Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled using Vibrio harveyi myovirus like

The adenine methyltransferase (DAM) gene methylates GATC sequences that have been demonstrated in various bacteria to be a powerful gene regulator functioning as an epigenetic switch, particularly with virulence gene regulation. However, overproduction of DAM can lead to mutations, giving rise to variability that may be important for adaptation to environmental change. While most bacterial hosts carry a DAM gene, not all bacteriophage carry this gene. Currently, there is no literature regarding the role DAM plays in life cycle regulation of bacteriophage. Vibrio campbellii strain 642 carries the bacteriophage Vibrio harveyi myovirus like (VHML) that has been proven to increase virulence. The complete genome sequence of VHML bacteriophage revealed a putative adenine methyltransferase gene. Using VHML, a new model of phage life cycle regulation, where DAM plays a central role between the lysogenic and lytic states, will be hypothesized. In short, DAM methylates the rha antirepressor gene and once methylation is removed, homologous CI repressor protein becomes repressed and non‐functional leading to the switching to the lytic cycle. Greater understanding of life cycle regulation at the genetic level can, in the future, lead to the genesis of chimeric bacteriophage with greater control over their life cycle for their safe use as probiotics within the aquaculture industry.     

Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation

Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.     

The tadpole of Scinax aromothyella (Anura: Hylidae) from Uruguay

We describe the tadpole of Scinax aromothyella from the surroundings of Quebrada de los Cuervos, Departamento de Treinta y Tres, Uruguay. It shares with other larvae of the Scinax catharinae clade the slightly depressed body, a dextral vent tube that reaches the free margin of the ventral fin, and the oral disc with a dorsal gap in the marginal row of papillae and with a concave posterior edge. It is most similar to the tadpole of Scinax berthae, from which it differs in the larger total length of S. aromothyella.

Describimos la larva de Scinax aromothyella de los alrededores de la Quebrada de los Cuervos, Departamento de Treinta y Tres, Uruguay. Comparte con las larvas de otras especies del clado de Scinax catharinae el tener el cuerpo levemente deprimido, el tubo proctodeal dextro que alcanza el borde libre de la aleta ventral, y el disco oral con un claro rostral en la hilera de papilas marginales y con su borde posterior cóncavo. Es muy parecida a la larva de Scinax berthae, de la que difiere en la mayor longitud total de S. aromothyella.     

Genome sequence of Phaeobacter daeponensis type strain (DSM 23529T), a facultatively anaerobic bacterium isolated from marine sediment,and emendation of Phaeobacter daeponensis

TF-218^T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218^T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218^T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.     

Comparative labellar micromorphology of Zygopetalinae (Orchidaceae)

Background and Aims

Molecular evidence indicates that the Neotropical sub-tribe Zygopetalinae is sister to Maxillariinae. Most members of the latter sub-tribe have deceit pollination strategies, but some species produce rewards such as nectar, pseudopollen, resin and wax, and are pollinated by a range of pollinators that include stingless bees (Meliponini), wasps and hummingbirds. By contrast, relatively little is known about the pollination of Zygopetalinae species. However, some are pollinated by fragrance-gathering, male euglossine bees or employ nectar deceit strategies. The aim of this study is to describe the labellar micromorphology of Zygopetalinae and to compare it with that of Maxillariinae sensu lato (s.l.) as part of an ongoing project to record the range of labellar characters found within the tribe Maxillarieae, and to assess whether these characters represent synapomorphies or homoplasies resulting from similar pollination pressures.

Methods

The labella of 31 species of Zygopetalinae, including Cryptarrhena R. Br. and representatives of the Zygopetalum, Huntleya and Warrea clades, were examined using light microscopy and scanning electron microscopy, and the range of labellar characters was recorded. These characters were subsequently compared with those of Maxillariinae s.l. which formed the subject of our previous investigations.

Key Results and Conclusions

The labellar micromorphology of Zygopetalinae is less diverse than that of Maxillariinae and does not reflect the currently accepted phylogeny of the former sub-tribe based on molecular studies. Instead, the relative uniformity in labellar micromorphology of Zygopetalinae is probably due to homoplasies resulting from similar pollinator pressures. Labellar trichomes are relatively uncommon in Zygopetalinae, but occur in certain members of both the Zygopetalum and Huntleya clades. Trichomes are unbranched, uniseriate and multicellular with rounded apices, or unbranched and unicellular, with tapering, pointed and flexuose apices. Hitherto, unicellular trichomes of this kind have been observed only for euglossophilous orchid taxa, and the adoption of a relatively limited range of pollination strategies by Zygopetalinae may have resulted in reduced investment in micromorphological labellar characters.     

Molecularly cloned SHIV-CN97001: a replication-competent, R5 simian/human immunodeficiency virus containing env of a primary Chinese HIV-1 clade C isolate

Background The increasing prevalence of human immunodeficiency virus type 1 (HIV‐1) subtype C infection worldwide calls for efforts to develop a relevant animal model for evaluating AIDS candidate vaccines. In China, the prevalent HIV strains comprise a circulating recombinant form, BC (CRF07_BC), in which the envelope belongs to subtype C. Methods To evaluate potential AIDS vaccines targeting Chinese viral strains in non‐human primate models, we constructed a simian/human immunodeficiency virus (SHIV) carrying most of the envelope sequence of a primary HIV‐1 clade C strain isolated from an HIV‐positive intravenous drug user from YunNan province in China. Furthermore, to determine whether in vivo adaptation would enhance the infectivity of SHIV‐CN97001, the parental infectious strain was serially passaged through eight Chinese rhesus macaques. Results Infection of six Chinese rhesus macaques with SHIV‐CN97001 resulted in a low level of viremia and no significant alteration in CD4+ T‐lymphocyte counts. However, the hallmarks of SHIV infectivity developed gradually, as shown by the increasingly elevated peak viremia with each passage. Conclusion These findings establish that the R5‐tropic SHIV‐CN97001/Chinese rhesus macaque model should be very useful for the evaluation of HIV‐1 subtype C vaccines in China.     

Toxins from strains of <Emphasis Type="Italic">Penicillium chrysogenum</Emphasis> isolated from buildings and other sources

In 2004, Scott et al. (Mycologia 2004; 96: 1095–1105) determined that there are four molecular species within P. chrysogenum, one of which (clade 4) was dominant in isolates in house dust in ~100 homes in southern Ontario, Canada. We collected additional strains from buildings across Canada and obtained some from DAOM. The large majority of our strains were in clade 4, with a modest number of strains in Clade 1. Because these strains came from across Canada, the dominance of clade 4 in buildings is apparently widespread. Most strains tested produced penicillin G, roquefortine C and unexpectedly, meleagrin in high yield. Additionally, there appeared to be strains differentiated by their ability to accumulate xanthocillin X. These studies allowed focused toxicity studies in vivo and with primary lung cell cultures to be undertaken on the basis of reliable information of the toxins that should be studied.     

Phylogeography of the high alpine plant Senecio halleri (Asteraceae) in the European Alps: in situ glacial survival with postglacial stepwise dispersal into peripheral areas

Whether alpine plant species survived Pleistocene glaciations in situ on high alpine nunatak mountains is still under debate. To test this hypothesis, Senecio halleri, a high alpine and endemic species with a narrow distribution range in the European Alps, was chosen as a model organism. Polymerase chain reaction-restriction fragment length polymorphisms of chloroplast DNA (cpDNA PCR-RFLPs) were used in a phylogeographic analysis of 14 populations of S. halleri, covering its total distribution area. The results of haplotype diversity and distribution gave evidence of in situ glacial survival on siliceous central-alpine nunatak mountains in two areas, southwest and northeast of the Aosta valley. According to the absence of genetic differentiation between these two nunatak areas (based on amova), nested clade analysis implied a history of preglacial gene flow, in situ survival and extinction of intermediate populations during glaciation and postglacial stepwise recolonization of peripheral and intermediate areas.     

Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies

Effective spatial management of coral reefs including design of marine protected areas requires an understanding of interpopulation genetic connectivity. We assessed gene flow along 355 km of the Florida reef system and between Florida and Belize in three commensal invertebrates occupying the same host sponge (Callyspongia vaginalis) but displaying contrasting reproductive dispersal strategies: the broadcast-spawning brittle star Ophiothrix lineata and two brooding amphipods Leucothoe kensleyi and Leucothoe ashleyae. Multiple analytical approaches to sequence variation in the mitochondrial COI gene demonstrated a high degree of overall connectivity for all three species along the Florida reef system. Ophiothrix lineata showed significant genetic structuring between Florida and Belize, and a pattern of isolation by distance but no significant genetic structuring along the Florida coastline. Bayesian estimates of migration detected a strong southerly dispersal bias for O. lineata along the Florida reef system, contrary to the general assumption of northerly gene flow in this region based on the direction of the Florida Current. Both amphipods, despite direct development, also showed high gene flow along the Florida reef system. Multiple inferences of long-distance dispersal from a nested clade analysis support the hypothesis that amphipod transport, possibly in detached sponge fragments, could generate the high levels of overall gene flow observed. However, this transport mechanism appears much less effective across deep water as connectivity between Florida and Belize (1072 km) is highly restricted.