Hobbes: optimized gram-based methods for efficient read alignment

Recent advances in sequencing technology have enabled the rapid generation of billions of bases at relatively low cost. A crucial first step in many sequencing applications is to map those reads to a reference genome. However, when the reference genome is large, finding accurate mappings poses a significant computational challenge due to the sheer amount of reads, and because many reads map to the reference sequence approximately but not exactly. We introduce Hobbes, a new gram-based program for aligning short reads, supporting Hamming and edit distance. Hobbes implements two novel techniques, which yield substantial performance improvements: an optimized gram-selection procedure for reads, and a cache-efficient filter for pruning candidate mappings. We systematically tested the performance of Hobbes on both real and simulated data with read lengths varying from 35 to 100 bp, and compared its performance with several state-of-the-art read-mapping programs, including Bowtie, BWA, mrsFast and RazerS. Hobbes is faster than all other read mapping programs we have tested while maintaining high mapping quality. Hobbes is about five times faster than Bowtie and about 2–10 times faster than BWA, depending on read length and error rate, when asked to find all mapping locations of a read in the human genome within a given Hamming or edit distance, respectively. Hobbes supports the SAM output format and is publicly available at http://hobbes.ics.uci.edu.     

The effect of training at the same time of day and tapering period on the diurnal variation of short exercise performances

The purpose of this investigation was to assess the effects of training and tapering at the same time of the day on the diurnal variations of short exercise performances. Thirty-one physically active men underwent 12 weeks of lower-extremity resistance training and 2 weeks of tapering. These subjects were matched and randomly assigned to a morning training group (MTG, training times 0700-0800 hours, n = 10), an evening training group (ETG, training times 1700-1800 hours, n = 11), and a control group (CG, completed all tests but did not train, n = 10). Muscular strength and power testing was conducted before (T0) and after 12 weeks of training (T1) and after 2 weeks of tapering (T2) in the morning (0700-0800 hours) and in the evening (1700-1800 hours). All morning and evening tests were performed in separate sessions (minimum interval = 36 hours) in a randomized design. In T0, the oral temperature and performances during the Wingate, vertical jump (squat jump and countermovement jump), and maximal voluntary contraction tests were higher in the evening than in the morning for all the groups. In T1, these diurnal variations were blunted in the MTG and persisted in the ETG and CG. In T2, the 2 weeks of tapering resulted in further time of day-specific adaptations and increases in short-term maximal performances. However, there was no significant difference in the relative increase between the MTG and the ETG after both training and tapering. From a practical point of view, if the time of competition is known, training and tapering sessions before a major competition must be conducted at the same time of the day at which one's critical performance is programmed. Moreover, if the time of the competition is not known, a tapering phase after resistance training program could be performed at any time of the day with the same benefit.     

The effect of warm-ups incorporating different volumes of dynamic stretching on 10- and 20-m sprint performance in highly trained male athletes

Recently, athletes have transitioned from traditional static stretching during warm-ups to incorporating dynamic stretching routines. However, the optimal volume of dynamic drills is yet to be identified. The aim of this repeated-measures study was to examine varying volumes (1, 2, and 3 sets) of active dynamic stretching (ADS) in a warm-up on 10- and 20-m sprint performance. With a within-subject design, 16 highly trained male participants (age: 20.9 ± 1.3 years; height: 179.7 ± 5.7 cm; body mass: 72.7 ± 7.9 kg; % body fat: 10.9 ± 2.4) completed a 5-minute general running warm-up before performing 3 preintervention measures of 10- to 20-m sprint. The interventions included 1, 2, and 3 sets of active dynamic stretches of the lower-body musculature (gastrocnemius, gluteals, hamstrings, quadriceps, and hip flexors) performed approximately 14 times for each exercise while walking (ADS1, ADS2, and ADS3). The active dynamic warm-ups were randomly allocated before performing a sprint-specific warm-up. Five minutes separated the end of the warm-up and the 3 postintervention measures of 10- to 20-m sprints. There were no significant time, condition, and interaction effects over the 10-m sprint time. For the 0- to 20-m sprint time, a significant main effect for the pre-post measurement (F = 10.81; p < 0.002), the dynamic stretching condition (F = 6.23; p = 0.004) and an interaction effect (F = 41.19; p = 0.0001) were observed. A significant decrease in sprint time (improvement in sprint performance) post-ADS1 (2.56%, p = 0.001) and post-ADS2 (2.61%, p = 0.001) was observed. Conversely, the results indicated a significant increase in sprint time (sprint performance impairment) post-ADS3 condition (2.58%, p = 0.001). Data indicate that performing 1-2 sets of 20 m of active dynamic stretches in a warm-up can enhance 20-m sprint performance. The results delineated that 3 sets of ADS repetitions could induce acute fatigue and impair sprint performance within 5 minutes of the warm-up.     

Aminomethylpiperazines as selective urotensin antagonists

Aminomethylpiperazines, reported previously as being kappa-opioid receptor agonists, were identified as lead compounds in the development of selective urotensin receptor antagonists. Optimized substitution of the piperazine moiety has provided high affinity urotensin receptor antagonists with greater than 100-fold selectivity over the kappa-opioid receptor. Select compounds were found to inhibit urotensin-induced vasoconstriction in isolated rat aortic rings consistent with the hypothesis that an urotensin antagonist may be useful for the treatment of hypertension.     

Potent and selective small-molecule human urotensin-II antagonists with improved pharmacokinetic profiles

Lead compound 1 was successfully redesigned to provide compounds with improved pharmacokinetic profiles for this series of human urotensin-II antagonists. Replacement of the 2-pyrrolidinylmethyl-3-phenyl-piperidine core of 1 with a substituted N-methyl-2-(1-pyrrolidinyl)ethanamine core as in compound 7 resulted in compounds with improved oral bioavailability in rats. The relationship between stereochemistry and selectivity for hUT over the kappa-opioid receptor was also explored.     

Reliability and validity of a modified Illinois change-of-direction test with ball dribbling speed in young soccer players

The purpose of this study was to assess test-retest reliability, discriminative and criterion-related validity of the modified Illinois change-of-direction (CoD) test with ball dribbling-speed (ICODT-BALL) in young soccer players of different biological maturity and playing levels. Sixty-five young male soccer players (11.4 ± 1.2 years) participated in this study. The participants were classified according to their biological maturity (pre- and circumpeak height velocity [PHV]) and playing-level (elite and amateur players). During the test-retest time period of two weeks, the following tests were performed during week one and as retest during week two: ICODT-BALL, ICODT, 4 × 9-m shuttle-run, countermovement-jump, triple-hop-test, maximum-voluntary isometric-contraction of back-extensors, Stork, Y-Balance, 10 and 30-m sprints. The ICODT-BALL showed excellent relative (r = 0.995, p < 0.001; ICC = 0.993) and absolute (SEM < 5%; SEM < SWCs_{(0.2, 0.6, 1.2)}) reliability. The circum-PHV (22.8 ± 1.7-s) and elite (22.5 ± 0.9-s) players showed better ICODT-BALL performance than their pre-PHV (24.2 ± 2.5-s) and amateur (25.1 ± 2.8-s) counterparts (p = 0.028 and p < 0.001, respectively). The ICODT-BALL showed “very good” (AUC = 0.81) discriminant validity when comparing the elite and amateur players, and “moderate” (AUC = 0.67) discriminant validity when compared to pre-PHV and circum-PHV boys. ICODT-BALL demonstrated “large” positive associations with the ICODT (r = 0.65; 41.8% shared-variance) and sprint tests (r ≥ 0.52; 27.3 to 34.8% shared-variance). In addition, results showed “moderate” negative associations between ICODT-BALL and strength, and power measures, as well as a “small” negative relationship with balance tests. In conclusion, the ICODT-BALL is a valid and reliable test to evaluate the ability to quickly change directions while ball dribbling in young soccer players. Therefore, practitioners can use the ICODT-BALL as a tool for talent identification.     

Two soluble glycosyltransferases glycosylate less efficiently in vivo than their membrane bound counterparts

Many Golgi glycosyltransferases are type II membrane proteins which are cleaved to produce soluble forms that are released from cells. Cho and Cummings recently reported that a soluble form of alpha1, 3- galactosyltransferase was comparable to its membrane bound counterpart in its ability to galactosylate newly synthesized glycoproteins (Cho,S.K. and Cummings,R.D. (1997) J. Biol. Chem., 272, 13622-13628). To test the generality of their findings, we compared the activities of the full length and soluble forms of two such glycosyltransferases, ss1,4 N-Acetylgalactosaminyltransferase (GM2/GD2/ GA2 synthase; GalNAcT) and beta galactoside alpha2,6 sialyltransferase (alpha2,6-ST; ST6Gal I), for production of their glycoconjugate products in vivo . Unlike the full length form of GalNAcT which produced ganglioside GM2 in transfected cells, soluble GalNAcT did not produce detectable GM2 in vivo even though it possessed in vitro GalNAcT activity comparable to that of full length GalNAcT. When compared with cells expressing full length alpha2,6-ST, cells expressing a soluble form of alpha2,6-ST contained 3-fold higher alpha2,6-ST mRNA levels and secreted 7-fold greater alpha2,6-ST activity as measured in vitro , but in striking contrast contained 2- to 4-fold less of the alpha2,6-linked sialic acid moiety in cellular glycoproteins in vivo . In summary these results suggest that unlike alpha1,3-galactosyltransferase the soluble forms of these two glycosyltransferases are less efficient at glycosylation of membrane proteins and lipids in vivo than their membrane bound counterparts.      

Bacterial species and evolution: Theoretical and practical perspectives

A discussion of the species problem in modern evolutionary biology serves as the point of departure for an exploration of how the basic science aspects of this problem relate to efforts to map bacterial diversity for practical pursuits—for prospecting among the bacteria for useful genes and gene-products. Out of a confusing array of species concepts, the Cohesion Species Concept seems the most appropriate and useful for analyzing bacterial diversity. Techniques of allozyme analysis and DNA fingerprinting can be used to put this concept into practice to map bacterial genetic diversity, though the concept requires minor modification to encompass cases of complete asexuality. Examples from studies of phenetically definedBacillus species provide very partial maps of genetic population structure. A major conclusion is that such maps frequently reveal deep genetic subdivision within the phenetically defined specles; divisions that in some cases are clearly distinct genetic species. Knowledge of such subdivisions is bound to make prospecting within bacterial diversity more effective. Under the general concept of genetic cohesion a hypothetical framework for thinking about the full range of species conditions that might exist among bacteria is developed and the consequences of each such model for species delineation, and species identification are discussed. Modes of bacterial evolution, and a theory of bacterial speciation with and without genetic recombination, are examined. The essay concludes with thoughts about prospects for very extensive mapping of bacterial diversity in the service of future efforts to find useful products. In this context, evolutionary biology becomes the handmaiden of important industrial activities. A few examples of past success in commercializing bacterial gene-products from species ofBacillus and a few other bacteria are reviewed.     

Lysosomal enzyme oligosaccharide phosphorylation in mouse lymphoma cells: specificity and kinetics of binding to the mannose 6-phosphate receptor in vivo

Phosphomannosyl residues on lysosomal enzymes serve as an essential component of the recognition marker necessary for binding to the mannose 6-phosphate (Man 6-P) receptor and translocation to lysosomes. The high mannose-type oligosaccharide units of lysosomal enzymes are phosphorylated by the following mechanism: N-acetylglucosamine 1-phosphate is transferred to the 6 position of a mannose residue to form a phosphodiester; then N- acetylglucosamine is removed to expose a phosphomonoester. We examined the kinetics of this phosphorylation pathway in the murine lymphoma BW5147.3 cell line to determine the state of oligosaccharide phosphorylation at the time the newly synthesized lysosomal enzymes bind to the receptor. Cells were labeled with [2-(3)H]mannose for 20 min and then chased for various times up to 4 h. The binding of newly synthesized glycoproteins to the Man 6-P receptor was followed by eluting the bound ligand with Man 6-P. Receptor-bound material was first detected at 30 min of chase and reached a maximum at 60 min of chase, at which time approximately 10 percent of the total phosphorylated oligosaccharides were associated with the receptor. During longer chase times, the total quantity of cellular phosphorylated oligosaccharides decreased with a half-time of 1.4 h, suggesting that the lysosomal enzymes had reached their destination and had been dephosphorylated. The structures of the phosphorylated aligosaccharides of the eluted ligand were then determined and compared with the phosphorylated oligosaccharides of molecules which were not bond to the receptor. The major phosphorylated oligosaccharide species present in the nonreceptor-bound material contained a single phosphosphodiester at all time examined. In contrast, receptor-bound oligosaccharides were greatly enriched in species possessing one and two phosphomonoesters. These results indicate that binding of newly synthesized lysosomal enzymes to the Man 6-P receptor occurs only after removal of the covering N- acetylglucosamine residues.