BACKGROUND: Previous studies have shown that inflammatory bowel disease (IBD) is associated with osteoporosis (OP) and bone mineral density (BMD), but the underlying genetic mechanisms are unclear. Our study wanted to explore the genetic and causal relationship between IBD and OP.
METHODS: Based on large-scale genome-wide association summary statistics and individual-level datasets (i.e., the UK Biobank), this study performed linkage disequilibrium score regression (LDSC), pleiotropic analysis under the composite null hypothesis (PLACO), and Mendelian randomization (MR) analyses to explore the genetic association, the pleiotropic genes and the causal relationship between IBD and BMD.
RESULTS: LDSC revealed significant genetic correlations between IBD and BMD (e.g., forearm BMD (rg = -0.3479, P = 0.019) and femoral neck BMD (rg = -0.1335, P = 0.0307). PLACO identified 14 overlapping pleiotropic loci, 1 shared risk gene (CDYL), and multiple shared pathways, revealing possible mechanisms for IBD and OP. MR analysis demonstrated a causal association between IBD and BMD.
CONCLUSIONS: Our study indicates that IBD may increase the risk of OP and reveals a complex genetic mechanism linking IBD and the risk of osteoporosis, which has important implications for diagnosing and treating IBD and OP.

Ovaries play key roles in fitness and evolution: they are essential female reproductive structures that develop and house the eggs in sexually reproducing animals. In Drosophila, the mature ovary contains multiple tubular egg-producing structures known as ovarioles. Ovarioles arise from somatic cellular structures in the larval ovary called terminal filaments (TFs), formed by TF cells and subsequently enclosed by sheath (SH) cells. As in many other insects, ovariole number per female varies extensively in Drosophila. At present, however, there is a striking gap of information on genetic mechanisms and evolutionary forces that shape the well-documented rapid interspecies divergence of ovariole numbers. To address this gap, here we studied genes associated with Drosophila melanogaster ovariole number or functions based on recent experimental and transcriptional datasets from larval ovaries, including TFs and SH cells, and assessed their rates and patterns of molecular evolution in five closely related species of the melanogaster subgroup that exhibit species-specific differences in ovariole numbers. From comprehensive analyses of protein sequence evolution (dN/dS), branch-site positive selection, expression specificity (tau), and phylogenetic regressions (phylogenetic generalized least squares), we report evidence of 42 genes that showed signs of playing roles in the genetic basis of interspecies evolutionary change of Drosophila ovariole number. These included the signaling genes upd2 and Ilp5 and extracellular matrix genes vkg and Col4a1, whose dN/dS predicted ovariole numbers among species. Together, we propose a model whereby a set of ovariole-involved gene proteins have an enhanced evolvability, including adaptive evolution, facilitating rapid shifts in ovariole number among Drosophila species.

UNASSIGNED: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and is prevalent in East Asia. Although genome-wide association studies (GWASs) of HCC have identified 23 risk regions, the susceptibility genes underlying these associations largely remain unclear. To identify novel candidate genes for HCC, we conducted liver single-tissue and cross-tissue transcriptome-wide association studies (TWASs) in two populations of East Asia.
UNASSIGNED: GWAS summary statistics of 2,514 subjects (1,161 HCC cases and 1,353 controls) from the Chinese Qidong cohort and 161,323 subjects (2,122 HCC cases and 159,201 controls) from the BioBank Japan project were used to conduct TWAS analysis. The single-tissue and cross-tissue TWAS approaches were both used to detect the association between susceptible genes and the risk of HCC. TWAS identified genes were further annotated by Metascape, UALCAN, GEPIA2, and DepMap.
UNASSIGNED: We identified 22 novel genes at 16 independent loci significantly associated with HCC risk after Bonferroni correction. Of these, 13 genes were located in novel regions. Besides, we found 83 genes overlapped in the Chinese and Japanese cohorts with P < 0.05, of which, three genes (NUAK2, HLA-DQA1, and ATP6V1G2) were discerned by both single-tissue and cross-tissue TWAS approaches. Among the genes identified through TWAS, a significant proportion of them exhibit a credible role in HCC biology, such as FAM96B, HSPA5, POLRMT, MPHOSPH10, and RABL2A. HLA-DQA1, NUAK2, and HSPA5 associated with the process of carcinogenesis in HCC as previously reported.
UNASSIGNED: Our findings highlight the value of leveraging the gene expression data to identify new candidate genes beyond the GWAS associations and could further provide a genetic insight for the biology of HCC.

BACKGROUND: Pine wood nematode (PWN; Bursaphelenchus xylophilus) is the causative agent of pine wilt disease (PWD), which is considered the most dangerous biohazard to conifer trees globally. The transmission of PWN relies on insect vectors, particularly the Japanese pine sawyer (JPS; Monochamus alternatus). However, the molecular mechanism underlying PWN-JPS assembly remains largely unknown.
RESULTS: Here, we found that both geographical and gender could significantly affect the PCA (PWN carrying amount) of JPS; thus, JPS transcriptomes from diverse locations and genders were explored regard to PWN loading. Due to the shortage of genomes, we developed a full-length reference transcriptome for analyzing next-generation sequencing data. A comparative genomic study was performed, and 11 248 potential PWN-carrying associate genes (β) were nominated in JPS by using the reported genomes of PWN and non-PWN carrier insect species. Then, 151 differentially expressed transcripts (DETs), 28 of them overlapped with β, correlated with the PCA of JPS were nominated by RNA-Seq, and found that fatty acid β-oxidation might be the key factor that affected the PCA of JPS. Furthermore, JPS fatty acid β-oxidation rates were experimentally decreased using the inhibitor Etomoxir, leading to an increased PCA of JPS. Meanwhile, silencing MaCPT1 in JPS by RNA interference led to a decreased fatty acid β-oxidation rate and increased PCA of JPS.
CONCLUSIONS: In conclusion, MaCPT1 was able to decrease the PWN-JPS assembly formation through the fatty acid β-oxidation of JPS. These results provide new insights for exploring the impact of PWN invasion on JPS. © 2024 Society of Chemical Industry.

Tuber plants are of great significance in the world as human food crops. Polysaccharides, important metabolites in tuber plants, also serve as a source of innovative drugs with significant pharmacological effects. These drugs are particularly known for their immunomodulation and antitumor properties. To fully exploit the potential value of tuber plant polysaccharides and establish a synthetic system for their targeted synthesis, it is crucial to dissect their metabolic processes and genetic regulatory mechanisms. In this article, we provide a comprehensive summary of the basic pathways involved in the synthesis of various types of tuber plant polysaccharides. We also outline the key research progress that has been made in this area in recent years. We classify the main types and functions of tuber plant polysaccharides and analyze the biosynthetic processes and genetic regulation mechanisms of key enzymes involved in the metabolic pathways of starch, cellulose, pectin, and fructan in tuber plants. We have identified hexokinase and glycosyltransferase as the key enzymes involved in the polysaccharide synthesis process. By elucidating the synthesis pathway of polysaccharides in tuber plants and understanding the underlying mechanism of action of key enzymes in the metabolic pathway, we can provide a theoretical framework for enhancing the yield of polysaccharides and other metabolites in plant culture cells. This will ultimately lead to increased production efficiency.

Porous sandstone geothermal water is an important geothermal resource, which is a low-carbon and clean resource, but lacks systematic research on a regional scale. The northern part of Jinan City is rich in geothermal resources, specifically porous sandstone thermal reservoirs. However, there is still incomplete research on the mechanism of geothermal genesis and the hydrochemical characteristics of geothermal water in porous sandstone. This study aims to address this gap by collecting 21 groundwater samples from northern Jinan and comparing their conventional ion and isotope characteristics to investigate the hydrochemical characteristics during the formation of geothermal water and uncover the genesis mechanism of porous sandstone geothermal water. The results indicate that the geothermal water is classified as Na-Cl type and Na-SO4-Cl type. The hydrochemical characteristics of geothermal water are primarily influenced by water-rock interaction and groundwater mixing. The water source primarily comes from the atmospheric precipitation in the Taiyi mountains, with an altitude of 910.75-1542.2 m.s.a.l.. The estimated temperature of the thermal reservoir ranges from 51 to 78 °C, and the depth of geothermal water circulation is estimated to be between 1316 and 2216 m. Based on the characteristics of the geothermal field, including the \"cap rock, water source, heat source, reservoir, and channel,\" a conceptual model of the porous sandstone geothermal water flow system is proposed. This model offers novel insights into the genesis mechanism of geothermal water under similar geological conditions.

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This study investigated the physiological and molecular responses of rice genotype \'9311\' to Cd stress and the mitigating effects of silicon oxide nanoparticles (SiO NPs). Cd exposure severely hindered plant growth, chlorophyll content, photosynthesis, and Cd accumulation. However, SiO NPs supplementation, particularly the SiONP100 treatment, significantly alleviated Cd-induced toxicity, mitigating the adverse effects on plant growth while maintaining chlorophyll content and photosynthetic attributes. The SiONP100 treatment also reduced Cd accumulation, indicating a preference for Si uptake in genotype 9311. Complex interactions among Cd, Si, Mg, Ca, and K were uncovered, with fluctuations in MDA and H2O2 contents. Distinct morphological changes in stomatal aperture and mesophyll cell structures were observed, including changes in starch granules, grana thylakoids, and osmophilic plastoglobuli. Moreover, following SiONP100 supplementation, genotype 9311 increased peroxidase, superoxide dismutase, and catalase activities by 56%, 44%, and 53% in shoots and 62%, 49%, and 65% in roots, respectively, indicating a robust defense mechanism against Cd stress. Notably, OsNramp5, OsHMA3, OsSOD-Cu/Zn, OsCATA, OsCATB, and OsAPX1 showed significant expression after SiO NPs treatment, suggesting potential Cd translocation within rice tissues. Overall, SiO NPs supplementation holds promise for enhancing Cd tolerance in rice plants while maintaining essential physiological functions.

Differential responses to viral infections are influenced by the genetic makeup of the host. Studies of resistance to retroviruses in human populations are complicated due to the inability to conduct proof-of-principle studies. Inbred mouse lines, which have a range of susceptible phenotypes to retroviruses, are an ideal tool to identify and characterize mechanisms of resistance and define their genetic underpinnings. YBR/Ei mice become infected with Mouse Mammary Tumor Virus, a mucosally transmitted murine retrovirus, but eliminate the virus from their pedigrees. Virus elimination correlates with a lack of virus-specific neonatal oral tolerance, which is a major mechanism for blocking the anti-virus response in susceptible mice. Virus control is unrelated to virus-neutralizing antibodies, cytotoxic CD8+ T cells, NK cells, and NK T cells, which are the best characterized mechanisms of resistance to retroviruses. We identified a single, dominant locus that controls the resistance mechanism, which we provisionally named attenuation of virus titers (Avt) and mapped to the distal region of chromosome 18. IMPORTANCE Elucidation of the mechanism that mediates resistance to retroviruses is of fundamental importance to human health, as it will ultimately lead to knowledge of the genetic differences among individuals in susceptibility to microbial infections.

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