431 research outputs found
Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies
Background
The most important challenge of performing insitu transcriptional profiling of the human ocular surface epithelial regions is obtaining samples in sufficient amounts, without contamination from adjacent tissue, as the region of interest is microscopic and closely apposed to other tissues regions. We have effectively collected ocular surface (OS) epithelial tissue samples from the Limbal Epithelial Crypt (LEC), limbus, cornea and conjunctiva of post-mortem cadaver eyes with laser microdissection (LMD) technique for gene expression studies with spotted oligonucleotide microarrays and Gene 1.0 ST arrays.
Methods
Human donor eyes (4 pairs for spotted oligonucleotide microarrays, 3 pairs for Gene 1.0 ST arrays) consented for research were included in this study with due ethical approval of the Nottingham Research Ethics Committee. Eye retrieval was performed within 36 hours of post-mortem period. The dissected corneoscleral buttons were immersed in OCT media and frozen in liquid nitrogen and stored at −80°C till further use. Microscopic tissue sections of interest were taken on PALM slides and stained with Toluidine Blue for laser microdissection with PALM microbeam systems. Optimisation of the laser microdissection technique was crucial for efficient and cost effective sample collection.
Results
The starting concentration of RNA as stipulated by the protocol of microarray platforms was taken as the cut-off concentration of RNA samples in our studies. The area of LMD tissue processed for spotted oligonucleotide microarray study ranged from 86,253 μm2 in LEC to 392,887 μm2 in LEC stroma. The RNA concentration of the LMD samples ranged from 22 to 92 pg/μl. The recommended starting concentration of the RNA samples used for Gene 1.0 ST arrays was 6 ng/5 μl. To achieve the desired RNA concentration the area of ocular surface epithelial tissue sample processed for the Gene 1.0 ST array experiments was approximately 100,0000 μm2 to 130,0000 μm2. RNA concentration of these samples ranged from 10.88 ng/12 μl to 25.8 ng/12 μl, with the RNA integrity numbers (RIN) for these samples from 3.3 to 7.9. RNA samples with RIN values below 2, that had failed to amplify satisfactorily were discarded.
Conclusions
The optimised protocol for sample collection and laser microdissection improved the RNA yield of the insitu ocular surface epithelial regions for effective microarray studies on spotted oligonucleotide and affymetrix platforms
Centrality and transverse momentum dependence of elliptic flow of multi-strange hadrons and meson in Au+Au collisions at = 200 GeV
We present high precision measurements of elliptic flow near midrapidity
() for multi-strange hadrons and meson as a function of
centrality and transverse momentum in Au+Au collisions at center of mass energy
200 GeV. We observe that the transverse momentum dependence of
and is similar to that of and , respectively,
which may indicate that the heavier strange quark flows as strongly as the
lighter up and down quarks. This observation constitutes a clear piece of
evidence for the development of partonic collectivity in heavy-ion collisions
at the top RHIC energy. Number of constituent quark scaling is found to hold
within statistical uncertainty for both 0-30 and 30-80 collision
centrality. There is an indication of the breakdown of previously observed mass
ordering between and proton at low transverse momentum in the
0-30 centrality range, possibly indicating late hadronic interactions
affecting the proton .Comment: 7 pages and 4 figures, Accepted for publication in Physical Review
Letter
Azimuthal anisotropy in U+U and Au+Au collisions at RHIC
Collisions between prolate uranium nuclei are used to study how particle
production and azimuthal anisotropies depend on initial geometry in heavy-ion
collisions. We report the two- and four-particle cumulants, and
, for charged hadrons from U+U collisions at =
193 GeV and Au+Au collisions at = 200 GeV. Nearly fully
overlapping collisions are selected based on the amount of energy deposited by
spectators in the STAR Zero Degree Calorimeters (ZDCs). Within this sample, the
observed dependence of on multiplicity demonstrates that ZDC
information combined with multiplicity can preferentially select different
overlap configurations in U+U collisions. An initial-state model with gluon
saturation describes the slope of as a function of multiplicity in
central collisions better than one based on Glauber with a two-component
multiplicity model.Comment: Final paper version accepted for publication in Phys. Rev. Lett. New
version includes comparisons to a constituent quark glauber mode
Isolation of Flow and Nonflow Correlations by Two- and Four-Particle Cumulant Measurements of Azimuthal Harmonics in 200 GeV Au+Au Collisions
A data-driven method was applied to measurements of Au+Au collisions at
200 GeV made with the STAR detector at RHIC to isolate
pseudorapidity distance -dependent and -independent
correlations by using two- and four-particle azimuthal cumulant measurements.
We identified a component of the correlation that is -independent,
which is likely dominated by anisotropic flow and flow fluctuations. It was
also found to be independent of within the measured range of
pseudorapidity . The relative flow fluctuation was found to be for particles of transverse momentum
less than GeV/. The -dependent part may be attributed to
nonflow correlations, and is found to be relative to the
flow of the measured second harmonic cumulant at
Observation of charge asymmetry dependence of pion elliptic flow and the possible chiral magnetic wave in heavy-ion collisions
We present measurements of and elliptic flow, , at
midrapidity in Au+Au collisions at 200, 62.4, 39, 27,
19.6, 11.5 and 7.7 GeV, as a function of event-by-event charge asymmetry,
, based on data from the STAR experiment at RHIC. We find that
() elliptic flow linearly increases (decreases) with charge asymmetry
for most centrality bins at and higher.
At , the slope of the difference of
between and as a function of exhibits a
centrality dependence, which is qualitatively similar to calculations that
incorporate a chiral magnetic wave effect. Similar centrality dependence is
also observed at lower energies.Comment: 6 pages, 4 figure
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