3,517 research outputs found
Noncoding DNA, isochores and gene expression: nucleosome formation potential
The nucleosome formation potential of introns, intergenic spacers and exons of human genes is shown here to negatively correlate with among-tissues breadth of gene expression. The nucleosome formation potential is also found to negatively correlate with the GC content of genomic sequences; the slope of regression line is steeper in exons compared with noncoding DNA (introns and intergenic spacers). The correlation with GC content is independent of sequence length; in turn, the nucleosome formation potential of introns and intergenic spacers positively (albeit weakly) correlates with sequence length independently of GC content. These findings help explain the functional significance of the isochores (regions differing in GC content) in the human genome as a result of optimization of genomic structure for epigenetic complexity and support the notion that noncoding DNA is important for orderly chromatin condensation and chromatin-mediated suppression of tissue-specific genes
Organismal complexity, cell differentiation and gene expression: human over mouse
We present a molecular and cellular phenomenon underlying the intriguing increase in phenotypic organizational complexity. For the same set of human–mouse orthologous genes (11 534 gene pairs) and homologous tissues (32 tissue pairs), human shows a greater fraction of tissue-specific genes and a greater ratio of the total expression of tissue-specific genes to housekeeping genes in each studied tissue, which suggests a generally higher level of evolutionary cell differentiation (specialization). This phenomenon is spectacularly more pronounced in those human tissues that are more directly involved in the increase of complexity, longevity and body size (i.e. it is reflected on the organismal level as well). Genes with a change in expression breadth show a greater human–mouse divergence of promoter regions and encoded proteins (i.e. the functional genomics data are supported by the structural analysis). Human also shows the higher expression of translation machinery. The upstream untranslated regions (5′UTRs) of human mRNAs are longer than mouse 5′UTRs (even after correction for the difference in genome sizes) and contain more uAUG codons, which suggest a more complex regulation at the translational level in human cells (and agrees well with the augmented cell specialization)
Nanostructured optical waveguide with a highly confined mode
We propose a transmission line working at telecom wavelengths with cross
section as small as , which is 1.6 times smaller than that of
optimized silicon waveguide. The proposed line can be implemented as a
subwavelength fiber with plasmonic cladding. This considerable decrease in the
line cross section is achieved by utilizing a plasmonic quasi-antisymmetric
mode. The required plasmonic cladding is rather thin, therefore, losses are
moderate and could be compensated by using amplifying core materials. Such a
transmission line can find applications in densely integrated optical systems
‘Genome design’ model and multicellular complexity: golden middle
Human tissue-specific genes were reported to be longer than housekeeping genes (both in coding and intronic parts). The competing neutralist and adaptationist models were proposed to explain this observation. Here I show that in human genome the longest are genes with the intermediate expression pattern. From the standpoint of information theory, the regulation of such genes should be most complex. In the genomewide context, they are found here to have the higher informational load on all available levels: from participation in protein interaction networks, pathways and modules reflected in Gene Ontology categories through transcription factor regulatory sets and protein functional domains to amino acid tuples (words) in encoded proteins and nucleotide tuples in introns and promoter regions. Thus, the intermediately expressed genes have the higher functional and regulatory complexity that is reflected in their greater length (which is consistent with the ‘genome design’ model). The dichotomy of housekeeping versus tissue-specific entities is more pronounced on the modular level than on the molecular level. There are much lesser intermediate-specific modules (modules overrepresented in the intermediately expressed genes) than housekeeping or tissue-specific modules (normalized to gene number). The dichotomy of housekeeping versus tissue-specific genes and modules in multicellular organisms is probably caused by the burden of regulatory complexity acted on the intermediately expressed genes
Isolation and Characterization of Human Colon Adenocarcinoma Stem-Like Cells Based on the Endogenous Expression of the Stem Markers.
BACKGROUND: Cancer stem cells\u27 (CSCs) self-maintenance is regulated via the pluripotency pathways promoting the most aggressive tumor phenotype. This study aimed to use the activity of these pathways for the CSCs\u27 subpopulation enrichment and separating cells characterized by the OCT4 and SOX2 expression.
METHODS: To select and analyze CSCs, we used the SORE6x lentiviral reporter plasmid for viral transduction of colon adenocarcinoma cells. Additionally, we assessed cell chemoresistance, clonogenic, invasive and migratory activity and the data of mRNA-seq and intrinsic disorder predisposition protein analysis (IDPPA).
RESULTS: We obtained the line of CSC-like cells selected on the basis of the expression of the OCT4 and SOX2 stem cell factors. The enriched CSC-like subpopulation had increased chemoresistance as well as clonogenic and migration activities. The bioinformatic analysis of mRNA seq data identified the up-regulation of pluripotency, development, drug resistance and phototransduction pathways, and the downregulation of pathways related to proliferation, cell cycle, aging, and differentiation. IDPPA indicated that CSC-like cells are predisposed to increased intrinsic protein disorder.
CONCLUSION: The use of the SORE6x reporter construct for CSCs enrichment allows us to obtain CSC-like population that can be used as a model to search for the new prognostic factors and potential therapeutic targets for colon cancer treatment
Deuteron and antideuteron production in Au+Au collisions at sqrt(s_NN)=200 GeV
The production of deuterons and antideuterons in the transverse momentum
range 1.1 < p_T < 4.3 GeV/c at mid-rapidity in Au + Au collisions at
sqrt(s_NN)=200 GeV has been studied by the PHENIX experiment at RHIC. A
coalescence analysis comparing the deuteron and antideuteron spectra with those
of protons and antiprotons, has been performed. The coalescence probability is
equal for both deuterons and antideuterons and increases as a function of p_T,
which is consistent with an expanding collision zone. Comparing (anti)proton
yields p_bar/p = 0.73 +/- 0.01, with (anti)deuteron yields: d_bar/d = 0.47 +/-
0.03, we estimate that n_bar/n = 0.64 +/- 0.04.Comment: 326 authors, 6 pages text, 5 figures, 1 Table. Submitted to PRL.
Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Mid-Rapidity Direct-Photon Production in p+p Collisions at sqrt(s) = 200 GeV
A measurement of direct photons in p+p collisions at sqrt(s)=200 GeV is
presented. A photon excess above background from pi^0 --> gamma+gamma, eta -->
gamma+gamma, and other decays is observed in the transverse momentum range 5.5
< p_T < 7 GeV/c. The result is compared to a next-to-leading-order perturbative
QCD calculation. Within errors, good agreement is found between the QCD
calculation and the measured result.Comment: 330 authors, 7 pages text, RevTeX, 2 figures, 2 tables. Submitted to
Physical Review D. Plain text data tables for the points plotted in figures
for this and previous PHENIX publications are (or will be) publicly available
at http://www.phenix.bnl.gov/papers.htm
Observation of direct-photon collective flow in sqrt(s_NN)=200 GeV Au+Au collisions
The second Fourier component v_2 of the azimuthal anisotropy with respect to
the reaction plane was measured for direct photons at midrapidity and
transverse momentum (p_T) of 1--13 GeV/c in Au+Au collisions at sqr(s_NN)=200
GeV. Previous measurements of this quantity for hadrons with p_T < 6 GeV/c
indicate that the medium behaves like a nearly perfect fluid, while for p_T > 6
GeV/c a reduced anisotropy is interpreted in terms of a path-length dependence
for parton energy loss. In this measurement with the PHENIX detector at the
Relativistic Heavy Ion Collider we find that for p_T > 4 GeV/c the anisotropy
for direct photons is consistent with zero, as expected if the dominant source
of direct photons is initial hard scattering. However, in the p_T < 4 GeV/c
region dominated by thermal photons, we find a substantial direct photon v_2
comparable to that of hadrons, whereas model calculations for thermal photons
in this kinematic region significantly underpredict the observed v_2.Comment: 384 authors, 6 pages, 3 figures, and 1 table. Submitted to Phys. Rev.
Lett. v2 has minor changes to match the submission version. Plain text data
tables for the points plotted in the figures are publicly available at
http://www.phenix.bnl.gov/phenix/WWW/info/data/ppg126_data.htm
Azimuthal anisotropy of pi^0 and eta mesons in Au+Au collisions at sqrt(s_NN)=200 GeV
The azimuthal anisotropy coefficients v_2 and v_4 of pi^0 and eta mesons are
measured in Au+Au collisions at sqrt(s_NN)=200 GeV, as a function of transverse
momentum p_T (1-14 GeV/c) and centrality. The extracted v_2 coefficients are
found to be consistent between the two meson species over the measured p_T
range. The ratio of v_4/v_2^2 for pi^0 mesons is found to be independent of p_T
for 1-9 GeV/c, implying a lack of sensitivity of the ratio to the change of
underlying physics with p_T. Furthermore, the ratio of v_4/v_2^2 is
systematically larger in central collisions, which may reflect the combined
effects of fluctuations in the initial collision geometry and finite viscosity
in the evolving medium.Comment: 384 authors, 71 institutions, 11 pages, 9 figures, and 2 tables.
Submitted to Physical Review C. Plain text data tables for the points plotted
in figures for this and previous PHENIX publications are (or will be)
publicly available at http://www.phenix.bnl.gov/papers.htm
Suppressed pi^0 Production at Large Transverse Momentum in Central Au+Au Collisions at sqrt(s_NN) = 200 GeV
Transverse momentum spectra of neutral pions in the range 1 < p_T < 10 GeV/c
have been measured at mid-rapidity by the PHENIX experiment at RHIC in Au+Au
collisions at sqrt(s_NN) = 200 GeV. The pi^0 multiplicity in central reactions
is significantly below the yields measured at the same sqrt(s_NN) in peripheral
Au+Au and p+p reactions scaled by the number of nucleon-nucleon collisions. For
the most central bin, the suppression factor is ~2.5 at p_T = 2 GeV/c and
increases to ~4-5 at p_T ~= 4 GeV/c. At larger p_T, the suppression remains
constant within errors. The deficit is already apparent in semi-peripheral
reactions and increases smoothly with centrality.Comment: 326 authors, 6 pages text, RevTeX, 3 figures, 2 tables. Submitted to
PRL. Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
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