bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional relevance of aromatic residues in the first transmembrane domain of P2X receptors
Authors: Jindrichova Marie , Vavra Vojtech , Obsil Tomas , Stojilkovic Stanko S. , Zemkova Hana 
Published: March 2009

J. Neurochem. (2009)109, 923–934.AbstractThe functional relevance of aromatic residues in the upper part of the transmembrane domain‐1 of purinergic P2X receptors (P2XRs) was examined. Replacement of the conserved Tyr residue with Ala had a receptor‐specific effect: the P2X1R was non‐functional, the P2X2R, P2X4R, and P2X3R exhibited enhanced sensitivity to ATP and αβ‐meATP accompanied by prolonged decay of current after washout of agonists, and the P2X7R sensitivity for agonists was not affected, though decay of current was delayed. The replacement of the P2X4R‐Tyr42 with other amino acids revealed the relevance of an aromatic residue at this position. Mutation of the neighboring Phe and ipsilateral Tyr/Trp residues, but not the contralateral Phe residue, also affected the P2X2R, P2X3R, and P2X4R function. Double mutation of ipsilateral Tyr42 and Trp46 P2X4R residues restored receptor function, whereas the corresponding P2X2R double mutant was not functional. In contrast, mutation of the contralateral Phe48 residue in the P2X4R‐Y42A mutant had no effect. These results indicate that aromatic residues in the upper part of TM1 play important roles in the three‐dimensional structure of the P2XRs and that they are required not only for ion conductivity but also for specificity of agonist binding and/or channel gating.
Effects of repeated injections of fibroblast‐stimulating lipopeptide‐1 on fever, formation of cytokines, and on the responsiveness to endotoxin in guinea‐pigs
Authors: Greis A. , Murgott J. , Gerstberger R. , Hübschle T. , Roth J. 
Published: March 2009

AbstractAims:  We investigated, whether the Toll‐like receptors (TLRs)‐2/6‐agonist fibroblast‐stimulating lipopeptide‐1 (FSL‐1), like the TLR‐4 agonist lipopolysaccharide (LPS), induces a state of tolerance. We further tested the influence of repeated pre‐treatment with FSL‐1 on the animals’ responsiveness to LPS.Methods:  Abdominal temperature was recorded in unrestrained guinea‐pigs with intra‐abdominally implanted radiotransmitters. Circulating concentrations of tumour necrosis factor (TNF) and interleukin‐6 (IL‐6) were measured with specific bioassays. We tested the effects of intra‐arterial (i.a.) or intraperitoneal (i.p.) injections of 100 μg kg−1 FSL‐1, repeated five times at intervals of 3 days. The animals’ responses to i.a. or i.p. injections of 10 μg kg−1 LPS were determined another 3 days later and compared to those of naïve guinea‐pigs.Results:  The FSL‐1‐induced TNF peak was significantly attenuated starting with the third i.a. administration, while fever was unimpaired and the IL‐6‐peak just tended to decrease. Fever and IL‐6 in response to i.a. injections of LPS were identical in both groups, while circulating TNF was higher in naïve compared to FSL‐1 pre‐treated animals. The effects of repeated i.p. injections of FSL‐1 were more pronounced resulting in attenuation of fever as well as circulating TNF and IL‐6, the strongest reduction observed after the third stimulation with FSL‐1. Repeated i.p. pre‐treatment with FSL‐1 induced hyporesponsiveness to i.p. administration of LPS compared to naïve animals with regard to fever and especially with regard to LPS‐induced formation of cytokines.Conclusions:  There is a development of tolerance to FSL‐1 and cross‐tolerance between FSL‐1 and LPS depending on the route of administration of the respective TLR‐2/6 and TLR‐4 agonists.
Myrip uses distinct domains in the cellular activation of myosin VA and myosin VIIA in melanosome transport
Authors: Ramalho José S. , Lopes Vanda S. , Tarafder Abul K. , Seabra Miguel C. , Hume Alistair N. 
Published: March 2009

SummaryMyrip is a Rab27a and MyosinVIIa (MyoVIIa) linking protein that may regulate melanosome transport in the retinal pigment epithelium (RPE). Myrip also binds MyosinVa (MyoVa) in vitro however it is unclear whether this interaction is of sufficient affinity to be physiologically relevant. Here, we addressed the questions of whether Myrip interacts with MyoVa in cells and the molecular basis of cellular activation of MyoVa and MyoVIIa by Myrip. To answer these questions we used melanosome transport in skin melanocytes and RPE cells as read‐outs of MyoVa and MyoVIIa activity. We found that Myrip recruits and activates MyoVa on skin melanosomes with similar efficiency to the established MyoVa activator Melanophilin (Mlph). Mutagenesis showed that a Myrip–Mlph conserved amphipathic helix (MMAH) is essential for MyoVa interaction while other Myrip regions, including the MyoVa exon F binding domain equivalent, play non‐essential roles in this interaction. This suggests that, in contrast to Mlph, Myrip interacts with MyoVa lacking melanocyte‐specific exon F. Parallel studies of RPE melanosome transport reveal that Myrip‐specific inserts, but not the MMAH, are essential for MyoVIIa activation. We conclude that Myrip is a versatile Rab27a‐associated myosin‐activating protein that mediates cellular activation of MyoVa and MyoVIIa via non‐overlapping domains.
REDD in the red: palm oil could undermine carbon payment schemes
Authors: Butler Rhett A. , Koh Lian Pin , Ghazoul Jaboury 
Published: March 2009

AbstractMechanisms to reduce carbon emissions from deforestation and forest degradation (REDD) have been gaining momentum as a way to combat global warming, fund forest conservation, and deliver economic benefits to rural populations. However, the economic viability of REDD schemes will depend on the profitability of alternative land uses. Oil palm agriculture has become a major driver of tropical deforestation over the last few decades. Here, we model and compare the profitability of converting forest to oil palm versus conserving it for an REDD project. We show that converting a hectare of forest for palm oil production will be more profitable (yielding net present values of $3,835–$9,630) to land owners than preserving it for carbon credits ($614–$994), which are currently restricted to voluntary carbon markets. Giving REDD credits price parity with carbon credits traded in compliance markets would boost the profitability of avoided deforestation (up to $6,605). Unless post‐2012 global climate policies legitimize the trading of carbon credits from avoided deforestation, REDD will not be able to compete with oil palm agriculture or other similarly profitable human activities as an economically attractive land‐use option, in which case REDD will not be able to fulfill its primary function of avoiding deforestation.
The Chromosomal Toxin Gene
yafQ
Is a Determinant of Multidrug Tolerance for
Escherichia coli
Growing in a Biofilm
Authors: Harrison Joe J. , Wade William D. , Akierman Sarah , Vacchi-Suzzi Caterina , Stremick Carol A. , Turner Raymond J. , Ceri Howard 
Published: March 2009

ABSTRACT

Escherichia coli
is refractory to elevated doses of antibiotics when it is growing in a biofilm, and this is potentially due to high numbers of multidrug-tolerant persister cells in the surface-adherent population. Previously, the chromosomal toxin-antitoxin loci
hipBA
and
relBE
have been linked to the frequency at which persister cells occur in
E. coli
populations. In the present study, we focused on the
dinJ
-
yafQ
-encoded toxin-antitoxin system and hypothesized that deletion of the toxin gene
yafQ
might influence cell survival in antibiotic-exposed biofilms. By using confocal laser scanning microscopy and viable cell counting, it was determined that a Δ
yafQ
mutant produced biofilms with a structure and a cell density equivalent to those of the parental strain. In-depth susceptibility testing identified that relative to wild-type
E. coli
, the Δ
yafQ
strain had up to a ∼2,400-fold decrease in cell survival after the biofilms were exposed to bactericidal concentrations of cefazolin or tobramycin. Corresponding to these data, controlled overexpression of
yafQ
from a high-copy-number plasmid resulted in up to a ∼10,000-fold increase in the number of biofilm cells surviving exposure to these bactericidal drugs. In contrast, neither the inactivation nor the overexpression of
yafQ
affected the tolerance of biofilms to doxycycline or rifampin (rifampicin). Furthermore, deletion of
yafQ
did not affect the tolerance of stationary-phase planktonic cells to any of the antibacterials tested. These results suggest that
yafQ
mediates the tolerance of
E. coli
biofilms to multiple but specific antibiotics; moreover, our data imply that this cellular pathway for persistence is likely different from that of multidrug-tolerant cells in stationary-phase planktonic cell cultures.
Construction of a Gene Knockout System for Application in
Paenibacillus alvei
CCM 2051
T
, Exemplified by the S-Layer Glycan Biosynthesis Initiation Enzyme WsfP
Authors: Zarschler Kristof , Janesch Bettina , Zayni Sonja , Schäffer Christina , Messner Paul 
Published: March 2009

ABSTRACT

The gram-positive bacterium
Paenibacillus alvei
CCM 2051
T
is covered by an oblique surface layer (S-layer) composed of glycoprotein subunits. The S-layer O-glycan is a polymer of [→3)-β-
d
-Gal
p
-(1[α-
d
-Glc
p
-(1→6)]→4)-β-
d
-Man
p
NAc-(1→] repeating units that is linked by an adaptor of -[GroA-2→OPO
2
→4-β-
d
-Man
p
NAc-(1→4)]→3)-α-
l
-Rha
p
-(1→3)-α-
l
-Rha
p
-(1→3)-α-
l
-Rha
p
-(1→3)-β-
d
-Gal
p
-(1→ to specific tyrosine residues of the S-layer protein. For elucidation of the mechanism governing S-layer glycan biosynthesis, a gene knockout system using bacterial mobile group II intron-mediated gene disruption was developed. The system is further based on the
sgsE
S-layer gene promoter of
Geobacillus stearothermophilus
NRS 2004/3a and on the
Geobacillus-Bacillus-Escherichia coli
shuttle vector pNW33N. As a target gene,
wsfP
, encoding a putative UDP-Gal:phosphoryl-polyprenol Gal-1-phosphate transferase, representing the predicted initiation enzyme of S-layer glycan biosynthesis, was disrupted. S-layer protein glycosylation was completely abolished in the insertional
P. alvei
CCM 2051
T
wsfP
mutant, according to sodium dodecyl sulfate-polyacrylamide gel electrophoresis evidence and carbohydrate analysis. Glycosylation was fully restored by plasmid-based expression of
wsfP
in the glycan-deficient
P. alvei
mutant, confirming that WsfP initiates S-layer protein glycosylation. This is the first report on the successful genetic manipulation of bacterial S-layer protein glycosylation in vivo, including transformation of and heterologous gene expression and gene disruption in the model organism
P. alvei
CCM 2051
T
.
Development of
cpn60
-Based Real-Time Quantitative PCR Assays for the Detection of 14
Campylobacter
Species and Application to Screening of Canine Fecal Samples
Authors: Chaban Bonnie , Musil Kristyna M. , Himsworth Chelsea G. , Hill Janet E. 
Published: March 2009

ABSTRACT

Campylobacter
species are important organisms in both human and animal health. The identification of
Campylobacter
currently requires the growth of organisms from complex samples and biochemical identification. In many cases, the condition of the sample being tested and/or the fastidious nature of many
Campylobacter
species has limited the detection of campylobacters in a laboratory setting. To address this, we have designed a set of real-time quantitative PCR (qPCR) assays to detect and quantify 14
Campylobacter
species,
C. coli, C. concisus, C. curvus, C. fetus, C. gracilis, C. helveticus, C. hyointestinalis, C. jejuni, C. lari, C. mucosalis, C. rectus, C. showae, C. sputorum
, and
C. upsaliensis
, directly from DNA extracted from feces. By use of a region of the
cpn60
(also known as
hsp60
or
groEL
) gene, which encodes the universally conserved 60-kDa chaperonin, species-specific assays were designed and validated. These assays were then employed to determine the prevalence of
Campylobacter
species in fecal samples from dogs. Fecal samples were found to contain detectable and quantifiable levels of
C. fetus, C. gracilis, C. helveticus, C. jejuni, C. showae
, and
C. upsaliensis
, with the majority of samples containing multiple
Campylobacter
species. This study represents the first report of
C. fetus, C. gracilis, C. mucosalis
, and
C. showae
detection in dogs and implicates dogs as a reservoir for these species. The qPCR assays described offer investigators a new tool to study many
Campylobacter
species in a culture-independent manner.
Bile-Inducible Efflux Transporter from
Bifidobacterium longum
NCC2705, Conferring Bile Resistance
Authors: Gueimonde Miguel , Garrigues Christel , van Sinderen Douwe , de los Reyes-Gavilán Clara G. , Margolles Abelardo 
Published: March 2009

ABSTRACT

Bifidobacteria are normal inhabitants of the human gut. Some strains of this genus are considered health promoting or probiotic, being included in numerous food products. In order to exert their health benefits, these bacteria must overcome biological barriers, including bile salts, to colonize and survive in specific parts of the intestinal tract. The role of multidrug resistance (MDR) transporters in bile resistance of probiotic bacteria and the effect of bile on probiotic gene expression are not fully understood. In the present study, the effect of subinhibitory concentrations of bile on the expression levels of predicted MDR genes from three different bifidobacterial strains, belonging to
Bifidobacterium longum
subsp.
longum, Bifidobacterium breve
, and
Bifidobacterium animalis
subsp.
lactis
, was tested. In this way, two putative MDR genes whose expression was induced by bile, BL0920 from
B. longum
and its homolog, Bbr0838, from
B. breve
, were identified. The expression of the BL0920 gene in
Escherichia coli
was shown to confer resistance to bile, likely to be mediated by active efflux from the cells. To the best of our knowledge, this represents the first identified bifidobacterial bile efflux pump whose expression is induced by bile.
Intestinal Endocellular Symbiotic Bacterium of the Macaque Louse
Pedicinus obtusus
: Distinct Endosymbiont Origins in Anthropoid Primate Lice and the Old World Monkey Louse
Authors: Fukatsu Takema , Hosokawa Takahiro , Koga Ryuichi , Nikoh Naruo , Kato Takuya , Hayama Shin-ichi , Takefushi Haruo , Tanaka Ichirou 
Published: March 2009

ABSTRACT

A symbiotic bacterium of the macaque louse,
Pedicinus obtusus
, was characterized. The symbiont constituted a gammaproteobacterial lineage distinct from the symbionts of anthropoid primate lice, localized in the midgut epithelium and the ovaries and exhibiting AT-biased genes and accelerated molecular evolution. The designation “
Candidatus
Puchtella pedicinophila” was proposed for it.
Cloning and In Situ Expression Studies of the
Hydrogenobaculum
Arsenite Oxidase Genes
Authors: Clingenpeel Scott R. , D'Imperio Seth , Oduro Harry , Druschel Greg K. , McDermott Timothy R. 
Published: March 2009

ABSTRACT

Novel arsenite [As(III)] oxidase structural genes (
aoxAB
) were cloned from
Hydrogenobaculum
bacteria isolated from an acidic geothermal spring. Reverse transcriptase PCR demonstrated expression throughout the outflow channel, and the
aoxB
cDNA clones exhibited distribution patterns relative to the physicochemical gradients in the spring. Microelectrode analyses provided evidence of quantitative As(III) transformation within the microbial mat.
Microbial Diversity of Septic Tank Effluent and a Soil Biomat
Authors: Tomaras Jill , Sahl Jason W. , Siegrist Robert L. , Spear John R. 
Published: March 2009

ABSTRACT
Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.
Empirical Leucine-to-Carbon Conversion Factors for Estimating Heterotrophic Bacterial Production: Seasonality and Predictability in a Temperate Coastal Ecosystem
Authors: Calvo-Díaz Alejandra , Morán Xosé Anxelu G. 
Published: March 2009

ABSTRACT

Leucine-to-carbon conversion factors (CFs) are needed for converting substrate incorporation into biomass production of heterotrophic bacteria. During 2006 we performed 20 dilution experiments for determining the spatiotemporal variability of empirical CFs in temperate Atlantic coastal waters. Values (0.49 to 1.92 kg C mol Leu
−1
) showed maxima in autumn to early winter and minima in summer. Spatially averaged CFs were significantly negatively correlated with in situ leucine incorporation rates (
r
= −0.91) and positively correlated with phosphate concentrations (
r
= 0.76). These relationships, together with a strong positive covariation between cell-specific leucine incorporation rates and carbon contents (
r
= 0.85), were interpreted as a strategy to maximize survival through protein synthesis and low growth rates under nutrient limitation (low CFs) until favorable conditions stimulate cell division relative to protein synthesis (high CFs). A multiple regression with in situ leucine incorporation rates and cellular carbon contents explained 96% of CF variance in our ecosystem, suggesting their potential prediction from more easily measurable routine variables. The use of the theoretical CF of 1.55 kg C mol Leu
−1
would have resulted in a serious overestimation (73%) of annual bacterial production rates. Our results emphasize the need for considering the temporal scale in CFs for bacterial production studies.
Inactivation of the SauI Type I Restriction-Modification System Is Not Sufficient To Generate
Staphylococcus aureus
Strains Capable of Efficiently Accepting Foreign DNA
Authors: Veiga Helena , Pinho Mariana G. 
Published: March 2009

ABSTRACT

Genetic manipulation of
Staphylococcus aureus
is limited by the availability of only a single strain, RN4220, that is capable of easily accepting foreign DNA. Inactivation of the
hsdR
gene of the SauI type I restriction-modification system was shown previously to be responsible for the high transformation efficiency of RN4220 (D. E. Waldron and J. A. Lindsay, J Bacteriol.
188:
5578-5585, 2006). However, deletion of this gene in three different
S. aureus
strains was not sufficient to make them readily transformable, which would be remarkably useful for genetic studies of this pathogenic organism. These results indicate that another unknown factor(s) is required for the transformable phenotype in
S. aureus
.
Stereospecific Biotransformation of Dihydrodaidzein into (3
S
)-Equol by the Human Intestinal Bacterium
Eggerthella
Strain Julong 732
Authors: Kim Mihyang , Kim Su-Il , Han Jaehong , Wang Xiu-Ling , Song Dae-Geun , Kim Soo-Un 
Published: March 2009

ABSTRACT

Stereochemical course of isoflavanone dihydrodaidzein (DHD) reduction into the isoflavan (3
S
)-equol via tetrahydrodaidzein (THD) by the human intestinal anaerobic bacterium
Eggerthella
strain Julong 732 was studied. THD was synthesized by catalytic hydrogenation, and each stereoisomer was separated by chiral high-performance liquid chromatography. Circular dichroism spectroscopy was used to elucidate the absolute configurations of four synthetic THD stereoisomers. Rapid racemization of DHD catalyzed by Julong 732 prevented the substrate stereospecificity in the conversion of DHD into THD from being confirmed. The absolute configuration of THD, prepared by reduction of DHD in the cell-free incubation, was assigned as (3
R
,4
S
) via comparison of the retention time to that of the authentic THD by chiral chromatography. Dehydroequol (DE) was unable to produce the (3
S
)-equol both in the cell-free reaction and in the bacterial transformation, negating the possible intermediacy of DE. Finally, the intermediate (3
R
,4
S
)-THD was reduced into (3
S
)-equol by the whole cell, indicating the inversion of stereochemistry at C-3 during the reduction. A possible mechanism accounting for the racemization of DHD and the inversion of configuration of THD during reduction into (3
S
)-equol is proposed.
Diversity of Bacteria in the Marine Sponge
Aplysina fulva
in Brazilian Coastal Waters
Authors: Hardoim C. C. P. , Costa R. , Araújo F. V. , Hajdu E. , Peixoto R. , Lins U. , Rosado A. S. , van Elsas J. D. 
Published: March 2009

ABSTRACT

Microorganisms can account for up to 60% of the fresh weight of marine sponges. Marine sponges have been hypothesized to serve as accumulation spots of particular microbial communities, but it is unknown to what extent these communities are directed by the organism or the site or occur randomly. To address this question, we assessed the composition of specific bacterial communities associated with
Aplysina fulva
, one of the prevalent sponge species inhabiting Brazilian waters. Specimens of
A. fulva
and surrounding seawater were collected in triplicate in shallow water at two sites, Caboclo Island and Tartaruga beach, Búzios, Brazil. Total community DNA was extracted from the samples using “direct” and “indirect” approaches. 16S rRNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the total bacterial community and of specific bacterial groups
—Pseudomonas
and
Actinobacteria—
revealed that the structure of these assemblages in
A. fulva
differed drastically from that observed in seawater. The DNA extraction methodology and sampling site were determinative for the composition of actinobacterial communities in
A. fulva
. However, no such effects could be gleaned from total bacterial and
Pseudomonas
PCR-DGGE profiles. Bacterial 16S rRNA gene clone libraries constructed from directly and indirectly extracted DNA did not differ significantly with respect to diversity and composition. Altogether, the libraries encompassed 15 bacterial phyla and the candidate division TM7. Clone sequences affiliated with the
Cyanobacteria
,
Chloroflexi
,
Gamma
- and
Alphaproteobacteria
,
Actinobacteria
,
Bacteroidetes
, and
Acidobacteria
were, in this order, most abundant. The bacterial communities associated with the
A. fulva
specimens were distinct and differed from those described in studies of sponge-associated microbiota performed with other sponge species.
Identification of Natural Target Proteins Indicates Functions of a Serralysin-Type Metalloprotease, PrtA, in Anti-Immune Mechanisms
Authors: Felföldi Gabriella , Marokházi Judit , Képiró Miklós , Venekei István 
Published: March 2009

ABSTRACTSerralysins are generally thought to function as pathogenicity factors of bacteria, but so far no hard evidence of this (e.g., specific substrate proteins that are sensitive to the cleavage by these proteases) has been found. We have looked for substrate proteins to a serralysin-type proteinase, PrtA, in a natural host-pathogen molecular interaction system involvingManduca sextaandPhotorhabdus luminescens. The exposure in vitro of hemolymph to PrtA digestion resulted in selective cleavage of 16 proteins, provisionally termed PAT (PrtA target) proteins. We could obtain sequence information for nine of these PrtA sensitive proteins, and by searching databases, we could identify six of them. Each has immune-related function involving every aspect of the immune defense: β-1,3 glucan recognition protein 2 (immune recognition), hemocyte aggregation inhibitor protein (HAIP), serine proteinase homolog 3, six serpin-1 variants, including serpin-1I (immune signaling and regulation), and scolexins A and B (coagulation cascade effector function). The functions of the identified PrtA substrate proteins shed new light on a possible participation of a serralysin in the virulence mechanism of a pathogen. Provided these proteins are targets of PrtA in vivo, this might represent, among others, a complex suppressive role on the innate immune response via interference with both the recognition and the elimination of the pathogen during the first, infective stage of the host-pathogen interaction. Our results also raise the possibility that the natural substrate proteins of serralysins of vertebrate pathogens might be found among the components of the innate immune system.