Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L.

To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica.

Inhibition of FABP5 attenuates inflammatory bowel disease by modulating macrophage alternative activation.

Fatty acid binding protein 5 (FABP5) is an intracellular chaperone of fatty acid molecules that regulates lipid metabolism and cell growth. However, its role in intestinal inflammation remains enigmatic. Through examination of human tissue samples and single-cell data, we observed a significant upregulation of FABP5 within the mucosa of patients afflicted with ulcerative colitis (UC) and Crohn's disease (CD), predominantly localized in intestinal macrophages. Herein, we investigate the regulation of FABP5-IN-1, a FABP5 inhibitor, on various cells of the gut in an inflammatory environment. Our investigations confirmed that FABP5 ameliorates DSS-induced colitis in mice by impeding the differentiation of macrophages into M1 macrophages in vitro and in vivo. Furthermore, following FABP5-IN-1 intervention, we observed a notable restoration of intestinal goblet cells and tuft cells, even under inflammatory conditions. Additionally, FABP5-IN-1 exhibits a protective effect against DSS-induced colitis by promoting the polarization of macrophages towards the M2 phenotype in vivo. In summary, FABP5-IN-1 confers protection against DSS-induced acute colitis through a multifaceted approach, encompassing the reduction of inflammatory macrophage infiltration, macrophage polarization, regulating Th17/Treg cells to play an anti-inflammatory role in IBD. The implications for IBD are underscored by the comprehensive in vivo and in vitro experiments presented in this article, thereby positioning FABP5 as a promising and novel therapeutic target for the treatment of IBD.

[Soil Heavy Metal Contamination, Sources, and Health Risk of Typical Drinking Water Sources in the Suspended Reach of the Lower Yellow River].

With the implementation of ecological protection and a high-quality development strategy in the Yellow River Basin, the environmental conditions around the Yellow River have attracted wide attention from scholars. In this study, the soil of drinking water sources(Heichi and Liuchi) in the typical suspended reach of the lower reaches of the Yellow River was selected as the research object. The geo-accumulation index and pollution load index were used to analyze the pollution characteristics of seven heavy metals(Cr, Ni, Cu, Zn, Cd, Pb, and As), and correlation analysis, principal component analysis, and absolute factor score-multiple linear regression(APCS-MLR) were employed to reveal the sources of soil heavy metals from both qualitative and quantitative perspectives. The health risk assessment model recommended by the United States Environmental Protection Agency(USEPA) was used to analyze the impact of soil heavy metals on human health, and the contribution rate of pollution sources to health risks was analyzed by combining the APCS-MLR model. The results showed that the average values of ω(Cr), ω(Ni), ω(Cu), ω(Zn), ω(Cd), ω(Pb), and ω(As) in the soil around the water source were 60.27, 30.00, 35.14, 77.75, 0.38, 21.74, and 9.70 mg·kg-1, respectively. Except for As, the contents of Cr, Ni, Cu, Zn, Cd, and Pb were higher than the background values of soil elements in the fluvo-aquic soil area of the lower Yellow River, whereas the contents of Cu and Zn in the soil around Liuchi were significantly higher than those in Heichi. Both the geo-accumulation index and the single-factor index showed that the black pond and the willow pond were slightly polluted by heavy metals, and Cd was the main pollution factor. The pollution load index model showed that the number of non-polluted and mildly polluted samples in the study area accounted for 5% and 95% of the total samples, respectively, indicating that the study area was at a mild pollution level. The source apportionment showed that Cr, Ni, Cu, and As were mainly affected by parent materials. The analysis results of the APCS-MLR model showed that the soil pollutants in the study area were mainly from natural sources, traffic sources, agricultural sources, and unknown sources, and their contribution rates were 42.95%, 23.39%, 16.95%, and 16.71%, respectively. The health risk assessment showed that As was the main non-carcinogenic factor, and Ni was the main carcinogenic factor. The non-carcinogenic risk of heavy metals to adults and children was negligible, and there was a tolerable carcinogenic risk to the human body. For both adults and children, the non-carcinogenic and carcinogenic risk contribution rates of the four pollution sources were:natural sources>unknown sources>traffic sources>agricultural sources, among which natural sources contributed the most to non-carcinogenic and carcinogenic risks. Therefore, it is of great significance to study the characteristics, sources, and effects of soil pollution on human health around the water source area of the suspended reach of the lower reaches of the Yellow River, which is of great significance for the protection of water sources and provides theoretical support for the high-quality development of the ecological environment along the Yellow River.

Effect of Fe(III) Species on the Stability of a Water-Model Oil Emulsion with an Anionic Sulfonate Surfactant as an Emulsifier.

The stability of an emulsion has an important effect on enhancing oil recovery. However, the effect of ions with different valences on the stability of the emulsion emulsified by an ionic surfactant is not fully understood. In this study, the effects of Fe(III) species on the stability, microscopic morphology of droplets, interfacial properties, and rheological properties of water-model oil emulsions emulsified by sodium dodecyl benzenesulfonate (SDBS) were explored. The effect of Fe(III) species on the stability of a W/O crude oil emulsion was also explored. The stability experiment results show that the addition of the Fe(III) species impairs the stability of the model oil-in-water (O/W) emulsion, in which the O/W model oil emulsion is inverted to a water-in-model oil (W/O) emulsion at ∼99 ppm. With the increase of Fe(III) species concentration, stable W/O model oil and W/O crude oil emulsions are obtained. The rheological results indicated that the existence of the Fe(III) species has a remarkable effect on the viscosity and viscoelastic behaviors of the water-model oil emulsion. The calculation results based on Derjaguin-Landau-Verwey-Overbeek (DLVO) theory are in accord with the stability experiment results. Furthermore, the addition of EO groups makes the phase inversion point appear at a higher Fe(III) species concentration, forming a more stable W/O model oil emulsion and a more unstable O/W model oil emulsion. The experimental results are helpful to comprehensively understand the effect of Fe(III) species on the stability of an emulsion emulsified by an anionic sulfonate surfactant, which can help to enhance the oil recovery.

Haze Occurrence Caused by High Gas-to-Particle Conversion in Moisture Air under Low Pollutant Emission in a Megacity of China.

Haze occurred in Zhengzhou, a megacity in the northern China, with the PM2.5 as high as 254 µg m-3 on 25 December 2019, despite the emergency response measure of restriction on the emission of anthropogenic pollutants which was implemented on December 19 for suppressing local air pollution. Air pollutant concentrations, chemical compositions, and the origins of particulate matter with aerodynamic diameter smaller than 2.5 µm (PM2.5) between 5-26 December were investigated to explore the reasons for the haze occurrence. Results show that the haze was caused by efficient SO2-to-suflate and NOx-to-nitrate conversions under high relative humidity (RH) condition. In comparison with the period before the restriction (5-18 December) when the PM2.5 was low, the concentration of PM2.5 during the haze (19-26 December) was 173 µg m-3 on average with 51% contributed by sulfate (31 µg m-3) and nitrate (57 µg m-3). The conversions of SO2-to-sulfate and NOx-to-nitrate efficiently produced sulfate and nitrate although the concentration of the two precursor gases SO2 and NOx was low. The high RH, which was more than 70% and the consequence of artificial water-vapor spreading in the urban air for reducing air pollutants, was the key factor causing the conversion rates to be enlarged in the constriction period. In addition, the last 48 h movement of the air parcels on 19-26 December was stagnant, and the air mass was from surrounding areas within 200 km, indicating weather conditions favoring the accumulation of locally-originated pollutants. Although emergency response measures were implemented, high gas-to-particle conversions in stagnant and moisture circumstances can still cause severe haze in urban air. Since the artificial water-vapor spreading in the urban air was one of the reasons for the high RH, it is likely that the spreading had unexpected side effects in some certain circumstances and needs to be taken into consideration in future studies.

Breaking the Linear Relation in the Dissociation of Nitrogen on Iron Surfaces.

Current industrial ammonia synthesis depends on the Haber-Bosch process, in which the activity of the catalyst is limited by the Brønsted-Evans-Polanyi (BEP) principle and Fe is used as a commercial catalyst. Herein, we found that the dissociation barriers of N2 on Fe(111), Fe(211), Fe(110), and Fe(100) surfaces do not follow the widely accepted BEP principle. N2 dissociation on Fe(111) surface has the smallest adsorption energy and the lowest energetic barrier. Such an abnormal phenomenon can be attributed to charge transfer from Fe surfaces to the anti-bonding orbital (π*) of the absorbed N2 . More charges transferred from the Fe surface to π* of N2 leads to a weaker N≡N triple bond and a lower adsorption energy of N atoms. However, the hydrogenation of N atoms and desorption of NH3 on the four Fe surfaces follow the BEP principle. Therefore, Fe(111) is found to be the most active surface to promote ammonia synthesis, and such a conclusion is also applicable to Ni and Mo surfaces.

Advances of supramolecular interaction systems for improved oil recovery (IOR).

Improved oil recovery (IOR) includes enhanced oil recovery (EOR) and other technologies (i.e. fracturing, water injection optimization, etc.), have become important methods to increase the oil/gas production in petroleum industry. However, conventional flooding systems always encounter the problems of low efficiency, high cost and complicated synthetic procedures for harsh reservoirs conditions. In recent decades, the supramolecular interactions are introduced into IOR processes to simplify the synthetic procedures, alter their structures and properties with bespoke functionalities and responsiveness suitable for different conditions. Herein, we primarily review the fundamentals of several supramolecular interactions, including hydrophobic association, hydrogen bond, electrostatic interaction, host-guest recognition, metal-ligand coordination and dynamic covalent bond from intrinsic principles and extrinsic functions. Then, the descriptions of supramolecular interactions in IOR processes from categories and advances are focused on the following variables: polymer, surfactant, surfactant/polymer (SP) complex for EOR and viscoelasticity surfactant (VES) for clean hydraulic fracturing aspects. Finally, the field applications, challenges and prospects for supramolecular interactions in IOR processes are involved and systematically addressed. The development of supramolecular interactions can open the way toward adaptive and evolutive IOR technology, a further step towards the cost-effective production of petroleum industry.

Amlodipine removal via peroxymonosulfate activated by carbon nanotubes/cobalt oxide (CNTs/Co3O4) in water.

Amlodipine (AML) is an effective drug that has been widely used for hypertension and angina. However, AML is frequently detected in aqueous environments, posing potential risks to human and ecological health. In this study, the degradation of AML via peroxymonosulfate (PMS) activated by CNTs/Co3O4 was investigated. CNTs/Co3O4 was prepared via a facile method, and multiple characterizations suggested that Co3O4 were uniformly dispersed on the surface of MWCNTs-COOH. Experimental results indicated that complete removal of 10 µM AML was achieved within 30 min by using 2 mg/L CNTs/Co3O4 and 4 µM PMS at 25 °C in PBS buffered solution (pH 7.0). The observed pseudo-first-order rate constant was calculated to be 0.1369 min-1. Interestingly, the presence of 100 mM Cl- resulted in a slight enhancement of AML removal rate from 0.0528 to 0.0642 min-1. The addition of 100 mM HCO3-, 5 mg/L Pony Lake fulvic acid (PLFA), or Suwannee River humic acid (SRHA) retarded AML degradation by 15.5, 0.7, and 1.6 times, respectively. As per the quenching experiments, SO4⦁- rather than ⦁OH were verified to be the dominant reactive oxygen species (ROS). Additionally, ten major intermediates were identified using TOF-LC-MS and three associated reaction pathways including ether bond broken, H-abstraction, and hydroxylation were proposed. We outlook these findings to advance the feasibility of organic contaminants removal via CNTs/Co3O4 + PMS systems that have extremely low-level PMS.

hsa-miR-195-5p inhibits cell proliferation of human thyroid carcinoma cells via modulation of p21/cyclin D1 axis.

BACKGROUND: Based on existing evidence, microRNAs (miRs) are gene regulators that undertake key functions in the oncogenesis and tumor progression of every single human malignant disease, such as thyroid carcinoma (TC). Previous clinical findings showed that expression of miR-195 is down-regulated in TC, which implies that miR-195 may be practically involved in TC pathogenesis. Nevertheless, the function of hsa-miR-195-5p in TC is still largely unclear. Herein, we detected the conceivable involvement of hsa-miR-195-5p in TC cell proliferation. METHODS: Real time PCR examination was performed to assess the expression level of hsa-miR-195-5p in TC cell lines TPC-1 and B-CPAP. TPC-1 cells were transfected with either hsa-miR-195-5p mimics or hsa-miR-195-5p inhibitor. After confirmation of transfection efficiency, the effect of hsa-miR-195-5p on proliferation and cell cycle of TPC-1 cells was assessed. The expression of cyclin D1 and p21 was simultaneously detected by western blotting. Moreover, targetScan 6.2 was used to predict hsa-miR-195-5p target genes. Subsequently, luciferase reporter was performed to examine whether there is a possible binding of hsa-miR-195-5p to 3'-UTR of cyclin D1 mRNA. Furthermore, cyclin D1 mRNA and protein levels were measured to check whether hsa-miR-195-5p exerts its function at the post-transcriptional level. In addition, to explore the function of cyclin D1 in TPC-1 cells overexpressing hsa-miR-195-5p, cyclin D1 siRNA was used to silence the expression of cyclin D1 in TPC-1 cells overexpressing hsa-miR-195-5p. RESULTS: We quantified the expression of hsa-miR-195-5p in TC cells and normal thyroid cells and found a remarkable decrease in hsa-miR-195-5p expression in TC cells. Over-expression of hsa-miR-195-5p obviously resulted in downgraded proliferation of TC cells. Moreover, hsa-miR-195-5p caused cell arrest at the GO/G1 phase. Further in silico analyses and the dual-luciferase reporter assay confirmed that 3'-UTR of cyclin D1 is a direct target of hsa-miR-195-5p. Western blot analysis uncovered that hsa-miR-195-5p over-expression led to decreased levels of cyclin D1 and p21. In mechanistic analyses, we found that silencing of cyclin D1 reversed the inhibitory effect of hsa-miR-195-5p on the proliferation of TC cells, which indicates that hsa-miR-195-5p suppresses TC cell proliferation by adversely regulating cyclin D1. CONCLUSIONS: We concluded that hsa-miR-195-5p is a candidate tumor-suppressor miRNA in TC and that the hsa-miR-195-5p/p21/cyclin D1 pathway could be a potential therapeutic target for TC.

A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton.

BACKGROUND: Cotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quality despite its potential value. Though some QTL controlling cottonseed quality have been identified, few of them that warrant further study are known. Identifying stable QTL controlling seed size, oil and protein content is necessary for improvement of cottonseed quality. RESULTS: In this study, a recombinant inbred line (RIL) population was developed from a cross between upland cotton cultivars/lines Yumian 1 and M11. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to construct a genetic map that covered 3353.15 cM with an average distance between consecutive markers of 0.48 cM. The seed index, together with kernel size, oil and protein content were further used to identify QTL. In total, 58 QTL associated with six traits were detected, including 13 stable QTL detected in all three environments and 11 in two environments. CONCLUSION: A high resolution genetic map including 7033 SNP loci was constructed through specific locus amplified fragment sequencing technology. A total of 13 stable QTL associated with six cottonseed quality traits were detected. These stable QTL have the potential for fine mapping, identifying candidate genes, elaborating molecular mechanisms of cottonseed development, and application in cotton breeding programs.

Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton.

BACKGROUND: Plant architecture and the vegetative-reproductive transition have major impacts on the agronomic success of crop plants, but genetic mechanisms underlying these traits in cotton (Gossypium spp.) have not been identified. RESULTS: We identify four natural mutations in GoCEN-Dt associated with cluster fruiting (cl) and early maturity. The situ hybridization shows that GhCEN is preferentially expressed in cotton shoot apical meristems (SAM) of the main stem and axillary buds. Constitutive GhCEN-Dt overexpression suppresses the transition of the cotton vegetative apex to a reproductive shoot. Silencing GoCEN leads to early flowering and determinate growth, and in tetraploids causes the main stem to terminate in a floral bud, a novel phenotype that exemplifies co-adaptation of polyploid subgenomes and suggests new research and/or crop improvement approaches. Natural cl variations are enriched in cottons adapted to high latitudes with short frost-free periods, indicating that mutants of GoCEN have been strongly selected for early maturity. CONCLUSION: We show that the cotton gene GoCEN-Dt, a homolog of Antirrhinum CENTRORADIALIS, is responsible for determinate growth habit and cluster fruiting. Insight into the genetic control of branch and flower differentiation offers new approaches to develop early maturing cultivars of cotton and other crops with plant architecture appropriate for mechanical harvesting.

Chromosome structural variation of two cultivated tetraploid cottons and their ancestral diploid species based on a new high-density genetic map.

A high-resolution genetic map is a useful tool for assaying genomic structural variation and clarifying the evolution of polyploid cotton. A total of 36956 SSRs, including 11289 released in previous studies and 25567 which were newly developed based on the genome sequences of G. arboreum and G. raimondii, were utilized to construct a new genetic map. The new high-density genetic map includes 6009 loci and spanned 3863.97 cM with an average distance of 0.64 cM between consecutive markers. Four inversions (one between Chr08 and Chr24, one between Chr09 and Chr23 and two between Chr10 and Chr20) were identified by homology analysis. Comparative genomic analysis between genetic map and two diploid cottons showed that structural variations between the A genome and At subgenome are more extensive than between D genome and Dt subgenome. A total of 17 inversions, seven simple translocations and two reciprocal translocations were identified between genetic map and G. raimondii. Good colinearity was revealed between the corresponding chromosomes of tetraploid G. hirsutum and G. barbadense genomes, but a total of 16 inversions were detected between them. These results will accelerate the process of evolution analysis of Gossipium genus.

Epidemiology and outcome of severe sepsis and septic shock in intensive care units in mainland China.

INTRODUCTION: Information about sepsis in mainland China remains scarce and incomplete. The purpose of this study was to describe the epidemiology and outcome of severe sepsis and septic shock in mixed ICU in mainland China, as well as the independent predictors of mortality. METHODS: We performed a 2-month prospective, observational cohort study in 22 closed multi-disciplinary intensive care units (ICUs). All admissions into those ICUs during the study period were screened and patients with severe sepsis or septic shock were included. RESULTS: A total of 484 patients, 37.3 per 100 ICU admissions were diagnosed with severe sepsis (n = 365) or septic shock (n = 119) according to clinical criteria and included into this study. The most frequent sites of infection were the lung and abdomen. The overall ICU and hospital mortality rates were 28.7% (n = 139) and 33.5% (n = 162), respectively. In multivariate analyses, APACHE II score (odds ratio[OR], 1.068; 95% confidential interval[CI], 1.027-1.109), presence of ARDS (OR, 2.676; 95%CI, 1.691-4.235), bloodstream infection (OR, 2.520; 95%CI, 1.142-5.564) and comorbidity of cancer (OR, 2.246; 95%CI, 1.141-4.420) were significantly associated with mortality. CONCLUSIONS: Our results indicated that severe sepsis and septic shock were common complications in ICU patients and with high mortality in China, and can be of help to know more about severe sepsis and septic shock in China and to improve characterization and risk stratification in these patients.

[Health risk assessment of soil heavy metals in residential communities built on brownfields].

Nine residential communities which were built on different brownfields in a city of Henan Province were chosen to investigate the health risks of heavy metals (As, Hg, Cd, and Pb) in surface soils. Concentrations of soil heavy metals were measured according to the methods described in the national standard. Based on the health risk models recommended by the U. S. Environmental Protection Agency (US EPA), non-carcinogenic and carcinogenic health risks of soil heavy metals were assessed. The results showed that compared with the original brownfields, the heavy metal concentrations in soils and their health risks in residential communities built on brownfields were significantly improved, and the concentrations and health risks of soil heavy metals in these communities were all higher than those in non-brownfield residential communities. The HQ and HI values of soil heavy metals in all the residential communities were lower than 1, which indicated that there was no non-carcinogenic risk in these communities. Meanwhile, the values of CR and TCR were slightly higher than the standard suggested by the US EPA, indicating that slight carcinogenic risks in the communities, but these values were lower than the lenient standard proposed by some experts. The HI value of the four metals for children was exactly seven times higher than that for adults. The contribution rate of HQ(As) to HI was about 75%, CR(AS) to TCR was about 80%, and therefore arsenic was the crucial factor for carcinogenic and non-carcinogenic risk in the residential communities of the city.

Aberrant DNA Methylation of P16, MGMT, and hMLH1 Genes in Combination with MTHFR C677T Genetic Polymorphism in gastric cancer.

OBJECTIVE: We aimed to explore the association of P16, MGMT and HMLH1 with gastric cancer and their relation with Methylenetetrahydrofolate reductase (MTHFR). METHODS: 322 gastric patients who were confirmed with pathological diagnosis were included in our study. Aberrant DNA methylation of P16, MGMT and HMLH1 and polymorphisms of MTHFR C677T and A1298C were detected using PCR-RFLP. RESULTS: The proportions of DNA hypermethylation in P16, MGMT and hMLH1 genes in gastric cancer tissues were 75.2% (242/322), 27.6% (89/322) and 5.3% (17/322), respectively. In the remote normal-appearing tissues, 29.5% (95/322) and 16.1%(52/322) showed hypermethylation in P16 and MGMT genes, respectively. We found a significantly higher proportion of DNA hypermethylation of P16 in patients with N1 TNM stage in cancer tissues and remote normal-appearing tissues (P<0.05). Similarly, we found DNA hypermethylation of MGMT had significantly higher proportion in N1 and M1 TNM stage (P<0.05). Individuals with homozygotes (TT) of MTHFR C677T had significant risk of DNA hypermethylation of MGMT in cancer tissues [OR (95% CI)=4.27(1.76-7.84)], and a significant risk was also found in those carrying MTHFR 677CT/TT genotype [OR (95% CI)= 3.27(1.21-4.77)]. CONCLUSION: We found the aberrant hypermethylation of cancer-related genes, such as P16, MGMT and HMLH1, could be predictive biomarkers for detection of gastric cancer.