ABSTRACT: This study was designed to look for differential gene expression in the annual dicot weed velvetleaf when it is grown in competition with corn relative to when it is grown in monoculture. Keywords: weed/crop competition Overall design: There were three biological replicates for each treatment [growth with corn (W1, W2, and W3) and growth in monoculture (C1, C2, and C3)]. These were compared directly in a rolling circle dye swap design and included two additional cross circle hybridizations.
Project description:Water shortage threatens agricultural sustainability in China, effective water-saving technologies urgently need to be developed. In this study, five treatments were conducted: rainfed (W0), a local supplemental irrigation (SI) practice (W1), and three treatments in which soil water content was tested prior to SI, specifically at 0-20 (W2), 0-40 (W3) and 0-60 cm (W4) soil layers. Soil water consumption in W3 had no differ with W2 but was higher than W1 and W4. Crop evapotranspiration in W1, W3 and W4 treatments were higher than that in W2. W3 treatment had higher leaf area index than W1 and W4 at later grain filling stages. The mean photosynthetically active radiation capture ratio in W3, especially at 20, 40 and 60 cm plant heights, were significantly higher than those in W1, W2 and W4. The chlorophyll content index, actual photosynthetic activities, catalase and superoxide dismutase activities of flag leaves from W3 were the highest after the middle grain filling stages. W3 treatment obtained the highest grain yield (9169 kg ha-1) and water use efficiency (20.8 kg ha-1 mm-1) in the two seasons. These benefits likely accrued through created a suitable soil moisture environment in W3 treatment.
Project description:Adolescent driving while alcohol/drug impaired (DWI) and parental monitoring knowledge may have notable interplay. However, the magnitude and direction of causality are unclear. This study examined possible reciprocal associations among adolescents between DWI and parental monitoring knowledge.The data were from waves 1, 2, and 3 (W1, W2, and W3) of the NEXT Generation Health Study, with longitudinal assessment of a nationally representative sample of 10th graders starting in 2009-2010 (n = 2,525 at W1) and analyzed in 2014. Those who had obtained an independent/unsupervised driving license were included for the analysis. Autoregressive cross-lagged path analysis was used to examine potential reciprocal associations between DWI and parental monitoring knowledge of both mothers and fathers, controlling for potential confounders.Stability of fathers' and mothers' monitoring knowledge across 3 consecutive interview waves was identified. W1 monitoring knowledge of both fathers and mothers was prospectively associated with DWI at W2 but not for W2 with W3. A significant negative association between adolescent DWI at W2 and mothers' monitoring knowledge at W3 was found but not between W1 and W2. None of the associations between DWI and fathers' monitoring knowledge from W1 to W2 or from W2 to W3 were significant.Early (10th grade) parental monitoring knowledge may predict lower adolescent self-reported DWI in 11th grade. More notably, adolescent DWI did not seem to increase parental monitoring knowledge. Future interventions are needed to improve parental monitoring knowledge and enhance awareness of the DWI risk in their adolescent novice drivers.
Project description:Winter wheat is threatened by drought in the Huang-Huai-Hai Plain of China, thus, effective water-saving irrigation practices are urgently required to maintain its high winter wheat production. This study was conducted from 2012 to 2014 to determine how supplemental irrigation (SI) affected soil moisture, photosynthesis, and dry matter (DM) production of winter wheat by measuring the moisture in 0-20 cm (W2), 0-40 cm (W3), and 0-60 cm (W4) soil profiles. Rainfed (W0) and local SI practice (W1, irrigation with 60 mm each at jointing and anthesis) treatments were designed as controls. The irrigation amount for W3 was significantly lower than that for W1 and W4 but higher than that for W2. The soil relative water content (SRWC) in 0-40 cm soil profiles at jointing after SI for W3 was significantly lower than that for W1 and W4 but higher than that for W2. W3 exhibited lower SRWC in 100-140 and 60-140 cm soil profiles at anthesis after SI and at maturity, respectively, but higher root length density in 60-100 cm soil profiles than W1, W2 and W4. Compared with W1, W2 and W4, photosynthetic and transpiration rates and stomatal conductance of flag leaves for W3 were significantly greater during grain filling, particularly at the mid and later stages. The total DM at maturity, DM in grain and leaves, post-anthesis DM accumulation and its contribution to grain and grain filling duration were higher for W3. The 1000-grain weight, grain yield and water use efficiency for W3 were the highest. Therefore, treatment of increasing SRWC in the 0-40 cm soil profiles to 65% and 70% field capacities at jointing and anthesis (W3), respectively, created a suitable soil moisture environment for winter wheat production, which could be considered as a high yield and water-saving treatment in Huang-Huai-Hai Plain, China.
Project description:The major changes in hormone levels that occur through the menstrual cycle have been postulated to affect the expression of hormone-regulated and proliferation-associated genes (PAGs) in premenopausal ER+ breast cancer. Whilst previous studies have demonstrated differences in gene expression, here, we investigated if there are within patient changes in the expression of oestrogen- and progesterone-regulated genes (ERGs and PRGs) and PAGs in ER+ breast cancer during the menstrual cycle. Samples from 96 patients in two independent prospective studies of the effect of menstrual cycle on ER+ breast cancer were used. Plasma hormone measurements were used to assign tumours to one of three pre-defined menstrual cycle windows: W1 (days 27-35 and 1-6; low oestradiol and low progesterone), W2 (days 7-16; high oestradiol and low progesterone) and W3 (days 17-26; intermediate oestradiol and high progesterone). RNA expression of 50 genes, including 27 ERGs, 11 putative PRGs and seven PAGs was measured. The AvERG (geomean of PGR, GREB1, TFF1 and PDZK1) was used as a composite measure of ERG expression and showed significant changes between the three windows of the menstrual cycle increasing over 2.2-fold between W1 and W2 and decreasing between W2 and W3 and between W3 and W1. Proliferation gene expression also varied significantly, following the same pattern of changes as ERG expression, but the changes were of lower magnitude (1.4-fold increase between W1 and W2). Significant changes in the expression of eight individual ERGs, including GREB1, PGR and TFF1, and two PAGs were observed between W1 and either W2 or W3 with all genes showing higher levels in W2 or W3 (1.3-2.4-fold; FDR 0.016-0.05). The AvProg, a composite measure of PRG expression, increased significantly (1.5-fold) in W3 compared to W1 or W2 but no significant changes were observed for individual PRGs. In conclusion, we observed significant changes in ERG, PRG and PAG expression in ER+ breast tumours during the menstrual cycle that may affect the assessment and interpretation of prominent biomarkers (e.g. PgR) and commonly used multigene prognostic signatures in premenopausal ER+ breast cancer.
Project description:The three yeast mutants sch9Δ, ras2Δ, tor1Δ show extended chronological life span up to three folds. This study aims to dissect the mechanisms that lead to the yeast life span extension. Keywords: Expression comparison between wild type and long-lived yeast mutant strain Overall design: We obtain gene expression profiles of sch9Mutant, ras2Mutant, tor1Mutant as well as that for a wild type at day 2.5 in SDC medium using Affymetrix Yeast2.0 arrays. Each sample has three replicates. We use a complicated pre-processing method and get the expression differntiation directly. We consider the issue of processing robustness and expression large differentiation. The normalization is carried out in a pairwise fashion. Namely, for each wild type sample (W1, W2, W3), three replicates of a mutant are normalized with respect to each reference. Take sch9Mutant (triplicates: S1, S2 and S3) for example, the normalized arrays with respect to W1, W2, W3 are respectively denoted by S1\W1, S2\W1, S3\W1, S1\W2, S2\W2, S3\W2, S1\W3, S2\W3, S3\W3. We group the wild type and normalized mutant arrays by the reference, and then summarize each group. We summarize the four arrays (the reference plus three normalized) W1, S1\W1, S2\W1, S3\W1 together. This leads to three estimates of expression fold changes of the mutant versus the wild type. In total, we have nine estimates from three wild type references, and we take their median difference as the final estimate. Expression fold change estimates (generated by the analysis) are given in the Series table.
Project description:PR1 is a pathogenesis-related protein encoded in the parsley genome by a family of three genes (PR1-1, PR1-2 and PR1-3). Loss- and gain-of-function experiments in a transient expression system demonstrated the presence of two fungal elicitor responsive elements in each of the PR1-1 and PR1-2 promoters. These elements, W1, W2 and W3, contain the sequence (T)TGAC(C) and mutations that disrupt this sequence abolish function. Gel shift experiments demonstrated that W1, W2 and W3 are bound specifically by similar nuclear proteins. Three cDNA clones encoding sequence-specific DNA-binding proteins were isolated by South-Western screening and these proteins, designated WRKY1, 2 and 3, also bind specifically to W1, W2 and W3. WRKY1, 2 and 3 are members of the family of sequence-specific DNA-binding proteins, which we call the WRKY family. Treatment of parsley cells with the specific oligopeptide elicitor Pep25 induced a transient and extremely rapid increase in mRNA levels of WRKY1 and 3. WRKY2 mRNA levels in contrast showed a concomitant transient decrease. These rapid changes in WRKY mRNA levels in response to a defined signal molecule suggest that WRKY1, 2 and 3 play a key role in a signal transduction pathway that leads from elicitor perception to PR1 gene activation.
Project description:This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8 stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8. Mechanisms underlying early season weed stress on crop growth are not well described. Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants. Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants. Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6. In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms. three biological replicates for each treatment and the control were collected and the resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had thre biological replicates for each growth condition amd two technical replicates for each biological sample.
Project description:OBJECTIVE:The goal of this study is to examine the cross-sectional prevalence of use and 3-year longitudinal pathways of cigar use in US youth (12-17 years), young adults (18-24 years), and adults 25+ (25 years or older). DESIGN:Data were drawn from the first three waves (2013-2016) of the Population Assessment of Tobacco and Health Study, a nationally representative, longitudinal cohort study of US youth and adults. Respondents with data at all three waves (youth, n=11 046; young adults, n=6478; adults 25+, n=17 188) were included in longitudinal analyses. RESULTS:Weighted cross-sectional prevalence of past 30-day (P30D) use was stable for adults 25+ (~6%), but decreased in youth (Wave 1 (W1) to Wave 3 (W3)=2.5% to 1.2%) and young adults (W1 to W3=15.7% to 14.0%). Among W1 P30D cigar users, over 50% discontinued cigar use (irrespective of other tobacco use) by Wave 2 (W2) or W3. Across age groups, over 70% of W1 P30D cigar users also indicated P30D use of another tobacco product, predominantly cigar polytobacco use with cigarettes. Discontinuing all tobacco use by W2 or W3 was greater in adult exclusive P30D cigar users compared with polytobacco cigar users. CONCLUSIONS:Although the majority of P30D cigar users discontinued use by W3, adult polytobacco users of cigars were less likely to discontinue all tobacco use than were exclusive cigar users. Tracking patterns of cigar use will allow further assessment of the population health impact of cigars.
Project description:Every individual (W1-W4) was hybridised 4 times, including 2 dye swaps: W1: 23573-23576; W2: 23577-23580; W3: 23581-23584; W4: 23585-23588. Only 2 of 4 hybridisations wer made at the same preparation Keywords: parallel sample
Project description:Femoral head collapse is a key reference point for determining a treatment regimen of femoral head osteonecrosis. However, there are no effective preventive measures and the efficacy of hip-preserving surgery is unsatisfactory due to the unclear mechanism of collapse. This study aimed to identify and validate miRNAs differentially expressed in collapse and non-collapse areas of the osteonecrotic femoral head, and to predict the target genes and pathways of these miRNAs.Nine samples passed the quality control test. A total of 2085 differentially expressed miRNAs were detected, among which 433 miRNAs showed differential expression in the T1 group compared to the W1 group; 344 miRNAs showed differential expression in the T2 group compared to the W2 group; 107 miRNAs showed differential expression in the T3 group compared to the W3 group. After combining data from all three patients, 10 miRNAs showed differential expression in the collapse area (T1+T2+T3) compared to the non-collapse area (W1+W2+W3). Compared to the normal area, has-miR-195-5p showed the most significant downregulation. Expression results from RT-PCR revealed that the expression of hsa-miR-195-5p in the collapse area (T1+T2+T3) was significantly lower than that in the non-collapse area (W1+W2+W3) and normal area (Z1+Z2+Z3). 157 genes were perdicted as the target gene of hsa-miR-195-5p.Femoral heads of three patients (2 males and 1 female) treated by total hip arthroplasty surgery for steroid-induced femoral head osteonecrosis were selected based on inclusion and exclusion criteria. Bone tissue samples were obtained from the collapse area (T), non-collapse area (W), and normal area (Z) according to the anatomical structure of osteonecrotic femoral heads. Total RNA was extracted from the samples and the microarray chip was scanned. miRNAs showing differential expressions of more than 1.5-fold were selected and was validated by RT-PCR. TargetScan, mirBase and miRanda bioinformatics software was used to predict target genes and identify possible pathways involving these genes.miR-195-5p showed the most significant difference in the collapse area of osteonecrotic femoral heads, suggesting that collapse may be related to the downregulation of miR-195-5p.