bluuebunny/crossref_metadata_2025 huggingface dataset:
Stable pediatric kidney transplant recipients run higher urine indoleamine 2, 3 dioxygenase (IDO) levels than healthy children
Authors: Khasawneh Eihab Al , Gupta Sushil , Tuli Sanjeev Y. , Shahlaee Amir H. , Garrett Timothy J. , Schechtman Kenneth B. , Dharnidharka Vikas R
Published: February 2014

Immune cells utilize the IDO enzymatic conversion of trp to kyn to determine T‐cell activation vs. anergy/apoptosis. In prior studies, urine IDO levels were higher in rejecting renal allografts than in stable state. However, urine IDO levels in healthy subjects or children are unknown. As a corollary to a larger longitudinal and prospective study of serum and urine IDO levels for transplant immune monitoring, here, we analyzed the difference between urine IDO levels in stable post‐transplant vs. healthy children. IDO levels were measured by tandem mass spectrometry and expressed as kyn/trp ratios. We compared one‐time urine samples, from 34 well children at general pediatric clinics, to the first‐month post‐transplant urine samples from 18 children, while in stable state (no acute rejection or major infection event in next 30 days). Urine kyn/trp ratios were significantly higher in stable children in first‐month post‐kidney transplant (median 16.6, range 3.9–44.0) vs. healthy children (median 9.2, range 3.51–17.0; p = 0.0057 by nonparametric Mann–Whitney test). Higher urine IDO levels even with stable transplant suggest a continuous ongoing low‐grade allorecognition/inflammatory process. Our data also provide baseline urine IDO levels in healthy subjects for use in future studies.
Panel Size and Overbooking Decisions for Appointment‐Based Services under Patient No‐Shows
Authors: Liu Nan , Ziya Serhan
Published: February 2014

Many service systems that work with appointments, particularly those in healthcare, suffer from high no‐show rates. While there are many reasons why patients become no‐shows, empirical studies found that the probability of a patient being a no‐show typically increases with the patient's appointment delay, i.e., the time between the call for the appointment and the appointment date. This paper investigates how demand and capacity control decisions should be made while taking this relationship into account. We use stylized single server queueing models to model the appointments scheduled for a provider, and consider two different problems. In the first problem, the service capacity is fixed and the decision variable is the panel size; in the second problem, both the panel size and the service capacity (i.e., overbooking level) are decision variables. The objective in both cases is to maximize some net reward function, which reduces to system throughput for the first problem. We give partial or complete characterizations for the optimal decisions, and use these characterizations to provide insights into how optimal decisions depend on patient's no‐show behavior in regards to their appointment delay. These insights especially provide guidance to service providers who are already engaged in or considering interventions such as sending reminders in order to decrease no‐show probabilities. We find that in addition to the magnitudes of patient show‐up probabilities, patients' sensitivity to incremental delays is an important determinant of how demand and capacity decisions should be adjusted in response to anticipated changes in patients' no‐show behavior.
Shareholder Value Effects of Voluntary Emissions Reduction
Authors: Jacobs Brian W.
Published: February 2014

The relationship between emissions reduction and firm financial performance has been studied with mixed results. We consider potential sources of this ambiguity by examining announcements of voluntary emissions reduction (VER) from 1990 to 2009. We measure the stock market reaction associated with VER announcements to estimate the effects of time, emissions type, and whether the reduction was announced ex ante or ex post. We find that the market reaction to VER significantly decreased over time. The changing nature of the market reaction to VER over time highlights the importance of evaluating the financial impact of any VER in the current context rather than relying on past findings. We also find that the market reaction is more positive if the reduction is for greenhouse gas (GHG) rather than other emissions types. In light of the increasing concern with GHGs, this finding should be welcome news for managers. Last, we find a more positive market reaction for VER announcements that are pledges or statements of intent rather than realized achievements of VER. Managers contemplating VER might find benefit (and at least no harm) in announcing their intent to reduce emissions rather than waiting until they have achieved the reduction.
The Strategic Role of Third‐Party Marketplaces in Retailing
Authors: Mantin Benny , Krishnan Harish , Dhar Tirtha
Published: February 2014

Retailers are increasingly adopting a dual‐format model. In addition to acting as traditional merchants (buying and reselling goods), these retailers provide a platform for third‐party (3P) sellers to access and compete for the same customers. We investigate the strategic rationale for a retailer to introduce a 3P marketplace. Our analysis provides insights into the growing prevalence of 3P marketplaces. We show that by committing to having an active 3P marketplace, the retailer creates an “outside option” that improves its bargaining position in negotiations with the manufacturer. This can explain the increasing prevalence of such marketplaces. On the other hand, the manufacturer would prefer to eliminate the retailer's outside option and should seek to limit or prevent sales through 3P marketplaces. This is consistent with actions that several manufacturers have taken to limit such sales. Interestingly, if the manufacturer fails to eliminate sales of competing products through the 3P marketplace, then the best strategy for the manufacturer is to allow the retailer to dictate the terms of their contract. This is because a powerful retailer will rely less on its outside option in generating profit, and therefore it will increase the fees charged to 3P sellers and soften the competition between 3P sellers and the manufacturer. The decrease in competition will lead to an increase in the value of outside option of the manufacturer and improve its profit. Additionally, we find that the presence of a 3P marketplace benefits consumers, but this benefit diminishes as the retailer becomes more powerful.
The Timing of Capacity Investment with Lead Times: When Do Firms Act in Unison?
Authors: Anderson Edward James , Sunny Yang Shu‐Jung
Published: February 2014

We study competitive capacity investment for the emergence of a new market. Firms may invest either in capacity leading demand or in capacity lagging demand at different costs. We show how the lead time and other operational factors including volume flexibility, existing capacity, and demand uncertainty impact equilibrium outcomes. Our results indicate that a type of bandwagon behavior is the most likely equilibrium outcome: if both firms are going to invest, then they are most likely to act in unison. Contrary to much received wisdom, we show that leader–follower behavior is very uncommon in equilibrium where firms do not have volume flexibility, and will not occur at all if lead times are sufficiently short. On the other hand, if there is volume flexibility in production, then the likelihood of this sequential investment behavior increases. Our findings underscore the importance of operational characteristics in determining the competitive dynamics of capacity investment timing.
Multiple‐Aetiology Enteric Infections Involving Non‐O157 Shiga Toxin‐Producing Escherichia coli – FoodNet, 2001–2010
Authors: Luna‐Gierke R. E. , Wymore K. , Sadlowski J. , Clogher P. , Gierke R. W. , Tobin‐D'Angelo M. , Palmer A. , Medus C. , Nicholson C. , McGuire S. , Martin H. , Garman K. , Griffin P. M. , Mody R. K.
Published: February 2014

We describe multiple‐aetiology infections involving non‐O157 Shiga toxin‐producing Escherichia coli (STEC) identified through laboratory‐based surveillance in nine FoodNet sites from 2001 to 2010. A multiple‐aetiology infection (MEI) was defined as isolation of non‐O157 STEC and laboratory evidence of any of the other nine pathogens under surveillance or isolation of >1 non‐O157 STEC serogroup from the same person within a 7‐day period. We compared exposures of patients with MEI during 2001–2010 with those of patients with single‐aetiology non‐O157 STEC infections (SEI) during 2008–2009 and with those of the FoodNet population from a survey conducted during 2006–2007. In total, 1870 non‐O157 STEC infections were reported; 68 (3.6%) were MEI; 60 included pathogens other than non‐O157 STEC; and eight involved >1 serogroup of non‐O157 STEC. Of the 68 MEI, 21 (31%) were part of six outbreaks. STEC O111 was isolated in 44% of all MEI. Of patients with MEI, 50% had contact with farm animals compared with 29% (P < 0.01) of persons with SEI; this difference was driven by infections involving STEC O111. More patients with non‐outbreak‐associated MEI reported drinking well water (62%) than respondents in a population survey (19%) (P < 0.01). Drinking well water and having contact with animals may be important exposures for MEI, especially those involving STEC O111.
Characterization of the anisotropic mechanical behaviour of colonic tissues: experimental activity and constitutive formulation
Authors: Carniel E. L. , Gramigna V. , Fontanella C. G. , Frigo A. , Stefanini C. , Rubini A. , Natali A. N.
Published: February 2014

New Findings

What is the central question of this study?

The wall of the colon shows an anisotropic and non‐linear mechanical response, because of the distribution and mechanical properties of sub‐components. This study aimed to provide, by a coupled experimental and computational approach, a constitutive framework to interpret the mechanics of colonic tissues.

What is the main finding and its importance?

Tensile tests on tissue samples from pig colon were developed. The experimental data were processed to define proper constitutive formulations. Constitutive parameters were identified by the inverse analysis of experimental tests. The reliability of parameters was assessed by agreement between the experimental and model results and the satisfaction of material thermomechanics principles. The developed constitutive framework is capable of interpreting the general anisotropic and non‐linear mechanical behaviour of colonic tissues.

The aim was to investigate the biomechanical behaviour of colonic tissues by a coupled experimental and numerical approach. The wall of the colon is composed of different tissue layers. Within each layer, different fibre families are distributed according to specific spatial orientations, which lead to a strongly anisotropic configuration. Accounting for the complex histology of the tissues, mechanical tests must be planned and designed to evaluate the behaviour of the colonic wall in different directions. Uni‐axial tensile tests were performed on tissue specimens from 15 fresh pig colons, accounting for six different loading directions (five specimens for each loading direction). The next step of the investigation was to define an appropriate constitutive framework and develop a procedure for identification of the constitutive parameters. A specific hyperelastic formulation was developed that accounted for the multilayered conformation of the colonic wall and the fibre‐reinforced configuration of the tissues. The parameters were identified by inverse analyses of the mechanical tests. The comparison of model results with experimental data, together with the evaluation of satisfaction of material thermomechanics principles, confirmed the reliability of the analysis developed. This work forms the basis for more comprehensive activities that aim to provide computational tools for the interpretation of surgical procedures that involve the gastrointestinal tract, considering the specific biomedical devices adopted.
Chemical mechanical planarization of gold
Authors: Karbasian Golnaz , Fay Patrick J. , Grace Xing Huili , Orlov Alexei O. , Snider Gregory L.
Published: February 2014

In this article, the authors investigate chemical mechanical planarization (CMP) of gold. Our experiments show that the oxidizer concentration, hardness of the adhesion layer, and surfactants added to stabilize the slurry are the main factors determining the outcome of the process. A combination of 30% H2O2 solution and an alumina based slurry in 1:3 volumetric ratio along with added sodium dodecyl sulfate and poly(vinyl pyrrolidone) was successfully used to pattern gold in a CMP Damascene process. After fabricating inlaid gold structures with CMP, the authors observed that pattern density, as opposed to feature size, is the major factor in determining the amount of metal thinning in inlaid features. 10 μm lines at 5% density were thinned down by 40 nm, while 150 μm pads at 75% density were recessed by 20 nm. The authors believe that in this process, metal recess, that is a chemical effect, outweighs dishing, a feature-size dependent factor, in controlling the severity of metal thinning.
Void-free direct bonding of InP to Si: Advantages of low H-content and ozone activation
Authors: Itawi A. , Pantzas K. , Sagnes I. , Patriarche G. , Talneau A.
Published: February 2014

Oxide-mediated direct bonding of InP to silicon has been investigated using a variety of oxidation and oxide-activation techniques to achieve void-free bonding without resorting to complex outgassing schemes. Void formation is shown to be related to the H content of the SiO2 layer. Transmission Fourier transformed infrared spectroscopy measurements corroborate this hypothesis. Finally, the use of ozone instead of oxygen plasma activation is also revealed to be beneficial for void-free bonding.
Atomic layer deposited high-κ nanolaminates for silicon surface passivation
Authors: Benner Frank , Jordan Paul M. , Richter Claudia , Simon Daniel K. , Dirnstorfer Ingo , Knaut Martin , Bartha Johann W. , Mikolajick Thomas
Published: February 2014

Nanolaminates comprising of TiO2 or HfO2 sublayers within an Al2O3 matrix are grown with atomic layer deposition. These nanolaminates provide an improved silicon surface passivation compared to conventional Al2O3 films. The physical properties of the nanolaminates can be described with a dynamic growth model that considers initial and steady-state growth rates for the involved metal oxides. This model links the cycle ratios of the different atomic layer deposition precursors to the thickness and the material concentrations of the nanolaminate, which are determined by means of spectroscopic ellipsometry. Effective carrier lifetime measurements show that Al2O3-TiO2 nanolaminates achieve values of up to 6.0 ms at a TiO2 concentration of 0.2%. In Al2O3-HfO2 nanolaminates, a maximum effective carrier lifetime of 5.5 ms is reached at 7% HfO2. Electrical measurements show that the TiO2 incorporation causes strong hysteresis effects, which are linked to the trapping of negative charges and result in an enhanced field effect passivation. For the Al2O3-HfO2 nanolaminates, the capacitance data clearly show a very low density of interface traps (below 5·1010 eV−1·cm−2) and a reduction of the fixed charge density with increasing HfO2 concentration. Due to the low number of recombination centers near the surface, the reduced field effect passivation only had a minor impact on the effective carrier lifetime.
Impedance characterization of nanogap interdigitated electrode arrays fabricated by tilted angle evaporation for electrochemical biosensor applications
Authors: Jeon Dae-Young , Jeong Park So , Kim Yongha , Shin Min-Ju , Soo Kang Pil , Kim Gyu-Tae
Published: February 2014

Nanogap interdigitated electrode (IDE) arrays were fabricated by tilted angle evaporation on dry etch SiO2 substrates, suggesting a simple, inexpensive, and controllable fabrication technique. The impedance characteristics in a KCl solution clearly showed the differences between nanogap and microscaled IDEs in terms of the peak positions of the phase shift and the ratio of the resistance amplitudes. Moreover, the effect of imperfections on the edge of electrodes was quantitatively discussed through the analysis of electric-field based on finite element method. Our results provide a better understanding of impedance behavior of nanogap IDE arrays for high-performance biochemical applications.
An efficient polyenergetic SART (pSART) reconstruction algorithm for quantitative myocardial CT perfusion
Authors: Lin Yuan , Samei Ehsan
Published: February 2014

Purpose:

In quantitative myocardial CT perfusion imaging, beam hardening effect due to dense bone and high concentration iodinated contrast agent can result in visible artifacts and inaccurate CT numbers. In this paper, an efficient polyenergetic Simultaneous Algebraic Reconstruction Technique (pSART) was presented to eliminate the beam hardening artifacts and to improve the CT quantitative imaging ability.

Methods:

Our algorithm made threea priori assumptions: (1) the human body is composed of several base materials (e.g., fat, breast, soft tissue, bone, and iodine); (2) images can be coarsely segmented to two types of regions, i.e., nonbone regions and noniodine regions; and (3) each voxel can be decomposed into a mixture of two most suitable base materials according to its attenuation value and its corresponding region type information. Based on the above assumptions, energy‐independent accumulated effective lengths of all base materials can be fast computed in the forward ray‐tracing process and be used repeatedly to obtain accurate polyenergetic projections, with which a SART‐based equation can correctly update each voxel in the backward projecting process to iteratively reconstruct artifact‐free images. This approach effectively reduces the influence of polyenergetic x‐ray sources and it further enables monoenergetic images to be reconstructed at any arbitrarily preselected target energies. A series of simulation tests were performed on a size‐variable cylindrical phantom and a realistic anthropomorphic thorax phantom. In addition, a phantom experiment was also performed on a clinical CT scanner to further quantitatively validate the proposed algorithm.

Results:

The simulations with the cylindrical phantom and the anthropomorphic thorax phantom showed that the proposed algorithm completely eliminated beam hardening artifacts and enabled quantitative imaging across different materials, phantom sizes, and spectra, as the absolute relative errors were reduced from [−7.5%, 12.1%] for SART to [−0.1%, 0.1%] for pSART. When using low kVp spectra and high reference energies, pSART also showed improved reconstruction efficiency in terms of convergence speed compared to the conventional SART algorithm. The phantom experiment on a clinical CT scanner indicated that the quantitative advantage of pSART is realizable in experimental CT acquisition, as the absolute relative errors across material inserts were less than 0.4%.

Conclusions:

By incorporatinga priori information (material attenuation coefficients, x‐ray source spectrum, and region type information) into the reconstruction process, the proposed pSART algorithm could effectively eliminate beam hardening artifacts, reconstruct the accurate attenuation coefficients for precise quantitative imaging, and accelerate the reconstruction process.
Identification of Bacteriophages for Biocontrol of the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae
Authors: Frampton Rebekah A. , Taylor Corinda , Holguín Moreno Angela V. , Visnovsky Sandra B. , Petty Nicola K. , Pitman Andrew R. , Fineran Peter C.
Published: February 2014

Pseudomonas syringae
pv. actinidiae is a reemerging pathogen which causes bacterial canker of kiwifruit (
Actinidia
sp.). Since 2008, a global outbreak of
P. syringae
pv. actinidiae has occurred, and in 2010 this pathogen was detected in New Zealand. The economic impact and the development of resistance in
P. syringae
pv. actinidiae and other pathovars against antibiotics and copper sprays have led to a search for alternative management strategies. We isolated 275 phages, 258 of which were active against
P. syringae
pv. actinidiae. Extensive host range testing on
P. syringae
pv. actinidiae, other pseudomonads, and bacteria isolated from kiwifruit orchards showed that most phages have a narrow host range. Twenty-four were analyzed by electron microscopy, pulse-field gel electrophoresis, and restriction digestion. Their suitability for biocontrol was tested by assessing stability and the absence of lysogeny and transduction. A detailed host range was performed, phage-resistant bacteria were isolated, and resistance to other phages was examined. The phages belonged to the
Caudovirales
and were analyzed based on morphology and genome size, which showed them to be representatives of
Myoviridae
,
Podoviridae
, and
Siphoviridae
. Twenty-one
Myoviridae
members have similar morphologies and genome sizes yet differ in restriction patterns, host range, and resistance, indicating a closely related group. Nine of these
Myoviridae
members were sequenced, and each was unique. The most closely related sequenced phages were a group infecting
Pseudomonas aeruginosa
and characterized by phages JG004 and PAK_P1. In summary, this study reports the isolation and characterization of
P. syringae
pv. actinidiae phages and provides a framework for the intelligent formulation of phage biocontrol agents against kiwifruit bacterial canker.
Genetic Manipulations of the Hyperthermophilic Piezophilic Archaeon Thermococcus barophilus
Authors: Thiel Axel , Michoud Grégoire , Moalic Yann , Flament Didier , Jebbar Mohamed
Published: February 2014

In this study, we developed a gene disruption system for
Thermococcus barophilus
using simvastatin for positive selection and 5-fluoroorotic acid (5-FOA) for negative selection or counterselection to obtain markerless deletion mutants using single- and double-crossover events. Disruption plasmids carrying flanking regions of each targeted gene were constructed and introduced by transformation into wild-type
T. barophilus
MP cells. Initially, a
pyrF
deletion mutant was obtained as a starting point for the construction of further markerless mutants. A deletion of the
hisB
gene was also constructed in the UBOCC-3256 (Δ
pyrF
) background, generating a strain (UBOCC-3260) that was auxotrophic for histidine. A functional
pyrF
or
hisB
allele from
T. barophilus
was inserted into the chromosome of UBOCC-3256 (Δ
pyrF
) or UBOCC-3260 (Δ
pyrF
Δ
hisB
), allowing homologous complementation of these mutants. The piezophilic genetic tools developed in this study provide a way to construct strains with multiple genetic backgrounds that will allow further genetic studies for hyperthermophilic piezophilic archaea.
Detection and Prevalence of Verotoxin-Producing Escherichia coli O157 and Non-O157 Serotypes in a Canadian Watershed
Authors: Johnson R. P. , Holtslander B. , Mazzocco A. , Roche S. , Thomas J. L. , Pollari F. , Pintar K. D. M.
Published: February 2014

Verotoxin-producing
Escherichia coli
(VTEC) strains are the cause of food-borne and waterborne illnesses around the world. Traditionally, surveillance of the human population as well as the environment has focused on the detection of
E. coli
O157:H7. Recently, increasing recognition of non-O157 VTEC strains as human pathogens and the German O104:H4 food-borne outbreak have illustrated the importance of considering the broader group of VTEC organisms from a public health perspective. This study presents the results of a comparison of three methods for the detection of VTEC in surface water, highlighting the efficacy of a direct VT immunoblotting method without broth enrichment for detection and isolation of O157 and non-O157 VTEC strains. The direct immunoblot method eliminates the need for an enrichment step or the use of immunomagnetic separation. This method was developed after 4 years of detecting low frequencies (1%) of
E. coli
O157:H7 in surface water in a Canadian watershed, situated within one of the FoodNet Canada integrated surveillance sites. By the direct immunoblot method, VTEC prevalence estimates ranged from 11 to 35% for this watershed, and
E. coli
O157:H7 prevalence increased to 4% (due to improved method sensitivity). This direct testing method provides an efficient means to enhance our understanding of the prevalence and types of VTEC in the environment. This study employed a rapid evidence assessment (REA) approach to frame the watershed findings with watershed
E. coli
O157:H7 prevalences reported in the literature since 1990 and the knowledge gap with respect to VTEC detection in surface waters.
Antiviral Properties of Silver Nanoparticles on a Magnetic Hybrid Colloid
Authors: Park SungJun , Park Hye Hun , Kim Sung Yeon , Kim Su Jung , Woo Kyoungja , Ko GwangPyo
Published: February 2014

Silver nanoparticles (AgNPs) are considered to be a potentially useful tool for controlling various pathogens. However, there are concerns about the release of AgNPs into environmental media, as they may generate adverse human health and ecological effects. In this study, we developed and evaluated a novel micrometer-sized magnetic hybrid colloid (MHC) decorated with variously sized AgNPs (AgNP-MHCs). After being applied for disinfection, these particles can be easily recovered from environmental media using their magnetic properties and remain effective for inactivating viral pathogens. We evaluated the efficacy of AgNP-MHCs for inactivating bacteriophage ϕX174, murine norovirus (MNV), and adenovirus serotype 2 (AdV2). These target viruses were exposed to AgNP-MHCs for 1, 3, and 6 h at 25°C and then analyzed by plaque assay and real-time TaqMan PCR. The AgNP-MHCs were exposed to a wide range of pH levels and to tap and surface water to assess their antiviral effects under different environmental conditions. Among the three types of AgNP-MHCs tested, Ag30-MHCs displayed the highest efficacy for inactivating the viruses. The ϕX174 and MNV were reduced by more than 2 log10after exposure to 4.6 × 109Ag30-MHCs/ml for 1 h. These results indicated that the AgNP-MHCs could be used to inactivate viral pathogens with minimum chance of potential release into environment.
Acidic pH Strongly Enhances
In Vitro
Biofilm Formation by a Subset of Hypervirulent ST-17 Streptococcus agalactiae Strains
Authors: D'Urzo Nunzia , Martinelli Manuele , Pezzicoli Alfredo , De Cesare Virginia , Pinto Vittoria , Margarit Immaculada , Telford John Laird , Maione Domenico
Published: February 2014

Streptococcus agalactiae
, also known as group B
Streptococcus
(GBS), is a primary colonizer of the anogenital mucosa of up to 40% of healthy women and an important cause of invasive neonatal infections worldwide. Among the 10 known capsular serotypes, GBS type III accounts for 30 to 76% of the cases of neonatal meningitis. In recent years, the ability of GBS to form biofilm attracted attention for its possible role in fitness and virulence. Here, a new
in vitro
biofilm formation protocol was developed to guarantee more stringent conditions, to better discriminate between strong-, low-, and non-biofilm-forming strains, and to facilitate interpretation of data. This protocol was used to screen the biofilm-forming abilities of 366 GBS clinical isolates from pregnant women and from neonatal infections of different serotypes in relation to medium composition and pH. The results identified a subset of isolates of serotypes III and V that formed strong biofilms under acidic conditions. Importantly, the best biofilm formers belonged to serotype III hypervirulent clone ST-17. Moreover, the abilities of proteinase K to strongly inhibit biofilm formation and to disaggregate mature biofilms suggested that proteins play an essential role in promoting GBS biofilm initiation and contribute to biofilm structural stability.
RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel
Authors: Tannock Gerald W. , Lawley Blair , Munro Karen , Sims Ian M. , Lee Julian , Butts Christine A. , Roy Nicole
Published: February 2014

Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope (
13
C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [
13
C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect
13
C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that
Bacteroides uniformis
,
Blautia glucerasea
,
Clostridium indolis
, and
Bifidobacterium animalis
were the main users of the
13
C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified.
B. uniformis
utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA–stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism.
Metabolic Responses of Lactobacillus plantarum Strains during Fermentation and Storage of Vegetable and Fruit Juices
Authors: Filannino P. , Cardinali G. , Rizzello C. G. , Buchin S. , De Angelis M. , Gobbetti M. , Di Cagno R.
Published: February 2014

Strains ofLactobacillus plantarumwere grown and stored in cherry (ChJ), pineapple (PJ), carrot (CJ), and tomato (TJ) juices to mimic the chemical composition of the respective matrices. Wheat flour hydrolysate (WFH), whey milk (W), and MRS broth were also used as representatives of other ecosystems. The growth rates and cell densities ofL. plantarumstrains during fermentation (24 h at 30°C) and storage (21 days at 4°C) differed only in part, being mainly influenced by the matrix. ChJ and PJ were the most stressful juices for growth and survival. Overall, the growth in juices was negatively correlated with the initial concentration of malic acid and carbohydrates. The consumption of malic acid was noticeable for all juices, but mainly during fermentation and storage of ChJ. Decreases of branched-chain amino acids (BCAA)—with the concomitant increase of their respective branched alcohols—and His and increases of Glu and gamma-aminobutyric acid (GABA) were the main traits of the catabolism of free amino acids (FAA), which were mainly evident under less acidic conditions (CJ and TJ). The increase of Tyr was found only during storage of ChJ. Some aldehydes (e.g., 3-methyl-butanal) were reduced to the corresponding alcohols (e.g., 3-methyl-1-butanol). After both fermentation and storage, acetic acid increased in all fermented juices, which implied the activation of the acetate kinase route. Diacetyl was the ketone found at the highest level, and butyric acid increased in almost all fermented juices. Data were processed through multidimensional statistical analyses. Except for CJ, the juices (mainly ChJ) seemed to induce specific metabolic traits, which differed in part among the strains. This study provided more in-depth knowledge on the metabolic mechanisms of growth and maintenance ofL. plantarumin vegetable and fruit habitats, which also provided helpful information to select the most suitable starters for fermentation of targeted matrices.
Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides
Authors: Erbilgin Onur , McDonald Kent L. , Kerfeld Cheryl A.
Published: February 2014

Bacterial microcompartments (BMCs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. The prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. It is increasingly apparent that diverse heterotrophic bacteria contain BMCs that are involved in catabolic reactions, and many of the BMCs are predicted to have novel functions. However, most of these putative organelles have not been experimentally characterized. In this study, we sought to discover the function of a conserved BMC gene cluster encoded in the majority of the sequenced planctomycete genomes. This BMC is especially notable for its relatively simple genetic composition, its remote phylogenetic position relative to characterized BMCs, and its apparent exclusivity to the enigmatic
Verrucomicrobia
and
Planctomycetes
. Members of the phylum
Planctomycetes
are known for their morphological dissimilarity to the rest of the bacterial domain: internal membranes, reproduction by budding, and lack of peptidoglycan. As a result, they are ripe for many discoveries, but currently the tools for genetic studies are very limited. We expanded the genetic toolbox for the planctomycetes and generated directed gene knockouts of BMC-related genes in
Planctomyces limnophilus
. A metabolic activity screen revealed that BMC gene products are involved in the degradation of a number of plant and algal cell wall sugars. Among these sugars, we confirmed that BMCs are formed and required for growth on
l
-fucose and
l
-rhamnose. Our results shed light on the functional diversity of BMCs as well as their ecological role in the planctomycetes, which are commonly associated with algae.
Comparative Analysis and Limitations of Ethidium Monoazide and Propidium Monoazide Treatments for the Differentiation of Viable and Nonviable Campylobacter Cells
Authors: Seinige Diana , Krischek Carsten , Klein Günter , Kehrenberg Corinna
Published: February 2014

The lack of differentiation between viable and nonviable bacterial cells limits the implementation of PCR-based methods for routine diagnostic approaches. Recently, the combination of a quantitative real-time PCR (qPCR) and ethidium monoazide (EMA) or propidium monoazide (PMA) pretreatment has been described to circumvent this disadvantage. In regard to the suitability of this approach forCampylobacterspp., conflicting results have been reported. Thus, we compared the suitabilities of EMA and PMA in various concentrations for aCampylobacterviability qPCR method. The presence of either intercalating dye, EMA or PMA, leads to concentration-dependent shifts toward higher threshold cycle (CT) values, especially after EMA treatment. However, regression analysis resulted in high correlation coefficient (R2) values of 0.99 (EMA) and 0.98 (PMA) betweenCampylobactercounts determined by qPCR and culture-based enumeration. EMA (10 μg/ml) and PMA (51.10 μg/ml) removed DNA selectively from nonviable cells in mixed samples at viable/nonviable ratios of up to 1:1,000. The optimized EMA protocol was successfully applied to 16Campylobacter jejuniandCampylobacter colifield isolates from poultry and indicated the applicability for field isolates as well. EMA-qPCR and culture-based enumeration ofCampylobacterspiked chicken leg quarters resulted in comparable bacterial cell counts. The correlation coefficient between the two analytical methods was 0.95. Nevertheless, larger amounts of nonviable cells (>104) resulted in an incomplete qPCR signal reduction, representing a serious methodological limitation, but double staining with EMA considerably improved the signal inhibition. Hence, the proposedCampylobacterviability EMA-qPCR provides a promising rapid method for diagnostic applications, but further research is needed to circumvent the limitation.
Microgravity Alters the Physiological Characteristics of Escherichia coli O157:H7 ATCC 35150, ATCC 43889, and ATCC 43895 under Different Nutrient Conditions
Authors: Kim H. W. , Matin A. , Rhee M. S.
Published: February 2014

The aim of this study is to provide understanding of microgravity effects on important food-borne bacteria,
Escherichia coli
O157:H7 ATCC 35150, ATCC 43889, and ATCC 43895, cultured in nutrient-rich or minimal medium. Physiological characteristics, such as growth (measured by optical density and plating), cell morphology, and pH, were monitored under low-shear modeled microgravity (LSMMG; space conditions) and normal gravity (NG; Earth conditions). In nutrient-rich medium, all strains except ATCC 35150 showed significantly higher optical density after 6 h of culture under LSMMG conditions than under NG conditions (
P
< 0.05). LSMMG-cultured cells were approximately 1.8 times larger than NG-cultured cells at 24 h; therefore, it was assumed that the increase in optical density was due to the size of individual cells rather than an increase in the cell population. The higher pH of the NG cultures relative to that of the LSMMG cultures suggests that nitrogen metabolism was slower in the latter. After 24 h of culturing in minimal media, LSMMG-cultured cells had an optical density 1.3 times higher than that of NG-cultured cells; thus, the higher optical density in the LSMMG cultures may be due to an increase in both cell size and number. Since bacteria actively grew under LSMMG conditions in minimal medium despite the lower pH, it is of some concern that LSMMG-cultured
E. coli
O157:H7 may be able to adapt well to acidic environments. These changes may be caused by changes in nutrient metabolism under LSMMG conditions, although this needs to be demonstrated in future studies.
Prokaryotic Communities in Pit Mud from Different-Aged Cellars Used for the Production of Chinese Strong-Flavored Liquor
Authors: Tao Yong , Li Jiabao , Rui Junpeng , Xu Zhancheng , Zhou Yan , Hu Xiaohong , Wang Xiang , Liu Menghua , Li Daping , Li Xiangzhen
Published: February 2014

Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4+, lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundantLactobacillusand high lactic acid and low pH levels. (ii) Phase II is a transition period. WhileLactobacillusabundance decreases dramatically, that ofBacteroidetesand methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.
Polysaccharides and Proteins Added to Flowing Drinking Water at Microgram-per-Liter Levels Promote the Formation of Biofilms Predominated by Bacteroidetes and Proteobacteria
Authors: Sack Eveline L. W. , van der Wielen Paul W. J. J. , van der Kooij Dick
Published: February 2014

Biopolymers are important substrates for heterotrophic bacteria in (ultra)oligotrophic freshwater environments, but information about their utilization at microgram-per-liter levels by attached freshwater bacteria is lacking. This study aimed at characterizing biopolymer utilization in drinking-water-related biofilms by exposing such biofilms to added carbohydrates or proteins at 10 μg C liter
−1
in flowing tap water for up to 3 months. Individually added amylopectin was not utilized by the biofilms, whereas laminarin, gelatin, and caseinate were. Amylopectin was utilized during steady-state biofilm growth with simultaneously added maltose but not with simultaneously added acetate. Biofilm formation rates (BFR) at 10 μg C liter
−1
per substrate were ranked as follows, from lowest to highest: blank or amylopectin (≤6 pg ATP cm
−2
day
−1
), gelatin or caseinate, laminarin, maltose, acetate alone or acetate plus amylopectin, and maltose plus amylopectin (980 pg ATP cm
−2
day
−1
). Terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene sequence analyses revealed that the predominant maltose-utilizing bacteria also dominated subsequent amylopectin utilization, indicating catabolic repression and (extracellular) enzyme induction. The accelerated BFR with amylopectin in the presence of maltose probably resulted from efficient amylopectin binding to and hydrolysis by inductive enzymes attached to the bacterial cells.
Cytophagia
,
Flavobacteriia
,
Gammaproteobacteria
, and
Sphingobacteriia
grew during polysaccharide addition, and
Alpha
-,
Beta
-, and
Gammaproteobacteria
,
Cytophagia
,
Flavobacteriia
, and
Sphingobacteriia
grew during protein addition. The succession of bacterial populations in the biofilms coincided with the decrease in the specific growth rate during biofilm formation. Biopolymers can clearly promote biofilm formation at microgram-per-liter levels in drinking water distribution systems and, depending on their concentrations, might impair the biological stability of distributed drinking water.
Distribution of Indigenous Bacterial Pathogens and Potential Pathogens Associated with Roof-Harvested Rainwater
Authors: Dobrowsky P. H. , De Kwaadsteniet M. , Cloete T. E. , Khan W.
Published: February 2014

The harvesting of rainwater is gaining acceptance among many governmental authorities in countries such as Australia, Germany, and South Africa, among others. However, conflicting reports on the microbial quality of harvested rainwater have been published. To monitor the presence of potential pathogenic bacteria during high-rainfall periods, rainwater from 29 rainwater tanks was sampled on four occasions (during June and August 2012) in a sustainable housing project in Kleinmond, South Africa. This resulted in the collection of 116 harvested rainwater samples in total throughout the sampling period. The identities of the dominant, indigenous, presumptive pathogenic isolates obtained from the rainwater samples throughout the sampling period were confirmed through universal 16S rRNA PCR, and the results revealed that
Pseudomonas
(19% of samples) was the dominant genus isolated, followed by
Aeromonas
(16%),
Klebsiella
(11%), and
Enterobacter
(9%). PCR assays employing genus-specific primers also confirmed the presence of
Aeromonas
spp. (16%),
Klebsiella
spp. (47%),
Legionella
spp. (73%),
Pseudomonas
spp. (13%),
Salmonella
spp. (6%),
Shigella
spp. (27%), and
Yersinia
spp. (28%) in the harvested rainwater samples. In addition, on one sampling occasion,
Giardia
spp. were detected in 25% of the eight tank water samples analyzed. This study highlights the diverse array of pathogenic bacteria that persist in harvested rainwater during high-rainfall periods. The consumption of untreated harvested rainwater could thus pose a potential significant health threat to consumers, especially children and immunocompromised individuals, and it is recommended that harvested rainwater be treated for safe usage as an alternative water source.
Vibrio Trends in the Ecology of the Venice Lagoon
Authors: Rahman Mohammad Shamsur , Martino Maria Elena , Cardazzo Barbara , Facco Pierantonio , Bordin Paola , Mioni Renzo , Novelli Enrico , Fasolato Luca
Published: February 2014

Vibrio
is a very diverse genus that is responsible for different human and animal diseases. The accurate identification of
Vibrio
at the species level is important to assess the risks related to public health and diseases caused by aquatic organisms. The ecology of
Vibrio
spp., together with their genetic background, represents an important key for species discrimination and evolution. Thus, analyses of population structure and ecology association are necessary for reliable characterization of bacteria and to investigate whether bacterial species are going through adaptation processes. In this study, a population of
Vibrionaceae
was isolated from shellfish of the Venice lagoon and analyzed in depth to study its structure and distribution in the environment. A multilocus sequence analysis (MLSA) was developed on the basis of four housekeeping genes. Both molecular and biochemical approaches were used for species characterization, and the results were compared to assess the consistency of the two methods. In addition, strain ecology and the association between genetic information and environment were investigated through statistical models. The phylogenetic and population analyses achieved good species clustering, while biochemical identification was demonstrated to be imprecise. In addition, this study provided a fine-scale overview of the distribution of
Vibrio
spp. in the Venice lagoon, and the results highlighted a preferential association of the species toward specific ecological variables. These findings support the use of MLSA for taxonomic studies and demonstrate the need to consider environmental information to obtain broader and more accurate bacterial characterization.
A Comparative Quantitative Proteomic Study Identifies New Proteins Relevant for Sulfur Oxidation in the Purple Sulfur Bacterium Allochromatium vinosum
Authors: Weissgerber Thomas , Sylvester Marc , Kröninger Lena , Dahl Christiane
Published: February 2014

In the present study, we compared the proteome response of
Allochromatium vinosum
when growing photoautotrophically in the presence of sulfide, thiosulfate, and elemental sulfur with the proteome response when the organism was growing photoheterotrophically on malate. Applying tandem mass tag analysis as well as two-dimensional (2D) PAGE, we detected 1,955 of the 3,302 predicted proteins by identification of at least two peptides (59.2%) and quantified 1,848 of the identified proteins. Altered relative protein amounts (≥1.5-fold) were observed for 385 proteins, corresponding to 20.8% of the quantified
A. vinosum
proteome. A significant number of the proteins exhibiting strongly enhanced relative protein levels in the presence of reduced sulfur compounds are well documented essential players during oxidative sulfur metabolism, e.g., the dissimilatory sulfite reductase DsrAB. Changes in protein levels generally matched those observed for the respective relative mRNA levels in a previous study and allowed identification of new genes/proteins participating in oxidative sulfur metabolism. One gene cluster (
hyd
; Alvin_2036-Alvin_2040) and one hypothetical protein (Alvin_2107) exhibiting strong responses on both the transcriptome and proteome levels were chosen for gene inactivation and phenotypic analyses of the respective mutant strains, which verified the importance of the so-called Isp hydrogenase supercomplex for efficient oxidation of sulfide and a crucial role of Alvin_2107 for the oxidation of sulfur stored in sulfur globules to sulfite. In addition, we analyzed the sulfur globule proteome and identified a new sulfur globule protein (SgpD; Alvin_2515).