bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photosensitivity skin disorders in childhood
Authors: Horkay Irene , Emri Gabriella , Varga Viktoria , Simics Eniko , Remenyik Eva 
Published: March 2008

SummaryPhotosensitivity in childhood is caused by a diverse group of diseases. It usually indicates idiopathic photodermatoses, first of all polymorphic light eruption. It may be an early symptom of genetic disorders such as porphyria or very rare genophotodermatoses. Photosensitivity secondary to topical or systemic external agents as well as photoexacerbated dermatoses is not so frequent in childhood. Here we present our experience with childhood photosensitivity skin diseases collected over a 40‐year period.
Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil
Authors: Peng Jingjing , Lü Zhe , Rui Junpeng , Lu Yahai 
Published: March 2008

ABSTRACT

Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH
4
production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15°C, 30°C, and 45°C). More CH
4
was produced in the straw treatment than root treatment. Increasing the temperature from 15°C to 45°C enhanced CH
4
production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that
Methanosarcinaceae
developed early in the incubations, whereas
Methanosaetaceae
became more abundant in the later stages.
Methanosarcinaceae
and
Methanosaetaceae
seemed to be better adapted at 15°C and 30°C, respectively, while the thermophilic
Methanobacteriales
and rice cluster I methanogens were significantly enhanced at 45°C. Straw residues promoted the growth of
Methanosarcinaceae
, whereas the root residues favored
Methanosaetaceae
. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H
2
) seems to be the key factor that regulates the shift of methanogenic community.
Genomic Insights into Mn(II) Oxidation by the Marine Alphaproteobacterium
Aurantimonas
sp. Strain SI85-9A1
Authors: Dick Gregory J. , Podell Sheila , Johnson Hope A. , Rivera-Espinoza Yadira , Bernier-Latmani Rizlan , McCarthy James K. , Torpey Justin W. , Clement Brian G. , Gaasterland Terry , Tebo Bradley M. 
Published: March 2008

ABSTRACT

Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium
Aurantimonas
sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O
2
concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca
2+
-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.
Microbes Enriched in Seawater after Addition of Coral Mucus
Authors: Allers Elke , Niesner Christina , Wild Christian , Pernthaler Jakob 
Published: March 2008

ABSTRACT

We investigated which microbial taxa in coastal Red Sea water were stimulated by addition of mucus from the coral
Fungia
sp. Decreases in the concentration and C/N ratio of particulate organic material during short-term incubations (50 h) were paralleled by a steep rise in the number of
Gammaproteobacteria
, particularly
Alteromonadaceae
, followed by
Vibrionaceae
. Two almost identical genotypes affiliated with
Alteromonas macleodii
accounted for up to >85% of all
Alteromonadaceae
(45% of the total cells) in the mucus-amended enrichments but were rare in unamended control incubations and in ambient seawater.
A. macleodii
-like bacteria might thus be important in the transfer of organic carbon from coral mucus to the pelagic microbial food webs of coral reefs.
Identification and Onion Pathogenicity of
Burkholderia cepacia
Complex Isolates from the Onion Rhizosphere and Onion Field Soil
Authors: Jacobs Janette L. , Fasi Anthony C. , Ramette Alban , Smith James J. , Hammerschmidt Raymond , Sundin George W. 
Published: March 2008

ABSTRACT

Burkholderia cepacia
complex strains are genetically related but phenotypically diverse organisms that are important opportunistic pathogens in patients with cystic fibrosis (CF,) as well as pathogens of onion and banana, colonizers of the rhizospheres of many plant species, and common inhabitants of bulk soil. Genotypic identification and pathogenicity characterization were performed on
B. cepacia
complex isolates from the rhizosphere of onion and organic soils in Michigan. A total of 3,798 putative
B. cepacia
complex isolates were recovered on
Pseudomonas cepacia
azelaic acid tryptamine and trypan blue tetracycline semiselective media during the 2004 growing season from six commercial onion fields located in two counties in Michigan. Putative
B. cepacia
complex isolates were identified by hybridization to a 16S rRNA gene probe, followed by duplex PCR using primers targeted to the 16S rRNA gene and
recA
sequences and restriction fragment length polymorphism analysis of the
recA
sequence. A total of 1,290 isolates, 980 rhizosphere and 310 soil isolates, were assigned to the species
B. cepacia
(160),
B. cenocepacia
(480),
B. ambifaria
(623), and
B. pyrrocinia
(27). The majority of isolates identified as
B. cepacia
(85%),
B. cenocepacia
(90%), and
B. ambifaria
(76%) were pathogenic in a detached onion bulb scale assay and caused symptoms of water soaking, maceration, and/or necrosis. A phylogenetic analysis of
recA
sequences from representative
B. cepacia
complex type and panel strains, along with isolates collected in this study, revealed that the
B. cenocepacia
isolates associated with onion grouped within the III-B lineage and that some strains were closely related to strain AU1054, which was isolated from a CF patient. This study revealed that multiple
B. cepacia
complex species colonize the onion rhizosphere and have the potential to cause sour skin rot disease of onion. In addition, the onion rhizosphere is a natural habitat and a potential environmental source of
B. cenocepacia
.
Impact of Nitrate on the Structure and Function of Bacterial Biofilm Communities in Pipelines Used for Injection of Seawater into Oil Fields
Authors: Schwermer Carsten U. , Lavik Gaute , Abed Raeid M. M. , Dunsmore Braden , Ferdelman Timothy G. , Stoodley Paul , Gieseke Armin , de Beer Dirk 
Published: March 2008

ABSTRACT

We studied the impact of NO
3
−
on the bacterial community composition, diversity, and function in in situ industrial, anaerobic biofilms by combining microsensor profiling,
15
N and
35
S labeling, and 16S rRNA gene-based fingerprinting. Biofilms were grown on carbon steel coupons within a system designed to treat seawater for injection into an oil field for pressurized oil recovery. NO
3
−
was added to the seawater in an attempt to prevent bacterial H
2
S generation and microbially influenced corrosion in the field. Microprofiling of nitrogen compounds and redox potential inside the biofilms showed that the zone of highest metabolic activity was located close to the metal surface, correlating with a high bacterial abundance in this zone. Upon addition, NO
3
−
was mainly reduced to NO
2
−
. In biofilms grown in the absence of NO
3
−
, redox potentials of <−450 mV at the metal surface suggested the release of Fe
2+
. NO
3
−
addition to previously untreated biofilms induced a decline (65%) in bacterial species richness, with
Methylophaga
- and
Colwellia
-related sequences having the highest number of obtained clones in the clone library. In contrast, no changes in community composition and potential NO
3
−
reduction occurred upon subsequent withdrawal of NO
3
−
. Active sulfate reduction was below detection levels in all biofilms, but S isotope fractionation analysis of sulfide deposits suggested that it must have occurred either at low rates or episodically. Scanning electron microscopy revealed that pitting corrosion occurred on all coupons, independent of the treatment. However, uniform corrosion was clearly mitigated by NO
3
−
addition.
Estimates of Biogenic Methane Production Rates in Deep Marine Sediments at Hydrate Ridge, Cascadia Margin
Authors: Colwell F. S. , Boyd S. , Delwiche M. E. , Reed D. W. , Phelps T. J. , Newby D. T. 
Published: March 2008

ABSTRACT

Methane hydrate found in marine sediments is thought to contain gigaton quantities of methane and is considered an important potential fuel source and climate-forcing agent. Much of the methane in hydrates is biogenic, so models that predict the presence and distribution of hydrates require accurate rates of in situ methanogenesis. We estimated the in situ methanogenesis rates in Hydrate Ridge (HR) sediments by coupling experimentally derived minimal rates of methanogenesis to methanogen biomass determinations for discrete locations in the sediment column. When starved in a biomass recycle reactor,
Methanoculleus submarinus
produced ca. 0.017 fmol methane/cell/day. Quantitative PCR (QPCR) directed at the methyl coenzyme M reductase subunit A gene (
mcrA
) indicated that 75% of the HR sediments analyzed contained <1,000 methanogens/g. The highest numbers of methanogens were found mostly from sediments <10 m below seafloor. By considering methanogenesis rates for starved methanogens (adjusted to account for in situ temperatures) and the numbers of methanogens at selected depths, we derived an upper estimate of <4.25 fmol methane produced/g sediment/day for the samples with fewer methanogens than the QPCR method could detect. The actual rates could vary depending on the real number of methanogens and various seafloor parameters that influence microbial activity. However, our calculated rate is lower than rates previously reported for such sediments and close to the rate derived using geochemical modeling of the sediments. These data will help to improve models that predict microbial gas generation in marine sediments and determine the potential influence of this source of methane on the global carbon cycle.
Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics
Authors: Sagova-Mareckova Marketa , Cermak Ladislav , Novotna Jitka , Plhackova Kamila , Forstova Jana , Kopecky Jan 
Published: March 2008

ABSTRACT

Seven methods of soil DNA extraction and purification were tested in a set of 14 soils differing in bedrock, texture, pH, salinity, moisture, organic matter content, and vegetation cover. The methods introduced in this study included pretreatment of soil with CaCO
3
or purification of extracted DNA by CaCl
2
. The performance of innovated methods was compared to that of the commercial kit Mo Bio PowerSoil and the phenol-chloroform-based method of D. N. Miller, J. E. Bryant, E. L. Madsen, and W. C. Ghiorse (Appl. Environ. Microbiol. 65:4715-4724, 1999). This study demonstrated significant differences between the tested methods in terms of DNA yield, PCR performance, and recovered bacterial diversity. The differences in DNA yields were correlated to vegetation cover, soil pH, and clay content. The differences in PCR performances were correlated to vegetation cover and soil pH. The innovative methods improved PCR performance in our set of soils, in particular for forest acidic soils. PCR was successful in 95% of cases by the method using CaCl
2
purification and in 93% of cases by the method based on CaCO
3
pretreatment, but only in 79% by Mo Bio PowerSoil, for our range of soils. Also, the innovative methods recovered a higher percentage of actinomycete diversity from a subset of three soils. Recommendations include the assessment of soil characteristics prior to selecting the optimal protocol for soil DNA extraction and purification.
Rapid Differentiation of Phenotypically Similar Yeast Species by Single-Strand Conformation Polymorphism Analysis of Ribosomal DNA
Authors: Wang Qi-Ming , Li Juan , Wang Shi-An , Bai Feng-Yan 
Published: March 2008

ABSTRACT

Single-strand conformation polymorphism (SSCP) analysis of ribosomal DNA (rDNA) was investigated for rapid differentiation of phenotypically similar yeast species. Sensitive tests indicated that some yeast strains with one, most strains with two, and all strains with three or more nucleotide differences in the internal transcribed spacer 1 (ITS1) or ITS2 region could be distinguished by PCR SSCP analysis. The discriminative power of SSCP in yeast species differentiation was demonstrated by comparative studies of representative groups of yeast species from ascomycetes and basidiomycetes, including
Saccharomyces
species, medically important
Candida
species, and phylloplane basidiomycetous yeast species. Though the species within each group selected are closely related and have relatively similar rDNA sequences, they were clearly differentiated by PCR-SSCP analysis of the ITS1 region, given the amplified fragments were less than 350 bp in sizes. By using SSCP analysis for rapid screening of yeast strains with different rDNA sequences, species diversity existing in a large collection of yeast strains from natural sources was effectively and thoroughly investigated with substantially reduced time and cost in subsequent DNA sequencing.
Ecological Dynamics of the Toxic Bloom-Forming Cyanobacterium
Microcystis aeruginosa
and Its Cyanophages in Freshwater
Authors: Yoshida Mitsuhiro , Yoshida Takashi , Kashima Aki , Takashima Yukari , Hosoda Naohiko , Nagasaki Keizo , Hiroishi Shingo 
Published: March 2008

ABSTRACT

The abundance of potentially
Microcystis aeruginosa
-infectious cyanophages in freshwater was studied using
g91
real-time PCR. A clear increase in cyanophage abundance was observed when
M. aeruginosa
numbers declined, showing that these factors were significantly negatively correlated. Furthermore, our data suggested that cyanophage dynamics may also affect shifts in microcystin-producing and non-microcystin-producing populations.
Effect of Wastewater Treatment Plant Effluent on Microbial Function and Community Structure in the Sediment of a Freshwater Stream with Variable Seasonal Flow
Authors: Wakelin Steven A. , Colloff Matt J. , Kookana Rai S. 
Published: March 2008

ABSTRACT

We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification of genes involved in the biogeochemical cycling of carbon and nitrogen was used to assess potential impacts on ecosystem functions. The effects of disturbance on bacterial community structure were assessed by PCR-denaturing gradient gel electrophoresis of 16S rRNA genes, and clone library analysis was used to phylogenetically characterize significant shifts. Significant (
P
< 0.05) shifts in bacterial community structures were associated with alteration of the sediment's physicochemical properties, particularly nutrient loading from the WWTP discharge. The effects were greatest at the sampling location 400 m downstream of the outfall where the stream flow is reduced. This highly affected stretch of sediment contained representatives of the gammaproteobacteria that were absent from less-disturbed sites, including
Oceanospirillales
and
Methylococcaceae
. 16S rRNA gene sequences from less-disturbed sites had representatives of the
Caulobacteraceae
,
Sphingomonadaceae
, and
Nitrospirae
which were not represented in samples from disturbed sediment. The diversity was lowest at the reference site; it increased with proximity to the WWTP outfall and declined toward highly disturbed (400 m downstream) sites (
P
< 0.05). The potential for biological transformations of N varied significantly with the stream sediment location (
P
< 0.05). The abundance of
amoA
,
narG
, and
nifH
genes increased with the distance downstream of the outfall. These processes are driven by N and C availability, as well as redox conditions. Together these data suggest cause and effect between nutrient loading into the creek, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of N.
Metabolic Engineering of
Escherichia coli
for
l
-Tyrosine Production by Expression of Genes Coding for the Chorismate Mutase Domain of the Native Chorismate Mutase-Prephenate Dehydratase and a Cyclohexadienyl Dehydrogenase from
Zymomonas mobilis
Authors: Chávez-Béjar María I. , Lara Alvaro R. , López Hezraí , Hernández-Chávez Georgina , Martinez Alfredo , Ramírez Octavio T. , Bolívar Francisco , Gosset Guillermo 
Published: March 2008

ABSTRACT

The expression of the feedback inhibition-insensitive enzyme cyclohexadienyl dehydrogenase (TyrC) from
Zymomonas mobilis
and the chorismate mutase domain from native chorismate mutase-prephenate dehydratase (PheA
CM
) from
Escherichia coli
was compared to the expression of native feedback inhibition-sensitive chorismate mutase-prephenate dehydrogenase (CM-TyrA
p
) with regard to the capacity to produce
l
-tyrosine in
E. coli
strains modified to increase the carbon flow to chorismate. Shake flask experiments showed that TyrC increased the yield of
l
-tyrosine from glucose (

Y

l
-Tyr/Glc

) by 6.8-fold compared to the yield obtained with CM-TyrA
p
. In bioreactor experiments, a strain expressing both TyrC and PheA
CM
produced 3 g/liter of
l
-tyrosine with a

Y

l
-Tyr/Glc

of 66 mg/g. These values are 46 and 48% higher than the values for a strain expressing only TyrC. The results show that the feedback inhibition-insensitive enzymes can be employed for strain development as part of a metabolic engineering strategy for
l
-tyrosine production.
Empirical Evaluation of a New Method for Calculating Signal-to-Noise Ratio for Microarray Data Analysis
Authors: He Zhili , Zhou Jizhong 
Published: March 2008

ABSTRACT

Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect-match (PM) and mismatch (MM) probes based upon four genes from
Shewanella oneidensis
MR-1. A new SNR calculation, called the signal-to-both-standard-deviations ratio (SSDR), was developed and evaluated, along with other two methods, the signal-to-standard-deviation ratio (SSR) and the signal-to-background ratio (SBR). At a low stringency, the thresholds of the SSR, SBR, and SSDR were 2.5, 1.60, and 0.80 with an oligonucleotide and a PCR amplicon as target templates and 2.0, 1.60, and 0.70 with genomic DNAs as target templates. Slightly higher thresholds were obtained under high-stringency conditions. The thresholds of the SSR and SSDR decreased with an increase in the complexity of targets (e.g., target types) and the presence of background DNA and a decrease in the compositions of targets, while the SBR remained unchanged in all situations. The lowest percentage of false positives and false negatives was observed with the SSDR calculation method, suggesting that it may be a better SNR calculation for more accurate determination of SNR thresholds. Positive spots identified by SNR thresholds were verified by the Student
t
test, and consistent results were observed. This study provides general guidance for users to select appropriate SNR thresholds for different samples under different hybridization conditions.
Relative Abundance ofBacteroidesspp. in Stools and Wastewaters as Determined by Hierarchical Oligonucleotide Primer Extension
Authors: Hong Pei-Ying , Wu Jer-Horng , Liu Wen-Tso 
Published: March 2008

ABSTRACTA molecular method, termed hierarchical oligonucleotide primer extension (HOPE), was used to determine the relative abundances of predominantBacteroidesspp. present in fecal microbiota and wastewaters. For this analysis, genomic DNA in feces of healthy human adults, bovines, and swine and in wastewaters was extracted and total bacterial 16S rRNA genes were PCR amplified and used as the DNA templates for HOPE. Nineteen oligonucleotide primers were designed to detect 14Bacteroidesspp. at different hierarchical levels (domain, order, cluster, and species) and were arranged into and used in six multiplex HOPE reaction mixtures. Results showed that species likeB. vulgatus,B. thetaiotaomicron,B. caccae,B. uniformis,B. fragilis,B. eggerthii, andB. massiliensiscould be individually detected in human feces at abundances corresponding to as little as 0.1% of PCR-amplified 16S rRNA genes. Minor species likeB. pyogenes,B. salyersiae, andB. nordiiwere detected only collectively using a primer that targeted theB. fragilissubgroup (corresponding to ∼0.2% of PCR-amplified 16S rRNA genes). Furthermore, Bac303-related targets (i.e., mostBacteroidales) were observed to account for 28 to 44% of PCR-amplified 16S rRNA genes from human fecal microbiota, and their abundances were higher than those detected in the bovine and swine fecal microbiota and in wastewaters by factors of five and two, respectively. These results were comparable to those obtained by quantitative PCR and to those reported previously from studies using whole-cell fluorescence hybridization and 16S rRNA clone library methods, supporting the conclusion that HOPE can be a sensitive, specific, and rapid method to determine the relative abundances ofBacteroidesspp. predominant in fecal samples.