bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Sensitivity Stable-Isotope Probing by a Quantitative Terminal Restriction Fragment Length Polymorphism Protocol
Authors: Andeer Peter , Strand Stuart E. , Stahl David A. 
Published: October 2011

ABSTRACT

Stable-isotope probing (SIP) has proved a valuable cultivation-independent tool for linking specific microbial populations to selected functions in various natural and engineered systems. However, application of SIP to microbial populations with relatively minor buoyant density increases, such as populations that utilize compounds as a nitrogen source, results in reduced resolution of labeled populations. We therefore developed a tandem quantitative PCR (qPCR)–TRFLP (terminal restriction fragment length polymorphism) protocol that improves resolution of detection by quantifying specific taxonomic groups in gradient fractions. This method combines well-controlled amplification with TRFLP analysis to quantify relative taxon abundance in amplicon pools of FAM-labeled PCR products, using the intercalating dye EvaGreen to monitor amplification. Method accuracy was evaluated using mixtures of cloned 16S rRNA genes, DNA extracted from low- and high-G+C bacterial isolates (
Escherichia coli
,
Rhodococcus
,
Variovorax
, and
Microbacterium
), and DNA from soil microcosms amended with known amounts of genomic DNA from bacterial isolates. Improved resolution of minor shifts in buoyant density relative to TRFLP analysis alone was confirmed using well-controlled SIP analyses.
Endosymbiont Transmission Mode in Bacterial Leaf Nodulation as Revealed by a Population Genetic Study of Psychotria leptophylla
Authors: Lemaire Benny , Janssens Steven , Smets Erik , Dessein Steven 
Published: October 2011

ABSTRACT

Leaf-nodulated plants are colonized by vertically inherited bacterial endosymbionts, which maintain symbioses throughout host generations. The permanent character of the interaction implies phylogenetic congruence between the host and the endosymbiont. However, the present population genetic study of
Psychotria leptophylla
provides evidence for a mixed symbiont transmission involving both vertical inheritance and horizontal transfers from the environment.
Iron Transformations Induced by an Acid-Tolerant Desulfosporosinus Species
Authors: Bertel Doug , Peck John , Quick Thomas J. , Senko John M. 
Published: October 2011

ABSTRACTThe mineralogical transformations of Fe phases induced by an acid-tolerant, Fe(III)- and sulfate-reducing bacterium,Desulfosporosinussp. strain GBSRB4.2 were evaluated under geochemical conditions associated with acid mine drainage-impacted systems (i.e., low pH and high Fe concentrations). X-ray powder diffractometry coupled with magnetic analysis by first-order reversal curve diagrams were used to evaluate mineral phases produced by GBSRB4.2 in media containing different ratios of Fe(II) and Fe(III). In medium containing Fe predominately in the +II oxidation state, ferrimagnetic, single-domain greigite (Fe3S4) was formed, but the addition of Fe(III) inhibited greigite formation. In media that contained abundant Fe(III) [as schwertmannite; Fe8O8(OH)6SO4·nH2O], the activities of strain GBSRB4.2 enhanced the transformation of schwertmannite to goethite (α-FeOOH), due to the increased pH and Fe(II) concentrations that resulted from the activities of GBSRB4.2.
Comparison of Assays for Sensitive and Reproducible Detection of Cell Culture-Infectious Cryptosporidium parvum and Cryptosporidium hominis in Drinking Water
Authors: Johnson Anne M. , Di Giovanni George D. , Rochelle Paul A. 
Published: October 2011

ABSTRACT

This study compared the three most commonly used assays for detecting
Cryptosporidium
sp. infections in cell culture: immunofluorescent antibody and microscopy assay (IFA), PCR targeting
Cryptosporidium
sp.-specific DNA, and reverse transcriptase PCR (RT-PCR) targeting
Cryptosporidium
sp.-specific mRNA. Monolayers of HCT-8 cells, grown in 8-well chamber slides or 96-well plates, were inoculated with a variety of viable and inactivated oocysts to assess assay performance. All assays detected infection with low doses of flow cytometry-enumerated
Cryptosporidium parvum
oocysts, including infection with one oocyst and three oocysts. All methods also detected infection with
Cryptosporidium hominis
. The RT-PCR assay, IFA, and PCR assay detected infection in 23%, 25%, and 51% of monolayers inoculated with three
C. parvum
oocysts and 10%, 9%, and 16% of monolayers inoculated with one oocyst, respectively. The PCR assay was the most sensitive, but it had the highest frequency of false positives with mock-infected cells and inactivated oocysts. IFA was the only infection detection assay that did not produce false positives with mock-infected monolayers. IFA was also the only assay that detected infections in all experiments with spiked oocysts recovered from Envirochek capsules following filtration of 1,000 liters of treated water. Consequently, cell culture with IFA detection is the most appropriate method for routine and sensitive detection of infectious
Cryptosporidium parvum
and
Cryptosporidium hominis
in drinking water.
Prevalence of Ca
2+
-ATPase-Mediated Carbonate Dissolution among Cyanobacterial Euendoliths
Authors: Ramírez-Reinat E. L. , Garcia-Pichel F. 
Published: October 2011

ABSTRACT

Recent physiological work has shown that the filamentous euendolithic cyanobacterium
Mastigocoleus testarum
(strain BC008) is able to bore into solid carbonates using Ca
2+
-ATPases to take up Ca
2+
from the medium at the excavation front, promoting dissolution of CaCO
3
there. It is not known, however, if this is a widespread mechanism or, rather, a unique capability of this model strain. To test this, we undertook a survey of multispecies euendolithic microbial assemblages infesting natural carbonate substrates in marine coastal waters of the Caribbean, Mediterranean, South Pacific, and Sea of Cortez. Microscopic examination revealed the presence of complex assemblages of euendoliths, encompassing 3 out of the 5 major cyanobacterial orders. 16S rRNA gene clone libraries detected even greater diversity, particularly among the thin-filamentous forms, and allowed us to categorize the endoliths in our samples into 8 distinct phylogenetic clades. Using real-time Ca
2+
imaging under a confocal laser scanning microscope, we could show that all communities displayed light-dependent formation of Ca
2+
-supersaturated zones in and around boreholes, a staple of actively boring phototrophs. In 3 out of 4 samples, boring activity was sensitive to at least one of two inhibitors of Ca
2+
-ATPase transporters (thapsigargin or
tert
-butylhydroquinone), indicating that the Ca
2+
-ATPase mechanism is widespread among cyanobacterial euendoliths but perhaps not universal. Function-community structure correlations point to one particular clade of baeocyte-forming euendoliths as the potential exception.
Engineering of Bacterial Methyl Ketone Synthesis for Biofuels
Authors: Goh Ee-Been , Baidoo Edward E. K. , Keasling Jay D. , Beller Harry R. 
Published: October 2011

ABSTRACT

We have engineered
Escherichia coli
to overproduce saturated and monounsaturated aliphatic methyl ketones in the C
11
to C
15
(diesel) range; this group of methyl ketones includes 2-undecanone and 2-tridecanone, which are of importance to the flavor and fragrance industry and also have favorable cetane numbers (as we report here). We describe specific improvements that resulted in a 700-fold enhancement in methyl ketone titer relative to that of a fatty acid-overproducing
E. coli
strain, including the following: (i) overproduction of β-ketoacyl coenzyme A (CoA) thioesters achieved by modification of the β-oxidation pathway (specifically, overexpression of a heterologous acyl-CoA oxidase and native FadB and chromosomal deletion of
fadA
) and (ii) overexpression of a native thioesterase (FadM). FadM was previously associated with oleic acid degradation, not methyl ketone synthesis, but outperformed a recently identified methyl ketone synthase (
Solanum habrochaites
MKS2 [
Sh
MKS2], a thioesterase from wild tomato) in β-ketoacyl-CoA-overproducing strains tested. Whole-genome transcriptional (microarray) studies led to the discovery that FadM is a valuable catalyst for enhancing methyl ketone production. The use of a two-phase system with decane enhanced methyl ketone production by 4- to 7-fold in addition to increases from genetic modifications.
Adhesive Bond Stiffness of Staphylococcus aureus with and without Proteins That Bind to an Adsorbed Fibronectin Film
Authors: Olsson Adam L. J. , Sharma Prashant K. , van der Mei Henny C. , Busscher Henk J. 
Published: October 2011

ABSTRACT

Staphylococcus aureus
is known to cause biomaterial-associated infections of implants and devices once it has breached the skin and mucosal barriers. Adhesion is the initial step in the development of a biomaterial-associated infection, and strategies to prevent staphylococcal adhesion and thus biomaterial-associated infections require understanding of the adhesive bond. The aim of this study was to compare the adhesive bond stiffnesses of two
S. aureus
strains with and without fibronectin-binding proteins (FnBPs) adhering to a fibronectin-coated quartz crystal microbalance (QCM) sensor surface on the basis of a coupled- resonance model. Both fibronectin adsorption and staphylococcal adhesion were accompanied by negative frequency shifts, regardless of the absence or presence of FnBPs on the staphylococcal cell surfaces. This is the opposite of the positive frequency shifts often observed for other bacterial strains adhering to bare sensor surfaces. Most likely, adhering staphylococci sink into and deform the adsorbed protein layer, creating stiff binding with the sensor surface due to an increased bacterium-substratum contact area.
S. aureus
8325-4 possesses FnBPs and yields less negative frequency shifts (Δ
f
) that are further away from the zero-crossing frequency than
S. aureus
DU5883. This suggests that FnBPs on
S. aureus
8325-4 create a stiffer bond to the fibronectin coating than has been observed for
S. aureus
DU5883. Due to a limited window of observation, as defined by the available resonance frequencies in QCM, we could not determine exact stiffness values.
Protective Effects of Passively Transferred Merozoite-Specific Antibodies against Theileria equi in Horses with Severe Combined Immunodeficiency
Authors: Mealey Robert H. , Kappmeyer Lowell S. , Ueti Massaro W. , Wagner Bettina , Knowles Donald P. 
Published: October 2011

ABSTRACTTheileria equiimmune plasma was infused into young horses (foals) with severe combined immunodeficiency. Although all foals became infected following intravenous challenge with homologousT. equimerozoite stabilate, delayed time to peak parasitemia occurred. Protective effects were associated with a predominance of passively transferred merozoite-specific IgG3.
Serum Antibody Responses to 10 Mycobacterium tuberculosis Proteins, Purified Protein Derivative, and Old Tuberculin in Natural and Experimental Tuberculosis in Rhesus Monkeys
Authors: Min Fangui , Zhang Yu , Huang Ren , Li Wende , Wu Yu'e , Pan Jinchun , Zhao Weibo , Liu Xiangmei 
Published: October 2011

ABSTRACT

Old tuberculin (OT) and purified protein derivative (PPD) are widely used for tuberculin skin testing (TST) in diagnosis of tuberculosis (TB) but often yield poor specificity and anergy in reaction. Therefore, it is necessary to develop new serological methods as a possible auxiliary diagnostic method for TB. In this study, we characterized the dynamic antibody responses of 10 purified recombinant antigens, PPD, and OT in rhesus monkeys experimentally infected with
Mycobacterium tuberculosis
and analyzed the time to antibody detection, antibody levels, and their association with the infectious doses. The antibodies were detected as early as 4 weeks after infection in response to 5 antigens (CFP10, CFP10-ESAT-6, U1, MPT64, and Ag85b). Antibodies against most of the other antigens were detected between 4 and 12 weeks after infection. The levels of antibodies were dose dependant. We further evaluated the serodiagnostic potential of these antigens by using indirect enzyme-linked immunosorbent assay in 71 TST-positive and 90 TST-negative serum samples from monkeys. For all 12 antigens, the median optical density values of TST-positive monkeys were statistically significantly higher than those of TST-negative monkeys (
P
< 0.001). Among those antigens, Ag85b and CFP10 showed higher diagnostic potential than others. A combination of results from Ag85b, the 38-kDa antigen (Ag38kDa), and Ag14kDa reaches a sensitivity of 95.77%, indicating that these antigens may be ideal cocktails in TB diagnosis.
Maintenance of Immune Response throughout Childhood following Serogroup C Meningococcal Conjugate Vaccination in Early Childhood
Authors: Khatami A. , Peters A. , Robinson H. , Williams N. , Thompson A. , Findlow H. , Pollard A. J. , Snape M. D. 
Published: October 2011

ABSTRACT

The objectives of this study were to evaluate the kinetics of antibody decline through childhood in a longitudinal study of a single cohort following serogroup C meningococcal (MenC) vaccine immunization in early childhood and to calculate the proportion of 11 to 13 year olds with protective levels of bactericidal antibody 10 years after immunization. United Kingdom children aged 11 to 13 years in 2010 who had previously taken part in a longitudinal study at the Oxford Vaccine Group had blood samples drawn between 2001 and 2010. Sera from each time point were analyzed for the MenC serum bactericidal antibody titer using a baby rabbit complement (rSBA) assay. The median age at MenC immunization was 21 months (range, 1 year 3 months to 3 years 9 months). The MenC rSBA geometric mean titer (GMT) at age 3.5 to 5 years was 8.0 (95% confidence interval, 6.5 to 9.9;
n
= 287). By age 11.5 to 13.5 years, the rSBA GMT had declined to 3.3 (2.5 to 4.4;
n
= 98). The percentage of children with rSBA titers of ≥1:8 (the threshold for protection) also declined from 38% (35% to 41%) to 15% (12% to 19%). We concluded that MenC rSBA titers wane rapidly following vaccination in early childhood and continue to decline into the second decade of life. Since nasopharyngeal colonization in adolescents probably provides the major reservoir for MenC in the population, declining immunity in this cohort is of concern. Sustaining high levels of antibody through booster vaccination in this cohort is likely necessary to avoid a resurgence of disease in the decade ahead.
Structural Correlates of Cytoplasmic and Chloroplast Lipid Body Synthesis in Chlamydomonas reinhardtii and Stimulation of Lipid Body Production with Acetate Boost
Authors: Goodson Carrie , Roth Robyn , Wang Zi Teng , Goodenough Ursula 
Published: October 2011

ABSTRACT

Light microscopy and deep-etch electron microscopy were used to visualize triacylglyceride (TAG)-filled lipid bodies (LBs) of the green eukaryotic soil alga
Chlamydomonas reinhardtii
, a model organism for biodiesel production. Cells growing in nitrogen-replete media contain small cytoplasmic lipid bodies (α-cyto-LBs) and small chloroplast plastoglobules. When starved for N, β-cyto-LB formation is massively stimulated. β-Cyto-LBs are intimately associated with both the endoplasmic reticulum membrane and the outer membrane of the chloroplast envelope, suggesting a model for the active participation of both organelles in β-cyto-LB biosynthesis and packaging. When
sta6
mutant cells, blocked in starch biosynthesis, are N starved, they produce β-cyto-LBs and also chloroplast LBs (cpst-LBs) that are at least 10 times larger than plastoglobules and eventually engorge the chloroplast stroma. Production of β-cyto-LBs and cpst-LBs under the conditions we used is dependent on exogenous 20 mM acetate. We propose that the greater TAG yields reported for N-starved
sta6
cells can be attributed to the strain's ability to produce cpst-LBs, a capacity that is lost when the mutant is complemented by a
STA6
transgene. Provision of a 20 mM acetate “boost” during N starvation generates
sta6
cells that become so engorged with LBs—at the expense of cytoplasm and most organelles—that they float on water even when centrifuged. This property could be a desirable feature for algal harvesting during biodiesel production.
The Intact
dupA
Cluster Is a More Reliable Helicobacter pylori Virulence Marker than
dupA
Alone
Authors: Jung Sung Woo , Sugimoto Mitsushige , Shiota Seiji , Graham David Y. , Yamaoka Yoshio 
Published: October 2011

ABSTRACT

The duodenal ulcer promoting (
dupA
) gene, located in the plasticity region of
Helicobacter pylori
, is associated with duodenal ulcer development.
dupA
was predicted to form a type IV secretory system (T4SS) with
vir
genes around
dupA
(
dupA
cluster). We investigated the prevalence of
dupA
and
dupA
clusters and clarified associations between the
dupA
cluster status and clinical outcomes in the U.S. population. In all, 245
H. pylori
strains were examined using PCR to evaluate the status of
dupA
and the adjacent
vir
genes predicted to form T4SS, in addition to the status of
cag
pathogenicity island (PAI). The associations between
dupA
cluster status and interleukin-8 (IL-8) and IL-12 production were also examined. The presence of
dupA
and all adjacent
vir
genes were defined as a complete
dupA
cluster. Many variations related to the status of
dupA
and
dupA
cluster genes were identified. Concurrent
H. pylori
infection and the presence of a complete
dupA
cluster increases duodenal ulcer risk compared to
H. pylori
infection with incomplete
dupA
cluster or without the
dupA
gene independent on the
cag
PAI status (adjusted odds ratio, 2.13; 95% confidence interval, 1.13 to 4.03). Gastric mucosal IL-8 levels were also significantly higher in the complete
dupA
cluster group than in other groups (
P
= 0.01). In conclusion, although the causal relationship between the
dupA
cluster and duodenal ulcer development is not proved, the presence of a complete
dupA
cluster but not
dupA
alone, is associated with duodenal ulcer development.
LipC (Rv0220) Is an Immunogenic Cell Surface Esterase of Mycobacterium tuberculosis
Authors: Shen Guomiao , Singh Krishna , Chandra Dinesh , Serveau-Avesque Carole , Maurin Damien , Canaan Stéphane , Singla Rupak , Behera Digambar , Laal Suman 
Published: October 2011

ABSTRACT

We have reported previously the identification of novel proteins of
Mycobacterium tuberculosis
by the immunoscreening of an expression library of
M. tuberculosis
genomic DNA with sera obtained from
M. tuberculosis
-infected rabbits at 5 weeks postinfection. In this study, we report the further characterization of one of these antigens, LipC (Rv0220). LipC is annotated as a member of the Lip family based on the presence of the consensus motif “GXSXG” characteristic of esterases. Although predicted to be a cytoplasmic enzyme, we provide evidence that LipC is a cell surface protein that is present in both the cell wall and the capsule of
M. tuberculosis
. Consistent with this localization, LipC elicits strong humoral immune responses in both HIV-negative (HIV
−
) and HIV-positive (HIV
+
) tuberculosis (TB) patients. The absence of anti-LipC antibodies in sera from purified protein derivative-positive (PPD
+
) healthy subjects confirms its expression only during active
M. tuberculosis
infection. Epitope mapping of LipC identified 6 immunodominant epitopes, 5 of which map to the exposed surface of the modeled LipC protein. The recombinant LipC (rLipC) protein also elicits proinflammatory cytokine and chemokine responses from macrophages and pulmonary epithelial cells. rLipC can hydrolyze short-chain esters with the carbon chain containing 2 to 10 carbon atoms. Together, these studies demonstrate that LipC is a novel cell surface-associated esterase of
M. tuberculosis
that is highly immunogenic and elicits both antibodies and cytokines/chemokines.
Association and Evidence for Linked Recognition of Type IV Secretion System Proteins VirB9-1, VirB9-2, and VirB10 in Anaplasma marginale
Authors: Morse Kaitlyn , Norimine Junzo , Palmer Guy H. , Sutten Eric L. , Baszler Timothy V. , Brown Wendy C. 
Published: October 2011

ABSTRACTLike several other bacterial pathogens,Anaplasma marginalehas an outer membrane that induces complete protection from infection and disease. However, the proteins that confer protective immunity and whether protection requires interacting proteins and/or linked T-cell and immunoglobulin G epitopes are not known. Our goal is to target the conserved type IV secretion system (T4SS) to identify conserved, immunogenic membrane proteins that are interacting and linked recognition candidates. Linked recognition is a process by which a B cell is optimally activated by a helper T cell that responds to the same, or physically associated, antigen.A. marginaleT4SS proteins VirB2, VirB4-1, VirB4-2, VirB6-1, VirB7, VirB8-2, VirB9-1, VirB9-2, VirB10, VirB11, and VirD4 were screened for their ability to induce IgG and to stimulate CD4+T cells from outer membrane-vaccinated cattle. VirB9-1, VirB9-2, and VirB10 induced the strongest IgG and T-cell responses in the majority of cattle, although three animals with major histocompatibility complex class II DRB3 restriction fragment length polymorphism types 8/23, 3/16, and 16/27 lacked T-cell responses to VirB9-1, VirB9-1 and VirB9-2, or VirB9-2 and VirB10, respectively. For these animals, VirB9-1-, VirB9-2-, and VirB10-specific IgG production may be associated with T-cell help provided by responses to an interacting protein partner(s). Interacting protein partners indicated by far-Western blotting were confirmed by immunoprecipitation assays and revealed, for the first time, specific interactions of VirB9-1 with VirB9-2 and VirB10. The immunogenicity and interactions of VirB9-1, VirB9-2, and VirB10 justify their testing as a linked protein vaccine againstA. marginale.
Innate Immune Responses and Modified Extracellular Matrix Regulation Characterize Bacterial Infection and Cellular/Connective Tissue Changes in Scarring Trachoma
Authors: Hu Victor H. , Weiss Helen A. , Ramadhani Athumani M. , Tolbert Sonda B. , Massae Patrick , Mabey David C. W. , Holland Martin J. , Bailey Robin L. , Burton Matthew J. 
Published: October 2011

ABSTRACT

Trachoma is the most common infectious cause of blindness and a major public health problem in many developing countries. It is caused by recurrent ocular infection with
Chlamydia trachomatis
in childhood, with conjunctival scarring seen later in life. The pathogenesis of trachomatous scarring, however, is poorly understood, and this study was carried out to investigate the immunofibrogenic correlates of trachomatous conjunctival scarring. A case-control study of 363 cases with conjunctival scarring and 363 control participants was conducted. Investigations included
in vivo
confocal microscopy (IVCM) assessment, quantitative real-time PCR gene expression,
C. trachomatis
detection, and nonchlamydial bacterial culture. Trachomatous scarring was found to be strongly associated with a proinflammatory, innate immune response with increased expression of psoriasin, interleukin-1β, tumor necrosis factor alpha, defensin-β4A, chemokine ligand 5, and serum amyloid A1. There was also differential expression of various modifiers of the extracellular matrix, including metalloproteinases 7, 9, 10, and 12, tissue inhibitor of matrix metalloproteinase 1, and secreted protein acidic cystein-rich-like 1. The expression of many of these genes was also significantly associated with the presence of nonchlamydial bacterial infection. These infections had a marked effect on conjunctival immune processes, including an increased inflammatory infiltrate and edema seen with IVCM. This study supports the possibility that the immunofibrogenic response in scarring trachoma is partly stimulated by nonchlamydial bacterial infection, which is characterized by the expression of innate factors.