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The upflow anaerobic sludge blanket (UASB) reactor is a microcosm for the methanogenic degradation of organic matter in anaerobic environments, and depends on the auto-formation of dense 3D biofilms of 1-3 mm in diameter, referred to as granular sludge (biogranules). Past research has shown that UASB and other methanogenic reactors are extremely stable functionally, but the underlying basis of the functional stability is not well understood. In this study, microbial dynamics in the communities residing in UASB biogranules were analysed to determine responses to short-term perturbations (change in reactor feed). The reactor was fed with simulated brewery wastewater (SBWW) for 1.5 months (phase 1), acetate/sulfate for 2 months (phase 2), acetate alone for 3 months (phase 3) and then a return to SBWW for 2 months (phase 4). Analysis of 16S rRNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB gene-based-clone libraries showed a relatively simple community composed mainly of the methanogenic archaea (Methanobacterium and Methanosaeta), members of the green non-sulfur (Chloroflexi) group of bacteria and Syntrophobacter, Spirochaeta, Acidobacteria and Cytophaga-related bacterial sequences. The mcrA clone libraries were dominated throughout by Methanobacterium- and Methanospirillum-related sequences. Although the reactor performance remained relatively stable throughout the experiment, community diversity levels generally decreased for all libraries in response to a change from SBWW to acetate alone feed. There was a large transitory increase noted in 1 6S diversity at the 2 month sampling on acetate alone, entirely related to an increase in bacterial diversity. Upon return to SBWW conditions in phase 4, all diversity measures returned to near phase 1 levels. Our results demonstrated that microbial communities, even highly structured ones such as in UASB biogranules, are very capable of responding to rapid and major changes in their environment. DOI 10.1099/mic.0.036715-0

The degradation of many structurally diverse aromatic compounds in Acinetobacter baylyi is accomplished by the [beta]-ketoadipate pathway. In addition to specific induction of expression by certain aromatic compounds, this pathway is regulated by complex mechanisms at multiple levels, which are the topic of this study. Multiple operons feeding into the [beta]-ketoadipate pathway are controlled by carbon catabolite repression (CCR) caused by succinate plus acetate. The pathways under study enable the catabolism of benzoate (ben), catechol (catA), cis,cis-muconate (catB, C,I,J,F,D), vanillate (van), hydroxycinnamates (hca), dicarboxylates (dca), salicylate (sal), anthranilate (ant) and benzyl esters (are). For analysis of CCR at the transcriptional level a luciferase reporter gene cassette was introduced into the operons. The Crc (catabolite repression control) protein is involved in repression of all operons (except for catA), as demonstrated by the analysis of respective crc strains. In addition, cross-regulation was demonstrated for the vanA,B, hca and dca operons. The presence of protocatechuate caused transcriptional repression of the vanA,B- and hca-encoded funnelling pathways (vertical regulation). Thus the results presented extend the understanding both of CCR and of the effects of Crc for all aromatic degradative pathways of A. baylyi and increase the number of operons known to be controlled by two additional mechanisms, cross-regulation and vertical regulation. DOI 10.1099/mic.0.037424-0

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.dsr.2008.10.002 Byline: Max Wisshak (a), Matthias Lopez Correa (a), Serge Gofas (b), Carmen Salas (b), Marco Taviani (c), Joachim Jakobsen (d), Andre Freiwald (a) Keywords: Oyster; Neopycnodonte zibrowii; Azores; Microstructure; Stable isotopes; Trace elements Abstract: A conspicuous new deep-sea oyster, Neopycnodonte zibrowii sp. n., is described from the Azores Archipelago, where it thrives in 420 to >500m water depth in high densities concealed underneath overhangs. The new species reaches a relatively large size, which may exceed 20cm, and is characterised by a very unusual hinge line morphology, straight without a bulge of the resilium. It is compared to the extant Indo-Pacific Empressostrea kostini Huber and Lorenz, 2007 and to the cosmopolitan Neopycnodonte cochlear (Poli, 1791), which has a broadly sympatric distribution at shallower depths in the Azores and Bay of Biscay. Radiocarbon dating reveals that individuals reach an impressive lifespan of one to more than five centuries, placing them among the longest-lived molluscs known to date. They often grow on top of each other, forming stacks that resemble dish piles -- an effective measure to optimise shell stability with minimal biomineralisation effort, but with the drawback of increased bioerosion ultimately leading to detachment. Three microstructure types are developed in N. zibrowii: (1) the cross-foliated, calcitic, dorsal to central endostracum and aragonitic ligostracum, (2) the porous vesicular structure of the calcitic ventral endostracum, and (3) the simple prismatic aragonitic myostracum. Foliated and vesicular shell portions show sub-millimetre-scale first-order increments delineated by conchiolin-rich growth breaks (interpreted as reproductive cyclicity), and less distinct second-order increments (interpreted as annual in nature). This pattern is clearly reflected by the elemental composition with the primary growth breaks lacking Ca and Sr but including Mg and S as organic matrix constituents. The second-order increments within the calcite are mirrored by moderately co-varying Mg/Ca and S/Ca fluctuations at stable Sr concentrations, reflecting varying proportions of organic matrix. Dorsal and central endostracum transects reveal a low inter-valve, but considerable inter-specimen variability with high Mg/Ca molar ratios and fluctuations (22.5[+ or -]17.6mmol/mol), low Sr/Ca values (0.2[+ or -]0.1mmol/mol), and a typical to high S/Ca content (6.9[+ or -]2.2mmol/mol), when compared to other calcitic bivalves. Unlike short-lived, shallow-water oysters, N. zibrowii thrives under very stable environmental conditions. Minimal temperature fluctuations and stable open marine salinity provide an optimal basis to recognise biological fractionation processes. Strong Mg/Ca fluctuations indicate a physiological control related to metabolism and biomineralisation, prohibiting the use of this ratio as a temperature or ocean chemistry proxy. Low Sr/Ca ratios indicate rather constant and low long-term accretion rates, while short-scale fluctuations may be attributed to short-term variations in growth rate and Mg incorporation. Oxygen isotopes yield a considerable spread of 1.8a[degrees] with a mean of 2.0[+ or -]0.3a[degrees][delta].sup.18O V-PDB, and low correlation between different contemporaneous parts of the shell and between specimens. These values surprisingly exceed expected equilibrium conditions, calculated from in situ temperature data (annual mean 12.3[+ or -]0.3[degrees]C) and seawater isotopic composition (0.5[+ or -]0.1a[degrees][delta].sup.18O SMOW), by 0.5a[degrees] on average. Such positively shifting vital effects, previously reported for limpets and barnacles, are often overlooked in high-temperature and high-amplitude settings and may be more common than is currently believed. Carbon isotopes range from 0.2 to 3.5a[degrees][delta].sup.13C V-PDB (mean 1.8[+ or -]0.7a[degrees]) and show an ontogenetic decrease, but may incorporate an environmental signal in adult portions, indicated by a strong correspondence of peaks between specimens. This signal is likely driven by a complex interplay of different factors, such as primary production, current-based food supply and metabolism. Author Affiliation: (a) GeoZentrum Nordbayern, Erlangen University, Loewenichstr. 28, D-91054 Erlangen, Germany (b) Departamento de Biologia Animal, Facultad de Ciencias, Universidad de Malaga, E-29071 Malaga, Spain (c) CNR-Istituto di Scienze Marine, Via Gobetti 101, I-40129 Bologna, Italy (d) Rebikoff-Niggeler Foundation, Rocha Vermelha, Praia do Almoxarife, 9900-451 Horta, Faial, Azores, Portugal Article History: Received 9 April 2008; Revised 30 September 2008; Accepted 10 October 2008

Bacillus subtilis produces [alpha]-L-arabinofuranosidases (EC 3.2.1.55; AFs) capable of releasing arabinosyl oligomers and L-arabinose from plant cell walls. Here, we show by insertion-deletion mutational analysis that genes abfA and xsa(asd), herein renamed abf2, encode AFs responsible for the majority of the intracellular AF activity in B. subtilis. Both enzyme activities were shown to be cytosolic and functional studies indicated that arabino-oligomers are natural substrates for the AFs. The products of the two genes were overproduced in Escherichia coli, purified and characterized. The molecular mass of the purified AbfA and Abf2 was about 58 kDa and 57 kDa, respectively. However, native PAGE gradient gel analysis and cross-linking assays detected higher-order structures (>250 kDa), suggesting a multimeric organization of both enzymes. Kinetic experiments at 37 [degrees]C, with p-nitrophenyl-[alpha]-L-arabinofuranoside as substrate, gave an apparent [K.sub.m] of 0.498 mM and 0.421 mM, and [V.sub.max] of 317 U [mg.sup.-1] and 311 U [mg.sup.-1] for AbfA and Abf2, respectively. The two enzymes displayed maximum activity at 50 [degrees]C and 60 [degrees]C, respectively, and both proteins were most active at pH 8.0. AbfA and Abf2 both belong to family 51 of the glycoside hydrolases but have different substrate specificity. AbfA acts preferentially on (1[right arrow]5) linkages of linear [alpha]-1,5-L-arabinan and [alpha]-1,5-linked arabino-oligomers, and is much less effective on branched sugar beet arabinan and arabinoxylan and arabinogalactan. In contrast, Abf2 is most active on (1[right arrow]2) and (1[right arrow]3) linkages of branched arabinan and arabinoxylan, suggesting a concerted contribution of these enzymes to optimal utilization of arabinosecontaining polysaccharides by B. subtilis.

Bacterial biodegradation of hydrocarbons, an important process for environmental remediation, requires the passage of hydrophobic substrates across the cell membrane. Here, we report crystal structures of two outer membrane proteins, Pseudomonas putida TodX and Ralstonia pickettii TbuX, which have been implicated in hydrocarbon transport and are part of a subfamily of the FadL fatty acid transporter family. The structures of TodX and TbuX show significant differences with those previously determined for Escherichia coli FadL, which may provide an explanation for the substrate-specific transport of TodX and TbuX observed with in vivo transport assays. The TodX and TbuX structures revealed 14-stranded [beta]-barrels with an N-terminal hatch domain blocking the barrel interior. A hydrophobic channel with bound detergent molecules extends from the extracellular surface and is contiguous with a passageway through the hatch domain, lined by both hydrophobic and polar or charged residues. The TodX and TbuX structures support a mechanism for transport of hydrophobic substrates from the extracellular environment to the periplasm via a channel through the hatch domain. membrane protein | x-ray structure

We investigated dissolved organic matter (DOM) metabolism by employing plug-flow biofilm reactors and ultra high resolution mass spectrometry of DOM isolated by C18 extraction in two forested stream ecosystems, a low DOM tropical stream sampled at baseflow and a higher DOM temperate stream sampled during a storm. On passage through the bioreactors, DOM concentrations in the tropical stream sample declined by 22%, whereas they declined by 42% in the temperate stream sample. The extracted DOM was subjected to electrospray ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry to obtain information on molecular weight distributions and elemental compositions for the thousands of compounds whose masses are calculated with sufficient accuracy to allow calculation of unique elemental formulas. In both streams, metabolism modifies DOM to lower molecular weight molecules, and oxygen-rich molecules are selectively biodegraded. Applying van Krevelen analyses for the unique elemental formulas of DOM constituents revealed that hydrogen-deficient molecules with low H : C ratios (assigned to black carbon--derived molecules) are present and generally not metabolized. Black carbon molecules are refractory to biodegradation compared with other components of DOM, supporting the suggestion that black carbon molecules in DOM flow to the ocean without experiencing significant microbial degradation.

Pseudomonas sp. strain MT1 is capable of degrading 4-and 5-chlorosalicylates via 4-chlorocatechol, 3-chloromuconate, and maleylacetate by a novel pathway. 3-Chloromuconate is transformed by muconate cycloisomerase of MT1 into protoanemonin, a dominant reaction product, as previously shown for other muconate cycloisomerases. However, kinetic data indicate that the muconate cycloisomerase of MT1 is specialized for 3-chloromuconate conversion and is not able to form cis-dienelactone. Protoanemonin is obviously a dead-end product of the pathway. A trans-dienelactone hydrolase (trans-DLH) was induced during growth on chlorosalicylates. Even though the purified enzyme did not act on either 3-chloromuconate or protoanemonin, the presence of muconate cylcoisomerase and trans-DLH together resulted in considerably lower protoanemonin concentrations but larger amounts of maleylacetate formed from 3-chloromuconate than the presence of muconate cycloisomerase alone resulted in. As trans-DLH also acts on 4-fluoromuconolactone, forming maleylacetate, we suggest that this enzyme acts on 4-chloromuconolactone as an intermediate in the muconate cycloisomerase-catalyzed transformation of 3-chloromuconate, thus preventing protoanemonin formation and favoring maleylacetate formation. The maleylacetate formed in this way is reduced by maleylacetate reductase. Chlorosalicylate degradation in MT1 thus occurs by a new pathway consisting of a patchwork of reactions catalyzed by enzymes from the 3-oxoadipate pathway (catechol 1,2-dioxygenase, muconate cycloisomerase) and the chlorocatechol pathway (maleylacetate reductase) and a trans-DLH.

A bacterial consortium comprising four different species was isolated from an Indonesian agricultural soil using a mixture of aniline and 4-chloroaniline (4CA) as principal carbon sources. The four species were identified as Chryseobacterium indologenes SB1, Comamonas testosteroni SB2, Pseudomonas corrugata SB4 and Stenotrophomonas maltophilia SB5. Growth studies on aniline and 4CA as single and mixed substrates demonstrated that the bacteria preferred to grow on and utilize aniline rather than 4CA, although both compounds were eventually depleted from the culture supernatant. However, despite 100% disappearance of the parent substrates, the degradation of 4CA was always characterized by incomplete dechlorination and 4-chlorocatechol accumulation. This result suggests that further degradation of 4-chlorocatechol may be the rate-limiting step in the metabolism of 4CA by the bacterial consortium. HPLC-UV analysis showed that 4-chlorocatechol was further degraded via an ortho-cleavage pathway by the bacterial consortium. This hypothesis was supported by the results from enzyme assays of the crude cell extract of the consortium revealing catechol 1,2-dioxygenase activity which converted catechol and 4-chlorocatechol to cis, cis-muconic acid and 3-chloro-cis, cis-muconic acid respectively. However, the enzyme had a much higher conversion rate for catechol [156 U [(g protein).sup.-1]] than for 4-chlorocatechol [17.2 U (g protein).sup.-1], indicating preference for non-chlorinated substrates. Members of the bacterial consortium were also characterized individually. All isolates were able to assimilate aniline. P. corrugata SB4 was able to grow on 4CA solely, while S. maltophilia SB5 was able to grow on 4-chlorocatechol. These results suggest that the degradation of 4CA in the presence of aniline by the bacterial consortium was a result of interspecies interactions.

Salmonella enterica forms polyhedral organelles during coenzyme [B.sub.12]-dependent growth on 1,2-propanediol (1,2-PD). Previously, these organelles were shown to consist of a protein shell partly composed of the PduA protein, the majority of the cell's [B.sub.12]-dependent diol dehydratase, and additional unidentified proteins. In this report, the polyhedral organelles involved in [B.sub.12]-dependent 1,2-PD degradation by S. enterica were purified by a combination of detergent extraction and differential and density gradient centrifugation. The course of the purification was monitored by electron microscopy and gel electrophoresis, as well as enzymatic assay of [B.sub.12]-dependent diol dehydratase. Following one-and two-dimensional gel electrophoresis of purified organelles, the identities and relative abundance of their constituent proteins were determined by N-terminal sequencing, protein mass fingerprinting, Western blotting, and densitometry. These analyses indicated that the organelles consisted of at least 15 proteins, including PduABB'CDEGHJKOPTU and one unidentified protein. Seven of the proteins identified (PduABB'JKTU) have some sequence similarity to the shell proteins of carboxysomes (a polyhedral organelle involved in autotrophic [CO.sub.2] fixation), suggesting that the S. enterica organelles and carboxysomes have a related multiprotein shell. In addition, S. enterica organelles contained four enzymes: [B.sub.12]-dependent diol dehydratase, its putative reactivating factor, aldehyde dehydrogenase, and ATP cob(I) alamin adenosyltransferase. This complement of enzymes indicates that the primary catalytic function of the S. enterica organelles is the conversion of 1,2-PD to propionyl coenzyme A (which is consistent with our prior proposal that the S. enterica organelles function to minimize aldehyde toxicity during growth on 1,2-PD). The possibility that similar protein-bound organelles may be more widespread in nature than currently recognized is discussed.

In this study, the genetic relationship of 19 Porphyromonas gingivalis isolates from patients with periodontitis was investigated by multilocus sequence analysis. Internal 400-600 bp DNA fragments of the 10 chromosomal genes ef-tu, ftsQ, hagB, gpdxJ, pepO, mcmA, dnaK, recA, pga and nah were amplified by PCR and sequenced. No two isolates were identical at all 10 loci. Phylogenetic analyses indicated a panmictic population structure of P. gingivalis. Split decomposition analysis, calculation of homoplasy ratios and analyses of clustered polymorphisms all indicate that recombination plays a major role in creating the genetic heterogeneity of P. gingivalis. A standardized index of association of 0.0898 indicates that the P. gingivalis genes analysed are close to linkage equilibrium.

The bacterial strain Delftia acidovorans P4a, isolated from an extreme environment (heavily contaminated with organochlorines, highly alkaline conditions in an aqueous environment), was found to mineralize 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid under alkaline conditions. Screening a genomic DNA library of the alkalitolerant strain for 2,4-D genes revealed the presence of the two 2,4-D gene clusters tfdCDEF and tfd[C.sub.II][E.sub.II]BKA, tfdR genes being located in the vicinity of each tfd gene cluster. The results showed that the putative genes of the complete 2,4-D degradation pathway are organized in a single genomic unit. Sequence similarities to homologous gene clusters indicate that the individual tfd elements of strain P4a do not share a common origin, but were brought together by recombination events. The entire region is flanked by insertion elements of the IS1071 and IS1380 families, forming a transposon-like structure of about 30 kb, of which 28.4 kb were analysed. This element was shown to be located on the bacterial chromosome. The present study provides the first reported case of a chromosomally located catabolic transposon which carries the genes for the complete 2,4-D degradation pathway.

Hydrothermal vent environments, particularly those associated with the vestimentiferan Riftia pachyptila, are believed to be among the highest chitin-producing systems. In order to elucidate the chitin cycle in these environments, we estimate the in situ chitin degradation rates of tube-worm exoskeletons. Our in situ experiments show that the tubes of Riftia are highly stable structures. Comparative measurements of the degradation rates of Riftia tubes and crab shells immersed at deep-sea vents show that the tubes would be degraded within 2.5 years, whereas the time for the total degradation of the vent crab (Bythograea thermydron) carapaces would not exceed 36 days. The importance of the microbial participation in this degradation was estimated for Riftia tubes. Based on previous work, we calculated chitin production by a population of Riftia tubes of about 750 g [m.sup.-2] [year.sup.-1] (763). From our in situ experiments, we estimated a microbial chitinolysis rate of about 500 g [m.sup.-2] [year.sup.-1] (496) (65% of the chitin produced). Exoskeletons containing [beta]-chitin appear more stable in natural environments than those containing [alpha]-chitin and would thus be less available as carbon and nitrogen sources. In contrast, isolated [beta]-chitin was hydrolysed faster than [alpha]-chitin during in vitro degradation experiments; for instance, Riftia [beta]-chitin was degraded about 3- to 4-fold faster than Bythograea [alpha]-chitin. A stabilization process by disulfide bonds of the proteins-chitin link, rather than the crystalline form of the chitin ([alpha]/[beta]), accounts for the resistance of Riftia tubes to enzymatic attacks.

Harvesting of the invasive Manila clam, Tapes philippinarum, is the main exploitative activity in the Venice lagoon, but the mechanical dredges used in this free-access regime produce a considerable disturbance of the lagoon ecosystem. An ecosystem approach to study the complex effects of clam harvesting was implemented using atrophic mass-balance model. The trophic relations in the ecosystem were quantified with a mixed trophic impact analysis and further evaluated by considering different explanations for the 'Tapes paradox', which consists of the apparent population enhancement of Manila clams by dredging and the apparent nutritional advantages that this species receives from re-suspended organic matter. The key-role played by this introduced species is highlighted by a network analysis that indicates a 'wasp-waist control' of the system by Manila clams. The model constructed to characterise the present state of the Venice lagoon ecosystem is compared with models produced for a reconstructed past lagoon and a projected future lagoon. The future model was obtained by simulating the elimination of clam dredging in 10 years. The three different models were compared using thermodynamic and informational indices. Simulating the elimination of clam dredging produced a 33% increase in artisanal fishery catches, carried out by means of static gears, even with no change in fishing effort. These simulations also forecast an increase in the mean trophic level of the artisanal fishery catches as a positive effect of eliminating mechanical clam harvesting.

Bacteria degrading the quorum-sensing (QS) signal molecule N-hexanoylhomoserine lactone were isolated from a tobacco rhizosphere. Twenty-five isolates degrading this homoserine lactone fell into six groups according to their genomic REP-PCR and rrs PCR-RFLP profiles. Representative strains from each group were identified as members of the genera Pseudomonas, Comamonas, Variovorax and Rhodococcus. All these isolates degraded N-acylhomoserine lactones other than the hexanoic acid derivative, albeit with different specificity and kinetics. One of these isolates, Rhodococcus erythropolis strain W2, was used to quench QS-regulated functions of other microbes. In vitro, W2 strongly interfered with violacein production by Chromobacterium violaceum, and transfer of pathogenicity in Agrobacterium tumefaciens. In planta, R. erythropolis W2 markedly reduced the pathogenicity of Pectobacterium carotovorum subsp, carotovorum in potato tubers. These series of results reveal the diversity of the QS-interfering bacteria in the rhizosphere and demonstrate the validity of targeting QS signal molecules to control pathogens with natural bacterial isolates.

Expression of the genes of the alkane degradation pathway encoded in the Pseudomonas putida OCT plasmid are subject to negative and dominant global control depending on the carbon source used and on the physiological status of the cell. We investigated the signals responsible for this control in chemostat cultures under conditions of nutrient or oxygen limitation. Our results show that this global control is not related to the growth rate and responds to two different signals. One signal is the concentration of the carbon source that generates the repressing effect (true catabolite repression control). The second signal is influenced by the level of expression of the cytochome o ubiquinol oxidase, which in turn depends on factors such as oxygen availability or the carbon source used. Since under carbon limitation conditions the first signal is relieved but the second signal is not, we propose that modulation mediated by the cytochrome o ubiquinol oxidase is not classical catabolite repression control but rather a more general physiological control mechanism. The two signals have an additive, but independent, effect, inhibiting induction of the alkane degradation pathway.

Clostridium cellulolyticum secretes large multienzymatic complexes with plant cell wail-degrading activities named cellulosomes. Most of the genes encoding cellulosomal components are located in a large gene cluster: cipC-cel48F-cel8C-cel9G-cel9E-orfX-cel9H-cel9J-man5K-cel9M. Downstream of the cel9M gene, a new open reading frame was discovered and named rgl11Y. Amino acid sequence analysis indicates that this gene encodes a multidomain pectinase, Rgl11Y, containing an N-terminal signal sequence, a catalytic domain belonging to family 11 of the polysaccharide lyases, and a C-terminal dockerin domain. The present report describes the biochemical characterization of a recombinant form of Rgl11Y. Rgl11Y cleaves the [alpha]-L-Rhap-(1[vector]4)-[alpha]-D-GalpA glycosidic bond in the backbone of rhamnogalacturonan I (RGI) via a [beta]-elimination mechanism. Its specific activity on potato pectic galactan and rhamnogalacturonan was found to be 28 and 3.6 IU/mg, respectively, indicating that Rgl11Y requires galactan decoration of the RGI backbone. The optimal pH of Rgl11Y is 8.5 and calcium is required for its activity. Rgl11Y was shown to be incorporated in the C. cellulolyticum cellulosome through a typical cohesin-dockerin interaction. Rgl11Y from C. cellulolyticum is the first cellulosomal rhamnogalacturonase characterized.

Mitochondrial release of cytochrome c in apoptotic cells activates caspases, which execute apoptotic cell death. However, the events themselves that culminate in caspase activation can have deleterious effects because caspase inhibitor-saved cells ultimately die in a caspase-independent manner. To determine what events may underlie this form of cell death, we examined bioenergetic changes in sympathetic neurons deprived of NGF in the presence of a broad-spectrum caspase inhibitor, boc-aspartyl-(OMe)-fluoromethylketone. Here, we report that NGF-deprived,boc-aspartyl-(OMe)-fluoromethylketone--saved neurons rely heavily on glycolysis for ATP generation and for survival. Second, the activity of F0F1 contributes to caspase-independent death, but has only a minor role in the maintenance of mitochondrial membrane potential, which is maintained primarily by electron transport. Third, permeability transition pore inhibition by cyclosporin A attenuates NGF deprivation-induced loss of mitochondrial proteins, suggesting that permeability transition pore opening may have a function in regulating the degradation of mitochondria after cytochrome c release. Identification of changes in caspase inhibitor-saved cells may provide the basis for rational strategies to augment the effectiveness of the therapeutic use of postmitochondrial interventions.

Cryptococcus neoformans is a pathogenic fungus that produces melanin when incubated in the presence of certain phenolic substrates such as L-3, 4-dihydroxyphenylalanine (L-dopa). Melanin is an enigmatic polymer that is deposited in the cell wall and contributes to virulence. Substantial progress has been made in understanding the synthesis of melanin and the mechanisms by which it contributes to virulence, but relatively little is known about how melanin is rearranged during growth and budding. In this study we used transmission and scanning electron microscopy and immunofluorescence of melanized cells and melanin 'ghosts' to study the process of melanization during replication. Budding in melanized C. neoformans results in focal disruption of cell-wall melanin at the bud site. In the presence of L-dopa, bud-related melanin defects are repaired and daughter cells are melanized. However, in the absence of substrate, mother cells cannot repair their melanin defects and daughter cells are non-melanized. Hence, melanin in the parent cell is not carried to the daughter cells, but rather is synthesized de novo in buds. These results imply that melanin remodelling occurs during cell growth in a process that involves degradation and synthesis at sites of budding.

The haem pigment of Porphyromonas gingivalis is composed of [micro]-oxo bishaem, [[Fe(III)PPIX].sub.2]O, but the nature of that generated by Prevotella species has not been established. Mossbauer, Raman and UV-visible spectrophotometry were used to characterize the haem pigment of Prevotella intermedia and Prevotella nigrescens. M6ssbauer and Raman spectroscopy revealed the major haem species to be monomeric iron protoporphyrin IX, Fe(III)PPIX.OH (haematin). The terminal growth pH of both species on blood agar was between 5.8 and 6.0, which favours the formation and maintenance of monomeric Fe(III)PPIX.OH. Incubation of Pr. nigrescens and Pr. intermedia with oxyhaemoglobin at pH 6.5 resulted in formation of aquomethaemoglobin which was degraded to generate Fe(III) PPIX.OH which in turn became cell-associated, whilst incubation at pH 7*5 resulted in formation of [[Fe(III)PPIX].sub.2]O. It is concluded that both Prevotella species degrade oxyhaemoglobin to form [[Fe(III)PPIX].sub.2]O as an intermediate, which is converted to Fe(III)PPIX.OH through a depression in pH. The low pH encourages cell-surface deposition of insoluble Fe(III)PPIX.OH which would act as a barrier against oxygen and reactive oxygen species, and also protect against [H.sub.2][O.sub.2] through its inherent catalase activity.

The development of protein-based vaccines remains a major challenge in the fields of immunology and drug delivery. Although numerous protein antigens have been identified that can generate immunity to infectious pathogens, the development of vaccines based on protein antigens has had limited success because of delivery issues. In this article, an acid-sensitive microgel material is synthesized for the development of protein-based vaccines. The chemical design of these microgels is such that they degrade under the mildly acidic conditions found in the phagosomes of antigen-presenting cells (APCs). The rapid cleavage of the microgels leads to phagosomal disruption through a colloid osmotic mechanism, releasing protein antigens into the APC cytoplasm for class I antigen presentation. Ovalbumin was encapsulated in microgel particles, 200-500 nm in diameter, prepared by inverse emulsion polymerization with a synthesized acid-degradable crosslinker. Ovalbumin is released from the acid-degradable microgels in a pH-dependent manner; for example, microgels containing ovalbumin release 80%. of their encapsulated proteins after 5 h at pH 5.0, but release only 10% at pH 7.4. APCs that phagocytosed the acid-degradable microgels containing ovalbumin were capable of activating ovalbumin-specific cytoxic T lymphocytes. The acid-degradable microgels developed in this article should therefore find applications as delivery vehicles for vaccines targeted against viruses and tumors, where the activation of cytoxic T lymphocytes is required for the development of immunity. polymer | crosslinker | encapsulation | vaccination | cytotoxic T lymphocyte

The second and third modules of human decay accelerating factor (DAF) are necessary and sufficient to accelerate decay of the classical pathway (CP) convertase of complement. No structure of a mammalian protein with decay-accelerating activity has been available to date. We therefore determined the solution structure of DAF modules 2 and 3 (DAF~2,3). Structure-guided analysis of 24 mutants identified likely contact points between DAF and the CP convertase. Three (R96, R69, and a residue in the vicinity of L171) lie on DAF~2,3's concave face. A fourth, consisting of K127 and nearby R100, is on the opposite face. Regions of module 3 remote from the semiflexible 2-3 interface seem not to be involved in binding to the CP convertase. DAF thus seems to occupy a groove on the CP convertase such that both faces of DAF close to the 2-3 junction (including a positively charged region that encircles the protein at this point) interact simultaneously. Alternative pathway convertase interactions with DAF require additional regions of CCP 3 lying away from the 2-3 interface, consistent with the established additional requirement of module 4 for alternative pathway regulation. CD55 | structure | complement control protein module

It has been proposed that the topoisomerase II (TOP2)[beta]-DNA covalent complex arrests transcription and triggers 26S proteasome-mediated degradation of TOP2[beta]. It is unclear whether the initial trigger for proteasomal degradation is due to DNA damage or transcriptional arrest. In the current study we show that the TOP2 catalytic inhibitor 4,4-(2,3-butanediyl)-bis(2,6-piperazinedione) (ICRF-193), which traps TOP2 into a circular clamp rather than the TOP2-DNA covalent complex, can also arrest transcription. Arrest of transcription, which is TOP[beta]dependent, is accompanied by proteasomal degradation of TOP2[beta]. Different from TOP2 poisons and other DNA-damaging agents, ICRF-193 did not induce proteasomal degradation of the large subunit of RNA polymerase II. These results suggest that proteasomal degradation of TOP2[beta] induced by the TOP2-DNA covalent complex or the TOP2 circular clamp is due to transcriptional arrest but not DNA damage. By contrast, degradation of the large subunit of RNA polymerase II is due to a DNA-damage signal.

Most of the substrates degraded by the proteasome are marked with polyubiquitin chains. However, there are a limited number of examples of nonubiquitinated proteins that are degraded by the proteasome. Here, we describe the degradation of the retinoblastoma family of tumor suppressor proteins by the proteasome in the absence of polyubiquitination. The retinoblastoma protein (p105), p107, and p130 are each targeted for degradation by the pp71 protein, which is encoded by the UL82 gene of human cytomegalovirus. It functions to direct their degradation in the absence of other viral proteins. While the pp71-mediated degradation of the retinoblastoma family of proteins requires proteasome function, it occurs without the attachment of ubiquitin to the substrates and in the absence of a functioning ubiquitin-conjugation system.

[beta]-Glucuronidase (GUSB) is a lysosomal enzyme important in the normal step-wise degradation of glycosaminoglycans. Deficiency of GUSB causes the lysosomal storage disease mucopolysaccharidosis VII (MPS VII, Sly disease). Affected patients have widespread progressive accumulation of [beta]-glucuronide-containing glycosaminoglycans in lysosomes. Enzyme replacement, bone marrow transplantation, and gene therapy can correct lysosomal storage in the MPS VII mouse model. Gene therapy in MPS VII patients and animals may result in massive overexpression of GUSB in individual tissues, and the toxicity of such overexpression is incompletely investigated. To gain insight into the effect of massive overexpression of GUSB, we established 19 transgenic mouse lines, two of which expressed very high levels of human GUSB in many tissues. The founder overexpressing mice had from >100- to several thousand-fold increases in tissue and serum GUSB. The enzyme expression in most tissues decreased in subsequent generations in one line, and expression in liver and marrow fell in subsequent generations of the other. Both lines had morphologically similar widespread lysosomal storage of GUSB and secondary elevations of other lysosomal enzymes, a finding characteristic of lysosomal storage disease. One line developed tumors, and one did not. These transgenic models show that massive overexpression of a lysosomal enzyme can be associated with dramatic morphological alterations, which, at least in one of the two lines, had little clinical consequence. For the other transgenic line, the high frequency of tumor development in [F.sub.2] FVB progeny suggests that the vector used to generate the transgenic lines has an integration site-dependent potential to be oncogenic, at least in this strain background. Sly disease | MPS VII | lysosomal storage disease | gene therapy | tumor susceptibility

Meiofauna from Avicennia marina leaf litter in a temperate mangrove forest was enumerated, and the nematode assemblages compared on the bases of leaf colour (used as a guide to leaf age) and shore horizon where samples were collected. Twenty-one putative nematode species were collected from 48 leaf litter samples. Univariate analyses indicated that neither the colour of the leaf nor the shore horizon significantly affected abundance of nematodes. However, of the four (2x2) treatment groups, rarefaction curves revealed highest diversity on brown leaves from under the shade of the tree canopy (H'=0.751 [+ or -] 0.126 SE, n=17). Species diversity of leaf litter nematodes was lower in this temperate mangrove system than reported from tropical mangrove studies. ANOSIM tests confirmed a significant effect of shore horizon on nematode assemblages. The dominant feeding group among nematodes was non-selective deposit feeders (7/21 species, but 77% of all nematodes). Epigrowth grazers were represented by 8/21 species of nematodes, but only 19% of the total number. Excised leaves became skeletonised by about 15 weeks. Shorter temporal scales of life cycles of nematodes compared with leaf degradation, and the dynamic nature of epibiontic assemblages, probably explain the similar assemblage structure on yellow and brown leaves.

Newly synthesized proteins that do not fold correctly in the ER are targeted for ER-associated protein degradation (ERAD) through distinct sorting mechanisms; soluble ERAD substrates require ER-Golgi transport and retrieval for degradation, whereas transmembrane ERAD substrates are retained in the ER. Retained transmembrane proteins are often sequestered into specialized ER subdomains, but the relevance of such sequestration to proteasomal degradation has not been explored. We used the yeast Saccharomyces cerevisiae and a model ERAD substrate, the cystic fibrosis transmembrane conductance regulator (CFTR), to explore whether CFTR is sequestered before degradation, to identify the molecular machinery regulating sequestration, and to analyze the relationship between sequestration and degradation. We report that CFTR is sequestered into ER subdomains containing the chaperone Kar2p, and that sequestration and CFTR degradation are disrupted in sec[12.sup.ts] strain (mutant in guanine-nucleotide exchange factor for Sar1p), sec[13.sup.ts] strain (mutant in the Sec13p component of COPII), and sec[23.sup.ts] strain (mutant in the Sec23p component of COPII) grown at restrictive temperature. The function of the Sar1p/COPII machinery in CFTR sequestration and degradation is independent of its role in ER-Golgi traffic. We propose that Sar1p/COPII-mediated sorting of CFTR into ER subdomains is essential for its entry into the proteasomal degradation pathway. These findings reveal a new aspect of the degradative mechanism, and suggest functional crosstalk between the secretory and the degradative pathways.

Research describes the alicyclic hydrocarbon, ethylcyclopentane, biodegradation under anaerobic conditions by a sulfate-reducing bacterial enrichment isolated from a gas condensate-contaminated aquifer. Results indicate that alicyclic hydrocarbons are anaerobically activated to form alkylsuccinate derivatives under sulfate-reducing conditions.

Research has been conducted on isolated light-harvesting proteins. The study of light-mediated degradation of these proteins and of oxygen free radicals involvement in the process has been carried out, and the results demonstrate that active oxygen is involved in light-harvesting protein degradation in these isolated subcomplexes.

Rsearch has been conducted on plant cell wall degradation by Clostridium cellulovorans. The hemicellulose degradation system of this bacterium has been investigated via the characterization of noncellulosomal alpha-arabinosidae genes, and the details are reported.

Research has been conducted on soluble cytoplasmic chemoreceptor. The characterization of this chemoreceptor has been carried out in investigating the hypothesis whether ClpX-mediated proteolysis may be commonly used to regulate chemotaxis mashinery during Caulobacter crescentus cell cycle, and the details are reposter.

Research has been conducted on polychlorinated biphenyl-degrading bacteria. The ability of these bacteria to differentiate between atropisomeric polychlorinated biphenyl congener enantiomers after growth in the presence of carvone, biphenyl, cymene or tryptone-soytone has been investigated, and the details are reported.

Research has been conducted on bacteria belonging to the genus Cycloclasticus. The role of these bacteria in petroleum polynuclear aromatic hydrocarbon biodegradation has been investigated in marine environment, and the results are reported.

Research has been conducted on gasoline oxygenate methyl tert-ether, a ground-water contaminant. Results suggest that improved microbial transport can lead to a bioaugmentation strategy for gasoline oxygenate methyl tert-ether-contaminated sites lacking indigenous oxygenate degraders.

Research has been conducted on biodegradative microbial populations. The effect of nutrients ammendments on these populations has been investigated, and the results are reported.

Research has been conducted on hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (RDX). The degradation of RDX by hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine-mineralizing strain, Klebsiella pneumoniae strain SCZ-1, has been investigated, and the details are reported.