bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinematic Analysis of Spatial Mechanical Systems Using Exponential Rotation Matrices
Authors: Özgören M. Kemal
Published: October 2007

The mathematical properties associated with the exponential rotation matrices are reviewed. By means of two typical mechanism examples, it is demonstrated that these properties constitute a versatile analytical tool, which can be used effectively in kinematic studies on spatial mechanical systems involving position, velocity, acceleration, and singularity analyses.
A Unified Approach to Solving Driving Forces in Spatial Parallel Manipulators With Less Than Six DOFs
Authors: Lu Yi , Hu Bo
Published: October 2007

A unified approach to solving driving forces in spatial parallel manipulators with less than six DOFs is proposed. First, the geometric constrained equations of the parallel manipulators are derived, and some independent pose parameters and a common transformation matrix with three translations and three Euler rotations are determined. Second, the common formulas for solving inverse kinematics, the Jacobian matrix, and velocity are derived. Third, a common virtual serial mechanism with three virtual prismatic joints and three virtual revolute joints corresponding to three Euler rotations is constructed. Fourth, a common analytic formula for solving driving forces in spatial parallel manipulators with less than six DOFs is derived by using the principle of virtual work and the virtual serial mechanism. Finally, a 3-SPR parallel manipulator with three DOFs and a 4SPS+SPR parallel manipulator with five DOFs are presented to illustrate the use of the unified approach to solve their inverse kinematics and the driving forces. The solving results are verified by the simulation mechanisms.
Contribution of Conserved ATP-Dependent Proteases ofCampylobacter jejunito Stress Tolerance and Virulence
Authors: Cohn Marianne Thorup , Ingmer Hanne , Mulholland Francis , Jørgensen Kirsten , Wells Jerry M. , Brøndsted Lone
Published: October 2007

In prokaryotic cells the ATP-dependent proteases Lon and ClpP (Clp proteolytic subunit) are involved in the turnover of misfolded proteins and the degradation of regulatory proteins, and depending on the organism, these proteases contribute variably to stress tolerance. We constructed mutants in thelonandclpPgenes of the food-borne human pathogenCampylobacter jejuniand found that the growth of both mutants was impaired at high temperature, a condition known to increase the level of misfolded protein. Moreover, the amounts of misfolded protein aggregates were increased when both proteases were absent, and we propose that both ClpP and Lon are involved in eliminating misfolded proteins inC. jejuni. In order to bind misfolded protein, ClpP has to associate with one of several Clp ATPases. Following inactivation of the ATPase genesclpAandclpX, only theclpXmutant displayed the same heat sensitivity as theclpPmutant, indicating that the ClpXP proteolytic complex is responsible for the degradation of heat-damaged proteins inC. jejuni. Notably, ClpP and ClpX are required for growth at 42°C, which is the temperature of the intestinal tract of poultry, one of the primary carriers ofC. jejuni. Thus, ClpP and ClpX may be suitable targets of new intervention strategies aimed at reducingC. jejuniin poultry production. Further characterization of theclpPandlonmutants revealed other altered phenotypes, such as reduced motility, less autoagglutination, and lower levels of invasion of INT407 epithelial cells, suggesting that the proteases may contribute to the virulence ofC. jejuni.
Actinobacterial Community Structure in Soils Receiving Long-Term Organic and Inorganic Amendments
Authors: Piao Zhe , Yang Linzhang , Zhao Liping , Yin Shixue
Published: October 2007

The impact of long-term organic and inorganic amendments on the actinobacterial community in soils was studied. Denaturing gradient gel electrophoresis patterns based on the V3 region of 16S rRNA suggested that there was no significant difference between the communities occurring in the different amendments. However, analysis of the clone libraries of the actinobacterial communities by the use of multiple statistical approaches showed that these communities were significantly different from each other. Results showed that long-term organic and inorganic soil amendments did not significantly alter the overall phylogenetic diversity of the actinobacterial communities but did significantly change the community structure.
CelAB, a Multifunctional Cellulase Encoded by
Teredinibacter turnerae
T7902
T
, a Culturable Symbiont Isolated from the Wood-Boring Marine Bivalve
Lyrodus pedicellatus
Authors: Ekborg Nathan A. , Morrill Wendy , Burgoyne Adam M. , Li Li , Distel Daniel L.
Published: October 2007

We characterized a multifunctional cellulase (CelAB) encoded by the endosymbiont
Teredinibacter turnerae
T7902
T
. CelAB contains two catalytic and two carbohydrate-binding domains, each separated by polyserine linker regions. CelAB binds cellulose and chitin, degrades multiple complex polysaccharides, and displays two catalytic activities, cellobiohydrolase (EC 3.2.1.91) and β-1,4(3) endoglucanase (EC 3.2.1.4).
A Metalloprotease Secreted by the Insect Pathogen
Photorhabdus luminescens
Induces Melanization
Authors: Held Kiara G. , LaRock Christopher N. , D'Argenio David A. , Berg Celeste A. , Collins Carleen M.
Published: October 2007

Photorhabdus luminescens
is a gram-negative insect pathogen that enters the hemocoel of infected hosts and produces a number of secreted proteins that promote colonization and subsequent death of the insect. In initial studies to determine the exact role of individual secreted proteins in insect pathogenesis, concentrated culture supernatants from various
P. luminescens
strains were injected into the tobacco hornworm
Manduca sexta
. Culture supernatants from
P. luminescens
TT01, the genome-sequenced strain, stimulated a rapid melanization reaction in
M. sexta
. Comparison of the profiles of secreted proteins from the various
Photorhabdus
strains revealed a single protein of approximately 37 kDa that was significantly overrepresented in the TT01 culture supernatant. This protein was purified by DEAE ion-exchange and Superdex 75 gel filtration chromatography and identified by matrix-assisted laser desorption ionization-time of flight analysis as the product of the TT01 gene plu1382 (NCBI accession number NC_005126); we refer to it here as PrtS. PrtS is a member of the M4 metalloprotease family. Injection of PrtS into larvae of
M. sexta
and
Galleria mellonella
and into adult
Drosophila melanogaster
and
D. melanogaster
melanization mutants (
Bc
) confirmed that the purified protein induced the melanization reaction. The
prtS
gene was transcribed by
P. luminescens
injected into
M. sexta
before death of the insect, suggesting that the protein was produced during infection. The exact function of this protease during infection is not clear. The bacteria might survive inside the insect despite the melanization process, or it might be that the bacterium is specifically activating melanization in an attempt to circumvent this innate immune response.
Identification of the Propionicin F Bacteriocin Immunity Gene (
pcfI
) and Development of a Food-Grade Cloning System for
Propionibacterium freudenreichii
Authors: Brede Dag Anders , Lothe Sheba , Salehian Zhian , Faye Therese , Nes Ingolf F.
Published: October 2007

This report describes the first functional analysis of a bacteriocin immunity gene from
Propionibacterium freudenreichii
and its use as a selection marker for food-grade cloning. Cloning of the
pcfI
gene (previously
orf5
[located as part of the
pcfABC
propionicin F operon]) rendered the sensitive host 1,000-fold more tolerant to the propionicin F bacteriocin. The physiochemical properties of the 127-residue large PcfI protein resemble those of membrane-bound immunity proteins from bacteriocin systems found in lactic acid bacteria. The high level of immunity conferred by
pcfI
allowed its use as a selection marker for plasmid transformation in
P. freudenreichii
. Electroporation of
P. freudenreichii
IFO12426 by use of the
pcfI
expression plasmid pSL102 and propionicin F selection (200 bacteriocin units/ml) yielded 10
7
transformants/μg DNA. The 2.7-kb
P. freudenreichii
food-grade cloning vector pSL104 consists of the pLME108 replicon, a multiple cloning site, and
pcfI
expressed from the constitutive P
pampS
promoter for selection. The pSL104 vector efficiently facilitated cloning of the propionicin T1 bacteriocin in
P. freudenreichii
. High-level propionicin T1 production (640 BU/ml) was obtained with the IFO12426 strain, and the food-grade propionicin T1 expression plasmid pSL106 was maintained by ∼91% of the cells over 25 generations in the absence of selection. To the best of our knowledge this is the first report of an efficient cloning system that facilitates the generation of food-grade recombinant
P. freudenreichii
strains.
Spread of Infectious Chronic Bee Paralysis Virus by Honeybee (
Apis mellifera
L.) Feces
Authors: Ribière M. , Lallemand P. , Iscache A.-L. , Schurr F. , Celle O. , Blanchard P. , Olivier V. , Faucon J.-P.
Published: October 2007

Knowledge of the spreading mechanism of honeybee pathogens within the hive is crucial to our understanding of bee disease dynamics. The aim of this study was to assess the presence of infectious chronic bee paralysis virus (CBPV) in bee excreta and evaluate its possible role as an indirect route of infection. Samples of paralyzed bees were (i) produced by experimental inoculation with purified virus and (ii) collected from hives exhibiting chronic paralysis. CBPV in bee heads or feces (crude or absorbed onto paper) was detected by reverse transcription-PCR. CBPV infectivity was assessed by intrathoracic inoculation of bees with virus extracted from feces and by placement of naive bees in cages previously occupied by contaminated individuals. CBPV RNA was systematically detected in the feces of naturally and experimentally infected bees and on the paper sheets that had been used to cover the floors of units containing bees artificially infected with CBPV or the floor of one naturally infected colony. Both intrathoracic inoculation of bees with virus extracted from feces and placement of bees in contaminated cages provoked overt disease in naive bees, thereby proving that the excreted virus was infectious and that this indirect route of infection could lead to overt chronic paralysis. This is the first experimental confirmation that infectious CBPV particles excreted in the feces of infected bees can infect naive bees and provoke overt disease by mere confinement of naive bees in a soiled environment.
Effect of Feeding Cows Genetically Modified Maize on the Bacterial Community in the Bovine Rumen
Authors: Wiedemann S. , Gürtler P. , Albrecht C.
Published: October 2007

Rumen-cannulated cows (
n
= 4) were fed successively silage made from either conventional or genetically modified (GM) maize. Results revealed no effects of GM maize on the dynamics of six ruminal bacterial strains (investigated by real-time PCR) compared to the conventional maize silage.
TiO
2
Photocatalysis Causes DNA Damage via Fenton Reaction-Generated Hydroxyl Radicals during the Recovery Period
Authors: Gogniat Gaëtan , Dukan Sam
Published: October 2007

Here, we show that resistance of
Escherichia coli
to TiO
2
photocatalysis involves defenses against reactive oxygen species. Results support the idea that TiO
2
photocatalysis generates damage which later becomes deleterious during recovery. We found this to be partly due to DNA attack via hydroxyl radicals generated by the Fenton reaction during recovery.
Phenotypic and Transcriptomic Analyses Demonstrate Interactions between the Transcriptional Regulators CtsR and Sigma B inListeria monocytogenes
Authors: Hu Yuewei , Raengpradub Sarita , Schwab Ute , Loss Chris , Orsi Renato H. , Wiedmann Martin , Boor Kathryn J.
Published: October 2007

Listeria monocytogenesσBpositively regulates the transcription of class II stress response genes; CtsR negatively regulates class III stress response genes. To identify interactions between these two stress response systems, we constructedL. monocytogenesΔctsRand ΔctsRΔsigBstrains, as well as a ΔctsRstrain expressingctsRintransunder the control of an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible promoter. These strains, along with a parent and a ΔsigBstrain, were assayed for motility, heat resistance, and invasion of human intestinal epithelial cells, as well as by whole-genome transcriptomic and quantitative real-time PCR analyses. Both ΔctsRand ΔctsRΔsigBstrains had significantly higher thermotolerances than the parent strain; however, full heat sensitivity was restored to the ΔctsRstrain whenctsRwas expressed intrans. Although log-phase ΔctsRwas not reduced in its ability to infect human intestinal cells, the ΔctsRΔsigBstrain showed significantly lower invasion efficiency than either the parent strain or the ΔsigBstrain, indicating that interactions between CtsR and σBcontribute to invasiveness. Statistical analyses also confirmed interactions between thectsRand thesigBnull mutations in both heat resistance and invasion phenotypes. Microarray transcriptomic analyses and promoter searches identified (i) 42 CtsR-repressed genes, (ii) 22 genes with lower transcript levels in the ΔctsRstrain, and (iii) at least 40 genes coregulated by both CtsR and σB, including genes encoding proteins with confirmed or plausible roles in virulence and stress response. Our data demonstrate that interactions between CtsR and σBplay an important role inL. monocytogenesstress resistance and virulence.
Identification of the Most Abundant
Lactobacillus
Species in the Crop of 1- and 5-Week-Old Broiler Chickens
Authors: Abbas Hilmi Hanan T. , Surakka Anu , Apajalahti Juha , Saris Per E. J.
Published: October 2007

Bacteria from crops of 1- and 5-week-old broiler chickens fed with two brands (diets A and B) of wheat-based diets were isolated on
Lactobacillus
-selective medium and identified (
n
= 300) based on partial 16S rRNA gene sequence. The most abundant
Lactobacillus
species were
L. reuteri
(33%),
L. crispatus
(18.7%), and
L. salivarius
(13.3%). Regardless of farm and feed,
L. reuteri
was the most abundant species (
P
< 0.005) in the crops of the younger chickens. However, the amount of
L. reuteri
was significantly reduced in the crops of the 5-week-old chickens regardless of the feed (
P
= 0.016). The diversity of
L. reuteri
isolates was studied by fatty acid analysis, and the 94
L. reuteri
isolates could be arranged into several clusters. The nisin sensitivities of the
L. reuteri
isolates were determined because nisin is a candidate coccidiostat. Sensitive isolates were found more frequently in younger chickens (77%) than in 5-week-old chickens (23%), whereas chickens fed with commercial feed B had a higher proportion of nisin-resistant isolates (73%) than did chickens fed with feed A (45%). Nisin-resistant strains are potential candidates for adjunct cultures for maintaining
L. reuteri
in its natural niche in the crop and are potential targets for genetic engineering with nisin-selectable food-grade vectors. The diversity of the
L. reuteri
population suggested that one should consider including several strains representing different clusters and nisin resistance phenotypes in candidate probiotic feed supplements for chickens.
Engineered Synthetic Pathway for Isopropanol Production in
Escherichia coli
Authors: Hanai T. , Atsumi S. , Liao J. C.
Published: October 2007

A synthetic pathway was engineered in
Escherichia coli
to produce isopropanol by expressing various combinations of genes from
Clostridium acetobutylicum
ATCC 824,
E. coli
K-12 MG1655,
Clostridium beijerinckii
NRRL B593, and
Thermoanaerobacter brockii
HTD4. The strain with the combination of
C. acetobutylicum thl
(acetyl-coenzyme A [CoA] acetyltransferase),
E. coli atoAD
(acetoacetyl-CoA transferase),
C. acetobutylicum adc
(acetoacetate decarboxylase), and
C. beijerinckii adh
(secondary alcohol dehydrogenase) achieved the highest titer. This strain produced 81.6 mM isopropanol in shake flasks with a yield of 43.5% (mol/mol) in the production phase. To our knowledge, this work is the first to produce isopropanol in
E. coli
, and the titer exceeded that from the native producers.
Effects of Disruption of Homocitrate Synthase Genes on
Nostoc
sp. Strain PCC 7120 Photobiological Hydrogen Production and Nitrogenase
Authors: Masukawa Hajime , Inoue Kazuhito , Sakurai Hidehiro
Published: October 2007

In the case of nitrogenase-based photobiological hydrogen production systems of cyanobacteria, the inactivation of uptake hydrogenase (Hup) leads to significant increases in hydrogen production activity. However, the high-level-activity stage of the Hup mutants lasts only a few tens of hours under air, a circumstance which seems to be caused by sufficient amounts of combined nitrogen supplied by active nitrogenase. The catalytic FeMo cofactor of nitrogenase binds homocitrate, which is required for efficient nitrogen fixation. It was reported previously that the nitrogenase from the homocitrate synthase gene (
nifV
) disruption mutant of
Klebsiella pneumoniae
shows decreased nitrogen fixation activity and increased hydrogen production activity under N
2
. The cyanobacterium
Nostoc
sp. strain PCC 7120 has two homocitrate synthase genes,
nifV1
and
nifV2
, and with the Δ
hupL
variant of
Nostoc
sp. strain PCC 7120 as the parental strain, we have constructed two single mutants, the Δ
hupL
Δ
nifV1
strain (with the
hupL
and
nifV1
genes disrupted) and the Δ
hupL
Δ
nifV2
strain, and a double mutant, the Δ
hupL
Δ
nifV1
Δ
nifV2
strain. Diazotrophic growth rates of the two
nifV
single mutants and the double mutant were decreased moderately and severely, respectively, compared with the rates of the parent Δ
hupL
strain. The hydrogen production activity of the Δ
hupL
Δ
nifV1
mutant was sustained at higher levels than the activity of the parent Δ
hupL
strain after about 2 days of combined-nitrogen step down, and the activity in the culture of the former became higher than that in the culture of the latter. The presence of N
2
gas inhibited hydrogen production in the Δ
hupL
Δ
nifV1
Δ
nifV2
mutant less strongly than in the parent Δ
hupL
strain and the Δ
hupL
Δ
nifV1
and Δ
hupL
Δ
nifV2
mutants. The alteration of homocitrate synthase activity can be a useful strategy for improving sustained photobiological hydrogen production in cyanobacteria.
Enumeration of Viable
Listeria monocytogenes
Cells by Real-Time PCR with Propidium Monoazide and Ethidium Monoazide in the Presence of Dead Cells
Authors: Pan Y. , Breidt F.
Published: October 2007

Propidium monoazide (PMA) and ethidium monoazide were used for enumeration of viable
Listeria monocytogenes
cells in the presence of dead cells. PMA had no antimicrobial effect on
L. monocytogenes
. Viable cell counts were linearly related to real-time PCR threshold cycle values for PMA-treated cells from planktonic and biofilm sources over a 4-log range.
Different Genotypes of Anatoxin-Producing Cyanobacteria Coexist in the Tarn River, France
Authors: Cadel-Six Sabrina , Peyraud-Thomas Caroline , Brient Luc , de Marsac Nicole Tandeau , Rippka Rosmarie , Méjean Annick
Published: October 2007

Repeated dog deaths occurred in 2002, 2003, and 2005 after the animals drank water from the shoreline of the Tarn River in southern France. Signs of intoxication indicated acute poisoning due to a neurotoxin. Floating scum and biofilms covering pebbles were collected in the summers of 2005 and 2006 from six different sites along 30 km from the border of this river. The cyanobacterial neurotoxic alkaloid anatoxin-a and/or its methyl homolog, homoanatoxin-a, was detected in the extracts of most samples examined by gas chromatography-mass spectrometry. Fifteen filamentous cyanobacteria of the order
Oscillatoriales
were isolated and displayed four distinct phenotypes based on morphological characteristics and pigmentation. Three of the phenotypes can be assigned to the genus
Oscillatoria
or
Phormidium
, depending on the taxonomic treatises (bacteriological/botanical) employed for identification. The fourth phenotype is typical of the genus
Geitlerinema
Anagnostidis 1989. Eight strains rendered axenic were analyzed for production of anatoxin-a and homoanatoxin-a, and all strains of
Oscillatoria
/
Phormidium
proved to be neurotoxic. The genetic relatedness of the new isolates was evaluated by comparison of the intergenic transcribed spacer sequences with those of six oscillatorian strains from the Pasteur Culture Collection of Cyanobacteria. These analyses showed that the neurotoxic representatives are composed of five different genotypes, three of which correspond to phenotypes isolated in this study. Our findings prove that neurotoxic oscillatorian cyanobacteria exist in the Tarn River and thus were most likely implicated in the reported dog poisonings. Furthermore, they reemphasize the importance of monitoring benthic cyanobacteria in aquatic environments to fully assess the health risks associated with these organisms.
Occurrence of Human Adenoviruses at Two Recreational Beaches of the Great Lakes
Authors: Xagoraraki Irene , Kuo David H.-W. , Wong Kelvin , Wong Mark , Rose Joan B.
Published: October 2007

Human adenoviruses (HAdVs) have been related to several waterborne diseases such as acute gastroenteritis, conjunctivitis, and respiratory illness, and it has been shown that an important human exposure pathway is through recreational waters. However, HAdV occurrence at recreational freshwater beaches has not been previously investigated. In this study, a total of 58 water samples were collected from two recreational beaches on Lake Michigan (i.e., Silver Beach and Washington Park Beach) during the summer of 2004. Occurrences of HAdVs in these lake samples were determined using two hexon-based real-time PCR assays (one for monitoring all 51 serotypes of HAdVs and another for specifically detecting F species HAdVs, i.e., serotypes 40 and 41) and compared to an integrated cell culture (ICC) PCR method. The real-time PCR results showed that 8 of 30 Silver Beach samples and 6 of 28 Washington Park Beach samples contained HAdVs, and F species HAdVs were detected in three of these positive samples. The concentrations of HAdVs ranged from (1.7 ± 0.7) × 10
1
to (3.4 ± 0.8) × 10
2
and from (7 ± 2) × 10
0
to (3.8 ± 0.3) × 10
3
virus particles/liter for Silver Beach and Washington Park Beach, respectively. F species HAdVs were detected at levels ranging from (4.8 ± 0.8) × 10
1
to (4.6 ± 1.5) × 10
2
virus particles/liter. Approximately 60% of the ICC-PCR analyses agreed with the real-time PCR results. This study revealed the occurrence of HAdVs at Lake Michigan recreational beaches. Given the potential health risks, further assessment regarding sources, virus transport, and survival is needed to improve the safety of the region.
Comparative Analyses of Prophage-Like Elements Present in Two
Lactococcus lactis
Strains
Authors: Ventura Marco , Zomer Aldert , Canchaya Carlos , O'Connell-Motherway Mary , Kuipers Oscar , Turroni Francesca , Ribbera Angela , Foroni Elena , Buist Girbe , Wegmann Udo , Shearman Claire , Gasson Michael J. , Fitzgerald Gerald F. , Kok Jan , van Sinderen Douwe
Published: October 2007

In this study, we describe the genetic organizations of six and five apparent prophage-like elements present in the genomes of the
Lactococcus lactis
subsp.
cremoris
strains MG1363 and SK11, respectively. Phylogenetic investigation as well bioinformatic analyses indicates that all 11 prophages belong to subdivisions of the lactococcal P335 group of temperate bacteriophages.
Production of Eight Different Hydride Complexes and Nitrite Release from 2,4,6-Trinitrotoluene by
Yarrowia lipolytica
Authors: Ziganshin Ayrat M. , Gerlach Robin , Borch Thomas , Naumov Anatoly V. , Naumova Rimma P.
Published: October 2007

2,4,6-Trinitrotoluene (TNT) transformation by the yeast strain
Yarrowia lipolytica
AN-L15 was shown to occur via two different pathways. Direct aromatic ring reduction was the predominant mechanism of TNT transformation, while nitro group reduction was observed to be a minor pathway. Although growth of
Y. lipolytica
AN-L15 was inhibited initially in the presence of TNT, TNT transformation was observed, indicating that the enzymes necessary for TNT reduction were present initially. Aromatic ring reduction resulted in the transient accumulation of eight different TNT-hydride complexes, which were characterized using high-performance liquid chromatography, UV-visible diode array detection, and negative-mode atmospheric pressure chemical ionization mass spectrometry (APCI-MS). APCI-MS analysis revealed three different groups of TNT-hydride complexes with molecular ions at
m/z
227, 228, and 230, which correspond to TNT-mono- and dihydride complexes and protonated dihydride isomers, respectively. One of the three protonated dihydride complex isomers detected appears to release nitrite in the presence of strain AN-L15. This release of nitrite is of particular interest since it can provide a pathway towards complete degradation and detoxification of TNT.
Molecular Epidemiology of
bla
CMY-2
Plasmids Carried by
Salmonella enterica
and
Escherichia coli
Isolates from Cattle in the Pacific Northwest
Authors: Daniels Joshua B. , Call Douglas R. , Besser Thomas E.
Published: October 2007

Restriction analyses of
bla
CMY-2
-bearing plasmids and
Salmonella
and
Escherichia coli
hosts identified (i) shared highly similar plasmids in these species in rare cases, (ii) a clonal host-plasmid relationship in
Salmonella enterica
serotype Newport, and (iii) a very high diversity of strain types and plasmids among commensal
E. coli
isolates.
Enhancement of Shiga Toxin Production in Enterohemorrhagic
Escherichia coli
Serotype O157:H7 by DNase Colicins
Authors: Toshima Hirono , Yoshimura Ayana , Arikawa Kentaro , Hidaka Ayumi , Ogasawara Jun , Hase Atsushi , Masaki Haruhiko , Nishikawa Yoshikazu
Published: October 2007

Colicins are proteins produced by and active against several strains of
Escherichia coli
. Previously we reported that colicinogenic bacteria seemed beneficial in preventing the clinical manifestations of infectious disease caused by enterohemorrhagic
E. coli
O157 in humans. The inhibitory effects could be due to a decrease in O157 levels and/or pathogenicity. This study investigated the effects of colicinogenic
E. coli
on the production of Shiga toxin (Stx) by O157. Standard strains of colicinogenic bacteria carrying plasmids for each type of colicin (E3/5/8/9) were used for the study. The O157 strains were cultured in the presence of colicinogenic bacteria or extracted colicins. Compared with results for controls, DNase colicins (E8/9) facilitated an 8- to 64-fold increase in production of Stx2, while RNase colicins (E3/5) suppressed Stx production in only two strains. Stx prophages were induced in synchrony with Stx production. Semiquantitative real-time reverse transcription-PCR (RT-PCR) was then performed to examine SOS gene expression. The RT-PCR results clearly indicated a marked increase in mRNA levels of SOS reaction-associated genes after the addition of DNase colicins. We believe that Stx prophages are induced by the SOS response to DNA damage caused by DNase colicins, thus leading to higher Stx production. These findings suggest that while colicinogenic bacteria can be antagonistic to O157 infection, DNase colicins may enhance Stx production. Thus, colicinogenic flora is likely to be involved in the complex pathogenic pathways of O157 infection, and further investigation should be performed before the use of colicinogenic bacteria as an intervention method.
Anaerobic Metabolism of 1-Amino-2-Naphthol-Based Azo Dyes (Sudan Dyes) by Human Intestinal Microflora
Authors: Xu Haiyan , Heinze Thomas M. , Chen Siwei , Cerniglia Carl E. , Chen Huizhong
Published: October 2007

The rates of metabolism of Sudan I and II and Para Red by human intestinal microflora were high compared to those of Sudan III and IV under anaerobic conditions. Metabolites of the dyes were identified as aniline, 2,4-dimethylaniline,
o
-toluidine, and 4-nitroaniline through high-performance liquid chromatography and liquid chromatography electrospray ionization tandem mass spectrometry analyses. These data indicate that human intestinal bacteria are able to reduce Sudan dyes to form potentially carcinogenic aromatic amines.
Conservation of the Chitin Utilization Pathway in the
Vibrionaceae
Authors: Hunt Dana E. , Gevers Dirk , Vahora Nisha M. , Polz Martin F.
Published: October 2007

Vibrionaceae
are regarded as important marine chitin degraders, and attachment to chitin regulates important biological functions; yet, the degree of chitin pathway conservation in
Vibrionaceae
is unknown. Here, a core chitin degradation pathway is proposed based on comparison of 19
Vibrio
and
Photobacterium
genomes with a detailed metabolic map assembled for
V. cholerae
from published biochemical, genomic, and transcriptomic results. Further, to assess whether chitin degradation is a conserved property of
Vibrionaceae
, a set of 54 strains from 32 taxa were tested for the ability to grow on various forms of chitin. All strains grew on
N
-acetylglucosamine (GlcNAc), the monomer of chitin. The majority of isolates grew on α (crab shell) and β (squid pen) chitin and contained chitinase A (
chiA
) genes.
chiA
sequencing and phylogenetic analysis suggest that this gene is a good indicator of chitin metabolism but appears subject to horizontal gene transfer and duplication. Overall, chitin metabolism appears to be a core function of
Vibrionaceae
, but individual pathway components exhibit dynamic evolutionary histories.
Evaluation of Removal of Noroviruses during Wastewater Treatment, Using Real-Time Reverse Transcription-PCR: Different Behaviors of Genogroups I and II
Authors: da Silva Allegra Kyria , Le Saux Jean-Claude , Parnaudeau Sylvain , Pommepuy Monique , Elimelech Menachem , Le Guyader Françoise S.
Published: October 2007

Noroviruses, an important cause of gastroenteritis, are excreted by infected individuals and are therefore present in wastewater. We quantified norovirus genogroup I (GI) and GII in wastewater at different locations in France and evaluated removal by a range of treatment types, including basic (waste stabilization pond), current industry standard (activated sludge), and state-of-the-art (submerged membrane bioreactor) treatments. Noroviruses were quantified using real-time reverse transcription-PCR (rRT-PCR). Mengovirus was used as a virus extraction control, and internal controls were used to verify the level of GI and GII rRT-PCR inhibition. A total of 161 (81 influent and 79 effluent) samples were examined; GI and GII were detected in 43 and 88% of the influent samples, respectively, and in 24 and 14% of the effluent samples, respectively. Physicians in France report far more cases of GII than GI during outbreaks; thus, the frequent presence of GI was unexpected. The GI influent concentrations were more variable, the peak GI influent concentrations were higher than the peak GII influent concentrations at all four sites (up to 1 × 10
9
and 6 × 10
7
genome copies/liter, respectively), and the average positive influent concentrations of GI were higher than the average positive influent concentrations of GII. The maximum effluent breakthrough concentrations were 6 × 10
6
and 3 × 10
6
genome copies/liter for GI and GII, respectively, indicating that the four treatment systems studied decreased the norovirus contamination load in receiving waters.
Physiological and Transcriptional Responses of
Saccharomyces cerevisiae
to Zinc Limitation in Chemostat Cultures
Authors: De Nicola Raffaele , Hazelwood Lucie A. , De Hulster Erik A. F. , Walsh Michael C. , Knijnenburg Theo A. , Reinders Marcel J. T. , Walker Graeme M. , Pronk Jack T. , Daran Jean-Marc , Daran-Lapujade Pascale
Published: October 2007

Transcriptional responses of the yeast
Saccharomyces cerevisiae
to Zn availability were investigated at a fixed specific growth rate under limiting and abundant Zn concentrations in chemostat culture. To investigate the context dependency of this transcriptional response and eliminate growth rate-dependent variations in transcription, yeast was grown under several chemostat regimens, resulting in various carbon (glucose), nitrogen (ammonium), zinc, and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified, and the set enabled the definition of the Zn-specific Zap1p regulon, comprised of 26 genes and characterized by a broader zinc-responsive element consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large number of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified.
Intestinal Integrity and
Akkermansia muciniphila
, a Mucin-Degrading Member of the Intestinal Microbiota Present in Infants, Adults, and the Elderly
Authors: Collado M. Carmen , Derrien Muriel , Isolauri Erika , de Vos Willem M. , Salminen Seppo
Published: October 2007

Fluorescence in situ hybridization and real-time PCR analysis targeting the 16S rRNA gene of
Akkermansia muciniphila
were performed to determine its presence in the human intestinal tract. These techniques revealed that an
A. muciniphila
-like bacterium is a common member of the human intestinal tract and that its colonization starts in early life and develops within a year to a level close to that observed in adults (10
8
cells/g) but decreases (
P
< 0.05) in the elderly.
Purification and Characterization of Two Highly Thermophilic Alkaline Lipases fromThermosyntropha lipolytica
Authors: Salameh Moh'd A. , Wiegel Juergen
Published: October 2007

Two thermostable lipases were isolated and characterized fromThermosyntropha lipolyticaDSM 11003, an anaerobic, thermophilic, alkali-tolerant bacterium which grows syntrophically with methanogens on lipids such as olive oil, utilizing only the liberated fatty acid moieties but not the glycerol. Lipases LipA and LipB were purified from culture supernatants to gel electrophoretic homogeneity by ammonium sulfate precipitation and hydrophobic interaction column chromatography. The apparent molecular masses of LipA and LipB determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis were 50 and 57 kDa, respectively. The temperature for maximal activity of LipA and LipB was around 96°C, which is, so far as is known, the highest temperature for maximal activity among lipases, and the pH optima for growth determined at 25°C (pH25°Coptima) were 9.4 and 9.6, respectively. LipA and LipB at 100°C and pH25°C8.0 retained 50% activity after 6 and 2 h of incubation, respectively. Both enzymes exhibited high activity with long-chain fatty acid glycerides, yielding maximum activity with trioleate (C18:1) and, among thep-nitrophenyl esters, withp-nitrophenyl laurate. Hydrolysis of glycerol ester bonds occurred at positions 1 and 3. The activities of both lipases were totally inhibited by 10 mM phenylmethylsulfonyl fluoride and 10 mM EDTA. Metal analysis indicated that both LipA and LipB contain 1 Ca2+and one Mn2+ion per monomeric enzyme unit. The addition of 1 mM MnCl2to dialyzed enzyme preparations enhanced the activities at 96°C of both LipA and LipB by threefold and increased the durations of their thermal stability at 60°C and 75°C, respectively, by 4 h.
Improving the Insecticidal Activity against Resistant
Culex quinquefasciatus
Mosquitoes by Expression of Chitinase Gene
chiAC
in
Bacillus sphaericus
Authors: Cai Yajun , Yan Jianpin , Hu Xiaomin , Han Bei , Yuan Zhiming
Published: October 2007

Expression of a chitinase gene,
chiAC
, from
Bacillus thuringiensis
in
B. sphaericus
2297 using the binary toxin promoter yielded a recombinant strain that was 4,297-fold more toxic than strain 2297 against resistant
Culex quinquefasciatus
. These results show that this chitinase can synergize the toxicity of the binary toxin against mosquitoes and thus may be useful in managing mosquito resistance to
B. sphaericus
.
Role of Iron in Human Serum Resistance of the Clinical and Environmental
Vibrio vulnificus
Genotypes
Authors: Bogard Ryan W. , Oliver James D.
Published: October 2007

We recently reported a simple PCR procedure that targets a sequence variation of the virulence-correlated gene locus
vcg
. It was found that 90% of all clinical isolates possessed the
vcgC
sequence variant, while 93% of all environmental isolates possessed the
vcgE
sequence variant. Here we report that the clinical genotype of
Vibrio vulnificus
is significantly better able to survive in human serum than is the environmental genotype. The presence of a siderophore-encoding gene,
viuB
, influenced serum survivability among all isolates of
V. vulnificus
tested. Those strains positive for
viuB
(all C-type strains but very few E-type strains) showed greater serum survivability than those lacking
viuB
(most E-type strains). The addition of iron (in the form of ferric ammonium citrate) to human serum restored the survival of E-type strains lacking
viuB
to levels not significantly different from those of C-type and E-type strains that possess
viuB
. These findings suggest that
viuB
may dictate serum survival in both C- and E-type strains of
V. vulnificus
and may explain why some strains (C- and E-type strains) are pathogenic and others (predominately E-type strains) are not. Additionally, C-type strains exhibited a cross-protective response against human serum, not exhibited by E-type strains, after incubation under nutrient and osmotic downshift conditions that mimicked estuarine waters. This suggests that the nutrient/osmotic environment may influence the survival of
V. vulnificus
following entry into the human body, leading to selection of the C genotype over the E genotype.
Aged HCT-8 Cell Monolayers Support
Cryptosporidium parvum
Infection
Authors: Sifuentes Laura Y. , Di Giovanni George D.
Published: October 2007

Cell culture assays in various formats have been used to study the infectivity of
Cryptosporidium
spp. as well as to determine the infectivity of naturally occurring oocysts in water. Currently, cell culture assays for infectious
Cryptosporidium
spp. in water have largely been limited to practice in research laboratories. One obstacle to the routine use of
Cryptosporidium
cell culture assays for the analysis of water samples is the coordination of water sample collection and processing with readiness of cell culture monolayers. For most
Cryptosporidium
cell culture assays, monolayers are allowed to develop for 24 to 48 h to reach 80 to 100% confluence prior to inoculation. In this study, we used immunofluorescent assay microscopy to evaluate freshly confluent (2-day-old) and aged (8- to 67-day-old) HCT-8 cell monolayers for their ability to support
Cryptosporidium parvum
infection. HCT-8 monolayers as old as 67 days were clearly shown to support infection. In two of three experiments, aged monolayers (8- to 11-day-old and 11- to 22-day-old, respectively) developed the same number of
C. parvum
clusters of infection as freshly confluent monolayers. Results suggest that it may be possible to use cell monolayers from freshly confluent to 3 weeks old on hand for infectivity assays without having to schedule sample processing to coincide with development of freshly confluent monolayers. This would make
Cryptosporidium
cell culture assays much more feasible for water quality and utility laboratories.
Enhanced UV Inactivation of Adenoviruses under Polychromatic UV Lamps
Authors: Linden Karl G. , Thurston Jeanette , Schaefer Raymond , Malley James P.
Published: October 2007

Adenovirus is recognized as the most UV-resistant waterborne pathogen of concern to public health microbiologists. The U.S. EPA has stipulated that a UV fluence (dose) of 186 mJ cm
−2
is required for 4-log inactivation credit in water treatment. However, all adenovirus inactivation data to date published in the peer-reviewed literature have been based on UV disinfection experiments using UV irradiation at 253.7 nm produced from a conventional low-pressure UV source. The work reported here presents inactivation data for adenovirus based on polychromatic UV sources and details the significant enhancement in inactivation achieved using these polychromatic sources. When full-spectrum, medium-pressure UV lamps were used, 4-log inactivation of adenovirus type 40 is achieved at a UV fluence of less than 60 mJ cm
−2
and a surface discharge pulsed UV source required a UV fluence of less than 40 mJ cm
−2
. The action spectrum for adenovirus type 2 was also developed and partially explains the improved inactivation based on enhancements at wavelengths below 230 nm. Implications for water treatment, public health, and the future of UV regulations for virus disinfection are discussed.
Hydrogen Peroxide-Dependent Uptake of Iodine by Marine
Flavobacteriaceae
Bacterium Strain C-21
Authors: Amachi Seigo , Kimura Koh , Muramatsu Yasuyuki , Shinoyama Hirofumi , Fujii Takaaki
Published: October 2007

The cells of the marine bacterium strain C-21, which is phylogenetically closely related to
Arenibacter troitsensis
, accumulate iodine in the presence of glucose and iodide (I
−
). In this study, the detailed mechanism of iodine uptake by C-21 was determined using a radioactive iodide tracer,
125
I
−
. In addition to glucose, oxygen and calcium ions were also required for the uptake of iodine. The uptake was not inhibited or was only partially inhibited by various metabolic inhibitors, whereas reducing agents and catalase strongly inhibited the uptake. When exogenous glucose oxidase was added to the cell suspension, enhanced uptake of iodine was observed. The uptake occurred even in the absence of glucose and oxygen if hydrogen peroxide was added to the cell suspension. Significant activity of glucose oxidase was found in the crude extracts of C-21, and it was located mainly in the membrane fraction. These findings indicate that hydrogen peroxide produced by glucose oxidase plays a key role in the uptake of iodine. Furthermore, enzymatic oxidation of iodide strongly stimulated iodine uptake in the absence of glucose. Based on these results, the mechanism was considered to consist of oxidation of iodide to hypoiodous acid by hydrogen peroxide, followed by passive translocation of this uncharged iodine species across the cell membrane. Interestingly, such a mechanism of iodine uptake is similar to that observed in iodine-accumulating marine algae.
Identification of a Chlorobenzene Reductive Dehalogenase in
Dehalococcoides
sp. Strain CBDB1
Authors: Adrian Lorenz , Rahnenführer Jan , Gobom Johan , Hölscher Tina
Published: October 2007

A chlorobenzene reductive dehalogenase of the anaerobic dehalorespiring bacterium
Dehalococcoides
sp. strain CBDB1 was identified. Due to poor biomass yields, standard protein isolation procedures were not applicable. Therefore, cell extracts from cultures grown on trichlorobenzenes were separated by native polyacrylamide gel electrophoresis and analyzed directly for chlorobenzene reductive dehalogenase activity within gel fragments. Activity was found in a single band, even though electrophoretic separation was performed under aerobic conditions. Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) and nano-liquid chromatography-MALDI MS analysis of silver-stained replicas of the active band on native polyacrylamide gels identified a protein product of the cbdbA84 gene, now called
cbrA
. The cbdbA84 gene is one of 32 reductive dehalogenase homologous genes present in the genome of strain CBDB1. The chlorobenzene reductive dehalogenase identified in our study represents a member of the family of corrinoid/iron-sulfur cluster-containing reductive dehalogenases. No orthologs of cbdbA84 were found in the completely sequenced genomes of
Dehalococcoides
sp. strains 195 and BAV1 nor among the genes amplified from
Dehalococcoides
sp. strain FL2 or mixed cultures containing
Dehalococcoides
. Another dehalogenase homologue (cbdbA80) was expressed in cultures that contained 1,2,4-trichlorobenzene, but its role is unclear. Other highly expressed proteins identified with our approach included the major subunit of a protein annotated as formate dehydrogenase, transporter subunits, and a putative S-layer protein.
Frequency of Secondary Symbiont Infection in an Invasive Psyllid Relates to Parasitism Pressure on a Geographic Scale in California
Authors: Hansen A. K. , Jeong G. , Paine T. D. , Stouthamer R.
Published: October 2007

Two endosymbionts, an obligate primary symbiont and a facultative secondary symbiont, are harbored within the invasive red gum (eucalyptus) lerp psyllid,
Glycaspis brimblecombei
, in California. An extensive survey of diversity and frequency of
G. brimblecombei
's secondary symbiont in multiple populations throughout the state of California was conducted using PCR detection, restriction enzymes, cloning, and sequencing. A total of 380
G. brimblecombei
individuals in 19 populations were screened for secondary symbionts. Based on molecular screening results, only one type of secondary symbiont was present in
G. brimblecombei
populations in California. Overall, 40% of the 380 psyllids screened were infected with the secondary symbiont. Interestingly, secondary symbiont infection frequencies in
G. brimblecombei
populations varied dramatically from 0 to 75% and were significantly related to parasitism pressure by
Psyllaphaegus bliteus
, a solitary endoparasitoid of the psyllid.
Genetic and Immunological Comparison of the Cladoceran Parasite
Pasteuria ramosa
with the Nematode Parasite
Pasteuria penetrans
Authors: Schmidt Liesbeth M. , Mouton Laurence , Nong Guang , Ebert Dieter , Preston James F.
Published: October 2007

Pasteuria penetrans
, an obligate endospore-forming parasite of
Meloidogyne
spp. (root knot nematodes), has been identified as a promising agent for biocontrol of these destructive agricultural crop pests.
Pasteuria ramosa
, an obligate parasite of water fleas (
Daphnia
spp.), has been shown to modulate cladoceran populations in natural ecosystems. Selected sporulation genes and an epitope associated with the spore envelope of these related species were compared. The
sigE
and
spoIIAA
/
spoIIAB
genes differentiate the two species to a greater extent than 16S rRNA and may serve as probes to differentiate the species. Single-nucleotide variations were observed in several conserved genes of five distinct populations of
P. ramosa
, and while most of these variations are silent single-nucleotide polymorphisms, a few result in conservative amino acid substitutions. A monoclonal antibody directed against an adhesin epitope present on
P. penetrans
P20 endospores, previously determined to be specific for
Pasteuria
spp. associated with several phytopathogenic nematodes, also detects an epitope associated with
P. ramosa
endospores. Immunoblotting provided patterns that differentiate
P. ramosa
from other
Pasteuria
spp. This monoclonal antibody thus provides a probe with which to detect and discriminate endospores of different
Pasteuria
spp. The presence of a shared adhesin epitope in two species with such ecologically distant hosts suggests that there is an ancient and ecologically significant recognition process in these endospore-forming bacilli that contributes to the virulence of both species in their respective hosts.
Ubericin A, a Class IIa Bacteriocin Produced by
Streptococcus uberis
Authors: Heng Nicholas C. K. , Burtenshaw Grace A. , Jack Ralph W. , Tagg John R.
Published: October 2007

Streptococcus uberis
, a causal agent of bovine mastitis, produces ubericin A, a 5.3-kDa class IIa (pediocin-like) bacteriocin, which was purified and characterized. The
uba
locus comprises two overlapping genes:
ubaA
(ubericin A precursor peptide) and
ubaI
(putative immunity protein). Ubericin A is the first streptococcal class IIa bacteriocin to be characterized.