On the genus Thaumatoconcha Kornicker and Sohn (Halocyprida) with description of two new species from Southern Ocean deep sea

Two new Thaumatoconcha Kornicker and Sohn, 1976a species, T. dandani n. sp. and T. quasiporosa n. sp., have been described in the present paper. Both species have been collected during two expeditions to the Southern Ocean and are found in the deep sea. The first species is most closely related to T. caraionae Kornicker and Sohn, 1976a, but it has a very specific appearance of copulatory organ, anterior part being covered in small spines. The second species is most closely related to T. porosa Kornicker, 1985, and they differ in the carapace shape and morphology, while they have almost identical appearance of the male copulatory organ. A list of Thaumatocyprididae species and a key to the species of Thaumatoconcha are also presented in this paper.     

Two ants (Insecta: Hymenoptera: Formicidae: Formicinae) from the Late Pliocene of Willershausen, Germany, with a nomenclatural note on the genus Camponotites

Two species of the genus Camponotites (Formicidae, Formicinae) are described from the Late Pliocene deposits of Willershausen, Lower Saxony, northern Germany: C. silvestris Steinbach, 1967, and C. steinbachi n. sp. The generic name Camponotites has been established for fossil (Tertiary) ants independently by Steinbach (Bericht der Naturhistorischen Gesellschaft zu Hannover 111:95–102, 1967) and by Dlussky (Trudy paleontologi?eskogo instituta, akademiâ nauk SSSR, 1981), each for materials of different stratigraphical and geographical origin. Though poorly described, Camponotites Steinbach, 1967, and the single included (type) species C. silvestris Steinbach, 1967 (a monotypic species from the Late Pliocene of Willershausen), were based upon indication in the sense of the ICZN. Therefore, both the generic and specific names are valid and available. Camponotites Dlussky, 1981 (and its type species C. macropterus Dlussky, 1981) were certainly introduced correctly and are therefore available, too; but due to its homonymy the generic name is not valid. The revision shows that in this rare case both generic names are not only homonyms but also synonyms.     

A morphometrical study of oribatid mites (Acari: Oribatida) of the genus Carabodes C.L. Koch, 1835 (Carabodidae) using a confocal laser scanning microscope: an alternative approach to quantitative analysis of various features

In the past, micro-arthropod taxonomists have mainly relied on qualitative characters to identify species, and relatively little attention has been paid to quantitative analysis. However, several taxonomic groups have high morphological variability, which creates problems in identification. Quantitative analysis of morphometrical data of specific characters could aid in understanding differences in the morphology of oribatid species. In this respect, confocal laser scanning microscopy and quantitative analysis were used to describe morphological traits of four oribatid mite species belonging to the genus Carabodes Koch, 1835—C. femoralis (Nicolet, 1855), C. labyrinthicus (Michael, 1879), C. ornatus Storkan, 1925 and C. subarcticus Trägårdh, 1902. All specimens were collected in Latvia. Thirteen morphological traits were measured for 838 adult individuals. The same traits were also measured with transmitted light microscopy, and results were compared. The impact of a number of environmental factors on traits was also assessed. High interspecific variability in size of most morphological features was observed. In many cases, sizes of the measured features correlated between different species. The ranges in length of notogastral setae p3 and h3 of C. femoralis did not overlap with those of C. labyrinthicus or C. ornatus. Significant correlations between body length and size of setal structures, as well as between setal structures, were detected. Size of morphological features was directly affected by the cover of lichens, a main food resource for Carabodes, and indirectly by the effect of soil moisture on lichen communities.     

A Mathematical and Numerical Investigation of the Hemodynamical Origins of Oscillations in Microvascular Networks

Evidence is presented to show that self-sustained oscillations of purely hemodynamical origin are possible in some arcade-type microvascular networks supplied with steady boundary conditions, but that in others the oscillations disappear with sufficient reduction of the time step Δt, showing them to be numerical artefacts. In an attempt to elucidate the mechanisms involved in the onset of fluctuations, we proceed to perform a linear stability analysis for the convective model of Kiani et al. (Microvasc. Res. 45:219–232, 1993; Am. J. Physiol. 266(35):H1822–H1828, 1994), and show that this leads via a system of delay differential equations to a nonlinear eigenvalue problem. This result generalises the characteristic equation obtained by Carr et al. (Ann. Biomed. Eng. 33:764–771, 2005) and Geddes et al. (SIAM J. Appl. Dyn. Syst. 6(4):694–727, 2007) who solved a special case in a two node network. An implicit numerical method is proposed for the computation of blood flows in networks using the convective model. In a moderate size subnetwork of one of the networks chosen by Kiani et al. (Am. J. Physiol. 266(35):H1822–H1828, 1994), the topology, vessel lengths, and diameters of which were based on microvascular networks in the rat mesentery, we compare results generated using the original explicit numerical method of Kiani et al. (Am. J. Physiol. 266(35):H1822–H1828, 1994) with those from our implicit scheme. From the linear stability theory, a critical value D _RBC,crit of a red blood cell diameter parameter D _RBC in the plasma skimming model of Fenton et al. (Pflügers Arch. 403:396–401, 1985b) is identified for the onset of oscillations about steady state and both the explicit and implicit methods are used to calculate the inflow hematocrit solutions in all vessels of the subnetwork at the critical parameter value, subject to perturbed initial conditions. The results of the implicit method are demonstrated to be in excellent and superior agreement with the predictions of the linear analysis in this case. For values of D _RBC slightly larger than D _RBC,crit the bifurcating periodic solutions calculated using either the explicit or implicit schemes are characteristic of those of a supercritical Hopf bifurcation and the graphs of D _RBC vs. oscillation amplitude would seem to converge as Δt→0.     

Missense mutations in the APOL1 gene are highly associated with end stage kidney disease risk previously attributed to the MYH9 gene

MYH9 has been proposed as a major genetic risk locus for a spectrum of nondiabetic end stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes Project to identify two western African-specific missense mutations (S342G and I384M) in the neighboring APOL1 gene, and demonstrate that these are more strongly associated with ESKD than previously reported MYH9 variants. The APOL1 gene product, apolipoprotein L-1, has been studied for its roles in trypanosomal lysis, autophagic cell death, lipid metabolism, as well as vascular and other biological activities. We also show that the distribution of these newly identified APOL1 risk variants in African populations is consistent with the pattern of African ancestry ESKD risk previously attributed to MYH9. Mapping by admixture linkage disequilibrium (MALD) localized an interval on chromosome 22, in a region that includes the MYH9 gene, which was shown to contain African ancestry risk variants associated with certain forms of ESKD (Kao et al. 2008; Kopp et al. 2008). MYH9 encodes nonmuscle myosin heavy chain IIa, a major cytoskeletal nanomotor protein expressed in many cell types, including podocyte cells of the renal glomerulus. Moreover, 39 different coding region mutations in MYH9 have been identified in patients with a group of rare syndromes, collectively termed the Giant Platelet Syndromes, with clear autosomal dominant inheritance, and various clinical manifestations, sometimes also including glomerular pathology and chronic kidney disease (Kopp 2010; Sekine et al. 2010). Accordingly, MYH9 was further explored in these studies as the leading candidate gene responsible for the MALD signal. Dense mapping of MYH9 identified individual single nucleotide polymorphisms (SNPs) and sets of such SNPs grouped as haplotypes that were found to be highly associated with a large and important group of ESKD risk phenotypes, which as a consequence were designated as MYH9-associated nephropathies (Bostrom and Freedman 2010). These included HIV-associated nephropathy (HIVAN), primary nonmonogenic forms of focal segmental glomerulosclerosis, and hypertension affiliated chronic kidney disease not attributed to other etiologies (Bostrom and Freedman 2010). The MYH9 SNP and haplotype associations observed with these forms of ESKD yielded the largest odds ratios (OR) reported to date for the association of common variants with common disease risk (Winkler et al. 2010). Two specific MYH9 variants (rs5750250 of S-haplotype and rs11912763 of F-haplotype) were designated as most strongly predictive on the basis of Receiver Operating Characteristic analysis (Nelson et al. 2010). These MYH9 association studies were then also extended to earlier stage and related kidney disease phenotypes and to population groups with varying degrees of recent African ancestry admixture (Behar et al. 2010; Freedman et al. 2009a, b; Nelson et al. 2010), and led to the expectation of finding a functional African ancestry causative variant within MYH9. However, despite intensive efforts including re-sequencing of the MYH9 gene no suggested functional mutation has been identified (Nelson et al. 2010; Winkler et al. 2010). This led us to re-examine the interval surrounding MYH9 and to the detection of novel missense mutations with predicted functional effects in the neighboring APOL1 gene, which are significantly more associated with ESKD than all previously reported SNPs in MYH9.     

Inhibition of platelet function by abciximab or high-dose tirofiban in patients with STEMI undergoing primary PCI: a randomised trial

BackgroundIn patients with ST-segment elevation myocardial infarction (STEMI) undergoing primary PCI, few data exist on the magnitude of platelet activation, aggregation and dosing of glycoprotein (GP) IIb/IIIa receptor inhibitors. Methods Sixty STEMI patients were randomised to abciximab, to high-dose tirofiban or to no additional GP IIb/IIIa inhibitor treatment. Platelet activation (P-selectin expression) was measured using flow cytometry and the level of inhibition of platelet aggregation was assessed using the Plateletworks assay. Additionally, the PFA-100 with the collagen/adenosine-diphosphate cartridge (CADP) was used to compare the levels of platelet inhibition. All measurements were performed at baseline (T₀), immediately after (T₁), 30 minutes (T₂), 60 minutes (T₃) and 120 minutes (T₄) after primary PCI. Results The level of platelet activation in both GP IIb/IIIa receptor inhibitor treated groups was significantly lower compared with the control group at all time points after primary PCI (p=0.04). Also the administration of the currently recommended dose of abciximab resulted in significantly lower levels of inhibition of aggregation compared with high-dose tirofiban (p<0.0001). In addition, the CADP closure times were significantly prolonged in both GP IIb/IIIa inhibitor treated groups compared with the control group at time points T1 (p=0.006) and T4 (p<0.0001). Conclusion The administration of high-dose tirofiban resulted in a significantly higher inhibition of platelet aggregation compared with the currently recommended dose of abciximab. Large clinical trials are needed to assess whether this laboratory superiority of high-dose tirofiban translates into higher clinical efficacy. (Neth Heart J 2007;15:375-81.)     

Taxonomic review of Kyphosus (Pisces: Kyphosidae) in the Atlantic and Eastern Pacific Oceans

The taxonomy of the Atlantic and Eastern Pacific species of Kyphosus is reviewed with K. bosquii (Lacepède 1802), K. incisor (Cuvier 1831), K. analogus (Gill 1862) and K. elegans (Peters 1869) considered valid, and K. atlanticus sp. nov. newly described. Kyphosus bosquii and K. atlanticus are both characterized by 12 dorsal- and 11 anal-fin soft rays, but differ in the number of longitudinal scale rows along the midbody (61–66, mode 63 vs. 50–56, mode 54). Kyphosus incisor and K. analogus, characterized by 14 dorsal- and 13 anal-fin soft rays, similarly differ from each other in midbody longitudinal scale row counts (57–64, mode 60 vs. 68–74, mode 70 or 72). Kyphosus elegans is characterized by 13 dorsal- and 12 anal-fin soft rays, and 51–57 midbody longitudinal scale rows. Kyphosus bosquii, K. atlanticus and K. incisor are distributed in the Atlantic Ocean, K. analogus and K. elegans occurring in the Eastern Pacific. The holotype of Pimelepterus flavolineatus Poey 1866, here regarded as a junior synonym of K. incisor, was located within a collection of Cuban fishes donated to the Smithsonian Institution by Poey in 1873. A neotype is designated here for K. analogus. Pimelepterus gallveii Cunningham 1910, Kyphosus palpebrosus Miranda-Ribeiro 1919 and K. metzelaari Jordan and Evermann 1927 are recognized as junior synonyms of K. bosquii. Pimelepterus sandwicensis Sauvage 1880 is a junior synonym of K. elegans. Perca saltatrix Linnaeus 1758, together with the replacement name Perca sectatrix Linnaeus 1766, is regarded as nomina dubia.     

A model of direction selectivity in the starburst amacrine cell network

Displaced starburst amacrine cells (SACs) are retinal interneurons that exhibit GABA _A receptor-mediated and Cl ^? cotransporter-mediated, directionally selective (DS) light responses in the rabbit retina. They depolarize to stimuli that move centrifugally through the receptive field surround and hyperpolarize to stimuli that move centripetally through the surround (Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006). They also play a key role in the activity of DS ganglion cells (DS GC; Amthor et al, Vis Neurosci 19:495–509 2002; Euler et al, Nature 418:845–852, 2002; Fried et al, Nature 420:411– 414, 2002; Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006; Lee and Zhou, Neuron 51:787–799 2006; Yoshida et al, Neuron 30:771–780, 2001). In this paper we present a model of strong DS behavior of SACs which relies on the GABA-mediated communication within a tightly interconnected network of these cells and on the glutamate signal that the SACs receive from bipolar cells (a presynaptic cell that receives input from cones). We describe how a moving light stimulus can produce a large, sustained depolarization of the SAC dendritic tips that point in the direction that the stimulus moves (i.e., centrifugal motion), but produce a minimal depolarization of the dendritic tips that point in the opposite direction (i.e., centripetal motion). This DS behavior, which is quantified based on the relative size and duration of the depolarizations evoked by stimulus motion at dendritic tips pointing in opposite directions, is robust to changes of many different parameter values and consistent with experimental data. In addition, the DS behavior is strengthened under the assumptions that the Cl^? cotransporters Na^?+?-K^?+?-Cl^?? and K^?+?-Cl^?? are located in different regions of the SAC dendritic tree (Gavrikov et al, PNAS 103(49):18793–18798, 2006) and that GABA evokes a long-lasting response (Gavrikov et al, PNAS 100(26):16047–16052, 2003, PNAS 103(49):18793–18798, 2006; Lee and Zhou, Neuron 51:787–799, 2006). A possible mechanism is discussed based on the generation of waves of local glutamate and GABA secretion, and their postsynaptic interplay as the waves travel between cell compartments.     

Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov

Recently we proposed that Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 be transferred to a novel genus, Prescottia, as Prescottia equi comb. nov. However, in accordance with Principle 2 and Rule 51b(4) of the Bacteriological Code (1990 Revision), the bacterial genus name Prescottia Jones et al. 2013 is deemed illegitimate as this name has been used previously for a plant genus within the family Orchidaceae. Consequently, a new genus name, Prescottella gen. nov. is proposed for the bacterial taxon and a new combination Prescottella equi comb. nov. is proposed for the type species.     

Thanetian gastropods from the Mesopotamian high folded zone in northern Iraq

An assemblage of gastropods from the Thanetian of the Kolosh Formation from the Zakho region in northern Iraq is documented for the first time. The ten species represent the families Campanilidae Douvillé 1904, Potamididae H. & A. Adams 1854, Batillariidae Thiele 1929, Thiaridae Gill 1871, Pachychilidae Fischer & Crosse 1892, Cerithiidae Fleming 1822 and Pseudolividae de Gregorio 1880, suggesting a littoral to shallow sublittoral depositional environment. Six of the species are new and five are formally described as new species. At least seven species are also known from the Thanetian and/or Early Ypresian of the Ankara region in Turkey. Only a single species occurs also in the Paleocene of the Paris Basin. No relation to Paleocene and Eocene faunas of Pakistan and India is detectable. This points to a considerably bioprovincialism along the northern coast of the Tethys. Consequently we suppose the existence of an Anatolian Province in the Thanetian/Ypresian Mediterranean Region of the Tethys Realm, represented by rather homogeneous mollusc faunas from western Turkey and northern Iraq. Campanile zakhoense nov. sp., Pyrazopsis hexagonpyramidalis nov. sp., Pachymelania islamogluae nov. sp., “Faunus” dominicii nov. sp. and Pseudoaluco mesopotamicus nov. sp. are introduced as new species. Varicipotamides Pacaud & Harzhauser nov. nom. is proposed as the replacement name for Exechestoma Cossmann (1889) non Brandt (1837).     

Constructions and headedness in derivation and compounding

The ??traditional?? distinction of compounds into endocentric (Eng. doorknob) and exocentric (pickpocket) is based on the presence or absence of a head constituent (Bloomfield, Language, Holt, New York, 1933); since the early eighties, the syntactic notion of ??head?? has been extended also to derivation, claiming that English derivational suffixes, as e.g. -ness, are heads, either in an absolute sense or in a categorial sense (see Williams Linguist Inq 12:245?C274, 1981; Lieber On the organization of the lexicon, Indiana university Linguistics Club, Bloomington, 1981; Lieber, in Yearbook of morphology 1989, Foris, Dordrecht, 1989; among others). In this paper, we shall first review some key issues in the morphological notion of head, illustrating well-known problematic cases, and then we shall discuss the Construction Morphology approach to headedness in derivation and compounding (Booij in The Oxford handbook of compounding, Oxford University Press, Oxford, 2009; Booij, in Cross-disciplinary issues in compounding, John Benjamins, Amsterdam, 2010a, 2010 Booij, Construction morphology, Oxford University Press, Oxford, 2010b). The stipulation of a hierarchical lexicon with subschemas expressing intermediate generalizations is a powerful theoretical device in accounting for a phenomenon as headedness variation, as we shall show with a Vietnamese case study; also, inconsistencies in word-class assignment in derivation will be dealt with in a constructionist perspective. Moreover, we shall discuss the consequences of a constructionist approach to the distinction between compounding and derivation.     

Redescriptions and reestablishments of some species belonging to the genus Prionospio (Polychaeta,Spionidae) and descriptions of three new species

Available type material of Prionospio heterobranchia Moore, 1907, P. (Prionospio) texana Hartman, 1951, P. spongicola Wesenberg-Lund, 1958 and P. (P.) newportensis Reish, 1959, as well as newly collected material from the Southern Gulf of Mexico and Chetumal Bay in the Caribbean Sea, was examined. Several important differences were found between P. heterobranchia, P. (Prionospio) texana, P. spongicola and P. (P.) newportensis, and as a result, these three species are removed from synonymy with P. heterobranchia Moore, 1907, and redescribed and reinstated as valid species. In addition, three new species were identified and described: P. caribensis sp. nov., P. rosariae sp. nov. and P. jamaicensis sp. nov. A key to all species of Prionospio with five pairs of branchiae is provided.     

An analysis of a ‘community-driven’ reconstruction of the human metabolic network

Following a strategy similar to that used in baker’s yeast (Herrgård et al. Nat Biotechnol 26:1155–1160, 2008). A consensus yeast metabolic network obtained from a community approach to systems biology (Herrgård et al. 2008; Dobson et al. BMC Syst Biol 4:145, 2010). Further developments towards a genome-scale metabolic model of yeast (Dobson et al. 2010; Heavner et al. BMC Syst Biol 6:55, 2012). Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network (Heavner et al. 2012) and in Salmonella typhimurium (Thiele et al. BMC Syst Biol 5:8, 2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella typhimurium LT2 (Thiele et al. 2011), a recent paper (Thiele et al. Nat Biotechnol 31:419–425, 2013). A community-driven global reconstruction of human metabolism (Thiele et al. 2013) described a much improved ‘community consensus’ reconstruction of the human metabolic network, called Recon 2, and the authors (that include the present ones) have made it freely available via a database at http://humanmetabolism.org/ and in SBML format at Biomodels (http://identifiers.org/biomodels.db/MODEL1109130000). This short analysis summarises the main findings, and suggests some approaches that will be able to exploit the availability of this model to advantage.     

Metalloproteins and the Pyrite-based Origin of Life: A Critical Assessment

We critically examine the proposal by Wächtershäuser (Prokaryotes 1:275?C283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787?C1808, 2006b) that putative transition metal binding sites in protein components of the translation machinery of hyperthermophiles provide evidence of a direct relationship with the FeS clusters of pyrite and thus indicate an autotrophic origin of life in volcanic environments. Analysis of completely sequenced cellular genomes of Bacteria, Archaea and Eucarya does not support the suggestion by Wächtershäuser (Prokaryotes 1:275?C283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787?C1808, 2006b) that aminoacyl-tRNA synthetases and ribosomal proteins bear sequence signatures typical of strong covalent metal bonding whose absence in mesophilic species reveals a process of adaptation towards less extreme environments.     

Revision and new data on the Coniacian ammonite genus Hemitissotia in the Iberian Peninsula (Spain and Portugal)

The types of the species of the Coniacian ammonite genus Hemitissotia Peron, 1897, identified in the Iberian Peninsula (Spain and Portugal), which are currently held in the Wiedmann (Universität Tübingen, Germany) and Choffat (Instituto Geológico e Mineiro, Portugal) collections, have been revised and refigured. New specimens of the taxa Hemitissotia ceadouroensis Choffat, 1898, Hemitissotia celtiberica Wiedmann, 1975b, Hemitissotia turzoi Karrenberg, 1935, Hemitissotia dullai (Karrenberg 1935) and Hemitissotia lenticeratiformis Wiedmann in Wiedmann and Kauffman, 1978 have also been presented. As results, H. celtiberica has been considered as a junior synonym of H. ceadouroensis, and the lectotype of this species and the neotypes of H. turzoi and H. dullai have been designated and figured. Additionally, the geographical and stratigraphical distributions of all of these species have been determined with precision, and several phylogenetic relationships between them have been identified, revealing morphologies that become progressively smaller and more depressed and ornamented (hydrodynamically less efficient), interpreted as an adaptative response to sea-level changes.     

A new record of the enigmatic lobster genus Stenodactylina Beurlen, 1928 (Crustacea: Decapoda: Erymidae) from the Middle Jurassic of south-western Germany

A second species of the previously monotypic lobster genus Stenodactylina Beurlen, 1928, Stenodactylina rogerfurzei n. sp. is recorded from the upper Aalenian of the Wutach area (Baden-Württemberg, SW Germany). Like the type species, Stenodactylina liasina Beurlen, 1928, the new species is based only on a single chela. Originally the type horizon of S. liasina was erroneously reported as being late Toarcian in age, but it in fact came from a bituminous limestone bed within the lower Toarcian Posidonia Shale. Hence, the known stratigraphical range of Stenodactylina is expanded from the early Toarcian to the late Aalenian.     

RNA phosphodiester backbone dynamics of a perdeuterated cUUCGg tetraloop RNA from phosphorus-31 NMR relaxation analysis

We have analyzed the relaxation properties of all ³¹P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R ₁ and R ₂ relaxation are observed in a protonated RNA sample at 600 MHz. These contributions can be suppressed using a perdeuterated RNA sample. In order to interpret the ³¹P relaxation data (R ₁, R ₂), we measured the ³¹P chemical shift anisotropy (CSA) by solid-state NMR spectroscopy under various salt and hydration conditions. A value of 178.5 ppm for the ³¹P CSA in the static state (S ² = 1) could be determined. In order to obtain information about fast time scale dynamics we performed a modelfree analysis on the basis of our relaxation data. The results show that subnanosecond dynamics detected around the phosphodiester backbone are more pronounced than the dynamics detected for the ribofuranosyl and nucleobase moieties of the individual nucleotides (Duchardt and Schwalbe, J Biomol NMR 32:295–308, 2005; Ferner et al., Nucleic Acids Res 36:1928–1940, 2008). Furthermore, the dynamics of the individual phosphate groups seem to be correlated to the 5′ neighbouring nucleobases.