bluuebunny/crossref_metadata_2025 huggingface dataset:
The functional consequences of diversity in plant–pollinator interactions
Authors: Perfectti Francisco , Gómez José M. , Bosch Jordi
Published: May 2009

The role of biological diversity in maintaining ecosystem functioning is a central issue in ecology. Most studies on diversity–functioning relationships have focused on ecosystem and community levels, leaving the extension of those relationships to other organization levels, such as populations, as a challenging and unsolved issue. Empirical studies have shown links between pollinator diversity and plant fecundity, suggesting that a diversity–functioning relationship at the population level may occur in pollination systems. We theoretically explored the effect of pollinator diversity on plant reproduction. We found that low pollinator diversity is beneficial when the most abundant pollinators are the most effective. In contrast, when the most effective pollinators are not the most abundant, we found an optimal value of pollinator diversity at which plant fecundity is maximized. When we parametrized our model with real data, we obtained that an increase in pollinator diversity was beneficial for the reproduction of some plants whereas it was harmful for other plants, the outcome depending exclusively on the differences in effectiveness among pollinators. Consequently, our theoretical approach suggests that in pollination systems the diversity–function relationship may be explained as the consequence of the interaction between among‐pollinator differences in effectiveness and frequency of interaction, without the need to invoke additional ecological mechanisms.
Resources and pollinators contribute to population sex‐ratio bias and pollen limitation inFragaria virginiana(Rosaceae)
Authors: Case Andrea L. , Ashman Tia‐Lynn
Published: May 2009

Populations of gynodioecious species vary in the ratio of female versus hermaphroditic individuals they contain, and many exhibit higher frequencies of females under poor resource conditions. One important factor limiting female frequencies within populations is predicted to be pollen limitation of seed production, caused by either low abundance of pollen donors or insufficient pollen transfer. However, empirical studies measuring variation in pollen limitation with population sex ratios or resource gradients in gynodioecious plants are inconsistent. Part of this inconsistency may be that pollen limitation and its causes are context‐dependent. Another possibility is that sex‐specific daily flower production and/or sex‐biased visitation are more relevant to the likelihood of pollen limitation than sex ratio based on counting individual plants. In this study, we examined context‐dependent pollen limitation in gynodioecious/subdioeciousFragaria virginiana. We specifically examined the potential for resource availability to influence sex‐specific daily flower production, sex‐biased pollinator visitation, and their relationships with pollen limitation in experimental populations that contained either high or low frequencies of female plants. High resource availability reduced apparent female frequency by increasing daily flower production by hermaphrodites relative to females. This is important because pollinators increasingly discriminated against female flowers as floral sex ratios became more female‐biased. Contrary to expectation, females in high‐female populations were not consistently more pollen limited than those in low‐female populations. The level of pollen limitation of females was better explained by sex–biased pollinator foraging and visitation frequency than by the plant sex ratio or floral sex ratio. Thus, negative frequency dependence of female pollen limitation was evident only considering sex ratio bias mediated by pollinator visitation.
Thomas Pynchon: Gravity’s Rainbow. The Ideas of the Opposite
Authors: Paz Menahem
Published: May 2009

Thomas Pynchon’s highly complex novel deals with the personal and social difficulty of accepting a new worldview. Set at the end of World War II and in its aftermath, the protagonists find themselves at the crossroads between Newtonian mechanics, epitomized by the V2 rockets, and the foreshadowed atom bomb, which is based on the theory of relativity and quantum mechanics.

The style of Gravity’s Rainbow resembles the scene of a subatomic world: it is presented as an ever‐changing kaleidoscope of characters, places, events and interactions, which are constantly redetermined in relation to each other in an unpredictable manner. Pynchon manages to create a unifying theme by making all the twists in the plot comprehensible as manifestations of the underlying attempt to reconstruct selfhood. In addition, he refers recurrently to the motif of light, both as a physical entity at the center of modern physics and as a literary symbol of classical stability. In the end, his main protagonist himself turns into a mysterious source of light.
Le “je” et son ombre. La mort imaginaire de Louis Sébastien Mercier à la lumière de Saint‐Martin
Authors: Barr Philippe
Published: May 2009

L’article explore l’influence de la pensée de Saint‐Martin sur l’écriture onirique de Louis Sébastien Mercier. L’analyse de « Je suis mort », un court texte tiré des Songes et visions philosophiques, démontre que la rencontre de la pensée du « philosophe inconnu » provoque chez Mercier un important bouleversement esthétique. Ce bouleversement se traduit par le recours à une première personne qui échappe aux exigences figuratives propres aux principaux genres du récit personnel du dix‐huitième siècle. L’écriture visionnaire de Mercier diffère de l’écriture du rêve dans la dissociation qu’elle opère entre le corps et l’esprit. Elle met de plus en scène une réforme du statut accordé au langage par l’entremise d’une représentation surnaturelle de la musique qui, analogue à la révolution qui se produit dans l’écriture du Moi de Mercier, conjugue à une critique de la pensée des Lumières une remise en question de son esthétique. L’esquisse de poétique anti‐représentative que présente le texte de Mercier invite ainsi à repenser non seulement la transition entre le dix‐huitième et le dix‐neuvième siècle, mais encore à considérer sous un nouveau jour les rapports entre l’esthétique allemande et française qui lui sont aujourd’hui inhérents.
Effects of dietary supplementation with conjugated linoleic acid on fatty acid composition and lipid oxidation in chicken breast meat
Authors: KAWAHARA Satoshi , TAKENOYAMA Shin‐ichi , TAKUMA Kazuaki , MUGURUMA Michio , YAMAUCHI Kiyoshi
Published: May 2009

We investigated the effects of dietary conjugated linoleic acid (CLA) on fatty acid composition and lipid oxidation in breast meat of broiler chickens. Broiler chickens (28‐day‐old females) were fed diets containing experimental oils at 20 g/kg diet for 28 days. The experimental oils consisted of either a 2:0, 1:1, or a 0:2 (wt : wt) ratio of safflower oil (high linoleic acid content) to a commercial CLA mixture. In this study, dietary CLA supplementation significantly increased the composition and content of CLA in chicken meat. The predominant CLA in meat from birds with supplemented diets was the cis‐9, trans‐11 isomer. The proportion of saturated fatty acid in meat significantly increased with increasing CLA supplementation, with a corresponding decrease in monounsaturated fatty acid. Dietary CLA also reduced thiobarbituric acid reactive substances (TBARS) values in raw meat during storage at 4°C for 5 days. These results provide evidence that CLA feeding is a practical strategy not only for adding nutritional benefits to chicken meat but also for improving meat quality including oxidative stability.
A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds
Authors: WU Yan‐Ping , GUAN Wei‐Jun , ZHAO Qian‐Jun , HE Xiao‐Hong , PU Ya‐Bin , HUO Jun‐Hong , XIE Jin‐Fang , HAN Jian‐Lin , RAO Shao‐Qi , MA Yue‐Hui
Published: May 2009

As the fast pace of genomic research continues to identify mitochondrial lineages in animals, it has become apparent that many independent studies are needed to support a robust phylogenetic inference. The aim of this study was thus to further characterize the maternal lineage, proposed to originate in southwestern region of China, using a wider survey of diverse goat breeds in China. To this end, we sequenced the mitochondrial hypervariable region 1 (HVR1) of the mtDNA control region in 145 goats of 12 Chinese breeds. Phylogenetic analysis revealed that Chinese goats were classified into four distinct lineages (A, B, C and D) as previously reported. A Mantel test and the analysis of Analysis of Molecular Variance (ANOVA) indicated that there was not an obvious geographic structure among Chinese goat breeds. Population expansion analysis based on mismatch distribution and Fu's Fs statistic indicate that two expansion events in Chinese goats occurred respectively at about 11 and 29 mutational time units ago, revealing two star‐like subclades in lineage B corresponding to two population expansion events. Moreover, lineage B sequences were presented only in the breeds of southwestern or surrounding regions of China. Multiple lines of evidence from this study and previous studies indicate that for Chinese goats mtDNA lineage B originated from the southwestern region of China.
Association of BoLA‐DRB3 alleles identified by a sequence‐based typing method with mastitis pathogens in Japanese Holstein cows
Authors: YOSHIDA Tatsuyuki , MUKOYAMA Harutaka , FURUTA Hiroki , KONDO Yasuko , TAKESHIMA Shin‐nosuke , AIDA Yoko , KOSUGIYAMA Motoaki , TOMOGANE Hiroshi
Published: May 2009

The association of the polymorphism of bovine leukocyte antigen (BoLA‐DRB3) genes identified by the polymerase chain reaction sequence‐based typing (PCR‐SBT) method with resistance and susceptibility to mastitis caused by pathogenic bacteria was investigated. Blood samples for DNA extraction were collected from 194 Holstein cows (41 healthy cows and 153 mastitis cows including 24 mixed‐infection cows infected with 2 or 3 species of pathogens) from 5 districts of Chiba prefecture, Japan. Sixteen BoLA‐DRB3 alleles were detected. The 4 main alleles of DRB3*0101, *1501, *1201, and *1101 constituted 56.8% of the total number of alleles detected. Mastitis cows were divided into 2 groups: group 1 with single‐infection cows and group 2 with all mastitis cows including 24 mixed‐infection cows. The differences in the frequencies of BoLA‐DRB3 alleles and the number of cows homozygous or heterozygous for each BoLA‐DRB3 allele between healthy cows and the 2 groups of mastitis cows were evaluated. Furthermore, similar comparisons were performed between healthy cows and the 2 groups of mastitis cows for each mastitis pathogen. It was considered that the 4 alleles, namely, DRB3*0101, *1501, *1201, and *1101 had specific resistance and susceptibility to 4 different mastitis pathogens. Thus, DRB3*0101 might be associated with susceptibility to coagulase‐negative Staphylococci and Escherichia coli, and DRB3*1501 might be associated with susceptibility to Escherichia coli. However, DRB3*1101 might be associated with resistance to Streptococci and coagulase‐negative Staphylococci, and DRB3*1201, with resistance to Streptococci, Escherichia coli, and Staphylococcus aureus.
Mary, the Reformation and some Scots! In Memory of John Macquarrie (1919–2007)
Authors: Cummings Owen F.
Published: May 2009

Since Vatican II great progress has been made towards an ecumenical understanding and appreciation of our Blessed Lady, even as there has been a certain development in Catholic understanding. This essay looks briefly at Reformation mariologies, those of Luther, Calvin and Zwingli before moving on to consider three Scots: John Knox, Edwin Muir and John Macquarrie. Arguably, John Macquarrie has shown one of the most careful retrievals of Marian theology, not least in his Principles of Christian Theology and Mary for All Christians. His final mariological sounding took him back to his Celtic roots, and is summarized here. John Macquarrie died in 2007, and this essay is dedicated to his memory.
Demography and population viability of polar bears in the Gulf of Boothia, Nunavut
Authors: Taylor Mitchell K. , Laake Jeff , McLoughlin Philip D. , Cluff H. Dean , Messier François
Published: May 2009

Abstract

We estimated demographic parameters and harvest risks for polar bears (Ursus maritimus) inhabiting the Gulf of Boothia, Nunavut, from 1976 to 2000. We computed survival and abundance from capture–recapture and recovery data (630 marks) using a Burnham joint live–dead model implemented in program MARK. Annual mean total survival (including harvest) was 0.889 ± 0.179 (x̄± 1 SE) for cubs, 0.883 ± 0.087 for subadults (ages 1–4), 0.919 ± 0.044 for adult females, and 0.917 ± 0.041 for adult males. Abundance in the last 3 yr of study was 1,592 ± 361 bears. Mean size of newborn litters was 1.648 ± 0.098 cubs. By age 7, 0.97 ± 0.30 of available females were producing litters. Harvest averaged 38.4 ± 4.2 bears/year in the last 5 yr of study; however, the 2002–2007 kill averaged 56.4 bears/yr. We used a harvested Population Viability Analysis (PVA) to examine impacts of increasing rates of harvest. We estimated the current population growth rate, λH, to be 1.025 ± 0.032. Although this suggests the population is growing, progressive environmental changes may require more frequent population inventory studies to maintain the same levels of harvest risk.
Exploring the Anomalous Positive Relationship between AIDS and Poverty in Africa
Authors: Gould B.
Published: May 2009

HIV/AIDS is very different from most epidemic diseases in the basis of its patterning at the local, national and international scales. Unlike most epidemic diseases, HIV/AIDS is not a disease directly associated with poverty and a lack of development; in Africa it disproportionately affects the wealthy, the educated and the mobile, and prevalence rates are much higher in richer Africa countries than in the poorest countries. The anomalous relationships between HIV/AIDS and poverty in Sub‐Saharan Africa are discussed to illustrate firstly, that the disease is not directly caused by extreme poverty, nor by lack of development in the region, as are most common communicable epidemic diseases, such as malaria or measles, and secondly, that it is not a disease that can be or will be eradicated or even greatly alleviated in its severity by ‘development’, as traditionally conceived in terms of rising incomes or better health services and public health.
Appraisal Detection Bias and Well‐Being in Close Relationships: Couples Experiencing Assisted Reproduction Treatment
Authors: Kienle Rolf , Luszczynska Aleksandra , Pfüller Bettina , Knoll Nina
Published: May 2009

Communication between partners about each other's individual stress appraisals is considered to be pivotal for dyadic coping. So far, very little effort has been made to investigate the effects of accurate or biased detection of the partner's stress appraisals. On the basis of a dyadic stress model we predicted low appraisal detection bias among partners to be associated with better emotional well‐being. Furthermore, we predicted appraisal detection bias to moderate the relationship between received support and well‐being. Indicators of affect and depressive symptoms, spousal emotional support, and self‐ and partner‐rated stress appraisals from 80 couples were assessed at two points in time during early phases of assisted reproduction treatment (in‐vitro fertilisation and intracytoplasmatic sperm injection). Results indicated a protective effect of low appraisal detection bias on partners' affect. Contrary to our prediction, little or no appraisal detection bias in support‐providing partners and higher emotional support were associated with an increase of depressive symptoms in support‐receiving partners. These findings are discussed in light of research on stress‐increasing effects of received social support.
Real-Time Infrared Detection of Cyanide Flip on Silver-Alumina NO

x

Removal Catalyst
Authors: Thibault-Starzyk Frédéric , Seguin Etienne , Thomas Sébastien , Daturi Marco , Arnolds Heike , King David A.
Published: May 2009

A Jump on Catalyst Kinetics

A common method for interrogating fast reaction kinetics is to create an abrupt initiation point, and, for reactions catalyzed by metals on oxide supports, one option is to induce a rapid temperature jump, provided that the part of the catalyst undergoing heating can be probed locally.

Thibault-Starzyk
et al.

(p.
1048
) used femtosecond laser pulses to heat catalysts for nitrogen oxide removal and followed the reaction with Fourier-transform infrared spectroscopy. These catalysts are designed to remove NO in fuel-efficient lean-burn engines through reaction with CO, rather than with hydrocarbons. A cyanide reaction intermediate was identified that moves from the silver nanoparticle to the alumina surface.
John Maddox (1925–2009)
Authors: Wade Nicholas
Published: May 2009

An unorthodox editor with a love of ideas enlivened science and single-handedly shook up the world of scientific publishing.
Lawsuit Challenges Legal Basis For Patenting Human Genes
Authors: Marshall Eliot
Published: May 2009

Patents have been awarded on human genes for decades, but until last week, no one had directly challenged the underlying idea that genes can be owned in a U.S. court. Now, a challenge has begun.
NASA Asks Augustine to Point the Way
Authors: Mervis Jeffrey
Published: May 2009

This month, Norman Augustine, former CEO of Lockheed Martin, agreed to lead a 90-day review of NASA's human space flight program. Augustine shared his thoughts with
Science
on a number of issues that the panel is likely to tackle.
Identification, Characterization, and Molecular Application of a Virulence-Associated Autotransporter from a Pathogenic
Pseudomonas fluorescens
Strain
Authors: Hu Yong-hua , Liu Chun-sheng , Hou Jin-hui , Sun Li
Published: May 2009

A gene,
pfa1
, encoding an autotransporter was cloned from a pathogenic
Pseudomonas fluorescens
strain, TSS, isolated from diseased fish. The expression of
pfa1
is enhanced during infection and is regulated by growth phase and growth conditions. Mutation of
pfa1
significantly attenuates the overall bacterial virulence of TSS and impairs the abilities of TSS in biofilm production, interaction with host cells, modulation of host immune responses, and dissemination in host blood. The putative protein encoded by
pfa1
is 1,242 amino acids in length and characterized by the presence of three functional domains that are typical for autotransporters. The passenger domain of PfaI contains a putative serine protease (Pap) that exhibits apparent proteolytic activity when expressed in and purified from
Escherichia coli
as a recombinant protein. Consistent with the important role played by PfaI in bacterial virulence, purified recombinant Pap has a profound cytotoxic effect on cultured fish cells. Enzymatic analysis showed that recombinant Pap is relatively heat stable and has an optimal temperature and pH of 50°C and pH 8.0. The domains of PfaI that are essential to autotransporting activity were localized, and on the basis of this, a PfaI-based autodisplay system (named AT1) was engineered to facilitate the insertion and transport of heterologous proteins. When expressed in
E. coli
, AT1 was able to deliver an integrated
Edwardsiella tarda
immunogen (Et18) onto the surface of bacterial cells. Compared to purified recombinant Et18, Et18 displayed by
E. coli
via AT1 induced significantly enhanced immunoprotection.
Genetic Modification of Carbon Catabolite Repression in
Trichoderma reesei
for Improved Protein Production
Authors: Nakari-Setälä Tiina , Paloheimo Marja , Kallio Jarno , Vehmaanperä Jari , Penttilä Merja , Saloheimo Markku
Published: May 2009

The cellulase and hemicellulase genes of the filamentous fungus
Trichoderma reesei
have been shown to be under carbon catabolite repression mediated by the regulatory gene
cre1
. In this study, strains were constructed in which the
cre1
gene was either completely removed or replaced by a truncated mutant variant,
cre1
-
1
, found previously in the Rut-C30 mutant strain with enhanced enzyme production capability. The
T
.
reesei
transformants with either deletion or truncation of
cre1
had clearly altered colony morphology compared with the parental strains, forming smaller colonies and fewer aerial hyphae and spores. Liquid cultures in a medium with glucose as a carbon source showed that the transformants were derepressed in cellulase and hemicellulase production. Interestingly, they also produced significantly elevated levels of these hydrolytic enzymes in fermentations carried out in a medium inducing the hydrolase genes. This suggests that
cre1
acts as a modulator of cellulase and hemicellulase gene expression under both noninducing and inducing conditions. There was no phenotypic difference between the Δ
cre1
and
cre1
-
1
mutant strains in any of the experiments done, indicating that the
cre1
-
1
gene is practically a null allele. The results of this work indicate that
cre1
is a valid target gene in strain engineering for improved enzyme production in
T
.
reesei
.
Identification of a Novel Toluene-Degrading Bacterium from the Candidate Phylum TM7, as Determined by DNA Stable Isotope Probing
Authors: Luo Chunling , Xie Shuguang , Sun Weimin , Li Xiangdong , Cupples Alison M.
Published: May 2009

The dominant bacterium responsible for carbon uptake from toluene in an agricultural soil was identified by stable isotope probing. Samples were amended with unlabeled toluene or labeled [ring-
13
C
6
]toluene, and DNA was extracted over time. Sequencing indicated that the organism involved belongs to the candidate phylum TM7. Microorganisms in this candidate phylum are of particular interest because although they have been found in a variety of habitats, no stable culture of any species exists, so their general metabolic capabilities are largely unknown.
Substrate Specificity of a Mannose-6-Phosphate Isomerase from
Bacillus subtilis
and Its Application in the Production of
l
-Ribose
Authors: Yeom Soo-Jin , Ji Jung-Hwan , Kim Nam-Hee , Park Chang-Su , Oh Deok-Kun
Published: May 2009

The uncharacterized gene previously proposed as a mannose-6-phosphate isomerase from
Bacillus subtilis
was cloned and expressed in
Escherichia coli
. The maximal activity of the recombinant enzyme was observed at pH 7.5 and 40°C in the presence of 0.5 mM Co
2+
. The isomerization activity was specific for aldose substrates possessing hydroxyl groups oriented in the same direction at the C-2 and C-3 positions, such as the
d
and
l
forms of ribose, lyxose, talose, mannose, and allose. The enzyme exhibited the highest activity for
l
-ribulose among all pentoses and hexoses. Thus,
l
-ribose, as a potential starting material for many
l
-nucleoside-based pharmaceutical compounds, was produced at 213 g/liter from 300-g/liter
l
-ribulose by mannose-6-phosphate isomerase at 40°C for 3 h, with a conversion yield of 71% and a volumetric productivity of 71 g liter
−1
h
−1
.
Bacterial Associates of Arboreal Ants and Their Putative Functions in an Obligate Ant-Plant Mutualism
Authors: Eilmus Sascha , Heil Martin
Published: May 2009

Bacterial communities are highly diverse and have great ecological importance. In the present study, we used an in silico analysis of terminal restriction fragments (tRF) to characterize the bacterial community of the plant ant
Pseudomyrmex ferrugineus
. This species is an obligate inhabitant of
Acacia
myrmecophytes and feeds exclusively on plant-derived food sources. Ants are the dominant insect group in tropical rain forests. Associations of ants with microbes, which contribute particularly to the ants’ nitrogen nutrition, could allow these insects to live on mostly or entirely plant-based diets and could thus contribute to the explanation of the high abundances that are reached by tropical ants. We found tRF patterns representing at least 30 prokaryotic taxa, of which the
Acidobacteria
,
Actinobacteria
,
Bacteroidetes
,
Firmicutes
,
Planctomycetes
,
Proteobacteria
, and
Spirochaetes
comprised 93%. Because most bacterial taxa were found in all ant-derived samples studied and because the bacteria detected on the ants’ host plant revealed little overlap with this community, we regard our results as reliably representing the bacterial community that is associated with
P. ferrugineus
. Genera with a likely function as ant symbionts were
Burkholderia
,
Pantoea
,
Weissella
, and several members of the
Enterobacteriaceae
. The presence of these and various other groups was confirmed via independent PCR and cultivation approaches. Many of the bacteria that we detected belong to purportedly N-fixing taxa. Bacteria may represent important further partners in ant-plant mutualisms, and their influences on ant nutrition can contribute to the extraordinary abundance and evolutionary success of tropical arboreal ants.
Diversity and Functional Analysis of LuxR-Type Transcriptional Regulators of Cyclic Lipopeptide Biosynthesis in
Pseudomonas fluorescens
Authors: de Bruijn I. , Raaijmakers J. M.
Published: May 2009

Cyclic lipopeptides (CLPs) are produced by many
Pseudomonas
species and have several biological functions, including a role in surface motility, biofilm formation, virulence, and antimicrobial activity. This study focused on the diversity and role of LuxR-type transcriptional regulators in CLP biosynthesis in
Pseudomonas
species and, specifically, viscosin production by
Pseudomonas fluorescens
strain SBW25. Phylogenetic analyses showed that CLP biosynthesis genes in
Pseudomonas
strains are flanked by LuxR-type regulators that contain a DNA-binding helix-turn-helix domain but lack
N
-acylhomoserine lactone-binding or response regulator domains. For SBW25, site-directed mutagenesis of the genes coding for either of the two identified LuxR-type regulators, designated ViscAR and ViscBCR, strongly reduced transcript levels of the
viscABC
biosynthesis genes and resulted in a loss of viscosin production. Expression analyses further showed that a mutation in either
viscAR
or
viscBCR
did not substantially (change of <2.5-fold) affect transcription of the other regulator. Transformation of the Δ
viscAR
mutant of SBW25 with a LuxR-type regulatory gene from
P. fluorescens
strain SS101 that produces massetolide, a CLP structurally related to viscosin, restored transcription of the
viscABC
genes and viscosin production. The results further showed that a functional
viscAR
gene was required for heterologous expression of the massetolide biosynthesis genes of strain SS101 in strain SBW25, leading to the production of both viscosin and massetolide. Collectively, these results indicate that the regulators flanking the CLP biosynthesis genes in
Pseudomonas
species represent a unique LuxR subfamily of proteins and that viscosin biosynthesis in
P. fluorescens
SBW25 is controlled by two LuxR-type transcriptional regulators.
Antibiotic Overproduction by
rpsL
and
rsmG
Mutants of Various Actinomycetes
Authors: Tanaka Yukinori , Komatsu Mamoru , Okamoto Susumu , Tokuyama Shinji , Kaji Akira , Ikeda Haruo , Ochi Kozo
Published: May 2009

Certain streptomycin resistance mutations (i.e.,
rpsL
and
rsmG
) result in the overproduction of antibiotics in various actinomycetes. Moreover,
rpsL rsmG
double-mutant strains show a further increase in antibiotic production.
rpsL
but not
rsmG
mutations result in a marked enhancement of oligomycin production in
Streptomyces avermitilis
and erythromycin production in
Saccharopolyspora erythraea
, accompanied by increased transcription of a key developmental regulator gene,
bldD
, in the latter organism.
Effects of
Bacillus thuringiensis
δ-Endotoxins on the Pea Aphid (
Acyrthosiphon pisum
)
Authors: Porcar Manuel , Grenier Anne-Marie , Federici Brian , Rahbé Yvan
Published: May 2009

Four
Bacillus thuringiensis
δ-endotoxins, Cry3A, Cry4Aa, Cry11Aa, and Cyt1Aa, were found to exhibit low to moderate toxicity on the pea aphid,
Acyrthosiphon pisum
, in terms both of mortality and growth rate. Cry1Ab was essentially nontoxic except at high rates. To demonstrate these effects, we had to use exhaustive buffer-based controls.
Metabolic Versatility and Indigenous Origin of the Archaeon
Thermococcus sibiricus
, Isolated from a Siberian Oil Reservoir, as Revealed by Genome Analysis
Authors: Mardanov Andrey V. , Ravin Nikolai V. , Svetlitchnyi Vitali A. , Beletsky Alexey V. , Miroshnichenko Margarita L. , Bonch-Osmolovskaya Elizaveta A. , Skryabin Konstantin G.
Published: May 2009

Thermococcus
species are widely distributed in terrestrial and marine hydrothermal areas, as well as in deep subsurface oil reservoirs.
Thermococcus sibiricus
is a hyperthermophilic anaerobic archaeon isolated from a well of the never flooded oil-bearing Jurassic horizon of a high-temperature oil reservoir. To obtain insight into the genome of an archaeon inhabiting the oil reservoir, we have determined and annotated the complete 1,845,800-base genome of
T
.
sibiricus
. A total of 2,061 protein-coding genes have been identified, 387 of which are absent in other members of the order
Thermococcales
. Physiological features and genomic data reveal numerous hydrolytic enzymes (e.g., cellulolytic enzymes, agarase, laminarinase, and lipases) and metabolic pathways, support the proposal of the indigenous origin of
T
.
sibiricus
in the oil reservoir, and explain its survival over geologic time and its proliferation in this habitat. Indeed, in addition to proteinaceous compounds known previously to be present in oil reservoirs at limiting concentrations, its growth was stimulated by cellulose, agarose, and triacylglycerides, as well as by alkanes. Two polysaccharide degradation loci were probably acquired by
T
.
sibiricus
from thermophilic bacteria following lateral gene transfer events. The first, a “saccharolytic gene island” absent in the genomes of other members of the order
Thermococcales
, contains the complete set of genes responsible for the hydrolysis of cellulose and β-linked polysaccharides. The second harbors genes for maltose and trehalose degradation. Considering that agarose and laminarin are components of algae, the encoded enzymes and the substrate spectrum of
T
.
sibiricus
indicate the ability to metabolize the buried organic matter from the original oceanic sediment.
Identification of a Polyketide Synthase Coding Sequence Specific for Anatoxin-a-Producing
Oscillatoria
Cyanobacteria
Authors: Cadel-Six Sabrina , Iteman Isabelle , Peyraud-Thomas Caroline , Mann Stéphane , Ploux Olivier , Méjean Annick
Published: May 2009

We report the identification of a sequence from the genome of
Oscillatoria
sp. strain PCC 6506 coding for a polyketide synthase. Using 50 axenic cyanobacteria, we found this sequence only in the genomes of
Oscillatoria
strains producing anatoxin-a or homoanatoxin-a, indicating its likely involvement in the biosynthesis of these toxins.
Influence of
Pythium oligandrum
Biocontrol on Fungal and Oomycete Population Dynamics in the Rhizosphere
Authors: Vallance Jessica , Le Floch Gaétan , Déniel Franck , Barbier Georges , Lévesque C. André , Rey Patrice
Published: May 2009

Fungal and oomycete populations and their dynamics were investigated following the introduction of the biocontrol agent
Pythium oligandrum
into the rhizosphere of tomato plants grown in soilless culture. Three strains of
P. oligandrum
were selected on the basis of their ability to form oospores (resting structures) and to produce tryptamine (an auxin-like compound) and oligandrin (a glycoprotein elicitor). Real-time PCR and plate counting demonstrated the persistence of large amounts of the antagonistic oomycete in the rhizosphere throughout the cropping season (April to September). Inter-simple-sequence-repeat analysis of the
P. oligandrum
strains collected from root samples at the end of the cropping season showed that among the three strains used for inoculation, the one producing the smallest amount of oospores was detected at 90%. Single-strand conformational polymorphism analysis revealed increases in the number of members and the complexity of the fungal community over time. There were no significant differences between the microbial ecosystems inoculated with
P. oligandrum
and those that were not treated, except for a reduction of
Pythium dissotocum
(ubiquitous tomato root minor pathogen) populations in inoculated systems during the last 3 months of culture. These findings raise interesting issues concerning the use of
P. oligandrum
strains producing elicitor and auxin molecules for plant protection and the development of biocontrol.
Induction of Immune Responses in Mice after Oral Immunization with RecombinantLactobacillus caseiStrains Expressing EnterotoxigenicEscherichia coliF41 Fimbrial Protein
Authors: Liu Jian-Kui , Hou Xi-Lin , Wei Chun-Hua , Yu Li-Yun , He Xiao-Jie , Wang Gui-Hua , Lee Jong-Soo , Kim Chul-Joong
Published: May 2009

In an effort to develop a safe and effective vaccine for the prevention of enterotoxigenicEscherichia coli(ETEC) F41 infections, we have developed a surface antigen display system using poly-γ-glutamate synthetase A (PgsA) as an anchoring matrix. The recombinant fusion proteins comprised of PgsA and fimbrial protein of F41 were stably expressed inLactobacillus casei525. Surface localization of the fusion protein was verified by immunoblotting, immunofluorescence microscopy, and flow cytometry. Oral inoculation of recombinantL. casei525 into specific-pathogen-free BALB/c mice resulted in significant mucosal immunoglobulin A (IgA) titers that remained elevated for >16 weeks. High levels of IgG responses in sera specific for F41 fimbriae were also induced, with prominent IgG1 titers as well as IgG2a and IgG2b titers. The helper T-cell (Th) response was Th2-cell dominant, as evidenced by increased mucosal and systemic interleukin-4-producing T cells and a concomitant elevation of serum IgG1 antibody responses. More than 80% of the mice were protected against challenge with a 2 × 104-fold 50% lethal dose of standard-type F41 (C83919). The induced antibodies were important for eliciting a protective immune response against F41 infection. These results indicated that the use of recombinantL. casei525 could be a valuable strategy for future vaccine development for ETEC.
mcrA
-Targeted Real-Time Quantitative PCR Method To Examine Methanogen Communities
Authors: Steinberg Lisa M. , Regan John M.
Published: May 2009

Methanogens are of great importance in carbon cycling and alternative energy production, but quantitation with culture-based methods is time-consuming and biased against methanogen groups that are difficult to cultivate in a laboratory. For these reasons, methanogens are typically studied through culture-independent molecular techniques. We developed a SYBR green I quantitative PCR (qPCR) assay to quantify total numbers of methyl coenzyme M reductase α-subunit (
mcrA
) genes. TaqMan probes were also designed to target nine different phylogenetic groups of methanogens in qPCR assays. Total
mcrA
and
mcrA
levels of different methanogen phylogenetic groups were determined from six samples: four samples from anaerobic digesters used to treat either primarily cow or pig manure and two aliquots from an acidic peat sample stored at 4°C or 20°C. Only members of the
Methanosaetaceae
,
Methanosarcina
,
Methanobacteriaceae
, and
Methanocorpusculaceae
and Fen cluster were detected in the environmental samples. The three samples obtained from cow manure digesters were dominated by members of the genus
Methanosarcina
, whereas the sample from the pig manure digester contained detectable levels of only members of the
Methanobacteriaceae
. The acidic peat samples were dominated by both
Methanosarcina
spp. and members of the Fen cluster. In two of the manure digester samples only one methanogen group was detected, but in both of the acidic peat samples and two of the manure digester samples, multiple methanogen groups were detected. The TaqMan qPCR assays were successfully able to determine the environmental abundance of different phylogenetic groups of methanogens, including several groups with few or no cultivated members.
Behavior of the Meat-Borne Bacterium
Lactobacillus sakei
during Its Transit through the Gastrointestinal Tracts of Axenic and Conventional Mice
Authors: Chiaramonte Fabrizio , Blugeon Sébastien , Chaillou Stéphane , Langella Philippe , Zagorec Monique
Published: May 2009

A
Lactobacillus sakei
strain named FLEC01 was isolated from human feces and characterized genotypically. Comparison of the genetic features of this strain with those of both the meat-borne
L. sakei
strain 23K and another human isolate, LTH5590, showed that they belong to different but closely related clusters. The three
L. sakei
strains did not persist and only transited through the gastrointestinal tracts (GITs) of conventional C3H/HeN mice. In contrast, they all colonized the GITs of axenic mice and rapidly reached a population of 10
9
CFU/g of feces, which remained stable until day 51. Five days after mice were fed, a first subpopulation, characterized by small colonies, appeared and reached 50% of the total
L. sakei
population in mice. Fifteen to 21 days after feeding, a second subpopulation, characterized by rough colonies, appeared. It coexisted with the two other populations until day 51, and its cell shapes were also affected, suggesting a dysfunction of the cell division or cell wall. No clear difference between the behaviors of the meat-borne strain and the two human isolates in both conventional and axenic mice was observed, suggesting that
L. sakei
is a food-borne bacterium rather than a commensal one and that its presence in human feces originates from diet. Previous observations of
Escherichia coli
strains suggest that the mouse GIT environment could induce mutations to increase their survival and colonization capacities. Here, we observed similar mutations concerning a food-grade gram-positive bacterium for the first time.
Retention and Release of
Cryptosporidium parvum
Oocysts by Experimental Biofilms Composed of a Natural Stream Microbial Community
Authors: Wolyniak E. A. , Hargreaves B. R. , Jellison K. L.
Published: May 2009

Cryptosporidium parvum
oocysts accumulate on biofilm surfaces. The percentage of oocysts attached to biofilms remained nearly constant while oocysts were supplied to the system but decreased to a new steady-state level once oocysts were removed from the feed. More oocysts attached to summer biofilm cultures than winter biofilm cultures.
Dispersion of Multidrug-Resistant
Enterococcus faecium
Isolates Belonging to Major Clonal Complexes in Different Portuguese Settings
Authors: Freitas Ana R. , Novais Carla , Ruiz-Garbajosa Patricia , Coque Teresa M. , Peixe Luísa
Published: May 2009

The population structure of 56
Enterococcus faecium
isolates selected from a collection of enterococci from humans, animals, and the environment in Portugal (1997 to 2007) was analyzed by multilocus sequence typing. We identified 41 sequence types clustering into CC17, CC5, CC9, CC22 and CC94, all clonal lineages comprising isolates from different hosts. Our findings highlight the role of community-associated hosts as reservoirs of enterococci able to cause human infections.
Detection, Distribution, and Organohalogen Compound Discovery Implications of the Reduced Flavin Adenine Dinucleotide-Dependent Halogenase Gene in Major Filamentous Actinomycete Taxonomic Groups
Authors: Gao Peng , Huang Ying
Published: May 2009

Halogenases have been shown to play a significant role in biosynthesis and introducing the bioactivity of many halogenated secondary metabolites. In this study, 54 reduced flavin adenine dinucleotide (FADH
2
)-dependent halogenase gene-positive strains were identified after the PCR screening of a large collection of 228 reference strains encompassing all major families and genera of filamentous actinomycetes. The wide distribution of this gene was observed to extend to some rare lineages with higher occurrences and large sequence diversity. Subsequent phylogenetic analyses revealed that strains containing highly homologous halogenases tended to produce halometabolites with similar structures, and halogenase genes are likely to propagate by horizontal gene transfer as well as vertical inheritance within actinomycetes. Higher percentages of halogenase gene-positive strains than those of halogenase gene-negative ones contained polyketide synthase genes and/or nonribosomal peptide synthetase genes or displayed antimicrobial activities in the tests applied, indicating their genetic and physiological potentials for producing secondary metabolites. The robustness of this halogenase gene screening strategy for the discovery of particular biosynthetic gene clusters in rare actinomycetes besides streptomycetes was further supported by genome-walking analysis. The described distribution and phylogenetic implications of the FADH
2
-dependent halogenase gene present a guide for strain selection in the search for novel organohalogen compounds from actinomycetes.
Novel Toxin-Antitoxin System Composed of Serine Protease and AAA-ATPase Homologues Determines the High Level of Stability and Incompatibility of the Tumor-Inducing Plasmid pTiC58
Authors: Yamamoto Shinji , Kiyokawa Kazuya , Tanaka Katsuyuki , Moriguchi Kazuki , Suzuki Katsunori
Published: May 2009

Stability of plant tumor-inducing (Ti) plasmids differs among strains. A high level of stability prevents basic and applied studies including the development of useful strains. The nopaline type Ti plasmid pTiC58 significantly reduces the transconjugant efficiency for incoming incompatible plasmids relative to the other type, such as octopine-type plasmids. In this study we identified a region that increases the incompatibility and stability of the plasmid. This region was located on a 4.3-kbp segment about 38 kbp downstream of the replication locus,
repABC
. We named two open reading frames in the segment,
ietA
and
ietS
, both of which were essential for the high level of incompatibility and stability. Plasmid stabilization by
ietAS
was accomplished by a toxin-antitoxin (TA) mechanism, where IetS is the toxin and IetA is the antitoxin. A database search revealed that putative IetA and IetS proteins are highly similar to AAA-ATPases and subtilisin-like serine proteases, respectively. Amino acid substitution experiments in each of the highly conserved characteristic residues, in both putative enzymes, suggested that the protease activity is essential and that ATP binding activity is important for the operation of the TA system. The
ietAS
-containing
repABC
plasmids expelled Ti plasmids even in strains which were tolerant to conventional Ti-curing treatments.
Redundant Hydrogen Peroxide Scavengers Contribute to
Salmonella
Virulence and Oxidative Stress Resistance
Authors: Hébrard Magali , Viala Julie P. M. , Méresse Stéphane , Barras Frédéric , Aussel Laurent
Published: May 2009

Salmonella enterica
serovar Typhimurium is an intracellular pathogen that can survive and replicate within macrophages. One of the host defense mechanisms that
Salmonella
encounters during infection is the production of reactive oxygen species by the phagocyte NADPH oxidase. Among them, hydrogen peroxide (H
2
O
2
) can diffuse across bacterial membranes and damage biomolecules. Genome analysis allowed us to identify five genes encoding H
2
O
2
degrading enzymes: three catalases (KatE, KatG, and KatN) and two alkyl hydroperoxide reductases (AhpC and TsaA). Inactivation of the five cognate structural genes yielded the HpxF
−
mutant, which exhibited a high sensitivity to exogenous H
2
O
2
and a severe survival defect within macrophages. When the phagocyte NADPH oxidase was inhibited, its proliferation index increased 3.7-fold. Moreover, the overexpression of
katG
or
tsaA
in the HpxF
−
background was sufficient to confer a proliferation index similar to that of the wild type in macrophages and a resistance to millimolar H
2
O
2
in rich medium. The HpxF
−
mutant also showed an attenuated virulence in a mouse model. These data indicate that
Salmonella
catalases and alkyl hydroperoxide reductases are required to degrade H
2
O
2
and contribute to the virulence. This enzymatic redundancy highlights the evolutionary strategies developed by bacterial pathogens to survive within hostile environments.
RsmC ofErwinia carotovorasubsp.carotovoraNegatively Controls Motility, Extracellular Protein Production, and Virulence by Binding FlhD and Modulating Transcriptional Activity of the Master Regulator, FlhDC
Authors: Chatterjee Asita , Cui Yaya , Chatterjee Arun K.
Published: May 2009

RsmC and FlhDC are global regulators controlling extracellular proteins/enzymes,rsmBRNA, motility, and virulence ofErwinia carotovorasubsp.carotovora. FlhDC, the master regulator of flagellar genes, controls these traits by positively regulatinggacA,fliA, andrsmCand negatively regulatinghexA. RsmC, on the other hand, is a negative regulator of extracellular proteins/enzymes, motility, and virulence since the deficiency of RsmC in FlhDC+strain results in overproduction of extracellular proteins/enzymes, hypermotility, and hypervirulence. These phenotypes are abolished in an RsmC−FlhDC−double mutant. We show that RsmC interferes with FlhDC action. Indeed, the expression of all three targets (i.e.,gacA,rsmC, andfliA) positively regulated inE.carotovorasubsp.carotovoraby FlhDC is inhibited by RsmC. RsmC also partly relieves the inhibition ofhexAexpression by FlhDC. The results of yeast two-hybrid analysis revealed that RsmC binds FlhD and FlhDC, but not FlhC. We propose that binding of RsmC with FlhD/FlhDC interferes with its regulatory functions and that RsmC acts as an anti-FlhD4FlhC2factor. We document here for the first time that RsmC interferes with activation offliAand motility in several members of theEnterobacteriaceaefamily. The extent ofE.carotovorasubsp.carotovoraRsmC-mediated inhibition of FlhDC-dependent expression offliAand motility varies depending upon enterobacterial species. The data presented here support the idea that differences in structural features in enterobacterial FlhD are responsible for differential susceptibility toE.carotovorasubsp.carotovoraRsmC action.
Survival of Pathogenic Mycobacteria in Macrophages Is Mediated through Autophosphorylation of Protein Kinase G
Authors: Scherr Nicole , Müller Philipp , Perisa Damir , Combaluzier Benoît , Jenö Paul , Pieters Jean
Published: May 2009

Pathogenic mycobacteria survive within macrophages through the inhibition of phagosome-lysosome fusion. A crucial factor for avoiding lysosomal degradation is the mycobacterial serine/threonine protein kinase G (PknG). PknG is released into the macrophage cytosol upon mycobacterial infection, suggesting that PknG might exert its activity by interfering with host signaling cascades, but the mode of action of PknG remains unknown. Here, we show that PknG undergoes autophosphorylation on threonine residues located at the N terminus. In contrast to all other mycobacterial kinases investigated thus far, autophosphorylation of PknG was not involved in the regulation of its kinase activity. However, autophosphorylation was crucial for the capacity of PknG to promote mycobacterial survival within macrophages. These results will contribute to a better understanding of the virulence mechanisms of pathogenic mycobacteria and may help to design improved inhibitors of PknG to be developed as antimycobacterial compounds.