bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light-Stimulated Bacterial Production and Amino Acid Assimilation by Cyanobacteria and Other Microbes in the North Atlantic Ocean
Authors: Michelou Vanessa K. , Cottrell Matthew T. , Kirchman David L. 
Published: July 2007

ABSTRACT

We examined the contribution of photoheterotrophic microbes—those capable of light-mediated assimilation of organic compounds—to bacterial production and amino acid assimilation along a transect from Florida to Iceland from 28 May to 9 July 2005. Bacterial production (leucine incorporation at a 20 nM final concentration) was on average 30% higher in light than in dark-incubated samples, but the effect varied greatly (3% to 60%). To further characterize this light effect, we examined the abundance of potential photoheterotrophs and measured their contribution to bacterial production and amino acid assimilation (0.5 nM addition) using flow cytometry.
Prochlorococcus
and
Synechococcus
were abundant in surface waters where light-dependent leucine incorporation was observed, whereas aerobic anoxygenic phototrophic bacteria were abundant but did not correlate with the light effect. The per-cell assimilation rates of
Prochlorococcus
and
Synechococcus
were comparable to or higher than those of other prokaryotes, especially in the light. Picoeukaryotes also took up leucine (20 nM) and other amino acids (0.5 nM), but rates normalized to biovolume were much lower than those of prokaryotes.
Prochlorococcus
was responsible for 80% of light-stimulated bacterial production and amino acid assimilation in surface waters south of the Azores, while
Synechococcus
accounted for on average 12% of total assimilation. However, nearly 40% of the light-stimulated leucine assimilation was not accounted for by these groups, suggesting that assimilation by other microbes is also affected by light. Our results clarify the contribution of cyanobacteria to photoheterotrophy and highlight the potential role of other photoheterotrophs in biomass production and dissolved-organic-matter assimilation.
Isolation of Polymer-Degrading Bacteria and Characterization of the Hindgut Bacterial Community from the Detritus-Feeding Larvae of
Tipula abdominalis
(Diptera: Tipulidae)
Authors: Cook Dana M. , DeCrescenzo Henriksen Emily , Upchurch Rima , Peterson Joy B. Doran 
Published: July 2007

ABSTRACT

The
Tipula abdominalis
larval hindgut microbial community presumably facilitates digestion of the lignocellulosic diet. The microbial community was investigated through characterization of bacterial isolates and analysis of 16S rRNA gene clone libraries. This initial study revealed novel bacteria and provides a framework for future studies of this symbiosis.
Persistence of Caliciviruses in Artificially Contaminated Oysters during Depuration
Authors: Ueki You , Shoji Mika , Suto Atsushi , Tanabe Toru , Okimura Yoko , Kikuchi Yoshihiko , Saito Noriyuki , Sano Daisuke , Omura Tatsuo 
Published: July 2007

ABSTRACT
The fate of calicivirus in oysters in a 10-day depuration was assessed. The norovirus gene was persistently detected from artificially contaminated oysters during the depuration, whereas feline calicivirus in oysters was promptly eliminated. The prolonged observation of norovirus in oysters implies the existence of a selective retention mechanism for norovirus within oysters.
Substrate Specificity-Conferring Regions of the Nonribosomal Peptide Synthetase Adenylation Domains Involved in Albicidin Pathotoxin Biosynthesis Are Highly Conserved within the SpeciesXanthomonas albilineans
Authors: Renier Adeline , Vivien Eric , Cociancich Stéphane , Letourmy Philippe , Perrier Xavier , Rott Philippe C. , Royer Monique 
Published: July 2007

ABSTRACTAlbicidin is a pathotoxin produced byXanthomonas albilineans, a xylem-invading pathogen that causes leaf scald disease of sugarcane. Albicidin is synthesized by a nonribosomal pathway via modular polyketide synthase and nonribosomal peptide synthetase (NRPS) megasynthases, and NRPS adenylation (A) domains are responsible for the recognition and activation of specific amino acid substrates. DNA fragments (0.5 kb) encoding the regions responsible for the substrate specificities of six albicidin NRPS A domains from 16 strains ofX. albilineansrepresenting the known diversity of this pathogen were amplified and sequenced. Polymorphism analysis of these DNA fragments at different levels (DNA, protein, and NRPS signature) showed that these pathogenicity loci were highly conserved. The conservation of these loci most likely reflects purifying selective pressure, as revealed by a comparison with the variability of nucleotide and amino acid sequences of two housekeeping genes (atpDandefp) ofX. albilineans. Nevertheless, the 16 strains ofX. albilineanswere differentiated into several groups by a phylogenetic analysis of the nucleotide sequences corresponding to the NRPS A domains. One of these groups was representative of the genetic diversity previously found within the pathogen by random fragment length polymorphism and amplified fragment length polymorphism analyses. This group, which differed by three single synonymous nucleotide mutations, contained only four strains ofX. albilineansthat were all involved in outbreaks of sugarcane leaf scald. The amount of albicidin produced in vitro in agar and liquid media varied among the 16 strains ofX. albilineans. However, no relationship among the amount of albicidin produced in vitro and the pathotypes and genetic diversity of the pathogen was found. The NRPS loci contributing to the synthesis of the primary structure of albicidin apparently are not involved in the observed pathogenicity differences among strains ofX. albilineans.
Cooccurring
Gentiana verna
and
Gentiana acaulis
and Their Neighboring Plants in Two Swiss Upper Montane Meadows Harbor Distinct Arbuscular Mycorrhizal Fungal Communities
Authors: Sýkorová Zuzana , Wiemken Andres , Redecker Dirk 
Published: July 2007

ABSTRACT

The community composition of arbuscular mycorrhizal fungi (AMF) was analyzed in roots of
Gentiana verna
,
Gentiana acaulis
, and accompanying plant species from two species-rich Swiss alpine meadows located in the same area. The aim of the study was to elucidate the impact of host preference or host specificity on the AMF community in the roots. The roots were analyzed by nested PCR, restriction fragment length polymorphism screening, and sequencing of ribosomal DNA small-subunit and internal transcribed spacer regions. The AMF sequences were analyzed phylogenetically and used to define monophyletic sequence types. The AMF community composition was strongly influenced by the host plant species, but compositions did not significantly differ between the two sites. Detailed analyses of the two cooccurring gentian species
G. verna
and
G. acaulis
, as well as of neighboring
Trifolium
spp., revealed that their AMF communities differed significantly. All three host plant taxa harbored AMF communities comprising multiple phylotypes from different fungal lineages. A frequent fungal phylotype from
Glomus
group B was almost exclusively found in
Trifolium
spp., suggesting some degree of host preference for this fungus in this habitat. In conclusion, the results indicate that within a relatively small area with similar soil and climatic conditions, the host plant species can have a major influence on the AMF communities within the roots. No evidence was found for a narrowing of the mycosymbiont spectrum in the two green gentians, in contrast to previous findings with their achlorophyllous relatives.
Metabolic Engineering of
Saccharomyces cerevisiae
for Conversion of
d
-Glucose to Xylitol and Other Five-Carbon Sugars and Sugar Alcohols
Authors: Toivari Mervi H. , Ruohonen Laura , Miasnikov Andrei N. , Richard Peter , Penttilä Merja 
Published: July 2007

ABSTRACT

Recombinant
Saccharomyces cerevisiae
strains that produce the sugar alcohols xylitol and ribitol and the pentose sugar
d
-ribose from
d
-glucose in a single fermentation step are described. A transketolase-deficient
S. cerevisiae
strain accumulated
d
-xylulose 5-phosphate intracellularly and released ribitol and pentose sugars (
d
-ribose,
d
-ribulose, and
d
-xylulose) into the growth medium. Expression of the xylitol dehydrogenase-encoding gene
XYL2
of
Pichia stipitis
in the transketolase-deficient strain resulted in an 8.5-fold enhancement of the total amount of the excreted sugar alcohols ribitol and xylitol. The additional introduction of the 2-deoxy-glucose 6-phosphate phosphatase-encoding gene
DOG1
into the transketolase-deficient strain expressing the
XYL2
gene resulted in a further 1.6-fold increase in ribitol production. Finally, deletion of the endogenous xylulokinase-encoding gene
XKS1
was necessary to increase the amount of xylitol to 50% of the 5-carbon sugar alcohols excreted.
Role of
laeA
in the Regulation of
alb1
,
gliP
, Conidial Morphology, and Virulence in
Aspergillus fumigatus
Authors: Sugui Janyce A. , Pardo Julian , Chang Yun C. , Müllbacher Arno , Zarember Kol A. , Galvez Eva M. , Brinster Lauren , Zerfas Patricia , Gallin John I. , Simon Markus M. , Kwon-Chung Kyung J. 
Published: July 2007

ABSTRACT

The
alb1
(
pksP
) gene has been reported as a virulence factor controlling the pigmentation and morphology of conidia in
Aspergillus fumigatus
. A recent report suggested that
laeA
regulates
alb1
expression and conidial morphology but not pigmentation in the
A. fumigatus
strain AF293.
laeA
has also been reported to regulate the synthesis of secondary metabolites, such as gliotoxin. We compared the role of
laeA
in the regulation of conidial morphology and the expression of
alb1
and
gliP
in strains B-5233 and AF293, which differ in colony morphology and nutritional requirements. Deletion of
laeA
did not affect conidial morphology or pigmentation in these strains, suggesting that
laeA
is not involved in
alb1
regulation during conidial morphogenesis. Deletion of
laeA
, however, caused down-regulation of
alb1
during mycelial growth in a liquid medium. Transcription of
gliP
, involved in the synthesis of gliotoxin, was drastically reduced in B-5233
laeAΔ
, and the gliotoxin level found in the culture filtrates was 20% of wild-type concentrations. While up-regulation of
gliP
in AF293 was comparable to that in B-5233, the relative mRNA level in AF293
laeAΔ
was about fourfold lower than that in B-5233
laeAΔ
. Strain B-5233
laeAΔ
caused slower onset of fatal infection in mice relative to that with B-5233. Histopathology of sections from lungs of infected mice corroborated the survival data. Culture filtrates from B-5233
laeAΔ
caused reduced death in thymoma cells and were less inhibitory to a respiratory burst of neutrophils than culture filtrates from B-5233. Our results suggest that while
laeA
is not involved in the regulation of
alb1
function in conidial morphology, it regulates the synthesis of gliotoxin and the virulence of
A. fumigatus.
EhLimA, a Novel LIM Protein, Localizes to the Plasma Membrane inEntamoeba histolytica
Authors: Wender Nomy , Villalobo Eduardo , Mirelman David 
Published: July 2007

ABSTRACTThe parasitic protozoanEntamoeba histolyticarelies on a very dynamic cytoskeleton in order to invade and survive in host tissues. Identification of cytoskeletal elements is key to understanding these processes. Here we present the characterization of EhLimA, the first LIM protein ofE. histolytica. EhLimA consists of a single LIM domain at its N terminus and exhibits the highest degree of homology with DdLimE fromDictyostelium discoideum. Immunofluorescence localization of EhLimA using anti-EhLimA antibodies revealed that EhLimA is highly concentrated at the plasma membrane of cells. Silencing or overexpression of the EhLimAgene did not have a significant effect on the growth or morphology of the parasite. EhLimA associates with the cytoskeleton as demonstrated by the enrichment of the protein in cytoskeleton fractions as well as in pull-down assays that revealed that cytoskeleton association involves interaction with actin. EhLimA binding to actin was shown to be dependent on the N-terminal LIM domain of EhLimA, as removal of even half of the LIM domain resulted in almost complete inhibition of the binding to actin. We also found that a portion of EhLimA floats to the lower-density regions of a sucrose gradient together with portions of the Gal-lectin light subunit and actin. Treatment of cells with the cholesterol-sequestering agent digitonin resulted in increased solubility of EhLimA. These results indicate that in addition to cytoskeletal association, EhLimA may also associate with lipid rafts in the parasite plasma membrane and suggest that EhLimA may be part of the molecular system connecting the actin cytoskeleton to membrane rafts.
Aspergillus nidulans
Conidiation Genes
dewA
,
fluG
, and
stuA
Are Differentially Regulated in Early Vegetative Growth
Authors: Breakspear Andrew , Momany Michelle 
Published: July 2007

ABSTRACT

Microarray analysis was used to identify transcriptional changes in early vegetative growth of the filamentous fungus
Aspergillus nidulans
. The results suggest that the previously identified conidiation genes
dewA
,
fluG
, and
stuA
may function in isotropic expansion during early vegetative growth and asexual reproduction.
VirB1* Promotes T-Pilus Formation in the
vir
-Type IV Secretion System of
Agrobacterium tumefaciens
Authors: Zupan John , Hackworth Cheryl A. , Aguilar Julieta , Ward Doyle , Zambryski Patricia 
Published: July 2007

ABSTRACT

The
vir
-type IV secretion system of
Agrobacterium
is assembled from 12 proteins encoded by the
virB
operon and
virD4
. VirB1 is one of the least-studied proteins encoded by the
virB
operon. Its N terminus is a lytic transglycosylase. The C-terminal third of the protein, VirB1*, is cleaved from VirB1 and secreted to the outside of the bacterial cell, suggesting an additional function. We show that both nopaline and octopine strains produce abundant amounts of VirB1* and perform detailed studies on nopaline VirB1*. Both domains are required for wild-type virulence. We show here that the nopaline type VirB1* is essential for the formation of the T pilus, a subassembly of the
vir
-T4SS composed of processed and cyclized VirB2 (major subunit) and VirB5 (minor subunit). A nopaline
virB1
deletion strain does not produce T pili. Complementation with full-length VirB1 or C-terminal VirB1*, but not the N-terminal lytic transglycosylase domain, restores T pili containing VirB2 and VirB5. T-pilus preparations also contain extracellular VirB1*. Protein-protein interactions between VirB1* and VirB2 and VirB5 were detected in the yeast two-hybrid assay. We propose that VirB1 is a bifunctional protein required for
vir
T4SS assembly. The N-terminal lytic transglycosylase domain provides localized lysis of the peptidoglycan cell wall to allow insertion of the T4SS. The C-terminal VirB1* promotes T-pilus assembly through protein-protein interactions with T-pilus subunits.
In Vivo Oligomerization of the F Conjugative Coupling Protein TraD
Authors: Haft Rembrandt J. F. , Gachelet Eliora G. , Nguyen Tran , Toussaint Luttrell , Chivian Dylan , Traxler Beth 
Published: July 2007

ABSTRACT
Type IV secretory systems are a group of bacterial transporters responsible for the transport of proteins and nucleic acids directly into recipient cells. Such systems play key roles in the virulence of some pathogenic organisms and in conjugation-mediated horizontal gene transfer. Many type IV systems require conserved “coupling proteins,” transmembrane polypeptides that are critical for transporting secreted substrates across the cytoplasmic membrane of the bacterium. In vitro evidence suggests that the functional form of coupling proteins is a homohexameric, ring-shaped complex. Using a library of tagged mutants, we investigated the structural and functional organization of the F plasmid conjugative coupling protein TraD by coimmunoprecipitation, cross-linking, and genetic means. We present direct evidence that coupling proteins form stable oligomeric complexes in the membranes of bacteria and that the formation of some of these complexes requires other F-encoded functions. Our data also show that different regions of TraD play distinct roles in the oligomerization process. We postulate a model for in vivo oligomerization and discuss the probable participation of individual domains of TraD in each step.
Pseudomonas aeruginosa
Psl Is a Galactose- and Mannose-Rich Exopolysaccharide
Authors: Ma Luyan , Lu Haiping , Sprinkle April , Parsek Matthew R. , Wozniak Daniel J. 
Published: July 2007

ABSTRACT

The
Pseudomonas aeruginosa
polysaccharide synthesis locus (
psl
) is predicted to encode an exopolysaccharide which is critical for biofilm formation. Here we used chemical composition analyses and mannose- or galactose-specific lectin staining, followed by confocal laser scanning microscopy and electron microscopy, to show that Psl is a galactose-rich and mannose-rich exopolysaccharide.
The Politics of Divine Presence: Temple as Locus of Conflict in the Gospel of Mark
Authors: Driggers Ira Brent 
Published: July 2007

AbstractThis paper examines the intersection of theology and politics in the Gospel of Mark as it pertains to Jesus' conflict with the so-called "leaders," giving special attention to the role of the Jerusalem temple within that conflict. It is argued that the temple as cultic institution does not concern the narrator as much as its affiliation with a priestly elite that abuses its God-given authority at the expense of those in need. As the mediator of God's presence Jesus exposes this abuse through a ministry of outreach, meeting rejection by the very ones charged to oversee the "house of God" (2:26; 11:17). This ironic rejection of the divine presence consists of both ignorance (failure to recognize Jesus as God's son) and self-interest (concern for honor and power). Jesus' climactic condemnation of the temple (11:11-25; 13:1-2) thus symbolizes his rejection of its caretakers, the "tenants" once commissioned by God to care for God's own vineyard (12:1-12).
The Lord's House and David's Lord: The Psalms and Mark's Perspective on Jesus and the Temple
Authors: Watts Rikk 
Published: July 2007

AbstractFour Davidic Psalms (2, 118, 110, and 22), each cited or alluded to at least twice, in this order, and at critical junctures in Mark's narrative, play a key role in his Gospel. In contemporary understanding Psalm 2 was associated with the future messianic purging of Jerusalem and especially the temple (e.g.4QFlor, Pss Sol 17). Psalm 118, concluding the Egyptian Hallel, spoke of Israel's future deliverance under a Davidic king with the restored temple as the goal of Israel's return from exile. Psalm 110's surprisingly elevated royal designation, uniquely expressed in Melchizedekian priestking terms, contributed to several portraits of exalted heavenly deliverers, some messianic, who would preside over Israel's restoration (e.g.11QMelch, 1 Enoch) while Psalm 22's Davidic suffering and vindication described the deliverance of righteous Zion (e.g.4QPs). Drawing from the dual perspective of their original contexts and contemporary interpretations, this paper proposes that Mark's careful arrangement of his psalm citations presents Jesus as both Israel's Davidic Messiah (Pss. 2, 118) and the temple's Lord (Ps. 110) who, coming to purge Jerusalem but rejected by the temple authorities, announces the present structure's destruction and, through his death and vindication (Ps. 22), its replacement with a new people-temple centered on himself.
Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) and of its relationship to H. zea
Authors: Behere Gajanan T , Tay Wee Tek , Russell Derek A , Heckel David G , Appleton Belinda R , Kranthi Keshav R , Batterham Philip 
Published: July 2007

Abstract

Background

Helicoverpa armigera and H. zea are amongst the most significant polyphagous pest lepidopteran species in the Old and New Worlds respectively. Separation of H. armigera and H. zea is difficult and is usually only achieved through morphological differences in the genitalia. They are capable of interbreeding to produce fertile offspring. The single species status of H. armigera has been doubted, due to its wide distribution and plant host range across the Old World. This study explores the global genetic diversity of H. armigera and its evolutionary relationship to H zea.

Results
We obtained partial (511 bp) mitochondrial DNA (mtDNA) Cytochrome Oxidase-I (COI) sequences for 249 individuals of H. armigera sampled from Australia, Burkina Faso, Uganda, China, India and Pakistan which were associated with various host plants. Single nucleotide polymorphisms (SNPs) within the partial COI gene differentiated H. armigera populations into 33 mtDNA haplotypes. Shared haplotypes between continents, low F-statistic values and low nucleotide diversity between countries (0.0017 – 0.0038) suggests high mobility in this pest. Phylogenetic analysis of four major Helicoverpa pest species indicates that H. punctigera is basal to H. assulta, which is in turn basal to H. armigera and H. zea. Samples from North and South America suggest that H. zea is also a single species across its distribution. Our data reveal short genetic distances between H. armigera and H. zea which seem to have been established via a founder event from H. armigera stock at around 1.5 million years ago.

Conclusion
Our mitochondrial DNA sequence data supports the single species status of H. armigera across Africa, Asia and Australia. The evidence for inter-continental gene flow observed in this study is consistent with published evidence of the capacity of this species to migrate over long distances. The finding of high genetic similarity between Old World H. armigera and New World H. zea emphasises the need to consider work on both pests when building pest management strategies for either.