Similar Datasets
Project description:Highly rearranged and mutated cancer genomes present major challenges in the identification of pathogenetic events driving the cancer process. Here, we engineered lymphoma-prone mice with chromosomal instability to assess the utility of mouse models in cancer gene discovery and the extent of cross-species overlap in cancer-associated copy number aberrations. Integrating with targeted re-sequencing, our comparative oncogenomic studies efficiently identified FBXW7 and PTEN as commonly deleted or mutated tumor suppressors in human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL). More generally, the murine cancers acquire widespread recurrent clonal amplifications and deletions targeting loci syntenic to alterations present in not only human T-ALL but also diverse tumors of hematopoietic, mesenchymal and epithelial types. These results thus support the view that murine and human tumors experience common biological processes driven by orthologous genetic events as they evolve towards a malignant phenotype. The highly concordant nature of genomic events encourages the use of genome unstable murine cancer models in the discovery of biologically relevant driver events in human cancer. Keywords: comparative genomic hybridization
2007-06-05 | GSE7603 | GEO
Project description:Referral for an assessment of tall stature is less common than for short stature. Tall stature is defined as a height more than two standard deviations above the mean for age. The majority of subjects with tall stature show a familial tall stature or a constitutional advance of growth (CAG), which is a diagnosis of exclusion. After a careful physical evaluation, tall subjects may be divided into two groups: tall subjects with normal appearance and tall subjects with abnormal appearance. In the case of normal appearance, the paediatric endocrinologist will have to evaluate the growth rate. If it is normal for age and sex, the subject may be classified as having familial tall stature, CAG or obese subject, while if the growth rate is increased it is essential to evaluate pubertal status and thyroid status. Tall subjects with abnormal appearance and dysmorphisms can be classified into those with proportionate and disproportionate syndromes.A careful physical examination and an evaluation of growth pattern are required before starting further investigations. Physicians should always search for a pathological cause of tall stature, although the majority of children are healthy and they generally do not need treatment to cease growth progression.The most accepted and effective treatment for an excessive height prediction is inducing puberty early and leading to a complete fusion of the epiphyses and achievement of final height, using testosterone in males and oestrogens in females. Alternatively, the most common surgical procedure for reducing growth is bilateral percutaneous epiphysiodesis of the distal femur and proximal tibia and fibula.This review aims to provide up-to-date information and suggestions about the diagnosis and management of children with tall stature.
| S-EPMC5543750 | biostudies-other
Project description:The closely related Coffea arabica cultivars ‘Tall Mokka’ and ‘Typica’, with excellent flavor, but differing distinctively in the size of aerial organs, branching pattern and branch numbers. Differential gene expression analysis of shoot tips of arabica coffee cultivars 'Tall Mokka' and 'Typica' were done using Potato cDNA microarray as cross-species platform. Using cross-species microarray hybridization, we identified a prolyl oligopeptidase (CaPOP) gene as differentially expressed between the shoot tips of ‘Tall Mokka’ and ‘Typica’. Isolation and sequencing of POP genes from coffee identified three paralogs, CaPOP1, CaPOP2 and CaPOP3. All three genes were present in both cultivars, which suggest that differences in the expression of CaPOP are caused by factor(s) regulating the transcription of CaPOPs. CaPOP1 differs in sequence from CaPOP2 primarily in having two large deletions in the promoter region. CaPOP genes are homologous to arabidopsis At1g20380, encoding a post-proline cleaving enzyme that acts on substrates shorter than 30 amino acids. Ectopic expression of CaPOP1 under its native promoter in transgenic arabidopsis resulted in more secondary branches than in the wild type. This is the first study to successfully isolate CaPOP genes and characterize their expression in the developing tissues of coffee. This study also identified a novel role for prolyl oligopeptidase in control of branching. Eight coffee trees of 'Typica' ('K') and six trees of 'Tall Mokka' ('M') cultivar were used in this study. The trees were equally divided into two groups 'A' and 'B' for each cultivar ('MA','MB', 'KA' and 'KB') and treated as biological replicates. Eight two channel microarray hybridizations were done in following pairs: MA x KA, MA x KB, MB x KA, MB x KB and dye swap replicate of each pair. Summary: Two-sample experiment: Tall Mokka vs. Typica . 8 Hybridizations. 2 Biological replicates per sample. 1 Dye swap per array.
2011-08-03 | E-GEOD-31179 | biostudies-arrayexpress
Project description: Not available
| S-EPMC8294929 | biostudies-literature
Project description:Purpose: We aimed to dissect heat response of tall fescue and possible roles of melatonin and 24-epibrassinolide during thermotolerance. Methods: A total amount of 3 µg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0). Results:In total, six samples with two biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis identified genes modulated by short term heat (2h) and long term heat (12h) treatments.
2018-03-02 | GSE101699 | GEO
Project description:Increases in nitrogen (N) inputs to the biosphere can exacerbate the introduction and spread of invasive non-native plant species. Often, with elevated soil N levels, invasive plants establish and further enrich soil N pools, changing overall ecosystem function. This study examined the relationship between soil N cycling and an increasingly prevalent, invasive plant species, tall oatgrass (Arrhenatherum elatius subsp. elatius), in foothills ecosystems between the Colorado Rocky Mountains and the Denver-Boulder Metropolitan area-similar to many Western US grasslands and woodlands. It focused on investigating differences in soil N transformations, inorganic N pools, and vegetation characteristics across invaded and uninvaded plots at three sites in two seasons (summer and autumn). There was a statistically significant effect of invasion on rates of net N mineralization, but it was dependent on site and season (p = 0.046). Site had a statistically significant effect on soil moisture and aboveground biomass C:N (p < 0.04). The interactions of invasion x site were statistically significant for ammonium pools (p < 0.03). These findings suggest that A. elatius invasion can be associated with accelerated N cycling, but that the nature of the relationship differs by location and season in the foothills. More broadly, this study contributes to determining how the N cycle is shifting in grassland ecosystems subject to increasing pressures from anthropogenic change.
| S-EPMC9226098 | biostudies-literature
Project description:The transpiration cycle in trees is powered by a negative water potential generated within the leaves, which pumps water up a dense array of xylem conduits. Synthetic trees can mimic this transpiration cycle, but have been confined to pumping water across a single microcapillary or microfluidic channels. Here, we fabricated tall synthetic trees where water ascends up an array of large diameter conduits, to enable transpiration at the same macroscopic scale as natural trees. An array of 19 tubes of millimetric diameter were embedded inside of a nanoporous ceramic disk on one end, while their free end was submerged in a water reservoir. After saturating the synthetic tree by boiling it underwater, water can flow continuously up the tubes even when the ceramic disk was elevated over 3 m above the reservoir. A theory is developed to reveal two distinct modes of transpiration: an evaporation-limited regime and a flow-limited regime.
| S-EPMC6959229 | biostudies-literature
Project description:illumina RNA sequencing of tall fescue leaves generated a total of raw 144,339 reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to functional databases. Further analysis revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. Totally, 1,862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs 24 h salt treatment. Protein interaction analysis revealed the high interaction of chaperonins and Rubisco proteins in 48h vs 24h salt treatment
2018-09-15 | GSE119957 | GEO