Cloning, expression, and purification of functional Sec11a and Sec11b, type I signal peptidases of the archaeon Haloferax volcanii

Across evolution, type I signal peptidases are responsible for the cleavage of secretory signal peptides from proteins following their translocation across membranes. In Archaea, type I signal peptidases combine domain-specific features with traits found in either their eukaryal or bacterial counterparts. Eukaryal and bacterial type I signal peptidases differ in terms of catalytic mechanism, pharmacological profile, and oligomeric status. In this study, genes encoding Sec11a and Sec11b, two type I signal peptidases of the halophilic archaeon Haloferax volcanii, were cloned. Although both genes are expressed in cells grown in rich medium, gene deletion approaches suggest that Sec11b, but not Sec11a, is essential. For purification purposes, tagged versions of the protein products of both genes were expressed in transformed Haloferax volcanii, with Sec11a and Sec11b being fused to a cellulose-binding domain capable of interaction with cellulose in hypersaline surroundings. By employing an in vitro signal peptidase assay designed for use with high salt concentrations such as those encountered by halophilic archaea such as Haloferax volcanii, the signal peptide-cleaving activities of both isolated membranes and purified Sec11a and Sec11b were addressed. The results show that the two enzymes differentially cleave the assay substrate, raising the possibility that the Sec11a and Sec11b serve distinct physiological functions.     

Sphingolipid depletion impairs endocytic traffic and inhibits Wingless signaling

Sphingolipids are an important part of the plasma membrane and implicated in a multitude of cellular processes. However, little is known about the role of sphingolipids in an epithelial context and their potential influence on the activity of signaling pathways. To shed light on these aspects we analyzed the consequences of changing ceramide levels in vivo in the Drosophila wing disc: an epithelial tissue in which the most fundamental signaling pathways, including the Wnt/Wg signaling pathway, are well characterized.We found that downregulation of Drosophila’s only ceramide synthase gene schlank led to defects in the endosomal trafficking of proteins. One of the affected proteins is the Wnt ligand Wingless (Wg) that accumulated. Unexpectedly, although Wg protein levels were raised, signaling activity of the Wg pathway was impaired. Recent work has spotlighted the central role of the endocytic trafficking in the transduction of the Wnt signal. Our results underscore this and support the view that sphingolipid levels are crucial in orchestrating epithelial endocytic trafficking in vivo. They further demonstrate that ceramide/sphingolipid levels can affect Wnt signaling.     

A bovine model of respiratory Chlamydia psittaci infection: challenge dose titration

This study aimed to establish and evaluate a bovine respiratory model of experimentally induced acute C. psittaci infection. Calves are natural hosts and pathogenesis may resemble the situation in humans. Intrabronchial inoculation of C. psittaci strain DC15 was performed in calves aged 2-3 months via bronchoscope at four different challenge doses from 10(6) to 10(9) inclusion-forming units (ifu) per animal. Control groups received either UV-inactivated C. psittaci or cell culture medium. While 10(6) ifu/calf resulted in a mild respiratory infection only, the doses of 10(7) and 10(8) induced fever, tachypnea, dry cough, and tachycardia that became apparent 2-3 days post inoculation (dpi) and lasted for about one week. In calves exposed to 10(9) ifu C. psittaci, the respiratory disease was accompanied by severe systemic illness (apathy, tremor, markedly reduced appetite). At the time point of most pronounced clinical signs (3 dpi) the extent of lung lesions was below 10% of pulmonary tissue in calves inoculated with 10(6) and 10(7) ifu, about 15% in calves inoculated with 10(8) and more than 30% in calves inoculated with 10(9) ifu C. psittaci. Beside clinical signs and pathologic lesions, the bacterial load of lung tissue and markers of pulmonary inflammation (i.e., cell counts, concentration of proteins and eicosanoids in broncho-alveolar lavage fluid) were positively associated with ifu of viable C. psittaci. While any effect of endotoxin has been ruled out, all effects could be attributed to infection by the replicating bacteria. In conclusion, the calf represents a suitable model of respiratory chlamydial infection. Dose titration revealed that both clinically latent and clinically manifest infection can be reproduced experimentally by either 10(6) or 10(8) ifu/calf of C. psittaci DC15 while doses above 10(8) ifu C. psittaci cannot be recommended for further studies for ethical reasons. This defined model of different clinical expressions of chlamydial infection allows studying host-pathogen interactions.     

Mutations in Leptin (LEP) Gene Are Associated with Carcass and Meat Quality Traits in Crossbreed Rabbits

Leptin is a hormone synthesized and secreted primarily in adipose cells that help to regulate energy balance. This study examined the associations of single nucleotide polymorphisms in the rabbit leptin gene with growth traits, slaughter traits and physicochemical parameters of New Zealand White (NZW) and Belgian Giant Grey (BGG) crossbreed rabbits. In total, 320 crossbreed animals were genotyped for polymorphisms within exon 2—g.16081633T>C, intron 1_2—g.16081420C>T, and within UTR—g.16079636C>G for association analysis. Identified polymorphisms within rabbits leptin gene showed significant differences for dissectible fat percentage in carcass and dissectible fat weight in intermediate part (g.16081633T>C). Moreover, meat traits like protein content (g.16081633T>C; g.16079636C>G), intramuscular fat content (g.16081633T>C; g.16079636C>G, g.16081420C>T), dry matter (g.16081420C>T), ash (g.16081420C>T), water (g.16081420C>T), and cohesiveness (g.16081420C>T, g.16079636C>G) were affected by polymorphisms in leptin gene. We conclude that polymorphism in the rabbit leptin gene influences important carcass and meat traits of NZW?×?BGG crossbreeds. Therefore, polymorphisms identified in this study may be used in selection as a meat trait markers.     

Design of recycling system for poly(methyl methacrylate) (PMMA). Part 2: process hazards and material flow analysis

Introduction

In this series of papers, we present a design of poly(methyl methacrylate) (PMMA) recycling system considering environmental impacts, chemical hazards, and resource availability. We applied life cycle assessment (LCA), environment, health, and safety (EHS) assessment as well as material flow analysis to the evaluation of the recycling system.

Purpose

Recycling systems for highly functional plastics such as PMMA have not been studied sufficiently. Along with the popularization of PMMA-containing products such as liquid crystal displays (LCDs), the use of PMMA is steadily increasing, which will result in more waste of PMMA in the next decades. In this study, pyrolysis process for recycling waste PMMA into methyl methacrylate (MMA) monomer was examined, considering not only general environmental impacts quantified by life cycle assessment but also local environment, health, and safety hazards, and raw material availability.

Methods

Process EHS hazards assessment was applied to quantify the local effects of the PMMA monomer recycling process. Process hazards are strongly connected with the hazardous properties of chemical substances and stream conditions within the process. Two alternative cooling methods exist, and their difference was analyzed by LCA and EHS assessment. Besides the process hazard, the availability of waste PMMA must be an important point for the feasibility of implementing the PMMA monomer recycling process. The available amount can be quantified by analyzing the material flow of PMMA-containing products. PMMA contained in LCDs as light guide panels was selected as a feasible source of waste PMMA, and the quantity of PMMA flows in the society was evaluated.

Results and discussion

In the case of PMMA, monomer recycling has less process hazard than the production of fresh MMA from crude oil. The implementation of circulated cooling water could significantly decrease the process hazard in PMMA pyrolysis attributable to chemical hazards. Material flow analysis revealed that the availability of waste PMMA shows a fluctuating trend in the next 20 years because of the sharp peak demand for LCD television sets. The fluctuation is strongly dependent on the lifetime of LCD television sets.

Conclusions

PMMA monomer recycling has a potential to reduce environmental impacts with a less process hazards than fresh MMA production from crude oil. The availability of waste PMMA has a strong relationship with the lifetime of LCD television sets. The multiple and comprehensive assessments can reveal various aspects of a process technology.     

Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals

The prothrombin (F2) 3' end formation signal is highly susceptible to thrombophilia-associated gain-of-function mutations. In its unusual architecture, the F2 3' UTR contains an upstream sequence element (USE) that compensates for weak activities of the non-canonical cleavage site and the downstream U-rich element. Here, we address the mechanism of USE function. We show that the F2 USE contains a highly conserved nonameric core sequence, which promotes 3' end formation in a position- and sequence-dependent manner. We identify proteins that specifically interact with the USE, and demonstrate their function as trans-acting factors that promote 3' end formation. Interestingly, these include the splicing factors U2AF35, U2AF65 and hnRNPI. We show that these splicing factors not only modulate 3' end formation via the USEs contained in the F2 and the complement C2 mRNAs, but also in the biocomputationally identified BCL2L2, IVNS and ACTR mRNAs, suggesting a broader functional role. These data uncover a novel mechanism that functionally links the splicing and 3' end formation machineries of multiple cellular mRNAs in an USE-dependent manner.     

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals — a cure and a vaccine – remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.

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