bluuebunny/crossref_metadata_2025 huggingface dataset:
Children's Beliefs About Self‐disclosure to Friends Regarding Academic Achievement
Authors: Zhang Zhenxin , Heyman Gail D. , Fu Genyue , Zhang Di , Yang Yue , Lee Kang
Published: July 2014

Self‐disclosure to friends is a potentially useful way for children to pursue a range of desired goals. Here we examined reasoning about the appropriateness of disclosing one's own academic outcomes in a sample of 7‐, 9‐, 11‐, 13‐, and 15‐year‐old Chinese participants (N = 150). The valence of (1) the outcomes to be disclosed and (2) the corresponding outcomes for the potential audience for the disclosure was manipulated factorially, and participants judged whether disclosure was advisable and explained their responses. Disclosure was seen as more appropriate under valence‐matching conditions than valence‐mismatching conditions. How participants judged each type of disclosure under valence‐mismatching conditions varied as a function of participant age: As compared with younger participants, older participants considered disclosure of weak performance to a stronger performer more acceptable and disclosure of strong performance to a weaker performer less acceptable. These findings suggest that older children are more likely than younger children to appreciate that self‐disclosing positive performance outcomes can bring social costs, and that self‐disclosing negative performance outcomes can bring social benefits.
Black–White Earnings Gap among Restaurant Servers: A Replication, Extension, and Exploration of Consumer Racial Discrimination in Tipping
Authors: Brewster Zachary W. , Lynn Michael
Published: July 2014

There is a rich history of social science research centering on racial inequalities that continue to be observed across various markets (e.g., labor, housing, and credit markets) and social milieus. Existing research on racial discrimination in consumer markets is, however, relatively scarce and that which has been done has disproportionately focused on consumers as the victims of race‐based mistreatment. As such, we know relatively little about how consumers contribute to inequalities in their roles as perpetrators of racial discrimination. In response, in this article, we elaborate on a line of research that is only in its infancy stages of development and yet is ripe with opportunities to advance the literature on consumer racial discrimination and racial earnings inequities among tip‐dependent employees in the United States. Specifically, we analyze data derived from an exit survey of restaurant consumers (N = 394) in an attempt to replicate, extend, and further explore the recently documented effect of service providers’ race on restaurant consumers’ tipping decisions. Our results indicate that both white and black restaurant customers discriminate against black servers by tipping them less than their white co‐workers. Importantly, we find no evidence that this black tip penalty is the result of inter‐racial differences in service skills possessed by black and white servers. We conclude by delineating directions for future research in this neglected but salient area of study.
“We Became Sceptics”: Fear and Media Hype in General Public Narrative on the Advent of Pandemic Influenza
Authors: Davis Mark , Lohm Davina , Flowers Paul , Waller Emily , Stephenson Niamh
Published: July 2014

In this article, we examine the apparent resistance of publics to messages regarding pandemic influenza. The 2009 H1N1 pandemic was addressed through media: governments used print, broadcast, and digital media to advise publics to enact hygiene practices and comply with social isolation; news media took up the pandemic as a lead story. Publics, however, rated the pandemic as not serious, even before it was widely known that it was mild for most. This problem is presently constructed as complacency: where individuals are seen to lack appropriate motivation to avoid risk. We combine perspectives on media reflexivity on the part of audiences with general public interviews and focus groups in Australia and the UK, to offer an alternative explanation for complacency. Publics endorse public health advice, but are skeptical of pandemic risk communication. They exhibit critical awareness of outbreak narrative and concomitant emotions, such as fear, which are coded into media stories. We, therefore, challenge the view that publics are complacent. Instead, governments must navigate an emerging terrain of ramified and critical media consumption to shape effective risk communication in time of global health emergency.
Optical coherence tomography applied to tests of skin care products in humans – a case study
Authors: Vasquez‐Pinto L. M. C. , Maldonado E. P. , Raele M. P. , Amaral M. M. , de Freitas A. Z.
Published: July 2014

Background/purpose

When evaluating skin care products for human skin, quantitative test methods need to be simple, precise and reliable. Optical coherence tomography (OCT), provides high‐resolution sectional images of translucent materials to a depth of a few millimeters, a technique usually applied to medical measurements in ophthalmology and dermatology. This study aimed to demonstrate the application of OCT as the main technique for monitoring changes in skin topography during tests of a wrinkle‐reduction product in humans.

Methods

We used a commercial OCT apparatus to perform clinical examinations of skin roughness in treated and non‐treated sites in the periorbital region of thirty human voluntaries who were using an anti‐aging product commercially available: Natura Chronos® Flavonóides de Passiflora 45+ FPS15, from Natura Cosméticos, Brazil. Measurements were performed days 0, 7, 14 and 28 of treatment. Equipment and software allowed real‐time recording of skin roughness parameters and wrinkle depths.

Results

The OCT measurements have allowed the monitoring of changes in skin roughness, which have shown reduction in treated sites around 10%. The obtained depth distributions also indicate reduction in the occurrence of wrinkles deeper than 170 μm. The verified results are consistent with those typically obtained after successful treatment with modern anti‐aging products.

Conclusion

By using the OCT technique, it was possible to quantify changes in skin roughness and in the distribution of depths of skin wrinkles, with adequate sensitivity. OCT imaging allows the direct visualization of the skin topography with resolution of micrometers, a reliable and interactive tool for clinical use. Therefore, for the first time, we demonstrated the use of OCT technique to verify the efficacy of cosmetic products in real time.
Imaging wavelength and light penetration depth for water content distribution measurement of skin
Authors: Arimoto H. , Egawa M.
Published: July 2014

Background/purpose

We investigate the measurement sensitivity for the water content distribution in Near‐infrared (NIR) imaging ranging up to 2 μm.

Methods

To evaluate the sensitivity, our attention is focused to the light penetration depth in the skin tissue because the thickness of a layer where the water content can be varied is very thin and deep light penetration decreases the signal variation. The light penetration depths in the wavelengths of 1300, 1450, and 1920 nm are calculated theoretically based on the Monte Carlo light transport simulation.

Results

It is clarified that the wavelength of 1920 nm gives the smallest penetration depth. A NIR imaging experiment is demonstrated to verify the difference of imaging sensitivity. The experiment result shows that the NIR image taken at 1920 nm gives the most sensitive measurement of the water content distribution in skin.
Identification of a soft tissue filler by ex vivo confocal microscopy and Raman spectroscopy in a case of adverse reaction to the filler
Authors: Cinotti E. , Perrot J. L. , Labeille B. , Boukenter A. , Ouerdane Y. , Cosmo P. , Douchet C. , Grivet D. , Cambazard F.
Published: July 2014

Background

Soft tissue fillers are usually identified in the skin using the conventional histopathologic examination. Ex vivo RCM has been used in one case and Raman spectroscopy (RS), which has been recently applied for the identification of skin foreign bodies, has never been employed for fillers. We report the use of both these new techniques, ex vivo RCM and RS, to confirm the diagnosis of adverse reaction to a soft tissue filler and to identify its composition.

Methods

We excised a skin nodule suspicious of adverse reaction to soft tissue filler, and we performed an ex vivo reflectance confocal microscopy (RCM) and an histopathologic examination, followed by a RS analysis.

Results

Ex vivo RCM showed numerous hypo‐reflective microspheres in the dermis that corresponded to rounded vacuoles at histopathologic examination, suggestive of polymethylmethacrylate (PMMA). RS showed a series of peaks at 600, 813, 970 1252, 1450, 1728, and 2951 cm−1 in correspondence to the microspheres, confirming the presence of PMMA.

Conclusion

These results suggest that ex vivo RCM and RS are additional tools to conventional histopathologic examination to characterize soft tissue fillers in case of adverse reaction. RCM has the advantage compared with the histopathologic examination that can be extemporaneously performed on a fresh surgical specimen. RS allow a precise chemical identification of the filler.
Acute UVB‐induced epidermal changes assessed by multiphoton laser tomography
Authors: Koehler M. J. , Kellner K. , Hipler U.‐C. , Kaatz M.
Published: July 2014

Background

In vivo multiphoton tomography (MPT) of human skin has become a valuable tool for non‐invasive examination of morphological and biophysical skin properties and their alterations. So far, skin changes after UVB irradiation were mainly evaluated clinically and histologically. The present study aimed at non‐invasive imaging of histological changes during acute UVB irradiation by multiphoton laser tomography.

Methods

In 10 volunteers, five areas were irradiated once with an erythematous UVB dose. Multiphoton measurements were performed four times, i.e. before irradiation (baseline), and 24, 48 and 72 h after irradiation, respectively. The data were evaluated for changes of epidermal pleomorphy, spongiosis, pigmentation and thickness.

Results

The four parameters were altered significantly by acute UVB irradiation, i.e. epidermal pleomorphy, spongiosis, pigmentation and thickness increased within 72 h after irradiation.

Conclusion

Thus, the study has shown that typical epidermal changes induced by acute UVB irradiation can be evaluated by MPT.
Endoplasmic reticulum aminopeptidase 1 function and its pathogenic role in regulating innate and adaptive immunity in cancer and major histocompatibility complex class I‐associated autoimmune diseases
Authors: Fruci D. , Romania P. , D'Alicandro V. , Locatelli F.
Published: July 2014

Major histocompatibility complex (MHC) class I molecules present antigenic peptides on the cell surface to alert natural killer (NK) cells and CD8+ T cells for the presence of abnormal intracellular events, such as virus infection or malignant transformation. The generation of antigenic peptides is a multistep process that ends with the trimming of N‐terminal extensions in the endoplasmic reticulum (ER) by aminopeptidases ERAP1 and ERAP2. Recent studies have highlighted the potential role of ERAP1 in reprogramming the immunogenicity of tumor cells in order to elicit innate and adaptive antitumor immune responses, and in conferring susceptibility to autoimmune diseases in predisposed individuals. In this review, we will provide an overview of the current knowledge about the role of ERAP1 in MHC class I antigen processing and how its manipulation may constitute a promising tool for cancer immunotherapy and treatment of MHC class I‐associated autoimmune diseases.
The origin of Lake Cheko and the 1908 Tunguska Event recorded by forest trees
Authors: Gasperini Luca , Stanghellini Carlo , Serra Romano
Published: July 2014

Several lines of evidence indicate that Cheko, a small lake close to the epicentre of the 1908 Tunguska Event (TE), fills a crater left behind by a fragment of the Tunguska Cosmic Body that impacted the ground downrange of the main explosion. It is thought that over 80 million trees were flattened or burnt as a consequence of the TE. However, a small number of trees in the devastated area survived the explosion and recorded in their growth‐ring patterns the environmental changes that followed this event. Some of those trees were found around Lake Cheko, ~10 km NW of the inferred TE epicentre. We analysed new data from the floor of Lake Cheko, including seismic‐reflection profiles, side‐scan sonar and video images, as well as dendrochronological evidence in tree samples collected along the shores, to test the hypothesis of a 1908 formation of the lake.
The condensin complexes play distinct roles to ensure normal chromosome morphogenesis during meiotic division in Arabidopsis
Authors: Smith Sarah J. , Osman Kim , Franklin F. Christopher H.
Published: July 2014

Meiosis is a specialized cell division essential for sexual reproduction. During meiosis the chromosomes are highly organized, and correct chromosome architecture is required for faithful segregation of chromosomes at anaphase I and II. Condensin is involved in chromosome organization during meiotic and mitotic cell divisions. Three condensin subunits, AtSMC4 and the condensin I and II specific subunits AtCAP‐D2 and AtCAP‐D3, respectively, have been studied for their role in meiosis. This has revealed that both the condensin I and condensin II complexes are required to maintain normal structural integrity of the meiotic chromosomes during the two nuclear divisions. Their roles appear functionally distinct in that condensin I is required to maintain normal compaction of the centromeric repeats and 45S rDNA, whereas loss of condensin II was associated with extensive interchromosome connections at metaphase I. Depletion of condensin is also associated with a slight reduction in crossover formation, suggesting a role during meiotic prophase I.
DIAGNOSTIC SENSITIVITY OF BONE SCINTIGRAPHY FOR EQUINE STIFLE DISORDERS
Authors: Graham Sarah , Solano Mauricio , Sutherland‐Smith James , Sato Amy F , Maranda Louise
Published: July 2014

Disorders of the stifle are a common cause of lameness in horses yet the accuracy of scintigraphy for diagnosis of stifle conditions is controversial. The aim of retrospective cross‐sectional study was to determine the diagnostic sensitivity (Se) of bone scintigraphy in detecting stifle disease and to determine if two orthogonal scintigraphic images improve diagnostic Se. Horses that underwent scintigraphic examination during a two‐year period were included. Horses were divided into two groups: group 1 (N= 23) had lameness that was localized to the stifle by intra‐articular analgesia and group 2 (N= 182) had lameness that was localized to a different location. Scintigraphic studies (one image or two images) were independently and retrospectively analyzed by two radiologists (R1 and R2). Sensitivity, specificity (Sp) and predictive values (PV), and were calculated for each type of study (one image or two images) and for each radiologist (R1 or R2). The Se to detect stifle disorders varied between radiologists (29.2% and 20.8%). The Sp was 84.5% and 88.3%. When two images were evaluated a decrease in the positive PV for both readers occurred. The Cohen kappa coefficient (κ) between readers was poor when one image (0.084) or two images (0.117) were evaluated. Findings from this study indicated that bone‐phase nuclear scintigraphy is reasonably specific but highly insensitive for detecting lameness originating from the stifle in a diverse population of both normal and affected horses. The addition of a caudal scintigraphic image acquisition did not improve diagnostic sensitivity.
DIAGNOSTIC SENSITIVITY OF ULTRASOUND, RADIOGRAPHY AND COMPUTED TOMOGRAPHY FOR GENDER DETERMINATION IN FOUR SPECIES OF LIZARDS
Authors: Di Ianni Francesco , Volta Antonella , Pelizzone Igor , Manfredi Sabrina , Gnudi Giacomo , Parmigiani Enrico
Published: July 2014

Gender determination is frequently requested by reptile breeders, especially for species with poor or absent sexual dimorphism. The aims of the current study were to describe techniques and diagnostic sensitivities of ultrasound, radiography, and computed tomography for gender determination (identification of hemipenes) in four species of lizards. Nineteen lizards of known sex, belonging to four different species (Pogona vitticeps, Uromastyx aegyptia, Tiliqua scincoides, Gerrhosaurus major) were prospectively enrolled. With informed owner consent, ultrasound, noncontrast CT, contrast radiography, and contrast CT (with contrast medium administered into the cloaca) were performed in conscious animals. Imaging studies were reviewed by three different operators, each unaware of the gender of the animals and of the results of the other techniques. The lizard was classified as a male when hemipenes were identified. Nineteen lizards were included in the study, 10 females and nine males. The hemipenes were seen on ultrasound in only two male lizards, and appeared as oval hypoechoic structures. Radiographically, hemipenes filled with contrast medium appeared as spindle‐shaped opacities. Noncontrast CT identified hemipenes in only two lizards, and these appeared as spindle‐shaped kinked structures with hyperattenuating content consistent with smegma. Hemipenes were correctly identified in all nine males using contrast CT (accuracy of 100%). Accuracy of contrast radiography was excellent (94.7%). Accuracy of ultrasound and of noncontrast CT was poor (64.3% and 63.1%, respectively). Findings from the current study supported the use of contrast CT or contrast radiography for gender determination in lizards.
IMAGING DIAGNOSIS—DUODENOBILIARY REFLUX OF BARIUM SULFATE DURING ESOPHAGOGASTROGRAPHY IN A DOG
Authors: Shaikh Layla , Sharma Ajay , Secrest Scott
Published: July 2014

A 4‐year‐old Australian cattle dog presented for regurgitation, 2 months after duodenal resection and anastomosis for a perforated duodenal ulcer. Duodenobiliary reflux of barium sulfate suspension was detected during fluoroscopic esophagogastrography. Follow‐up radiography 2 hours later demonstrated persistence of the barium in the gallbladder and biliary tree. Ultrasonography showed an open sphincter of Oddi but no other morphological abnormalities with the gallbladder or biliary system. No side effects or bloodwork abnormalities were noted. This is the first case report of duodenobiliary reflux of barium in a dog. The pathophysiology of this phenomenon and its incidence and significance in human medicine are discussed.
ZnO/porous-Si and TiO2/porous-Si nanocomposite nanopillars
Authors: Wang Dong , Yan Yong , Schaaf Peter , Sharp Thomas , Schönherr Sven , Ronning Carsten , Ji Ran
Published: July 2014

Porous Si nanopillar arrays are used as templates for atomic layer deposition of ZnO and TiO2, and thus, ZnO/porous-Si and TiO2/porous-Si nanocomposite nanopillars are fabricated. The diffusion of the precursor molecules into the inside of the porous structure occurs via Knudsen diffusion and is strongly limited by the small pore size. The luminescence of the ZnO/porous-Si nanocomposite nanopillars is also investigated, and the optical emission can be changed and even quenched after a strong plasma treatment. Such nanocomposite nanopillars are interesting for photocatalysis and sensors.
Tunable electrical properties of TaNx thin films grown by ionized physical vapor deposition
Authors: Choi Miri , Dubourdieu Catherine , Kellock Andrew J. , Lee Kam Leung , Haight Richard A. , Pyzyna Adam , Frank Martin M. , Demkov Alexander A. , Narayanan Vijay
Published: July 2014

Tantalum nitride (TaNx) amorphous thin films with varying nitrogen content were grown on SiO2/Si using ionized physical vapor deposition. The composition of the films was examined by Rutherford back scattering spectrometry. The carrier density and the resistivity of TaNx films were measured by Hall effect and Van Der Pauw's method. TaNx thin films showed increased electrical resistivity and reduced carrier density as the amount of nitrogen was increased. By controlling the nitrogen content, the carrier density can be tuned within a large range of 1019–1022 cm−3 for 3 and 15 nm thick TaNx films. The metallicity of the films was confirmed using ultraviolet photoemission spectroscopy. For 3 nm thick TaNx films, carrier densities of ∼1021 cm−3 were obtained with the N2 flow rate in the range of 10–15 sccm. Such films have potential application in a quantum metal field effect transistor.
A 3D MR‐acquisition scheme for nonrigid bulk motion correction in simultaneous PET‐MR
Authors: Kolbitsch Christoph , Prieto Claudia , Tsoumpas Charalampos , Schaeffter Tobias
Published: July 2014

Purpose:

Positron emission tomography (PET) is a highly sensitive medical imaging technique commonly used to detect and assess tumor lesions. Magnetic resonance imaging (MRI) provides high resolution anatomical images with different contrasts and a range of additional information important for cancer diagnosis. Recently, simultaneous PET‐MR systems have been released with the promise to provide complementary information from both modalities in a single examination. Due to long scan times, subject nonrigid bulk motion, i.e., changes of the patient's position on the scanner table leading to nonrigid changes of the patient's anatomy, during data acquisition can negatively impair image quality and tracer uptake quantification. A 3D MR‐acquisition scheme is proposed to detect and correct for nonrigid bulk motion in simultaneously acquired PET‐MR data.

Methods:

A respiratory navigated three dimensional (3D) MR‐acquisition with Radial Phase Encoding (RPE) is used to obtain T1‐ and T2‐weighted data with an isotropic resolution of 1.5 mm. Healthy volunteers are asked to move the abdomen two to three times during data acquisition resulting in overall 19 movements at arbitrary time points. The acquisition scheme is used to retrospectively reconstruct dynamic 3D MR images with different temporal resolutions. Nonrigid bulk motion is detected and corrected in this image data. A simultaneous PET acquisition is simulated and the effect of motion correction is assessed on image quality and standardized uptake values (SUV) for lesions with different diameters.

Results:

Six respiratory gated 3D data sets with T1‐ and T2‐weighted contrast have been obtained in healthy volunteers. All bulk motion shifts have successfully been detected and motion fields describing the transformation between the different motion states could be obtained with an accuracy of 1.71 ± 0.29 mm. The PET simulation showed errors of up to 67% in measured SUV due to bulk motion which could be reduced to less than 10% with the proposed motion compensation approach.

Conclusions:

A MR acquisition scheme which yields both high resolution 3D anatomical data and highly accurate nonrigid motion information without an increase in scan time is presented. The proposed method leads to a strong improvement in both MR and PET image quality and ensures an accurate assessment of tracer uptake.
Dose‐to‐water conversion for the backscatter‐shielded EPID: A frame‐based method to correct for EPID energy response to MLC transmitted radiation
Authors: Zwan Benjamin J. , King Brian W. , O'Connor Daryl J. , Greer Peter B.
Published: July 2014

Purpose:

To develop a frame‐by‐frame correction for the energy response of amorphous silicon electronic portal imaging devices (a‐Si EPIDs) to radiation that has transmitted through the multileaf collimator (MLC) and to integrate this correction into the backscatter shielded EPID (BSS‐EPID) dose‐to‐water conversion model.

Methods:

Individual EPID frames were acquired using a Varian frame grabber and iTools acquisition software then processed using in‐house software developed inMATLAB. For each EPID image frame, the region below the MLC leaves was identified and all pixels in this region were multiplied by a factor of 1.3 to correct for the under‐response of the imager to MLC transmitted radiation. The corrected frames were then summed to form a corrected integrated EPID image. This correction was implemented as an initial step in the BSS‐EPID dose‐to‐water conversion model which was then used to compute dose planes in a water phantom for 35 IMRT fields. The calculated dose planes, with and without the proposed MLC transmission correction, were compared to measurements in solid water using a two‐dimensional diode array.

Results:

It was observed that the integration of the MLC transmission correction into the BSS‐EPID dose model improved agreement between modeled and measured dose planes. In particular, the MLC correction produced higher pass rates for almost all Head and Neck fields tested, yielding an average pass rate of 99.8% for 2%/2 mm criteria. A two‐sample independentt‐test and fisher F‐test were used to show that the MLC transmission correction resulted in a statistically significant reduction in the mean and the standard deviation of the gamma values, respectively, to give a more accurate and consistent dose‐to‐water conversion.

Conclusions:

The frame‐by‐frame MLC transmission response correction was shown to improve the accuracy and reduce the variability of the BSS‐EPID dose‐to‐water conversion model. The correction may be applied as a preprocessing step in any pretreatment portal dosimetry calculation and has been shown to be beneficial for highly modulated IMRT fields.
Germination of Aspergillus niger Conidia Is Triggered by Nitrogen Compounds Related to
l
-Amino Acids
Authors: Hayer Kimran , Stratford Malcolm , Archer David B.
Published: July 2014

Conidial germination is fundamentally important to the growth and dissemination of most fungi. It has been previously shown (K. Hayer, M. Stratford, and D. B. Archer, Appl. Environ. Microbiol. 79:6924–6931, 2013,
http://dx.doi.org/10.1128/AEM.02061-13
), using sugar analogs, that germination is a 2-stage process involving triggering of germination and then nutrient uptake for hyphal outgrowth. In the present study, we tested this 2-stage germination process using a series of nitrogen-containing compounds for the ability to trigger the breaking of dormancy of
Aspergillus niger
conidia and then to support the formation of hyphae by acting as nitrogen sources. Triggering and germination were also compared between
A. niger
and
Aspergillus nidulans
using 2-deoxy-
d
-glucose (trigger),
d
-galactose (nontrigger in
A. niger
but trigger in
A. nidulans
), and an N source (required in
A. niger
but not in
A. nidulans
). Although most of the nitrogen compounds studied served as nitrogen sources for growth, only some nitrogen compounds could trigger germination of
A. niger
conidia, and all were related to
l
-amino acids. Using
l
-amino acid analogs without either the amine or the carboxylic acid group revealed that both the amine and carboxylic acid groups were essential for an
l
-amino acid to serve as a trigger molecule. Generally, conidia were able to sense and recognize nitrogen compounds that fitted into a specific size range. There was no evidence of uptake of either triggering or nontriggering compounds over the first 90 min of
A. niger
conidial germination, suggesting that the germination trigger sensors are not located within the spore.
Functional and Structural Responses of Hyporheic Biofilms to Varying Sources of Dissolved Organic Matter
Authors: Wagner Karoline , Bengtsson Mia M. , Besemer Katharina , Sieczko Anna , Burns Nancy R. , Herberg Erik R. , Battin Tom J.
Published: July 2014

Headwater streams are tightly connected with the terrestrial milieu from which they receive deliveries of organic matter, often through the hyporheic zone, the transition between groundwater and streamwater. Dissolved organic matter (DOM) from terrestrial sources (that is, allochthonous) enters the hyporheic zone, where it may mix with DOM from
in situ
production (that is, autochthonous) and where most of the microbial activity takes place. Allochthonous DOM is typically considered resistant to microbial metabolism compared to autochthonous DOM. The composition and functioning of microbial biofilm communities in the hyporheic zone may therefore be controlled by the relative availability of allochthonous and autochthonous DOM, which can have implications for organic matter processing in stream ecosystems. Experimenting with hyporheic biofilms exposed to model allochthonous and autochthonous DOM and using 454 pyrosequencing of the 16S rRNA (targeting the “active” community composition) and of the 16S rRNA gene (targeting the “bulk” community composition), we found that allochthonous DOM may drive shifts in community composition whereas autochthonous DOM seems to affect community composition only transiently. Our results suggest that priority effects based on resource-driven stochasticity shape the community composition in the hyporheic zone. Furthermore, measurements of extracellular enzymatic activities suggest that the additions of allochthonous and autochthonous DOM had no clear effect on the function of the hyporheic biofilms, indicative of functional redundancy. Our findings unravel possible microbial mechanisms that underlie the buffering capacity of the hyporheic zone and that may confer stability to stream ecosystems.
Gammaproteobacterial Methanotrophs Dominate Cold Methane Seeps in Floodplains of West Siberian Rivers
Authors: Oshkin Igor Y. , Wegner Carl-Eric , Lüke Claudia , Glagolev Mikhail V. , Filippov Illiya V. , Pimenov Nikolay V. , Liesack Werner , Dedysh Svetlana N.
Published: July 2014

A complex system of muddy fluid-discharging and methane (CH
4
)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH
4
flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH
4
h
−1
, while some seeps emitted up to 5.54 g CH
4
h
−1
. The δ
13
C value of methane released from these seeps varied between −71.1 and −71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low
in situ
temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH
4
ml
−1
day
−1
) were measured in mud samples. Fluorescence
in situ
hybridization detected 10
7
methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of
pmoA
genes, encoding particulate methane monooxygenase. A total of 53,828
pmoA
gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the
Methylobacter-Methylovulum-Methylosoma
group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH
4
sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies.
A Desaturase Gene Involved in the Formation of 1,14-Nonadecadiene in Synechococcus sp. Strain PCC 7002
Authors: Mendez-Perez Daniel , Herman Nicolaus A. , Pfleger Brian F.
Published: July 2014

The marine cyanobacterium
Synechococcus
sp. strain PCC 7002 synthesizes two alkenes, 1-nonadecene and 1,14-nonadecadiene. Whereas the genetic basis for the biosynthesis of the terminal double bond in both alkenes has been characterized, the origin of the internal double bond in 1,14-nonadecadiene has not. In this study, we demonstrate that a gene encoding an uncharacterized desaturase is involved in the formation of the internal double bond of 1,14-nonadecadiene. Further, at low temperatures, the desaturase gene is essential for growth, and in wild-type cells the levels of 1,14-nonadecadiene increase relative to that of cells grown at 38°C. These data suggest that 1,14-nonadecadiene plays a role in responding to cold stress.
Screening of a Leptospira biflexa Mutant Library To Identify Genes Involved in Ethidium Bromide Tolerance
Authors: Pětrošová Helena , Picardeau Mathieu
Published: July 2014

Leptospira
spp. are spirochete bacteria comprising both pathogenic and free-living species. The saprophyte
L. biflexa
is a model bacterium for studying leptospiral biology due to relative ease of culturing and genetic manipulation. In this study, we constructed a library of 4,996 random transposon mutants in
L. biflexa
. We screened the library for increased susceptibility to the DNA intercalating agent, ethidium bromide (EtBr), in order to identify genetic determinants that reduce
L. biflexa
susceptibility to antimicrobial agents. By phenotypic screening, using subinhibitory EtBr concentrations, we identified 29 genes that, when disrupted via transposon insertion, led to increased sensitivity of the bacteria to EtBr. At the functional level, these genes could be categorized by function as follows: regulation and signaling (
n
= 11), transport (
n
= 6), membrane structure (
n
= 5), stress response (
n
= 2), DNA damage repair (
n
= 1), and other processes (
n
= 3), while 1 gene had no predicted function. Genes involved in transport (including efflux pumps) and regulation (two-component systems, anti-sigma factor antagonists, etc.) were overrepresented, demonstrating that these genes are major contributors to EtBr tolerance. This finding suggests that transport genes which would prevent EtBr to enter the cell cytoplasm are critical for EtBr resistance. We identified genes required for the growth of
L. biflexa
in the presence of sublethal EtBr concentration and characterized their potential as antibiotic resistance determinants. This study will help to delineate mechanisms of adaptation to toxic compounds, as well as potential mechanisms of antibiotic resistance development in pathogenic
L. interrogans
.
Microbial Community Stratification Controlled by the Subseafloor Fluid Flow and Geothermal Gradient at the Iheya North Hydrothermal Field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331)
Authors: Yanagawa Katsunori , Breuker Anja , Schippers Axel , Nishizawa Manabu , Ijiri Akira , Hirai Miho , Takaki Yoshihiro , Sunamura Michinari , Urabe Tetsuro , Nunoura Takuro , Takai Ken
Published: July 2014

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the
Chloroflexi
and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I
Thaumarchaeota
dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments.
FLP-FRT-Based Method To Obtain Unmarked Deletions of
CHU
_
3237
(
porU
) and Large Genomic Fragments of Cytophaga hutchinsonii
Authors: Wang Ying , Wang Zhiquan , Cao Jing , Guan Zhiwei , Lu Xuemei
Published: July 2014

Cytophaga hutchinsonii
is a widely distributed cellulolytic bacterium in the phylum
Bacteroidetes
. It can digest crystalline cellulose rapidly without free cellulases or cellulosomes. The mechanism of its cellulose utilization remains a mystery. We developed an efficient method based on a linear DNA double-crossover and FLP-FRT recombination system to obtain unmarked deletions of both single genes and large genomic fragments in
C. hutchinsonii
. Unmarked deletion of
CHU
_
3237
(
porU
), an ortholog of the C-terminal signal peptidase of a type IX secretion system (T9SS), resulted in defects in colony spreading, cellulose degradation, and protein secretion, indicating that it is a component of the T9SS and that T9SS plays an important role in cellulose degradation by
C. hutchinsonii
. Furthermore, deletions of four large genomic fragments were obtained using our method, and the sizes of the excised fragments varied from 9 to 19 kb, spanning from 6 to 22 genes. The customized FLP-FRT method provides an efficient tool for more rapid progress in the cellulose degradation mechanism and other physiological aspects of
C. hutchinsonii
.
Biofilm Formation on Biotic and Abiotic Surfaces in the Presence of Antimicrobials by Escherichia coli Isolates from Cases of Bovine Mastitis
Authors: Silva Vitor O. , Soares Larissa O. , Silva Júnior Abelardo , Mantovani Hilário C. , Chang Yung-Fu , Moreira Maria Aparecida S.
Published: July 2014

Escherichia coli
is a highly adaptive microorganism, and its ability to form biofilms under certain conditions can be critical for antimicrobial resistance. The adhesion of four
E. coli
isolates from bovine mastitis to bovine mammary alveolar (MAC-T) cells, biofilm production on a polystyrene surface, and the expression profiles of the genes
fliC
,
csgA
,
fimA
, and
luxS
in the presence of enrofloxacin, gentamicin, co-trimoxazole, and ampicillin at half of the MIC were investigated. Increased adhesion of
E. coli
isolates in the presence of antimicrobials was not observed; however, increased internalization of some isolates was observed by confocal microscopy. All of the antimicrobials induced the formation of biofilms by at least one isolate, whereas enrofloxacin and co-trimoxazole decreased biofilm formation by at least one isolate. Quantitative PCR analysis revealed that all four genes were differentially expressed when bacteria were exposed to subinhibitory concentrations of antimicrobials, with expression altered on the order of 1.5- to 22-fold. However, it was not possible to associate gene expression with induction or reduction of biofilm formation in the presence of the antimicrobials. Taken together, the results demonstrate that antimicrobials could induce biofilm formation by some isolates, in addition to inducing MAC-T cell invasion, a situation that might occur
in vivo
, potentially resulting in a bacterial reservoir in the udder, which might explain some cases of persistent mastitis in herds.
“Candidatus Liberibacter asiaticus” Prophage Late Genes May Limit Host Range and Culturability
Authors: Fleites Laura A. , Jain Mukesh , Zhang Shujian , Gabriel Dean W.
Published: July 2014

“
Candidatus
Liberibacter asiaticus” is an uncultured alphaproteobacterium that systemically colonizes its insect host both inter- and intracellularly and also causes a severe, crop-destroying disease of citrus called huanglongbing, or citrus “greening.”
In planta
, “
Ca
. Liberibacter asiaticus” is also systemic but phloem limited. “
Ca
. Liberibacter asiaticus” strain UF506 carries two predicted prophages, SC1 and SC2. Bacteriophage particles have been observed in experimentally “
Ca
. Liberibacter asiaticus”-infected periwinkle but not in any other host. Comparative gene expression analysis of predicted SC1 late genes showed a much higher level of late gene expression, including holin transcripts (SC1_gp110), in “
Ca
. Liberibacter asiaticus”-infected periwinkle relative to “
Ca
. Liberibacter asiaticus”-infected citrus. To functionally characterize predicted holin and endolysin activity, SC1_gp110 and two predicted endolysins, one within SC1 (SC1_gp035) and another well outside the predicted prophage region (CLIBASIA_04790), were cloned and expressed in
Escherichia coli
. Both SC1 genes inhibited bacterial growth consistent with holin and endolysin function. The holin (SC1_gp110) promoter region was fused with a
uidA
reporter on pUFR071, a wide bacterial host range (repW) replicon, and used to transform
Liberibacter crescens
strain BT-1 by electroporation. BT-1 is the only liberibacter strain cultured to date and was used as a proxy for “
Ca
. Liberibacter asiaticus.” pUFR071 was >95% stable without selection in BT-1 for over 20 generations. The reporter construct exhibited strong constitutive glucuronidase (GUS) activity in culture-grown BT-1 cells. However, GUS reporter activity in BT-1 was suppressed in a dose-dependent manner by crude aqueous extracts from psyllids. Taken together with plant expression data, these observations indicate that “
Ca
. Liberibacter asiaticus” prophage activation may limit “
Ca
. Liberibacter asiaticus” host range and culturability.
Genomic Characterization and Transcriptional Studies of the Starch-Utilizing Strain Bifidobacterium adolescentis 22L
Authors: Duranti Sabrina , Turroni Francesca , Lugli Gabriele Andrea , Milani Christian , Viappiani Alice , Mangifesta Marta , Gioiosa Laura , Palanza Paola , van Sinderen Douwe , Ventura Marco
Published: July 2014

Bifidobacteria are members of the gut microbiota, but the genetic basis for their adaptation to the human gut is poorly understood. The analysis of the 2,203,222-bp genome of
Bifidobacterium adolescentis
22L revealed a nutrient acquisition strategy that targets diet/plant-derived glycans, in particular starch and starch-like carbohydrates. Starch-like carbohydrates were shown to support the growth of
B. adolescentis
22L. Transcriptome profiling of 22L cultures grown under
in vitro
conditions or during colonization of the murine gut by RNA sequencing and quantitative real-time PCR assays revealed the expression of a set of chromosomal loci responsible for starch metabolism as well as for pilus production. Such extracellular structures include so-called sortase-dependent and type IVb pili, which may be involved in gut colonization of 22L through adhesion to extracellular matrix proteins.
Effects of High Hydrostatic Pressure on Coastal Bacterial Community Abundance and Diversity
Authors: Marietou Angeliki , Bartlett Douglas H.
Published: July 2014

Hydrostatic pressure is an important parameter influencing the distribution of microbial life in the ocean. In this study, the response of marine bacterial populations from surface waters to pressures representative of those under deep-sea conditions was examined. Southern California coastal seawater collected 5 m below the sea surface was incubated in microcosms, using a range of temperatures (16 to 3°C) and hydrostatic pressure conditions (0.1 to 80 MPa). Cell abundance decreased in response to pressure, while diversity increased. The morphology of the community also changed with pressurization to a predominant morphotype of small cocci. The pressure-induced community changes included an increase in the relative abundance of
Alphaproteobacteria
,
Gammaproteobacteria
,
Actinobacteria
, and
Flavobacteria
largely at the expense of
Epsilonproteobacteria
. Culturable high-pressure-surviving bacteria were obtained and found to be phylogenetically similar to isolates from cold and/or deep-sea environments. These results provide novel insights into the response of surface water bacteria to changes in hydrostatic pressure.
Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit
Authors: Mansfeldt Cresten B. , Rowe Annette R. , Heavner Gretchen L. W. , Zinder Stephen H. , Richardson Ruth E.
Published: July 2014

A cDNA-microarray was designed and used to monitor the transcriptomic profile of
Dehalococcoides mccartyi
strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6 ± 0.6 μM Cl
−
/h)- and fast (22.9 ± 9.6 μM Cl
−
/h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (
n
= 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all
Dehalococcoides
strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112).
Dynamics of Mitochondrial RNA-Binding Protein Complex in Trypanosoma brucei and Its Petite Mutant under Optimized Immobilization Conditions
Authors: Huang Zhenqiu , Kaltenbrunner Sabine , Šimková Eva , Stanĕk David , Lukeš Julius , Hashimi Hassan
Published: July 2014

There are a variety of complex metabolic processes ongoing simultaneously in the single, large mitochondrion of
Trypanosoma brucei
. Understanding the organellar environment and dynamics of mitochondrial proteins requires quantitative measurement
in vivo
. In this study, we have validated a method for immobilizing both procyclic stage (PS) and bloodstream stage (BS)
T. brucei brucei
with a high level of cell viability over several hours and verified its suitability for undertaking fluorescence recovery after photobleaching (FRAP), with mitochondrion-targeted yellow fluorescent protein (YFP). Next, we used this method for comparative analysis of the translational diffusion of mitochondrial RNA-binding protein 1 (MRP1) in the BS and in
T. b. evansi
. The latter flagellate is like petite mutant
Saccharomyces cerevisiae
because it lacks organelle-encoded nucleic acids. FRAP measurement of YFP-tagged MRP1 in both cell lines illuminated from a new perspective how the absence or presence of RNA affects proteins involved in mitochondrial RNA metabolism. This work represents the first attempt to examine this process in live trypanosomes.