Determination of the size of the Azotobacter vinelandii chromosome

The chromosome of Azotobacter vinelandii UW was digested separately with the rape cutter restriction endonucleases Swal (5-ATTTAAAT), PmeI (5GTTTAAAC) and Pacl (5-TTAATTAA) and the products were separated by pulsed-field gel electrophoresis. The size of the chromosome was determined to be approximately 4.5 megabase pairs (Mb) based on the sum of the sizes of the restriction fragments. This is almost the same as the size of the chromosome of Escherichia coli. The inability of the undigested DNA to enter the gel has led us to infer that the chromosome is circular.     

THE INFLUENCE OF THE MATING SYSTEM ON SEED SIZE VARIATION IN CRINUM ERUBESCENS (AMARYLLIDACEAE)

We present evidence that extreme seed size variation in fruits of Crinum erubescens (range: 0.1 to 66.5 g per seed) occurs when mating pairs are inbred, either from selfing or biparental inbreeding. Several relatively uniform seeds of intermediate size are produced when pollen from several pollen donors is applied simultaneously to a flower. Selfed fruits and some fruits pollinated with a single pollen donor produce both large and small seeds, although selfed fruits produce fewer seeds than outcrossed fruit. These results are contrary to the hypothesis that variation in seed size is attributable to either pollen competition or differential allocation of maternal resource to seeds of different genotypes.     

Spatially-correlated extinction in a metapopulation model of Leadbeater's Possum

The importance of considering spatially-correlated extinction in metapopulation viability analyses was investigated using a model of the population dynamics of Gymnobelideus leadbeateri McCoy (Leadbeater's Possum). Fire caused local extinction of G. leadbeateri and induced changes in the suitability of the habitat over a period of decades and centuries. Spatially-correlated fires, in which the correlation between the incidence of fire declines with distance, and uniformly-correlated fires were simulated. The predicted risk of metapopulation extinction increased: (i) as the variance in the number of fires each year increased, (ii) as the mean fire interval decreased, and (iii) as the mean dispersal distance decreased. Incorporating spatial correlation in the incidence of fires between patches had little effect on the results, provided the variance in the number of fires per year remained the same and fires modified habitat quality. The predicted risk of metapopulation extinction was greater for spatially-correlated fires than for uniformly-correlated fires when fires only caused local extinction but did not change habitat suitability. Incorporating spatial correlation in the incidence of fire within patches, which allowed partial burning of patches, reduced the predicted risk of extinction. This effect was only slight when patches were smaller than about 50 ha. The results of our simulations demonstrate the importance of considering correlations in disturbance regimes in metapopulation models, especially if these models are used to assist the design of nature reserves.     

Sex allocation and clutch size in the gregarious larval endoparasitoid wasp, Cotesia glomerata

The ability of the gregarious larval endoparasitoid Cotesia glomerata L. (Hymenoptera: Braconidae) to adjust progeny sex ratio and clutch size was investigated. The sex ratios (proportion of males) of field clusters were diverse, but many (70%) were female-biased. Nearly 10% yielded males only, suggesting a low percentage of unmated females in the field. In over half of the clusters containing females, the sex ratio was below 0.3. Superparasitism was common in the field, and females were believed to increase progeny sex ratio when attacking previously-parasitized hosts. However, in a single oviposition bout, sex allocation was not precisely controlled both in the field and laboratory. In the laboratory, the number of eggs laid in a day tended to decrease with increasing female age. For females which were offered two hosts per day and for those offered three hosts per day, this value became nearly the same several days after the start of oviposition. The total number of hosts which a female could parasitize during her lifetime was often less than 40. Some of the old females which attacked more than 40 hosts produced male-biased clutches; this was due to sperm depletion, because sperm remained viable throughout a female's lifetime. The amount of sperm used in a single oviposition bout seemed fixed and was not dependent on the number of eggs laid. Females with much oviposition experience did not produce new eggs to compensate for deposited eggs, and the efficiency of egg use (deposited eggs/total eggs) was more than 80%.     

Genetic and phenotypic variation in juvenile development in relation to temperature and developmental pathway in a geometrid moth

Life histories show genetic population-level variation due to spatial variation in selection pressures. Phenotypic plasticity in life histories is also common, facilitating fine-tuning of the phenotype in relation to the prevailing selection regime. In multivoltine (≥ 2 generations per year) insects, individuals following alternative developmental pathways (diapause/direct development) experience different selection regimes. We studied the genetic and phenotypic components of juvenile development in Cabera exanthemata (Lepidoptera: Geometridae) in a factorial split-brood experiment. F(2) offspring of individuals originating from populations in northern and central Finland were divided among manipulations defined by temperature (14°C/20°C) and day length (24 h/15 h). Short day length invariably induced diapause, whereas continuous light almost invariably induced direct development in both regions, although northern populations are strictly univoltine in the wild. Individuals from northern Finland had higher growth rates, shorter development times and higher pupal masses than individuals from central Finland across the conditions, indicating genetic differences between regions. Individuals that developed directly into adults tended to have higher growth rates, shorter development times and higher pupal masses than those entering diapause, indicating phenotypic plasticity. Temperature-induced plasticity was substantial; growth rate was much higher, development time much shorter and pupal mass higher at 20°C than at 14°C. The degree of plasticity in relation to developmental pathway was pronounced at 20°C in growth rate and development time and at 14°C in pupal mass, emphasizing multidimensionality of reaction norms. The observed genetic variation and developmental plasticity seem adaptive in relation to time-stress due to seasonality.     

Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.     

Molecular Modelling reveals the inhibition mechanism and structure–activity relationship of curcumin and its analogues to Staphylococcal aureus Sortase A

Previous studies found that the activity of Sortase A, a bacterial surface protein from Staphylococcus aureus, was inhibited by curcumin and its analogues. To explore this inhibitory mechanism, Sortase A and its inhibitors in complex systems were studied by molecular docking, molecular modelling, binding energy decomposition calculation and steered molecular dynamics simulations. Energy decomposition analysis indicated that PRO-163, LEU-169, GLN-172, ILE-182 and ILE-199 are key residues in Sortase A-inhibitor complexes. Furthermore, interactions between the methoxyl group on the benzene ring in the conjugated molecule (curcumin, demethoxycurcumin, bisdemethoxycurcumin) and VAL-168, LEU-169 and GLN-172 induce the inhibitory activity based on the energy decomposition and distance analyses between the whole residues and inhibitors. However, because of its coiled structure, the non-conjugated molecule, tetrahydrocurcumin, with key residues in the binding sites of Sortase A, interacted weakly with SrtA, leading to the loss of inhibitory activity. Based on these results, the methoxyl group on the benzene ring in the conjugated molecule largely influenced the inhibitory activity of the Sortase A inhibitors.     

Systematic review of Atractus schach (Serpentes: Dipsadidae) species complex from the Guiana Shield with description of three new species

The Guiana Shield harbours one of the best preserved and largest extents of tropical forest on Earth and an immense biodiversity. The herpetofauna of this region remains poorly known. The species-rich snake genus Atractus contains ～140 species, many with complicated taxonomic histories, including A. schach. Examination of specimens in museums and newly collected material from French Guiana has allowed the illustration of hemipenial morphology for the first time and an expanded diagnosis. Concatenated molecular phylogenetic (mitochondrial and nuclear genes) and phenotypic (morphometrics, external and hemipenial morphology) analyses confirm non-monophyly of the A. flammigerus group and indicate that A. schach is a species complex with three new species described here. The geographic distribution of A. schach sensu stricto is restricted to Guiana, Surinam, and French Guiana north of Tumucumaque massif. Populations tentatively assigned to A. schach from the east from French Guiana in the Roura lowlands to Almeirim, and from central Amazonia between the Negro and Trombetas rivers in Brazil are also recognized as new species. Our results suggest that populations from south of the Amazon River are not conspecific with those from the Guiana Shield.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:A7AE40BC-4716-4302-B3BE-1F43600B0A72     

Characterizing symbiont inheritance during host–microbiota evolution: Application to the great apes gut microbiota

Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful association with their hosts (i.e. strict vertical transmission), or transmitted with occasional host switches (i.e. vertical transmission with horizontal switches). These different modes of inheritance affect microbes’ diversification, which at the two extremes can be independent from that of their associated host or follow host diversification. The few existing quantitative tools for investigating the inheritance of symbiotic organisms rely on cophylogenetic approaches, which require knowledge of both host and symbiont phylogenies, and are therefore often not well adapted to DNA metabarcoding microbial data. Here, we develop a model‐based framework for identifying vertically transmitted microbial taxa. We consider a model for the evolution of microbial sequences on a fixed host phylogeny that includes vertical transmission and horizontal host switches. This model allows estimating the number of host switches and testing for strict vertical transmission and independent evolution. We test our approach using simulations. Finally, we illustrate our framework on gut microbiota high‐throughput sequencing data of the family Hominidae and identify several microbial taxonomic units, including fibrolytic bacteria involved in carbohydrate digestion, that tend to be vertically transmitted.     

Tinocladia sanrikuensis sp. nov. (Ectocarpales s.l., Phaeophyceae) from Japan

The new species Tinocladia sanrikuensis sp. nov. H.Kawai, K.Takeuchi & T.Hanyuda (Ectocarpales s.l., Phaeophyceae) is described from the Pacific coast of the Tohoku region, northern Japan based on morphology and DNA sequences. The species is a spring–summer annual growing on lower intertidal to upper subtidal rocks and cobbles on relatively protected sites. T. sanrikuensis has a slimy, cylindrical, multiaxial erect thallus, slightly hollow when fully developed, branching once to twice, and resembles T. crassa in gross morphology. The erect thalli are composed of a dense medullary layer, long subcortical filaments, and assimilatory filaments of 11–35 cells, up to 425 μm long and curved in the upper portion. Unilocular zoidangia are formed on the basal part of assimilatory filaments. The species is genetically most closely related to T. crassa and has the same basic thallus structures but differs in having thinner and longer assimilatory filaments. DNA sequences of the mitochondrial cox1 and cox3, chloroplast atpB, psaA, psbA and rbcL genes support the distinctness of this species.