bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Community Composition and Denitrifying Enzyme Activities in Salt Marsh Sediments
Authors: Cao Yiping , Green Peter G. , Holden Patricia A. 
Published: November 2008

ABSTRACT

Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (
nirS
) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh.
Terminal Restriction Fragment Length Polymorphism for Identification of
Cryptosporidium
Species in Human Feces
Authors: Waldron L. S. , Ferrari B. C. , Gillings M. R. , Power M. L. 
Published: November 2008

ABSTRACT

Effective management of human cryptosporidiosis requires efficient methods for detection and identification of the species of
Cryptosporidium
isolates. Identification of isolates to the species level is not routine for diagnostic assessment of cryptosporidiosis, which leads to uncertainty about the epidemiology of the
Cryptosporidium
species that cause human disease. We developed a rapid and reliable method for species identification of
Cryptosporidium
oocysts from human fecal samples using terminal restriction fragment polymorphism (T-RFLP) analysis of the 18S rRNA gene. This method generated diagnostic fragments unique to the species of interest. A panel of previously identified isolates of species was blind tested to validate the method, which determined the correct species identity in every case. The T-RFLP profiles obtained for samples spiked with known amounts of
Cryptosporidium hominis
and
Cryptosporidium parvum
oocysts generated the two expected diagnostic peaks. The detection limit for an individual species was 1% of the total DNA. This is the first application of T-RFLP to protozoa, and the method which we developed is a rapid, repeatable, and cost-effective method for species identification.
Biotechnological Process for Production of β-Dipeptides from Cyanophycin on a Technical Scale and Its Optimization
Authors: Sallam Ahmed , Kast Alene , Przybilla Simon , Meiswinkel Tobias , Steinbüchel Alexander 
Published: November 2008

ABSTRACT

A triphasic process was developed for the production of β dipeptides from cyanophycin (CGP) on a large scale. Phase I comprises an optimized acid extraction method for technical isolation of CGP from biomass. It yielded highly purified CGP consisting of aspartate, arginine, and a little lysine. Phase II comprises the fermentative production of an extracellular CGPase (CphE
al
) from
Pseudomonas alcaligenes
strain DIP1 on a 500-liter scale in mineral salts medium, with citrate as the sole carbon source and CGP as an inductor. During optimization, it was shown that 2 g liter
−1
citrate, pH 6.5, and 37°C are ideal parameters for CphE
al
production. Maximum enzyme yields were obtained after induction in the presence of 50 mg liter
−1
CGP or CGP dipeptides for 5 or 3 h, respectively. Aspartate at a concentration of 4 g liter
−1
induced CphE
al
production with only about 30% efficiency in comparison to that with CGP. CphE
al
was purified utilizing its affinity for the substrate and its specific binding to CGP. CphE
al
turned out to be a serine protease with maximum activity at 50°C and at pH 7 to 8.5. Phase III comprises degradation of CGP to β-aspartate-arginine and β-aspartate-lysine dipeptides with a purity of over 99% (by thin-layer chromatography and high-performance liquid chromatography), employing a crude CphE
al
preparation. Optimum degradation parameters were 100 g liter
−1
CGP, 10 g liter
−1
crude CphE
al
powder, and 4 h of incubation at 50°C. The overall efficiency of phase III was 91%, while 78% (wt/wt) of the used CphE
al
powder with sustained activity toward CGP was recovered. The optimized process was performed with industrial materials and equipment and is applicable to any desired scale.
Abundances of Hyperthermophilic Autotrophic Fe(III) Oxide Reducers and Heterotrophs in Hydrothermal Sulfide Chimneys of the Northeastern Pacific Ocean
Authors: Ver Eecke Helene C. , Kelley Deborah S. , Holden James F. 
Published: November 2008

ABSTRACTThe abundances of hyperthermophilic heterotrophs, methanogens, and autotrophic reducers of amorphous Fe(III) oxide in 18 samples of deep-sea hydrothermal vent sulfide chimneys of the Endeavour Segment were measured. The results indicate that conditions favor the growth of iron reducers toward the interiors of these deposits and that of heterotrophs toward the outer surfaces near high-temperature polychaete worms (Paralvinella sulfincola).
Developmental and Microbiological Analysis of the Inception of Bioluminescent Symbiosis in the Marine FishNuchequula nuchalis(Perciformes: Leiognathidae)
Authors: Dunlap Paul V. , Davis Kimberly M. , Tomiyama Shinichi , Fujino Misato , Fukui Atsushi 
Published: November 2008

ABSTRACTMany marine fish harbor luminous bacteria as bioluminescent symbionts. Despite the diversity, abundance, and ecological importance of these fish and their apparent dependence on luminous bacteria for survival and reproduction, little is known about developmental and microbiological events surrounding the inception of their symbioses. To gain insight on these issues, we examined wild-caught larvae of the leiognathid fishNuchequula nuchalis, a species that harborsPhotobacterium leiognathias its symbiont, for the presence, developmental state, and microbiological status of the fish's internal, supraesophageal light organ. Nascent light organs were evident in the smallest specimens obtained, flexion larvae of 6.0 to 6.5 mm in notochord length (NL), a developmental stage at which the stomach had not yet differentiated and the nascent gasbladder had not established an interface with the light organ. Light organs of certain of the specimens in this size range apparently lacked bacteria, whereas light organs of other specimens of 6.5 mm in NL and of all larger specimens harbored large populations of bacteria, representatives of which were identified asP. leiognathi. Bacteria identified asVibrio harveyiwere also present in the light organ of one larval specimen. Light organ populations were composed typically of two or three genetically distinct strain types ofP. leiognathi, similar to the situation in adult fish, and the same strain type was only rarely found in light organs of different larval, juvenile, or adult specimens. Light organs of larvae carried a smaller proportion of strains merodiploid for thelux-riboperon, 79 of 249 strains, than those of adults (75 of 91 strains). These results indicate that light organs ofN. nuchalisflexion and postflexion larvae of 6.0 to 6.7 mm in NL are at an early stage of development and that inception of the symbiosis apparently occurs in flexion larvae of 6.0 to 6.5 mm in NL. Ontogeny of the light organ therefore apparently precedes acquisition of the symbiotic bacteria. Furthermore, bacterial populations in larval light organs near inception of the symbiosis are genetically diverse, like those of adult fish.
Prevalence and Genotypes of
Anaplasma
Species and Habitat Suitability for Ticks in a Mediterranean Ecosystem
Authors: Torina Alessandra , Alongi Angelina , Naranjo Victoria , Estrada-Peña Agustín , Vicente Joaquín , Scimeca Salvatore , Marino Anna M. F. , Salina Felice , Caracappa Santo , de la Fuente José 
Published: November 2008

ABSTRACT

Anaplasma
species are tick-transmitted pathogens that impact veterinary and human health. Sicily is one of the locations where these pathogens are endemic. Sicily represents a typical Mediterranean ecosystem to study
Anaplasma
infection and tick habitat suitability. The aims of this study were (i) to characterize by 16S rRNA and species-specific
msp4
gene PCR the prevalence and genotypes of
A. marginale
,
A. phagocytophilum
, and
A. ovis
in the most abundant host species in Sicilian provinces and (ii) to correlate differences between hosts and between western and eastern Sicily with the habitat suitability for ticks in these regions. Differences were found in the prevalence of
Anaplasma
spp. between different hosts and between western and eastern provinces. The differences in
Anaplasma
prevalence between different hosts may be explained by pathogen host tropism. The differences between western and eastern provinces correlated with the tick habitat suitability in these regions. The analysis of
Anaplasma
genotypes suggested a higher host and regional specificity for
A. phagocytophilum
than for
A. marginale
and
A. ovis
strains, a finding probably associated with the broader host range of
A. phagocytophilum
. The presence of identical
A. marginale
genotypes in the two regions may reflect cattle movement. The results for
A. ovis
suggested the possibility of some genotypes being host specific. These results provide information potentially useful for the management of tick-borne diseases caused by
Anaplasma
spp. in Sicily and other Mediterranean regions and may contribute to the development of models to predict the risks for these tick-borne pathogens.
Selective Extraction of Bacterial DNA from the Surfaces of Macroalgae
Authors: Burke Catherine , Kjelleberg Staffan , Thomas Torsten 
Published: November 2008

ABSTRACTA novel method has been developed for the selective extraction of DNA from surface-associated bacterial communities from the two model marine benthic algaeUlva australisandDelisea pulchra. The extracted DNA had no detectable contamination with host DNA, was recovered in high yield and quality, and was representative of the bacterial community on the algal surfaces. The DNA is suitable for a variety of subsequent applications, including the construction of large-insert clone libraries and metagenomic sequencing.
Use of 4-Sulfophenyl Isothiocyanate Labeling and Mass Spectrometry To Determine the Site of Action of the Streptococcolytic Peptidoglycan Hydrolase Zoocin A
Authors: Gargis Shaw R. , Heath Harry E. , Heath Lucie S. , LeBlanc Paul A. , Simmonds Robin S. , Abbott Brian D. , Timkovich Russell , Sloan Gary L. 
Published: November 2008

ABSTRACT

Zoocin A is a streptococcolytic peptidoglycan hydrolase with an unknown site of action that is produced by
Streptococcus equi
subsp.
zooepidemicus
4881. Zoocin A has now been determined to be a
d
-alanyl-
l
-alanine endopeptidase by digesting susceptible peptidoglycan with a combination of mutanolysin and zoocin A, separating the resulting muropeptides by reverse-phase high-pressure liquid chromatography, and analyzing them by mass spectrometry (MS) in both the positive- and negative-ion modes to determine their compositions. In order to distinguish among possible structures for these muropeptides, they were N-terminally labeled with 4-sulfophenyl isothiocyanate (SPITC) and analyzed by tandem MS in the negative-ion mode. This novel application of SPITC labeling and MS/MS analysis can be used to analyze the structure of peptidoglycans and to determine the sites of action of other peptidoglycan hydrolases.
Effect of Tree Species and Mycorrhizal Colonization on the Archaeal Population of Boreal Forest Rhizospheres
Authors: Bomberg Malin , Timonen Sari 
Published: November 2008

ABSTRACT

Group 1.1c
Crenarchaeota
are the predominating archaeal group in acidic boreal forest soils. In this study, we show that the detection frequency of 1.1c crenarchaeotal 16S rRNA genes in the rhizospheres of the boreal forest trees increased following colonization by the ectomycorrhizal fungus
Paxillus involutus
. This effect was very clear in the fine roots of
Pinus sylvestris
,
Picea abies
, and
Betula pendula
, the most common forest trees in Finland. The nonmycorrhizal fine roots had a clearly different composition of archaeal 16S rRNA genes in comparison to the mycorrhizal fine roots. In the phylogenetic analysis, the 1.1c crenarchaeotal 16S rRNA gene sequences obtained from the fine roots formed a well-defined cluster separate from the mycorrhizal ones.
Alnus glutinosa
differed from the other trees by having high diversity and detection levels of
Crenarchaeota
both on fine roots and on mycorrhizas as well as by harboring a distinct archaeal flora. The similarity of the archaeal populations in rhizospheres of the different tree species was increased upon colonization by the ectomycorrhizal fungus. A minority of the sequences obtained from the mycorrhizas belonged to
Euryarchaeota
(order
Halobacteriales
).
Identification and Characterization of the Asperthecin Gene Cluster of
Aspergillus nidulans
Authors: Szewczyk Edyta , Chiang Yi-Ming , Oakley C. Elizabeth , Davidson Ashley D. , Wang Clay C. C. , Oakley Berl R. 
Published: November 2008

ABSTRACT

The sequencing of
Aspergillus
genomes has revealed that the products of a large number of secondary metabolism pathways have not yet been identified. This is probably because many secondary metabolite gene clusters are not expressed under normal laboratory culture conditions. It is, therefore, important to discover conditions or regulatory factors that can induce the expression of these genes. We report that the deletion of
sumO
, the gene that encodes the small ubiquitin-like protein SUMO in
A. nidulans
, caused a dramatic increase in the production of the secondary metabolite asperthecin and a decrease in the synthesis of austinol/dehydroaustinol and sterigmatocystin. The overproduction of asperthecin in the
sumO
deletion mutant has allowed us, through a series of targeted deletions, to identify the genes required for asperthecin synthesis. The asperthecin biosynthesis genes are clustered and include genes encoding an iterative type I polyketide synthase, a hydrolase, and a monooxygenase. The identification of these genes allows us to propose a biosynthetic pathway for asperthecin.
Cloning of the
Trichoderma reesei
cDNA Encoding a Glucuronan Lyase Belonging to a Novel Polysaccharide Lyase Family
Authors: Konno Naotake , Igarashi Kiyohiko , Habu Naoto , Samejima Masahiro , Isogai Akira 
Published: November 2008

ABSTRACT

The filamentous fungus
Trichoderma reesei
produces glucuronan lyase (TrGL) when it is grown on β-(1→4)-polyglucuronate (cellouronate) as a sole carbon source. The cDNA encoding TrGL was cloned, and the recombinant enzyme was heterologously expressed in
Pichia pastoris
. The cDNA of TrGL includes a 777-bp open reading frame encoding a 20-amino-acid signal peptide and the 238-amino-acid mature protein. The amino acid sequence showed no similarity to the amino acid sequences of previously described functional proteins, indicating that the enzyme should be classified in a novel polysaccharide lyase (PL) family. Recombinant TrGL catalyzed depolymerization of cellouronate endolytically by β-elimination and was highly specific for cellouronate. The enzyme was most active at pH 6.5 and 50°C, and its activity and thermostability increased in the presence of Ca
2+
, suggesting that its calcium dependence is similar to that of other PLs, such as pectate lyases.
Case-Control Study To Determine whether River Water Can Spread Tetracycline Resistance to Unexposed Impala (
Aepyceros melampus
) in Kruger National Park (South Africa)
Authors: Mariano V. , McCrindle C. M. E. , Cenci-Goga B. , Picard J. A. 
Published: November 2008

ABSTRACT

A case-control study was performed in the Kruger National Park (KNP), South Africa, to find out whether impala (
Aepyceros melampus
) were more likely to harbor tetracycline-resistant
Escherichia coli
(TREC) in their feces when they drank from rivers that contained these bacteria than when they drank from rivers that were uncontaminated with TREC. The following five perennial rivers were selected: the Crocodile, the Letaba, the Olifants, the Sabie, and the Sand. Samples of river water (
n
= 33) and feces (
n
= 209), collected at 11 different sites, were cultured for
E. coli.
The resulting colonies were screened for tetracycline resistance by use of the Lederberg replica plating method (breakpoint, 4 mg/liter). A resistant and/or a susceptible isolate was then selected from each sample and subjected to the CLSI MIC broth microdilution test for tetracyclines. Among the 21 water specimens contaminated by
E. coli
, 19.05% (
n
= 4) were found to be resistant by the MIC method (breakpoint, ≥8 mg/liter). This led to the Crocodile, Olifants, and Letaba rivers being classified as TREC positive. Among the 209 impala feces sampled, 191 were positive for the presence of
E. coli
(91.38%). Within these (
n
= 191), 9.95% (
n
= 19) of the isolates were shown to be TREC by the MIC method. It was found that 1.11% (
n
= 1) of the
E. coli
isolates cultured from the feces of the control group (
n
= 90) were TREC, in comparison with 17.82% (
n
= 18) of those in feces from the exposed group (
n
= 101). The calculation of the odds ratio showed that impala drinking from TREC-contaminated rivers were 19.3 (2.63 to 141.69) times more likely to be infected with TREC than were unexposed impala. This is a significant finding, indicating that surface water could be a possible source of antimicrobial resistance in naïve animal populations and that impala could act as sentinels for antimicrobial resistance.
Detection and Characterization of the Fimbrial
sfp
Cluster in Enterohemorrhagic
Escherichia coli
O165:H25/NM Isolates from Humans and Cattle
Authors: Bielaszewska Martina , Prager Rita , Vandivinit Liz , Müsken Anne , Mellmann Alexander , Holt Nicholas J. , Tarr Phillip I. , Karch Helge , Zhang Wenlan 
Published: November 2008

ABSTRACT

The
sfp
cluster, encoding Sfp fimbriae and located in the large plasmid of sorbitol-fermenting (SF) enterohemorrhagic
Escherichia coli
(EHEC) O157 (pSFO157), has been considered a unique characteristic of this organism. We discovered and then characterized the
sfp
cluster in EHEC O165:H25/NM (nonmotile) isolates of human and bovine origin. All seven strains investigated harbored a complete
sfp
cluster (carrying
sfpA
,
sfpH
,
sfpC
,
sfpD
,
sfpJ
,
sfpF
, and
sfpG
) of 6,838 bp with >99% nucleotide sequence homology to the
sfp
cluster of SF EHEC O157:NM. The
sfp
cluster in EHEC O165:H25/NM strains was located in an ∼80-kb (six strains) or ∼120-kb (one strain) plasmid which differed in structure, virulence genes, and
sfp
flanks from pSFO157. All O165:H25/NM strains belonged to the same multilocus sequence type (ST119) and were only distantly phylogenetically related to SF EHEC O157:NM (ST11). The highly conserved
sfp
cluster in different clonal backgrounds suggests that this segment was acquired independently by EHEC O165:H25 and SF EHEC O157:NM. Its presence in an additional EHEC serotype extends the diagnostic utility of PCR targeting
sfpA
as an easy and efficient approach to seek EHEC in patients' stools. The reasons for the convergence of pathogenic EHEC strains on a suite of virulence loci remain unknown.
Genetic Diversity and Ecological Success of
Staphylococcus aureus
Strains Colonizing Humans
Authors: Sakwinska Olga , Kuhn Gerrit , Balmelli Carlo , Francioli Patrick , Giddey Marlyse , Perreten Vincent , Riesen Andrea , Zysset Frédéric , Blanc Dominique S. , Moreillon Philippe 
Published: November 2008

ABSTRACT

The genetic determinants and phenotypic traits which make a
Staphylococcus aureus
strain a successful colonizer are largely unknown. The genetic diversity and population structure of 133
S. aureus
isolates from healthy, generally risk-free adult carriers were investigated using four different typing methods: multilocus sequence typing (MLST), amplified fragment length polymorphism analysis (AFLP), double-locus sequence typing (DLST), and
spa
typing were compared. Carriage isolates displayed great genetic diversity which could only be revealed fully by DLST. Results of AFLP and MLST were highly concordant in the delineation of genotypic clusters of closely related isolates, roughly equivalent to clonal complexes.
spa
typing and DLST provided considerably less phylogenetic information. The resolution of
spa
typing was similar to that of AFLP and inferior to that of DLST. AFLP proved to be the most universal method, combining a phylogeny-building capacity similar to that of MLST with a much higher resolution. However, it had a lower reproducibility than sequencing-based MLST, DLST, and
spa
typing. We found two cases of methicillin-resistant
S. aureus
colonization, both of which were most likely associated with employment at a health service. Of 21 genotypic clusters detected, 2 were most prevalent: cluster 45 and cluster 30 each colonized 24% of the carrier population. The number of bacteria found in nasal samples varied significantly among the clusters, but the most prevalent clusters were not particularly numerous in the nasal samples. We did not find much evidence that genotypic clusters were associated with different carrier characteristics, such as age, sex, medical conditions, or antibiotic use. This may provide empirical support for the idea that genetic clusters in bacteria are maintained in the absence of adaptation to different niches. Alternatively, carrier characteristics other than those evaluated here or factors other than human hosts may exert selective pressure maintaining genotypic clusters.
UV Disinfection of Adenoviruses: Molecular Indications of DNA Damage Efficiency
Authors: Eischeid Anne C. , Meyer Joel N. , Linden Karl G. 
Published: November 2008

ABSTRACT
Adenovirus is a focus of the water treatment community because of its resistance to standard, monochromatic low-pressure (LP) UV irradiation. Recent research has shown that polychromatic, medium-pressure (MP) UV sources are more effective than LP UV for disinfection of adenovirus when viral inactivation is measured using cell culture infectivity assays; however, UV-induced DNA damage may be repaired during cell culture infectivity assays, and this confounds interpretation of these results. Objectives of this work were to study adenoviral response to both LP and MP UV using (i) standard cell culture infectivity assays and (ii) a PCR assay to directly assess damage to the adenoviral genome without introducing the virus into cell culture. LP and MP UV dose response curves were determined for (i) log inactivation of the virus in cell culture and (ii) UV-induced lesions per kilobase of viral DNA as measured by the PCR assay. Results show that LP and MP UV are equally effective at damaging the genome; MP UV is more effective at inactivating adenovirus in cell culture. This work suggests that the higher disinfection efficacy of MP UV cannot be attributed to a difference in DNA damage induction. These results enhance our understanding of the fundamental mechanisms of UV disinfection of viruses—especially double-stranded DNA viruses that infect humans—and improve the ability of the water treatment community to protect public health.