microRNA Expression during Trophectoderm Specification

Segregation of the trophectoderm from the inner cell mass of the embryo represents the first cell-fate decision of mammalian development. Transcription factors essential for specifying trophectoderm have been identified, but the role of microRNAs (miRNAs) in modulating this fate-choice has been largely unexplored. We have compared miRNA expression in embryonic stem cell (ESC)-derived trophectoderm and in staged murine embryos to identify a set of candidate miRNAs likely to be involved in trophectoderm specification.We profiled embryonic stem cells (ESCs) as they were induced to differentiate into trophectodermal cells by ectopic expression of HRas/Q61L. We also profiled murine embryos at progressive stages of preimplantation development (zygote, 2-cell, 4-cell, 8-cell, morula, and blastocyst), which includes the time window in which the trophectoderm is specified in vivo Q61L/H.We describe miRNA expression changes that occur during trophectoderm specification and validate that our in vitro system faithfully recapitulates trophectoderm specification in vivo. By comparing our in vitro and in vivo datasets, we have identified a minimal set of candidate miRNAs likely to play a role in trophectoderm specification. These miRNAs are predicted to regulate a host of development-associated target genes, and many of these miRNAs have previously reported roles in development and differentiation. Additionally, we highlight a number of miRNAs whose tight developmental regulation may reflect a functional role in other stages of embryogenesis. Our embryo profiling data may be useful to investigators studying trophectoderm specification and other stages of preimplantation development

Quark Distributions of Octet Baryons from SU(3) Symmetry

SU(3) symmetry relations between the octet baryons are introduced in order to connect both the unpolarized and polarized quark distributions of the octet baryons with those of the nucleon. Two different parametrizations of the nucleon quark distributions are used. A new scenario of quark flavor and spin structure of the $\Lambda$ is found and compared with two other models: a perturbative QCD based analysis and a quark diquark model. The $u$ and $d$ quarks inside the $\Lambda$ are predicted to be positively polarized at large Bjorken variable $x$ in the new scenario. By using an approximate relation connecting the quark fragmentation functions with the quark distributions, the hadron polarizations of the octet baryons in $e^+e^-$-annihilation, polarized charged lepton deep inelastic scattering (DIS) processes, and neutrino (antineutrino) DIS processes are predicted. The predictions for $\Lambda$ polarizations in several processes are compatible with the available data at large fragmentation momentum fraction $z$, and support the prediction of positively polarized $u$ and $d$ quarks inside the $\Lambda$ at large $x$. Predictions for Drell-Yan processes from $\Sigma^{\pm}$ and $\Xi^-$ beams on an isoscalar target are also given and discussed.Comment: 29 latex pages, 16 figures, to appear in PR

Poly A- Transcripts Expressed in HeLa Cells

BACKGROUND: Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts. CONCLUSION/SIGNIFICANCE: Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts

Realistic optical cell modeling and diffraction imaging simulation for study of optical and morphological parameters of nucleus

Coherent light scattering presents complex spatial patterns that depend on morphological and molecular features of biological cells. We present a numerical approach to establish realistic optical cell models for generating virtual cells and accurate simulation of diffraction images that are comparable to measured data of prostate cells. With a contourlet transform algorithm, it has been shown that the simulated images and extracted parameters can be used to distinguish virtual cells of different nuclear volumes and refractive indices against the orientation variation. These results demonstrate significance of the new approach for development of rapid cell assay methods through diffraction imaging.ECU Open Access Publishing Support Fun

Label-free classification of cultured cells through diffraction imaging

Automated classification of biological cells according to their 3D morphology is highly desired in a flow cytometer setting. We have investigated this possibility experimentally and numerically using a diffraction imaging approach. A fast image analysis software based on the gray level co-occurrence matrix (GLCM) algorithm has been developed to extract feature parameters from measured diffraction images. The results of GLCM analysis and subsequent classification demonstrate the potential for rapid classification among six types of cultured cells. Combined with numerical results we show that the method of diffraction imaging flow cytometry has the capacity as a platform for high-throughput and label-free classification of biological cells

Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06)

The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21–22, 2006. Twenty-six peer-reviewed papers were selected for publication in this special issue of BMC Bioinformatics. These papers cover a broad range of topics including bioinformatics theories, algorithms, applications and tool development. The main technical topics contain gene expression analysis, sequence analysis, genome analysis, phylogenetic analysis, gene function prediction, molecular interaction and system biology, genetics and population study, immune strategy, protein structure prediction and proteomics

Quark Structure of Λ\Lambda from Λ\Lambda-Polarization in Z Decays

The flavor and spin structure for the quark distributions of the $\Lambda$-baryon is studied in a perturbative QCD (pQCD) analysis and in the SU(6) quark-diquark model, and then applied to calculate the $\Lambda$-polarization of semi-inclusive $\Lambda$ production in $e^+e^-$-annihilation near the $Z$-pole. It is found that the quark-diquark model gives very good description of the available experimental data. The pQCD model can also give good description of the data by taking into account the suppression of quark helicities compared to the naive SU(6) quark model spin distributions. Further information is required for a clean distinction between different predictions concerning the flavor and spin structure of the $\Lambda$.Comment: 25 latex pages, eight eps figures, small changes in references and discussions, final version to be published in PRD 61(2000