Genotoxicity of lomefloxacin--an antibacterial drug in somatic and germ cells of Swiss albino mice in vivo

The in vivo genotoxicity of lomefloxacin, a diflourinated antibacterial drug, was evaluated by employing mouse in vivo chromosomal aberration test in bone marrow cells and dominant lethal mutation assay in germ cells. Statistically significant reduction in mitotic index, increase in chromosomal aberrations (CAs)/cell and percent abnormal metaphase was observed only at the highest dose (160 mg/kg b.w.) of the drug. In the dominant lethal mutation assay, a statistically significant decrease in the number of implants/female, compared to vehicle control, was noticed only in the females mated with males treated with 32 mg/kg b.w. during the third week of mating, while statistically significant reduction in live implants/female was noticed at both the doses during the second and third weeks of mating. Nevertheless, no significant change in the number of dead implants/female was observed after lomefloxacin treatment. These results seems to indicate that lomefloxacin is a weak clastogen in the bone marrow cells and non-mutagenic in the germ cells of mouse in vivo.     

Toll and interleukin-1 receptor (TIR) domain-containing proteins in plants: a genomic perspective

Toll and interleukin-1 receptor (TIR) domains were originally described from comparisons of proteins found in mammals and Drosophila. They are now known to occur in several organisms, with the most TIR proteins being found in ARABIDOPSIS: our analysis of the sequenced Arabidopsis genome has revealed the presence of at least 135 proteins containing TIR domains. Several novel types of TIR-domain-containing proteins are found in Arabidopsis that are not found in other genomes. Here, we discuss the roles of TIR-domain-containing proteins in pathogen resistance and as candidate signaling modules.     

A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein,Frigg, as a protein kinase A substrate

Although proteins phosphorylated on tyrosine residues can be enriched by immunoprecipitation with anti-phosphotyrosine antibodies, it has been difficult to identify proteins that are phosphorylated on serine/threonine residues because of lack of immunoprecipitating antibodies. In this report, we describe several antibodies that recognize phosphoserine/phosphothreonine-containing proteins by Western blotting. Importantly, these antibodies can be used to enrich for proteins phosphorylated on serine/threonine residues by immunoprecipitation, as well. Using these antibodies, we have immunoprecipitated proteins from untreated cells or those treated with calyculin A, a serine/threonine phosphatase inhibitor. Mass spectrometry-based analysis of bands from one-dimensional gels that were specifically observed in calyculin A-treated samples resulted in identification of several known serine/threonine-phosphorylated proteins including drebrin 1, alpha-actinin 4, and filamin-1. We also identified a protein, poly(A)-binding protein 2, which was previously not known to be phosphorylated, in addition to a novel protein without any obvious domains that we designate as Frigg. Frigg is widely expressed and was demonstrated to be a protein kinase A substrate in vitro. We identified several in vivo phosphorylation sites by tandem mass spectrometry using Frigg protein immunoprecipitated from cells. Our method should be applicable as a generic strategy for enrichment and identification of serine/threonine-phosphorylated substrates in signal transduction pathways.     

A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes

We have undertaken a systematic proteomic approach to purify and identify secreted factors that are differentially expressed in preadipocytes versus adipocytes. Using one-dimensional gel electrophoresis combined with nanoelectrospray tandem mass spectrometry, proteins that were specifically secreted by 3T3-L1 preadipocytes or adipocytes were identified. In addition to a number of previously reported molecules that are up- or down-regulated during this differentiation process (adipsin, adipocyte complement-related protein 30 kDa, complement C3, and fibronectin), we identified four secreted molecules that have not been shown previously to be expressed differentially during the process of adipogenesis. Pigment epithelium-derived factor, a soluble molecule with potent antiangiogenic properties, was found to be highly secreted by preadipocytes but not adipocytes. Conversely, we found hippocampal cholinergic neurostimulating peptide, neutrophil gelatinase-associated lipocalin, and haptoglobin to be expressed highly by mature adipocytes. We also used liquid chromatography-based separation followed by automated tandem mass spectrometry to identify proteins secreted by mature adipocytes. Several additional secreted proteins including resistin, secreted acidic cysteine-rich glycoprotein/osteonectin, stromal cell-derived factor-1, cystatin C, gelsolin, and matrix metalloprotease-2 were identified by this method. To our knowledge, this is the first study to identify several novel secreted proteins by adipocytes by a proteomic approach using mass spectrometry.     

Muscle oxygenation during incremental arm and leg exercise in men and women

The purpose of this study was to compare the rates of muscle deoxygenation in the exercising muscles during incremental arm cranking and leg cycling exercise in healthy men and women. Fifteen men and 10 women completed arm cranking and leg cycling tests to exhaustion in separate sessions in a counterbalanced order. Cardiorespiratory measurements were monitored using an automated metabolic cart interfaced with an electrocardiogram. Tissue absorbency was recorded continuously at 760 nm and 850 nm during incremental exercise and 6 min of recovery, with a near infrared spectrometer interfaced with a computer. Muscle oxygenation was calculated from the tissue absorbency measurements at 30%, 45%, 60%, 75% and 90% of peak oxygen uptake (V˙O₂) during each exercise mode and is expressed as a percentage of the maximal range observed during exercise and recovery (%Mox). Exponential regression analysis indicated significant inverse relationships (P < 0.01) between %Mox and absolute V˙O₂ during arm cranking and leg cycling in men (multiple R = −0.96 and −0.99, respectively) and women (R =−0.94 and −0.99, respectively). No significant interaction was observed for the %Mox between the two exercise modes and between the two genders. The rate of muscle deoxygenation per litre of V˙O₂ was 31.1% and 26.4% during arm cranking and leg cycling, respectively, in men, and 26.3% and 37.4% respectively, in women. It was concluded that the rate of decline in %Mox for a given increase in V˙O₂ between 30% and 90% of the peak V˙O₂ was independent of exercise mode and gender. Accepted: 31 March 1998     

Rice Pangenome Genotyping Array: an efficient genotyping solution for pangenome-based accelerated genetic improvement in rice

The advent of the pangenome era has unraveled previously unknown genetic variation existing within diverse crop plants, including rice. This untapped genetic variation is believed to account for a major portion of phenotypic variation existing in crop plants. However, the use of conventional single reference-guided genotyping often fails to capture a large portion of this genetic variation leading to a reference bias. This makes it difficult to identify and utilize novel population/cultivar-specific genes for crop improvement. Thus, we developed a Rice Pangenome Genotyping Array (RPGA) harboring probes assaying 80K single-nucleotide polymorphisms (SNPs) and presence–absence variants spanning the entire 3K rice pangenome. This array provides a simple, user-friendly and cost-effective (60–80 USD per sample) solution for rapid pangenome-based genotyping in rice. The genome-wide association study (GWAS) conducted using RPGA-SNP genotyping data of a rice diversity panel detected a total of 42 loci, including previously known as well as novel genomic loci regulating grain size/weight traits in rice. Eight of these identified trait-associated loci (dispensable loci) could not be detected with conventional single reference genome-based GWAS. A WD repeat-containing PROTEIN 12 gene underlying one of such dispensable locus on chromosome 7 (qLWR7) along with other non-dispensable loci were subsequently detected using high-resolution quantitative trait loci mapping confirming authenticity of RPGA-led GWAS. This demonstrates the potential of RPGA-based genotyping to overcome reference bias. The application of RPGA-based genotyping for population structure analysis, hybridity testing, ultra-high-density genetic map construction and chromosome-level genome assembly, and marker-assisted selection was also demonstrated. A web application ( http://www.rpgaweb.com ) was further developed to provide an easy to use platform for the imputation of RPGA-based genotyping data using 3K rice reference panel and subsequent GWAS.     

Increased aortic stiffness in the insulin-resistant Zucker fa/fa rat

Accumulating clinical evidence indicates increased aortic stiffness, an independent risk factor for cardiovascular and all-cause mortality, in type 2 diabetic and glucose-intolerant individuals. The present study sought to determine whether increased mechanical stiffness, an altered extracellular matrix, and a profibrotic gene expression profile could be observed in the aorta of the insulin-resistant Zucker fa/fa rat. Mechanical testing of Zucker fa/fa aortas showed increased vascular stiffness in longitudinal and circumferential directions compared with Zucker lean controls. Unequal elevations in developed strain favoring the longitudinal direction resulted in a loss of anisotropy. Real-time quantitative PCR and immunohistochemistry revealed increased expression of fibronectin and collagen IV alpha 3 in the Zucker fa/fa aorta. In addition, expression of transforming growth factor-beta and several Smad proteins was increased in vessels from insulin-resistant animals. In rat vascular smooth muscle cells, 12-18 h of exposure to insulin (100 nmol/l) enhanced transforming growth factor-beta1 mRNA expression, implicating a role for hyperinsulinemia in vascular stiffness. Thus there is mechanical, structural, and molecular evidence of arteriosclerosis in the Zucker fa/fa rat at the glucose-intolerant, hyperinsulinemic stage.     

Probabilistic model of the human protein-protein interaction network

A catalog of all human protein-protein interactions would provide scientists with a framework to study protein deregulation in complex diseases such as cancer. Here we demonstrate that a probabilistic analysis integrating model organism interactome data, protein domain data, genome-wide gene expression data and functional annotation data predicts nearly 40,000 protein-protein interactions in humans-a result comparable to those obtained with experimental and computational approaches in model organisms. We validated the accuracy of the predictive model on an independent test set of known interactions and also experimentally confirmed two predicted interactions relevant to human cancer, implicating uncharacterized proteins into definitive pathways. We also applied the human interactome network to cancer genomics data and identified several interaction subnetworks activated in cancer. This integrative analysis provides a comprehensive framework for exploring the human protein interaction network.     

Circadian clocks: neural and peripheral pacemakers that impact upon the cell division cycle

Circadian clocks are pervasive entities that allow organisms to maintain rhythms of approximately 24h, independently of external cues, thereby adapting them to the solar cycle. Recent studies have shown that molecular circadian clocks are important for the proper orchestration of the cell division cycle. For the first time, this provides a framework to understand the interactions between these two evolutionarily linked timers. Here we review the current model of the circadian clock and the molecular methods that can be used to investigate its function. We then map out links to the cell cycle at the cellular level. Furthermore, we review recent progress that has linked dysfunction of the clockwork with the pathogenesis of cancer. Disruption of circadian timing (as occurs in jet-lag, shift work and dementia) thus has far reaching consequences for normal regulation of cell division. The implications of this for the health of a "24-h society" are apparent.