bluuebunny/crossref_metadata_2025 huggingface dataset:
Steady Flow Hemodynamic and Energy Loss Measurements in Normal and Simulated Calcified Tricuspid and Bicuspid Aortic Valves
Authors: Seaman Clara , George Akingba A. , Sucosky Philippe
Published: January 2014

The bicuspid aortic valve (BAV), which forms with two leaflets instead of three as in the normal tricuspid aortic valve (TAV), is associated with a spectrum of secondary valvulopathies and aortopathies potentially triggered by hemodynamic abnormalities. While studies have demonstrated an intrinsic degree of stenosis and the existence of a skewed orifice jet in the BAV, the impact of those abnormalities on BAV hemodynamic performance and energy loss has not been examined. This steady-flow study presents the comparative in vitro assessment of the flow field and energy loss in a TAV and type-I BAV under normal and simulated calcified states. Particle-image velocimetry (PIV) measurements were performed to quantify velocity, vorticity, viscous, and Reynolds shear stress fields in normal and simulated calcified porcine TAV and BAV models at six flow rates spanning the systolic phase. The BAV model was created by suturing the two coronary leaflets of a porcine TAV. Calcification was simulated via deposition of glue beads in the base of the leaflets. Valvular performance was characterized in terms of geometric orifice area (GOA), pressure drop, effective orifice area (EOA), energy loss (EL), and energy loss index (ELI). The BAV generated an elliptical orifice and a jet skewed toward the noncoronary leaflet. In contrast, the TAV featured a circular orifice and a jet aligned along the valve long axis. While the BAV exhibited an intrinsic degree of stenosis (18% increase in maximum jet velocity and 7% decrease in EOA relative to the TAV at the maximum flow rate), it generated only a 3% increase in EL and its average ELI (2.10 cm2/m2) remained above the clinical threshold characterizing severe aortic stenosis. The presence of simulated calcific lesions normalized the alignment of the BAV jet and resulted in the loss of jet axisymmetry in the TAV. It also amplified the degree of stenosis in the TAV and BAV, as indicated by the 342% and 404% increase in EL, 70% and 51% reduction in ELI and 48% and 51% decrease in EOA, respectively, relative to the nontreated valve models at the maximum flow rate. This study indicates the ability of the BAV to function as a TAV despite its intrinsic degree of stenosis and suggests the weak dependence of pressure drop on orifice area in calcified valves.
An In Vitro Model of Aortic Stenosis for the Assessment of Transcatheter Aortic Valve Implantation
Authors: Maleki Hoda , Shahriari Shahrokh , Labrosse Michel , Pibarot Philippe , Kadem Lyes
Published: January 2014

A significant number of elderly patients with severe symptomatic aortic stenosis are denied surgical aortic valve replacement (SAVR) because of high operative risk. Transcatheter aortic valve implantation (TAVI) has emerged as a valid alternative to SAVR in these patients. One of the main characteristics of TAVI, when compared to SAVR, is that the diseased native aortic valve remains in place. For hemodynamic testing of new percutaneous valves and clinical training, one should rely on animal models. However, the development of an appropriate animal model of severe aortic stenosis is not straightforward. This work aims at developing and testing an elastic model of the ascending aorta including a severe aortic stenosis. The physical model was built based on a previous silicone model and tested experimentally in this study. Experimental results showed that the error between the computer-aided design (CAD) file and the physical elastic model was <5%, the compliance of the ascending aorta was 1.15 ml/mm Hg, the effective orifice area (EOA) of the stenotic valve was 0.86 cm2, the peak jet velocity was 4.9 m/s and mean transvalvular pressure gradient was 50 mm Hg, consistent with as severe. An EDWARDS-SAPIEN 26 mm valve was then implanted in the model leading to a significant increase in EOA (2.22 cm2) and a significant decrease in both peak jet velocity (1.29 m/s) and mean transvalvular pressure gradient (3.1 mm Hg). This model can be useful for preliminary in vitro testing of percutaneous valves before more extensive animal and in vivo tests.
Assessment of Giardia and Cryptosporidium spp. as a Microbial Source Tracking Tool for Surface Water: Application in a Mixed-Use Watershed
Authors: Prystajecky Natalie , Huck Peter M. , Schreier Hans , Isaac-Renton Judith L.
Published: January 2014

Knowledge of host specificity, combined with genomic sequencing of
Giardia
and
Cryptosporidium
spp., has demonstrated a microbial source tracking (MST) utility for these common waterborne microbes. To explore the source attribution potential of these pathogens, water samples were collected in a mixed rural-urban watershed in the Township of Langley, in southwestern British Columbia (BC), Canada, over a 2-year period.
Cryptosporidium
was detected in 63% of surface water samples at concentrations ranging from no positive detection (NPD) to 20,600 oocysts per 100 liters.
Giardia
was detected in 86% of surface water samples at concentrations ranging from NPD to 3,800 cysts per 100 liters of water. Sequencing at the 18S rRNA locus revealed that 50% of
Cryptosporidium
samples and 98% of
Giardia
samples contained species/genotypes (
Cryptosporidium
) or assemblages (
Giardia
) that are capable of infecting humans, based on current knowledge of host specificity and taxonomy.
Cryptosporidium
genotyping data were more promising for source tracking potential, due to the greater number of host-adapted (i.e., narrow-host-range) species/genotypes compared to
Giardia
, since 98% of
Giardia
isolates were zoonotic and the potential host could not be predicted. This report highlights the benefits of parasite genomic sequencing to complement Method 1623 (U.S. Environmental Protection Agency) and shows that
Cryptosporidium
subtyping for MST purposes is superior to the use of
Giardia
subtyping, based on better detection limits for
Cryptosporidium
-positive samples than for
Giardia
-positive samples and on greater host specificity among
Cryptosporidium
species. These additional tools could be used for risk assessment in public health and watershed management decisions.
Phylogenetic Differences in Attached and Free-Living Bacterial Communities in a Temperate Coastal Lagoon during Summer, Revealed via High-Throughput 16S rRNA Gene Sequencing
Authors: Mohit Vani , Archambault Philippe , Toupoint Nicolas , Lovejoy Connie
Published: January 2014

Most of what is known about coastal free-living and attached bacterial diversity is based on open coasts, with high particulate and nutrient riverine supply, terrestrial runoffs, and anthropogenic activities. The Magdalen Islands in the Gulf of St. Lawrence (Canada) are dominated by shallow lagoons with small, relatively pristine catchments and no freshwater input apart from rain. Such conditions provided an opportunity to investigate coastal free-living and attached marine bacterial diversity in the absence of confounding effects of steep freshwater gradients. We found significant differences between the two communities and marked temporal patterns in both. Taxonomic richness and diversity were greater in the attached than in the free-living community, increasing over summer, especially within the least abundant bacterial phyla. The highest number of reads fell within the SAR 11 clade (
Pelagibacter
,
Alphaproteobacteria
), which dominated free-living communities. The attached communities had deeper phylum-level diversity than the free-living fraction. Distance-based redundancy analysis indicated that the particulate organic matter (POM) concentration was the main variable separating early and late summer samples with salinity and temperature changes also significantly correlated to bacterial community structure. Our approach using high-throughput sequencing detected differences in free-living versus attached bacteria in the absence of riverine input, in keeping with the concept that marine attached communities are distinct from cooccurring free-living taxa. This diversity likely reflects the diverse microhabitats of available particles, implying that the total bacterial diversity in coastal systems is linked to particle supply and variability, with implications for understanding microbial biodiversity in marine systems.
Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393
Authors: Hong Pei-Ying , Iakiviak Michael , Dodd Dylan , Zhang Meiling , Mackie Roderick I. , Cann Isaac
Published: January 2014

Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium
Bacteroides intestinalis
DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The
xyn8A
gene encodes an endoxylanase (Xyn8A), and
rex8A
encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X
5
) and xylohexaose (X
6
) to a mixture of xylobiose (X
2
) and xylotriose (X
3
), while Rex8A hydrolyzed X
3
through X
6
to a mixture of xylose (X
1
) and X
2
. Moreover,
rex8A
is located downstream of a GH3 gene (
xyl3A
) that was demonstrated to exhibit β-xylosidase activity and would be able to further hydrolyze X
2
to X
1
. Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the
Bacteroidetes
, indicating that these genes contribute to xylan utilization in the human gut.
A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum
Authors: Koch Marion , Delmotte Nathanaël , Ahrens Christian H. , Omasits Ulrich , Schneider Kathrin , Danza Francesco , Padhi Barnali , Murset Valérie , Braissant Olivier , Vorholt Julia A. , Hennecke Hauke , Pessi Gabriella
Published: January 2014

Rhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. In this study,
Bradyrhizobium japonicum
USDA 110 was found to be able to utilize oxalate as the sole carbon source. A proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. A mutant of the key pathway genes
oxc
(for oxalyl-coenzyme A decarboxylase) and
frc
(for formyl-coenzyme A transferase) was constructed and shown to be (i) impaired in growth on arabinose and (ii) unable to grow on oxalate. Oxalate was detected in roots and, at elevated levels, in root nodules of four different
B. japonicum
host plants. Mixed-inoculation experiments with wild-type and
oxc-frc
mutant cells revealed that oxalotrophy might be a beneficial trait of
B. japonicum
at some stage during legume root nodule colonization.
Thermostability Improvement of a Streptomyces Xylanase by Introducing Proline and Glutamic Acid Residues
Authors: Wang Kun , Luo Huiying , Tian Jian , Turunen Ossi , Huang Huoqing , Shi Pengjun , Hua Huifang , Wang Caihong , Wang Shuanghe , Yao Bin
Published: January 2014

Protein engineering is commonly used to improve the robustness of enzymes for activity and stability at high temperatures. In this study, we identified four residues expected to affect the thermostability of
Streptomyces
sp. strain S9 xylanase XynAS9 through multiple-sequence analysis (MSA) and molecular dynamic simulations (MDS). Site-directed mutagenesis was employed to construct five mutants by replacing these residues with proline or glutamic acid (V81P, G82E, V81P/G82E, D185P/S186E, and V81P/G82E/D185P/S186E), and the mutant and wild-type enzymes were expressed in
Pichia pastoris
. Compared to the wild-type XynAS9, all five mutant enzymes showed improved thermal properties. The activity and stability assays, including circular dichroism and differential scanning calorimetry, showed that the mutations at positions 81 and 82 increased the thermal performance more than the mutations at positions 185 and 186. The mutants with combined substitutions (V81P/G82E and V81P/G82E/D185P/S186E) showed the most pronounced shifts in temperature optima, about 17°C upward, and their half-lives for thermal inactivation at 70°C and melting temperatures were increased by >9 times and approximately 7.0°C, respectively. The mutation combination of V81P and G82E in adjacent positions more than doubled the effect of single mutations. Both mutation regions were at the end of long secondary-structure elements and probably rigidified the local structure. MDS indicated that a long loop region after positions 81 and 82 located at the end of the inner β-barrel was prone to unfold. The rigidified main chain and filling of a groove by the mutations on the bottom of the active site canyon may stabilize the mutants and thus improve their thermostability.
Vibrio coralliilyticus Strain OCN008 Is an Etiological Agent of Acute Montipora White Syndrome
Authors: Ushijima Blake , Videau Patrick , Burger Andrew H. , Shore-Maggio Amanda , Runyon Christina M. , Sudek Mareike , Aeby Greta S. , Callahan Sean M.
Published: January 2014

Identification of a pathogen is a critical first step in the epidemiology and subsequent management of a disease. A limited number of pathogens have been identified for diseases contributing to the global decline of coral populations. Here we describe
Vibrio coralliilyticus
strain OCN008, which induces acute
Montipora
white syndrome (aMWS), a tissue loss disease responsible for substantial mortality of the coral
Montipora capitata
in Kāne‘ohe Bay, Hawai‘i. OCN008 was grown in pure culture, recreated signs of disease in experimentally infected corals, and could be recovered after infection. In addition, strains similar to OCN008 were isolated from diseased coral from the field but not from healthy
M. capitata
. OCN008 repeatedly induced the loss of healthy
M. capitata
tissue from fragments under laboratory conditions with a minimum infectious dose of between 10
7
and 10
8
CFU/ml of water. In contrast,
Porites compressa
was not infected by OCN008, indicating the host specificity of the pathogen. A decrease in water temperature from 27 to 23°C affected the time to disease onset, but the risk of infection was not significantly reduced. Temperature-dependent bleaching, which has been observed with the
V. coralliilyticus
type strain BAA-450, was not observed during infection with OCN008. A comparison of the OCN008 genome to the genomes of pathogenic
V. coralliilyticus
strains BAA-450 and P1 revealed similar virulence-associated genes and quorum-sensing systems. Despite this genetic similarity, infections of
M. capitata
by OCN008 do not follow the paradigm for
V. coralliilyticus
infections established by the type strain.
Environmental Survival of Mycobacterium avium subsp. paratuberculosis in Different Climatic Zones of Eastern Australia
Authors: Eppleston Jeffrey , Begg Douglas J. , Dhand Navneet K. , Watt Bruce , Whittington Richard J.
Published: January 2014

The duration of survival of both the S and C strains of
Mycobacterium avium
subsp.
paratuberculosis
in feces was quantified in contrasting climatic zones of New South Wales, Australia, and detailed environmental temperature data were collected. Known concentrations of S and C strains in feces placed on soil in polystyrene boxes were exposed to the environment with or without the provision of shade (70%) at Bathurst, Armidale, Condobolin, and Broken Hill, and subsamples taken every 2 weeks were cultured for the presence of
M. avium
subsp.
paratuberculosis
. The duration of survival ranged from a minimum of 1 week to a maximum of 16 weeks, and the provision of 70% shade was the most important factor in extending the survival time. The hazard of death for exposed compared to shaded samples was 20 and 9 times higher for the S and C strains, respectively. Site did not affect the survival of the C strain, but for the S strain, the hazard of death was 2.3 times higher at the two arid zone sites (Broken Hill and Condobolin) than at the two temperate zone sites (Bathurst and Armidale). Temperature measurements revealed maximum temperatures exceeding 60°C and large daily temperature ranges at the soil surface, particularly in exposed boxes.
Distribution of Sequence-Based Types of Legionella pneumophila Serogroup 1 Strains Isolated from Cooling Towers, Hot Springs, and Potable Water Systems in China
Authors: Qin Tian , Zhou Haijian , Ren Hongyu , Guan Hong , Li Machao , Zhu Bingqing , Shao Zhujun
Published: January 2014

Legionella pneumophila
serogroup 1 causes Legionnaires' disease. Water systems contaminated with
Legionella
are the implicated sources of Legionnaires' disease. This study analyzed
L. pneumophila
serogroup 1 strains in China using sequence-based typing. Strains were isolated from cooling towers (
n
= 96), hot springs (
n
= 42), and potable water systems (
n
= 26). Isolates from cooling towers, hot springs, and potable water systems were divided into 25 sequence types (STs; index of discrimination [IOD], 0.711), 19 STs (IOD, 0.934), and 3 STs (IOD, 0.151), respectively. The genetic variation among the potable water isolates was lower than that among cooling tower and hot spring isolates. ST1 was the predominant type, accounting for 49.4% of analyzed strains (
n
= 81), followed by ST154. With the exception of two strains, all potable water isolates (92.3%) belonged to ST1. In contrast, 53.1% (51/96) and only 14.3% (6/42) of cooling tower and hot spring, respectively, isolates belonged to ST1. There were differences in the distributions of clone groups among the water sources. The comparisons among
L. pneumophila
strains isolated in China, Japan, and South Korea revealed that similar clones (ST1 complex and ST154 complex) exist in these countries. In conclusion, in China, STs had several unique allelic profiles, and ST1 was the most prevalent sequence type of environmental
L. pneumophila
serogroup 1 isolates, similar to its prevalence in Japan and South Korea.
New
In Situ
Capture Quantitative (Real-Time) Reverse Transcription-PCR Method as an Alternative Approach for Determining Inactivation of Tulane Virus
Authors: Wang Dapeng , Xu Shuxia , Yang David , Young Glenn M. , Tian Peng
Published: January 2014

Human noroviruses (HuNoVs) are the major cause of epidemic nonbacterial gastroenteritis. Although quantitative (real-time) reverse transcription-PCR (qRT-PCR) is widely used for detecting HuNoVs, it only detects the presence of viral RNA and does not indicate viral infectivity. Human blood group antigens (HBGAs) have been identified as receptors/co-receptors for both HuNoVs and Tulane virus (TV) and are crucial for viral infection. We propose that viral infectivity can be evaluated with a molecular assay based on receptor-captured viruses. In this study, we employed TV as an HuNoV surrogate to validate the HBGA-based capture qRT-PCR method against the 50% tissue culture infectious dose (TCID
50
) method. We employed type B HBGA on an immuno-well module to concentrate TV, followed by amplification of the captured viral genome by
in situ
qRT-PCR. We first demonstrated that this
in situ
capture qRT-PCR (ISC-qRT-PCR) method could effectively concentrate and detect TV. We then treated TV under either partial or full inactivation conditions and measured the remaining infectivity by ISC-qRT-PCR and a tissue culture-based amplification method (TCID
50
). We found that the ISC-qRT-PCR method could be used to evaluate virus inactivation deriving from damage to the capsid and study interactions between the capsid and viral receptor. Heat, chlorine, and ethanol treatment primarily affect the capsid structure, which in turns affects the ability of the capsid to bind to viral receptors. Inactivation of the virus by these methods could be reflected by the ISC-qRT-PCR method and confirmed by TCID
50
assay. However, the loss of the infectivity caused by damage to the viral genome (such as that from UV irradiation) could not be effectively reflected by this method. Despite this limitation, the ISC-qRT-PCR provides an alternative approach to determine inactivation of Tulane virus. A particular advantage of the ISC-qRT-PCR method is that it is also a faster and easier method to effectively recover and detect the viruses, as there is no need to extract viral RNA or to transfer the captured virus from magnetic beads to PCR tubes for further amplification. Therefore, ISC-qRT-PCR can be easily adapted for use in automated systems for multiple samples.
Transcription Factor RFX1 Is Crucial for Maintenance of Genome Integrity in Fusarium graminearum
Authors: Min Kyunghun , Son Hokyoung , Lim Jae Yun , Choi Gyung Ja , Kim Jin-Cheol , Harris Steven D. , Lee Yin-Won
Published: January 2014

The survival of cellular organisms depends on the faithful replication and transmission of DNA. Regulatory factor X (RFX) transcription factors are well conserved in animals and fungi, but their functions are diverse, ranging from the DNA damage response to ciliary gene regulation. We investigated the role of the sole RFX transcription factor, RFX1, in the plant-pathogenic fungus
Fusarium graminearum
. Deletion of
rfx1
resulted in multiple defects in hyphal growth, conidiation, virulence, and sexual development. Deletion mutants of
rfx1
were more sensitive to various types of DNA damage than the wild-type strain. Septum formation was inhibited and micronuclei were produced in the
rfx1
deletion mutants. The results of the neutral comet assay demonstrated that disruption of
rfx1
function caused spontaneous DNA double-strand breaks (DSBs). The transcript levels of genes involved in DNA DSB repair were upregulated in the
rfx1
deletion mutants. DNA DSBs produced micronuclei and delayed septum formation in
F. graminearum
. Green fluorescent protein (GFP)-tagged RFX1 localized in nuclei and exhibited high expression levels in growing hyphae and conidiophores, where nuclear division was actively occurring. RNA-sequencing-based transcriptomic analysis revealed that RFX1 suppressed the expression of many genes, including those required for the repair of DNA damage. Taken together, these findings indicate that the transcriptional repressor
rfx1
performs crucial roles during normal cell growth by maintaining genome integrity.
Regulation of Acetate Kinase Isozymes and Its Importance for Mixed-Acid Fermentation in Lactococcus lactis
Authors: Puri Pranav , Goel Anisha , Bochynska Agnieszka , Poolman Bert
Published: January 2014

Acetate kinase (ACK) converts acetyl phosphate to acetate along with the generation of ATP in the pathway for mixed-acid fermentation in
Lactococcus lactis
. The reverse reaction yields acetyl phosphate for assimilation purposes. Remarkably,
L. lactis
has two ACK isozymes, and the corresponding genes are present in an operon. We purified both enzymes (AckA1 and AckA2) from
L. lactis
MG1363 and determined their oligomeric state, specific activities, and allosteric regulation. Both proteins form homodimeric complexes, as shown by size exclusion chromatography and static light-scattering measurements. The turnover number of AckA1 is about an order of magnitude higher than that of AckA2 for the reaction in either direction. The

K
m

values for acetyl phosphate, ATP, and ADP are similar for both enzymes. However, AckA2 has a higher affinity for acetate than does AckA1, suggesting an important role under acetate-limiting conditions despite the lower activity. Fructose-1,6-bisphosphate, glyceraldehyde-3-phosphate, and phospho-
enol
-pyruvate inhibit the activities of AckA1 and AckA2 to different extents. The allosteric regulation of AckA1 and AckA2 and the pool sizes of the glycolytic intermediates are consistent with a switch from homolactic to mixed-acid fermentation upon slowing of the growth rate.
Contribution of Many Charged Residues at the Stator-Rotor Interface of the Na
+
-Driven Flagellar Motor to Torque Generation in Vibrio alginolyticus
Authors: Takekawa Norihiro , Kojima Seiji , Homma Michio
Published: January 2014

In torque generation by the bacterial flagellar motor, it has been suggested that electrostatic interactions between charged residues of MotA and FliG at the rotor-stator interface are important. However, the actual role(s) of those charged residues has not yet been clarified. In this study, we systematically made mutants of
Vibrio alginolyticus
whose charged residues of PomA (MotA homologue) and FliG were replaced by uncharged or charge-reversed residues and characterized the motilities of those mutants. We found that the members of a group of charged residues, 7 in PomA and 6 in FliG, collectively participate in torque generation of the Na
+
-driven flagellar motor in
Vibrio
. An additional specific interaction between PomA-E97 and FliG-K284 is critical for proper performance of the
Vibrio
motor. Our results also reveal that more charged residues are involved in the PomA-FliG interactions in the
Vibrio
Na
+
-driven motor than in the MotA-FliG interactions in the H
+
-driven one. This suggests that a larger number of conserved charged residues at the PomA-FliG interface contributes to the robustness of the
Vibrio
motor against mutations. The interaction surfaces of the stator and rotor of the Na
+
-driven motor seem to be more complex than those previously proposed in the H
+
-driven motor.
Nonclassical Transpeptidases of Mycobacterium tuberculosis Alter Cell Size, Morphology, the Cytosolic Matrix, Protein Localization, Virulence, and Resistance to β-Lactams
Authors: Schoonmaker Maia K. , Bishai William R. , Lamichhane Gyanu
Published: January 2014

Virtually all bacteria possess a peptidoglycan layer that is essential for their growth and survival. The β-lactams, the most widely used class of antibiotics in human history, inhibit
d,d
-transpeptidases, which catalyze the final step in peptidoglycan biosynthesis. The existence of a second class of transpeptidases, the
l,d
-transpeptidases, was recently reported.
Mycobacterium tuberculosis
, an infectious pathogen that causes tuberculosis (TB), is known to possess as many as five proteins with
l,d
-transpeptidase activity. Here, for the first time, we demonstrate that loss of
l,d
-transpeptidases 1 and 2 of
M. tuberculosis
(Ldt
Mt1
and Ldt
Mt2
) alters cell surface morphology, shape, size, organization of the intracellular matrix, sorting of some low-molecular-weight proteins that are targeted to the membrane or secreted, cellular physiology, growth, virulence, and resistance of
M. tuberculosis
to amoxicillin-clavulanate and vancomycin.
Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon
Authors: Majerczyk Charlotte , Brittnacher Mitchell , Jacobs Michael , Armour Christopher D. , Radey Mathew , Schneider Emily , Phattarasokul Somsak , Bunt Richard , Greenberg E. Peter
Published: January 2014

Burkholderia thailandensis
contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify
B. thailandensis
quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of
B. thailandensis
, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of
B. thailandensis
and the closely related pathogenic
Burkholderia pseudomallei
and
Burkholderia mallei
.
Influence of O Polysaccharides on Biofilm Development and Outer Membrane Vesicle Biogenesis in Pseudomonas aeruginosa PAO1
Authors: Murphy Kathleen , Park Amber J. , Hao Youai , Brewer Dyanne , Lam Joseph S. , Khursigara Cezar M.
Published: January 2014

Pseudomonas aeruginosa
is a common opportunistic human pathogen known for its ability to adapt to changes in its environment during the course of infection. These adaptations include changes in the expression of cell surface lipopolysaccharide (LPS), biofilm development, and the production of a protective extracellular exopolysaccharide matrix. Outer membrane vesicles (OMVs) have been identified as an important component of the extracellular matrix of
P. aeruginosa
biofilms and are thought to contribute to the development and fitness of these bacterial communities. The goal of this study was to examine the relationships between changes in the cell surface expression of LPS O polysaccharides, biofilm development, and OMV biogenesis in
P. aeruginosa
. We compared wild-type
P. aeruginosa
PAO1 with three chromosomal knockouts. These knockouts have deletions in the
rmd
,
wbpM
, and
wbpL
genes that produce changes in the expression of common polysaccharide antigen (CPA), O-specific antigen (OSA), or both. Our results demonstrate that changes in O polysaccharide expression do not significantly influence OMV production but do affect the size and protein content of OMVs derived from both CPA
−
and OSA
−
cells; these mutant cells also exhibited different physical properties from wild-type cells. We further examined biofilm growth of the mutants and determined that CPA
−
cells could not develop into robust biofilms and exhibit changes in cell morphology and biofilm matrix production. Together these results demonstrate the importance of O polysaccharide expression on
P. aeruginosa
OMV composition and highlight the significance of CPA expression in biofilm development.
Kinetics and mechanism of oxidation of Cr(II) ions by tetrachloromethane
Authors: Ševčík Peter , Khír Miroslav
Published: January 2014

Kinetics of the redox reaction of Cr(II) ions with tetrachloromethane has been studied in H2O-CH3OH-HClO4 and H2O-CH3COOH-HClO4. In the redox reaction 2 moles of Cr(II) are consumed per one mol of CCl4, and CrCl2+ and CrCCL2+3 ions are formed in the same amounts. Second order rate constants (k293 = 2.31 mol-1 s -1 in 50% CH3OH, k293 = 1.66 l . mol-1 s-1 in 50% CH3COOH) are independent of H+ ions concentration.The rate determining step is an inner sphere transfer of the halogen from CCl4 to Cr(II), the Cr-Cl-C bridge structure being retained in both media.
Kinetics and mechanism of redox reaction of U(III) ions with trichloroacetic acid
Authors: Adamčíková Ľubica , Treindl Ľudovít
Published: January 2014

The kinetics and mechanism of redox reaction of U3+ ions with trichloroacetic acid in the medium of perchloric acid were studied. The form of the dependence of the rate constant on the concentration of H3O+ ions suggests that the U3+ion reacts in the first elementary step with the CCL3.COO- anion under formation of an intermediary radical which reacts rapidly in the second step.The results of kinetic measurements of all three chloro substituted acetic acids are compared. A detailed study of the influence of binary mixtures on kinetic parameters of the studied reaction (especially of water-tert-butanol mixtures) shows that the reduction of chloroacetic acids with U3+ ions proceeds by the outer sphere mechanism of the electron transfer.
Statistical treatment of material balance of separation operations
Authors: Madron František
Published: January 2014

A method of complex statistical treatment of material balances of separation operations without chemical reactions has been proposed. The method which is suitable for checking of correctness of material balance of separation operations in the laboratoty and industrial size is simple and easy for programming on digital computer. The computational procedure is illustrated on an example of material balance of an absorption unit.
Citrate complexes of uranyl in solutions with high citrate concentrations
Authors: Vaňura Petr , Kuča Libor
Published: January 2014

The composition and stability of uranyl citrate complexes in aqueous solutions of the ionic medium of 1M-(H,Na,(UO2)0.5)A3 (where H3A represents citric acid) were studied based on the potentiometric and spectrophotometric data. The best fit to the experimental data was obtained with the set of complexes UO2A-, (UO2A)22-, HUO2A, (HUO2A)2, and H2UO2A+, the former three complexes being significant in the whole concentration region.
The reactions of gallium, indium and thallium with 2-(2-pyridylazo)-1-naphthol-4-sulphonic acid and their spectrophotometric determination
Authors: Voznica Petr , Havel Josef , Sommer Lumír
Published: January 2014

The complex equilibria of gallium, indium and thallium(III) with analytically important 2-(2-pyridylazo)-1-naphthol-4-sulphonate were studied spectrophotometrically using graphical analysis of the absorbance curves and minimization procedures for the absorbance data using the SPEKTFOT program on the Tesla 200 computer. The study yielded a complete picture of the reaction mechanism of these elements with heterocyclic azodyes. Optimum conditions for the spectrophotometric determination of gallium, indium and thallium using this reagent were found.
Trimethylammoniodiformylmethylide: Structure and charge distribution
Authors: Král Vladimír , Arnold Zdeněk
Published: January 2014

Geometric arrangement of trimethylammoniodiformylmethylide (I) and charge distribution in this compound were calculated by quantum chemical methods (EHT, CNDO/2, INDO, PCILO, MINDO/2, ab initio). Total energy minimum was found for the arrangement If. The experimentally found dipole moment agrees very well with that calculated for this conformation.
Study of some aliphatic ammonium ylides by semiempirical and ab initio methods: Structure and charge distribution
Authors: Král Vladimír , Arnold Zdeněk
Published: January 2014

Structure of, and charge distribution in, some aliphatic ammonium ylides were determined by quantum chemical methods (CNDO/2, INDO, MINDO/2, PCILO, ab initio-STO-3G and 4-31G bases). Non-stabilized ylides were found to have pyramidal arrangement of bonds on the ylide carbon whereas the stabilized ylides have a planar arrangement. The charge distribution in stabilized ylides indicates a significant transfer of the negative charge from the ylide carbon to the electronegative groups. The calculated dipole moments for the previously prepared compounds, as well as for the derivatives VII and X, described in this paper, agree well with the experimental value.
Aluminium chloride induced isomerisation of 1,1,2-trichlorotrifluoroethane and 1,2-difluorotetrachloroethane
Authors: Paleta Oldřich , Liška František , Pošta Antonín , Dědek Václav
Published: January 2014

Under comparable conditions, the isomerisation of 1,1,2-trichlorotrifluoroethane (I) to 1,1,1-trichlorotrifluoroethane (II) is more difficult than the isomerisation of 1,2-difluorotetrachloroethane (III) to 1,1-difluorotetrachloroethane (IV). Advantageously, III was isomerised to IV in the presence of I or II. The degree of isomerisation of the starting compounds I and III was 95-99%, the preparative yield of IV being 65-74%. The C-F bond energies in I-IVwere derived from correlation diagram and the physico-chemical aspects of the isomerisation are discussed.
Solvent effects on the decomposition of 7-cumyl hydroperoxide in the presence of the phthalocyanines of cobalt and nickel
Authors: Kropf Heinz , Ivanov Slavi K. , Spangenberg Jochen , Timmermann Ute , Unger Wolfgang
Published: January 2014

The decomposition of 7-cumyl hydroperoxide catalyzed by cobalt phthalocyanine in the solvent system decalin-3-chlorotoluene (40°C) follows the 2nd order kinetics in the absence of N-(2-naphthyl)aniline and that of the 1st order in the presence of the inhibitor. The effect of composition of the solvent system on the rate constants and on the quotient of the initial rates in presence and in absence of inhibitor and the mechanism of the decomposition are discussed. Nickel phthalocyanine has an inhibiting effect on the decomposition of 7-cumyl hydroperoxide in the solvent systems decalin-1-chloronaphthalene and 3-chlorotoluene-1-chloronaphthalene (120°C). Decomposition starts after addition of N-(2-naphthyl)aniline. After an autocatalytical phase the reaction follows 1st order kinetics. The rate constants depend on the composition of the solvent system. The temperature dependence of the decomposition on 1-chloronaphthalene was determined. The anomalous slope of the Arrhenius plot is discussed.
Spectral properties and intramolecular hydrogen bonding in 1-methyl(phenyl)-4(5)-substituted 6-oxo-1H-pyridazin-4(5)-ols
Authors: Kováč Štefan , Konečný Václav
Published: January 2014

Infrared, ultraviolet and 1H-NMR spectral data of 53 1-methyl(phenyl)-4(5)-substituted 6-oxo-1H-pyridazin-4(5)-ols are listed. Intramolecular hydrogen bondings are discussed; relatively strong hydrogen bondings OH...S were found, which are comparable in terms of strength with those of OH...O=C. Wavenumbers of ν(C=O) and ν(O-H) bands linearly correlated with substituent constants σ*, σR and σF.
Galvanostatic dissolution of mercury from the surface of glassy carbon into thiocyanate solution
Authors: Opekar František , Holub Karel
Published: January 2014

The galvanostatic dissolution of mercury from the surface of glassy carbon into a thiocyanate solution proceeds in accord with theoretical assumptions, as manifested by the constant product of the dissolution current and transition time. Under certain relations between the amount of oxidised mercury and concentration of thiocyanate at the electrode surface, however, a small part of the mercury dissolves at more positive potentials than correspond to the Nernst equation. This dissolution can be accompanied by potential oscillations. The anomalous behaviour is elucidated by the concept about coverage of a certain part of mercury with a film of sparingly soluble compounds of SCN- ions with mercury. This film is formed at the end of the galvanostatic dissolution on certain places of the electrode surface covered with mercury droplets, where SCN- ions are much exhausted as a result of a high current density.
Determination of critical micelle concentration of 1-carbethoxypentadecyltrimethylammonium bromide
Authors: Čermáková Ludmila , Rosendorfová Jitka , Malát Miroslav
Published: January 2014

The critical concentration of 1-carbethoxypentadecyltrimethylammonium bromide, cc = 7.7.10-4 mol l-1, was determined from surface tension measurements by using the method of the maximum bubble pressure. The cc value decreases markedly if a strong electrolyte (NaCl, NaNO3) is added even in very low quantities; further increase of the electrolyte concentration - 0.1 to 1.0 mol l-1 - does not bring about appreciable additional changes of cc.
An experimental study of gas phase back mixing under the counter-current gas-liquid flow on a vertical expanded metal sheet packing by static tracer technique
Authors: Červenka Jan , Endršt Mirko , Kolář Václav
Published: January 2014

Gas phase back mixing has been measured in a column packed with vertical expanded metal sheet under the counter-current flow of gas and liquid by the static method using a tracer. The observed experimental concentration profiles has not confirmed our earlier proposed model of back mixing, based on the concentration profiles in absorption runs. These profiles do not even conform with the axially dispersed plug flow model currently used to describe axial mixing in packed bed columns. The concentration profiles may be described by a combination of the axially dispersed plug flow model with back flow.
Mechanistic aspects of chain initiation in radical addition reactions induced by metal ions
Authors: Ponec Robert , Málek Jaroslav
Published: January 2014

Bersuker's concept of redox charge transfer in catalysis has been adopted to study initiating activity of metal ions in radical addition reactions of model organic addends with alkenes. It was found that the most important factor determining the activity of the metal ions was the magnitude of the redox charge transfer δq. Additionally, the spin-allowedness or spin-forbiddenness of the redox step was essential. Two-valent metal ions with configuration d5-d9 do not exhibit, regardless of the spin-allowedness of the redox step, a significant oxidation activity owing to low values of δq. Three-valent metal ions with configurations d1-d3 are also inactive because of relatively lowest values of δq and spin-forbiddenness of the redox step. A transient position is occupied by the Mn3+ (d4) ion for which the redox step is still spin-forbidden, but the value of δq is high enough to evoke satisfactory oxidation activity. Three-valent ions Fe3+, Ni3+ with configurations d5-d7 as well as four-valent ions Pb4+ and Mn4+ show, according to the magnitude of δq, the highest oxidation activity in chain initiation.
Kinetics of alkaline hydrolysis of diphenic and terephthalic acid monomethyl esters
Authors: Holba Vladislav , Benko Ján , Kozánková Jana
Published: January 2014

The dependence of the rate constant of alkaline hydrolysis of diphenic acid monomethyl ester and terephthalic acid monomethyl ester on ionic strength and temperature was studied together with the specific influence of some electrolytes on the reaction rate. Thermodynamic activation parameters extrapolated to zero ionic strength and critical interionic distances of reacting ions were calculated from the temperature dependences of the rate constants.
5,7-Cyclo-B-homopregnane derivatives with the corticoid ketol side chain
Authors: Šanda Vlastimil , Kohout Ladislav , Fajkoš Jan
Published: January 2014

Syntheses of the epimeric 5,7-cyclo-B-homopregnane derivatives carrying an oxygen function in positions 17α and 21 are described and the structures of the products are established by spectral means.
Synthesis of analogues of the melanocyte-stimulating hormone release-inhibiting factor containing 2-oxoimidazolidine-1-carboxylic acid
Authors: Kasafírek Evžen , Krejčí Ivan , Felt Vladimír
Published: January 2014

2-Oxoimidazolidine-1-carbonyl-leucyl-glycine amide (I), 2-oxoimidazolidine-1-carbonyl-leucyl-β-alanine amide (II), and 2-oxoimidazolidine-1-carbonyl-leucine amide (III) were synthesized by the acylation of corresponding dipeptide or amino-acid esters with 2-oxoamidazolidine-1-carbonyl chloride and following ammonolysis. Analogues I and II, containing 2-oxoimidazolidine-1-carboxylic acid instead of proline, exhibited the antiamnestic activity in the doses of 1 mg per kg subcutaneously, III was without effect.
Molecular geometries - Accuracy test of the PCILO method
Authors: Havlas Zdeněk , Maloň Petr
Published: January 2014

Applicability of the PCILO method for investigation of stationary points of the energy hypersurface has been tested with a set of 11 small organic molecules. From comparison of the molecular geometries, completely optimized with the use of the Payne algorithm, with experimental data and with the results obtained by the MINDO/3 and MNDO methods it follows that the PCILO method is suitable for semiquantitative estimate of molecular geometry (mean error in the bond length determination 5 . 10-3 nm, valence angles 3.4°). The Payne algorithm is little efficient, if the starting geometry is far from the stationary point and if the assumption of quadratic form of the hypersurface is not fulfilled.
Analysis of 1H-NMR spectra of cinnamaldehyde type model substances of lignin
Authors: Liptaj Tibor , Remko Milan , Polčin Ján
Published: January 2014

1H-NMR spectra of the following lignin model substances have been analyzed: cinnamaldehyde, 2-methoxycinnamaldehyde, 3-methoxycinnamaldehyde, 4-methoxycinnamaldehyde, 3,4-dimethoxycinnamaldehyde, 3-methoxy-4-hydroxycinnamaldehyde and 3,4,5-trimethoxycinnamaldehyde. From the NMR spectra analysis it follows that the studied compounds exist in solutions as trans isomers. Theoretical (PCILO) calculations in agreement with the NMR data have shown that the more stable conformer has trans orientation of C=O group with respect to the double bond of the conjugated side chain.
Solvation and redox properties of [Co(en)3]3+-[Co(en)3]2+ system
Authors: Kotočová Adéla , Mayer Ulrich
Published: January 2014

The solvation effect of a number of nonaqueous polar solvents was studied on the oxidation-reduction properties of the [Co(en)3]3+-[Co(en)3]2+ system. Interactions of these ions with the solvent molecules are discussed in terms of their coordination, which is accompanied by a specific interaction of the Lewis acid-base type, namely formation of a hydrogen bond between the interacting particles. This is the main controlling factor of the redox properties of the studied system.
Association of radical anions with alkali metal cations; I. Modified π(PPP-like) method for the investigation of ion pairs
Authors: Miertuš Stanislav , Kyseľ Ondrej , Mach Pavol
Published: January 2014

A simple π-approximation (PPP-like) method was modified to enable study of the association of radical anions with alkali metals. The possible uses of the method are demonstrated by the calculations of the different properties of the pyrazine-Me (Me = Li, Na, Cs) system.
Association of radical anions with alkali metal cations; II. Quantum-chemical study of the associates of glyoxal, nitrobenzene and fluorenone with lithium
Authors: Miertuš Stanislav , Kyseľ Ondrej , Mach Pavol
Published: January 2014

Some radical anions (glyoxal, fluorenone and nitrobenzene) were investigated by the modified LHP method. The calculated effects of cations (in ion pairs) and the effect of the polarity of the medium on energy ratios, conformation, hyperfine splitting constants and electronic spectra in the systems agree well with the available experimental data. It seems that the proposed modified LHP method can be useful in the study of ion-radical systems derived from larger conjugated molecules.
Association of radical anions alkali metal cations. III. Experimental and theoretical study of the associates of nitrobenzene radical anions with Li+, Na+, K+, Cs+ and (n-C4H9)4N+ cations
Authors: Miertuš Stanislav , Kyseľ Ondrej , Danciger Juraj
Published: January 2014

The nitrobenzene radical anion prepared by electrolysis was studied by UV spectroscopy. Formation of associates with Li+, Na+, K+, Cs+ and n(C4H9)4N+ cations was examined. It has been found that associates are also formed in a polar medium such as dimethylformamide. The enthalpy of the associated-free ion equilibrium was estimated as being equal to 6+4 kJ/mol-1. The quantum-chemical LHP method (in the π-approximation) was employed to study a simple ion pair model used for calculation of the most stable geometrical structure.
Association of radical anion with alkali cations. IV. ESR study of the 4-nitrobenzophenone radical anion
Authors: Miertuš Stanislav , Kyseľ Ondrej
Published: January 2014

The 4-nitrobenzophenone radical anion prepared by electrolysis was studied by ESR spectroscopy. On the basis of the interpretation of ESR spectra, the conformation of this system was estimated. The effect of the concentration of supporting electrolyte and of the presence of a proton-donor agent (C2H5OH) was examined. It is assumed that changes in hyperfine splitting constants are caused by association.
Solvolysis of diphenyl amidophosphates in aqueous alcoholic media
Authors: Kašpárek František , Mollin Jiří
Published: January 2014

Influence of substituent on the reaction rate of the alkali-catalyzed solvolysis of the studied compound set has been followed. The activation entropy has also been determined. The reaction products have been identified, and their concentration ratio has been determined. The reaction selectivity is mostly influenced by sterical effects in the substrate molecule. The results obtained agree with the SN2 mechanism.