The Escherichia coli O157:H7 cattle immunoproteome includes outer membrane protein A (OmpA), a modulator of adherence to bovine rectoanal junction squamous epithelial (RSE) cells.

Building on previous studies, we defined the repertoire of proteins comprising the immunoproteome (IP) of Escherichia coli O157:H7 (O157) cultured in DMEM supplemented with norepinephrine (O157 IP), a β-adrenergic hormone that regulates E. coli O157 gene expression in the gastrointestinal tract, using a variation of a novel proteomics-based platform proteome mining tool for antigen discovery, called "proteomics-based expression library screening" (PELS; Kudva et al., 2006).

Integrative genome analysis reveals an oncomir/oncogene cluster regulating glioblastoma survivorship.

Using a multidimensional genomic data set on glioblastoma from The Cancer Genome Atlas, we identified hsa-miR-26a as a cooperating component of a frequently occurring amplicon that also contains CDK4 and CENTG1, two oncogenes that regulate the RB1 and PI3 kinase/AKT pathways, respectively. By integrating DNA copy number, mRNA, microRNA, and DNA methylation data, we identified functionally relevant targets of miR-26a in glioblastoma, including PTEN, RB1, and MAP3K2/MEKK2. We demonstrate that miR-26a alone can transform cells and it promotes glioblastoma cell growth in vitro and in the mouse brain by decreasing PTEN, RB1, and MAP3K2/MEKK2 protein expression, thereby increasing AKT activation, promoting proliferation, and decreasing c-JUN N-terminal kinase-dependent apoptosis.

Cytogenetic and array-CGH characterization of a complex de novo rearrangement involving duplication and deletion of 9p and clinical findings in a 4-month-old female.

Approximately 15 patients with partial trisomy 9p involving de novo duplications have been previously described. Here, we present clinical, cytogenetic, FISH and aCGH findings in a patient with a de novo complex rearrangement in the short arm of chromosome 9 involving an inverted duplication at 9p24-->p21.3 and a deletion at 9pter-->p24.

Integrative predictive model of coronary artery calcification in atherosclerosis.

Background: Many different genetic and clinical factors have been identified as causes or contributors to atherosclerosis. We present a model of preclinical atherosclerosis based on genetic and clinical data that predicts the presence of coronary artery calcification in healthy Americans of European descent 45 to 84 years of age in the Multi-Ethnic Study of Atherosclerosis (MESA).

Methods And Results: We assessed 712 individuals for the presence or absence of coronary artery calcification and assessed their genotypes for 2882 single-nucleotide polymorphisms.

Characterization of human skeletal muscle biopsy samples using shotgun proteomics.

We characterized the human muscle proteome by studying muscle biopsy specimens through four different workflows, using 1 or 2D peptide separation, SDS gels, or differential solubilization. By performing MS/MS analyses of 178 4-h LC separations derived from 31 patients, we identified more than 2000 proteins, and determined how 370 very abundant proteins behave upon differential solubilization. The resulting semiquantitative database should serve as a resource for muscle biochemistry.

Fast-twitch sarcomeric and glycolytic enzyme protein loss in inclusion body myositis.

Inclusion body myositis (IBM) is an inflammatory disease of skeletal muscle of unknown cause. To further understand the nature of the tissue injury in this disease, we developed methods for large-scale detection and quantitation of proteins in muscle biopsy samples and analyzed proteomic data produced by these methods together with histochemical, immunohistochemical, and microarray data. Twenty muscle biopsy samples from patients with inflammatory myopathies (n = 17) or elderly subjects without neuromuscular disease (n = 3) were profiled by proteomic studies using liquid chromatographic separation of peptides followed by mass spectrometry.

Genetic mechanisms in Apc-mediated mammary tumorigenesis.

Many components of Wnt/beta-catenin signaling pathway also play critical roles in mammary tumor development, yet the role of the tumor suppressor gene APC (adenomatous polyposis coli) in breast oncongenesis is unclear. To better understand the role of Apc in mammary tumorigenesis, we introduced conditional Apc mutations specifically into two different mammary epithelial populations using K14-cre and WAP-cre transgenic mice that express Cre-recombinase in mammary progenitor cells and lactating luminal cells, respectively. Only the K14-cre-mediated Apc heterozygosity developed mammary adenocarcinomas demonstrating histological heterogeneity, suggesting the multilineage progenitor cell origin of these tumors.

Epigenetics meets next-generation sequencing.

Next-generation sequencing is poised to unleash dramatic changes in every area of molecular biology. In the past few years, chromatin immunoprecipitation (ChIP) on tiled microarrays (ChIP-chip) has been an important tool for genome-wide mapping of DNA-binding proteins or histone modifications. Now, ChIP followed by direct sequencing of DNA fragments (ChIP-seq) offers superior data with less noise and higher resolution and is likely to replace ChIP-chip in the near future.

Predictive genomics of cardioembolic stroke.

Cardioembolic stroke is a complex disease resulting from the interaction of numerous factors. Using data from Genes Affecting Stroke Risk and Outcome Study (GASROS), we show that a multivariate predictive model built using Bayesian networks is able to achieve a predictive accuracy of 86% on the fitted values as computed by the area under the receiver operating characteristic curve relative to that of the individual single nucleotide polymorphism with the highest prognostic performance (area under the receiver operating characteristic curve=60%).

Experimental design and data analysis for array comparative genomic hybridization.

Array comparative genomic hybridization (aCGH) is a technique for measuring chromosomal aberrations in genomic DNA. With the availability of high-resolution microarrays, detailed characterization of the cancer genome has become possible. In this review, we discuss several issues in the generation and interpretation of aCGH data, including array platforms, experimental design, and data analysis.

The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome.

The male-specific lethal (MSL) complex upregulates the single male X chromosome to achieve dosage compensation in Drosophila melanogaster. We have proposed that MSL recognition of specific entry sites on the X is followed by local targeting of active genes marked by histone H3 trimethylation (H3K36me3). Here we analyze the role of the MSL3 chromodomain in the second targeting step.

The autistic neuron: troubled translation?

Autism is a complex genetic disorder, but single-gene disorders with a high prevalence of autism offer insight into its pathogenesis. Recent evidence suggests that some molecular defects in autism may interfere with the mechanisms of synaptic protein synthesis. We propose that aberrant synaptic protein synthesis may represent one possible pathway leading to autistic phenotypes, including cognitive impairment and savant abilities.

Loss of Rb1 in the gastrointestinal tract of Apc1638N mice promotes tumors of the cecum and proximal colon.

To examine the role of Rb1 in gastrointestinal (GI) tumors, we generated mice with an Apc(1638N) allele, Rb(tm2brn) floxed alleles, and a villin-cre transgene (RBVCA). These animals had exon 19 deleted from Rb1 throughout the GI tract. We have shown previously that Rb1 deficiency is insufficient for GI tumor initiation, with inactivation of an Apc allele capable of overcoming the insufficiency.

A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome.

The Drosophila MSL complex associates with active genes specifically on the male X chromosome to acetylate histone H4 at lysine 16 and increase expression approximately 2-fold. To date, no DNA sequence has been discovered to explain the specificity of MSL binding. We hypothesized that sequence-specific targeting occurs at "chromatin entry sites," but the majority of sites are sequence independent.

Nucleosome positioning in human HOX gene clusters.

The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes. Toward this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines.

nuScore: a web-interface for nucleosome positioning predictions.

Unlabelled: Sequence-directed mapping of nucleosome positions is of major biological interest. Here, we present a web-interface for estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence. Our approach is based on assessment of the energy cost of imposing the deformations required to wrap DNA around the histone surface.

SCFbeta-TRCP controls oncogenic transformation and neural differentiation through REST degradation.

The RE1-silencing transcription factor (REST, also known as NRSF) is a master repressor of neuronal gene expression and neuronal programmes in non-neuronal lineages. Recently, REST was identified as a human tumour suppressor in epithelial tissues, suggesting that its regulation may have important physiological and pathological consequences. However, the pathways controlling REST have yet to be elucidated.

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms.

Unlabelled: Accurate estimation of DNA copy numbers from array comparative genomic hybridization (CGH) data is important for characterizing the cancer genome. An important part of this process is the segmentation of the log-ratios between the sample and control DNA along the chromosome into regions of different copy numbers. However, multiple algorithms are available in the literature for this procedure and the results can vary substantially among these.

Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes.

Motivation: DNA copy number aberrations (CNAs) and gene expression (GE) changes provide valuable information for studying chromosomal instability and its consequences in cancer. While it is clear that the structural aberrations and the transcript levels are intertwined, their relationship is more complex and subtle than initially suspected. Most studies so far have focused on how a CNA affects the expression levels of those genes contained within that CNA.

Analysis of TBX1 variation in patients with psychotic and affective disorders.

A significant portion of patients with 22q11 deletion syndrome (22q11DS) develop psychiatric disorders, including schizophrenia and other psychotic and affective symptoms, and the responsible gene/s are assumed to also play a significant role in the etiology of nonsyndromic psychiatric disease. The most common psychiatric diagnosis among patients with 22q11DS is schizophrenia, thought to result from neurotransmitter imbalances and also from disturbed brain development. Several genes in the 22q11 region with known or suspected roles in neurotransmitter metabolism have been analyzed in patients with isolated schizophrenia; however, their contribution to the disease remains controversial.

Regional control of chromatin organization by noncoding roX RNAs and the NURF remodeling complex in Drosophila melanogaster.

Dosage compensation in Drosophila is mediated by a histone-modifying complex that upregulates transcription of genes on the single male X chromosome. The male-specific lethal (MSL) complex contains at least five proteins and two noncoding roX (RNA on X) RNAs. The mechanism by which the MSL complex targets the X chromosome is not understood.

Tumor progression in Apc(1638N) mice with Exo1 and Fen1 deficiencies.

Flap endonuclease 1 (Fen1) and exonuclease 1 (Exo1) have sequence homology and similar nuclease capabilities. Both function in multiple pathways of DNA metabolism, but appear to have distinct in vivo nucleic acid substrates, and therefore distinct metabolic roles. When combined with Apc(1638N), Fen1 promotes tumor progression.

Anaphase initiation is regulated by antagonistic ubiquitination and deubiquitination activities.

The spindle checkpoint prevents chromosome mis-segregation by delaying sister chromatid separation until all chromosomes have achieved bipolar attachment to the mitotic spindle. Its operation is essential for accurate chromosome segregation, whereas its dysregulation can contribute to birth defects and tumorigenesis. The target of the spindle checkpoint is the anaphase-promoting complex (APC), a ubiquitin ligase that promotes sister chromatid separation and progression to anaphase.

MSL complex associates with clusters of actively transcribed genes along the Drosophila male X chromosome.

Dosage compensation in Drosophila serves as a model system for understanding the targeting of chromatin-modifying complexes to their sites of action. The MSL (male-specific lethal) complex up-regulates transcription of the single male X chromosome, thereby equalizing levels of transcription of X-linked genes between the sexes. Recruitment of the MSL complex to its binding sites on the male X chromosome requires each of the MSL proteins and at least one of the two large noncoding roX RNAs.

Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC.

We describe a new cloning method, sequence and ligation-independent cloning (SLIC), which allows the assembly of multiple DNA fragments in a single reaction using in vitro homologous recombination and single-strand annealing. SLIC mimics in vivo homologous recombination by relying on exonuclease-generated ssDNA overhangs in insert and vector fragments, and the assembly of these fragments by recombination in vitro. SLIC inserts can also be prepared by incomplete PCR (iPCR) or mixed PCR.