Gsw-fi: a GLM model incorporating shrinkage and double-weighted strategies for identifying cancer driver genes with functional impact.

BACKGROUND: Cancer, a disease with high morbidity and mortality rates, poses a significant threat to human health. Driver genes, which harbor mutations accountable for the initiation and progression of tumors, play a crucial role in cancer development. Identifying driver genes stands as a paramount objective in cancer research and precision medicine. RESULTS: In the present work, we propose a method for identifying driver genes using a Generalized Linear Regression Model (GLM) with Shrinkage and double-Weighted strategies based on Functional Impact, which is named GSW-FI. Firstly, an estimating model is proposed for assessing the background functional impacts of genes based on GLM, utilizing gene features as predictors. Secondly, the shrinkage and double-weighted strategies as two revising approaches are integrated to ensure the rationality of the identified driver genes. Lastly, a statistical method of hypothesis testing is designed to identify driver genes by leveraging the estimated background function impacts. Experimental results conducted on 31 The Cancer Genome Altas datasets demonstrate that GSW-FI outperforms ten other prediction methods in terms of the overlap fraction with well-known databases and consensus predictions among different methods. CONCLUSIONS: GSW-FI presents a novel approach that efficiently identifies driver genes with functional impact mutations using computational methods, thereby advancing the development of precision medicine for cancer.

Spatiotemporal transcriptomics and metabolic profiling provide insights into gene regulatory networks during lentil seed development.

Lentil (Lens culinaris Medik.) is a nutritious legume with seeds rich in protein, minerals and an array of diverse specialized metabolites. The formation of a seed requires regulation and tight coordination of developmental programs to form the embryo, endosperm and seed coat compartments, which determines the structure and composition of mature seed and thus its end-use quality. Understanding the molecular and cellular events and metabolic processes of seed development is essential for improving lentil yield and seed nutritional value. However, such information remains largely unknown, especially at the seed compartment level. In this study, we generated high-resolution spatiotemporal gene expression profiles in lentil embryo, seed coat and whole seeds from fertilization through maturation. Apart from anatomic differences between the embryo and seed coat, comparative transcriptomics and weighted gene co-expression network analysis revealed embryo- and seed coat-specific genes and gene modules predominant in specific tissues and stages, which highlights distinct genetic programming. Furthermore, we investigated the dynamic profiles of flavonoid, isoflavone, phytic acid and saponin in seed compartments across seed development. Coupled with transcriptome data, we identified sets of candidate genes involved in the biosynthesis of these metabolites. The global view of the transcriptional and metabolic changes of lentil seed tissues throughout development provides a valuable resource for dissecting the genetic control of secondary metabolism and development of molecular tools for improving seed nutritional quality.

Maternal Dietary Cholesterol and Egg Intake during Pregnancy and Large-for-Gestational-Age Infants: A Prospective Cohort Study.

BACKGROUND: Cholesterol plays a vital role in fetal growth and development during pregnancy. There remains controversy over whether pregnant females should limit their cholesterol intake. OBJECTIVES: The objective of this study was to investigate the association between maternal dietary cholesterol intake during pregnancy and infant birth weight in a Chinese prospective cohort study. METHODS: A total of 4146 mother-child pairs were included based on the Jiangsu Birth Cohort study. Maternal dietary information was assessed with a semiquantitative food-frequency questionnaire. Birth weight z-scores and large-for-gestational-age (LGA) infants were converted by the INTERGROWTH-21st neonatal weight-for-gestational-age standard. Poisson regression and generalized estimating equations were employed to examine the relationships between LGA and maternal dietary cholesterol across the entire pregnancy and trimester-specific cholesterol intake, respectively. RESULTS: The median intake of maternal total dietary cholesterol during the entire pregnancy was 671.06 mg/d, with eggs being the main source. Maternal total dietary cholesterol and egg-sourced cholesterol were associated with an increase in birth weight z-score, with per standard deviation increase in maternal total and egg-sourced dietary cholesterol being associated with an increase of 0.16 [95% confidence interval (CI): 0.07, 0.25] and 0.06 (95% CI: 0.03, 0.09) in birth weight z-score, respectively. Egg-derived cholesterol intake in the first and third trimesters was positively linked to LGA, with an adjusted relative risk of 1.11 (95% CI: 1.04, 1.18) and 1.09 (95% CI: 1.00, 1.18). Compared with mothers consuming ≤7 eggs/wk in the third trimester, the adjusted relative risk for having an LGA newborn was 1.37 (95% CI: 1.09, 1.72) for consuming 8-10 eggs/wk and 1.45 (95% CI: 1.12, 1.86) for consuming >10 eggs/wk (P-trend = 0.015). CONCLUSIONS: Maternal total dietary cholesterol intake, as well as consuming over 7 eggs/wk during pregnancy, displayed significant positive relationships with the incidence of LGA, suggesting that mothers should avoid excessive cholesterol intake during pregnancy to prevent adverse birth outcomes.

Assisted reproductive technology and neurodevelopment in children at 1 year of age: a longitudinal birth cohort study.

BACKGROUND: With remarkable advancements in assisted reproductive technology (ART), the number of ART-conceived children continues to increase. Despite increased research investigating the outcomes of ART children, evidence on neurodevelopment remains controversial. OBJECTIVE: The aim of this study was to investigate the association between ART use and neurodevelopment in children at 1 year of age and to determine whether the characteristics of parental infertility and specific ART procedures affect neurodevelopment in children. STUDY DESIGN: The Jiangsu Birth Cohort enrolled couples who received ART treatment and who conceived spontaneously (2014-2020) in Jiangsu Province, China. In this study, we included 3531 pregnancies with 3840 cohort children who completed neurodevelopment assessment at 1 year of age, including 1906 infants conceived by ART (including 621 twins). Poisson regressions were fitted to estimate unadjusted and adjusted risk ratios (RRs) and 95% confidence intervals (CIs) for ART use with neurodevelopmental outcomes (cognition, receptive communication, expressive communication, fine motor, and gross motor) in children. RESULTS: Among singletons, ART use was associated with a 24% to 34% decrease in the risk for noncompetent development in 3 domains (cognition, adjusted RR, 0.66; 95% CI, 0.53-0.82; receptive communication, 0.76; 0.64-0.91; expressive communication, 0.69; 0.51-0.93) after adjustment for conventional covariates. However, an inverse association was observed in the gross motor domain, with ART singletons having a greater risk of being noncompetent in gross motor development than their non-ART counterparts (adjusted RR, 1.41; 95% CI, 1.11-1.79). Compared with singletons, twins resulting from ART treatment demonstrated compromised neurodevelopment in several domains. Furthermore, we continued to observe that the transfer of 'poor' quality embryos was associated with greater risks for noncompetent development in receptive communication (adjusted RR, 1.50; 95% CI, 1.05-2.14) and gross motor domains (1.55; 1.02-2.36) among ART singletons. CONCLUSION: These results generally provide reassuring evidence among singletons born after ART in the cognition, communication, and fine motor domains, but drawn attention to their gross motor development. The quality of transferred embryos in ART treatment might be associated with offspring neurodevelopment; however, the potential associations warrant further validation in independent studies, and the clinical significance needs careful interpretation.

Prenatal Parental Exposure to Metals and Birth Defects: A Prospective Birth Cohort Study.

While maternal exposure to high metal levels during pregnancy is an established risk factor for birth defects, the role of paternal exposure remains largely unknown. We aimed to assess the associations of prenatal paternal and maternal metal exposure and parental coexposure with birth defects in singletons. This study conducted within the Jiangsu Birth Cohort recruited couples in early pregnancy. We measured their urinary concentrations for 25 metals. A total of 1675 parent-offspring trios were included. The prevalence of any birth defects among infants by one year of age was 7.82%. Paternal-specific gravity-corrected urinary concentrations of titanium, vanadium, chromium, manganese, cobalt, nickel, copper, and selenium and maternal vanadium, chromium, nickel, copper, selenium, and antimony were associated with a 21-91% increased risk of birth defects after adjusting for covariates. These effects persisted after mutual adjustment for the spouse's exposure. Notably, when assessing the parental mixture effect by Bayesian kernel machine regression, paternal and maternal chromium exposure ranked the highest in relative importance. Parental coexposure to metal mixture showed a pronounced joint effect on the risk of overall birth defects, as well as for some specific subtypes. Our findings suggested a couple-based prevention strategy for metal exposure to reduce birth defects in offspring.

Titanium exposure and gestational diabetes mellitus: associations and potential mediation by perturbation of amino acids in early pregnancy.

BACKGROUND: Several recent studies reported the potential adverse effects of titanium exposure on glucose homeostasis among the non-pregnant population, but the association of titanium exposure with gestational diabetes mellitus (GDM) is scarce. METHODS: The present study of 1,449 pregnant women was conducted within the Jiangsu Birth Cohort (JBC) study in China. Urine samples were collected in the early pregnancy, and urinary titanium concentration and non-targeted metabolomics were measured. Poisson regression estimated the association of titanium exposure in the early pregnancy with subsequent risk of GDM. Multiple linear regression screened for titanium-related urine metabolites. Mediation analyses assessed the mediating effects of candidate metabolites and pathways. RESULTS: As parameterized in tertiles, titanium showed positive dose-response relationship with GDM risk (P for trend = 0.008), with women at the highest tertile of titanium exposure having 30% increased risk of GDM [relative risk (RR) = 1.30 (95% CI: 1.06, 1.61)] when compared to those exposure at the first tertile level. Meanwhile, we identified the titanium-related metabolites involved in four amino acid metabolic pathways. Notably, the perturbation of the aminoacyl-tRNA biosynthesis and alanine, aspartate and glutamate metabolism mediated 27.1% and 31.0%, respectively, of the relative effect of titanium exposure on GDM. Specifically, three titanium-related metabolites, choline, creatine and L-alanine, demonstrated predominant mediation effects on the association between titanium exposure and GDM risk. CONCLUSIONS: In this prospective study, we uniquely identified a correlation between early pregnancy titanium exposure and increased GDM risk. We unveiled novel insights into how perturbations in amino acid metabolism may mediate the link between titanium exposure and GDM. Notably, choline, creatine, and L-alanine emerged as key mediators influencing this association. Our findings imply that elevated titanium exposure in early pregnancy can lead to amino acid dysmetabolism, thereby elevating GDM risk.

Associations of inflammation related prenatal adversities with neurodevelopment of offspring in one year: a longitudinal prospective birth cohort study.

BACKGROUND: The recent Maternal Immune Activation (MIA) theory suggests maternal systemic inflammation may serve as a mediator in associations between prenatal maternal adversities and neurodevelopmental diseases in offspring. Given the co-exposure to multiple adversities may be experienced by pregnant person, it is unclear whether a quantitative index can be developed to characterize the inflammation related exposure level, and whether this index is associated with neurodevelopmental delays in offspring. METHODS: Based on Jiangsu Birth Cohort (JBC), a total of 3051 infants were included in the analysis. Inflammation related Prenatal Adversity Index (IPAI) was constructed using maternal data. Neurodevelopmental outcomes were assessed using the Bayley Scales of Infant and Toddler Development, third edition, screening test in one year. Multivariate linear regression and Poisson regression model were performed to analyze the associations between IPAI and neurodevelopment in offspring. RESULTS: Compared with "low IPAI" group, offspring with "high IPAI" have lower scores of cognition, receptive communication, expressive communication, and fine motor. The adjusted ß were - 0.23 (95%CI: -0.42, -0.04), -0.47 (95%CI: -0.66, -0.28), -0.30 (95%CI: -0.49, -0.11), and - 0.20 (95%CI: -0.33, -0.06). Additionally, the elevated risk for noncompetent development of cognition and receptive communication among "high IPAI" group was observed. The relative risk [RR] and 95% confidence interval [CI] were 1.35 (1.01, 1.69) and 1.37 (1.09, 1.72). CONCLUSIONS: Our results revealed a significant association between higher IPAI and lower scores across cognition, receptive communication, expressive communication, and fine motor domains, and an increased risk of noncompetent development in the cognition and receptive communication domains.

Effect of prenatal perfluoroheptanoic acid exposure on spermatogenesis in offspring mice.

BACKGROUND: Perfluoroheptanoic acid (PFHpA), a persistent organic pollutant widespread in the environment, is suspected as an environmental endocrine disruptor for its disturbance effect on hormone homeostasis and reproductive development. Whereas the effect of intrauterine PFHpA exposure during gestation on spermatogenesis of male offspring mice is still unknown. OBJECTIVE: This study aimed to explore the effect of prenatal PFHpA exposure on the reproductive development of male offspring mice and the role of N6-methyladenosine (m6A) during the process. METHODS: Fifty-six C57BL/6 pregnant mice were randomly divided into 4 groups. During the gestation period, the pregnant mice were exposed to 0, 0.0015, 0.015, and 0.15 mg/kg bw/d PFHpA from gestational day 1 (GD1) to GD16 by oral gavage. The male offspring mice were sacrificed by spinal dislocation at 7 weeks old. The body weight, testicular weight, and brain weight were weighed, and the intra-testicular testosterone was detected. The sperm qualities were analyzed with computer-aided sperm analysis (CASA). The testicular tissues were taken to analyze the pathological changes and examine the global m6A RNA methylation levels. Quantitative real-time PCR (qRT-PCR) was adopted to figure out the mRNA expression levels of m6A-related enzymes in testicular tissues of different PFHpA treated groups. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was applied to further explore the m6A RNA methylation at a whole-genome scale. RESULTS: Compared with the control group, no significant differences were observed in body weight, testicular weight, testicular coefficient, and the visceral-brain ratio of testicular tissue in the PFHpA treated groups. And no significant change was observed in intra-testicular testosterone among the four groups. CASA results showed a decrease of sperm count, sperm concentration, and total cell count, as well as an increase of sperm progressive cells' head area after prenatal PFHpA exposure (P < 0.05). Hematoxylin and eosin staining of pathological sections showed seminiferous tubules morphological change, disorder arrangement of seminiferous epithelium, and reduction of spermatogenic cells in the PFHpA treated groups. PFHpA significantly decreased global levels of m6A RNA methylation in testicular tissue (P < 0.05). Besides, qRT-PCR results showed significant alteration of the mRNA expression levels of seven m6A-related enzymes (Mettl3, Mettl5, Mettl14, Pcif1, Wtap, Hnrnpa2b1, and Hnrnpc) in the PFHpA treated groups (P < 0.05). MeRIP-seq results showed a correlation between prenatal PFHpA exposure and activation and binding of cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). Cnga3 and Mpzl3 showed differential expression in the enrichment subcategories or pathways. CONCLUSIONS: Exposure to PFHpA during the gestation period would adversely affect the development of seminiferous tubules and testicular m6A RNA methylation in offspring mice, which subsequently interferes with spermatogenesis and leads to reproductive toxicity.

Persistent visible luminescence of SrF2:Pr3+ for ratiometric thermometry.

Luminescence-based thermometry, especially the ratiometric temperature sensing technology, has attracted considerable attention recently due to its characteristics such as non-contact operating mode and strong capacity of resisting disturbance. Differing from the conventional strategy that usually needs continuous excitation, here an optical thermometry, which we have named the persistent luminescence intensity ratio (PLIR) thermometry, is proposed. The PLIR thermometry relies on the optical material SrF2:Pr3+ that could emit luminescence for several hours and even longer after being charged by X-ray. It has been demonstrated that the PLIR is sensitive to the variation of temperature and complies with the Boltzmann distribution. More importantly, the reliability of the proposed PLIR thermometry is verified. Our work may inspire others to develop more persistent luminescence thermometry.

Boltzmann-distribution-dominated persistent luminescence ratiometric thermometry in NaYF4:Pr3.

A novel, to the best of our knowledge, optical temperature measurement method is proposed, i.e., persistent luminescence intensity ratio (PLIR) thermometry. The PLIR thermometry relies on the micro-sized NaYF4:Pr3+ material that can emit persistent luminescence (PersL) uninterruptedly after being charged by x ray irradiation. The 3P1→3H5 and 3P0→3H5 PersL transitions, locating separately at ∼ 522 and 538 nm, have been confirmed to follow the Boltzmann distribution. The emitting intensity ratio of this pair of PersL lines is thus found to be a good indicator of the variation of temperature. Our work is expected to enrich the optical temperature sensing family.

A metabolomic study on the effect of prenatal exposure to Benzophenone-3 on spontaneous fetal loss in mice.

Benzophenone-3 (BP-3) is widely used in a variety of cosmetics and is prevalent in drinking water or food, and women were under notable high exposure burden of BP-3. Reports show the associations between prenatal exposure to BP-3 and the risk of fetal loss, but its underlying mechanism remains largely unknown. Pregnant ICR mice were gavaged with BP-3 from gestational day (GD) 0 to GD 6 at doses of 0.1, 10 and 1000 mg/kg/day. The samples were collected on GD 12. Ultra-performance liquid chromatography coupled with mass spectrometry-based metabolomics was used to detect metabolome changes in fetal mice, the uterus and the placenta to identify the underlying mechanism. The results showed that the body weight and relative organ weights of the liver, brain and uterus of pregnant mice were not significantly changed between the control group and the treatment group. BP-3 increased fetal loss, and induced placental thrombosis and tissue necrosis with enhancement of platelet aggregation. Metabolomic analysis revealed that fructose and mannose metabolism, the TCA cycle, arginine and proline metabolism in the fetus, arginine and proline metabolism and biotin metabolism in the uterus, and arginine biosynthesis and pyrimidine metabolism in the placenta were the key changed pathways involved in the above changes. Our study indicates that exposure to BP-3 can induce placental thrombosis and fetal loss via the disruption of maternal and fetal metabolism in mice, providing novel insights into the influence of BP-3 toxicity on the female reproductive system.

Association between mercury exposure and thyroid hormones levels: A meta-analysis.

BACKGROUND: The relationship between mercury (Hg) exposure and thyroid hormones (THs) levels in the general population has been inconclusive. We conducted a random effects model meta-analysis to identify the association between Hg exposure and THs levels in the general population. METHODS: This meta-analysis were performed based on the PECO questions (P = general population; E =1ug/L Hg in blood and urine; C =1ug/L incremental increase on; and O = variation of THs levels). We searched four electronic databases including PubMed, Web of Science, Embase, and Cochrane Library for studies published on or before 20th July 2020. Prospective and cross-sectional studies that evaluated the association between Hg exposure and the levels of thyroid stimulating hormone (TSH), triiodothyronine (T3), thyroxine (T4), free triiodothyronine (FT3), and free thyroxine (FT4) were included. We also assessed aggregate risks for the reliability of the included studies. RESULTS: Initially, we retrieved 4889 articles. 18 studies met our inclusion criteria after screening and 13 articles were eligible to be included in the meta-analysis. The meta-analysis results suggest that blood Hg may be significantly associated with THs levels. The presence of Hg in blood may significantly increase the levels of TSH (ß=0.55; 95%CI: 0.20,0.90; p < 0.001) and FT4 (ß=0.47; 95%CI: 0.11,0.82; p < 0.001), with the opposite association in T4 (ß=-0.02; 95%CI: 0.02, -0.01; p < 0.001). For the subgroup analysis, blood Hg was positively correlated with TSH levels in children and adolescents (ß=0.62; 95%CI: 0.09, 1.15; p < 0.001) and FT4 levels in pregnant women (ß=1.00; 95%CI: 0.99, 1.00; p < 0.001) respectively. CONCLUSIONS: This meta-analysis indicates that exposure to Hg in blood could significantly corrrelate with the levels of TSH, T4, and FT4 in the general population. Therefore, it is crucial to control the use of Hg and strengthen protection of the thyroid.

Stress, anxiety, and depression in infertile couples are not associated with a first IVF or ICSI treatment outcome.

BACKGROUND: Psychological distress may exert a negative influence on reproductive function of couples at reproductive age. Couples seeking assisted reproductive technology (ART) treatment may have a higher prevalence of psychological distress than fertile couples. However, whether psychological distress is associated with the outcome of ART treatment remains unknown. We aimed to investigate the association of pre-treatment psychological distress and clinical pregnancy rate among infertility couples undergoing in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) treatment. METHODS: This nested case-control study was conducted based on women who underwent their first fresh IVF or ICSI cycle in the Jiangsu Birth Cohort Study (JBC) between November 2015 and January 2019. A total of 150 women who did not obtain clinical pregnancy after first IVF or ICSI fresh embryo transfer were identified as cases, and a total of 300 age matched women who obtained clinical pregnancy were identified as controls. Conditional logistic regression analyses were used to investigate the association between psychological distress and the outcome of first IVF or ICSI treatment, adjusting for multiple potential confounders. RESULTS: No statistically significant association was observed between score of maternal symptoms of psychological distress and clinical pregnancy. Adjusted ORs of logistic regression were 1.00 (95% CI 0.97-1.03) for anxiety, 0.98 (95% CI 0.95-1.02) for depression, and 0.98 (95% CI 0.95-1.01) for perceived stress, respectively. When treat depression and anxiety as categorical variables, 62 (13.8%) were classified as clinical depression, 11 (2.4%) were classified as clinical anxiety, among 450 women in the present study. Psychological distress symptoms were also not associated with clinical pregnancy rate. Adjusted ORs of logistic regression were 0.27 (95% CI 0.03-2.33) for anxiety, 0.88 (95% CI 0.46-1.68) for depression, respectively. CONCLUSIONS: Our findings firstly indicated that psychological distress experienced prior to IVF/ICSI treatment was not associated with clinical pregnancy.

Hypomethylation of PRDM1 is associated with recurrent pregnancy loss.

Recurrent pregnancy loss (RPL) rates have continued to rise during the last few decades, yet the underlying mechanisms remain poorly understood. An emerging area of interest is the mediation of gene expression by DNA methylation during early pregnancy. Here, genome-wide DNA methylation from placental villi was profiled in both RPL patients and controls. Subsequently, differentially expressed genes were analysed for changes in gene expression. Many significant differentially methylated regions (DMRs) were identified near genes dysregulated in RPL including PRDM1. Differentially expressed genes were enriched in immune response pathways indicating that abnormal immune regulation contributes to RPL. Integrated analysis of DNA methylome and transcriptome demonstrated that the expression level of PRDM1 is fine-tuned by DNA methylation. Specifically, hypomethylation near the transcription start site of PRDM1 can recruit other transcription factors, like FOXA1 and GATA2, leading to up-regulation of gene expression and resulting in changes to trophoblast cell apoptosis and migration. These phenotypic differences may be involved in RPL. Overall, our study provides new insights into PRDM1-dependent regulatory effects during RPL and suggests both a mechanistic link between changes in PRDM1 expression, as well as a role for PRDM1 methylation as a potential biomarker for RPL diagnosis.

Effect of endometrial thickness and embryo quality on live-birth rate of fresh IVF/ICSI cycles: a retrospective cohort study.

BACKGROUND: Successful implantation and delivery require both the functional embryo and receptive endometrium in assisted reproductive technology (ART) cycles. However, little is known about embryo-endometrial interaction on live-birth. We aimed to investigate the independent effect and interaction of endometrial thickness (EMT) and embryo quality on live-birth in fresh embryo transfer (ET) cycles. METHODS: We conducted a retrospective cohort study including 15,012 ART cycles between 2013 and 2016 in three centers in China. Poisson regression with generalized estimating equations was employed to calculate relative risks (RRs) and 95% confidence intervals (CIs). We estimated the interaction of embryo quality and EMT on live-birth rate (LBR). RESULTS: The LBR per cycle was 42.8% overall. LBR increased with increasing EMT and reached a plateau (50.6 to 54.2%) when EMT was 11 mm or thicker. Embryo quality represented by cumulative score was associated with LBR independently of number of embryos transferred and EMT. LBR was not increased with thicker EMT when only Q1 cleavage-stage embryo transferred (aRR 0.95, 95%CI 0.61-1.46). LBR was not increased significantly with thicker EMT with transfer of two good-quality cleavage-stage embryos and any blastocyst combination except Q1 group. There was significant interaction between EMT and embryo quality on LBR for cleavage-stage ETs (P=0.023). CONCLUSIONS: This study demonstrated the nonlinear EMT-LBR association and the EMT cut-off value of 11 mm which may be of more clinical significance for predicting live-birth. Embryo quality is an independent prognostic tool for LBR. Our finding of significant embryo-endometrial interaction indicates combination of EMT and embryos quality might improve the prognostic value in clinical practice for live-birth in patients undergoing transfer of 1-2 fresh cleavage-stage embryos.

Comparative Transcriptome Analysis Combining SMRT- and Illumina-Based RNA-Seq Identifies Potential Candidate Genes Involved in Betalain Biosynthesis in Pitaya Fruit.

To gain more valuable genomic information about betalain biosynthesis, the full-length transcriptome of pitaya pulp from 'Zihonglong' (red pulp) and 'Jinghonglong' (white pulp) in four fruit developmental stages was analyzed using Single-Molecule Real-Time (SMRT) sequencing corrected by Illumina RNA-sequence (Illumina RNA-Seq). A total of 65,317 and 91,638 genes were identified in 'Zihonglong' and 'Jinghonglong', respectively. A total of 11,377 and 15,551 genes with more than two isoforms were investigated from 'Zihonglong' and 'Jinghonglong', respectively. In total, 156,955 genes were acquired after elimination of redundancy, of which, 120,604 genes (79.63%) were annotated, and 30,875 (20.37%) sequences without hits to reference database were probably novel genes in pitaya. A total of 31,169 and 53,024 simple sequence repeats (SSRs) were uncovered from the genes of 'Zihonglong' and 'Jinghonglong', and 11,650 long non-coding RNAs (lncRNAs) in 'Zihonglong' and 11,113 lncRNAs in 'Jinghonglong' were obtained herein. qRT-PCR was conducted on ten candidate genes, the expression level of six novel genes were consistent with the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values. In conclusion, we firstly undertook SMRT sequencing of the full-length transcriptome of pitaya, and the valuable resource that was acquired through this sequencing facilitated the identification of additional betalain-related genes. Notably, a list of novel putative genes related to the synthesis of betalain in pitaya fruits was assembled. This may provide new insights into betalain synthesis in pitaya.

Maternal pentachlorophenol exposure induces developmental toxicity mediated by autophagy on pregnancy mice.

Pentachlorophenol (PCP) is often used as chlorinated hydrocarbon herbicides and insecticides, which has been suggested that toxicity of carcinogenic effect, teratogenic effect and reproductive system. However, there was still precious known about the underlying molecular mechanism of PCP on mammalian early development. To explore the developmental toxicity of PCP and its potential mechanism, pregnancy ICR mice except controls were exposed to PCP (0.02, 0.2 or 2 mg/kg) during gestation day (GD) 0.5 to GD8.5 in this study. We found that the fetal loss rate was increased and placental chorionic villi structure was disorder in hematoxylin-eosin staining (HE) on GD16.5. Meanwhile, autophagosomes were observed in chorionic villi through Transmission Electron Microscope (TEM). Moreover, the mRNA and/or protein expression of P62, LC3-ІІ/LC3-І and Beclin1 were increased in placenta, indicating the occurrence of autophagy. Then, to further explore the autophagy mechanism, microRNA (miR)-30a-5p, an expression inhibitor of Beclin1, was predicted through bioinformatics predictions and RT-PCR, and it was reduced in PCP-treated mice. Transfection and luciferase reporter gene test were used to verify the interaction between Beclin1 and miR-30a-5p. These results firstly indicate that, PCP exposure could downregulate the expression of miR-30a-5p, and then induced autophagy through upregulation of Beclin1 to result in fetal loss. Our study laid a foundation for understanding the PCP developmental toxicity through autophagy.

Metabolic Profiling of Pitaya (Hylocereus polyrhizus) during Fruit Development and Maturation.

Pitaya (Hylocereus polyrhizus) has attracted much interest from consumers as it is a novelty fruit with high nutrient content and a tolerance to drought stress. As a group of attractive pigment- and health-promoting natural compounds, betalains represent a visual feature for pitaya fruit quality. However, little information on the correlation between betalains and relevant metabolites exists so far. Currently, color (Commission International del'Eclairage, CIE) parameters, betalain contents, and untargeted metabolic profiling (gas chromatography-time-of-flight-mass spectrometry, GC⁻MS and liquid chromatography tandem mass spectrometry, LC⁻MS) have been examined on 'Zihonglong' fruits at nine different developmental stages, and the variation character of the metabolite contents was simultaneously investigated between peel and pulp. Furthermore, principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) were used to explore metabolite profiles from the fruit samples. Our results demonstrated that the decrease of amino acid, accompanied by the increase of sugars and organic acid, might contribute to the formation of betalains. Notably, as one of four potential biomarker metabolites, citramalic acid might be related to betalain formation.

Phaseic Acid, an Endogenous and Reversible Inhibitor of Glutamate Receptors in Mouse Brain.

Phaseic acid (PA) is a phytohormone regulating important physiological functions in higher plants. Here, we show the presence of naturally occurring (-)-PA in mouse and rat brains. (-)-PA is exclusively present in the choroid plexus and the cerebral vascular endothelial cells. Purified (-)-PA has no toxicity and protects cultured cortical neurons against glutamate toxicity through reversible inhibition of glutamate receptors. Focal occlusion of the middle cerebral artery elicited a significant induction in (-)-PA expression in the cerebrospinal fluid but not in the peripheral blood. Importantly, (-)-PA induction only occurred in the penumbra area, indicting a protective role of PA in the brain. Indeed, elevating the (-)-PA level in the brain reduced ischemic brain injury, whereas reducing the (-)-PA level using a monoclonal antibody against (-)-PA increased ischemic injury. Collectively, these studies showed for the first time that (-)-PA is an endogenous neuroprotective molecule capable of reversibly inhibiting glutamate receptors during ischemic brain injury.

Interaction between Y chromosome haplogroup O3* and 4-n-octylphenol exposure reduces the susceptibility to spermatogenic impairment in Han Chinese.

Certain genetic background (mainly Y chromosome haplogroups, Y-hg) may modify the susceptibility of certain environmental exposure to some diseases. Compared with respective main effects of genetic background or environmental exposure, interactions between them reflect more realistic combined effects on the susceptibility to a disease. To identify the interactions on spermatogenic impairment, we performed Y chromosome haplotyping and measurement of 9 urinary phenols concentrations in 774 infertile males and 520 healthy controls in a Han Chinese population, and likelihood ratio tests were used to examine the interactions between Y-hgs and phenols. Originally, we observed that Y-hg C and Y-hg F* might modify the susceptibility to male infertility with urinary 4-n-octylphenol (4-n-OP) level (Pinter = 0.005 and 0.019, respectively). Subsequently, based on our results, two panels were tested to identify the possible protective sub-branches of Y-hg F* to 4-n-OP exposure, and Y-hg O3* was uncovered to interact with 4-n-OP (Pinter = 0.019). In conclusion, while 4-n-OP shows an adverse effect on spermatogenesis, Y-hg O3* makes individuals more adaptive to such an effect for maintaining basic reproductive capacity.