Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus

The dimorphic prosthecate bacteria (DPB) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.     

Support for a rare pattern of temperature-dependent sex determination in archaic reptiles: evidence from two species of tuatara (Sphenodon)

Background

In many birds, day length (=photoperiod) regulates reproductive cycle. The photoperiodic environment varies between different seasons and latitudes. As a consequence, species at different latitudes may have evolved separate photoperiodic strategies or modified them as per their adaptive need. We studied this using house sparrow as a model since it is found worldwide and is widely investigated. In particular, we examined whether photoperiodism in house sparrows (Passer domesticus) at 27°N, 81°E shared features with those exhibited by its conspecifics at high latitudes.

Results

Initial experiment described in the wild and captive conditions the gonad development and molt (only in captives) cycles over a 12-month period. Both male and female sparrows had similar seasonal cycles, linked with annual variations in day length; this suggested that seasonal reproduction in house sparrows was under the photoperiodic control. However, a slower testis and attenuated follicular growth among captives indicated that other (supplementary) factors are also involved in controlling the reproductive cycle. Next experiment examined if sparrows underwent seasonal variations in their response to stimulatory effects of long day lengths. When birds were transferred every month over a period of 1 year to 16 hours light:8 hours darkness (16L:8D) for 17–26 weeks, there was indeed a time-of-year effect on the growth-regression cycle of gonads. The final experiment investigated response of house sparrows to a variety of light-dark (LD) cycles. In the first set, sparrows were exposed for 31 weeks to photoperiods that were close to what they receive in between the period from sunrise to sunset at this latitude: 9L:15D (close to shortest day length in December), 12L:12D (equinox, in March and September) 15L:9D (close to longest day length in June). They underwent testicular growth and regression and molt in 12L and 15L photoperiods, but not in 9L photoperiod. In the second set, sparrows were exposed for 17 weeks to photoperiods with light periods extending to different duration of the daily photosensitivity rhythm (e.g. 2L:22D, 6L:18D, 10L:14D, 14L:10D, 18L:6D and 22L:2D). Interestingly, a slow and small testicular response occurred under 2L and 10L photoperiods; 6L:18D was non-inductive. On the other hand, 14L, 18L and 22L photoperiods produced testicular growth and subsequent regression response as is typical of a long day photostimulation.

Conclusion

Subtropical house sparrows exhibit photoperiodic responses similar to that is reported for its population living at high latitudes. This may suggest the conservation of the photoperiodic control mechanisms in birds evolved over a long period of time, as a physiological strategy in a temporally changing environment ensuring reproduction at the best suited time of the year.     

Rickettsia prowazekii Transports UMP and GMP, but Not CMP, as Building Blocks for RNA Synthesis

Rickettsia prowazekii, the etiological agent of epidemic typhus, is an obligate intracellular bacterium and is apparently unable to synthesize ribonucleotides de novo. Here, we show that as an alternative, isolated, purified R. prowazekii organisms transported exogenous uridyl- and guanylribonucleotides and incorporated these labeled precursors into their RNA in a rifampin-sensitive manner. Transport systems for nucleotides, which we have shown previously and show here are present in rickettsiae, have never been reported in free-living bacteria, and the usual nucleobase and nucleoside transport systems are absent in rickettsiae. There was a clear preference for the monophosphate form of ribonucleotides as the transported substrate. In contrast, rickettsiae did not transport cytidylribonucleotides. The source of rickettsial CTP appears to be the transport of UMP followed by its phosphorylation and the amination of intrarickettsial UTP to CTP by CTP synthetase. A complete schema of nucleotide metabolism in rickettsiae is presented that is based on a combination of biochemical, physiological, and genetic information.     

Multiple sources of isotopic variation in a terrestrial arthropod community: challenges for disentangling food webs

Documenting trophic links in a food web has traditionally required complex exclusion experiments coupled with extraordinarily labor-intensive direct observations of predator foraging. Newer techniques such as stable isotope analysis (SIA) may facilitate relatively quick and accurate assessments of consumer feeding behavior. Ratios of N and C isotopes are thought to be useful for determining species' trophic position (e.g., 1 degrees consumer, 2 degrees consumer, or omnivore) and their original carbon source (e.g., C3 or C4 plants; terrestrial or marine nutrients). Thus far, however, applications of stable isotopes to terrestrial arthropod food webs have suggested that high taxon-specific variation may undermine the effectiveness of this method. We applied stable isotope analysis to a pear orchard food web, in which biological control of a dominant pest, pear psylla (Cacopsylla pyricola), involves primarily generalist arthropod predators with a high frequency of omnivory. We found multiple sources of isotopic variation in this food web, including differences among plant tissues; time, stage, and taxon-specific differences among herbivores (despite similar feeding modes); and high taxon-specific variation among predators (with no clear evidence of omnivory). Collectively, these multiple sources of isotopic variation blur our view of the structure of this food web. Idiosyncrasies in consumer trophic shifts make ad hoc application of SIA to even moderately complex food webs intractable. SIA may not be a generally applicable "quick and dirty" method for delineating terrestrial food web structure-not without calibration of specific consumer food trophic shifts.     

Detection of antineoplastic agent induced cardiotoxicity by 31P NMR of perfused rat hearts

Development of dose dependent chronic irreversible cardiotoxicity is a key problem encountered in chemotherapy with adriamycin. Here it has been demonstrated that infusion of this agent produced distinct and largely irreversible changes in levels of phosphate metabolites and substantial acidosis that are detected by 31P NMR of the Langendorf perfused heart. Administration of the antioxidant, butylated hydroxytoluene minimizes these spectral changes but does not substantially diminish the antineoplastic activity of adriamycin. Bisantrene (CL 216,942), a noncardiotoxic anthracene with antineoplastic activity, produces only minor perturbations of the 31P spectrum of the perfused rat heart. These studies demonstrate the potential utility of employing 31P NMR to monitor acute or chronic cardiotoxicity in the perfused rat heart and for developing noninvasive in vivo NMR techniques for monitoring cardiotoxicity in experimental animals and humans.     

Monoclonal antibodies to Escherichia coli 50S ribosomes.

Hybridoma cell lines that produce monoclonal antibodies directed against 50S Ribosomal proteins have been isolated. Spleen cells (from BALB/c mice immunized with 50S ribosomal subunits extracted from Escherichia coli) were fused to mouse myeloma cell line SP2/O-Ag 14. The initial screening for antibody producing hybridomas was carried out by a double antibody sandwich method; hybridomas were subsequently cloned in soft agar. Antibodies were characterized by their specific binding to individual 50S ribsomal proteins separated on phosphocellulose columns and in two-dimensional polyacrylamide gels. The assignments were confirmed with purified single ribosomal proteins. Of four clones analyzed thus far, two are identical with specificity for r-protein L5. The other clones produce two different antibodies directed against r-protein L20. Each monoclonal antibody formed ribosome dimers visualizable in the electron microscope. Dimers could be reacted with a different second antibody to form chains containing 8 or more ribosomes, which may be useful for structural studies.     

Comparison of phosphorus deficiency indices during a spring phytoplankton bloom in a eutrophic reservoir

1. Phosphorus limitation was studied along the eutrophic, canyon-type ?ímov reservoir (Czech Republic) during a spring phytoplankton bloom. Concentration of soluble reactive phosphorus (SRP), C:P molar ratio in seston, extracellular alkaline phosphatase activity (APA), and P limitation (bioassay) were used as indices for phosphorus deficiency in the phytoplankton. 2. SRP, C:P, APA, and P limitation indicated a moderate P deficiency in the downstream, but not upper, part of the reservoir. 3. Significant correlations between these parameters were found in the downstream part. Chlorophyll a concentration correlated with APA and P limitation in the upper part. 4. APA was significantly enhanced in the phosphorus-deficient phytoplankton. However, APA was apparently not related to total biomass or species composition of the phytoplankton. 5. Generally, APA was closely correlated with pH in the reservoir. However, extracellular alkaline phosphatases, with a pH optimum above 9.0, were induced and active only during the phytoplankton bloom, whereas low background activity of extracellular phosphatases was found at low chlorophyll a concentrations (winter, clear-water phase).     

A trnL-F based phylogeny for species ofPelargonium (Geraniaceae) with small chromosomes

Phylogenetic analysis was performed of 921 positions of trnL (UAA) 5 exon — trnF (GAA) exon chloroplast DNA regions from 68 representatives ofPelargonium sectt.Campylia, Cortusina, Glaucophyllum, Hoarea, Isopetalum, Ligularia, Otidia, Pelargonium, Peristera, Polyactium, andReniformia, together with five putative outgroup species from sectionsCiconium, Chorisma andJenkinsonia. The total data set therefore comprised 67.2 kb of DNA sequence. Two main ingroup clades were identified: one clade contains sectionsPeristera, Reniformia, andIsopetalum, the other contains sectionsCampylia, Cortusina, Glaucophyllum, Hoarea, Ligularia, Otidia, Pelargonium, Polyactium and two species currently grouped in sect.Peristera. Branching order among five main clades within the latter clade was not resolved. The trnL-F sequence data support monophyly only for sectionsReniformia andHoarea, the remainder of the currently recognized sections ofPelargonium being either paraphyletic or polyphyletic. The data further suggest that sect.Polyactium is diphyletic and that sect.Glaucophyllum is nested within sect.Pelargonium. One relatively derived clade, which represents half of the genus, contains predominantly geophytic and succulent species, occurring in the geographically restricted winter rainfall region of the South African Cape. This pattern is interpreted as reflecting explosive radiation, possibly as an adaptive response to recent aridification in the western Cape.     

Nuclear mitochondrial pseudogenes as molecular outgroups for phylogenetically isolated taxa: a case study in Sphenodon

'Living fossil' taxa, by definition, have no close relatives, and therefore no outgroup to provide a root to phylogenetic trees. We identify and use a molecular outgroup in the sole extant lineage of sphenodontid reptiles, which separated from other reptiles 230 million years ago. We isolated and sequenced a partial nuclear copy of the mitochondrial cytochrome b gene. We confirm the copy is indeed not mitochondrial, is older than all extant mitochondrial copies in Sphenodon (tuatara), and is therefore useful as a molecular outgroup. Under phylogenetic analysis, the nuclear copy places the root of the tuatara mitochondrial gene tree between the northern and the southern (Cook Strait) groups of islands of New Zealand that are the last refugia for Sphenodon. This analysis supports a previous mid-point rooted mitochondrial gene tree. The mitochondrial DNA tree conflicts with allozyme analyses which place a Cook Strait population equidistant to all northern and other Cook Strait populations. This population on North Brother Island is the only natural population of extant S. guntheri; thus, we suggest that the current species designations of tuatara require further investigation.