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.     

Obesity in Older Adults: Technical Review and Position Statement of the American Society for Nutrition and NAASO,The Obesity Society

Obesity causes serious medical complications and impairs quality of life. Moreover, in older persons, obesity can exacerbate the age‐related decline in physical function and lead to frailty. However, appropriate treatment for obesity in older persons is controversial because of the reduction in relative health risks associated with increasing body mass index and the concern that weight loss could have potential harmful effects in the older population. This joint position statement from the American Society for Nutrition and NAASO, The Obesity Society reviews the clinical issues related to obesity in older persons and provides health professionals with appropriate weight‐management guidelines for obese older patients. The current data show that weight‐loss therapy improves physical function, quality of life, and the medical complications associated with obesity in older persons. Therefore, weight‐loss therapy that minimizes muscle and bone losses is recommended for older persons who are obese and who have functional impairments or medical complications that can benefit from weight loss.     

Electrophysiological evidence for the autoregulation of β-cell secretion by insulin

Electrophysiological studies of cultured rat pancreatic β-cells using intracellular microelectrodes show that exogenous insulin over the range of 0.1–10.0 μg/ml inhibits the electrical activity due to 27.8 mM glucose in a dose-related manner. This inhibitory effect is manifested by a mean increase of the membrane potential from about ?20 to ?30 mV and inhibition of the manner of cells impaled showing spike activity from 60 to less than 10%. The inhibitory influence of insulin is rapid occuring within 5 min for the highest level used. The results provide evidence for a negative feedback role of insulin in regulating its own release.     

Benzylpenicillin-induced filament formation of Clostridium perfringens

Growth of Clostridium perfringens with low concentrations of benzylpenicillin inhibited septum formation and division of the organisms. This resulted in continued growth of the organisms as aseptate filaments. The effect was reversed on removal of the antibiotic. The composition of walls isolated from organisms grown with the antibiotic was similar to that of walls from untreated bacteria. In addition, both contained non-N-acetylated glucosamine residues in their peptidoglycan. No differences were detected in the degree of cross-linkage of peptidoglycan. Clostridium perfringens contains six membrane-associated penicillin-binding proteins (PBPs) which have different affinities for [3H]benzylpenicillin. Concentrations of the antibiotic which were sufficient to cause filamentation of apparently all organisms in a culture caused almost complete saturation of PBPs 3, 4, 5 and 6. At these concentrations there was no measurable interaction with PBPs 1 and 2. Thus interaction of the antibiotic with the lower molecular weight PBPs is correlated with the inhibition of septum formation in C. perfringens.     

X-ray diffraction and time-resolved fluorescence analyses of Aequorea green fluorescent protein crystals

The energy transfer protein, green fluorescent protein, from the hydromedusan jellyfish Aequorea victoria has been crystallized in two morphologies suitable for x-ray diffraction analysis. Hexagonal plates have been obtained in the P6122 or P6522 space group with a = b = 77.5, c = 370 A, and no more than three molecules per asymmetric unit. Monoclinic parallel-epipeds have been obtained in the C2 space group with a = 93.3, b = 66.5, c = 45.5 A, beta = 108 degrees, and one molecule per asymmetric unit. The monoclinic form is better suited for use in a structure determination, and a data set was collected from the native crystal. Time-resolved fluorescence measurements of large single crystals are possible due to the unique, covalently bound chromophore present in this molecule. Fluorescence emission spectra of Aequorea green fluorescent protein in solution and from either the hexagonal or monoclinic single crystal show similar profiles suggesting that the conformations of protein in solution and in the crystal are similar. Multifrequency phase fluorimetric data obtained from a single crystal were best fit by a single fluorescence lifetime very close to that exhibited by the protein in solution. The complementary structural data obtained from fluorescence spectroscopy and x-ray diffraction crystallography will aid in the elucidation of this novel protein's structure-function relationship.     

Genetic comparisons of New and Old World coregonid fishes*

The genetic relationships among New and Old World coregonid fishes were studied by electrophoresis. The genetic composition of 60 populations, representing perhaps nine commonly recognized species of Coregonus and Stenodus from Europe and North America was determined for 37 genetic loci. Six distinct genetic groups were evident. The first contained only populations of the inconnu, Stenodus leucichthys (Güldenstadt). The Nei genetic distance between Stenodus and Coregonus was 0.305, a relatively small value as compared to other salmonid inter-generic comparisons. The second genetic grouping contained the Arctic cisco, C. autumnalis (Pallas), the N. American lake cisco, C. artedii Lesueur, and the Irish pollan, C. autumnalis pollan Thompson. These three taxa appear to be conspecific on the basis of genetic distances. The third genetic grouping contained the European whitefish, C. lavaretus (L.), and the N. American lake whitefish, C. clupeaformis (Mitchill). European and lake whitefish may be conspecific. Lake whitefish from northwestern N. America were more closely related to European whitefish (genetic distance 0.038) than to lake whitefish from central N. America (genetic distance 0.098). The fourth group contained the broad whitefish, C. nasus (Pallas), which is perhaps more closely related to the European/lake whitefish groups than other coregonids. The fifth genetic grouping contained only the Asian endemic, C. peled (Gmelin), and the sixth contained the least cisco, C. sardinella Valenciennes, and vendace, C. albula (L.), which also appear to be conspecific. The widespread genetic groupings obtained for ciscoes indicate that they do not constitute a single closely related group within the genus Coregonus.     

Trans-epidermal Transport and Storage of Calcium in Holthuisana transversa (Brachyura; Sundathelphusidae) During Premoult

Holthuisana transversa reabsorbs much of its exoskeletal calcium in the last 3 days before ecdysis and stores it in circulating granules in the haemocoel and in non-circulating granules in the subepidermal connective tissue. Calcium enters the epidermal cells from the moulting fluid, probably through their apical microvilli and is either incorporated into intracellular calcium granules or exits the cell via the basolateral membranes to be used in formation of two other granule types. Intracellular granules (0.4–2 μm long) form in large masses in the apical cytoplasm of the epidermal cells. They are formed as membrane-bound vesicles by the Golgi, and calcium and organic matrix material are added from the surrounding cytoplasm. As development proceeds, lamellae appear and calcium carbonate is deposited in the matrix. Granule masses move basally and are stored in the connective tissue. Calcium is also incorporated into extracellular large granules (0.8–3.8 μm long) which are formed in narrow intercellular channels between epidermal cells. A third granule type (small granules, 0.26 μm diameter) is formed in subepidermal connective tissue cells and released into the haemolymph in very large numbers. Calcium was identified in the two larger granule types using X-ray microanalysis and significant amounts of phosphorus and potassium were also present in the large granules. A model for ion cycling between the exoskeleton and granules is presented.