bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathway of Propionate Oxidation by a Syntrophic Culture of
Smithella propionica
and
Methanospirillum hungatei
Authors: de Bok F. A. M. , Stams A. J. M. , Dijkema C. , Boone D. R. 
Published: July 2002

ABSTRACT

The pathway of propionate conversion in a syntrophic coculture of
Smithella propionica
and
Methanospirillum hungatei
JF1 was investigated by
13
C-NMR spectroscopy. Cocultures produced acetate and butyrate from propionate. [3-
13
C]propionate was converted to [2-
13
C]acetate, with no [1-
13
C]acetate formed. Butyrate from [3-
13
C]propionate was labeled at the C2 and C4 positions in a ratio of about 1:1.5. Double-labeled propionate (2,3-
13
C) yielded not only double-labeled acetate but also single-labeled acetate at the C1 or C2 position. Most butyrate formed from [2,3-
13
C]propionate was also double labeled in either the C1 and C2 atoms or the C3 and C4 atoms in a ratio of about 1:1.5. Smaller amounts of single-labeled butyrate and other combinations were also produced. 1-
13
C-labeled propionate yielded both [1-
13
C]acetate and [2-
13
C]acetate. When
13
C-labeled bicarbonate was present, label was not incorporated into acetate, propionate, or butyrate. In each of the incubations described above,
13
C was never recovered in bicarbonate or methane. These results indicate that
S. propionica
does not degrade propionate via the methyl-malonyl-coenzyme A (CoA) pathway or any other of the known pathways, such as the acryloyl-CoA pathway or the reductive carboxylation pathway. Our results strongly suggest that propionate is dismutated to acetate and butyrate via a six-carbon intermediate.
Microbiological Analysis of Tube-Well Water in a Rural Area of Bangladesh
Authors: Islam M. S. , Siddika A. , Khan M. N. H. , Goldar M. M. , Sadique M. A. , Kabir A. N. M. H. , Huq Anwar , Colwell R. R. 
Published: July 2002

ABSTRACT
Five tube-wells in Matlab, Bangladesh, were selected for analysis of selected biophysicochemical parameters. The results showed that all tube-well water samples contained zooplankton and bacteria. Results for some of the parameters were outside the accepted limits recommended by the World Health Organization for drinking water. It is concluded that water from tube-wells should be treated if used as drinking water.
Cloning, Sequencing, and Expression of the Cold-Inducible
hutU
Gene from the Antarctic Psychrotrophic Bacterium
Pseudomonas syringae
Authors: Janiyani Kamala L. , Ray M. K. 
Published: July 2002

ABSTRACT

A promoter-fusion study with a Tn
5
-based promoter probe vector had earlier found that the
hutU
gene which encodes the enzyme urocanase for the histidine utilization pathway is upregulated at a lower temperature (4° C) in the Antarctic psychrotrophic bacterium
Pseudomonas syringae
. To examine the characteristics of the urocanase gene and its promoter elements from the psychrotroph, the complete
hutU
and its upstream region from
P. syringae
were cloned, sequenced, and analyzed in the present study. Northern blot and primer extension analyses suggested that the
hutU
gene is inducible upon a downshift of temperature (22 to 4°C) and that there is more than one transcription initiation site. One of the initiation sites was specific to the cells grown at 4°C, which was different from the common initiation sites observed at both 4 and 22°C. Although no typical promoter consensus sequences were observed in the flanking region of the transcription initiation sites, there was a characteristic CAAAA sequence at the −10 position of the promoters. Additionally, the location of the transcription and translation initiation sites suggested that the
hutU
mRNA contains a long 5′-untranslated region, a characteristic feature of many cold-inducible genes of mesophilic bacteria. A comparison of deduced amino acid sequences of urocanase from various bacteria, including the mesophilic and psychrotrophic
Pseudomonas
spp., suggests that there is a high degree of similarity between the enzymes. The enzyme sequence contains a signature motif (GXGX
2
GX
10
G) of the Rossmann fold for dinucleotide (NAD
+
) binding and two conserved cysteine residues in and around the active site. The psychrotrophic enzyme, however, has an extended N-terminal end.
Cloning, Sequence Analysis, and Expression in
Escherichia coli
of the Gene Encoding an α-Amino Acid Ester Hydrolase from
Acetobacter turbidans
Authors: Polderman-Tijmes Jolanda J. , Jekel Peter A. , de Vries Erik J. , van Merode Annet E. J. , Floris René , van der Laan Jan-Metske , Sonke Theo , Janssen Dick B. 
Published: July 2002

ABSTRACT

The α-amino acid ester hydrolase from
Acetobacter turbidans
ATCC 9325 is capable of hydrolyzing and synthesizing β-lactam antibiotics, such as cephalexin and ampicillin. N-terminal amino acid sequencing of the purified α-amino acid ester hydrolase allowed cloning and genetic characterization of the corresponding gene from an
A. turbidans
genomic library. The gene, designated
aehA
, encodes a polypeptide with a molecular weight of 72,000. Comparison of the determined N-terminal sequence and the deduced amino acid sequence indicated the presence of an N-terminal leader sequence of 40 amino acids. The
aehA
gene was subcloned in the pET9 expression plasmid and expressed in
Escherichia coli
. The recombinant protein was purified and found to be dimeric with subunits of 70 kDa. A sequence similarity search revealed 26% identity with a glutaryl 7-ACA acylase precursor from
Bacillus laterosporus
, but no homology was found with other known penicillin or cephalosporin acylases. There was some similarity to serine proteases, including the conservation of the active site motif, GXSYXG. Together with database searches, this suggested that the α-amino acid ester hydrolase is a β-lactam antibiotic acylase that belongs to a class of hydrolases that is different from the Ntn hydrolase superfamily to which the well-characterized penicillin acylase from
E. coli
belongs. The α-amino acid ester hydrolase of
A. turbidans
represents a subclass of this new class of β-lactam antibiotic acylases.
Diversity of Nitrite Reductase (
nirK
and
nirS
) Gene Fragments in Forested Upland and Wetland Soils
Authors: Priemé Anders , Braker Gesche , Tiedje James M. 
Published: July 2002

ABSTRACT

The genetic heterogeneity of nitrite reductase gene (
nirK
and
nirS
) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods.
nirK
gene fragments could be amplified from both soils, whereas
nirS
gene fragments could be amplified only from the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of
nirK
clones was lower than the diversity of
nirS
clones. Among the 54 distinct
nirK
RFLP patterns identified in the two soils, only one pattern was found in both soils and in each soil two dominant groups comprised >35% of all clones. No dominance and few redundant patterns were seen among the
nirS
clones. Phylogenetic analysis of deduced amino acids grouped the
nirK
sequences into five major clusters, with one cluster encompassing most marsh clones and all upland clones. Only a few of the
nirK
clone sequences branched with those of known denitrifying bacteria. The
nirS
clones formed two major clusters with several subclusters, but all
nirS
clones showed less than 80% identity to
nirS
sequences from known denitrifying bacteria. Overall, the data indicated that the denitrifying communities in the two soils have many members and that the soils have a high richness of different
nir
genes, especially of the
nirS
gene, most of which have not yet been found in cultivated denitrifiers.
Transformation of Isopropylamine to
l
-Alaninol by
Pseudomonas
sp. Strain KIE171 Involves
N
-Glutamylated Intermediates
Authors: de Azevedo Wäsch Susana I. , van der Ploeg Jan R. , Maire Tere , Lebreton Alice , Kiener Andreas , Leisinger Thomas 
Published: July 2002

ABSTRACT

Pseudomonas
sp. strain KIE171 was able to grow with isopropylamine or
l
-alaninol [
S
-(+)-2-amino-1-propanol] as the sole carbon source, but not with
d
-alaninol. To investigate the hypothesis that
l
-alaninol is an intermediate in the degradation of isopropylamine, two mini-Tn
5
mutants unable to utilize both isopropylamine and
l
-alaninol were isolated. Whereas mutant KIE171-BI transformed isopropylamine to
l
-alaninol, mutant KIE171-BII failed to do so. The two genes containing a transposon insertion were cloned, and the DNA regions flanking the insertions were sequenced. Two clusters, one comprising eight
ipu
(isopropylamine utilization) genes (
ipuABCDEFGH
) and the other encompassing two genes (
ipuI
and
orf259
), were identified. Comparisons of sequences of the deduced Ipu proteins and those in the database suggested that isopropylamine is transported into the cytoplasm by a putative permease, IpuG. The next step, the formation of γ-glutamyl-isopropylamide from isopropylamine, ATP, and
l
-glutamate, was shown to be catalyzed by IpuC, a γ-glutamylamide synthetase. γ-Glutamyl-isopropylamide is then subjected to stereospecific monooxygenation by the hypothetical four-component system IpuABDE, thereby yielding γ-glutamyl-
l
-alaninol [γ(
l
-glutamyl)-
l
-hydroxy-isopropylamide]. Enzymatic hydrolysis by a hydrolase, IpuF, was shown to finally liberate
l
-alaninol and to regenerate
l
-glutamate. No gene(s) encoding an enzyme for the next step in the degradation of isopropylamine was found in the
ipu
clusters. Presumably,
l
-alaninol is oxidized by an alcohol dehydrogenase to yield
l
-2-aminopropionaldehyde or it is deaminated by an ammonia lyase to propionaldehyde. Genetic evidence indicated that the aldehyde formed is then further oxidized by the hypothetical aldehyde dehydrogenases IpuI and IpuH to either
l
-alanine or propionic acid, compounds which can be processed by reactions of the intermediary metabolism.
Immobilization of Radionuclides and Heavy Metals through Anaerobic Bio-Oxidation of Fe(II)
Authors: Lack Joseph G. , Chaudhuri Swades K. , Kelly Shelly D. , Kemner Kenneth M. , O'Connor Susan M. , Coates John D. 
Published: July 2002

ABSTRACT

Adsorption of heavy metals and radionuclides (HMR) onto iron and manganese oxides has long been recognized as an important reaction for the immobilization of these compounds. However, in environments containing elevated concentrations of these HMR the adsorptive capacity of the iron and manganese oxides may well be exceeded, and the HMR can migrate as soluble compounds in aqueous systems. Here we demonstrate the potential of a bioremediative strategy for HMR stabilization in reducing environments based on the recently described anaerobic nitrate-dependent Fe(II) oxidation by
Dechlorosoma
species. Bio-oxidation of 10 mM Fe(II) and precipitation of Fe(III) oxides by these organisms resulted in rapid adsorption and removal of 55 μM uranium and 81 μM cobalt from solution. The adsorptive capacity of the biogenic Fe(III) oxides was lower than that of abiotically produced Fe(III) oxides (100 μM for both metals), which may have been a result of steric hindrance by the microbial cells on the iron oxide surfaces. The binding capacity of the biogenic oxides for different heavy metals was indirectly correlated to the atomic radius of the bound element. X-ray absorption spectroscopy indicated that the uranium was bound to the biogenically produced Fe(III) oxides as U(VI) and that the U(VI) formed bidentate and tridentate inner-sphere complexes with the Fe(III) oxide surfaces.
Dechlorosoma suillum
oxidation was specific for Fe(II), and the organism did not enzymatically oxidize U(IV) or Co(II). Small amounts (less than 2.5 μM) of Cr(III) were reoxidized by
D. suillum
; however, this appeared to be inversely dependent on the initial concentration of the Cr(III). The results of this study demonstrate the potential of this novel approach for stabilization and immobilization of HMR in the environment.
Neutrophilic Fe-Oxidizing Bacteria Are Abundant at the Loihi Seamount Hydrothermal Vents and Play a Major Role in Fe Oxide Deposition
Authors: Emerson David , Moyer Craig L. 
Published: July 2002

ABSTRACT

A number of hydrothermal vent sites exist on the summit of the Loihi Seamount, a shield volcano that is part of the Hawaiian archipelago. The vents are 1,100 to 1,325 m below the surface and range in temperature from slightly above ambient (10°C) to high temperature (167°C). The vent fluid is characterized by high concentrations of CO
2
(up to 17 mM) and Fe(II) (up to 268 μM), but there is a general paucity of H
2
S. Most of the vents are surrounded by microbial mats that have a gelatinous texture and are heavily encrusted with rust-colored Fe oxides. Visually, the Fe oxides appeared homogeneous. However, light microscopy revealed that the oxides had different morphologies, which fell into three classes: (i) sheaths, (ii) twisted or irregular filaments, and (iii) amorphous oxides. A morphological analysis of eight different samples indicated that the amorphous oxides were overall the most abundant; however, five sites had >50% sheaths and filamentous oxides. These latter morphologies are most likely the direct result of microbial deposition. Direct cell counts revealed that all of the oxides had abundant microbial populations associated with them, from 6.9 × 10
7
to 5.3 × 10
8
cells per ml of mat material. At most sites, end point dilution series for lithotrophic Fe oxidizers were successful out to dilutions of 10
−6
and 10
−7
. A pure culture was obtained from a 10
−7
dilution tube; this strain, JV-1, was an obligate, microaerophilic Fe oxidizer that grew at 25 to 30°C. A non-cultivation-based molecular approach with terminal-restriction fragment length polymorphism also indicated the common presence of Fe-oxidizing bacteria at Loihi. Together, these results indicate that Fe-oxidizing bacteria are common at the Loihi Seamount and probably play a major role in Fe oxidation. A review of the literature suggests that microbially mediated Fe oxidation at hydrothermal vents may be important globally.
Analysis of the 16S rRNA Gene Sequence ofAnaplasma centraleand Its Phylogenetic Relatedness to Other Ehrlichiae
Authors: Inokuma Hisashi , Terada Yutaka , Kamio Tugihiko , Raoult Didier , Brouqui Philippe 
Published: July 2002

ABSTRACTThe nucleotide sequence of theAnaplasma centrale16S rRNA gene was determined and compared with the sequences of ehrlichial bacteria. The sequence ofA. centralewas closely related toAnaplasma marginaleby both level-of-similarity (98.08% identical) and distance analysis. A species-specific PCR was developed based upon the alignment data. The PCR can detectA. centraleDNA extracted from 10 infected bovine red blood cells in a reaction mixture.A. centraleDNA was amplified in the reaction, but not other related ehrlichial species.
Adherence of Probiotic Bacteria to Human Intestinal Mucus in Healthy Infants and during Rotavirus Infection
Authors: Juntunen M. , Kirjavainen P. V. , Ouwehand A. C. , Salminen S. J. , Isolauri E. 
Published: July 2002

ABSTRACT

The concentration of fecal mucin and the adhesion of specific probiotics and their combinations in the intestinal mucus of infants during and after rotavirus diarrhea and in healthy children were determined. Mucus was prepared from fecal samples from 20 infants during and after rotavirus diarrhea and from 10 healthy age-matched children. Mucin concentration was determined, and the adhesion of five probiotics—
Lactobacillus rhamnosus
GG,
Lactobacillus casei
Shirota,
Lactobacillus paracasei
F19,
Lactobacillus acidophilus
LA5, and
Bifidobacterium lactis
Bb12—and their combinations was tested in vitro. The mean concentrations of fecal mucin during and after rotavirus diarrhea, 15.2 and 14.1 mg/g, were comparable to that in healthy children, 14.9 mg/g. The adherence of probiotics ranged from 1 to 34% in healthy subjects as indicated for the following strains:
L. rhamnosus
GG, 34%;
B. lactis
Bb12, 31%;
L. acidophilus
LA5, 4%;
L. paracasei
F19, 3%; and
L. casei
Shirota, 1% (
P
= 0.0001). The distinctive pattern of probiotic adherence was not influenced by rotavirus diarrhea. The adhesion of Bb12 in the presence of GG increased from 31 to 39% in healthy infants (
P
= 0.018) and in episodes of diarrhea increased from 26 to 44% (
P
= 0.001). Rotavirus diarrhea does not decrease the production of fecal mucin or with respect to the adhesion of probiotic bacteria tested in vitro. Combination of specific probiotic strains may enhance adherence in a synergistic manner. Optimal clinical application of these interactions may offer novel therapeutic guidelines for the treatment and prevention of gastrointestinal infections.
Effect of Intranasal Administration ofLactobacillus caseiShirota on Influenza Virus Infection of Upper Respiratory Tract in Mice
Authors: Hori Tetsuji , Kiyoshima Junko , Shida Kan , Yasui Hisako 
Published: July 2002

ABSTRACTIn mice administeredLactobacillus caseistrain Shirota (LcS) intranasally, potent induction of interleukin 12, gamma interferon, and tumor necrosis factor alpha, which play a very important role in excluding influenza virus (IFV), was evident in mediastinal lymph node cells. In this model of upper respiratory IFV infection, the titers of virus in the nasal wash of mice inoculated with 200 μg of LcS for three consecutive days (LcS 200 group) before infection were significantly (P< 0.01) lower than those of mice not inoculated with LcS (control group) (100.9 ± 0.6versus 102.1 ± 1.0). The IFV titer was decreased to about 1/10 of the control level. Using this infection model with modifications, we investigated whether the survival rate of mice was increased by intranasal administration of LcS. The survival rate of the mice in the LcS 200 group was significantly (P< 0.05) greater than that of the mice in the control group (69% versus 15%). It seems that the decrease in the titer of virus in the upper respiratory tract to 1/10 of the control level was important in preventing death. These findings suggest that intranasal administration of LcS enhances cellular immunity in the respiratory tract and protects against influenza virus infection.
Antibody Maturation in
Trypanosoma cruzi
-Infected Rats
Authors: Marcipar Iván S. , Risso Marikena G. , Silber Ariel M. , Revelli Silvia , Marcipar Alberto J. 
Published: July 2002

ABSTRACT

The study of antibody avidity changes during infection has improved the understanding of the pathologic processes involved in several infectious diseases. In some infections, like toxoplasmosis, this information is being used for diagnostic purposes. Results of the evolution of antibody avidity for different specific antigens in
Trypanosome cruzi
-infected rats are presented. A Western blotting technique, combined with avidity analysis to identify antigens that elicit high-avidity antibodies, is suggested. In this system, antibodies showed high avidity values only during the chronic phase of infection and only in relation to antibodies against 21-, 33-, 41-, 42-, 56-, 58-, 66-, and 72-kDa antigens. Finally, a 97-kDa
T. cruzi
antigen, which was recognized by high-avidity antibodies and occurred in noninfected rats, was identified. These results allow us to evaluate the different antigens in chagasic infection. Our results show that with the correct choice of antigen it is possible to detect differences in maturation of antibodies and to discriminate, in an experimental model, between recent (acute) and chronic infections.
Treatment of Giardiasis
Authors: Gardner Timothy B. , Hill David R. 
Published: July 2002

SUMMARYGiardia lamblia is both the most common intestinal parasite in the United States and a frequent cause of diarrheal illness throughout the world. In spite of its recognition as an important human pathogen, there have been relatively few agents used in therapy. This paper discusses each class of drugs used in treatment, along with their mechanism of action, in vitro and clinical efficacy, and side effects and contraindications. Recommendations are made for the preferred treatment in different clinical situations. The greatest clinical experience is with the nitroimidazole drugs, i.e., metronidazole, tinidazole, and ornidazole, which are highly effective. A 5- to 7-day course of metronidazole can be expected to cure over 90% of individuals, and a single dose of tinidazole or ornidazole will cure a similar number. Quinacrine, which is no longer produced in the United States, has excellent efficacy but may be poorly tolerated, especially in children. Furazolidone is an effective alternative but must be administered four times a day for 7 to 10 days. Paromomycin may be used during early pregnancy, because it is not systematically absorbed, but it is not always effective. Patients who have resistant infection can usually be cured by a prolonged course of treatment with a combination of a nitroimidazole with quinacrine.
Pandemic Threat Posed by Avian Influenza A Viruses
Authors: Horimoto Taisuke , Kawaoka Yoshihiro 
Published: July 2002

SUMMARY
Influenza pandemics, defined as global outbreaks of the disease due to viruses with new antigenic subtypes, have exacted high death tolls from human populations. The last two pandemics were caused by hybrid viruses, or reassortants, that harbored a combination of avian and human viral genes. Avian influenza viruses are therefore key contributors to the emergence of human influenza pandemics. In 1997, an H5N1 influenza virus was directly transmitted from birds in live poultry markets in Hong Kong to humans. Eighteen people were infected in this outbreak, six of whom died. This avian virus exhibited high virulence in both avian and mammalian species, causing systemic infection in both chickens and mice. Subsequently, another avian virus with the H9N2 subtype was directly transmitted from birds to humans in Hong Kong. Interestingly, the genes encoding the internal proteins of the H9N2 virus are genetically highly related to those of the H5N1 virus, suggesting a unique property of these gene products. The identification of avian viruses in humans underscores the potential of these and similar strains to produce devastating influenza outbreaks in major population centers. Although highly pathogenic avian influenza viruses had been identified before the 1997 outbreak in Hong Kong, their devastating effects had been confined to poultry. With the Hong Kong outbreak, it became clear that the virulence potential of these viruses extended to humans.