Transplantation, 2001 Sep 15, 72(5), 818 - 22 Neuropathy in miniature swine after administration of the mutant diphtheria toxin-based immunotoxin, pCD3-CRM9; Gargollo P et al.; BACKGROUND: Effective in vivo T-cell depletion is a critical component of many transplantation tolerance protocols . We have previously demonstrated T-cell depletion in miniature swine using a CRM9-based CD3-immunotoxin, pCD3-CRM9 . CRM9 is a mutant form of diphtheria toxin (DT) that binds less efficiently than wild-type DT to the DT receptor (proHB-EGF) of primates . In this report, we describe and characterize the dose-dependent neurotoxicity associated with CRM9-based immunotoxin administration in swine . METHODS: Miniature swine were treated with varying doses of pCD3-CRM9 followed by daily monitoring for symptoms of neuropathy, including limb weakness, paresis, sluggishness, and/or respiratory distress . Animals demonstrating severe respiratory distress were euthanized and peripheral nerve, spinal cord, and skeletal muscle tissue samples were obtained at autopsy for microscopic examination . Unconjugated CRM9 was administered to one animal to define its toxicity independent of the effects of T-cell depletion . RESULTS: Excellent T-cell depletion was obtained using doses of pCD3-CRM9 greater than 0.1 mg/kg . However, neurotoxicity was observed at these doses, as manifested by transient muscle weakness or paresis, which in some cases progressed to respiratory failure and death . Dorsal root ganglia samples revealed pathological changes typical of diphtheritic polyneuropathy . The animal receiving unconjugated CRM9 exhibited the same neurotoxic side effects as those receiving the pCD3-CRM9 conjugate . CONCLUSIONS: Administration of pCD3-CRM9 immunotoxin provides excellent T-cell depletion in miniature swine but is associated with significant dose-dependent neurotoxicity . A possible reason for CRM9-associated neurotoxicity in swine, but not primates, is suggested on the basis of a known amino acid difference in the exodomain of the DT receptor (proHB-EGF) of swine compared with that of primates. Appl Environ Microbiol, 2001 Oct, 67(10), 4850 - 7 Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris; Dedysh SN et al.; Two 16S rRNA-targeted oligonucleotide probes, Mcell-1026 and Mcell-181, were developed for specific detection of the acidophilic methanotroph Methylocella palustris using fluorescence in situ hybridization (FISH) . The fluorescence signal of probe Mcell-181 was enhanced by its combined application with the oligonucleotide helper probe H158 . Mcell-1026 and Mcell-181, as well as 16S rRNA oligonucleotide probes with reported group specificity for either type I methanotrophs (probes M-84 and M-705) or the Methylosinus/Methylocystis group of type II methanotrophs (probes MA-221 and M-450), were used in FISH to determine the abundance of distinct methanotroph groups in a Sphagnum peat sample of pH 4.2 . M . palustris was enumerated at greater than 10(6) cells per g of peat (wet weight), while the detectable population size of type I methanotrophs was three orders of magnitude below the population level of M . palustris . The cell counts with probe MA-221 suggested that only 10(4) type II methanotrophs per g of peat (wet weight) were present, while the use of probe M-450 revealed more than 10(6) type II methanotroph cells per g of the same samples . This discrepancy was due to the fact that probe M-450 targets almost all currently known strains of Methylosinus and Methylocystis, whereas probe MA-221, originally described as group specific, does not detect a large proportion of Methylocystis strains . The total number of methanotrophic bacteria detected by FISH was 3.0 (+/-0.2) x 10(6) cells per g (wet weight) of peat . This was about 0.8% of the total bacterial cell number . Thus, our study clearly suggests that M . palustris and a defined population of Methylocystis spp . were the predominant methanotrophs detectable by FISH in an acidic Sphagnum peat bog. Appl Environ Microbiol, 2001 Oct, 67(10), 4773 - 80 The glycogen-bound polyphosphate kinase from Sulfolobus acidocaldarius is actually a glycogen synthase; Cardona S et al.; Inorganic polyphosphate (polyP) is obtained by the polymerization of the terminal phosphate of ATP through the action of the enzyme polyphosphate kinase (PPK) . Despite the presence of polyP in every living cell, a gene homologous to that of known PPKs is missing from the currently sequenced genomes of Eukarya, Archaea, and several bacteria . To further study the metabolism of polyP in Archaea, we followed the previously published purification procedure for a glycogen-bound protein of 57 kDa with PPK as well as glycosyl transferase (GT) activities from Sulfolobus acidocaldarius (R . Skorko, J . Osipiuk, and K . O . Stetter, J . Bacteriol . 171:5162-5164, 1989) . In spite of using recently developed specific enzymatic methods to analyze polyP, we could not reproduce the reported PPK activity for the 57-kDa protein and the polyP presumed to be the product of the reaction most likely corresponded to glycogen-bound ATP under our experimental conditions . Furthermore, no PPK activity was found associated to any of the proteins bound to the glycogen-protein complex . We cloned the gene corresponding to the 57-kDa protein by using reverse genetics and functionally characterized it . The predicted product of the gene did not show similarity to any described PPK but to archaeal and bacterial glycogen synthases instead . In agreement with these results, the recombinant protein showed only GT activity . Interestingly, the GT from S . acidocaldarius was phosphorylated in vivo . In conclusion, our results convincingly demonstrate that the glycogen-protein complex of S . acidocaldarius does not contain a PPK activity and that what was previously reported as being glycogen-bound PPK is a bacterial enzyme-like thermostable glycogen synthase. Appl Environ Microbiol, 2001 Oct, 67(10), 4765 - 72 Copper-induced inhibition of growth of Desulfovibrio desulfuricans G20: assessment of its toxicity and correlation with those of zinc and lead; Sani RK et al.; The toxicity of copper {Cu(II)} to sulfate-reducing bacteria (SRB) was studied by using Desulfovibrio desulfuricans G20 in a medium (MTM) developed specifically to test metal toxicity to SRB (R . K . Sani, G . Geesey, and B . M . Peyton, Adv . Environ . Res . 5:269-276, 2001) . The effects of Cu(II) toxicity were observed in terms of inhibition in total cell protein, longer lag times, lower specific growth rates, and in some cases no measurable growth . At only 6 microM, Cu(II) reduced the maximum specific growth rate by 25% and the final cell protein concentration by 18% compared to the copper-free control . Inhibition by Cu(II) of cell yield and maximum specific growth rate increased with increasing concentrations . The Cu(II) concentration causing 50% inhibition in final cell protein was evaluated to be 16 microM . A Cu(II) concentration of 13.3 microM showed 50% inhibition in maximum specific growth rate . These results clearly show significant Cu(II) toxicity to SRB at concentrations that are 100 times lower than previously reported . No measurable growth was observed at 30 microM Cu(II) even after a prolonged incubation of 384 h . In contrast, Zn(II) and Pb(II), at 16 and 5 microM, increased lag times by 48 and 72 h, respectively, but yielded final cell protein concentrations equivalent to those of the zinc- and lead-free controls . Live/dead staining, based on membrane integrity, indicated that while Cu(II), Zn(II), and Pb(II) inhibited growth, these metals did not cause a loss of D . desulfuricans membrane integrity . The results show that D . desulfuricans in the presence of Cu(II) follows a growth pattern clearly different from the pattern followed in the presence of Zn(II) or Pb(II) . It is therefore likely that Cu(II) toxicity proceeds by a mechanism different from that of Zn(II) or Pb(II) toxicity. Appl Environ Microbiol, 2001 Oct, 67(10), 4694 - 700 Response of the endophytic diazotroph Gluconacetobacter diazotrophicus on solid media to changes in atmospheric partial O(2) pressure; Pan B et al.; Gluconacetobacter diazotrophicus is an N(2)-fixing endophyte isolated from sugarcane . G . diazotrophicus was grown on solid medium at atmospheric partial O(2) pressures (pO(2)) of 10, 20, and 30 kPa for 5 to 6 days . Using a flowthrough gas exchange system, nitrogenase activity and respiration rate were then measured at a range of atmospheric pO(2) (5 to 60 kPa) . Nitrogenase activity was measured by H(2) evolution in N(2)-O(2) and in Ar-O(2), and respiration rate was measured by CO(2) evolution in N(2)-O(2) . To validate the use of H(2) production as an assay for nitrogenase activity, a non-N(2)-fixing (Nif(-)) mutant of G . diazotrophicus was tested and found to have a low rate of uptake hydrogenase (Hup(+)) activity (0.016 +/- 0.009 micromol of H(2) 10(10) cells(-1) h(-1)) when incubated in an atmosphere enriched in H(2) . However, Hup(+) activity was not detectable under the normal assay conditions used in our experiments . G . diazotrophicus fixed nitrogen at all atmospheric pO(2) tested . However, when the assay atmospheric pO(2) was below the level at which the colonies had been grown, nitrogenase activity was decreased . Optimal atmospheric pO(2) for nitrogenase activity was 0 to 20 kPa above the pO(2) at which the bacteria had been grown . As atmospheric pO(2) was increased in 10-kPa steps to the highest levels (40 to 60 kPa), nitrogenase activity decreased in a stepwise manner . Despite the decrease in nitrogenase activity as atmospheric pO(2) was increased, respiration rate increased marginally . A large single-step increase in atmospheric pO(2) from 20 to 60 kPa caused a rapid 84% decrease in nitrogenase activity . However, upon returning to 20 kPa of O(2), 80% of nitrogenase activity was recovered within 10 min, indicating a "switch-off/switch-on" O(2) protection mechanism of nitrogenase activity . Our study demonstrates that colonies of G . diazotrophicus can fix N(2) at a wide range of atmospheric pO(2) and can adapt to maintain nitrogenase activity in response to both long-term and short-term changes in atmospheric pO(2). BMC Microbiol . 2001;1(1):19 . Epub 2001 Aug 31. amiA is a negative regulator of acetamidase expression in Mycobacterium smegmatis; Parish T et al.; BACKGROUND: The acetamidase of Mycobacterium smegmatis is a highly inducible enzyme . Expression of this enzyme is increased 100-fold when the substrate acetamide is present . The acetamidase gene is found immediately downstream of three open reading frames . Two of these are proposed to be involved in regulation . RESULTS: We constructed a deletion mutant in one of the upstream ORFs (amiA) . This mutant (Mad1) showed a constitutively high level of acetamidase expression . We identified four promoters in the upstream region using a beta-galactosidase reporter gene . One of these (P2) was inducible in the wild-type, but was constitutively active in Mad1 . CONCLUSIONS: These results demonstrate that amiA encodes a negative regulatory protein which interacts with P2 . Since amiA has homology to DNA-binding proteins, it is likely that it exerts the regulatory effect by binding to the promoter to prevent transcription. Protein Expr Purif, 2001 Oct, 23(1), 22 - 32 Formation of soluble inclusion bodies by hpv e6 oncoprotein fused to maltose-binding protein; Nomine Y et al.; Many polypeptides overexpressed in bacteria are produced misfolded and accumulate as solid structures called inclusion bodies . Inclusion-body-prone proteins have often been reported to escape precipitation when fused to maltose-binding protein (MBP) . Here, we have examined the case of HPV 16 oncoprotein E6 . The unfused sequence of E6 is overexpressed as inclusion bodies in bacteria . By contrast, fusions of E6 to the C-terminus of MBP are produced soluble . We have analyzed preparations of soluble MBP-E6 fusions by using three independent approaches: dynamic light scattering, lateral turbidimetry, and sandwich ELISA . All three methods showed that MBP-E6 preparations contain highly aggregated material . The behavior of these soluble aggregates under denaturating conditions suggests that they are formed by agglomeration of misfolded E6 moieties . However, precipitation is prevented by the presence of the folded and highly soluble MBP moieties, which maintain the aggregates in solution . Therefore, the fact that a protein or protein domain is produced soluble when fused to the C-terminus of a carrier protein does not guarantee that the protein of interest is properly folded and active . We suggest that aggregation of fusion proteins should be systematically assayed, especially when these fusions are to be used for binding measurements or activity tests . Biotechniques, 2001 Sep, 31(3), 541 - 5 Development of a new epitope tag recognized by a monoclonal antibody to Rickettsia typhi; Lee JR et al.; The epitope recognized by a mouse monoclonal antibody (MAb) to the crystalline surface layer protein of Rickettsia typhi, SRT10, was mapped to 10 amino acid residues (SRTag TFIGAIATDT) . The oligonucleotide sequence covering the epitope recognized by SRT10 was inserted into a mammalian expression vector together with multiple cloning sites . When the SRTag was fused in frame to the coding region of the NCC27/CLIC1 gene and expressed in mammalian cells, the MAb SRT10 could detect the tagged protein by immunoblotting, immunocytochemistry, and immunoprecipitation . In addition to the SRT-NCC27/CLIC1, SRT10 could detect N-terminal-tagged MEF2D and C-terminal-tagged CD4 by immunocytochemistry . We suggest that this specific recognition of the SRTag by SRT10 is generally applicable to cellular and molecular biology research that requires the expression and detection of fusion proteins. C R Acad Sci III, 2001 Oct, 324(10), 929 - 33 {Discovery of the first virus, the tobacco mosaic virus: 1892 or 1898?}; Lecoq H; Two scientists contributed to the discovery of the first virus, Tobacco mosaic virus . Ivanoski reported in 1892 that extracts from infected leaves were still infectious after filtration through a Chamberland filter-candle . Bacteria are retained by such filters, a new world was discovered: filterable pathogens . However, Ivanovski probably did not grasp the full meaning of his discovery . Beijerinck, in 1898, was the first to call 'virus', the incitant of the tobacco mosaic . He showed that the incitant was able to migrate in an agar gel, therefore being an infectious soluble agent, or a 'contagium vivum fluidum' and definitively not a 'contagium fixum' as would be a bacteria . Ivanovski and Beijerinck brought unequal but decisive and complementary contributions to the discovery of viruses . Since then, discoveries made on Tobacco mosaic virus have stood out as milestones of virology history. Biofactors, 2001, 14(1-4), 87 - 92 Evolution of selenocysteine-containing proteins: significance of identification and functional characterization of selenoproteins; Gladyshev VN et al.; In the genetic code, UGA serves as either a signal for termination or a codon for selenocysteine (Sec) . Sec rarely occurs in protein and is different from other amino acids in that much of the biosynthetic machinery governing its incorporation into protein is unique to this amino acid . Sec-containing proteins have diverse functions and lack a common amino acid motif or consensus sequence . Sec has previously been considered to be a relic of the primordial genetic code that was counter-selected by the presence of oxygen in the atmosphere . In the present report, it is proposed that Sec was added to the already existing genetic code and its use has accumulated during evolution of eukaryotes culminating in vertebrates . The more recently evolved selenoproteins appear to take advantage of unique redox properties of Sec that are superior to those of Cys for specific biological functions . Further understanding of the evolution of selenoproteins as well as biological properties and biomedical applications of the trace element selenium requires identification and functional characterization of all mammalian selenoproteins. Biofactors, 2001, 14(1-4), 75 - 83 Selenoprotein synthesis in archaea; Rother M et al.; The availability of the genome sequences from several archaea has facilitated the identification of the encoded selenoproteins and also of most of the components of the machinery for selenocysteine biosynthesis and insertion . Until now, selenoproteins have been identified solely in species of the genera Methanococcus (M.) and Methanopyrus . Apart from selenophosphate synthetase, they include only enzymes with a function in energy metabolism . Like in bacteria and eukarya, selenocysteine insertion is directed by a UGA codon in the mRNA and involves the action of a specific tRNA and of selenophosphate as the selenium donor . Major differences to the bacterial system, however, are that no homolog for the bacterial selenocysteine synthase was found and, especially, that the SECIS element of the mRNA is positioned in the 3' nontranslated region . The characterisation of a homolog for the bacterial SelB protein showed that it does not bind to the SECIS element necessitating the activity of at least a second protein . The use of the genetic system of M . maripaludis allowed the heterologous expression of a selenoprotein gene from M . jannaschii and will facilitate the elucidation of the mechanism of the selenocysteine insertion process in the future. J Bacteriol, 2001 Oct, 183(20), 6135 - 9 Glycerol 3-phosphate inhibits swarming and aggregation of Myxococcus xanthus; Moraleda-Munoz A et al.; We have cloned a gene of Myxococcus xanthus with similarities to the permease for glycerol 3-phosphate (G3P) of other bacteria . Expression of the gene increased significantly during the first hours of starvation . Swarming of the wild-type strain was inhibited and aggregation was delayed by G3P . Conversely, a DeltaglpT strain aggregated even on rich medium . These results indicate that G3P may function to regulate the timing of aggregation in M . xanthus. J Bacteriol, 2001 Oct, 183(20), 6119 - 25 The alternative sigma factor SigH regulates major components of oxidative and heat stress responses in Mycobacterium tuberculosis; Raman S et al.; Mycobacterium tuberculosis is a specialized intracellular pathogen that must regulate gene expression to overcome stresses produced by host defenses during infection . SigH is an alternative sigma factor that we have previously shown plays a role in the response to stress of the saprophyte Mycobacterium smegmatis . In this work we investigated the role of sigH in the M . tuberculosis response to heat and oxidative stress . We determined that a M . tuberculosis sigH mutant is more susceptible to oxidative stresses and that the inducible expression of the thioredoxin reductase/thioredoxin genes trxB2/trxC and a gene of unknown function, Rv2466c, is regulated by sigH via expression from promoters directly recognized by SigH . We also determined that the sigH mutant is more susceptible to heat stress and that inducible expression of the heat shock genes dnaK and clpB is positively regulated by sigH . The induction of these heat shock gene promoters but not of other SigH-dependent promoters was markedly greater in response to heat versus oxidative stress, consistent with their additional regulation by a heat-labile repressor . To further understand the role of sigH in the M . tuberculosis stress response, we investigated the regulation of the stress-responsive sigma factor genes sigE and sigB . We determined that inducible expression of sigE is regulated by sigH and that basal and inducible expression of sigB is dependent on sigE and sigH . These data indicate that sigH plays a central role in a network that regulates heat and oxidative-stress responses that are likely to be important in M . tuberculosis pathogenesis. J Bacteriol, 2001 Oct, 183(20), 5997 - 6008 Recombination in the ompA gene but not the omcB gene of Chlamydia contributes to serovar-specific differences in tissue tropism, immune surveillance, and persistence of the organism; Millman KL et al.; Sequences of the major outer membrane protein (MOMP) gene (ompA) and the outer membrane complex B protein gene (omcB) from Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci were analyzed for evidence of intragenic recombination and for linkage equilibrium . The Sawyer runs test, compatibility matrices, and index of association analyses provided substantial evidence that there has been a history of intragenic recombination at ompA including one instance of interspecies recombination between the C . trachomatis mouse pneumonitis strain and the C . pneumoniae horse N16 strain . Although none of these methods detected intragenic recombination within omcB, differences in divergence reported in earlier studies suggested that there has been intergenic recombination involving omcB, and the analyses presented in this study are consistent with this . For C . trachomatis, index-of-association analyses suggested a higher degree of recombination for C class than for B class strains and a higher degree of recombination in the downstream half of ompA . In concordance with these findings, many significant breakpoints were found in variable segments 3 and 4 of MOMP for the recombinant strains D/B120, G/UW-57, E/Bour, and LGV-98 identified in this study . We provide examples of how genetic diversity generated by repeated recombination in these regions may be associated with evasion of immune surveillance, serovar-specific differences in tissue tropism, and persistence. Biophys J, 2001 Oct, 81(4), 2395 - 402 Reliable and global measurement of fluorescence resonance energy transfer using fluorescence microscopes; Xia Z et al.; Green fluorescence protein (GFP)-based fluorescence resonance energy transfer (FRET) is increasingly used in investigation of inter- and intramolecular interactions in living cells . In this report, we present a modified method for FRET quantification in cultured cells using conventional fluorescence microscopy . To reliably measure FRET, three positive control constructs in which a cyan fluorescence protein and a yellow fluorescence protein were linked by peptides of 15, 24, or 37 amino acid residues were prepared . FRET was detected using a spectrofluorometer, a laser scanning confocal microscope, and an inverted fluorescence microscope . Three calculation methods for FRET quantification using fluorescence microscopes were compared . By normalization against expression levels of GFP fusion proteins, the modified method gave consistent FRET values that could be compared among different cells with varying protein expression levels . Whole-cell global analysis using this method allowed FRET measurement with high spatial resolutions . Using such a procedure, the interaction of synaptic proteins syntaxin and the synaptosomal associated protein of 25 kDa (SNAP-25) was examined in PC12 cells, which showed strong FRET on plasma membranes . These results demonstrate the effectiveness of the modified method for FRET measurement in live cell systems. Biophys J, 2001 Oct, 81(4), 2314 - 9 Early photocycle kinetic behavior of the E46A and Y42F mutants of photoactive yellow protein: femtosecond spectroscopy; Devanathan S et al.; In the photoactive yellow protein, PYP, both Glu46 and Tyr42 form hydrogen bonds to the phenolic OH group of the p-hydroxycinnamoyl chromophore . Previous work on replacement of the carboxyl group of Glu46 by an amide group (Glu46Gln) has shown that changing the nature of this hydrogen bond has a minimal effect on the rate constant for the formation of the first intermediate (I(0)) and on the excited state lifetime, whereas the rate constants for the formation of the second (I(0)( not equal)) and third (I(1)) intermediates were increased by factors of approximately 30 and 5, respectively . In the present experiments, two additional mutants (Glu46Ala and Tyr42Phe) have been studied . These two mutants are shown to behave kinetically very similarly to one another . In both cases, the rate constant for I(0) formation is decreased by a factor of approximately 2, with little or no effect on the photochemical yield as a consequence of a compensating increase in the excited state lifetime . Although we are unable to resolve the rate constant for the formation of the second intermediate from that of the first intermediate, the rate constant for the formation of the third intermediate is increased by a factor of approximately 100 . The structural implications of these results are discussed. Biophys J, 2001 Oct, 81(4), 2082 - 99 Two-dimensional kinetic analysis suggests nonsequential gating of mechanosensitive channels in Xenopus oocytes; Gil Z et al.; Xenopus oocytes express mechanosensitive (MS(XO)) channels that can be studied in excised patches of membrane with the patch-clamp technique . This study examines the steady-state kinetic gating properties of MS(XO) channels using detailed single-channel analysis . The open and closed one-dimensional dwell-time distributions were described by the sums of 2-3 open and 5-7 closed exponential components, respectively, indicating that the channels enter at least 2-3 open and 5-7 closed kinetic states during gating . Dependency plots revealed that the durations of adjacent open and closed intervals were correlated, indicating two or more gateway states in the gating mechanism for MS channels . Maximum likelihood fitting of two-dimensional dwell-time distributions to both generic and specific models was used to examine gating mechanism and rank models . A kinetic scheme with five closed and five open states, in which each closed state could make a direct transition to an open state (two-tiered model) could account for the major features of the single-channel data . Two-tiered models that allowed direct transitions to subconductance open states in addition to the fully open state were also consistent with multiple gateway states . Thus, the gating mechanism of MS(XO) channels differs from the sequential (linear) gating mechanisms considered for MS channels in bacteria, chick skeletal muscle, and Necturus proximal tubule. J Hazard Mater, 2001 Oct 12, 87(1-3), 11 - 21 Toxic effect of sulfur compounds on anaerobic biogranule; Lin CY et al.; The effects of sulfide, sulfite and sulfate on degradation of volatile fatty acid (VFA) in UASB process have been studied by using serum bottle assay and septage-leachate acclimated biogranules . The relative toxicity of the compounds towards methane production and degradation of total VFA varied as SO(4)(2-) -S>S(2-)>SO(3)(2-) -S and SO(4)(2-) -S>SO(3)(2-) -S>S(2-), respectively . The difference of this order shows the importance of choosing monitoring factor in evaluating the effect of sulfur compounds on a UASB system . For the individual VFA the effects of sulfur compounds depended on the types of VFA . The VFA-degrading activity of anaerobic biogranules was decreased by 50% when 34, 26 and 20mg of S(2-), SO(3)(2-) -S and SO(4)(2-) -S were added to each gram of biomass, respectively . A comparison of the toxicity-resistance between two different anaerobic biogranules that acclimatized with septage-leachate mixture and septage was also made.In the presence of the leachate, the toxicity-resistance of biogranules was not weakened to sulfide and sulfate but was enhanced to sulfite. J Biotechnol, 2001 Oct 4, 91(2-3), 127 - 41 Evaluation of plant growth promoting and colonization ability of endophytic diazotrophs from deep water rice; Verma SC et al.; A study of the diversity of endophytic bacteria present in seeds of a deepwater rice variety revealed the presence of seven types of BOX-PCR fingerprints . In order to evaluate the plant growth promoting potential the presence of nitrogenase, indole acetic acid production and mineral phosphate solubilization were estimated in the representative BOX-PCR types . The seven representatives of BOX-PCR types produced indole acetic acid, reduced acetylene and showed specific immunological cross-reaction with anti-dinitrogenase reductase antibody . Only four types showed mineral phosphate solubilizing ability . Comparison of cellulase and pectinase activities showed differences among different BOX-PCR types . PCR fingerprinting data showed that one strain isolated from the surface sterilized seeds as well as the aerial parts of the seedlings of rice variety showed low cellulase and pectinase but relatively high ARA . On the basis of 16S rDNA nucleotide sequence and BIOLOG system of bacterial identification, this strain was identified as Pantoea agglomerans . For studying the endophytic colonization this strain was genetically tagged with the reporter gene, gusA . Histochemical analysis of the seedling grown in hydroponics showed that the tagged strain colonized the root surface, root hairs, root cap, points of lateral root emergence, root cortex and the stelar region . Treatment of the roots with 2,4-D produced short thickened lateral roots which showed better colonization by P . agglomerans. Clin Chim Acta, 2001 Sep 25, 311(2), 119 - 23 Increased serum amylase and lipase in fructose malabsorbers; Ledochowski M et al.; BACKGROUND: Fructose malabsorption is frequently seen in the general population and is characterised by the inability to absorb fructose efficiently . Due to fructose malabsorption, fructose reaches the colon where it is broken down by bacteria to short fatty acids, CO(2) and H(2) . Bloating, cramps, osmotic diarrhea and other symptoms of irritable bowel syndrome are the consequence . We recently found that fructose malabsorption is associated with low plasma folic acid concentrations and low serum tryptophan and zinc . Because fructose malabsorption apparently is associated not only with malabsorption of other nutrients, but also with abdominal discomfort, it was of interest to examine whether mild pancreatitis may be involved . METHODS: We retrospectively examined our data in 159 otherwise healthy adults (110 females, 49 males) aged 14-84 years (mean 45.6+/-14.4 S.D.) with gastrointestinal complaints for serum amylase and serum lipase concentrations . The patients have been tested earlier for fructose malabsorption and lactose maldigestion by measuring breath H(2) concentrations after an oral dose of 25 g fructose and 50 g lactose, respectively, 1 week apart . RESULTS: Fructose malabsorption (H(2) concentrations > or =20 ppm over baseline values) was detected in 107 of 159 individuals (67.3%) . These subjects with fructose malabsorption presented with significantly higher serum amylase concentrations (73.1 U/l+/-25.7 S.D.) compared to individuals with normal fructose absorption (59.6 U/l+17.9 S.D; p=0.0009) . Fructose malabsorbers also presented with higher serum lipase concentrations (122.0 U/l+/-100.3 S.D.) compared to normals (89.5 U/l+/-46.5 S.D.; p<0.05) . To determine whether this finding is a consequence of any sort of malabsorption syndrome or whether it is specific for fructose malabsorption, all subjects were screened for lactose maldigestion . Lactose maldigestion (H(2) concentrations>20 ppm over baseline after lactose loading) was found in 50 of 159 individuals (31.4%) . There were no significant differences in either amylase or lipase concentrations in lactose maldigestors . CONCLUSION: Serum amylase and lipase concentrations are higher in subjects with fructose malabsorption compared to normals . Therefore, fructose malabsorption should be considered as a differential diagnosis in moderately elevated serum amylase. Arch Biochem Biophys, 2001 Oct 1, 394(1), 76 - 86 A role for rubredoxin in oxidative stress protection in Desulfovibrio vulgaris: catalytic electron transfer to rubrerythrin and two-iron superoxide reductase; Coulter ED et al.; Desulfovibrio vulgaris rubredoxin, which contains a single {Fe(SCys)4} site, is shown to be a catalytically competent electron donor to two enzymes from the same organism, namely, rubrerythrin and two-iron superoxide reductase (a.k.a . rubredoxin oxidoreductase or desulfoferrodoxin) . These two enzymes have been implicated in catalytic reduction of hydrogen peroxide and superoxide, respectively, during periods of oxidative stress in D . vulgaris, but their proximal electron donors had not been characterized . We further demonstrate the incorrectness of a previous report that rubredoxin is not an electron donor to the superoxide reductase and describe convenient assays for demonstrating the catalytic competence of all three proteins in their respective functions . Rubrerythrin is shown to be an efficient rubredoxin peroxidase in which the rubedoxin:hydrogen peroxide redox stoichiometry is 2:1 mol:mol . Using spinach ferredoxin-NADP+ oxidoreductase (FNR) as an artificial, but proficient, NADPH:rubredoxin reductase, rubredoxin was further found to catalyze rapid and complete reduction of all Fe3+ to Fe2+ in rubrerythrin by NADPH under anaerobic conditions . The combined system, FNR/rubredoxin/rubrerythrin, was shown to function as a catalytically competent NADPH peroxidase . Another small rubredoxin-like D . vulgaris protein, Rdl, could not substitute for rubredoxin as a peroxidase substrate of rubrerythrin . Similarly, D . vulgaris rubredoxin was demonstrated to efficiently catalyze reduction of D . vulgaris two-iron superoxide reductase and, when combined with FNR, to function as an NADPH:superoxide oxidoreductase . We suggest that, during periods of oxidative stress, rubredoxin could divert electron flow from the electron transport chain of D . vulgaris to rubrerythrin and superoxide reductase, thereby simultaneously protecting autoxidizable redox enzymes and lowering intracellular hydrogen peroxide and superoxide levels . Biochem Biophys Res Commun, 2001 Sep 28, 287(3), 789 - 800 Differences in HAC1 mRNA processing and translation between yeast and mammalian cells indicate divergence of the eukaryotic ER stress response; Bowring CE et al.; Perturbation of normal endoplasmic reticulum (ER) function induces a stress response found throughout eukaryotes, sometimes termed the unfolded protein response (UPR) . In yeast, auxotrophic mutants have identified two genes, IRE1 and HAC1, whose products are key components . Normally HAC1 mRNA is not translated owing to a 252-nt "intron." Disruption of ER function activates Ire1p to remove this intron through endogenous endoribonuclease activity . Together with tRNA ligase, cleavage and splicing produces a translatable HAC1 mRNA to give Hac1p, a transcription factor that upregulates the expression of genes responsive to ER stress . No Hac1p homologue has been identified in mammalian cells, but Ire1p homologues exist with endoribonuclease activity required for a fully functional UPR, raising the possibility that the key features of the yeast UPR might be conserved in higher eukaryotic cells . To address this, we expressed yeast HAC1 in HeLa and HEK 293T human cell lines, both on its own and as fusions with yellow fluorescent protein (YFP) to investigate its processing and translation . HAC1 mRNA was not processed, but efficiently translated irrespective of whether the cells were subjected to ER stress . Expression of exogenous HAC1 mRNA constructs in yeast showed UPR-induced splicing required the presence of its 3' UTR . These results suggest that the mammalian ER stress response has diverged from the yeast UPR . Water Environ Res, 2001 Mar-Apr, 73(2), 223 - 32 pH as a key factor in the competition between glycogen-accumulating organisms and phosphorus-accumulating organisms; Filipe CD et al.; The effects of pH on the anaerobic metabolism of glycogen-accumulating organisms (GAOs) and phosphorus-accumulating organisms (PAOs) were compared using models for the kinetics of acetate uptake . The comparison revealed that GAOs take up acetate faster than PAOs when the pH of the anaerobic zone is less than 7.25, but that PAOs remove acetate faster than GAOs at pHs greater than 7.5 . It was also found that the growth efficiencies of the two organisms are similar . Furthermore, the amount of polyhydroxy-alkanoates available after replenishment of the polymers used during acetate uptake under anaerobic conditions is similar for the two organisms, making GAOs highly competitive in nutrient removal systems . The effects of pH on the competition between the two organisms were demonstrated during the operation of a laboratory-scale sequencing batch reactor . When the overall pH of the system was low, poor phosphate removal was observed . When the pH of the system was allowed to increase to a maximum of 7.5, phosphate removal improved, but was still incomplete . Total removal was only achieved when the pH of the system was never allowed to drop lower than 7.25 . After the minimum pH in the system was increased, total removal of phosphate was achieved in 14 days . The results showed that pH control is a promising strategy for minimizing the accumulation of GAOs and increasing the reliability of biological excess phosphorus removal systems. Water Environ Res, 2001 Mar-Apr, 73(2), 213 - 22 Effects of pH on the rates of aerobic metabolism of phosphate-accumulating and glycogen-accumulating organisms; Filipe CD et al.; The effect of pH on the aerobic metabolism of phosphorus-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) was studied using aerobic batch experiments performed at pH 6.5, 7.0, and 7.5 . For PAOs, the rates of phosphate uptake, polyhydroxy-alkanoates consumption, and biomass growth observed at pH 6.5 were 42, 70, and 53%, respectively, of the rates observed at pH 7.0 . In contrast, the rates for GAOs were relatively independent of pH for the range tested . The results suggest that the stability of biological excess phosphorus removal (BEPR) is strongly dependent on the pH in the aerobic zone . If the pH is low, growth of PAOs will be inhibited whereas the growth of GAOs will be only mildly affected . This may lead to the proliferation of GAOs in BEPR systems, resulting in reduced phosphorus removal. Water Environ Res, 2001 Mar-Apr, 73(2), 154 - 64 Ammonia inhibition in the anaerobic treatment of fishery effluents; Aspe E et al.; Inhibition of the organic matter consumption rate of a saline and rich proteic effluent by free ammonia was assessed in anaerobic filters at 37 degrees C . Inhibition of substrate (total organic carbon, TOC) consumption rate by ammonia was fitted by the Luong and noncompetitive models . Calculated kinetic parameters using the Luong model were maximum specific growth rate, micromax = 0.28 day(-1); average saturation constant, Ks = 568 mg TOC/L; Luong inhibition parameter, KNH3 = 1707mg ammonia-nitrogen (NH3-N)/L; and Luong exponent, gamma = 0.283 and the noncompetitive calculated parameters were umax= 0.26 day(-1), Ks = 703 mg TOC/L, and inhibition parameter, INH3 = 325 mg NH3-N/L . The Luong and noncompetitive models predicted 50% inhibition of the substrate consumption rate at ammonia concentrations of 147 and 325 mg NH3-N/L, respectively, suggesting biomass adaptation to the ammonia concentration (80 mg NH3-N/L as average) at which the anaerobic filters were previously operating . Ammonia formation by anaerobic digestion of fishing effluent would produce a maximum of 65.1 and 58.6% inhibition of the efficiency, predicted by the Luong and noncompetitive models, respectively . Ammonia influence on the digestion steps was determined by comparing fishing effluent with volatile fatty acids as substrates . The noncompetitive model predicted a 50% inhibition of methane production rate at ammonia concentrations of 196.6 and 188.6 mg NH3-N/L for fishing effluent and volatile fatty acids, respectively, suggesting that the methanogenic step is the one most affected by ammonia. Int J Parasitol, 2001 Sep, 31(11), 1166 - 76 Inhibition of apoptosis by intracellular protozoan parasites; Heussler VT et al.; Protozoan parasites which reside inside a host cell avoid direct destruction by the immune system of the host . The infected cell, however, still has the capacity to counteract the invasive pathogen by initiating its own death, a process which is called programmed cell death or apoptosis . Apoptotic cells are recognised and phagocytosed by macrophages and the parasite is potentially eliminated together with the infected cell . This potent defence mechanism of the host cell puts strong selective pressure on the parasites which have, in turn, evolved strategies to modulate the apoptotic program of the host cell to their favour . Within the last decade, the existence of cellular signalling pathways which inhibit the apoptotic machinery has been demonstrated . It is not surprising that intracellular pathogens subvert these pathways to ensure their own survival in the infected cell . Molecular mechanisms which interfere with apoptotic pathways have been studied extensively for viruses and parasitic bacteria, but protozoan parasites have come into focus only recently . Intracellular protozoan parasites which have been reported to inhibit the apoptotic program of the host cell, are Toxoplasma gondii, Trypanosoma cruzi, Leishmania sp., Theileria sp., Cryptosporidium parvum, and the microsporidian Nosema algerae . Although these parasites differ in their mechanism of host cell entry and in their final intracellular localisation, they might activate similar pathways in their host cells to inhibit apoptosis . In this respect, two families of molecules, which are known for their capacity to interrupt the apoptotic program, are currently discussed in the literature . First, the expression of heat shock proteins is often induced upon parasite infection and can directly interfere with molecules of the cellular death machinery . Secondly, a more indirect effect is attributed to the parasite-dependent activation of NF-kappaB, a transcription factor that regulates the transcription of anti-apoptotic molecules. Mem Inst Oswaldo Cruz, 2001 Aug, 96(6), 865 - 73 A new continuous cell line from the mosquito Psorophora confinnis (Diptera: Culicidae) and its susceptibility to infections with some arboviruses; Bello FJ et al.; A new cell line, PC-0199-BR, was established from embryonated eggs of the mosquito Psorophora confinnis . To date (September 2000) it has had 62 continuous passages . This is the first report of a cell line of mosquitoes belonging to the genus Psorophora . Cell growth initially was achieved in the MM/VP12 medium, supplemented with 20% fetal bovine serum; however, the subcultures were later adapted to Grace's medium with 10% fetal bovine serum . Cell morphology in the primary cultures was heterogeneous; but later in the established cell line, the predominant cell type was epithelioid . Cultured cells were predominantly diploid (2n=6); however, chromosome abnormalities were observed in a small proportion of the cells in later passages . C and G band patterns were also determined in the karyotype . The cell line isozyme profiles coincided with pupae and adult samples of the species taken from the same colony . A preliminary arbovirus susceptibility study for the cell line was undertaken . No evidence was observed of contamination of the cell line with bacteria, fungi or mycoplasma. J Biol Chem, 2001 Nov 16, 276(46), 43152 - 9 Epub 2001 Sep 18. Structural determinants of Ca2+ transport in the Arabidopsis H+/Ca2+ antiporter CAX1; Shigaki T et al.; Ca(2+) levels in plants, fungi, and bacteria are controlled in part by H(+)/Ca(2+) exchangers; however, the relationship between primary sequence and biological activity of these transporters has not been reported . The Arabidopsis H(+)/cation exchangers, CAX1 and CAX2, were identified by their ability to suppress yeast mutants defective in vacuolar Ca(2+) transport . CAX1 has a much higher capacity for Ca(2+) transport than CAX2 . An Arabidopsis thaliana homolog of CAX1, CAX3, is 77% identical (93% similar) and, when expressed in yeast, localized to the vacuole but did not suppress yeast mutants defective in vacuolar Ca(2+) transport . Chimeric constructs and site-directed mutagenesis showed that CAX3 could suppress yeast vacuolar Ca(2+) transport mutants if a nine-amino acid region of CAX1 was inserted into CAX3 (CAX3-9) . Biochemical analysis in yeast showed CAX3-9 had 36% of the H(+)/Ca(2+) exchange activity as compared with CAX1; however, CAX3-9 and CAX1 appear to differ in their transport of other ions . Exchanging the nine-amino acid region of CAX1 into CAX2 doubled yeast vacuolar Ca(2+) transport but did not appear to alter the transport of other ions . This nine-amino acid region is highly variable among the plant CAX-like transporters . These findings suggest that this region is involved in CAX-mediated Ca(2+) specificity. Curr Pharm Des, 2001 Nov, 7(17), 1839 - 62 Peptide-nucleic acids (PNAs): a tool for the development of gene expression modifiers; Gambari R; Peptide nucleic acids (PNAs) represent nucleic acid analogues with unique biochemical properties and of great interest for the development of therapeutic agents . The firstly designed and tested PNAs are molecules in which the sugar-phosphate backbone of DNA was replaced with a pseudopeptide chain constituted by N-(2-aminoethyl) glycine monomers . Nucleobases can be linked to this backbone through a carboxymethyl moiety, which allows to maintain a two atom spacer between the backbone and the bases . Since the first reports on PNAs based on N-(2-aminoethyl) glycine backbone, other PNA analogues have been synthesized, with the main purpose of improve biological activities as well as stability and efficient delivery to target cells . Of great interest are chiral PNAs, PNA analogues bearing phosphate groups (PHONA), PNA-DNA and PNA-peptide chimeras, PNA linked to non-peptide vectors . PNAs hybridize to DNA and RNA with high efficiency following the Watson-Crick hybridization rules, forming highly stable PNA/DNA and PNA/RNA duplexes . In addition, homopyrimidine PNAs, as well as PNAs containing a high pyrimidine:purine ratio, are able to bind to DNA or RNA forming highly stable (PNA)(2)-DNA triple helices . Accordingly, therapeutic PNA and PNA analogues could act as antigene as well as antisense molecules . In addition, recent studies provide evidences for the possible use of PNA-based therapeutic molecules as artificial promoters, as decoy or ribozyme facilitator . Among the therapeutic applications of PNA-based molecules, the most pomising include anti-cancer and anti-viral experimental strategies, but activity of PNAs against bacteria and medically important parasitic organisms have been also reported. Biochemistry, 2001 Sep 25, 40(38), 11472 - 82 Pigment organization and their interactions in reaction centers of photosystem II: optical spectroscopy at 6 K of reaction centers with modified pheophytin composition; Germano M et al.; Photosystem II reaction centers (RC) with selectively exchanged pheophytin (Pheo) molecules as described in {Germano, M., Shkuropatov, A . Ya., Permentier, H., Khatypov, R . A., Shuvalov, V . A., Hoff, A . J., and van Gorkom, H . J . (2000) Photosynth . Res . 64, 189-198} were studied by low-temperature absorption, linear and circular dichroism, and triplet-minus-singlet absorption-difference spectroscopy . The ratio of extinction coefficients epsilon(Pheo)/epsilon(Chl) for Q(Y) absorption in the RC is approximately 0.40 at 6 K and approximately 0.45 at room temperature . The presence of 2 beta-carotenes, one parallel and one perpendicular to the membrane plane, is confirmed . Absorption at 670 nm is due to the perpendicular Q(Y) transitions of the two peripheral chlorophylls (Chl) and not to either Pheo . The "core" pigments, two Pheo and four Chl absorb in the 676-685 nm range . Delocalized excited states as predicted by the "multimer model" are seen in the active branch . The inactive Pheo and the nearby Chl, however, mainly contribute localized transitions at 676 and 680 nm, respectively, although large CD changes indicate that exciton interactions are present on both branches . Replacement of the active Pheo prevents triplet formation, causes an LD increase at 676 and 681 nm, a blue-shift of 680 nm absorbance, and a bleach of the 685 nm exciton band . The triplet state is mainly localized on the Chl corresponding to B(A) in purple bacteria . Both Pheo Q(Y) transitions are oriented out of the membrane plane . Their Q(X) transitions are parallel to that plane, so that the Pheos in PSII are structurally similar to their homologues in purple bacteria. Biochemistry, 2001 Sep 25, 40(38), 11460 - 71 Light-induced proton release and proton uptake reactions in the cyanobacterial phytochrome Cph1; van Thor JJ et al.; The P(r) to P(fr) transition of recombinant Synechocystis PCC 6803 phytochrome Cph1 and its N-terminal sensor domain Cph1Delta2 is accompanied by net acidification in unbuffered solution . The extent of this net photoreversible proton release was measured with a conventional pH electrode and increased from less than 0.1 proton released per P(fr) formed at pH 9 to between 0.6 (Cph1) and 1.1 (Cph1Delta2) H(+)/P(fr) at pH 6 . The kinetics of the proton release were monitored at pH 7 and pH 8 using flash-induced transient absorption measurements with the pH indicator dye fluorescein . Proton release occurs with time constants of approximately 4 and approximately 20 ms that were also observed in parallel measurements of the photocycle (tau(3) and tau(4)) . The number of transiently released protons per P(fr) formed is about one . This H(+) release phase is followed by a proton uptake phase of a smaller amplitude that has a time constant of approximately 270 ms (tau(5)) and is synchronous with the formation of P(fr) . The acidification observed in the P(r) to P(fr) transition with pH electrodes is the net effect of these two sequential protonation changes . Flash-induced transient absorption measurements were carried out with Cph1 and Cph1Delta2 at pH 7 and pH 8 . Global analysis indicated the presence of five kinetic components (tau(1)-tau(5): 5 and 300 micros and 3, 30, and 300 ms) . Whereas the time constants were approximately pH independent, the corresponding amplitude spectra (B(1), B(3), and B(5)) showed significant pH dependence . Measurements of the P(r)/P(fr) photoequilibrium indicated that it is pH independent in the range of 6.5-9.0 . Analysis of the pH dependence of the absorption spectra from 6.5 to 9.0 suggested that the phycocyanobilin chromophore deprotonates at alkaline pH in both P(r) and P(fr) with an approximate pK(a) of 9.5 . The protonation state of the chromophore at neutral pH is therefore the same in both P(r) and P(fr) . The light-induced deprotonation and reprotonation of Cph1 at neutral pH are thus due to pK(a) changes in the protein moiety, which are linked to conformational transitions occurring around 4 and 270 ms after photoexcitation . These transient structural changes may be relevant for signal transduction by this cyanobacterial phytochrome. Exp Parasitol, 2001 Aug, 98(4), 171 - 9 Encephalitozoon cuniculi (Microspora): characterization of a phospholipid metabolic pathway potentially linked to therapeutics; El Alaoui H et al.; Phospholipid metabolism of the microsporidian Encephalitozoon cuniculi, an obligate intracellular parasite, has been investigated . Labeled precursor incorporation experiments have shown that phosphatidylserine decarboxylase and phosphatidylethanolamine N-methyltransferase are more active in cells infected by E . cuniculi than in uninfected cells . In contrast, no difference was observed in the activity of Kennedy pathway's enzymes, the mammalian pathway . This suggests the occurrence in microsporidia of a bacteria- and fungi-typical pathway for phospholipid synthesis, which is supported by the identification of two genes implicated in this pathway, the cds gene encoding the key enzyme CDP-diacylglycerol synthase (E.C . 2.7.7.41) and the pss gene for CDP-alcohol phosphatidyltransferase . The pss gene could encode phosphatidylserine synthase (E.C . 2.7.8.8.), which catalyses the de novo synthesis of phosphatidylserine in bacteria and fungi . The complete CDP-diacylglycerol synthase messenger has been isolated and shows very short 5' and 3' untranslated regions . This is strong evidence for the functionality of a metabolic pathway which could be a potential target against microsporidia which infect humans . Biofizika, 2001 Jul-Aug, 46(4), 656 - 60 {Model of dynamics of the insect cellular immune system}; Nedorezov LV et al.; A mathematical model for the dynamics of functioning of an insect immune subsystem is considered . It is assumed that the interaction between hemocytes and bacteria corresponds to the Volterra principle of "pair interactions": the rate at which bacteria enter the system decreases in proportion to the rate of interaction of hemocytes with bacteria . In the absence of interaction, the intrinsic dynamics of bacteria is described by the Malthus law . Dynamic regimes of the model for different values of the parameters were analyzed . In particular, it was shown that, depending on the initial values of variables and the values of the parameters, there exist two regimes, the regime of death of the organism and the regime of elimination of bacteria. Water Environ Res, 2001 Jan-Feb, 73(1), 118 - 26 Biological sulfate reduction using molasses as a carbon source; Annachhatre AP et al.; The feasibility of using a laboratory-scale upflow anaerobic sludge blanket process for sulfate reduction with molasses as a carbon source was demonstrated . Competition between methane-producing bacteria (MPB) and sulfate-reducing bacteria (SRB) was influenced by the chemical oxygen demand-to-sulfur (COD:S) ratio in the feed . Sulfate removal greater than 80% could be achieved at COD:S greater than 10 when MPB predominated . Activity of MPB and SRB was inhibited at a dissolved sulfide concentration of approximately 200 mg/L . Competition between MPB and SRB was intense as the COD:S was reduced from 5 to 2 . Further reduction in the COD:S to 0.7 led to the formation of sulfidogenic granules . The COD removal decreased to approximately 30% at a COD:S less than 2 because of accumulation of sulfurous precipitates and the nonbiodegradable portion of molasses in the sludge . Reduced gas production rates further imposed limitations on diffusion of the organic substrate into granules . Sulfidogenic process operation yielded sulfate removal as great as 70% at a COD:S of approximately 3.5. Water Environ Res, 2001 Jan-Feb, 73(1), 103 - 9 Anaerobic treatment of condensates: trial at a kraft pulp and paper mill; Dufresne R et al.; The Domtar Papers pulp and paper mill in Windsor, Quebec, Canada, investigated the potential for anaerobic treatment of contaminated kraft mill condensates . The objectives of this project were to assess the technical feasibility of replacing the steam stripper with anaerobic treatment, to provide basic information for the design of an anaerobic treatment process for condensates, and to provide information on treated condensate quality for eventual reuse . The project involved extensive chemical characterization of condensates, followed by treatability tests . The tests included laboratory bench-scale tests and on-site pilot testing using direct feed from the process . Characterization showed that the organic content of the condensates was essentially methanol, as expected, but that foul evaporator condensates had high sulfide contents . It was found that undiluted foul condensates at the Windsor mill are toxic to the anaerobic biomass because of these high concentrations of sulfides . Treatment of combined condensates is possible at an approximate volumetric loading of 10 to 12 g/L.d chemical oxygen demand (COD) with good production of biogas (0.35 L/g of COD removed) and excellent methanol removal (better than 95%) . The biogas produced is of excellent fuel quality with close to 90% methane, but with a high sulfide content (close to 4%). Mikrobiologiia, 2001 Jul-Aug, 70(4), 444 - 51 {Growth of mesophilic methanotrophs at low temperatures}; Kevbrina MV et al.; The optimal growth of mesophilic methanotrophic bacteria (collection strains of the genera Methylocystis, Methylomonas, Methylosinus, and Methylobacter) occurred within temperature ranges of 31-34 degrees C and 23-25 degrees C . None of the strains studied were able to grow at 1.5 or 4 degrees C . Representatives of six methanotrophic species (strains Mcs . echinoides 2, Mm . methanica 12, Mb . bovis 89, Mcs . pyriformis 14, Mb . chroococcum 90, and Mb . vinelandii 87) could grow at 10 degrees C (with a low specific growth rate) . The results obtained suggest that some mesophilic methane-oxidizing bacteria display psychrotolerant (psychrotrophic) but not psychrophilic properties . In general, the Rosso model, which describes bacterial growth rate as a function of temperature, fits well the experimental data, although, for most methanotrophs, with symmetrical approximations for optimal temperature. Aust Fam Physician, 2001 Jul, 30(7), 681 - 4 Herbal medicine in infectious disease; Pinn G; This eighth article in the series looks at the current role of plant therapy in infection . Plant chemicals are useful for infection control and, until the advent of antibiotics (many themselves of natural origin) were the only remedies available . The current role of plants in this area could be summarised as treating minor acute infections, topical therapy for skin or wound infections and perhaps a supportive role in chronic infection . With increasing resistance of bacteria, viruses and malaria to standard therapy, alternative treatments are being re-explored with some urgency. Nature, 2001 Sep 13, 413(6852), 211 - 8 How the olfactory system makes sense of scents; Firestein S; The human nose is often considered something of a luxury, but in the rest of the animal world, from bacteria to mammals, detecting chemicals in the environment has been critical to the successful organism . An indication of the importance of olfactory systems is the significant proportion - as much as 4% - of the genomes of many higher eukaryotes that is devoted to encoding the proteins of smell . Growing interest in the detection of diverse compounds at single-molecule levels has made the olfactory system an important system for biological modelling. Nature, 2001 Sep 13, 413(6852), 128 - 9 Nitrogen fixation . Endocrine disrupters and flavonoid signalling; Fox JE et al.; Nitrogen fixation is a symbiotic process initiated by chemical signals from legumes that are recognized by soil bacteria . Here we show that some endocrine-disrupting chemicals (EDCs), so called because of their effect on hormone-signalling pathways in animal cells, also interfere with the symbiotic signalling that leads to nitrogen fixation . Our results raise the possibility that these phytochemically activated pathways may have features in common with hormonal signalling in vertebrates, thereby extending the biological and ecological impact of EDCs. Science, 2001 Oct 26, 294(5543), 818 - 23 Epub 2001 Sep 13. Biogeography and ecological setting of Indian Ocean hydrothermal vents; Van Dover CL et al.; Within the endemic invertebrate faunas of hydrothermal vents, five biogeographic provinces are recognized . Invertebrates at two Indian Ocean vent fields (Kairei and Edmond) belong to a sixth province, despite ecological settings and invertebrate-bacterial symbioses similar to those of both western Pacific and Atlantic vents . Most organisms found at these Indian Ocean vent fields have evolutionary affinities with western Pacific vent faunas, but a shrimp that ecologically dominates Indian Ocean vents closely resembles its Mid-Atlantic counterpart . These findings contribute to a global assessment of the biogeography of chemosynthetic faunas and indicate that the Indian Ocean vent community follows asymmetric assembly rules biased toward Pacific evolutionary alliances. Mol Biol Evol, 2001 Oct, 18(10), 1919 - 28 Mitochondrial type iron-sulfur cluster assembly in the amitochondriate eukaryotes Trichomonas vaginalis and Giardia intestinalis, as indicated by the phylogeny of IscS; Tachezy J et al.; Pyridoxal-5'-phosphate-dependent cysteine desulfurase (IscS) is an essential enzyme in the assembly of FeS clusters in bacteria as well as in the mitochondria of eukaryotes . Although FeS proteins are particularly important for the energy metabolism of amitochondrial anaerobic eukaryotes, there is no information about FeS cluster formation in these organisms . We identified and sequenced two IscS homologs of Trichomonas vaginalis (TviscS-1 and TviscS-2) and one of Giardia intestinalis (GiiscS) . TviscS-1, TviscS-2, and GiiscS possess the typical conserved regions implicated in cysteine desulfurase activity . N-termini of TviscS-1 and TviscS-2 possess eight amino acid extensions, which resemble the N-terminal presequences that target proteins to hydrogenosomes in trichomonads . No presequence was evident in GiiscS from Giardia, an organism that apparently lacks hydrogenosmes or mitochondria . Phylogenetic analysis showed a close relationship among all eukaryotic IscS genes including those of amitochondriates . IscS of proteobacteria formed a sister group to the eukaryotic clade, suggesting that isc-related genes were present in the proteobacterial endosymbiotic ancestor of mitochondria and hydrogenosomes . NifS genes of nitrogen-fixing bacteria, which are IscS homologs required for specific formation of FeS clusters in nitrogenase, formed a more distant group . The phylogeny indicates the presence of a common mechanism for FeS cluster formation in mitochondriates as well as in amitochondriate eukaryotes . Furthermore, the analyses support a common origin of Trichomonas hydrogenosomes and mitochondria, as well as secondary loss of mitochondrion/hydrogenosome-like organelles in Giardia. Phytochemistry, 2001 Oct, 58(3), 441 - 9 Isolation, characterization, and systematic significance of 2-pyrone-4,6-dicarboxylic acid in Rosaceae; Wilkes S et al.; 2-Pyrone-4,6-dicarboxylic acid was isolated from Potentilla anserina . Until now this substance was only found in bacteria and not in higher plants . By sterile cultivation it was verified that this compound is genuine also in plants . In addition the systematic relevance of 2-pyrone-4,6-dicarboxylic acid within the Rosaceae was tested . The compound seems to be a chemotaxonomic marker for the Rosoideae sensu stricto proposed by Morgan et al . (Morgan, D.R., Soltis, D.E., Robertson, K.R., 1994 . Systematic and evolutionary implications of rbcL sequence variation in Rosaceae . American Journal of Botany 81, 890-903). Brain Pathol, 2001 Oct, 11(4), 452 - 64 Polymerase chain reaction as a diagnostic adjunct in herpesvirus infections of the nervous system; Kleinschmidt-DeMasters BK et al.; Polymerase chain reaction (PCR) is a powerful technique that allows detection of minute quantities of DNA or RNA in cerebrospinal fluid (CSF), vesicle and endoneurial fluids, blood, fresh-frozen, and even formalin-fixed tissues . Various infectious agents can be detected with high specificity and sensitivity, including bacteria, parasites, rickettsia and viruses . PCR analysis of CSF has revolutionized the diagnosis of nervous system viral infections, particularly those caused by human herpesviruses (HHV), and has now replaced brain biopsy as the gold standard for diagnosis of herpes simplex virus (HSV) encephalitis . PCR analysis of both CSF and nervous system tissues has also broadened our understanding of the spectrum of disease caused by HSV-1 and -2, cytomegalovirus (CMV), Epstein-Barr virus (EBV), varicella zoster virus (VZV), and HHV-6 . Nonetheless, positive tissue PCR results must be interpreted cautiously, especially in cases that lack corroborating clinical and neuropathologic evidence of infection . Moreover, positive PCR results from tissues do not distinguish latent from productive (lytic) viral infections . In several neurological diseases, negative PCR results have provided strong evidence against a role for herpesviruses as the causative agents . This review focuses on the use of PCR tests to diagnose HSV and VZV infections of the nervous system. Vox Sang, 2001, 81(2), 87 - 92 Granulocyte transfusion: a review; Yeghen T et al.; Neutrophils are the body's main defence against invasion by bacteria and fungi and, below a level of 1 x 10(9)/l, there is a direct relationship between their circulating number and the risk of systemic infection . Despite advances in supportive care, such as improved broad-spectrum antibiotics and the haemopoietic growth factors, neutropenia following myelosuppressive chemotherapy for malignant disease remains the most important cause of treatment-related morbidity and mortality and its most important dose-limiting toxicity . Although there is clear theoretical, experimental and anecdotal clinical evidence supporting the use of transfused granulocytes to prevent and treat infection in neutropenia, early attempts at exploiting this clinically were unsuccessful, mainly because of difficulties in collecting a sufficient number of cells . Improvements in the technology of collection, including the use of red cell sedimenting agents, glucocorticoids and, more recently, granulocyte-colony-stimulating factor, now allow granulocyte doses within the therapeutic range to be routinely collected . Preliminary evidence suggests clinical efficacy . However, well-designed trials with clinically relevant end-points will be required before granulocyte transfusion can become part of routine clinical practice. Mol Microbiol, 2001 Sep, 41(5), 1077 - 89 SREA is involved in regulation of siderophore biosynthesis, utilization and uptake in Aspergillus nidulans; Oberegger H et al.; Under conditions of low iron availability, most fungi excrete siderophores in order to mobilize extracellular iron . We show that lack of the GATA-type transcription factor SREA in Aspergillus nidulans not only leads to derepression of siderophore biosynthesis but also to deregulation of siderophore-bound iron uptake and ornithine esterase expression . Furthermore, SREA deficiency causes increased accumulation of ferricrocin, the siderophore responsible for intracellular iron storage . In sreA deletion strains, extracellular siderophore production is derepressed but still regulated negatively by iron availability, indicating the presence of an additional iron-regulatory mechanism . In contrast, iron affects ferricrocin accumulation in a positive way, suggesting a protective role for this siderophore in detoxification of intracellular iron excess . The harmfulness of deregulated iron uptake in this mutant is demonstrated by increased expression of genes encoding the antioxidative enzymes catalase CATB and the superoxide dismutases SODA and SODB . It is noteworthy that iron starvation was found to repress catB expression in wild-type (wt) and SREA-deficient strains, consistent with catB being subject to SREA-independent iron regulation . Differential display led to the identification of putative SREA target genes amcA and mirA . The deduced MIRA amino acid sequence displays significant similarity to recently characterized siderophore permeases of Saccharomyces cerevisiae . amcA encodes a putative mitochondrial carrier for the siderophore precursor ornithine, indicating cross-regulation of siderophore and ornithine metabolism. Mol Ecol, 2001 Aug, 10(8), 2101 - 6 Wolbachia infection shared among planthoppers (Homoptera: Delphacidae) and their endoparasite (Strepsiptera: Elenchidae): a probable case of interspecies transmission; Noda H et al.; Wolbachia, a group of parasitic bacteria of arthropods, are believed to be horizontally transmitted among arthropod taxa . We present a new probable example of interspecies horizontal transmission of Wolbachia by way of an endoparasite based on the conformity of Wolbachia gene sequences . Field samples of two rice planthoppers, Laodelphax striatellus and Sogatella furcifera possessed identical Wolbachia . Among three major endoparasites of planthoppers, a strepsipteran, Elenchus japonicus, harboured the identical Wolbachia strain, suggesting strepsipteran transmission of Wolbachia from one planthopper to the other . No Wolbachia was detected in a mermithid nematode Agamermis unka, and dryinid wasps possessed different types of Wolbachia. J Oral Pathol Med, 2001 Oct, 30(9), 560 - 3 Helicobacter pylori colonization of tongue mucosa--increased incidence in atrophic glossitis and burning mouth syndrome (BMS); Gall-Troselj K et al.; Nested polymerase chain reaction (PCR) was performed to detect the presence of Helicobacter pylori in tongue mucosa in 268 patients divided into four groups according to their diagnosis: 87 with atrophic glossitis, 37 with benign migratory glossitis and 144 with burning mouth syndrome (BMS) . The latter group was subdivided according to anatomic site of burning sensation: subgroup A (54 patients) with complaints limited to tongue and subgroup B (90 patients) with burning sensations in other parts of oral mucosa . H . pylori was found in 43 samples (16%) . Bacteria were significantly less present in tongue mucosa affected with benign migratory glossitis compared with atrophic glossitis and BMS (P=0.025) . This difference was more obvious when compared with atrophic glossitis only (P=0.006) . Mucosal changes in these conditions might make the oral environment more acceptable for H . pylori colonization compared with normal mucosa, and this mechanism may play a role in its oro-oral transmission. Anal Biochem, 2001 Sep 15, 296(2), 162 - 6 Pellet pestle homogenization of agarose gel slices at 45 degrees C for deoxyribonucleic acid extraction; Kurien BT et al.; A simple method for extracting DNA from agarose gel slices is described . The extraction is rapid and does not involve harsh chemicals or sophisticated equipment . The method involves homogenization of the excised gel slice (in Tris-EDTA buffer), containing the DNA fragment of interest, at 45 degrees C in a microcentrifuge tube with a Kontes pellet pestle for 1 min . The "homogenate" is then centrifuged for 30 s and the supernatant is saved . The "homogenized" agarose is extracted one more time and the supernatant obtained is combined with the previous supernatant . The DNA extracted using this method lent itself to restriction enzyme analysis, ligation, transformation, and expression of functional protein in bacteria . This method was found to be applicable with 0.8, 1.0, and 2.0% agarose gels . DNA fragments varying from 23 to 0.4 kb were extracted using this procedure and a yield ranging from 40 to 90% was obtained . The yield was higher for fragments 2.0 kb and higher (70-90%) . This range of efficiency was maintained when the starting material was kept between 10 and 300 ng . The heat step was found to be critical since homogenization at room temperature failed to yield any DNA . Extracting DNA with our method elicited an increased yield (up to twofold) compared with that extracted with a commercial kit . Also, the number of transformants obtained using the DNA extracted with our method was at least twice that obtained using the DNA extracted with the commercial kit . Infect Immun, 2001 Oct, 69(10), 6541 - 4 Mouse cytokine profiles associated with Brucella abortus RB51 vaccination or B . abortus 2308 infection; Pasquali P et al.; This study indicated that mice immunized with Brucella abortus RB51 bacteria and subsequently challenged with B . abortus 2308 were protected from reinfection . After vaccination, both Th1 and Th2 cytokine patterns were observed . Of those, the early production of gamma interferon seems to have the prominent role in inducing an immunologically based protection. Infect Immun, 2001 Oct, 69(10), 6427 - 33 Bartonella henselae-specific cell-mediated immune responses display a predominantly Th1 phenotype in experimentally infected C57BL/6 mice; Arvand M et al.; Immune responses of the immunocompetent host to Bartonella henselae infection were investigated in the murine infection model using C57BL/6 mice . Following intraperitoneal infection with human-derived B . henselae strain Berlin-1, viable bacteria could be recovered from livers and spleens during the first week postinfection, while Bartonella DNA remained detectable by PCR in the liver for up to 12 weeks after infection . Granulomatous lesions developed in livers of infected mice, reached maximal density at 12 weeks after infection, and persisted for up to 20 weeks, indicating that B . henselae induced a chronic granulomatous hepatitis in the immunocompetent murine host . T-cell-mediated immune responses were analyzed in vitro by means of spleen cell proliferation and cytokine release assays as well as analysis of immunoglobulin G (IgG) isotypes . Spleen cells from infected mice proliferated specifically upon stimulation with heat-killed Bartonella antigen . Proliferative responses were mainly mediated by CD4+ T cells, increased during the course of infection, peaked at 8 weeks postinfection, and decreased thereafter . Gamma interferon, but not interleukin-4, was produced in vitro by spleen cells from infected animals upon stimulation with Bartonella antigens . Bartonella-specific IgG was detectable in serum of infected mice by 2 weeks, and the antibody concentration peaked at 12 weeks postinfection . IgG2b was the prominent isotype among the Bartonella-specific serum IgG antibodies . These data indicate that B . henselae induces cell-mediated immune responses with a Th1 phenotype in immunocompetent C57BL/6 mice. Infect Immun, 2001 Oct, 69(10), 6348 - 63 High extracellular levels of Mycobacterium tuberculosis glutamine synthetase and superoxide dismutase in actively growing cultures are due to high expression and extracellular stability rather than to a protein-specific export mechanism; Tullius MV et al.; Glutamine synthetase (GS) and superoxide dismutase (SOD), large multimeric enzymes that are thought to play important roles in the pathogenicity of Mycobacterium tuberculosis, are among the bacterium's major culture filtrate proteins in actively growing cultures . Although these proteins lack a leader peptide, their presence in the extracellular medium during early stages of growth suggested that they might be actively secreted . To understand their mechanism of export, we cloned the homologous genes (glnA1 and sodA) from the rapid-growing, nonpathogenic Mycobacterium smegmatis, generated glnA1 and sodA mutants of M . smegmatis by allelic exchange, and quantitated expression and export of both mycobacterial and nonmycobacterial GSs and SODs in these mutants . We also quantitated expression and export of homologous and heterologous SODs from M . tuberculosis . When each of the genes was expressed from a multicopy plasmid, M . smegmatis exported comparable proportions of both the M . tuberculosis and M . smegmatis GSs (in the glnA1 strain) or SODs (in the sodA strain), in contrast to previous observations in wild-type strains . Surprisingly, recombinant M . smegmatis and M . tuberculosis strains even exported nonmycobacterial SODs . To determine the extent to which export of these large, leaderless proteins is expression dependent, we constructed a recombinant M . tuberculosis strain expressing green fluorescent protein (GFP) at high levels and a recombinant M . smegmatis strain coexpressing the M . smegmatis GS, M . smegmatis SOD, and M . tuberculosis BfrB (bacterioferritin) at high levels . The recombinant M . tuberculosis strain exported GFP even in early stages of growth and at proportions very similar to those of the endogenous M . tuberculosis GS and SOD . Similarly, the recombinant M . smegmatis strain exported bacterioferritin, a large (approximately 500-kDa), leaderless, multimeric protein, in proportions comparable to GS and SOD . In contrast, high-level expression of the large, leaderless, multimeric protein malate dehydrogenase did not lead to extracellular accumulation because the protein was highly unstable extracellularly . These findings indicate that, contrary to expectations, export of M . tuberculosis GS and SOD in actively growing cultures is not due to a protein-specific export mechanism, but rather to bacterial leakage or autolysis, and that the extracellular abundance of these enzymes is simply due to their high level of expression and extracellular stability . The same determinants likely explain the presence of other leaderless proteins in the extracellular medium of actively growing M . tuberculosis cultures. Infect Immun, 2001 Oct, 69(10), 6131 - 9 Mannheimia haemolytica leukotoxin activates a nonreceptor tyrosine kinase signaling cascade in bovine leukocytes, which induces biological effects; Jeyaseelan S et al.; The leukotoxin (LktA) produced by Mannheimia haemolytica binds to bovine lymphocyte function-associated antigen 1 (LFA-1) and induces biological effects in bovine leukocytes in a cellular and species-specific fashion . We have previously shown that LktA also binds to porcine LFA-1 without eliciting any effects . These findings suggest that the specificity of LktA effects must entail both binding to LFA-1 and activation of signaling pathways which are present in bovine leukocytes . However, the signaling pathways leading to biological effects upon LktA binding to LFA-1 have not been characterized . In this context, several reports have indicated that ligand binding to LFA-1 results in activation of a nonreceptor tyrosine kinase (NRTK) signaling cascade . We designed experiments with the following objectives: (i) to determine whether LktA binding to LFA-1 leads to activation of NRTKs, (ii) to examine whether LktA-induced NRTK activation is target cell specific, and (iii) to determine whether LktA-induced NRTK activation is required for biological effects . We used a biologically inactive mutant leukotoxin (DeltaLktA) for comparison with LktA . Our results indicate that LktA induces tyrosine phosphorylation (TP) of the CD18 tail of LFA-1 in bovine leukocytes . The DeltaLktA mutant does not induce TP of the CD18 tail, albeit binding to bovine LFA-1 . LktA-induced TP of the CD18 tail was attenuated by an NRTK inhibitor, herbimycin A; a phosphatidylinositol 3'-kinase (PI 3-kinase) inhibitor, wortmannin; and a Src kinase inhibitor, PP2, in a concentration-dependent manner . Furthermore, LktA induces TP of the CD18 tail in bovine, but not porcine, leukocytes . Moreover, LktA-induced intracellular calcium ({Ca2+}i) elevation was also inhibited by herbimycin A, wortmannin, and PP2 . Thus, our data represent the first evidence that binding of LktA to bovine LFA-1 induces a species-specific NRTK signaling cascade involving PI 3-kinase and Src kinases and that this signaling cascade is required for LktA-induced biological effects. Infect Immun, 2001 Oct, 69(10), 6038 - 43 Role of ADP-ribosyltransferase activity of pertussis toxin in toxin-adhesin redundancy with filamentous hemagglutinin during Bordetella pertussis infection; Alonso S et al.; Pertussis toxin (PT) and filamentous hemagglutinin (FHA) are two major virulence factors of Bordetella pertussis . FHA is the main adhesin, whereas PT is a toxin with an A-B structure, in which the A protomer expresses ADP-ribosyltransferase activity and the B moiety is responsible for binding to the target cells . Here, we show redundancy of FHA and PT during infection . Whereas PT-deficient and FHA-deficient mutants colonized the mouse respiratory tract nearly as efficiently as did the isogenic parent strain, a mutant deficient for both factors colonized substantially less well . This was not due to redundant functions of PT and FHA as adhesins, since in vitro studies of epithelial cells and macrophages indicated that FHA, but not PT, acts as an adhesin . An FHA-deficient B . pertussis strain producing enzymatically inactive PT colonized as poorly as did the FHA-deficient, PT-deficient strain, indicating that the ADP-ribosyltransferase activity of PT is required for redundancy with FHA . Only strains producing active PT induced a local transient release of tumor necrosis factor alpha (TNF-alpha), suggesting that the pharmacological effects of PT are the basis of the redundancy with FHA, through the release of TNF-alpha . This may lead to damage of the pulmonary epithelium, allowing the bacteria to colonize even in the absence of FHA. Vet Immunol Immunopathol, 2001 Sep 20, 81(3-4), 251 - 4 The ACVD task force on canine atopic dermatitis (XIII): threshold phenomenon and summation of effects; Marsella R et al.; The concepts of a threshold for pruritus and a threshold for canine atopic dermatitis (AD) are useful in the understanding of the development of clinical manifestations of this disease . Multiple flare factors, such as infections with bacteria and yeasts, can contribute to the severity of clinical signs in affected patients. Environ Microbiol, 2001 Jul, 3(7), 460 - 70 Evidence for anaerobic syntrophic acetate oxidation during methane production in the profundal sediment of subtropical Lake Kinneret (Israel); Nusslein B et al.; Methane production was measured in samples of the profundal sediment from Lake Kinneret . Production rates of CH(4) were higher at 30 degrees C than at the in situ temperature of 15 degrees C and were higher in the top 5 cm layer than below . Turnover of {2-(14)C}-acetate resulted in the production of (14)CH(4) and (14)CO(2) with turnover times of < 42 min . However, < 30% of the added radioactivity was converted to gaseous products, indicating that only part of the acetate pool was microbially available . The calculated acetate turnover rates were sufficient to account for total CH(4) production, indicating that CH(4) was produced exclusively from acetate . This conclusion was confirmed by inhibition of methanogens with chloroform, which resulted in an almost stoichiometric accumulation of acetate . However, a large percentage (30-60%) of {2-(14)C}-acetate was converted to (14)CO(2), despite lack of reducible sulphate or other oxidants in the sediment . Anoxic preincubation of the sediment did not result in reduced production of (14)CO(2) . Therefore, part of the acetate must have been oxidized rather than methanogenically cleaved . Conversion of {(14)C}-bicarbonate to (14)CH(4) indicated that 30-50% of total CH(4) production originated from reduction of CO(2) . To reconcile the relatively high contribution of H(2)/CO(2)-dependent methanogenesis with the relatively high oxidative conversion of acetate, we assume that part of the acetate was used syntrophically by consortia of acetate-oxidizing bacteria and H(2)/CO(2)-using methanogens . This conclusion is supported by favourable thermodynamic conditions for syntrophic acetate oxidation under in situ conditions and complete inhibition of {2-(14)C}-acetate turnover at high H(2) partial pressures . Further evidence to support this conclusion comes from the analysis of the structure of the archaeal community . Terminal restriction fragment length polymorphism (T-RFLP) and partial sequence analysis of the SSU rRNA genes amplified from DNA extracts of the sediment showed Methanomicrobiaceae as the dominant methanogenic group, whereas acetoclastic methanogens could not be detected. Cell Microbiol, 2001 Sep, 3(9), 623 - 32 Evidence of a leading role for VEGF in Bartonella henselae-induced endothelial cell proliferations; Kempf VA et al.; Bartonella henselae causes the vasculoproliferative disorders bacillary angiomatosis (BA) and bacillary peliosis (BP) . The pathomechanisms of these tumorous proliferations are unknown . Our results suggest a novel bacterial two-step pathogenicity strategy, in which the pathogen triggers growth factor production for subsequent proliferation of its own host cells . In fact, B . henselae induces host cell production of the angiogenic factor vascular endothelial growth factor (VEGF), leading to proliferation of endothelial cells . The presence of B . henselae pili was associated with host cell VEGF production, as a Pil- mutant of B . henselae was unable to induce VEGF production . In turn, VEGF-stimulated endothelial cells promoted the growth of B . henselae . Immunohistochemistry for VEGF in specimens from patients with BA or BP revealed increased VEGF expression in vivo . These findings suggest a novel bacteria-dependent mechanism of tumour growth. ANZ J Surg, 2001 Oct, 71(10), 574 - 6 Prevalence of Helicobacter pylori in gastric cancer in a South-East Asian population by 14C-urea breath test; Chung AY et al.; BACKGROUND: Helicobacter pylori is believed to play an important role in the aetiology of gastric cancer . There is a great variability in seropositivity and histological frequency of H . pylori in gastric cancer . The present prospective study investigates the prevalence of H . pylori infection in gastric cancer patients using 14C-urea breath testing . METHODS: Patients with endoscopic biopsy-proven gastric cancer were fasted for 6 h prior to ingesting 18.5 x 104 Bq of 14C-urea cocktail orally . Breath samples were collected after 20 min by asking them to blow into a hyamine solution and measurements were read in a scintillation counter . RESULTS: Fifty out of 51 patients (98%) with gastric cancer were positive on the 14C-urea breath test compared to 29 patients (61%) who were positive on histology . There was no association between sex, age or tumour site, stage, differentiation, Lauren type and H . pylori status . The test was negative in one patient with cardial tumour in which histology of the resected specimen was also negative for the bacteria . CONCLUSIONS: Active H . pylori infection is highly prevalent in gastric cancer in a South-East Asian population . The 14C-urea breath test is a highly sensitive method for detecting the presence of H . pylori even in gastric adenocarcinoma irrespective of the stage. Khirurgiia (Mosk), 2001, (8), 17 - 20 {Ultrasound-controlled minimally invasive surgical interventions in abdominal abscesses}; Ektov VN et al.; Results of ultrasound-controlled minimally invasive surgical interventions (UAMISI) for abdominal abscesses are analyzed . 84 operations were performed in 72 patients with good results . Puncture method was used in 12 patients, drainage operation--in 58, endoscopy-guided puncture method--in 2 patients . Indications for different ultrasonic-assisted interventions are developed . It is concluded that at present the UAMISI are the alternative to conventional "open" treatment of abdominal abscesses. J Biol Chem, 2001 Nov 23, 276(47), 44044 - 51 Epub 2001 Sep 10. Conformational component in the coupled transfer of multiple electrons and protons in a monomeric tetraheme cytochrome; Louro RO et al.; Cell metabolism relies on energy transduction usually performed by complex membrane-spanning proteins that couple different chemical processes, e.g . electron and proton transfer in proton-pumps . There is great interest in determining at the molecular level the structural details that control these energy transduction events, particularly those involving multiple electrons and protons, because tight control is required to avoid the production of dangerous reactive intermediates . Tetraheme cytochrome c(3) is a small soluble and monomeric protein that performs a central step in the bioenergetic metabolism of sulfate reducing bacteria, termed "proton-thrusting," linking the oxidation of molecular hydrogen with the reduction of sulfate . The mechano-chemical coupling involved in the transfer of multiple electrons and protons in cytochrome c(3) from Desulfovibrio desulfuricans ATCC 27774 is described using results derived from the microscopic thermodynamic characterization of the redox and acid-base centers involved, crystallographic studies in the oxidized and reduced states of the cytochrome, and theoretical studies of the redox and acid-base transitions . This proton-assisted two-electron step involves very small, localized structural changes that are sufficient to generate the complex network of functional cooperativities leading to energy transduction, while using molecular mechanisms distinct from those established for other Desulfovibrio sp . cytochromes from the same structural family. J Biol Chem, 2001 Dec 14, 276(50), 47563 - 74 Epub 2001 Sep 10. Phosphatidylinositol 3-kinase-dependent pathways oppose Fas-induced apoptosis and limit chloride secretion in human intestinal epithelial cells . Implications for inflammatory diarrheal states; Abreu MT et al.; The epithelial lining of the intestine serves as a barrier to lumenal bacteria and can be compromised by pathologic Fas-mediated epithelial apoptosis . Phosphatidylinositol (PI)3-kinase signaling has been described to limit apoptosis in other systems . We hypothesized that PI3-kinase-dependent pathways regulate Fas-mediated apoptosis and barrier function in intestiynal epithelial cells (IEC) . IEC lines (HT-29 and T84) were exposed to agonist anti-Fas antibody in the presence or absence of chemical inhibitors of PI3-kinase (LY294002 and wortmannin) . Apoptosis, barrier function, changes in short circuit current (DeltaI(sc)), and expression of adhesion molecules were assessed . Inhibition of PI3-kinase strongly sensitized IEC to Fas-mediated apoptosis . Expression of constitutively active Akt, a principal downstream effector of the PI3-kinase pathway, protected against Fas-mediated apoptosis to an extent that was comparable with expression of a genetic caspase inhibitor, p35 . PI3-kinase inhibition sensitized to apoptosis by increasing and accelerating Fas-mediated caspase activation . Inhibition of PI3-kinase combined with cross-linking Fas was associated with increased permeability to molecules that were <400 Da but not those that were >3,000 Da . Inhibition of PI3-kinase resulted in chloride secretion that was augmented by cross-linking Fas . Confocal analyses revealed polymerization of actin and maintenance of epithelial cell adhesion molecule-mediated interactions in monolayers exposed to anti-Fas antibody in the context of PI3-kinase inhibition . PI3-kinase-dependent pathways, especially Akt, protect IEC against Fas-mediated apoptosis . Inhibition of PI3-kinase in the context of Fas signaling results in increased chloride secretion and barrier dysfunction . These findings suggest that agonists of PI3-kinase such as growth factors may have a dual effect on intestinal inflammation by protecting epithelial cells against immune-mediated apoptosis and limiting chloride secretory diarrhea. Biochemistry, 2001 Sep 18, 40(37), 11270 - 8 Mouse alpha1-syntrophin binding to Grb2: further evidence of a role for syntrophin in cell signaling; Oak SA et al.; Syntrophins have been proposed to serve as adapter proteins . Syntrophins are found in the dystrophin glycoprotein complex (DGC); defects in the constituents of this complex are linked to various muscular dystrophies . Blot overlay experiments demonstrate that alpha-dystroglycan, beta-dystroglycan, and syntrophins all bind Grb2, the growth factor receptor bound adapter protein . Mouse alpha1-syntrophin sequences were produced as chimeric fusion proteins in bacteria and found to also bind Grb2 in a Ca2+-independent manner . This binding was localized to the proline rich sequences adjacent to and overlapping with the N-terminal pleckstrin homology domain (PH1) . Grb2 bound syntrophin with an apparent KD of 563 +/- 15 nM . Grb2-C-SH3 domain bound syntrophin with slightly higher affinity than Grb2-N-SH3 domain . Crk-L, an SH2/SH3 protein of similar domain structure but different specificity, does not bind these syntrophin sequences. Biochemistry, 2001 Sep 18, 40(37), 11227 - 33 Ceramide inhibition of mammalian phospholipase D1 and D2 activities is antagonized by phosphatidylinositol 4,5-bisphosphate; Singh IN et al.; Ceramides inhibit phospholipase D (PLD) activity in several mammalian cell types . These effects have been related to preventing activation by ARF1, RhoA, and protein kinase C-alpha and -beta and therefore indicate that PLD1 is inhibited . In the present work, we investigated the effects of ceramides in inhibiting both PLD1 and PLD2 and the interaction with another activator, phosphatidylinositol 4,5-bisphosphate (PIP2) . PLD1 and PLD2 were overexpressed separately in Sf9 insect cells using baculovirus vectors . In our cell-free system, PLD1 activity was inhibited completely by C2-ceramide at sub-optimum concentrations of PIP2 (3 and 6 microM), whereas at supra-optimum PIP2 concentrations (18 and 24 microM) C2-ceramide did not inhibit PLD1 activity . Partially purified PLD2 exhibited an absolute requirement for PIP2 when the activity was measured using Triton X-100 micelles . Ceramides inhibited PLD2 activity, and this inhibition was decreased as PIP2 concentrations increased . However, C2-ceramide also reversibly inhibited the activity of PLD1 and PLD2 mutants in which binding of PIP2 was decreased, indicating that ceramides are interacting with the catalytic core of the mammalian PLDs . By contrast, C2-ceramide failed to produce a significant inhibition of PLDs from bacteria and plants . Our results provide a novel demonstration that ceramides reversibly inhibit mammalian PLD2 as well as PLD1 activities and that both of these actions are more pronounced when PIP2 concentrations are rate-limiting. Appl Microbiol Biotechnol, 2001 Aug, 56(3-4), 350 - 60 Flow cytometry in biotechnology; Rieseberg M et al.; Flow cytometry is a general method for rapidly analyzing large numbers of cells individually using light-scattering, fluorescence, and absorbence measurements . The power of this method lies both in the wide range of cellular parameters that can be determined and in the ability to obtain information on how these parameters are distributed in the cell population . Flow cytometric assays have been developed to determine both cellular characteristics such as size, membrane potential, and intracellular pH, and the levels of cellular components such as DNA, protein, surface receptors, and calcium . Measurements that reveal the distribution of these parameters in cell populations are important for biotechnology, because they better describe the population than the average values obtained from traditional techniques . This Mini-Review provides an overview of the principles of flow cytometry, with descriptions of methods used to measure various cellular parameters and examples of the application of flow cytometry in biotechnology . Finally, a discussion of the challenges and limitations of the method is presented along with a future outlook. Morfologiia, 2001, 119(2), 40 - 4 {Interaction of artificial carbon-mineral sorption preparations with the wound content}; Maiborodin IV et al.; The surface of SUMS1 was studied using scanning electron microscopy after contact with the wound contact . In vivo sorbent action was found to differ from in vitro adsorption properties of sorption drugs, as during the contact with organism tissue in the inflammation focus granule active surface is covered by fibrin, to which necrotic tissues, bacteria and immunocompetent cells adhere . The use of sorption drainage in acute and chronic inflammation lowers the challenge on lymphatic tissue because removal of sorption preparations also causes elimination of large fragments of non viable tissues, antigens and protein-cellular conglomerates that might block lymphatic vessels and regional lymph nodes. IUBMB Life, 2001 Mar, 51(3), 165 - 73 Oxygen signal transduction; Gilles-Gonzalez MA; Although manifestations of O2 adaptation have long been examined, only now are biochemical mechanisms of O2 regulation beginning to be understood . This article comments on the current state of knowledge about proteins that function as direct sensors of molecular oxygen and makes predictions about as yet undiscovered sensors. Mol Cell, 2001 Aug, 8(2), 251 - 62 DExD/H box RNA helicases: from generic motors to specific dissociation functions; Tanner NK et al.; RNA helicases of the DEAD box and related DExD/H proteins form a very large superfamily of proteins conserved from bacteria and viruses to humans . They have seven to eight conserved motifs, the characteristics of which are used to subgroup members into individual families . They are associated with all processes involving RNA molecules, including transcription, editing, splicing, ribosome biogenesis, RNA export, translation, RNA turnover, and organelle gene expression . Analysis of the three-dimensional structures obtained through the crystallization of viral and cellular RNA helicases reveals a strong structural homology to DNA helicases . In this review, we discuss our current understanding of RNA helicases and their biological function. J Mol Microbiol Biotechnol, 2001 Oct, 3(4), 611 - 7 A new class of glutaminase from Aspergillus oryzae; Thammarongtham C et al.; The koji mold Aspergillus oryzae is able to produce glutaminase which converts glutamine to glutamic acid, one of the most important flavor components in soy sauce . We present here the isolation and the complete nucleotide sequence of the glutaminase- encoding gene from A . oryzae U212, an industrial strain used in Thailand . N-terminal and internal amino acid sequences were determined from purified glutaminase . A 700-bp fragment was amplified by PCR using oligonucleotide primers designed from partial amino acid sequences . This PCR fragment was used as a homologous probe for screening an A . oryzae genomic DNA library . RT-PCR showed that the gene contained seven short introns . Sequence analysis revealed an open reading frame that encodes a protein of 690 amino-acid residues with a predicted molecular mass of 76 kDa . The N-terminal and internal amino acid sequences of the deduced protein exactly matched the ones determined from the purified protein . Comparison of the amino acid sequence with glutaminase sequences from other origins showed that A . oryzae glutaminase shares little homology with those of bacteria, eukaryote and mammals . The A . oryzae glutaminase gene was expressed in A . nidulans to confirm the presence of a functional glutaminase gene in the cloned DNA . To our knowledge, this is the first reported glutaminase gene cloned from filamentous fungi. Nature, 2001 Sep 6, 413(6851), 70 - 4 Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ line; Bessereau JL et al.; Transposons have been enormously useful for genetic analysis in both Drosophila and bacteria . Mutagenic insertions constitute molecular tags that are used to rapidly clone the mutated gene . Such techniques would be especially advantageous in the nematode Caenorhabditis elegans, as the entire sequence of the genome has been determined . Several different types of endogenous transposons are present in C . elegans, and these can be mobilized in mutator strains (reviewed in ref . 1) . Unfortunately, use of these native transposons for regulated transposition in C . elegans is limited . First, all strains contain multiple copies of these transposons and thus new insertions do not provide unique tags . Second, mutator strains tend to activate the transposition of several classes of transposons, so that the type of transposon associated with a particular mutation is not known . Here we demonstrate that the Drosophila mariner element Mos1 can be mobilized in C . elegans . First, efficient mobilization of Mos1 is possible in somatic cells . Second, heritable insertions of the transposon can be generated in the germ line . Third, genes that have been mutated by insertion can be rapidly identified using inverse polymerase chain reaction . Fourth, these insertions can subsequently be remobilized to generate deletion and frameshift mutations by imperfect excision. J Immunol, 2001 Sep 15, 167(6), 3375 - 82 The effect of an anti-HLA-B27 immune response on CTL recognition of Chlamydia; Popov I et al.; The interplay between triggering bacteria and HLA-B27 in the pathogenesis of the spondyloarthropathies remains one of the most active areas of investigation in the rheumatic diseases . This has proved difficult to study systematically in the clinical setting, and in this study we utilized a rat model to address the influence that B27-related immunity may have on the process of generating anti-Chlamydia immunity . When splenocytes from HLA-B27 DNA-immunized Lewis (LEW) animals received restimulation in vitro with Chlamydia-treated cells from B27-transgenic LEW rats, we observed that in addition to the expected CTL recognition of HLA-B27, there was also anti-Chlamydia CTL killing of Chlamydia-sensitized syngeneic fibroblast targets . This was not seen when responding cells in vitro were naive LEW splenocytes . To confirm the existence of CTLs recognizing both HLA-B27 and Chlamydia, LEW rats were immunized with B27-transgenic LEW cells, instead of the B27 DNA construct . Splenocytes from the immune rats were restimulated in vitro with Chlamydia-treated B27-transgenic LEW cells . In this instance, the CTLs retained the allele-specific recognition of HLA-B27, as well as recognition of Chlamydia-sensitized syngeneic fibroblasts . Thus, if there is prior expansion of an immune response against HLA-B27, then the resulting splenocytes demonstrate a reduced threshold for generating a primary anti-Chlamydia CTL response . These studies implicate a dynamic interrelationship between recognition of HLA-B27 and Chlamydia trachomatis . The results may have implications for deciphering the cellular basis of Chlamydia-induced reactive arthritis. J Bacteriol, 2001 Oct, 183(19), 5544 - 53 Genetics and regulation of chitobiose utilization in Borrelia burgdorferi; Tilly K et al.; Borrelia burgdorferi spends a significant proportion of its life cycle within an ixodid tick, which has a cuticle containing chitin, a polymer of N-acetylglucosamine (GlcNAc) . The B . burgdorferi celA, celB, and celC genes encode products homologous to transporters for cellobiose and chitobiose (the dimer subunit of chitin) in other bacteria, which could be useful for bacterial nutrient acquisition during growth within ticks . We found that chitobiose efficiently substituted for GlcNAc during bacterial growth in culture medium . We inactivated the celB gene, which encodes the putative membrane-spanning component of the transporter, and compared growth of the mutant in various media to that of its isogenic parent . The mutant was no longer able to utilize chitobiose, while neither the mutant nor the wild type can utilize cellobiose . We propose renaming the three genes chbA, chbB, and chbC, since they probably encode a chitobiose transporter . We also found that the chbC gene was regulated in response to growth temperature and during growth in medium lacking GlcNAc. J Bacteriol, 2001 Oct, 183(19), 5491 - 5 Properties of a thermostable nitrate reductase from the hyperthermophilic archaeon Pyrobaculum aerophilum; Afshar S et al.; The nitrate reductase of the hyperthermophilic archaeon Pyrobaculum aerophilum was purified 137-fold from the cytoplasmic membrane . Based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, the enzyme complex consists of three subunits with apparent molecular weights of 130,000, 52,000, and 32,000 . The enzyme contained molybdenum (0.8-mol/mol complex), iron (15.4-mol/mol complex) and cytochrome b (0.49-mol/mol complex) as cofactors . The P . aerophilum nitrate reductase distinguishes itself from nitrate reductases of mesophilic bacteria and archaea by its very high specific activity using reduced benzyl viologen as the electron donor (V(max) with nitrate, 1,162 s(-1) (326 U/mg); V(max) with chlorate, 1,348 s(-1) (378 U/mg) {assayed at 75 degrees C}) . The K(m) values for nitrate and chlorate were 58 and 140 microM, respectively . Azide was a competitive inhibitor and cyanide was a noncompetitive inhibitor of the nitrate reductase activity . The temperature optimum for activity was > 95 degrees C . When incubated at 100 degrees C, the purified nitrate reductase had a half-life of 1.5 h . This study constitutes the first description of a nitrate reductase from a hyperthermophilic archaeon. Genomics, 2001 Sep, 77(1-2), 65 - 70 The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders; Kenmochi N et al.; Mitochondria possess their own translational machinery, which is composed of components distinct from their cytoplasmic counterparts . To investigate the possible involvement of mitochondrial ribosomal defects in human disease, we mapped nuclear genes that encode mitochondrial ribosomal proteins (MRPs) . We generated sequence-tagged sites (STSs) of individual MRP genes that were able to be detected by PCR . They were placed on an STS content map of the human genome by typing of radiation hybrid panels . We located 54 MRP genes on the STS-content map and assigned these genes to cytogenetic bands of the human chromosomes . Although mitochondria are thought to have originated from bacteria, in which the genes encoding ribosomal proteins are clustered into operons, the mapped MRP genes are widely dispersed throughout the genome, suggesting that transfer of each MRP gene to the nuclear genome occurred individually . We compared the assigned positions with candidate regions for mendelian disorders and found certain genes that might be involved in particular diseases . This map provides a basis for studying possible roles of MRP defects in mitochondrial disorders. Geochim Cosmochim Acta, 2000 Dec, 64(23), 4049 - 81 Elongated prismatic magnetite crystals in ALH84001 carbonate globules: potential Martian magnetofossils; Thomas-Keprta KL et al.; Using transmission electron microscopy (TEM), we have analyzed magnetite (Fe3O4) crystals acid-extracted from carbonate globules in Martian meteorite ALH84001 . We studied 594 magnetites from ALH84001 and grouped them into three populations on the basis of morphology: 389 were irregularly shaped, 164 were elongated prisms, and 41 were whisker-like . As a possible terrestrial analog for the ALH84001 elongated prisms, we compared these magnetites with those produced by the terrestrial magnetotactic bacteria strain MV-1 . By TEM again, we examined 206 magnetites recovered from strain MV-1 cells . Natural (Darwinian) selection in terrestrial magnetotactic bacteria appears to have resulted in the formation of intracellular magnetite crystals having the physical and chemical properties that optimize their magnetic moment . In this study, we describe six properties of magnetite produced by biologically controlled mechanisms (e.g., magnetotactic bacteria), properties that, collectively, are not observed in any known population of inorganic magnetites . These criteria can be used to distinguish one of the modes of origin for magnetites from samples with complex or unknown histories . Of the ALH84001 magnetites that we have examined, the elongated prismatic magnetite particles (similar to 27% of the total) are indistinguishable from the MV-1 magnetites in five of these six characteristics observed for biogenically controlled mineralization of magnetite crystals. J Geophys Res, 2000 May 25, 105(E5), 11981 - 90 Greenhouse warming by CH4 in the atmosphere of early Earth; Pavlov AA et al.; Earth appears to have been warm during its early history despite the faintness of the young Sun . Greenhouse warming by gaseous CO2 and H2O by itself is in conflict with constraints on atmospheric CO2 levels derived from paleosols for early Earth . Here we explore whether greenhouse warming by methane could have been important . We find that a CH4 mixing ratio of 10(-4) (100 ppmv) or more in Earth's early atmosphere would provide agreement with the paleosol data from 2.8 Ga . Such a CH4 concentration could have been readily maintained by methanogenic bacteria, which are thought to have been an important component of the biota at that time . Elimination of the methane component of the greenhouse by oxidation of the atmosphere at about 2.3-2.4 Ga could have triggered the Earth's first widespread glaciation. Polar Biol, 1999 May, 21(5), 285 - 94 Ciliated protozoa of two antarctic lakes: analysis by quantitative protargol staining and examination of artificial substrates; Kepner RL Jr et al.; Planktonic and artificial substrate-associated ciliates have been identified in two perennially ice-covered antarctic lakes of the McMurdo Dry Valleys . Abundances estimated by quantitative protargol staining ranged from < 5 to 31690 cells l-1, levels that are comparable to those previously obtained using other methods . Nineteen ciliate taxa were identified from these lakes, with the most frequently encountered genera being Plagiocampa, Askenasia, Monodinium, Sphaerophrya and Vorticella . The taxonomic findings compare favorably with those of previous investigators; however four previously unreported genera were observed in both Lakes Fryxell and Hoare . The variability in the depth distributions of ciliates in Lake Fryxell is explained in terms of lake physicochemical properties and ciliate prey distributions, while factors related to temporal succession in the Lake Hoare assemblage remain unexplained . Local marine or temperate zone freshwater habitats are a more likely source than the surrounding dry valleys soils for present ciliate colonists in these lakes . Although the taxonomic uncertainties require further examination, our results suggest that ciliate populations in these antarctic lakes undergo significant fluctuations and are more diverse than was previously recognized. Gravit Space Biol Bull, 2000 Jun, 13(2), 13 - 23 Metazoans in extreme environments: adaptations of hydrothermal vent and hydrocarbon seep fauna; McMullin ER et al.; Some of the most extreme environments where animals survive are associated with active vents and seeps in the deep sea . In addition to the extreme pressure, low temperatures, and lack of light that characterize the deep sea in general, a variety of other factors that are hostile to most animals prevail in these environments . Hydrothermal vent regions show extremes in temperature, areas of very low oxygen, and the presence of toxic hydrogen sulfide and heavy metals . Hydrocarbon seeps, though much cooler than vents, also have regions of very low oxygen and high hydrogen sulfide, as well as other potentially harmful substances such as crude oil and supersaturated brine . Specially adapted animals not only tolerate these conditions, they often thrive under them . In most cases this tolerance is due to a combination of physiological and behavioral adaptations that allow animals to avoid the extremes of their habitats and yet benefit from the chemoautotrophic production characteristic of these environments. Eur J Protistol, 1999 Oct 15, 35(3), 327 - 37 Devescovinid trichomonad with axostyle-based rotary motor ("Rubberneckia"): taxonomic assignment as Caduceia versatilis sp . nov; d'Ambrosio U et al.; An amitochondriate trichomonad cell of the family Devescovinidae (Class Parabasalia), helped demonstrate the fluid model of lipoprotein cell membranes . This wood-ingesting symbiont in the hindgut of the dry wood-eating termite Cryptotermes cavifrons is informally known to cell biologists as "Rubberneckia" . As the microtubular axo-style complex generates force causing clockwise movement of the entire anterior portion of the cell at the shear zone the protist displays "head" rotation . Studies by phase contrast and videomicroscopy of live cells, of whole mounts by scanning, and thin sections by transmission electron microscopy extend the observations of Tamm and Tamm {24-26} and Tamm {19-23} . Habitat, cell shape, size, nuclear features, parabasal apparatus and other morphological details permit the assignment of "Rubberneckia" to Kirby's cosmopolitan genus Caduceia . This large-sized devescovinid has distinctive parabasal gyres, an axostylar rotary, motor, and regularly-associated nonflagellated, fusiform and flagellated rod epibiotic surface bacteria . In addition to regularly aligned epibionts intranuclear and endocytoplasmic bacteria are abundant and hydrogenosomes are Present . "Rubberneckia" is compared here to the other seven species of Caduceia . Since it is clearly sufficiently distinctive to warrant new species status, we named it C . versatilis. Proc NIPR Symp Antarct Meteorites, 1995 Oct, 8, 258 - 67 Geochemical characteristics of organic compounds in a permafrost sediment core sample from northeast Siberia, Russia; Matsumoto GI et al.; We studied total organic carbon (TOC), hydrocarbons and fatty acids in a permafrost sediment core sample (well 6-90, length 32.0 m, 1.5-2.5 Ma BP) from northeast Siberia (approximately 70 degrees N, 158 degrees E), Russia, to elucidate their geochemical features in relation to source organisms and paleoenvironmental conditions . Long-chain n-alkanes and n-alkanoic acids (>C19) were most predominant hydrocarbons and fatty acids, respectively, so organic matter in the sediment core was derived mainly from vascular plants and, to a much smaller extent, from bacteria . Low concentrations of unsaturated fatty acids revealed that organic matter in the sediment core was considerably degraded during and/or after sedimentation . The predominance of vascular plant components, the major ionic components of nonmarine sources, and geological data strongly implied that the sediment layers were formed in shal