bluuebunny/crossref_metadata_2025_split huggingface dataset:
In search for more accurate alignments in the twilight zone
Authors: Jaroszewski Lukasz , Li Weizhong , Godzik Adam 
Published: July 2002

AbstractA major bottleneck in comparative modeling is the alignment quality; this is especially true for proteins whose distant relationships could be reliably recognized only by recent advances in fold recognition. The best algorithms excel in recognizing distant homologs but often produce incorrect alignments for over 50% of protein pairs in large fold‐prediction benchmarks. The alignments obtained by sequence–sequence or sequence–structure matching algorithms differ significantly from the structural alignments. To study this problem, we developed a simplified method to explicitly enumerate all possible alignments for a pair of proteins. This allowed us to estimate the number ofsignificantly differentalignments for a given scoring method that score better than the structural alignment. Using several examples of distantly related proteins, we show that for standard sequence–sequence alignment methods, the number of significantly different alignments is usually large, often about 1010alternatives. This distance decreases when the alignment method is improved, but the number is still too large for the brute force enumeration approach. More effective strategies were needed, so we evaluated and compared two well‐known approaches for searching the space of suboptimal alignments. We combined their best features and produced a hybrid method, which yielded alignments that surpassed the original alignments for about 50% of protein pairs with minimal computational effort.
Genetic Divergence of Human Immunodeficiency Virus Type 1 Ethiopian Clade C Reverse Transcriptase (RT) and Rapid Development of Resistance against Nonnucleoside Inhibitors of RT
Authors: Loemba Hugues , Brenner Bluma , Parniak Michael A. , Ma'ayan Shlomo , Spira Bonnie , Moisi Daniela , Oliveira Maureen , Detorio Mervi , Wainberg Mark A. 
Published: July 2002

ABSTRACT

We sequenced and phylogenetically analyzed the reverse transcriptase (RT) region of five human immunodeficiency virus type 1 isolates from treatment-naive Ethiopian émigrés to Israel. Heteroduplex mobility assays were performed to confirm the clade C status of
env
genomic regions. The RT sequences showed that the strains clustered phylogenetically with clade C viruses, and a KVEQ-specific motif of silent mutations (amino acids 65, 106, 138, and 161, respectively) at resistance sites was present in the polymerase region of all studied Ethiopian isolates and subtype C reference strains. In addition, many other silent mutations were observed in the clade C viruses at various resistance sites. In general, the Ethiopian isolates were more closely related genotypically to a clade C reference strain from Botswana (southern Africa) than to previously sequenced Ethiopian reference strains. Genotypic analysis showed that two Ethiopian isolates naturally harbored the mutations K70R and G190A associated with resistance to ZDV and nonnucleoside reverse transcriptase inhibitors, respectively. Phenotypic assays revealed that the K70R substitution in this context did not reduce susceptibility to ZDV, whereas the G190A substitution resulted in high-level resistance to nevirapine (NVP). Moreover, variants resistant to NVP, delavirdine (DLV), and efavirenz (EFV) were more rapidly selected at lower drug doses culture with clade C than with clade B wild-type isolates. In the case of subtype C, selection with NVP and/or EFV led to the appearance of several previously unseen mutations in RT, i.e., V106M and S98I, as well as other mutations that have been previously reported (e.g., K103N, V106A, V108I, and Y181C). After selection with DLV, a polymorphism, A62A, initially observed in the Ethiopian isolate 4762, mutated to A62V; the latter is a secondary substitution associated with multidrug resistance against nucleoside RT inhibitors. Phenotypic analysis of clade C mutants selected against NVP, DLV, and EFV revealed broad cross-resistance, particularly in regard to NVP and DLV. These findings suggest that RT genotypic diversity may influence the emergence of drug resistance.
Enzymes Associated with Reductive Activation and Action of Nitazoxanide, Nitrofurans, and Metronidazole in
Helicobacter pylori
Authors: Sisson Gary , Goodwin Avery , Raudonikiene Ausra , Hughes Nicky J. , Mukhopadhyay Asish K. , Berg Douglas E. , Hoffman Paul S. 
Published: July 2002

ABSTRACT

Nitazoxanide (NTZ) is a redox-active nitrothiazolyl-salicylamide prodrug that kills
Helicobacter pylori
and also many anaerobic bacterial, protozoan, and helminthic species. Here we describe development and use of a spectrophotometric assay, based on nitroreduction of NTZ at 412 nm, to identify
H. pylori
enzymes responsible for its activation and mode of action. Three enzymes that reduce NTZ were identified: two related NADPH nitroreductases, which also mediate susceptibility to metronidazole (MTZ) (RdxA and FrxA), and pyruvate oxidoreductase (POR). Recombinant His-tagged RdxA, FrxA, and POR, overexpressed in nitroreductase-deficient
Escherichia coli
, each rapidly reduced NTZ, whereas only FrxA and to a lesser extent POR reduced nitrofuran substrates (furazolidone, nitrofurantoin, and nitrofurazone). POR exhibited no MTZ reductase activity either in extracts of
H. pylori
or following overexpression in
E. coli
; RdxA exhibited no nitrofuran reductase activity, and FrxA exhibited no MTZ reductase activity. Analysis of mutation to rifampin resistance (Rif
r
) indicated that NTZ was not mutagenic and that nitrofurans were only weakly mutagenic. Alkaline gel DNA electrophoresis indicated that none of these prodrugs caused DNA breakage. In contrast, MTZ caused DNA damage and was strongly mutagenic. We conclude that POR, an essential enzyme, is responsible for most or all of the bactericidal effects of NTZ against
H. pylori
. While loss-of-function mutations in
rdxA
and
frxA
produce a Mtz
r
phenotype, they do not contribute much to the innate susceptibility of
H. pylori
to NTZ or nitrofurans.
Novel Class 1 Integron (InS21) Carrying
bla
CTX-M-2
in
Salmonella enterica
Serovar Infantis
Authors: Di Conza José , Ayala Juan A. , Power Pablo , Mollerach Marta , Gutkind Gabriel 
Published: July 2002

ABSTRACT

The genetic organization of the region coding for CTX-M-2 in
Salmonella enterica
serovar Infantis was determined by PCR mapping. This gene seems to have been mobilized from the
Kluyvera ascorbata
chromosome to a complex
sulI
-type integron, similar to In6 and In7.
In Vivo Activity of Posaconazole againstMucorspp. in an Immunosuppressed-Mouse Model
Authors: Sun Qiu N. , Najvar Laura K. , Bocanegra Rosie , Loebenberg David , Graybill John R. 
Published: July 2002

ABSTRACTThe in vivo activities of posaconazole, itraconazole, and amphotericin B in neutropenic mice with zygomycosis were compared. The in vitro MICs of posaconazole and itraconazole for the strains ofMucorspp. used in this study ranged from 0.125 to 8 μg/ml and 0.25 to 8 μg/ml, respectively. The in vitro MIC range for amphotericin B is 0.125 to 0.25 μg/ml. At twice-daily doses of ≥15 mg/kg of body weight, posaconazole prolonged the survival of the mice and reduced tissue burden.
Hexapeptide Derivatives of Glycopeptide Antibiotics: Tools for Mechanism of Action Studies
Authors: Allen Norris E. , LeTourneau Deborah L. , Hobbs Joe N. , Thompson Richard C. 
Published: July 2002

ABSTRACT

Hexapeptide (des-
N
-methylleucyl) derivatives of LY264826 were prepared in order to examine further the role of N-substituted hydrophobic side chains in defining the mechanisms of action of semisynthetic glycopeptide antibiotics. The hexapeptide of LY264826 binds to the cell wall intermediate analog
l
-Lys-
d
-Ala-
d
-Ala with a 100-fold lower affinity than LY264826 and inhibits
Micrococcus luteus
almost 200-fold more poorly than LY264826 does. Alkylation of the 4-epi-vancosamine moiety of the disaccharide significantly enhanced the antibacterial activity of the hexapeptide. Alkylation did not affect the binding affinity for
d
-alanyl-
d
-alanine residues; however, it did enhance dimerization 7,000-fold and enhanced binding to bacterial membrane vesicles noticeably compared with the levels of dimerization and binding for the unsubstituted hexapeptide. The findings from this study complement those presented in an earlier report (N. E. Allen, D. L. LeTourneau, and J. N. Hobbs, Jr., J. Antibiot. 50:677-684, 1997) and are consistent with the conclusion that the enhanced antibacterial activities of semisynthetic glycopeptide antibiotics derive from the ability of the hydrophobic side chain to markedly affect both dimerization and binding to bacterial membranes.
N-Arylsulfonyl Hydrazones as Inhibitors of IMP-1 Metallo-β-Lactamase
Authors: Siemann Stefan , Evanoff Darryl P. , Marrone Laura , Clarke Anthony J. , Viswanatha Thammaiah , Dmitrienko Gary I. 
Published: July 2002

ABSTRACTMembers of a family ofN-arylsulfonyl hydrazones have been identified as novel inhibitors of IMP-1, a metallo-β-lactamase of increasing prevalence. Structure-activity relationship studies have indicated a requirement for bulky aromatic substituents on each side of the sulfonyl hydrazone backbone for these compounds to serve as efficient inhibitors of IMP-1. Molecular modeling has provided insight into the structural basis for the anti-metallo-β-lactamase activity exhibited by this class of compounds.
Distribution of
mef
(A) in Gram-Positive Bacteria from Healthy Portuguese Children
Authors: Luna Vicki A. , Heiken Marc , Judge Kathleen , Ulep Catherine , Van Kirk Nicole , Luis Henrique , Bernardo Mario , Leitao Jose , Roberts Marilyn C. 
Published: July 2002

ABSTRACT

We screened 615 gram-positive isolates from 150 healthy children for the presence of the
erm
(A),
erm
(B),
erm
(C),
erm
(F), and
mef
(A) genes. The
mef
(A) genes were found in 20 (9%) of the macrolide-resistant isolates, including
Enterococcus
spp.,
Staphylococcus
spp., and
Streptococcus
spp. Sixteen of the 19 gram-positive isolates tested carried the other seven open reading frames (ORFs) described in Tn
1207.1
, a genetic element carrying
mef
(A) recently described in
Streptococcus pneumoniae
. The three
Staphylococcus
spp. did not carry
orf1
to
orf3
. A gram-negative
Acinetobacter junii
isolate also carried the other seven ORFs described in Tn
1207.1.
A
Staphylococcus aureus
isolate, a
Streptococcus intermedius
isolate, a
Streptococcus
sp. isolate, and an
Enterococcus
sp. isolate had their
mef
(A) genes completely sequenced and showed 100% identity at the DNA and amino acid levels with the
mef
(A) gene from
S. pneumoniae
.
In Vitro Evaluation of AZD2563, a Novel Oxazolidinone, against 603 Recent Staphylococcal Isolates
Authors: Anderegg Tamara R. , Biedenbach Douglas J. , Jones Ronald N. 
Published: July 2002

ABSTRACT

AZD2563, a novel oxazolidinone, and a selection of comparator drugs that included linezolid, erythromycin, clindamycin, quinolones, and gentamicin were tested against 384
Staphylococcus aureus
(176 oxacillin-resistant
S. aureus
[ORSA]) and 219 coagulase-negative staphylococci (CoNS; 162 oxacillin resistant) by reference microdilution (all strains) and agar dilution (30 strains) methods. The following results were noted for AZD2563. (Note that, for comparison only, a breakpoint of ≤4 μg/ml [the breakpoint of linezolid] was used for this study, although a susceptibility breakpoint for AZD2563 has not been determined.) For
S. aureus
, the MIC at which 50% of the isolates tested are inhibited (MIC
50
) was 1 μg/ml, the MIC
90
was 2 μg/ml, and the percent susceptibility was 100%. For CoNS, the MIC
50
was 0.5 μg/ml, the MIC
90
was 1 μg/ml, and the percent susceptibility was 100%. ORSA and OR-CoNS strains were equally inhibited by AZD2563 and linezolid. AZD2563 demonstrated antistaphylococcal activity comparable to that of linezolid.
Activities of ABT-773 against Microaerophilic and Fastidious Organisms
Authors: Finegold Sydney M. , Molitoris Denise , Phan V. T. , Vaisanen M.-L. , Wexler Hannah M. 
Published: July 2002

ABSTRACT
ABT-773 was tested against 317 fastidious isolates; it inhibited 99% of organisms at a concentration of 4.0 μg/ml. With ampicillin-sulbactam and levofloxacin, only 2 and 6% of these strains, respectively, were resistant at the breakpoint. With clindamycin, penicillin G, and metronidazole, 22, 26, and 58% of the strains, respectively, were resistant.
Members of the Family
Comamonadaceae
as Primary Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate)-Degrading Denitrifiers in Activated Sludge as Revealed by a Polyphasic Approach
Authors: Khan Shams Tabrez , Horiba Yoko , Yamamoto Masamitsu , Hiraishi Akira 
Published: July 2002

ABSTRACT

The distribution and phylogenetic affiliations of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)-degrading denitrifying bacteria in activated sludge were studied by a polyphasic approach including culture-independent biomarker and molecular analyses as well as cultivation methods. A total of 23 strains of PHBV-degrading denitrifiers were isolated from activated sludges from different sewage treatment plants. 16S ribosomal DNA (rDNA) sequence comparisons showed that 20 of the isolates were identified as members of the family
Comamonadaceae
, a major group of β-
Proteobacteria.
When the sludges from different plants were acclimated with PHBV under denitrifying conditions in laboratory scale reactors, the nitrate removal rate increased linearly during the first 4 weeks and reached 20 mg NO
3
−
-N h
−1
g of dry sludge
−1
at the steady state. The bacterial-community change in the laboratory scale sludges during the acclimation was monitored by rRNA-targeted fluorescence in situ hybridization and quinone profiling. Both approaches showed that the population of β-
Proteobacteria
in the laboratory sludges increased sharply during acclimation regardless of their origins. 16S rDNA clone libraries were constructed from two different acclimated sludges, and a total of 37 clones from the libraries were phylogenetically analyzed. Most of the 16S rDNA clones were grouped with members of the family
Comamonadaceae
. The results of our polyphasic approach indicate that β-
Proteobacteria
, especially members of the family
Comamonadaceae
, are primary PHBV-degrading denitrifiers in activated sludge. Our data provide useful information for the development of a new nitrogen removal system with solid biopolymer as an electron donor.
Process and Metabolic Strategies for Improved Production of
Escherichia coli
-Derived 6-Deoxyerythronolide B
Authors: Pfeifer Blaine , Hu Zhihao , Licari Peter , Khosla Chaitan 
Published: July 2002

ABSTRACT

Recently, the feasibility of using
Escherichia coli
for the heterologous biosynthesis of complex polyketides has been demonstrated. In this report, the development of a robust high-cell-density fed-batch procedure for the efficient production of complex polyketides is described. The effects of various physiological conditions on the productivity and titers of 6-deoxyerythronolide B (6dEB; the macrocyclic core of the antibiotic erythromycin) in recombinant cultures of
E. coli
were studied in shake flask cultures. The resulting data were used as a foundation to develop a high-cell-density fermentation procedure by building upon procedures reported earlier for recombinant protein production in
E. coli
. The fermentation strategy employed consistently produced ∼100 mg of 6dEB per liter, whereas shake flask conditions generated between 1 and 10 mg per liter. The utility of an accessory thioesterase (TEII from
Saccharopolyspora erythraea
) for enhancing the productivity of 6dEB in
E. coli
was also demonstrated (increasing the final titer of 6dEB to 180 mg per liter). In addition to reinforcing the potential for using
E. coli
as a heterologous host for wild-type- and engineered-polyketide biosynthesis, the procedures described in this study may be useful for the production of secondary metabolites that are difficult to access by other routes.
Identification of anopd(Organophosphate Degradation) Gene in anAgrobacteriumIsolate
Authors: Horne Irene , Sutherland Tara D. , Harcourt Rebecca L. , Russell Robyn J. , Oakeshott John G. 
Published: July 2002

ABSTRACTWe isolated a bacterial strain,Agrobacterium radiobacterP230, which can hydrolyze a wide range of organophosphate (OP) insecticides. A gene encoding a protein involved in OP hydrolysis was cloned fromA. radiobacterP230 and sequenced. This gene (calledopdA) had sequence similarity toopd, a gene previously shown to encode an OP-hydrolyzing enzyme inFlavobacteriumsp. strain ATCC 27551 andBrevundimonas diminutaMG. Insertional mutation of theopdAgene produced a strain lacking the ability to hydrolyze OPs, suggesting that this is the only gene encoding an OP-hydrolyzing enzyme inA. radiobacterP230. The OPH and OpdA proteins, encoded byopdandopdA, respectively, were overexpressed and purified as maltose-binding proteins, and the maltose-binding protein moiety was cleaved and removed. Neither protein was able to hydrolyze the aliphatic OP malathion. The kinetics of the two proteins for diethyl OPs were comparable. For dimethyl OPs, OpdA had a higherkcatthan OPH. It was also capable of hydrolyzing the dimethyl OPs phosmet and fenthion, which were not hydrolyzed at detectable levels by OPH.
tfdA
-Like Genes in 2,4-Dichlorophenoxyacetic Acid-Degrading Bacteria Belonging to the
Bradyrhizobium-Agromonas-Nitrobacter-Afipia
Cluster in α-
Proteobacteria
Authors: Itoh Kazuhito , Kanda Rie , Sumita Yoko , Kim Hongik , Kamagata Yoichi , Suyama Kousuke , Yamamoto Hiroki , Hausinger Robert P. , Tiedje James M. 
Published: July 2002

ABSTRACT

The 2,4-dichlorophenoxyacetate (2,4-D)/α-ketoglutarate dioxygenase gene (
tfdA
) homolog designated
tfdAα
was cloned and characterized from 2,4-D-degrading bacterial strain RD5-C2. This Japanese upland soil isolate belongs to the
Bradyrhizobium-Agromonas-Nitrobacter-Afipia
cluster in the α subdivision of the class
Proteobacteria
on the basis of its 16S ribosomal DNA sequence. Sequence analysis showed 56 to 60% identity of
tfdAα
to representative
tfdA
genes. A MalE-TfdAα fusion protein expressed in
Escherichia coli
exhibited about 10 times greater activity for phenoxyacetate than 2,4-D in an α-ketoglutarate- and Fe(II)-dependent reaction. The deduced amino acid sequence of TfdAα revealed a conserved His-X-Asp-X
146
-His-X
14
-Arg motif characteristic of the active site of group II α-ketoglutarate-dependent dioxygenases. The
tfdAα
genes were also detected in 2,4-D-degrading α-
Proteobacteria
previously isolated from pristine environments in Hawaii and in Saskatchewan, Canada (Y. Kamagata, R. R. Fulthorpe, K. Tamura, H. Takami, L. J. Forney, and J. M. Tiedje, Appl. Environ. Microbiol.
63:
2266-2272, 1997). These findings indicate that the
tfdA
genes in β- and γ-
Proteobacteria
and the
tfdAα
genes in α-
Proteobacteria
arose by divergent evolution from a common ancestor.
Fitness of
Salmonella enterica
serovar Thompson in the Cilantro Phyllosphere
Authors: Brandl Maria T. , Mandrell Robert E. 
Published: July 2002

ABSTRACT

The epiphytic fitness of
Salmonella enterica
was assessed on cilantro plants by using a strain of
S. enterica
serovar Thompson that was linked to an outbreak resulting from cilantro.
Salmonella
serovar Thompson had the ability to colonize the surface of cilantro leaves, where it was detected by confocal laser scanning microscopy (CLSM) at high densities on the veins and in natural lesions. The population sizes of two common colonizers of plant surfaces,
Pantoea agglomerans
and
Pseudomonas chlororaphis
, were 10-fold higher than that of the human pathogen on cilantro incubated at 22°C. However,
Salmonella
serovar Thompson achieved significantly higher population levels and accounted for a higher proportion of the total culturable bacterial flora on cilantro leaves when the plants were incubated at warm temperatures, such as 30°C, after inoculation, indicating that the higher growth rates exhibited by
Salmonella
serovar Thompson at warm temperatures may increase the competitiveness of this organism in the phyllosphere. The tolerance of
Salmonella
serovar Thompson to dry conditions on plants at 60% relative humidity was at least equal to that of
P. agglomerans
and
P. chlororaphis
. Moreover, after exposure to low humidity on cilantro,
Salmonella
serovar Thompson recovered under high humidity to achieve its maximum population size in the cilantro phyllosphere. Visualization by CLSM of green fluorescent protein-tagged
Salmonella
serovar Thompson and dsRed-tagged
P. agglomerans
inoculated onto cilantro revealed that the human pathogen and the bacterial epiphyte formed large heterogeneous aggregates on the leaf surface. Our studies support the hypothesis that preharvest contamination of crops by
S. enterica
plays a role in outbreaks linked to fresh fruits and vegetables.
Evidence of Association of Salmonellae with Tomato Plants Grown Hydroponically in Inoculated Nutrient Solution
Authors: Guo Xuan , van Iersel Marc W. , Chen Jinru , Brackett Robert E. , Beuchat Larry R. 
Published: July 2002

ABSTRACT

The possibility of uptake of salmonellae by roots of hydroponically grown tomato plants was investigated. Within 1 day of exposure of plant roots to Hoagland nutrient solution containing 4.46 to 4.65 log
10
CFU of salmonellae/ml, the sizes of the pathogen populations were 3.01 CFU/g of hypocotyls and cotyledons and 3.40 log
10
CFU/g of stems for plants with intact root systems (control) and 2.55 log
10
CFU/g of hypocotyls and cotyledons for plants from which portions of the roots had been removed. A population of ≥3.38 log
10
CFU/g of hypocotyls-cotyledons, stems, and leaves of plants grown for 9 days was detected regardless of the root condition. Additional studies need to be done to unequivocally demonstrate that salmonellae can exist as endophytes in tomato plants grown under conditions that simulate commonly used agronomic practices.
Catalase, a Specific Antigen in the Feces of Human Subjects Infected with
Helicobacter pylori
Authors: Suzuki Nobuyuki , Wakasugi Masahiko , Nakaya Seigo , Kokubo Naomi , Sato Masami , Kajiyama Hirofumi , Takahashi Ryoki , Hirata Haruhisa , Ezure Yohji , Fukuda Yoshihiro , Shimoyama Takashi 
Published: July 2002

ABSTRACT

Recently, we reported the production of three new monoclonal antibodies with high specificity for a
Helicobacter pylori
antigen suitable for diagnosis of
H. pylori
infection. The aim of the present study was to identify the antigen recognized by these monoclonal antibodies concerning both
H. pylori
and the feces of human subjects infected with
H. pylori
. The cellular antigen was purified from an
H. pylori
cell extract by immunoaffinity column chromatography with the monoclonal antibody as a ligand. The amino-terminal amino acid sequences (eight residues) of the purified antigen and
H. pylori
catalase were the same. The molecular weights of native and subunit, specific catalase activity, and UV and visible spectra of the purified antigen were in good agreement with those of
H. pylori
catalase. The human fecal antigens were purified from two fecal samples of two
H. pylori
-positive subjects by ammonium sulfate precipitation, CM-Sephadex C
50
chromatography, and the same immunoaffinity chromatography used for the
H. pylori
cellular antigen. The fecal antigens had catalase activity. The amino-terminal amino acid sequences (five residues) of the human fecal antigen and
H. pylori
catalase were the same. The monoclonal antibodies reacted with the native cellular antigen, but did not react with the denatured antigen, human catalase, and bovine catalase. The results show that the target antigen of the monoclonal antibodies is native
H. pylori
catalase and that the monoclonal antibodies are able to specifically detect the antigen, which exists in an intact form, retaining the catalase activity in human feces.