bluuebunny/crossref_metadata_2025 huggingface dataset:
GldI Is a Lipoprotein That Is Required for
Flavobacterium johnsoniae
Gliding Motility and Chitin Utilization
Authors: McBride Mark J. , Braun Timothy F.
Published: April 2004

Cells of
Flavobacterium johnsoniae
glide rapidly over surfaces by an unknown mechanism. Seven genes (
gldA
,
gldB
,
gldD
,
gldF
,
gldG
,
gldH
, and
ftsX
) that are required for gliding motility have been described. Complementation of the nonmotile mutants UW102-41, UW102-85, and UW102-92 identified another gene,
gldI
, that is required for gliding motility.
gldI
mutants formed nonspreading colonies, and individual cells were completely nonmotile. They were also resistant to bacteriophages that infect wild-type cells, and they failed to digest chitin. Introduction of wild-type
gldI
on a plasmid restored colony spreading, cell motility, phage sensitivity, and the ability to digest chitin to the
gldI
mutants.
gldI
encodes a predicted 199-amino-acid protein that localized to the membrane fraction. Labeling studies with [
3
H]palmitate indicated that GldI is a lipoprotein. GldI is similar to peptidyl-prolyl
cis/trans
-isomerases of the FK506-binding protein family and may be involved in folding cell envelope protein components of the motility machinery.
A 12-Base-Pair Deletion in the Flagellar Master Control Gene
flhC
Causes Nonmotility of the Pathogenic German Sorbitol-Fermenting
Escherichia coli
O157:H
−
Strains
Authors: Monday Steven R. , Minnich Scott A. , Feng Peter C. H.
Published: April 2004

An atypical, Stx2-producing, pathogenic
Escherichia coli
O157:H
−
strain has been isolated with increasing frequency from hemolytic uremic syndrome patients in Germany. The lack of the H7 antigen coupled with the strain's ability to ferment sorbitol and express β-glucuronidase have complicated its detection and identification. In this study, we have determined that the loss of motility in these German sorbitol-fermenting (SF) O157 strains is due to a 12-bp in-frame deletion in
flhC
that is required for transcriptional activation of genes involved in flagellum biosynthesis. Either complementation with a functional
flhC
or repair of this mutation restored H7 antigen expression and motility. PCR analysis of several nonmotile
E. coli
O157 strains from various geographical sources confirmed that the 12-bp
flhC
deletion is found only in the cluster of German SF O157 strains, providing a potentially useful marker by which these atypical strains can be identified. The loss of motility via mutations in the
flhDC
operon that we observed in the German SF O157 strains is consistent with a similar phenomenon currently observed in a significant subset of other important gram-negative pathogens.
A New Amidohydrolase from
Bordetella
or
Alcaligenes
Strain FB188 with Similarities to Histone Deacetylases
Authors: Hildmann Christian , Ninkovic Milena , Dietrich Rüdiger , Wegener Dennis , Riester Daniel , Zimmermann Thomas , Birch Olwen M. , Bernegger Christine , Loidl Peter , Schwienhorst Andreas
Published: April 2004

The full-length gene encoding the histone deacetylase (HDAC)-like amidohydrolase (HDAH) from
Bordetella
or
Alcaligenes
(
Bordetella/Alcaligenes
) strain FB188 (DSM 11172) was cloned using degenerate primer PCR combined with inverse-PCR techniques and ultimately expressed in
Escherichia coli
. The expressed enzyme was biochemically characterized and found to be similar to the native enzyme for all properties examined. Nucleotide sequence analysis revealed an open reading frame of 1,110 bp which encodes a polypeptide with a theoretical molecular mass of 39 kDa. Interestingly, peptide sequencing disclosed that the N-terminal methionine is lacking in the mature wild-type enzyme, presumably due to the action of methionyl aminopeptidase. Sequence database searches suggest that the new amidohydrolase belongs to the HDAC superfamily, with the closest homologs being found in the subfamily assigned acetylpolyamine amidohydrolases (APAH). The APAH subfamily comprises enzymes or putative enzymes from such diverse microorganisms as
Pseudomonas aeruginosa
,
Archaeoglobus fulgidus
, and the actinomycete
Mycoplana ramosa
(formerly
M. bullata
). The FB188 HDAH, however, is only moderately active in catalyzing the deacetylation of acetylpolyamines. In fact, FB188 HDAH exhibits significant activity in standard HDAC assays and is inhibited by known HDAC inhibitors such as trichostatin A and suberoylanilide hydroxamic acid (SAHA). Several lines of evidence indicate that the FB188 HDAH is very similar to class 1 and 2 HDACs and contains a Zn
2+
ion in the active site which contributes significantly to catalytic activity. Initial biotechnological applications demonstrated the extensive substrate spectrum and broad optimum pH range to be excellent criteria for using the new HDAH from
Bordetella/Alcaligenes
strain FB188 as a biocatalyst in technical biotransformations, e.g., within the scope of human immunodeficiency virus reverse transcriptase inhibitor synthesis.
The Gas Vesicle Gene Cluster from
Microcystis aeruginosa
and DNA Rearrangements That Lead to Loss of Cell Buoyancy
Authors: Mlouka Alyssa , Comte Katia , Castets Anne-Marie , Bouchier Christiane , Tandeau de Marsac Nicole
Published: April 2004

Microcystis aeruginosa
is a planktonic unicellular cyanobacterium often responsible for seasonal mass occurrences at the surface of freshwater environments. An abundant production of intracellular structures, the gas vesicles, provides cells with buoyancy. A 8.7-kb gene cluster that comprises twelve genes involved in gas vesicle synthesis was identified. Ten of these are organized in two operons,

gvpA
I

A
II

A
III

CNJX
and
gvpKFG
, and two,
gvpV
and
gvpW
, are individually expressed. In an attempt to elucidate the basis for the frequent occurrence of nonbuoyant mutants in laboratory cultures, four gas vesicle-deficient mutants from two strains of
M. aeruginosa
, PCC 7806 and PCC 9354, were isolated and characterized. Their molecular analysis unveiled DNA rearrangements due to four different insertion elements that interrupted
gvpN
,
gvpV
, or
gvpW
or led to the deletion of the

gvpA
I

-A
III

region. While
gvpA
, encoding the major gas vesicle structural protein, was expressed in the
gvpN
,
gvpV
, and
gvpW
mutants, immunodetection revealed no corresponding GvpA protein. Moreover, the absence of a gas vesicle structure was confirmed by electron microscopy. This study brings out clues concerning the process driving loss of buoyancy in
M. aeruginosa
and reveals the requirement for gas vesicle synthesis of two newly described genes,
gvpV
and
gvpW
.
Burkholderia
spp. Alter
Pseudomonas aeruginosa
Physiology through Iron Sequestration
Authors: Weaver Valerie B. , Kolter Roberto
Published: April 2004

Pseudomonas aeruginosa
and members of the
Burkholderia cepacia
complex often coexist in both the soil and the lungs of cystic fibrosis patients. To gain an understanding of how these different species affect each other's physiology when coexisting, we performed a screen to identify
P. aeruginosa
genes that are induced in the presence of
Burkholderia
. A random gene fusion library was constructed in
P. aeruginosa
PA14 by using a transposon containing a promoterless
lacZ
gene. Fusion strains were screened for their ability to be induced in the presence of
Burkholderia
strains in a cross-streak assay. Three fusion strains were induced specifically by
Burkholderia
species; all three had transposon insertions in genes known to be iron regulated. One of these fusion strains, containing a transposon insertion in gene PA4467, was used to characterize the inducing activity from
Burkholderia
. Biochemical and genetic evidence demonstrate that ornibactin, a siderophore produced by nearly all
B. cepacia
strains, can induce
P. aeruginosa
PA4467. Significantly, PA4467 is induced early in coculture with an ornibactin-producing but not an ornibactin-deficient
B. cepacia
strain, indicating that ornibactin can be produced by
B. cepacia
and detected by
P. aeruginosa
when the two species coexist.
Identification of a Phosphotransferase System of
Escherichia coli
Required for Growth on
N
-Acetylmuramic Acid
Authors: Dahl Ulrike , Jaeger Tina , Nguyen Bao Trâm , Sattler Julia M. , Mayer Christoph
Published: April 2004

We report here that wild-type
Escherichia coli
grows on
N
-acetylmuramic acid (MurNAc) as the sole source of carbon and energy. Analysis of mutants defective in
N
-acetylglucosamine (GlcNAc) catabolism revealed that the catabolic pathway for MurNAc merges into the GlcNAc pathway on the level of GlcNAc 6-phosphate. Furthermore, analysis of mutants defective in components of the phosphotransferase system (PTS) revealed that a PTS is essential for growth on MurNAc. However, neither the glucose-, mannose/glucosamine-, nor GlcNAc-specific PTS (PtsG, ManXYZ, and NagE, respectively) was found to be necessary. Instead, we identified a gene at 55 min on the
E. coli
chromosome that is responsible for MurNAc uptake and growth. It encodes a single polypeptide consisting of the EIIB and C domains of a so-far-uncharacterized PTS that was named
murP
. MurP lacks an EIIA domain and was found to require the activity of the
crr
-encoded enzyme IIA-glucose (EIIA
Glc
), a component of the major glucose transport system for growth on MurNAc.
murP
deletion mutants were unable to grow on MurNAc as the sole source of carbon; however, growth was rescued by providing
murP
in
trans
expressed from an isopropylthiogalactopyranoside-inducible plasmid. A functional His
6
fusion of MurP was constructed, isolated from membranes, and identified as a polypeptide with an apparent molecular mass of 37 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis. Close homologs of MurP were identified in the genome of several bacteria, and we believe that these organisms might also be able to utilize MurNAc.
Genetic Analysis of theSalmonella entericaType III Secretion-Associated ATPase InvC Defines Discrete Functional Domains
Authors: Akeda Yukihiro , Galán Jorge E.
Published: April 2004

An essential component of all type III secretion systems is a highly conserved ATPase that shares significant amino acid sequence similarity to the β subunit of the F0F1ATPases and is thought to provide the energy for the secretion process. We have performed a genetic and functional analysis of InvC, the ATPase associated with theSalmonella entericatype III secretion system encoded within its pathogenicity island 1. Through a mutagenesis analysis, we have identified amino acid residues that are essential for specific activities of InvC, such as nucleotide hydrolysis and membrane binding. This has allowed us to define discrete domains of InvC that are specifically associated with different essential activities of this protein.
ZipA Is Required for Targeting ofDMinC/DicB, but NotDMinC/MinD, Complexes to Septal Ring Assemblies inEscherichia coli
Authors: Johnson Jay E. , Lackner Laura L. , Hale Cynthia A. , de Boer Piet A. J.
Published: April 2004

The MinC division inhibitor is required for accurate placement of the septal ring at the middle of theEscherichia colicell. The N-terminal domain of MinC (ZMinC) interferes with FtsZ assembly, while the C-terminal domain (DMinC) mediates both dimerization and complex formation with either MinD or DicB. Binding to either of these activators greatly enhances the division-inhibitory activity of MinC in the cell. The MinD ATPase plays a crucial role in the rapid pole-to-pole oscillation of MinC that is proposed to force FtsZ ring formation to midcell. DicB is encoded by one of the cryptic prophages on theE. colichromosome (Qin) and is normally not synthesized. Binding of MinD or DicB toDMinC produces complexes that have high affinities for one or more septal ring-associated targets. Here we show that the FtsZ-binding protein ZipA is required for both recruitment of theDMinC/DicB complex to FtsZ rings and the DicB-inducible division block normally seen in MinC+cells. In contrast, none of the known FtsZ-associated factors, including ZipA, FtsA, and ZapA, appear to be specifically required for targeting of theDMinC/MinD complex to rings, implying that the two MinC/activator complexes must recognize distinct features of FtsZ assemblies. MinD-dependent targeting of MinC may occur in two steps of increasing topological specificity: (i) recruitment of MinC from the cytoplasm to the membrane, and (ii) specific targeting of the MinC/MinD complex to nascent septal ring assemblies on the membrane. Using membrane-tethered derivatives of MinC, we obtained evidence that both of these steps contribute to the efficiency of MinC/MinD-mediated division inhibition.
Expression Islands Clustered on the Symbiosis Island of the
Mesorhizobium loti
Genome
Authors: Uchiumi Toshiki , Ohwada Takuji , Itakura Manabu , Mitsui Hisayuki , Nukui Noriyuki , Dawadi Pramod , Kaneko Takakazu , Tabata Satoshi , Yokoyama Tadashi , Tejima Kouhei , Saeki Kazuhiko , Omori Hirofumi , Hayashi Makoto , Maekawa Takaki , Sriprang Rutchadaporn , Murooka Yoshikatsu , Tajima Shigeyuki , Simomura Kenshiro , Nomura Mika , Suzuki Akihiro , Shimoda Yoshikazu , Sioya Kouki , Abe Mikiko , Minamisawa Kiwamu
Published: April 2004

Rhizobia are symbiotic nitrogen-fixing soil bacteria that are associated with host legumes. The establishment of rhizobial symbiosis requires signal exchanges between partners in microaerobic environments that result in mutualism for the two partners. We developed a macroarray for
Mesorhizobium loti
MAFF303099, a microsymbiont of the model legume
Lotus japonicus
, and monitored the transcriptional dynamics of the bacterium during symbiosis, microaerobiosis, and starvation. Global transcriptional profiling demonstrated that the clusters of genes within the symbiosis island (611 kb), a transmissible region distinct from other chromosomal regions, are collectively expressed during symbiosis, whereas genes outside the island are downregulated. This finding implies that the huge symbiosis island functions as clustered expression islands to support symbiotic nitrogen fixation. Interestingly, most transposase genes on the symbiosis island were highly upregulated in bacteroids, as were
nif
,
fix
,
fdx
, and
rpoN
. The genome region containing the
fixNOPQ
genes outside the symbiosis island was markedly upregulated as another expression island under both microaerobic and symbiotic conditions. The symbiosis profiling data suggested that there was activation of amino acid metabolism, as well as
nif-fix
gene expression. In contrast, genes for cell wall synthesis, cell division, DNA replication, and flagella were strongly repressed in differentiated bacteroids. A highly upregulated gene in bacteroids, mlr5932 (encoding 1-aminocyclopropane-1-carboxylate deaminase), was disrupted and was confirmed to be involved in nodulation enhancement, indicating that disruption of highly expressed genes is a useful strategy for exploring novel gene functions in symbiosis.
The Teicoplanin-Associated Locus Regulator (TcaR) and the Intercellular Adhesin Locus Regulator (IcaR) Are Transcriptional Inhibitors of the
ica
Locus in
Staphylococcus aureus
Authors: Jefferson Kimberly K. , Pier Danielle B. , Goldmann Donald A. , Pier Gerald B.
Published: April 2004

Infections involving
Staphylococcus aureus
are often more severe and difficult to treat when the organism assumes a biofilm mode of growth. The polysaccharide poly-
N
-acetylglucosamine (PNAG), also known as polysaccharide intercellular adhesin, is synthesized by the products of the intercellular adhesin (
ica
) locus and plays a key role in biofilm formation. Numerous conditions and exogenous factors influence
ica
transcription and PNAG synthesis, but the regulatory factors and pathways through which these environmental stimuli act have been only partially characterized. We developed a DNA affinity chromatography system to purify potential regulatory proteins that bind to the
ica
promoter region. Using this technique, we isolated four proteins, including the staphylococcal gene regulator SarA, a MarR family transcriptional regulator of the teicoplanin-associated locus TcaR, DNA-binding protein II, and topoisomerase IV, that bound to the
ica
promoter. Site-directed deletion mutagenesis of
tcaR
indicated that TcaR was a negative regulator of
ica
transcription, but deletion of
tcaR
alone did not induce any changes in PNAG production or in adherence to polystyrene. We also investigated the role of IcaR, encoded within the
ica
locus but divergently transcribed from the biosynthetic genes. As has been shown previously in
Staphylococcus epidermidis
, we found that IcaR was also a negative regulator of
ica
transcription in
S. aureus
. We also demonstrate that mutation of
icaR
augmented PNAG production and adherence to polystyrene. Transcription of the
ica
locus, PNAG production, and adherence to polystyrene were further increased in a
tcaR icaR
double mutant. In summary, TcaR appeared to be a weak negative regulator of transcription of the
ica
locus, whereas IcaR was a strong negative regulator, and in their absence PNAG production and biofilm formation were enhanced.
The CoreEscherichia coliSignal Recognition Particle Receptor Contains Only the N and G Domains of FtsY
Authors: Eitan Asa , Bibi Eitan
Published: April 2004

Previous studies have proposed that the N-terminal A domain (∼200 amino acid residues) of theEscherichia colisignal recognition particle (SRP) receptor, FtsY, is required for membrane targeting. In contrast to this suggestion, we show that A domain-truncated versions of FtsY, harboring only domains N and G, are functional. Therefore, we propose that N and G domains constitute the core SRP receptor.
Clostridium difficileIStron CdISt1: Discovery of a Variant Encoding Two Complete Transposase-Like Proteins
Authors: Hasselmayer Oliver , Braun Veit , Nitsche Claudia , Moos Michael , Rupnik Maja , von Eichel-Streiber Christoph
Published: April 2004

Screening aClostridium difficilestrain collection for the chimeric element CdISt1, we identified two additional variants, designated CdISt1-0 and CdISt1-III. In in vitro assays, we could prove the self-splicing ribozyme activity of these variants. Structural comparison of all known CdISt1variants led us to define four types of IStrons that we designated CdISt1-0 through CdISt1-III. Since CdISt1-0 encodes two complete transposase-like proteins (TlpA and TlpB), we suggest that it represents the original genetic element, hypothesized before to have originated by fusion of a group I intron and an insertion sequence element.
On the discovery of a unique terrestrial faunal assemblage in the classic Pennsylvanian section at Joggins, Nova Scotia
Authors: Hebert Brian L , Calder John H
Published: March 2004

A rich fossil assemblage discovered from the classic Pennsylvanian locality of Joggins, Nova Scotia, is here described for the first time. The 2 m-thick Hebert sandstone, within the lower Joggins Formation of early Langsettian age, is the most productive stratum at Joggins of terrestrial tetrapods and the pulmonate gastropod Dendropupa vetusta exclusive of the historic fossil forest locality of Dawson and Lyell, and the most productive Pennsylvanian locality in the world of the large unionoid bivalve genus Archanodon. Although the land snailarchanodontid bivalvetetrapod assemblage of the Hebert Sandstone comprises a unique late Paleozoic terrestrial dryland biota, individual taxa were not endemic to drylands alone.
B chromosomes and genome size in flowering plants
Authors: Trivers Robert , Burt Austin , Palestis Brian G
Published: April 2004

B chromosomes are extra chromosomes found in some, but not all, individuals within a species, often maintained by giving themselves an advantage in transmission, i.e. they drive. Here we show that the presence of B chromosomes correlates to and varies strongly and positively with total genome size (excluding the Bs and corrected for ploidy) both at a global level and via a comparison of independent taxonomic contrasts. B chromosomes are largely absent from species with small genomes; however, species with large genomes are studied more frequently than species with small genomes and Bs are more likely to be reported in well-studied species. We controlled for intensity of study using logistic regression. This regression analysis also included effects of degree of outbreeding, which is positively associated with Bs and genome size, and chromosome number, which is negatively associated with Bs and genome size, as well as variable ploidy (more than one ploidy level in a species). Genome size, breeding system and chromosome number all contribute independently to the distribution of B chromosomes, while variable ploidy does not have a significant effect. The genome size correlates are consistent with reduced selection against extra DNA in species with large genomes and with increased generation of B sequences from large A genomes.Key words: B chromosomes, genome size, selfish genetic elements, breeding system, ploidy.
The transfer and characterization of resistance to common root rot from Thinopyrum ponticum to wheat
Authors: Li Hongjie , Conner Robert L , Chen Qin , Li Haiyan , Laroche André , Graf Robert J , Kuzyk Allan D
Published: April 2004

Common root rot, caused by Cochliobolus sativus (Ito and Kurib) Drechs. ex Dastur, is a major soil-borne disease of spring and winter wheat (Triticum aestivum L. em Thell.) on the Canadian prairies. Resistance to common root rot from Thinopyrum ponticum (Podp.) Liu and Wang was transferred into wheat via crossing with Agrotana, a resistant wheat – Th. ponticum partial amphiploid line. Evaluation of common root rot reactions showed that selected advanced lines with blue kernel color derived from a wheat × Agrotana cross expressed more resistance than the susceptible T. aestivum 'Chinese Spring' parent and other susceptible wheat check cultivars. Cytological examination revealed 41 to 44 chromosomes in the advanced lines. Genomic in situ hybridization, using total genomic DNA from Pseudoroegneria strigosa (M. Bieb) A. Löve (St genome) as a probe, demonstrated that the blue kernel plants had two pairs of spontaneously translocated J–Js and Js–J chromosomes derived from the J and Js genome of Th. ponticum. The presence of these translocated chromosomes was associated with increased resistance of wheat to common root rot. The lines with blue aleurone color always had a subcentromeric Js–J translocated chromosome. The subtelocentric J–Js translocated chromosome was not responsible for the blue kernel color. The genomic in situ hybridization analysis on meiosis revealed that the two spontaneous translocations were not reciprocal translocations.Key words: Cochliobolus sativus, genomic in situ hybridization, blue kernel color.
M chromosome of the wild silkworm, Bombyx mandarina (n = 27), corresponds to two chromosomes in the domesticated silkworm, Bombyx mori (n = 28)
Authors: Banno Yutaka , Nakamura Takashi , Nagashima Eiichi , Fujii Hiroshi , Doira Hiroshi
Published: April 2004

Chromosomes of Bombyx mori (n = 28) and of Bombyx mandarina (n = 27) were studied cytogenetically to resolve the origin of the large M chromosome in the Japaneses type of B. mandarina. In the F1 progeny from the reciprocal cross between B. mandarina and B. mori, the mitotic chromosome number was 2n = 55, and a chromosome configuration of 26 bivalents plus 1 trivalent was observed at metaphase I of germ cells. The trivalent chromosome consisted of the M chromosome from B. mandarina and two chromosomes from B. mori. When males of B. mori were mated to the F1 females, nuclei with two types of chromosome number (2n = 55 and 2n = 56) and two sets of chromosome pairs (26 bivalents plus 1 trivalent versus 28 bivalents) were observed in the metaphase I stage. Linkage analysis showed that the 14th chromosome of B. mori was involved in these two types of chromosome segregation. This result indicates that the M chromosome in B. mandarina arose from a fusion between a chromosome corresponding to the 14th linkage group and another, yet unidentified linkage group.Key words: Bombyx mandarina, Bombyx mori, chromosome dimorphism, linkage, karyotype.
Confocal analysis of chromosome behavior in wheat × maize zygotes
Authors: Mochida Keiichi , Tsujimoto Hisashi , Sasakuma Tetsuo
Published: April 2004

Herein, we profile the first embryonic mitosis in a hybrid of wheat and maize by using a whole-mount genomic in situ hybridization method and immunofluorescence staining with a tubulin-specific antibody. We have successfully captured the dynamics of each set of parental chromosomes in the first zygotic division of the hybrid embryo 24-28 h after crossing. During the first zygotic metaphase, although both sets of parental chromosomes congressed into the equatorial plate of the zygote, the maize chromosomes tended to lag in comparison with the wheat chromosomes. During anaphase, each parental chromosome separated into its sister chromosomes; however, some of the maize chromosomes lagged around the metaphase plate as segregants. The maize sister chromosomes that did move toward the pole showed delayed and asymmetric movement as compared with the wheat ones. Immunological staining of tubulin revealed a bipolar spindle structure in the first zygotic metaphase. The kinetochores of the maize chromosomes that lagged around the metaphase plate did not attach to the spindle microtubules. These results suggest that factors on the kinetochores of maize chromosomes that are required to control chromosome movement are deficient in the zygotic cell cycle.Key words: whole-mount, GISH, chromosome elimination, hybrid embryogenesis.
Biosynthesis, transport, and modification of lipid A
Authors: Trent M Stephen
Published: April 2004

Lipopolysaccharide (LPS) is the major surface molecule of Gram-negative bacteria and consists of three distinct structural domains: O-antigen, core, and lipid A. The lipid A (endotoxin) domain of LPS is a unique, glucosamine-based phospholipid that serves as the hydrophobic anchor of LPS and is the bioactive component of the molecule that is associated with Gram-negative septic shock. The structural genes encoding the enzymes required for the biosynthesis of Escherchia coli lipid A have been identified and characterized. Lipid A is often viewed as a constitutively synthesized structural molecule. However, determination of the exact chemical structures of lipid A from diverse Gram-negative bacteria shows that the molecule can be further modified in response to environmental stimuli. These modifications have been implicated in virulence of pathogenic Gram-negative bacteria and represent one of the molecular mechanisms of microbial surface remodeling used by bacteria to help evade the innate immune response. The intent of this review is to discuss the enzymatic machinery involved in the biosynthesis of lipid A, transport of the molecule, and finally, those enzymes involved in the modification of its structure in response to environmental stimuli.Key words: lipopolysaccharides, lipid A, endotoxin, outer membrane, MsbA.
Product diversity and regulation of type II fatty acid synthases
Authors: Lu Ying-Jie , Zhang Yong-Mei , Rock Charles O
Published: April 2004

Fatty acid biosynthesis is catalyzed in most bacteria by a group of highly conserved proteins known as the type II fatty acid synthase (FAS II) system. FAS II has been extensively studied in the Escherichia coli model system, and the recent explosion of bioinformatic information has accelerated the investigation of the pathway in other organisms, mostly important human pathogens. All FAS II systems possess a basic set of enzymes for the initiation and elongation of acyl chains. This review focuses on the variations on this basic theme that give rise to the diversity of products produced by the pathway. These include multiple mechanisms to generate unsaturated fatty acids and the accessory components required for branched-chain fatty acid synthesis in Gram-positive bacteria. Most of the known mechanisms that regulate product distribution of the pathway arise from the fundamental biochemical properties of the expressed enzymes. However, newly identified transcriptional factors in bacterial fatty acid biosynthetic pathways are a fertile field for new investigation into the genetic control of the FAS II system. Much more work is needed to define the role of these factors and the mechanisms that regulate their DNA binding capability, but there appear to be fundamental differences in how the expression of the pathway genes is controlled in Gram-negative and in Gram-positive bacteria.Key words: fatty acid synthase, bacteria.
Effects of ethanol and haloperidol on plasma levels of hepatic enzymes, lipid profile, and apolipoprotein in rats
Authors: Vasconcelos S M.M , Pereira R F , Alves R S , Filho A C.V. Arruda , Aguiar L M.V , Macedo D S , Freitas R M , Queiroz M G.R , Sousa F C.F , Viana G S.B
Published: April 2004

This work studied the effects of ethanol in the absence and presence of haloperidol under two experimental conditions. In protocol 1, rats were treated daily with ethanol (4 g/kg, p.o.) for 7 days, and received only haloperidol (1 mg/kg, i.p.) from the 8th day to the 14th day. In protocol 2, animals received ethanol, and the treatment continued with ethanol and haloperidol from the 8th day to the 14th day. Results show increases in alanine transaminase (ALT; 48% and 55%) and aspartate transaminase (AST; 32% and 22%) levels after ethanol or haloperidol (14 days) treatments, as compared with controls. Apolipoprotein A-1 (APO A1) levels were increased by haloperidol, after 7- (148%) but not after 14-day treatments, as compared with controls. Levels of lipoprotein (high-density lipoprotein (HDL-C)) tended to be increased only by ethanol treatment for 14 days. ALT (80%) and AST (43%) levels were increased in the haloperidol plus ethanol group (protocol 2), as compared with controls. However, an increase in APO A1 levels was observed in the haloperidol group pretreated with ethanol (protocol 1), as compared with controls and ethanol 7-day treatments. Triglyceride (TG) levels were increased in the combination of ethanol and haloperidol in protocol 1 (234%) and 2 (106%), as compared with controls. Except for a small decrease in haloperidol groups, with or without ethanol, as related to ethanol alone, no other effect was observed in HDL-C levels. In conclusion, we showed that haloperidol might be effective in moderating lipid alterations caused by chronic alcohol intake.Key words: ethanol, haloperidol, hepatic enzymes, lipid profiles.
The role of disulfide bonds in the conformational stability and catalytic activity of phytase
Authors: Wang Xiao-Yun , Meng Fan-Guo , Zhou Hai-Meng
Published: April 2004

Previous studies have predicted five disulfide bonds in Aspergillus niger phytase (phy A). To investigate the role of disulfide bonds, intrinsic fluorescence spectra, far-ultraviolet circular dichroism (CD) spectra, and an enzyme activity assay were used to compare the differences of catalytic activity and conformational stability of phytase during denaturation in urea in the presence and absence of dithiothreitol (DTT). In the presence of 2 mM DTT, the inactivation and unfolding were greatly enhanced at the same concentration of denaturant. The fluorescence emission maximum red shift and decreases of ellipticity at 222 nm were in accord with the changes of catalytic activity. The kinetics of the unfolding courses were a biphasic process consisting of two first-order reactions in the absence of DTT and a monophasic process of a first-order reaction in the presence of DTT. The results suggested that the loss of enzymatic activity was most likely because of a conformational change, and that disulfide bonds played an important role in three-dimensional structure and catalytic activity.Key words: phytase, urea denaturation, inactivation, disulfide bond.
Zebrafish tyrosylprotein sulfotransferase: molecular cloning, expression, and functional characterization
Authors: Mishiro Emi , Liu Ming-Yih , Sakakibara Yoichi , Suiko Masahito , Liu Ming-Cheh
Published: April 2004

By employing the reverse transcriptase – polymerase chain reaction technique in conjunction with 3' rapid amplification of cDNA ends, a full-length cDNA encoding a zebrafish (Danio rerio) tyrosylprotein sulfotransferase (TPST) was cloned and sequenced. Sequence analysis revealed that this zebrafish TPST is, at the amino acid sequence level, 66% and 60% identical to the human and mouse TPST-1 and TPST-2, respectively. The recombinant form of the zebrafish TPST, expressed in COS-7 cells, exhibited a pH optimum at 5.75. Manganese appeared to exert a stimulatory effect on the zebrafish TPST. The activity of the enzyme determined in the presence of 20 mM MnCl2was more than 2.5 times that determined in the absence of MnCl2. Of the other nine divalent metal cations tested at a 10 mM concentration, Co2+also showed a considerable stimulatory effect, while Ca2+, Pb2+, and Cd2+exerted some inhibitory effects. The other four divalent cations, Fe2+, Cu2+, Zn2+, and Hg2+, inhibited completely the sulfating activity of the zebrafish TPST. Using the wild-type and mutated P-selectin glycoprotein ligand-1 N-terminal peptides as substrates, the zebrafish TPST was shown to exhibit a high degree of substrate specificity for the tyrosine residue on the C-terminal side of the peptide. These results constitute a first study on the cloning, expression, and characterization of a zebrafish cytosolic TPST.Key words: zebra fish, tyrosylprotein sulfotransferase, molecular cloning.
Molecular regulation of SREBP function: the Insig-SCAP connection and isoform-specific modulation of lipid synthesis
Authors: McPherson Ruth , Gauthier Andre
Published: April 2004

Sterol regulatory element binding proteins (SREBPs) are a family of membrane-bound transcription factors that play a unique and fundamental role in both cholesterol and fatty acid metabolism, relevant to human disease. There are three SREBPs that regulate the expression of over 30 genes. SREBPs are subject to regulation at three levels: proteolytic cleavage, rapid degradation by the ubiquitin-proteasome pathway, and sumoylation. Recently, there have been exciting advances in our understanding of the molecular mechanism of SREBP trafficking and processing with new information on the role of insulin-induced genes and the differential role and regulation of SREBP-1c and -2, which may ultimately lead to novel strategies for the treatment of dyslipidemia and insulin resistance.Key words: SREBP, Insig, SCAP, cholesterol synthesis, lipid metabolism.
Cell membranes and apoptosis: role of cardiolipin, phosphatidylcholine, and anticancer lipid analogues
Authors: Wright Marcia M , Howe Alicia G , Zaremberg Vanina
Published: April 2004

The apoptotic program utilizes cellular membranes to transduce and generate operative signals. Lipids are major components of cellular membranes and have the potential to control the effectiveness of the signal by directing it to the proper location, being a source of new signals or as mediators in the response. These possible lipid functions are illustrated in the present review, focussing on the role that two different phospholipids, cardiolipin and phospha tidyl choline, play in apoptosis. Mitochondria have a central role in apoptosis, and many important aspects of the process mediated by this organelle converge through its distinctive lipid cardiolipin. Specifically, changes in cardiolipin metabolism have been detected in early steps of the death program and it is postulated (i) to mediate recruitment of pro apop totic proteins like Bid to the mitochondria surface and (ii) to actively participate in the release of proteins relevant for the execution phase of apoptosis, like cytochrome c. Unlike the organelle specific distribution of cardiolipin, phos pha tidylcholine is widely distributed among all organelles of the cell. The importance of phosphatidylcholine in apop tosis has been approached mainly through the study of the mode of action of (i) phosphatidylcholine anticancer analogues such as edelfosine and (ii) molecules that alter phosphatidylcholine metabolism, such as farnesol. The contribution of phosphatidylcholine metabolism to the apoptotic program is discussed, analyzing the experimental evidence available and pointing out some controversies in the proposed mechanisms of action.Key words: cardiolipin, phosphatidylcholine, apoptosis, edelfosine, farnesol.
Multiple variants and a differential splicing pattern of kinectin in human hepatocellular carcinoma
Authors: Wang Hong-Cheng , Su Yan-Rong , Han Ke-Jun , Pang Xue-Wen , Peng Ji-Run , Liang Bin , Wang Shan , Chen Wei-Feng
Published: April 2004

To extend the search for hepatocellular carcinoma (HCC) associated antigens with immunogenicity for clinical applications, we constructed a cDNA expression library using resected human HCC tissue sample and screened it by serological analysis of recombinant cDNA expression library (SEREX) with autologous and allogeneic sera. A total of 24 distinct antigens were isolated and kinectin was the antigen most frequently identified. We found that kinectin was alternatively spliced at four sites and obtained all eight theoretical forms of variant, six by SEREX and two by RT-PCR, from the different splicing combinations of the last three sites. In addition, the splicing patterns of four sites were analyzed. Variant containing D2 was overexpressed in cancerous tissues and this alteration may be tumor associated. The four splicing sites, the variants generated by alternative splicing, and the humoral immune response in HCC patients, may help to analyze the role of kinectin in human HCC cell biology.Key words: alternative splicing, antibody response, hepatocellular carcinoma, kinectin, serological analysis of recombinant cDNA expression library (SEREX).
Predicting total trihalomethane formation in finished water using artificial neural networks
Authors: Lewin Nicola , Zhang Qing , Chu Lingling , Shariff Riyaz
Published: April 2004

This paper reports on the application of artificial neural network (ANN) techniques for predicting the concentration of trihalomethanes (THMs) in finished water at the E.L. Smith Water Treatment Plant (WTP) in Edmonton, Alberta, Canada. The formation of THMs in finished water involves many complex chemical reactions and interactions that are difficult to model using conventional methods. The formation of THMs has been found to be correlated to raw and treated water quality characteristics such as colour, pH, and temperature and chemical addition such as chlorine, alum, and powder activated carbon (PAC). Three models were derived using raw water, post clarification water, and a combination of raw and post clarification water parameter inputs. The model that most successfully predicted the concentration of THMs in finished water is the model that uses clarifier effluent parameter inputs. This model can be used at the E.L. Smith WTP for early detection of potentially high THM concentrations in finished water and gives plant operators enough advanced warning to reduce THM precursors. With an adequate understanding of water treatment plant processes and THM formation potential it will be fairly easy for any water treatment facility, which has a few years of historical plant data, to develop its own ANN model for predicting the formation of THM in finished water. Key words: artificial neural networks, water treatment process, water treatment modeling, trihalomethane formation.
Internal workings of feed-forward neural networks
Authors: Zhang Qing J , Stanley Stephen J , Smith Daniel W
Published: April 2004

This paper describes the authors' recent research on the theories about internal workings of feed-forward artificial neural networks (ANNs). Knowledge of the inner workings of ANNs progresses with the evolution of ANN modelling techniques. In the early stages, neural networks consisted of perceptrons and were easy to interpret. Since the emergence of backpropagation learning in the 1980s, ANN models have become much more complex. Even today, many users still consider ANN models as black-box type models. In this paper, a systematic approach is demonstrated to study the behaviours of ANN models in an attempt to open up the ANN "black box". The authors emphasise that feed-forward ANN models are functions, and use a graphical interpretation technique to open the ANN models and show the detailed activities of each inner component through several case studies. These studies include how the training process changes the internal components of an ANN model, how noise impacts the training process, and how the sensitivity of ANN models is affected by the training data. Key words: artificial neural network, ANN black box, artificial neuron, connection weight, activation function, knowledge extraction.
Advanced process control techniques for water treatment using artificial neural networks
Authors: Shariff Riyaz , Cudrak Audrey , Zhang Qing , Stanley Stephen J
Published: April 2004

Virtually all water utilities are looking at improving the operation of their plants to keep control of costs and to meet stringent water quality regulations. Better process control and automation of the plants can help achieve these goals. However, traditional control techniques such as proportionalintegralderivative (PID) can be inadequate when automating certain water treatment processes such as turbidity, organics, or hardness removal in a clarification process. Advanced process control techniques are alternatives to mitigate this impediment. At the cornerstone of many advanced process control techniques is a model of the process being controlled, which can be developed using artificial neural networks (ANNs). This paper describes various advanced process control techniques, the potentially large role of ANN models in implementing these techniques, and issues and solutions when using ANN in a real-time control system. Key words: artificial neural networks, model-based control, proportional-integral-derivative control, forward and inverse models, direct and indirect control.
Biotransformation of theStreptomyces scabiesphytotoxin thaxtomin A by the fungusAspergillus niger
Authors: Lazarovits George , Hill Jackie , King Russell R , Calhoun Larry A
Published: April 2004

Of several hundred microorganisms randomly selected from the environment, only a fungal isolate identified as Aspergillus niger van Tiegham var. niger was found to transform the phytotoxin thaxtomin A to much less toxic metabolites. The rate and extent of transformation of thaxtomin A was tested under a variety of conditions, including different growth media, biomass concentrations, incubation periods, and shaker speeds. Under optimum conditions the fungus converted thaxtomin A into two major and five minor metabolites. The two major metabolites and three of the five minor metabolites were fully characterized by a combination of mass spectral and nuclear magnetic resonance techniques. When assayed on aseptically produced mini-tubers, the major metabolites proved to be much less phytotoxic than thaxtomin A.Key words: Aspergillus niger van Tiegham var. niger, biotransformation, common scab, phytotoxins, Streptomyces scabies, thaxtomin A.
Salmonella entericasubsp.entericaserovar Enteritidis harbours ColE1, ColE2, and rolling-circle-like replicating plasmids
Authors: Gregorova Daniela , Matiasovicova Jitka , Sebkova Alena , Faldynova Marcela , Rychlik Ivan
Published: April 2004

Using DNA hybridization, at least three distinct groups of low molecular mass plasmids were identified in Salmonella enterica subsp. enterica serovar Enteritidis. After sequencing representative plasmids from each group, we concluded that they belonged to ColE1, ColE2, and rolling-circle-like replicating plasmids. Plasmid pK (4245 bp) is a representative of widely distributed ColE1 plasmids. Plasmid pP (4301 bp) is homologous to ColE2 plasmids and was present predominantly in single-stranded DNA form. The smallest plasmids pJ (2096 bp) and pB (1983 bp) were classified as rolling-circle-like replicating plasmids. Both encoded only a single protein essential for their own replication, and they must have existed in an unusual molecular structure, as (i) they were capable of hybridization without denaturation, (ii) their DNA could be linearized with S1 nuclease, and (iii) even after such treatment, the ability to hybridize without denaturation did not disappear.Key words:Salmonella enterica subsp. enterica serovar Enteritidis, ColE1, ColE2, RCR, plasmid, rolling-circle replication.
A local approach to reduce industrial uranium wound contamination in rats
Authors: Houpert P , Chazel V , Paquet F
Published: April 2004

The aim of this work is to develop a new approach to partially decontaminate wounds after industrial uranium contamination, during the interval of time between contamination and transfer of the patient to the infirmary. A wound dressing and a paste mixed or not with uranium-chelating ligands, ethane-1-hydroxy-1,1-bisphosphonate (EHBP) and carballylic amido bis phosphonic acid (CAPBP), were tested in vitro on muscles and in vivo on rats after deposit of uranium oxide compounds. The dressing and the paste, composed of carboxymethylcellulose-based hydrocolloids known to be highly absorbent, were applied on simulated wounds a few minutes after the contamination. The incorporation of chelating ligands did not improve the efficacy of the dressing or paste, and the best results were obtained with the dressing. In vivo, after 1 h of contact with the wound, the dressing absorbed about 30% and 60% of a UO4 compound deposited intra- and intermuscularly, respectively. After intramuscular deposit, the efficacy of the dressing was not reduced if the contact time decreased from 1 h to 15 min. Therefore, this wound dressing could be a practical option to treat uranium-contaminated wounds, but its efficacy depends on the localization of the uranium deposit.Key words: uranium, wound, rat, treatment.
Ginsenosides 20(S)-protopanaxadiol and Rh2 reduce cell proliferation and increase sub-G1cells in two cultured intestinal cell lines, Int-407 and Caco-2
Authors: Popovich David G , Kitts David D
Published: April 2004

Ginsenosides derived from 20(S)-protopanaxatriol (PT) and 20(S)-protopanaxadiol (PD) groups had similar characteristic cytotoxic effects on the growth of two intestinal cells lines, Int-407 and Caco-2. Pure Rh2, a ginsenoside structurally related to PD, inhibited intestinal cell growth at greater than twice the concentration of PD, while Rh1, a ginsenoside structurally related to aglycone PT, had no cytotoxic effect. Concentrations causing growth inhibition of 50% of cells (LC50) for the compounds PD, PT, and Rh2 were 23, 26, and 53 µg/mL, respectively, for Int-407 cells. In comparison, the LC50for PD and PT was determined to be 24 µg/mL, and that for Rh2 was 55 µg/mL in Caco-2 cells. A standardized North American ginseng extract with a known ginsenosides composition did not induce cytotoxicity in either of the intestinal cell lines. Cell cycle analysis showed characteristically different (P = 0.05) effects of ginsen o sides PD, Rh2, and PT in both cell lines. Rh2 treatment of Int-407 caused a significantly (P = 0.05) higher production of sub-G1(apoptotic) cells (35% ± 1%) compared with untreated cells (14% ± 0.3%) after 24 h. PD and Rh2 treatments were both significantly (P < 0.05) higher in apoptotic cells than in untreated cells after 48 and 72 h. Similar results were obtained for treatment of Caco-2 cells. Lactate dehydrogenase (LDH) activity in both cell lines was similar for PD and Rh2 and higher (P = 0.05) than for PT treatment at most time periods. These results show a specific structure–function relationship for bioactive ginsenosides in two contrasting intestinal cell types.Key words: ginseng, ginsenosides, protopanaxadiol, protopanaxatriol, Rh2, apoptosis.