bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative effect of lens care solutions on blink rate, ocular discomfort and visual performance
Authors: Yang Shun‐nan , Tai Yu‐chi , Sheedy James E , Kinoshita Beth , Lampa Matthew , Kern Jami R
Published: July 2012

Citation information: Yang N, Tai C, Sheedy JE, Kinoshita B, Lampa M & Kern JR. Comparative effect of lens care solutions on blink rate, ocular discomfort and visual performance. Ophthalmic Physiol Opt 2012, 32, 412–420. doi: 10.1111/j.1475‐1313.2012.00922.x

Purpose:  To help maintain clear vision and ocular surface health, eye blinks occur to distribute natural tears over the ocular surface, especially the corneal surface. Contact lens wearers may suffer from poor vision and dry eye symptoms due to difficulty in lens surface wetting and reduced tear production. Sustained viewing of a computer screen reduces eye blinks and exacerbates such difficulties. The present study evaluated the wetting effect of lens care solutions (LCSs) on blink rate, dry eye symptoms, and vision performance.

Methods:  Sixty‐five adult habitual soft contact lens wearers were recruited to adapt to different LCSs (Opti‐free, ReNu, and ClearCare) in a cross‐over design. Blink rate in pictorial viewing and reading (measured with an eyetracker), dry eye symptoms (measured with the Ocular Surface Disease Index questionnaire), and visual discrimination (identifying tumbling E) immediately before and after eye blinks were measured after 2 weeks of adaption to LCS. Repeated measures anova and mixed model ancova were conducted to evaluate effects of LCS on blink rate, symptom score, and discrimination accuracy.

Results:  Opti‐Free resulted in lower dry eye symptoms (p = 0.018) than ClearCare, and lower spontaneous blink rate (measured in picture viewing) than ClearCare (p = 0.014) and ReNu (p = 0.041). In reading, blink rate was higher for ClearCare compared to ReNu (p = 0.026) and control (p = 0.024). Visual discrimination time was longer for the control (daily disposable lens) than for Opti‐Free (p = 0.007), ReNu (p = 0.009), and ClearCare (0.013) immediately before the blink.

Conclusions:  LCSs differently affected blink rate, subjective dry eye symptoms, and visual discrimination speed. Those with wetting agents led to significantly fewer eye blinks while affording better ocular comfort for contact lens wearers, compared to that without. LCSs with wetting agents also resulted in better visual performance compared to wearing daily disposable contact lenses. These presumably are because of improved tear film quality.
Computer‐related visual symptoms in office workers
Authors: Portello Joan K , Rosenfield Mark , Bababekova Yuliya , Estrada Jorge M , Leon Alejandro
Published: July 2012

Citation information: Portello JK, Rosenfield M, Bababekova Y, Estrada JM & Leon A. Computer‐related visual symptoms in office workers. Ophthalmic Physiol Opt 2012, 32, 375–382. doi: 10.1111/j.1475‐1313.2012.00925.x

Purpose:  Many individuals report visual symptoms during office work and specifically computer use. This study determined the prevalence of symptoms in a population of office workers, and examined the association between these symptoms and both dry eye disease and other demographic factors.

Method:  A written questionnaire was used to quantify the prevalence of symptoms in 520 New York City office workers, and to determine the effect of risk factors including gender, ethnicity, age, smoking, type of refractive correction and hours spent doing computer work. The questionnaire also examined the prevalence of ocular surface disease.

Results:  A significant positive correlation was observed between the symptom score and the number of hours spent working on a computer in a typical day. The most prevalent symptom was tired eyes, which was reported by approximately 40% of subjects as occurring ‘at least half the time’. 32% and 31% of subjects reported symptoms of dry eye and eye discomfort, respectively. Symptoms varied significantly with gender (being greater in females), ethnicity (being greater in Hispanics) and the use of rewetting drops. A significant positive correlation was observed between computer‐related visual symptoms and the Ocular Surface Disease Index (OSDI), a measure of dry eye.

Conclusions:  Visual symptoms associated with computer use occur frequently in the general population producing discomfort for extended periods of time. They are strongly associated with ocular surface disease. Therapeutic regimens need to be developed for this widespread condition.
How Choice Experiment Design Affects Estimated Valuation of Use of Gestation Crates
Authors: Pozo Veronica F. , Tonsor Glynn T. , Schroeder Ted C.
Published: July 2012

This study utilises a split‐sample experimental approach where six different choice experiment designs that vary in the number of attributes are used to control for the effects of design dimensions and consumer inferences in assessing consumer demand. Our application is in the use of gestation stalls (crates) in pork production. Our findings suggest that effects of both the mixture of attributes included in the design and consumer inferences on the specific attributes presented in experiments influence estimated willingness‐to‐pay and consumer welfare. Implications are that when researchers limit their studies to the use of a unique choice experiment design, resulting willingness‐to‐pay estimates might not be robust to different specifications.
Beyond Neurovascular: Migraine as a Dysfunctional Neurolimbic Pain Network
Authors: Maizels Morris , Aurora Sheena , Heinricher Mary
Published: July 2012

No single model of migraine explains all of the known features of the disorder. Migraine has recently been characterized as an abnormality in pain‐modulating circuits in the brainstem. The periaqueductal gray appears to have a critical role in migraine genesis and has been labeled the “migraine generator.” The concept of a “pain matrix,” rather than a specific locus of pain, is widely accepted in the pain literature and offers a new dimension to understanding migraine. Recent neuroimaging studies of migraineurs suggest altered functional connectivity between brainstem pain‐modulating circuits and cortical (limbic) centers. Numerous clinical observations suggest that limbic influences play an important role in migraine expression. We propose a model of migraine as a dysfunction of a “neurolimbic” pain network. The influence between brainstem and cortical centers is bidirectional, reflecting the bidirectional interaction of pain and mood. Neurolimbic dysfunction may increase as migraine becomes more chronic or refractory. The neurolimbic model expands the model of migraine as a dysfunction of brainstem nuclei. A neurolimbic model may help bridge a gap in understanding the migraine attack, the interictal dysfunctions of episodic migraine, the progression to chronic migraine, and the common comorbidities with other disorders (such as fibromyalgia, irritable bowel syndrome, and mood and anxiety disorders), which may also be considered neurolimbic. A neurolimbic model of migraine may be a useful heuristic that would impact both clinical treatment and research agendas, as well as education of physicians and patients.
Remembering and Voting: Theory and Evidence from Amnesic Patients
Authors: Coronel Jason C. , Duff Melissa C. , Warren David E. , Federmeier Kara D. , Gonsalves Brian D. , Tranel Daniel , Cohen Neal J.
Published: July 2012

One of the most prominent claims to emerge from the field of public opinion is that citizens can vote for candidates whose issue positions best reflect their own beliefs even when they cannot remember previously learned stances associated with the candidates. The current experiment provides a unique and powerful examination of this claim by determining whether individuals with profound amnesia, whose severe memory impairments prevent them from remembering specific issue information associated with any particular candidate, can vote for candidates whose issue positions come closest to their own political views. We report here that amnesic patients, despite not being able to remember any issue information, consistently voted for candidates with favored political positions. Thus, sound voting decisions do not require recall or recognition of previously learned associations between candidates and their issue positions. This result supports a multiple memory systems model of political decision making.
Evaluating Body Mass Index–Specific Trimester Weight Gain Recommendations: Differences Between Black and White Women
Authors: Fontaine Patricia L. , Hellerstedt Wendy L. , Dayman Caitlyn E. , Wall Melanie M. , Sherwood Nancy E.
Published: July 2012

Introduction: We compared the gestational weight gains of black and white women with the 2009 Institute of Medicine (IOM) recommendations to better understand the potential for successful implementation of these guidelines in clinical settings.

Methods: Prenatal and birth data for 2760 women aged 18 to 40 years with term singleton births from 2004 through 2007 were abstracted. We examined race differences in mean trimester weight gains with adjusted linear regression and compared race differences in the distribution of women who met the IOM recommendations with chi‐square analyses. We stratified all analyses by prepregnancy body mass index.

Results: Among normal‐weight and obese women, black women gained less weight than white women in the first and second trimesters. Overweight black women gained significantly less than white women in all trimesters. For both races in all body mass index categories, a minority of women (range 9.9%‐32.4%) met the IOM recommended gains for the second and third trimesters. For normal‐weight, overweight, and obese black and white women, 49% to 80% exceeded the recommended gains in the third trimester, with higher rates of excessive gain for white women.

Discussion: Less than half of the sample gained within the IOM recommended weight gain ranges in all body mass index groups and in all trimesters. The risk of excessive gain was higher for white women. For both races, excessive weight gain began by the second trimester, suggesting that counseling about the importance of weight gain during pregnancy should begin earlier, in the first trimester or prior to conception.
Normal vs. disordered bereavement‐related depression: are the differences real or tautological?
Authors: Wakefield J. C. , Schmitz M. F.
Published: July 2012

Objective: To evaluate whether the DSM distinction between uncomplicated (normal) and complicated (disordered) bereavement‐related depression (BRD) has discriminant validity on a range of pathology indicators. The DSM’s major depression bereavement exclusion (BE) excludes BRDs from diagnosis when they are uncomplicated (defined by brief duration, non‐severe impairment, and lack of certain pathosuggestive symptoms) but classifies all other (“complicated”) BRDs as major depression. A previous report seemed to support the uncomplicated/complicated distinction’s discriminant validity. However, those arguing for eliminating the BE from DSM‐5 dismiss the findings as ‘tautological,’ attributing the validator differences to definitional biases (e.g. ‘uncomplicated’ requires ‘no suicidal ideation,’ yet ‘lifetime suicide attempt’ was a validator). This study empirically tests whether the uncomplicated/complicated differences are real or tautological.

Method: Using National Comorbidity Survey data, confounds between definitional criteria for ‘uncomplicated’ and pathology validators were identified and corrected by deleting the biasing criteria and recalculating the corresponding validator’s outcome.

Results: Six validators (interference with life, suicide attempt, melancholic depression, duration, hospitalization, and number of symptoms) were reanalyzed using unbiased definitions for ‘uncomplicated.’ All still yielded significantly lower pathology levels for uncomplicated BRDs, disconfirming the ‘tautology’ hypothesis. Regression analysis revealed that ‘uncomplicated’ offered incremental validity over severity alone in predicting pathology, so ‘uncomplicated’ cannot be equated with ‘mild.’

Conclusion: Uncomplicated BRDs’ lower pathology validator levels are because of real syndromal differences, not definitional tautologies, supporting the BE’s validity.
Common mental disorders and long‐term sickness absence in a general working population. The Hordaland Health Study
Authors: Knudsen A. K. , Harvey S. B. , Mykletun A. , Øverland S.
Published: July 2012

Objective:  To examine and compare the prospective effect of the common mental disorders (CMD) anxiety and depression on duration and recurrence of sickness absence (SA), and to investigate whether the effect of CMD on SA is detectable over time.

Method:  Information from a large epidemiological health study (N = 13 436) was linked with official records of SA episodes lasting ≥16 days up to 6 years after participation. Common mental disorders were assessed with the Hospital Anxiety and Depression Scale (HADS). Associations were analysed with Cox regression and multinomial logistic regression models controlling for potential covariates.

Results:  Comorbid anxiety and depression, and anxiety only were significant risk factors for SA after adjusting for covariates, whilst depression only was not. Anxiety and depression were stronger predictors for longer duration of SA episodes compared with shorter duration and associated with more frequent recurrence of SA. There was a general trend toward the effect of CMD on SA becoming weaker over time; however, the effect of anxiety only on SA remained stable throughout the follow‐up.

Conclusion:  Common mental disorders are long‐lasting predictors of onset, duration and recurrence of SA. Anxiety appears to be a more important contributor to long‐term SA than previously described in the literature.
Integrons, β‐lactamase and qnr genes in multidrug resistant clinical isolates of Proteus mirabilis and P. vulgaris
Authors: Mokracka Joanna , Gruszczyńska Beata , Kaznowski Adam
Published: July 2012

Thirty‐three isolates of Proteus mirabilis and two P. vulgaris were examined for their antimicrobial resistance, the presence of integrons with regard to gene cassette content, and genetic determinants of β‐lactam and low‐level quinolone resistance. Integrons were detected in 23 (69.7%) P. mirabilis isolates; six (18.2%) of them had class 1 integrons, 11 (33.3%) possessed class 2 integrons and six (18.2%) carried integrons of both classes. One P. vulgaris strain possessed class 1 and class 2 integrons. The presence of integrons was associated with increased frequency of resistance to gentamicin, ciprofloxacin, sulfamethoxazole and co‐trimoxazole. Moreover, integron presence was associated with increased resistance range in terms of both the number of antimicrobials and the number of classes of antimicrobials to which a strain was resistant. Class 1 integrons contained aadA1, aadB‐aadA1, dfrA1‐aadA1, blaPSE‐1‐aadA1 and aacA4‐orfA‐orfB‐aadA1 gene cassette arrays, whereas all class 2 integrons had a dfrA1‐sat2‐aada1 array. β‐lactamase genes not associated with integrons comprised blaTEM‐2, blaDHA‐1 and blaCMY‐15. Plasmid‐mediated fluoroquinolone resistance was determined by qnrD and qnrS1 genes. This is the first report of P. vulgaris strains harbouring qnrD genes in Europe.
Intratumoral T but not B lymphocytes are related to clinical outcome in prostate cancer
Authors: Flammiger Anna , Bayer Florian , Cirugeda‐Kühnert Ana , Huland Hartwig , Tennstedt Pierre , Simon Ronald , Minner Sarah , Bokemeyer Carsten , Sauter Guido , Schlomm Thorsten , Trepel Martin
Published: July 2012

The number of tumor‐infiltrating lymphocytes is functionally important and correlates with clinical outcome in several tumor entities. Herein we explore the impact of the density of T and B lymphocytes in prostate cancer tissue on prostate‐specific antigen (PSA) recurrence after prostatectomy in 3261 prostate cancer tissue samples. The number of prostate cancer‐infiltrating CD3‐positive T cells and CD20‐positive B cells per tissue spot in a tissue microarray format was determined by immunohistochemistry and was correlated with clinical and pathological data from the same patient cohort. Patients with very low and very high numbers of CD3‐positive T cells per tissue spot had a significantly shorter PSA recurrence‐free survival compared to patients with intermediate numbers of T cells (p = 0.0188). Furthermore, a high number of CD3‐positive T cells per tissue spot was associated with fusion type prostate cancer identified by ERG expression analysis. The number of CD20‐positive B cells per tissue spot was not associated with other clinical and histopathological parameters. This study indicates that the density of T but not B cells plays a functional role in the biology of prostate cancer and may have an impact on clinical outcome in this frequent neoplasia.
Biochemical aspects of bean resistance to anthracnose mediated by silicon
Authors: Polanco L.R. , Rodrigues F.A. , Nascimento K.J.T. , Shulman P. , Silva L.C. , Neves F.W. , Vale F.X.R.
Published: July 2012

This study investigated the effect of silicon (Si) on resistance of bean plants (cv. ‘Peróla’) to anthracnose, caused by Colletotrichum lindemuthianum, grown in a nutrient solution containing 0 (−Si) or 2 mmol Si L−1 (+Si). The concentration of Si in leaf tissue and the incubation period increased by 55.2% and 14.3%, respectively, in +Si plants in relation to −Si plants. The area under anthracnose progress curve and the severity estimated by the software QUANT significantly decreased by 32.9% and 27%, respectively, for +Si plants. Si did not affect the concentration of total soluble phenolics. Chitinases activity was higher in the advanced stages of infection by C. lindemuthianum for leaves of −Si plants. β‐1,3‐Glucanase activity increased after C. lindemuthianum infection, but it was not enhanced by Si. Peroxidase and polyphenoloxidase activities had no apparent effect on the resistance of bean plants to anthracnose, regardless of the presence of Si. The increase in lignin concentration as well as on the phenylalanine ammonia‐lyase and lipoxygenase activities were important for the resistance of +Si plants against anthracnose. The results of this study suggest that Si may increase resistance to anthracnose in bean plants by enhancing certain biochemical mechanisms of defence as opposed to just acting as a physical barrier to penetration by C. lindemuthianum.
Evaluation of Darwin's fecundity advantage hypothesis in Parthenium beetle, Zygogramma bicolorata
Authors:   Omkar , Afaq Uzma
Published: July 2012

In the Parthenium beetle, Zygogramma bicolorata Pallister (Coleoptera: Chrysomelidae), variation in body size exists between and within the sexes. The females are larger than the males. Darwin (1874) proposed the fecundity advantage hypothesis, that is, large‐sized females produce more progeny, with subsequent studies supporting, as well as, refuting the hypothesis. Thus, in order to evaluate whether this hypothesis stands in Z. bicolorata we performed experiments to investigate the role of body size in influencing: (i) assortative mating; (ii) reproductive attributes; and (iii) growth, development and survival of offspring. It is the first attempt in this beetle. We found that size influenced assortative mating, reproductive output and offspring fitness. Larger males and females were preferred as mates over smaller ones. The pairs, having larger adults as mates, had higher fecundity, while the egg viability was influenced by the male size only. The offspring of larger parents had fast development and higher survival, indicating thereby possible better nutrient allotment by the female and supply of accessory gland proteins by the male in addition to better quality of genes.
Reconsidering Duration in Assessing the Character of Precipitation
Authors: Brommer David M.
Published: July 2012

In general, previous research has only tangentially addressed questions about the duration of precipitation events and the spatial and temporal variability associated with accumulating precipitation, from local to global scales. As precipitation rates and intensities change with variations in the climate, it is imperative that changes in the duration of precipitation events are also considered. Impacts from changes in precipitation duration, coupled with changes in precipitation intensity and frequency, have significant implications for changes in extreme events such as droughts and floods, but also the potential changes in moderate to light precipitation events. Accurately depicting changes in precipitation duration will help answer fundamental questions about precipitation characteristics that have not been addressed previously. A review of previous research incorporating precipitation duration is presented in this manuscript, with an example of how sub‐daily precipitation data can be used to provide additional insight into the overall nature of precipitation.
Angular dependences of SiO2 etch rates in C4F6/O2/Ar and C4F6/CH2F2/O2/Ar plasmas
Authors: Cho Sung-Woon , Kim Chang-Koo , Lee Jin-Kwan , Moon Sang Heup , Chae Heeyeop
Published: July 2012

The angular dependences of SiO2 etch rates for C4F6/O2/Ar and C4F6/CH2F2/O2/Ar plasmas were investigated using a Faraday cage system. In the absence of CH2F2, the steady-state fluorocarbon film that formed on the SiO2 surface was thin enough (<10 Å) for ions to penetrate through the film. The normalized etch yield (NEY) curve in this case showed a maximum value of 1.74 at an ion-incident angle of 70°, illustrating that physical sputtering was a major contributor to the SiO2 etching. The addition of CH2F2 to C4F6/O2/Ar plasmas produced thicker and more etch-resistant fluorocarbon films, leading to a decrease in the ion energy transfer depth through the steady-state films. This implies that physical sputtering was suppressed when CH2F2 was present in the plasma, demonstrated by a decrease in the maximum NEY and the ion-incident angle at the maximum NEY.
A higher-order split-step Fourier parabolic-equation sound propagation solution scheme
Authors: Lin Ying-Tsong , Duda Timothy F.
Published: July 2012

A three-dimensional Cartesian parabolic-equation model with a higher-order approximation to the square-root Helmholtz operator is presented for simulating underwater sound propagation in ocean waveguides. The higher-order approximation includes cross terms with the free-space square-root Helmholtz operator and the medium phase speed anomaly. It can be implemented with a split-step Fourier algorithm to solve for sound pressure in the model. Two idealized ocean waveguide examples are presented to demonstrate the performance of this numerical technique.
A Tissue Engineering Solution for Segmental Defect Regeneration in Load-Bearing Long Bones
Authors: Reichert Johannes C. , Cipitria Amaia , Epari Devakara R. , Saifzadeh Siamak , Krishnakanth Pushpanjali , Berner Arne , Woodruff Maria A. , Schell Hanna , Mehta Manav , Schuetz Michael A. , Duda Georg N. , Hutmacher Dietmar W.
Published: July 2012

A polycaprolactone-tricalcium phosphate scaffold with recombinant human BMP-7 heals critical-sized bone defects in sheep.
Association of Fecal Indicator Bacteria with Human Viruses and Microbial Source Tracking Markers at Coastal Beaches Impacted by Nonpoint Source Pollution
Authors: McQuaig Shannon , Griffith John , Harwood Valerie J.
Published: July 2012

Water quality was assessed at two marine beaches in California by measuring the concentrations of culturable fecal indicator bacteria (FIB) and by library-independent microbial source tracking (MST) methods targeting markers of human-associated microbes (human polyomavirus [HPyV] PCR and quantitative PCR,
Methanobrevibacter smithii
PCR, and
Bacteroides
sp. strain HF183 PCR) and a human pathogen (adenovirus by nested PCR). FIB levels periodically exceeded regulatory thresholds at Doheny and Avalon Beaches for enterococci (28.5% and 31.7% of samples, respectively) and fecal coliforms (20% and 5.8%, respectively). Adenoviruses were detected at four of five sites at Doheny Beach and were correlated with detection of HPyVs and human
Bacteroides
HF183; however, adenoviruses were not detected at Avalon Beach. The most frequently detected human source marker at both beaches was
Bacteroides
HF183, which was detected in 27% of samples. Correlations between FIBs and human markers were much more frequent at Doheny Beach than at Avalon Beach; e.g., adenovirus was correlated with HPyVs and HF183. Human sewage markers and adenoviruses were routinely detected in samples meeting FIB regulatory standards. The toolbox approach of FIB measurement coupled with analysis of several MST markers targeting human pathogens used here demonstrated that human sewage is at least partly responsible for the degradation of water quality, particularly at Doheny Beach, and resulted in a more definitive assessment of recreational water quality and human health risk than reliance on FIB concentrations alone could have provided.
The Bacterium Pantoea stewartii Uses Two Different Type III Secretion Systems To Colonize Its Plant Host and Insect Vector
Authors: Correa Valdir R. , Majerczak Doris R. , Ammar El-Desouky , Merighi Massimo , Pratt Richard C. , Hogenhout Saskia A. , Coplin David L. , Redinbaugh Margaret G.
Published: July 2012

Plant- and animal-pathogenic bacteria utilize phylogenetically distinct type III secretion systems (T3SS) that produce needle-like injectisomes or pili for the delivery of effector proteins into host cells.
Pantoea stewartii
subsp.
stewartii
(herein referred to as
P. stewartii
), the causative agent of Stewart's bacterial wilt and leaf blight of maize, carries phylogenetically distinct T3SSs. In addition to an Hrc-Hrp T3SS, known to be essential for maize pathogenesis,
P. stewartii
has a second T3SS (
Pantoea
secretion island 2 [PSI-2]) that is required for persistence in its flea beetle vector,
Chaetocnema pulicaria
(Melsh). PSI-2 belongs to the Inv-Mxi-Spa T3SS family, typically found in animal pathogens. Mutagenesis of the PSI-2
psaN
gene, which encodes an ATPase essential for secretion of T3SS effectors by the injectisome, greatly reduces both the persistence of
P. stewartii
in flea beetle guts and the beetle's ability to transmit
P. stewartii
to maize. Ectopic expression of the
psaN
gene complements these phenotypes. In addition, the PSI-2
psaN
gene is not required for
P. stewartii
pathogenesis of maize and is transcriptionally upregulated in insects compared to maize tissues. Thus, the Hrp and PSI-2 T3SSs play different roles in the life cycle of
P. stewartii
as it alternates between its insect vector and plant host.
Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales
Authors: Stratilo Chad W. , Bader Douglas E.
Published: July 2012

Environmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (
Bison bison
) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park.
Bacillus anthracis
spores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. Confirmed
B. anthracis
isolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA).
B. anthracis
isolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing of
Bacillus anthracis
.
Mercury Resistance and Mercuric Reductase Activities and Expression among Chemotrophic Thermophilic Aquificae
Authors: Freedman Zachary , Zhu Chengsheng , Barkay Tamar
Published: July 2012

Mercury (Hg) resistance (
mer
) by the reduction of mercuric to elemental Hg is broadly distributed among the
Bacteria
and
Archaea
and plays an important role in Hg detoxification and biogeochemical cycling. MerA is the protein subunit of the homodimeric mercuric reductase (MR) enzyme, the central function of the
mer
system. MerA sequences in the phylum
Aquificae
form the deepest-branching lineage in Bayesian phylogenetic reconstructions of all known MerA homologs. We therefore hypothesized that the
merA
homologs in two thermophilic
Aquificae
,
Hydrogenobaculum
sp. strain Y04AAS1 (AAS1) and
Hydrogenivirga
sp. strain 128-5-R1-1 (R1-1), specified Hg resistance. Results supported this hypothesis, because strains AAS1 and R1-1 (i) were resistant to >10 μM Hg(II), (ii) transformed Hg(II) to Hg(0) during cellular growth, and (iii) possessed Hg-dependent NAD(P)H oxidation activities in crude cell extracts that were optimal at temperatures corresponding with the strains' optimal growth temperatures, 55°C for AAS1 and 70°C for R1-1. While these characteristics all conformed with the
mer
system paradigm, expression of the
Aquificae
mer
operons was not induced by exposure to Hg(II) as indicated by unity ratios of
merA
transcripts, normalized to
gyrA
transcripts for hydrogen-grown AAS1 cultures, and by similar MR specific activities in thiosulfate-grown cultures with and without Hg(II). The Hg(II)-independent expression of
mer
in the deepest-branching lineage of MerA from bacteria whose natural habitats are Hg-rich geothermal environments suggests that regulated expression of
mer
was a later innovation likely in environments where microorganisms were intermittently exposed to toxic concentrations of Hg.
Comparative Assessment of Nitrogen Fixation Methodologies, Conducted in the Oligotrophic North Pacific Ocean
Authors: Wilson Samuel T. , Böttjer Daniela , Church Matthew J. , Karl David M.
Published: July 2012

Resolution of the nitrogen (N) cycle in the marine environment requires an accurate assessment of dinitrogen (N
2
) fixation. We present here an update on progress in conducting field measurements of acetylene reduction (AR) and
15
N
2
tracer assimilation in the oligotrophic North Pacific Subtropical Gyre (NPSG). The AR assay was conducted on discrete seawater samples using a headspace analysis system, followed by quantification of ethylene (C
2
H
4
) with a reducing compound photodetector. The rates of C
2
H
4
production were measurable for nonconcentrated seawater samples after an incubation period of 3 to 4 h. The
15
N
2
tracer measurements compared the addition of
15
N
2
as a gas bubble and dissolved as
15
N
2
enriched seawater. On all sampling occasions and at all depths, a 2- to 6-fold increase in the rate of
15
N
2
assimilation was measured when
15
N
2
-enriched seawater was added to the seawater sample compared to the addition of
15
N
2
as a gas bubble. In addition, we show that the
15
N
2
-enriched seawater can be prepared prior to its use with no detectable loss (<1.7%) of dissolved
15
N
2
during 4 weeks of storage, facilitating its use in the field. The ratio of C
2
H
4
production to
15
N
2
assimilation varied from 7 to 27 when measured simultaneously in surface seawater samples. Collectively, the modifications to the AR assay and the
15
N
2
assimilation technique present opportunities for more accurate and high frequency measurements (e.g., diel scale) of N
2
fixation, providing further insight into the contribution of different groups of diazotrophs to the input of N in the global oceans.
Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability
Authors: Morrow Kathleen M. , Moss Anthony G. , Chadwick Nanette E. , Liles Mark R.
Published: July 2012

Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean,Montastraea faveolataandPorites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here thatM. faveolataandP. astreoidesharbor distinct, host-specific bacteria but that specificity varies by species and site.P. astreoidesgenerally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus,Endozoicomonas, within the orderOceanospirillales. The bacterial assemblages associated withM. faveolataare significantly more diverse and exhibit higher specificity at the family level thanP. astreoidesassemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.
Novel Mutations Associated with Resistance to Bacillus sphaericus in a Polymorphic Region of the Culex quinquefasciatus cqm1 Gene
Authors: Chalegre Karlos Diogo de Melo , Romão Tatiany Patrícia , Tavares Daniella Aliny , Santos Eloína Mendonça , Ferreira Lígia Maria , Oliveira Cláudia Maria Fontes , de-Melo-Neto Osvaldo Pompílio , Silva-Filha Maria Helena Neves Lobo
Published: July 2012

Bin toxin fromBacillus sphaericusacts onCulex quinquefasciatuslarvae by binding to Cqm1 midgut-bound receptors, and disruption of thecqm1gene is the major cause of resistance. The goal of this work was to screen for a laboratory-selected resistancecqm1RECallele in field populations in the city of Recife, Brazil, and to describe other resistance-associated polymorphisms in thecqm1gene. Thecqm1RECallele was detected in the four nontreated populations surveyed at frequencies from 0.001 to 0.017, and sequence analysis from these samples revealed a novel resistant allele (cqm1REC-D16) displaying a 16-nucletotide (nt) deletion which is distinct from the 19-nt deletion associated withcqm1REC. Yet a third resistant allele (cqm1REC-D25), displaying a 25-nt deletion, was identified in samples from a treated area exposed toB. sphaericus. A comparison of the three deletion events revealed that all are located within the same 208-nt region amplified during the screening procedure. They also introduce equivalent frameshifts in the sequence and generate the same premature stop codon, leading to putative transcripts encoding truncated proteins which are unable to locate to the midgut epithelium. The populations analyzed in this study contained a variety of alleles with mutations disrupting the function of the corresponding Bin toxin receptor. Their locations reveal a hot spot that can be exploited to assess the resistance risk through DNA screening.
Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly
Authors: Emerson Joanne B. , Thomas Brian C. , Andrade Karen , Allen Eric E. , Heidelberg Karla B. , Banfield Jillian F.
Published: July 2012

Viruses of theBacteriaandArchaeaplay important roles in microbial evolution and ecology, and yet viral dynamics in natural systems remain poorly understood. Here, we createdde novoassemblies from 6.4 Gbp of metagenomic sequence from eight community viral concentrate samples, collected from 12 h to 3 years apart from hypersaline Lake Tyrrell (LT), Victoria, Australia. Through extensive manual assembly curation, we reconstructed 7 complete and 28 partial novel genomes of viruses and virus-like entities (VLEs, which could be viruses or plasmids). We tracked these 35 populations across the eight samples and found that they are generally stable on the timescale of days and transient on the timescale of years, with some exceptions. Cross-detection of the 35 LT populations in three previously described haloviral metagenomes was limited to a few genes, and most previously sequenced haloviruses were not detected in our samples, though 3 were detected upon reducing our detection threshold from 90% to 75% nucleotide identity. Similar results were obtained when we applied our methods to haloviral metagenomic data previously reported from San Diego, CA: 10 contigs that we assembled from that system exhibited a variety of detection patterns on a timescale of weeks to 1 month but were generally not detected in LT. Our results suggest that most haloviral populations have a limited or, possibly, a temporally variable global distribution. This study provides high-resolution insight into viral biogeography and dynamics and it places “snapshot” viral metagenomes, collected at a single time and location, in context.
Weak Transcription of the
cry1Ac
Gene in Nonsporulating Bacillus thuringiensis Cells
Authors: Yang Hui , Wang Pinshu , Peng Qi , Rong Rong , Liu Chunxia , Lereclus Didier , Zhang Jie , Song Fuping , Huang Dafang
Published: July 2012

The
cry1Ac
gene of
Bacillus thuringiensis
subsp.
kurstaki
HD-73 (
B. thuringiensis
HD-73) is a typical example of a sporulation-dependent crystal gene and is controlled by sigma E and sigma K during sporulation. To monitor the production and accumulation of Cry1Ac at the cellular level, we developed a green fluorescent protein-based reporter system. The production of Cry1Ac was monitored in
spo0A
,
sigE
, and
sigK
mutants, and these mutants were able to express the Cry1Ac-green fluorescent protein fusion protein. In nonsporulating
B. thuringiensis
HD-73 cells, low-level expression of
cry1Ac
was also observed. Reverse transcription-PCR and Western blotting results confirmed that the
cry1Ac
promoter has low activity in nonsporulating
B. thuringiensis
cells. A beta-galactosidase assay demonstrated that the transcription of the
cry1Ac
gene during exponential and transition phases is positively regulated by Spo0A. Additional bioassay results indicated that
spo0A
and
sigE
mutants containing the
cry1Ac-gfp
fusion exhibited insecticidal activity against
Plutella xylostella
larvae.
A Convenient and Robust
In Vivo
Reporter System To Monitor Gene Expression in the Human Pathogen Helicobacter pylori
Authors: Vannini Andrea , Agriesti Francesca , Mosca Flaviana , Roncarati Davide , Scarlato Vincenzo , Danielli Alberto
Published: July 2012

Thirty years of intensive research have significantly contributed to our understanding of
Helicobacter pylori
biology and pathogenesis. However, the lack of convenient genetic tools, in particular the limited effectiveness of available reporter systems, has notably limited the toolbox for fundamental and applied studies. Here, we report the construction of a bioluminescent
H. pylori
reporter system based on the
Photorhabdus luminescens luxCDABE
cassette. The system is constituted of a promoterless
lux
acceptor strain in which promoters and sequences of interest can be conveniently introduced by double homologous recombination of a suicide transformation vector. We validate the robustness of this new
lux
reporter system in noninvasive
in vivo
monitoring of dynamic transcriptional responses of inducible as well as repressible promoters and demonstrate its suitability for the implementation of genetic screens in
H. pylori
.
Significance of the Bacteriophage Treatment Schedule in Reducing Salmonella Colonization of Poultry
Authors: Bardina Carlota , Spricigo Denis A. , Cortés Pilar , Llagostera Montserrat
Published: July 2012

Salmonella
remains the major cause of food-borne diseases worldwide, with chickens known to be the main reservoir for this zoonotic pathogen. Among the many approaches to reducing
Salmonella
colonization of broilers, bacteriophage offers several advantages. In this study, three bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) obtained from our collection that exhibited a broad host range against
Salmonella enterica
serovar Enteritidis and
Salmonella enterica
serovar Typhimurium were characterized with respect to morphology, genome size, and restriction patterns. A cocktail composed of the three bacteriophages was more effective in promoting the lysis of
S.
Enteritidis and
S.
Typhimurium cultures than any of the three bacteriophages alone. In addition, the cocktail was able to lyse the
Salmonella enterica
serovars Virchow, Hadar, and Infantis. The effectiveness of the bacteriophage cocktail in reducing the concentration of
S.
Typhimurium was tested in two animal models using different treatment schedules. In the mouse model, 50% survival was obtained when the cocktail was administered simultaneously with bacterial infection and again at 6, 24, and 30 h postinfection. Likewise, in the White Leghorn chicken specific-pathogen-free (SPF) model, the best results, defined as a reduction of
Salmonella
concentration in the chicken cecum, were obtained when the bacteriophage cocktail was administered 1 day before or just after bacterial infection and then again on different days postinfection. Our results show that frequent treatment of the chickens with bacteriophage, and especially prior to colonization of the intestinal tract by
Salmonella
, is required to achieve effective bacterial reduction over time.
Enumerating Viruses by Using Fluorescence and the Nature of the Nonviral Background Fraction
Authors: Pollard Peter C.
Published: July 2012

Bulk fluorescence measurements could be a faster and cheaper way of enumerating viruses than epifluorescence microscopy, flow cytometry, or transmission electron microscopy (TEM). However, since viruses are not imaged, the background fluorescence compromises the signal, and we know little about its nature. In this paper the size ranges of nucleotides that fluoresce in the presence of SYBR gold were determined for wastewater and a range of freshwater samples using a differential filtration method. Fluorescence excitation-emission matrices (FEEMs) showed that >70% of the SYBR fluorescence was in the <10-nm size fraction (background) and was not associated with intact viruses. This was confirmed using TEM. The use of FEEMs to develop a fluorescence-based method for counting viruses is an approach that is fundamentally different from the epifluorescence microscopy technique used for enumerating viruses. This high fluorescence background is currently overlooked, yet it has had a most pervasive influence on the development of a simple fluorescence-based method for quantifying viral abundance in water.
Fast and Sensitive Detection of Bacillus anthracis Spores by Immunoassay
Authors: Morel Nathalie , Volland Hervé , Dano Julie , Lamourette Patricia , Sylvestre Patricia , Mock Michèle , Créminon Christophe
Published: July 2012

Bacillus anthracis
is one of the most dangerous potential biological weapons, and it is essential to develop a rapid and simple method to detect
B. anthracis
spores in environmental samples. The immunoassay is a rapid and easy-to-use method for the detection of
B. anthracis
by means of antibodies directed against surface spore antigens. With this objective in view, we have produced a panel of monoclonal antibodies against
B. anthracis
and developed colorimetric and electrochemiluminescence (ECL) immunoassays. Using Meso Scale Discovery ECL technology, which is based on electrochemiluminescence (ECL) detection utilizing a sulfo-Tag label that emits light upon electrochemical stimulation (using a dedicated ECL plate reader, an electrical current is placed across the microplate with electrodes integrated into the bottom of the plate, resulting in a series of electrically induced reactions leading to a luminescent signal), a detection limit ranging between 0.3 × 10
3
and 10
3
CFU/ml (i.e., 30 to 100 spores per test), depending on the
B. anthracis
strain assayed, was achieved. In complex matrices (5 mg/ml of soil or simulated powder), the detection level (without any sample purification or concentration) was never altered more than 3-fold compared with the results obtained in phosphate-buffered saline.
Contribution of Surfactin and SwrA to Flagellin Expression, Swimming, and Surface Motility in Bacillus subtilis
Authors: Ghelardi Emilia , Salvetti Sara , Ceragioli Mara , Gueye Sokhna A. , Celandroni Francesco , Senesi Sonia
Published: July 2012

Multicellular communities produced by
Bacillus subtilis
can adopt sliding or swarming to translocate over surfaces. While sliding is a flagellum-independent motility produced by the expansive forces in a growing colony, swarming requires flagellar functionality and is characterized by the appearance of hyperflagellated swarm cells that associate in bundles or rafts during movement. Previous work has shown that swarming by undomesticated
B. subtilis
strains requires
swrA
, a gene that upregulates the expression of flagellar genes and increases swimming motility, and surfactin, a lipopeptide biosurfactant that also facilitates sliding. Through an analysis of
swrA
+
and
swrA
mutant laboratory strains with or without a mutation in
sfp
(a gene involved in surfactin production), we show that both
swrA
and surfactin upregulate the transcription of the flagellin gene and increase bacterial swimming. Surfactin also allows the nonswarming
swrA
mutant strain to efficiently colonize moist surfaces by sliding. Finally, we reconfirm the essential role of
swrA
in swarming and show that surfactin, which increases surface wettability, allows
swrA
+
strains to produce swarm cells on media at low humidity.
Impact of Short-Term Acidification on Nitrification and Nitrifying Bacterial Community Dynamics in Soilless Cultivation Media
Authors: Cytryn Eddie , Levkovitch Irit , Negreanu Yael , Dowd Scot , Frenk Sammy , Silber Avner
Published: July 2012

Soilless medium-based horticulture systems are highly prevalent due to their capacity to optimize growth of high-cash crops. However, these systems are highly dynamic and more sensitive to physiochemical and pH perturbations than traditional soil-based systems, especially during nitrification associated with ammonia-based fertilization. The objective of this study was to assess the impact of nitrification-generated acidification on ammonia oxidation rates and nitrifying bacterial community dynamics in soilless growth media. To achieve this goal, perlite soilless growth medium from a commercial bell pepper greenhouse was incubated with ammonium in bench-scale microcosm experiments. Initial quantitative real-time PCR analysis indicated that betaproteobacterial ammonia oxidizers were significantly more abundant than ammonia-oxidizing archaea, and therefore, research focused on this group. Ammonia oxidation rates were highest between 0 and 9 days, when pH values dropped from 7.4 to 4.9. Pyrosequencing of betaproteobacterial ammonia-oxidizing
amoA
gene fragments indicated that r-strategist-like
Nitrosomonas
was the dominant ammonia-oxidizing bacterial genus during this period, seemingly due to the high ammonium concentration and optimal growth conditions in the soilless media. Reduction of pH to levels below 4.8 resulted in a significant decrease in both ammonia oxidation rates and the diversity of ammonia-oxidizing bacteria, with increased relative abundance of the r-strategist-like
Nitrosospira
. Nitrite oxidizers (
Nitrospira
and
Nitrobacter
) were on the whole more abundant and less sensitive to acidification than ammonia oxidizers. This study demonstrates that nitrification and nitrifying bacterial community dynamics in high-N-load intensive soilless growth media may be significantly different from those in
in-terra
agricultural systems.