBs) formation. In vitro functional analysis revealed that the defects of DSBs formation may be a result of a lower expression level of MEI1 protein in the mutant. Therefore, the NOA in this patient is likely caused by the single novel mutation in the MEI1 gene leading to meiotic arrest. Our report expands the mutation spectrum of MEI1 and provides new evidence that the MEI1 gene may serve as a diagnostic marker for genetic counseling in NOA patients. [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 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]

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]

While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co‐occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 Pocillopora corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of Pocillopora, most of which cannot be reliably identified based on morphology: P. meandrina (42.9%), P. tuahiniensis (25.1%), P. verrucosa (12.2%), P. acuta (10.4%), P. grandis (7.73%), and P. cf. effusa (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used psbAncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of Pocillopora species differed across habitats within the reef. Sister taxa P. verrucosa and P. tuahiniensis had similar niche breadths and hosted the same specialist symbiont species (mostly Cladocopium pacificum) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa P. meandrina and P. grandis had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly C. latusorum). Pocillopora acuta had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, Durusdinium gynnii. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth—Pocillopora species with a broader habitat niche also had a broader symbiont niche. Our results show how fine‐scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated. [ABSTRACT FROM AUTHOR]

Stem rust is a serious disease of many gramineous plants including small grain staples such as wheat, barley, rye and triticale. Separate formae speciales (ff. spp.) of the causal fungus, Puccinia graminis, predominantly infect certain host plant genera. However, despite these taxonomic subdivisions, many P. graminis ff. spp. are genetically too similar to distinguish using existing genetic markers. For those infecting cereals, this is particularly challenging for P. graminis f. sp. tritici (Pgt) and P. graminis f. sp. secalis (Pgs). Herein we harnessed newly available genomic data for 39 Pgt and Pgs isolates and identified four regions of structural variation that were used to design four simple PCR‐based assays to distinguish the aforementioned formae speciales. These genomic regions display large presence/absence variation between Pgt and Pgs isolates, and yet a high degree of sequence conservation within shared neighbouring regions, facilitating primer design. We also confirmed lack of amplification in host plant genera analysed, which included assessment of the shared alternate host of Pgt and Pgs, Berberis vulgaris. Accurate classification of P. graminis ff. spp. infections on B. vulgaris is exceptionally valuable to rapidly define plants harbouring P. graminis inoculum when adjacent to cereal crops. Finally, we demonstrated utility of these four genetic markers to correctly distinguish a genetically diverse array of Pgt and Pgs isolates. This strategy could now be readily applied to other pathogens of interest, which will be of increasing value as genomic resources continue to rapidly expand for many key biotic threats to agricultural productivity. [ABSTRACT FROM AUTHOR]

Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost‐effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water‐soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non‐exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step‐up from traditional barcoding and universal markers, the genome‐wide custom loci targeted by Orchidinae‐205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids. [ABSTRACT FROM AUTHOR]

Mastitis is a significant factor that decreases milk production in cows of different breeds in Kazakhstan. The objective of this study was to determine the genetic makeup of Holstein cows by analysing specific gene loci (SELL, MX1, CXCR1+291C>T and CXCR1+1093C>T) that are linked to resistance against mastitis. The goal was to identify cows with favourable genotypes that are less prone to udder diseases. At the SELL gene locus c.567T>C, all three genetic variants were identified in the control population with the respective frequencies: TT (0.20), CT (0.44), and CC (0.36). Genetic variation was also detected at the MX1 gene c.567T>C, CXCR1 c.+291C>T and CXCR1+1093C>T loci. Deviation from the expected Hardy–Weinberg equilibrium was observed for two gene loci, MX1 g.143182088 and CXCR1+1093C>T, with increased chi‐square values of 10.6261 and 9.7137, respectively. The analysis of subclinical mastitis incidence indicates that cows carrying the heterozygous CT genotype at the L‐selectin gene locus exhibit greater resistance to the disease. Animals carrying the CCCCCT genotype at the MX1 c.567T>C, CXCR1 c.+291C>T and CXCR1+1093C>T gene loci were discovered to have a significant likelihood of developing subclinical mastitis. This suggests that these genes could serve as potential indicators of susceptibility to the condition. The practical significance of this study lies in determining the frequency of genotypes linked to mammary gland morbidity in Holstein breeding farms in Kazakhstan. [ABSTRACT FROM AUTHOR]

Pod shattering is a major production constraint of soybean [Glycine max (L.)]. The objectives of this study were to (i) estimate heritability for pod shattering resistance, (ii) determine the frequency of the pod shattering resistance allele pdh1 in the International Institute for Tropical Agriculture (IITA) soybean germplasm and Zambian commercial varieties, and (iii) determine the effectiveness of the DNA marker for the pod shattering resistance allele pdh1. A total of 59 genotypes were evaluated for pod shattering in field trials conducted in Malawi and Zambia and genotyped with a marker for pdh1. TGx2002‐8FM and TGx2002‐9FM were the most resistant among genotypes in early and medium maturity classes and can be used for genetic enhancement of pod shattering resistance in these specific maturity classes. Narrow sense heritability estimates for pod shattering ranged from 0.27 to 0.80. Of the 59 genotypes, 57 (96.6%) carried the resistance allele pdh1 while only two genotypes (3.6%) carried the susceptible allele, suggesting near‐fixation of the resistance allele pdh1 in the IITA germplasm. The marker for pdh1 was highly effective in selecting resistant genotypes. [ABSTRACT FROM AUTHOR]

Climate‐driven ecosystem shifts occur through turnover in the foundation species which structure the landscape. Therefore, to predict the fate of areas undergoing climate‐driven ecosystem shifts, one approach is to characterize ecological and evolutionary responses of foundation species along dynamic environmental gradients. One such gradient is the ecotone between tidal marshes and maritime forests in coastal areas of the US Mid‐Atlantic region where accelerated sea‐level rise and coastal storms of increased frequency and intensity are driving forest dieback and inland marsh migration. Mid‐Atlantic tidal marshes are structured by marsh grasses which act as foundation species, and these grasses exhibit trait variation across their distribution from established marsh interior to their inland migration front. We conducted a reciprocal transplant experiment with Spartina patens, a dominant high marsh grass and foundation species, between established populations in the high marsh and range edge populations in the forest understory at three Mid‐Atlantic sites. We monitored environmental conditions in marsh and forest understory habitats, measured plant traits (above‐ and belowground biomass, specific leaf area, leaf N and C concentrations) in transplanted and reference non‐transplanted individuals, and used microsatellite markers to determine the genetic identity of transplants to quantify clonality between habitats and sites. Individuals transplanted into the forest understory exhibited a plastic shift in resource allocation to aboveground structures associated with light acquisition, with shifts in transplants making them more morphologically similar to reference individuals sampled from the forest habitat. Clonal diversity and genetic distance among transplants were relatively high at two of three sites, but individuals at all sites exhibited trans‐habitat plasticity regardless of clonal diversity or a lack thereof. Individuals grown in the forest understory showed lower vegetative and reproductive fitness. Nevertheless, the trait plasticity exhibited by this species allowed individuals from the forest that were transplanted into the marsh to recoup significant biomass in only a single growing season. We predict high plasticity will facilitate the persistence of colonizing S. patens individuals under suboptimal forest shade conditions until forest dieback increases light availability, ultimately promoting continued inland migration of this foundation species under sea‐level rise. [ABSTRACT FROM AUTHOR]

Objective: This study aims to investigate the mechanisms underlying the impaired healing response by diabetes after periodontal therapy. Background: Outcomes of periodontal therapy in patients with diabetes are impaired compared with those in patients without diabetes. However, the mechanisms underlying impaired healing response to periodontal therapy have not been sufficiently investigated. Materials and Methods: Zucker diabetic fatty (ZDF) and lean (ZL) rats underwent experimental periodontitis by ligating the mandibular molars for one week. The gingiva at the ligated sites was harvested one day after ligature removal, and gene expression was comprehensively analyzed using RNA‐Seq. In patients with and without type 2 diabetes (T2D), the corresponding gene expression was quantified in the gingiva of the shallow sulcus and residual periodontal pocket after non‐surgical periodontal therapy. Results: Ligation‐induced bone resorption and its recovery after ligature removal were significantly impaired in the ZDF group than in the ZL group. The RNA‐Seq analysis revealed 252 differentially expressed genes. Pathway analysis demonstrated the enrichment of downregulated genes involved in the peroxisome proliferator‐activated receptor (PPAR) signaling pathway. PPARα and PPARγ were decreased in mRNA level and immunohistochemistry in the ZDF group than in the ZL group. In clinical, probing depth reduction was significantly less in the T2D group than control. Significantly downregulated expression of PPARα and PPARγ were detected in the residual periodontal pocket of the T2D group compared with those of the control group, but not in the shallow sulcus between the groups. Conclusions: Downregulated PPAR subtypes expression may involve the impaired healing of periodontal tissues by diabetes. [ABSTRACT FROM AUTHOR]

An astonishing range of morphologies and life strategies has arisen across the vast diversity of protists, allowing them to thrive in most environments. In model protists, like Tetrahymena, Dictyostelium, or Trypanosoma, life cycles involving multiple life stages with different morphologies have been well characterized. In contrast, knowledge of the life cycles of free‐living protists, which primarily consist of uncultivated environmental lineages, remains largely fragmentary. Various life stages and lineage‐specific cellular innovations have been observed in the field for uncultivated protists, but such innovations generally lack functional characterization and have unknown physiological and ecological roles. In the actual state of knowledge, evidence of sexual processes is confirmed for 20% of free‐living protist lineages. Nevertheless, at the onset of eukaryotic diversification, common molecular trends emerged to promote genetic recombination, establishing sex as an inherent feature of protists. Here, we review protist life cycles from the viewpoint of life cycle transitions and genetics across major eukaryotic lineages. We focus on the scarcely observed sexual cycle of free‐living protists, summarizing evidence for its existence and describing key genes governing its progression, as well as, current methods for studying the genetics of sexual cycles in both cultivable and uncultivated protist groups. [ABSTRACT FROM AUTHOR]

Aim Methods Results Conclusions Gamma‐glutamyltransferase (GGT) is known as an oxidative stress marker, induced by alcohol consumption and metabolic disorders, and is reported as a predictor of hepatocellular carcinoma (HCC) development after hepatitis C virus (HCV) elimination. However, it is not clear whether GGT serves simply as a surrogate marker for overlapping metabolic diseases or reflects HCV‐specific carcinogenicity. We investigated the association between GGT and hepatocarcinogenesis after achieving a sustained viral response (SVR), accounting for drinking habits or diabetes, and examined predisposing factors associated with GGT levels after SVR.This is a prospective, multicenter, and observational study using the database of 1001 patients after HCV eradication with direct‐acting antiviral agents. The association of GGT at SVR with cumulative HCC development was examined in a multivariate analysis using Cox proportional hazard models after adjustment for covariates including alcohol and diabetes. The association between oxidative stress markers or genetic factors and GGT levels was analyzed.High GGT levels at SVR were associated with HCC development (HR] 2.38, 95% CI 1.10–5.17). This association was also significant when restricted to patients without alcohol consumption or diabetes (HR 8.38, 95% CI 2.87–24.47). GGT levels were correlated with serum growth differentiation factor 15 levels, a marker of mitochondrial dysfunction. Single‐nucleotide polymorphisms of ZNF827 and GDF15 were associated with high GGT levels.High GGT levels at SVR were associated with HCC development after accounting for alcohol consumption and diabetes. GGT levels are influenced by genetic predisposition and may reflect mitochondrial dysfunction after HCV eradication. [ABSTRACT FROM AUTHOR]

The recent advances in sequencing technologies, phylogenomics and divergence dating methods call for an integrative review of the current state of Hymenoptera systematics. We here explore the impact of these latest developments on the Hymenoptera phylogeny and our understanding of the timing of Hymenoptera evolution, while identifying the current methodological constraints and persistent knowledge gaps that warrant further investigation. Our review highlights the lack of consensus among the backbone phylogeny of Hymenoptera between key phylogenomic studies, as the higher level phylogeny remains unresolved in key nodes such as the relationships among Eusymphyta, the relationships within the Infraorder Proctotrupomorpha and the placements of the superfamilies Ichneumonoidea, Ceraphronoidea and Vespoidea. Furthermore, we underline the huge variation in divergence age estimates for Hymenoptera and detect several major gaps and/or disagreements between the fossil record and available age estimates, either due to the poorly studied fossil record or problematic age estimates, or both. To better understand the timing of Hymenoptera evolution and the role of key diversification factors, we will need continuous efforts to (i) reconcile conflicts among morphological and molecular phylogenies, by improving taxon sampling of underrepresented lineages, applying novel techniques to study morphology, making use of genome‐scale data and critically assessing incongruences in genetic markers; (ii) improve the Hymenoptera fossil record, by exercising integrative taxonomy and bringing together paleontologists and neontologists; and (iii) reconcile age estimates, by relying on tip dating approaches to bridge fossils, morphology and genomes across time. [ABSTRACT FROM AUTHOR]

The present drainage network of Bulgaria is the result of a complex Neogene and Quaternary evolution. Karst, which has developed on 23% of the territory, further complicates the hydrological pattern. Fresh waters of Bulgaria drain into the Black Sea and the Aegean Sea basins and can be roughly divided into the Danube (Middle and Lower Danube), non‐Danube Black Sea, East Aegean, and West Aegean hydrological regions. Phoxinus, a small leuciscid fish, has a mosaic distribution in all four of these regions, inhabiting small mountainous and semi‐mountainous streams. Based on morphology, it was identified as three species, Phoxinus phoxinus in the Danube, Phoxinus strandjae in the non‐Danube, and Phoxinus strymonicus in West Aegean region. Later, molecular data revealed Phoxinus csikii and Phoxinus lumaireul in the Middle Danube and P. csikii in the Lower Danube. Phoxinus has been the focus of many studies, showing a high molecular and morphological diversity, which is not entirely consistent with previous morphology‐only‐based taxonomic concepts. In this study, molecular (a mitochondrial marker and a nuclear marker) and morphological data from both historical and recently sampled collections were analysed to assess the applicability of the integrative approach in Phoxinus. The results showed a significant influence of the complex paleo‐ and recent hydrology on the currently observed genetic structure of the considered populations and species. Furthermore, the study also demonstrated a strong influence of phenotypic plasticity on the morphological analysis of Phoxinus and the lack of a clear differentiation between P. csikii and P. strandjae. A barcoded specimen was designated as neotype to fix the species named P. strandjae in the current taxonomic concept. Finally, a significant discordance between genetically delimited clades and phenotypic groups did not allow a proper delineation of the species distributed in Bulgaria, demonstrating that more molecular markers are needed for further taxonomic study of the Phoxinus complex. [ABSTRACT FROM AUTHOR]

The capture and reduction of atmospheric dinitrogen gas to ammonium can be accomplished through the enzyme nitrogenase in a process known as biological nitrogen fixation (BNF), by a class of microbes known as diazotrophs. The diazotroph Azotobacter vinelandii is a model organism for the study of aerobic nitrogen fixation, and in recent years has been promoted as a potential producer of biofertilizers. Prior reports have demonstrated the potential to partially deregulate BNF in A. vinelandii, resulting in accumulation and extracellular release of ammonium. In many cases, deregulation requires the introduction of transgenic genes or elements to yield the desired phenotype, and the long‐term stability of these strains has been reported to be somewhat problematic. In this work, we constructed two strains of A. vinelandii where regulation can be precisely controlled without the addition of any foreign genes or genetic markers. Regulation is maintained through native promoters found in A. vinelandii that can be induced through the addition of extraneous galactose. These strains result in varied degrees of regulation of BNF, and as a result, the release of extracellular ammonium is controlled in a precise, and galactose concentration‐dependent manner. In addition, these strains yield high biomass levels, similar to the wild‐type A. vinelandii strain and are further able to produce high percentages of the bioplastic polyhydroxybutyrate. [ABSTRACT FROM AUTHOR]

Objectives: To assess the role of TNF‐α/TNFR2 axis on promoting angiogenesis in oral squamous cell carcinoma (OSCC) cells and uncover the underlying mechanisms. Materials and Methods: The expression of TNFR2 and CD31 in OSCC tissues was examined; gene expression relationship between TNF‐α/TNFR2 and angiogenic markers or signaling molecules was analyzed; the expression of angiogenic markers, signaling molecules, TNFR1, and TNFR2 in TNF‐α‐stimulated OSCC cells treated with or without TNFR2 neutralizing antibody (TNFR2 Nab) were assessed; the concentration of angiogenic markers in the supernatant of OSCC cells was detected; conditioned mediums of OSCC cells treated with TNF‐α or TNF‐α + TNFR2 Nab were applied to human umbilical vein endothelial cells (HUVECs), followed by tube formation and cell migration assays. Results: Significantly elevated expression of TNFR2 and CD31 in OSCC tissues was observed. A positive gene expression correlation was identified between TNF‐α/TNFR2 and angiogenic markers or signaling molecules. TNFR2 Nab inhibited the effects of TNF‐α on enhancing the expression of angiogenic factors and TNFR2, the phosphorylation of the Akt/mTOR signaling pathway, HUVECs migration, and tube formation. Conclusions: TNFR2 Nab counteracts the effect of TNF‐α on OSCC cells through the TNFR2/Akt/mTOR axis, indicating that blocking TNFR2 might be a promising strategy against cancer. [ABSTRACT FROM AUTHOR]

Objective: To investigate whether genes in the Wnt pathway, which have been previously associated with both oral clefts and oral squamous cell carcinoma, are also associated with oral potentially malignant disorders (leukoplakia, erythroplakia and lichen planus). Materials and Methods: Case–control study: Dataset consisted of clinical information linked to DNA samples from affected subjects diagnosed with oral potential malignant disorders and oral cancer and their matched controls. Individual samples, clinical history, and potential risk factors were obtained through the Dental Registry and DNA Repository project of the School of Dental Medicine, University of Pittsburgh. The rs1533767 (WNT11), rs9879992 (GSK3B), and rs3923087 (AXIN2) were tested. After genomic DNA had been extracted, genotyping was performed blindly to clinical diagnosis status. Representation of genotypes and alleles in affected subjects in comparison to the unaffected individuals was determined using PLINK. Additional analysis was performed to investigate associations between environmental (socioeconomic/lifestyle) risk factors and the oral pathologies studied using STATA. Results: Two of the SNPs tested (rs9879992 in GSK3B and rs3923087 in AXIN2) were statistically, significantly associated with the pathologies studied (p = 0.039 and 0.038, respectively). Conclusion: Single‐nucleotide polymorphisms in genes in the Wnt pathway were associated with oral potentially malignant disorders. [ABSTRACT FROM AUTHOR]

Objectives: The pathology of Tardive Dyskinesia (TD) has yet to be fully understood, but there have been proposed hypotheses for the cause of this condition. Our team previously reported a possible association of TD with the Complement Component C4 gene in the HLA region. In this study, we explored the HLA region further by examining two previously identified schizophrenia‐associated HLA‐region single‐nucleotide polymorphisms (SNPs), namely rs13194504 and rs210133. Methods: The SNPs rs13194504 and rs210133 were tested for association with the occurrence and severity of TD in a sample of 172 schizophrenia patients who were recruited for four studies from three different clinical sites in Canada and USA. Results: The rs13194504 AA genotype was associated with decreased severity for TD as measured by Abnormal Involuntary Movement Scale (AIMS) scores (p = 0.047) but not for TD occurrence. SNP rs210133 was not significantly associated with either TD occurrence or AIMS scores. Conclusion: Our findings suggest that the rs13194504 AA genotype may play a role in TD severity, while SNP rs210133 may not have a major role in the risk or severity of TD. [ABSTRACT FROM AUTHOR]

Aim: Our aim was to assess the population structure, genetic diversity and demographic history of the wolverine (Gulo gulo) throughout its entire Eurasian range. Additionally, we aimed to contextualize and put into perspective the state of the endangered Fennoscandian population by emphasizing its connectivity to other populations. Location: The main study area covered most of the Eurasian wolverine range, with samples from Finland, Russia, Kazakhstan and Mongolia. Methods: Using a 495 bp fragment of the mitochondrial DNA control region and a frequently used set of 14 microsatellite markers on an extensive dataset of samples, we assessed the population structure, genetic diversity, and demographic history of wolverines with a variety of population genetic analyses. Results: According to both nuclear and mitochondrial genetic markers, Eurasian wolverines exhibit substructure, with the most distinct population located in Fennoscandia. The Fennoscandian population has undergone a genetic bottleneck, likely influencing its genetic diversity, which is notably the lowest in Eurasia. Genetic diversity in the rest of Eurasia gradually rises towards the central part of the range and decreases again in the east, although not as significantly as in the west. Main Conclusions: This study reveals the population structure of wolverines across Eurasia and provides direction for allocating conservation efforts to sustain a diverse and connected wolverine population. While most of the Eurasian populations seem to be well‐connected and genetically diverse, the Fennoscandian wolverines may need better connectivity to the other Eurasian populations to ensure gene flow and long‐term persistence. Our study further highlights the importance of considering the population genetic structure and diversity of the entire species range when planning management strategies. [ABSTRACT FROM AUTHOR]

The ITS‐2‐rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free‐living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS‐1 intergenic spacer and the region spanning ITS‐1_5.8S_ITS‐2. These databases comprise 2645, 254, 13,461 and 10,107 unique full‐length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS‐1 database includes the largest number of unique full‐length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short‐read or long‐read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum. [ABSTRACT FROM AUTHOR]

In polygynous species, male reproductive success is often determined by their ability to dominate female harems. Harem‐holders sire a disproportionate number of offspring. Male dominance tends to correlate with age, but intense competition and early male mortality limit most males from achieving high social status. To maximize reproductive success despite low rank, offspring sex ratio adjustment may have evolved, favoring the sex with higher fitness. If traits influencing dominance are heritable and confer reproductive advantages, we expect fathers with higher reproductive success to produce more sons, as they are more likely to become dominant. In contrast, subordinate males with lower success may benefit from siring more daughters. We tested this hypothesis on a colony of southern elephant seals breeding on the Kerguelen Archipelago. We used genetic markers to link the paternity of 540 pups to 58 breeding males. We found that the probability of siring a son increases from 43% to 54% with paternal relative reproductive success, supporting the offspring sex ratio adjustment hypothesis. Given that various factors influence sex ratio in a population, future studies should tease apart these ecological processes (e.g., paternal dominance, maternal condition, local density, or adult sex ratio) and investigate how they interact with each other. [ABSTRACT FROM AUTHOR]

Summary: Despite advancements in utilizing genetic markers to enhance acute myeloid leukaemia (AML) outcome prediction, significant disease heterogeneity persists, hindering clinical management. To refine survival predictions, we assessed the transcriptome of non‐acute promyelocytic leukaemia chemotherapy‐treated AML patients from five cohorts (n = 975). This led to the identification of a 4‐gene prognostic index (4‐PI) comprising CYP2E1, DHCR7, IL2RA and SQLE. The 4‐PI effectively stratified patients into risk categories, with the high 4‐PI group exhibiting TP53 mutations and cholesterol biosynthesis signatures. Single‐cell RNA sequencing revealed enrichment for leukaemia stem cell signatures in high 4‐PI cells. Validation across three cohorts (n = 671), including one with childhood AML, demonstrated the reproducibility and clinical utility of the 4‐PI, even using cost‐effective techniques like real‐time quantitative polymerase chain reaction. Comparative analysis with 56 established prognostic indexes revealed the superior performance of the 4‐PI, highlighting its potential to enhance AML risk stratification. Finally, the 4‐PI demonstrated to be potential marker to reclassified patients from the intermediate ELN2017 category to the adverse category. In conclusion, the 4‐PI emerges as a robust and straightforward prognostic tool to improve survival prediction in AML patients. [ABSTRACT FROM AUTHOR]

This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron‐oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron‐oxidation at circumneutral pH. Over 1000 proteins were identified under both iron‐ and hydrogen‐oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron‐oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β‐barrel structure of Cyc2. This cluster potentially encodes a biological nanowire‐like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron‐oxidizing conditions was confirmed by quantitative reverse transcription‐PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three‐electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation. [ABSTRACT FROM AUTHOR]

The use of animal manure to fertilize soil is an emerging concern contributing to the transfer of antimicrobial‐resistant pathogens to vegetables. Hence, assessing antimicrobial susceptibility profile of Escherichia coli in vegetable farms is essential to design appropriate interventions against antimicrobial resistance (AMR) in the food chain. This study assessed antimicrobial resistance profile and associated genetic markers among E. coli isolated from vegetable farms fertilized with animal manure in Addis Ababa, Ethiopia. A total of 1044 samples were collected using convenience sampling: soil (n = 271), manure (n = 375), and vegetables (n = 398) from 81 vegetable farms in Addis Ababa, Ethiopia. Antimicrobial susceptibility test was conducted for 100 E. coli isolates and antimicrobial resistance genes (ARGs) were tested by polymerase chain reaction (PCR). Of the 1044 collected samples, 25.3% were positive for E. coli, with significantly higher prevalence in the manure sample and samples collected from Akaki Kality sub‐city (p <.05). The highest resistance rate was recorded for tetracycline (72%), followed by streptomycin (63%), and sulfamethoxazole +trimethoprim (56%). Multidrug resistance was detected in 61% of the E. coli isolates. The aac(3)‐IV (76.9%), blaTEM (65.4%), aadA (60.3%), tet(A) (58.3%), and sulI (51.7%) were the commonly detected resistance genes. The current study showed a high burden of antimicrobial resistance among E. coli isolated from manure‐amended vegetable farms, with potential of playing a significant role in the dissemination of antimicrobial resistance in the food chain. Efforts should be made to reduce the burden of resistant organisms and ARGs through prudent use of antimicrobials in livestock and application of appropriate composting techniques before using manure as fertilizer. [ABSTRACT FROM AUTHOR]

Narcolepsy is a life‐long neurological disorder with well‐established genetic risk factors. Human leukocyte antigen‐DQB1*06:02 remains the strongest genetic predeterminant; however, polymorphisms in genes encoding the T‐cell receptor alpha chain are also strongly linked. This case report shows the inheritance pathway of these genetic markers contributing to narcolepsy onset in a 17‐year‐old female. [ABSTRACT FROM AUTHOR]

Marbling is one of the most important beef quality traits. An association between a non‐synonymous variant located in EGFLAM (EGF‐like fibronectin and laminin G) and marbling in Hanwoo cattle has recently been published. We therefore investigated the association between this SNP (rs109436056 SNP) and marbling in Limousin cattle. A total of 355 animals were phenotyped for marbling and genotyped for this SNP. Significant association (p < 0.05) was observed, in which genotype CC exhibited higher marbling. This SNP could be used for the genetic improvement of marbling in Limousin cattle. [ABSTRACT FROM AUTHOR]

As an important component of wheat (Triticum aestivum L.) yield, 1000‐kernel weight (TKW) has played a crucial role in yield improvement in recent decades. Marker‐assisted selection is an effective tool for improving quantitative traits; however, most markers have not been effectively applied in TKW improvement despite the identification of many loci associated with TKW. In this study, association mapping was performed using local cultivated varieties, and a previous linkage analysis was integrated to identify 10 candidate intervals. The corresponding kompetitive allele‐specific PCR markers associated with TKW were successfully developed and screened in 1153 F4 breeding lines. Three markers, namely, Ktkw‐5B2, Ktkw‐5D, and Ktkw‐7D, were proved to be significantly related to TKW according to large‐scale association mapping, and their ability to increase TKW was enhanced in combination. We applied the three markers in 150 F6 breeding lines and obtained 25 high‐TKW lines, indicating the availability in marker‐assisted selection. The TKW‐increasing allele for Ktkw‐5D was heavily selected in the present breeding program, while that for Ktkw‐5B2 was low and for Ktkw‐7D tended to increase after 2000. Furthermore, strategies for gene exploration in the three significant intervals were proposed. These results are expected to provide an efficient route for improving TKW in wheat high‐yield breeding. Core Ideas: Three significant loci for 1000‐kernel weight were identified by genetic analysis.The markers were applied in breeding lines to generate varieties with high 1000‐kernel weight.The application progress of the three loci was clarified.Strategies for gene exploration in the three significant intervals were proposed. [ABSTRACT FROM AUTHOR]