ATP‐dependent looping of DNA by ISWI

Snf2 related chromatin remodelling enzymes possess an ATPase subunit similar to that of the SF‐II helicases which hydrolyzes ATP to track along DNA. Translocation and any resulting torque in the DNA could drive chromatin remodeling. To determine whether the ISWI protein can translocate and generate torque, tethered particle motion experiments and atomic force microscopy have been performed using recombinant ISWI expressed in E. coli. In the absence of ATP, ISWI bound to and wrapped DNA thereby shortening the overall contour length measured in atomic force micrographs. Although naked DNA only weakly stimulates ATP hydrolysis by ISWI, both atomic force microscopy and tethered particle motion data indicate that the protein generated loops in the presence of ATP. The duration of the looped state of the DNA measured using tethered particle motion was ATP‐dependent. Finally, ISWI relaxed positively supercoiled plasmids visualized by atomic force microscopy. While other chromatin remodeling ATPases catalyze either DNA wrapping or looping, both are catalyzed by ISWI. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The phylogenetic distribution and morphological variation of the ‘pouch’ in female snakes

Siegel D.S., Miralles A, Trauth S.E. and Aldridge R.D. 2011. The phylogenetic distribution and morphological variation of the ‘pouch’ in female snakes. —Acta Zoologica (Stockholm) 93 : 400–408. The urodaeum of female snakes is a chamber that receives the oviducts, urinary ducts, and intestine. Previous studies have indicated that a derived region of unknown function persists between the urodaeum and oviducts in some snakes of the Colubroides. This structure was recently termed the ‘pouch’; however, it is also commonly referred to as the vaginal pouch. A broad sampling of female snakes revealed that the pouch evolved once on the branch leading to Colubroides. The presence of the pouch in Colubroides is not unambiguous, as this feature was lost in some members of the Atractaspididae and Lamprophiidae. Variation was also observed in pouch morphology between taxa of the Colubroides. Variation included the following: (1) whether the pouch was bifurcated and if so, were the arms of the pouch separated caudally, (2) whether separated pouch arms were split by a caudal bifurcation of the urodaeum or through medial septa of the pouch arms, and (3) the absence or presence of oviducal papillae invading the cranial/lateral extremity of the pouch. The variation in pouch morphology observed does not appear to be correlated with the evolutionary history of Colubroides and polymorphism within families is common.     

DNA as a ‘Nanomaterial’

DNA is recognized as a nanomaterial, not as a biological material, in the research field of nanotechnology. This article reviews recent research on nanowires, nanoarchitectures, computing, aptamers, biocatalysts, devices, and machines using DNA. In these works, the characteristics of DNA including facile synthesis by the solid-phase method, self-assembly, electro-conductivity, information elements, amplification, switching, molecular recognition, and catalytic functions, were appropriately applied. Multiple functions of DNA could be used simultaneously, and activated independently, by molecular switching. Therefore, the combinations of functional sequences of DNA can produce unique materials. It is obvious that the DNA molecule is one of the most promising functional nanomaterials. However, the application of DNA molecules is still under study because of the big gap that exists between theory and practice. We eagerly anticipate a ‘coming out’ of DNA due to breakthroughs in nanobiotechnology.     

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.     

‘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.     

Biogeography of ‘Cyprinella lutrensis’: intensive genetic sampling from the Pecos River ‘melting pot’ reveals a dynamic history and phylogenetic complexity

Thorough sampling is necessary to delineate lineage diversity for polytypic ‘species’ such as Cyprinella lutrensis. We conducted extensive mtDNA sampling (cytochrome b and ND4) from the Pecos River, Rio Grande, and South Canadian River, New Mexico. Our study focussed on the Pecos River due to its complex geological history and potential to harbour multiple lineages. We used geometric–morphometric, morphometric, and meristic analyses to test for phenotypic divergence and combined nucDNA with mtDNA to test for cytonuclear disequilibrium and combined our sequences with published data to conduct a phylogenetic re‐assessment of the entire C. lutrensis clade. We detected five co‐occurring mtDNA lineages in the Pecos River, but no evidence for cytonuclear disequilibrium or phenotypic divergence. Recognized species were interspersed amongst divergent lineages of ‘C. lutrensis’. Allopatric divergence among drainages isolated in the Late Miocene and Pliocene apparently produced several recognized species and major divisions within ‘C. lutrensis’. Pleistocene re‐expansion and subsequent re‐fragmentation of a centralized lineage founded younger, divergent lineages throughout the Rio Grande basin and Edwards Plateau. There is also evidence of recent introductions to the Rio Grande, Pecos and South Canadian Rivers. Nonetheless, deeply divergent lineages have coexisted since the Pleistocene.     

Structural mechanism of ATP‐dependent DNA binding and DNA end bridging by eukaryotic Rad50

The Mre11–Rad50–Nbs1 (MRN) complex is a central factor in the repair of DNA double‐strand breaks (DSBs). The ATP‐dependent mechanisms of how MRN detects and endonucleolytically processes DNA ends for the repair by microhomology‐mediated end‐joining or further resection in homologous recombination are still unclear. Here, we report the crystal structures of the ATPγS‐bound dimer of the Rad50^NBD (nucleotide‐binding domain) from the thermophilic eukaryote Chaetomium thermophilum (Ct) in complex with either DNA or CtMre11^RBD (Rad50‐binding domain) along with small‐angle X‐ray scattering and cross‐linking studies. The structure and DNA binding motifs were validated by DNA binding experiments in vitro and mutational analyses in Saccharomyces cerevisiae in vivo. Our analyses provide a structural framework for the architecture of the eukaryotic Mre11–Rad50 complex. They show that a Rad50 dimer binds approximately 18 base pairs of DNA along the dimer interface in an ATP‐dependent fashion or bridges two DNA ends with a preference for 3′ overhangs. Finally, our results may provide a general framework for the interaction of ABC ATPase domains of the Rad50/SMC/RecN protein family with DNA.     

ATP‐dependent/‐independent enzymatic ring reductions involved in the anaerobic catabolism of naphthalene

Polycyclic aromatic hydrocarbons are among the most hazardous environmental pollutants. However, in contrast to aerobic degradation, the respective degradation pathways in anaerobes are greatly unknown which has so far prohibited many environmental investigations. In this work, we studied the enzymatic dearomatization reactions involved in the degradation of the PAH model compounds naphthalene and 2‐methylnaphthalene in the sulfate‐reducing enrichment culture N47. Cell extracts of N47 grown on naphthalene catalysed the sodium dithionite‐dependent four‐electron reduction of the key intermediate 2‐naphthoyl‐coenzyme A (NCoA) to 5,6,7,8‐tetrahydro‐2‐naphthoyl‐CoA (THNCoA). The NCoA reductase activity was independent of ATP and was, surprisingly, not sensitive to oxygen. In cell extracts in the presence of various electron donors the product THNCoA was further reduced by a two‐electron reaction to most likely a conjugated hexahydro‐2‐naphthoyl‐CoA isomer (HHNCoA). The reaction assigned to THNCoA reductase strictly depended on ATP and was oxygen‐sensitive with a half‐life time between 30 s and 1 min when exposed to air. The rate was highest with NADH as electron donor. The results indicate that two novel and completely different dearomatizing ring reductases are involved in anaerobic naphthalene degradation. While the THNCoA reducing activity shows some properties of ATP‐dependent class I benzoyl‐CoA reductases, NCoA reduction appears to be catalysed by a previously unknown class of dearomatizing aryl‐carboxyl‐CoA reductases.     

Developmental evolution: Going beyond the ‘just so’

Two new protocols for infecting non-mammalian embryos with viruses, together with RNA inhibition, have provided evolutionary developmental biologists with the tools to study the effects of manipulating gene activity in a wide range of species, allowing them to test hypotheses rather than rely on inference from similarity.     

Identifying ‘prime suspects’: symbioses and the evolution of multicellularity

The possible involvement of symbioses in the evolution of multicellularity is explored. Evidence is drawn principally from the biology of present day associations of plants and animals with prokaryotes. A particular emphasis is placed on future research opportunities in this area of biology that have been provided by the advent of specific molecular techniques and new model systems. With the application of new approaches that result from these advances, a more holistic understanding of the biology of the coevolved communities, composed of animals or plants and their associated prokaryotes, is within the reach of biologists over the next few decades.     

‘Native’ Culture and Self‐advocacy

Book reviewed in this article: Takashi Irimoto and Takako Yamada (eds). Circumpolar Ethnicity and Identity.     

Making sense of ‘lower’ and ‘upper’ stem‐group Euarthropoda,with comments on the strict use of the name Arthropoda von Siebold, 1848

The ever‐increasing number of studies that address the origin and evolution of Euarthropoda – whose extant representatives include chelicerates, myriapods, crustaceans and hexapods – are gradually reaching a consensus with regard to the overall phylogenetic relationships of some of the earliest representatives of this phylum. The stem‐lineage of Euarthropoda includes numerous forms that reflect the major morphological transition from a lobopodian‐type to a completely arthrodized body organization. Several methods of classification that aim to reflect such a complex evolutionary history have been proposed as a consequence of this taxonomic diversity. Unfortunately, this has also led to a saturation of nomenclatural schemes, often in conflict with each other, some of which are incompatible with cladistic‐based methodologies. Here, I review the convoluted terminology associated with the classification of stem‐group Euarthropoda, and propose a synapomorphy‐based distinction that allows ‘lower stem‐Euarthropoda’ (e.g. lobopodians, radiodontans) to be separated from ‘upper stem‐Euarthropoda’ (e.g. fuxianhuiids, Cambrian bivalved forms) in terms of the structural organization of the head region and other aspects of overall body architecture. The step‐wise acquisition of morphological features associated with the origins of the crown‐group indicate that the node defining upper stem‐Euarthropoda is phylogenetically stable, and supported by numerous synapomorphic characters; these include the presence of a deutocerebral first appendage pair, multisegmented head region with one or more pairs of post‐ocular differentiated limbs, complete body arthrodization, posterior‐facing mouth associated with the hypostome/labrum complex, and post‐oral biramous arthropodized appendages. The name ‘Deuteropoda’ nov. is proposed for the scion (monophyletic group including the crown‐group and an extension of the stem‐group) that comprises upper stem‐Euarthropoda and Euarthropoda. A brief account of common terminological inaccuracies in recent palaeontological studies evinces the utility of Deuteropoda nov. as a reference point for discussing aspects of early euarthropod phylogeny.     

The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution

The earliest evolution of the animals remains a taxing biological problem, as all extant clades are highly derived and the fossil record is not usually considered to be helpful. The rise of the bilaterian animals recorded in the fossil record, commonly known as the ‘Cambrian explosion’, is one of the most significant moments in evolutionary history, and was an event that transformed first marine and then terrestrial environments. We review the phylogeny of early animals and other opisthokonts, and the affinities of the earliest large complex fossils, the so‐called ‘Ediacaran’ taxa. We conclude, based on a variety of lines of evidence, that their affinities most likely lie in various stem groups to large metazoan groupings; a new grouping, the Apoikozoa, is erected to encompass Metazoa and Choanoflagellata. The earliest reasonable fossil evidence for total‐group bilaterians comes from undisputed complex trace fossils that are younger than about 560 Ma, and these diversify greatly as the Ediacaran–Cambrian boundary is crossed a few million years later. It is generally considered that as the bilaterians diversified after this time, their burrowing behaviour destroyed the cyanobacterial mat‐dominated substrates that the enigmatic Ediacaran taxa were associated with, the so‐called ‘Cambrian substrate revolution’, leading to the loss of almost all Ediacara‐aspect diversity in the Cambrian. Why, though, did the energetically expensive and functionally complex burrowing mode of life so typical of later bilaterians arise? Here we propose a much more positive relationship between late‐Ediacaran ecologies and the rise of the bilaterians, with the largely static Ediacaran taxa acting as points of concentration of organic matter both above and below the sediment surface. The breaking of the uniformity of organic carbon availability would have signalled a decisive shift away from the essentially static and monotonous earlier Ediacaran world into the dynamic and burrowing world of the Cambrian. The Ediacaran biota thus played an enabling role in bilaterian evolution similar to that proposed for the Savannah environment for human evolution and bipedality. Rather than being obliterated by the rise of the bilaterians, the subtle remnants of Ediacara‐style taxa within the Cambrian suggest that they remained significant components of Phanerozoic communities, even though at some point their enabling role for bilaterian evolution was presumably taken over by bilaterians or other metazoans. Bilaterian evolution was thus an essentially benthic event that only later impacted the planktonic environment and the style of organic export to the sea floor.     

Cleaner Wrasses Keep Track of the ‘When’ and ‘What’ in a Foraging Task1

In recent years evidence has accumulated that at least some animals can remember the ‘what’, ‘where’ and ‘when’ of personal experiences. Currently, evidence for such ability is taxonomically restricted to birds and mammals. Here, we demonstrate for the first time that cleaner wrasses Labroides dimidiatus are able to remember when they interacted with what after a single event. In nature, cleaners remove ectoparasites from other reef fishes, so‐called clients. Clients are depleted, non‐stationary food patches at the end of an interaction and replenished only after a delay. In our experiments, we presented twelve cleaners every 2.5 min, a choice between two of a total of four plates with different colours and patterns. One plate was always accessible but contained a non‐preferred food item while the other three contained a preferred food item, but allowed a next feeding event only after 5, 10 or 15 min. Thus, to maximise food intake, cleaners had to remember for each choice when they had last interacted with which plate. When confronted with two plates offering preferred food, cleaners showed an overall significant preference for the plate that allowed access during the trial. For six cleaners, the preference was significant. Also, on trials involving the always accessible plate, cleaners discriminated between trials in which they had to eat the non‐preferred food and trials on which they could eat the preferred food. In conclusion, cleaners are able to track the ‘when’ and ‘what’ (or possibly ‘who’) within a biologically meaningful time period.     

Molecular phylogenies,morphological homologies and the evolution of moth ‘ears’

The recent suggestion that complex hearing organs (‘ears’) may have been evolved just once in the stem lineage of a clade of ditrysian moths including the pyraloids and ‘Macroheterocera’ is discussed. It is argued that homology between ears situated in different segments and in different morphological territories (dorsal or ventral) of the same segment must be ruled out, and that therefore the number of independent origins of ears in the said clade is three at the very least. Mechanical protection of the ventral abdominal base by the backwards slanting metacoxae permits an attenuation of the body wall which would facilitate multiple independent origins of ears exactly in this region.     

Taxonomy of the ‘Synargis axenus complex’ belonging to the ‘Synargis regulus’ species group,with a phylogenetic reassessment of the genus Synargis Hübner, 1819 (Lepidoptera: Riodinidae: Nymphidiini)

Three new species of Synargis Hübner, 1819, from Paraguay and southern and central Brazil are described: Synargis fandanga sp. nov. from Paraguay (Amambay and Paraguari) and southern Brazil (Paraná and Santa Catarina), Synargis rasqueada sp. nov. from central Brazil (Mato Grosso), and Synargis gorpa sp. nov. from southern Brazil (Paraná, Santa Catarina, and Rio Grande do Sul). Lectotypes are designated for Lemonias axenus Hewitson, 1876, Ematurgina axenus ochrophlegma Sitchel, 1911, Ematurgina acervata Seitz, 1932, and Ematurgina perrupta Seitz, 1932. Ematurgina ochrophlegma f. dissimilis Hayward, 1949, is a new synonym of Synargis bifasciata (Mengel, 1902), and Ematurgina ochrophlegma f. distincta Hayward, 1949, is a new synonym of Synargis axenus (Hewitson, 1876). The revalidation of E. perrupta Seitz, 1932, and the new status Synargis ochrophlegma (Stichel, 1911) are proposed. Ematurgina perrupta ab. roeberi Seitz, 1932, and Ematurgina bifasciata ochrophlegma ab. leucomelaina Breyer, 1930, are considered unavailable names. Based on a previous phylogenetic hypothesis, the phylogeny of the genus Synargis is reassessed, adding these new and revalidated taxa, and nine additional characters. The ‘Synargis regulus’ species group and the ‘Synargis axenus complex’ are recovered as monophyletic, with S. gorpa sp. nov. sister to the remaining species of the ‘S. axenus complex’. Additionally, an up‐to‐date geographical distribution map and a dichotomous key are provided, and the taxonomy of the taxa involved is discussed. © 2013 The Linnean Society of London     

‘Dancing the image’: materiality and spirituality in Andean religious ‘images’

In the Christian tradition, representing the divine has often been considered both an impossible and yet necessary endeavour rooted in the human need in certain moments of weakness to visualize God. In this article, based on research findings from fieldwork carried out with urban indigenous groups in La Paz, Bolivia, I suggest that the articulation of local and Catholic representational traditions and practices has produced an understanding of the religious image not so much as an object of detached contemplation or a reference to a religious symbol but rather as an energized element which physically shapes the relationship and exchange between the material and the spiritual world. I suggest that through a study of Andean religious images we may be able to produce an alternative ontological perspective on the relationship between the spiritual, material, and living worlds.

Résumé

Dans la tradition chrétienne, la représentation du divin est souvent considérée comme une gageure impossible et pourtant nécessaire, motivée par la nécessité humaine de visualiser Dieu dans les moments de faiblesse. À partir des matériaux de terrain obtenus auprès de groupes autochtones urbains à La Paz, en Bolivie, l'auteur suggère ici que l'articulation des traditions et pratiques de représentation locales et catholiques a conduit à concevoir l'image religieuse moins comme un objet de contemplation détachée ou une référence à un symbole religieux que comme un élément chargé d'énergie, qui donne physiquement forme à la relation et aux échanges entre le monde matériel et le monde spirituel. L'article suggère qu'à travers l'étude des images religieuses andines, on pourrait élaborer un autre point de vue ontologique sur la relation entre les mondes spirituel, matériel et vivant.     

‘Not anymore,not yet’: Australian–Hungarians rediscover the ‘old‐new’ Hungary

This article examines the return visits of Australian‐Hungarians to their homeland after 1989 and the different types of homecoming experiences after an extended period of separation. The focus of the paper is returnees’ perceptions of changes to Hungary or lack thereof. I analyse the distinction between the ‘desired/nostalgic past’, which Hungarian returnees nurtured during the decades of separation and expected to rediscover upon return, and the ‘disdained past’ of the Communist dictatorship, which they had fled and hoped never to encounter again. The findings demonstrate that people interpret both past and present in relation to hopes, expectations and disappointments situated within particular nationalist imaginaries, political projects and ideological prisms. This allows us to analyse the nexus between local, national and diasporic belonging through post‐socialist identities, orientations toward democracy and understandings of ‘nation’.