bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species identification and sibship assignment of sympatric larvae in the yucca moths Tegeticula synthetica and Tegeticula antithetica (Lepidoptera: Prodoxidae)
Authors: DRUMMOND CHRISTOPHER S. , SMITH CHRISTOPHER I. , PELLMYR OLLE 
Published: April 2009

AbstractEcological interactions between yucca moths (Tegeticula, Prodoxidae) and their host plants (Yucca, Agavaceae) are exemplary of obligate plant–pollinator mutualism and co‐evolution. We describe a multiplex microsatellite DNA protocol for species identification and sibship assignment of sympatric larvae from Tegeticula synthetica and Tegeticula antithetica, pollinators of the Joshua tree (Yucca brevifolia). Bayesian clustering provides correct diagnosis of species in 100% of adult moths, with unambiguous identification of sympatric larvae. Sibship assignments show that larvae within a single fruit are more likely to be full‐sibs or half‐sibs than larvae from different fruit, consistent with the hypothesis that larval clutches are predominantly the progeny of an individual female.
A Mechanical Fourier Series Generator: An Exact Solution
Authors: Bucher Izhak 
Published: April 2009

Abstract
A vibrating system is constructed such that its natural frequencies are exact integer multiples of a base frequency. This system requires little energy to produce a periodic motion whose period is determined by the base frequency. The ability to amplify integer multiples of a base frequency makes this device an effective mechanical Fourier series generator. The proposed topology makes use of symmetry to assign poles and zeros at optimal frequencies. The system zeros play the role of suppressing the energy at certain frequencies while the poles amplify the input at their respective frequencies. An exact, non-iterative procedure is adopted to provide the stiffness and mass values of a discrete realization. It is shown that the spatial distributions of mass and stiffness are smooth; thus it is suggested that a continuous realization of a mechanical Fourier series generator is a viable possibility. A laboratory experiment and numerical examples are briefly described to validate the theory.
Effect of pH and Temperature on Denitrification Gene Expression and Activity in
Pseudomonas mandelii
Authors: Saleh-Lakha Saleema , Shannon Kelly E. , Henderson Sherri L. , Goyer Claudia , Trevors Jack T. , Zebarth Bernie J. , Burton David L. 
Published: April 2009

ABSTRACT

Pseudomonas mandelii
liquid cultures were studied to determine the effect of pH and temperature on denitrification gene expression, which was quantified by quantitative reverse transcription-PCR. Denitrification was measured by the accumulation of nitrous oxide (N
2
O) in the headspace in the presence of acetylene. Levels of gene expression of
nirS
and
cnorB
at pH 5 were 539-fold and 6,190-fold lower, respectively, than the levels of gene expression for cells grown at pH 6, 7, and 8 between 4 h and 8 h. Cumulative denitrification levels were 28 μmol, 63 μmol, and 22 μmol at pH 6, 7, and 8, respectively, at 8 h, whereas negligible denitrification was measured at pH 5.
P. mandelii
cells grown at 20°C and 30°C exhibited 9-fold and 94-fold increases in levels of
cnorB
expression between 0 h and 2 h, respectively, and an average 17-fold increase in levels of
nirS
gene expression. In contrast, induction of
cnorB
and
nirS
gene expression for
P. mandelii
cells grown at 10°C did not occur in the first 4 h. Levels of cumulative denitrification at 10 h were 6.6 μmol for
P. mandelii
cells grown at 10°C and 20°C and 30 μmol for cells grown at 30°C. Overall, levels of
cnorB
and
nirS
expression were relatively insensitive to pH values over the range of pH 6 to 8 but were substantially reduced at pH 5, whereas gene expression was sensitive to temperature, with induction and time to achieve maximum gene expression delayed as the temperature decreased from 30°C. Low pH and temperature negatively affected denitrification activity.
The Haloprotease CPI Produced by the Moderately Halophilic Bacterium
Pseudoalteromonas ruthenica
Is Secreted by the Type II Secretion Pathway
Authors: Sánchez-Porro Cristina , Mellado Encarnación , Pugsley Anthony P. , Francetic Olivera , Ventosa Antonio 
Published: April 2009

ABSTRACT

The gene (
cpo
) encoding the extracellular protease CPI produced by the moderately halophilic bacterium
Pseudoalteromonas ruthenica
CP76 was cloned, and its nucleotide sequence was analyzed. The
cpo
gene encodes a 733-residue protein showing sequence similarity to metalloproteases of the M4 family. The type II secretion apparatus was shown to be responsible for secretion of the haloprotease CPI.
Regulation of Expression of Genes Involved in Quinate and Shikimate Utilization in
Corynebacterium glutamicum
Authors: Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki 
Published: April 2009

ABSTRACT

The utilization of the hydroaromatic compounds quinate and shikimate by
Corynebacterium glutamicum
was investigated.
C. glutamicum
grew well with either quinate or shikimate as the sole carbon source. The disruption of
qsuD
, encoding quinate/shikimate dehydrogenase, completely suppressed growth with either substrate but did not affect growth with glucose, indicating that the enzyme encoded by
qsuD
catalyzes the first step of the catabolism of quinate/shikimate but is not involved in the shikimate pathway required for the biosynthesis of various aromatic compounds. On the chromosome of
C. glutamicum
, the
qsuD
gene is located in a gene cluster also containing
qsuA, qsuB
, and
qsuC
genes, which are probably involved in the quinate/shikimate utilization pathway to form protocatechuate. Reverse transcriptase PCR analyses revealed that the expression of the
qsuABCD
genes was markedly induced during growth with either quinate or shikimate relative to expression during growth with glucose. The induction level by shikimate was significantly decreased by the disruption of
qsuR
, which is located immediately upstream of
qsuA
in the opposite direction and encodes a LysR-type transcriptional regulator, suggesting that QsuR acts as an activator of the
qsuABCD
genes. The high level of induction of
qsuABCD
genes by shikimate was still observed in the presence of glucose, and simultaneous consumption of glucose and shikimate during growth was observed.
Characterization of Bacterial Magnetotactic Behaviors by Using a Magnetospectrophotometry Assay
Authors: Lefèvre Christopher T. , Song Tao , Yonnet Jean-Paul , Wu Long-Fei 
Published: April 2009

ABSTRACT

Magnetotactic bacteria have the unique capacity of synthesizing intracellular single-domain magnetic particles called magnetosomes. The magnetosomes are usually organized in a chain that allows the bacteria to align and swim along geomagnetic field lines, a behavior called magnetotaxis. Two mechanisms of magnetotaxis have been described. Axial magnetotactic cells swim in both directions along magnetic field lines. In contrast, polar magnetotactic cells swim either parallel to the geomagnetic field lines toward the North Pole (north seeking) or antiparallel toward the South Pole (south seeking). In this study, we used a magnetospectrophotometry (MSP) assay to characterize both the axial magnetotaxis of “
Magnetospirillum magneticum
” strain AMB-1 and the polar magnetotaxis of magneto-ovoid strain MO-1. Two pairs of Helmholtz coils were mounted onto the cuvette holder of a common laboratory spectrophotometer to generate two mutually perpendicular homogeneous magnetic fields parallel or perpendicular to the light beam. The application of magnetic fields allowed measurements of the change in light scattering resulting from cell alignment in a magnetic field or in absorbance due to bacteria swimming across the light beam. Our results showed that MSP is a powerful tool for the determination of bacterial magnetism and the analysis of alignment and swimming of magnetotactic bacteria in magnetic fields. Moreover, this assay allowed us to characterize south-seeking derivatives and non-magnetosome-bearing strains obtained from north-seeking MO-1 cultures. Our results suggest that oxygen is a determinant factor that controls magnetotactic behavior.
Possible Environmental Origin of Resistance of
Aspergillus fumigatus
to Medical Triazoles
Authors: Snelders Eveline , Huis in 't Veld Robert A. G. , Rijs Anthonius J. M. M. , Kema Gert H. J. , Melchers Willem J. G. , Verweij Paul E. 
Published: April 2009

ABSTRACT

We reported the emergence of resistance to medical triazoles of
Aspergillus fumigatus
isolates from patients with invasive aspergillosis. A dominant resistance mechanism was found, and we hypothesized that azole resistance might develop through azole exposure in the environment rather than in azole-treated patients. We investigated if
A. fumigatus
isolates resistant to medical triazoles are present in our environment by sampling the hospital indoor environment and soil from the outdoor environment. Antifungal susceptibility, resistance mechanisms, and genetic relatedness were compared with those of azole-resistant clinical isolates collected in a previous study. Itraconazole-resistant
A. fumigatus
(five isolates) was cultured from the indoor hospital environment as well as from soil obtained from flower beds in proximity to the hospital (six isolates) but never from natural soil. Additional samples of commercial compost, leaves, and seeds obtained from a garden center and a plant nursery were also positive (four isolates). Cross-resistance was observed for voriconazole, posaconazole, and the azole fungicides metconazole and tebuconazole. Molecular analysis showed the presence of the dominant resistance mechanism, which was identical to that found in clinical isolates, in 13 of 15 environmental isolates, and it showed that environmental and clinical isolates were genetically clustered apart from nonresistant isolates. Patients with azole-resistant aspergillosis might have been colonized with azole-resistant isolates from the environment.
Uncultivated Magnetotactic Cocci from Yuandadu Park in Beijing, China
Authors: Lin Wei , Pan Yongxin 
Published: April 2009

ABSTRACT

In the present study, we investigated a group of uncultivated magnetotactic cocci, which was magnetically isolated from a freshwater pond in Beijing, China. Light and transmission electron microscopy showed that these cocci ranged from 1.5 to 2.5 μm and contained two to four chains of magnetite magnetosomes, which sometimes were partially disorganized. Overall, the size of the disorganized magnetosomes was significantly smaller than that arranged in chains. All characterized magnetosome crystals were elongated (shape factor = 0.64) and fall into the single-domain size range (30 to 115 nm). Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization showed that the enriched bacteria were a virtually homogeneous population and represented a novel lineage in the
Alphaproteobacteria
. The closest cultivated relative was magnetotactic coccoid strain MC-1 (88% sequence identity). First-order reversal curve diagrams revealed that these cocci had relatively strong magnetic interactions compared to the single-chain magnetotactic bacteria. Low-temperature magnetic measurements showed that the Verwey transition of them was ∼108 K, confirming magnetite magnetosomes, and the delta ratio δ
FC
/δ
ZFC
was >2. Based on the structure, phylogenetic position and magnetic properties, the enriched magnetotactic cocci of
Alphaproteobacteria
are provisionally named as “
Candidatus
Magnetococcus yuandaducum.”
Rhizobiumsp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems
Authors: Schmeisser Christel , Liesegang Heiko , Krysciak Dagmar , Bakkou Nadia , Le Quéré Antoine , Wollherr Antje , Heinemeyer Isabelle , Morgenstern Burkhard , Pommerening-Röser Andreas , Flores Margarita , Palacios Rafael , Brenner Sydney , Gottschalk Gerhard , Schmitz Ruth A. , Broughton William J. , Perret Xavier , Strittmatter Axel W. , Streit Wolfgang R. 
Published: April 2009

ABSTRACTRhizobiumsp. strain NGR234 is a unique alphaproteobacterium (orderRhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule.
Differential
Listeria monocytogenes
Strain Survival and Growth in Katiki, a Traditional Greek Soft Cheese, at Different Storage Temperatures
Authors: Kagkli Dafni-Maria , Iliopoulos Vassilios , Stergiou Virginia , Lazaridou Anna , Nychas George-John 
Published: April 2009

ABSTRACT

Katiki Domokou is a traditional Greek cheese, which has received the Protected Designation of Origin recognition since 1994. Its microfloras have not been studied although its structure and composition may enable (or even favor) the survival and growth of several pathogens, including
Listeria monocytogenes
. The persistence of
L. monocytogenes
during storage at different temperatures has been the subject of many studies since temperature abuse of food products is often encountered. In the present study, five strains of
L. monocytogenes
were aseptically inoculated individually and as a cocktail in Katiki Domokou cheese, which was then stored at 5, 10, 15, and 20°C. Pulsed-field gel electrophoresis was used to monitor strain evolution or persistence during storage at different temperatures in the case of the cocktail inoculum. The results suggested that strain survival of
L. monocytogenes
was temperature dependent since different strains predominated at different temperatures. Such information is of great importance in risk assessment studies, which typically consider only the presence or absence of the pathogen.
Generation of Electricity and Analysis of Microbial Communities in Wheat Straw Biomass-Powered Microbial Fuel Cells
Authors: Zhang Yifeng , Min Booki , Huang Liping , Angelidaki Irini 
Published: April 2009

ABSTRACT

Electricity generation from wheat straw hydrolysate and the microbial ecology of electricity-producing microbial communities developed in two-chamber microbial fuel cells (MFCs) were investigated. The power density reached 123 mW/m
2
with an initial hydrolysate concentration of 1,000 mg chemical oxygen demand (COD)/liter, while coulombic efficiencies ranged from 37.1 to 15.5%, corresponding to the initial hydrolysate concentrations of 250 to 2,000 mg COD/liter. The suspended bacteria found were different from the bacteria immobilized in the biofilm, and they played different roles in electricity generation from the hydrolysate. The bacteria in the biofilm were consortia with sequences similar to those of
Bacteroidetes
(40% of sequences),
Alphaproteobacteria
(20%),
Bacillus
(20%),
Deltaproteobacteria
(10%), and
Gammaproteobacteria
(10%), while the suspended consortia were predominately
Bacillus
(22.2%). The results of this study can contribute to improving understanding of and optimizing electricity generation in microbial fuel cells.
Spatial Patterns in Hyphal Growth and Substrate Exploitation within Norway Spruce Stems Colonized by the Pathogenic White-Rot Fungus
Heterobasidion parviporum
Authors: Hietala Ari M. , Nagy Nina E. , Steffenrem Arne , Kvaalen Harald , Fossdal Carl G. , Solheim Halvor 
Published: April 2009

ABSTRACT

In Norway spruce, a fungistatic reaction zone with a high pH and enrichment of phenolics is formed in the sapwood facing heartwood colonized by the white-rot fungus
Heterobasidion parviporum
. Fungal penetration of the reaction zone eventually results in expansion of this xylem defense. To obtain information about mechanisms operating upon heartwood and reaction zone colonization by the pathogen, hyphal growth and wood degradation were investigated using real-time PCR, microscopy, and comparative wood density analysis of naturally colonized trees with extensive stem decay. The hyphae associated with delignified wood at stump level were devoid of any extracellular matrix, whereas incipient decay at the top of decay columns was characterized by a carbohydrate-rich hyphal sheath attaching hyphae to tracheid walls. The amount of pathogen DNA peaked in aniline wood, a narrow darkened tissue at the colony border apparently representing a compromised region of the reaction zone. Vigorous production of pathogen conidiophores occurred in this region. Colonization of aniline wood was characterized by hyphal growth within polyphenolic lumen deposits in tracheids and rays, and the hyphae were fully encased in a carbohydrate-rich extracellular matrix. Together, these data indicate that the interaction of the fungus with the reaction zone involves a local concentration of fungal biomass that forms an efficient translocation channel for nutrients. Finally, the enhanced production of the hyphal sheath may be instrumental in lateral expansion of the decay column beyond the reaction zone boundary.
CpxRA Influences
Xenorhabdus nematophila
Colonization Initiation and Outgrowth in
Steinernema carpocapsae
Nematodes through Regulation of the
nil
Locus
Authors: Herbert Tran Erin E. , Andersen Aaron W. , Goodrich-Blair Heidi 
Published: April 2009

ABSTRACT

The gammaproteobacterium
Xenorhabdus nematophila
mutualistically colonizes an intestinal region of a soil-dwelling nematode and is a blood pathogen of insects. The
X. nematophila
CpxRA two-component regulatory system is necessary for both of these host interactions (E. Herbert et al., Appl. Environ. Microbiol. 73:7826-7836, 2007). Mutualistic association of
X. nematophila
with its nematode host consists of two stages: initiation, where a small number of bacterial cells establish themselves in the colonization site, and outgrowth, where these cells grow to fill the space. In this study, we show that the Cpx system is necessary for both of these stages.
X. nematophila
Δ
cpxR1
colonized fewer nematodes than its wild-type parent and did not achieve as high a density as did the wild type within a portion of the colonized nematodes. To test whether the Δ
cpxR1
host interaction phenotypes are due to its overexpression of
mrxA
, encoding the type I pilin subunit protein, we assessed the colonization phenotype of a Δ
cpxR1
Δ
mrxA1
double mutant. This mutant displayed the same colonization defect as Δ
cpxR1
, indicating that CpxR negative regulation of
mrxA
does not play a detectable role in
X. nematophila
-host interactions. CpxR positively regulates expression of
nilA
,
nilB
, and
nilC
genes necessary for nematode colonization. Here we show that the nematode colonization defect of the Δ
cpxR1
mutant is rescued by elevating
nil
gene expression through mutation of
nilR
, a negative regulator of
nilA
,
nilB
, and
nilC
. These data suggest that the nematode colonization defect previously observed in Δ
cpxR1
is caused, at least in part, by altered regulation of
nilA
,
nilB
, and
nilC
.
Detection of Live
Salmonella
sp. Cells in Produce by a TaqMan-Based Quantitative Reverse Transcriptase Real-Time PCR Targeting
invA
mRNA
Authors: González-Escalona Narjol , Hammack Thomas S. , Russell Mindi , Jacobson Andrew P. , De Jesús Antonio J. , Brown Eric W. , Lampel Keith A. 
Published: April 2009

ABSTRACT

Salmonella enterica
contamination in foods is a significant concern for public health. When DNA detection methods are used for analysis of foods, one of the major concerns is false-positive results from the detection of dead cells. To circumvent this crucial issue, a TaqMan quantitative real-time RT-PCR (qRT-PCR) assay with an RNA internal control was developed.
invA
RNA standards were used to determine the detection limit of this assay as well as to determine
invA
mRNA levels in mid-exponential-, late-exponential-, and stationary-phase cells. This assay has a detection limit of 40 copies of
invA
mRNA per reaction. The levels of
invA
mRNA in mid-exponential-, late-exponential-, and stationary-phase
S. enterica
cells was approximately 1 copy per 3 CFU, 1 copy per CFU, and 4 copies per 10
3
CFU, respectively. Spinach, tomatoes, jalapeno peppers, and serrano peppers were artificially contaminated with four different
Salmonella
serovars at levels of 10
5
and less than 10 CFU. These foods were analyzed with qRT-PCR and with the FDA's
Bacteriological Analytical Manual Salmonella
culture method (W. A. Andrews and T. S. Hammack,
in
G. J. Jackson et al., ed., Bacteriological analytical manual online,
http://www.cfsan.fda.gov/∼ebam/bam-5.html
, 2007). Comparable results were obtained by both methods. Only live
Salmonella
cells could be detected by this qRT-PCR assay, thus avoiding the dangers of false-positive results from nonviable cells. False negatives (inhibition of the PCR) were also ruled out through the use of an RNA internal control. This assay allows for the fast and accurate detection of viable
Salmonella
spp. in spinach, tomatoes, and in both jalapeno and serrano peppers.
Effect of Octenidine Hydrochloride on Planktonic Cells and Biofilms of
Listeria monocytogenes
Authors: Amalaradjou Mary Anne Roshni , Norris Carol E. , Venkitanarayanan Kumar 
Published: April 2009

ABSTRACT

Listeria monocytogenes
is a food-borne pathogen capable of forming biofilms and persisting in food processing environments for extended periods of time, thereby potentially contaminating foods. The efficacy of octenidine hydrochloride (OH) for inactivating planktonic cells and preformed biofilms of
L. monocytogenes
was investigated at 37, 21, 8, and 4°C in the presence and absence of organic matter (rehydrated nonfat dry milk). OH rapidly killed planktonic cells and biofilms of
L. monocytogenes
at all four temperatures. Moreover, OH was equally effective in killing
L. monocytogenes
biofilms on polystyrene and stainless steel matrices in the presence and absence of organic matter. The results underscore OH's ability to prevent establishment of
L. monocytogenes
biofilms by rapidly killing planktonic cells and to eliminate preformed biofilms, thus suggesting that it could be used as a disinfectant to prevent
L. monocytogenes
from persisting in food processing environments.