NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes

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.     

Effect of pathogenic mutations on the structure and dynamics of Alzheimer’s Aβ42-amyloid oligomers

Converging lines of evidence suggest that soluble Aβ-amyloid oligomers play a pivotal role in the pathogenesis of Alzheimer’s disease, and present direct effectors of synaptic and cognitive dysfunction. Three pathological E22-Aβ-amyloid point mutants (E22G, E22K, E22Q) and the deletion mutant E22Δ exhibit an enhanced tendency to form prefibrillar aggregates. The present study assessed the effect of these four mutations using molecular dynamics simulations and subsequent structural and energetic analyses. Our data shows that E22 plays a unique role in wild type Aβ, since it has a destabilising effect on the oligomer structure due to electrostatic repulsion between adjacent E22 side chains. Mutations in which E22 is replaced by an uncharged residue result in higher oligomer stability. This effect is also observed to a lesser extent for the E22K mutation and is consistent with its lower pathogenicity compared to other mutants. Interestingly, deletion of E22 does not destroy the amyloid fold but is compensated by local changes in the backbone geometry that allow the preservation of a structurally important salt bridge. The finding that all mutant oligomers investigated exhibit higher internal stability than the wild type offers an explanation for the experimentally observed enhanced oligomer formation and stability.     

Logistic population growth under random dispersal

Various diffusion processes employed for modelling logistic growth are briefly summarized. A discrete-time, discrete-state space stochastic process for population growth is proposed and analyzed with either Bose-Einstein or Maxwell-Boltzmann statistics for the distribution of offspring in available sites in a restricted region. A diffusion approximation is constructed, which differs from those previously employed. The logistic law is a natural deterministic analog of the diffusion process.     

Thermal adaptations in lizard muscle function

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     

Trilobites Calmoniidae de l'Ordovicien supérieur du Maroc et les origines de la Province Malvino-Cafre

A re-examination of the trilobite Baniaspis globosa Destombes (Phacopina) from the Ashgill of the Anti-Atlas (Morocco) shows that it has several derived characters which allow us to classify it in the family Calmoniidae. Calmoniids were characteristic members of the Malvino-Kaffric province during the Lower Devonian. Hence we regard the origins of this palaeogeographic province as located on the northern Gondwanan margin as early as Ashgill, or even Caradoc, times. We agree with those authors who have suggested that the trilobite associations present in the Anti-Atlas, the Montagne Noire (France) and Bohemia during the earlier Ordovician argue against the existence of a 'proto-Tethys' ocean.     

Increased Concentrations of 3-Hydroxykynurenine in Vitamin B6 Deficient Neonatal Rat Brain

Increased concentrations of the endogenous tryptophan metabolite 3-hydroxykynurenine (3-HK) were measured in the brains of vitamin B6 deficient neonatal rats. Mean concentrations of 3-HK in B6 deficient cerebellum, corpus striatum, frontal cortex, and pons/medulla ranged from 9.7 to 18.6 and 102 to 142 nmol/g of wet tissue at 14 and 18 days of age, respectively. 3-HK was not significantly increased in control neonatal or adult rat brain, vitamin B6 deficient rat brain at 7 days of age, or in brains from adult rats deprived of vitamin B6 for 58 days. The administration of daily intraperitoneal injections of vitamin B6 from the 14th to the 18th day of age decreased the concentration of 3-HK to control levels. 3-HK has been shown by other investigators to produce seizures when injected into the cerebral ventricles of adult rodents. Thus, our studies show the accumulation in brain of a putative endogenous convulsant as the result of a nutritional deficiency.     

Gabaculine Inhibition of Chlorophyll Biosynthesis and Nodulation in Phaseolus lunatus L

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.