bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uniaxial Tension of a Class of Compressible Solids With Plastic
Non-Normality
Authors: Mohan Nisha , Cheng Justine , Greer Julia R. , Needleman Alan 
Published: July 2013

Abstract
Motivated by a model that qualitatively captured the response of vertically aligned carbon nanotube (VACNT) pillars in uniaxial compression, we consider the uniaxial tensile response of a class of compressible elastic-viscoplastic solids. In Hutchens et al. [“Analysis of Uniaxial Compression of Vertically Aligned Carbon Nanotubes,” J. Mech. Phys. Solids, 59, pp. 2227–2237 (2011), Erratum 60, 1753–1756 (2012)] an elastic viscoplastic constitutive relation with plastic compressibility, plastic non-normality, and a hardening-softening-hardening hardness function was used to model experimentally obtained uniaxial compression data of cylindrical VACNT micropillars. Complex deformation modes were found in uniaxial compression, which include a sequential buckling-like collapse of the type seen in experiments. These complex deformation modes led to the overall stress-strain signature of the pillar not being of the same form as the input material hardness function. A fundamental question that motivates exploring the deformation of this class of materials—both experimentally and theoretically—is how to extract the intrinsic material response from simple tests. In this study we explore the relation between the input material response and the overall stress strain behavior in uniaxial tension using the constitutive framework of Hutchens et al. A simple one-dimensional analysis reveals the types of instability modes to be expected. Dynamic, finite deformation finite element calculations are carried out to explore the dependence of diffuse necking, localized necking, and propagating band deformation modes on characteristics of the hardness function. Attention is devoted to uncovering implications for obtaining intrinsic material properties of complex hierarchical structures; for example, vertically aligned carbon nanotubes (VACNTs), from uniaxial tension experiments.
Evolution of Pseudomonas aeruginosa Virulence as a Result of Phage Predation
Authors: Hosseinidoust Zeinab , van de Ven Theo G. M. , Tufenkji Nathalie 
Published: July 2013

ABSTRACT

The rapid increase in the emergence of antibiotic-resistant bacteria has attracted attention to bacteriophages for treating and preventing bacterial infections. Bacteriophages can drive the diversification of
Pseudomonas aeruginosa
, giving rise to phage-resistant variants with different phenotypes from their ancestral hosts. In this study, we sought to investigate the effect of phage resistance on cytotoxicity of host populations toward cultured mammalian cells. The library of phage-resistant
P. aeruginosa
PAO1 variants used was developed previously via experimental evolution of an isogenic host population using phages PP7 and E79. Our results presented herein indicate that the phage-resistant variants developed in a heterogeneous phage environment exhibit a greater ability to impede metabolic action of cultured human keratinocytes and have a greater tendency to cause membrane damage even though they cannot invade the cells in large numbers. They also show a heightened resistance to phagocytosis by model murine macrophages. Furthermore, all isolates produced higher levels of at least one of the secreted virulence factors, namely, total proteases, elastase, phospholipase C, and hemolysins. Reverse transcription-quantitative PCR (RT-qPCR) revealed upregulation in the transcription of a number of genes associated with virulence of
P. aeruginosa
for the phage-resistant variants. The results of this study indicate a significant change in the
in vitro
virulence of
P. aeruginosa
following phage predation and highlight the need for caution in the selection and design of phages and phage cocktails for therapeutic use.
Comparison of Listeria monocytogenes Exoproteomes from Biofilm and Planktonic State: Lmo2504, a Protein Associated with Biofilms
Authors: Lourenço António , de Las Heras Aitor , Scortti Mariela , Vazquez-Boland Jose , Frank Joseph F. , Brito Luisa 
Published: July 2013

ABSTRACT

The food-borne pathogen
Listeria monocytogenes
is the causative agent of the severe human and animal disease listeriosis. The persistence of this bacterium in food processing environments is mainly attributed to its ability to form biofilms. The search for proteins associated with biofilm formation is an issue of great interest, with most studies targeting the whole bacterial proteome. Nevertheless, exoproteins constitute an important class of molecules participating in various physiological processes, such as cell signaling, pathogenesis, and matrix remodeling. The aim of this work was to quantify differences in protein abundance between exoproteomes from a biofilm and from the planktonic state. For this, two field strains previously evaluated to be good biofilm producers (3119 and J311) were used, and a procedure for the recovery of biofilm exoproteins was optimized. Proteins were resolved by two-dimensional difference gel electrophoresis and identified by electrospray ionization-tandem mass spectrometry. One of the proteins identified in higher abundance in the biofilm exoproteomes of both strains was the putative cell wall binding protein Lmo2504. A mutant strain with deletion of the gene for Lmo2504 was produced (3119Δ
lmo2504
), and its biofilm-forming ability was compared to that of the wild type using the crystal violet and the ruthenium red assays as well as scanning electron microscopy. The results confirmed the involvement of Lmo2504 in biofilm formation, as strain 3119Δ
lmo2504
showed a significantly (
P
< 0.05) lower biofilm-forming ability than the wild type. The identification of additional exoproteins associated with biofilm formation may lead to new strategies for controlling this pathogen in food processing facilities.
An Extracellular Serine/Threonine-Rich Protein from Lactobacillus plantarum NCIMB 8826 Is a Novel Aggregation-Promoting Factor with Affinity to Mucin
Authors: Hevia Arancha , Martínez Noelia , Ladero Víctor , Álvarez Miguel A. , Margolles Abelardo , Sánchez Borja 
Published: July 2013

ABSTRACT

Autoaggregation in lactic acid bacteria is directly related to the production of certain extracellular proteins, notably, aggregation-promoting factors (APFs). Production of aggregation-promoting factors confers beneficial traits to probiotic-producing strains, contributing to their fitness for the intestinal environment. Furthermore, coaggregation with pathogens has been proposed to be a beneficial mechanism in probiotic lactic acid bacteria. This mechanism would limit attachment of the pathogen to the gut mucosa, favoring its removal by the human immune system. In the present paper, we have characterized a novel aggregation-promoting factor in
Lactobacillus plantarum
. A mutant with a knockout of the D1 gene showed loss of its autoaggregative phenotype and a decreased ability to bind to mucin, indicating an adhesion role of this protein. In addition, heterologous production of the D1 protein or an internal fragment of the protein, characterized by its abundance in serine/threonine, strongly induced autoaggregation in
Lactococcus lactis
. This result strongly suggested that this internal fragment is responsible for the bioactivity of D1 as an APF. To our knowledge, this is the first report on a gene coding for an aggregation-promoting factor in
Lb. plantarum
.
Reconstitution of Active Mycobacterial Binuclear Iron Monooxygenase Complex in Escherichia coli
Authors: Furuya Toshiki , Hayashi Mika , Kino Kuniki 
Published: July 2013

ABSTRACTBacterial binuclear iron monooxygenases play numerous physiological roles in oxidative metabolism. Monooxygenases of this type found in actinomycetes also catalyze various useful reactions and have attracted much attention as oxidation biocatalysts. However, difficulties in expressing these multicomponent monooxygenases in heterologous hosts, particularly inEscherichia coli, have hampered the development of engineered oxidation biocatalysts. Here, we describe a strategy to functionally express the mycobacterial binuclear iron monooxygenase MimABCD inEscherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of themimABCDgene expression inE. colirevealed that the oxygenase components MimA and MimC were insoluble. Furthermore, although the reductase MimB was expressed at a low level in the soluble fraction ofE. colicells, a band corresponding to the coupling protein MimD was not evident. This situation rendered the transformedE. colicells inactive. We found that the following factors are important for functional expression of MimABCD inE. coli: coexpression of the specific chaperonin MimG, which caused MimA and MimC to be soluble inE. colicells, and the optimization of themimDnucleotide sequence, which led to efficient expression of this gene product. These two remedies enabled this multicomponent monooxygenase to be actively expressed inE. coli. The strategy described here should be generally applicable to theE. coliexpression of other actinomycetous binuclear iron monooxygenases and related enzymes and will accelerate the development of engineered oxidation biocatalysts for industrial processes.
Characterization of Pleurotus ostreatus Biofilms by Using the Calgary Biofilm Device
Authors: Pesciaroli Lorena , Petruccioli Maurizio , Fedi Stefano , Firrincieli Andrea , Federici Federico , D'Annibale Alessandro 
Published: July 2013

ABSTRACT

The adequacy of the Calgary biofilm device, often referred to as the MBEC system, as a high-throughput approach to the production and subsequent characterization of
Pleurotus ostreatus
biofilms was assessed. The hydroxyapatite-coating of pegs was necessary to enable biofilm attachment, and the standardization of vegetative inocula ensured a uniform distribution of
P. ostreatus
biofilms, which is necessary for high-throughput evaluations of several antimicrobials and exposure conditions. Scanning electron microscopy showed surface-associated growth, the occurrence of a complex aggregated growth organized in multilayers or hyphal bundles, and the encasement of hyphae within an extracellular matrix (ECM), the extent of which increased with time. Chemical analyses showed that biofilms differed from free-floating cultures for their higher contents of total sugars (TS) and ECM, with the latter being mainly composed of TS and, to a lesser extent, protein. Confocal laser scanning microscopy analysis of 4-day-old biofilms showed the presence of interspersed interstitial voids and water channels in the mycelial network, the density and compactness of which increased after a 7-day incubation, with the novel occurrence of ECM aggregates with an α-glucan moiety. In 4- and 7-day-old biofilms, tolerance to cadmium was increased by factors of 3.2 and 11.1, respectively, compared to coeval free-floating counterparts.
Posttranslational Maturation of the Invasion Acyl Carrier Protein of Salmonella enterica Serovar Typhimurium Requires an Essential Phosphopantetheinyl Transferase of the Fatty Acid Biosynthesis Pathway
Authors: Viala Julie P. M. , Puppo Rémy , My Lætitia , Bouveret Emmanuelle 
Published: July 2013

ABSTRACT

Salmonella
pathogenicity island 1 (SPI-1) carries genes required for the formation of a type 3 secretion system, which is necessary for the invasion process of
Salmonella
. Among the proteins encoded by SPI-1 is IacP, a homolog of acyl carrier proteins. Acyl carrier proteins are mainly involved in fatty acid biosynthesis, and they require posttranslational maturation by addition of a 4′-phosphopantetheine prosthetic group to be functional. In this study, we analyzed IacP maturation
in vivo
. By performing matrix-assisted laser desorption ionization–time-of-flight (MALDI-TOF) mass spectrometry analysis of intact purified proteins, we showed that IacP from
Salmonella enterica
serovar Typhimurium was matured by addition of 4′-phosphopantetheine to the conserved serine 38 residue. Therefore, we searched for the phosphopantetheinyl transferases in charge of IacP maturation. A bacterial two-hybrid approach revealed that IacP interacted with AcpS, an enzyme normally required for the maturation of the canonical acyl carrier protein (ACP), which is involved in fatty acid biosynthesis. The creation of a conditional
acpS
mutant then demonstrated that AcpS was necessary for the maturation of IacP. However, although IacP was similar to ACP and matured by using the same enzyme, IacP could not replace the essential function of ACP in fatty acid synthesis. Hence, the demonstration that IacP is matured by AcpS establishes a cross-connection between virulence and fatty acid biosynthesis pathways.
Copper Efflux Is Induced during Anaerobic Amino Acid Limitation in Escherichia coli To Protect Iron-Sulfur Cluster Enzymes and Biogenesis
Authors: Fung Danny Ka Chun , Lau Wai Yin , Chan Wing Tat , Yan Aixin 
Published: July 2013

ABSTRACT

Adaptation to changing environments is essential to bacterial physiology. Here we report a unique role of the copper homeostasis system in adapting
Escherichia coli
to its host-relevant environment of anaerobiosis coupled with amino acid limitation. We found that expression of the copper/silver efflux pump CusCFBA was significantly upregulated during anaerobic amino acid limitation in
E. coli
without the supplement of exogenous copper. Inductively coupled plasma mass spectrometry analysis of the total intracellular copper content combined with transcriptional assay of the P

cusC

-
lacZ
reporter in the presence of specific Cu(I) chelators indicated that anaerobic amino acid limitation led to the accumulation of free Cu(I) in the periplasmic space of
E. coli
, resulting in Cu(I) toxicity. Cells lacking
cusCFBA
and another copper transporter,
copA
, under this condition displayed growth defects and reduced ATP production during fumarate respiration. Ectopic expression of the Fe-S cluster enzyme fumarate reductase (Frd), or supplementation with amino acids whose biosynthesis involves Fe-S cluster enzymes, rescued the poor growth of Δ
cusC
cells. Yet, Cu(I) treatment did not impair the Frd activity
in vitro
. Further studies revealed that the alternative Fe-S cluster biogenesis system Suf was induced during the anaerobic amino acid limitation, and Δ
cusC
enhanced this upregulation, indicating the impairment of the Fe-S cluster assembly machinery and the increased Fe-S cluster demands under this condition. Taken together, we conclude that the copper efflux system CusCFBA is induced during anaerobic amino acid limitation to protect Fe-S cluster enzymes and biogenesis from the endogenously originated Cu(I) toxicity, thus facilitating the physiological adaptation of
E. coli
.
Identification of a Ligand on the Wip1 Bacteriophage Highly Specific for a Receptor on Bacillus anthracis
Authors: Kan Sherry , Fornelos Nadine , Schuch Raymond , Fischetti Vincent A. 
Published: July 2013

ABSTRACT

Tectiviridae
is a family of tailless bacteriophages with Gram-negative and Gram-positive hosts. The family model PRD1 and its close relatives all infect a broad range of enterobacteria by recognizing a plasmid-encoded conjugal transfer complex as a receptor. In contrast, tectiviruses with Gram-positive hosts are highly specific to only a few hosts within the same bacterial species. The cellular determinants that account for the observed specificity remain unknown. Here we present the genome sequence of Wip1, a tectivirus that infects the pathogen
Bacillus anthracis
. The Wip1 genome is related to other tectiviruses with Gram-positive hosts, notably, AP50, but displays some interesting differences in its genome organization. We identified Wip1 candidate genes for the viral spike complex, the structure located at the capsid vertices and involved in host receptor binding. Phage adsorption and inhibition tests were combined with immunofluorescence microscopy to show that the Wip1 gene product p23 is a receptor binding protein. His-p23 also formed a stable complex with p24, a Wip1 protein of unknown function, suggesting that the latter is involved with p23 in host cell recognition. The narrow host range of phage Wip1 and the identification of p23 as a receptor binding protein offer a new range of suitable tools for the rapid identification of
B. anthracis
.
NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO
Authors: Wang Shuning , Huang Haiyan , Kahnt Jörg , Mueller Alexander P. , Köpke Michael , Thauer Rudolf K. 
Published: July 2013

ABSTRACT

Flavin-based electron bifurcation is a recently discovered mechanism of coupling endergonic to exergonic redox reactions in the cytoplasm of anaerobic bacteria and archaea. Among the five electron-bifurcating enzyme complexes characterized to date, one is a heteromeric ferredoxin- and NAD-dependent [FeFe]-hydrogenase. We report here a novel electron-bifurcating [FeFe]-hydrogenase that is NADP rather than NAD specific and forms a complex with a formate dehydrogenase. The complex was found in high concentrations (6% of the cytoplasmic proteins) in the acetogenic
Clostridium autoethanogenum
autotrophically grown on CO, which was fermented to acetate, ethanol, and 2,3-butanediol. The purified complex was composed of seven different subunits. As predicted from the sequence of the encoding clustered genes (
fdhA/hytA-E
) and from chemical analyses, the 78.8-kDa subunit (FdhA) is a selenocysteine- and tungsten-containing formate dehydrogenase, the 65.5-kDa subunit (HytB) is an iron-sulfur flavin mononucleotide protein harboring the NADP binding site, the 51.4-kDa subunit (HytA) is the [FeFe]-hydrogenase proper, and the 18.1-kDa (HytC), 28.6-kDa (HytD), 19.9-kDa (HytE1), and 20.1-kDa (HytE2) subunits are iron-sulfur proteins. The complex catalyzed both the reversible coupled reduction of ferredoxin and NADP
+
with H
2
or formate and the reversible formation of H
2
and CO
2
from formate. We propose the complex to have two functions
in vivo
, namely, to normally catalyze CO
2
reduction to formate with NADPH and reduced ferredoxin in the Wood-Ljungdahl pathway and to catalyze H
2
formation from NADPH and reduced ferredoxin when these redox mediators get too reduced during unbalanced growth of
C. autoethanogenum
on CO (
E
0′
= −520 mV).
Characterization of SAV7471, a TetR-Family Transcriptional Regulator Involved in the Regulation of Coenzyme A Metabolism in Streptomyces avermitilis
Authors: Liu Yanping , Yan Tingting , Jiang Libin , Wen Ying , Song Yuan , Chen Zhi , Li Jilun 
Published: July 2013

ABSTRACT

The role of a
tetR
transcriptional regulatory gene (
SAV7471
) in avermectin production in the Gram-positive soil bacterium
Streptomyces avermitilis
was investigated by gene deletion, complementation, and overexpression experiments. Gene deletion of the
SAV7471
open reading frame resulted in avermectin overproduction. The deletion also resulted in overexpression of
SAV7472-SAV7473
transcripts, which encode a protein of unknown function and a flavoprotein possibly involved in pantothenate and coenzyme A (CoA) metabolism. EMSAs and footprinting assays showed that SAV7471 can bind to two palindromic sequences with high similarity in the intergenic region between
SAV7471
and
SAV7472
, a region that contains the apparent transcription start sites for each gene detected by rapid amplification of 5′ cDNA ends (5′-RACE). In addition to
SAV7472-SAV7473
, at least two genes (
SAV1104
and
SAV1258
) involved in CoA metabolism are negatively controlled by SAV7471. By negatively regulating the transcription of the target genes
SAV7472-SAV7473
and other genes involved in CoA metabolism, SAV7471 may affect cellular metabolic flux and may thereby indirectly regulate avermectin biosynthesis.
Autoantibody prevalence in active tuberculosis: reactive or pathognomonic?
Authors: Shen Chieh-Yu , Hsieh Song-Chou , Yu Chia-Li , Wang Jann-Yuan , Lee Li-Na , Yu Chong-Jen 
Published: July 2013

ObjectivesTo evaluate the autoantibody in patients without corresponding symptoms, whether these autoantibody are pathognomonic or not. We hypothesised that autoantibody may be reactive to chronic infection, such as tuberculosis (TB).DesignRandomised, case–control cohort study.SettingA tertiary centre in Taiwan.ParticipantsWe randomly chose 100 patients out of the data bank of patients with TB in a tertiary medical centre. All patients completed the sera sampling. We chose 100 patients according to autoantibody prevalence in previous literature. We also chose 100 medical staff as control group.InterventionsWe tested anti-SSA, anti-SSB, anti-Sm, anti ribonucleoprotein, anti-Scl 70, anticentromere, anti-double-stranded DNA, anticardiolipin IgG and IgM in all patient and control groups. The clinical symptoms and the underlying disease were all recorded.Primary and secondary outcome measuresThe result of sera antibody titre was recorded. For those with specific positive serology results, following examination was carried out after a 3-month anti-TB medication.ResultsAnticardiolipin IgG titre was significantly higher in patients with TB than in control group. We compared the result with previous population study and found that anti-Scl70 is also significantly higher in patients with TB. The following up data in anti-Scl70 revealed decreased titre after treatment. No correlation between sera titre and clinical conditions was observed.ConclusionsIn TB endemic areas, a significant proportion (32%) of patients with TB have elevated autoantibody titres, especially anticardiolipin IgG and anti-Scl-70. Mycobacterial studies should be performed in patients with elevated serum autoantibody titres but without the typical or multiple manifestations of autoimmune diseases.Trial registrationThe study was approved by the Institutional Review Board of the hospital (NTUH REC: 9561707008) after informed consent had been obtained from the patients.
EP1: a novel rabbit monoclonal antibody for detection of oestrogen receptor α
Authors: Badve Sunil , Vladislav I Tudor , Spaulding Betsy , Strickland Anna , Hernandez Sylvia , Bird-Turner Lisa , Dodson Cecelia , Elleby Bjorn , Phillips Therese 
Published: July 2013

AimsAssessment of hormone receptor expression is part of routine examination of every breast cancer. In this study, we report the characterisation of a novel rabbit monoclonal antibody, clone EP1, directed against oestrogen receptor (ER) α. Additionally, its immunohistochemical performance characteristics in archival tissues are evaluated in normal tissues and two distinct cohorts of breast cancer patients.MethodsComparative analyses between EP1 and the anti-ERα component of the ER/PR pharmDx kit (cocktail of mouse monoclonal antibody clones 1D5 and ER-2-123) and between EP1 and another commercially available rabbit monoclonal antibody, clone SP1, are described.ResultsClone EP1 specifically detects nuclear ER in all tissues examined; cytoplasmic staining was not observed. The analysis shows a high degree of concordance (∼95%) between EP1 and both the ERα component of the Dako ER/PR pharmDx kit and Ventana clone SP1. However, the use of EP1 antibody together with Dako EnVision FLEX detection system resulted in a stronger staining intensity as compared with SP1 antibody using the Ventana ultraView DAB detection system resulting in better ‘ease of use.’ConclusionsThe use of EPI can result in better interpretation of the results of the ER analysis.