Enzyme electrophoretograms in the analysis of taxon relatedness of Micrococcus cryophilus, Branhamella catarrhalis and atypical Neisserias.

Extracts were prepared from Micrococcus cryophilus, several strains of Branhamella catarrhalis and Neisseria spp. Esterases, NADP-dependent isocitrate dehydrogenase and malate dehydrogenase activities were assayed after electrophoresis of extracts of polyacrylamide gels. Except for Neisseria perflava and N. sicca which resolved activity bands for the acetate-esterase only, the remaining bacteria exhibited species-specific esterase patterns also for the propionate and butyrate substrates. The multiple esterase patterns from B. catarrhalis ATCC25238 were qualitatively and quantitatively different from those of B. catarrhalis ATCC23246. This finding and other evidence supports a taxonomic shift of the latter to a species level of that genus. The atypical neisserias N. caviae and N. ovis appeared to exhibit an intrageneric specificity in their esterase patterns with those from B. catarrhalis but not to the other Neisseria spp. tested. The malate dehydrogenase patterns from the atypical neisserias and B. catarrhalis ATCC23246 were qualitatively similar; however, the patterns of isocitrate dehydrogenase activity were variable for these species. Micrococcus cryophilus was distinct in its esterase and dehydrogenase bands, strongly suggesting its taxon unrelatedness to the genus Branhammella or the atypical neisserias. Of the enzymes assayed, esterase proved to be the most reliable for taxonomic identifications.     

Population genetic structure of Nantucket pine tip moth

Summary Variation at polymorphic isozyme loci was analyzed in Nantucket pine tip moth (NPTM) populations from 5 geographic locations. At the North Carolina location, populations representing 3 generations at 3 local sites were also studied. Four of the loci investigated (LAP, MDH, -GPDH and AK), although variable, had few alleles per locus (3–5) and few differences among populations in allele frequencies. At each locus, all populations had the same allele at a high frequency.At the PGM locus, fifteen alleles were identified and allelic frequencies varied among populations. At least eight alleles were present within a population and, in most populations, two or more alleles had high frequencies that differed among populations. An excess of homozygotes over Hardy-Weinberg expectations was found for 7 out of the 10 populations studied, indicating the probable existence of some form of inbreeding structure or populational subdivision within sampled stands.Joint consideration of the results observed for PGM and the other four loci is counterindicative of neutrality at all loci and strongly indicative of genetic differentiation among locally disjunct populations.Published as Paper No. 6751 of the Journal Series of the North Carolina Agricultural Research Service     

Baseplate protein of bacteriophage T4 with both structural and lytic functions.

Analyses of a new bacteriophage T4 mutant that permits lysis of infected cells in the absence of e lysozyme showed that the strain carried a suppressor mutation in gene 5, a gene whose polypeptide product (gp5) is an integral component of the virion baseplate. Indirect experiments indicated that cell lysis was caused by the lytic action of mutant gp5. With regard to the physiological role of normal gp5, we speculate that it functions in the initiation of infection by catalyzing local cell wall digestion to facilitate penetration of the tail tube through the cell envelope. The proposed lytic activity of gp5 may also be responsible for the well-known phenomenon of lysis from without observed with T4.     

The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants

The photosynthetic gene rbcL has been lost or dramatically altered in some lineages of nonphotosynthetic parasitic plants, but the dynamics of these events following loss of photosynthesis and whether rbcL has sustained functionally significant changes in photosynthetic parasitic plants are unknown. To assess the changes to rbcL associated with the loss of functional constraints for photosynthesis, nucleotide sequences from nonparasitic and parasitic plants of Scrophulariales were used for phylogeny reconstruction and character analysis. Plants in this group display a broad range of parasitic abilities, from photosynthetic ("hemiparasites") to nonphotosynthetic ("holoparasites"). With the exception of Conopholis (Orobanchaceae), the rbcL locus is present in all parasitic plants of Scrophulariales examined. Several holoparasitic genera included in this study, including Boschniakia, Epifagus, Orobanche, and Hyobanche, have rbcL pseudogenes. However, the holoparasites Alectra orobanchoides, Harveya capensis, Harveya purpurea, Lathraea clandestina, Orobanche corymbosa, O. fasciculata, and Striga gesnerioides have intact open reading frames (ORFs) for the rbcL gene. Phylogenetic hypotheses based on rbcL are largely in agreement with those based on sequences of the nonphotosynthetic genes rps2 and matK and show a single origin of parasitism, and loss of photosynthesis and pseudogene formation have been independently derived several times in Scrophulariales. The mutations in rbcL in nonparasitic and hemiparasitic plants would result in largely conservative amino acid substitutions, supporting the hypothesis that functional proteins can experience only a limited range of changes, even in minimally photosynthetic plants. In contrast, ORFs in some holoparasites had many previously unobserved missense substitutions at functionally important amino acid residues, suggesting that rbcL genes in these plants have evolved under relaxed or altered functional constraints.      

Groundwater nitrogen dynamics at the terrestrial-lotic interface of a small catchment in the Central Amazon basin

Processes operating at the terrestrial-lotic interface may significantly alter dissolved nitrogen concentrations in groundwater as a result of shifting redox conditions and microbial communities. We monitored concentrations of total dissolved nitrogen, NO ₄ ^– , NH ₄ ^– , O₂ and Fe²⁺ for 10 months along two transects tracing groundwater flow from an upland (terra firme) forest, beneath the riparian forest, and into the stream channel of a small Central Amazonian catchment. Our aim was to examine the role of near-stream processes in regulating groundwater transfers of dissolved nitrogen from terrestrial to lotic ecosystems in the Central Amazon. We found pronounced compositional differences in inorganic nitrogen chemistry between upland, riparian, and stream hydrologic compartments. Nitrate dominated (average 89% of total inorganic nitrogen; TIN) the inorganic nitrogen chemistry of oxygenated upland groundwater but decreased markedly upon crossing the upland-riparian margin. Conversely, NH ₄ ^– dominated (average 93% of TIN) the inorganic chemistry of apparently anoxic riparian groundwater; NH ₄ ^– and TIN concentrations decreased markedly across the riparian-stream channel margin. In the oxygenated streamwater, NO ₃ ^– again dominated (average 82% of TIN) inorganic nitrogen chemistry. Denitrification followed by continued ammonification is hypothesized to effect the shift in speciation observed at the upland-riparian margin, while a combination of several processes may control the shift in speciation and loss of TIN observed at the riparian-stream margin. Dissolved organic nitrogen concentrations did not vary significantly between upland and riparian groundwater, but decreased across the riparian-stream margin. Our data suggest that extensive transformation reactions focused at the upland and stream margins of the riparian zone strongly regulate and diminish transfers of inorganic nitrogen from groundwater to streamwater in the catchment. This suggestion questions the veracity of attempts in the literature to link stream nitrogen chemistry with nutrient status in adjacent forests of similar catchments in the Central Amazon. It also complicates efforts to model nitrogen transfers across terrestrial-lotic interfaces in response to deforestation and changing climate.     

Rapid purification of synthetic oligonucleotides: a convenient alternative to high-performance liquid chromatography and polyacrylamide gel electrophoresis

A new method has been developed to purify and detritylate milligram amounts of synthetic oligonucleotides. Dimethoxytrityl oligonucleotides from 15 to 100 nucleotides in length are applied in triethylammonium acetate or concentrated ammonium hydroxide to a disposable chromatographic cartridge, the NENSORB PREP Nucleic Acid Purification Cartridge. Salts, failure sequences and synthetic by-products are washed away while the desired, full-length, dimethoxytrityl oligonucleotide remains bound to the cartridge. The trityl group is hydrolyzed from the 5'-end of the oligonucleotide with an acid wash and then the purified oligonucleotide is eluted with 35% methanol. Oligonucleotides are recovered salt-free with purities greater than 95%. NENSORB PREP-purified primers provide superior sequence data compared to similar primers used without purification and equivalent data to primers purified by polyacrylamide gel electrophoresis when used in manual radiometric Sanger sequencing.     

Looking at proteins: representations, folding, packing, and design. Biophysical Society National Lecture, 1992.

Looking at proteins is an active process of interpretation and selection, emphasizing some features and deleting others. Multiple representations are needed, for such purposes as showing motions or conveying both the chain connectivity and the three-dimensional shape simultaneously. In studying and comparing protein structures, ideas are suggested about the determinants of tertiary structure and of folding (e.g., that Greek key beta barrels may fold up two strands at a time). The design and synthesis of new proteins "from scratch" provides a route toward the experimental testing of such ideas. It has also been a fruitful new perspective from which to look at structures, requiring such things as statistics on very narrowly defined structural categories and explicit attention to "negative design" criteria that actively block unwanted alternatives (e.g., reverse topology of a helix bundle, or edge-to-edge aggregation of beta sheets). Recently, the field of protein design has produced a rather unexpected general result: apparently we do indeed know enough to successfully design proteins that fold into approximately correct structures, but not enough to design unique, native-like structures. The degree of order varies considerably, but even the best designed material shows multiple conformations by NMR, more similar to a "molten globule" folding intermediate than to a well ordered native tertiary structure. In response to this conclusion, we are now working on systems that test useful questions with approximate structures (such as determining which factors most influence the choice of helix-bundle topology) and also analyzing how natural proteins achieve unique core conformations (e.g., for side chains on the interior side of a beta sheet, illustrated in the kinemages).     

Zinc supplementation inhibits hepatic apoptosis in mice subjected to a long-term ethanol exposure

Hepatocyte apoptosis has been documented in both clinical and experimental alcoholic liver disease. This study was undertaken to examine the effect of dietary zinc supplementation on hepatic apoptosis in mice subjected to a long-term ethanol exposure. Male adult 129S6 mice fed an ethanol-containing liquid diet for 6 months developed hepatitis, as indicated by neutrophil infiltration and elevation of hepatic keratinocyte chemoattractant (KC) and monocyte chemoattractant protein-1 (MCP-1) levels. Apoptotic cell death was detected in ethanol-exposed mice by a terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay and was confirmed by the increased activities of caspase-3 and -8. Zinc supplementation attenuated alcoholic hepatitis and reduced the number of TUNEL-positive cells in association with inhibition of caspase activities. Ethanol exposure caused oxidative stress, as indicated by reactive oxygen species accumulation, mitochondrial glutathione depletion, and decreased metallothionein levels in the liver, which were suppressed by zinc supplementation. The mRNA levels of tumor necrosis factor (TNF)-alpha, TNF-R1, FasL, Fas, Fas-associated factor-1, and caspase-3 in the liver were upregulated by ethanol exposure, which were attenuated by zinc supplementation. Zinc supplementation also prevented ethanol-elevated serum and hepatic TNF-alpha levels and TNF-R1 and Fas proteins in the liver. In conclusion, zinc supplementation prevented hepatocyte apoptosis in mice subjected to long-term ethanol exposure, and the action of zinc is likely through suppression of oxidative stress and death receptor-mediated pathways.     

Abundance–occupancy relationships in deep sea wood fall communities

The generally positive relationship between the number of sites a species occupies and its average abundance within those sites provides an important link between population processes occurring at different spatial scales. Although such abundance–occupancy relationships (AORs) have been documented across a very wide range of taxa and in many different environments, little is known of such patterns in Earth's largest ecosystem, the deep sea. Wood falls – derived from natural or anthropogenic inputs of wood into the oceans – constitute an important deep‐sea habitat, habouring their own unique communities ultimately entirely dependent on the wood for chemical energy. In this study we take advantage of the unique features of an experimental wood fall deployment to examine AORs for the first time in deep‐sea invertebrates. The study design combines advantages of both experimental (tractability, control of key environmental parameters) and observational (natural colonisation by taxonomically diverse communities) studies. We show that the interspecific AOR is strongly positive across the 48 species occurring over 32 wood fall communities. The precise form of the AOR is mediated by both species‐level life history (body size) and by the colonisation stage at which communities were harvested, but not by environmental energy (wood fall size). Temporal dynamics within species are also generally consistent with positive intraspecific AORs. This support for positive AORs in the deep sea is an important extension of a macroecological generality into a new environment offering considerable potential for further testing and developing mechanistic macroecological theories.