Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the ...smallest of the 12 rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.
OBJECTIVEThis study evaluates the ability of perflubron to inhibit pulmonary neutrophil accumulation during partial liquid ventilation (PLV) in the setting of acute lung injury.
DESIGNRandomized, ...controlled, nonblinded study.
SETTINGResearch laboratory at a university.
SUBJECTSMale, Sprague-Dawley rats (n = 120, 506 +/- 42 g).
INTERVENTIONSAnimals were divided into eight groups (n = 15 in each group, of which n = 12 for myeloperoxidase content and n = 3 for histologic neutrophil counting)a) GV-CVF group, animals received gas ventilation (GV) with the induction of lung injury using cobra venom factor (CVF); b) PLV-CVF group, animals received partial liquid ventilation before the induction of lung injury; c) PEEP-CVF group, animals received positive end-expiratory pressure (PEEP) before the administration of cobra venom factor; d) CVF-PLV group, animals received partial liquid ventilation after cobra venom factor; e) CVF-PEEP group, animals received PEEP after cobra venom factor; f) PLV only group, animals received partial liquid ventilation only; g) GV only group, animals received gas ventilation only; and h) NVSBA group, nonventilated spontaneous breathing animals.
MEASUREMENTS AND MAIN RESULTSAfter the experimental period, total lung myeloperoxidase content was significantly decreased in the PLV-CVF (0.29 +/- 0.08, p = .02) and PEEP-CVF (0.34 +/- 0.04, p = .01) groups when compared with the GV-CVF group (0.62 +/- 0.07). When compared with the GV-CVF group, a trend toward a reduction in myeloperoxidase was observed in the CVF-PLV (0.42 +/- 0.05, p = .07) and the CVF-PEEP (0.39 +/- 0.06, p = .07) groups. When compared with the cobra venom factor only group (GV-CVF 47 +/- 2 neutrophils/high-power field), reductions in neutrophil count were observed in all groups (neutrophils/high-power field)PLV-CVF (20 +/- 2, p = .009); PEEP-CVF (24 +/- 1, p = .01); CVF-PLV (30 +/- 2, p = .03); and CVF-PEEP (37 +/- 1, p = .04).
CONCLUSIONThese data suggest that both partial liquid ventilation and PEEP result in a reduction in neutrophil accumulation in the setting of acute lung injury. (Crit Care Med 1998; 26:1716-1724)
An attempt is made to formulate the relationship between age and chromospheric emission (CE) in late-type dwarf stars. Evidence is reviewed that a deterministic relationship of this type actually ...exists, and that for stars of known age, either a power-law relation or a curve corresponding to a constant star formation rate fits equally well. Further observations should be able to demonstrate either that there is a real excess of young stars near the sun or that the evolution of CE for a low-mass star goes through a slow initial decline, a rapid decline at intermediate ages, and finally a slow decline for old stars like the sun. 100 refs.
The Texas brown tide alga (strain TBA-2) is described as Aureoumbra lagunensis Stockwell, DeYoe, Hargraves, et Johnson, gen. et sp. nov. Pigment composition, chloroplast structure, and 18S ribosomal ...RNA gene sequence data indicate that A. lagunensis and the east coast brown tide alga Aureococcus anophagefferens (originally placed in the Chrysophyceae) belong in the class Pelagophyceae. The new genus Aureoumbra with A. lagunensis the type species differs from Aureococcus in 18S ribosomal RNA gene sequence, pyrenoid form, nitrogen physiology, and possession of basal bodies. The genus Aureococcus is placed in the order Pelagomonadales and family Pelagomonadaceae while ordinal placement of Aureoumbra is deferred.
Prostate cancer is the second leading cause of cancer deaths among American men. The loss of Y chromosome has been frequently observed in primary prostate cancer as well as other types of cancer. ...Earlier, we showed that introduction of the human Y chromosome suppresses the in vivo tumorigenicity of the prostate cancer cell line PC-3. To further characterize the Y chromosome, we have developed a high-density bacterial artificial chromosome (BAC) microarray containing 178 BAC clones from the human Y chromosome. BAC microarray was used for array comparative genomic hybridization on prostate cancer samples and cell lines. The most prominent observation on prostate cancer specimens was a deletion at Yp11.2 containing the TSPY tandem gene array. Out of 36 primary prostate tumors analyzed, 16 (44.4%) samples exhibited loss of TSPY gene copies. Notably, we observed association between the number of TSPY copies in the blood and the incidence of prostate cancer. Moreover, PC-3 hybrids with an intact Yp11.2 did not grow tumors in nude mice, whereas PC-3 hybrids with a deletion at Yp11.2 grew tumors in nude mice.
R Aquarii is a symbiotic binary star system surrounded by a complex extended optical nebulosity. Recent observations have ruled out the the possibility that the radio components in the system's jet ...were formed in a single explosive event but suggest instead that they were ejected in "bullets" at intervals of about 20 years into a narrow cone.
Abstract
The unconventional normal-state properties of the cuprates are often discussed in terms of emergent electronic order that onsets below a putative critical doping of
x
c
≈ 0.19. Charge ...density wave (CDW) correlations represent one such order; however, experimental evidence for such order generally spans a limited range of doping that falls short of the critical value
x
c
, leading to questions regarding its essential relevance. Here, we use X-ray diffraction to demonstrate that CDW correlations in La
2−
x
Sr
x
CuO
4
persist up to a doping of at least
x
= 0.21. The correlations show strong changes through the superconducting transition, but no obvious discontinuity through
x
c
≈ 0.19, despite changes in Fermi surface topology and electronic transport at this doping. These results demonstrate the interaction between CDWs and superconductivity even in overdoped cuprates and prompt a reconsideration of the role of CDW correlations in the high-temperature cuprate phase diagram.
The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides 'Level 3' data, which have been processed using a pipeline specific to that resource. However, we have ...found using experimentally derived data that this pipeline produces gene-expression values that vary considerably across biological replicates. In addition, some RNA-Sequencing analysis tools require integer-based read counts, which are not provided with the Level 3 data. As an alternative, we have reprocessed the data for 9264 tumor and 741 normal samples across 24 cancer types using the Rsubread package. We have also collated corresponding clinical data for these samples. We provide these data as a community resource.
We compared TCGA samples processed using either pipeline and found that the Rsubread pipeline produced fewer zero-expression genes and more consistent expression levels across replicate samples than the TCGA pipeline. Additionally, we used a genomic-signature approach to estimate HER2 (ERBB2) activation status for 662 breast-tumor samples and found that the Rsubread data resulted in stronger predictions of HER2 pathway activity. Finally, we used data from both pipelines to classify 575 lung cancer samples based on histological type. This analysis identified various non-coding RNA that may influence lung-cancer histology.
The RNA-Sequencing and clinical data can be downloaded from Gene Expression Omnibus (accession number GSE62944). Scripts and code that were used to process and analyze the data are available from https://github.com/srp33/TCGA_RNASeq_Clinical.
stephen_piccolo@byu.edu or andreab@genetics.utah.edu
Supplementary material is available at Bioinformatics online.
PDF
