From signal perception to signal transduction: ligand‐induced dimeric switch of DctB sensory domain in solution

Sinorhizobium meliloti DctB is a typical transmembrane sensory histidine kinase, which senses C₄‐dicarboxylic acids (DCA) and regulates the expression of DctA, the DCA transporter. We previously reported the crystal structures of its periplasmic sensory domain (DctBp) in apo and succinate‐bound states, and these structures showed dramatic conformational changes at dimeric level. Here we show a ligand‐induced dimeric switch in solution and a strong correlation between DctBp's dimerization states and the in vivo activities of DctB. Using site‐directed mutagenesis, we identify important determinants for signal perception and transduction. Specifically, we show that the ligand‐binding pocket is essential for DCA‐induced ‘on’ activity of DctB. Mutations at different sections of DctBp's dimerization interface can lock full‐length DctB at either ‘on’ or ‘off’ state, independent of ligand binding. Taken together, these results suggest that DctBp's signal perception and transduction occur through a ‘ligand‐induced dimeric switch’, in which the changes in the dimeric conformations upon ligand binding are responsible for the signal transduction in DctB.     

Remote touch prey‐detection by Madagascar crested ibises Lophotibis cristata urschi

Birds that forage by probing must often rely on sensory systems other than vision to detect their buried prey. Such senses may include hearing (e.g. Australian magpies (Atramidae), American robins (Turdidae)) or chemical senses/olfaction (e.g. kiwi (Apterygidae) and some shorebirds (Scolopacidae)). Probe foraging kiwi and shorebirds are also able to use vibrotactile cues to locate prey buried in the substrate at some distance from their bill‐tips (‘remote touch’). These birds possess an organ consisting of a honey‐comb of sensory pits in bone of the bill‐tips, packed with mechanoreceptive nerve ending (Herbst corpuscles). Such a bill‐tip organ has recently also been described in ibises (Threskiornithinae), but its function not elucidated. We designed a foraging experiment presenting mealworm prey to three captive Madagascar crested ibises Lophotibis cristata urschi under a variety of trial conditions to discover whether they were using remote touch, mediated by their bill‐tip organ; chemosense/olfaction; or hearing to locate buried prey. The ibises were reliant on remote touch for prey detection – the first time this sensory system has been demonstrated for this group of birds. They did not appear to use hearing or chemical senses/olfaction to aid in prey detection.     

Beyond the senses: perception,the environment,and vision impairment

The ‘sensory turn’ in anthropology has generated a significant literature on sensory perception and experience. Whilst much of this literature is critical of the compartmentalization of particular ‘senses’, there has been limited exploration of how anthropologists might examine sensory perception beyond ‘the senses’. Based on ethnographic fieldwork with people who have impaired vision walking the South Downs landscape in England, this article develops such an approach. It suggests that the experiences of seeing in blindness challenge the conceptualization of ‘vision’ (and ‘non-vision’). In place of ‘vision’ (as a sense), the article explores ‘activities of seeing’ – an approach that contextualizes the visual to examine the biographically constituted and idiosyncratic nature of perception within an environment. Through an ethnography of seeing with anatomical eyes and ‘seeing in the mind's eye’, it articulates an approach that avoids associating perception with anatomy, or compartmentalizing experience into ‘senses’.     

Nutrient depletion may trigger the Yersinia pestis OmpR‐EnvZ regulatory system to promote flea‐borne plague transmission

The flea’s lumen gut is a poorly documented environment where the agent of flea‐borne plague, Yersinia pestis, must replicate to produce a transmissible infection. Here, we report that both the acidic pH and osmolarity of the lumen’s contents display simple harmonic oscillations with different periods. Since an acidic pH and osmolarity are two of three known stimuli of the OmpR‐EnvZ two‐component system in bacteria, we investigated the role and function of this Y. pestis system in fleas. By monitoring the in vivo expression pattern of three OmpR‐EnvZ‐regulated genes, we concluded that the flea gut environment triggers OmpR‐EnvZ. This activation was not, however, correlated with changes in pH and osmolarity but matched the pattern of nutrient depletion (the third known stimulus for OmpR‐EnvZ). Lastly, we found that the OmpR‐EnvZ and the OmpF porin are needed to produce the biofilm that ultimately obstructs the flea’s gut and thus hastens the flea‐borne transmission of plague. Taken as a whole, our data suggest that the flea gut is a complex, fluctuating environment in which Y. pestis senses nutrient depletion via OmpR‐EnvZ. Once activated, the latter triggers a molecular program (including at least OmpF) that produces the biofilm required for efficient plague transmission.     

Origin of pre‐islamic architecture in West‐Africa

’Cultural theory’, launched by social anthropologist Mary Douglas, has been highly influential in the inter‐disciplinary field concerned with the study of risk perception and risk communication. The theory derives from the grid‐group analyses that Douglas developed in the 1970s. Cultural theory aims to explain universal ‘cultural bias’ by way of a general typology of group formation and a concomitant cosmology or world view. This article critically examines cultural theory and the study of hazards as culturally construed phenomena.     

Adolescents' perceived weight associated with depression in young adulthood: a longitudinal study

Objective: The objective of this study is to examine whether adolescents’ measured BMI and self‐ or mother's perception of weight status at age 14 are associated with depression at age 21. Research Methods and Procedures: The study participants were a subsample of 2017 participants of the Mater–University of Queensland Study of Pregnancy and Its Outcomes, a population‐based birth cohort study, which commenced in 1981 in Brisbane, Australia, for whom measured BMI at ages 14 and 21 and information on self‐reported mental health problems were available at the age 21 follow‐up. A total of 1802 individuals had measured BMI and reported weight perception in a supplementary questionnaire at 14 years, and their self‐reported mental health problems were reported at 21 years. Mental health was measured using Center for Epidemiology Studies Depression Scale and Young Adults Self‐Reported depression/anxiety at 21 years of age. Results: We found that both young adult males and females who perceived themselves as overweight at age 14 had more mental health problems compared with those who perceived themselves as the right weight. When we combined adolescents’ weight perception with their measured BMI categories, weight perception but not measured overweight was associated with mental health problems for males and females at age 21. This association remained after adjusting for potential confounders, including adolescents’ behavioral problems, family meals, diet, physical activity, and television watching. Conclusions: This study suggests that the perception of being overweight during adolescence is a significant risk factor for depression in young adult men and women. The perception of being overweight during adolescence should be considered a possible target for a prevention intervention.     

Care Giver Perception of Children's Obesity‐Related Health Risk: A Study of African American Families

Objective: To examine care giver perception of children's weight‐related health risk in African American families. Research Methods and Procedures: One‐hundred and eleven families (representing 48 boys and 63 girls) screened for participation in a diabetes prevention study participated. Care givers completed a health awareness questionnaire that assessed their perception of the child's weight, eating habits, appearance, exercise habits, and health risk. The care givers also reported each subject's family history of obesity, diabetes, and other chronic diseases. After a physical examination, height and weight were used to compute an age‐ and sex‐adjusted body mass index for each child. Results: Despite the fact that a substantial number of children were obese (57%) and super‐obese (12%), only 44% of the care givers perceived the child's weight to be a potential health problem. Regression analysis showed that 21% of the variance in parental perception of obesity‐related health risk could be predicted by child age, body mass index, perception of frame size, and perception of exercise habits. Discussion: A number of reasons for the apparent minimization of child health risk are discussed, including cultural differences in the acceptance of a large body habitus, lack of knowledge about the connection between childhood obesity and future health risk, and an optimistic bias in the perception of personal health risk.     

Biogeography and evolution of the Holarctic zooplankton genus Leptodora (Crustacea: Branchiopoda: Haplopoda)

Aim To reconstruct the phylogeographic history of the Holarctic carnivorous genus Leptodora (Crustacea: Cladocera: Haplopoda). Location We studied the DNA of between one and five specimens each from 28 populations distributed across the Holarctic, but with emphasis on Eurasia. Methods We sequenced a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (elongation factor‐1α) gene, and combined this molecular information with geological and palaeoclimatological data. Haplotype networks and phylogenetic trees were constructed using a Bayesian and maximum likelihood approach. A molecular clock was applied. Results Leptodora consists of three clades (Leptodora kindtii in Europe, Leptodora richardi in China and Japan, and Leptodora sp. in North America), with insular subclades in Japan and in the eastern Mediterranean. The North American clade was not studied in detail. Leptodora richardi is the more thermophilic of the three. It extends from the Tropic of Cancer in the south to the Heilong Basin in the north. The western European L. kindtii is more cold‐water adapted than the eastern Mediterranean subclade. ‘West European’ and ‘Chinese’ clades are broadly separated by a hybrid zone in Siberia and European Russia as far west as the Volga. These hybrids have the mitochondrial DNA of L. kindtii, the nuclear DNA of L. richardi and the low‐temperature preference of L. kindtii, and may have formed as recently as the Holocene hypsithermal. A pure L. kindtii population in the Upper Irtysh catchment, east of the Dzungarian Gates, has been sequestered in endorheic Lake Wulungu, Xinjiang, since the mid‐Pleistocene. Main conclusions Application of a molecular clock places the most recent common ancestor of the North American, East Asian and European populations in the mid‐Miocene. The North American taxon is still living in isolation, while the Eurasian taxa, separated by the Alpine folding, made contact again in the Pleistocene, when the cold‐stenothermic L. kindtii repeatedly moved eastwards across Siberia and back. The population in Xinjiang is a relict of an early wave coming from western Europe: it crossed the Dzungarian Gates during a humid mid‐Pleistocene event, probably corresponding to the Apsheron transgression in the Caspian Basin. Later aridity isolated it there, and it started accumulating private haplotypes. The Holocene Euro‐Siberian hybrid zone may eventually engulf all European populations.     

Altered sensitivity to ethylene in ‘Tardivo’, a late‐ripening mutant of Clementine mandarin

‘Tardivo’ mandarin is a mutant of ‘Comune’ Clementine with a delay in peel degreening and coloration, allowing late harvesting. In this work, we have explored if the late‐harvesting phenotype of ‘Tardivo’ mandarin is related to altered perception and sensitivity to ethylene. The peel degreening rate was examined after a single ethephon treatment or during a continuous ethylene application in fruits at two maturation stages. In general, ethylene‐induced peel degreening was considerably delayed and reduced in fruits of ‘Tardivo’, as well as the concomitant reduction of chlorophyll (Chl) and chloroplastic carotenoids, and the accumulation of chromoplastic carotenoids. Analysis of the expression of genes involved in Chl degradation, carotenoids, ABA, phenylpropanoids and ethylene biosynthesis revealed an impairment in the stimulation of most genes by ethylene in the peel of ‘Tardivo’ fruits with respect to ‘Comune’, especially after 5 days of ethylene application. Moreover, ethylene‐induced expression of two ethylene receptor genes, ETR1 and ETR2, was also reduced in mutant fruits. Expression levels of two ethylene‐responsive factors, ERF1 and ERF2, which were repressed by ethylene, were also impaired to a different extent, in fruits of both genotypes. Collectively, results suggested an altered sensitivity of the peel of ‘Tardivo’ to ethylene‐induced physiological and molecular responses, including fruit degreening and coloration processes, which may be time‐dependent since an early moderated reduction in the responses was followed by the latter inability to sustain ethylene action. These results support the involvement of ethylene in the regulation of at least some aspects of peel maturation in the non‐climacteric citrus fruit.     

Origin and diversification of the cryptic ant genus Stenamma Westwood (Hymenoptera: Formicidae), inferred from multilocus molecular data,biogeography and natural history

The genus Stenamma Westwood comprises a group of cryptic, cold tolerant ants that occur throughout the Holarctic and Middle American regions. Traditional approaches to taxonomy and phylogeny are confounded by multiple factors, including the conservative and often convergent morphology of workers and the rarity of reproductive castes in collections. Monophyly of Stenamma and relationships within the genus are uncertain as nearly all previous taxonomic work has been regional in scope. Furthermore, the sister group to Stenamma has not been well established. Here an extensive molecular dataset consisting of ten genes (～8 kb of data), 48 ingroup taxa (20 Nearctic, 6 Palaearctic and 22 Neotropical) and 8 outgroup taxa (6 closely related non‐Stenamma and 2 additional myrmicines) is used to investigate the broad‐scale phylogeny and evolutionary history of Stenamma. Phylogenetic analysis is performed under maximum likelihood and Bayesian frameworks on individual genes and several alternate concatenated datasets, which are used to investigate the effects of inclusion or exclusion of COI and intronic regions. The timing of Stenamma evolution is inferred in beast and ancestral areas are reconstructed using both the s‐diva and DEC methods, as implemented in the programs rasp and lagrange , respectively. Stenamma is revealed as monophyletic with high support and tentatively is sister to a group of New World species placed currently in Aphaenogaster Mayr and Messor Forel. Within Stenamma, two major clades are recovered: a ‘Holarctic clade’ (HOC) and a ‘Middle American clade’ (MAC). The HOC consists of the European S. striatulum Emery sister to two well‐supported groups, the informal ‘debile’ and ‘brevicorne’ clades. The ‘brevicorne’ clade is entirely Nearctic, whereas the ‘debile’ clade includes both Nearctic and Palaearctic representatives. The MAC occurs from the southern United States to northern South America and, with the exception of S. huachucanum Smith, is almost completely isolated geographically from the HOC. It includes a depauperate northern clade and the ‘MAC core’, which is a diverse assemblage of wet forest adapted species found throughout Central America. Divergence dating and biogeographic reconstruction show that Stenamma is most likely to have originated in the Nearctic at the Eocene–Oligocene boundary (～35 Ma) and diversified more rapidly at 16 and 8 Ma for the HOC and MAC, respectively. Potential environmental factors affecting the evolution of Stenamma include the intense global cooling of the late Eocene combined with aridification and mountain building. The phylogenetic results are discussed in relation to the current Stenamma species groups and several new morphological characters are presented to help in identification.     

Effects of transgenic American chestnut leaf litter on growth and survival of wood frog larvae

Biotechnology offers a new approach for the restoration of tree species affected by exotic pathogens; however, nontarget impacts of this novel strategy on other organisms have not been comprehensively assessed. We evaluated the effect of transgenic American chestnut (Castanea dentata) leaf litter on the growth and survival of larval wood frogs (Lithobates sylvaticus), a forest‐dwelling amphibian species widely sympatric with American chestnut, that forage almost entirely on periphyton and litter detritus that accumulate in temporary vernal pools in forests. We reared wood frog larvae on Castanea leaf litter (American chestnut genetically engineered for blight tolerance, nontransgenic American chestnut, Chinese chestnut [Castanea mollissima], and an American–Chinese chestnut hybrid) and litter from two non‐Castanea, nontransgenic “control” tree species, coupled with two levels of supplementary food. We observed no differences in growth or survival of wood frog larvae reared on transgenic versus nontransgenic American chestnut leaves. Without supplementary food, wood frog larvae provided leaves from American chestnut (both types) developed faster and grew larger than those exposed to other leaf litter treatments. Results of this study provide preliminary evidence that (1) American chestnut may have formerly been an important source of food for forest‐dwelling amphibians and (2) transgenic American chestnut litter generated as part of chestnut restoration efforts is unlikely to present direct novel risks to developing amphibian larvae in the forest environment.     

Epidermal jasmonate perception is sufficient for all aspects of jasmonate‐mediated male fertility in Arabidopsis

Jasmonate (JA) signaling is essential for several environmental responses and reproductive development in many plant species. In Arabidopsis thaliana, the most obvious phenotype of JA biosynthetic and perception mutants is profound sporophytic male sterility characterized by failure of stamen filament elongation, severe delay of anther dehiscence and pollen inviability. The site of action of JA in the context of reproductive development has been discussed, but the ideas have not been tested experimentally. To this end we used targeted expression of a COI1‐YFP transgene in the coi1‐1 mutant background. As COI1 is an essential component of the JA co‐receptor complex, the null coi1‐1 mutant is male sterile due to lack of JA perception. We show that expression of COI1‐YFP in the epidermis of the stamen filament and anther in coi1 mutant plants is sufficient to rescue filament elongation, anther dehiscence and pollen viability. In contrast, filament expression alone or expression in the tapetum do not restore dehiscence and pollen viability. These results demonstrate that epidermal JA perception is sufficient for anther function and pollen viability, and suggest the presence of a JA‐dependent non‐autonomous signal produced in the anther epidermis to synchronize both anther dehiscence and pollen maturation.     

Chlorella variabilis and Micractinium reisseri sp. nov. (Chlorellaceae,Trebouxiophyceae): Redescription of the endosymbiotic green algae of Paramecium bursaria (Peniculia,Oligohymenophorea) in the 120th year

Symbiotic algae of the ciliate Paramecium bursaria (Ehrenberg) Focker are key species in the fields of virology and molecular evolutionary biology as well as in the biology of symbiotic relationships. These symbiotic algae were once identified as Zoochlorella conductrix Brandt by the Dutch microbiologist, Beijerinck 120 years ago. However, after many twists and turns, the algae are today treated as nameless organisms. Recent molecular analyses have revealed several different algal partners depending on P. bursaria strains, but nearly all P. bursaria contains a symbiont belonging to either the so‐called ‘American’ or ‘European’ group. The absence of proper names for these algae is beginning to provoke ill effects in the above‐mentioned study areas. In the present study, we confirmed the genetic autonomy of the ‘American’ and ‘European’ groups and described the symbionts as Chlorella variabilis Shihira et Krauss and Micractinium reisseri Hoshina, Iwataki et Imamura sp. nov., respectively (Chlorellaceae, Trebouxiophyceae).     

The odour of things: Smell and the cultural elaboration of disgust in Eastern Indonesia

Recent years have witnessed an increasing number of calls for anthropology to devote more attention to non‐visual modes of perception. Frequently, the implicit suggestion of these calls has been that the acknowledgement of different ways of organising the senses could help us escape the supposed malaise of modern ‘ocular‐centrism ‘. This paper explores the sense and symbolism of smell in Buli, a village in eastern Indonesia, to argue that smell is part of an ontology that catches Buli people in a malaise of their own. ‘Bad’ smell attests to an ambiguous moral order that can be traced across myth, ritual and everyday life. Ambiguity is ever‐present because ‘bad’ or disgusting smells destabilise the very conceptual order they also help support. The analysis of smells as they relate to local notions of disgust is therefore suggested as an alternative way to conceptualise the contradictory nature of power.     

Oligomeric states of the Shigella translocator protein IpaB provide structural insights into formation of the type III secretion translocon

The Shigella flexneri Type III secretion system (T3SS) senses contact with human intestinal cells and injects effector proteins that promote pathogen entry as the first step in causing life threatening bacillary dysentery (shigellosis). The Shigella Type III secretion apparatus (T3SA) consists of an anchoring basal body, an exposed needle, and a temporally assembled tip complex. Exposure to environmental small molecules recruits IpaB, the first hydrophobic translocator protein, to the maturing tip complex. IpaB then senses contact with a host cell membrane, forming the translocon pore through which effectors are delivered to the host cytoplasm. Within the bacterium, IpaB exists as a heterodimer with its chaperone IpgC; however, IpaB's structural state following secretion is unknown due to difficulties isolating stable protein. We have overcome this by coexpressing the IpaB/IpgC heterodimer and isolating IpaB by incubating the complex in mild detergents. Interestingly, preparation of IpaB with n‐octyl‐oligo‐oxyethylene (OPOE) results in the assembly of discrete oligomers while purification in N,N‐dimethyldodecylamine N‐oxide (LDAO) maintains IpaB as a monomer. In this study, we demonstrate that IpaB tetramers penetrate phospholipid membranes to allow a size‐dependent release of small molecules, suggesting the formation of discrete pores. Monomeric IpaB also interacts with liposomes but fails to disrupt them. From these and additional findings, we propose that IpaB can exist as a tetramer having inherent flexibility, which allows it to cooperatively interact with and insert into host cell membranes. This event may then lay the foundation for formation of the Shigella T3SS translocon pore.     

Out of sight, out of mind: high cryptic diversity obscures the identities and histories of geminate species in the marine bivalve subgenus Acar

Aim The rise of the Isthmus of Panama and the formation of ‘geminate’ species pairs serves as an important model of allopatric speciation. However, to function as a model system, hypothesized geminates must first be shown to be each other’s closest living relatives. If the presence of cryptic taxa obscures true relationships, the biogeographical histories of transisthmian taxa are likely to be misinterpreted. We have therefore completed a phylogeographic survey of the transisthmian bivalve subgenus Acar in the genus Barbatia to characterize patterns of tropical American diversity and to place transisthmian taxa in a regional phylogeographic context. Location Tropical America. Methods Mitochondrial cytochrome c oxidase I (COI) and nuclear internal transcribed spacer (ITS) sequences were obtained from 233 specimens of Acar. Sequences were analysed using cladistic and Bayesian methods. Divergence times between species were inferred from net nucleotide divergences and a coalescence‐based method. Results The survey revealed 22 COI clades that were also monophyletic at ITS, indicating that the taxonomy of Acar is potentially greater than a fivefold diversity underestimate. The lone previously recognized geminate [Barbatia (Acar) gradata and Barbatia (Acar) domingensis] is composed of 15 clades. Among the four transisthmian lineages identified, two diverged more than 14 Ma; the two other geminates split just prior to the time of final seaway closure. In addition to a fourfold increase in the number of known geminates, our data show that within‐basin diversification has been more impressive, with one geminate splitting into five monophyletic clades in the Western Atlantic alone since seaway closure. Electron microscopy of the larval shells of specimens indicates that the transisthmian lineage with the greatest rate of post‐Isthmian diversification possesses non‐planktonic larvae, a life‐history feature linked to high speciation rates. Main conclusions Our analyses revealed that the identities of geminate pairs split by the Isthmus of Panama were obscured by extremely high tropical American cryptic diversity. Although we have identified four geminates, only two appear to have been split by the Isthmus. Our uncovering of extensive post‐Isthmian diversification is consistent with the palaeontological perspective that the final closure of the Central American Seaway was followed by high rates of subgeneric diversification, particularly in the tropical Western Atlantic.     

SYSTEMATIC REVISION OF PSEUDOBEACONIA BORDAS, 1944, AND MENDOCINICHTHYS WHITLEY, 1953 (ACTINOPTERYGII: ‘PERLEIDIFORMES’) FROM THE TRIASSIC OF ARGENTINA

Abstract: The ‘perleidiform’Mendocinichthys and Pseudobeaconia from the Potrerillos and Santa Clara Abajo formations (Upper Triassic; Argentina) are reviewed. Mendocinichthys has been known from a review of this species that is not based on the type material, but on referred specimens in the American Museum of Natural History. However, those specimens are found here to represent a new species of Pseudobeaconia, P. celestae sp. nov. Consequently, Mendocinichthys is restricted here to the type material and, within it, to the only specimen that clearly represents a distinct taxon and is thus designated lectotype. We further performed a cladistic analysis and propose a new family, Pseudobeaconiidae for these two South American Triassic genera, which is mainly characterized by the presence of an incomplete dorsal ridge of spine‐like scales between the skull and the dorsal fin, and scales with straight posterior border, an elevated central region and marginal concentric ridges of ganoine. The cladistic analysis further indicates the existence of some lineages endemic to certain areas of Gondwana and Europe. Pseudobeaconia celestae sp. nov. represents the first record of Pseudobeaconia in the Cacheuta sub‐basin of the Cuyana Basin. The genus was previously known from the Santa Clara sub‐basin of the Cuyana Basin only, and the new record confirms the previous hypothesis of correlation between the sedimentary infilling of these sub‐basins.     

A regulatory gene network related to the porcine umami taste receptor (TAS1R1/TAS1R3)

Taste perception plays an important role in the mediation of food choices in mammals. The first porcine taste receptor genes identified, sequenced and characterized, TAS1R1 and TAS1R3, were related to the dimeric receptor for umami taste. However, little is known about their regulatory network. The objective of this study was to unfold the genetic network involved in porcine umami taste perception. We performed a meta‐analysis of 20 gene expression studies spanning 480 porcine microarray chips and screened 328 taste‐related genes by selective mining steps among the available 12 320 genes. A porcine umami taste‐specific regulatory network was constructed based on the normalized coexpression data of the 328 genes across 27 tissues. From the network, we revealed the ‘taste module’ and identified a coexpression cluster for the umami taste according to the first connector with the TAS1R1/TAS1R3 genes. Our findings identify several taste‐related regulatory genes and extend previous genetic background of porcine umami taste.