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21.
Gabriel A. Al-Ghalith Emmanuel Montassier Henry N. Ward Dan Knights 《PLoS computational biology》2016,12(1)
The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs). NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the “concatesome,” as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop. 相似文献
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23.
Henry B. John-Alder Albert F. Bennett 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1987,157(2):241-252
Summary This study was undertaken to investigate thermal adaptations in muscle contractile properties in closely-related lizards with different preferred body temperatures (PBT). The species examined all belong to theSphenomorphus group of Australian skinks (Scincidae: Lygosominae). Preferred body temperatures are conservative at the generic level as follows:Ctenotus, 35°C;Sphenomorphus, 30°C;Eremiascincus, 25°C. Contractile properties of the fast glycolytic portion of the iliofibularis muscle were measured. Translational adaptations are evident in several isometric factors, including tetanic tension (Po), twitch tension (Pt), twitch time to peak tension (TPT), and twitch half-relaxation time (1/2 RT). Capacity adaptations are not evident in rates of tetanic tension development (dPo/dt) or in maximal velocities of isotonic shortening (V
max). Rotational adaptations are not evident in any contractile properties. Thermal limits on upper response temperatures are about 5°C warmer inCtenotus than in the more cryophilic species, indicative of resistance adaptation in muscle performance. Despite these adaptive shifts, there is little indication that muscle functional capacities are optimized or equalized at PBT in these lizards.Abbreviations
FG
fast glycolytic
-
IF
iliofibularis muscle
-
PBT
preferred body temperature
-
Po
tetanic tension
-
Pt
twitch tension
- 1/2RT
twitch half relaxation time
-
TPT
twitch time to peak tension 相似文献
24.
Gabaculine Inhibition of Chlorophyll Biosynthesis and Nodulation in Phaseolus lunatus L 总被引:1,自引:1,他引:0 下载免费PDF全文
Gabaculine (3-amino-2,3-dihydrobenzoic acid) was an inhibitor of in vivo chlorophyll biosynthesis in lima bean (Phaseolus lunatus L. cv Henderson). When applied to roots of 9-day-old plants, 10 micromolar gabaculine was sufficient to terminate biosynthesis of new chlorophyll. The trifoliolate leaves which emerged after gabaculine treatment were yellow. Gabaculine-treated plants had slightly lower dry weights; yet, overall plant size showed very little change. Chlorophyll fluorescence induction kinetics and CO2 exchange measurements were used to monitor both immediate and long-term effects of gabaculine on photosynthesis. A lowered rate of the decline from the maximum level of fluorescence was observed after 10 hours for nitrate-supplemented plants, and all treated plants showed a slightly increased level of original fluorescence after 6 days. No change was observed in the rate of photosynthesis by unifoliolate leaves. The trifoliolate leaves, though not able to photosynthesize, were able to continue respiration. This suggested that heme biosynthesis for mitochondrial cytochromes was not abolished. In untreated lima bean, root nodules were induced by Rhizobium sp. 127E15. Following gabaculine treatment, root nodules formed, but were largely ineffective in nitrogen fixation. Nodule dry weight, nitrogen fixation activity, and leghemoglobin content were decreased by gabaculine. 相似文献
25.
Coordinate regulation of phospholipid biosynthesis by serine in Saccharomyces cerevisiae. 总被引:6,自引:4,他引:2 下载免费PDF全文
The addition of L-serine to inositol-containing growth medium repressed membrane-associated CDPdiacylglycerol synthase (CTP:phosphatidate cytidylyltransferase, EC 2.7.7.41) and phosphatidylserine synthase (CDPdiacylglycerol:L-serine O-phosphatidyltransferase, EC 2.7.8.8) activities and subunit levels in wild-type Saccharomyces cerevisiae. Enzyme activities and subunit levels were not repressed when inositol was absent from the growth medium. The addition of L-serine to the growth medium did not affect the phospholipid composition of wild-type cells. CDPdiacylglycerol synthase and phosphatidylserine synthase were not regulated in the S. cerevisiae inositol biosynthesis ino2, ino4, and opi1 regulatory mutants, suggesting that regulation by inositol plus L-serine is coupled to inositol synthesis. Inositol and L-serine did not affect the activities of purified CDPdiacylglycerol synthase and phosphatidylserine synthase. The addition of compounds structurally related to L-serine to the growth medium of wild-type cells also resulted in a repression of CDPdiacylglycerol synthase and phosphatidylserine synthase but only in the presence of inositol. Phosphatidylinositol synthase (CDPdiacylglycerol:myo-inositol 3-phosphatidyltransferase, EC 2.7.8.11) was not regulated by inositol plus L-serine. 相似文献
26.
Co-purification and characterization of ATP-sulfurylase and adenosine-5'-phosphosulfate kinase from rat chondrosarcoma 总被引:1,自引:0,他引:1
D H Geller J G Henry J Belch N B Schwartz 《The Journal of biological chemistry》1987,262(15):7374-7382
The two sulfate-activating enzymes, ATP-sulfurylase (EC 2.7.7.4) and adenosine-5'-phosphosulfate kinase (adenylylsulfate kinase, EC 2.7.1.25), were each purified about 2000-fold from crude rat chondrosarcoma homogenate. Throughout a purification protocol which included Sephacryl S-300 gel filtration, DEAE-Sephadex ion exchange, hydroxylapatite, and ATP-agarose affinity chromatography, these two activities consistently co-purified. ATP-sulfurylase and adenosine-5'-phosphosulfate kinase each showed a pH optima of 7.0-7.4 and a bimodal temperature optima of 46 and 52-54 degrees C. Both activities preferred Mg2+ as their divalent cation source over Mn2+, Co2+, or Zn2+. The apparent Km values determined for adenosine 5'-phosphosulfate in both assays was 1-5 microM; the Km for pyrophosphate in the sulfurylase reaction was 40 microM and for ATP in the kinase reaction was 5 mM. Gel electrophoresis indicated major bands at Mr = 160,000 in nondenaturing systems and 35,000-37,000 and 60,000 under dissociative conditions, whereas gel filtration of the most highly purified fractions yielded a coincident peak in the molecular weight range 260,000. 相似文献
27.
28.
Henry A. F. Stephens Robert W. Vaughan Lazaros I. Sakkas Ken I. Welsh Gabriel S. Panayi 《Immunogenetics》1989,30(3):149-155
Despite extensive analysis of the incidence ofHLA-DR andHLA-DQ allele frequencies in defined autoimmune disease groups, there is very little information available onHLA-DP allele frequencies. This is largely becauseHLA-DP typing has until recently been restricted to primed lymphocyte typing (PLT). However, allelic polymorphism of theHLA-DP subregion can now be studied by Southern blot analysis or genotyping withDPA1 andDPB1 probes. By direct counting of allele-specific DNA fragments, we have analyzed the frequencies of five majorDP genotypes (DPw1, DPw2, DPw3/6, DPw4, andDPw5), in a large number of Caucasoid rheumatoid arthritis (RA) patients (n=74), and controls (n=91). The predicted frequency
ofDP alleles in both patient and control groups was comparable to PLT-determinedDP allele frequencies in normal Caucasoids. However, the gene frequency ofDPw4 was increased in the RA patients, with 51% of the patients studied scoring asDPw4, 4 homozygotes. With the exception of one possible combination (DPw5 andDRw6) in the controls, no significant linkage disequilibrium was detected betweenDP andDR alleles in either patient or control groups. Thus the prevalence ofDPw4 in the RA patients is independent of any disease association with theDR loci, and may represent a new class II association with RA. 相似文献
29.
30.
Roger Lennard Henry Huddart 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1989,159(1):105-113
Summary The interaction of adrenaline and adenosine was examined in cardiac tissue of the flounderPlatichthys flesus.When applied alone both agents increased contractility in both auricular and ventricular myocardial strips. This positive inotropic effect was associated with a small depolarization in the tissues examined by the sucrose gap technique. Simultaneous application of adrenaline and adenosine gave an inhibition of the control responses seen with either agent alone in both auricle and ventricle.Radiocalcium flux studies on ventricular tissue showed that influx was increased by adrenaline or adenosine alone above control values, but when applied together radiocalcium influx was reduced. Radiocalcium efflux from cardiac microsomes was stimulated by challenge with adrenaline or adenosine alone. This stimulation was not seen following simultaneous challenge by both agents.The effect of adrenaline on responses of hypoxic flounder hearts was less than that seen in normoxic hearts. This situation was reversed by pretreatment with the purine receptor blocker caffeine. Caffeine pretreatment also reduced the positive inotropic effect seen in normoxic hearts challenged with adenosine.TLC studies gave strong evidence that hearts perfused with hypoxic salines produced both adenosine and adrenaline.The results are discussed as evidence for a mechanism of heart regulation which the flounder may use as a defence against severe acute hypoxic stress. 相似文献