Vif Proteins from Diverse Primate Lentiviral Lineages Use the Same Binding Site in APOBEC3G

APOBEC3G (A3G) is a cytidine deaminase that restricts human immunodeficiency virus type 1 (HIV-1) and other lentiviruses. Most of these viruses encode a Vif protein that directly binds A3G and leads to its proteasomal degradation. Both Vif proteins of HIV-1 and African green monkey simian immunodeficiency virus (SIVagm) bind residue 128 of A3G. However, this position does not control the A3G degradation by Vif variants derived from HIV-2 and SIVmac, which both originated from SIV of sooty mangabey monkeys (SIVsmm), suggesting that the A3G binding site for Vif proteins of the SIVsmm/HIV-2 lineage differs from that of HIV-1. To map the SIVsmm Vif binding site of A3G, we performed immunoprecipitations of individual A3G domains, Vif/A3G degradation assays and a detailed mutational analysis of human A3G. We show that A3G residue 129, but not the adjacent position 128, confers susceptibility to degradation by SIVsmm Vif. An artificial A3G mutant, the P129D mutant, was resistant to degradation by diverse Vifs from HIV-1, HIV-2, SIVagm, and chimpanzee SIV (SIVcpz), suggesting a conserved lentiviral Vif binding site. Gorilla A3G naturally contains a glutamine (Q) at position 129, which makes its A3G resistant to Vifs from diverse lineages. We speculate that gorilla A3G serves as a barrier against SIVcpz strains. In summary, we show that Vif proteins from distinct lineages bind to the same A3G loop, which includes positions 128 and 129. The multiple adaptations within this loop among diverse primates underscore the importance of counteracting A3G in lentiviral evolution.     

A comparison of the strength of biodiversity effects across multiple functions

In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.     

Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo‐West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach‐cast, remote‐biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population‐level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as‐yet‐unnamed species off northern Australia).     

Common and divergent functions of Beclin 1 and Beclin 2

In a recent paper published in Cell, He and colleagues reported the identification and functional characterization of Beclin 2, a mammal-specific homolog of the evolutionarily conserved autophagy-regulatory and oncosuppressive factor Beclin 1. In spite of a non-negligible degree of sequence identity, Beclin 1 and Beclin 2 differ from each other in multiple aspects, including their functional profile as well as the genomic organization of the respective loci.Originally identified as a BCL-2-interacting partner capable of protecting mice from viral encephalitis¹, Beclin 1 — the mammalian ortholog of yeast Atg6 — is nowadays well known as a core component of the class III phosphoinosite-3-kinase (PI3K) enzymatic complex that initiates the formation of autophagosomes in the course of macroautophagy (hereafter referred to as autophagy)². Presumably owing to the critical function of autophagy in embryonic development, mice lacking both copies of the Beclin 1-coding gene (Becn1) die early during embryogenesis. Moreover, Becn1^+/− mice suffer from a high incidence of spontaneous tumors, indicating that Beclin 1 acts as a haploinsufficient tumor suppressor³. At least in part, this reflects the central role that autophagy plays in the maintenance of intracellular homeostasis. Indeed, baseline levels of autophagy mediate the removal of various cytoplasmic entities that might favor oncogenesis, including damaged mitochondria and protein aggregates⁴. Conversely, established neoplasms often harness the cytoprotective functions of autophagy to their own benefit². The pathophysiological relevance of autophagy is not limited to cancer, but extends to a large panel of human diseases, including neurodegenerative, cardiovascular and infectious conditions⁵. Thus, during the last decade autophagy-regulatory signaling pathways have been intensively investigated.Until now, Beclin 1 was considered as the only Beclin encoded by the mammalian genome, sharing some degree of structural homology with so-called “BH3-only” proteins, pro-apoptotic members of the BCL-2 family that are involved in the activation of cell death in response to stress⁶. In a recent paper published in Cell, the research group led by Beth Levine⁷ identified a human and a mouse protein sharing 57% and 44% sequence identity with human and mouse Beclin 1, respectively, de facto unveiling the existence of an additional, mammal-specific ortholog of Atg6, Beclin 2. The mouse Beclin 2 mRNA was detected in multiple organs including the brain, skeletal muscle, placenta, thymus and uterus, as was the human protein in both fetal and adult brain tissues. These data demonstrate that the current classification of mouse and human Beclin 2-encoding genes (i.e., {"type":"entrez-nucleotide","attrs":{"text":"NG_022940","term_id":"298676453","term_text":"NG_022940"}}NG_022940 and {"type":"entrez-nucleotide","attrs":{"text":"NG_028451","term_id":"331028236","term_text":"NG_028451"}}NG_028451) as pseudogenes is incorrect.The knockdown of Beclin 2 reduced several manifestations of basal or starvation-induced autophagy in cultured mammalian cells, including the degradation of the autophagic substrate p62, the aggregation of a fluorescent form of LC3 into cytoplasmic dots and the lipidation of endogenous LC3. All such effects, which were not due to an increased autophagosomal turnover (as verified in the presence of the lysosomal inhibitor bafilomycin A1), could be rescued upon the transgene-driven expression of a non-interferable Beclin 2 variant. Thus, similar to Beclin 1, Beclin 2 regulates autophagy⁷. In fact, Beclin 2 turned out to physically interact with several (but not all) components of the class III PI3K complex organized around Beclin 1, including the catalytic subunit VPS34 as well as the regulatory factors ATG14, AMBRA1 and UVRAG, but not RUBICON (Figure 1A). Beclin 2 also appeared to share with Beclin 1 the ability to bind BCL-2, although only the latter gets dissociated from such an interaction in the course of stress-induced autophagy^7,8. As the greatest divergence between mammalian Beclins involves their N terminus, He and colleagues employed the N-terminal domain of Beclin 2 as a bait in a yeast two-hybrid screen, and identified G protein-coupled receptor (GPCR)-associated sorting protein 1 (GASP1) as a Beclin 2-specific interactor. Thus, similar to GASP1 (but not to Beclin 1), Beclin 2 was required for the agonist-induced lysosomal degradation of a subset of GPCRs including opioid receptor δ1 (DOR) and cannabinoid receptor 1 (CB1R). Importantly, such an activity, but not the capacity of Beclin 2 to regulate autophagic responses, appears to rely on the physical interaction between Beclin 2 and GASP1.Open in a separate windowFigure 1Common and divergent functions of mammalian Beclins. Specificity of the main interactors (A) and functions (B) ascribed to mammalian Beclin 1 and Beclin 2 to date. GPCR, G protein-coupled receptor; RTK, receptor tyrosine kinase.To obtain insights into the physiological functions of Beclin 2, He and colleagues attempted to generate Becn2^−/− mice, finding that these animals survived embryonic and early post-natal development at sub-Mendelian rates (approximately 4%). Not only Becn2^+/− and Becn2^−/− mouse embryonic fibroblasts, but also the brain of Becn2^+/− animals exhibited significant autophagic defects, corroborating the role of Beclin 2 in the regulation of autophagy in vivo. Moreover, these genotypes were associated with increased basal levels of multiple GPCRs, including CB1R and dopamine receptor D2 (DRD2)⁷. In line with the notion that increased CB1R signaling accrues food intake and hence favors obesity and insulin resistance, while pharmacological or genetic CB1R inhibition has opposite effects⁹, Becn2^+/− mice accumulated more weight than their wild-type littermates in response to a standard (as well as to a high-fat) diet. At odds with their Becn1^+/− counterparts, Becn2^+/− mice also exhibited impaired glucose tolerance and decreased insulin sensitivity, two effects that could be reverted by a chemical CB1R antagonist⁷. Taken together, these data demonstrate that besides regulating autophagy, Beclin 2 plays a unique role in glucose metabolism.Beclin 1 is known to regulate various processes other than autophagy, including vacuolar protein sorting and the degradation of specific growth factor receptors¹⁰. Thus, in spite of 44% - 57% sequence identity, the two mammalian Beclins described to date are relatively different from each other, exhibiting functional profiles that overlap to a limited degree (Figure 1B). Interestingly, He and colleagues have previously shown that defects in stimulus-induced autophagy (including those introduced by the Becn1^+/− genotype) are coupled to decreased endurance and altered glucose metabolism during acute exercise, as well as with an impaired capacity of training to protect mice against diet-induced glucose intolerance⁸. Part of these phenomena were shown to reflect defects in the AMP-activated protein kinase (AMPK)-dependent exposure of glucose transporters on the plasma membrane of skeletal muscle cells. It is therefore tempting to speculate that the metabolic phenotype of Becn2^+/− may in part originate from peripheral defects in glucose handling linked to autophagy. Thus, although the force driving the divergence of mammalian Beclins remains to be elucidated, it may reflect the need for an integrated regulation of central and peripheral mechanisms of metabolic homeostasis. Further studies are required to address this hypothesis.     

Life Cycle Impact Assessment—where we are, trends, and next steps: a late report from a UNEP/SETAC Life Cycle Initiative workshop and a few updates from recent developments

Purpose

The paper provides a late report from the United Nations Environment Program (UNEP)/Society of Environmental Toxicology and Chemistry (SETAC) Life Cycle Initiative workshop “Life Cycle Impact Assessment (LCIA)—where we are, trends, and next steps;” it embeds this report into recent development with regard to the envisaged development of global guidance on environmental life cycle impact assessment indicators and related methodologies.

Methods

The document is the output of the UNEP/SETAC Life Cycle Initiative’s workshop on “Life Cycle Impact Assessment—where we are, trends, and next steps.” The presentations and discussions held during the workshop reviewed the first two phases of the Life Cycle Initiative and provided an overview of current LCIA activities being conducted by the Initiative, governments and academia, as well as corporate approaches. The outcomes of the workshop are reflected in light of the implementation of the strategy for Phase 3 of the Life Cycle Initiative.

Results

The range of views provided during the workshop indicated different user needs, with regards to, amongst other things, the required complexity of the LCIA methodology, associated costs, and the selection of LCIA categories depending on environmental priorities. The workshop’s results signified a number of potential focus areas for Phase 3 of the Initiative, including capacity building efforts concerning LCIA in developing countries and emerging economies, the preparation of training materials on LCIA, the production of global guidance on LCIA, and the potential development of a broader sustainability indicators framework.

Conclusions

These suggestions have been taken into account in the strategy for Phase 3 of the Life Cycle Initiative in two flagship projects, one on global capability development on life cycle approaches and the other on global guidance on environmental life cycle impact assessment indicators. In the context of the latter project, first activities are being organized and planned. Moreover, UNEP has included the recommendations in its Rio + 20 Voluntary Commitments: UNEP and SETAC through the UNEP/SETAC Life Cycle Initiative commit to facilitate improved access to good quality life cycle data and databases as well as expanded use of key environmental indicators that allows the measurement and monitoring of progress towards the environmental sustainability of selected product chains.     

A UNEP/SETAC approach towards a life cycle sustainability assessment—our contribution to Rio+20

Purpose

To contribute to the upcoming United Nations Conference on Sustainable Development (Rio+20) in 2012 by introducing a life cycle sustainability assessment (LCSA) and showing how it can play a crucial role in moving towards sustainable consumption and production. The publication, titled Towards a Life Cycle Sustainability Assessment, and published by the UNEP/SETAC Life Cycle Initiative aims to show how three life cycle techniques—(environmental) LCA, S-LCA and LCC—can be combined as part of an over-arching LCSA.

Methods

The method was demonstrated by evaluating the characteristics of each phase for each life cycle technique. In defining the goal and scope of an LCSA, for example, different aspects should be taken into account to establish the aim of the study as well as the functional unit, system boundaries, impact category and allocation. Then, the data to be collected for the life cycle sustainability inventory can be either in a unit process or on an organisational level. They can also be quantitative or qualitative. Life cycle sustainability impact assessment should consider the relevance of the impacts as well as the perspective of stakeholders. The interpretation should not add up the results, but rather evaluate them jointly. In order to clarify the approach, a case study is presented to evaluate three types of marble according to the proposed method.

Results and discussion

The authors have identified that while LCSA is feasible, following areas need more development: data production and acquisition, methodological development, discussion about LCSA criteria (e.g. cutoff rules), definitions and formats of communication and dissemination of LCSA results and the expansion of research and applications combining (environmental) LCA, LCC and S-LCA. The authors also indicate that it is necessary to develop more examples and cases to improve user capacity to analyse the larger picture and therefore address the three dimensions or pillars of sustainability in a systematic way. Software and database providers are called for in order to facilitate user-friendly and accessible tools to promote LCSAs.

Conclusions

The application demonstrated that, although methodological improvements are still needed, important steps towards an overarching sustainability assessment have been accomplished. LCSA is possible and should be pursued; however, more efforts should be made to improve the technique and facilitate the studies in order to contribute to a greener economy.     

Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle,independently of its on-target effect

The small-molecule inhibitor of phosphoglycerate dehydrogenase, NCT-503, reduces incorporation of glucose-derived carbons into serine in vitro. Here we describe an off-target effect of NCT-503 in neuroblastoma cell lines expressing divergent phosphoglycerate dehydrogenase (PHGDH) levels and single-cell clones with CRISPR-Cas9-directed PHGDH knockout or their respective wildtype controls. NCT-503 treatment strongly reduced synthesis of glucose-derived citrate in all cell models investigated compared to the inactive drug control and independent of PHGDH expression level. Incorporation of glucose-derived carbons entering the TCA cycle via pyruvate carboxylase was enhanced by NCT-503 treatment. The activity of citrate synthase was not altered by NCT-503 treatment. We also detected no change in the thermal stabilisation of citrate synthase in cellular thermal shift assays from NCT-503-treated cells. Thus, the direct cause of the observed off-target effect remains enigmatic. Our findings highlight off-target potential within a metabolic assessment of carbon usage in cells treated with the small-molecule inhibitor, NCT-503.     

Phytochemical Compounds from the Crop Byproducts of Tunisian Globe Artichoke Cultivars

The phytochemical composition in two Tunisian globe artichoke cultivars (bracts, leaves, and floral stems) was evaluated in the plant byproducts. The results indicated that the bracts contain the highest levels of total phenols, o‐diphenols, and flavonoids, whereas tannins seem to be more abundant in the leaves. Bracts from the ‘Violet d'Hyères’ cultivar possessed more total phenols (160.8 mg/g DW), flavonoids (64.9 mg/g DW), and anthocyanins (15.3 μg/g DW) than the ‘Blanc d'Oran’ bracts (134.5 mg/g DW, 51.2 mg/g DW, and 8.3 μg/g DW, resp.). Sixty‐four volatile compounds were identified in the headspace of globe artichoke material, particularly in the bracts. The volatile profile showed that sesquiterpene hydrocarbons and non‐terpene derivatives were the main volatiles emitted by the bracts in both cultivars. These results suggest that globe artichoke byproducts might represent a potential source of natural compounds, which could be used as nutraceuticals or as ingredients in the design of functional foods.     

Connectivity in the network macrostructure of Tursiops truncatus in the Pelagos Sanctuary (NW Mediterranean Sea): does landscape matter?

The bottlenose dolphin (Tursiops truncatus Montagu, 1821) is a regularly observed species in the Mediterranean Sea, but its network organization has never been investigated on a large scale. We described the network macrostructure of the bottlenose dolphin (meta)population inhabiting the Pelagos Sanctuary (a wide protected area located in the north-western portion of the Mediterranean basin) and we analysed its connectivity in relation to the landscape traits. We pooled effort and sighting data collected by 13 different research institutions operating within the Pelagos Sanctuary from 1994 to 2011 to examine the distribution of bottlenose dolphins in the Pelagos study area and then we applied a social network analysis, investigating the association patterns of the photo-identified dolphins (806 individuals in 605 sightings). The bottlenose dolphin (meta)population inhabiting the Pelagos Sanctuary is clustered in discrete units whose borders coincide with habitat breakages. This complex structure seems to be shaped by the geo-morphological and ecological features of the landscape, through a mechanism of local specialization of the resident dolphins. Five distinct clusters were identified in the (meta)population and two of them were solid enough to be further investigated and compared. Significant differences were found in the network parameters, suggesting a different social organization of the clusters, possibly as a consequence of the different local specialization.     

Effects of temperature on the development,performance and fitness of the corn leafhopper Dalbulus maidis (DeLong) (Hemiptera: Cicadellidae): implications on its distribution under climate change

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