A metabolic and genomic assessment of sugar fermentation profiles of the thermophilic Thermotogales,Fervidobacterium pennivorans

A metabolic, genomic and proteomic assessment of Fervidobacterium pennivorans strains was undertaken to clarify the metabolic and genetic capabilities of this Thermotogales species. The type strain Ven5 originally isolated from a hot mud spa in Italy, and a newly isolated strain (DYC) from a hot spring at Ngatamariki, New Zealand, were compared for metabolic and genomic differences. The fermentation profiles of both strains on cellobiose generated similar major end products (acetate, alanine, glutamate, H₂, and CO₂). The vast majority of end products produced were redox neutral, and carbon balances were in the range of 95–115%. Each strain showed distinct fermentation profiles on sugar substrates. The genome of strain DYC was sequenced and shown to have high sequence similarity and synteny with F. pennivorans Ven5 genome, suggesting they are the same species. The unique genome regions in Ven5, corresponded to genes involved in the Entner–Doudoroff pathway confirming our observation of DYC’s inability to utilize gluconate. Genome analysis was able to elucidate pathways involved in production of the observed end-products with the exception of alanine and glutamate synthesis which were resolved with less clarity due to poor sequence identity and missing critical enzymes within the pathway, respectively.

     

PHYLOGENETIC EXAMINATION OF FEMALE INCORPORATION OF EJACULATE IN DROSOPHILA

Males of some invertebrate species transfer large ejaculates, and many of the substances contained therein are incorporated by females into their somatic and ovarian tissues. These incorporated substances are expected to be energetically costly for males to produce, but benefit males by enhancing their fertilization success and/or the viability of their offspring. A better understanding of the evolution and maintenance of this important reproductive strategy should come from phylogenetic examination. We therefore quantified the extent of ejaculate incorporation by females of 34 species of Drosophila. Substantive amounts of male-derived proteins were more frequently detected in female somatic tissue than in ovarian tissue. Substantive ejaculate incorporation by females was found to have arisen numerous times across the phylogeny and tended to be lineage specific in expression. The extent to which evolution of a nutritive function of the ejaculate may have been influenced by phylogenetic history in the genus Drosophila is discussed. Macroevolutionary relationships between the amount of ejaculate incorporated by females and other features of species' reproductive and life-history biology, including body size, sperm length, the formation of an insemination reaction in females, and sex-specific ages of reproductive maturity, also were examined after controlling for phylogenetic effects.     

Bacteriophage T4 regA protein binds RNA as a monomer, overcoming dimer interactions.

The stoichiometry of the complex formed between the T4 translational repressor protein regA and the 16 nt gene 44 recognition element (gene 44RE) RNA has been determined. Under quantitative binding conditions, the association of wild-type regA protein with gene 44RE RNA exhibits saturation at a 1:1 ratio of protein to RNA. It is known that regA protein exists as a dimer in protein crystals. Thus, the stoichiometry may be indicative of a regA dimer bound to two RNAs or a regA monomer bound to one RNA. Gel filtration through Sephadex G-75 revealed that wild-type and R91L regA proteins (14.6 kDa) elute at a mass of 29 kDa, consistent with the mass of a dimer. However, wild-type regA preincubated with gene 44RE (1:1) resulted in a complex that eluted at approximately 20 kDa, consistent with a regA monomer-RNA complex. Covalent crosslinking of surface lysines with glutaraldehyde confirmed that wild-type and R91L proteins exist as dimers and higher oligomers in solution. However, the addition of RNA to wild-type regA protein prior to crosslinking inhibited the formation of crosslinked dimers. Thus, the regA protein-protein interactions observed in solution are disrupted or blocked in the presence of gene 44RE RNA. Together, these studies demonstrate that regA protein binds RNA as a monomer, although free protein exists predominantly as a dimer.     

Toward a (Dys)functional Anthropology of Drinking: Ambivalence and the American Indian Experience with Alcohol

This article explores the complex and contradictory experiences of urban American Indian drinkers. While previous anthropological accounts have emphasized the functions served by American Indian drinking, the testimony of drinkers also documents their awareness of the destructive effects of heavy drinking, particularly the way in which it often interferes with their ability to meet social obligations. Nevertheless, people often continue to use alcohol, and this means that many are profoundly ambivalent about their drinking; they see it simultaneously as something that is embedded in certain important relationships, but also something that is destructive of much that they value. Drawing on interviews with 35 self-defined problem drinkers, this article details the ambiguous nature of the American Indian experience with alcohol, highlighting the need for clinically sophisticated anthropology of alcohol, [alcohol, American Indians, functional ism, clinical approaches]     

Generation of accurate peptide retention data for targeted and data independent quantitative LC‐MS analysis: Chromatographic lessons in proteomics

The emergence of data‐independent quantitative LC‐MS/MS analysis protocols further highlights the importance of high‐quality reproducible chromatographic procedures. Knowing, controlling and being able to predict the effect of multiple factors that alter peptide RP‐HPLC separation selectivity is critical for successful data collection for the construction of ion libraries. Proteomic researchers have often regarded RP‐HPLC as a “black box”, while vast amount of research on peptide separation is readily available. In addition to obvious parameters, such as the type of ion‐pairing modifier, stationary phase and column temperature, we describe the “mysterious” effects of gradient slope, column size and flow rate on peptide separation selectivity. Retention time variations due to these parameters are governed by the linear solvent strength (LSS) theory on a peptide level by the value of its slope S in the basic LSS equation—a parameter that can be accurately predicted. Thus, the application of shallower gradients, higher flow rates, or smaller columns will each increases the relative retention of peptides with higher S‐values (long species with multiple positively charged groups). Simultaneous changes to these parameters that each drive shifts in separation selectivity in the same direction should be avoided. The unification of terminology represents another pressing issue in this field of applied proteomics that should be addressed to facilitate further progress.     

Limited proteolysis studies on the Escherichia coli single-stranded DNA binding protein. Evidence for a functionally homologous domain in both the Escherichia coli and T4 DNA binding proteins

Limited proteolysis can be used to remove either 42 or 62 amino acids at the COOH terminus of the 18,873-dalton Escherichia coli single-stranded DNA binding protein (SSB). Since poly(dT), but not d(pT)16, increases the rate of this reaction, it appears that cooperative SSB binding to single-stranded DNA (ssDNA) is associated with a conformational change that increases the exposure of the COOH terminus to proteolysis. As a result of this DNA-induced conformational change, we presume that the COOH-terminal region of SSB will become more accessible for interacting with other proteins that utilize the SSB:ssDNA complex as a substrate and that are involved in E. coli DNA replication, repair, and recombination. Removal of this COOH-terminal domain from SSB results in a stronger helix-destabilizing protein which suggests this region may be important for controlling the ability of SSB to denature double-stranded DNA. Since similar results have previously been reported for the bacteriophage T4 gene 32 protein (Williams, K.R., and Konigsberg, W. (1978) J. Biol. Chem. 253, 2463-2470; Hosoda, J., and Moise, H. (1978) J. Biol. Chem. 253, 7547-7555), the acidic, COOH-terminal domains of these two single-stranded DNA binding proteins may be functionally homologous. Preliminary evidence is cited that suggests other prokaryotic and eukaryotic DNA binding proteins may contain similar functional domains essential for controlling their ability to invade double helical DNA.     

Cytochemical Localization of Certain Phosphatases in Escherichia coli

Cytochemical studies of Escherichia coli at the light and electron microscopic levels have revealed alkaline phosphatase, hexose monophosphatase, and cyclic phosphodiesterase reaction products in the periplasmic space and at the cell surface. In preparations for both light and electron microscopy, reaction product filled polar caplike enlargements of the periplasmic space, such as those described in plasmolyzed cells, indicating significant terminal concentrations of these enzymes; dense substance was often seen within these polar caps in morphological specimens. Staining of the bacterial surface was commonly encountered, but could represent artifactual accumulation of precipitate along the cell wall. Alkaline phosphatase was demonstrated with several substrates (ethanolamine phosphate, glycerophosphate, p-nitrophenylphosphate, and glucose-6-phosphate) over a wide pH range in a bacterial strain (C-90) known to be constitutive for this enzyme, whereas strains deficient in this enzyme (U-7, repressed K-37), showed no activity with these substrates. Hexose monophosphatase and cyclic phosphodiesterase activities were characterized by reaction-product deposition with specific substrates at acid or neutral, but not at alkaline, pH in strains of E. coli lacking alkaline phosphatase (U-7 and repressed K-37). Fixation in Formalin or the use of calcium as a capture reagent seemed to interfere with periplasmic staining in cells prepared for electron microscopy. Formalin fixation had little effect on biochemical assays of the phosphatase activity of intact cells in suspension, but partially reduced the activity evident in sonically treated extracts or in suspensions of dispersed cryostat sections. Glutaraldehyde treatment impaired enzyme activity more drastically.     

Coexistence of acid phosphatase and acid mucosubstance in the nucleoid of human blood platelet granules

Summary Fine structural localization of acid phosphatase and acid mucosubstance in the human blood platelet has shown that these two components coexist in the platelet granules. Within the granules acid phosphatase activity and acid mucosubstance both appear confined to the nucleoid region. Additionally, heavy acid phosphatase activity filled occasional small cytoplasmic bodies as well as elongated irregular cell organelles which latter appeared to correspond with atypical granules in morphologic preparations. A complex of mucosubstance with nonenzymatic protein, sequestering the lysosomal enzyme, or a complex of mucosubstance with the enzyme reversibly inactivating it, might explain the cytochemical latency of acid phosphatase in certain lysosomes and the masked dialyzed iron affinity in these sites after glutaraldehyde fixation.     

FERRITIN PARTICLES IN MACROPHAGES AND IN ASSOCIATED MAST CELLS

In a variety of tissues (lymph node and glandular stroma), mast cells have been found in close and often intimate association with macrophages containing numerous ferritin-like particles in their cytoplasm and within cytoplasmic vacuoles (siderosomes). Phagocytic vacuoles in a given macrophage differed markedly. Some contained abundant Prussian blue-reactive material and others contained periodic acid-Schiff reactive substance at the light microscope level, and ultrastructurally some were filled with ferritin particles and others were not. Ferritin-like particles have also been observed occasionally in the mast cells associated with macrophages and even within the matrix of some of the granules in these mast cells.