On estimating the directionality distribution in pedicle trabecular bone from micro-CT images.

Our interest in the trabecular alignment within bone stems from the need to better understand the manner in which it can affect ultrasound propagation, particularly in pedicles. Within long bones it is well established that trabecular structures are aligned in an organized manner associated with the direction of load distribution; however, for smaller bones there are limited alignment studies. To investigate the directionality distribution in a quantitative manner we used a micro-CT to obtain three-dimensional (3D) structural data and developed analytical methods based on the special properties of Gabor filters.

Mechanistic models for muscle diseases and disorders originating in the sarcoplasmic reticulum.

This review focuses on muscle disorders and diseases caused by defects in the Ca(2+) release channels of the sarcoplasmic reticulum, the ryanodine receptors, and in the luminal, low affinity, high capacity Ca(2+)-binding proteins, calsequestrins. It provides a time line over the past half century of the highlights of research on malignant hyperthermia (MH), central core disease (CCD) and catecholaminergic polymorphic ventricular tachycardia (CPVT), that resulted in the identification of the ryanodine receptor (RYR), calsequestrin (CASQ) and dihydropyridine receptor (CACNA1S) genes as sites of disease-causing mutations. This is followed by a description of approaches to functional analysis of the effects of disease-causing mutations on protein function, focusing on studies of how mutations affect spontaneous (store overload-induced) Ca(2+)-release from the sarcoplasmic reticulum, the underlying cause of MH and CPVT.

Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells.

The contribution of steroidogenic factor 1 (SF-1) to the gene expression profile of Y1 mouse adrenocortical cells was evaluated using short hairpin RNAs to knockdown SF-1. The reduced level of SF-1 RNA was associated with global changes that affected the accumulation of more than 2000 transcripts. Among the down-regulated transcripts were several with functions in steroidogenesis that were affected to different degrees--i.

Large-scale studies to identify biomarkers for heart disease: a role for proteomics?

Background: In clinical practice, timely detection of disease and accurate diagnosis are highly important for the effective treatment of various patient populations. Biomarkers offer a new and innovative means of assessing the disease state during early, mid and late stages of progression.

Objective: Advancements in various proteomic platforms used to study the disease proteome and their applications to the field of clinical medicine are reviewed.

MAID : an effect size based model for microarray data integration across laboratories and platforms.

Background: Gene expression profiling has the potential to unravel molecular mechanisms behind gene regulation and identify gene targets for therapeutic interventions. As microarray technology matures, the number of microarray studies has increased, resulting in many different datasets available for any given disease. The increase in sensitivity and reliability of measurements of gene expression changes can be improved through a systematic integration of different microarray datasets that address the same or similar biological questions.

Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR.

The interaction of Escherichia coli AllR regulator with operator DNA is disrupted by the effector molecule glyoxylate. This is a general, yet uncharacterized regulatory mechanism for the large IclR family of transcriptional regulators to which AllR belongs. The crystal structures of the C-terminal effector-binding domain of AllR regulator and its complex with glyoxylate were determined at 1.

A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription.

Background: Systematic identification and functional characterization of novel types of noncoding (nc)RNA in genomes is more difficult than it is for protein coding mRNAs, since ncRNAs typically do not possess sequence features such as splicing or translation signals, or long open reading frames. Recent "tiling" microarray studies have reported that a surprisingly larger proportion of mammalian genomes is transcribed than was previously anticipated. However, these non-genic transcripts often appear to be low in abundance, and their functional significance is not known.

High-throughput production of prokaryotic membrane proteins.

Membrane proteins constitute ~30% of prokaryotic and eukaryotic genomes but comprise a small fraction of the entries in protein structural databases. A number of features of membrane proteins render them challenging targets for the structural biologist, among which the most important is the difficulty in obtaining sufficient quantities of purified protein. We are exploring procedures to express and purify large numbers of prokaryotic membrane proteins.

Enzyme genomics: Application of general enzymatic screens to discover new enzymes.

In all sequenced genomes, a large fraction of predicted genes encodes proteins of unknown biochemical function and up to 15% of the genes with "known" function are mis-annotated. Several global approaches are routinely employed to predict function, including sophisticated sequence analysis, gene expression, protein interaction, and protein structure. In the first coupling of genomics and enzymology, Phizicky and colleagues undertook a screen for specific enzymes using large pools of partially purified proteins and specific enzymatic assays.

Probing microRNAs with microarrays: tissue specificity and functional inference.

MicroRNAs (miRNAs) are short, stable, noncoding RNAs involved in post-transcriptional gene silencing via hybridization to mRNA. Few have been thoroughly characterized in any species. Here, we describe a method to detect miRNAs using micro-arrays, in which the miRNAs are directly hybridized to the array.

The promise of functional genomics: completing the encyclopedia of a cell.

Genome sequencing provides complete parts lists of organisms. This presents the obvious challenge of determining how each gene contributes to the life of the organism. This task seems increasingly feasible; however, progress to date suggests that increased interaction between systematic efforts and individual investigators will be critical to completing the encyclopedia of the yeast cell.

The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase activities.

In all mature tRNAs, the 3'-terminal CCA sequence is synthesized or repaired by a template-independent nucleotidyltransferase (ATP(CTP):tRNA nucleotidyltransferase; EC 2.7.7.

Central core disease mutations R4892W, I4897T and G4898E in the ryanodine receptor isoform 1 reduce the Ca2+ sensitivity and amplitude of Ca2+-dependent Ca2+ release.

Three CCD (central core disease) mutants, R4892W (Arg4892-->), I4897T and G4898E, in the pore region of the skeletal-muscle Ca2+-release channel RyR1 (ryanodine receptor 1) were characterized using a newly developed assay that monitored Ca2+ release in the presence of Ca2+ uptake in microsomes isolated from HEK-293 cells (human embryonic kidney 293 cells), co-expressing each of the three mutants together with SERCA1a (sarcoplasmic/endoplasmic-reticulum Ca2+-ATPase 1a). Both Ca2+ sensitivity and peak amplitude of Ca2+ release were either absent from or sharply decreased in homotetrameric mutants. Co-expression of wild-type RyR1 with mutant RyR1 (heterotetrameric mutants) restored Ca2+ sensitivity partially, in the ratio 1:2, or fully, in the ratio 1:1.

Bridging structural biology and genomics: assessing protein interaction data with known complexes.

Currently, there is a major effort to map protein-protein interactions on a genome-wide scale. The utility of the resulting interaction networks will depend on the reliability of the experimental methods and the coverage of the approaches. Known macromolecular complexes provide a defined and objective set of protein interactions with which to compare biochemical and genetic data for validation.

Bridging structural biology and genomics: assessing protein interaction data with known complexes.

Currently, there is a major effort to map protein-protein interactions on a genome-wide scale. The utility of the resulting interaction networks will depend on the reliability of the experimental methods and the coverage of the approaches. Known macromolecular complexes provide a defined and objective set of protein interactions with which to compare biochemical and genetic data for validation.

Yeast and drug discovery.

Advanced genetic techniques, along with the high degree of conservation of basic cellular processes, have made the yeast Saccharomyces cerevisiae a valuable system for identification of new drug targets, target-based and non-target-based drug screening, and detailed analysis of the cellular effects of drugs. Yeast also presents a convenient system for antifungal drug discovery because it is closely related to Candida albicans, a major human pathogen. Many yeast genes remain poorly characterized, and most of the sophisticated techniques in yeast have been in widespread use less than a decade - a period shorter than the typical cycle from target identification to marketing approval for a new drug.

Gene expression: the close coupling of transcription and splicing.

Increasing evidence indicates that the transcriptional machinery can influence the efficiency of splicing as well as splice-site selection. Surprisingly, it has now been demonstrated that splicing components influence the efficiency of transcription. This mutual stimulation has important implications for the regulation of gene expression.

A ribosomal ATPase is a target for hygromycin B inhibition on Escherichia coli ribosomes.

We demonstrate that the transfer of fully charged aminoacyl-tRNAs into peptides directed by the MS2 RNA template requires both ATP and GTP, initiation factors (IF1, IF2, and IF3), elongation factors (EF-Tu, EF-Ts, and EF-G), and the ribosomal ATPase (RbbA). The nonhydrolyzable analogue AMPPCP inhibits the reactions, suggesting that hydrolysis of ATP is required for synthesis. The RbbA protein occurs bound to ribosomes and stimulates the ATPase activity of Escherichia coli 70S and 30S particles.

Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases.

Exonic splicing enhancers (ESEs) are discrete sequences within exons that promote both constitutive and regulated splicing. The precise mechanism by which ESEs facilitate the assembly of splicing complexes has been controversial. However, recent studies have provided insights into this question and have led to a new model for ESE function.

Site-directed disulfide mapping of helices M4 and M6 in the Ca2+ binding domain of SERCA1a, the Ca2+ ATPase of fast twitch skeletal muscle sarcoplasmic reticulum.

In an attempt to define the spatial relationships among SERCA1a transmembrane helices M4, M5, M6, and M8, involved in Ca2+ binding, all six cysteine residues were removed from predicted transmembrane sequences by substitution with Ser or Ala. The cysteine-depleted protein retained 44% of wild type Ca2+ transport activity. Pairs of cysteine residues were then reintroduced to determine whether their juxtaposition would result in the formation of disulfide cross-links between transmembrane helices.