bluuebunny/crossref_metadata_2025 huggingface dataset:
Melting and melt segregation in the aureole of the Glenmore Plug, Ardnamurchan
Authors: HOLNESS M. B. , DANE K. , SIDES R. , RICHARDSON C. , CADDICK M.
Published: February 2005

Contact metamorphism caused by the Glenmore plug in Ardnamurchan, a magma conduit active for 1 month, resulted in partial melting, with melt now preserved as glass. The pristine nature of much of the aureole provides a natural laboratory in which to investigate the distribution of melt. A simple thermal model, based on the first appearance of melt on quartz–feldspar grain boundaries, the first appearance of quartz paramorphs after tridymite and a plausible magma intrusion temperature, provides a time‐scale for melting. The onset of melting on quartz–feldspar grain boundaries was initially rapid, with an almost constant further increase in melt rim thickness at an average rate of 0.5–1.0 × 10−9 cm s−1. This rate was most probably controlled by the distribution of limited amounts of H2O on the grain boundaries and in the melt rims.

The melt in the inner parts of the aureole formed an interconnected grain‐boundary scale network, and there is evidence for only limited melt movement and segregation. Layer‐parallel segregations and cross‐cutting veins occur within 0.6 m of the contact, where the melt volume exceeded 40%. The coincidence of the first appearance of these signs of the segregation of melt in parts of the aureole that attained the temperature at which melting in the Qtz–Ab–Or system could occur, suggests that internally generated overpressure consequent to fluid‐absent melting was instrumental in the onset of melt movement.
CD226 is expressed on the megakaryocytic lineage from hematopoietic stem cells/progenitor cells and involved in its polyploidization
Authors: Ma Dongchu , Sun Yinghui , Lin Di , Wang Haoyang , Dai Bing , Zhang Xinghai , Ouyang Weiming , Jian Jinlong , Jia Wei , Xu Xiaoguang , Jin Boquan
Published: February 2005

Abstract:  Objectives:  In this study, we examined the expression of CD226 on megakaryocytic, granulocytic and erythroid lineage from hematopoietic stem cells/progenitor cells in adult and fetus and its potential role in megakaryocytic maturation. Methods: CD34+ cells from adult and fetus were induced to differentiate toward the megakaryocytic lineage by thrombopoietin (TPO) and the granulocytic lineage by granulocyte colony‐stimulating factor (G‐CSF), respectively. Mononuclear cells from fetal liver and CD34+ cells from adult were induced to differentiate toward erythroid‐lineage by erythropoiesis (EPO). We investigated the expression of CD226 and lymphocyte function associated antigen‐1 (LFA‐1) (CD11a) during hemopoiesis. We also studied the effect of CD226 monoclonal antibody (MoAb) and LFA‐1 MoAb on megakaryocyte with antibody cross‐liking technique. Results: CD34+ cells from adult and fetus and TPO‐induced CD41+ cells all expressed CD226 molecule. CD226 was not expressed on erythroid progenitor cells and erythroblasts and most cells of granulocytic lineage although G‐CSF induced a significant increase of the expression of CD226 on CD34+ cells in early period of time. CD226 MoAb acts on megakaryocytes by inducing intracellular calcium mobilization. The expression of LFA‐1 decreased significantly at late stage of differentiation and maturation of fetal megakaryocytes whereas the expression of LFA‐1 on adult megakaryocytes retained at a high level. CD226 MoAb in combination with LFA‐1 MoAb shifted the ploidy of generated megakaryocytes from adult‐derived CD34+ cells to higher classes significantly although CD226 and LFA‐1 MoAb slightly increased the ploidy of the generated megakaryocytes individually. CD226 MoAb or LFA‐1 MoAb or CD226 MoAb plus LFA‐1 MoAbs did not increase the ploidy of the generated megakaryocytes from fetus‐derived CD34+ cells. Conclusion: CD226 molecules play an important role in maturation of the megakaryocytes in combination with LFA‐1.
Successful treatment with splenectomy and interferon alpha against recurred hemophagocytic syndrome in remission state of anaplastic large cell lymphoma following high‐dose therapy and autologous peripheral blood stem cell transplantation
Authors: Cho Seok Goo , Koh Yong Bok , Chang Hong Seok , Park Gyeongsin , Kang Chang Suk , Park Jong Won , Min Woo Sung
Published: February 2005

Abstract:  A 25‐yr‐old man had been diagnosed as having CD30+ anaplastic large cell lymphoma associated with hemophagocytic syndrome (HS). He received aggressive frontline chemotherapies and consolidation with autologous peripheral blood stem cell transplantation (PBSCT) following high‐dose chemotherapy combined with splenic irradiation (720 cGy in fraction of 180 cGy). However, HS recurred on day 50 of PBSCT without radiologic evidence of lymphoma relapse. On day 56 of PBSCT, splenectomy was performed and pathology showed massive sinusoidal infiltration of histiocytes. On day 68 of PBSCT, administration of interferon alpha was started and maintained for 24 months. HS was completely resolved and he has been alive well and in complete remission (CR), 60 months after initial diagnosis.
Successful treatment of mediastinal lymphomatoid granulomatosis with rituximab monotherapy
Authors: Jordan Karin , Grothey Axel , Grothe Wilfried , Kegel Thomas , Wolf Hans‐Heinrich , Schmoll Hans‐Joachim
Published: February 2005

Abstract:  Lymphomatoid granulomatosis is a rare Epstein–Barr virus (EBV)‐positive‐B‐cell lymphoproliferative disorder. Treatment options include corticosteroids, antiviral therapy, interferon‐alpha and chemotherapy. However, long‐term prognosis is poor and no therapeutic standard has been established yet. In a 21‐year‐old woman, a biopsy of mediastinal mass revealed lymphomatoid granulomatosis. Combined therapy with valganciclovir and interferon‐alpha proved ineffective. In view of the CD20 expression of the tumor cells, monotherapy with rituximab was intiated. After 3 months a complete remission was achieved. Rituximab was continued for another 6 months with subsequent consolidation radiotherapy. This is the first report of an enduring complete remission (20 months) of a non‐CNS lymphomatoid granulomatosis treated with rituximab.
Hepatitis B virus reactivation and alemtuzumab therapy
Authors: Iannitto Emilio , Minardi Viviana , Calvaruso Giuseppina , Mulè Antonino , Ammatuna Emanuele , Trapani Rosa D. , Ferraro Donatella , Abbadessa Vincenzo , Craxí Antonio , Stefano Rosa D.
Published: February 2005

Abstract:  Reactivation of hepatitis B virus infection in subjects receiving cytotoxic treatment for heamatological malignancies occurs in 21–53% of chronic HBsAg carriers and in an unknown number of HBsAg negative subjects harbouring occult HBV infection. Immunotherapy with alemtuzumab, a humanized monoclonal antibody against CD52 epitopes on lymphocytes cells produces deep immunosuppression. We describe two subjects with chronic lymphocytic leukaemia and occult HBV infection who developed a virological and biochemical flare of hepatitis B following immunotherapy with alemtuzumab. One of them developed full blown hepatitis with seroreversion from anti‐HBs to HBsAg after four weeks of alemtuzumab therapy. Lamivudine (100 mg die) achieved a complete clinical recovery and HBV‐DNA clearance from blood within 8 weeks. The second patient (HBsAg and HBV‐DNA seronegative, anti‐HBs and anti‐HBc positive before treatment) was kept under prophylaxis with lamivudine up to three months after alemtuzumab. Two months after withdrawal of lamivudine, clinical and laboratory features of acute hepatitis B developed. Lamivudine therapy was restarted and a prompt recovery was obtained with HBsAg and HBV‐DNA clearance.
Safety of oral iron chelator deferiprone in young thalassaemics
Authors: Naithani Rahul , Chandra Jagdish , Sharma Sharad
Published: February 2005

Abstract:  Deferiprone is now widely used for iron chelation in patients with thalassaemia. Studies on its efficacy and safety have largely included older children and adults. Objective: To assess the safety of deferiprone in children <6 yr of age. Methods: The study is based on scrutiny of follow‐up data of 44 patients of age <6 yr receiving deferiprone for a variable period of time. Occurrence of various side effects including gastrointestinal, osteoarticular were noticed and complete blood counts were performed every 2–4 wk. Results: Nausea and vomiting were noticed in 12 (27.2%), joint symptoms were reported by four (9.1%) and neutropenia was observed in only two patients (4.5%). None of the patient had agranulocytosis. Thrombocytopenia was observed in 20 patients (45.45%), which occurred 3 months to 1 yr after deferiprone therapy. Interruption of deferiprone for 2–4 wk led to reversal of symptoms in all but two patients. Conclusion: Thrombocytopenia is one of the major side effects in young thalassaemics and necessitates frequent close monitoring of blood counts but its resolution after discontinuation and absence of clinical evidence of bleeding does not preclude its use.
Neurological toxicity of long‐term (>1 yr) thalidomide therapy in patients with multiple myeloma
Authors: Tosi Patrizia , Zamagni Elena , Cellini Claudia , Plasmati Rosaria , Cangini Delia , Tacchetti Paola , Perrone Giulia , Pastorelli Francesca , Tura Sante , Baccarani Michele , Cavo Michele
Published: February 2005

Objective: Thalidomide is remarkably active in advanced relapsed and refractory multiple myeloma (MM), so that its use has been recently proposed either in newly diagnosed patients or as maintenance treatment after conventional or high‐dose therapy. This latter therapeutic approach has risen the concern of side‐effects of long‐term therapy with this drug. Methods: We analysed long‐term toxicity of 40 patients (27 M, 13 F, median age = 61.5 yr) who received salvage therapy with thalidomide ± dexamethasone for longer than 12 months (median 15, range 12–44) at our centre. All the patients had achieved at least a stable disease upon treatment with thalidomide alone (200–400 mg/d, n = 20) or thalidomide (200 mg/d) and dexamethasone (40 mg/d for 4 d every 4 wk) (n = 20). Results and conclusions: Neurotoxicity was the most troublesome and frequent toxic effect that was observed after long‐term treatment, the incidence averaging 75%. Among these 30 patients symptoms included paraesthesias, tremor and dizziness. Neurotoxicity was grade 1 in six patients (15%); grade 2 in 13 patients (32.5%), thus determining thalidomide dose reduction to 100 mg/d; and grade 3 in 11 patients (27.5%) who had subsequently to interrupt therapy despite their response. Electromyographic study, performed in patients with grade ≥2 neurotoxicity, revealed a symmetrical, mainly sensory peripheral neuropathy, with minor motor involvement. The severity of neurotoxicity was not related to cumulative or daily thalidomide dose, but only to the duration of the disease prior to thalidomide treatment, although no patients presented neurological symptoms at study entry. These results suggest that long‐term thalidomide therapy in MM may be hampered by the remarkable neurotoxicity of the drug, and that a neurological evaluation should be mandatory prior to thalidomide treatment, in order to identify patients at risk of developing a peripheral neuropathy.
A case of post‐transplant lymphoproliferative disease presenting as CD20‐expressing, Epstein–Barr‐virus positive Hodgkin lymphoma
Authors: Stern M. , Herrmann R. , Rochlitz C. , Dirnhofer S. , Pless M.
Published: February 2005

Abstract:  Classical Hodgkin lymphoma (HL) is a rare complication after solid organ transplantation. We describe the first case of a patient developing CD20‐positive HL after renal transplantation treated with the monoclonal antibody rituximab. Treatment with single agent rituximab led to partial remission. Subsequent combined modality treatment consisting of chemotherapy (adriamycin, bleomycin, vindesin and dacarbacin), immunotherapy (rituximab) and involved field irradiation achieved complete remission. Different therapeutic strategies in the treatment of patients developing lymphoproliferative disease – and particularly HL – after solid organ transplantation are discussed.
Crystal Structure of a Complex Between the Catalytic and Regulatory (RIα) Subunits of PKA
Authors: Kim Choel , Xuong Nguyen-Huu , Taylor Susan S.
Published: February 2005

The 2.0-angstrom structure of the cyclic adenosine monophosphate (cAMP)–dependent protein kinase (PKA) catalytic subunit bound to a deletion mutant of a regulatory subunit (RIα) defines a previously unidentified extended interface. The complex provides a molecular mechanism for inhibition of PKA and suggests how cAMP binding leads to activation. The interface defines the large lobe of the catalytic subunit as a stable scaffold where Tyr
247
in the G helix and Trp
196
in the phosphorylated activation loop serve as anchor points for binding RIα. These residues compete with cAMP for the phosphate binding cassette in RIα. In contrast to the catalytic subunit, RIα undergoes major conformational changes when the complex is compared with cAMP-bound RIα. The inhibitor sequence docks to the active site, whereas the linker, also disordered in free RIα, folds across the extended interface. The β barrel of cAMP binding domain A, which is the docking site for cAMP, remains largely intact in the complex, whereas the helical subdomain undergoes major reorganization.
Dynamic Complex Formation During the Yeast Cell Cycle
Authors: de Lichtenberg Ulrik , Jensen Lars Juhl , Brunak Søren , Bork Peer
Published: February 2005

To analyze the dynamics of protein complexes during the yeast cell cycle, we integrated data on protein interactions and gene expression. The resulting time-dependent interaction network places both periodically and constitutively expressed proteins in a temporal cell cycle context, thereby revealing previously unknown components and modules. We discovered that most complexes consist of both periodically and constitutively expressed subunits, which suggests that the former control complex activity by a mechanism of just-in-time assembly. Consistent with this, we show that additional regulation through targeted degradation and phosphorylation by Cdc28p (Cdk1) specifically affects the periodically expressed proteins.
Saturn's Temperature Field from High-Resolution Middle-Infrared Imaging
Authors: Orton G. S. , Yanamandra-Fisher P. A.
Published: February 2005

Saturn was imaged between 8 and 24.5 micrometers at ∼3000-kilometer resolution with the Keck I Telescope. Saturn's atmosphere has zonal temperature bands, which are mostly uncorrelated with visible cloud reflectivity, strong 100-millibar zonal temperature oscillations near 32°S, a warm south polar cap, and a compact hot point within 3° of the south pole.
Aconitase Couples Metabolic Regulation to Mitochondrial DNA Maintenance
Authors: Chen Xin Jie , Wang Xiaowen , Kaufman Brett A. , Butow Ronald A.
Published: February 2005

Mitochondrial DNA (mtDNA) is essential for cells to maintain respiratory competency and is inherited as a protein-DNA complex called the nucleoid. We have identified 22 mtDNA-associated proteins in yeast, among which is mitochondrial aconitase (Aco1p). We show that this Krebs-cycle enzyme is essential for mtDNA maintenance independent of its catalytic activity. Regulation of
ACO1
expression by the HAP and retrograde metabolic signaling pathways directly affects mtDNA maintenance. When constitutively expressed, Aco1p can replace the mtDNA packaging function of the high-mobility-group protein Abf2p. Thus, Aco1p may integrate metabolic signals and mtDNA maintenance.
Use of Ethidium Monoazide and PCR in Combination for Quantification of Viable and Dead Cells in Complex Samples
Authors: Rudi Knut , Moen Birgitte , Drømtorp Signe Marie , Holck Askild L.
Published: February 2005

The distinction between viable and dead cells is a major issue in many aspects of biological research. The current technologies for determining viable versus dead cells cannot readily be used for quantitative differentiation of specific cells in mixed populations. This is a serious limitation. We have solved this problem by developing a new concept with the viable/dead stain ethidium monoazide (EMA) in combination with real-time PCR (EMA-PCR). A dynamic range of approximately 4 log
10
was obtained for the EMA-PCR viable/dead assay. Viable/dead differentiation is obtained by covalent binding of EMA to DNA in dead cells by photoactivation. EMA penetrates only dead cells with compromised membrane/cell wall systems. DNA covalently bound to EMA cannot be PCR amplified. Thus, only DNA from viable cells can be detected. We evaluated EMA-PCR with the major food-borne bacterium
Campylobacter jejuni
as an example. Traditional diagnosis of this bacterium is very difficult due to its specific growth requirements and because it may enter a state where it is viable but not cultivable. The conditions analyzed included detection in mixed and natural samples, survival in food, and survival after disinfection or antibiotic treatment. We obtained reliable viable/dead quantifications for all conditions tested. Comparison with standard fluorescence-based viable/dead techniques showed that the EMA-PCR has a broader dynamic range and enables quantification in mixed and complex samples. In conclusion, EMA-PCR offers a novel real-time PCR method for quantitative distinction between viable and dead cells with potentially very wide application.
Transcriptional Organization of Genes for Protocatechuate and Quinate Degradation from
Acinetobacter
sp. Strain ADP1
Authors: Dal Süreyya , Trautwein Gaby , Gerischer Ulrike
Published: February 2005

Quinate and protocatechuate are both abundant plant products and can serve, along with a large number of other aromatic or hydroaromatic compounds, as growth substrates for
Acinetobacter
sp. strain ADP1. The respective genes are part of the chromosomal
dca-pca-qui-pob-hca
cluster encoding these pathways. The adjacent
pca
and
qui
gene clusters, which encode enzymes for protocatechuate breakdown via the β-ketoadipate pathway and for the conversion of quinate or shikimate to protocatechuate, respectively, have the same direction of transcription and are both expressed inducibly in response to protocatechuate. The
pca
genes are governed by the transcriptional activator-repressor PcaU. The mechanism governing
qui
gene expression was previously unknown. Here we report data suggesting the existence of a large 14-kb primary transcript covering the
pca
and
qui
genes. The area between the
pca
and
qui
genes contains no promoter activity, whereas a weak, constitutive promoter was identified upstream of
quiA
(
quiAp
). The 5′ end of the
quiA
transcript was mapped. Northern blot analysis allowed the identification of a 12-kb transcript spanning
pcaI
to
quiX
. An analysis of the
pca
and
qui
gene transcripts in a strain missing the structural gene promoter
pcaIp
led to the identification of two
pcaIp
-independent transcripts (4 and 2.4 kb). The 2.4-kb transcript makes up about 25% of the total transcript abundance of
quiA
, and thus the majority of transcription of the last gene of the area is also driven by
pcaIp
. This report strongly supports the organization of the
pca
and
qui
genes as a
pca-qui
operon and, furthermore, suggests that PcaU is the regulator governing its expression.
Desulfitobacterium hafniense
Is Present in a High Proportion within the Biofilms of a High-Performance Pentachlorophenol-Degrading, Methanogenic Fixed-Film Reactor
Authors: Lanthier M. , Juteau P. , Lépine F. , Beaudet R. , Villemur R.
Published: February 2005

We developed a pentachlorophenol (PCP)-degrading, methanogenic fixed-film reactor by using broken granular sludge from an upflow anaerobic sludge blanket reactor. This methanogenic consortium was acclimated with increasing concentrations of PCP. After 225 days of acclimation, the reactor was performing at a high level, with a PCP removal rate of 1,173 μM day
−1
, a PCP removal efficiency of up to 99%, a degradation efficiency of approximately 60%, and 3-chlorophenol as the main chlorophenol residual intermediate. Analyses by PCR-denaturing gradient gel electrophoresis (DGGE) showed that
Bacteria
and
Archaea
in the reactor stabilized in the biofilms after 56 days of operation. Important modifications in the profiles of
Bacteria
between the original granular sludge and the reactor occurred, as less than one-third of the sludge DGGE bands were still present in the reactor. Fluorescence in situ hybridization experiments with probes for
Archaea
or
Bacteria
revealed that the biofilms were composed mostly of
Bacteria
, which accounted for 70% of the cells. With PCR species-specific primers, the presence of the halorespiring bacterium
Desulfitobacterium hafniense
in the biofilm was detected very early during the reactor acclimation period.
D. hafniense
cells were scattered in the biofilm and accounted for 19% of the community. These results suggest that the presence of PCP-dehalogenating
D. hafniense
in the biofilm was crucial for the performance of the reactor.
Propionate Oxidation by and Methanol Inhibition of Anaerobic Ammonium-Oxidizing Bacteria
Authors: Güven Didem , Dapena Ana , Kartal Boran , Schmid Markus C. , Maas Bart , van de Pas-Schoonen Katinka , Sozen Seval , Mendez Ramon , Op den Camp Huub J. M. , Jetten Mike S. M. , Strous Marc , Schmidt Ingo
Published: February 2005

Anaerobic ammonium oxidation (anammox) is a recently discovered microbial pathway and a cost-effective way to remove ammonium from wastewater. Anammox bacteria have been described as obligate chemolithoautotrophs. However, many chemolithoautotrophs (i.e., nitrifiers) can use organic compounds as a supplementary carbon source. In this study, the effect of organic compounds on anammox bacteria was investigated. It was shown that alcohols inhibited anammox bacteria, while organic acids were converted by them. Methanol was the most potent inhibitor, leading to complete and irreversible loss of activity at concentrations as low as 0.5 mM. Of the organic acids acetate and propionate, propionate was consumed at a higher rate (0.8 nmol min
−1
mg of protein
−1
) by Percoll-purified anammox cells. Glucose, formate, and alanine had no effect on the anammox process. It was shown that propionate was oxidized mainly to CO
2
, with nitrate and/or nitrite as the electron acceptor. The anammox bacteria carried out propionate oxidation simultaneously with anaerobic ammonium oxidation. In an anammox enrichment culture fed with propionate for 150 days, the relative amounts of anammox cells and denitrifiers did not change significantly over time, indicating that anammox bacteria could compete successfully with heterotrophic denitrifiers for propionate. In conclusion, this study shows that anammox bacteria have a more versatile metabolism than previously assumed.
Association ofCryptosporidium parvumwith Suspended Particles: Impact on Oocyst Sedimentation
Authors: Searcy Kristin E. , Packman Aaron I. , Atwill Edward R. , Harter Thomas
Published: February 2005

The association ofCryptosporidium parvumoocysts with suspended particles can alter the oocysts' effective physical properties and influence their transport in aquatic systems. To assess this behavior,C. parvumoocysts were mixed with various suspended sediments under a variety of water chemical conditions, and the resulting settling of the oocysts was observed. Direct microscopic observations showed that oocysts attached to suspended sediments. Settling column and batch experiments demonstrated that oocysts are removed from suspension at a much higher rate when associated with sediments. The rate of oocyst sedimentation depended primarily on the type of sediment with which the oocysts were mixed. Changes in background water conditions had a relatively small impact on the extent of oocyst-particle association and the resulting oocyst deposition. We believe that the ubiquitous association ofC. parvumoocysts with suspended particles enhances the sedimentation of oocysts in natural waters and that this interaction should generally be considered when predicting the migration of pathogens in the environment.
Phylogenetic Characterization of 16S rRNA Gene Clones from Deep-Groundwater Microorganisms That Pass through 0.2-Micrometer-Pore-Size Filters
Authors: Miyoshi Tatsuo , Iwatsuki Teruki , Naganuma Takeshi
Published: February 2005

A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-μm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-μm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-μm-pore-size filters were largely affiliated with
Betaproteobacteria
.
Discovery of
glpC
, an Organic Solvent Tolerance-Related Gene in
Escherichia coli
, Using Gene Expression Profiles from DNA Microarrays
Authors: Shimizu Kazunori , Hayashi Shuhei , Kako Takeshi , Suzuki Maiko , Tsukagoshi Norihiko , Doukyu Noriyuki , Kobayashi Takeshi , Honda Hiroyuki
Published: February 2005

Gene expression profiles were collected from
Escherichia coli
strains (OST3410, TK33, and TK31) before and after exposure to organic solvents, and the six genes that showed higher gene expression were selected. Among these genes,
glpC
encoding the anaerobic glycerol-3-phosphate dehydrogenase subunit C remarkably increased the organic solvent tolerance.
Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)
Authors: Besemer Katharina , Moeseneder Markus M. , Arrieta Jesus M. , Herndl Gerhard J. , Peduzzi Peter
Published: February 2005

Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition.
Key Role of Cysteine Residues in Catalysis and Subcellular Localization of Sulfur Oxygenase-Reductase of
Acidianus tengchongensis
Authors: Chen Zhi-Wei , Jiang Cheng-Ying , She Qunxin , Liu Shuang-Jiang , Zhou Pei-Jin
Published: February 2005

Analysis of known sulfur oxygenase-reductases (SORs) and the SOR-like sequences identified from public databases indicated that they all possess three cysteine residues within two conserved motifs (V-G-P-K-V-C
31
and C
101
-X-X-C
104
; numbering according to the
Acidianus tengchongensis
numbering system). The thio-modifying reagent
N
-ethylmaleimide and Zn
2+
strongly inhibited the activities of the SORs of
A. tengchongensis
, suggesting that cysteine residues are important. Site-directed mutagenesis was used to construct four mutant SORs with cysteines replaced by serine or alanine. The purified mutant proteins were investigated in parallel with the wild-type SOR. Replacement of any cysteine reduced SOR activity by 98.4 to 100%, indicating that all the cysteine residues are crucial to SOR activities. Circular-dichroism and fluorescence spectrum analyses revealed that the wild-type and mutant SORs have similar structures and that none of them form any disulfide bond. Thus, it is proposed that three cysteine residues, C
31
and C
101
-X-X-C
104
, in the conserved domains constitute the putative binding and catalytic sites of SOR. Furthermore, enzymatic activity assays of the subcellular fractions and immune electron microscopy indicated that SOR is not only present in the cytoplasm but also associated with the cytoplasmic membrane of
A. tengchongensis
. The membrane-associated SOR activity was colocalized with the activities of sulfite:acceptor oxidoreductase and thiosulfate:acceptor oxidoreductase. We tentatively propose that these enzymes are located in close proximity on the membrane to catalyze sulfur oxidation in
A. tengchongensis
.
Identification of Cyanophage Ma-LBP and Infection of the Cyanobacterium
Microcystis aeruginosa
from an Australian Subtropical Lake by the Virus
Authors: Tucker Stephen , Pollard Peter
Published: February 2005

Viruses can control the structure of bacterial communities in aquatic environments. The aim of this project was to determine if cyanophages (viruses specific to cyanobacteria) could exert a controlling influence on the abundance of the potentially toxic cyanobacterium
Microcystis aeruginosa
(host).
M. aeruginosa
was isolated, cultured, and characterized from a subtropical monomictic lake—Lake Baroon, Sunshine Coast, Queensland, Australia. The viral communities in the lake were separated from cyanobacterial grazers by filtration and chloroform washing. The natural lake viral cocktail was incubated with the
M. aeruginosa
host growing under optimal light and nutrient conditions. The specific growth rate of the host was 0.023 h
−1
; generation time, 30.2 h. Within 6 days, the host abundance decreased by 95%. The density of the cyanophage was positively correlated with the rate of
M. aeruginosa
cell lysis (
r
2
= 0.95). The cyanophage replication time was 11.2 h, with an average burst size of 28 viral particles per host cell. However, in 3 weeks, the cultured host community recovered, possibly because the host developed resistance (immunity) to the cyanophage. The multiplicity of infection was determined to be 2,890 virus-like particles/cultured host cell, using an undiluted lake viral population. Transmission electron microscopy showed that two types of virus were likely controlling the host cyanobacterial abundance. Both viruses displayed T7-like morphology and belonged to the
Podoviridiae
group (short tails) of viruses that we called cyanophage Ma-LBP. In Lake Baroon, the number of the cyanophage Ma-LBP was 5.6 × 10
4
cyanophage · ml
−1
, representing 0.23% of the natural viral population of 2.46 × 10
7
 · ml
−1
. Our results showed that this cyanophage could be a major natural control mechanism of
M. aeruginosa
abundance in aquatic ecosystems like Lake Baroon. Future studies of potentially toxic cyanobacterial blooms need to consider factors that influence cyanophage attachment, infectivity, and lysis of their host alongside the physical and chemical parameters that drive cyanobacterial growth and production.
Fate of Pathogens Present in Livestock Wastes Spread onto Fescue Plots
Authors: Hutchison Mike L. , Walters Lisa D. , Moore Tony , Thomas D. John I. , Avery Sheryl M.
Published: February 2005

Fecal wastes from a variety of farmed livestock were inoculated with livestock isolates ofEscherichia coliO157,Listeria monocytogenes,Salmonella,Campylobacter jejuni, andCryptosporidium parvumoocysts at levels representative of the levels found in naturally contaminated wastes. The wastes were subsequently spread onto a grass pasture, and the decline of each of the zoonotic agents was monitored over time. There were no significant differences among the decimal reduction times for the bacterial pathogens. The mean bacterial decimal reduction time was 1.94 days. A range of times between 8 and 31 days for a 1-log reduction inC. parvumlevels was obtained, demonstrating that the protozoans were significantly more hardy than the bacteria. Oocyst recovery was more efficient from wastes with lower dry matter contents. The levels of most of the zoonotic agents had declined to below detectable levels by 64 days. However, for some waste types, 128 days was required for the complete decline ofL. monocytogeneslevels. We were unable to find significant differences between the rates of pathogen decline in liquid (slurry) and solid (farmyard manure) wastes, although concerns have been raised that increased slurry generation as a consequence of more intensive farming practices could lead to increased survival of zoonotic agents in the environment.
Relationship of Temporal and Spatial Variabilities of Ammonia-Oxidizing Bacteria to Nitrification Rates in Monterey Bay, California
Authors: O'Mullan G. D. , Ward B. B.
Published: February 2005

Temporal and spatial dynamics of ammonia-oxidizing bacteria (AOB) were examined using genes encoding 16S rRNA and ammonia monooxygenase subunit A (AmoA) in Monterey Bay, Calif. Samples were collected from three depths in the water column on four dates at one mid-bay station. Diversity estimators for the two genes showed a strong positive correlation, indicating that overlapping bacterial populations had been sampled by both sets of clone libraries. Some samples that were separated by only 15 m in depth had less genetic similarity than samples that were collected from the same depth months apart. Clone libraries from the Monterey Bay AOB community were dominated byNitrosospira-like sequences and clearly differentiated from the adjacent AOB community in Elkhorn Slough. Many Monterey Bay clones clustered with previously identified 16S rRNA andamoAgroups composed entirely of marine sequences, supporting the hypothesis that these groups are specific to the marine environment and are dominant marine AOB. In addition, novel, phylogenetically distinct groups of AOB sequences were identified and compared to sequences in the database. Only one cluster of gammaproteobacterial AOB was detected using 16S rRNA genes. Although significant genetic variation was detected in AOB populations from both vertical and temporal samples, no significant correlation was detected between diversity and environmental variables or the rate of nitrification.
Accumulation and Fate of Microorganisms and Microspheres in Biofilms Formed in a Pilot-Scale Water Distribution System
Authors: Långmark Jonas , Storey Michael V. , Ashbolt Nicholas J. , Stenström Thor-Axel
Published: February 2005

The accumulation and fate of model microbial “pathogens” within a drinking-water distribution system was investigated in naturally grown biofilms formed in a novel pilot-scale water distribution system provided with chlorinated and UV-treated water. Biofilms were exposed to 1-μm hydrophilic and hydrophobic microspheres,
Salmonella
bacteriophages 28B, and
Legionella pneumophila
bacteria, and their fate was monitored over a 38-day period. The accumulation of model pathogens was generally independent of the biofilm cell density and was shown to be dependent on particle surface properties, where hydrophilic spheres accumulated to a larger extent than hydrophobic ones. A higher accumulation of culturable legionellae was measured in the chlorinated system compared to the UV-treated system with increasing residence time. The fate of spheres and fluorescence in situ hybridization-positive legionellae was similar and independent of the primary disinfectant applied and water residence time. The more rapid loss of culturable legionellae compared to the fluorescence in situ hybridization-positive legionellae was attributed to a loss in culturability rather than physical desorption. Loss of bacteriophage 28B plaque-forming ability together with erosion may have affected their fate within biofilms in the pilot-scale distribution system. The current study has demonstrated that desorption was one of the primary mechanisms affecting the loss of microspheres, legionellae, and bacteriophage from biofilms within a pilot-scale distribution system as well as disinfection and biological grazing. In general, two primary disinfection regimens (chlorination and UV treatment) were not shown to have a measurable impact on the accumulation and fate of model microbial pathogens within a water distribution system.
Kinetic Studies and Biochemical Pathway Analysis of Anaerobic Poly-(
R
)-3-Hydroxybutyric Acid Synthesis in
Escherichia coli
Authors: Carlson Ross , Wlaschin Aaron , Srienc Friedrich
Published: February 2005

Poly-(
R
)-3-hydroxybutyric acid (PHB) was synthesized anaerobically in recombinant
Escherichia coli
. The host anaerobically accumulated PHB to more than 50% of its cell dry weight during cultivation in either growth or nongrowth medium. The maximum specific PHB production rate during growth-associated synthesis was approximately 2.3 ± 0.2 mmol of PHB/g of residual cell dry weight/h. The by-product secretion profiles differed significantly between the PHB-synthesizing strain and the control strain. PHB production decreased acetate accumulation for both growth and nongrowth-associated PHB synthesis. For instance under nongrowth cultivation, the PHB-synthesizing culture produced approximately 66% less acetate on a glucose yield basis as compared to a control culture. A theoretical biochemical network model was used to provide a rational basis to interpret the experimental results like the fermentation product secretion profiles and to study
E. coli
network capabilities under anaerobic conditions. For example, the maximum theoretical carbon yield for anaerobic PHB synthesis in
E. coli
is 0.8. The presented study is expected to be generally useful for analyzing, interpreting, and engineering cellular metabolisms.
Effects of Diverse Environmental Conditions on φLC3 Prophage Stability in
Lactococcus lactis
Authors: Lunde Merete , Aastveit Are Halvor , Blatny Janet Martha , Nes Ingolf F.
Published: February 2005

The effects of various growth conditions on spontaneous φLC3 prophage induction in
Lactococcus lactis
subsp.
cremoris
IMN-C1814 was analyzed with a half fraction of a 4
4
factorial experimental design. The four factors included in the study were nutrient availability, acidity, osmolarity, and temperature, each applied at four levels. These environmental factors are related to the fermentation processes in the dairy industry, in which bacteriophage attacks on sensitive starter strains are a constant threat to successful fermentation processes. The frequency of spontaneous φLC3 induction was determined by quantitative analyses of restored DNA attachment sites (
attB
) on the bacterial chromosomes in a population of lysogenic cells. Statistical analysis revealed that all four environmental factors tested affected φLC3 prophage stability and that the environmental factors were involved in interactions (interactions exist when the effect of one factor depends on the level of another factor). The spontaneous φLC3 induction frequency varied from 0.08 to 1.76%. In general, the induction frequency remained at the same rate or decreased when level 1 to 3 of the four environmental factors was applied. At level 4, which generally gave the least favorable growth conditions, the induction frequency was either unchanged, decreased, or increased, depending on the type of stress. It appeared that the spontaneous induction frequency was independent of the growth behavior of the host. It was the environmental growth conditions that were the decisive factor in induction frequency.
Tetracycline-Dependent Conditional Gene Knockout in
Bacillus subtilis
Authors: Kamionka Annette , Bertram Ralph , Hillen Wolfgang
Published: February 2005

Reversible tetracycline-dependent gene regulation allows induction of expression with the tetracycline repressor (TetR) or gene silencing with the newly developed reverse mutant revTetR. We report here the implementation of both approaches with full regulatory range in gram-positive bacteria as exemplified in
Bacillus subtilis
. A chromosomally located gene is controlled by one or two
tet
operators. The precise adjustment of regulatory windows is accomplished by adjusting
tetR
or
revtetR
expression via different promoters. The most efficient induction was 300-fold in the presence of 0.4 μM anhydrotetracycline obtained with a
Pr-xylA-tetR
fusion. Reversible 500-fold gene knockouts were obtained in
B. subtilis
after adjusting expression of revTetR by synthetically designed promoters. We anticipate that these tools will also be useful in many other gram-positive bacteria.
Escherichia coli
Behavior in the Presence of Organic Matter Released by Algae Exposed to Water Treatment Chemicals
Authors: Bouteleux C. , Saby S. , Tozza D. , Cavard J. , Lahoussine V. , Hartemann P. , Mathieu L.
Published: February 2005

When exposed to oxidation, algae release dissolved organic matter with significant carbohydrate (52%) and biodegradable (55 to 74%) fractions. This study examined whether algal organic matter (AOM) added in drinking water can compromise water biological stability by supporting bacterial survival.
Escherichia coli
(1.3 × 10
5
cells ml
−1
) was inoculated in sterile dechlorinated tap water supplemented with various qualities of organic substrate, such as the organic matter coming from chlorinated algae, ozonated algae, and acetate (model molecule) to add 0.2 ± 0.1 mg of biodegradable dissolved organic carbon (BDOC) liter
−1
. Despite equivalent levels of BDOC,
E. coli
behavior depended on the source of the added organic matter. The addition of AOM from chlorinated algae led to an
E. coli
growth equivalent to that in nonsupplemented tap water; the addition of AOM from ozonated algae allowed a 4- to 12-fold increase in
E. coli
proliferation compared to nonsupplemented tap water. Under our experimental conditions, 0.1 mg of algal BDOC was sufficient to support
E. coli
growth, whereas the 0.7 mg of BDOC liter
−1
initially present in drinking water and an additional 0.2 mg of BDOC acetate liter
−1
were not sufficient. Better maintenance of
E. coli
cultivability was also observed when AOM was added; cultivability was even increased after addition of AOM from ozonated algae. AOM, likely to be present in treatment plants during algal blooms, and thus potentially in the treated water may compromise water biological stability.
Monte Carlo Simulation of Pathogen Behavior during the Sprout Production Process
Authors: Montville Rebecca , Schaffner Donald
Published: February 2005

Food-borne disease outbreaks linked to the consumption of raw sprouts have become a concern over the past decade. A Monte Carlo simulation model of the sprout production process was created to determine the most-effective points for pathogen control. Published literature was reviewed, and relevant data were compiled. Appropriate statistical distributions were determined and used to create the Monte Carlo model with Analytica software. Factors modeled included initial pathogen concentration and prevalence, seed disinfection effectiveness, and sampling of seeds prior to sprouting, sampling of irrigation water, or sampling of the finished product. Pathogen concentration and uniformity of seed contamination had a large effect on the fraction of contaminated batches predicted by the simulation. The model predicted that sprout sampling and irrigation water sampling at the end of the sprouting process would be more effective in pathogen detection than seed sampling prior to production. Day of sampling and type of sample (sprout or water) taken had a minimal effect on rate of detection. Seed disinfection reduced the proportion of contaminated batches, but in some cases it also reduced the ability to detect the pathogen when it was present, because cell numbers were reduced below the detection limit. Both the amount sampled and the pathogen detection limit were shown to be important variables in determining sampling effectiveness. This simulation can also be used to guide further research and compare the levels of effectiveness of different risk reduction strategies.
Repeat-Length-Independent Broad-Spectrum Shuffling, a Novel Method of Generating a Random Chimera Library In Vivo
Authors: Mori Koichi , Mukaihara Takafumi , Uesugi Yoshiko , Iwabuchi Masaki , Hatanaka Tadashi
Published: February 2005

We describe a novel method of random chimeragenesis based on highly frequent deletion formation in the
Escherichia coli ssb-3
strain and a deletion-directed chimera selection system that uses the
rpsL
+
gene as a reporter. It enables the selection of chimeras without target gene expression and can therefore be applied to cytotoxic targets. When this system was applied to phospholipase D genes from
Streptomyces septatus
TH-2 and
Streptomyces halstedii
subsp.
scabies
K6 (examples of cytotoxic targets), chimeragenesis occurred between short identical sequences at the corresponding position of the parental genes with large variations. Chimeragenesis was >1,000 times more frequent in the
ssb-3
background than in the
ssb
+
background. We called this system repeat-length-independent broad-spectrum shuffling. It enables the convenient chimeragenesis and functional study of chimeric proteins. In fact, we found two amino acid residues related to the thermostability of phospholipase D (Phe426 and Thr433) by comparing thermostability among the chimeric enzymes obtained.
New Strategy for Identification of Novel
cry
-Type Genes from
Bacillus thuringiensis
Strains
Authors: Berón Corina M. , Curatti Leonardo , Salerno Graciela L.
Published: February 2005

We designed five degenerate primers for detection of novel
cry
genes from
Bacillus thuringiensis
strains. An efficient strategy was developed based on a two-step PCR approach with these primers in five pair combinations. In the first step, only one of the primer pairs is used in the PCR, which allows amplification of DNA fragments encoding protein regions that include consensus domains of representative proteins belonging to different Cry groups. A second PCR is performed by using the first-step amplification products as DNA templates and the set of five primer combinations. Cloning and sequencing of the last-step amplicons allow both the identification of known
cry
genes encoding Cry proteins covering a wide phylogenetic distance and the detection and characterization of
cry
-related sequences from novel
B. thuringiensis
isolates.
gerR
, a Novel
ger
Operon Involved in
l
-Alanine- and Inosine-Initiated Germination of
Bacillus cereus
ATCC 14579
Authors: Hornstra Luc M. , de Vries Ynte P. , de Vos Willem M. , Abee Tjakko , Wells-Bennik Marjon H. J.
Published: February 2005

Bacillus cereus
endospores germinate in response to particular nutrients. Spores are able to sense these nutrients in the environment by receptors encoded by the
gerA
family of operons. Analysis of the
Bacillus cereus
ATCC 14579 genome revealed seven
gerA
family homologues. Using a transposon Tn
917
-based insertional mutagenesis approach followed by an enrichment procedure to select for
l
-alanine-induced germination mutants, we isolated a mutant with a defect in the
l
-alanine germination pathway. The transposon disrupted the last gene of a tricistronic
gerA
family operon, designated
gerR
, with the order
gerRA
,
gerRC, gerRB
. A second mutant was created by insertion of pMUTIN4 in
gerRC
. Both mutants showed the same phenotype for nutrient-induced germination. Spores of the
gerR
mutant strains were blocked in their
l
-alanine-initiated germination pathway and showed a delayed inosine-induced germination response. Apparently, germination mediated by
l
-alanine and inosine cannot be compensated for completely by the other germinant receptors, and this points towards an essential role of the
gerR
-encoded receptor in the receptor complex. In food products, spores of the mutant strains showed a reduced germination response compared to spores of the parental strain. High-pressure-initiated germination was not affected by the
gerR
mutations, as experiments with 100 and 550 MPa showed no difference with spores of the parental strain.