bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stenoxybacter acetivorans
gen. nov., sp. nov., an Acetate-Oxidizing Obligate Microaerophile among Diverse O
2
-Consuming Bacteria from Termite Guts
Authors: Wertz John T. , Breznak John A. 
Published: September 2007

ABSTRACT

In termite hindguts, fermentative production of acetate—a major carbon and energy source for the insect—depends on efficient removal of inwardly diffusing oxygen by microbes residing on and near the hindgut wall. However, little is known about the identity of these organisms or about the substrate(s) used to support their respiratory activity. A cultivation-based approach was used to isolate O
2
-consuming organisms from hindguts of
Reticulitermes flavipes
. A consistently greater (albeit not statistically significant) number of colonies developed under hypoxia (2% [vol/vol] O
2
) than under air, and the increase coincided with the appearance of morphologically distinct colonies of a novel, rod-shaped, obligately microaerophilic β-proteobacterium that was <95% similar (based on the 16S rRNA gene sequence) to its closest known relative (
Eikenella corrodens
). Nearly identical organisms (and/or their 16S rRNA genes) were obtained from geographically separated and genetically distinct populations of
Reticulitermes
. PCR-based procedures implied that the novel isolates were autochthonous to the hindgut of
R. flavipes
and comprised ca. 2 to 7% of the hindgut prokaryote community. Representative strain TAM-DN1 utilized acetate and a limited range of other organic and amino acids as energy sources and possessed catalase and superoxide dismutase. On solid medium, the optimal O
2
concentration for growth was about 2%, and no growth occurred with O
2
concentrations above 4% or under anoxia. However, cells in liquid medium could grow with higher O
2
concentrations (up to 16%), but only after proportionately extended lag phases. The genetic and physiological distinctiveness of TAM-DN1 and related strains supports their recognition as a new genus and species, for which the name
Stenoxybacter acetivorans
gen. nov., sp. nov. is proposed.
Phylogenetic Ecology of the Freshwater
Actinobacteria
acI Lineage
Authors: Newton Ryan J. , Jones Stuart E. , Helmus Matthew R. , McMahon Katherine D. 
Published: September 2007

ABSTRACT

The acI lineage of freshwater
Actinobacteria
is a cosmopolitan and often numerically dominant member of lake bacterial communities. We conducted a survey of acI 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions from 18 Wisconsin lakes and used standard nonphylogenetic and phylogenetic statistical approaches to investigate the factors that determine acI community composition at the local scale (within lakes) and at the regional scale (across lakes). Phylogenetic reconstruction of 434 acI 16S rRNA genes revealed a well-defined and highly resolved phylogeny. Eleven previously unrecognized monophyletic clades, each with ≥97.9% within-clade 16S rRNA gene sequence identity, were identified. Clade community similarity positively correlated with lake environmental similarity but not with geographic distance, implying that the lakes represent a single biotic region containing environmental filters for communities that have similar compositions. Phylogenetically disparate clades within the acI lineage were most abundant at the regional scale, and local communities were comprised of more closely related clades. Lake pH was a strong predictor of the community composition, but only when lakes with a pH below 6 were included in the data set. In the remaining lakes (pH above 6) biogeographic patterns in the landscape were instead a predictor of the observed acI community structure. The nonrandom distribution of the newly defined acI clades suggests potential ecophysiological differences between the clades, with acI clades AI, BII, and BIII preferring acidic lakes and acI clades AII, AVI, and BI preferring more alkaline lakes.
Detection and Visualization of an Exopolysaccharide Produced byXylella fastidiosaIn Vitro and In Planta
Authors: Roper M. Caroline , Greve L. Carl , Labavitch John M. , Kirkpatrick Bruce C. 
Published: September 2007

ABSTRACTMany phytopathogenic bacteria, such asRalstonia solanacearum,Pantoea stewartii, andXanthomonas campestris, produce exopolysaccharides (EPSs) that aid in virulence, colonization, and survival. EPS can also contribute to host xylem vessel blockage. The genome ofXylella fastidiosa, the causal agent of Pierce's disease (PD) of grapevine, contains an operon that is strikingly similar to theX. campestris gumoperon, which is responsible for the production of xanthan gum. Based on this information, it has been hypothesized thatX. fastidiosais capable of producing an EPS similar in structure and composition to xanthan gum but lacking the terminal mannose residue. In this study, we raised polyclonal antibodies against a modified xanthan gum polymer similar to the predictedX. fastidiosaEPS polymer. We used enzyme-linked immunosorbent assay to quantify production of EPS fromX. fastidiosacells grown in vitro and immunolocalization microscopy to examine the distribution ofX. fastidiosaEPS in biofilms formed in vitro and in planta and assessed the contribution ofX. fastidiosaEPS to the vascular occlusions seen in PD-infected grapevines.
Methanobrevibacter ruminantium
as an Indicator of Domesticated-Ruminant Fecal Pollution in Surface Waters
Authors: Ufnar Jennifer A. , Wang Shiao Y. , Ufnar David F. , Ellender R. D. 
Published: September 2007

ABSTRACT

A PCR-based assay (Mrnif) targeting the
nifH
gene of
Methanobrevibacter ruminantium
was developed to detect fecal pollution from domesticated ruminants in environmental water samples. The assay produced the expected amplification product only when the reaction mixture contained DNA extracted from
M. ruminantium
culture, bovine (80%), sheep (100%), and goat (75%) feces, and water samples from a bovine waste lagoon (100%) and a creek contaminated with bovine lagoon waste (100%). The assay appears to be specific and sensitive and can distinguish between domesticated- and nondomesticated-ruminant fecal pollution in environmental samples.
Stenotrophomonas maltophiliaSeITE02, a New Bacterial Strain Suitable for Bioremediation of Selenite-Contaminated Environmental Matrices
Authors: Antonioli Paolo , Lampis Silvia , Chesini Irene , Vallini Giovanni , Rinalducci Sara , Zolla Lello , Righetti Pier Giorgio 
Published: September 2007

ABSTRACTBiochemical and proteomic tools have been utilized for investigating the mechanism of action of a newStenotrophomonas maltophiliastrain (SeITE02), a gammaproteobacterium capable of resistance to high concentrations of selenite [SeO32−, Se(IV)], reducing it to nontoxic elemental selenium under aerobic conditions; this strain was previously isolated from a selenite-contaminated mining soil. Biochemical analysis demonstrated that (i) nitrite reductase does not seem to take part in the process of selenite reduction by the bacterial strain SeITE02, although its involvement in this process had been hypothesized in other cases; (ii) nitrite strongly interferes with selenite removal when the two oxyanions (NO2−and SeO32−) are simultaneously present, suggesting that the two reduction/detoxification pathways share a common enzymatic step, probably at the level of cellular transport; (iii) in vitro, selenite reduction does not take place in the membrane or periplasmic fractions but only in the cytoplasm, where maximum activity is exhibited at pH 6.0 in the presence of NADPH; and (iv) glutathione is involved in the selenite reduction mechanism, since inhibition of its synthesis leads to a considerable delay in the onset of reduction. As far as the proteomic findings are concerned, the evidence was reached that 0.2 mM selenite and 16 mM nitrite, when added to the culture medium, caused a significant modulation (ca. 10%, i.e., 96 and 85 protein zones, respectively) of the total proteins visualized in the respective two-dimensional maps. These spots were identified by mass spectrometry analysis and were found to belong to the following functional classes: nucleotide synthesis and metabolism, damaged-protein catabolism, protein and amino acid metabolism, and carbohydrate metabolism along with DNA-related proteins and proteins involved in cell division, oxidative stress, and cell wall synthesis.
Application of DNA Bar Codes for Screening of Industrially Important Fungi: the Haplotype of
Trichoderma harzianum
Sensu Stricto Indicates Superior Chitinase Formation
Authors: Nagy Viviana , Seidl Verena , Szakacs George , Komoń-Zelazowska Monika , Kubicek Christian P. , Druzhinina Irina S. 
Published: September 2007

ABSTRACT

Selection of suitable strains for biotechnological purposes is frequently a random process supported by high-throughput methods. Using chitinase production by
Hypocrea lixii/Trichoderma harzianum
as a model, we tested whether fungal strains with superior enzyme formation may be diagnosed by DNA bar codes. We analyzed sequences of two phylogenetic marker loci, internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA-encoding gene cluster and the large intron of the elongation factor 1-alpha gene,
tef1
, from 50 isolates of
H. lixii/T. harzianum
, which were also tested to determine their ability to produce chitinases in solid-state fermentation (SSF). Statistically supported superior chitinase production was obtained for strains carrying one of the observed ITS1 and ITS2 and
tef1
alleles corresponding to an allele of
T. harzianum
type strain CBS 226.95. A
tef1
-based DNA bar code tool,
Tricho
CHIT, for rapid identification of these strains was developed. The geographic origin of the strains was irrelevant for chitinase production. The improved chitinase production by strains containing this haplotype was not due to better growth on
N
-acetyl-β-
d
-glucosamine or glucosamine. Isoenzyme electrophoresis showed that neither the isoenzyme profile of
N
-acetyl-β-glucosaminidases or the endochitinases nor the intensity of staining of individual chitinase bands correlated with total chitinase in the culture filtrate. The superior chitinase producers did not exhibit similarly increased cellulase formation. Biolog Phenotype MicroArray analysis identified lack of
N
-acetyl-β-
d
-mannosamine utilization as a specific trait of strains with the chitinase-overproducing haplotype. This observation was used to develop a plate screening assay for rapid microbiological identification of the strains. The data illustrate that desired industrial properties may be an attribute of certain populations within a species, and screening procedures should thus include a balanced mixture of all genotypes of a given species.
Multiple Introductions of the Old World Begomovirus
Tomato yellow leaf curl virus
into the New World
Authors: Duffy Siobain , Holmes Edward C. 
Published: September 2007

ABSTRACT

A phylogenetic analysis of three genomic regions revealed that
Tomato yellow leaf curl virus
(TYLCV) from western North America is distinct from TYLCV isolated in eastern North America and the Caribbean. This analysis supports a second introduction of this Old World begomovirus into the New World, most likely from Asia.
Autecology of an Arsenite Chemolithotroph: Sulfide Constraints on Function and Distribution in a Geothermal Spring
Authors: D'Imperio Seth , Lehr Corinne R. , Breary Michele , McDermott Timothy R. 
Published: September 2007

ABSTRACT

Previous studies in an acid-sulfate-chloride spring in Yellowstone National Park found that microbial arsenite [As(III)] oxidation is absent in regions of the spring outflow channel where H
2
S exceeds ∼5 μM and served as a backdrop for continued efforts in the present study. Ex situ assays with microbial mat samples demonstrated immediate As(III) oxidation activity when H
2
S was absent or at low concentrations, suggesting the presence of As(III) oxidase enzymes that could be reactivated if H
2
S is removed. Cultivation experiments initiated with mat samples taken from along the H
2
S gradient in the outflow channel resulted in the isolation of an As(III)-oxidizing chemolithotroph from the low-H
2
S region of the gradient. The isolate was phylogenetically related to
Acidicaldus
and was characterized in vitro for spring-relevant properties, which were then compared to its distribution pattern in the spring as determined by denaturing gradient gel electrophoresis and quantitative PCR. While neither temperature nor oxygen requirements appeared to be related to the occurrence of this organism within the outflow channel, H
2
S concentration appeared to be an important constraint. This was verified by in vitro pure-culture modeling and kinetic experiments, which suggested that H
2
S inhibition of As(III) oxidation is uncompetitive in nature. In summary, the studies reported herein illustrate that H
2
S is a potent inhibitor of As(III) oxidation and will influence the niche opportunities and population distribution of As(III) chemolithotrophs.
Mutated Cadherin Alleles from a Field Population of
Helicoverpa armigera
Confer Resistance to
Bacillus thuringiensis
Toxin Cry1Ac
Authors: Yang Yajun , Chen Haiyan , Wu Yidong , Yang Yihua , Wu Shuwen 
Published: September 2007

ABSTRACT

The cotton bollworm
Helicoverpa armigera
is the major insect pest targeted by cotton genetically engineered to produce the
Bacillus thuringiensis
toxin (transgenic Bt cotton) in the Old World. The evolution of this pest's resistance to
B. thuringiensis
toxins is the main threat to the long-term effectiveness of transgenic Bt cotton. A deletion mutation allele (
r

1

) of a cadherin gene (
Ha_BtR
) was previously identified as genetically linked with Cry1Ac resistance in a laboratory-selected strain of
H. armigera
. Using a biphasic screen strategy, we successfully trapped two new cadherin alleles (
r

2

and
r

3

) associated with Cry1Ac resistance from a field population of
H. armigera
collected from the Yellow River cotton area of China in 2005. The
r

2

and
r

3

alleles, respectively, were created by inserting the long terminal repeat of a retrotransposon (designated
HaRT1
) and the intact
HaRT1
retrotransposon at the same position in exon 8 of
Ha_BtR
, which results in a truncated cadherin containing only two ectodomain repeats in the N terminus of
Ha_BtR
. This is the first time that the
B. thuringiensis
resistance alleles of a target insect of Bt crops have been successfully detected in the open field. This study also demonstrated that bollworm larvae carrying two resistance alleles can complete development on Bt cotton. The cadherin locus should be an important target for intensive DNA-based screening of field populations of
H. armigera
.
Effects of Salivary Gland Hypertrophy Virus on the Reproductive Behavior of the Housefly,
Musca domestica
Authors: Lietze Verena-Ulrike , Geden Christopher J. , Blackburn Patrick , Boucias Drion G. 
Published: September 2007

ABSTRACT
Pathological studies demonstrated that the salivary gland hypertrophy virus of houseflies (MdSGHV) shuts down reproduction in infected females. The mechanism that underlay the disruption of reproduction functioned on several levels. Females infected at the previtellogenic stage did not produce eggs, reflecting a block in the gonadotropic cycle. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blot analysis of hemolymph samples demonstrated that MdSGHV infection reduced the levels of both the female-specific hexamerin and egg yolk proteins. Furthermore, reverse transcriptase quantitative real-time PCR data demonstrated that infection blocked hexamerin and yolk protein gene transcription. When females were allowed to develop eggs prior to infection (postvitellogenic stage), the outcome of mating attempts depended upon when mating took place. If egg-containing, virus-infected females were mated within 24 h of infection, they copulated and deposited a single batch of fertilized eggs. However, if mating was delayed for a longer period, the egg-containing females refused to copulate with healthy males. Both of these results suggested that a virus-induced signal influenced the central nervous system, shutting down female receptivity and egg production. All experiments demonstrated that MdSGHV-infected males did not display azoospermia and were fertile. Both healthy females mated with infected males, and the resulting F1 progeny were free of salivary gland hypertrophy symptoms, which suggests that the virus is not sexually or vertically transmitted.
Identification of anEntamoeba histolyticaSerine-, Threonine-, and Isoleucine-Rich Protein with Roles in Adhesion and Cytotoxicity
Authors: MacFarlane Ryan C. , Singh Upinder 
Published: September 2007

ABSTRACTEntamoeba histolyticais a leading cause of parasitic death globally. However, the molecular framework regulating pathogenesis is poorly understood. We have previously used expression profiling to identifyEntamoebagenes whose expressions were strictly associated with virulent strains (R. C. MacFarlane and U. Singh, Infect. Immun. 74:340-351, 2006). One gene, which we have named EhSTIRP (Entamoebahistolyticaserine-,threonine-, andisoleucine-richprotein), was exclusively expressed in virulent but not in nonvirulentEntamoebastrains. EhSTIRP is predicted to be a transmembrane protein and is encoded by a multigene family. In order to characterize its function in amebic biology, we used a double-stranded RNA-based approach and were able to selectively down-regulate expression of this gene family. Upon EhSTIRP down-regulation, we were able to ascribe cytotoxic and adhesive properties to the protein family using lactate dehydrogenase release and Chinese hamster ovary cell adhesion assays. EhSTIRP thus likely represents a novel determinant of virulence inEntamoeba histolytica. This work validates the fact that genes expressed exclusively in virulent strains may represent virulence determinants and highlights the need for further functional analyses of other genes with similar expression profiles.
The Deoxycytidine Pathway for Thymidylate Synthesis in
Escherichia coli
Authors: Weiss Bernard 
Published: September 2007

ABSTRACT

When thymidylate production is diminished by a mutation affecting dCTP deaminase,
Escherichia coli
is known to use an alternate pathway involving deoxycytidine as an intermediate. The pathway requires the gene for any of three nucleoside diphosphate kinases (
ndk
,
pykA
, or
pykF
) and the gene for a 5′-nucleotidase (
yfbR
).
Transcriptome Analysis of the
Vibrio fischeri
LuxR-LuxI Regulon
Authors: Antunes Luis Caetano M. , Schaefer Amy L. , Ferreira Rosana B. R. , Qin Nan , Stevens Ann M. , Ruby Edward G. , Greenberg E. Peter 
Published: September 2007

ABSTRACT

The
Vibrio fischeri
quorum-sensing signal
N
-3-oxohexanoyl-
l
-homoserine lactone (3OC6-HSL) activates expression of the seven-gene luminescence operon. We used microarrays to unveil 18 additional 3OC6-HSL-controlled genes, 3 of which had been identified by other means previously. We show most of these genes are regulated by the 3OC6-HSL-responsive transcriptional regulator LuxR directly. This demonstrates that
V. fischeri
quorum sensing regulates a substantial number of genes other than those involved in light production.
The
Mesorhizobium loti purB
Gene Is Involved in Infection Thread Formation and Nodule Development in
Lotus japonicus
Authors: Okazaki Shin , Hattori Yoshiyuki , Saeki Kazuhiko 
Published: September 2007

ABSTRACT

The
purB
and
purH
mutants of
Mesorhizobium loti
exhibited purine auxotrophy and nodulation deficiency on
Lotus japonicus
. In the presence of adenine, only the
purH
mutant induced nodule formation and the
purB
mutant produced few infection threads, suggesting that 5-aminoimidazole-4-carboxamide ribonucleotide biosynthesis catalyzed by PurB is required for the establishment of symbiosis.
DivL Performs Critical Cell Cycle Functions inCaulobacter crescentusIndependent of Kinase Activity
Authors: Reisinger Sarah J. , Huntwork Sarah , Viollier Patrick H. , Ryan Kathleen R. 
Published: September 2007

ABSTRACTTheCaulobactercell cycle is regulated by a network of two-component signal transduction proteins. Phosphorylation and stability of the master transcriptional regulator CtrA are controlled by the CckA-ChpT phosphorelay, and CckA activity is modulated by another response regulator, DivK. In a screen to identify suppressors of the cold-sensitivedivK341mutant, we found point mutations in the essential genedivL. DivL is similar to histidine kinases but has a tyrosine instead of a histidine at the conserved phosphorylation site (Y550). Surprisingly, we found that the ATPase domain of DivL is not essential forCaulobacterviability. We show that DivL selectively affects CtrA phosphorylation but not CtrA proteolysis, indicating that DivL acts in a pathway independent of the CckA-ChpT phosphorelay.divLcan be deleted in a strain overproducing the phosphomimetic protein CtrAD51E, but unlike ΔctrAcells expressing CtrAD51E, this strain is profoundly impaired in the control of chromosome replication and cell division. Thus, DivL performs a second function in addition to promoting CtrA phosphorylation. DivL is required for bipolar DivK localization and positively regulates DivK phosphorylation. Our results show that DivL controls two key cell cycle regulators, CtrA and DivK, and that phosphoryl transfer is not DivL's essential cellular activity.
Enterococcal Surface Protein Esp Is Important for Biofilm Formation of
Enterococcus faecium
E1162
Authors: Heikens Esther , Bonten Marc J. M. , Willems Rob J. L. 
Published: September 2007

ABSTRACT

Enterococci have emerged as important nosocomial pathogens with resistance to multiple antibiotics. Adhesion to abiotic materials and biofilm formation on medical devices are considered important virulence properties. A single clonal lineage of
Enterococcus faecium
, complex 17 (CC17), appears to be a successful nosocomial pathogen, and most CC17 isolates harbor the enterococcal surface protein gene,
esp
. In this study, we constructed an
esp
insertion-deletion mutant in a clinical
E. faecium
CC17 isolate. In addition, initial adherence and biofilm assays were performed. Compared to the wild-type strain, the
esp
insertion-deletion mutant no longer produced Esp on the cell surface and had significantly lower initial adherence to polystyrene and significantly less biofilm formation, resulting in levels of biofilm comparable to those of an
esp
-negative isolate. Capacities for initial adherence and biofilm formation were restored in the insertion-deletion mutant by in
trans
complementation with
esp
. These results identify Esp as the first documented determinant in
E. faecium
CC17 with an important role in biofilm formation, which is an essential factor in infection pathogenesis.