bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer
Authors: Rabaey Korneel , Boon Nico , Siciliano Steven D. , Verhaege Marc , Verstraete Willy 
Published: September 2004

ABSTRACTMicrobial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2of electrode surface to a maximal level of 4.31 W m−2(664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1day−1and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such asAlcaligenes faecalisandEnterococcus gallinarum, which are capable of hydrogen production.Pseudomonas aeruginosaand otherPseudomonasspecies were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced byP. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components.
Simultaneous Fluorescence In Situ Hybridization of mRNA and rRNA in Environmental Bacteria
Authors: Pernthaler Annelie , Amann Rudolf 
Published: September 2004

ABSTRACT

We developed for
Bacteria
in environmental samples a sensitive and reliable mRNA fluorescence in situ hybridization (FISH) protocol that allows for simultaneous cell identification by rRNA FISH. Samples were carbethoxylated with diethylpyrocarbonate to inactivate intracellular RNases and pretreated with lysozyme and/or proteinase K at different concentrations. Optimizing the permeabilization of each type of sample proved to be a critical step in avoiding false-negative or false-positive results. The quality of probes as well as a stringent hybridization temperature were determined with expression clones. To increase the sensitivity of mRNA FISH, long ribonucleotide probes were labeled at a high density with
cis
-platinum-linked digoxigenin (DIG). The hybrid was immunocytochemically detected with an anti-DIG antibody labeled with horseradish peroxidase (HRP). Subsequently, the hybridization signal was amplified by catalyzed reporter deposition with fluorochrome-labeled tyramides.
p
-Iodophenylboronic acid and high concentrations of NaCl substantially enhanced the deposition of tyramides and thus increased the sensitivity of our approach. After inactivation of the antibody-delivered HRP, rRNA FISH was performed by following routine protocols. To show the broad applicability of our approach, mRNA of a key enzyme of aerobic methane oxidation, particulate methane monooxygenase (subunit A), was hybridized with different types of samples: pure cultures, symbionts of a hydrothermal vent bivalve, and even sediment, one of the most difficult sample types with which to perform successful FISH. By simultaneous mRNA FISH and rRNA FISH, single cells are identified and shown to express a particular gene. Our protocol is transferable to many different types of samples with the need for only minor modifications of fixation and permeabilization procedures.
Identification of Members of the Metabolically Active Microbial Populations Associated with
Beggiatoa
Species Mat Communities from Gulf of Mexico Cold-Seep Sediments
Authors: Mills Heath J. , Martinez Robert J. , Story Sandra , Sobecky Patricia A. 
Published: September 2004

ABSTRACT

In this study, the composition of the metabolically active fraction of the microbial community occurring in Gulf of Mexico marine sediments (water depth, 550 to 575 m) with overlying filamentous bacterial mats was determined. The mats were mainly composed of either orange- or white-pigmented
Beggiatoa
spp. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from three different sediment depths (0 to 2, 6 to 8, and 10 to 12 cm) that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct 12 different 16S crDNA libraries containing 333
Archaea
and 329
Bacteria
clones. Analysis of the
Archaea
clones indicated that all sediment depths associated with overlying orange- and white-pigmented microbial mats were almost exclusively dominated by ANME-2 (95% of total
Archaea
clones), a lineage related to the methanogenic order
Methanosarcinales
. In contrast, bacterial diversity was considerably higher, with the dominant phylotype varying by sediment depth. An equivalent number of clones detected at 0 to 2 cm, representing a total of 93%, were related to the γ and δ classes of
Proteobacteria
, whereas clones related to δ-
Proteobacteria
dominated the metabolically active fraction of the bacterial community occurring at 6 to 8 cm (79%) and 10 to 12 cm (85%). This is the first phylogenetics-based evaluation of the presumptive metabolically active fraction of the
Bacteria
and
Archaea
community structure investigated along a sediment depth profile in the northern Gulf of Mexico, a hydrocarbon-rich cold-seep region.
Experimental and Theoretical Bases of Specific Affinity, a Cytoarchitecture-Based Formulation of Nutrient Collection Proposed To Supercede the Michaelis-Menten Paradigm of Microbial Kinetics
Authors: Button D. K. , Robertson Betsy , Gustafson Elizabeth , Zhao Xiaoming 
Published: September 2004

ABSTRACT

A theory for solute uptake by whole cells was derived with a focus on the ability of oligobacteria to sequester nutrients. It provided a general relationship that was used to obtain the kinetic constants for in situ marine populations in the presence of naturally occurring substrates. In situ affinities of 0.9 to 400 liters g of cells
−1
h
−1
found were up to 10
3
times smaller than those from a “
Marinobacter arcticus
” isolate, but springtime values were greatly increased by warming. Affinities of the isolate for usual polar substrates but not for hydrocarbons were diminished by ionophores. A kinetic curve or Monod plot was constructed from the best available data for cytoarchitectural components of the isolate by using the theory together with concepts and calculations from first principles. The order of effect of these components on specific affinity was membrane potential > cytoplasmic enzyme concentration > cytoplasmic enzyme affinity > permease concentration > area of the permease site > translation coefficient > porin concentration. Component balance was influential as well; a small increase in cytoplasmic enzyme concentration gave a large increase in the effect of permease concentration. The effect of permease concentration on specific affinity was large, while the effect on

K
m

was small. These results are in contrast to the Michaelis-Menten theory as applied by Monod that has uptake kinetics dependent on the quality of the permease molecules, with

K
m

as an independent measure of affinity. Calculations demonstrated that most oligobacteria in the environment must use multiple substrates simultaneously to attain sufficient energy and material for growth, a requirement consistent with communities largely comprising few species.
Blakeslea trispora
Genes for Carotene Biosynthesis
Authors: Rodríguez-Sáiz M. , Paz B. , de la Fuente J. L. , López-Nieto M. J. , Cabri W. , Barredo J. L. 
Published: September 2004

ABSTRACT

We cloned the
carB
and
carRA
genes involved in β-carotene biosynthesis from overproducing and wild-type strains of
Blakeslea trispora
. The
carB
gene has a length of 1,955 bp, including two introns of 141 and 68 bp, and encodes a protein of 66.4 kDa with phytoene dehydrogenase activity. The
carRA
gene contains 1,894 bp, with a single intron of 70 bp, and encodes a protein of 69.6 kDa with separate domains for lycopene cyclase and phytoene synthase. The estimated transcript sizes for
carB
and
carRA
were 1.8 and 1.9 kb, respectively. CarB from the β-carotene-overproducing strain
B. trispora
F-744 had an S528R mutation and a TAG instead of a TAA stop codon. The overproducing strain also had a P143S mutation in CarRA. Both
B. trispora
genes could complement mutations in orthologous genes in
Mucor circinelloides
and could be used to construct transformed strains of
M. circinelloides
that produced higher levels of β-carotene than did the nontransformed parent. The results show that these genes are conserved across the zygomycetes and that the
B. trispora carB
and
carRA
genes are functional and potentially useable to increase carotenoid production.
Cloning and Characterization of the Bile Salt Hydrolase Genes (
bsh
) from
Bifidobacterium bifidum
Strains
Authors: Kim Geun-Bae , Miyamoto Carol M. , Meighen Edward A. , Lee Byong H. 
Published: September 2004

ABSTRACT

Biochemical characterization of the purified bile salt hydrolase (BSH) from
Bifidobacterium bifidum
ATCC 11863 revealed some distinct characteristics not observed in other species of
Bifidobacterium
. The
bsh
gene was cloned from
B. bifidum
, and the DNA flanking the
bsh
gene was sequenced. Comparison of the deduced amino acid sequence of the cloned gene with previously known sequences revealed high homology with BSH enzymes from several microorganisms and penicillin V amidase (PVA) of
Bacillus sphaericus
. The proposed active sites of PVA were highly conserved, including that of the Cys-1 residue. The importance of the SH group in the N-terminal cysteine was confirmed by substitution of Cys with chemically and structurally similar residues, Ser or Thr, both of which resulted in an inactive enzyme. The transcriptional start point of the
bsh
gene has been determined by primer extension analysis. Unlike
Bifidobacterium longum bsh
,
B. bifidum bsh
was transcribed as a monocistronic unit, which was confirmed by Northern blot analysis. PCR amplification with the type-specific primer set revealed the high level of sequence homology in their
bsh
genes within the species of
B. bifidum
.
Implications of Amino Acid Substitutions in GyrA at Position 83 in Terms of Oxolinic Acid Resistance in Field Isolates ofBurkholderia glumae, a Causal Agent of Bacterial Seedling Rot and Grain Rot of Rice
Authors: Maeda Yukiko , Kiba Akinori , Ohnishi Kouhei , Hikichi Yasufumi 
Published: September 2004

ABSTRACTOxolinic acid (OA), a quinolone, inhibits the activity of DNA gyrase composed of GyrA and GyrB and shows antibacterial activity againstBurkholderia glumae. SinceB. glumaecauses bacterial seedling rot and grain rot of rice, both of which are devastating diseases, the emergence of OA-resistant bacteria has important implications on rice cultivation in Japan. Based on the MIC of OA, 35B. glumaefield isolates isolated from rice seedlings grown from OA-treated seeds in Japan were divided into sensitive isolates (OSs; 0.5 μg/ml), moderately resistant isolates (MRs; 50 μg/ml), and highly resistant isolates (HRs; ≥100 μg/ml). Recombination withgyrAof an OS, Pg-10, led MRs and HRs to become OA susceptible, suggesting thatgyrAmutations are involved in the OA resistance of field isolates. The amino acid at position 83 in the GyrA of all OSs was Ser, but in all MRs and HRs it was Arg and Ile, respectively. Ser83Arg and Ser83Ile substitutions in the GyrA of an OS, Pg-10, resulted in moderate and high OA resistance, respectively. Moreover, Arg83Ser and Ile83Ser substitutions in the GyrA of MRs and HRs, respectively, resulted in susceptibility to OA. These results suggest that Ser83Arg and Ser83Ile substitutions in GyrA are commonly responsible for resistance to OA inB. glumaefield isolates.
Identification and Functional Characterization of a
Xenorhabdus nematophila
Oligopeptide Permease
Authors: Orchard Samantha S. , Goodrich-Blair Heidi 
Published: September 2004

ABSTRACT

The bacterium
Xenorhabdus nematophila
is a mutualist of
Steinernema carpocapsae
nematodes and a pathogen of insects. Presently, it is not known what nutrients the bacterium uses to thrive in these host environments. In other symbiotic bacteria, oligopeptide permeases have been shown to be important in host interactions, and we therefore sought to determine if oligopeptide uptake is essential for growth or symbiotic functions of
X. nematophila
in laboratory or host environments. We identified an
X. nematophila
oligopeptide permease (
opp
) operon of two sequential
oppA
genes, predicted to encode oligopeptide-binding proteins, and putative permease-encoding genes
oppB
,
oppC
,
oppD
, and
oppF
. Peptide-feeding studies indicated that this
opp
operon encodes a functional oligopeptide permease. We constructed strains with mutations in
oppA
1
,
oppA
2
, or
oppB
and examined the ability of each mutant strain to grow in a peptide-rich laboratory medium and to interact with the two hosts. We found that the
opp
mutant strains had altered growth phenotypes in the laboratory medium and in hemolymph isolated from larval insects. However, the
opp
mutant strains were capable of initiating and maintaining both mutualistic and pathogenic host interactions. These data demonstrate that the
opp
genes allow
X. nematophila
to utilize peptides as a nutrient source but that this function is not essential for the existence of
X. nematophila
in either of its host niches. To our knowledge, this study represents the first experimental analysis of the role of oligopeptide transport in mediating a mutualistic invertebrate-bacterium interaction.
Molecular Fingerprinting of Dairy Microbial Ecosystems by Use of Temporal Temperature and Denaturing Gradient Gel Electrophoresis
Authors: Ogier J.-C. , Lafarge V. , Girard V. , Rault A. , Maladen V. , Gruss A. , Leveau J.-Y. , Delacroix-Buchet A. 
Published: September 2004

ABSTRACT

Numerous microorganisms, including bacteria, yeasts, and molds, constitute the complex ecosystem present in milk and fermented dairy products. Our aim was to describe the bacterial ecosystem of various cheeses that differ by production technology and therefore by their bacterial content. For this purpose, we developed a rapid, semisystematic approach based on genetic profiling by temporal temperature gradient electrophoresis (TTGE) for bacteria with low-G+C-content genomes and denaturing gradient gel electrophoresis (DGGE) for those with medium- and high-G+C-content genomes. Bacteria in the unknown ecosystems were assigned an identity by comparison with a comprehensive bacterial reference database of ∼150 species that included useful dairy microorganisms (lactic acid bacteria), spoilage bacteria (e.g.,
Pseudomonas
and
Enterobacteriaceae
), and pathogenic bacteria (e.g.,
Listeria monocytogenes
and
Staphylococcus aureus
). Our analyses provide a high resolution of bacteria comprising the ecosystems of different commercial cheeses and identify species that could not be discerned by conventional methods; at least two species, belonging to the
Halomonas
and
Pseudoalteromonas
genera, are identified for the first time in a dairy ecosystem. Our analyses also reveal a surprising difference in ecosystems of the cheese surface versus those of the interior; the aerobic surface bacteria are generally G+C rich and represent diverse species, while the cheese interior comprises fewer species that are generally low in G+C content. TTGE and DGGE have proven here to be powerful methods to rapidly identify a broad range of bacterial species within dairy products.
Effect of
Escherichia coli
Morphogene
bolA
on Biofilms
Authors: Vieira Helena L. A. , Freire Patrick , Arraiano Cecília M. 
Published: September 2004

ABSTRACT

Biofilm physiology is established under a low growth rate. The morphogene
bolA
is mostly expressed under stress conditions or in stationary phase, suggesting that
bolA
could be implicated in biofilm development. In order to verify this hypothesis, we tested the effect of
bolA
on biofilm formation. Overexpression of
bolA
induces biofilm development, while
bolA
deletion decreases biofilms.
Methanogenic Inhibition by Arsenic Compounds
Authors: Sierra-Alvarez Reyes , Cortinas Irail , Yenal Umur , Field Jim A. 
Published: September 2004

ABSTRACT
The acute acetoclastic methanogenic inhibition of several inorganic and organic arsenicals was assayed. Trivalent species, i.e., methylarsonous acid and arsenite, were highly inhibitory, with 50% inhibitory concentrations of 9.1 and 15.0 μM, respectively, whereas pentavalent species were generally nontoxic. The nitrophenylarsonate derivate, roxarsone, displayed moderate toxicity.
Widespread Occurrence of a Novel Division of Bacteria Identified by 16S rRNA Gene Sequences Originally Found in Deep Marine Sediments
Authors: Webster Gordon , Parkes R. John , Fry John C. , Weightman Andrew J. 
Published: September 2004

ABSTRACT
Phylogenetic analysis of 16S rRNA gene sequences from deep marine sediments identified a deeply branching clade, designated candidate division JS1. Primers for PCR amplification of partial 16S rRNA genes that target the JS1 division were developed and used to detect JS1 sequences in DNA extracted from various sedimentary environments, including, for the first time, coastal marine and brackish sediments.
Repertaxin, a novel inhibitor of rat CXCR2 function, inhibits inflammatory responses that follow intestinal ischaemia and reperfusion injury
Authors: Souza Danielle G , Bertini Riccardo , Vieira Angelica T , Cunha Fernando Q , Poole Steve , Allegretti Marcello , Colotta Francesco , Teixeira Mauro M 
Published: September 2004

Neutrophils are thought to play a major role in the mediation of reperfusion injury. CXC chemokines are known inducers of neutrophil recruitment. Here, we assessed the effects of Repertaxin, a novel low molecular weight inhibitor of human CXCL8 receptor activation, on the local, remote and systemic injuries following intestinal ischaemia and reperfusion (I/R) in the rat.
Pre‐incubation of rat neutrophils with Repertaxin (10−11–10−6M) inhibited the chemotaxis of neutrophils induced by human CXCL8 or rat CINC‐1, but not that induced by fMLP, PAF or LTB4, in a concentration‐dependent manner. Repertaxin also prevented CXCL8‐induced calcium influx but not CXCL8 binding to purified rat neutrophils.
In a model of mild I/R injury (30 min of ischaemia and 30 min of reperfusion), Repertaxin dose‐dependently (3–30 mg kg−1) inhibited the increase in vascular permeability and neutrophil influx. Maximal inhibition occurred at 30 mg kg−1.
Following severe I/R injury (120 min of ischaemia and 120 min of reperfusion), Repertaxin (30 mg kg−1) markedly prevented neutrophil influx, the increase in vascular permeability both in the intestine and the lungs. Moreover, there was prevention of haemorrhage in the intestine of reperfused animals.
Repertaxin effectively suppressed the increase in tissue (intestine and lungs) and serum concentrations of TNF‐α and the reperfusion‐associated lethality.
For comparison, we also evaluated the effects of an anti‐CINC‐1 antibody in the model of severe I/R injury. Overall, the antibody effectively prevented tissue injury, systemic inflammation and lethality. However, the effects of the antibody were in general of lower magnitude than those of Repertaxin.
In conclusion, CINC‐1 and possibly other CXC chemokines, acting on CXCR2, have an important role during I/R injury. Thus, drugs, such as Repertaxin, developed to block the function of the CXCR2 receptor may be effective at preventing reperfusion injury in relevant clinical situations.

British Journal of Pharmacology (2004) 143, 132–142. doi:10.1038/sj.bjp.0705862
Lipoxins and novel 15‐epi‐lipoxin analogs display potent anti‐inflammatory actions after oral administration
Authors: Bannenberg Gerard , Moussignac Rose‐Laure , Gronert Karsten , Devchand Pallavi R , Schmidt Birgitta A , Guilford William J , Bauman John G , Subramanyam Babu , Daniel Perez H , Parkinson John F , Serhan Charles N 
Published: September 2004

Lipoxins (LX) and aspirin‐triggered 15‐epi‐lipoxins (ATL) exert potent anti‐inflammatory actions. In the present study, we determined the anti‐inflammatory efficacy of endogenous LXA4 and LXB4, the stable ATL analog ATLa2, and a series of novel 3‐oxa‐ATL analogs (ZK‐996, ZK‐990, ZK‐994, and ZK‐142) after intravenous, oral, and topical administration in mice.
LXA4, LXB4, ATLa2, and ZK‐994 were orally active, exhibiting potent systemic inhibition of zymosan A‐induced peritonitis at very low doses (50 ng kg−1–50 μg kg−1).
Intravenous ZK‐994 and ZK‐142 (500 μg kg−1) potently attenuated hind limb ischemia/reperfusion‐induced lung injury, with 32±12 and 53±5% inhibition (P<0.05), respectively, of neutrophil accumulation in lungs. The same dose of ATLa2 had no significant protective action.
Topical application of ATLa2, ZK‐994, and ZK‐142 (∼20 μg cm−2) prevented vascular leakage and neutrophil infiltration in LTB4/PGE2‐stimulated ear skin inflammation. While ATLa2 and ZK‐142 displayed approximately equal anti‐inflammatory efficacy in this model, ZK‐994 displayed a slower onset of action.
In summary, native LXA4 and LXB4, and analogs ATLa2, ZK‐142, and ZK‐994 retain broad anti‐inflammatory effects after intravenous, oral, and topical administration. The 3‐oxa‐ATL analogs, which have enhanced metabolic and chemical stability and a superior pharmacokinetic profile, provide new opportunities to explore the actions and therapeutic potential for LX and ATL.

British Journal of Pharmacology (2004) 143, 43–52. doi:10.1038/sj.bjp.0705912
The Silent Sinus Syndrome: A Case Series and Literature Review
Authors: Vander Meer Joseph B. , Harris Gerald , Toohill Robert J. , Smith Timothy L. 
Published: September 2004

AbstractPurpose The purpose of this study is to describe the clinical and pathologic features of a form of chronic maxillary atelectasis referred to as the silent sinus syndrome, which is characterized by progressive enophthalmos secondary to maxillary collapse resulting from maxillary sinus hypoventilation.Methods A retrospective medical record analysis was carried out to identify patients with enophthalmos secondary to maxillary collapse. Clinical records, including ophthalmology and otolaryngology evaluations as well as computed tomography scans and operative reports, were carefully examined. A complete literature review for relevant studies was performed to examine possible pathophysiology and similar cases.Results Four patients with enophthalmos and asymptomatic maxillary sinus disease were identified. On computed tomography, all four of the patients had opacified, partially collapsed maxillary sinuses with osteopenia of the sinus walls and orbital floor displacement resulting in enophthalmos. All four underwent successful functional endoscopic sinus surgery and transconjunctival orbital floor repair.Conclusion In some instances, chronic maxillary atelectasis can present with enophthalmos secondary to collapse of the maxillary sinus. For reasons that are unclear, the sinus component of the disease remains asymptomatic and is discovered only after thorough evaluation of the enophthalmos.