Free-living and aggregate-associated Planctomycetes in the Black Sea

We examined the distribution of uncultured Planctomycetes phylotypes along depth profiles spanning the redox gradient of the Black Sea suboxic zone to gain insight into their respective ecological niches. Planctomycetes phylogeny correlated with depth and chemical profiles, implying similar metabolisms within phylogenetic groups. A suboxic zone sample was split into >?30 and ?30?μm fraction except for members of the Scalindua genus, which were apparently free-living. Sequences from Candidatus Scalindua, known to carry out the anammox process, formed two distinct clusters with nonoverlapping depth ranges. One cluster, only 97.1% similar to the named species, was present at high nitrite/nitrate and low ammonium concentrations in the upper suboxic zone. We propose this sequence type be named 'Candidatus Scalindua richardsii'. A second cluster, containing sequences more similar to 'Candidatus Scalindua sorokinii', was present at high ammonium and low nitrite conditions in the lower suboxic zone. Sequences obtained from the sulfidic zone (1000?m depth) yielded Planctomycetes from two uncharacterized Planctomycetacia clusters and three potentially new genera as well as sequences from the uncultured OP3 phylum.     

Molecular genetic analysis reveals that a nonribosomal peptide synthetase-like (NRPS-like) gene in Aspergillus nidulans is responsible for microperfuranone biosynthesis

Genome sequencing of Aspergillus species including Aspergillus nidulans has revealed that there are far more secondary metabolite biosynthetic gene clusters than secondary metabolites isolated from these organisms. This implies that these organisms can produce additional secondary metabolites, which have not yet been elucidated. The A. nidulans genome contains 12 nonribosomal peptide synthetase (NRPS), one hybrid polyketide synthase/NRPS, and 14 NRPS-like genes. The only NRPS-like gene in A. nidulans with a known product is tdiA, which is involved in terrequinone A biosynthesis. To attempt to identify the products of these NRPS-like genes, we replaced the native promoters of the NRPS-like genes with the inducible alcohol dehydrogenase (alcA) promoter. Our results demonstrated that induction of the single NRPS-like gene AN3396.4 led to the enhanced production of microperfuranone. Furthermore, heterologous expression of AN3396.4 in Aspergillus niger confirmed that only one NRPS-like gene, AN3396.4, is necessary for the production of microperfuranone.     

A versatile and efficient gene-targeting system for Aspergillus nidulans

Aspergillus nidulans is an important experimental organism, and it is a model organism for the genus Aspergillus that includes serious pathogens as well as commercially important organisms. Gene targeting by homologous recombination during transformation is possible in A. nidulans, but the frequency of correct gene targeting is variable and often low. We have identified the A. nidulans homolog (nkuA) of the human KU70 gene that is essential for nonhomologous end joining of DNA in double-strand break repair. Deletion of nkuA (nkuA delta) greatly reduces the frequency of nonhomologous integration of transforming DNA fragments, leading to dramatically improved gene targeting. We have also developed heterologous markers that are selectable in A. nidulans but do not direct integration at any site in the A. nidulans genome. In combination, nkuA delta and the heterologous selectable markers make up a very efficient gene-targeting system. In experiments involving scores of genes, 90% or more of the transformants carried a single insertion of the transforming DNA at the correct site. The system works with linear and circular transforming molecules and it works for tagging genes with fluorescent moieties, replacing genes, and replacing promoters. This system is efficient enough to make genomewide gene-targeting projects feasible.     

First-principles calculations of protein circular dichroism in the far-ultraviolet and beyond

Understanding the relationship between the amino acid sequence of a protein and its unique, compact three-dimensional structure is one of the grand challenges in molecular biophysics. One exciting approach to the protein-folding problem is fast time-resolved spectroscopy in the ultra-violet (UV). Time-resolved electronic circular dichroism (CD) spectroscopy offers resolution on a nanosecond (or faster) timescale, but does not provide the spatial resolution of techniques like X-ray crystallography or NMR. There is a need to underpin fast timescale spectroscopic studies of protein folding with a stronger theoretical foundation. We review some recent studies in this regard and briefly highlight how modern quantum chemical models of aromatic groups have improved the accuracy of calculations of protein CD spectra near-UV. On the other side of the far-UV, we describe calculations indicating that charge-transfer transitions are likely to be responsible for bands observed in the vacuum UV in protein CD.     

Diazotrophic endophytes of native black cottonwood and willow

Poplar and willow are economically-important, fast-growing tree species with the ability to colonize nutrient-poor environments. To initiate a study on the possible contribution of endophytes to this ability, we isolated bacteria from within surface-sterilized stems of native poplar (Populus trichocarpa) and willow (Salix sitchensis) in a riparian system in western Washington state. Several of the isolates grew well in nitrogen-limited medium. The presence ofnifH, a gene encoding one of the subunits of nitrogenase, was confirmed in several of the isolates including species ofBurkholderia, Rahnella, Sphingomonas, andAcinetobacter. Nitrogenase activity (as measured by the acetylene reduction assay) was also confirmed in some of the isolates. The presence of these diazotrophic microorganisms may help explain the ability of these pioneering tree species to grow under nitrogen limitation.     

UV-induced RPA phosphorylation is increased in the absence of DNA polymerase eta and requires DNA-PK

Signaling from arrested replication forks plays a role in maintaining genome stability. We have investigated this process in xeroderma pigmentosum variant cells that carry a mutation in the POLH gene and lack functional DNA polymerase eta (poleta). Poleta is required for error-free bypass of UV-induced cyclobutane pyrimidine dimers; in the absence of poleta in XPV cells, DNA replication is arrested at sites of UV-induced DNA damage, and mutagenic bypass of lesions is ultimately carried out by other, error-prone, DNA polymerases. The present study investigates whether poleta expression influences the activation of a number of UV-induced DNA damage responses. In a stably transfected XPV cell line (TR30-9) in which active poleta can be induced by addition of tetracycline, expression of poleta determines the extent of DNA double-strand break formation following UV-irradiation. UV-induced phosphorylation of replication protein A (RPA), a key DNA-binding protein involved in DNA replication, repair and recombination, is increased in cells lacking poleta compared to when poleta is expressed in the same cell line. To identify the protein kinase responsible for increased UV-induced hyperphosphorylation of the p34 subunit of RPA, we have used NU7441, a specific small molecule inhibitor of DNA-PK. DNA-PK is necessary for RPA p34 hyperphosphorylation, but DNA-PK-mediated phosphorylation is not required for recruitment of RPA p34 into nuclear foci in response to UV-irradiation. The results demonstrate that activation of a UV-induced DNA damage response pathway, involving phosphorylation of RPA p34 by DNA-PK, is enhanced in cells lacking poleta.     

Stem cell transplantation: potential impact on heart failure

Cell transplantation is a promising new modality in treating damaged myocardium after myocardial infarction and in preventing postmyocardial infarction LV remodelling. Two strategies are plausible: the first uses adult tissue stem cells to replace the scar tissues and amend the lost myocardium, whilst the second strategy uses embryonic stem cells in an attempt to regenerate myocardium and/or blood vessels.     

Taste responses of human chorda tympani nerve

Records from humans of summated action potential dischargesof the chorda tympani nerve were examined. The magnitudes ofneural and psychophysical responses were well related only whenthe comparison was made within a given taste quality. The responseto a mixture of 0 02 M citric acid and 0.5 M sucrose was lessthan the sum of the separate responses to the mixture components.Citric acid failed to cross-adapt the response to sucrose, implyingthe receptor sites for sucrose are independent of citric acid.The human chorda tympani nerve shows vigorous responses to mechanicalstimulation and cooling of the tongue that are maintained aftertreatment of the tongue with a water extract of the herb Gymnemasylvestre. Gymnema extract selectively suppressed the responseto all sweeteners tested (sucrose, fructose, saccharin and cyclamate)and also suppressed by – 50% the water-after-citric-acidresponse which has a predominantly sweet taste. Gymnema suppressedby 0 – 10% the water-rinse response following NaCl. fructoseand sucrose that have a predominantly bitter-sour taste. Water-rinseresponses were present even when mechanical and thermal stimulationof the tongue were minimized. The human chorda tympani nerveappears to have positive water-rinse taste responses. Theseare solute-specific off-responses that are probably mediatedby receptor sites independent of those responsible for the on-responseto the given solute.     

Habitat management for tanks and Tuans: Evolving approaches at Puckapunyal Military Area

Through a combination of on-ground actions, policies and plans, this military training area – set within an important Box–Ironbark Ecosystem – is being managed in a manner that provides compatibility with the conservation of biodiversity.     

Comparative tests of evolutionary trade-offs in a palinurid lobster acoustic system

Communication structures vary greatly in size and can be structurally and behaviorally integrated with other systems. In structurally integrated systems, dramatic changes in size may impose trade-offs with the size of neighboring structures. In spiny lobsters (Palinuridae), there is a fivefold difference in size of the antennular plate, on which sound producing apparatus is located, such that the antennular plate reaches 38% carapace length in some sound producers (Stridentes) compared to only 4% carapace length in non-sound producing spiny lobsters (Silentes). We examined whether this major variation in antennular plate size imposes trade-offs with the adjoining antennae, specifically in the context that the signal producing structures and antennae are both used in predator defense. We recorded and analyzed lobster sounds in order to test whether size increases in the acoustic morphology were correlated with production of particular signal features. Antennal and antennular plate structures were measured across the family, including both Stridentes and Silentes. Phylogenetic comparative methods were used to test for correlated evolutionary change among the structures and signal features. We analyzed the phylogenetic relationships of the Palinuridae based on morphological characters and ribosomal DNA evidence (16S, 18S and 28S nuclear and mitochondrial ribosomal RNA gene regions). We found that the number of sound pulses was positively correlated with length of the sound producing apparatus. Opposite to the predicted trade-offs, we found that the size of the antennular plate was positively correlated with size of the surrounding antennae within Stridentes. Nevertheless, when Stridentes were compared to Silentes, the latter had relatively larger antennae for a given antennular plate size than did the sound producing taxa. These results suggest that body size does not limit size increases in acoustic structures within Stridentes, however the presence and associated constructional costs of a sound producing apparatus may impose a trade-off when taxa with and without the apparatus are compared. Alternatively, since both systems are used in predator defense, this pattern may indicate greater selection for antennal force production in Silentes, which lack the additional acoustic mode of predator defense.