Project description:Hormones effect various plant developmental processes by altering gene expression. The expression of several genes is regulated by plant hormones and many of these genes are regulated commonly and specifically by various hormones. We used microarrays to study the global effect of plant hormones on rice gene expression and identify the genes involved in operlapping and specific transcriptional responses. Rice seedlings of IR64 variety were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark. Seedlings were incubated in water (control) or 50 µM solution of indole-3-acetic acid (auxin, IAA) and benzyl aminopurine (cytokinin, BAP) and 100 µM solution of abscisic acid (ABA), 1-aminocyclopropane-1-carboxylic acid (ethylene derivative, ACC), salicylic acid (SA) and jasmonic acid (JA) for 3h. The 5 micrograms of total RNA sample isolated from each tissue sample was processed for microarray analysis according to Affymetrix protocol. Two biological replicates for each sample (two controls, IAA, BAP, ABA, ACC, SA and JA) were used for microarray analysis.
Project description:Hormones effect various plant developmental processes by altering gene expression. The expression of several genes is regulated by plant hormones and many of these genes are regulated commonly and specifically by various hormones. We used microarrays to study the global effect of plant hormones on rice gene expression and identify the genes involved in operlapping and specific transcriptional responses.
Project description:Individual plant parts from two to three specimens of one representative species of each subgeneric clade of Euphorbia were sampled (E. horrida Boiss., subg. Athymalus, three specimens; E. hirta L., subg. Chamaesyce, two specimens; E. lathyris L., subg. Esula, two specimens; E. milii Des Moul., subg. Euphorbia, two specimens) in the Botanical Garden in Copenhage, Denmark. Approximately 200 mg fresh plant material of each individual plant part was collected in 1.5 ml Eppendorf tubes and flash frozen under liquid nitrogen. The frozen plant material was disrupted in plastic tubes (Qiagen, RB 2 mL) in 1.3 ml 50/50 vol/vol methanol (Fisher Scientific, HPLC Grade)/acetonitrile (Fisher Scientific, Optima LC/MS) with stainless steel beads (VWR International, 5 mm) using a tissue lyser (Qiagen, TissueLyser II) at 25 Hz during 10 min. The samples were then extracted under sonication (Fisher Scientific) at 40 C during 15 min and centrifuged (Eppendorf Centrifuge 5418) for 10 min at 11,000 r.p.m. The extract supernatant was transferred to new plastic tubes and lyophilized to dryness (Labcono, Acid Resistant CentriVap Concentrator). Dried extracts were dissolved in 50/50 vol/vol methanol (Fisher Scientific, HPLC Grade)/acetonitrile (Fisher Scientific, Optima LC/MS) to a concentration of 1 mg/ml, 100 uL of each extract were transferred to a 96-well plate (Falcon, 96-well plates, 0.34 ml, polypropylene), sealed with Zone-Free Sealing Film (Excel Scientific) and centrifuged for 30 min. at 2000 r.p.m. at 4 C. 20 uL of each extract were injected into the LC-MS/MS equipment. For more details refer to the Material and Methods section and Supplementary Material in Ernst et al., (2019).
Project description:Summary
1. Purpose and Objective: The purpose of this study is to test the feasibility of rapid acquisition of point of care 3D ultrasound in obtaining abdominal and/or pelvic images. The study will use a newly developed acquisition method and post-processing technique to create three dimensional image models of the abdomen and/or pelvis.
2. Study activities and population group. The study population will be a convenience sample of patients of any age presenting to the Emergency Department with complaints necessitating a clinical abdominal and/or pelvic imaging. The study intervention includes acquisition of research ultrasound images, which will not be used for clinical care, and comparison of these images with clinically obtained images. Other clinical data such as surgical and pathology reports will also be reviewed. 3.Data analysis and risk/safety issues. This is a pilot study intended to determine feasibility and to refine image reconstruction algorithms. Research images will be compared to clinical images. Comparison of research images with final diagnosis will also occur. The research intervention, an ultrasound exam, has no known safety risks. The only risk to subjects is loss of confidentiality.
This study is observational, not interventional, because the experimental ultrasound will be performed in all subjects and will not be used in the clinical care of patients (consequently, will not have the opportunity to affect clinical outcomes). Experimental images will be reviewed after completion of clinical care and will not be provided to the clinicians caring for the subjects. The investigators are not measuring the effect of the ultrasound examination on the subjects’ outcomes.
Project description:We reported 4 single-sample cases and 3 control-sample cases of inflammatory cardiomyopathy using deep RNA-seq for detection of pathogenic agents. We identified various bacterial infections, analyzed genetic variants in patients and their differential gene expression caused by these infections in control-sample cases.
Project description:To investigate HCM mutation-associated molecular details at the early stage of disease development, we performed bulk RNA-seq analysis at Day 15 of differentiation using RNA isolated from the isogenic control and mutant hiPSC-CMs. We performed pair-end sequencing with >30 million reads per sample with clean read counts of more than 96% for each sample.