Influence of Planting Density on Sweet Potato Storage Root Formation by Regulating Carbohydrate and Lignin Metabolism.

An appropriate planting density could realize the maximum yield potential of crops, but the mechanism of sweet potato storage root formation in response to planting density is still rarely investigated. Four planting densities, namely D15, D20, D25, and D30, were set for 2-year and two-site field experiments to investigate the carbohydrate and lignin metabolism in potential storage roots and its relationship with the storage root number, yield, and commercial characteristics at the harvest period. The results showed that an appropriate planting density (D20 treatment) stimulated cambium cell differentiation, which increased carbohydrate accumulation and inhibited lignin biosynthesis in potential storage roots. At canopy closure, the D20 treatment produced more storage roots, particularly developing ones. It increased the yield by 10.18-19.73% compared with the control D25 treatment and improved the commercial features by decreasing the storage root length/diameter ratio and increasing the storage root weight uniformity. This study provides a theoretical basis for the high-value production of sweet potato.

Feasibility Study of Using Hydrophobic Geopolymer-Based as Aggregate Substitution in Asphalt Mixture.

Hydrophobic aggregates have the great ability to prevent asphalt pavement roads from stripping-off of the asphalt in presence of water. In addition, they give the option to consume less asphalt and save cost. On the other hand, natural aggregates have been found to be non-renewable and rare. Geopolymer based artificial aggregates are great materials as they demonstrated to have exceptional features, such as high strength, superior durability, and greater resistance to fire exposure. In this study, a new hydrophobic geopolymer based aggregate has been produced with rice ash (RA) and fly ash as precursors as well as, Sodium Hydroxide (NaOH) and Sodium Silicate (Na2SiO3) as activators. The mechanical properties combined with the softening coefficient, surface properties of samples, contact angle and adhesion were characterized as well as microstructure X-ray diffraction (XRD) and Scanning electron microscopy (SEM) test. The results indicate that the activators Na2SiO3/NaOH at a mix ratio of 1 have a suitable effect on the pores and the compressive strength of the new artificial aggregate most particularly sodium hydroxide. Nonetheless, it has been found that coating the artificial aggregate with asphalt showed a great improvement of the hydrophobic nature of the produced artificial aggregate based geopolymer. Hence, indicates the possibility of using it as recycle aggregate pavement. From a microstructure point, the hydrophobic nature of the new alkali-activated artificial aggregate can be improved by increasing the quantity of mullite in the mix proportion design.

The Regulatory Network of Sweet Corn (Zea mays L.) Seedlings under Heat Stress Revealed by Transcriptome and Metabolome Analysis.

Heat stress is an increasingly significant abiotic stress factor affecting crop yield and quality. This study aims to uncover the regulatory mechanism of sweet corn response to heat stress by integrating transcriptome and metabolome analyses of seedlings exposed to normal (25 °C) or high temperature (42 °C). The transcriptome results revealed numerous pathways affected by heat stress, especially those related to phenylpropanoid processes and photosynthesis, with 102 and 107 differentially expressed genes (DEGs) identified, respectively, and mostly down-regulated in expression. The metabolome results showed that 12 or 24 h of heat stress significantly affected the abundance of metabolites, with 61 metabolites detected after 12 h and 111 after 24 h, of which 42 metabolites were detected at both time points, including various alkaloids and flavonoids. Scopoletin-7-o-glucoside (scopolin), 3-indolepropionic acid, acetryptine, 5,7-dihydroxy-3',4',5'-trimethoxyflavone, and 5,6,7,4'-tetramethoxyflavanone expression levels were mostly up-regulated. A regulatory network was built by analyzing the correlations between gene modules and metabolites, and four hub genes in sweet corn seedlings under heat stress were identified: RNA-dependent RNA polymerase 2 (RDR2), UDP-glucosyltransferase 73C5 (UGT73C5), LOC103633555, and CTC-interacting domain 7 (CID7). These results provide a foundation for improving sweet corn development through biological intervention or genome-level modulation.

Double sodium channel mutation, I265T/L1014F, is possibly related to pyrethroid-resistant in Thrips palmi.

Thrips palmi Karny (Thysanoptera: Thripidae) can harm a variety of agricultural crops and transmit plant viruses, causing heavy economic losses. In the Hainan province of China, pyrethroids were sprayed widely to control T. palmi, which leaded to resistance to pyrethroids in T. palmi. The bioassay has shown that the resistance ratio of T. palmi to pyrethroids increases annually. Resistance ratio to λ-cyhalothrin has increased from 10.711 to 23.321 and to cypermethrin has increased from 5.507 to 23.051 for 3 years, 2020-2022. The double mutation (I265T/L1014F) was identified from the field strain for the first time, which were located in the domains I and II of the voltage-gated sodium channel of T. palmi, respectively. The double mutation is probably the reason for the higher resistance of T. palmi in Hainan. The frequencies of the double mutation were 53.33% in HN2020, 70.00% in HN2021, and 96.67% in HN2022. Results indicated that T. palmi had developed different degrees of resistance to pyrethroids in Hainan. This study provides theoretical guidance for the use of insecticides in the field control of thrips.

Characterization of leachates from drainage asphalt pavement under multi-factor environmental treatments.

Pavement leachates could cause considerable environmental contamination. However, the influence of multiple environmental factors on the compositions of pavement leachates is still ill-understood. Therefore, it is necessary to analyse the variation of bitumen leachates with environmental factors and accordingly clarify the leaching mechanism. For this reason, a multi-environment device was invented to perform single-factor, two-factor and full-climate environmental treatments on open-graded friction courses (OGFC) asphalt mixtures. Subsequently, the acidity and alkalinity (pH) value, metal element composition and conductivity of the bitumen leachates with varying environmental treatments were characterized and analysed. Based on this, the leaching mechanism of bitumen leachates dissolved in water was proposed. The results indicated that the bitumen compositions were influenced by different environmental treatments, inducing the variation of pavement leachates. The primary substances of pavements leachates were composed of the organic acid substances and minor metal element ions. Accordingly, the experiment results demonstrated the increase of conductivity, and partial metal element concentration with the extension of treatment time. In terms of the pH value, an initial increase followed by a progressive decrease was observed.

A Temperature-Independent Methodology for Polymer Bitumen Modification Evaluation Based on DSR Measurement.

Owing to the continuous increase of traffic loads, bitumen modification has been manifested as an efficient methodology to enhance asphaltic pavement performance. Currently, the modification index, defined as the ratio of mechanical properties (e.g., complex modulus) before and after bitumen modification, is extensively adopted to evaluate the modification degree. However, bituminous materials behave as temperature-dependent, which indicates that the mechanical property varies with measured temperatures. As a result, the calculated modification index also shows temperature-dependent property, which inhibits the use of modification index. For this reason, this study introduced a method to eliminate the temperature-dependency of the modification index. In specific, a mathematical model considering the properties of modifiers was firstly established to predict the modification index-temperature curve (MI-T curve). In what follows, the temperature-dependency of modification index was analyzed to verify the proposed model on three types of modifiers, which were graphene, Styrene-Butadiene-Styrene (SBS), and Ethyl-Vinyl-Acetate (EVA), respectively. The results indicated that the developed model could efficiently predict the MI-T curves. Besides, the effective modification area (EMA) and optimal modification index (OMI) were two reasonable indicators that evaluate the bitumen modification without considering the temperature-dependency.

Prospective Study on the Postoperative Use of Levosimendan After Conventional Heart Valve Replacement.

BACKGROUND The aim of this study was to explore the effect of levosimendan in patients after heart valve replacement and its influence on postoperative recovery. MATERIAL AND METHODS This prospective study included 185 patients with valvular diseases undergoing conventional valve replacement. Patients were divided into 2 groups using a random number table before surgery. Patients in the levosimendan group were administrated levosimendan intravenous infusion immediately after entering the Intensive Care Unit (ICU). The left ventricular ejection fraction (LVEF), cardiac output, and heart failure-related index, such as B-type natriuretic peptide (BNP) level, were recorded at 1, 3, and 7 days after surgery. The dosage and administration time of dopamine and epinephrine, mechanical ventilation time, ICU length of stay, and postoperative adverse events were recorded. RESULTS Cardiac output and LVEF of patients in the levosimendan group were significantly higher than those in the control group at different time points (P<0.05), and BNP level was lower than that of the control group (P<0.0001). Dosage and administration time of dopamine and epinephrine in the levosimendan group were lower than those of the control group (P<0.0001, P<0.0001, respectively). ICU length of stay and total incidence of postoperative adverse events were lower than those of the control group (P<0.0001, P=0.002, respectively). CONCLUSIONS Levosimendan administration immediately after heart valve replacement effectively improved the heart function of patients, reduced administration of vasoactive drugs, shortened length of ICU stay, reduced incidence of postoperative adverse events, and promoted recovery of patients after surgery.

Salt Stress Modulates the Landscape of Transcriptome and Alternative Splicing in Date Palm (Phoenix dactylifera L.).

Date palm regards as a valuable genomic resource for exploring the tolerance genes due to its ability to survive under the sever condition. Although a large number of differentiated genes were identified in date palm responding to salt stress, the genome-wide study of alternative splicing (AS) landscape under salt stress conditions remains unknown. In the current study, we identified the stress-related genes through transcriptomic analysis to characterize their function under salt. A total of 17,169 genes were differentially expressed under salt stress conditions. Gene expression analysis confirmed that the salt overly sensitive (SOS) pathway genes, such as PdSOS2;1, PdSOS2;2, PdSOS4, PdSOS5, and PdCIPK11 were involved in the regulation of salt response in date palm, which is consistent with the physiological analysis that high salinity affected the Na+/K+ homeostasis and amino acid profile of date palm resulted in the inhibition of plant growth. Interestingly, the pathway of "spliceosome" was enriched in the category of upregulation, indicating their potential role of AS in date palm response to salt stress. Expectedly, many differentially alternative splicing (DAS) events were found under salt stress conditions, and some splicing factors, such as PdRS40, PdRSZ21, PdSR45a, and PdU2Af genes were abnormally spliced under salt, suggesting that AS-related proteins might participated in regulating the salt stress pathway. Moreover, the number of differentially DAS-specific genes was gradually decreased, while the number of differentially expressed gene (DEG)-specific genes was increased with prolonged salt stress treatment, suggesting that AS and gene expression could be distinctively regulated in response to salt stress. Therefore, our study highlighted the pivotal role of AS in the regulation of salt stress and provided novel insights for enhancing the resistance to salt in date palm.

Pre-miR-149 rs71428439 polymorphism is associated with increased cancer risk and AKT1/cyclinD1 signaling in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the most common lethal malignancies in the world, and the current knowledge on the molecular and genetic basis of HCC is still limited. Previous study has shown miR-149 plays a tumor suppressive role in HCC, here we aimed to investigate the association between rs71428439 polymorphism, which located in the pre-miR-149, and the risk of HCC in a Chinese Han population. A total of 177 HCC patients and 103 healthy controls were genotyped, by a multivariate logistic regression, we found that individuals with GG genotype have significantly higher risk of HCC (adjusted OR=3.397, 95% CI=1.565-7.375, P=0.002) compared with those with AA genotype, similar results were also observed in recessive model (adjusted OR=2.563, 95% CI=1.300-5.054, P=0.007) and dominant model (adjusted OR=2.074, 95% CI=1.147-3.752, P=0.016). We further observed that tumor tissues in patients with GG genotype expressed lower level of miR-149 compared with those with AA or AG genotype, and consequently, AKT1, a pre-validated miR-149 target in vitro, was found to have higher expression level in tumors with GG genotype. In summary, our data indicated that rs71428439 may be a genetic risk factor of HCC in the Chinese Han population, and its mechanism possibly involves downregulated miR-149 expression and upregulated AKT1 expression.

Toolbox for mobile-element insertion detection on cancer genomes.

Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram.

Toolbox for mobile-element insertion detection on cancer genomes.

Mobile elements constitute greater than 45% of the human genome as a result of repeated insertion events during human genome evolution. Although most of mobile elements are fixed within the human population, some elements (including ALU, long interspersed elements (LINE) 1 (L1), and SVA) are still actively duplicating and may result in life-threatening human diseases such as cancer, motivating the need for accurate mobile-element insertion (MEI) detection tools. We developed a software package, TANGRAM, for MEI detection in next-generation sequencing data, currently serving as the primary MEI detection tool in the 1000 Genomes Project. TANGRAM takes advantage of valuable mapping information provided by our own MOSAIK mapper, and until recently required MOSAIK mappings as its input. In this study, we report a new feature that enables TANGRAM to be used on alignments generated by any mainstream short-read mapper, making it accessible for many genomic users. To demonstrate its utility for cancer genome analysis, we have applied TANGRAM to the TCGA (The Cancer Genome Atlas) mutation calling benchmark 4 dataset. TANGRAM is fast, accurate, easy to use, and open source on https://github.com/jiantao/Tangram.

Tangram: a comprehensive toolbox for mobile element insertion detection.

BACKGROUND: Mobile elements (MEs) constitute greater than 50% of the human genome as a result of repeated insertion events during human genome evolution. Although most of these elements are now fixed in the population, some MEs, including ALU, L1, SVA and HERV-K elements, are still actively duplicating. Mobile element insertions (MEIs) have been associated with human genetic disorders, including Crohn's disease, hemophilia, and various types of cancer, motivating the need for accurate MEI detection methods. To comprehensively identify and accurately characterize these variants in whole genome next-generation sequencing (NGS) data, a computationally efficient detection and genotyping method is required. Current computational tools are unable to call MEI polymorphisms with sufficiently high sensitivity and specificity, or call individual genotypes with sufficiently high accuracy. RESULTS: Here we report Tangram, a computationally efficient MEI detection program that integrates read-pair (RP) and split-read (SR) mapping signals to detect MEI events. By utilizing SR mapping in its primary detection module, a feature unique to this software, Tangram is able to pinpoint MEI breakpoints with single-nucleotide precision. To understand the role of MEI events in disease, it is essential to produce accurate individual genotypes in clinical samples. Tangram is able to determine sample genotypes with very high accuracy. Using simulations and experimental datasets, we demonstrate that Tangram has superior sensitivity, specificity, breakpoint resolution and genotyping accuracy, when compared to other, recently developed MEI detection methods. CONCLUSIONS: Tangram serves as the primary MEI detection tool in the 1000 Genomes Project, and is implemented as a highly portable, memory-efficient, easy-to-use C++ computer program, built under an open-source development model.

Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data.

BACKGROUND: DNA capture technologies combined with high-throughput sequencing now enable cost-effective, deep-coverage, targeted sequencing of complete exomes. This is well suited for SNP discovery and genotyping. However there has been little attention devoted to Copy Number Variation (CNV) detection from exome capture datasets despite the potentially high impact of CNVs in exonic regions on protein function. RESULTS: As members of the 1000 Genomes Project analysis effort, we investigated 697 samples in which 931 genes were targeted and sampled with 454 or Illumina paired-end sequencing. We developed a rigorous Bayesian method to detect CNVs in the genes, based on read depth within target regions. Despite substantial variability in read coverage across samples and targeted exons, we were able to identify 107 heterozygous deletions in the dataset. The experimentally determined false discovery rate (FDR) of the cleanest dataset from the Wellcome Trust Sanger Institute is 12.5%. We were able to substantially improve the FDR in a subset of gene deletion candidates that were adjacent to another gene deletion call (17 calls). The estimated sensitivity of our call-set was 45%. CONCLUSIONS: This study demonstrates that exonic sequencing datasets, collected both in population based and medical sequencing projects, will be a useful substrate for detecting genic CNV events, particularly deletions. Based on the number of events we found and the sensitivity of the methods in the present dataset, we estimate on average 16 genic heterozygous deletions per individual genome. Our power analysis informs ongoing and future projects about sequencing depth and uniformity of read coverage required for efficient detection.

Mapping copy number variation by population-scale genome sequencing.

Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies.

COMIT: identification of noncoding motifs under selection in coding sequences.

Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences. We present the COMIT algorithm to detect functional noncoding motifs in coding regions using sequence conservation, explicitly separating nucleotide from amino acid effects. COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs. Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.

Deoxycholic acid induces the overexpression of intestinal mucin, MUC2, via NF-kB signaling pathway in human esophageal adenocarcinoma cells.

BACKGROUND: Mucin alterations are a common feature of esophageal neoplasia, and alterations in MUC2 mucin have been associated with tumor progression in the esophagus. Bile acids have been linked to esophageal adenocarcinoma and mucin secretion, but their effects on mucin gene expression in human esophageal adenocarcinoma cells is unknown. METHODS: Human esophageal adenocarcinoma cells were treated 18 hours with 50-300 muM deoxycholic acid, chenodeoxycholic acid, or taurocholic acid. MUC2 transcription was assayed using a MUC2 promoter reporter luciferase construct and MUC2 protein was assayed by Western blot analysis. Transcription Nuclear factor-kappaB activity was measured using a Nuclear factor-kappaB reporter construct and confirmed by Western blot analysis for Nuclear factor-kappaB p65. RESULTS: MUC2 transcription and MUC2 protein expression were increased four to five fold by bile acids in a time and dose-dependent manner with no effect on cell viability. Nuclear factor-kappaB activity was also increased. Treatment with the putative chemopreventive agent aspirin, which decreased Nuclear factor-kappaB activity, also decreased MUC2 transcription. Nuclear factor-kappaB p65 siRNA decreased MUC2 transcription, confirming the significance of Nuclear factor-kappaB in MUC2 induction by deoxycholic acid. Calphostin C, a specific inhibitor of protein kinase C (PKC), greatly decreased bile acid induced MUC2 transcription and Nuclear factor-kappaB activity, whereas inhibitors of MAP kinase had no effect. CONCLUSION: Deoxycholic acid induced MUC2 overexpression in human esophageal adenocarcinoma cells by activation of Nuclear factor-kappaB transcription through a process involving PKC-dependent but not PKA, independent of activation of MAP kinase.

[Role of bile in rat gastric mucosal injury due to duodenogastric reflux].

OBJECTIVE: To explore the effect of bile in inducing gastric mucosal injury in rats. METHODS: SD rats were divided into 4 groups, namely bile duct ligation group, duodenogastric reflux (DGR) group, DGR plus bile duct ligation group and normal control group. The pathological changes in the gastric mucosa and tight junction 3 months after gastrojejunostomy were observed and compared with the findings in the normal control rats. RESULTS: Compared with the rats in DGR plus bile duct ligation group, the rats in DGR group showed obvious gastric mucosal hyperemia, foveolar hyperplasia and severely impaired tight junction between the gastric mucosal cells. CONCLUSION: Bile plays an important role in gastric mucosal injury due to DGR.