Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small‐scale reproducibility

DNA sequencing of ancient permafrost samples can be used to reconstruct past plant, animal and bacterial communities. In this study, we assess the small‐scale reproducibility of taxonomic composition obtained from sequencing four molecular markers (mitochondrial 12S ribosomal DNA (rDNA), prokaryote 16S rDNA, mitochondrial cox1 and chloroplast trnL intron) from two soil cores sampled 10 cm apart. In addition, sequenced control reactions were used to produce a contaminant library that was used to filter similar sequences from sample libraries. Contaminant filtering resulted in the removal of 1% of reads or 0.3% of operational taxonomic units. We found similar richness, overlap, abundance and taxonomic diversity from the 12S, 16S and trnL markers from each soil core. Jaccard dissimilarity across the two soil cores was highest for metazoan taxa detected by the 12S and cox1 markers. Taxonomic community distances were similar for each marker across the two soil cores when the chi‐squared metric was used; however, the 12S and cox1 markers did not cluster well when the Goodall similarity metric was used. A comparison of plant macrofossil vs. read abundance corroborates previous work that suggests eastern Beringia was dominated by grasses and forbs during cold stages of the Pleistocene, a habitat that is restricted to isolated sites in the present‐day Yukon.     

Production of milk-derived bioactive peptides as precursor chimeric proteins in chloroplasts of Chlamydomonas reinhardtii

Bioactive peptides are considered high value-added ingredients in functional foods, and the main sources of these are milk, egg, plants, among others. A major limitation in their commercial use is the cost of production. This study deals with the design and production of a chimeric protein in chloroplasts of the microalgae Chlamydomonas reinhardtii to generate bioactive peptides of antihypertensive, opioid, antimicrobial, and hypocholesterolemic activities. A synthetic gene, designated as NCQ, coding for the selected chimeric protein, is transferred to C. reinhardtii using biolistic bombardment. Transplastomic transformants have been identified by PCR and Western blots following selection on a spectinomycin-containing medium. An ELISA quantification assay has revealed that the expressed NCQ protein accumulated at levels ranging between 0.16 and 2.4 % of total soluble protein. These findings demonstrate that chloroplasts of C. reinhardtii could serve as a robust expression platform for production of bioactive peptides.     

Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

? The internal transcribed spacer (ITS) of the nuclear ribosomal DNA region is a widely used species marker for plants and fungi. Recent metagenomic studies using next-generation sequencing, however, generate only partial ITS sequences. Here we compare the performance of partial and full-length ITS sequences with several classification methods. ? We compiled a full-length ITS data set and created short fragments to simulate the read lengths commonly recovered from current next-generation sequencing platforms. We compared recovery, erroneous recovery, and coverage for the following methods: best BLAST hit classification, MEGAN classification, and automated phylogenetic assignment using the Statistical Assignment Program (SAP). ? We found that summarizing results with more inclusive taxonomic ranks increased recovery and reduced erroneous recovery. The similarity-based methods BLAST and MEGAN performed consistently across most fragment lengths. Using a phylogeny-based method, SAP runs with queries 400 bp or longer worked best. Overall, BLAST had the highest recovery rates and MEGAN had the lowest erroneous recovery rates. ? A high-throughput ITS classification method should be selected, taking into consideration read length, an acceptable tradeoff between maximizing the total number of classifications and minimizing the number of erroneous classifications, and the computational speed of the assignment method.     

Advanced glycation endproducts and their pathogenic roles in neurological disorders

Glycation is implicated in neurological disorders. In some cases it plays a key role in the pathogenesis, in others it plays a co-adjuvant role or it appears as a consequence of degenerative changes and protein accumulation stemming from other pathways. In this work, we attempt to provide a concise, updated review of the major recent findings concerning glycation in neurological diseases. After a short introduction covering advanced glycation endproducts (AGEs) and the receptor for AGEs (RAGE), we will discuss the impact of glycation in central nervous system disorders including Alzheimer’s, Parkinson’s and Creutzfeldt–Jakob disease, as well as peripheral diabetic polyneuropathies. Therapies directed at lowering the concentrations of RAGE ligands including AGEs, blocking RAGE signaling, preventing oxidative stress or lowering methylglyoxal (MGO) levels may significantly decrease the development of AGE-related pathologies in patients with neurological disorders. Many drugs are on the pipeline and the future clinical trials will reveal if the promising results translate into clinical application.     

Self‐association of streptococcus pyogenes collagen‐like constructs into higher order structures

A number of bacterial collagen‐like proteins with Gly as every third residue and a high Pro content have been observed to form stable triple‐helical structures despite the absence of hydroxyproline (Hyp). Here, the high yield cold‐shock expression system is used to obtain purified recombinant collagen‐like protein (V‐CL) from Streptococcus pyogenes containing an N‐terminal globular domain V followed by the collagen triple‐helix domain CL and the modified construct with two tandem collagen domains V‐CL‐CL. Both constructs and their isolated collagenous domains form stable triple‐helices characterized by very sharp thermal transitions at 35–37°C and by high values of calorimetric enthalpy. Procedures for the formation of collagen SLS crystallites lead to parallel arrays of in register V‐CL‐CL molecules, as well as centrosymmetric arrays of dimers joined at their globular domains. At neutral pH and high concentrations, the bacterial constructs all show a tendency towards aggregation. The isolated collagen domains, CL and CL‐CL, form units of diameter 4–5 nm which bundle together and twist to make larger fibrillar structures. Thus, although this S. pyogenes collagen‐like protein is a cell surface protein with no indication of participation in higher order structure, the triple‐helix domain has the potential of forming fibrillar structures even in the absence of hydroxyproline. The formation of fibrils suggests bacterial collagen proteins may be useful for biomaterials and tissue engineering applications.     

Arginase-negative mutants of Arabidopsis exhibit increased nitric oxide signaling in root development

Mutation of either arginase structural gene (ARGAH1 or ARGAH2 encoding arginine [Arg] amidohydrolase-1 and -2, respectively) resulted in increased formation of lateral and adventitious roots in Arabidopsis (Arabidopsis thaliana) seedlings and increased nitric oxide (NO) accumulation and efflux, detected by the fluorogenic traps 3-amino,4-aminomethyl-2',7'-difluorofluorescein diacetate and diamino-rhodamine-4M, respectively. Upon seedling exposure to the synthetic auxin naphthaleneacetic acid, NO accumulation was differentially enhanced in argah1-1 and argah2-1 compared with the wild type. In all genotypes, much 3-amino,4-aminomethyl-2',7'-difluorofluorescein diacetate fluorescence originated from mitochondria. The arginases are both localized to the mitochondrial matrix and closely related. However, their expression levels and patterns differ: ARGAH1 encoded the minor activity, and ARGAH1-driven beta-glucuronidase (GUS) was expressed throughout the seedling; the ARGAH2::GUS expression pattern was more localized. Naphthaleneacetic acid increased seedling lateral root numbers (total lateral roots per primary root) in the mutants to twice the number in the wild type, consistent with increased internal NO leading to enhanced auxin signaling in roots. In agreement, argah1-1 and argah2-1 showed increased expression of the auxin-responsive reporter DR5::GUS in root tips, emerging lateral roots, and hypocotyls. We propose that Arg, or an Arg derivative, is a potential NO source and that reduced arginase activity in the mutants results in greater conversion of Arg to NO, thereby potentiating auxin action in roots. This model is supported by supplemental Arg induction of adventitious roots and increased NO accumulation in argah1-1 and argah2-1 versus the wild type.     

Predicted and verified distributions of <Emphasis Type="Italic">Ateles geoffroyi</Emphasis> and <Emphasis Type="Italic">Alouatta palliata</Emphasis> in Oaxaca,Mexico

Primate conservation requires a better knowledge of the distributions and statuses of populations in both large areas of habitat and in areas for which we currently have no information. We focused on spider monkeys (Ateles geoffroyi) and howler monkeys (Alouatta palliata) in the state of Oaxaca, Mexico. This Mexican state has protected large tracts of forest, and has historical records for both primates, although very little is known about them. To update our knowledge of the distributions of these primates and identify potential areas in which they are present, we modeled their geographic distributions by characterizing their ecological niches using the genetic algorithm for rule-set production (GARP), performed interviews and carried out field surveys. The predicted distributions, surveys and interviews indicate that the distributions of these primates are restricted to northeastern Oaxaca. The results suggest that spider monkeys occupy a wider area and elevational range than howler monkeys. Throughout that range there is a wide variety of suitable habitats for these primates. Most of the sites where monkeys were recorded in the field are not officially protected and there was evidence of hunting and habitat destruction. It is important to improve protection, economic alternatives and environmental education as we move towards an integral solution for the conservation of these species. Validation of the GARP model was done for A. geoffroyi, since we had obtained enough field data for this species; this validation indicated that the predicted distribution of the species was statistically better than expected by chance. Hence, ecological niche modeling is a useful approach when performing an initial assessment to identify distribution patterns, detecting suitable areas for future exploration, and for conservation planning. Our findings provide an improved basis for primate conservation and productive fieldwork in Oaxaca.