Identification of simple sequence repeat biomarkers through cross-species comparison in a tag cloud representation.

Simple sequence repeats (SSRs) are not only applied as genetic markers in evolutionary studies but they also play an important role in gene regulatory activities. Efficient identification of conserved and exclusive SSRs through cross-species comparison is helpful for understanding the evolutionary mechanisms and associations between specific gene groups and SSR motifs. In this paper, we developed an online cross-species comparative system and integrated it with a tag cloud visualization technique for identifying potential SSR biomarkers within fourteen frequently used model species. Ultraconserved or exclusive SSRs among cross-species orthologous genes could be effectively retrieved and displayed through a friendly interface design. Four different types of testing cases were applied to demonstrate and verify the retrieved SSR biomarker candidates. Through statistical analysis and enhanced tag cloud representation on defined functional related genes and cross-species clusters, the proposed system can correctly represent the patterns, loci, colors, and sizes of identified SSRs in accordance with gene functions, pattern qualities, and conserved characteristics among species.

Chitosan reduces plasma adipocytokines and lipid accumulation in liver and adipose tissues and ameliorates insulin resistance in diabetic rats.

Chitosan is a natural product derived from chitin. To investigate the hypoglycemic and anti-obesity effects of chitosan, male Sprague-Dawley rats were divided into four groups: normal control, diabetic, and diabetic fed 5% or 7% chitosan. Diabetes was induced in rats by injecting streptozotocin/nicotinamide. After 10 weeks of feeding, the elevated plasma glucose, tumor necrosis factor-α, and interleukin-6 and lower adiponetin levels caused by diabetes were effectively reversed by chitosan treatment. In addition, 7% chitosan feeding also elevated plasma glucagon-like peptide-1 levels and lowered the insulin resistance index (homeostasis model assessment) in diabetic rats. Lower adipocyte granular intensities and higher lipolysis rates in adipose tissues were noted in the 7% chitosan group. Moreover, chitosan feeding reduced hepatic triglyceride and cholesterol contents and increased hepatic peroxisomal proliferator-activated receptor α expression in diabetic rats. Our results indicate that long-term administration of chitosan may reduce insulin resistance through suppression of lipid accumulation in liver and adipose tissues and amelioration of chronic inflammation in diabetic rats.

An online conserved SSR discovery through cross-species comparison.

Simple sequence repeats (SSRs) play important roles in gene regulation and genome evolution. Although there exist several online resources for SSR mining, most of them only extract general SSR patterns without providing functional information. Here, an online search tool, CG-SSR (Comparative Genomics SSR discovery), has been developed for discovering potential functional SSRs from vertebrate genomes through cross-species comparison. In addition to revealing SSR candidates in conserved regions among various species, it also combines accurate coordinate and functional genomics information. CG-SSR is the first comprehensive and efficient online tool for conserved SSR discovery.

Different temporal expressions of Tilapia (Oreochromis mossambicus) insulin-like growth factor-I and IGF binding protein-3 after growth hormone induction.

In vertebrates the insulin-like growth factor-I (IGF-I) is well recognized for its important roles in prenatal and postnatal processes. Liver is the major endocrine organ in mammals to produce IGF-I and its modulators, the insulin-like growth factor binding proteins (IGFBPs), which form a binary complex with IGF-I in circulation or in extracellular fluid. In the complex, IGFBP-3 accounts for the majority of IGFBPs that interact with IGF-I in circulation. To date, we know little of fish IGF-I regulation at the gene or protein level. In this preliminary experiment, we isolated tilapia IGFBP-3 complementary DNA sequence by degenerate polymerase chain reaction cloning. This identified clone contained a partial open reading frame of 635 bp and lacked both 5' and 3' end cDNA sequence information. The deduced 211 amino acid residues shared approximately 50% identity with mammalian counterparts. This tilapia IGFBP-3 transcript was expressed in every tissue examined with the highest level found in liver. In a growth hormone time course experiment, both IGF-I and IGFBP-3 message levels increased sharply, and after 24 hours of injection, IGF-I and IGFBP-3 was increased 1.97 and 2.15 fold, respectively. The relative message ratio of IGF-I to IGFBP-3 was 1.58, 1.09, 0.94, 0.91, and 0.92 for 3, 6, 9, 12, and 24 hours, respectively. After 9 hours of treatment, the IGF-I/IGFBBP-3 message ratio maintained a constant value of approximately 0.9 throughout the experiment. This is the first report to demonstrate a fish counterpart of IGFBP-3 at the cDNA level and its message expression ratio with IGF-I under growth hormone induction.

Gene expression of insulin-like growth factor-I receptor and p53 suppressor during zebrafish (Danio rerio) embryogenesis.

In vertebrates insulin-like growth factors (IGFs) regulate important cellular activities involving proliferation, differentiation, and antiapoptosis and their biological activities are mediated through the insulin-like growth factor-I receptor (IGF-IR). To understand the functions of IGF-IR in zebrafish embryogenesis, the polymerase chain reaction (PCR) cloning technique was applied to isolate the IGF-IR gene. A 5'-truncated 3285-nucleotide zebrafish IGF-IR sequence was assembled from 3 overlapping clones. This contained a partial coding region of 1550 nucleotides and a 1735-nucleotide 3' untranslated region. The deduced 515 amino acid residues included the conserved kinase domain and shared 60.9%, 61.1%, and 59.9% homology to human, mouse, and frog, respectively. To understand the relationship of IGF-IR with p53 suppressor gene during embryogenesis, expression of both genes was analyzed in parallel by semicompetitive reverse transcriptase PCR and whole-mount in situ hybridization. This analysis indicated that messenger RNA of both genes was of maternal origin, but the p53 suppressor mRNA was relatively more abundant than the IGF-IR message in most of the developmental stages, except possibly at 28 hours postfertilization. At this stage the IGF-I receptor message was highly expressed and visible in whole internal organ regions by whole-mount in situ hybridization, while p53 message was concentrated in the head portion and barely detectable in the trunk portion. The results suggest that IGF-IR and p53 mRNA are expressed at different places and different times. However, the temporal and spatial relationship of IGF-IR and its relationship to p53 suppressor protein during developmental processes remain unknown.