bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coupling Short‐Term Changes in Ambient UV‐B levels with Induction of UV‐Screening Compounds†
Authors: Sullivan Joe H. , Gitz Dennis C. , Liu‐Gitz Lan , Xu Chenping , Gao Wei , Slusser James 
Published: July 2010

ABSTRACTA substantial number of studies have been conducted over the last several decades to assess the potential impacts of long‐term increases in ultraviolet‐B radiation (UV‐B between 280 and 320 nm) that will result from continued depletion of stratospheric ozone. However, seasonal changes, tropospheric chemistry and cloudiness are the dominant factors controlling ambient UV‐B levels on a short‐term or daily basis. The effects of short‐term changes in UV‐B on plant growth, phytochemistry and physiological processes have received relatively little attention. The USDA UV‐B Monitoring and Research Program provides an excellent network of stations that provide an opportunity to monitor long‐term changes in solar UV‐B radiation and evaluate the responses of plants to short‐term variation in UV‐B levels on a near‐real‐time basis. In this study barley (Hordeum vulgareL.) and soybean (Glycine max[L] Merr.) were used as model systems. Emerging seedlings of these species were grown under either near‐ambient levels of UV‐B or under reduced levels (ca90% reduction) in the field. Periodic measurements of foliar UV‐screening compounds were made on separate groups of seedlings planted at intervals over the growing season during contrasting periods of ambient levels of UV radiation. The levels of UV‐screening compounds correlated with UV‐B levels in both species and with UV‐A in soybean but the sensitivity of the response differed between the two species and among the soybean cultivars. Response differences among species may be related to unique secondary chemistry of each species, so one response estimate or action spectrum may not be appropriate for all species.
Effect of X‐Radiation on Lipid Peroxidation and Antioxidant Systems in Rats Treated with Saponin‐containing Compounds
Authors: Yalinkilic Omer , Enginar Huseyin 
Published: July 2010

AbstractThe aim of this study was to investigate the effect of three saponin‐containing plant species extracts (Aesculuc hippocastanum L. seed extract [AHE], Medicago sativa L. extract [MSE] and Spinacia oleracea L. extract [SOE]) on lipid peroxidation and on antioxidant systems in rats exposed to X‐rays (XR). The rats were divided into three categories. The first category served as controls and received only a standard diet. The second category served as the radiation group and received 5 and 10 Gy XR dose. The third category (XR+extract‐treated) received plant extracts (25.0 or 50.0 mg kg−1 live weight) and 5 or 10 Gy XR dose. Blood samples were analyzed for their content of malondialdehyde (MDA), reduced glutathione (GSH), plasma vitamin C, β‐carotene and retinol. In animals receiving XR, the plasma MDA (P < 0.001) value significantly increased but the level of GSH (P < 0.01), vitamin C (P < 0.001), retinol and β‐carotene (P < 0.001) decreased significantly with increasing XR doses. In the XR+extract‐treated groups, the concentrations of MDA increased significantly with increasing radiation but their concentrations decreased significantly with increasing extract concentrations. Plasma concentrations of GSH, β‐carotene, retinol and vitamin C in XR+extract‐treated groups decreased significantly with increasing XR dose but their concentrations increased with increasing extract doses. Further, comparison of blood samples of XR+extract‐treated groups with those from the control group showed that GSH, β‐carotene, retinol and vitamin C values increased significantly but that MDA values decreased significantly. The results showed that all extracts have enhanced the antioxidant status and decreased the incidence of free radical‐induced lipid peroxidation in blood samples of rats exposed to XR. However, the antioxidant effect of AHE‐administered animals was more effective than that of MSE‐ and SOE‐administered whole‐body XR rats. We conclude that the supplementation with saponin‐containing extracts may serve to reinforce the antioxidant systems, thus having protective effect against cell damage by XR.
Perspectives on Therapeutic Jurisprudence in Dependency Court in Cases Involving Battered Mothers
Authors: Maze Candice L. , Hannah Stefanie A. 
Published: July 2010

ABSTRACTA qualitative study was conducted involving clients, victim advocates, and judges participating in one of Miami‐Dade County's (Florida) “therapeutic” juvenile court based programs, the Dependency Court Intervention Program for Family Violence (DCIPFV). The primary objective of this study was to assess how battered mothers’ perceptions of the dependency court judges’ actions impacted the women's motivation to take appropriate actions to promote their own, and their child(ren)'s safety.
Cellotriose and Cellotetraose as Inducers of the Genes Encoding Cellobiohydrolases in the Basidiomycete
Phanerochaete chrysosporium
Authors: Suzuki Hitoshi , Igarashi Kiyohiko , Samejima Masahiro 
Published: July 2010

ABSTRACT

The wood decay basidiomycete
Phanerochaete chrysosporium
produces a variety of cellobiohydrolases belonging to glycoside hydrolase (GH) families 6 and 7 in the presence of cellulose. However, no inducer of the production of these enzymes has yet been identified. Here, we quantitatively compared the transcript levels of the genes encoding GH family 6 cellobiohydrolase (
cel6A
) and GH family 7 cellobiohydrolase isozymes (
cel7A
to
cel7F/G
) in cultures containing glucose, cellulose, and cellooligosaccharides by real-time quantitative PCR, in order to evaluate the transcription-inducing effect of soluble sugars. Upregulation of transcript levels in the presence of cellulose compared to glucose was observed for
cel7B
,
cel7C
,
cel7D
,
cel7F/G
, and
cel6A
at all time points during cultivation. In particular, the transcription of
cel7C
and
cel7D
was strongly induced by cellotriose or cellotetraose. The highest level of
cel7C
transcripts was observed in the presence of cellotetraose, whereas the highest level of
cel7D
transcripts was found in the presence of cellotriose, amounting to 2.7 × 10
6
and 1.7 × 10
6
copies per 10
5
actin gene transcripts, respectively. These numbers of
cel7C
and
cel7D
transcripts were higher than those in the presence of cellulose. In contrast, cellobiose had a weaker transcription-inducing effect than either cellotriose or cellotetraose for
cel7C
and had little effect in the case of
cel7D
. These results indicate that cellotriose and cellotetraose, but not cellobiose, are possible natural cellobiohydrolase gene transcription inducers derived from cellulose.
Presence of
Mycobacterium avium
subsp.
paratuberculosis
in Environmental Samples Collected on Commercial Dutch Dairy Farms
Authors: Eisenberg Susanne W. F. , Koets Ad P. , Hoeboer Jeroen , Bouman Marina , Heederik Dick , Nielen Mirjam 
Published: July 2010

ABSTRACT

Mycobacterium avium
subsp.
paratuberculosis
, the causative agent of Johne's disease in cattle, was identified in settled-dust samples of Dutch commercial dairy farms, both in the dairy barn and in the young stock housing. Bioaerosols may play a role in within-farm
M. avium
subsp.
paratuberculosis
transmission.
Biotransformation of Flurbiprofen byCunninghamellaSpecies
Authors: Amadio Jessica , Gordon Katherine , Murphy Cormac D. 
Published: July 2010

ABSTRACTThe biotransformation of the fluorinated anti-inflammatory drug flurbiprofen was investigated inCunninghamellaspp. Mono- and dihydroxylated metabolites were detected using gas chromatography-mass spectrometry and fluorine-19 nuclear magnetic resonance spectroscopy, and the major metabolite 4′-hydroxyflurbiprofen was isolated by preparative high-pressure liquid chromatography (HPLC).Cunninghamella elegansDSM 1908 andC. blakesleeanaDSM 1906 also produced a phase II (conjugated) metabolite, which was identified as the sulfated drug via deconjugation experiments.
New Method for Counting Bacteria Associated with Coral Mucus
Authors: Garren Melissa , Azam Farooq 
Published: July 2010

ABSTRACT

The ability to count bacteria associated with reef-building corals in a rapid, reliable, and cost-effective manner has been hindered by the viscous and highly autofluorescent nature of the coral mucus layer (CML) in which they live. We present a new method that disperses bacterial cells by trypsinization prior to 4′,6-diamidino-2-phenylindole (DAPI) staining and quantification by epifluorescence microscopy. We sampled seawater and coral mucus from
Porites lobata
from 6 reef sites influenced by wastewater intrusion and 2 reef sites unaffected by wastewater in Hawaii. Bacterial and zooxanthella abundances and cell sizes were quantified for each sample. Bacteria were more abundant in coral mucus (ranging from 5.3 × 10
5
± 1.0 × 10
5
cells ml
−1
to 1.8 × 10
6
± 0.2 × 10
6
cells ml
−1
) than in the surrounding seawater (1.9 × 10
5
± 0.1 × 10
5
cells ml
−1
to 4.2 × 10
5
± 0.2 × 10
5
cells ml
−1
), and the mucus-associated cells were significantly smaller than their seawater counterparts at all sites (
P
< 0.0001). The difference in cell size between mucus- and seawater-associated bacteria decreased at wastewater-influenced sites, where simultaneously mucus bacteria were larger and seawater bacteria were smaller than those at uninfluenced sites. The abundance of zooxanthellae in mucus ranged from 1.1 × 10
5
± 0.1 × 10
5
cells ml
−1
to 3.4 × 10
5
± 0.3 × 10
5
cells ml
−1
. The frequency of dividing cells (FDC) was higher in the surrounding seawater than in mucus, despite finding that a 1,000-fold-higher zooxanthella biovolume than bacterial biovolume existed in the CML. Establishment of a standardized protocol for enumeration will provide the field of coral microbial ecology with the urgently needed ability to compare observations across studies and regions.
Scent of Danger: Floc Formation by a Freshwater Bacterium Is Induced by Supernatants from a Predator-Prey Coculture
Authors: Blom Judith F. , Zimmermann Yannick S. , Ammann Thomas , Pernthaler Jakob 
Published: July 2010

ABSTRACT

We investigated predator-prey interactions in a model system consisting of the bacterivorous flagellate
Poterioochromonas
sp. strain DS and the freshwater bacterium
Sphingobium
sp. strain Z007. This bacterial strain tends to form a subpopulation of grazing-resistant microscopic flocs, presumably by aggregation. Enhanced formation of such flocs could be demonstrated in static batch culture experiments in the presence of the predator. The ratio of aggregates to single cells reached >0.1 after 120 h of incubation in an oligotrophic growth medium. The inoculation of bacteria into supernatants from cocultures of bacteria and flagellates (grown in oligotrophic or in rich media) also resulted in a substantially higher level of floc formation than that in supernatants from bacterial monocultures only. After separation of supernatants on a C
18
cartridge, the aggregate-inducing activity could be assigned to the 50% aqueous methanolic fraction, and further separation of this bioactive fraction could be achieved by high-pressure liquid chromatography. These results strongly suggest the involvement of one or several chemical factors in the induction of floc formation by
Sphingobium
sp. strain Z007 that are possibly released into the surrounding medium by flagellate grazing.
Pseudohyphal Regulation by the Transcription Factor Rfg1p in Candida albicans
Authors: Cleary Ian A. , Mulabagal Priyadarshini , Reinhard Sara M. , Yadev Nishant P. , Murdoch Craig , Thornhill Martin H. , Lazzell Anna L. , Monteagudo Carlos , Thomas Derek P. , Saville Stephen P. 
Published: July 2010

ABSTRACT

The opportunistic human fungal pathogen
Candida albicans
is a major cause of nosocomial infections. One of the fundamental features of
C. albicans
pathogenesis is the yeast-to-hypha transition. Hypha formation is controlled positively by transcription factors such as Efg1p and Cph1p, which are required for hyphal growth, and negatively by Tup1p, Rfg1p, and Nrg1p. Previous work by our group has shown that modulating
NRG1
gene expression, hence altering morphology, is intimately linked to the capacity of
C. albicans
to cause disease. To further dissect these virulence mechanisms, we employed the same strategy to analyze the role of Rfg1p in filamentation and virulence. Studies using a
tet-RFG1
strain revealed that
RFG1
overexpression does not inhibit hypha formation
in vitro
or in the mouse model of hematogenously disseminated candidiasis. Interestingly,
RFG1
overexpression drives formation of pseudohyphae under yeast growth conditions—a phenotype similar to that of
C. albicans
strains with mutations in one of several mitotic regulatory genes. Complementation assays and real-time PCR analysis indicate that, although the morphology of the
tet-RFG1
strain resembles that of the mitotic regulator mutants, Rfg1p overexpression does not impact expression of these genes.
A Developmentally Regulated Gene,
ASI2
, Is Required for Endocycling in the Macronuclear Anlagen of Tetrahymena
Authors: Yin Lihui , Gater Susan T. , Karrer Kathleen M. 
Published: July 2010

ABSTRACT

Ciliated protozoa contain two types of nuclei, germ line micronuclei (Mic) and transcriptionally active macronuclei (Mac). During sexual reproduction, the parental Mac degenerates and a new Mac develops from a mitotic product of the zygotic Mic. Macronuclear development involves extensive endoreplication of the genome. The present study shows that endoreplication of macronuclear DNA in
Tetrahymena
is an example of endocyling, a variant of the mitotic cycle with alternating S and G phases in the absence of cell division. Thus, endocycling is conserved from ciliates to multicellular organisms. The gene
ASI2
in
Tetrahymena thermophila
encodes a putative signal transduction receptor.
ASI2
is nonessential for vegetative growth, but it is upregulated during development of the new Mac. Cells that lack
ASI2
in the developing Mac anlagen are arrested in endoreplication of the DNA and die. This study shows that
ASI2
is also transcribed in the parental Mac early in conjugation and that transcription of
ASI2
in the parental Mac supports endoreplication of the DNA during early stages of development of the Mac anlagen. Other molecular events in Mac anlage development, including developmentally regulated DNA rearrangement, occur normally in matings between
ASI2
knockouts, suggesting that
ASI2
specifically regulates endocycling in
Tetrahymena
.
The
UPC2
Promoter in Candida albicans Contains Two
cis
-Acting Elements That Bind Directly to Upc2p, Resulting in Transcriptional Autoregulation
Authors: Hoot Samantha J. , Brown Ryan P. , Oliver Brian G. , White Theodore C. 
Published: July 2010

ABSTRACT

In
Candida albicans
, ergosterol biosynthetic genes, including
ERG11
, which encodes the target of azole antifungal drugs, are regulated by the transcriptional regulator Upc2p. To initially characterize the promoter of the
UPC2
gene, 5′ rapid amplification of cDNA ends was used to identify two transcriptional initiation sites upstream of the ATG codon. The regions within the
UPC2
promoter required for azole regulation of the
UPC2
promoter were then identified using nested deletions fused to a luciferase reporter which were tested for azole inducibility in wild-type (WT) and
upc2
Δ
/upc2
Δ strains. Two distinct regions important for azole induction were identified: a Upc2p-dependent region (UDR) between bp −450 and −350 upstream of the ATG codon and a Upc2p-independent region (UIR) between bp −350 and −250 upstream of the ATG codon. Within the UDR, loss or mutation of the sterol response element (SRE), so named because of homology to the
Saccharomyces cerevisiae
Upc2p binding site, resulted in a decrease in both basal and induced expression in the WT strain but did not affect azole inducibility in the
upc2
Δ/
upc2
Δ deletion strain. Gel shift analyses using the DNA binding domain of Upc2p confirmed binding of the protein to two SRE-related sequences within the
UPC2
promoter, with strongest binding to the UDR SRE. Detailed gel shift analyses of the UDR SRE shows that Upc2p binds to a bipartite element within the
UPC2
promoter, including the previously identified SRE and a new, adjacent element, the short direct repeat (SDR), with partial homology to the SRE.
The Human Oral Microbiome
Authors: Dewhirst Floyd E. , Chen Tuste , Izard Jacques , Paster Bruce J. , Tanner Anne C. R. , Yu Wen-Han , Lakshmanan Abirami , Wade William G. 
Published: July 2010

ABSTRACT

The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (
www.homd.org
). The HOMD includes 619 taxa in 13 phyla, as follows:
Actinobacteria
,
Bacteroidetes
,
Chlamydiae
,
Chloroflexi
,
Euryarchaeota
,
Firmicutes
,
Fusobacteria
,
Proteobacteria
,
Spirochaetes
, SR1,
Synergistetes
,
Tenericutes
, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.
Characterization of the PduS Cobalamin Reductase of
Salmonella
enterica
and Its Role in the Pdu Microcompartment
Authors: Cheng Shouqiang , Bobik Thomas A. 
Published: July 2010

ABSTRACT

Salmonella enterica
degrades 1,2-propanediol (1,2-PD) in a coenzyme B
12
(adenosylcobalamin, AdoCbl)-dependent fashion.
Salmonella
obtains AdoCbl by assimilation of complex precursors, such as vitamin B
12
and hydroxocobalamin. Assimilation of these compounds requires reduction of their central cobalt atom from Co
3+
to Co
2+
to Co
+
, followed by adenosylation to AdoCbl. In this work, the His
6
-tagged PduS cobalamin reductase from
S. enterica
was produced at high levels in
Escherichia coli
, purified, and characterized. The anaerobically purified enzyme reduced cob(III)alamin to cob(II)alamin at a rate of 42.3 ± 3.2 μmol min
−1
mg
−1
, and it reduced cob(II)alamin to cob(I)alamin at a rate of 54.5 ± 4.2 nmol min
−1
mg
−1
protein. The apparent
K

m

values of PduS-His
6
were 10.1 ± 0.7 μM for NADH and 67.5 ± 8.2 μM for hydroxocobalamin in cob(III)alamin reduction. The apparent
K

m

values for cob(II)alamin reduction were 27.5 ± 2.4 μM with NADH as the substrate and 72.4 ± 9.5 μM with cob(II)alamin as the substrate. High-performance liquid chromatography (HPLC) and mass spectrometry (MS) indicated that each monomer of PduS contained one molecule of noncovalently bound flavin mononucleotide (FMN). Genetic studies showed that a
pduS
deletion decreased the growth rate of
Salmonella
on 1,2-PD, supporting a role in cobalamin reduction
in vivo
. Further studies demonstrated that the PduS protein is a component of the Pdu microcompartments (MCPs) used for 1,2-PD degradation and that it interacts with the PduO adenosyltransferase, which catalyzes the terminal step of AdoCbl synthesis. These studies further characterize PduS, an unusual MCP-associated cobalamin reductase, and, in conjunction with prior results, indicate that the Pdu MCP encapsulates a complete cobalamin assimilation system.
Pathogenicity-Associated Islands in Extraintestinal PathogenicEscherichia coliAre Fitness Elements Involved in Intestinal Colonization
Authors: Diard Médéric , Garry Louis , Selva Marjorie , Mosser Thomas , Denamur Erick , Matic Ivan 
Published: July 2010

ABSTRACTThe virulence of many human pathogens does not seem to be an evolutionarily selected trait, but an accidental by-product of the selection that operates in another ecological context. We investigated the possibility that virulence of theextraintestinalpathogenicEscherichiacoli(ExPEC) strains, which frequently cause disease in the host in which they asymptomatically colonize the intestine, is the consequence of commensalism. Most of the ExPEC virulence factors are clustered on genomic islands calledpathogenicity-associatedislands (PAIs). We constructed and characterized several mutants of the ExPEC 536 strain with either (i) deletions of each single PAI or (ii) a complete deletion of all seven PAIs.In vitrophenotypic characterization of 536 mutants showed that the seven PAIs were dispensable for growth in the absence of external stress, as well as under a range of biologically relevant stressors, i.e., serum, bile, and oxidative, nitrosative, hyperosmotic, and acidic stress. However, challenge against the wild-type (WT) strain in a murine model shows that the deletion of all seven PAIs drastically reduces the fitness of 536 during persistent intestinal colonization. This defect seems to be linked to the hypermotility observed for mutants devoid of all seven PAIs. In addition, we show that PAIs diminish fitness of their carrier during growth in urine, suggesting that urinary tract infections are unlikely to provide selective pressure for the maintenance of ExPEC PAIs. Our results are in accordance with the coincidental-evolution hypothesis postulating that extraintestinalE. colivirulence is a by-product of commensalism.
Cell Selection as Driving Force in Lung and Colon Carcinogenesis
Authors: Schöllnberger Helmut , Beerenwinkel Niko , Hoogenveen Rudolf , Vineis Paolo 
Published: July 2010

Abstract
Carcinogenesis is the result of mutations and subsequent clonal expansions of mutated, selectively advantageous cells. To investigate the relative contributions of mutation versus cell selection in tumorigenesis, we compared two mathematical models of carcinogenesis in two different cancer types: lung and colon. One approach is based on a population genetics model, the Wright-Fisher process, whereas the other approach is the two-stage clonal expansion model. We compared the dynamics of tumorigenesis predicted by the two models in terms of the time period until the first malignant cell appears, which will subsequently form a tumor. The mean waiting time to cancer has been calculated approximately for the evolutionary colon cancer model. Here, we derive new analytic approximations to the median waiting time for the two-stage lung cancer model and for a multistage approximation to the Wright-Fisher process. Both equations show that the waiting time to cancer is dominated by the selective advantage per mutation and the net clonal expansion rate, respectively, whereas the mutation rate has less effect. Our comparisons support the idea that the main driving force in lung and colon carcinogenesis is Darwinian cell selection. Cancer Res; 70(17); 6797–803. ©2010 AACR.