Simultaneous Quantification of the Acetylome and Succinylome by ‘One‐Pot’ Affinity Enrichment

Protein posttranslational modifications (PTMs) are of increasing interest in biomedical research, yet studies rarely examine more than one PTM. One barrier to multi‐PTM studies is the time cost for both sample preparation and data acquisition, which scale linearly with the number of modifications. The most prohibitive requirement is often the need for large amounts of sample, which must be increased proportionally with the number of PTM enrichment steps. Here, a streamlined, quantitative label‐free proteomic workflow—“one‐pot” PTM enrichment—that enables comprehensive identification and quantification of peptides containing acetylated and succinylated lysine residues from a single sample containing as little as 1 mg mitochondria protein is described. Coupled with a label‐free, data‐independent acquisition (DIA), 2235 acetylated and 2173 succinylated peptides with the one‐pot method are identified and quantified and peak areas are shown to be highly correlated between the one‐pot and traditional single‐PTM enrichments. The ‘one‐pot’ method makes possible detection of multiple PTMs occurring on the same peptide, and it is shown that it can be used to make unique biological insights into PTM crosstalk. Compared to single‐PTM enrichments, the one‐pot workflow has equivalent reproducibility and enables direct assessment of PTM crosstalk from biological samples in less time from less tissue.     

Multiculturalism,Latin Americans and ‘Indigeneity’ in Australia

What are the relations between the discourse of ‘multiculturalism’ and that of ‘indigeneity’ in Australia? In problematising these relations this paper explores the affiliations that Latin American migrants and political refugees living in Adelaide have with the notion of indigeneity. For some Latin Americans affiliations with the struggle of Aboriginal people and indigeneity is a product of strong political identification with the political left and the struggle for human rights in their countries of origin. At the same time references to Latin Americans' indigeneity are often evoked within Australian multicultural settings and performances that promote ‘cultural diversity’ and are consumed by White Australians for their exotic otherness and as forms of cultural enrichment. Such representations work to marginalise further the migrants (and the ‘indigenous’) into a cultural sphere which marks them as the tolerated ethnic ‘Other’.     

‘I am helping them’: ‘Traffickers’, ‘anti‐traffickers’ and economies of bad faith

For several years, aid programs in the Mekong region have taken an increasing interest in cross‐border mobility and human trafficking and its relationship with development. More recently, there has been an increasing interest in the identification of trafficked victims and the investigation, arrest and prosecution of traffickers. Whereas anti‐trafficking programs ubiquitously define themselves as being in a battle with traffickers, this article argues that although they are not homologous social actors, both engage in acts of bad faith. The article elaborates this argument by drawing attention to the recruitment process within the Lao sex industry as well as to the way in which aid programs attempt to identify trafficked victims. It concludes that imaginary aspects of development underpin a simultaneous disjuncture yet enable the social reproduction of the life worlds of ‘traffickers’ and ‘anti‐traffickers’ alike.     

Interaction of ‘toxic’ and ‘immunogenic’ A‐gliadin peptides with a membrane‐mimetic environment

Celiac disease (CD) is characterized by abnormally high concentrations of certain peptides in the small bowel. These peptides can be grouped in ‘toxic’ and ‘immunogenic’ classes, which elicit an innate immune response and an HLA‐mediated adaptive response, respectively. It is not clear on which molecular mechanisms responses to these different classes are based, but the 31–43 (P31–43) and the 56–68 (P56–68) A‐gliadin fragments are usually adopted as sequence representatives of toxic and immunogenic peptides, respectively. Here we report fluorescence experiments aiming to mimic the interaction of these peptides with the cell membrane surface by using sodium dodecyl sulphate (SDS) as a membrane‐mimetic medium. We show that P31–43 is able to bind SDS micelles in a way that resembles mixed micelle formation. On the other hand, no binding at all could be detected for P56–68. This different behaviour could be related to the paracellular or transcellular route through which gluten peptides may cross the intestinal epithelium, and open new insights into the pathogenetic mechanisms of CD. Copyright © 2009 John Wiley & Sons, Ltd.     

The contingency of ‘rights’: Locating a global discourse in Aboriginal Central Australia

The United Nations Declaration on the Rights of Indigenous Peoples was adopted by the United Nations (UN) General Assembly in 2007 and endorsed by the Australian Labor government two years later. This achievement is an essential element in the global politics of Indigenous recognition and includes unique rights, such as the right to a cultural collectivity and Indigenous Cultural and Intellectual Property, while reinforcing the right to self‐determination. Yet this new Indigenous rights regime is both underpinned and constrained by the UN human rights system, the implications of which include constraint within a secular neo‐imperialist liberal paradigm. However, this human rights paradigm can also offer generative potential to challenge existing relations of power. According to Kymlicka, the UN's system of human rights has, after all, been ‘one of the great moral achievements of the twentieth century’. How can these tensions between the aspirations to universal secularism and the right to culture, for instance, be accommodated within the Indigenous human rights discourse? And how does this new international legal and norm‐setting instrument speak to the glaring disjunct between declaration of rights and social fact in central Australia, the focus of this research? The move toward an anthropology of human rights looks squarely at this conundrum and attempts to locate spaces of continuity and co‐option or, conversely, subversion and rejection as local cultures of human rights are articulated.     

Detection and Identification of ‘Candidatus Phytoplasma prunorum’, ‘Candidatus Phytoplasma mali’ and ‘Candidatus Phytoplasma pyri’ in Stone Fruit Trees in Poland

A survey was made to determine the incidence of phytoplasmas in 39 sweet and sour cherry, peach, nectarine, apricot and plum commercial and experimental orchards in seven growing regions of Poland. Nested polymerase chain reaction (PCR) using the phytoplasma‐universal primer pairs P1/P7 followed by R16F2n/R16R2 showed the presence of phytoplasmas in 29 of 435 tested stone fruit trees. The random fragment length polymorphism (RFLP) patterns obtained after digestion of the nested PCR products separately with RsaI, AluI and SspI endonucleases indicated that selected Prunus spp. trees were infected by phytoplasmas belonging to three different subgroups of the apple proliferation group (16SrX‐A, ‐B, ‐C). Nucleotide sequence analysis of 16S rDNA fragment amplified with primers R16F2n/R16R2 confirmed the PCR/Restriction Fragment Length Polymorphism (RFLP) results and revealed that phytoplasma infecting sweet cherry cv. Regina (Reg), sour cherry cv. Sokowka (Sok), apricots cv. Early Orange (EO) and AI/5, Japanese plum cv. Ozark Premier (OzPr) and peach cv. Redhaven (RedH) was closely related to isolate European stone fruit yellows‐G1 of the ‘Candidatus Phytoplasma prunorum’ (16SrX‐B). Sequence and phylogenetic analyses resulted in the highest similarity of the 16S rDNA fragment of phytoplasma from nectarine cv. Super Queen (SQ) with the parallel sequence of the strain AP15 of the ‘Candidatus Phytoplasma mali’ (16SrX‐A). The phytoplasma infecting sweet cherry cv. Kordia (Kord) was most similar to the PD1 strain of the ‘Candidatus Phytoplasma pyri’ (16SrX‐C). This is the first report of the occurrence of ‘Ca. P. prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ in naturally infected stone fruit trees in Poland.     

Comparing ecological restoration in South Africa and Western Australia: the benefits of a ‘travelling workshop’

Researchers and practitioners of ecological restoration from South Africa and Western Australia recently undertook a travelling workshop across several South African biomes to discuss and evaluate the various approaches currently being utilised in the field. Key findings from the workshop highlighted the contrasting nature of ecological restoration undertaken in these two ecologically similar, but socially and politically different regions.     

Nature,Work and ‘the Environment’: Contesting Sentiments and Identities in the Southwest of Western Australia

Contesting discourses about natural resource development present a rich arena for ethnographic investigation. This paper focuses on interviews with environmental activists and forest industry defenders to document a struggle over the meaning of land, work and nature in the southwest of Western Australia. While Green activists condemn what they regard as crimes against nature, this moral challenge to rural communities from urban-based environmentalism is inverted by those working in the industry, such that local cultural practices are celebrated in the face of what is seen as emotional and non-scientific rhetoric. Conflicts about resource development are thus driven in significant respects by identity politics. The paper argues for the importance of cultural analysis, focused particularly on concepts of identity and ‘place’, in the study of contesting moral claims about what should be done with ‘the environment’.     

Revisiting the ‘bank of microscopic forms’ in macroalgal‐dominated ecosystems

Theoretical ecological models, such as succession and facilitation, were defined in terrestrial habitats, and subsequently applied to marine and freshwater habitats in intertidal and then subtidal realms. One such model is the soil seed bank, defined as all viable seeds (or fruits) found near the soil surface that facilitate community restoration/recovery. “Banks of microscopic forms” have been hypothesized in aquatic habitats and recent work from aquaculture has highlighted dormancy in algal life cycle stages. To reinvigorate the discussions about these algal banks, we discuss differences in life cycles, dispersal, and summarize research on banks of macroalgal stages in aquatic ecosystems that may be easier to explore with modern advances in molecular technology. With focus on seminal work in global kelp forest ecosystems, we present a pilot study in northern California as proof of concept that Nereocystis luetkeana and Alaria marginata stages can be detected within kelp forests in the biofilm of rocks and bedrock using targeted primers long after zoospore release. Considering the increased interest in algae as an economic resource, [blue] carbon sink, and as ecosystem engineers, the potential for “banking” macroalgal forms could be a mechanism of resilience and recovery in aquatic populations that have complex life cycles and environmental cues for reproduction. Molecular barcoding is becoming an important tool for identifying banks of macroalgal forms in marine communities. Understanding banks of macroalgal stages, especially in deforested habitats with intense disturbance and grazer pressure, will allow researchers and marine resource managers to facilitate this natural process in recovery of the aquatic system.     

Potential ‘costs of reproduction’ in a skink: Inter‐ and intrapopulational variation

Reproductive costs are important determinants of reproductive effort in squamate reptiles. Consequently, differences in costs of reproduction between populations of geographically or climatically widespread species are likely to result in different patterns of reproductive effort. In the present study, the effect of pregnancy on sprint speed was examined in a small viviparous skink, Niveoscincus ocellatus (Gray 1845), from two populations at the climatic extremes of its distribution. Decreased sprint speed has the potential to be an important cost of reproduction in this species, through a reduced ability to avoid predation and/or decreased foraging efficiency. Lizards inhabiting the colder site were larger than those from the warmer site and, contrary to predictions from life history theory, had a higher reproductive effort. In both populations, sprint speed was lower in pregnant lizards than in either the same individuals after birth or non‐pregnant control lizards. Within each population, sprint speed was unrelated to the level of reproductive effort of the female in terms of either absolute mass of the reproductive burden or the burden relative to her post‐partum body mass. However, within each population, the mass of the clutch that an individual female was carrying relative to snout–vent length was an important determinant of her sprint speed while pregnant. Thus, within each population, a relatively high reproductive burden may potentially increase costs of reproduction in this species. Despite this relationship and predictions from life history theory suggesting that annual reproductive effort will be lower in populations with a large body size and delayed maturity, it is suggested that a higher reproductive effort at the cold site is possible because they have a higher absolute sprint speed because of their larger size and a relatively higher abundance of cover at the cold site, and differences in predation pressure may alter selective pressures on reproductive investment.     

‘Poking the skunk’: Ethical and medico‐legal concerns in research about patients’ experiences of medical injury

Improving how health care providers respond to medical injury requires an understanding of patients’ experiences. Although many injured patients strongly desire to be heard, research rarely involves them. Institutional review boards worry about harming participants by asking them to revisit traumatic events, and hospital staff worry about provoking lawsuits. Institutions’ reluctance to approve this type of research has slowed progress toward responses to injuries that are better able to meet patients’ needs. In 2015–2016, we were able to surmount these challenges and interview 92 injured patients and families in the USA and New Zealand. This article explores whether the ethical and medico‐legal concerns are, in fact, well‐founded. Consistent with research about trauma‐research‐related distress, our participants’ accounts indicate that the pervasive fears about retraumatization are unfounded. Our experience also suggests that because being heard is an important (but often unmet) need for injured patients, talking provides psychological benefits and may decrease rather than increase the impetus to sue. Our article makes recommendations to institutional review boards and researchers. The benefits to responsibly conducted research with injured patients outweigh the risks to participants and institutions.     

The AAT1 locus is critical for the biosynthesis of esters contributing to ‘ripe apple’ flavour in ‘Royal Gala’ and ‘Granny Smith’ apples

The ‘fruity’ attributes of ripe apples (Malus × domestica) arise from our perception of a combination of volatile ester compounds. Phenotypic variability in ester production was investigated using a segregating population from a ‘Royal Gala’ (RG; high ester production) × ‘Granny Smith’ (GS; low ester production) cross, as well as in transgenic RG plants in which expression of the alcohol acyl transferase 1 (AAT1) gene was reduced. In the RG × GS population, 46 quantitative trait loci (QTLs) for the production of esters and alcohols were identified on 15 linkage groups (LGs). The major QTL for 35 individual compounds was positioned on LG2 and co‐located with AAT1. Multiple AAT1 gene variants were identified in RG and GS, but only two (AAT1‐RGa and AAT1‐GSa) were functional. AAT1‐RGa and AAT1‐GSa were both highly expressed in the cortex and skin of ripe fruit, but AAT1 protein was observed mainly in the skin. Transgenic RG specifically reduced in AAT1 expression showed reduced levels of most key esters in ripe fruit. Differences in the ripe fruit aroma could be perceived by sensory analysis. The transgenic lines also showed altered ratios of biosynthetic precursor alcohols and aldehydes, and expression of a number of ester biosynthetic genes increased, presumably in response to the increased substrate pool. These results indicate that the AAT1 locus is critical for the biosynthesis of esters contributing to a ‘ripe apple’ flavour.     

Cycles of coral reef ‘turn‐on’, rapid growth and ‘turn‐off’ over the past 8500 years: a context for understanding modern ecological states and trajectories

Human activities threaten reef ecosystems globally, forcing ecological change at rates and scales regarded as unprecedented in the Holocene. These changes are so profound that a cessation of reef accretion (reef ‘turn‐off’) and net erosion of reef structures is argued by many as the ultimate and imminent trajectory. Here, we use a regional scale reef growth dataset, based on 76 core records (constrained by 211 radiometric dates) from 22 reefs along and across the inner‐shelf of the Great Barrier Reef, Australia, to examine the timing of different phases of reef initiation (‘turn‐on’), growth and ‘turn‐off’ during the Holocene. This dataset delineates two temporally discrete episodes of reef‐building over the last 8500 years: the first associated with the Holocene transgression‐early highstand period [～8.5–5.5 k calibrated years bp (cal ybp )]; the second since ～2.3 k cal ybp . During both periods, reefs accreted rapidly to sea level before entering late evolutionary states – states naturally characterized by reduced coral cover and low accretion potential – and a clear hiatus occurs between these reef‐building episodes for which no records of reef initiation exist. These transitions mimic those projected under current environmental disturbance regimes, but have been driven entirely by natural forcing factors. Our results demonstrate that, even through the late Holocene, reef health and growth has fluctuated through cycles independent of anthropogenic forcing. Consequently, degraded reef states cannot de facto be considered to automatically reflect increased anthropogenic stress. Indeed, in many cases degraded or nonaccreting reef communities may reflect past reef growth histories (as dictated by reef growth–sea level interactions) as much as contemporary environmental change. Recognizing when changes in reef condition reflect these natural ‘turn‐on’– growth –‘turn‐off’ cycles and how they interact with on‐going human disturbance is critical for effective coral reef management and for understanding future reef ecological trajectories.     

Identification and Molecular Characterization of ‘Candidatus Phytoplasma mali’ Isolates in North‐western Italy

Apple proliferation (AP) is an important disease and is prevalent in several European countries. The causal agent of AP is ‘Candidatus Phytoplasma mali’ (‘Ca. Phytoplasma mali’). In this work, isolates of ‘Ca. Phytoplasma mali’ were detected and characterized through polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analyses of 16S rRNA gene and non‐ribosomal DNA fragment. The presence of three AP subtypes (AT‐1, AT‐2 and AP‐15) was identified in 31 symptomatic apple trees and two samples each constituted by a pool of five insects, collected in north‐western Italy, where AT‐1 is a dominant subtype. Subsequent nucleotide sequence analysis of the PCR‐amplified 1.8 kb (P1/P7) fragment, containing the 16S rDNA, the 16S–23S intergenic ribosomal region and the 5′‐end of the 23S rDNA, revealed the presence of at least two phytoplasmal genetic lineages within the AT‐1 subtype, designed AT‐1a and AT‐1b. Moreover, in silico single nucleotide polymorphism (SNP) analysis based on 16S rDNA sequence can differentiate AT‐1 subtype from AT‐2 and AP‐15 subtypes. Our data showed a high degree of genetic diversity among ‘Ca. Phytoplasma mali’ population in north‐western Italy and underlined the possible use of the 16S rDNA analysis for the identification and the geographical origin assignation of isolates of AP phytoplasma. Molecular markers on 16S rDNA, here identified, could be useful for studying the epidemiology of AP disease.     

From clear lakes to murky waters – tracing the functional response of high‐latitude lake communities to concurrent ‘greening’ and ‘browning’

Climate change and the intensification of land use practices are causing widespread eutrophication of subarctic lakes. The implications of this rapid change for lake ecosystem function remain poorly understood. To assess how freshwater communities respond to such profound changes in their habitat and resource availability, we conducted a space‐for‐time analysis of food‐web structure in 30 lakes situated across a temperature‐productivity gradient equivalent to the predicted future climate of subarctic Europe (temperature +3°C, precipitation +30% and nutrient +45 μg L^?1 total phosphorus). Along this gradient, we observed an increase in the assimilation of pelagic‐derived carbon from 25 to 75% throughout primary, secondary and tertiary consumers. This shift was overwhelmingly driven by the consumption of pelagic detritus by benthic primary consumers and was not accompanied by increased pelagic foraging by higher trophic level consumers. Our data also revealed a convergence of the carbon isotope ratios of pelagic and benthic food web endmembers in the warmest, most productive lakes indicating that the incorporation of terrestrial derived carbon into aquatic food webs increases as land use intensifies. These results, reflecting changes along a gradient characteristic of the predicted future environment throughout the subarctic, indicate that climate and land use driven eutrophication and browning are radically altering the function and fuelling of aquatic food webs in this biome.     

The long‐term persistence of phytoplankton resting stages in aquatic ‘seed banks’

In the past decade, research on long‐term persistence of phytoplankton resting stages has intensified. Simultaneously, insight into life‐cycle variability in the diverse groups of phytoplankton has also increased. Aquatic ‘seed banks’ have tremendous significance and show many interesting parallels to terrestrial seed beds of vascular plants, but are much less studied. It is therefore timely to review the phenomenon of long‐term persistence of aquatic resting stages in sediment seed banks. Herein we compare function, morphology and physiology of phytoplankton resting stages to factors central for persistence of terrestrial seeds. We review the types of resting stages found in different groups of phytoplankton and focus on the groups for which long‐term (multi‐decadal) persistence has been shown: dinoflagellates, diatoms, green algae and cyanobacteria. We discuss the metabolism of long‐term dormancy in phytoplankton resting stages and the ecological, evolutionary and management implications of this important trait. Phytoplankton resting stages exhibiting long‐term viability are characterized by thick, often multi‐layered walls and accumulation vesicles containing starch, lipids or other materials such as pigments, cyanophycin or unidentified granular materials. They are reported to play central roles in evolutionary resilience and survival of catastrophic events. Promising areas for future research include the role of hormones in mediating dormancy, elucidating the mechanisms behind metabolic shut‐down and testing bet‐hedging hypotheses.     

Ontogeny,morphology and taxonomy of the soft‐bodied Cambrian ‘mollusc’ Wiwaxia

The soft‐bodied Cambrian organism Wiwaxia poses a taxonomic conundrum. Its imbricated dorsal scleritome suggests a relationship with the polychaete annelid worms, whereas its mouthparts and naked ventral surface invite comparison with the molluscan radula and foot. 476 new and existing specimens from the 505‐Myr‐old Burgess Shale cast fresh light on Wiwaxia's sclerites and scleritome. My observations illuminate the diversity within the genus and demonstrate that Wiwaxia did not undergo discrete moult stages; rather, its scleritome developed gradually, with piecewise addition and replacement of individually secreted sclerites. I recognize a digestive tract and creeping foot in Wiwaxia, solidifying its relationship with the contemporary Odontogriphus. Similarities between the scleritomes of Wiwaxia, halkieriids, Polyplacophora and Aplacophora hint that the taxa are related. A molluscan affinity is robustly established, and Wiwaxia provides a good fossil proxy for the ancestral aculiferan – and perhaps molluscan – body plan.