Sex hormones and risk of lung and colorectal cancers in women: a Mendelian randomization study.

The roles of sex hormones such as estradiol, testosterone, and sex hormone-binding globulin (SHBG) in the etiology of lung and colorectal cancers in women, among the most common cancers after breast cancer, are unclear. This Mendelian randomization (MR) study evaluated such potential causal associations in women of European ancestry. We used summary statistics data from genome-wide association studies (GWASs) on sex hormones and from the Trøndelag Health (HUNT) Study and large consortia on cancers. There was suggestive evidence of genetically predicted 1-standard deviation increase in total testosterone levels being associated with a lower risk of lung non-adenocarcinoma (hazard ratio (HR) 0.60, 95% CI 0.37-0.98) in the HUNT Study. However, this was not confirmed by using data from a larger consortium. In general, we did not find convincing evidence to support a causal role of sex hormones on risk of lung and colorectal cancers in women of European ancestry.

OsCOPT7 is a copper exporter at the tonoplast and endoplasmic reticulum and controls Cu translocation to the shoots and grain of rice.

Copper (Cu) is an essential micronutrient for all living organisms but is also highly toxic in excess. Cellular homoeostasis of Cu is maintained by various transporters and metallochaperones. Here, we investigated the biological function of OsCOPT7, a member of the copper transporters (COPT) family, in Cu homoeostasis in rice. OsCOPT7 was mainly expressed in the roots and the expression was upregulated by Cu deficiency. OsCOPT7 was localized at the tonoplast and the endoplasmic reticulum. Knockout of OsCOPT7 increased Cu accumulation in the roots but decreased Cu concentrations in the shoots and grain. The knockout mutants contained higher concentrations of Cu in the roots cell sap but markedly lower concentrations of Cu in the xylem sap than wild-type plants. Seed setting and grain yield were reduced significantly in the knockout mutants grown in a low Cu soil. Knockout mutants were more tolerant to Cu toxicity. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsCOPT7 interacts physically with the rice Cu chaperone antioxidant protein 1 (OsATX1). Taken together, our results indicate that OsCOPT7 is a specific Cu transporter functioning to export Cu from the vacuoles and the ER and plays an important role in controlling the root-to-shoot Cu translocation in rice.

Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies.

BACKGROUND: Clinical, molecular, and genetic epidemiology studies displayed remarkable differences between ever- and never-smoking lung cancer. METHODS: We conducted a stratified multi-population (European, East Asian, and African descent) association study on 44,823 ever-smokers and 20,074 never-smokers to identify novel variants that were missed in the non-stratified analysis. Functional analysis including expression quantitative trait loci (eQTL) colocalization and DNA damage assays, and annotation studies were conducted to evaluate the functional roles of the variants. We further evaluated the impact of smoking quantity on lung cancer risk for the variants associated with ever-smoking lung cancer. RESULTS: Five novel independent loci, GABRA4, intergenic region 12q24.33, LRRC4C, LINC01088, and LCNL1 were identified with the association at two or three populations (P < 5 × 10-8). Further functional analysis provided multiple lines of evidence suggesting the variants affect lung cancer risk through excessive DNA damage (GABRA4) or cis-regulation of gene expression (LCNL1). The risk of variants from 12 independent regions, including the well-known CHRNA5, associated with ever-smoking lung cancer was evaluated for never-smokers, light-smokers (packyear ≤ 20), and moderate-to-heavy-smokers (packyear > 20). Different risk patterns were observed for the variants among the different groups by smoking behavior. CONCLUSIONS: We identified novel variants associated with lung cancer in only ever- or never-smoking groups that were missed by prior main-effect association studies. IMPACT: Our study highlights the genetic heterogeneity between ever- and never-smoking lung cancer and provides etiologic insights into the complicated genetic architecture of this deadly cancer.

N-acetylaspartate from fat cells regulates postprandial body temperature.

N-acetylaspartate (NAA), the brain's second most abundant metabolite, provides essential substrates for myelination through its hydrolysis. However, activities and physiological roles of NAA in other tissues remain unknown. Here, we show aspartoacylase (ASPA) expression in white adipose tissue (WAT) governs systemic NAA levels for postprandial body temperature regulation. Proteomics and mass spectrometry revealed NAA accumulation in WAT of Aspa knockout mice stimulated the pentose phosphate pathway and pyrimidine production. Stable isotope tracing confirmed higher incorporation of glucose-derived carbon into pyrimidine metabolites in Aspa knockout cells. Additionally, serum NAA positively correlates with the pyrimidine intermediate orotidine and this relationship predicted lower body mass index in humans. Using whole-body and tissue-specific knockout mouse models, we demonstrate that fat cells provided plasma NAA and suppressed postprandial body temperature elevation. Furthermore, exogenous NAA supplementation reduced body temperature. Our study unveils WAT-derived NAA as an endocrine regulator of postprandial body temperature and physiological homeostasis.

BiMGCL: rumor detection via bi-directional multi-level graph contrastive learning.

The rapid development of large language models has significantly reduced the cost of producing rumors, which brings a tremendous challenge to the authenticity of content on social media. Therefore, it has become crucially important to identify and detect rumors. Existing deep learning methods usually require a large amount of labeled data, which leads to poor robustness in dealing with different types of rumor events. In addition, they neglect to fully utilize the structural information of rumors, resulting in a need to improve their identification and detection performance. In this article, we propose a new rumor detection framework based on bi-directional multi-level graph contrastive learning, BiMGCL, which models each rumor propagation structure as bi-directional graphs and performs self-supervised contrastive learning based on node-level and graph-level instances. In particular, BiMGCL models the structure of each rumor event with fine-grained bidirectional graphs that effectively consider the bi-directional structural characteristics of rumor propagation and dispersion. Moreover, BiMGCL designs three types of interpretable bi-directional graph data augmentation strategies and adopts both node-level and graph-level contrastive learning to capture the propagation characteristics of rumor events. Experimental results on real datasets demonstrate that our proposed BiMGCL achieves superior detection performance compared against the state-of-the-art rumor detection methods.

Comprehensive analysis of HOXC8 associated with tumor microenvironment characteristics in colorectal cancer.

Background: Accumulating evidence have highlighted the essential roles of HOX genes in embryonic development and carcinogenesis. As a member of the HOX gene family, the abnormal expression of HOXC8 gene is associated with the progression and metastasis of various tumors. However, potential roles of HOXC8 in colorectal cancer (CRC) prognosis and tumor microenvironment (TME) remodeling remain unclear. Methods: We conducted an integrated analysis of clinical and molecular characteristics, relevant oncogenic and immune regulation roles and drug sensitivity features of HOXC8 in CRC. Results: HOXC8 expression was markedly high expressed in CRC samples compared to normal samples, and the upregulated expression of HOXC8 was associated with poor prognosis. High HOXC8 expression was significantly associated with invasion-related pathways especially epithelial-mesenchymal transition (EMT). In vitro experiments showed significantly up-regulated HOXC8 expression in some CRC cell lines and its promoting effect on EMT and cell proliferation. TME categorization through transcriptomic analysis of CRC patients with high HOXC8 expression identified two different TME subtypes known as immune-enriched with fibrotic subtype and immune-depleted subtype. Patients with immune-enriched, fibrotic subtype exhibited significantly longer progression-free survival (PFS), upregulated PD-L1 and CTLA4 expression and higher TMB than those with the immune-depleted subtype. Conclusions: HOXC8 overexpression was associated with poor prognosis and specific TME subtypes in CRC. This study provided valuable resource for further exploring the potential mechanisms and therapeutic targets of HOX genes in CRC.

Long-Term Exposure to Microcystin-LR Induces Gastric Toxicity by Activating the Mitogen-Activated Protein Kinase Signaling Pathway.

Previous studies have primarily concentrated on the hepatotoxicity of MC-LR, whereas its gastric toxicity effects and mechanisms of long-term exposure under low dosage remain unknown. Herein, the gastric tissue from C57BL/6 mice fed with drinking water contaminated by low-dose MC-LR (including 1, 60, and 120 µg/L) was investigated. The results obtained showed that exposure to different concentrations of MC-LR resulted in significant shedding and necrosis of gastric epithelial cells in mice, and a down-regulation of tight junction markers, including ZO-1, Claudin1, and Occludin in the stomach, which might lead to increased permeability of the gastric mucosa. Moreover, the protein expression levels of p-RAF/RAF, p-ERK1/2/ERK1/2, Pink1, Parkin, and LC3-II/LC-3-I were increased in the gastric tissue of mice exposed to 120 µg/L of MC-LR, while the protein expression level of P62 was significantly decreased. Furthermore, we found that pro-inflammatory factors, including IL-6 and TNF-ɑ, were dramatically increased, while the anti-inflammatory factor IL-10 was significantly decreased in the gastric tissue of MC-LR-exposed mice. The activation of the MAPK signaling pathway and mitophagy might contribute to the development of gastric damage by promoting inflammation. We first reported that long-term exposure to MC-LR induced gastric toxicity by activating the MAPK signaling pathway, providing a new insight into the gastric toxic mechanisms caused by MC-LR.

Immune-Ageing Evaluation of Peripheral T and NK Lymphocyte Subsets in Chinese Healthy Adults.

Ageing is often accompanied with a decline in immune system function, resulting in immune ageing. Numerous studies have focussed on the changes in different lymphocyte subsets in diseases and immunosenescence. The change in immune phenotype is a key indication of the diseased or healthy status. However, the changes in lymphocyte number and phenotype brought about by ageing have not been comprehensively analysed. Here, we analysed T and natural killer (NK) cell subsets, the phenotype and cell differentiation states in 43,096 healthy individuals, aged 20-88 years, without known diseases. Thirty-six immune parameters were analysed and the reference ranges of these subsets were established in different age groups divided into 5-year intervals. The data were subjected to random forest machine learning for immune-ageing modelling and confirmed using the neural network analysis. Our initial analysis and machine modelling prediction showed that naïve T cells decreased with ageing, whereas central memory T cells (Tcm) and effector memory T cells (Tem) increased cluster of differentiation (CD) 28-associated T cells. This is the largest study to investigate the correlation between age and immune cell function in a Chinese population, and provides insightful differences, suggesting that healthy adults might be considerably influenced by age and sex. The age of a person's immune system might be different from their chronological age. Our immune-ageing modelling study is one of the largest studies to provide insights into 'immune-age' rather than 'biological-age'. Through machine learning, we identified immune factors influencing the most through ageing and built a model for immune-ageing prediction. Our research not only reveals the impact of age on immune parameter differences within the Chinese population, but also provides new insights for monitoring and preventing some diseases in clinical practice. Supplementary Information: The online version contains supplementary material available at 10.1007/s43657-023-00106-0.

Study of polycyclic aromatic hydrocarbons accumulation in bioretention facilities and its influence on microbial community structure.

Bioretention facilities are one of the most widely used measures for urban stormwater control and utilization. In this study, the accumulation characteristics of polycyclic aromatic hydrocarbons (PAHs) in bioretention facilities and the effects of PAHs on the structure of microbial communities were explored by combining on-site monitoring and water distribution simulation experiments. The correlation between pollutant accumulation and dominant microorganisms in the bioretention systems was also clarified. The results showed that all 16 priority PAHs were detected in the bioretention facilities in the sponge city pilot area. The PAH concentrations in the soil during the non-rainy season were higher than those in the rainy season and medium- and high-ring PAHs dominated. PAHs in the study area were mainly derived from coal and biomass combustion. The potential carcinogenic risk of PAHs accumulated in the bioretention facilities in the study area was low. The microbial diversity during the non-rainy season was greater than that during the rainy season. Firmicutes, Bacteroidetes, Bacteroides, and Massilia were strongly correlated with naphthalene (NAP), pyrene (PYR), fluoranthene (FLT), and benzo[a]pyrene (BaP). According to the results of the small-scale water distribution test, the addition of PAHs had little effect on the decline in water quantity, and there was no significant regularity in the reduction of water quality including TP, NH4+-N, NO3-N, and TN. The addition of PAHs had a significant effect on the microbial community structure and an inhibitory effect on enzyme activity.

Anisotropic Phonon Behavior and Phase Transition in Monolayer ReSe2 Discovered by High Pressure Raman Scattering.

Re-based transition metal dichalcogenides have attracted extensive attention owing to their anisotropic structure and excellent properties in applications such as optoelectronic devices and electrocatalysis. The present study methodically investigated the evolution of specific Raman phonon mode behaviors and phase transitions in monolayer and bulk ReSe2 under high pressure. Considering the distinctive anisotropic characteristics and the vibration vectors of Re and Se atoms exhibited by monolayer ReSe2, we perform phonon dispersion calculations and propose a methodology utilizing pressure-dependent polarized Raman measurements to explore the precise structural evolution of monolayer ReSe2 under the stress fields. Varied behaviors of the Eg-like and Ag-like modes, along with their specific vector transformations, have been identified in the pressure range 0-14.59 GPa. The present study aims to offer original perspectives on the physical evolution of Re-based transition metal dichalcogenides, elucidating their fundamental anisotropic properties and exploring potential applicability in diverse devices.

Dynamic Characteristic Model of Giant Magnetostrictive Transducer with Double Terfenol-D Rods.

Giant magnetostrictive transducer can be widely used in active vibration control, micro-positioning mechanism, energy harvesting system, and ultrasonic machining. Hysteresis and coupling effects are present in transducer behavior. The accurate prediction of output characteristics is critical for a transducer. A dynamic characteristic model of a transducer is proposed, by providing a modeling methodology capable of characterizing the nonlinearities. To attain this objective, the output displacement, acceleration, and force are discussed, the effects of operating conditions on the performance of Terfenol-D are studied, and a magneto-mechanical model for the behavior of transducer is proposed. A prototype of the transducer is fabricated and tested to verify the proposed model. The output displacement, acceleration, and force have been theoretically and experimentally studied at different working conditions. The results show that, the displacement amplitude, acceleration amplitude, and force amplitude are about 49 µm, 1943 m/s2, and 20 N. The error between the model and experimental results are 3 µm, 57 m/s2, and 0.2 N. Calculation results and experimental results show a good agreement.

Microcystin-LR-Exposure-Induced Kidney Damage by Inhibiting MKK6-Mediated Mitophagy in Mice.

Previous studies have reported that microcystin-LR (MC-LR) levels are highly correlated with abnormal renal function indicators, suggesting that MC-LR is an independent risk factor for kidney damage. However, the evidence for the exact regulation mechanism of MC-LR on kidney damage is still limited, and further in-depth exploration is needed. In addition, the mitochondria-related mechanism of MC-LR leading to kidney damage has not been elucidated. To this end, the present study aimed to further explore the mechanism of mitophagy related to kidney damage induced by MC-LR through in vitro and in vivo experiments. Male C57BL/6 mice were fed with a standard rodent pellet and exposed daily to MC-LR (20 µg/kg·bw) via intraperitoneal injections for 7 days. Moreover, HEK 293 cells were treated with MC-LR (20 µM) for 24 h. The histopathological results exhibited kidney damage after MC-LR exposure, characterized by structurally damaged nephrotomies, with inflammatory cell infiltration. Similarly, a significant increase in renal interstitial fibrosis was observed in the kidneys of MC-LR-treated mice compared with those of the control group (CT) mice. MC-LR exposure caused impaired kidney function, with markedly increased blood urea nitrogen (BUN), creatinine (Cr), and uric acid (UA) levels in mice. Ultrastructural analysis exhibited obviously swollen, broken, and disappearing mitochondrial crests, and partial mitochondrial vacuoles in the MC-LR-treated HEK 293 cells. The Western blotting results demonstrated that exposure to MC-LR significantly increased the protein expressions of MKK6, p-p38, and p62, while the expression of mitophagy-related proteins was significantly inhibited in the kidneys of mice and HEK293 cells, including parkin, TOM20, and LC3-II, indicating the inhibition of mitophagy. Therefore, our data suggest that the inhibition of MKK6-mediated mitophagy might be the toxicological mechanism of kidney toxicity in mice with acute exposure to MC-LR.

Mosaic Chromosomal Alterations Are Associated With Increased Lung Cancer Risk: Insight From the INTEGRAL-ILCCO Cohort Analysis.

INTRODUCTION: Mosaic chromosomal alterations (mCAs) detected in white blood cells represent a type of clonal hematopoiesis (CH) that is understudied compared with CH-related somatic mutations. A few recent studies indicated their potential link with nonhematological cancers, especially lung cancer. METHODS: In this study, we investigated the association between mCAs and lung cancer using the high-density genotyping data from the OncoArray study of INTEGRAL-ILCCO, the largest single genetic study of lung cancer with 18,221 lung cancer cases and 14,825 cancer-free controls. RESULTS: We identified a comprehensive list of autosomal mCAs, ChrX mCAs, and mosaic ChrY (mChrY) losses from these samples. Autosomal mCAs were detected in 4.3% of subjects, in addition to ChrX mCAs in 3.6% of females and mChrY losses in 9.6% of males. Multivariable logistic regression analysis indicated that the presence of autosomal mCAs in white blood cells was associated with an increased lung cancer risk after adjusting for key confounding factors, including age, sex, smoking status, and race. This association was mainly driven by a specific type of mCAs: copy-neutral loss of heterozygosity on autosomal chromosomes. The association between autosome copy-neutral loss of heterozygosity and increased risk of lung cancer was further confirmed in two major histologic subtypes, lung adenocarcinoma and squamous cell carcinoma. In addition, we observed a significant increase of ChrX mCAs and mChrY losses in smokers compared with nonsmokers and racial differences in certain types of mCA events. CONCLUSIONS: Our study established a link between mCAs in white blood cells and increased risk of lung cancer.

Effects of Kinesio Taping for Chronic Nonspecific Low Back Pain: A Systematic Review and Meta-analysis.

Context: Chronic nonspecific low back pain (CNLBP) is a common musculoskeletal disorder that seriously affects patients' quality of life (QoL). Clinicians have used Kinesio Taping (KT) in the treatment of CNLBP patients, but evidence is still lacking on the benefits of KT for CNLBP. Objective: The study aimed to perform a systematic review and meta-analysis of the currently published randomized controlled trails (RCTs) to determine KT's efficacy for CNLBP patients. Design: The research team performed a literature search using five major electronic databases-PubMed, Embase, Web of science, Cochrane Library, MEDLINE and OpenGrey-and included studies form inception to January 2018. The search used the keywords "kinesio tap*", "kinesio*", and "chronic low back pain (CLBP)" or "CNLBP". Setting: The study took place in the 942 Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army. Outcome Measures: The research team performed the meta-analysis using RevMan 5.3 software. The team selected studies that used pain intensity and disability as the primary outcome measures, and if the study used other outcomes, they had to be the secondary outcomes. Results: The systematic review included nine RCTs in the meta-analysis. KT can significantly reduce pain intensity between baseline and immediately postintervention (SMD = -0.47, 95% CI -0.93 to -0.02, P = .04) and between baseline and the short-term follow-up period (SMD = -0.67, 95% CI -0.44 to -0.20, P = .03). However, no significant differences existed between KT's ability to relieve other symptoms of CNLBP-disability, trunk flexion range of motion (ROM), change in status, fear of movement, isometric endurance of the trunk muscles, or extension-when compared to either sham taping or KT as an adjunct to physical therapy. Conclusions: KT can have immediate and short-term positive effects on reducing pain intensity, but existing evidence doesn't support KT's superiority to other interventions in improving functions for individuals with CNLBP.

Interaction between the PI3K/AKT pathway and mitochondrial autophagy in macrophages and the leukocyte count in rats with LPS-induced pulmonary infection.

This study examined the effects of the PI3K/AKT pathway and mitochondrial autophagy in macrophages and the leukocyte count after pulmonary infection. Sprague‒Dawley rats were subjected to tracheal injection of lipopolysaccharide (LPS) to establish animal models of pulmonary infection. By inhibiting the PI3K/AKT pathway or inhibiting/inducing mitochondrial autophagy in macrophages, the severity of the pulmonary infection and the leukocyte count were altered. The PI3K/AKT inhibition group did not show a significant difference in leukocyte counts compared with the infection model group. Mitochondrial autophagy induction alleviated the pulmonary inflammatory response. The infection model group had significantly higher levels of LC3B, Beclin1, and p-mTOR than the control group. The AKT2 inhibitor group exhibited significantly increased levels of LC3B and Beclin1 compared with the control group (P < 0.05), and the Beclin1 level was significantly higher than that in the infection model group (P < 0.05). Compared with the infection model group, the mitochondrial autophagy inhibitor group exhibited significantly decreased levels of p-AKT2 and p-mTOR, whereas the levels of these proteins were significantly increased in the mitochondrial autophagy inducer group (P < 0.05). PI3K/AKT inhibition promoted mitochondrial autophagy in macrophages. Mitochondrial autophagy induction activated the downstream gene mTOR of the PI3K/AKT pathway, alleviated pulmonary inflammatory reactions, and decreased leukocyte counts.

Expansion of human megakaryocyte-biased hematopoietic stem cells by biomimetic Microniche.

Limited numbers of available hematopoietic stem cells (HSCs) limit the widespread use of HSC-based therapies. Expansion systems for functional heterogenous HSCs remain to be optimized. Here, we present a convenient strategy for human HSC expansion based on a biomimetic Microniche. After demonstrating the expansion of HSC from different sources, we find that our Microniche-based system expands the therapeutically attractive megakaryocyte-biased HSC. We demonstrate scalable HSC expansion by applying this strategy in a stirred bioreactor. Moreover, we identify that the functional human megakaryocyte-biased HSCs are enriched in the CD34+CD38-CD45RA-CD90+CD49f lowCD62L-CD133+ subpopulation. Specifically, the expansion of megakaryocyte-biased HSCs is supported by a biomimetic niche-like microenvironment, which generates a suitable cytokine milieu and supplies the appropriate physical scaffolding. Thus, beyond clarifying the existence and immuno-phenotype of human megakaryocyte-biased HSC, our study demonstrates a flexible human HSC expansion strategy that could help realize the strong clinical promise of HSC-based therapies.

Construction and application of sponge city resilience evaluation system: a case study in Xi'an, China.

Urban vulnerability is evident when highly complex flood risks overlap with diverse cities, and it is important to enhance the resilience of cities to flood shocks. In this study, a sponge city resilience assessment system is established considering engineering, environmental and social indicators, and the grey relational analysis method (GRA) is used to quantify sponge city resilience. At the same time, a multi-objective optimization model is established based on the three dimensions of water ecological environment, drainage safety, and waterlogging safety. The optimal configuration of grey-green infrastructure is weighed by combining the ideal point method, aiming to ensure that cities effectively reduce flood risk through the optimal configuration scheme. Taking the Xiaozhai area in Xi'an as the study area, the evaluation results show that the grey relational degree (GRD) of the resilience indexes of the original scheme is between 0.390 and 0.661 under the seven different return periods, while the optimization scheme ranges from 0.648 to 0.765, with the best sponge city resilience at a return period of 2a. Compared with the original scheme, the optimized sponge city resilience level increases from level II to nearly level I in the low return period and from level IV to level II in the high return period, indicating that city's ability to cope with waterlogging and pollution is enhanced significantly. Besides, the main factor affecting the sponge city resilience is the runoff control rate, followed by pollutant load reduction rate, which can provide a methodological framework for the assessment and improvement of sponge city resilience.

Study on non-point source pollution characteristics under different spatial scales: a case study of Hanjiang River Basin, China.

In recent years, the research on non-point source (NPS) pollution has been deepening, but it is focused on the large-scale watershed or region. There are a few studies on the scales of small watershed and runoff plot, and it is even less to analyze the characteristics and mechanism of non-point source pollution in certain watershed by combining three different scales. Based on the combination of natural rainfall monitoring and MIKE model simulation, the Shaanxi section of Hanjiang River Basin in China was taken as an example to study the characteristics of NPS pollution at different spatial scales. The results showed that there was an obvious correlation between rainfall and runoff/sediment yield. The order of runoff yield/sediment yield per unit area was as follows: woodland > forested and grassy land > arable land. There was a significant relationship between the loss of total phosphorus and the sediment yield in the runoff plots. The total nitrogen pollution was serious, with an average concentration of 3.8 mg/L. The nutrient loss was in the form of nitrate nitrogen, with an average proportion of 63.06%. For small watershed scale, the characteristics of rainfall runoff pollution generation were like runoff plot scale, both have obvious initial scour phenomenon. However, compared with runoff plot scale, the pollutant loss concentration increases with a strong lag. The MIKE model based on the coupling of hydrology, hydrodynamics, and pollution load had a strong applicability in the basin. The critical source areas of NPS pollution were identified, and five scenarios were laid out in the areas for the control of NPS pollution. Centralized livestock and poultry farming had the best reduction effect.

Rapid identification of high and low cadmium (Cd) accumulating rice cultivars using machine learning models with molecular markers and soil Cd levels as input data.

Excessive accumulation of cadmium (Cd) in rice grains threatens food safety and human health. Growing low Cd accumulating rice cultivars is an effective approach to produce low-Cd rice. However, field screening of low-Cd rice cultivars is laborious, time-consuming, and subjected to the influence of environment × genotype interactions. In the present study, we investigated whether machine learning-based methods incorporating genotype and soil Cd concentration can identify high and low-Cd accumulating rice cultivars. One hundred and sixty-seven locally adapted high-yielding rice cultivars were grown in three fields with different soil Cd levels and genotyped using four molecular markers related to grain Cd accumulation. We identified sixteen cultivars as stable low-Cd accumulators with grain Cd concentrations below the 0.2 mg kg-1 food safety limit in all three paddy fields. In addition, we developed eight machine learning-based models to predict low- and high-Cd accumulating rice cultivars with genotypes and soil Cd levels as input data. The optimized model classifies low- or high-Cd cultivars (i.e., the grain Cd concentration below or above 0.2 mg kg-1) with an overall accuracy of 76%. These results indicate that machine learning-based classification models constructed with molecular markers and soil Cd levels can quickly and accurately identify the high- and low-Cd accumulating rice cultivars.

Bovine HOXA11 Gene Identified from RNA-Seq: mRNA Profile Analysis and Genetic Variation Detection Using ME Method and Their Associations with Carcass Traits.

The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.