The identification of quantitative trait locus (QTL) or genes responsible for key agronomic traits has significantly enhanced genetic improvement through marker-assisted selection (MAS). However, the impacts of MAS on genetic parameters and subsequent selection processes have not been thoroughly characterised. Here, through genome-wide selective sweep analysis, we identified a diverse set of genes involved in oocyte meiosis, including PPP3CA, AR, PPP1CB, SPDYA, MAD1L1, and BMPR1B. The genome-wide association study (GWAS) further identified three genes UNC5C, BMPR1B, and PDLIM5 as being associated with lambing rate in Hu sheep. From these analyses, the FecB loci emerged as a potential molecular marker for lambing rate. with an increase of 0.5 lambs per G allele. The heritability of the lambing rate was estimated to be 0.19 (±0.02). Moreover, based on 10-fold cross-validation, the accuracy of genomic selection (GS) was found to be 0.30. Simulated MAS resulted in a reduction of the additive genetic variance components, with estimated heritability dropping to 0.14 (±0.02) and GS accuracy decreasing to 0.18-representing a decline of 26.42% and 34.81%, respectively. To address the reduced GS accuracy, we performed GWAS on the reference set to identify weighted single nucleotide polymorphisms (SNPs). This method has the potential to increase accuracy by 13.8%. Our study found that MAS has a negative impact on GS. To address this issue, we integrated prior information on SNPs from GWAS, which exhibit pleiotropic genetic architecture. This integration enables us to utilise genetic markers for complex traits more effectively, thereby improving the accuracy and efficiency of GS.

Marker assisted breeding (MAB) supports breeding by identifying individuals or molecular markers associated with important traits. MAB methods include genome-wide association studies (GWAS) and genomic selection (GS). Local haplotypes are regions of DNA that are inherited together due to high levels of linkage disequilibrium. Local haplotypes can improve the prediction accuracy and power of GS and GWAS. Currently available local haplotyping tools improve GWAS power through fine-mapping of candidate regions or through haplotype-based GWAS. However, no local haplotyping tools utilize the benefits of haplotypes for GS. Here we present HaploVar, a local haplotyping tool designed to improve both GWAS and GS pipelines by identifying local haplotypes and formatting the output to be compatible with all major GWAS and GS tools. HaploVar can be used in any haplotype-based MAB study. HaploVar can be downloaded from CRAN with R > 4.0.0 (DOI: 10.32614/CRAN.package.HaploVar). HaploVar and a tutorial vignette is available on GitHub (https://github.com/TessaMacNish/HaploVar). HaploVar is available under an MIT license. Supplementary material is available at Bioinformatics online.

Design of CellProfiler-based pipelines enabling the attribution of molecular stress markers to specific tissue and subcellular compartments of the colonic mucosa.

The genus Geum , comprises about 72 species, most frequently distributed in North America, Asia, and Europe, with a few representatives in South America, South Africa, Australia, and New Zealand. Previous phylogenetic analyses based on several molecular markers have contributed to understanding the delimitation of Geum , but the phylogenetic relationships within the genus remain unresolved. Moreover, only a few chloroplast (cp) genomes of Geum species have been reported, and no comparative cp genome analyses among Geum species have been conducted to date, limiting our understanding of cp genome evolution. This study is the first to conduct comparative genomic analyses on the cp genomes of 32 accessions representing 11 Geum taxa. The Geum cp genomes showed a typical quadripartite structure, similar to that of most other land plants, with a total of 129 genes, including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The Geum cp genomes were conserved in structure, size, GC content, gene order, and gene content. Eleven highly variable regions ( 3′-trnK-UUU-matK , psbZ-trnG-GCC , trnR-UCU-atpA , petA-psbJ , 5′-trnK-UUU-rps16 , rps16-trnQ-UUG , rpl32-trnL-UAG , ndhF-rpl32 , trnS-GCU-trnG-UCC , ndhC-trnV-UAC , and petN-psbM ) were identified as candidate molecular markers for future studies on population genetics and systematic evolution of Geum species. Phylogenetic analyses provided new insights into the relationships among Geum species and supported Smedmark’s recircumscription of Geum in a broad sense, corroborating the inclusion of Acomastylis , Coluria , and Taihangia within Geum . Twenty-three genes with sites under positive selection were detected, and the adaptive evolution of these genes may play important roles in the adaptation of Geum species to their habitats. Overall, this study enhances our understanding of the cp genome characteristics, phylogeny, and adaptive evolution of Geum species.

Colorectal cancer (CRC) is the third most prevalent cancer and one of the leading causes of cancer-related mortality in the world. Early detection is crucial in preventing deaths, but current screening methods have various limitations. So today, much attention is focused on genetic changes, including mutations in oncogenes and tumor suppressor genes, and epigenetic modifications such as aberrant methylation and alterations in the expression of specific microRNAs that contribute to CRC development. This has led to the discovery of more specific and sensitive molecular biomarkers. Furthermore, the use of liquid biopsy, which has a high potential for identifying molecular tumor markers, provides a perspective for overcoming the limitations of conventional screening methods. In this review, we first discuss the intricate molecular processes involved in the development of colorectal tumors. We then delve into the concept of liquid biopsy, exploring its traceable components such as extracellular vesicles, circulating tumor cells, circulating tumor DNAs, and circulating tumor RNAs. We also examine various methods for analyzing these components to identify molecular biomarkers for CRC screening. Additionally, we refer to the development of new diagnostic kits for CRC, such as Epi proColon, ColoSure, and Cologuard, which offer non-invasive utilization of genetic and epigenetic biomarkers. Lastly, we address the current challenges faced in using these biomarkers in a clinical setting. Despite the obstacles, these non-invasive and reliable markers have the potential to enable early detection of CRC and likely increase screening uptake, potentially replacing current modalities.

Ovarian cancer biosensors: established glycoproteins to emerging molecular biomarkers.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory loss, and neuronal degeneration. Current treatments offer limited efficacy. Elaeocarpus angustifolius Blume (Rudraksha), used traditionally in Ayurveda for neurological disorders, has shown potential for cognitive health, warranting investigation in AD models. This study aimed to evaluate the neuroprotective efficacy of an alkaloid-rich fraction of E. angustifolius (EAF) in an AlCl₃-induced rat model of AD. AD-like symptoms were induced by oral administration of AlCl₃ (100mg/kg) for 60 days, followed by a 30-day oral treatment with EAF (200 and 400mg/kg). Cognitive performance was assessed using the Morris water maze, elevated plus maze, novel object recognition, and locomotor activity tests. Biochemical and molecular markers were analysed, and hippocampal histopathology was conducted. AlCl₃ exposure caused significant cognitive and motor deficits, elevated Aβ1-42 and phosphorylated tau, decreased acetylcholine and dopamine, increased glutamate and NF-κB, and reduced NRF-2 expression, indicating oxidative stress and neuroinflammation. EAF treatment significantly improved behavioral outcomes, reduced Aβ1-42 and tau levels, restored neurotransmitter balance, enhanced antioxidant markers (GSH, SOD, CAT), and reduced MDA. It suppressed NF-κB and upregulated NRF-2, suggesting antioxidant and anti-inflammatory effects. Histopathological analysis confirmed hippocampal neuroprotection. EAF exhibited significant neuroprotective effects by mitigating oxidative stress, neuroinflammation, and AD-related pathologies, including amyloid accumulation and cholinergic dysfunction. These findings support the potential of EAF as a therapeutic candidate for AD prevention and management.

Carnation and Dianthus (Dianthus spp) are globally cultivated as a cut flower, yet high summer temperatures in Taiwan significantly reduce the yield and quality of commercial cultivars. To enhance stress tolerance traits such as heat resistance and disease resistance, interspecific and intergeneric hybridization with native species is a viable approach. Since the success of hybridization is influenced by genetic distance, this study aimed to clarify the phylogenetic relationships among native species, commercial cultivars, and interspecific hybrids using internal transcribed spacer (ITS) and random amplified polymorphic DNA (RAPD) markers. Phylogenetic analysis based on RAPD markers effectively differentiated among native Taiwanese species, commercial varieties, interspecific hybrids, and outgroup taxa. ITS markers, on the other hand, were more informative for identifying parent-offspring relationships. Notably, Dianthus superbus var. longicalycinus from Taiwan and Japan, despite sharing the same scientific name, exhibited clear distinctions in both morphological traits and molecular profiles. The combined use of RAPD and ITS markers provides complementary insights into the genetic relationships within the Dianthus genus. These findings not only support the strategic use of molecular markers in breeding programs but also highlight the need to reassess taxonomic classifications among morphologically similar varieties. This study provides genetics, breeding tools, and germplasm information for future Dianthus breeding.

Age-related cognitive decline and individual differences in dementia susceptibility are increasingly explained through the concept of cognitive reserve (CR). CR reflected the brain’s adaptive capacity to sustain cognitive performance despite Alzheimer’s disease (AD)-related pathology, extending beyond traditional biomarkers that captured the molecular or structural changes, but often failed to account for clinical heterogeneity. This review provided a comprehensive synthesis of how CR was operationalized through three major methodological approaches: sociobehavioral proxies, residual variance frameworks, and neurobiological indicators within the context of longitudinal study designs. The review included evidences from a structured PubMed and Scopus search restricted to English-language studies examining the incidence of mild cognitive impairment (MCI) or AD. Findings consistently demonstrated that higher CR, most commonly estimated through sociobehavioral proxies, such as educational level, occupational complexity, bilingualism, and engagement in cognitively stimulating activities, was associated with a delayed onset of impairment, lower dementia risk, and better clinical outcomes, despite a comparable neuropathological burden. Residual variance approaches provided complementary insights by quantifying cognitive performance that exceeded the predicted levels from underlying pathology, thereby capturing unexplained variance by structural or molecular disease markers. These residual-based methods extend CR concept beyond life-course experiences, offering statistical evidence of resilience within longitudinal trajectories of aging and disease. Additional evidence from electrophysiological and genetic investigations further suggested that CR enhanced the neural efficiency, flexibility, and the recruitment of compensatory networks. Finally, neuroimaging studies provided the mechanistic evidence that CR was supported by alterations in brain structure, functional connectivity, and activation patterns, though findings on long-term trajectories remained inconsistent. Overall, CR emerged as a multidimensional and modifiable construct that enhanced resilience to aging and dementia. Future research should prioritize the integrative longitudinal designs, combining sociobehavioral, residual variance, genetic, electrophysiological, and neuroimaging approaches to clarify mechanisms, establishing robust measurement frameworks and advance clinical translation.

Aphids that feed on alfalfa (Medicago sativa) are widespread pests, causing significant losses in yield and forage quality through direct feeding damage and the transmission of plant viruses. In this study, we assessed aphid resistance in 239 genetically diverse alfalfa accessions across multiple field environments by quantifying aphid infestation levels. Leveraging more than 1.9million high-quality single nucleotide polymorphisms, a genome-wide association study identified 22 genomic loci significantly associated with aphid resistance. These loci were distributed across all eight alfalfa chromosomes and collectively explained between 4.05% and 24.19% of the observed phenotypic variance. Functional annotation of the candidate genes revealed their involvement in key biological pathways, including ubiquitin-mediated proteolysis, ABC transporter activity, and immune signaling processes. Notably, two NLR-type resistance genes, Msa.H.0143490 and Msa.H.0461950, emerged as strong candidates for enhancing aphid resistance through genetic improvement. These findings provide valuable insights into the genetic architecture of aphid resistance and offer molecular markers that can be utilized in marker-assisted selection to develop more resilient alfalfa cultivars.

Esaxerenone inhibits renal macrophage proliferation through MR/TGF-β1 pathway in db/db mice.

SIRT1 targeted bioengineered extracellular vesicles chrono-reprogram microglia to reverse non-dipping hypertension - myocardial remodeling and comorbid neuropsychiatric disorders under stress.

From exposure to outcomes: How air pollutants impact maternal and foetal health.

Ornamental plants exhibit the capacity to augment visual appeal through their diverse morphological features, encompassing floral forms, hues, foliage, and numerous other attributes. These botanical specimens find application in landscaping, floral arrangements, container gardening, and various commercial endeavors. As a result, there exists a persistent need for the creation of novel cultivars to satisfy market demands. Traditional plant breeding is slow and takes a lot of work. This has led to the use of biotechnology, especially molecular breeding. Molecular breeding lets breeders target specific, difficult-to-change traits like flower color, scent, and plant shape. It uses advanced methods like marker-assisted selection and genome-wide selection to speed up improvements and reduce the time it takes to develop new varieties. Molecular breeding may revolutionize agriculture in the 21st century by making genetic improvements faster and more efficient. Thanks to advances in genomics, gene editing, and molecular plant breeding, we now understand molecular markers much better. This has improved breeding strategies and given us a deeper understanding of crop diversity. This review elucidates the importance of various commercially valuable ornamental traits and delineates the research endeavors and accomplishments in enhancing floral characteristics through molecular breeding techniques.

Underreporting of molecular targets in surgically treated patients with peritoneal metastasis of gastric cancer.

Cigarette smoke disrupts osteogenic-adipogenic balance via Nrf2/HERC2 axis-driven ferroptosis.

Geographical distribution and incidence of pesticide resistance mutations in spider mite and thrips species from North Vietnam.

A sex-determining loci in koi carp(Cyprinus carpio) based on whole genome resequencing technology.

Transcriptomic dynamics and immune-associated SNP discovery in Monopterus albus infected with Chinese rice-field eel rhabdovirus.

Immune-like response and autophagy modulation in gill epithelial cells of rainbow trout challenged with Piscirickettsia salmonis.