bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simplified Method for Optimal Sensor Distribution for Process Fault Diagnosis in Multistation Assembly Processes
Authors: Xinmin Lai , Zhaoqing Tian , Zhongqin Lin 
Published: September 2008

Abstract
The fault diagnosis plays an important role for product quality improvement in the multistation assembly processes (MAPs) and the efficiency of diagnosis significantly depends on the sensor distribution strategy, such as the number and location of the sensor. The diagnosis-oriented sensor distribution optimization in MAP has been studied for the purpose of a full diagnosis of the process faults with the minimum sensing stations number as well as the minimum sensor number. However, the existing studies are time consuming with the complex analysis and calculation processes, and no intuitive principles are given directly according to the process configuration. In this paper, a simplified method for the optimal sensor distribution is presented for a fully diagnosis of the process faults. First, two different types of assembly modes are defined and the variation transmissibility ratios for these two assembly modes are discussed based on the process configuration. Then, the conditions for between-station diagnosability and within-station diagnosability are analyzed, respectively. Based on the results, the optimal sensor distribution method is derived finally. After comparing with the former methods, the optimal sensor distribution in this paper is based only on the process configuration without using for model-based matrix computation. Therefore, the proposed method greatly simplified the process.
Characterization of the Community Structure of a Dechlorinating Mixed Culture and Comparisons of Gene Expression in Planktonic and Biofloc-Associated “Dehalococcoides” andMethanospirillumSpecies
Authors: Rowe Annette R. , Lazar Brendan J. , Morris Robert M. , Richardson Ruth E. 
Published: September 2008

ABSTRACTThis study sought to characterize bacterial and archaeal populations in a perchloroethene- and butyrate-fed enrichment culture containing hydrogen-consuming “Dehalococcoides ethenogenes” strain 195 and aMethanospirillum hungateistrain. Phylogenetic characterization of this microbial community was done via 16S rRNA gene clone library and gradient gel electrophoresis analyses. Fluorescence in situ hybridization was used to quantify populations of “Dehalococcoides” andArchaeaand to examine the colocalization of these two groups within culture bioflocs. A technique for enrichment of planktonic and biofloc-associated biomass was developed and used to assess differences in population distribution and gene expression patterns following provision of substrate. On a per-milliliter-of-culture basis, mostD. ethenogenesgenes (the hydrogenase genehupL; the highly expressed gene for an oxidoreductase of unknown function,fdhA; the RNA polymerase subunit generpoB; and the 16S rRNA gene) showed no statistical difference in expression between planktonic and biofloc enrichments at either time point studied (1 to 2 and 6 h postfeeding). Normalization of transcripts to ribosome (16S rRNA) levels supported that planktonic and biofloc-associatedD. ethenogeneshad similar gene expression profiles, with one notable exception; planktonicD. ethenogenesshowed higher expression oftceArelative to biofloc-associated cells at 6 h postfeeding. These trends were compared to those for the hydrogen-consuming methanogen in the culture,M. hungatei. The vast majority ofM. hungateicells, ribosomes (16S rRNA), and transcripts of the hydrogenase genemvrDand the housekeeping generpoEwere observed in the biofloc enrichments. This suggests that, unlike the comparable activity ofD. ethenogenesfrom both enrichments, planktonicM. hungateiis responsible for only a small fraction of the hydrogenotrophic methanogenesis in this culture.
Novel Carotenoid-Based Biosensor for Simple Visual Detection of Arsenite: Characterization and Preliminary Evaluation for Environmental Application
Authors: Yoshida Kazuyuki , Inoue Koichi , Takahashi Yuko , Ueda Shunsaku , Isoda Katsuhiro , Yagi Kiyohito , Maeda Isamu 
Published: September 2008

ABSTRACT

A novel whole-cell arsenite biosensor was developed using the photosynthetic bacterium
Rhodopseudomonas palustris
no. 7 and characterized. A sensor plasmid containing the operator-promoter region of the
ars
operon and
arsR
gene from
Escherichia coli
and the
crtI
gene from
R. palustris
no. 7 was introduced into a blue-green mutant with
crtI
deleted,
R. palustris
no. 711. The biosensor changed color in response to arsenite, and the change was obvious to the naked eye after 24 h without further manipulation. Real-time reverse transcription-PCR showed that the
crtI
mRNA was induced 3-fold at 3 h and 2.5-fold at 6 h after addition of 50 μg/liter arsenite compared with the no-arsenite control, and consistent with this, the relative levels of lycopene and rhodopin also increased compared with the control. Colorimetric analysis of the bacteria showed that the hue angle had clearly shifted from green-yellow toward red in an arsenic dose-dependent manner at 24 h after arsenite addition. This obvious shift occurred irrespective of the culture conditions before arsenite was added, indicating that the color change of the biosensor is stable in water samples containing various concentrations of dissolved oxygen. Finally, assays using samples prepared in various types of mineral water indicated that this biosensor could be used to screen groundwater samples for the presence of arsenite in a variety of locations, even where electricity is not available.
Phylogenetic Comparison of the Methanogenic Communities from an Acidic, Oligotrophic Fen and an Anaerobic Digester Treating Municipal Wastewater Sludge
Authors: Steinberg Lisa M. , Regan John M. 
Published: September 2008

ABSTRACT

Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (
mcrA
) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and
mcrA
within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for
mcrA
within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the
Methanomicrobiales
, although members of the
Methanosarcinales
and
Methanobacteriales
were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both
mcrA
libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.
AbiV, a Novel Antiphage Abortive Infection Mechanism on the Chromosome of
Lactococcus lactis
subsp.
cremoris
MG1363
Authors: Haaber Jakob , Moineau Sylvain , Fortier Louis-Charles , Hammer Karin 
Published: September 2008

ABSTRACT

Insertional mutagenesis with pGhost9::IS
S1
resulted in independent insertions in a 350-bp region of the chromosome of
Lactococcus lactis
subsp.
cremoris
MG1363 that conferred phage resistance to the integrants. The orientation and location of the insertions suggested that the phage resistance phenotype was caused by a chromosomal gene turned on by a promoter from the inserted construct. Reverse transcription-PCR analysis confirmed that there were higher levels of transcription of a downstream open reading frame (ORF) in the phage-resistant integrants than in the phage-sensitive strain
L. lactis
MG1363. This gene was also found to confer phage resistance to
L. lactis
MG1363 when it was cloned into an expression vector. A subsequent frameshift mutation in the ORF completely eliminated the phage resistance phenotype, confirming that the ORF was necessary for phage resistance. This ORF provided resistance against virulent lactococcal phages belonging to the 936 and c2 species with an efficiency of plaquing of 10
−4
, but it did not protect against members of the P335 species. A high level of expression of the ORF did not affect the cellular growth rate. Assays for phage adsorption, DNA ejection, restriction/modification activity, plaque size, phage DNA replication, and cell survival showed that the ORF encoded an abortive infection (Abi) mechanism. Sequence analysis revealed a deduced protein consisting of 201 amino acids which, in its native state, probably forms a dimer in the cytosol. Similarity searches revealed no homology to other phage resistance mechanisms, and thus, this novel Abi mechanism was designated AbiV. The mode of action of AbiV is unknown, but the activity of AbiV prevented cleavage of the replicated phage DNA of 936-like phages.
In Situ Detection of Freshwater Fungi in an Alpine Stream by New Taxon-Specific Fluorescence In Situ Hybridization Probes
Authors: Baschien Christiane , Manz Werner , Neu Thomas R. , Marvanová Ludmila , Szewzyk Ulrich 
Published: September 2008

ABSTRACT

New rRNA-targeting oligonucleotide probes permitted the fluorescence in situ hybridization (FISH) identification of freshwater fungi in an Austrian second-order alpine stream. Based on computer-assisted comparative sequence analysis, nine taxon-specific probes were designed and evaluated by whole-fungus hybridizations. Oligonucleotide probe MY1574, specific for a wide range of
Eumycota
, and the genus (
Tetracladium
)-specific probe TCLAD1395, as well as the species-specific probes ALacumi1698 (
Alatospora acuminata
), TRIang322 (
Tricladium angulatum
), and Alongi340 (
Anguillospora longissima
), are targeted against 18S rRNA, whereas probes TmarchB10, TmarchC1_1, TmarchC1_2, and AlongiB16 are targeted against the 28S rRNA of
Tetracladium marchalianum
and
Anguillospora longissima
, respectively. After 2 weeks and 3 months of exposure of polyethylene slides in the stream, attached germinating conidia and growing hyphae of freshwater fungi were accessible for FISH. Growing hyphae and germinating conidia on leaves and in membrane cages were also visualized by the new FISH probes.
Hydrogenomics of the Extremely Thermophilic Bacterium
Caldicellulosiruptor saccharolyticus
Authors: van de Werken Harmen J. G. , Verhaart Marcel R. A. , VanFossen Amy L. , Willquist Karin , Lewis Derrick L. , Nichols Jason D. , Goorissen Heleen P. , Mongodin Emmanuel F. , Nelson Karen E. , van Niel Ed W. J. , Stams Alfons J. M. , Ward Donald E. , de Vos Willem M. , van der Oost John , Kelly Robert M. , Kengen Servé W. M. 
Published: September 2008

ABSTRACT

Caldicellulosiruptor saccharolyticus
is an extremely thermophilic, gram-positive anaerobe which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO
2
, and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to coutilize glucose and xylose make this bacterium an attractive candidate for microbial bioenergy production. Here, the complete genome sequence of
C. saccharolyticus
, consisting of a 2,970,275-bp circular chromosome encoding 2,679 predicted proteins, is described. Analysis of the genome revealed that
C. saccharolyticus
has an extensive polysaccharide-hydrolyzing capacity for cellulose, hemicellulose, pectin, and starch, coupled to a large number of ABC transporters for monomeric and oligomeric sugar uptake. The components of the Embden-Meyerhof and nonoxidative pentose phosphate pathways are all present; however, there is no evidence that an Entner-Doudoroff pathway is present. Catabolic pathways for a range of sugars, including rhamnose, fucose, arabinose, glucuronate, fructose, and galactose, were identified. These pathways lead to the production of NADH and reduced ferredoxin. NADH and reduced ferredoxin are subsequently used by two distinct hydrogenases to generate hydrogen. Whole-genome transcriptome analysis revealed that there is significant upregulation of the glycolytic pathway and an ABC-type sugar transporter during growth on glucose and xylose, indicating that
C. saccharolyticus
coferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks is a highly desirable feature of this lignocellulose-utilizing, biofuel-producing bacterium.
Formulation of a Defined V8 Medium for Induction of Sexual Development of
Cryptococcus neoformans
Authors: Kent Cory R. , Ortiz-Bermúdez Patricia , Giles Steven S. , Hull Christina M. 
Published: September 2008

ABSTRACT

For over 3 decades, sexual development in the human fungal pathogen
Cryptococcus neoformans
and other fungi has been initiated by growing compatible mating partners on V8 juice medium. Although this medium is an efficient inducer of sexual development, the mechanism by which it promotes the process is unknown. To understand how V8 juice medium induces sexual development, we attempted to purify inducing factors from V8 juice, and we carried out a complete compositional analysis of V8 juice. We discovered that no single factor is responsible for the effects of V8 juice medium. Rather, the unique composition of V8 juice medium provides the proper nutrient composition for inducing and sustaining complete sexual development. Utilizing these findings, we developed a defined V8 (DV8) medium that mimics V8 juice medium in sexual development assays. Then, using DV8 as a tool, we explored the roles that specific molecules play in enhancing sexual development. Surprisingly, we discovered that copper is a key factor, leading to an upregulation of the mating pheromone genes
MF

a

and
MF
α, both required for the initial steps in sexual development. The utilization of DV8 to investigate the effects of copper on sexual development presented here is an example of how defining the conditions that induce sexual development will advance the study of
C. neoformans
.
Occurrence of Free-Living Amoebae in Communities of Low and High Endemicity for Buruli Ulcer in Southern Benin
Authors: Eddyani Miriam , De Jonckheere Johan F. , Durnez Lies , Suykerbuyk Patrick , Leirs Herwig , Portaels Françoise 
Published: September 2008

ABSTRACT

Buruli ulcer or
Mycobacterium ulcerans
disease occurs mainly in areas in proximity to standing or slowly running freshwater, habitats in which free-living amoebae occur. For this reason, a possible link between the habitat of
M. ulcerans
and free-living amoebae was investigated. Free-living amoebae and mycobacteria were isolated from water and biofilm specimens taken from protected and unprotected sources of water in villages known to have either high or low endemicity for Buruli ulcer in Benin. Amoebae were isolated from 78.8% of samples. A greater proportion of water bodies in areas of high endemicity had amoebae than in areas of low endemicity (83.3% versus 66.7%). Protected sources of water were significantly more likely to contain amoebae in areas of high endemicity than in areas of low endemicity (88.0% versus 11.1%). Several pathogenic free-living amoebae and mycobacteria were isolated. However, no
M. ulcerans
was isolated and no specimen was positive for IS
2404
PCR. Our results show that the study area has a water hygiene problem, which is greater in areas of high Buruli ulcer endemicity than in areas of low endemicity. Our observations indicate that additional studies are required to explore the possible link between free-living amoebae and mycobacteria.
Salmonella enterica
Serovar Enteritidis Genes Induced during Oviduct Colonization and Egg Contamination in Laying Hens
Authors: Gantois I. , Ducatelle R. , Pasmans F. , Haesebrouck F. , Van Immerseel F. 
Published: September 2008

ABSTRACT

Salmonella enterica
serovar Enteritidis is the predominant serovar associated with salmonellosis worldwide, which is in part due to its ability to contaminate the internal contents of the hen's egg. It has been shown that
S. enterica
serovar Enteritidis has an unusual tropism for the avian reproductive tract and an ability to persist in the oviduct and ovary. Factors allowing
S. enterica
serovar Enteritidis strains to contaminate eggs could be a specific interaction with the oviduct tissue, leading to persisting oviduct colonization. In vivo expression technology, a promoter-trap strategy, was used to identify genes expressed during oviduct colonization and egg contamination with
S. enterica
serovar Enteritidis. A total of 25 clones with in vivo-induced promoters were isolated from the oviduct tissue and from laid eggs. Among the 25 clones, 7 were isolated from both the oviducts and the eggs. DNA sequencing of the cloned promoters revealed that genes involved in amino acid and nucleic acid metabolism, motility, cell wall integrity, and stress responses were highly expressed in the reproductive tract tissues of laying hens.
Histo-Blood Group Antigen Assay for Detecting Noroviruses in Water
Authors: Cannon Jennifer L. , Vinjé Jan 
Published: September 2008

ABSTRACT
We evaluated a novel, magnetic-bead-based histo-blood group antigen assay for the recovery of low numbers of norovirus particles. Using this assay, with Norwalk virus seeded in environmental waters as a model, we were able to recover 30 to 300 genomic copies of the virus.
Cryptosporidium
Source Tracking in the Potomac River Watershed
Authors: Yang Wenli , Chen Plato , Villegas Eric N. , Landy Ronald B. , Kanetsky Charles , Cama Vitaliano , Dearen Theresa , Schultz Cherie L. , Orndorff Kenneth G. , Prelewicz Gregory J. , Brown Miranda H. , Young Kim Roy , Xiao Lihua 
Published: September 2008

ABSTRACT

To better characterize
Cryptosporidium
in the Potomac River watershed, a PCR-based genotyping tool was used to analyze 64 base flow and 28 storm flow samples from five sites in the watershed. These sites included two water treatment plant intakes, as well as three upstream sites, each associated with a different type of land use. The uses, including urban wastewater, agricultural (cattle) wastewater, and wildlife, posed different risks in terms of the potential contribution of
Cryptosporidium
oocysts to the source water.
Cryptosporidium
was detected in 27 base flow water samples and 23 storm flow water samples. The most frequently detected species was
C. andersoni
(detected in 41 samples), while 14 other species or genotypes, almost all wildlife associated, were occasionally detected. The two common human-pathogenic species,
C. hominis
and
C. parvum
, were not detected. Although
C. andersoni
was common at all four sites influenced by agriculture, it was largely absent at the urban wastewater site. There were very few positive samples as determined by Environmental Protection Agency method 1623 at any site; only 8 of 90 samples analyzed (9%) were positive for
Cryptosporidium
as determined by microscopy. The genotyping results suggest that many of the
Cryptosporidium
oocysts in the water treatment plant source waters were from old calves and adult cattle and might not pose a significant risk to human health.
First Cultivation and Ecological Investigation of a Bacterium Affiliated with the Candidate Phylum OP5 from Hot Springs
Authors: Mori Koji , Sunamura Michinari , Yanagawa Katsunori , Ishibashi Jun-ichiro , Miyoshi Youko , Iino Takao , Suzuki Ken-ichiro , Urabe Tetsuro 
Published: September 2008

ABSTRACT

The phylogenetic group termed OP5 was originally discovered in the Yellowstone National Park hot spring and proposed as an uncultured phylum; the group was afterwards analyzed by applying culture-independent approaches. Recently, a novel thermophilic chemoheterotrophic filamentous bacterium was obtained from a hot spring in Japan that was enriched through various isolation procedures. Phylogenetic analyses of the isolate have revealed that it is closely related to the OP5 phylum that has mainly been constructed with the environmental clones retrieved from thermophilic and mesophilic anaerobic environments. It appears that the lineage is independent at the phylum level in the domain
Bacteria
. Therefore, we designed a primer set for the 16S rRNA gene to specifically target the OP5 phylum and performed quantitative field analysis by using the real-time PCR method. Thus, the 16S rRNA gene of the OP5 phylum was detected in some hot-spring samples with the relative abundance ranging from 0.2% to 1.4% of the prokaryotic organisms detected. The physiology of the above-mentioned isolate and the related environmental clones indicated that they are scavengers contributing to the sulfur cycle in nature.
Nitric Oxide as a Signaling Factor To Upregulate the Death-Specific Protein in a Marine Diatom,
Skeletonema costatum
, during Blockage of Electron Flow in Photosynthesis
Authors: Chung Chih-Ching , Hwang Sheng-Ping L. , Chang Jeng 
Published: September 2008

ABSTRACT

To determine the physiological functions of a novel death-specific protein gene,
Skeletonema costatum DSP-1
(Sc
DSP-1
) in a marine diatom,
Skeletonema costatum
, the mRNA abundance of Sc
DSP-1
was measured in cultures subjected to light manipulation and treatments with various chemicals. When cells were transferred to a dim light intensity of 15 μmol m
−2
s
−1
, Sc
DSP-1
mRNA levels showed a transient increase of 1 to 17.2 μmol (mol 18S rRNA)
−1
in 60 h. Furthermore, treatments with the photoinhibitors 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-
p
-benzoquinone (DBMIB) resulted in high Sc
DSP-1
mRNA levels, which reached 943 and 72 μmol (mol 18S rRNA)
−1
, respectively. Treatment with the nitric oxide (NO) donor diethylamine nitric oxide also induced Sc
DSP-1
expression, and this inducible expression was inhibited by the NO scavenger hemoglobin. Additionally, the expression of Sc
DSP-1
mRNA elicited by DCMU and DBMIB was efficiently reduced when cultures were pretreated with the cell-penetrating NO scavenger 2-(4-carboxyphenyl)-4,5-dihydro-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide. In contrast, treatment with another photoinhibitor, paraquat, had no effect on Sc
DSP-1
expression. Our results indicated that NO is the crucial secondary messenger which signals the expression of Sc
DSP-1
when electron flow between photosystem II and photosystem I is blocked in
S. costatum
cells. In addition, the discovery of a similar gene, Sc
DSP-2
, is briefly described.