Chromosome‐level hybrid de novo genome assemblies as an attainable option for nonmodel insects

The emergence of third‐generation sequencing (3GS; long‐reads) is bringing closer the goal of chromosome‐size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of nonmodel organisms. However, long‐read technologies result in higher sequencing error rates and therefore impose an elevated cost of sufficient coverage to achieve high enough quality. In this context, hybrid assemblies, combining short‐reads and long‐reads, provide an alternative efficient and cost‐effective approach to generate de novo, chromosome‐level genome assemblies. The array of available software programs for hybrid genome assembly, sequence correction and manipulation are constantly being expanded and improved. This makes it difficult for nonexperts to find efficient, fast and tractable computational solutions for genome assembly, especially in the case of nonmodel organisms lacking a reference genome or one from a closely related species. In this study, we review and test the most recent pipelines for hybrid assemblies, comparing the model organism Drosophila melanogaster to a nonmodel cactophilic Drosophila, D. mojavensis. We show that it is possible to achieve excellent contiguity on this nonmodel organism using the dbg2olc pipeline.     

Using richness of native and non-native aquatic species along a climatic gradient to test the intermediate disturbance hypothesis

The intermediate disturbance hypothesis (IDH) has been thoroughly investigated, but much controversy has been found for supporting its assumptions, which rely largely on the nature of the disturbance, spatial scale, and biological predictors tested. In this paper, richness of native and non-native species along a suite of Neotropical aquatic ecosystems across a broad latitudinal and geographical range was used to test the IDH predictions. An extensive literature survey was performed to compile native species richness and the occurrence of several taxonomic groups listed as non-native for twenty-four coastal rivers and bays evenly distributed into three climatic zones (tropical, transitional, and subtropical). The climatic gradient was confirmed by NMDS and PERMANOVA, but IDH predictions were only significantly supported for native and total species richness in the coastal bays. The distribution patterns of non-native marine species showed a linear instead unimodal pattern of increase with latitudinal climatic gradient, but the responses are complex and dependent of many non-exclusive factors, such as the sampling effort per ecosystem and the potential interference of other disturbance gradients that should be further addressed to unravel the role of IDH for non-native species distribution.

     

Parotocinclus jacksoni,a new hypoptopomatine catfish (Siluriformes: Loricariidae) from the Rio Mamanguape basin,north-eastern Brazil

A new species of Parotocinclus is described from the Rio Mamanguape basin, in the State of Paraíba, north-eastern Brazil. The new species can be distinguished from all of its congeners, except for P. bahiensis, P. cesarpintoi, P. jumbo, P. nandae and P. spilosoma, by the presence of an abdomen covered by a few small and dispersed platelets (vs. an abdomen entirely covered by large plates in adult individuals or the absence of plates in that region). The new species differs from those mentioned above with respect to several features, such as an exposed pectoral girdle and supporting odontodes medially and laterally, the number of premaxillary and dentary teeth, odontodes covering only the lateral portion of the cleithrum and the absence of irregular golden lines on the head and body (colour in vivo). The new species was collected only in the upper and middle portions of the Rio Mamanguape basin, suggesting a geographic distribution restricted to the Caatinga biome.     

The signaling requirements for mouse embryonic stem cells

Comment on: ten Berge D, et al. Nat Cell Biol 2011; 13:1070-5. doi:10.1038/ncb2314     

Solid-Phase Synthesis of Oligodeoxyribonucleotide Analogues Containing 5, 6-Dihydroimidazo [1, 2-c] Pyrimidin-5-One as a Base Moiety

Abstract

The synthesis on a polyacrylamide resin of oligonucleotides containing 5,6-dihydroimidazo [1, 2-c] pyrimidin-5-one (X) as a base residue is described. Perliminary results on enzymatic hydrolysis of the modified octanucleotide d(TXAATTCA) (21), containing. the recognition sequence for the endonuclease -ECO RI where dG is replaced by dX (1), are reported.     

Synthesis of Bridged Pyrimidine Nucleosides and Triazo [4, 3-c] Pyrimidine Nucleoside Analogues

Abstract

The synthesis and the spectral characterization of a number of N⁴-N⁴ bridged pyrimidine nucleosides and triazo [4, 3-c] pyrimidine nucleoside analogues are reported.     

Metagenomic Analysis of a Tropical Composting Operation at the S?o Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.     

A Cell System for Phenotypic Screening of Modifiers of SMN2 Gene Expression and Function

Spinal muscular atrophy (SMA) is an inherited neurodegenerative disease caused by homozygous inactivation of the SMN1 gene and reduced levels of the survival motor neuron (SMN) protein. Since higher copy numbers of the nearly identical SMN2 gene reduce disease severity, to date most efforts to develop a therapy for SMA have focused on enhancing SMN expression. Identification of alternative therapeutic approaches has partly been hindered by limited knowledge of potential targets and the lack of cell-based screening assays that serve as readouts of SMN function. Here, we established a cell system in which proliferation of cultured mouse fibroblasts is dependent on functional SMN produced from the SMN2 gene. To do so, we introduced the entire human SMN2 gene into NIH3T3 cell lines in which regulated knockdown of endogenous mouse Smn severely decreases cell proliferation. We found that low SMN2 copy number has modest effects on the cell proliferation phenotype induced by Smn depletion, while high SMN2 copy number is strongly protective. Additionally, cell proliferation correlates with the level of SMN activity in small nuclear ribonucleoprotein assembly. Following miniaturization into a high-throughput format, our cell-based phenotypic assay accurately measures the beneficial effects of both pharmacological and genetic treatments leading to SMN upregulation. This cell model provides a novel platform for phenotypic screening of modifiers of SMN2 gene expression and function that act through multiple mechanisms, and a powerful new tool for studies of SMN biology and SMA therapeutic development.     

Full Inhibition of Spinal FAAH Leads to TRPV1-Mediated Analgesic Effects in Neuropathic Rats and Possible Lipoxygenase-Mediated Remodeling of Anandamide Metabolism

Neuropathic pain elevates spinal anandamide (AEA) levels in a way further increased when URB597, an inhibitor of AEA hydrolysis by fatty acid amide hydrolase (FAAH), is injected intrathecally. Spinal AEA reduces neuropathic pain by acting at both cannabinoid CB1 receptors and transient receptor potential vanilloid-1 (TRPV1) channels. Yet, intrathecal URB597 is only partially effective at counteracting neuropathic pain. We investigated the effect of high doses of intrathecal URB597 on allodynia and hyperalgesia in rats with chronic constriction injury (CCI) of the sciatic nerve. Among those tested, the 200 µg/rat dose of URB597 was the only one that elevated the levels of the FAAH non-endocannabinoid and anti-inflammatory substrates, oleoylethanolamide (OEA) and palmitoylethanolamide (PEA), and of the endocannabinoid FAAH substrate, 2-arachidonoylglycerol, and fully inhibited thermal and tactile nociception, although in a manner blocked almost uniquely by TRPV1 antagonism. Surprisingly, this dose of URB597 decreased spinal AEA levels. RT-qPCR and western blot analyses demonstrated altered spinal expression of lipoxygenases (LOX), and baicalein, an inhibitor of 12/15-LOX, significantly reduced URB597 analgesic effects, suggesting the occurrence of alternative pathways of AEA metabolism. Using immunofluorescence techniques, FAAH, 15-LOX and TRPV1 were found to co-localize in dorsal spinal horn neurons of CCI rats. Finally, 15-hydroxy-AEA, a 15-LOX derivative of AEA, potently and efficaciously activated the rat recombinant TRPV1 channel. We suggest that intrathecally injected URB597 at full analgesic efficacy unmasks a secondary route of AEA metabolism via 15-LOX with possible formation of 15-hydroxy-AEA, which, together with OEA and PEA, may contribute at producing TRPV1-mediated analgesia in CCI rats.     

Preadult Parental Diet Affects Offspring Development and Metabolism in Drosophila melanogaster

When Drosophila melanogaster larvae are reared on isocaloric diets differing in their amounts of protein relative to sugar, emerging adults exhibit significantly different development times and metabolic pools of protein, glycogen and trigylcerides. In the current study, we show that the influence of larval diet experienced during just one generation extends into the next generation, even when that subsequent generation had been shifted to a standard diet during development. Offspring of flies that were reared on high protein relative to sugar underwent metamorphosis significantly faster, had higher reproductive outputs, and different metabolic pool contents compared to the offspring of adults from low protein relative to sugar diets. In addition, isofemale lines differed in the degree to which parental effects were observed, suggesting a genetic component to the observed transgenerational influences.