Large-scale comparative genomic analyses of cytoplasmic membrane transport systems in prokaryotes

The recent advancements in genome sequencing make it possible for the comparative analyses of essential cellular processes like transport in organisms across the three domains of life. Membrane transporters play crucial roles in fundamental cellular processes and functions in prokaryotic systems. Between 3 and 16% of open reading frames in prokaryotic genomes were predicted to encode membrane transport proteins, emphasizing the importance of transporters in their lifestyles. Hierarchical clustering of phylogenetic profiles of transporter families, which are derived from the presence or absence of a certain transporter family, showed distinct clustering patterns for obligate intracellular organisms, plant/soil-associated microbes and autotrophs. Obligate intracellular organisms possess the fewest types and number of transporters presumably due to their relatively stable living environment, while plant/soil-associated organisms generally encode the largest variety and number of transporters. A group of autotrophs are clustered together largely due to their absence of transporters for carbohydrate and organic nutrients and the presence of transporters for inorganic nutrients. Inside of each group, organisms are further clustered by their phylogenetic properties. These findings strongly suggest the correlation of transporter profiles to both evolutionary history and the overall physiology and lifestyles of the organisms.     

Beta-D-(1→4)-galactan-containing side chains in RG-I regions of pectic polysaccharides from Biophytum petersianum Klotzsch. contribute to expression of immunomodulating activity against intestinal Peyer's patch cells and macrophages

The aerial parts of the medicinal plant Biophytum petersianum have a long tradition for being used in Mali and other West-African countries against various ailments such as wound healing and malaria. Previous studies on polysaccharides from water extracts of the aerial parts showed the presence of pectic like polymers with an effect on the human complement system as well as the ability to activate macrophages and dendritic cells.The present study shows that pectic polysaccharide fragments (BPII.1 and BPII.2) as well as the original pectic polysaccharide (BPII) expressed immunomodulating activity against Peyer’s patch immunocompetent cells. Exo-β-d-(1 → 3)-galactanase digestion succeeded to decrease IL-6 production enhancing activity against Peyer’s patch cells of BPII.2, but the activity of BPII.1 did not decrease. Endo-β-d-(1 → 4)-galactanase digestion reduced the activities of both BPII.1 and BPII.2. BPII.1 and BPII.2 also stimulated IL-6 production enhancing activity against macrophages, and the activities of both pectic fragments were significantly decreased by either enzymic digestion with exo-β-d-(1 → 3)-galactanase or endo-β-d-(1 → 4)-galactanase. Trimming of terminal GlcA by exo-β-d-glucuronidase digestion did not affect IL-6 production enhancing activity against macrophages of both pectic fragments. Methylation analyses of endo-β-d-(1 → 4)-galactanase digestion products showed the characteristic decrement of 4-linked Gal residues in the pectic fragments. These results suggest that β-d-(1 → 4)-galactan-containing side chains in BPII.1 and BPII.2 play an important role for expression of immunomodulating activity against both Peyer’s patch immunocompetent cells and macrophages in addition to β-d-(1 → 3,6)-galactan chains.     

UDP-Gal: GlcNAc-R β1,4-galactosyltransferase—a target enzyme for drug design. Acceptor specificity and inhibition of the enzyme

Galactosyltransferases are important enzymes for the extension of the glycan chains of glycoproteins and glycolipids, and play critical roles in cell surface functions and in the immune system. In this work, the acceptor specificity and several inhibitors of bovine β1,4-Gal-transferase T1 (β4GalT, EC 2.4.1.90) were studied. Series of analogs of N-acetylglucosamine (GlcNAc) and GlcNAc-carrying glycopeptides were synthesized as acceptor substrates. Modifications were made at the 3-, 4- and 6-positions of the sugar ring of the acceptor, in the nature of the glycosidic linkage, in the aglycone moiety and in the 2-acetamido group. The acceptor specificity studies showed that the 4-hydroxyl group of the sugar ring was essential for β4GalT activity, but that the 3-hydroxyl could be replaced by an electronegative group. Compounds having the anomeric β-configuration were more active than those having the α-configuration, and O-, S- and C-glycosyl compounds were all active as substrates. The aglycone was a major determinant for the rate of Gal-transfer. Derivatives containing a 2-naphthyl aglycone were inactive as substrates although quinolinyl groups supported activity. Several compounds having a bicyclic structure as the aglycone were found to bind to the enzyme and inhibited the transfer of Gal to control substrates. The best small hydrophobic GlcNAc-analog inhibitor was found to be 1-thio-N-butyrylGlcNβ-(2-naphthyl) with a K_i of 0.01 mM. These studies help to delineate β4GalT–substrate interactions and will aid in the development of biologically applicable inhibitors of the enzyme.     

An In Vivo Model for Studying Function of Brain Tissue Temporarily Devoid of Glial Cell Metabolism: The Use of Fluorocitrate

The effect of intrastriatal injection of fluorocitrate on amino acid pattern, cell enzyme markers, and ultrastructural appearance was investigated. A dose of 1 nmol of fluorocitrate resulted in temporarily decreased levels of glutamine, glutamate, and aspartate, whereas the level of alanine was increased. The glutamine level was severely reduced after 4 h but was reversed after 24 h. The activity of different cellular enzyme markers did not change markedly after this dose. Ultrastructural changes in glial cells were observed, concomitant with the biochemical changes. A dose of greater than or equal to 2 nmol of fluorocitrate resulted in more marked and irreversible changes in amino acid levels. By 24-72 h after the injection of this dose, several marker enzyme activities decreased markedly. The ultrastructural changes affected the neurons as well as the glial cells and were not reversible. The use of microinjection of 1 nmol of fluorocitrate into the neostriatum of the rat to provide a model for studying transmitter amino acid metabolism in brain devoid of glial cell activity is discussed.     

Protein domains required for formation of stable monomeric Lhca1- and Lhca4-complexes

The peripheral light-harvesting complex of Photosystem I consists of two subpopulations, LHC I-680 and LHC I-730. The latter is composed of the two apoproteins Lhca1 and Lhca4. Recently, reconstitution of monomeric LHC I using bacterially overexpressed Lhca1 or Lhca4 was achieved. In order to obtain insight into the structure requirements for formation of monomeric light-harvesting complexes, we produced a series of N- and C-terminal deletion mutants and used the overexpressed proteins for reconstitution experiments. We found the entire extrinsic N-terminal region dispensable for monomer formation in Lhca1 and Lhca4. Also at the C-terminus, both subunits revealed similarity since all amino acids up to the end of the fourth helix could be removed without abolishing monomer formation. In connection with former corresponding results for Lhcb1, the dispensability of these regions appears to be a general feature in LHC-formation. In LHC I, however, a stabilising effect can be ascribed to these regions since the yield of complexes was decreased. In the majority of the mutant LHC I versions no effect on pigment binding was detected. However, in the LHC with the most extensively N-terminally truncated mutant of Lhca4 a dramatic shift in the 77 K fluorescence emission to shorter wavelengths was observed. This suggests that chlorophylls involved in long wavelength fluorescence emission are located in the chlorophyll array located towards the stromal face of the thylakoid membrane assuming a pigment arrangement corresponding to that in LHC II and CP29. This revised version was published online in June 2006 with corrections to the Cover Date.     

Tissue distribution and functional analyses of the constitutively active orphan G protein coupled receptors, GPR26 and GPR78

GPR26 and GPR78 are orphan GPCRs (oGPCRs) that share 51% amino acid sequence identity and are widely expressed in selected tissues of the human brain as well as the developing and adult mouse brain. Investigation of the functional activity of GPR26 and GPR78 via expression in HEK293 cells showed that both proteins are constitutively active and coupled to elevated cAMP production. Accordingly, in yeast, GPR26 demonstrated apparent agonist-independent coupling to a chimeric Gpa1 protein in which the 5 C-terminal amino acids were from Galphas. A comparison of the proteins revealed an atypical glutamine residue in GPR78 in place of the conserved arginine residue (R3.50) in the so-called DRY box. Site-directed mutants R3.50 in GPR26 were constructed and retained their constitutive activity suggesting that these 2 receptors activate G proteins in a manner that is distinct from other group 1 GPCRs.     

Dynamics of dissolved organic nitrogen in subalpine Castle Lake,California

Dissolved organic nitrogen (DON) concentrations were measured in meso-oligotrophic Castle Lake, California during the ice-free season in 1982, 1983 and 1984. No consistent relationships were found between DON and particulate-N, primary productivity rates or chlorophyll concentrations. However, increases in DON concentrations were observed in the early growing season of 1982 and 1984 when water temperature was rising and a diatom bloom was senescing. DON increased at a high rate (0.31 mg atom N m^–3 day^–1), and then rapidly disappeared. Sediment released appared to be the most important source of DON. Dissolved free amino acids were always less than 7.5% of the DON pool, and did not vary in the composition of specific amino acids during the growing season.     

Macrorestriction Analysis of Caenorhabditis Elegans Genomic DNA

The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a ``macrorestriction mapping' procedure for Caenorhabditis elegans that we have applied to this endeavor. High molecular weight, genomic DNA is digested with infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probed with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobases and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applications of this technique. (1) We determined that the amount of DNA in a previously uncloned region is <220 kb. (2) We mapped the mes-1 gene to a cosmid, by detecting polymorphic restriction fragments associated with a deletion allele of the gene. The 25-kb deletion was initially detected using as a probe sequences located ~400 kb away from the gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the unc-38-dpy-5 region have very complex molecular structures, containing internal rearrangements and deletions.     

Theoretical temperature distributions produced by an annular phased array-type system in CT-based patient models

Theoretical calculations for the specific absorption rate (SAR) and the resulting temperature distributions produced by an annular phased array (APA)-type system are made. The finite element numerical method is used in the formulation of both the electromagnetic (EM) and thermal boundary value problems. A number of detailed two-dimensional patient models based on CT-scan data from the pelvic, visceral, and thoracic regions are generated to simulate a variety of tumor locations and surrounding normal tissues. The SAR values from the EM solution are put into the bioheat transfer equation, and steady-state temperature distributions are calculated for a wide range of blood flow rates. Based on our theoretical modeling, the APA shows no preferential heating of superficial over deep-seated tumors. However, in most cases for all three regions of the human trunk only fair thermal profiles (therapeutic area near 60%) are obtained in tumors with little or no blood flow and poor temperature patterns (therapeutic area less than 50%) are found in tumors with moderate to high perfusion rates. These theoretical calculations should aid the clinician in the evaluation of the effectiveness of APA-type devices in heating tumors located in the trunk region.