Prediction of novel pre-microRNAs with high accuracy through boosting and SVM

High-throughput deep-sequencing technology has generated an unprecedented number of expressed short sequence reads, presenting not only an opportunity but also a challenge for prediction of novel microRNAs. To verify the existence of candidate microRNAs, we have to show that these short sequences can be processed from candidate pre-microRNAs. However, it is laborious and time consuming to verify these using existing experimental techniques. Therefore, here, we describe a new method, miRD, which is constructed using two feature selection strategies based on support vector machines (SVMs) and boosting method. It is a high-efficiency tool for novel pre-microRNA prediction with accuracy up to 94.0% among different species. AVAILABILITY: miRD is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/rpg/mird/mird.php.     

Liver-specific inactivation of the abetalipoproteinemia gene completely abrogates very low density lipoprotein/low density lipoprotein production in a viable conditional knockout mouse

Conventional knockout of the microsomal triglyceride transfer protein large subunit (lMTP) gene is embryonic lethal in the homozygous state in mice. We have produced a conditional lMTP knockout mouse by inserting loxP sequences flanking exons 5 and 6 by gene targeting. Homozygous floxed mice were born live with normal plasma lipids. Intravenous injection of an adenovirus harboring Cre recombinase (AdCre1) produced deletion of exons 5 and 6 and disappearance of lMTP mRNA and immunoreactive protein in a liver-specific manner. There was also disappearance of plasma apolipoprotein (apo) B-100 and marked reduction in apoB-48 levels. Wild-type mice showed no response, and heterozygous mice, an intermediate response, to AdCre1. Wild-type mice doubled their plasma cholesterol level following a high cholesterol diet. This hypercholesterolemia was abolished in AdCre1-treated lMTP-/- mice, the result of a complete absence of very low/intermediate/low density lipoproteins and a slight reduction in high density lipoprotein. Heterozygous mice showed an intermediate lipoprotein phenotype. The rate of accumulation of plasma triglyceride following Triton WR1339 treatment in lMTP-/- mice was <10% that in wild-type animals, indicating a failure of triglyceride-rich lipoprotein production. Pulse-chase experiments using hepatocytes isolated from wild-type and lMTP-/- mice revealed a failure of apoB secretion in lMTP-/- animals. Therefore, the liver-specific inactivation of the lMTP gene completely abrogates apoB-100 and very low/intermediate/low density lipoprotein production. These conditional knockout mice are a useful in vivo model for studying the role of MTP in apoB biosynthesis and the biogenesis of apoB-containing lipoproteins.     

Diversity and Biogeography of Rhizobia Isolated from Root Nodules of <Emphasis Type="Italic">Glycine max</Emphasis> Grown in Hebei Province,China

A total of 215 rhizobial strains were isolated and analyzed with 16S rRNA gene, 16S–23S intergenic spacer, housekeeping genes atpD, recA, and glnII, and symbiotic genes nifH and nodC to understand the genetic diversity of soybean rhizobia in Hebei province, China. All the strains except one were symbiotic bacteria classified into nine genospecies in the genera of Bradyrhizobium and Sinorhizobium. Surveys on the distribution of these rhizobia in different regions showed that Bradyrhizobium japonicum and Bradyrhizobium elkanii strains were found only in neutral to slightly alkaline soils whereas Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense-related strains and strains of five Sinorhizobium genospecies were found in alkaline–saline soils. Correspondence and canonical correspondence analyses on the relationship of rhizobial distribution and their soil characteristics reveal that high soil pH, electrical conductivity, and potassium content favor distribution of the B. yuanmingense and the five Sinorhizobium species but inhibit B. japonicum and B. elkanii. High contents of available phosphorus and organic matters benefit Sinorhizobium fredii and B. liaoningense-related strains and inhibit the others groups mentioned above. The symbiotic gene (nifH and nodC) lineages among B. elkanii, B. japonicum, B. yuanmingense, and Sinorhizobium spp. were observed in the strains, signifying that vertical gene transfer was the main mechanism to maintain these genes in the soybean rhizobia. However, lateral transfer of symbiotic genes commonly in Sinorhizobium spp. and rarely in Bradyrhizobium spp. was also detected. These results showed the genetic diversity, the biogeography, and the soil determinant factors of soybean rhizobia in Hebei province of China.     

Lipid pattern and Na+−K+-dependent adenosine triphosphatase activity in the salt gland of duck before and after adaptation to hypertonic saline

Summary Ducks (Anas platyrhynchos) were fed hypertonic saline for eight days, resulting in an activation and hypertrophy of the salt gland. The Na⁺–K⁺-dependent adenosine triphosphatase, an enzyme generally assumed to be part of the active Na transport system, increased its specific activity by about 200% during this activation. Sulfatides, the major glycolipids of the salt gland, increased their concentration to the same extent. Cholesterol, cerebrosides, and six phospholipid classes showed an increase of 20–80%.A preliminary report on this work was given at the Second International Meeting of the International Society for Neurochemistry, Milan, September 1–5, 1969, and at the XIIIth International Conference on the Biochemistry of Lipids, Athens, September 7–12, 1969.     

Conformational analysis of potent sweet taste ligands by NMR and computer simulations

We report the conformational analysis by ¹H‐nmr and computer simulations of five potent sweet molecules, N‐(3,3‐dimethylbutyl)‐L ‐aspartyl‐S‐(α‐methyl)phenylalanine methylester (1; 5000 times more potent than sucrose), L ‐aspartyl‐D ‐valine (S)‐α‐methoxycarbonylmethylbenzylamide (2; 1400 times more potent than sucrose), L ‐aspartyl‐D ‐valine α‐phenylcyclopentylamide (3; 1200 times more potent than sucrose), L ‐aspartyl‐D ‐α‐aminobutyric acid (S)‐α‐cyclohexylpropylamide (4; 2300 times more potent than sucrose), and L ‐aspartyl‐D ‐valine (R)‐α‐methylthiomethylbenzylamide (5; 3000 times more potent than sucrose). The “L‐shaped” structure, which we believe to be responsible for sweet taste, is accessible to all five sweet compounds in solution. This structure is characterized by a zwitterionic ring formed by the A‐H and B containing moieties located in the +y axis and by the hydrophobic group X pointing into the +x axis. Other accessible conformations of these flexible molecules are extended conformations with the A‐H and B containing moieties in the +y axis and the hydrophobic group X pointing in the −y axis and reversed L‐shaped structures with the hydrophobic group X projecting along the −x axis. The remarkable potency of the N‐alkylated compound 1 supports our recent hypothesis that a second hydrophobic binding domain in addition to interactions arising from the L‐shaped structure leads to an enhancement of sweetness potency. © 1999 John Wiley & Sons, Inc. Biopoly 49: 525–539, 1999     

Synthesis and characterization of pyrrolidine derivatives as potent agonists of the human melanocortin-4 receptor

A series of trans-4-phenylpyrrolidine-3-carboxamides were synthesized and characterized as potent ligands of the human melanocortin-4 receptor. Interestingly, a pair of diastereoisomers 20f-1 and 20f-2 displayed potent functional agonist and antagonist activity, respectively. Thus, the 3S,4R-compound 20f-1 possessed a K(i) of 11nM and an EC(50) of 24nM, while its 3R,4S-isomer 20f-2 exhibited a K(i) of 8.6 and an IC(50) of 65nM. Both compounds were highly selective over other melanocortin receptor subtypes. The MC4R agonist 20f-1 also demonstrated efficacy in diet-induced obese rats.     

Isolation and characterization of microsatellite DNA loci from Russell's snapper (Lutjanus russellii)

A total of 37 microsatellite loci from the Russell's snapper, Lutjanus russellii, were successfully isolated and characterized. Thirty‐four loci were polymorphic in L. russellii samples. Twenty of the 37 markers did not differ significantly from Hardy–Weinberg expected genotype proportions. Significant linkage disequilibrium was detected in one pairwise comparison. The numbers of alleles and observed heterozygosities in polymorphic loci ranged from two to 16 and from 0.41 to 0.95, respectively. These markers will be useful for studying the population genetic structure of this species.     

Main changes in the new edition of the International Code of Botanical Nomenclature——the “Vienna Code”

The rules that govern scientific naming in botany (including phycology and mycology) are revised at Nomenclature Section meetings at successive International Botanical Congresses. The most recent edition of the International Code of Botanical Nomenclature (Vienna Code) embodies the decisions of the XVII International Botanical Congress held in Vienna in 2005 and supersedes the Saint Louis Code. This paper presents an account of the main differences between the two Codes, including those related with starting points, effective publication, valid publication, fossil plants, pleomorphic fungi, orthography, and the Appendices.     

Gender-specific links between hepatic 11beta reduction of cortisone and adipokines

Objective: Reduction of cortisone to cortisol is mediated by 11β‐hydroxysteroid dehydrogenase type 1 (11βHSD1), a putative key enzyme in obesity‐related complications. Experimental studies suggest that adipokines, notably leptin and tumor necrosis factor‐α (TNF‐α), are of importance for 11βHSD1 activity. We hypothesized that the regulation of hepatic preceptor glucocorticoid metabolism is gender‐specific and associated with circulating levels of leptin and TNF‐α receptors and/or sex hormones. Research Methods and Procedures: A total of 34 males and 38 women (14 premenopausal and 22 postmenopausal) underwent physical examination and fasting blood sampling. Insulin sensitivity was tested by euglycemic hyperinsulinemic clamps, and hepatic 11βHSD1 enzyme activity was estimated by the conversion of orally‐ingested cortisone to cortisol. Results: Hepatic 11βHSD1 activity was negatively associated with leptin and soluble TNF (sTNF) r1 and sTNFr2 in males. These correlations remained significant after adjustment for age and insulin sensitivity, and for sTNF‐α receptors also after adjustment of BMI and waist circumference. In contrast, 11β reduction of cortisone was positively associated to leptin in females after adjustment for BMI and waist circumference. Discussion: Hepatic 11β reduction shows different links to circulating adipocyte‐derived hormones in males and females. This emphasizes the need for further studies on tissue‐specific regulation of 11βHSD1 in both genders.     

Upregulation of PHLDA2 in Dicer knockdown HEK293 cells

It has been reported that RNAi-dependent chromatin silencing in vertebrates is not restricted to the centromeres. To address whether RNAi machinery could regulate the chromatin structure of imprinted genes, we knocked down Dicer in HEK293 cells and found that the expression of PHLDA2, one of the several genes in the imprinted gene domain of 11p15.5, was specifically upregulated. This was accompanied by a shift towards more activated chromatin at PHLDA2 locus as indicated by change in H3K9 acetylation, however, the methylation state at this locus was not affected. Furthermore, we found that PHLDA2 was downregulated in growth-arrested HEK293 cells induced by either serum deprivation or contact inhibition. This suggests that PHLDA2 upregulation might be a direct result of Dicer depletion rather than the consequence of growth arrest induced by Dicer knockdown. Considering the reports that there is consistent placental outgrowth in PHLDA2 knockout mice and that PHLDA2 overexpression in mice causes growth inhibition, we speculate that PHLDA2 may be a candidate for contributing to the reduced growth rate of Dicer-deficient cells and the very early embryonic lethality in Dicer knockout mice.