Novel attempts launched toward universal Sarbecovirus vaccine

The emergence of severe acute respiratory syndrome corona-virus 2 (SARS-CoV-2) variants and new coronaviruses raise the demand for universal vaccines.In recent ...     

Structural and biochemical insights into 7β‐hydroxysteroid dehydrogenase stereoselectivity

Hydroxysteroid dehydrogenases are of great interest as biocatalysts for transformations involving steroid substrates. They feature a high degree of stereo‐ and regio‐selectivity, acting on a defined atom with a specific configuration of the steroid nucleus. The crystal structure of 7β‐hydroxysteroid dehydrogenase from Collinsella aerofaciens reveals a loop gating active‐site accessibility, the bases of the specificity for NADP⁺, and the general architecture of the steroid binding site. Comparison with 7α‐hydroxysteroid dehydrogenase provides a rationale for the opposite stereoselectivity. The presence of a C‐terminal extension reshapes the substrate site of the β‐selective enzyme, possibly leading to an inverted orientation of the bound substrate. Proteins 2016; 84:859–865. © 2016 Wiley Periodicals, Inc.     

Tools and methodologies to support more sustainable biofuel feedstock production

Increasingly, government regulations, voluntary standards, and company guidelines require that biofuel production complies with sustainability criteria. For some stakeholders, however, compliance with these criteria may seem complex, costly, or unfeasible. What exiting tools, then, might facilitate compliance with a variety of biofuel-related sustainability criteria? This paper presents four existing tools and methodologies that can help stakeholders assess (and mitigate) potential risks associated with feedstock production, and can thus facilitate compliance with requirements under different requirement systems. These include the Integrated Biodiversity Assessment Tool (IBAT), the ARtificial Intelligence for Ecosystem Services (ARIES) tool, the Responsible Cultivation Areas (RCA) methodology, and the related Biofuels + Forest Carbon (Biofuel + FC) methodology.     

Coupling solid phase microextraction to complementary separation platforms for metabotyping of <Emphasis Type="Italic">E. coli</Emphasis> metabolome in response to natural antibacterial agents

Introduction

Essential oils are known to possess antimicrobial activity; thus, their use has played an important role over the years in medicine and for food preservation purposes.

Objective

The effect of clove oil and its major constituents as bactericidal agents on the global metabolic profiling of E. coli bacteria was assessed by means of metabolic alterations, using solid phase microextraction (SPME) as a sample preparation method coupled to complementary analytical platforms.

Method

E. Coli cultures treated with clove oil and its major individual components were sampled by HS-SPME-GCxGC-ToF/MS and SPME-UPLC–MS. Full factorial design was applied in order to estimate the most effective antibacterial agent towards E. coli. Central composite design and factorial design were applied to investigate parameters influencing metabolite coverage and efficiency by SPME.

Results

The metabolic profile, including 500 metabolites identified by LC–MS and 789 components detected by GCxGC-ToF/MS, 125 of which were identified as dysregulated metabolites, revealed changes in the metabolome provoked by the antibacterial activity of clove oil, and in particular its major constituent eugenol. Analyses of individual components selected using orthogonal projections to latent structures discriminant analysis showed a neat differentiation between control samples in comparison to treated samples in various sets of metabolic pathways.

Conclusions

The combination of a sample preparation method capable of providing cleaner extracts coupled to different analytical platforms was successful in uncovering changes in metabolic pathways associated with lipids biodegradation, changes in the TCA cycle, amino acids, and enzyme inhibitors in response to antibacterial treatment.

     

A framework for the practical science necessary to restore sustainable,resilient, and biodiverse ecosystems

Demand for restoration of resilient, self‐sustaining, and biodiverse natural ecosystems as a conservation measure is increasing globally; however, restoration efforts frequently fail to meet standards appropriate for this objective. Achieving these standards requires management underpinned by input from diverse scientific disciplines including ecology, biotechnology, engineering, soil science, ecophysiology, and genetics. Despite increasing restoration research activity, a gap between the immediate needs of restoration practitioners and the outputs of restoration science often limits the effectiveness of restoration programs. Regrettably, studies often fail to identify the practical issues most critical for restoration success. We propose that part of this oversight may result from the absence of a considered statement of the necessary practical restoration science questions. Here we develop a comprehensive framework of the research required to bridge this gap and guide effective restoration. We structure questions in five themes: (1) setting targets and planning for success, (2) sourcing biological material, (3) optimizing establishment, (4) facilitating growth and survival, and (5) restoring resilience, sustainability, and landscape integration. This framework will assist restoration practitioners and scientists to identify knowledge gaps and develop strategic research focused on applied outcomes. The breadth of questions highlights the importance of cross‐discipline collaboration among restoration scientists, and while the program is broad, successful restoration projects have typically invested in many or most of these themes. Achieving restoration ecology's goal of averting biodiversity losses is a vast challenge: investment in appropriate science is urgently needed for ecological restoration to fulfill its potential and meet demand as a conservation tool.     

Additive effect of TAp63 deficiency on the adrenocortical dysplasia (acd) phenotype

Adrenocortical dysplasia (acd) is a spontaneous autosomal recessive mouse mutation exhibiting caudal truncation, vertebral segmentation defects, hydronephrosis, limb hypoplasia, and perinatal lethality. Acd encodes TPP1, a component of the shelterin complex that maintains telomere integrity, and consequently acd mutant mice have telomere dysfunction and genomic instability. We previously showed that apoptosis is the primary mechanism causing the acd skeletal phenotype, and that p53 deficiency rescues the skeletal defects of the acd phenotype but has no effect on the perinatal lethality. The Trp63 gene encodes multiple isoforms, which play a role in proliferation, apoptosis, and stem/progenitor cell maintenance. Different p63 isoforms exhibit both proapoptotic (TAp63) and antiapoptotic (ΔNp63) functions. We hypothesized that deficiency of proapoptotic TAp63 isoforms might rescue the acd skeletal phenotype, similar to our previous observations with deficiency of p53. Mice heterozygous for a null allele of TAp63 were crossed to heterozygous acd mice to determine the effect of TAp63 deficiency on the acd mutant phenotype. In contrast to our results with the acd?×?p53 cross, skeletal anomalies were not rescued by deficiency of TAp63. In fact, the limb and vertebral anomalies observed in double-mutant embryos were more severe than those of embryos with the acd mutation alone, demonstrating a dose-dependent effect. These studies suggest that TAp63 isoforms do not facilitate p53-like apoptosis during development in response to acd-mediated telomere dysfunction and are consistent with the proposed roles of TAp63 in maintaining genomic stability.     

The role of apolipoprotein A-I helix 10 in apolipoprotein-mediated cholesterol efflux via the ATP-binding cassette transporter ABCA1

Recent studies of Tangier disease have shown that the ATP-binding cassette transporter A1 (ABCA1)/apolipoprotein A-I (apoA-I) interaction is critical for high density lipoprotein particle formation, apoA-I integrity, and proper reverse cholesterol transport. However, the specifics of this interaction are unknown. It has been suggested that amphipathic helices of apoA-I bind to a lipid domain created by the ABCA1 transporter. Alternatively, apoA-I may bind directly to ABCA1 itself. To better understand this interaction, we created several truncation mutants of apoA-I and then followed up with more specific point mutants and helix translocation mutants to identify and characterize the locations of apoA-I required for ABCA1-mediated cholesterol efflux. We found that deletion of residues 221-243 (helix 10) abolished ABCA1-mediated cholesterol efflux from cultured RAW mouse macrophages treated with 8-bromo-cAMP. Point mutations in helix 10 that affected the helical charge distribution reduced ABCA1-mediated cholesterol efflux versus the wild type. We noted a strong positive correlation between cholesterol efflux and the lipid binding characteristics of apoA-I when mutations were made in helix 10. However, there was no such correlation for helix translocations in other areas of the protein as long as helix 10 remained intact at the C terminus. From these observations, we propose an alternative model for apolipoprotein-mediated efflux.