Transcriptome pathways unique to dehydration tolerant relatives of modern wheat

Among abiotic stressors, drought is a major factor responsible for dramatic yield loss in agriculture. In order to reveal differences in global expression profiles of drought tolerant and sensitive wild emmer wheat genotypes, a previously deployed shock-like dehydration process was utilized to compare transcriptomes at two time points in root and leaf tissues using the Affymetrix GeneChip(R) Wheat Genome Array hybridization. The comparison of transcriptomes reveal several unique genes or expression patterns such as differential usage of IP(3)-dependent signal transduction pathways, ethylene- and abscisic acid (ABA)-dependent signaling, and preferential or faster induction of ABA-dependent transcription factors by the tolerant genotype that distinguish contrasting genotypes indicative of distinctive stress response pathways. The data also show that wild emmer wheat is capable of engaging known drought stress responsive mechanisms. The global comparison of transcriptomes in the absence of and after dehydration underlined the gene networks especially in root tissues that may have been lost in the selection processes generating modern bread wheats

Bovine acute-phase response after different doses of corticotropin-releasing hormone challenge¹,²,³

The objective was to compare the acute-phase response of steers receiving different doses of bovine corticotropin-releasing hormone (CRH). Fourteen weaned Angus steers (BW = 191 ± 2.1 kg, age = 167 ± 4.7 d) fitted with an indwelling jugular catheter and a rectal temperature (RT) monitoring device were assigned to receive 1 of 3 treatments (intravenous infusion): 1) 0.1 μg of CRH/kg of BW (CRH1; n = 5), 2) 0.5 μg of CRH/kg of BW (CRH5; n = 5), and 3) 10 mL of saline (0.9%; n = 4). Blood samples were collected via catheters, relative to treatment infusion (0 h), hourly from –2 to 0 h and 4 to 8 h and every 30 min from 0 to 4 h. Rectal temperatures were recorded every 30 min from −2 to 8 h. Blood samples were also collected via jugular venipuncture and rectal temperatures assessed using a digital thermometer every 6 h from 12 to 72 h and every 24 h from 96 to 168 h. All plasma samples collected during the study were analyzed for concentrations of haptoglobin. All plasma samples collected from –2 to 8 h were analyzed for cortisol concentrations. Serum samples collected hourly from −2 to 8 h were analyzed for concentrations of NEFA, IL-6, tumor necrosis factor (TNF)-α, and interferon-γ. Cortisol peaked at 0.5 h for CRH1 steers but returned to baseline concentrations at 1 h relative to infusion (time effect; P 0.37). Mean serum TNF-α concentrations in CRH1 steers after treatment infusion were greater compared with saline (P = 0.02), tended to be greater (P = 0.08) compared with CRH5, and were similar (P = 0.40) between CRH5 and saline steers. Mean RT in CRH1 steers after treatment infusion were greater (P 0.45). In conclusion, the bovine acute-phase response stimulated by CRH infusion is dependent on the CRH dose and the subsequent response in circulating cortisol.This is the publisher’s final pdf. The published article is copyrighted by the American Society of Animal Science and can be found at: http://jas.fass.org/Keywords: bovine, acute-phase proteins, corticotropin-releasing hormone, proinflammatory cytokines, acute-phase respons

Daily and alternate day supplementation of urea or soybean meal to ruminants consuming low-quality cool-season forage: II. Effects on ruminal fermentation

Five ruminally cannulated steers (initial BW=464 ± 26 kg) consuming low-quality forage (5% CP; 78% NDF; DM basis) were used in an incomplete 5 x 4 Latin square with four 18-d periods to determine the influence of supplemental N source and supplementation frequency (SF) on ruminal fermentation dynamics. Treatments, arranged as a 2 x 2 factorial with a negative control, consisted of urea or soybean meal (SBM) supplements offered daily (D) or alternate days (2D) plus an unsupplemented treatment (CON). Urea supplements were provided to meet 100% of the degradable intake protein requirement while SBM supplements were provided on an isonitrogenous basis. All supplemented treatments received an equal quantity of supplemental N over a 2-d period. Ruminal indigestible acid detergent fiber (IADF) passage rate was increased with supplementation (P ≤ 0.03) on the days when D and 2D supplements were provided, as well as when only D supplements were provided. In contrast, ruminal liquid fill and dilution rate were not affected by supplementation, N source, or SF on the days when D and 2D supplements were provided (P ≥ 0.24). However, when only D supplements were offered, ruminal liquid dilution rate was greater (P=0.03) for SBM supplemented steers compared with cohorts receiving supplemental urea, whereas ruminal liquid fill was greater (P=0.03) for steers fed urea supplements. Nitrogen supplementation increased (P = 0.50). In summary, providing a urea-based supplement, as infrequently as every-other-day, was an effective alternative to a SBM-based supplement in maintaining acceptable ruminal fermentation of steers consuming low-quality, cool-season forage. (C) 2013 Elsevier B.V. All rights reserved.Keywords: Non-protein N, Forage, Urea, Soybean meal, Supplementation frequencyKeywords: Non-protein N, Forage, Urea, Soybean meal, Supplementation frequenc

A molecularly characterized preclinical platform of subcutaneous renal cell carcinoma (RCC) patient-derived xenograft models to evaluate novel treatment strategies

Renal cell carcinoma (RCC) is a kidney cancer with an onset mainly during the sixth or seventh decade of the patient’s life. Patients with advanced, metastasized RCC have a poor prognosis. The majority of patients develop treatment resistance towards Standard of Care (SoC) drugs within months. Tyrosine kinase inhibitors (TKIs) are the backbone of first-line therapy and have been partnered with an immune checkpoint inhibitor (ICI) recently. Despite the most recent progress, the development of novel therapies targeting acquired TKI resistance mechanisms in advanced and metastatic RCC remains a high medical need. Preclinical models with high translational relevance can significantly support the development of novel personalized therapies. It has been demonstrated that patient-derived xenograft (PDX) models represent an essential tool for the preclinical evaluation of novel targeted therapies and their combinations. In the present project, we established and molecularly characterized a comprehensive panel of subcutaneous RCC PDX models with well-conserved molecular and pathological features over multiple passages. Drug screening towards four SoC drugs targeting the vascular endothelial growth factor (VEGF) and PI3K/mTOR pathway revealed individual and heterogeneous response profiles in those models, very similar to observations in patients. As unique features, our cohort includes PDX models from metastatic disease and multi-tumor regions from one patient, allowing extended studies on intra-tumor heterogeneity (ITH). The PDX models are further used as basis for developing corresponding in vitro cell culture models enabling advanced high-throughput drug screening in a personalized context. PDX models were subjected to next-generation sequencing (NGS). Characterization of cancer-relevant features including driver mutations or cellular processes was performed using mutational and gene expression data in order to identify potential biomarker or treatment targets in RCC. In summary, we report a newly established and molecularly characterized panel of RCC PDX models with high relevance for translational preclinical research

Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde

Overexpression of a Common Wheat Gene TaSnRK2.8 Enhances Tolerance to Drought, Salt and Low Temperature in Arabidopsis

Drought, salinity and low temperatures are major factors limiting crop productivity and quality. Sucrose non-fermenting1-related protein kinase 2 (SnRK2) plays a key role in abiotic stress signaling in plants. In this study, TaSnRK2.8, a SnRK2 member in wheat, was cloned and its functions under multi-stress conditions were characterized. Subcellular localization showed the presence of TaSnRK2.8 in the cell membrane, cytoplasm and nucleus. Expression pattern analyses in wheat revealed that TaSnRK2.8 was involved in response to PEG, NaCl and cold stresses, and possibly participates in ABA-dependent signal transduction pathways. To investigate its role under various environmental stresses, TaSnRK2.8 was transferred to Arabidopsis under control of the CaMV-35S promoter. Overexpression of TaSnRK2.8 resulted in enhanced tolerance to drought, salt and cold stresses, further confirmed by longer primary roots and various physiological characteristics, including higher relative water content, strengthened cell membrane stability, significantly lower osmotic potential, more chlorophyll content, and enhanced PSII activity. Meanwhile, TaSnRK2.8 plants had significantly lower total soluble sugar levels under normal growing conditions, suggesting that TaSnRK2.8 might be involved in carbohydrate metabolism. Moreover, the transcript levels of ABA biosynthesis (ABA1, ABA2), ABA signaling (ABI3, ABI4, ABI5), stress-responsive genes, including two ABA-dependent genes (RD20A, RD29B) and three ABA-independent genes (CBF1, CBF2, CBF3), were generally higher in TaSnRK2.8 plants than in WT/GFP controls under normal/stress conditions. Our results suggest that TaSnRK2.8 may act as a regulatory factor involved in a multiple stress response pathways