1,434 research outputs found
ArrayQuest: a web resource for the analysis of DNA microarray data
BACKGROUND: Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the Internet enhances the applicability and utility of these analytic software tools. RESULTS: Here we present ArrayQuest, a web-based DNA microarray analysis process controller. Key features of ArrayQuest are that (1) it is capable of executing numerous analysis programs such as those written in R, BioPerl and C++; (2) new analysis programs can be added to ArrayQuest Methods Library at the request of users or developers; (3) input DNA microarray data can be selected from public databases (i.e., the Medical University of South Carolina (MUSC) DNA Microarray Database or Gene Expression Omnibus (GEO)) or it can be uploaded to the ArrayQuest center-point web server into a password-protected area; and (4) analysis jobs are distributed across computers configured in a backend cluster. To demonstrate the utility of ArrayQuest we have populated the methods library with methods for analysis of Affymetrix DNA microarray data. CONCLUSION: ArrayQuest enables browser-based implementation of DNA microarray data analysis programs that can be executed on a Linux-based platform. Importantly, ArrayQuest is a platform that will facilitate the distribution and implementation of new analysis algorithms and is therefore of use to both developers of analysis applications as well as users. ArrayQuest is freely available for use at
GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms
MEASUREMENT OF THE BLACK HOLE MASS IN NGC 1332 FROM ALMA OBSERVATIONS AT 0.044 ARCSECOND RESOLUTION
We present Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 3 observations of CO(2-1) emission from the circumnuclear disk in the E/S0 galaxy NGC 1332 at 0.″044 resolution. The disk exhibits regular rotational kinematics and central high-velocity emission (±500 km s ) consistent with the presence of a compact central mass. We construct models for a thin, dynamically cold disk in the gravitational potential of the host galaxy and black hole and fit the beam-smeared model line profiles directly to the ALMA data cube. Model fits successfully reproduce the disk kinematics out to r = 200 pc. Fitting models just to spatial pixels within projected r = 50 pc of the nucleus (two times larger than the black hole's gravitational radius of influence), we find M =(6.64 ) × 10 M . This observation demonstrates ALMA's powerful capability to determine the masses of supermassive black holes by resolving gas kinematics on small angular scales in galaxy nuclei. -1 +0.65 8 BH -0.63
A Precision Measurement of the Mass of the Black Hole in NGC 3258 from High-Resolution ALMA Observations of its Circumnuclear Disk
We present resolution Atacama Large
Millimeter/submillimeter Array (ALMA) CO(21) imaging of the arcsecond-scale
( pc) dusty molecular disk in the giant elliptical galaxy NGC
3258. The data provide unprecedented resolution of cold gas disk kinematics
within the dynamical sphere of influence of a supermassive black hole,
revealing a quasi-Keplerian central increase in projected rotation speed rising
from 280 km s at the disk's outer edge to km s near the
disk center. We construct dynamical models for the rotating disk and fit
beam-smeared model CO line profiles directly to the ALMA data cube. Our models
incorporate both flat disks and tilted-ring disks that provide a better fit of
the mildly warped structure in NGC 3258. We show that the exceptional angular
resolution of the ALMA data makes it possible to infer the host galaxy's mass
profile within pc solely from the ALMA CO kinematics, without relying
on optical or near-infrared imaging data to determine the stellar mass profile.
Our model therefore circumvents any uncertainty in the black hole mass that
would result from the substantial dust extinction in the galaxy's central
region. The best model fit yields
with a statistical model-fitting uncertainty of just 0.18\%, and systematic
uncertainties of 0.62\% from various aspects of the model construction and 12\%
from uncertainty in the distance to NGC 3258. This observation demonstrates the
full potential of ALMA for carrying out highly precise measurements of
in early-type galaxies containing circumnuclear gas disksComment: Accepted for publication in ApJ. 32 pages, 22 figure
Targeted disruption of cubilin reveals essential developmental roles in the structure and function of endoderm and in somite formation
BACKGROUND: Cubilin is a peripheral membrane protein that interacts with the integral membrane proteins megalin and amnionless to mediate ligand endocytosis by absorptive epithelia such as the extraembryonic visceral endoderm (VE). RESULTS: Here we report the effects of the genetic deletion of cubilin on mouse embryonic development. Cubilin gene deletion is homozygous embryonic lethal with death occurring between 7.5–13.5 days post coitum (dpc). Cubilin-deficient embryos display developmental retardation and do not advance morphologically beyond the gross appearance of wild-type 8–8.5 dpc embryos. While mesodermal structures such as the allantois and the heart are formed in cubilin mutants, other mesoderm-derived tissues are anomalous or absent. Yolk sac blood islands are formed in cubilin mutants but are unusually large, and the yolk sac blood vessels fail to undergo remodeling. Furthermore, somite formation does not occur in cubilin mutants. Morphological abnormalities of endoderm occur in cubilin mutants and include a stratified epithelium in place of the normally simple columnar VE epithelium and a stratified cuboidal epithelium in place of the normally simple squamous epithelium of the definitive endoderm. Cubilin-deficient VE is also functionally defective, unable to mediate uptake of maternally derived high-density lipoprotein (HDL). CONCLUSION: In summary, cubilin is required for embryonic development and is essential for the formation of somites, definitive endoderm and VE and for the absorptive function of VE including the process of maternal-embryo transport of HDL
The acute transcriptome response of the midbrain/diencephalon to injury in the adult mummichog (\u3cem\u3eFundulus heteroclitus\u3c/em\u3e)
Adult fish produce new cells throughout their central nervous system during the course of their lives and maintain a tremendous capacity to repair damaged neural tissue. Much of the focus on understanding brain repair and regeneration in adult fish has been directed at regions of the brainstem and forebrain; however, the mesencephalon (midbrain) and diencephalon have received little attention. We sought to examine differential gene expression in the midbrain/diencephalon in response to injury in the adult fish using RNA-seq. Using the mummichog (Fundulus heteroclitus), we administered a mechanical lesion to the midbrain/diencephalon and examined differentially expressed genes (DEGs) at an acute recovery time of 1 h post-injury. Comparisons of whole transcriptomes derived from isolated RNA of intact and injured midbrain/diencephalic tissue identified 404 DEGs with the vast majority being upregulated. Using qPCR, we validated the upregulation of DEGs pim-2-like, syndecan-4-like, and cd83. Based on genes both familiar and novel regarding the adult brain response to injury, these data provide an extensive molecular profile giving insight into a range of cellular processes involved in the injury response of a brain regenerative-capable vertebrate
The acute transcriptome response of the midbrain/diencephalon to injury in the adult mummichog (\u3cem\u3eFundulus heteroclitus\u3c/em\u3e)
Adult fish produce new cells throughout their central nervous system during the course of their lives and maintain a tremendous capacity to repair damaged neural tissue. Much of the focus on understanding brain repair and regeneration in adult fish has been directed at regions of the brainstem and forebrain; however, the mesencephalon (midbrain) and diencephalon have received little attention. We sought to examine differential gene expression in the midbrain/diencephalon in response to injury in the adult fish using RNA-seq. Using the mummichog (Fundulus heteroclitus), we administered a mechanical lesion to the midbrain/diencephalon and examined differentially expressed genes (DEGs) at an acute recovery time of 1 h post-injury. Comparisons of whole transcriptomes derived from isolated RNA of intact and injured midbrain/diencephalic tissue identified 404 DEGs with the vast majority being upregulated. Using qPCR, we validated the upregulation of DEGs pim-2-like, syndecan-4-like, and cd83. Based on genes both familiar and novel regarding the adult brain response to injury, these data provide an extensive molecular profile giving insight into a range of cellular processes involved in the injury response of a brain regenerative-capable vertebrate
S1P, dihydro-S1P and C24:1-ceramide levels in the HDL-containing fraction of serum inversely correlate with occurrence of ischemic heart disease
BACKGROUND: The lysosphingolipid sphingosine 1-phosphate (S1P) is carried in the blood in association with lipoproteins, predominantly high density lipoproteins (HDL). Emerging evidence suggests that many of the effects of HDL on cardiovascular function may be attributable to its S1P cargo. METHODS: Here we have evaluated how levels of S1P and related sphingolipids in an HDL-containing fraction of human serum correlate with occurrence of ischemic heart disease (IHD). To accomplish this we used liquid chromatography-mass spectrometry to measure S1P levels in the HDL-containing fraction of serum (depleted of LDL and VLDL) from 204 subjects in the Copenhagen City Heart Study (CCHS). The study group consisted of individuals having high serum HDL cholesterol (HDL-C) (females:≥73.5 mg/dL; males:≥61.9 mg/dL) and verified IHD; subjects with high HDL-C and no IHD; individuals with low HDL-C (females:≤38.7 mg/dL; males:≤34.1 mg/dL) and IHD, and subjects with low HDL-C and no IHD. RESULTS: The results show a highly significant inverse relationship between the level of S1P in the HDL-containing fraction of serum and the occurrence of IHD. Furthermore, an inverse relationship with IHD was also observed for two other sphingolipids, dihydro-S1P and C24:1-ceramide, in the HDL-containing fraction of serum. Additionally, we demonstrated that the amount of S1P on HDL correlates with the magnitude of HDL-induced endothelial cell barrier signaling. CONCLUSIONS: These findings indicate that compositional differences of sphingolipids in the HDL-containing fraction of human serum are related to the occurrence of IHD, and may contribute to the putative protective role of HDL in IHD
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