UBA1-CDK16 : A Sex-Specific Chimeric RNA and Its Role in Immune Sexual Dimorphism.

RNA processing mechanisms, such as alternative splicing and RNA editing, have been recognized as critical means to expand the transcriptome. Chimeric RNAs formed by intergenic splicing provide another potential layer of RNA diversification. By analyzing a large set of RNA-Seq data and validating results in over 1,200 blood samples, we identified UBA1-CDK16 , a female-specific chimeric transcript. Intriguingly, both parental genes, are expressed in males and females. Mechanistically, UBA1-CDK16 is produced by cis-splicing between the two adjacent X-linked genes, originating from the inactive X chromosome. A female-specific chromatin loop, formed between the junction sites, facilitates the alternative splicing of its readthrough precursor. This unique chimeric transcript exhibits evolutionary conservation, evolving to be female-specific from non-human primates to humans. Furthermore, our investigation reveals that UBA1-CDK16 is enriched in the myeloid lineage and plays a regulatory role in myeloid differentiation. Notably, female COVID-19 patients who tested negative for this chimeric transcript displayed higher counts of neutrophils, highlighting its potential role in disease pathogenesis. These findings support the notion that chimeric RNAs represent a new repertoire of transcripts that can be regulated independently from the parental genes, and a new class of RNA variance with potential implications in sexual dimorphism and immune responses.

Exosomes from Intrahepatic Cholestasis of Pregnancy Induce Cell Apoptosis Through the miRNA-6891-5p/YWHAE Pathway.

BACKGROUND: Intrahepatic cholestasis of pregnancy (ICP) is associated with adverse pregnancy outcomes; however, the underlying mechanisms are not fully understood. AIMS: This study aimed to determine the role of exosomal miR-6891-5p in placental trophoblast dysfunction in ICP and identify new biomarkers for ICP diagnosis. METHODS: Serum samples were collected from ICP patients and healthy pregnant women, and serum exosomes were extracted and identified. Fluorescent dye labeling of exosomes and cell-verified cell phagocytosis were performed. In vitro experiments were conducted by adding taurocholic acid to simulate the ICP environment. Cell proliferation and apoptosis levels were detected using flow cytometry and the cell counting kit-8 assay. Mimics were constructed to overexpress miR-6891-5p in cells, and the binding site between miR-6891-5p and YWHAE was verified using luciferase reporter genes. RESULTS: miR-6891-5p expression was significantly decreased in serum exosomes of ICP patients. Co-culturing with exosomes derived from ICP patients' serum (ICP-Exos) decreased HTR-8/SVeno cell proliferation and increased apoptosis levels. miR-6891-5p upregulation in HTR-8/SVeno cells significantly increased cell viability and reduced cell apoptosis levels, as determined by the cell counting kit-8 assay and flow cytometry. A double luciferase assay confirmed that miR-6891-5p affected the expression of the downstream YWHAE protein. CONCLUSIONS: This study indicates that serum exosomes from ICP patients can impact the apoptosis of placental trophoblast HTR-8/SVeno cells through the miR-6891-5P/YWHAE pathway and can serve as specific molecular markers for ICP diagnosis.

The role of ERp29/FOS/EMT pathway in excessive apoptosis of placental trophoblast cells in intrahepatic cholestasis of pregnancy.

BACKGROUND: Abnormal bile acid metabolism leading to changes in placental function during pregnancy. To determine whether endoplasmic reticulum protein 29 (ERp29) can mediate the pregnancy effects of cholestasis by altering the level of trophoblast cell apoptosis. METHODS: ERp29 in serum of 66 intrahepatic cholestasis of pregnancy (ICP) pregnant women and 74 healthy were detected by ELISA. Subcutaneous injection of ethinyl estradiol (E2) was used to induce ICP in pregnant rats. Taurocholic acid (TCA) was used to simulate the ICP environment, and TGF-ß1 was added to induce the epithelial mesenchymal transformation (EMT) process. The scratch, migration, and invasion test were used to detect the EMT process. ERp29 overexpression/knockdown vector were constructed and transfected to verify the role of ERp29 in the EMT process. Downstream gene was obtained through RNA-seq. RESULTS: Compared with the healthy pregnant women, the expression levels of ERp29 in serum of ICP pregnancy women were significantly increased (P < 0.001). ERp29 in the placenta tissue of the ICP pregnant rats increased significantly, and the level of apoptosis increased. The placental tissues of the ICP had high expression of E-cadherin and low expression of N-cadherin, snail1, vimentin. After HTR-8/SVneo cells were induced by TCA, EMT was inhibited, while the ERp29 increased. Cell and animal experiments showed that, knockdown of ERp29 reduced the inhibition of EMT, the ICP progress was alleviated. Overexpression of FOS salvaged the inhibitory effects of ERp29 on cell EMT. DISCUSSION: The high level of ERp29 in placental trophoblast cells reduced FOS mRNA levels, inhibited the EMT process and aggravated the occurrence and development of ICP.

A protein-encoding CCDC7 circular RNA inhibits the progression of prostate cancer by up-regulating FLRT3.

Circular RNAs (circRNAs) are a family of endogenous RNAs that have become a focus of biological research in recent years. Emerging evidence has revealed that circRNAs exert biological functions by acting as transcriptional regulators, microRNA sponges, and binding partners with RNA-binding proteins. However, few studies have identified coding circRNAs, which may lead to a hidden repertoire of proteins. In this study, we unexpectedly discovered a protein-encoding circular RNA circCCDC7(15,16,17,18,19) while we were searching for prostate cancer related chimeric RNAs. circCCDC7(15,16,17,18,19) is derived from exon 19 back spliced to exon 15 of the CCDC7 gene. It is significantly downregulated in patients with high Gleason score. Prostate cancer patients with decreased circCCDC7(15,16,17,18,19) expression have a worse prognosis, while linear CCDC7 had no such association. Overexpressed circCCDC7(15,16,17,18,19) inhibited prostate cancer cell migration, invasion, and viability, supporting classification of circCCDC7(15,16,17,18,19) as a bona fide tumor suppressor gene. We provide evidence that its tumor suppressive activity is driven by the protein it encodes, and that circCCDC7(15,16,17,18,19) encodes a secretory protein. Consistently, conditioned media from circCCDC7(15,16,17,18,19) overexpressing cells has the same tumor suppressive activity. We further demonstrate that the tumor suppressive activity of circCCDC7(15,16,17,18,19) is at least partially mediated by FLRT3, whose expression also negatively correlates with Gleason score and clinical prognosis. In conclusion, circCCDC7(15,16,17,18,19) functions as a tumor suppressor in prostate cancer cells through the circCCDC7-180aa secretory protein it encodes, and is a promising therapeutic peptide for prostate cancer.

Elevated CO2 concentration enhances drought resistance of soybean by regulating cell structure, cuticular wax synthesis, photosynthesis, and oxidative stress response.

The atmospheric [CO2] and the frequency and intensity of extreme weather events such as drought are increased, leading to uncertainty to soybean production. Elevated [CO2] (eCO2) partially mitigates the adverse effects of drought stress on crop growth and photosynthetic performance, but the mitigative mechanism is not well understood. In this study, soybean seedlings under drought stress simulated by PEG-6000 were grown in climate chambers with different [CO2] (400 µmol mol-1 and 700 µmol mol-1). The changes in anatomical structure, wax content, photosynthesis, and antioxidant enzyme were investigated by the analysis of physiology and transcriptome sequencing (RNA-seq). The results showed that eCO2 increased the thickness of mesophyll cells and decreased the thickness of epidermal cells accompanied by reduced stomatal conductance, thus reducing water loss in soybean grown under drought stress. Meanwhile, eCO2 up-regulated genes related to wax anabolism, thus producing more epidermal wax. Under drought stress, eCO2 increased net photosynthetic rate (PN), ribulose-1,5-bisphosphate carboxylase/oxygenase activity, and alerted the gene expressions in photosynthesis. The increased sucrose synthesis and decreased sucrose decomposition contributed to the progressive increase in the soluble saccharide contents under drought stress with or without eCO2. In addition, eCO2 increased the expressions of genes associated with peroxidase (POD) and proline (Pro), thus enhancing POD activity and Pro content and improving the drought resistance in soybean. Taken together, these findings deepen our understanding of the effects of eCO2 on alleviating drought stress in soybean and provide potential target genes for the genetic improvement of drought tolerance in soybean.

The effect of anxiety, depression, and structural social capital on life satisfaction among people with hearing disabilities: a cross-sectional study in Shanghai, China.

Background: Life satisfaction (LS) serves as a crucial indicator of social wellbeing and plays a significant role in formulating strategies aimed at enhancing health outcomes among the hearing-disabled population. This study aimed to examine the effect of anxiety, depression, and structural social capital on life satisfaction among people with hearing disabilities in Shanghai, China. Methods: A cross-sectional study was conducted in Shanghai, China. As of March 2022, 337 people with hearing disabilities were recruited from the Shanghai Disabled Persons' Federation. An online survey was conducted using a four-part questionnaire to collect data including demographic characteristics, the Hospital Anxiety and Depression Scale (HADS), the Social Capital Scale (SCS), and a single-item question to measure life satisfaction. One-sample t-tests, Pearson's correlation analysis, and hierarchical multiple regression analysis were performed. Results: Anxiety (ß = - 0.153) and depression (ß = - 0.242) were significant factors influencing life satisfaction among people with hearing disabilities. Structural social capital also played an influential role in life satisfaction, and people with hearing disabilities who lack social networks (ß = 0.125) and social support (ß = 0.121) reported significantly lower levels of life satisfaction. However, no significant relationship was found in this study between LS and other components of structural social capital, such as social participation. Conclusion: This study shows that paying attention to mental health is critical for people with hearing disabilities to achieve social wellbeing and promote LS improvement. At the same time, the government and society also need to focus on the structural social capital, provide various social service programs, enhance social support, and expand social networks, improving LS for people with hearing disabilities.

Gold nanoparticle dimer-based immunochromatography for in situ ultrasensitive detection of porcine epidemic diarrhea virus.

The low detection sensitivity of lateral-flow immunochromatography assay (LFIA) based on spherical gold nanoparticle (AuNP) limits its wide applications. In the present study, AuNP dimers with strong plasma scattering and robust signal output were synthesized via the Ag ion soldering (AIS) strategy and used as labeled probes in LFIA to boost the sensitivity without any extra operation process and equipment. The established LFIA exhibited high sensitivity with a limit of detection (LOD) of 2.0 × 102 TCID50/mL for PEDV, which provides 50 times higher sensitivity than commercial LFIA based on spherical colloidal gold. In addition, the AuNP dimer-based LFIA showed strong specificity, good reproducibility, high stability, and good accordance to reverse transcription polymer chain reaction (RT-PCR) when detecting 109 clinical samples. Thus, the AuNP dimers is a promising probe for LFIA and the developed AuNP dimer-based LFIA is suitable for the rapid detection of PEDV in the field.

Identification and validation of potential hypoxia-related genes associated with coronary artery disease.

Introduction: Coronary artery disease (CAD) is one of the most life-threatening cardiovascular emergencies with high mortality and morbidity. Increasing evidence has demonstrated that the degree of hypoxia is closely associated with the development and survival outcomes of CAD patients. However, the role of hypoxia in CAD has not been elucidated. Methods: Based on the GSE113079 microarray dataset and the hypoxia-associated gene collection, differential analysis, machine learning, and validation of the screened hub genes were carried out. Results: In this study, 54 differentially expressed hypoxia-related genes (DE-HRGs), and then 4 hub signature genes (ADM, PPFIA4, FAM162A, and TPBG) were identified based on microarray datasets GSE113079 which including of 93 CAD patients and 48 healthy controls and hypoxia-related gene set. Then, 4 hub genes were also validated in other three CAD related microarray datasets. Through GO and KEGG pathway enrichment analyses, we found three upregulated hub genes (ADM, PPFIA4, TPBG) were strongly correlated with differentially expressed metabolic genes and all the 4 hub genes were mainly enriched in many immune-related biological processes and pathways in CAD. Additionally, 10 immune cell types were found significantly different between the CAD and control groups, especially CD8 T cells, which were apparently essential in cardiovascular disease by immune cell infiltration analysis. Furthermore, we compared the expression of 4 hub genes in 15 cell subtypes in CAD coronary lesions and found that ADM, FAM162A and TPBG were all expressed at higher levels in endothelial cells by single-cell sequencing analysis. Discussion: The study identified four hypoxia genes associated with coronary heart disease. The findings provide more insights into the hypoxia landscape and, potentially, the therapeutic targets of CAD.

Identification of INHBA as a potential biomarker for gastric cancer through a comprehensive analysis.

Inhibin subunit beta A (INHBA) is a member of the transforming growth factor-beta (TGF-ß) superfamily that plays a fundamental role in various cancers. However, a systematic analysis of the exact role of INHBA in patients with gastric cancer (GC) has not yet been conducted. We evaluated the expression levels of INHBA and the correlation between INHBA and GC prognosis in GC. The relationship between INHBA expression, immune infiltration levels, and type markers of immune cells in GC was also explored. In addition, we studied INHBA mutations, promoter methylation, and functional enrichment analysis. Besides, high expression levels of INHBA in GC were significantly related to unfavorable prognosis. INHBA was negatively correlated with B cell infiltration, but positively correlated with macrophage and most anticancer immunity steps. INHBA expression was positively correlated with the type markers of CD8+ T cells, neutrophils, macrophages, and dendritic cells. INHBA has a weak significant methylation level change between tumor and normal tissues and mainly enriched in cancer-related signaling pathways. The present study implies that INHBA may serve as a potential biomarker for predicting the prognosis of patients with GC. INHBA is a promising predictor of immunotherapy response, with higher levels of INHBA indicating greater sensitivity.

Construction of the panoptosis-related gene model and characterization of tumor microenvironment infiltration in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is the most common fatal cancer worldwide, patients with HCC have a high mortality rate and poor prognosis. PANoptosis is a novel discovery of programmed cell death associated with cancer development. However, the role of PANoptosis in HCC remains obscure. In this study, we enrolled 274 PANoptosis-related genes (PANRGs) and screened 8 genes to set up a prognostic model. A previous scoring system calculated PANscore was utilized to quantify the individual risk level of each HCC patient, and the reliability of the prognostic model has been validated in an external cohort. Nomogram constructed with PANscore and clinical characteristics were used to optimize individualized treatment for each patient. Single-cell analysis revealed a PANoptosis model associated with tumor immune cell infiltration, particularly natural killer (NK) cells. Further exploration of hub genes and assessment of the prognostic role of these 4 hub genes in HCC by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC). In conclusion, we evaluated a PANoptosis-based prognostic model as a potential prognostic biomarker for HCC patients.

Trade-offs between wheat soil N2O emissions and C sequestration under straw return, elevated CO2 concentration, and elevated temperature.

The feedback between nitrous oxide (N2O) emissions, straw management and future climate scenarios is not well understood, especially in wheat ecosystems. In this study, the changes in N2O emissions, soil properties, enzymes, and functional genes involved in N cycling were measured with straw return (incorporation and mulching) and straw removal, under elevated [CO2] (+200 µmol mol-1 above ambient [CO2]), elevated temperature (+2 °C above ambient temperature), and their combination. The net global warming potential (NGWP) and greenhouse gas intensity (GHGI) were evaluated in combination with greenhouse gas emissions, yield, and soil organic carbon (C) sequestration. Compared with the ambient condition, elevated [CO2] and elevated temperature suppressed N2O emission by 41 %-46 %. Straw return significantly increased N2O emission by 31 %-109 % through increasing soil C and N substrates and denitrifying genes abundance, compared with straw removal. In addition, the impact of straw return on N2O emission was greater than that of elevated [CO2] or temperature. Straw return generally reduced NGWP by 166.2-3353.3 kg CO2-eq ha-1 and GHGI by 0.4-1.1 kg CO2-eq kg-1 through increasing soil organic C sequestration by 0.1-1.1 t C ha-1 and grain yield by 280.8 kg ha-1-1595.4 kg ha-1. Straw return would stimulate N2O emissions from this wheat cropping system under future warmer, elevated [CO2] climates, but simultaneously increase grain yield and soil organic C sequestration to a greater extent. Overall, straw return is beneficial to climate change mitigation; in particular, straw incorporation would be more effective than straw mulching.

Effects of elevated CO2 concentration on cell structure and stress resistance physiology of Setaria italica under drought stress.

The frequency of drought will increase under further warming. The increase in atmospheric CO2 concentration, along with more frequent drought, will affect crop growth. We examined the changes of cell structure, photosynthetic physiology, antioxidant enzymes, osmotic regulatory substances, and yield of foxtail millet (Setaria ita-lica) leaves under different CO2 concentrations (ambient air CO2 concentration and ambient atmospheric CO2 concentration + 200 µmol·mol-1) and water treatment (soil moisture content maintained at 45%-55%, and 70%-80% of field capacity, representing mild drought and normal water condition, respectively). The results showed that elevated CO2 concentration increased the number of starch grains, the area of single starch grains, and the total area of starch grains in the chloroplast of millet mesophyll cells. Under mild drought condition, elevated CO2 concentration increased net photosynthetic rate of millet leaves at the booting stage by 37.9%, but did not affect water use efficiency at this stage. Elevated CO2 concentration increased net photosynthetic rate and water use efficiency of millet leaves under mild drought condition at the filling stage by 15.0% and 44.2%, respectively. Under mild drought condition, elevated CO2 concentration increased the content of peroxidase (POD) and soluble sugar in millet leaves at the booting stage by 39.3% and 8.0%, respectively, but decreased proline content by 31.5%. It increased the content of POD in millet leaves at the filling stage by 26.5% but decreased the content of MDA and proline by 37.2% and 39.3%, respectively. Under mild drought condition, elevated CO2 concentration significantly increased the number of grain spikes by 44.7% and yield by 52.3% in both years compared with normal water condition. The effect of elevated CO2 concentration on grain yield under mild drought conditions was higher than that under normal water condition. Under mild drought conditions, elevated CO2 concentration increased leaf thickness, vascular bundle sheath cross-sectional area, net photosynthetic rate, and water use efficiency of millet, improved the antioxidant oxidase activity, and changed the concentration of osmotic regulatory substances, alleviated the nega-tive effect of drought on foxtail millet, and finally increased the number of grains per ear and yield of foxtail millet. This study would provide a theoretical basis for millet production and sustainable agricultural development in arid areas under future climate change.

Simultaneous quantitative determination of residues of abamectin, ivermectin, albendazole and its three metabolites in beef and chicken by HPLC-PDA.

Antimicrobial drugs are frequently used in a combination or shuttle way to cope with coinfection of bacteria or parasites and prevent drug resistance, thus the accurate quantification of multiple drug residues in animal-derived foods is crucial to ensure food safety. Here, a simple and efficient high-performance liquid chromatography-photodiode array (HPLC-PDA) method was established for the simultaneous quantitative screening of six common residues of antiparasitic drugs, including abamectin (ABM), ivermectin (IVM), albendazole (ABZ) and the three metabolites of ABZ in beef and chicken. The LODs and LOQs for six target compounds in beef and chicken are determined to be 3.2 to 12.5 µg/kg and 9.0 to 30.0 µg/kg, respectively. The calibration curves show good linearity (R2 ≥ 0.9990) between the peak area and concentration. The recoveries from the fortified blank samples are all above 85.10%. Finally, the applicability of the HPLC-PDA method is successfully demonstrated by the real sample analysis.

Physiological and transcriptome analysis of response of soybean (Glycine max) to cadmium stress under elevated CO2 concentration.

The continuous accumulation of Cd has long-lasting detrimental effects on plant growth and food safety. Although elevated CO2 concentration (EC) has been reported to reduce Cd accumulation and toxicity in plants, evidence on the functions of elevated CO2 concentration and its mechanisms in the possible alleviation of Cd toxicity in soybean are limited. Here, we used physiological and biochemical methods together with transcriptomic comparison to explore the effects of EC on Cd-stressed soybean. Under Cd stress, EC significantly increased the weight of roots and leaves, promoted the accumulations of proline, soluble sugars, and flavonoid. In addition, the enhancement of GSH activity and GST gene expressions promoted Cd detoxification. These defensive mechanisms reduced the contents of Cd2+, MDA, and H2O2 in soybean leaves. The up-regulation of genes encoding phytochelatin synthase, MTPs, NRAMP, and vacuoles protein storage might play vital roles in the transportation and compartmentalization process of Cd. The MAPK and some transcription factors such as bHLH, AP2/ERF, and WRKY showed changed expressions and might be engaged in mediation of stress response. These findings provide a boarder view on the regulatory mechanism of EC on Cd stress and provide numerous potential target genes for future engineering of Cd-tolerant cultivars in soybean breeding programs under climate changes scenarios.

RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data.

Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor ( https://github.com/sandybioteck/RTCpredictor ) has less memory requirements and faster execution time.

Roles of non-coding RNAs in eye development and diseases.

The prevalence of ocular disorders is dramatically increasing worldwide, especially those that cause visual impairment and permanent loss of vision, including cataract, glaucoma, age-related macular degeneration, and diabetic retinopathy. Extensive evidence has shown that ncRNAs are key regulators in various biogenesis and biological functions, controlling gene expression related to histogenesis and cell differentiation in ocular tissues. Aberrant expression and function of ncRNA can lead to dysfunction of visual system and mediate progression of eye disorders. Here, we mainly offer an overview of the role of precise modulation of ncRNAs in eye development and function in patients with eye diseases. We also highlight the challenges and future perspectives in conducting ncRNA studies, focusing specifically on the role of ncRNAs that may hold expanded promise for their diagnostic and therapeutic applications in various eye diseases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.

Investigation of interfacial adsorption between microplastics and methylparaben in aqueous solution.

Microplastics and parabens are considered to be a global contaminants, especially in the aquatic ecosystem. The interfacial interaction between four types of microplastics including polystyrene, polyethylene, polyethylene terephthalate, and polyvinyl chloride, and methylparaben were investigated in this study. The results showed that molecular layer dominates the adsorption, with the rate significantly affected by both internal diffusion and external diffusion. Among the four types, polystyrene and polyvinyl chloride showed the smallest and biggest adsorption capability, with the values were 0.656 and 1.269 mg g-1, respectively. For the adsorption capability, smaller particle size and higher pH value possessed positive effects. However, the existence of metal ions could inhibit the adsorption process, except for a weak promotion at low salinity. Physical adsorption effects, such as electrostatic interaction, hydrogen bond formation, and covalent bond formation, had been identified that dominated the adsorption. This finding could be served as a speculative foundation for the further study of the toxicity, migration, and ecological risk assessment of microplastics in aquatic ecosystem.

Coupling life cycle assessment and global sensitivity analysis to evaluate the uncertainty and key processes associated with carbon footprint of rice production in Eastern China.

An accurate and objective evaluation of the carbon footprint of rice production is crucial for mitigating greenhouse gas (GHG) emissions from global food production. Sensitivity and uncertainty analysis of the carbon footprint evaluation model can help improve the efficiency and credibility of the evaluation. In this study, we combined a farm-scaled model consisting of widely used carbon footprint evaluation methods with a typical East Asian rice production system comprising two fertilization strategies. Furthermore, we used Morris and Sobol' global sensitivity analysis methods to evaluate the sensitivity and uncertainty of the carbon footprint model. Results showed that the carbon footprint evaluation model exhibits a certain nonlinearity, and it is the most sensitive to model parameters related to CH4 emission estimation, including EFc (baseline emission factor for continuously flooded fields without organic amendments), SFw (scaling factor to account for the differences in water regime during the cultivation period), and t (cultivation period of rice), but is not sensitive to activity data and its emission factors. The main sensitivity parameters of the model obtained using the two global sensitivity methods were essentially identical. Uncertainty analysis showed that the carbon footprint of organic rice production was 1271.7 ± 388.5 kg CO2eq t-1 year-1 (95% confidence interval was 663.9-2175.8 kg CO2eq t-1 year-1), which was significantly higher than that of conventional rice production (926.0 ± 213.6 kg CO2eq t-1 year-1, 95% confidence interval 582.5-1429.7 kg CO2eq t-1 year-1) (p<0.0001). The carbon footprint for organic rice had a wider range and greater uncertainty, mainly due to the greater impact of CH4 emissions (79.8% for organic rice versus 53.8% for conventional rice). EFc , t, Y, and SFw contributed the most to the uncertainty of carbon footprint of the two rice production modes, wherein their correlation coefficients were between 0.34 and 0.55 (p<0.01). The analytical framework presented in this study provides insights into future on-farm advice related to GHG mitigation of rice production.

An optimistic future of C4 crop broomcorn millet (Panicum miliaceum L.) for food security under increasing atmospheric CO2 concentrations.

Broomcorn millet, a C4 cereal, has better tolerance to environmental stresses. Although elevated atmospheric CO2 concentration has led to grain nutrition reduction in most staple crops, studies evaluating its effects on broomcorn millet are still scarce. The yield, nutritional quality and metabolites of broomcorn millet were investigated under ambient CO2 (aCO2, 400 µmol mol-1) and elevated CO2 (eCO2, aCO2+ 200 µmol mol-1) for three years using open-top chambers (OTC). The results showed that the yield of broomcorn millet was markedly increased under eCO2 compared with aCO2. On average, eCO2 significantly increased the concentration of Mg (27.3%), Mn (14.6%), and B (21.2%) over three years, whereas it did not affect the concentration of P, K, Fe, Ca, Cu or Zn. Protein content was significantly decreased, whereas starch and oil concentrations were not changed by eCO2. With the greater increase in grain yield, eCO2 induced increase in the grain accumulations of P (23.87%), K (29.5%), Mn (40.08%), Ca (22.58%), Mg (51.31%), Zn (40.95%), B (48.54%), starch (16.96%) and oil (28.37%) on average for three years. Flavonoids such as kaempferol, apigenin, eriodictyol, luteolin, and chrysoeriol were accumulated under eCO2. The reduction in L-glutamine and L-lysine metabolites, which were the most representative amino acid in grain proteins, led to a reduction of protein concentration under eCO2. Broomcorn millet has more desirable nutritional traits for combating hidden hunger. This may potentially be useful for breeding more nutritious plants in the era of climate change.

Profile of chimeric RNAs and TMPRSS2-ERG e2e4 isoform in neuroendocrine prostate cancer.

PURPOSE: Specific gene fusions and their fusion products (chimeric RNA and protein) have served as ideal diagnostic markers and therapeutic targets for cancer. However, few systematic studies for chimeric RNAs have been conducted in neuroendocrine prostate cancer (NEPC). In this study, we explored the landscape of chimeric RNAs in different types of prostate cancer (PCa) cell lines and aimed to identify chimeric RNAs specifically expressed in NEPC. METHODS: To do so, we employed the RNA-seq data of eight prostate related cell lines from Cancer Cell Line Encyclopedia (CCLE) for chimeric RNA identification. Multiple filtering criteria were used and the candidate chimeric RNAs were characterized at multiple levels and from various angles. We then performed experimental validation on all 80 candidates, and focused on the ones that are specific to NEPC. Lastly, we studied the clinical relevance and effect of one chimera in neuroendocrine process. RESULTS: Out of 80 candidates, 15 were confirmed to be expressed preferentially in NEPC lines. Among them, 13 of the 15 were found to be specifically expressed in NEPC, and four were further validated in another NEPC cell line. Importantly, in silico analysis showed that tumor malignancy may be correlated to the level of these chimeric RNAs. Clinically, the expression of TMPRSS2-ERG (e2e4) was elevated in tumor tissues and indicated poor clinical prognosis, whereas the parental wild type transcripts had no such association. Furthermore, compared to the most frequently detected TMPRSS2-ERG form (e1e4), e2e4 encodes 31 more amino acids and accelerated neuroendocrine process of prostate cancer. CONCLUSIONS: In summary, these findings painted the landscape of chimeric RNA in NEPC and supported the idea that some chimeric RNAs may represent additional biomarkers and/or treatment targets independent of parental gene transcripts.