bluuebunny/crossref_metadata_2025 huggingface dataset:
High‐resolution molecular karyotyping uncovers pairing between ancestrally related Brassica chromosomes
Authors: Mason Annaliese S. , Batley Jacqueline , Bayer Philipp Emanuel , Hayward Alice , Cowling Wallace A. , Nelson Matthew N.
Published: January 2014

How do chromosomal regions with differing degrees of homology and homeology interact at meiosis? We provide a novel analytical method based on simple genetics principles which can help to answer this important question. This method interrogates high‐throughput molecular marker data in order to infer chromosome behavior at meiosis in interspecific hybrids.

We validated this method using high‐resolution molecular marker karyotyping in two experimental Brassica populations derived from interspecific crosses among B. juncea, B. napus and B. carinata, using a single nucleotide polymorphism chip.

This method of analysis successfully identified meiotic interactions between chromosomes sharing different degrees of similarity: full‐length homologs; full‐length homeologs; large sections of primary homeologs; and small sections of secondary homeologs.

This analytical method can be applied to any allopolyploid species or fertile interspecific hybrid in order to detect meiotic associations. This genetic information can then be used to identify which genomic regions share functional homeology (i.e., retain enough similarity to allow pairing and segregation at meiosis). When applied to interspecific hybrids for which reference genome sequences are available, the question of how differing degrees of homology and homeology affect meiotic interactions may finally be resolved.
Postprocedure Mapping of Cardiac Resynchronization Lead Position Using Standard Fluoroscopy Systems: Implications for the Nonresponder with Scar
Authors: PARKER KATHERINE M. , BUNTING ETHAN , MALHOTRA ROHIT , CLARKE SAMANTHA A. , MASON PAMELA , DARBY ANDREW E. , KRAMER CHRISTOPHER M. , SALERNO MICHAEL , HOLMES JEFFREY W. , BILCHICK KENNETH C.
Published: January 2014

Background

The relationship between cardiac resynchronization therapy (CRT), left ventricular (LV) lead position, scar, and regional mechanical function influences CRT response.

Objective

To determine LV lead position relative to LV structural characteristics in standard clinical practice, we developed and validated a practical yet mathematically rigorous method to register procedural fluoroscopic LV lead position with pre‐CRT cardiac magnetic resonance (CMR).

Methods

After one‐time calibration of the standard fluoroscopic suite, we identified the projected CMR LV lead position using three reference landmarks on both CMR and fluoroscopy. This predicted lead position was validated in a canine model by histology and in eight “validation group” patients based on postoperative computed tomography scans (n = 7) or CMR coronary sinus venography (n = 1). The methodology was applied in an additional eight patients with CRT nonresponse and infarction‐related myocardial scar.

Results

The projected and actual lead positions were within 1.2 mm in the canine model. The median distance between projected and actual lead positions for the validation group (n = 8) and animal validation case was 11.3 mm (interquartile range 9.2–14.6 mm). In the application (nonresponder) group (n = 8), the lead mapped to the scar periphery in three patients, the core of the scar in one patient, and more than 3 cm from scar in four patients.

Conclusions

This methodology projects procedural fluoroscopic LV lead position onto pre‐CRT CMR using standard fluoroscopic equipment and a one‐time calibration, enabling assessment of LV lead position with sufficient accuracy to identify the lead position relative to regional function and infarction‐related scar in CRT nonresponders.
Novel method for isolating human melanoblasts from keratinocyte culture
Authors: Cho Eun‐Gyung , Bin Bum‐Ho , Choi Hyunjung , Park Phil June , Kang Hak Hee , Lee Tae Ryong
Published: January 2014

The characterization of melanoblasts is important for understanding their in vivo development, melanoma formation, and pigment‐related disorders. However, no methods have been reported for the isolation of melanoblasts from human skin. Using a ‘calcium‐pulse’ technique, involving the differentiation of human keratinocytes with high calcium and the subsequent spontaneous separation of the epidermal sheets, we effectively isolated human melanoblasts (keratinocyte‐adapted melanoblasts, KaMBs) from keratinocyte culture. The KaMBs expressed early melanogenesis‐related genes, including BRN2, which is a known melanoblast marker. Moreover, the KaMBs displayed much higher proliferative and growth capacities than the primary melanocytes. Considering that keratinocytes might provide an in vivo‐like environment for KaMBs during isolation and in vitro culture, the ‘calcium‐pulse’ technique offers an unprecedented, easy, and efficient method for the isolation of human melanoblasts, retaining the original characteristics of these cells.
Preparation and Characterization of Uniform Near IR Polystyrene Nanoparticles
Authors: Pellach Michal , Margel Shlomo
Published: January 2014

Biomaterials for in vivo fluorescence imaging are required to be biocompatible, nontoxic, photostable and highly fluorescent. Fluorescence must be in the near infrared (NIR) region of the electromagnetic spectrum to avoid absorption and autofluorescence of endogenous tissues. NIR fluorescent polystyrene nanoparticles may be considered ideal biomaterials for in vivo imaging applications. These NIR nanoparticles were prepared by a swelling process of polystyrene template nanoparticles with a hydrophobic NIR dye dissolved in a water‐miscible swelling solvent, a method developed for preparation of nonbiodegradable nanoparticles, for NIR fluorescent bioimaging applications. This method overcomes common problems that occur with dye entrapment during nanoparticle formation such as loss of fluorescence and size polydispersity. Fluorescence intensity of the nanoparticles was found to be size dependent, and was optimized for differently sized nanoparticles. The resulting NIR nanoparticles were also found to be more fluorescent and highly photostable compared to the free dye in solution, showing their potential as biomaterials for in vivo fluorescence imaging.
Skatole Metabolism in the Pigs with Reduced Testicular Oestrogen Synthesis
Authors: Zamaratskaia G , Berger T
Published: January 2014

Content

The objectives of the study were to investigate the involvement of oestrogens in the regulation of skatole levels in pigs. In total, 44 intact male pigs, siblings from 10 litters, were included in the study. Pigs were orally treated weekly with either 0.1 mg letrozole/kg body weight to reduce endogenous oestrogens or the canola oil vehicle. Fat and liver samples were collected at slaughter at 16, 20 and 40 weeks of age. Skatole and androstenone levels in fat and activities of hepatic cytochrome P4501A1, CYP1A2, CYP2A19 and CYP2E1 were analysed. Letrozole treatment did not significantly change either the levels of skatole or activities of skatole‐metabolising enzymes, suggesting that oestrogens are not responsible for gender‐related differences in skatole concentrations in porcine tissues.
Creative Activism and Art Against Urban Renaissance and Social Exclusion – Space Sensitive Approaches to the Study of Collective Action and Belonging
Authors: Youkhana Eva
Published: January 2014

Creative activism and urban art are increasingly being used as an instrument to collectively re‐appropriate the urban space and thus articulate urban belonging and citizenship from below. In cities worldwide, where different politics of place stimulate capitalist appropriation, individuals and groups use the public space as a laboratory for resistance, creative act, and as a medium for communication. As such, creative activism is a strategy for those who are widely excluded from social, political, cultural, and economic participation. Collectives are built through joint actions and experiences that are translated into the production situated forms of urban belonging. By drawing on space sensitive and situationist approaches and the power of creativity as an important moment in the analysis of action, the paper provides examples of how collective action and belonging is produced under conditions of contentious politics and exclusion that go beyond social norms, the social containment of institutions,and imposed collective identities.
Neighborhood Scale and Collective Efficacy: Does Size Matter?
Authors: Stein Rachel E.
Published: January 2014

The theory of collective efficacy emphasizes the role of the neighborhood as a unit of social control that can deter crime. The neighborhood unit is most often defined as a census tract or a similar administratively defined measure. These neighborhood definitions are not always sociologically meaningful. That is, administratively defined geographical areas do not necessarily align with residents' perceptions of their neighborhood's boundaries, which incorporate the familiarity with an area and interactions with other residents. Officially defined neighborhoods often present an inaccurate representation of collective efficacy, as these areas are not likely to function as a cohesive social unit. An alternative measure of “bespoke” neighborhoods is presented in geographical research. The bespoke neighborhood identifies a neighborhood area as the distance from a specific point or the number of people situated nearest to a specific location. This concept takes into consideration each resident's unique definition of the neighborhood. In addition, the bespoke neighborhood can be assessed on different scales to identify the most appropriate neighborhood size, where patterns of behavior are most meaningful. Bespoke neighborhoods can be used to identify sociologically meaningful neighborhoods that can inform the theory of collective efficacy.
Cardamine hirsuta: a versatile genetic system for comparative studies
Authors: Hay Angela S. , Pieper Bjorn , Cooke Elizabeth , Mandáková Terezie , Cartolano Maria , Tattersall Alexander D. , Ioio Raffaele D. , McGowan Simon J. , Barkoulas Michalis , Galinha Carla , Rast Madlen I. , Hofhuis Hugo , Then Christiane , Plieske Jörg , Ganal Martin , Mott Richard , Martinez‐Garcia Jaime F. , Carine Mark A. , Scotland Robert W. , Gan Xiangchao , Filatov Dmitry A. , Lysak Martin A. , Tsiantis Miltos
Published: January 2014

A major goal in biology is to identify the genetic basis for phenotypic diversity. This goal underpins research in areas as diverse as evolutionary biology, plant breeding and human genetics. A limitation for this research is no longer the availability of sequence information but the development of functional genetic tools to understand the link between changes in sequence and phenotype. Here we describe Cardamine hirsuta, a close relative of the reference plant Arabidopsis thaliana, as an experimental system in which genetic and transgenic approaches can be deployed effectively for comparative studies. We present high‐resolution genetic and cytogenetic maps for C. hirsuta and show that the genome structure of C. hirsuta closely resembles the eight chromosomes of the ancestral crucifer karyotype and provides a good reference point for comparative genome studies across the Brassicaceae. We compared morphological and physiological traits between C. hirsuta and A. thaliana and analysed natural variation in stamen number in which lateral stamen loss is a species characteristic of C. hirsuta. We constructed a set of recombinant inbred lines and detected eight quantitative trait loci that can explain stamen number variation in this population. We found clear phylogeographic structure to the genetic variation in C. hirsuta, thus providing a context within which to address questions about evolutionary changes that link genotype with phenotype and the environment.
A Dynamin Homolog Promotes the Transition from Hemifusion to Content Mixing in Intracellular Membrane Fusion
Authors: Kulkarni Aditya , Alpadi Kannan , Sirupangi Tirupataiah , Peters Christopher
Published: January 2014

The convergence of the antagonistic reactions of membrane fusion and fission at the hemifusion/hemifission intermediate has generated a captivating enigma of whether Soluble N‐ethylmaleimide sensitive factor Attachment Protein Receptor (SNAREs) and dynamin have unusual counter‐functions in fission and fusion, respectively. SNARE‐mediated fusion and dynamin‐driven fission are fundamental membrane flux reactions known to occur during ubiquitous cellular communication events such as exocytosis, endocytosis and vesicle transport. Here we demonstrate the influence of the dynamin homolog Vps1 (Vacuolar protein sorting 1) on lipid mixing and content mixing properties of yeast vacuoles, and on the incorporation of SNAREs into fusogenic complexes. We propose a novel concept that Vps1, through its oligomerization and SNARE domain binding, promotes the hemifusion‐content mixing transition in yeast vacuole fusion by increasing the number of trans‐SNAREs.
Optimization of a Hybrid Double-Side Jet Impingement Cooling System for High-Power Light Emitting Diodes
Authors: Kim Sun-Min , Kim Kwang-Yong
Published: January 2014

Optimization of a hybrid double-side jet impingement cooling system for high-power light emitting diodes (LEDs) was performed using a hybrid multi-objective evolutionary approach and three-dimensional numerical analysis for steady incompressible laminar flow and conjugate heat transfer using Navier–Stokes equations. For optimization, two design variables, i.e., ratios of the diameter of jet holes and the distance from the exit of upper impinging hole to chips to thickness of substrate were chosen out of the various geometric parameters affecting the performance of the cooling system. To evaluate cooling performance and pressure loss of the system, two objective functions, viz., the ratio of the maximum temperature to average temperature on the chips and pressure coefficient, were selected. Surrogate modeling of the objective functions was performed using response surface approximation. The Pareto-optimal solutions were obtained using a multi-objective evolutionary algorithm, and performances of three representative Pareto-optimal designs were discussed compared to a reference design. In the optimal designs, higher level of uniform cooling was generally achieved with higher pressure coefficient. The Pareto-sensitivity analysis between the objective function and design variable was also performed.
Advances in the Development of a Microturbine Engine
Authors: Dessornes O. , Landais S. , Valle R. , Fourmaux A. , Burguburu S. , Zwyssig C. , Kozanecki Z.
Published: January 2014

To reduce the size and weight of power generation machines for portable devices, several systems to replace the currently used heavy batteries are being investigated worldwide. As micro gas turbines are expected to offer the highest power density, several research groups launched programs to develop ultra micro gas turbines: IHI firm (Japan), PowerMEMS Consortium (Belgium). At Onera, a research program called DecaWatt is under development in order to realize a demonstrator of a micro gas turbine engine in the 50 to 100 Watts electrical power range. A single-stage gas turbine is currently being studied. First of all, a calculation of the overall efficiency of the micro gas turbine engine has been carried out according to the pressure ratio, the turbine inlet temperature, and the compressor and turbine efficiencies. With realistic hypotheses, we could obtain an overall efficiency of about 5% to 10%, which leads to around 200 W/kg when taking into account the mass of the micro gas turbine engine, its electronics, fuel and packaging. Moreover, the specific energy could be in the range 300 to 600 Wh/kg, which largely exceeds the performance of secondary batteries. To develop such a micro gas turbine engine, experimental and computational work focused on: (1) a 10-mm diameter centrifugal compressor, with the objective to obtain a pressure ratio of about 2.5; (2) a radial inflow turbine; (3) journal and thrust gas bearings (lobe bearings and spiral grooves) and their manufacturing; (4) a small combustor working with hydrogen or hydrocarbon gaseous fuel (propane); (5) a high rotation speed microgenerator; and (6) the choice of materials. Components of this tiny engine were tested prior to the test with all the parts assembled together. Tests of the generator at 700,000 rpm showed a very good efficiency of this component. In the same way, compressor testing was performed up to 500,000 rpm and showed that the nominal compression rate at the 840,000 rpm nominal speed should nearly be reached.
Design and Development of a Specially Modified Positive Displacement Rotary Screw Pump and Relevant Hydraulic Circuit to Enhance “Entrained Air Handling” Capability in a Closed Loop Lube Oil System
Authors: Berti Simone , Fracassi Pietro , Mattioli Alessandra , Reddy Potula Varuna , Lotti Cristiano
Published: January 2014

Rotary screw type positive displacement (RSPD) pumps are commonly used in oil and gas industry for pumping of mineral lube oil in services where they can be mechanically driven by gears coupled to a train driver. Installation of these pumps is critical and should be designed jointly by vendors and users according to project specific restrictions (i.e., the arrangement of the entire oil circulation system). This paper describes a real case in which restrictions due to lube oil system arrangement have produced low pump suction head and have amplified the influence of air bubbles that remained entrained in oil despite lube oil tank degassing. The investigations have been directed toward the mathematical modeling of the aeration phenomenon coupled with experimental measurements of critical parameters taken on the shop plant. Among corrective actions identified and considered there are reduction of quantity of air entering the lube oil system and revamping of the entire lube oil system with changes in piping, tank and also in pump model together with special modifications of internal path to enhance air handling capabilities. In order to validate pump behavior with reference to resistance to aeration (monitoring noise and vibration) a special simulation setup was jointly developed by end user and manufacturer on a pilot test bench to carry out the various performance tests. The numerical data collected during shop aeration test have confirmed that the pump was able to handle the expected amount of entrained air with noise and vibrations within industrial limits. The pumps tested in the pilot bench were installed at user's site and the effectiveness of the synergic corrective actions listed above was successfully verified. The study concludes that an early estimation of entrained air in the lube oil system is critical for design and development of either the RSPD pump or the entire lube oil circuit of a motor compressor train. When a critical quantity of entrained air is likely to be reached at pump suction (near 10% in volume), pump manufacturers and end users should apply some basic rules related to “design for aeration” of the pump and agree on a nonroutine test to be performed at manufacturer's shop before pump installation at site. This will serve as a reliable prediction of pump air handling capabilities, without which effective operation, reliability and durability of the pump could be jeopardized.
Laser Induced Chemical Deposition of Ferrihydrite Nanotubes: Exploring Growth Rate and Crystal Structure
Authors: Liu Zhikun , Richard Liu C.
Published: January 2014

This paper is one of three papers exploring and confirming a novel high rate nanomanufacturing method using laser to induce and accelerate chemical synthesis and deposition of nanotubes. We have shown elsewhere that the growth rate of SnO2 nanotubes by this method is a few orders faster than that by the state of the art electrochemical deposition method, the growth rate of the nanotubes is favorably affected by increasing the laser power under a constant number of scanning passes, and the process can grow nanotubes coalesced from ultrasmall particle size as small as 2 nm (Liu and Liu, 2013, "Laser Induced Chemical Solution Deposition of Nanomaterials: A Novel Process Demonstrated by Manufacturing SnO2 Nanotubes," Manuf. Lett., 1(1), pp. 42–35). In the second paper, we have shown that this novel method is generic, demonstrated by synthesizing various metal oxide and sulfide nanotubes (Liu and Liu, "Laser-Induced Solution Synthesis and Deposition: A Generic Method to Make Metal Chalcogenide Nanotubes at High Rate With High Consistency," J. Nanoeng. Nanosyst. (accepted)). Since the performance and properties of nanomaterials are highly dependent on its structure, we explore here how the basic processing variables affect the growth rate and crystal size. Our initial finding is that (1) the growth rate can be increased by increasing the pH value of the solution, resulting in little change on the crystal size and (2) the crystal size of the manufactured ferrihydrite nanotube arrays can be controlled by changing laser scanning passes. We found the increase of the pH value from 1.33 to 2.16 almost tripled the growth rate of ferrihydrite nanotubes, while the crystal size remained little changed as revealed by the transmission electron microscopy studies. However, increasing the number of laser scanning passes at a given power could coarsen the ferrihydrite nanocrystals. The crystal structure of the nanotubes could be converted to haematite by dry furnace annealing. These initial findings demonstrated the capability and controllability of the novel process.
Investigation of Mechanical Behavior of Membrane in Polymer Electrolyte Fuel Cells Subject to Dynamic Load Changes
Authors: Verma A. , Pitchumani R.
Published: January 2014

One of the major barriers for polymer electrolyte membrane (PEM) fuel cells to be commercially viable for stationary and transportation applications is the durability of membranes undergoing chemical and mechanical degradation over the period of operation. Toward understanding the effects of operating parameters on membrane durability, this paper presents numerical simulations for a single channel PEM fuel cell undergoing changes in load, by subjecting a unit cell to step changes in voltage. The objective is to elucidate the mechanical response of the membrane, which is subjected to hygral (water) loading and unloading cycles at constant temperature. Detailed three-dimensional (3D) computational fluid dynamics (CFD) simulations are conducted, taking into account the complex interactions of water transport dynamics and load changes, to accurately capture the water content in the membrane with changes in cell voltage. The water content obtained through CFD simulations is, in turn, used to carry out two-dimensional (2D) finite element (FE) analysis to predict the mechanical response of the membrane undergoing cyclic change in water content, as the operating voltage is cycled. The effects of cyclic changes in cell potential on the stresses induced, amount of plastic strain, and its localization are analyzed for various inlet cathode humidity values for two sections along the length of the fuel cell.
A New Incremental Formulation of Elastic–Plastic Deformation of Two-Phase Particulate Composite Materials
Authors: Teng Hong
Published: January 2014

In this study the double-inclusion model, originally developed to determine the effective linear elastic properties of composite materials, is reformulated in incremental form and extended to predict the effective nonlinear elastic–plastic response of two-phase particulate composites reinforced with spherical particles. The study is limited to composites consisting of purely elastic particles and elastic–plastic matrix of von Mises yield criterion with isotropic strain hardening. The resulting nonlinear problem of elastic–plastic deformation of a double inclusion embedded in an infinite reference medium (that has the elastic–plastic properties of the matrix) subjected to an incrementally applied far-field strain is linearized at each load increment through the use of the matrix tangent moduli. The proposed incremental double-inclusion model is evaluated by comparison of the model predictions to the exact results of the direct approach using representative volume elements containing many particles, and to the available experimental results. It is shown that the incremental double-inclusion formulation gives accurate prediction of the effective elastic–plastic response of two-phase particulate composites at moderate particle volume fractions. In particular, the incremental double-inclusion model is capable of capturing the Bauschinger effect often exhibited by heterogeneous materials. A unique feature of the proposed incremental formulation is that the composite matrix is treated as a two-phase material consisting of both an elastic and a plastic region.
Thermal Spreading Analysis of Rectangular Heat Spreader
Authors: Thompson S. M. , Ma H. B.
Published: January 2014

A unique nondimensional scheme that employs a source-to-substrate “area ratio” (e.g., footprint), has been utilized for analytically determining the steady-state temperature field within a centrally-heated, cuboidal heat spreader with square cross-section. A modified Laplace equation was solved using a Fourier expansion method providing for an infinite cosine series solution. This solution can be used to analyze the effects of Biot number, heat spreader thickness, and area ratio on the heat spreader's nondimensional maximum temperature and nondimensional thermal spreading resistance. The solution is accurate only for low Biot numbers (Bi < 0.001); representative of highly-conductive, two-phase heat spreaders. Based on the solution, a unique method for estimating the effective thermal conductivity of a two-phase heat spreader is also presented.
Two-Phase Upward Flow in a Slightly Deviated Pipe
Authors: Abdulahi Abolore , Azzopardi Barry J.
Published: January 2014

This study was undertaken to look at the effect of a slight inclination of pipe on upward flow characteristics especially at 10 deg from vertical position. Air-silicone oil flows in a 67 mm diameter pipe have been investigated using a capacitance wire mesh sensor (WMS) and electrical capacitance tomography (ECT). They provide time and cross-sectionally resolved data on void fraction. Superficial gas and liquid velocities of 0.05–1.9 and 0.05–0.5 were studied. Statistical methods and visual observation methods were used to characterize the fluid flows obtained into different flow patterns. From the output results from the tomography instruments, flow patterns were identified using both the reconstructed images as well as the characteristic signatures of Probability density function (PDF) plots of the time series of cross-sectionally averaged void fraction. Bubbly, cap bubble, slug, and churn flows were observed when the pipe was deviated by 10 deg from vertical pipe for the range of superficial gas velocities considered.
On the Effective Viscosity Expression for Modeling Squeeze-Film Damping at Low Pressure
Authors: Pantano Maria F. , Pagnotta Leonardo , Nigro Salvatore
Published: January 2014

While at high pressure, the classical Navier–Stokes equation is suitable for modeling squeeze-film damping, at low pressure, it needs some modification in order to consider fluid rarefaction. According to a common approach, fluid rarefaction can be included in this equation by substituting the standard fluid viscosity with a fictitious quantity, known as effective viscosity, for which different formulations were proposed. In order to identify which expression works better, the results obtained when either formulation is implemented inside the Navier–Stokes equation (that is then solved by both analytical and numerical means) are compared with already available experimental data. At the end, a novel expression is discussed, derived from a computer-assessed optimization procedure.
Refined NrfA Phylogeny Improves PCR-Based
nrfA
Gene Detection
Authors: Welsh Allana , Chee-Sanford Joanne C. , Connor Lynn M. , Löffler Frank E. , Sanford Robert A.
Published: January 2014

Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products). The nitrite reductase NrfA catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in DNRA. Although well studied biochemically, the diversity and phylogeny of this enzyme had not been rigorously analyzed. A phylogenetic analysis of 272 full-length NrfA protein sequences distinguished 18 NrfA clades with robust statistical support (>90% Bayesian posterior probabilities). Three clades possessed a CXXCH motif in the first heme-binding domain, whereas all other clades had a CXXCK motif in this location. The analysis further identified a KXRH or KXQH motif between the third and fourth heme-binding motifs as a conserved and diagnostic feature of all pentaheme NrfA proteins. PCR primers targeting a portion of the heme-binding motifs that flank this diagnostic region yielded the expected 250-bp-long amplicons with template DNA from eight pure cultures and 16 new
nrfA
-containing isolates.
nrfA
amplicons obtained with template DNA from two geomorphically distinct agricultural soils could be assigned to one of the 18 NrfA clades, providing support for this expanded classification. The extended NrfA phylogeny revealed novel diagnostic features of DNRA populations and will be useful to assess nitrate/nitrite fate in natural and engineered ecosystems.
Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia
Authors: Men Yujie , Seth Erica C. , Yi Shan , Allen Robert H. , Taga Michiko E. , Alvarez-Cohen Lisa
Published: January 2014

Corrinoids are essential cofactors of reductive dehalogenases inDehalococcoides mccartyi, an important bacterium in bioremediation, yet sequencedD. mccartyistrains do not possess the complete pathway forde novocorrinoid biosynthesis.Pelosinussp. andDesulfovibriosp. have been detected in dechlorinating communities enriched from contaminated groundwater without exogenous cobalamin corrinoid. To investigate the corrinoid-related interactions among key members of these communities, we constructed consortia by growingD. mccartyistrain 195 (Dhc195) in cobalamin-free, trichloroethene (TCE)- and lactate-amended medium in cocultures withDesulfovibrio vulgarisHildenborough (DvH) orPelosinus fermentansR7 (PfR7) and with both in tricultures. Only the triculture exhibited sustainable dechlorination and cell growth when a physiological level of 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, was provided. In the triculture, DvH provided hydrogen while PfR7 provided corrinoids to Dhc195, and the initiation of dechlorination and Dhc195 cell growth was highly dependent on the growth of PfR7. Corrinoid analysis indicated that Dhc195 imported and remodeled the phenolic corrinoids produced by PfR7 into cobalamin in the presence of DMB. Transcriptomic analyses of Dhc195 showed the induction of the CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes during corrinoid salvaging and remodeling. In contrast, another operon annotated to encode a putative iron/cobalamin ABC transporter (DET1174-DET1176) was induced when cobalamin was exogenously provided. Interestingly, a global upregulation of phage-related genes was observed when PfR7 was present. These findings provide insights into both the gene regulation of corrinoid salvaging and remodeling in Dhc195 when it is grown without exogenous cobalamin and microbe-to-microbe interactions in dechlorinating microbial communities.
Whole-Genome Single-Nucleotide-Polymorphism Analysis for Discrimination of Clostridium botulinum Group I Strains
Authors: Gonzalez-Escalona Narjol , Timme Ruth , Raphael Brian H. , Zink Donald , Sharma Shashi K.
Published: January 2014

Clostridium botulinum
is a genetically diverse Gram-positive bacterium producing extremely potent neurotoxins (botulinum neurotoxins A through G [BoNT/A-G]). The complete genome sequences of three strains harboring only the BoNT/A1 nucleotide sequence are publicly available. Although these strains contain a toxin cluster (HA
+
OrfX
−
) associated with hemagglutinin genes, little is known about the genomes of subtype A1 strains (termed HA
−
OrfX
+
) that lack hemagglutinin genes in the toxin gene cluster. We sequenced the genomes of three BoNT/A1-producing
C. botulinum
strains: two strains with the HA
+
OrfX
−
cluster (69A and 32A) and one strain with the HA
−
OrfX
+
cluster (CDC297). Whole-genome phylogenic single-nucleotide-polymorphism (SNP) analysis of these strains along with other publicly available
C. botulinum
group I strains revealed five distinct lineages. Strains 69A and 32A clustered with the
C. botulinum
type A1 Hall group, and strain CDC297 clustered with the
C. botulinum
type Ba4 strain 657. This study reports the use of whole-genome SNP sequence analysis for discrimination of
C. botulinum
group I strains and demonstrates the utility of this analysis in quickly differentiating
C. botulinum
strains harboring identical toxin gene subtypes. This analysis further supports previous work showing that strains CDC297 and 657 likely evolved from a common ancestor and independently acquired separate BoNT/A1 toxin gene clusters at distinct genomic locations.
Persistence of Infectious Shiga Toxin-Encoding Bacteriophages after Disinfection Treatments
Authors: Allué-Guardia Anna , Martínez-Castillo Alexandre , Muniesa Maite
Published: January 2014

In Shiga toxin-producingEscherichia coli(STEC), induction of Shiga toxin-encoding bacteriophages (Stx phages) causes the release of free phages that can later be found in the environment. The ability of Stx phages to survive different inactivation conditions determines their prevalence in the environment, the risk ofstxtransduction, and the generation of new STEC strains. We evaluated the infectivity and genomes of two Stx phages (Φ534 and Φ557) under different conditions. Infectious Stx phages were stable at 4, 22, and 37°C and at pH 7 and 9 after 1 month of storage but were completely inactivated at pH 3. Infective Stx phages decreased moderately when treated with UV (2.2-log10reduction for an estimated UV dose of 178.2 mJ/cm2) or after treatment at 60 and 68°C for 60 min (2.2- and 2.5-log10reductions, respectively) and were highly inactivated (3 log10) by 10 ppm of chlorine in 1 min. Assays in a mesocosm showed lower inactivation of all microorganisms in winter than in summer. The number of Stx phage genomes did not decrease significantly in most cases, and STEC inactivation was higher than phage inactivation under all conditions. Moreover, Stx phages retained the ability to lysogenizeE. coliafter some of the treatments.
Life History Analysis of Integrative and Conjugative Element Activation in Growing Microcolonies of Pseudomonas
Authors: Reinhard Friedrich , van der Meer Jan Roelof
Published: January 2014

Integrative and conjugative elements (ICE) are in some ways parasitic mobile DNA that propagate vertically through replication with the bacterial host chromosome but at low frequencies can excise and invade new recipient cells through conjugation and reintegration (horizontal propagation). The factors that contribute to successful horizontal propagation are not very well understood. Here, we study the influence of host cell life history on the initiation of transfer of a model ICE named ICE
clc
in bacteria of the genus
Pseudomonas
. We use time-lapse microscopy of growing and stationary-phase microcolonies of ICE
clc
bearing cells in combination with physiological staining and gene reporter analysis in stationary-phase suspended cells. We provide evidence that cell age and cell lineage are unlikely to play a role in the decision to initiate the ICE
clc
transfer program. In contrast, cells activating ICE
clc
show more often increased levels of reactive oxygen species and membrane damage than nonactivating cells, suggesting that some form of biochemical damage may make cells more prone to ICE
clc
induction. Finally, we find that ICE
clc
active cells appear spatially at random in a microcolony, which may have been a selective advantage for maximizing ICE
clc
horizontal transmission to new recipient species.
Identification and Characterization of a Second Quorum-Sensing System in Agrobacterium tumefaciens A6
Authors: Wang Chao , Yan Chunlan , Fuqua Clay , Zhang Lian-Hui
Published: January 2014

Quorum sensing (QS) is a widespread mechanism of bacterial communication in which individual cells produce and respond to small chemical signals. In
Agrobacterium tumefaciens
, an acylhomoserine lactone-dependent QS mechanism is known to regulate the replication and conjugation of the tumor-inducing (Ti) plasmid. Most of the QS regulatory proteins are encoded within the Ti plasmid. Among them, TraI is the LuxI-type enzyme synthesizing the QS signal
N
-3-oxooctanoyl-
l
-homoserine lactone (3OC8HSL), TraR is the LuxR-type transcriptional factor that recognizes 3OC8HSL, and TraM is an antiactivator that antagonizes TraR. Recently, we identified a TraM homolog encoded by the
traM2
gene in the chromosomal background of
A. tumefaciens
A6. In this study, we further identified additional homologs (TraI2 and TraR2) of TraI and TraR in this strain. We showed that similar to TraI, TraI2 could predominantly synthesize the QS signal 3OC8HSL. We also showed that TraR2 could recognize 3OC8HSL and activate the
tra
box-containing promoters as efficiently as TraR. Further analysis showed that
traM2
,
traI2
, and
traR2
are physically linked on a mobile genetic element that is not related to the Ti plasmid. These findings indicate that
A. tumefaciens
A6 carries a second QS system that may play a redundant role in the regulation of the replication and conjugation of the Ti plasmid.
Relation between adsorption from binary solutions and adsorption of pure gaseous components on the same adsorbent. The effect of the bulk liquid phase
Authors: Šišková Marie
Published: January 2014

The thermodynamic consistency test proposed by Sircar and Myers was employed to show the effect of the bulk liquid phase on the adsorption from solutions on a solid adsorbent. This effect can invalidate the prediction of the isotherm of the concentration change in a solution from experimental adsorption isotherms of pure components adsorbed from the gaseous phase on the same adsorbent.
Behaviour of CoNaA zeolites in interaction with water
Authors: Wichterlová Blanka , Kubelková Ludmila , Jírů Pavel
Published: January 2014

The influence of dehydration and adsorption of water on the coordination of cations, the state of adsorbed water, and stretching vibrations of CoNaA and NaA zeolites was investigated by means of electronic and infrared spectroscopy. Complexes of Co2+ change their symmetry from octahedral through tetrahedral to planar trigonal. The role of ligands play both skeletal oxygens and molecular water. The formation of OH groups either on skeleton or on Co2+ ions was not found; the existence of these groups was assumed in the literature to explain the catalytic activity of CoNaA zeolites in the isomerization of butenes.
Densities and molar volumes of the Ca(NO3)2-CaBr2-H2O system
Authors: Kodejš Zdeněk , Sláma Ivo
Published: January 2014

Molar volumes and densities of mixtures consisting of water, calcium nitrate, and calcium bromide have been determined in the range of molar ratio of water within 3 to 18 and in the temperature range of 20 to 80° C. The obtained results have been described by an equation derived under the assumption that additivity of molar volumes of the components is valid.
13C-NMR spectra of aldoses in molybdate complexes
Authors: Alföldi Juraj , Bílik Vojtech , Petruš Ladislav
Published: January 2014

Analysis of 13C-NMR spectra has shown that ribose, talose and allose behave as trident donors in their molybdate complexes using hydroxyl groups at C(2), C(3) and C(4), whereas lyxose and mannose use hydroxyl groups at C(1), C(2) and C(3).
Reactions and spectral properties of ethyl 5-aminofuroate and its derivatives
Authors: Prousek Josef , Jurášek Adolf , Kováč Jaroslav
Published: January 2014

Ethyl 5-aminofuroate (II), prepared by reduction of ethyl 5-nitrofuroate (I), served for preparation of bifunctional α,β-substituted aminofurans IV-IX, acyl derivatives IIIa, IIIb and condensation product X. The latter reacted with diazomethane directly to afford the corresponding aziridine derivative XI. The synthesized compounds were characterized by spectral data (IR, UV, 1H-NMR, 13C-NMR (XI) and mass spectra.)
Synthesis and reactions of alkyl 3-bromomethyl-3-(2-furyl)-2-propenoates with sulfur containing nucleophiles
Authors: Špirková Katarína , Kováč Jaroslav , Konečný Václav , Dandárová Miloslava , Černayová Marta
Published: January 2014

Preparation and nucleophilic displacement reactions of alkyl 3-bromomethyl-3-(2-furyl)-2-propenoates with sulfur containing nucleophiles is described. The UV, IR and 1H-NMR spectra of the synthesized compounds are interpreted.
Opening of the furan ring in 5-azido-2-furaldehyde
Authors: Považanec František , Kováč Jaroslav , Hesek Dušan
Published: January 2014

Fission of the furan ring in 5-azido-2-furaldehyde is described. α-Furylnitrene, formed from α-azido furan derivatives, is stabilized by the furan ring fission. Transformation of the intermediate to quinoxaline and pyrazole derivatives is also studied.
5-Nitro-2-furylvinylation of secondary and tertiary amines
Authors: Végh Daniel , Kováč Jaroslav , Dandárová Miloslava , Ivančo Lubor
Published: January 2014

Reaction of 12 secondary amines and trimethylamine with (Z) and (E)-5-nitro-2-furylvinyl bromide (I) was studied. Whereas the enamines II, obtained from secondary amines, have the E configuration, the quaternisation of trimethylamine affords stereospecifically the corresponding (Z) or (E) vinylammonium salts III.
Endo-D-galacturonanase immobilized by a covalent binding to hydroxyalkyl methacrylate gels. Preparation and properties
Authors: Rexová-Benková Lubomíra , Mračková Marta , Babor Karol
Published: January 2014

Insoluble derivatives of endo-D-galacturonanase were prepared by a covalent binding to hydroxyalkyl methacrylate gels (Spherons) by a cyanogen bromide method. Gels of various pore size were used. The amount of the attached enzyme, its activity and kinetic constants were determined. The effect of covalent binding on the pH activity curves, heat stability, storage stability at 4°C and the operational stability of the enzyme were investigated.
Study of the nature of the complexes present in PdCl2 aqueous solution
Authors: Kaszonyi Alexander , Vojtko Ján , Hrušovský Mikuláš
Published: January 2014

The existence of complexes of palladium chlorides in aqueous solutions was examined for different chloride-to-palladium molar ratios. Spectral and potentiometric methods were employed in conjunction with the cryoscopic technique, and the complexes of palladium with chlorides were found to be only mononuclear ; the existence of binuclear complexes can be practically ruled out.
Theoretical study of [10] and [12]annulenes
Authors: Loos Dušan , Leška Jaroslav
Published: January 2014

Equilibrium geometries of various geometrical isomers of annulenes have been calculated by the quantum-chemical methods EHT, CNDO/2, MINDO/2, MINDO/3 and the method of empirical potentials. Automatic method of full optimization has been used for some [10]annulenes and all isomers of [12]annulene. The bond strengths and degree of delocalization have been determined from the bond overlap populations and the Wiberg indices. Relative stabilities of the isomers have been determined by comparison of the formation enthalpies calculated by MINDO/3, MINDO/2 and empirical potential methods. Strain energy has been calculated, and degree of aromaticity of the isomers has been characterized by several aromaticity indices.
Experimental and calculated (PPP) electronic spectra of flavonoid, stilbene and coumarone structures
Authors: Remko Milan , Polčin Ján
Published: January 2014

Electronic spectra of seven hydroxy and methoxy substituted flavones as well as nine hydroxy and methoxy substituted flavoneles have been studied experimentally and theoretically with the use of the semiempirical SCF LCI PPP method. The same method has been applied to electronic spectra of some model compounds of lignin of stilbene and coumarone type. The calculated excitation energies agree well with the observed ones. Results of our experimental and theoretical studies of electronic spectra of basic chromophoric structural units of lignin are summarized from the viewpoint of their contribution to color of lignin.
The use of catalyzed decomposition of cupric formate for study of properties of palladium catalysts
Authors: Červený Libor , Marhoul Antonín , Červinka Karel , Růžička Vlastimil
Published: January 2014

The decomposition of cupric formate induced by palladium catalysts has been studied in aqueous solution. Effects of the carrier and the proper active component on the cupric formate concentration decrease have been separated. Kinetic data of the decomposition reaction have been obtained, and processes affecting the decomposition have been followed. The decomposition rates found with the use of various catalysts enabled to test the effects of preparation methods of palladium catalysts on their activity. The values found agree with hydrogenation activity of the catalysts.
Pyrolysis of hydrocarbons in the presence of elemental sulfur
Authors: Bajus Martin , Veselý Václav
Published: January 2014

The effect of elemental sulfur on the kinetics and selectivity of conversion of heptane was studied with regard to the inhibition of the coke formation during pyrolysis of raffinates from naphtha reforming. The experiments were conducted in stainless steel tubular through-flow reactors at atmospheric pressure. The heptane decomposition rate in the absence of sulfur was compared with that in the presence of 0.01, 0.02, and 0.1 wt.% sulfur at 700°C and with the steam-to-feed ratio 3:1. The influence of the inner surface of the reactor was investigated by using reactors with different equivalent volumes. The effect of sulfur on the coke formation during the pyrolysis of the reformer raffinate was examined at 820°C without any inert diluent.
Reactions of thiourea with chloro- and bromoacetic acids
Authors: Kaválek Jaromír , El-Bahaie Said , Štěrba Vojeslav
Published: January 2014

The reaction of chloroacetic acid with thiourea represents an SN2 substitution of chlorine by sulphur atom and is about two orders of magnitude slower than that of bromoacetic acid. Chloroacetate ion reacts slower than chloroacetic acid only about 30%. The acid catalyzed splitting off of hydroxyl group from the formed tetrahedral intermediate is rate-limiting in the cyclization of the S-carboxylatomethyleneisothiouronium salt, formation of the intermediate being rate-limiting below pH 2.
The synthesis and mass spectra of some oxygen-bridged 5α-cholestane and B-homo-5α-cholestane derivatives
Authors: Tureček František , Kočovský Pavel
Published: January 2014

The synthesis and mass spectrometric behaviour of a series of oxygen-bridged α-cholestans and B-homo-5α-cholestans I-X are described. The differences in fragmentation patterns of these compounds are discussed in dependence on the position of the oxygen bridge, position and configuration of additional substituents and conformation of the A and B rings of the steroid skeleton.