The presence of the WGD motif in CC8 heterodimeric disintegrin increases its inhibitory effect on alphaII(b)beta3, alpha(v)beta3, and alpha5beta1 integrins

Two highly homologous dimeric disintegrins, CC5 and CC8, have been isolated from the venom of the North African sand viper Cerastes cerastes. CC5 is a homodimer containing an RGD motif in its subunits. CC8 is a heterodimer. The CC8A and CC8B subunits contain RGD and WGD tripeptide sequence in their respective integrin-binding loops. Both CC5 and CC8 inhibited platelet aggregation and the adhesion of cells expressing integrins alphaII(b)beta3, alpha(v)beta3, and alpha5beta1 to appropriate ligands. However, the inhibitory activity of CC8 was at least 1 order of magnitude higher than that of CC5. Enhanced activity of CC8 over CC5 was also observed in the induction of LIBS epitopes on beta1 and beta3 integrins. Synthetic peptides in which the arginyl residue of the RGD motif had been replaced with tryptophans exhibited increased inhibitory activity toward integrins alpha5beta1, alphaII(b)beta3, and alpha(v)beta3. Moreover, alanine substitution of the aspartic acid of the WGD motif of these peptides decreased their inhibitory ability, whereas the same substitution in the RGD sequence almost completely abolished the activity of the peptides. We conclude that the WGD motif enhances the inhibitory activity of disintegrins toward alphaII(b)beta3, alpha(v)beta3, and alpha5beta1 integrins.     

Alkaloids of Lycopodium paniculatum: The structure of paniculine

Three new alkaloids isolated from Lycopodium paniculatum were identified as paniculine (7α-hydroxy-acetyldihydrolycopodine), deacetylpaniculine and anhydrodeacetylpaniculine. Other known alkaloids isolated include flabellidine, lycoclavine, together with deacetyllycoclavine previously obtained as a degradation product of lycoclavine.     

Effect of olive oil mill wastewater on extracellular ligninolytic enzymes produced by Phanerochaete flavido-alba

Four genes, fagA, B, C and D, encoding products with 32-47% identity to proteins involved in bacterial iron uptake systems, were identified immediately downstream of the Corynebacterium pseudotuberculosis phospholipase D gene. beta-Galactosidase assays on a C. pseudotuberculosis strain carrying a fagA-lacZ fusion indicated that the putative fagABC operon was poorly expressed in iron-rich media. However, similar experiments in iron-limited media resulted in an approximately three-fold increase in beta-galactosidase activity, suggesting that this operon is regulated by iron in vitro. Although no defect in iron utilization could be determined for a C. pseudotuberculosis fagB(C) mutant in vitro, this mutant showed reduced virulence compared to wild-type in a goat model of caseous lymphadenitis. Thus, expression of the fag genes in the host appears to contribute to virulence.     

Cloning and expression of the human T-type channel Ca(v)3.3: insights into prepulse facilitation

The full-length human Ca(v)3.3 (alpha(1I)) T-type channel was cloned, and found to be longer than previously reported. Comparison of the cDNA sequence to the human genomic sequence indicates the presence of an additional 4-kb exon that adds 214 amino acids to the carboxyl terminus and encodes the 3' untranslated region. The electrophysiological properties of the full-length channel were studied after transient transfection into 293 human embryonic kidney cells using 5 mM Ca(2+) as charge carrier. From a holding potential of -100 mV, step depolarizations elicited inward currents with an apparent threshold of -70 mV, a peak of -30 mV, and reversed at +40 mV. The kinetics of channel activation, inactivation, deactivation, and recovery from inactivation were very similar to those reported previously for rat Ca(v)3.3. Similar voltage-dependent gating and kinetics were found for truncated versions of human Ca(v)3.3, which lack either 118 or 288 of the 490 amino acids that compose the carboxyl terminus. A major difference between these constructs was that the full-length isoform generated twofold more current. These results suggest that sequences in the distal portion of Ca(v)3.3 play a role in channel expression. Studies on the voltage-dependence of activation revealed that a fraction of channels did not gate as low voltage-activated channels, requiring stronger depolarizations to open. A strong depolarizing prepulse (+100 mV, 200 ms) increased the fraction of channels that gated at low voltages. In contrast, human Ca(v)3.3 isoforms with shorter carboxyl termini were less affected by a prepulse. Therefore, Ca(v)3.3 is similar to high voltage-activated Ca(2+) channels in that depolarizing prepulses can regulate their activity, and their carboxy termini play a role in modulating channel activity.     

Phage-host associations in a full-scale activated sludge plant during sludge bulking

Sludge bulking, a notorious microbial issue in activated sludge plants, is always accompanied by dramatic changes in the bacterial community. Despite large numbers of phages in sludge systems, their responses to sludge bulking and phage-host associations during bulking are unknown. In this study, high-throughput sequencing of viral metagenomes and bacterial 16S rRNA genes were employed to characterize viral and bacterial communities in a sludge plant under different sludge conditions (sludge volume index (SVI) of 180, 132, and 73 ml/g). Bulking sludges (SVI > 125 ml/g) taken about 10 months apart exhibited similar bacterial and viral composition. This reflects ecological resilience of the sludge microbial community and indicates that changes in viral and bacterial populations correlate closely with each other. Overgrowth of “Candidatus Microthrix parvicella” led to filamentous bulking, but few corresponding viral genotypes were identified. In contrast, sludge viromes were characterized by numerous contigs associated with “Candidatus Accumulibacter phosphatis,” suggesting an abundance of corresponding phages in the sludge viral community. Notably, while nitrifiers (mainly Nitrosomonadaceae and Nitrospiraceae) declined significantly along with sludge bulking, their corresponding viral contigs were identified more frequently and with greater abundance in the bulking viromes, implying that phage-mediated lysis might contribute to the loss of autotrophic nitrifiers under bulking conditions.     

swinger: a user‐friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information

Captive breeding programmes are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programmes have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group‐breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding. Molecular‐based estimates of relatedness and inbreeding may instead be used to select breeding groups (≥two individuals) that minimize relatedness and filter out inbred individuals. swinger constructs breeding groups based on molecular estimates of relatedness and inbreeding. The number of possible combinations of breeding groups quickly becomes intractable by hand. swinger was designed to overcome this major issue in ex situ conservation biology. The user can specify parameters within swinger to reach breeding solutions that suit the mating system of the target species and available resources. We provide evidence of the efficiency of the software with an empirical example and using simulations. The only data required are a typical molecular marker data set, such as a microsatellite or SNP data set, from which estimates of inbreeding and pairwise relatedness may be obtained. Such molecular data sets are becoming easier to gather from non‐model organisms with next‐generation sequencing technology. swinger is an open‐source software with a user‐friendly interface and is available at http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/ and https://github.com/Yuma248/Swinger .     

Over the top: do thermal barriers along elevation gradients limit biotic similarity?

Organismal dispersal through mountain passes should be more constrained by temperature‐related differences between lowland and highland sites in montane environments. This may lead to higher rates of diversification through isolation of existing lineages toward the tropics. This mechanism, proposed by Janzen, could influence broad‐scale patterns of biodiversity across mountainous regions and more broadly across latitudinal gradients. We constructed two complementary analyses to test this hypothesis. First, we measured topographically‐derived thermal gradients using recently‐developed climatic data across the Americas, reviewing the main expectations from Janzen's climatic model. Then, we evaluated whether thermal barriers predict assemblage similarity for amphibians and mammals along elevational gradients across most of their latitudinal extent in the Americas. Thermal barriers between low and high elevation areas, initially proposed to be unique to tropical environments, are comparably strong in some temperate regions, particularly along the western slopes of North American dividing ranges. Biotic similarity for both mammals and amphibians decreases between sites that are separated by elevation‐related thermal barriers. That is, the stronger the thermal barrier separating pairs of sites across the latitudinal gradient, the lower the similarity of their species assemblages. Thermal barriers explain 10–35% of the variation in latitudinal gradients of biotic similarity, effects that were stronger in comparisons of sites at high elevations. Mammals' stronger dispersal capacities and homeothermy may explain weaker effects of thermal barriers on gradients of assemblage similarity than among amphibians. Understanding how temperature gradients have shaped gradients of montane biological diversity in the past will improve understanding of how changing environments may affect them in the future.     

Habitat selection,diet and food availability of European Golden Plover Pluvialis apricaria chicks in Swedish Lapland

Fennoscandian alpine tundra habitats support large numbers of breeding waders, but relatively little is known about their breeding ecology despite the fact that this habitat is threatened by climate change. We studied habitat selection, diet and prey availability of European (Eurasian) Golden Plover Pluvialis apricaria chicks at the Vindelfjällen Nature Reserve, Ammarnäs, Sweden. Information from 22 chicks tracked using radio‐transmitters was analysed. By analysing 149 faecal samples, four main prey taxa were identified, Coleoptera (40%), Bibionidae (31%), Hymenoptera (13%) and Tipulidae (10%). We found that chicks switched from feeding on Tipulidae to feeding on Bibionidae as they grew, and that this switch coincided with a shift from the use of the habitat where Tipulidae were abundant (alpine meadow/heathland) to the use of the habitat were Bibionidae were abundant (Willow shrub). Although chicks track food availability to some extent, the link between prey availability and habitat use was not perfect, indicating that additional factors other than food abundance, such as shelter from predators, determine habitat selection. Bibionidae are an important prey for Golden Plover chicks as it is the only prey group that has a late summer flush in abundance, in contrast to the general decline of total arthropod biomass during the chick‐rearing period. However, Bibionidae imagoes only occurred in 2011 and were virtually absent in 2013, which relates to the species’ ecology with 2‐ to 5‐year cycles in mass occurrence. Extreme annual variation in an essential food source such as Bibionidae imagoes might have an important effect on the condition and survival of Golden Plover chicks, an important subject for future studies. The foraging conditions for Golden Plover chicks in Fennoscandia appear to be different to those in the UK, where the chicks rely mainly on a Tipulidae flush only.     

Analysing the representativeness of local‐scale palaeodiversity measurements: a case from the Lower Cretaceous plant assemblage of Hautrage (Mons Basin,Belgium)

Two plant fossil‐bearing beds from the middle Barremian of Belgium were analysed to ascertain how experimental designs affect conclusions regarding palaeodiversity at a local scale. We analysed eight lateral samples per bed taken regularly every 3 m using an exhaustive sub‐sampling method. The Clench equation was used to evaluate the completeness of the taxonomic inventory of the samples and the sampling effort needed to obtain a reliable representation of diversity. The number of replicates needed to obtain the same representation of diversity from different nearby lateral samples of the same bed ranged from 5 to 19. Richness (S), Evenness (J) and the number of equiprobable taxa (2^H’) greatly varied between samples from the same bed, even over short distances. Only one of the studied samples was representative of the taxonomic inventory of its bed. Our study shows that 1) the selection bias of the sampling area is reduced by increasing the number of lateral samples taken in a bed, enabling more reliable conclusions about local‐scale diversity; 2) intense sub‐sampling methods are needed to account for statistically independent observations of detailed lateral variation; and 3) sampling methods in palaeodiversity analyses must look for a similar degree of representativeness in samples rather than a homogeneous sample size. Using a sampling effort analysis provides evidence for the completeness of the data set, adjusting the amount of work required. Implementing the Clench equation in palaeodiversity analyses improves the performance of data acquisition in palaeoecological studies and provides a quality test of the data sets derived from them.     

1,2‐Diacylglycerol choline phosphotransferase catalyzes the final step in the unique Treponema denticola phosphatidylcholine biosynthesis pathway

Treponema denticola synthesizes phosphatidylcholine through a licCA‐dependent CDP‐choline pathway identified only in the genus Treponema. However, the mechanism of conversion of CDP‐choline to phosphatidylcholine remained unclear. We report here characterization of TDE0021 (herein designated cpt) encoding a 1,2‐diacylglycerol choline phosphotransferase homologous to choline phosphotransferases that catalyze the final step of the highly conserved Kennedy pathway for phosphatidylcholine synthesis in eukaryotes. T. denticola Cpt catalyzed in vitro phosphatidylcholine formation from CDP‐choline and diacylglycerol, and full activity required divalent manganese. Allelic replacement mutagenesis of cpt in T. denticola resulted in abrogation of phosphatidylcholine synthesis. T. denticola Cpt complemented a Saccharomyces cerevisiae CPT1 mutant, and expression of the entire T. denticola LicCA‐Cpt pathway in E. coli resulted in phosphatidylcholine biosynthesis. Our findings show that T. denticola possesses a unique phosphatidylcholine synthesis pathway combining conserved prokaryotic choline kinase and CTP:phosphocholine cytidylyltransferase activities with a 1,2‐diacylglycerol choline phosphotransferase that is common in eukaryotes. Other than in a subset of mammalian host‐associated Treponema that includes T. pallidum, this pathway is found in neither bacteria nor Archaea. Molecular dating analysis of the Cpt gene family suggests that a horizontal gene transfer event introduced this gene into an ancestral Treponema well after its divergence from other spirochetes.