bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple and Safe Method for Simultaneous Isolation of Microbial RNA and DNA from Problematic Populations
Authors: McIlroy Simon , Porter Kate , Seviour Robert J. , Tillett Daniel 
Published: September 2008

ABSTRACT
We describe a novel, rapid, and safe method for extracting RNA and DNA from refractory microbes, which avoids the use of phenol or chloroform. It has been used successfully to isolate high-quality nucleic acids from pure cultures and environmental populations known to resist widely used extraction protocols.
Mutational Analysis of the Class IIa Bacteriocin Curvacin A and Its Orientation in Target Cell Membranes
Authors: Haugen Helén Sophie , Kristiansen Per Eugen , Fimland Gunnar , Nissen-Meyer Jon 
Published: September 2008

ABSTRACT
To analyze the orientation in target cell membranes of the pediocin-like bacteriocin (antimicrobial peptide) curvacin A, 55 variants were generated by site-directed mutagenesis and their potencies against four different target cells determined. The result suggest that the somewhat hydrophilic short central helix (residues 19 to 24), along with the N-terminal β-sheet-like structure (residues 1 to 16), inserts in the interface region of the target cell membrane, with Ala22 close to the hydrophobic core of the membrane. The following hinge region, with Gly28 as an important residue, may then form a turn wherein Gly28 becomes positioned near the border between the interface and the hydrophobic regions, thus permitting the longer and more-hydrophobic C-terminal helix (residues 29 to 41) to insert into the hydrophobic core of the membrane. This helix contains three glycine residues (G33, G37, and G40) that form a putative helix-helix-interacting GxxxGxxG motif. The replacement of any of these glycines with a larger residue was very detrimental, suggesting their possible involvement in helix-helix interactions with a membrane-embedded receptor protein.
Evaluating the Insecticidal Genes and Their Expressed Products in
Bacillus thuringiensis
Strains by Combining PCR with Mass Spectrometry
Authors: Sun Yunjun , Fu Zujiao , Ding Xuezhi , Xia Liqiu 
Published: September 2008

ABSTRACT

By a combination of PCR and mass spectrometry, a total of five
cry
genes (
cry1Aa, cry1Ac, cry2Aa, cry2Ab
, and
cry1Ia
) were detected in genomic DNA from the wild-type
Bacillus thuringiensis
strain 4.0718, and three protoxins (Cry1Aa, Cry1Ac, and Cry2Aa) were identified in the strain's parasporal crystals. These results indicated that this complementary method may be useful in evaluating
B. thuringiensis
strains at both the gene and protein levels.
Role of DNA Protection and Repair in Resistance of
Bacillus subtilis
Spores to Ultrahigh Shock Pressures Simulating Hypervelocity Impacts
Authors: Moeller Ralf , Horneck Gerda , Rabbow Elke , Reitz Günther , Meyer Cornelia , Hornemann Ulrich , Stöffler Dieter 
Published: September 2008

ABSTRACT

Impact-induced ejections of rocks from planetary surfaces are frequent events in the early history of the terrestrial planets and have been considered as a possible first step in the potential interplanetary transfer of microorganisms. Spores of
Bacillus subtilis
were used as a model system to study the effects of a simulated impact-caused ejection on rock-colonizing microorganisms using a high-explosive plane wave setup. Embedded in different types of rock material, spores were subjected to extremely high shock pressures (5 to 50 GPa) lasting for fractions of microseconds to seconds. Nearly exponential pressure response curves were obtained for spore survival and linear dependency for the induction of sporulation-defective mutants. Spores of strains defective in major small, acid-soluble spore proteins (SASP) (α/β-type SASP) that largely protect the spore DNA and spores of strains deficient in nonhomologous-end-joining DNA repair were significantly more sensitive to the applied shock pressure than were wild-type spores. These results indicate that DNA may be the sensitive target of spores exposed to ultrahigh shock pressures. To assess the nature of the critical physical parameter responsible for spore inactivation by ultrahigh shock pressures, the resulting peak temperature was varied by lowering the preshock temperature, changing the rock composition and porosity, or increasing the water content of the samples. Increased peak temperatures led to increased spore inactivation and reduced mutation rates. The data suggested that besides the potential mechanical stress exerted by the shock pressure, the accompanying high peak temperatures were a critical stress parameter that spores had to cope with.
Distribution of Different Species of the
Bacteroides fragilis
Group in Individuals with Japanese Cedar Pollinosis
Authors: Odamaki Toshitaka , Xiao Jin-Zhong , Sakamoto Mitsuo , Kondo Shizuki , Yaeshima Tomoko , Iwatsuki Keiji , Togashi Hideo , Enomoto Tadao , Benno Yoshimi 
Published: September 2008

ABSTRACT

We investigated associations of species of the
Bacteroides fragilis
group with Japanese cedar pollinosis (JCPsis). Cell numbers of
Bacteroides fragilis
and
Bacteroides intestinalis
were significantly higher in JCPsis subjects than in non-JCPsis subjects before the pollen season. They correlated positively with both symptom scores and JCPsis-specific immunoglobulin E levels.
Molecular Characterization of a Variant of
Bacillus anthracis
-Specific Phage AP50 with Improved Bacteriolytic Activity
Authors: Sozhamannan Shanmuga , McKinstry Michael , Lentz Shannon M. , Jalasvuori Matti , McAfee Farrell , Smith Angela , Dabbs Jason , Ackermann Hans-W. , Bamford Jaana K. H. , Mateczun Alfred , Read Timothy D. 
Published: September 2008

ABSTRACT

The genome sequence of a
Bacillus anthracis
-specific clear plaque mutant phage, AP50c, contains 31 open reading frames spanning 14,398 bp, has two mutations compared to wild-type AP50t, and has a colinear genome architecture highly similar to that of gram-positive
Tectiviridae
phages. Spontaneous AP50c-resistant
B. anthracis
mutants exhibit a mucoid colony phenotype.
Broiler
Campylobacter
Contamination and Human Campylobacteriosis in Iceland
Authors: Callicott Kenneth A. , Harðardóttir Hjördís , Georgsson Franklín , Reiersen Jarle , Friðriksdóttir Vala , Gunnarsson Eggert , Michel Pascal , Bisaillon Jean-Robert , Kristinsson Karl G. , Briem Haraldur , Hiett Kelli L. , Needleman David S. , Stern Norman J. 
Published: September 2008

ABSTRACT

To examine whether there is a relationship between the degree of
Campylobacter
contamination observed in product lots of retail Icelandic broiler chicken carcasses and the incidence of human disease, 1,617 isolates from 327 individual product lots were genetically matched (using the
flaA
short variable region [SVR[) to 289 isolates from cases of human campylobacteriosis whose onset was within approximately 2 weeks from the date of processing. When there was genetic identity between broiler isolates and human isolates within the appropriate time frame, a retail product lot was classified as implicated in human disease. According to the results of this analysis, there were multiple clusters of human disease linked to the same process lot or lots. Implicated and nonimplicated retail product lots were compared for four lot descriptors: lot size, prevalence, mean contamination, and maximum contamination (as characterized by direct rinse plating). For retail product distributed fresh, Mann-Whitney U tests showed that implicated product lots had significantly (
P
= 0.0055) higher mean contamination than nonimplicated lots. The corresponding median values were 3.56 log CFU/carcass for implicated lots and 2.72 log CFU/carcass for nonimplicated lots. For frozen retail product, implicated lots were significantly (
P
= 0.0281) larger than nonimplicated lots. When the time frame was removed, retail product lots containing
Campylobacter flaA
SVR genotypes also seen in human disease had significantly higher mean and maximum contamination numbers than lots containing no genotypes seen in human disease for both fresh and frozen product. Our results suggest that cases of broiler-borne campylobacteriosis may occur in clusters and that the differences in mean contamination levels may provide a basis for regulatory action that is more specific than a presence-absence standard.
Transcriptional Regulation of
xyr1
, Encoding the Main Regulator of the Xylanolytic and Cellulolytic Enzyme System in
Hypocrea jecorina
Authors: Mach-Aigner Astrid R. , Pucher Marion E. , Steiger Matthias G. , Bauer Gudrun E. , Preis Sonja J. , Mach Robert L. 
Published: September 2008

ABSTRACT

In
Hypocrea jecorina
, Xyr1 (xylanase regulator 1) is the main transcription activator of hydrolase-encoding genes, such as
xyn1
,
xyn2
,
bxl1
,
cbh1
,
cbh2
,
egl1
, and
bgl1
. Even though Xyr1 mediates the induction signal for all these genes derived from various inducing carbon sources and compounds,
xyr1
transcription itself is not inducible by any of these substances. However, cultivation on glucose as the carbon source provokes carbon catabolite repression of
xyr1
transcription mediated by Cre1. In addition,
xyr1
transcription is repressed by the specific transcription factor Ace1. Moreover, Xyr1 is permanently available in the cell, and no de novo synthesis of this factor is needed for a first induction of
xyn1
transcription. The constitutive expression of
xyr1
leads to a significant elevation/deregulation of the
xyn1
,
xyn2
, and
bxl1
transcription compared to what is seen for the parental strain. Overall, the corresponding xylanolytic enzyme activities are clearly elevated in a constitutively
xyr1
-expressing strain, emphasizing this factor as an auspicious target for genetically engineered strain improvement.
Involvement of a Novel Enzyme, MdpA, in Methyl
tert
-Butyl Ether Degradation in
Methylibium petroleiphilum
PM1
Authors: Schmidt Radomir , Battaglia Vince , Scow Kate , Kane Staci , Hristova Krassimira R. 
Published: September 2008

ABSTRACT

Methylibium petroleiphilum
PM1 is a well-characterized environmental strain capable of complete metabolism of the fuel oxygenate methyl
tert
-butyl ether (MTBE). Using a molecular genetic system which we established to study MTBE metabolism by PM1, we demonstrated that the enzyme MdpA is involved in MTBE removal, based on insertional inactivation and complementation studies. MdpA is constitutively expressed at low levels but is strongly induced by MTBE. MdpA is also involved in the regulation of
tert
-butyl alcohol (TBA) removal under certain conditions but is not directly responsible for TBA degradation. Phylogenetic comparison of MdpA to related enzymes indicates close homology to the short-chain hydrolyzing alkane hydroxylases (AH1), a group that appears to be a distinct subfamily of the AHs. The unique, substrate-size-determining residue Thr
59
distinguishes MdpA from the AH1 subfamily as well as from AlkB enzymes linked to MTBE degradation in
Mycobacterium austroafricanum
.
Time-Lapse Microscopy of
Streptomyces coelicolor
Growth and Sporulation
Authors: Jyothikumar Vinod , Tilley Emma J. , Wali Rashmi , Herron Paul R. 
Published: September 2008

ABSTRACT

Bacteria from the genus
Streptomyces
are among the most complex of all prokaryotes; not only do they grow as a complex mycelium, they also differentiate to form aerial hyphae before developing further to form spore chains. This developmental heterogeneity of streptomycete microcolonies makes studying the dynamic processes that contribute to growth and development a challenging procedure. As a result, in order to study the mechanisms that underpin streptomycete growth, we have developed a system for studying hyphal extension, protein trafficking, and sporulation by time-lapse microscopy. Through the use of time-lapse microscopy we have demonstrated that
Streptomyces coelicolor
germ tubes undergo a temporary arrest in their growth when in close proximity to sibling extension sites. Following germination, in this system, hyphae extended at a rate of ∼20 μm h
−1
, which was not significantly different from the rate at which the apical ring of the cytokinetic protein FtsZ progressed along extending hyphae through a spiraling movement. Although we were able to generate movies for streptomycete sporulation, we were unable to do so for either the erection of aerial hyphae or the early stages of sporulation. Despite this, it was possible to demonstrate an arrest of aerial hyphal development that we suggest is through the depolymerization of FtsZ-enhanced green fluorescent protein (GFP). Consequently, the imaging system reported here provides a system that allows the dynamic movement of GFP-tagged proteins involved in growth and development of
S. coelicolor
to be tracked and their role in cytokinesis to be characterized during the streptomycete life cycle.
Transport of Glucose byBifidobacterium animalissubsp.lactisOccurs via Facilitated Diffusion
Authors: Briczinski E. P. , Phillips A. T. , Roberts R. F. 
Published: September 2008

ABSTRACTTwo strains ofBifidobacterium animalissubsp.lactiswere indistinguishable by several nucleic acid-based techniques; however, the type strain DSMZ 10140 was glucose utilization positive, while RB 4825, an industrially employed strain, was unable to grow rapidly on glucose as the principal carbon source. This difference was attributed to the presence of a low-affinity facilitated-diffusion glucose transporter identified in DSMZ 10140 but lacking in RB 4825. Uptake ofd-[U-14C]glucose in DSMZ 10140 was stimulated by monovalent cations (ammonium, sodium, potassium, and lithium) and inhibited by divalent cations (calcium and magnesium). When competitor carbohydrates were included in the uptake assays, stereospecific inhibition was exhibited, with greater competition by methyl-β-glucoside than methyl-α-glucoside. Significant inhibition (>30%) was observed with phloretin, an inhibitor of facilitated diffusion of glucose, whereas there was no inhibition by sodium fluoride, iodoacetate, sodium arsenate, sodium azide, 2,4-dinitrophenol, monensin, or valinomycin, which typically reduce energy-driven transport. Based on kinetic analyses, the mean values forKtandVmaxwere 14.8 ± 3.4 mMd-glucose and 0.13 ± 0.03 μmol glucose/min/mg cell protein, respectively. Glucose uptake by several glucose-utilizing commercial strains ofB. animalissubsp.lactiswas also inhibited by phloretin, indicating the presence of facilitated diffusion glucose transporters in those strains. Since DSMZ 10140 has been previously reported to lack a functional glucose phosphoenolpyruvate phosphotransferase system, the glucose transporter identified here is responsible for much of the organism's glucose uptake.
Host Ranges of
Listeria
-Specific Bacteriophages from the Turkey Processing Plant Environment in the United States
Authors: Kim Jae-Won , Siletzky Robin M. , Kathariou Sophia 
Published: September 2008

ABSTRACT

Even though at least 400
Listeria
phages have been isolated from various sources, limited information is available on phages from the food processing plant environment. Phages in the processing plant environment may play critical roles in determining the
Listeria
population that becomes established in the plant. In this study, we pursued the isolation of
Listeria
-specific phages from environmental samples from four turkey processing plants in the United States. These environmental samples were also utilized to isolate
Listeria
spp. Twelve phages were isolated and classified into three groups in terms of their host range. Of these, nine (group 1) showed a wide host range, including multiple serotypes of
Listeria monocytogenes
, as well as other
Listeria
spp. (
L. innocua
,
L. welshimeri
,
L. seeligeri
, and
L. ivanovii
). The remaining phages mostly infected
L. monocytogenes
serotype 4b as well as
L. innocua
,
L. ivanovii
, and/or
L. welshimeri
. All but one of the strains of the serotype 4b complex (4b, 4d, 4e) from the processing plant environment could be readily infected by the wide-host-range phages isolated from the environment of the processing plants. However, many strains of other serotypes (1/2a [or 3a] and 1/2b [or 3b]), which represented the majority of
L. monocytogenes
strains isolated from the environmental samples, were resistant to infection by these phages. Experiments with two phage-resistant strains showed reduced phage adsorption onto the host cells. These findings suggest that phage resistance may be an important component of the ecology of
L. monocytogenes
in the turkey processing plants.
Diverse Phage-Encoded Toxins in a Protective Insect Endosymbiont
Authors: Degnan Patrick H. , Moran Nancy A. 
Published: September 2008

ABSTRACTThe lysogenic bacteriophage APSE infects “CandidatusHamiltonella defensa,” a facultative endosymbiont of aphids and other sap-feeding insects. This endosymbiont has established a beneficial association with aphids, increasing survivorship following attack by parasitoid wasps. Although APSE and “Ca. Hamiltonella defensa” are effectively maternally transmitted between aphid generations, they can also be horizontally transferred among insect hosts, which results in genetically distinct “Ca. Hamiltonella defensa” strains infecting the same aphid species and sporadic distributions of both APSE and “Ca. Hamiltonella defensa” among hosts. Aphids infected only with “Ca. Hamiltonella defensa” have significantly less protection than those infected with both “Ca. Hamiltonella defensa” and APSE. This protection has been proposed to be connected to eukaryote-targeted toxins previously discovered in the genomes of two characterized APSE strains. In this study, we have sequenced partial genomes from seven additional APSE strains to address the evolution and extent of toxin variation in this phage. The APSE lysis region has been a hot spot for nonhomologous recombination of novel virulence cassettes. We identified four new toxins from three protein families, Shiga-like toxin, cytolethal distending toxin, and YD-repeat toxins. These recombination events have also resulted in reassortment of the downstream lysozyme and holin genes. Analysis of the conserved APSE genes flanking the variable toxin cassettes reveals a close phylogenetic association with phage sequences from two other facultative endosymbionts of insects. Thus, phage may act as a conduit for ongoing gene exchange among heritable endosymbionts.
Mechanistic Dissection of the Enzyme Complexes Involved in Biosynthesis of Lacticin 3147 and Nisin
Authors: Kuipers Anneke , Meijer-Wierenga Jenny , Rink Rick , Kluskens Leon D. , Moll Gert N. 
Published: September 2008

ABSTRACT

The thioether rings in the lantibiotics lacticin 3147 and nisin are posttranslationally introduced by dehydration of serines and threonines, followed by coupling of these dehydrated residues to cysteines. The prepeptides of the two-component lantibiotic lacticin 3147, LtnA1 and LtnA2, are dehydrated and cyclized by two corresponding bifunctional enzymes, LtnM1 and LtnM2, and are subsequently processed and exported via one bifunctional enzyme, LtnT. In the nisin synthetase complex, the enzymes NisB, NisC, NisT, and NisP dehydrate, cyclize, export, and process prenisin, respectively. Here, we demonstrate that the combination of LtnM2 and LtnT can modify, process, and transport peptides entirely different from LtnA2 and that LtnT can process and transport unmodified LtnA2 and unrelated peptides. Furthermore, we demonstrate a higher extent of NisB-mediated dehydration in the absence of thioether rings. Thioether rings apparently inhibited dehydration, which implies alternating actions of NisB and NisC. Furthermore, certain (but not all) NisC-cyclized peptides were exported with higher efficiency as a result of their conformation. Taken together, these data provide further insight into the applicability of
Lactococcus lactis
strains containing lantibiotic enzymes for the design and production of modified peptides.
Codon Optimization Increases Steady-State mRNA Levels in
Aspergillus oryzae
Heterologous Gene Expression
Authors: Tokuoka Masafumi , Tanaka Mizuki , Ono Kazuhisa , Takagi Shinobu , Shintani Takahiro , Gomi Katsuya 
Published: September 2008

ABSTRACT

We investigated the effect of codon optimization on the expression levels of heterologous proteins in
Aspergillus oryzae
, using the mite allergen Der f 7 as a model protein. A codon-optimized Der f 7 gene was synthesized according to the frequency of codon usage in
A. oryzae
by recursive PCR. Both native and optimized Der f 7 genes were expressed under the control of a high-level-expression promoter with their own signal peptides or in a fusion construct with
A. oryzae
glucoamylase (GlaA). Codon optimization markedly increased protein and mRNA production levels in both nonfused and GlaA-fused Der f 7 constructs. For constructs with native codons, analysis by 3′ rapid amplification of cDNA ends revealed that poly(A) tracts tended to be added within the coding region, producing aberrant mRNAs that lack a termination codon. Insertion of a termination codon between the carrier GlaA and native Der f 7 proteins in the GlaA fusion construct resulted in increases in mRNA and secreted-carrier-GlaA levels. These results suggested that mRNAs without a termination codon as a result of premature polyadenylation are degraded, possibly through the nonstop mRNA decay pathway. We suggest that codon optimization in
A. oryzae
results in elimination of cryptic polyadenylation signals in native Der f 7, thereby circumventing the production of truncated transcripts and resulting in an increase in steady-state mRNA levels.
Kinetics of Reduction of Fe(III) Complexes by Outer Membrane Cytochromes MtrC and OmcA ofShewanella oneidensisMR-1
Authors: Wang Zheming , Liu Chongxuan , Wang Xuelin , Marshall Matthew J. , Zachara John M. , Rosso Kevin M. , Dupuis Michel , Fredrickson James K. , Heald Steve , Shi Liang 
Published: September 2008

ABSTRACTBecause of their cell surface locations, the outer membranec-type cytochromes MtrC and OmcA ofShewanella oneidensisMR-1 have been suggested to be the terminal reductases for a range of redox-reactive metals that form poorly soluble solids or that do not readily cross the outer membrane. In this work, we determined the kinetics of reduction of a series of Fe(III) complexes with citrate, nitrilotriacetic acid (NTA), and EDTA by MtrC and OmcA using a stopped-flow technique in combination with theoretical computation methods. Stopped-flow kinetic data showed that the reaction proceeded in two stages, a fast stage that was completed in less than 1 s, followed by a second, relatively slower stage. For a given complex, electron transfer by MtrC was faster than that by OmcA. For a given cytochrome, the reaction was completed in the order Fe-EDTA > Fe-NTA > Fe-citrate. The kinetic data could be modeled by two parallel second-order bimolecular redox reactions with second-order rate constants ranging from 0.872 μM−1s−1for the reaction between MtrC and the Fe-EDTA complex to 0.012 μM−1s−1for the reaction between OmcA and Fe-citrate. The biphasic reaction kinetics was attributed to redox potential differences among the heme groups or redox site heterogeneity within the cytochromes. The results of redox potential and reorganization energy calculations showed that the reaction rate was influenced mostly by the relatively large reorganization energy. The results demonstrate that ligand complexation plays an important role in microbial dissimilatory reduction and mineral transformation of iron, as well as other redox-sensitive metal species in nature.