The DAPK family: a structure–function analysis

DAP-kinase (DAPK) is the founding member of a family of highly related, death associated Ser/Thr kinases that belongs to the calmodulin (CaM)-regulated kinase superfamily. The family includes DRP-1 and ZIP-kinase (ZIPK), both of which share significant homology within the common N-terminal kinase domain, but differ in their extra-catalytic domains. Both DAPK and DRP-1 possess a conserved CaM autoregulatory domain, and are regulated by calcium-activated CaM and by an inhibitory auto-phosphorylation within the domain. ZIPK’s activity is independent of CaM but can be activated by DAPK. The three kinases share some common functions and substrates, such as induction of autophagy and phosphorylation of myosin regulatory light chain leading to membrane blebbing. Furthermore, all can function as tumor suppressors. However, they also each possess unique functions and intracellular localizations, which may arise from the divergence in structure in their respective C-termini. In this review we will introduce the DAPK family, and present a structure/function analysis for each individual member, and for the family as a whole. Emphasis will be placed on the various domains, and how they mediate interactions with additional proteins and/or regulation of kinase function.     

The CCN family: a new class of inflammation modulators?

Uncontrolled or sustained inflammation is the underlying cause of or actively contributes to the progression of many chronic pathologies such as atherosclerosis, arthritis, or neuroinflammatory diseases. Matricellular proteins of the CCN family (CYR61/CTGF/NOV) have emerged as localized multitasking signal integrators. These structurally conserved secreted proteins specifically interact with and signal through various extracellular partners, in particular integrins, which enable them to play crucial roles in various processes including development, angiogenesis, wound healing and diseases such as fibrosis, vascular disease and cancer. In this review, we discuss the possibility that the CCN family members could represent a putative new class of modulators of inflammation. In this context, we focused on their relationship with cytokines and chemokines. In vitro, CCN expression is finely regulated by diverse inflammatory mediators including cytokines (TNFα, IL1β, TGF-β), small factors such as prostaglandins, nitric oxide, histamine and serotonin, and extracellular matrix enzymes. In addition, CCN proteins acting alone or in concert with their specific partners appear to be potent regulators of the production of cytokines and chemokines in a context-dependent manner. Finally, emerging studies suggest a potential role for CCN proteins in chronic inflammatory diseases such as atherosclerosis, rheumatoid arthritis, inflammatory kidney diseases and neuroinflammatory pathologies such as Alzheimer’s disease. CCN members could therefore represent new potential therapeutic targets for drug development against such diseases.     

Long-term ecological change in a conservation hotspot: the fossil avifauna of Mé Auré Cave,New Caledonia

Through the continuing accumulation of fossil evidence, it is clear that first human arrival on islands around the world was linked to a rise in the extinction rate for vertebrates. Bones in human-era fossil sites can also reveal changes in the composition and structure of ecological communities due to human environmental impacts. New Caledonia is a large and biogeographically distinct island in the southwest Pacific and is considered a critical priority for biodiversity conservation. We examined fossil birds from the Mé Auré Cave site (WMD007), located in lowland dry forest on the west coast of New Caledonia. Accumulation of bird skeletal material in the cave was primarily through deposition in barn owl (Tyto alba) pellets. The site recorded the island-wide extinction of two species and extirpation of at least two other species from the lowlands in the past 1200 years. Species richness of birds in the stratigraphic deposit was quite high, reflecting the catholic diet of barn owls on islands, and many species have continued to persist near the site despite loss and degradation of the dry forest. However, we found substantial turnover in relative abundance of species in the cave deposit, with edge and open country birds becoming more common through time. These changes may reflect the severe reduction of dry forest habitat during the colonial period. This work provides a temporal record of avifaunal and environmental change in the threatened dry forest habitat that should be particularly informative for ongoing conservation and restoration efforts.     

Macroevolutionary patterns in Rhynchocephalia: is the tuatara (Sphenodon punctatus) a living fossil?

The tuatara, Sphenodon punctatus, known from 32 small islands around New Zealand, has often been noted as a classic ‘living fossil’ because of its apparently close resemblance to its Mesozoic forebears and because of a long, low‐diversity history. This designation has been disputed because of the wide diversity of Mesozoic forms and because of derived adaptations in living Sphenodon. We provide a testable definition for ‘living fossils’ based on a slow rate of lineage evolution and a morphology close to the centroid of clade morphospace. We show that through their history since the Triassic, rhynchocephalians had heterogeneous rates of morphological evolution and occupied wide morphospaces during the Triassic and Jurassic, and these then declined in the Cretaceous. In particular, we demonstrate that the extant tuatara underwent unusually slow lineage evolution, and is morphologically conservative, being located near the centre of the morphospace for all Rhynchocephalia.     

The low-density lipoprotein receptor gene family: a cellular Swiss army knife?

The low-density lipoprotein receptor gene family is an evolutionarily conserved group of cell-surface receptors produced by mammals and other organisms. Initially thought to be endocytic receptors that mediate the uptake of lipoproteins, recent findings have shown that these receptors have other roles in a range of cellular processes. Among other activities, members of this family act as signal transducers in neuronal migration processes, regulate synaptic plasticity or control vitamin homeostasis. Such multifunctionality is achieved by interaction with diverse cell-surface proteins including glycolipid-anchored receptors, G-protein-coupled receptors and ion channels. Here, we review the molecular interactions of this protein family with other cell-surface proteins that provide specificity and versatility - a versatility that may be reminiscent of a cellular Swiss army knife.     

The BAR-domain family of proteins: a case of bending and binding?

BAR-domains recently took centre stage in science through a report on the crystal structure of this domain in Drosophila Amphiphysin. Though only weakly conserved at the sequence level, the structure of the BAR domain shows striking similarity to the GTPase-binding domain of Arfaptin 2, an effector of Rho- and Arf- GTPases. On the basis of this sequence and structural similarity, these two proteins have been classified as belonging to the same family, the BAR-domain family, and they probably also have similar functional characteristics. Presented here are the results of a database search for the sequence of the BAR domain of Amphiphysin and Arfaptin 2. This search identified a variety of related proteins, most of which are involved in intracellular transport and especially in endocytosis. For example, the BAR-domain family includes Endophilins, GTPase-activating proteins of the Centaurinbeta family and Oligophrenins, the adaptor proteins APPL1 and APPL2 that were recently shown to interact with the small GTPase Rab5, as well as members of the Sorting nexin family. On the basis of the structures of Amphiphysin and Arfaptin 2 and the cellular role of Amphiphysins in the early steps of endocytosis, the functions of the BAR domain have been defined as a dimerization motif and as sensing and inducing membrane curvature. However, data on Arfaptin 2 and now also on the Adaptor proteins APPL1 and 2 suggest that another function of the BAR domain is to bind to small GTPases.     

The ‘death roll’ of giant fossil crocodyliforms (Crocodylomorpha: Neosuchia): allometric and skull strength analysis

In the evolution of crocodylomorphs, there were at least three giant-dimension genera: Deinosuchus from late Cretaceous of North America, Sarcosuchus from middle Cretaceous of Africa and South America, and Purussaurus from Miocene of South America. It has been suggested that these predators could have fed on very large prey as dinosaurs and megamammals. The ‘death roll’ is a spinning manoeuver executed to subdue and dismember large prey; therefore, it has been previously suggested that giant cocrodylomorphs may have used this manoeuver. However, this manoeuver can generate torsional stresses in the skull. We propose a biomechanical model to estimate the capability of a crocodylomorphs for withstanding this torsional stresses. Our results show a good correlation between a ‘death roll’ capability indicator and the feeding categories related with the actual use of ‘death roll’ in 16 living species. Here, for the first time, we propose a biomechanical approach of the implications of ‘death roll’ in fossil crocodylomorphs. We suggest that Deinosuchus and Purussaurus were able to execute death roll over dinosaurs and large mammals, respectively, but Sarcosuchus probably was not. We also found some allometry effects and, finally, we discuss palaeobiological implications based on our results.     

Paramesopsocidae,a new Mesozoic psocid family (Insecta: Psocodea “Psocoptera”: Psocomorpha)

Paramesopsocus lu n. gen., n. sp. and Paramesopsocus adibi n. sp. are respectively described from the Early Cretaceous amber of Lebanon and from the Late Jurassic limestone of Karatau (Kazakhstan). They are placed within the suborder Psocomorpha, and in the Mesozoic extinct family Paramesopsocidae n. fam. A cladistic phylogeny for Psocomorpha is given including our fossil taxa. The discovery of these new taxa demonstrates the necessity of a deep cladistic redefinition of the currently admitted major subdivisions of this suborder.     

The roots—a short history of industrial microbiology and biotechnology

Early biotechnology (BT) had its roots in fascinating discoveries, such as yeast as living matter being responsible for the fermentation of beer and wine. Serious controversies arose between vitalists and chemists, resulting in the reversal of theories and paradigms, but prompting continuing research and progress. Pasteur’s work led to the establishment of the science of microbiology by developing pure monoculture in sterile medium, and together with the work of Robert Koch to the recognition that a single pathogenic organism is the causative agent for a particular disease. Pasteur also achieved innovations for industrial processes of high economic relevance, including beer, wine and alcohol. Several decades later Buchner, disproved the hypothesis that processes in living cells required a metaphysical ‘vis vitalis’ in addition to pure chemical laws. Enzymes were shown to be the chemical basis of bioconversions. Studies on the formation of products in microbial fermentations, resulted in the manufacture of citric acid, and chemical components required for explosives particularly in war time, acetone and butanol, and further products through fermentation. The requirements for penicillin during the Second World War lead to the industrial manufacture of penicillin, and to the era of antibiotics with further antibiotics, like streptomycin, becoming available. This was followed by a new class of high value-added products, mainly secondary metabolites, e.g. steroids obtained by biotransformation. By the mid-twentieth century, biotechnology was becoming an accepted specialty with courses being established in the life sciences departments of several universities. Starting in the 1970s and 1980s, BT gained the attention of governmental agencies in Germany, the UK, Japan, the USA, and others as a field of innovative potential and economic growth, leading to expansion of the field. Basic research in Biochemistry and Molecular Biology dramatically widened the field of life sciences and at the same time unified them considerably by the study of genes and their relatedness throughout the evolutionary process. The scope of accessible products and services expanded significantly. Economic input accelerated research and development, by encouraging and financing the development of new methods, tools, machines and the foundation of new companies. The discipline of ‘New Biotechnology’ became one of the lead sciences. Although biotechnology has historical roots, it continues to influence diverse industrial fields of activity, including food, feed and other commodities, for example polymer manufacture, biofuels and energy production, providing services such as environmental protection, and the development and production of many of the most effective drugs. The understanding of biology down to the molecular level opens the way to create novel products and efficient environmentally acceptable methods for their production.     

The Høylandet area – patterns and processes of a pristine boreal-subalpine ecosystem – a synopsis

The research activities on soil–freshwaterinteractions and freshwater biotic structure andprocesses in the Høylandet area during the years 1986–89are presented in this issue ofHydrobiologia. The 9 papers cover a range of topicsfrom physiochemical gradients and processes in soilsand freshwaters to selected aspects of freshwaterbiotic community structure and temporal variability.This synopsis aims (a) to present an overview of majorfindings, (b) to interpret the results in the contextof air pollution effects and (c) to outlinesuggestions for future research activities inHøylandet. The area has a sub-oceanic climate varyingfrom 1100 to 2200 mm of precipitation normallyoriginating from unpolluted airmasses from the NorthAtlantic. It is chemically dominated by sea salts, haslow concentrations and low deposition of mineralacids. The catchment geology is variable and complexand consists mainly of various granites and gneisses.The soils are undisturbed ancient soils,primarily iron podzols associated with forests, orintact histosols with strong organic characterassociated with mires, often quite acidic.They are sensitive because occurrence of predominantlyinsoluble unstable Al-complexes may leach out ifexposed to anthropogenically acidified soil drainagewater and turn up as toxic inorganic aqueous Al insurface runoff. Small amounts of locally generatednitrogen compounds are mostly retained in thecatchment. The water qualities of these Høylandetsites are run by inputs of sea salts, hydrologicalprocesses including dilution of the base flow, orlateral surface or overland flow and in-catchmentprocesses. Relative to affected areas, it appears thatthe inputs and catchment processes are in balance,i.e., that the inputs of strong acid anions, hydrogenions and sea salts are equilibrated by internalweathering and other processes and integrated withinapparently intact biogeochemical cycles. The overallresult is that these soils remain a net source ofalkalinity to the runoff. These results are confirmedby regional studies of water quality both at low andhigh flow which show that the humus and ionic contentof the water decreased with elevation, headwatersbeing more dominated by sea salts and dilutionprocesses. Excess sulphate concentrations are low, andfew if any sites appear anthropogenically acidified,the most acid pHs reflecting presence of natural weakorganic acids.The resulting surface water quality allows a diverseaquatic fauna and flora with representatives of manyacid-sensitive groups. The fish fauna consists ofself-reproducing salmonid populations with normaldemography and ecological interactions. Despite highin-lake mortality, both brown trout and Arctic charrexhibited normal age-class compositions, with noindication of the recruitment failure or highpost-spawning mortality commonly observed inacid-stressed situations. The zooplankton and benthos in the lakesare inhabited by populations of several acid sensitivespecies, like Daphnia spp and Gammaruslacustris, and with dominance of mayfly species ofthe genus Baetis in the stream fauna. Thediatom flora includes many species which are rare orabsent in acidified waters. The observed gradients indiversity and biomass seem dominated by localenvironmental conditions which reflect natural ratherthan man-made processes. The pristine nature of thearea also emerges from the paleoecological studies inLake Røyrtjønna which show that the low acidity ofthis lake evironment has persisted from preindustrialtill present times. Suggestion for future researchactivities in Høylandet are outlined.     

内蒙古中始新世一似ameghinornithid鸟类(鸟纲:Cariamae:Ameghinornithidae?)

内蒙古二连盆地额尔登敖包剖面(相当于伊尔丁曼哈组)的中始新世早期地层中新发现的一件标本显示其属于一个与ameghinornithid相似的种,代表了Ameghinomithidae在亚洲的首个记录.新标本具有外踝半圆形,缺失骨质腱桥,伸肌沟外侧具有大而平的结节,以及其他与ameghinomithid和似ameghinomithid鸟类共有的特征.内蒙古标本与欧洲最古老的ameghinomithids记录大体属同一时代(约48 Ma).与同时期内蒙古哺乳动物群主要由亚洲类群组成兼有少量与北美有关的绝灭类群不同,这类鸟类中始新世时在北美缺失,而存在于欧洲和亚洲.加上埃及法尤姆早渐新世地层中发现的似ameghinomithid鸟类,这类已经绝灭的鸟类的地理分布似乎比过去所认为的要广泛得多.     

“Out-of-India” dispersal for Adina (tribe Naucleeae; family Rubiaceae): evidence from the early Eocene fossil record from India

This study reports the oldest fossil record of the genus Adina, A. vastanenesis n. sp., from the early Eocene of Vastan lignite mine (Cambay Shale Formation), Surat district, Gujarat. This fossil wood is characterized by diffuse porous wood, predominantly solitary tylosed vessels, simple perforations, scanty paratracheal to diffuse to sometimes diffuse in aggregate axial parenchyma, predominantly uniseriate to occasionally biseriate rays, and non septate fibres with bordered pits and shows its best resemblance with the modern species, Adina multifolia Haviland, belonging to the tribe Naucleeae (subfamily Cinchonoideae) of the family Rubiaceae. The present discovery becomes the first fossil record of the wood of Adina, which provides an insight about the Gondwanan origin either for the genus Adina or the tribe Naucleeae and its further dispersal to Southeast Asia.     

Anamylopsoraceae — a new family of lichenized ascomycetes with stipitate apothecia (Lecanorales: Agyriineae)

The anatomy, chemistry and developmental morphology ofAnamylopsora pulcherrima is investigated. Some characters, including the ascus structure, suggest a close affinity with theAgyriaceae. However, the chemistry and the pycnidial structure differ as well as the ascoma ontogeny.Anamylopsora has a gymnocarpous ascoma development and the ascogonia are produced in stipes.Trapelia coarctata, as a typical member of theAgyriaceae, shows a hemiangiocarpous ascoma ontogeny. The anatomical, chemical and ontogenetical characters of several families are compared withAnamylopsora and it is shown that the genus is best placed in a monotypic familyAnamylopsoraceae Lumbsch & Lunke, fam. nova, which is placed in theAgyriineae (Lecanorales).This paper is dedicated to Prof. DrAino Henssen (Marburg) on the occasion of the 70th birthday.     

The first fossil spider cricket (Orthoptera: Gryllidae: Phalangopsinae): 20 million years of troglobiomorphosis or exaptation in the dark?

A new spider cricket (Orthoptera: Gryllidae: Phalangopsinae) is described from an adult female preserved in Early Miocene (Burdigalian) amber from the Dominican Republic. Araneagryllus dylani gen. et sp. nov. represents the first fossil record of Phalangopsinae, and is assigned to the tribe Luzarini, subtribe Amphiacustina stat. nov. A cladistic analysis of Amphiacustina places Araneagryllus gen. nov. within a clade comprising Arachnopsita, Leptopedetes, Longuripes, Mayagryllus, Nemoricantor, and Prolonguripes. This clade is the sister group to a clade comprising Amphiacusta, Cantrallia, and Noctivox. The results of this analysis suggest that: (1) the common ancestor of all Amphiacustina was epigean, and was likely to have been cavicolous and/or straminicolous; (2) strict troglobitism evolved twice within Amphiacustina, once in the lineage leading to Noctivox and again in the clade comprising Mayagryllus, Arachnopsita, Longuripes, and Prolonguripes; and (3) Prolonguripes is secondarily epigean, having reverted to life above ground. The occurrence of Araneagryllus gen. nov. in amber indicates that it was not troglobitic, but was instead more likely to have been straminicolous, living on the ground and foraging amongst leaf litter. Araneagryllus gen. nov. possesses a number of characters that are usually considered to be adaptive to a troglobitic life history, suggesting that many so‐called troglobiomorphies are not adaptations to life in caves, but are instead likely to have been exaptive. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 56–65.     

Insertion of a short repetitive sequence (D881) in a sea urchin gene: A typical interspersed repeat?

Summary A comparison has been made between the Sp88 gene regions of the DNAs of the sea urchinsStrongylocentrotus purpuratus (Sp.) andStrongylocentrotus drobachiensis (Sd.). Examination of the 3 terminal part of the transcribed region revealed a short repetitive sequence present in Sd. but absent from Sp. A 12-nucleotide sequence present once in Sp. is almost perfectly duplicated at both ends of the repeat in Sd., suggesting that a mobile repeat was inserted in the Sd. genome. Other members of this family of repeated sequences occur in many interspersed locations in the genomes of both species. Except for the insertion duplication, the inserted sequence lacks direct or reverse repeats.     

The DNA-polymerase-X family: controllers of DNA quality?

Synthesis of the genetic material of the cell is achieved by a large number of DNA polymerases. Besides replicating the genome, they are involved in DNA-repair processes. Recent studies have indicated that certain DNA-polymerase-X-family members can synthesize unusual DNA structures, and we propose that these DNA structures might serve as 'flag wavers' for the induction of DNA-repair and/or DNA-damage-checkpoint pathways.