bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct and indirect effects of Mediterranean vegetation on runoff and soil loss
Authors: Garcia‐Estringana P. , Alonso‐Blázquez N. , Marques M. J. , Bienes R. , Alegre J.
Published: February 2010

Vegetation cover acts in a complex way in influencing runoff and soil loss and a great deal of information is needed to model these effects. In the Mediterranean, the abandonment of land is important under extensive land‐use. Abandoned lands typically have a rolling landscape with steep slopes, and are dominated by herbaceous communities that grow on pasture land interspersed by shrubs. To characterize communities of vegetation such as these, which grow in central Spain, and to evaluate their direct and indirect effects on runoff and soil loss, we carried out experiments with simulated rain. We assessed separately the effects of pasture land and of four species of shrubs (Dorycnium pentaphyllum Scop., Medicago strasseri Greuter et al., Colutea arborescens L. and Retama sphaerocarpa, L.). The infiltration rates under herbaceous vegetation were 7.9 times greater than those obtained on bare land (92.2 mm hour−1 compared with 11.7 mm hour−1), and 88% of these differences could be attributed to direct effects. On the pasture land, as the proportion of covered land increased, the runoff decreased linearly, whereas the soil loss decreased exponentially. On the land covered by shrubs, the average infiltration rate was 82.5 mm hour−1. Under D. pentaphyllum and M. strasseri infiltration rates were greater than 105 mm hour−1, whereas for R. sphaerocarpa the infiltration rate was 57 mm hour−1. For D. pentaphyllum and M. strasseri soil loss was less than 4.5 g m−2, whereas for C. arborescens soil loss was 61.4 g m−2. Unlike the results for the pasture land, for the shrub‐type vegetation the increases in infiltration rates could be attributed to indirect effects: they explained 47% of the increase in infiltration for C. arborescens, 69% for R. sphaerocarpa, 75% for D. pentaphyllum and 100% for M. strasseri.
Changes in fitness, body mass index and obesity in 9–10 year olds
Authors: Boddy L. M. , Hackett A. F. , Stratton G.
Published: February 2010

Background:  The prevalence of obesity in children has increased substantially in recent years and, paediatric obesity and poor fitness are risk factors for disease. The present study aimed to assess changes in body mass index (BMI), the prevalence of obesity and changes in aerobic endurance over time in 9–10‐year‐old schoolchildren.

Methods:  Participants were recruited by the SportsLinx project from primary schools across Liverpool. Height and weight data were used to calculate BMI. The prevalence of obesity and overweight were estimated using age‐ and sex‐specific cut‐off points. Performance on the 20‐m multi‐stage shuttle runs test (20 mMST) was used as a marker of aerobic endurance. Data were available for 13 418 (6572 boys, 6846 girls) 9–10‐year‐old children. Analysis of covariance was completed to assess year‐on‐year changes in BMI controlling for deprivation (IMD) and 20 mMST performance, and 20 mMST performance controlling for IMD and BMI.

Results:  No significant changes in BMI from baseline were observed (P > 0.05). Obesity prevalence reduced in girls (2005 = 10.3%, 2008 = 8.52% in 2008). The data for boys showed no reductions in prevalence (2005 = 6.77%, 2008 = 7.87%). The most recent cohort for boys and two most recent cohorts for girls had lower levels of aerobic endurance than baseline (2004–2005) (P ≤ 0.01).

Conclusions:  The data suggest a plateau in the yearly increases in BMI in 9–10 year olds independent of deprivation and fitness and a declining prevalence of obesity in girls. Levels of aerobic endurance have declined independent of BMI and deprivation. The current obesity interventions in place appear to be having some impact on BMI, but further investment is urged to promote fitness in children.
Increased risk of low birthweight and small for gestational age infants among women with tuberculosis
Authors: Lin H‐C , Lin H‐C , Chen S‐F
Published: February 2010

Please cite this paper as: Lin H‐C, Lin H‐C, Chen S‐F. Increased risk of low birthweight and small for gestational age infants among women with tuberculosis. BJOG 2010;117:585–590.

Objective  As the relationship between tuberculosis (TB) and fetal outcomes remains unclear, this study used a 3‐year nationwide population‐based data set to determine the risk of adverse pregnancy outcomes [low birthweight (LBW), preterm birth and small for gestational age (SGA) infants] among women with TB.

Design  A cross‐sectional retrospective study.

Setting  Taiwan.

Sample  Linking the Taiwan birth certificate registry and the Taiwan National Health Insurance Research Dataset, we identified 761 women who gave birth from 2001 to 2003 and who had received medication treatment for TB during their pregnancy, together with 3805 unaffected women matched in terms of age and year of delivery.

Methods  Conditional logistic regression analyses were performed to compare the risk of LBW, preterm birth and SGA for mothers with TB and unaffected mothers.

Main outcome measures  The risk of LBW, preterm birth and SGA.

Results  Mothers diagnosed with TB had significantly higher percentages of LBW (8.5 versus 6.4%, P = 0.033) and SGA (19.7 versus 16.7%, P = 0.048) infants than unaffected mothers. However, there was no significant difference in preterm birth (8.0 versus 8.0%, P = 0.961) between these two groups. The adjusted odds ratios of having LBW and SGA infants for mothers with TB were 1.35 (95% CI = 1.01–1.81) and 1.22 (95% CI = 1.00–1.49), respectively, compared with unaffected mothers.

Conclusions  We concluded that women diagnosed with TB during pregnancy are at increased risk for having LBW and SGA babies, compared with unaffected mothers. We suggest that clinicians should make women with TB aware of the potential risks before planning a child.
Pregnancy outcome in women with repaired versus unrepaired isolated ventricular septal defect
Authors: Yap S‐C , Drenthen W , Pieper PG , Moons P , Mulder BJM , Vliegen HW , van Dijk APJ , Meijboom FJ , Jaddoe VWV , Steegers EAP , Boersma E , Roos‐Hesselink JW ,   on behalf of the ZAHARA investigators
Published: February 2010

Please cite this paper as: Yap S‐C, Drenthen W, Pieper P, Moons P, Mulder B, Vliegen H, van Dijk A, Meijboom F, Jaddoe V, Steegers E, Boersma E, Roos‐Hesselink J on behalf of the ZAHARA investigators. Pregnancy outcome in women with repaired versus unrepaired isolated ventricular septal defect. BJOG 2010; DOI: 10.1111/j.1471‐0528.2010.02512.x.

Objective  To compare the risks of pregnancy complications in women with repaired and unrepaired isolated ventricular septal defect (VSD).

Design  A retrospective multicentre study.

Setting  Tertiary centres in the Netherlands and Belgium.

Methods  Women were identified using two congenital heart disease registries. Eighty‐eight women were identified who had experienced 202 pregnancies, including 46 miscarriages and nine terminations of pregnancy. Information on each completed pregnancy (n = 147; unrepaired VSD, n = 104; repaired VSD, n = 43) was obtained using medical records and telephone interviews. Data from the Generation R database (prospective cohort study; n = 9667) were used to determine the background risk (controls). Odds ratios and 95% CI were estimated using general estimation equation analysis adjusted for multiple pregnancies per woman, maternal age and parity status.

Main outcome measures  Adjusted odds ratios (AORs) for developing pregnancy complications in relation to corrective status.

Results  Pregnancies in women with an unrepaired VSD were associated with a higher risk of pre‐eclampsia (AOR 4.59, 95% CI 2.01–10.5, P < 0.001) compared with controls. No differences were observed when comparing women with repaired VSD and controls. Pregnancies in women with repaired VSD were associated with a higher risk of premature labour (AOR 4.02, 95% CI 1.12–14.4, P = 0.03) and small‐for‐gestational‐age (SGA) births (AOR 4.09, 95% CI 1.27–13.2, P = 0.02) compared with women with unrepaired VSD.

Conclusions  Women with unrepaired VSD are at increased risk of pre‐eclampsia, which suggests that it is not a benign condition. In addition, women with repaired VSD are at increased risk of premature labour and SGA births compared with women with unrepaired VSD.
Chronic in vitro ketosis is neuroprotective but not anti‐convulsant
Authors: Samoilova Marina , Weisspapir Michael , Abdelmalik Peter , Velumian Alexander A. , Carlen Peter L.
Published: February 2010

J. Neurochem. (2010) 113, 826–835.

The ketogenic diet (KD), used successfully to treat a variety of epilepsy syndromes in humans and to attenuate seizures in different animal models, also provides powerful neuroprotection in various CNS injury models. Yet, a direct role for ketone bodies in limiting seizure and neuronal damage remains poorly understood. Using organotypic hippocampal slice cultures, we established an in vitro model of chronic ketosis for parallel studies of its neuroprotective and anti‐convulsant effects. Chronic in vitro treatment with a ketone body, d‐β‐hydroxybutyrate, protected the cultures against chronic hypoglycemia, oxygen‐glucose deprivation, and NMDA‐induced excitotoxicity, but failed to suppress intrinsic and induced seizure‐like activity, indicating improved neuroprotection is not directly translated into seizure control. However, chronic in vitro ketosis abolished hippocampal network hyperexcitability following a metabolic insult, hypoxia, demonstrating for the first time a direct link between metabolic resistance and better control of excessive, synchronous, abnormal electrical activity. These findings suggest that the KD and, possibly, exogenous ketone administration, can be more beneficial for the treatment of seizures associated with metabolic stress or underlying metabolic abnormalities, and can potentially be used to optimize clinical applications of the traditional KD or its variants.
Simulated climate conditions in Europe during the Marine Isotope Stage 3 stadial
Authors: KJELLSTRÖM ERIK , BRANDEFELT JENNY , NÄSLUND JENS‐OVE , SMITH BEN , STRANDBERG GUSTAV , VOELKER ANTJE H. L. , WOHLFARTH BARBARA
Published: February 2010

Kjellström, E., Brandefelt, J., Näslund, J.‐O., Smith, B., Strandberg, G., Voelker, A. H. L. & Wohlfarth, B. 2010: Simulated climate conditions in Europe during the Marine Isotope Stage 3 stadial. Boreas, 10.1111/j.1502‐3885.2010.00143.x. ISSN 0300‐9483.

State‐of‐the‐art climate models were used to simulate climate conditions in Europe during Greenland Stadial (GS) 12 at 44 ka BP. The models employed for these simulations were: (i) a fully coupled atmosphere–ocean global climate model (AOGCM), and (ii) a regional atmospheric climate model (RCM) to dynamically downscale results from the global model for a more detailed investigation of European climate conditions. The vegetation was simulated off‐line by a dynamic vegetation model forced by the climate from the RCM. The resulting vegetation was then compared with the a priori vegetation used in the first simulation. In a subsequent step, the RCM was rerun to yield a new climate more consistent with the simulated vegetation. Forcing conditions included orbital forcing, land–sea distribution, ice‐sheet configuration, and atmospheric greenhouse gas concentrations representative for 44 ka BP. The results show a cold climate on the global scale, with global annual mean surface temperatures 5 °C colder than the modern climate. This is still significantly warmer than temperatures derived from the same model system for the Last Glacial Maximum (LGM). Regional, northern European climate is much colder than today, but still significantly warmer than during the LGM. Comparisons between the simulated climate and proxy‐based sea‐surface temperature reconstructions show that the results are in broad agreement, albeit with a possible cold bias in parts of the North Atlantic in summer. Given a prescribed restricted Marine Isotope Stage 3 ice‐sheet configuration, with large ice‐free regions in Sweden and Finland, the AOGCM and RCM model simulations produce a cold and dry climate in line with the restricted ice‐sheet configuration during GS 12. The simulated temperature climate, with prescribed ice‐free conditions in south‐central Fennoscandia, is favourable for the development of permafrost, but does not allow local ice‐sheet formation as all snow melts during summer.
CDKN2A promoter methylation is related to the tumor location and histological subtype and associated with Helicobacter pylori flaA(+) strains in gastric adenocarcinomas
Authors: ALVES MARKÊNIA KÉLIA SANTOS , LIMA VALESKA PORTELA , FERRASI ADRIANA CAMARGO , RODRIGUES MARIA APARECIDA , DE MOURA CAMPOS PARDINI MARIA INÊS , RABENHORST SILVIA HELENA BAREM
Published: February 2010

Alves MKS, Lima VP, Ferrasi AC, Rodrigues MA, de Moura Campos Pardini MI, Rabenhorst SHB. CDKN2A promoter methylation is related to the tumor location and histological subtype and associated with Helicobacter pylori flaA(+) strains in gastric adenocarcinomas. APMIS 2010; 118: 297–307.

Promoter hypermethylation of CDKN2A (p16INK4A protein) is the main mechanism of gene inactivation. However, its association with Helicobacter pylori infection is a controversial issue. Therefore, we examined a series of gastric adenocarcinomas to assess the association between p16INK4A inactivation and H. pylori genotype (vacA, cagA, cagE, virB11 and flaA) according to the location and histological subtype of the tumors. p16INK4A expression and CDKN2A promoter methylation were found in 77 gastric adenocarcinoma samples by immunohistochemistry and methylation‐specific PCR, respectively. Helicobacter pylori infection and genotype were determined by PCR. A strong negative correlation between immunostaining and CDKN2A promoter region methylation was found. In diffuse subtype tumors, the inactivation of p16INK4A by promoter methylation was unique in noncardia tumors (p = 0.022). In addition, H. pylori‐bearing flaA was associated with non‐methylation tumors (p = 0.008) and H. pylori strain bearing cagA or vacAs1m1 genes but without flaA was associated with methylated tumors (p = 0.022 and 0.003, respectively). Inactivation of p16INK4A in intestinal and diffuse subtypes showed distinct carcinogenic pathways, depending on the tumor location. Moreover, the process of methylation of the CDKN2A promoter seems to depend on the H. pylori genotype. The present data suggest that there is a differential influence and relevance of H. pylori genotype in gastric cancer development.
NURSE–PATIENT COMMUNICATION WHILE PERFORMING HOME DIALYSIS: THE PATIENTS’ PERCEPTIONS
Authors: Sadala Maria Lúcia Araújo , Miranda Marcelo Guimarães , Lorençon Marisa , De Campos Pereira Estela Pacheco
Published: February 2010

This study aimed at describing patients’ perception of their communication with nurses when performing home dialysis. Data were collected from interviews guided by the question: “What is communication like, between you and nurses, during home dialysis treatment?” Results show participants’ perception of treatment during home peritoneal dialysis [Continuous ambulatory peritoneal dialysis (CAPD)]; relationship with nurses and family and the effects of treatment on one's existence. Patients can be self‐caring and they learn to value the autonomy in their own care. However, some are unable to assume the responsibility for self‐care. It was discovered that the connotation of “inspection” that some participants attributed to the nurse's visits, led to an alienation from the education process in the CAPD education. Findings suggest that effective communication and the development of the relationship of a working partnership with patients is crucial. Improvement in the nurses’ communication, aiming at adapting it to the characteristics, limitations and specific needs of each patient, is significant for achieving better outcomes.
WHO CARES…………FOR THE CARERS?
Authors: Kelly Mike
Published: February 2010

This paper is about carers; a family member or members who provide unpaid care to a loved one with a chronic condition. Caring for someone who is chronically ill permeates every aspect of life. Dreams may be shattered, plans for the future may have to be radically altered or shelved permanently. Psychological stress is common, but many carers find it difficult to access services. Resources are there to support the person diagnosed, or, on treatment. What resources are directed to the care and support of carers? Drawing on relevant literature and my own clinical experience I give examples of the demands, often unrelenting, and difficulties carers face. I suggest some interventions that can support and facilitate carers, enabling them to continue their role in a healthy, life giving manner.
EXPLORING SYMPTOMS IN PATIENTS MANAGED WITHOUT DIALYSIS: A QUALITATIVE RESEARCH STUDY
Authors: Noble Helen , Meyer Professor Julienne , Bridge Dr Jackie , Johnson Dr Barbara , Kelly Dr Daniel
Published: February 2010

Little is known about the prevalence and burden of symptoms in patients managed without dialysis. This study was the result of a larger study exploring the experiences of 30 such patients and their trajectories to death. Data were analysed relating to symptoms once the patients had been referred to a Renal Supportive Care Service based in the East End of London, UK. A high symptom prevalence was found with 30 different symptoms reported at first consultation. Widely reported symptoms impacting on daily living included breathlessness, oedema, pruritus, nausea and vomiting and pain. Findings indicate that as symptoms escalate and death approaches, some symptoms, such as fluid overload and lethargy become difficult to treat indicating that death is close. This new knowledge can help staff as they attempt to determine when the end of life is approaching in order to support and care for patients appropriately. This paper highlights a need for effective identification and management of symptoms as they arise and further exploration of the effects of these symptoms on daily living.
Focused Ion-Beam Based Nanohole Modeling, Simulation, Fabrication, and Application
Authors: Zhou Jack , Yang Guoliang
Published: February 2010

There are three major steps toward the fabrication of a single-digit nanohole: (1) preparing the free-standing thin film by epitaxial deposition and electrochemical etching, (2) making submicron holes (0.2–0.02 μm) by focused ion beam (FIB), and (3) reducing the hole to less than 10 nm by FIB-induced deposition. One specific aim for this paper is to model, simulate, and control the focused ion-beam machining process to fabricate holes that can reach a single-digit nanometer scale on solid-state thin films. Preliminary work has been done on the thin film (30 nm in thickness) preparation, submicron hole fabrication, and ion-beam-induced deposition, and the results are presented.
Automated Part Centering With Impulse Actuation
Authors: Furst S. J. , Dow T. A. , Garrard K. , Sohn A.
Published: February 2010

Centering a part on a spindle for precision machining is a tedious, time-consuming task. Currently, a skilled operator must measure the run-out of a part using a displacement gauge, then tap the part into place using a plastic or rubber hammer. This paper describes a method to automatically center a part on a vacuum chuck with initial run-out as large as 2.5 mm. The method involves measuring the magnitude and direction of the radial run-out and then actuating the part until the part and spindle centerlines are within 5 μm of each other. The run-out can be measured with either a touch probe mounted to a machine axis or an electronic gauge. The part is tapped into place with a linear actuator driven by a voice coil motor. This paper includes an analysis of run-out measurement uncertainty as well as the design, performance modeling, and testing of the alignment actuator. This actuator was employed for part realignment and successfully positioned a hemispherical part with an initial run-out of 1–2.5 mm to within 5 μm of the spindle centerline. This capability shows that the run-out of a part manually placed on flat vacuum chuck can be automatically corrected.
The Effect of Laser Beam Geometry on Cut Path Deviation in Diode Laser Chip-Free Cutting of Glass
Authors: Nisar Salman , Sheikh M. A. , Li Lin , Pinkerton Andrew J. , Safdar Shakeel
Published: February 2010

In laser cleaving of brittle materials using the controlled fracture technique, thermal stresses are used to induce a single crack and the material is separated along the cutting path by extending the crack. One of the problems in laser cutting of glass with the controlled fracture technique is the cut deviation at the leading and the trailing edges of the glass sheet. This work is about minimizing this deviation through an optimization process, which includes laser beam geometry. It has been established that the thermal stresses generated during laser scanning are strongly dependent upon laser beam geometry. Experimental techniques are used to quantify cut deviation for soda-lime glass sheets under a set of conditions while finite element modeling is used to optimize the process and reduce (or eliminate) cut deviation. The experimental results of the effect of different laser beam geometries on cut path deviation have been presented in this study, along with the finite element modeling of the cutting process to simulate the transient effects of the moving beam and predict thermal fields and stress distribution. These predictions are compared with the experimental data. In comparison to other beam geometries, the triangular-forward beam at the leading edge and triangular-reverse and circular beam geometry at the trailing edge produces lower tensile stresses (σxx) and hence minimizes the cut path deviation. The work also shows that beam divergence inside the glass plays a significant role in changing the cut path deviation at the bottom leading and trailing edges of the glass.
Development Process for Custom Three-Dimensional Printing (3DP) Material Systems
Authors: Utela Ben R. , Storti Duane , Anderson Rhonda L. , Ganter Mark
Published: February 2010

The development of a new material system for three-dimensional printing (3DP) can be difficult without experience in the field, since the flexibility of the 3DP process implies a large number of material and processing parameters. This paper presents a detailed explanation of the steps involved in developing specific implementations of 3DP, along with tools and insight for each step. This material system development procedure should provide a clear understanding of the 3DP process steps and development decisions to help the user take advantage of the considerable flexibility of 3DP and expedite a new system development. The paper concludes with a demonstration of how the guidance provided is applied in the development of fully dense ceramic dental copings; a research problem uniquely suited to the flexibility of 3DP.
Modeling of the Thread Milling Operation in a Combined Thread/Drilling Operation: Thrilling
Authors: Jun Martin B. G. , Araujo Anna Carla
Published: February 2010

This paper investigates a thread making process called thrilling, which performs both drilling and thread milling with one tool. A chip thickness and mechanistic cutting force model has been developed for a thread milling operation with a thrilling tool. The model considers the complex geometry of a thrilling tool and the unique tool paths associated with the thread milling operation. Experiments have been conducted to validate the developed model. Comparison of the average torque and forces between experiment and simulation results shows that the model predicts the experimental results within 12% error.
A more thorough analysis of water rockets: Moist adiabats, transient flows, and inertial forces in a soda bottle
Authors: Gommes Cedric J.
Published: February 2010

Although water rockets are widely used to illustrate first year physics principles, accurate measurements show that they outperform the usual textbook analysis at the beginning of the thrust phase. This paper gives a more thorough analysis of this problem. It is shown that the air expansion in the rocket is accompanied by water vapor condensation, which provides an extra thrust; the downward acceleration of water within the rocket also contributes to the thrust, an effect that is negligible in other types of rockets; the apparent gravity resulting from the acceleration of the rocket contributes as much to water ejection as does the pressure difference between the inside and outside of the rocket; and the water flow is transient, which precludes the use of Bernoulli’s equation. Although none of these effects is negligible, they mostly cancel each other, and the overall accuracy of the analysis is only marginally improved. There remains a difference between theory and experiment with water rockets.
Lorentz-invariant three-vectors and alternative formulation of relativistic dynamics
Authors: Rȩbilas Krzysztof
Published: February 2010

Besides the well-known scalar invariants, there also exist vectorial invariants in special relativity. It is shown that the three-vector (dp⃗/dt)∥+γv(dp⃗/dt)⊥ is invariant under the Lorentz transformation. The subscripts ∥ and ⊥ denote the respective components with respect to the direction of the velocity of the body v⃗, and p⃗ is the relativistic momentum. We show that this vector is equal to a force F⃗R, which satisfies the classical Newtonian law F⃗R=ma⃗R in the instantaneous inertial rest frame of an accelerating body. Therefore, the relation F⃗R=(dp⃗/dt)∥+γv(dp⃗/dt)⊥, based on the Lorentz-invariant vectors, may be used as an invariant (not merely a covariant) relativistic equation of motion in any inertial system of reference. An alternative approach to classical electrodynamics based on the invariant three-vectors is proposed.
Local pinning of trial wave functions: An optimization method without integrals for finding approximate solutions of field equations
Authors: Theodorakis Stavros , Kindyni Nitsa
Published: February 2010

We present an optimization method that requires no integrations for obtaining approximate solutions of field equations of the form F(Ψ(r⃗))=0. The expression F(Ψ(r⃗)) would be identically zero everywhere if Ψ(r⃗) were an exact solution. The method consists of selecting an appropriate trial function Ψ0(r⃗), which depends on several parameters, and requiring that the values of these parameters be such that F(Ψ0(r⃗)) equal zero in certain regions of space, especially around singularities. This requirement yields a locally pinned trial wave function that approximates the exact solution. We illustrate the method by applying it to a simple harmonic oscillator, a vortex in a superfluid, to the ground state of a Bose–Einstein condensate and to the ground state of the helium atom.
Interferometry using a noisy moving source
Authors: Gersten Joel I.
Published: February 2010

Interferometry using a broadband noise source and a narrow band receiver is studied. It is shown that interferometry kinematic information relating to trains may be obtained using only a radio receiver and a watch.
Environmental Determinants of and Impact on Childhood Asthma by the Bacterial Community in Household Dust
Authors: Maier Raina M. , Palmer Michael W. , Andersen Gary L. , Halonen Marilyn J. , Josephson Karen C. , Maier Robert S. , Martinez Fernando D. , Neilson Julia W. , Stern Debra A. , Vercelli Donata , Wright Anne L.
Published: February 2010

Asthma increased dramatically in the last decades of the 20th century and is representative of chronic diseases that have been linked to altered microbial exposure and immune responses. Here we evaluate the effects of environmental exposures typically associated with asthma protection or risk on the microbial community structure of household dust (dogs, cats, and day care). PCR-denaturing gradient gel analysis (PCR-DGGE) demonstrated that the bacterial community structure in house dust is significantly impacted by the presence of dogs or cats in the home (
P
= 0.0190 and 0.0029, respectively) and by whether or not children attend day care (
P
= 0.0037). In addition, significant differences in the dust bacterial community were associated with asthma outcomes in young children, including wheezing (
P
= 0.0103) and specific IgE (
P
= 0.0184). Our findings suggest that specific bacterial populations within the community are associated with either risk or protection from asthma.
Identification and Analysis of the Biosynthetic Gene Cluster Encoding the Thiopeptide Antibiotic Cyclothiazomycin in
Streptomyces hygroscopicus
10-22
Authors: Wang Jiang , Yu Yi , Tang Kexuan , Liu Wen , He Xinyi , Huang Xi , Deng Zixin
Published: February 2010

Thiopeptide antibiotics are an important class of natural products resulting from posttranslational modifications of ribosomally synthesized peptides. Cyclothiazomycin is a typical thiopeptide antibiotic that has a unique bridged macrocyclic structure derived from an 18-amino-acid structural peptide. Here we reported cloning, sequencing, and heterologous expression of the cyclothiazomycin biosynthetic gene cluster from
Streptomyces hygroscopicus
10-22. Remarkably, successful heterologous expression of a 22.7-kb gene cluster in
Streptomyces lividans
1326 suggested that there is a minimum set of 15 open reading frames that includes all of the functional genes required for cyclothiazomycin production. Six genes of these genes,
cltBCDEFG
flanking the structural gene
cltA
, were predicted to encode the enzymes required for the main framework of cyclothiazomycin, and two enzymes encoded by a putative operon,
cltMN
, were hypothesized to participate in the tailoring step to generate the tertiary thioether, leading to the final cyclization of the bridged macrocyclic structure. This rigorous bioinformatics analysis based on heterologous expression of cyclothiazomycin resulted in an ideal biosynthetic model for us to understand the biosynthesis of thiopeptides.
Experimental Adaptation of
Burkholderia cenocepacia
to Onion Medium Reduces Host Range
Authors: Ellis Crystal N. , Cooper Vaughn S.
Published: February 2010

It is unclear whether adaptation to a new host typically broadens or compromises host range, yet the answer bears on the fate of emergent pathogens and symbionts. We investigated this dynamic using a soil isolate of
Burkholderia cenocepacia
, a species that normally inhabits the rhizosphere, is related to the onion pathogen
B. cepacia
, and can infect the lungs of cystic fibrosis patients. We hypothesized that adaptation of
B. cenocepacia
to a novel host would compromise fitness and virulence in alternative hosts. We modeled adaptation to a specific host by experimentally evolving 12 populations of
B. cenocepacia
in liquid medium composed of macerated onion tissue for 1,000 generations. The mean fitness of all populations increased by 78% relative to the ancestor, but significant variation among lines was observed. Populations also varied in several phenotypes related to host association, including motility, biofilm formation, and quorum-sensing function. Together, these results suggest that each population adapted by fixing different sets of adaptive mutations. However, this adaptation was consistently accompanied by a loss of pathogenicity to the nematode
Caenorhabditis elegans
; by 500 generations most populations became unable to kill nematodes. In conclusion, we observed a narrowing of host range as a consequence of prolonged adaptation to an environment simulating a specific host, and we suggest that emergent pathogens may face similar consequences if they become host-restricted.
Characterization of Environmentally Persistent
Escherichia coli
Isolates Leached from an Irish Soil
Authors: Brennan Fiona P. , Abram Florence , Chinalia Fabio A. , Richards Karl G. , O'Flaherty Vincent
Published: February 2010

Soils are typically considered to be suboptimal environments for enteric organisms, but there is increasing evidence that
Escherichia coli
populations can become resident in soil under favorable conditions. Previous work reported the growth of autochthonous
E. coli
in a maritime temperate Luvic Stagnosol soil, and this study aimed to characterize, by molecular and physiological means, the genetic diversity and physiology of environmentally persistent
E. coli
isolates leached from the soil. Molecular analysis (16S rRNA sequencing, enterobacterial repetitive intergenic consensus PCR, pulsed-field gel electrophoresis, and a multiplex PCR method) established the genetic diversity of the isolates (
n
= 7), while physiological methods determined the metabolic capability and environmental fitness of the isolates, relative to those of laboratory strains, under the conditions tested. Genotypic analysis indicated that the leached isolates do not form a single genetic grouping but that multiple genotypic groups are capable of surviving and proliferating in this environment. In physiological studies, environmental isolates grew well across a broad range of temperatures and media, in comparison with the growth of laboratory strains. These findings suggest that certain
E. coli
strains may have the ability to colonize and adapt to soil conditions. The resulting lack of fecal specificity has implications for the use of
E. coli
as an indicator of fecal pollution in the environment.
Role ofGeobacter sulfurreducensOuter Surfacec-Type Cytochromes in Reduction of Soil Humic Acid and Anthraquinone-2,6-Disulfonate
Authors: Voordeckers James W. , Kim Byoung-Chan , Izallalen Mounir , Lovley Derek R.
Published: February 2010

Deleting individual genes for outer surfacec-type cytochromes inGeobacter sulfurreducenspartially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.
Fermentation of Glycerol to Succinate by Metabolically Engineered Strains of
Escherichia coli
Authors: Zhang Xueli , Shanmugam K. T. , Ingram Lonnie O.
Published: February 2010

The fermentative metabolism of
Escherichia coli
was reengineered to efficiently convert glycerol to succinate under anaerobic conditions without the use of foreign genes. Formate and ethanol were the dominant fermentation products from glycerol in wild-type
Escherichia coli
ATCC 8739, followed by succinate and acetate. Inactivation of pyruvate formate-lyase (
pflB
) in the wild-type strain eliminated the production of formate and ethanol and reduced the production of acetate. However, this deletion slowed growth and decreased cell yields due to either insufficient energy production or insufficient levels of electron acceptors. Reversing the direction of the gluconeogenic phosphoenolpyruvate carboxykinase reaction offered an approach to solve both problems, conserving energy as an additional ATP and increasing the pool of electron acceptors (fumarate and malate). Recruiting this enzyme through a promoter mutation (
pck*
) to increase expression also increased the rate of growth, cell yield, and succinate production. Presumably, the high NADH/NAD
+
ratio served to establish the direction of carbon flow. Additional mutations were also beneficial. Glycerol dehydrogenase and the phosphotransferase-dependent dihydroxyacetone kinase are regarded as the primary route for glycerol metabolism under anaerobic conditions. However, this is not true for succinate production by engineered strains. Deletion of the
ptsI
gene or any other gene essential for the phosphotranferase system was found to increase succinate yield. Deletion of
pflB
in this background provided a further increase in the succinate yield. Together, these three core mutations (
pck
*,
ptsI
, and
pflB
) effectively redirected carbon flow from glycerol to succinate at 80% of the maximum theoretical yield during anaerobic fermentation in mineral salts medium.
The Second Extracellular Loop of Pore-Forming Subunits of ATP-Binding Cassette Transporters for Basic Amino Acids Plays a Crucial Role in Interaction with the Cognate Solute Binding Protein(s)
Authors: Eckey Viola , Weidlich Daniela , Landmesser Heidi , Bergmann Ulf , Schneider Erwin
Published: February 2010

In the thermophile
Geobacillus stearothermophilus
, the uptake of basic amino acids is mediated by an ABC transporter composed of the substrate binding protein (receptor) ArtJ and a homodimer each of the pore-forming subunit, ArtM, and the nucleotide-binding subunit, ArtP. We recently identified two putative binding sites in ArtJ that might interact with the Art(MP)
2
complex, thereby initiating the transport cycle (A. Vahedi-Faridi et al., J. Mol. Biol. 375:448-459, 2008). Here we investigated the contribution of charged amino acid residues in the second extracellular loop of ArtM to contact with ArtJ. Our results demonstrate a crucial role for residues K177, R185, and E188, since mutations to oppositely charged amino acids or glutamine led to a complete loss of ArtJ-stimulated ATPase activity of the complex variants in proteoliposomes. The defects could not be suppressed by ArtJ variants carrying mutations in site I (K39E and K152E) or II (E163K and D170K), suggesting a more complex interplay than that by a single salt bridge. These findings were supported by cross-linking assays demonstrating physical proximity between ArtJ(N166C) and ArtM(E182C). The importance of positively charged residues for receptor-transporter interaction was underscored by mutational analysis of the closely related transporter HisJ/LAO-HisQMP
2
of
Salmonella enterica
serovar Typhimurium. While transporter variants with mutated positively charged residues in HisQ displayed residual ATPase activities, corresponding mutants of HisM could no longer be stimulated by HisJ/LAO. Interestingly, the ATPase activity of the HisQM(K187E)P
2
variant was inhibited by
l
- and
d
-histidine in detergent, suggesting a role of the residue in preventing free histidine from gaining access to the substrate binding site within HisQM.
Role of FlgT in Anchoring the Flagellum of
Vibrio cholerae
Authors: Martinez Raquel M. , Jude Brooke A. , Kirn Thomas J. , Skorupski Karen , Taylor Ronald K.
Published: February 2010

Flagellar motility has long been regarded as an important virulence factor. In
Vibrio cholerae
, the single polar flagellum is essential for motility as well as for proper attachment and colonization. In this study, we demonstrate that the novel flagellar protein FlgT is involved in anchoring the flagellum to the
V. cholerae
cell. A screen for novel colonization factors by use of Tn
phoA
mutagenesis identified
flgT
. An in-frame deletion of
flgT
established that FlgT is required for attachment, colonization, and motility. Transmission electron microscopy revealed that while the
flgT
mutant is capable of assembling a phenotypically normal flagellum, the
flgT
population is mostly aflagellate compared to the wild-type population. Further analyses indicated that the flagellum of the
flgT
mutant is released into the culture supernatant from the cell upon completion of assembly. Additionally, hook basal body complexes appear to be released along with the filament. These results indicate that FlgT functions to stabilize the flagellar apparatus at the pole of the cell.
Di-Adenosine Tetraphosphate (Ap4A) Metabolism Impacts Biofilm Formation byPseudomonas fluorescensvia Modulation of c-di-GMP-Dependent Pathways
Authors: Monds Russell D. , Newell Peter D. , Wagner Jeffrey C. , Schwartzman Julia A. , Lu Wenyun , Rabinowitz Joshua D. , O'Toole George A.
Published: February 2010

Dinucleoside tetraphosphates are common constituents of the cell and are thought to play diverse biological roles in organisms ranging from bacteria to humans. In this study we characterized two independent mechanisms by which di-adenosine tetraphosphate (Ap4A) metabolism impacts biofilm formation byPseudomonas fluorescens. Null mutations inapaH, the gene encoding nucleoside tetraphosphate hydrolase, resulted in a marked increase in the cellular level of Ap4A. Concomitant with this increase, Pho regulon activation in low-inorganic-phosphate (Pi) conditions was severely compromised. As a consequence, anapaHmutant was not sensitive to Pho regulon-dependent inhibition of biofilm formation. In addition, we characterized a Pho-independent role for Ap4A metabolism in regulation of biofilm formation. In Pi-replete conditions Ap4A metabolism was found to impact expression and localization of LapA, the major adhesin regulating surface commitment byP. fluorescens. Increases in the level of c-di-GMP in theapaHmutant provided a likely explanation for increased localization of LapA to the outer membrane in response to elevated Ap4A concentrations. Increased levels of c-di-GMP in theapaHmutant were associated with increases in the level of GTP, suggesting that elevated levels of Ap4A may promotede novopurine biosynthesis. In support of this suggestion, supplementation with adenine could partially suppress the biofilm and c-di-GMP phenotypes of theapaHmutant. We hypothesize that changes in the substrate (GTP) concentration mediated by altered flux through nucleotide biosynthetic pathways may be a significant point of regulation for c-di-GMP biosynthesis and regulation of biofilm formation.
Central Role of the Early Colonizer
Veillonella
sp. in Establishing Multispecies Biofilm Communities with Initial, Middle, and Late Colonizers of Enamel
Authors: Periasamy Saravanan , Kolenbrander Paul E.
Published: February 2010

Human dental biofilm communities comprise several species, which can interact cooperatively or competitively. Bacterial interactions influence biofilm formation, metabolic changes, and physiological function of the community. Lactic acid, a common metabolite of oral bacteria, was measured in the flow cell effluent of one-, two- and three-species communities growing on saliva as the sole nutritional source. We investigated single-species and multispecies colonization by using known initial, early, middle, and late colonizers of enamel. Fluorescent-antibody staining and image analysis were used to quantify the biomass in saliva-fed flow cells. Of six species tested, only the initial colonizer
Actinomyces oris
exhibited significant growth. The initial colonizer
Streptococcus oralis
produced lactic acid but showed no significant growth. The early colonizer
Veillonella
sp. utilized lactic acid in two- and three-species biofilm communities. The biovolumes of all two-species biofilms increased when
Veillonella
sp. was present as one of the partners, indicating that this early colonizer promotes mutualistic community development. All three-species combinations exhibited enhanced growth except one, i.e.,
A. oris
,
Veillonella
sp., and the middle colonizer
Porphyromonas gingivalis
, indicating specificity among three-species communities. Further specificity was seen when
Fusobacterium nucleatum
(a middle colonizer),
Aggregatibacter actinomycetemcomitans
(a late colonizer), and
P. gingivalis
did not grow with
S. oralis
in two-species biofilms, but inclusion of
Veillonella
sp. resulted in growth of all three-species combinations. We propose that commensal veillonellae use lactic acid for growth in saliva and that they communicate metabolically with initial, early, middle, and late colonizers to establish multispecies communities on enamel.
Analysis of Protein Expression Regulated by theHelicobacter pyloriArsRS Two-Component Signal Transduction System
Authors: Loh John T. , Gupta Shobhana S. , Friedman David B. , Krezel Andrzej M. , Cover Timothy L.
Published: February 2010

Previous studies have shown that theHelicobacter pyloriArsRS two-component signal transduction system contributes to acid-responsive gene expression. To identify additional members of the ArsRS regulon and further investigate the regulatory role of the ArsRS system, we analyzed protein expression in wild-type andarsSnull mutant strains. Numerous proteins were differentially expressed in anarsSmutant strain compared to a wild-type strain when the bacteria were cultured at pH 5.0 and also when they were cultured at pH 7.0. Genes encoding 14 of these proteins were directly regulated by the ArsRS system, based on observed binding of ArsR to the relevant promoter regions. The ArsRS-regulated proteins identified in this study contribute to acid resistance (urease and amidase), acetone metabolism (acetone carboxylase), resistance to oxidative stress (thioredoxin reductase), quorum sensing (Pfs), and several other functions. These results provide further definition of the ArsRS regulon and underscore the importance of the ArsRS system in regulating expression ofH. pyloriproteins during bacterial growth at both neutral pH and acidic pH.
High levels of fatty acids increase contractile function of neonatal rabbit hearts during reperfusion following ischemia
Authors: Ito Masayoshi , Jaswal Jagdip S. , Lam Victoria H. , Oka Tatsujiro , Zhang Liyan , Beker Donna L. , Lopaschuk Gary D. , Rebeyka Ivan M.
Published: February 2010

In the neonatal heart the transition from using carbohydrates to using fatty acids has not fully matured and oxidative metabolism/ATP generation may be limiting contractile function after ischemia. This study tested the hypothesis that increasing fatty acid availability increases recovery of left ventricular (LV) work by increasing palmitate oxidation, tricarboxylic acid (TCA) cycle activity, and ATP generation. Isolated working hearts from 7-day-old rabbits were perfused with Krebs solution containing low (0.4 mM) or high (2.4 mM) palmitate and 5.5 mM glucose. Hearts were subjected to 35-min global ischemia before 40-min reperfusion, and rates of glycolysis, glucose oxidation, and palmitate oxidation were assessed. LV work was similar before ischemia but was greater during reperfusion in hearts perfused with 2.4 mM palmitate compared with hearts perfused with 0.4 mM palmitate [6.98 ± 0.14 ( n = 15) vs. 3.01 ± 0.23 ( n = 16) mJ·beat−1·g dry wt−1; P < 0.05]. This was accompanied by increased LV energy expenditure during reperfusion [35.98 ± 0.16 ( n = 8) vs. 19.92 ± 0.18 ( n = 6) mJ·beat−1·g dry wt−1; P < 0.05]. During reperfusion the rates of palmitate oxidation [237.5 ± 28.10 ( n = 7) vs. 86.0 ± 9.7 ( n = 6) nmol·g dry wt−1·min−1; P < 0.05], total TCA cycle activity [2.65 ± 0.39 ( n = 7) vs. 1.36 ± 0.14 ( n = 6) μmol acetyl-CoA·g dry wt−1·min−1; P < 0.05], and ATP generation attributable to palmitate oxidation [26.6 ± 3.1 ( n = 7) vs. 12.6 ± 1.7 ( n = 6) μmol·g dry wt−1·min−1; P < 0.05] were greater in hearts perfused with 2.4 mM palmitate. These data indicate that the neonatal heart has decreased energy reserve, and, in contrast to the mature heart, increasing availability of fatty acid substrate increases energy production and improves recovery of function after ischemia.