bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vitiligo as an inflammatory skin disorder: a therapeutic perspective
Authors: Taïeb Alain 
Published: November 2011

SummaryFrom a therapeutic standpoint, vitiligo is still regarded by many physicians as a simple problem of regenerative medicine, with the main aim to repopulate the depigmented skin with functional melanocytes from the margins of the lesions or from intact progenitors in hair follicles. However, recent research in vitiligo suggests that various local triggers alert the skin immune innate system and may precede adaptive immune responses targeting melanocytes. This scenario is close to that of other common skin inflammatory disorders like psoriasis and atopic, and suggests to target as a priority this clinically silent inflammatory component of he disease. This perspective highlights possible targets for intervention.
Molecular Clues To Understand the Aerotolerance Phenotype of Bifidobacterium animalis subsp. lactis
Authors: Ruiz Lorena , Gueimonde Miguel , Ruas-Madiedo Patricia , Ribbera Angela , de los Reyes-Gavilán Clara G. , Ventura Marco , Margolles Abelardo , Sánchez Borja 
Published: November 2011

ABSTRACT

Oxygen is one of the abiotic factors negatively affecting the survival of
Bifidobacterium
strains used as probiotics, mainly due to the induction of lethal oxidative damage. Aerobic conditions are present during the process of manufacture and storage of functional foods, and aerotolerance is a desired trait for bifidobacteria intended for use in industry. In the present study, the molecular response of
Bifidobacterium animalis
subsp.
lactis
IPLA4549 to aerobic conditions is presented. Molecular targets affected by oxygen were studied using two-dimensional electrophoresis (2DE) and quantitative reverse transcriptase (qRT) PCR. Globally, oxygen stress induced a shift in the glycolytic pathway toward the production of acetic acid with a concomitant increase in ATP formation. Several changes in the expression of genes coding for enzymes involved in redox reactions were detected, although the redox ratio remained unaltered. Interestingly, cells grown under aerobic conditions were characterized by higher activity of coproporphyrinogen III oxidase, which can directly detoxify molecular oxygen, and by higher NADH oxidase specific activity, which can oxidize NADH using hydrogen peroxide. In turn, this is in agreement with the glycolytic shift toward acetate production, in that more NADH molecules may be available due to the lower level of lactic acid formation. These findings further our ability to elucidate the mechanisms by which
B. animalis
copes with an oxygen-containing atmosphere.
Effect of a Synbiotic Yogurt on Levels of Fecal Bifidobacteria, Clostridia, and Enterobacteria
Authors: Palaria Amrita , Johnson-Kanda Ivy , O'Sullivan Daniel J. 
Published: November 2011

ABSTRACT

While ingestion of synbiotic yogurts containing
Bifidobacterium animalis
subsp.
lactis
and inulin is increasing, their effect on certain microbial groups in the human intestine is unclear. To further investigate this, a large-scale, crossover-design, placebo-controlled study was utilized to evaluate the effect of a synbiotic yogurt containing
B. animalis
subsp.
lactis
Bb-12 and inulin on the human intestinal bifidobacteria, clostridia, and enterobacteria. Fecal samples were collected at 14 time points from 46 volunteers who completed the study, and changes in the intestinal bacterial levels were monitored using real-time PCR. Strain Bb-12 could not be detected in feces after 2 weeks of washout. A live/dead PCR procedure indicated that the Bb-12 strain detected in the fecal samples was alive. A significant increase (
P
< 0.001) in the total bifidobacterial numbers was seen in both groups of subjects during the final washout period compared to the prefeeding period. This increase in total bifidobacteria corresponded with a significant decrease (
P
< 0.05) in numbers of clostridia but not enterobacteria. No significant differences in numbers of bifidobacteria, clostridia, or enterobacteria were observed between the probiotic and placebo groups during any of the feeding periods. However, subgrouping subjects based on lower initial bifidobacterial numbers or higher initial clostridial numbers did show corresponding significant differences between the synbiotic yogurt and placebo groups. This was not observed for a subgroup with higher initial enterobacterial numbers. While this synbiotic yogurt can increase bifidobacterial numbers and decrease clostridial numbers (but not enterobacterial numbers) in some individuals, it cannot modulate these microbial groups in the majority of individuals.
Production of 7-
O
-Methyl Aromadendrin, a Medicinally Valuable Flavonoid, in Escherichia coli
Authors: Malla Sailesh , Koffas Mattheos A. G. , Kazlauskas Romas J. , Kim Byung-Gee 
Published: November 2011

ABSTRACT

7-
O
-Methyl aromadendrin (7-OMA) is an aglycone moiety of one of the important flavonoid-glycosides found in several plants, such as
Populus alba
and
Eucalyptus maculata
, with various medicinal applications. To produce such valuable natural flavonoids in large quantity, an
Escherichia coli
cell factory has been developed to employ various plant biosynthetic pathways. Here, we report the generation of 7-OMA from its precursor,
p
-coumaric acid, in
E. coli
for the first time. Primarily, naringenin (NRN) (flavanone) synthesis was achieved by feeding
p
-coumaric acid and reconstructing the plant biosynthetic pathway by introducing the following structural genes: 4-coumarate–coenzyme A (CoA) ligase from
Petroselinum crispum
, chalcone synthase from
Petunia hybrida
, and chalcone isomerase from
Medicago sativa.
In order to increase the availability of malonyl-CoA, a critical precursor of 7-OMA, genes for the acyl-CoA carboxylase α and β subunits (
nfa9890
and
nfa9940
), biotin ligase (
nfa9950
), and acetyl-CoA synthetase (
nfa3550
) from
Nocardia farcinica
were also introduced. Thus, produced NRN was hydroxylated at position 3 by flavanone-3-hydroxylase from
Arabidopsis thaliana
, which was further methylated at position 7 to produce 7-OMA in the presence of 7-
O
-methyltransferase from
Streptomyces avermitilis
. Dihydrokaempferol (DHK) (aromadendrin) and sakuranetin (SKN) were produced as intermediate products. Overexpression of the genes for flavanone biosynthesis and modification pathways, along with malonyl-CoA overproduction in
E. coli
, produced 2.7 mg/liter (8.9 μM) 7-OMA upon supplementation with 500 μM
p
-coumaric acid in 24 h, whereas the strain expressing only the flavanone modification enzymes yielded 30 mg/liter (99.2 μM) 7-OMA from 500 μM NRN in 24 h.
Bacterial Chitin Hydrolysis in Two Lakes with Contrasting Trophic Statuses
Authors: Köllner Krista E. , Carstens Dörte , Keller Esther , Vazquez Francisco , Schubert Carsten J. , Zeyer Josef , Bürgmann Helmut 
Published: November 2011

ABSTRACT

Chitin, which is a biopolymer of the amino sugar glucosamine (GlcN), is highly abundant in aquatic ecosystems, and its degradation is assigned a key role in the recycling of carbon and nitrogen. In order to study the significance of chitin decomposition in two temperate freshwater lakes with contrasting trophic and redox conditions, we measured the turnover rate of the chitin analog methylumbelliferyl-
N
,
N
′-diacetylchitobioside (MUF-DC) and the presence of chitinase (
chiA
) genes in zooplankton, water, and sediment samples. In contrast to the eutrophic and partially anoxic lake,
chiA
gene fragments were detectable throughout the oligotrophic water column and
chiA
copy numbers per ml of water were up to 15 times higher than in the eutrophic waters. For both lakes, the highest
chiA
abundance was found in the euphotic zone—the main habitat of zooplankton, but also the site of production of easily degradable algal chitin. The bulk of chitinase activity was measured in zooplankton samples and the sediments, where recalcitrant chitin is deposited. Both,
chiA
abundance and chitinase activity correlated well with organic carbon, nitrogen, and concentrations of particulate GlcN. Our findings show that chitin, although its overall contribution to the total organic carbon is small (∼0.01 to 0.1%), constitutes an important microbial growth substrate in these temperate freshwater lakes, particularly where other easily degradable carbon sources are scarce.
Indole Production Promotes Escherichia coli Mixed-Culture Growth with Pseudomonas aeruginosa by Inhibiting Quorum Signaling
Authors: Chu Weihua , Zere Tesfalem R. , Weber Mary M. , Wood Thomas K. , Whiteley Marvin , Hidalgo-Romano Benjamin , Valenzuela Ernesto , McLean Robert J. C. 
Published: November 2011

ABSTRACT

Indole production by
Escherichia coli
, discovered in the early 20th century, has been used as a diagnostic marker for distinguishing
E. coli
from other enteric bacteria. By using transcriptional profiling and competition studies with defined mutants, we show that cyclic AMP (cAMP)-regulated indole formation is a major factor that enables
E. coli
growth in mixed biofilm and planktonic populations with
Pseudomonas aeruginosa
. Mutants deficient in cAMP production (
cyaA
) or the cAMP receptor gene (
crp
), as well as indole production (
tnaA
), were not competitive in coculture with
P. aeruginosa
but could be restored to wild-type competitiveness by supplementation with a physiologically relevant indole concentration.
E. coli
sdiA
mutants, which lacked the receptor for both indole and
N
-acyl-homoserine lactones (AHLs), showed no change in competitive fitness, suggesting that indole acted directly on
P. aeruginosa
. An
E. coli
tnaA
mutant strain regained wild-type competiveness if grown with
P. aeruginosa
AHL synthase (
rhlI
and
rhlI lasI
) mutants. In contrast to the wild type,
P. aeruginosa
AHL synthase mutants were unable to degrade indole. Indole produced during mixed-culture growth inhibited pyocyanin production and other AHL-regulated virulence factors in
P. aeruginosa
. Mixed-culture growth with
P. aeruginosa
stimulated indole formation in
E. coli
cpdA
, which is unable to regulate cAMP levels, suggesting the potential for mixed-culture gene activation via cAMP. These findings illustrate how indole, an early described feature of
E. coli
central metabolism, can play a significant role in mixed-culture survival by inhibiting quorum-regulated competition factors in
P. aeruginosa
.
Natural Niche for Organohalide-Respiring Chloroflexi
Authors: Krzmarzick Mark J. , Crary Benjamin B. , Harding Jevon J. , Oyerinde Oyenike O. , Leri Alessandra C. , Myneni Satish C. B. , Novak Paige J. 
Published: November 2011

ABSTRACTThe phylumChloroflexicontains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals. The distribution and role of theseChloroflexiin uncontaminated terrestrial environments, where abundant natural organohalogens could function as potential electron acceptors, have not been studied. Soil samples (116 total, including 6 sectioned cores) from a range of uncontaminated sites were analyzed for the number ofDehalococcoides-likeChloroflexi16S rRNA genes present.Dehalococcoides-likeChloroflexipopulations were detected in all but 13 samples. The concentrations of organochlorine ([organochlorine]), inorganic chloride, and total organic carbon (TOC) were obtained for 67 soil core sections. The number ofDehalococcoides-likeChloroflexi16S rRNA genes positively correlated with [organochlorine]/TOC while the number ofBacteria16S rRNA genes did not.Dehalococcoides-likeChloroflexiwere also observed to increase in number with a concomitant accumulation of chloride when cultured with an enzymatically produced mixture of organochlorines. This research provides evidence that organohalide-respiringChloroflexiare widely distributed as part of uncontaminated terrestrial ecosystems, they are correlated with the fraction of TOC present as organochlorines, and they increase in abundance while dechlorinating organochlorines. These findings suggest that organohalide-respiringChlorofleximay play an integral role in the biogeochemical chlorine cycle.
Characterization, Ecological Distribution, and Population Dynamics of Saccharomyces Sensu Stricto Killer Yeasts in the Spontaneous Grape Must Fermentations of Southwestern Spain
Authors: Maqueda Matilde , Zamora Emiliano , Álvarez María L. , Ramírez Manuel 
Published: November 2011

ABSTRACTKiller yeasts secrete protein toxins that are lethal to sensitive strains of the same or related yeast species. Among the four types ofSaccharomyceskiller yeasts already described (K1, K2, K28, and Klus), we found K2 and Klus killer yeasts in spontaneous wine fermentations from southwestern Spain. Both phenotypes were encoded by medium-size double-stranded RNA (dsRNA) viruses,Saccharomyces cerevisiaevirus (ScV)-M2 and ScV-Mlus, whose genome sizes ranged from 1.3 to 1.75 kb and from 2.1 to 2.3 kb, respectively. The K2 yeasts were found in all the wine-producing subareas for all the vintages analyzed, while the Klus yeasts were found in the warmer subareas and mostly in the warmer ripening/harvest seasons. The middle-size isotypes of the M2 dsRNA were the most frequent among K2 yeasts, probably because they encoded the most intense K2 killer phenotype. However, the smallest isotype of the Mlus dsRNA was the most frequent for Klus yeasts, although it encoded the least intense Klus killer phenotype. The killer yeasts were present in most (59.5%) spontaneous fermentations. Most were K2, with Klus being the minority. The proportion of killer yeasts increased during fermentation, while the proportion of sensitive yeasts decreased. The fermentation speed, malic acid, and wine organoleptic quality decreased in those fermentations where the killer yeasts replaced at least 15% of a dominant population of sensitive yeasts, while volatile acidity and lactic acid increased, and the amount of bacteria in the tumultuous and the end fermentation stages also increased in an unusual way.
Salivaricin D, a Novel Intrinsically Trypsin-Resistant Lantibiotic from Streptococcus salivarius 5M6c Isolated from a Healthy Infant
Authors: Birri Dagim Jirata , Brede Dag Anders , Nes Ingolf F. 
Published: November 2011

ABSTRACT

In this work, we purified and characterized a newly identified lantibiotic (salivaricin D) from
Streptococcus salivarius
5M6c. Salivaricin D is a 34-amino-acid-residue peptide (3,467.55 Da); the locus of the gene encoding this peptide is a 16.5-kb DNA segment which contains genes encoding the precursor of two lantibiotics, two modification enzymes (dehydratase and cyclase), an ABC transporter, a serine-like protease, immunity proteins (lipoprotein and ABC transporters), a response regulator, and a sensor histidine kinase. The immunity gene (
salI
) was heterologously expressed in a sensitive indicator and provided significant protection against salivaricin D, confirming its immunity function. Salivaricin D is a naturally trypsin-resistant lantibiotic that is similar to nisin-like lantibiotics. It is a relatively broad-spectrum bacteriocin that inhibits members of many genera of Gram-positive bacteria, including the important human pathogens
Streptococcus pyogenes
and
Streptococcus pneumoniae
. Thus,
Streptococcus salivarius
5M6c may be a potential biological agent for the control of oronasopharynx-colonizing streptococcal pathogens or may be used as a probiotic bacterium.
Enterococcus faecium of the
vanA
Genotype in Rural Drinking Water, Effluent, and the Aqueous Environment
Authors: Morris Dearbháile , Galvin Sandra , Boyle Fiona , Hickey Paul , Mulligan Martina , Cormican Martin 
Published: November 2011

ABSTRACT

Total enterococci and vancomycin-resistant enterococci (VRE) were enumerated in samples of effluent (
n
= 50) and water (
n
= 167) from a number of sources. VRE were detected in the outflow of a wastewater treatment plant and in a single rural drinking water supply, suggesting potential for transmission to humans through environmental contamination.
Preliminary Safety Evaluation of a New Bacteroides xylanisolvens Isolate
Authors: Ulsemer Philippe , Toutounian Kawe , Schmidt Jens , Karsten Uwe , Goletz Steffen 
Published: November 2011

ABSTRACT

Besides conferring some health benefit to the host, a bacterial strain must present an unambiguous safety status to be considered a probiotic. We here present the preliminary safety evaluation of a new
Bacteroides xylanisolvens
strain (DSM 23964) isolated from human feces. First results suggest that it may be able to provide probiotic health benefits. Its identity was confirmed by biochemical analysis, by sequencing of its 16S rRNA genes, and by DNA-DNA hybridization. Virulence determinants known to occur in the genus
Bacteroides
, such the
bft
enterotoxin and other enzymatic activities involved in the degradation of the extracellular matrix and the capsular polysaccharide PS A, were absent in this strain. The investigation of the antibiotic susceptibility indicated that strain DSM 23964 was sensitive to metronidazole, meropenem agents, and clindamycin. Resistance to penicillin and ampicillin was identified to be conferred by the β-lactamase
cepA
gene and could therefore be restored by adding β-lactamase inhibitors. The localization of the
cepA
gene in the genome of strain DSM 23964 and the absence of detectable plasmids further suggest that a transfer of β-lactamase activity or the acquisition of other antibiotic resistances are highly improbable. Taken together, the presented data indicate that the strain
B. xylanisolvens
DSM 23964 has no virulence potential. Since it also resists the action of gastric enzymes and low-pH conditions, this strain is an interesting candidate for further investigation of its safety and potential health-promoting properties.
Streptomycin-Induced Expression in Bacillus subtilis of YtnP, a Lactonase-Homologous Protein That Inhibits Development and Streptomycin Production in Streptomyces griseus
Authors: Schneider Johannes , Yepes Ana , Garcia-Betancur Juan C. , Westedt Isa , Mielich Benjamin , López Daniel 
Published: November 2011

ABSTRACT

Bacillus subtilis
induces expression of the gene
ytnP
in the presence of the antimicrobial streptomycin, produced by the Gram-positive bacterium
Streptomyces griseus
.
ytnP
encodes a lactonase-homologous protein that is able to inhibit the signaling pathway required for the streptomycin production and development of aerial mycelium in
S. griseus
.
Role of IncP-1β Plasmids pWDL7::
rfp
and pNB8c in Chloroaniline Catabolism as Determined by Genomic and Functional Analyses
Authors: Król J. E. , Penrod J. T. , McCaslin H. , Rogers L. M. , Yano H. , Stancik A. D. , Dejonghe W. , Brown C. J. , Parales R. E. , Wuertz S. , Top E. M. 
Published: November 2011

ABSTRACT

Broad-host-range catabolic plasmids play an important role in bacterial degradation of man-made compounds. To gain insight into the role of these plasmids in chloroaniline degradation, we determined the first complete nucleotide sequences of an IncP-1 chloroaniline degradation plasmid, pWDL7::
rfp
and its close relative pNB8c, as well as the expression pattern, function, and bioaugmentation potential of the putative 3-chloroaniline (3-CA) oxidation genes. Based on phylogenetic analysis of backbone proteins, both plasmids are members of a distinct clade within the IncP-1β subgroup. The plasmids are almost identical, but whereas pWDL7::
rfp
carries a duplicate inverted catabolic transposon, Tn
6063
, containing a putative 3-CA oxidation gene cluster,
dcaQTA1A2BR
, pNB8c contains only a single copy of the transposon. No genes for an aromatic ring cleavage pathway were detected on either plasmid, suggesting that only the upper 3-CA degradation pathway was present. The
dcaA1A2B
gene products expressed from a high-copy-number vector were shown to convert 3-CA to 4-chlorocatechol in
Escherichia coli
. Slight differences in the
dca
promoter region between the plasmids and lack of induction of transcription of the pNB8c
dca
genes by 3-CA may explain previous findings that pNB8C does not confer 3-CA transformation. Bioaugmentation of activated sludge with pWDL7::
rfp
accelerated removal of 3-CA, but only in the presence of an additional carbon source. Successful bioaugmentation requires complementation of the upper pathway genes with chlorocatechol cleavage genes in indigenous bacteria. The genome sequences of these plasmids thus help explain the molecular basis of their catabolic activities.
Mur Regulates the Gene Encoding the Manganese Transporter MntH in Brucella abortus 2308
Authors: Menscher Evan A. , Caswell Clayton C. , Anderson Eric S. , Roop R. Martin 
Published: November 2011

ABSTRACT

MntH is the only high-affinity manganese transporter identified in
Brucella
. A previous study showed that MntH is required for the wild-type virulence of
Brucella abortus
2308 in mice (Anderson ES, et al., Infect. Immun.
77:
3466–3474, 2009) and indicated that the
mntH
gene is regulated in a manganese-responsive manner in this strain by a Mur homolog. In the study presented here, the transcriptional start site for
mntH
in
B. abortus
2308 was determined by primer extension analysis. Specific interactions between Mur and the
mntH
promoter region were demonstrated in an electrophoretic mobility shift assay (EMSA), and a Mur binding site was identified in the −55 to −24 region of the
mntH
promoter by DNase I footprint analysis. The specificity of the interaction of Mur with the putative Mur box was further evaluated by EMSA employing oligonucleotides in which the consensus nucleotides in this region were substituted. These studies not only confirm a direct role for Mur in the Mn-responsive regulation of
mntH
expression in
Brucella abortus
2308 but also identify the
cis
-acting elements upstream of
mntH
that are responsible for this regulation.
Sequential Closure of the Cytoplasm and Then the Periplasm during Cell Division in Escherichia coli
Authors: Skoog Karl , Söderström Bill , Widengren Jerker , von Heijne Gunnar , Daley Daniel O. 
Published: November 2011

ABSTRACT

To visualize the latter stages of cell division in live
Escherichia coli
, we have carried out fluorescence recovery after photobleaching (FRAP) on 121 cells expressing cytoplasmic green fluorescent protein and periplasmic mCherry. Our data show conclusively that the cytoplasm is sealed prior to the periplasm during the division event.
The Vibrio cholerae Mannitol Transporter Is Regulated Posttranscriptionally by the MtlS Small Regulatory RNA
Authors: Mustachio Lisa Maria , Aksit Selime , Mistry Ronak H. , Scheffler Robert , Yamada Akikuni , Liu Jane M. 
Published: November 2011

ABSTRACT

Vibrio cholerae
continues to pose a health threat in many developing nations and regions of the world struck by natural disasters. It is a pathogen that rapidly adapts to aquatic environments and the human small intestine. Small regulatory RNAs (sRNAs) may contribute to this adaptability. Specifically, the mannitol operon sRNA (MtlS sRNA; previously designated the IGR7 sRNA) is transcribed antisense to the 5′ untranslated region of the
mtl
operon, encoding the mannitol-specific phosphotransferase system. Mannitol is a six-carbon sugar alcohol that accumulates in the human small intestine, the primary site of
V. cholerae
colonization. To better understand the
V. cholerae
mtl
operon at a molecular level, we investigated
mtlA
expression in the presence of various carbon sources and the role of the MtlS sRNA. We observed that MtlA protein is present only in cells grown on mannitol sugar, whereas MtlS sRNA is expressed during growth on all sugars other than mannitol. In contrast,
mtlA
mRNA is expressed in similar amounts regardless of the carbon source used for bacterial growth. These observations suggest that the regulation of MtlA protein expression is a posttranscriptional event. We further demonstrate that MtlS sRNA overexpression repressed MtlA synthesis without affecting the stability of the messenger and that this process is largely independent of Hfq. We propose a model in which, when carbon sources other than mannitol are present, MtlS sRNA is transcribed, base pairs with the 5′ untranslated region of the
mtlA
mRNA, occluding the ribosome binding site, and inhibits the synthesis of the mannitol-specific phosphotransferase system.