bluuebunny/crossref_metadata_2025 huggingface dataset:
Weight Suppression in Bulimia Nervosa: Relationship with Cognitive Behavioral Therapy Outcome
Authors: Dawkins Hayley , Watson Hunna J. , Egan Sarah J. , Kane Robert T.
Published: April 2013

Objective

In light of prior inconsistent findings, this study revisits the relationship between weight suppression and treatment outcome in bulimia nervosa. Aside from differences in methodology, we propose that moderator effects may assist the field in interpreting previous inconsistency. In this study, we considered moderators that might place individuals at risk of broad cognitive and biobehavioral mechanisms implicated in weight (dys)regulation and binge eating, and that within the context of a history of weight suppression, might be associated with especially poor outcomes.

Method

Participants were 117 female outpatients aged 16–54 years (M = 25.5) with bulimic disorders treated with enhanced cognitive behavioral therapy.

Results

Logistic regression indicated that higher pretreatment weight suppression did not predict drop‐out or poor treatment outcome (nonabstinence from binging and purging). Moderators of parental history of overweight, childhood body shape, pretreatment body mass index, and the difference between highest and lowest ever adult body weight were analyzed, but no moderator effects were apparent.

Discussion

This study, along with other negative studies, calls into question the association between weight suppression and treatment outcome. We maintain that moderators may account for inconsistencies, but no candidates were identified in this study. Moderator models could assist us to refine conceptualizations of why some patients high in weight suppression may be vulnerable to poor treatment adherence and outcome and to establish clinical interventions that enhance prognosis. © 2013 Wiley Periodicals, Inc. (Int J Eat Disord 2013; 46:586–593)
A Littoral Fauna Index for assessing the impact of lakeshore alterations in Alpine lakes
Authors: Urbanič Gorazd
Published: April 2013

Lakeshore deterioration is a major threat to the ecological integrity of lakes worldwide. In this study, the relationship between littoral benthic invertebrates and the Lakeshore Modification Index (LMI) was examined. The influence of the taxonomic resolution on littoral benthic invertebrate community response to LMI was assessed using the results of the canonical correspondence analysis and the relationship between the taxa richness, Shannon–Wiener diversity index and the LMI. Benthic invertebrates were sampled in summer between 2006 and 2011 in two natural and two artificial Alpine lakes using a littoral microhabitat type sampling scheme. Ordination analyses show a similar explanation power when the lowest available taxonomic level was used in comparison with the family level. Taxa richness and the Shannon–Wiener diversity index indicate that lakeshore modifications impair littoral biological conditions with a loss of richness and diversity independently of lake type and used taxonomic level. For 64 families, a lakeshore modification indicative value between one and nine were set on the basis of distribution among five lakeshore modification classes. A Littoral Fauna Index (LFI) was then derived by summation of the lakeshore modification indicative values recorded at each site. A validation dataset from natural and artificial lakes confirmed the good relationships between LMI and LFI but revealed some differences in the relationships. The results show that the impacts of lakeshore modifications can be assessed using littoral benthic invertebrate assemblages with a family‐level‐based LFI, which makes this method cost effective and appropriate for routine monitoring. Copyright © 2013 John Wiley & Sons, Ltd.
EMIC waves growth and guiding in the presence of cold plasma density irregularities
Authors: de Soria‐Santacruz M. , Spasojevic M. , Chen L.
Published: April 2013

Intense electromagnetic ion cyclotron (EMIC) waves are observed within plasmaspheric plumes during geomagnetic storms and are believed to be a significant driver of loss of both ring current protons and radiation belt electrons. In this study, we use ray tracing together with path‐integrated linear growth calculations to analyze the amplification and propagation of EMIC waves within cold plasma density irregularities characteristic of the plasmaspheric plume. All waves are launched at the equator in the range of L = 5 to 7, and wave amplification is analyzed as a function of frequency and initial wave normal angle. These results are compared to a baseline case without irregularities, which show that guiding is possible for irregularity sizes on the order of the EMIC wavelength. Results suggest that typical structures with density levels above and below the average value can result in both areas of increased as well as suppressed wave activity.
Surf zone flushing on embayed beaches
Authors: Castelle Bruno , Coco Giovanni
Published: April 2013

Using a numerical model, we show that the surf zone of embayed beaches systematically flushes out more floating material (simulated using passive tracers) than on open beaches, with most exits occurring through the headland rips. For obliquely incident waves, a headland rip acts as a persistent conduit for transporting floating material out of the surf zone and into the inner shelf region. Wave angle and embayment size determine which headland rip (upwave or downwave) flushes out more the surf zone material. For narrow embayed beaches, passive drifters exit the surf zone through the upwave headland rip. For wider embayed beaches, the longshore current has enough room to develop and is further deflected against the downwave headland where most drifters exit the surf zone. Our results indicate that wave‐exposed rugged coasts strongly enhance exchange of floating matter (e.g., pollutants and nutrients) at the ocean/continent interface.
Uncertainty of snow water equivalent retrieved from AMSR‐E brightness temperature in northeast Asia
Authors: Byun Kyuhyun , Choi Minha
Published: April 2013

Accurate estimation of snow water equivalent (SWE) has been significantly recognized to improve management and analyses of water resource in specific regions. Although several studies have focused on developing SWE values based on remotely sensed brightness temperatures obtained by microwave sensor systems, it is known that there are still a number of uncertainties in SWE values retrieved from microwave radiometers. Therefore, further research for improving remotely sensed SWE values including global validation should be conducted in unexplored regions such as Northeast Asia. In this regard, we evaluated SWE through comparison of values produced by the Advanced Microwave Scanning Radiometer Earth Observing System (AMSR‐E) from December 2002 to February 2011 with in situ SWE values converted from snow‐depth observation data from four regions in the South Korea. The results from three areas showed similarities which indicated that the AMSR‐E SWE values were overestimated when compared with in situ SWE values, and their Mean Absolute Errors (MAE) by month were relatively small (1.1 to 6.5 mm). Contrariwise, the AMSR‐E SWE values of one area were significantly underestimated when compared with in situ SWE values and the MAE were much greater (4.9 to 35.2 mm). These results were closely related to AMSR‐E algorithm‐related error sources, which we analyzed with respect to topographic characteristics and snow properties. In particular, we found that snow density data used in the AMSR‐E SWE algorithm should be based on reliable in situ data as the current AMSR‐E SWE algorithm cannot reflect the spatio‐temporal variability of snow density values. Additionally, we derived better results considering saturation effect of AMSR‐E SWE. Despite the demise of AMSR‐E, this study's analysis is significant for providing a baseline for the new sensor and suggests parameters important for obtaining more reliable SWE. Copyright © 2013 John Wiley & Sons, Ltd.
The importance of the tropical tropopause layer for equatorial Kelvin wave propagation
Authors: Flannaghan T. J. , Fueglistaler S.
Published: April 2013

We analyze the propagation of equatorial Kelvin waves from the troposphere to the stratosphere using a new filtering technique applied to ERA‐Interim data (very similar results for Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) temperatures) that allows separation of wave activity into number of waves and wave amplitude. The phase speed of Kelvin waves (order 20 m/s) is similar to the magnitude of zonal wind in the tropical tropopause layer (TTL), and correspondingly, we find that the seasonal and interannual variability of Kelvin wave propagation is dominated by the variability in the wind field and less by tropospheric convectively coupled wave activity. We show that local relations between wave activity and zonal wind are ambiguous, and only full ray tracing calculations can explain the observed patterns of wave activity. Easterlies amplify and deflect the eastward traveling waves upward. Westerlies have the opposite effect. During boreal winter, the strong dipole of zonal winds in the TTL centered at the dateline confines wave propagation into the stratosphere to a window over the Atlantic‐Indian Ocean sector (30°W to 90°E), which casts a lasting “shadow” into the lower stratosphere that explains the remarkable zonal asymmetry in wave activity there. During boreal summer, the upper level monsoon circulation leads to maximum easterlies, and wave amplitude (but not number of waves) maximizes over the Indian Ocean sector (30°E to 90°E). Interannual variability in wave propagation due to El‐Niño/Southern Oscillation, for example, is well explained by its modification of the zonal wind field.
Effects of matrix elasticity and cell density on human mesenchymal stem cells differentiation
Authors: Xue Ruyue , Li Julie Yi‐Shuan , Yeh Yiting , Yang Li , Chien Shu
Published: April 2013

Human mesenchymal stem cells (hMSCs) can differentiate into various cell types, including osteogenic and chondrogenic cells. The matrix elasticity and cell seeding density are important factors in hMSCs differentiation. We cultured hMSCs at different seeding densities on polyacrylamide hydrogels with different stiffness corresponding to Young's moduli of 1.6 ± 0.3 and 40 ± 3.6 kPa. The promotion of osteogenic marker expression by hard gel is overridden by a high seeding density. Cell seeding density, however, did not influence the chondrogenic marker expressions induced by soft gel. These findings suggest that interplays between cell–matrix and cell–cell interactions contribute to hMSCs differentiation. The promotion of osteogenic differentiation on hard matrix was shown to be mediated through the Ras pathway. Inhibition of Ras (RasN17) significantly decreased ERK, Smad1/5/8 and AKT activation, and osteogenic markers expression. However, constitutively active Ras (RasV12) had little effect on osteogenic marker expression, suggesting that the Ras pathways are necessary but not sufficient for osteogenesis. Taken together, our results indicate that matrix elasticity and cell density are important microenvironmental cues driving hMSCs proliferation and differentiation. © 2013 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 31:1360–1365, 2013
Proteomic and cytokine plasma biomarkers for predicting progression from colorectal adenoma to carcinoma in human patients
Authors: Choi Jung‐Won , Liu Hao , Shin Dong Hoon , Yu Gyeong Im , Hwang Jae Seok , Kim Eun Soo , Yun Jong Won
Published: April 2013

In the present study, we screened proteomic and cytokine biomarkers between patients with adenomatous polyps and colorectal cancer (CRC) in order to improve our understanding of the molecular mechanisms behind turmorigenesis and tumor progression in CRC. To this end, we performed comparative proteomic analysis of plasma proteins using a combination of 2DE and MS as well as profiled differentially regulated cytokines and chemokines by multiplex bead analysis. Proteomic analysis identified 11 upregulated and 13 downregulated plasma proteins showing significantly different regulation patterns with diagnostic potential for predicting progression from adenoma to carcinoma. Some of these proteins have not previously been implicated in CRC, including upregulated leucine‐rich α‐2‐glycoprotein, hemoglobin subunit β, Ig α‐2 chain C region, and complement factor B as well as downregulated afamin, zinc‐α‐2‐glycoprotein, vitronectin, and α‐1‐antichymotrypsin. In addition, plasma levels of three cytokines/chemokines, including interleukin‐8, interferon gamma‐induced protein 10, and tumor necrosis factor α, were remarkably elevated in patients with CRC compared to those with adenomatous polyps. Although further clinical validation is required, these proteins and cytokines can be established as novel biomarkers for CRC and/or its progression from colon adenoma.
A general synthetic method toward uridylylated picornavirus VPg proteins
Authors: van der Heden van Noort Gerbrand J. , Schein Catherine H. , Overkleeft Herman S. , van der Marel Gijsbert A. , Filippov Dmitri V.
Published: April 2013

Small proteins called viral protein genome‐linked (VPg), attached to the 5′‐end of the viral RNA genome are found as common structure in the large family of picornaviruses. The replication of these viruses is primed by this VPg protein linked to a single uridylyl residue. We report a general procedure to obtain such nucleoproteins employing a pre‐uridylylated tyrosine building block in an on‐line solid phase‐based approach. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Real-time monitoring of cell viability and cell density on the basis of a three dimensional optical reflectance method (3D-ORM): investigation of the effect of sub-lethal and lethal injuries
Authors: Brognaux Alison , Bugge Jörg , Schwartz Friedel H , Thonart Philippe , Telek Samuel , Delvigne Frank
Published: April 2013

Cell density and cell viability have been followed on-line by using a three-dimensional optical reflectance method (3D-ORM) probe. This method has allowed to highlight the differences between a well-mixed and a scale-down bioreactor configured in order to reproduce mixing deficiencies during a fed-batch culture of Escherichia coli. These differences have been observed both for the obscuration factor (OBF) and the coincidence probability delivered by the probe. These parameters are correlated to flow cytometry measurement based on the PI-uptake test and cell density based on optical density measurement. This first set of results has pointed out the fact that the 3D-ORM probe is sensitive to sub-lethal injuries encountered by microbial cells in process-related conditions. The effect of lethal injuries has been further investigated on the basis of additional experiments involving heat stress and a sharp increase of the OBF has been observed indicating that cells are effectively injured by the increase of temperature. However, further improvement of the probe are needed in order to give access to single-cell measurements.
A Review of Genetic Counseling for Charcot Marie Tooth Disease (CMT)
Authors: Siskind Carly E. , Panchal Seema , Smith Corrine O. , Feely Shawna M. E. , Dalton Joline C. , Schindler Alice B. , Krajewski Karen M.
Published: April 2013

Charcot Marie Tooth disease (CMT) encompasses the inherited peripheral neuropathies. While four genes have been found to cause over 90 % of genetically identifiable causes of CMT (PMP22, GJB1, MPZ, MFN2), at least 51 genes and loci have been found to cause CMT when mutated, creating difficulties for clinicians to find a genetic subtype for families. Here, the classic features of CMT as well as characteristic features of the most common subtypes of CMT are described, as well as methods for narrowing down the possible subtypes. Psychosocial concerns particular to the CMT population are identified. This is the most inclusive publication for CMT‐specific genetic counseling.
“Nothing is Absolute in Life”: Understanding Uncertainty in the Context of Psychiatric Genetic Counseling from the Perspective of those with Serious Mental Illness
Authors: Hippman Catriona , Lohn Zoe , Ringrose Andrea , Inglis Angela , Cheek Joanna , Austin Jehannine C
Published: April 2013

No genetic tests are currently clinically available for serious mental illnesses such as schizophrenia and bipolar disorder. Rather, the full spectrum of genetic variants that confer susceptibility remain unknown, and estimates of probability of condition recurrence typically have the form of ranges rather than single absolute numbers. Genetic counselors have been shown to feel that the information that can be provided for patients with serious mental illness could be more confusing than helpful. However, how those with serious mental illness perceive this uncertainty remains unknown. So, to investigate this, individuals with serious mental illness participated in a psychiatric genetic counseling (GC) session and responded to a single open ended question about their reactions towards the uncertainty that they encountered in their GC session immediately and one month post‐counseling (from which themes were identified), and completed the Genetic Counseling Satisfaction Scale immediately post‐session (descriptive statistics applied). While some of the 37 participants were disappointed with the uncertainty, twice as many were unconcerned. Overall, responses from immediately and one month after GC were very similar; participants were very satisfied with, and found value in GC despite uncertainty, and four approaches to coping with uncertainty emerged. Ultimately, these findings offer insight into providing GC for those with serious mental illness, and potentially could be applied to other areas of GC where uncertainty lies, with downstream impact on GC practice and future research.
A Rapid Method for Determining the Oxidative Stability of Oils Suitable for Breeder Size Samples
Authors: Przybylski R. , Wu J. , Eskin N. A. M.
Published: April 2013

A method utilizing thin‐layer chromatography with a flame ionization detector (TLC‐FID) was developed for assessing the stability of breeder's oil seed samples based on the formation of polar compounds. The results showed a linear relationship between peroxide value (PV) and the content of polar material in the oxidized oil. Oil samples oxidized very readily on chromarods, even at low temperature, which is a particular advantage for antioxidant screening. At 45 °C, the oil oxidation rate was relatively low, but the relationship between the content of polar material and reaction time was linear. At 65 °C, if the content of polar material was below 50 %, the above relationship was still linear. At different temperatures, the action of tocopherol appeared to vary slightly. For example, at 65 °C, the oxidative stability of the oil sample was determined by the content of tocopherol, especially γ‐tocopherol. At 45 and 55 °C, the oxidative stability was determined by both the content of tocopherol and polyunsaturated fatty acids. Of the tocopherol isomers, γ‐tocopherol exhibited the highest antioxidant potency, consistent with the published literature. These results suggest that chromarods provide good media for monitoring oil oxidation for antioxidant screening. A particular advantage is the use of very small oil samples, usually 1–2 μL, and the ability to analyze multiple samples at the same time.
Strategies for Reducing Radiation Exposure from Multidetector Computed Tomography in the Acute Care Setting
Authors: Sodickson Aaron
Published: April 2013

Many tools and strategies exist to enable reduction of radiation exposure from computed tomography (CT). The common CT metrics of x-ray output, the volume CT dose index and the dose-length product, are explained and serve as the basis for monitoring radiation exposure from CT. Many strategies to dose-optimize CT protocols are explored that, in combination with available hardware and software tools, allow robust diagnostic quality CT to be performed with a radiation exposure appropriate for the clinical scenario and the size of the patient. Specific emergency department example protocols are used to demonstrate these techniques.
Effects of commercial citrate‐containing juices on urolithiasis in a Drosophila model
Authors: Ho Chien‐Yi , Chen Yung‐Hsiang , Wu Pei‐Yin , Chang Chiao‐Hui , Chen Huey‐Yi , Man Kee‐Ming , Shen Jui‐Lung , Tsai Fuu‐Jen , Lin Wei‐Yong , Lee Yuan‐Ju , Chen Wen‐Chi
Published: April 2013

Diet modification plays an important role in nephrolithiasis. Development of an easy, ready‐to‐use beverage such as a commercial juice drink to use as a preventive treatment for renal calculi formation would be widely welcomed. We previously developed a novel Drosophila model for the study of nephrolithiasis. It provides a new well‐established drug discovery platform for this common disease. In our current study, we used the Drosophila model to investigate the preventive effects of various commercial juices as potential treatments for nephrolithiasis. Our results showed that apple, cranberry, orange, and pomegranate juices failed to reduce calcium oxalate (CaOx) crystal formation, whereas our positive control—potassium citrate (K‐citrate)—significantly prevented CaOx crystal formation. Unlike the commercial fruit juices that were tested, the administration of K‐citrate significantly ameliorated the ethylene glycol (EG)‐induced life‐span reduction in treated flies. These results indicate that EG‐induced CaOx nephrolithiasis in Drosophila can be prevented by K‐citrate, but not by commercial citrate‐containing juices. However, the inhibitory capability of citrate‐containing juices to reduce renal stone formation in humans requires further elucidation.
Position effect on
FGF13
associated with X-linked congenital generalized hypertrichosis
Authors: DeStefano Gina M. , Fantauzzo Katherine A. , Petukhova Lynn , Kurban Mazen , Tadin-Strapps Marija , Levy Brynn , Warburton Dorothy , Cirulli Elizabeth T. , Han Yujun , Sun Xiaoyun , Shen Yufeng , Shirazi Maryam , Jobanputra Vaidehi , Cepeda-Valdes Rodrigo , Cesar Salas-Alanis Julio , Christiano Angela M.
Published: April 2013

X-linked congenital generalized hypertrichosis (Online Mendelian Inheritance in Man 307150) is an extremely rare condition of hair overgrowth on different body sites. We previously reported linkage in a large Mexican family with X-linked congenital generalized hypertrichosis cosegregating with deafness and with dental and palate anomalies to Xq24-27. Using SNP oligonucleotide microarray analysis and whole-genome sequencing, we identified a 389-kb interchromosomal insertion at an extragenic palindrome site at Xq27.1 that completely cosegregates with the disease. Among the genes surrounding the insertion, we found that Fibroblast Growth Factor 13 (
FGF13
) mRNA levels were significantly reduced in affected individuals, and immunofluorescence staining revealed a striking decrease in FGF13 localization throughout the outer root sheath of affected hair follicles. Taken together, our findings suggest a role for FGF13 in hair follicle growth and in the hair cycle.
Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry
Authors: Hu Wenbing , Walters Benjamin T. , Kan Zhong-Yuan , Mayne Leland , Rosen Laura E. , Marqusee Susan , Englander S. Walter
Published: April 2013

The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry technology. The results show that folding proceeds through distinct intermediates in a stepwise pathway that sequentially incorporates cooperative native-like structural elements to build the native protein. Each step is seen as a concerted transition of one or more segments from an HX-unprotected to an HX-protected state. Deconvolution of the data to near amino acid resolution shows that each step corresponds to the folding of a secondary structural element of the native protein, termed a “foldon.” Each folded segment is retained through subsequent steps of foldon addition, revealing a stepwise buildup of the native structure via a single dominant pathway. Analysis of the pertinent literature suggests that this model is consistent with experimental results for many proteins and some current theoretical results. Two biophysical principles appear to dictate this behavior. The principle of cooperativity determines the central role of native-like foldon units. An interaction principle termed “sequential stabilization” based on native-like interfoldon interactions orders the pathway.
PhenoMiner: quantitative phenotype curation at the rat genome database
Authors: Laulederkind Stanley J F , Liu Weisong , Smith Jennifer R , Hayman G Thomas , Wang Shur-Jen , Nigam Rajni , Petri Victoria , Lowry Timothy F , de Pons Jeff , Dwinell Melinda R , Shimoyama Mary
Published: April 2013

The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses >40 000 rat gene records as well as human and mouse orthologs, >2000 rat and 1900 human quantitative trait loci (QTLs) records and >2900 rat strain records. Biological information curated for these data objects includes disease associations, phenotypes, pathways, molecular functions, biological processes and cellular components. Recently, a project was initiated at RGD to incorporate quantitative phenotype data for rat strains, in addition to the currently existing qualitative phenotype data for rat strains, QTLs and genes. A specialized curation tool was designed to generate manual annotations with up to six different ontologies/vocabularies used simultaneously to describe a single experimental value from the literature. Concurrently, three of those ontologies needed extensive addition of new terms to move the curation forward. The curation interface development, as well as ontology development, was an ongoing process during the early stages of the PhenoMiner curation project.

Database URL: http://rgd.mcw.edu
Evolution of neutron star + He star binaries: an alternative evolutionary channel to intermediate-mass binary pulsars
Authors: Chen Wen-Cong , Liu Wei-Min
Published: April 2013

It is difficult for intermediate-mass X-ray binaries to form compact intermediate-mass binary pulsars (IMBPs) with a short orbital-period ( ≲ 3 d), which have heavy ( ≳ 0.4 M⊙) CO or ONeMg white dwarf (WD) companions. Since neutron star + He star binaries may experience common-envelope evolution, they have some advantage to account for the formation of short orbital-period IMBPs. In this work, we explore the probability of IMBPs formed by this evolutionary channel. Using Eggleton's stellar evolution code, considering that the dead pulsars were spun up by the accreting material and angular momentum from the He star companions, we have calculated the evolution of a large number of neutron star + He star binaries. Our simulated results indicate that the NS + He star evolutionary channel can produce IMBPs with a WD of ∼ 0.5-1.1 M⊙ and an orbital period of 0.03–20 d, in which pulsars have a spin period of 1.4–200 ms. Comparing the calculated results with the observational parameters (spin period and orbital period) of nine compact IMBPs, the NS + He star evolutionary channel can account for the formation of four sources. Therefore, NS + He star binaries offer an alternative evolutionary channel to compact IMBPs.
The star formation rate and stellar mass limits for submillimetre galaxies implied by recent interferometric observations
Authors: Hayward Christopher C.
Published: April 2013

Explaining the observed number counts of submillimetre (submm) galaxies (SMGs) has been a longstanding challenge for theoretical models. Surprisingly, recent observations have suggested that the brightest SMGs are almost exclusively multiple fainter sources blended into a single source in the single-dish surveys. This result is in contrast with the predictions of our previously presented theoretical model, which includes some effects of blending. In this Letter, we consider the implications of an upper limit on the submm flux density for the demographics of the SMG population. Using a relation amongst submm flux, star formation rate (SFR) and dust mass (Md) from our previous work, we infer the maximum SFR for a range of flux density limits. For Md = 2 × 109(5 × 108) M⊙, the SFR limit that corresponds to an 870-μm flux density (S870) limit in the range 9–12.5 mJy is in the range $\sim 630\hbox{--}1400 (3600\hbox{--}7700)\, \mathrm{M_{{\odot }}\,{\rm yr}^{-1}}$. The SFR limit implies a correspondingly sharp, redshift-dependent cutoff in the stellar mass (M⋆) function, the value of which we predict using the S870–M⋆ relation predicted by our model. The M⋆ limit decreases with increasing redshift: for an S870 limit of 9–12.5 mJy, the M⋆ limit ranges from ∼4–7 × 1012 M⊙ at z ∼ 1 to ∼3–5 × 1011 M⊙ at z ∼ 6. We discuss the few interferometrically detected SMGs that may be brighter than the proposed cutoff. Although such objects are certainly interesting, inferences based on such objects may not apply to most SMGs.
Alicyclobacillus

consociatus sp. nov., isolated from a human clinical specimen
Authors: Glaeser Stefanie P. , Falsen Enevold , Martin Karin , Kämpfer Peter
Published: April 2013

A Gram-stain-positive, aerobic organism, isolated from a blood sample from a 51-year-old woman, was studied for its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain CCUG 53762T was grouped into the genus

Alicyclobacillus

, most closely related to the type strain of

Alicyclobacillus pohliae

(94.7 %). The 16S rRNA gene sequence similarity to other species of the genus

Alicyclobacillus

was ≤91 % and similarity to species of the genus

Tumebacillus

was 91.3–93 %. The occurrence of menaquinone MK-7 as the major respiratory quinone, meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall and the fatty acid profile supported the allocation of the strain to the genus

Alicyclobacillus

. Major fatty acids were iso- and anteiso-branched fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The absence of the iso-branched fatty acids iso-C16 : 0 and iso-C17 : 0 allowed differentiation of strain CCUG 53762T from

A. pohliae

CIP 109385T. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain CCUG 53762T from this most closely related species. The G+C content of the DNA was 47 mol%. Strain CCUG 53762T therefore represents a novel species of the genus

Alicyclobacillus

, for which we propose the name

Alicyclobacillus

consociatus sp. nov., with CCUG 53762T ( = CCM 8439T) as the type strain.
Genomes of the class

Erysipelotrichia

clarify the firmicute origin of the class

Mollicutes
Authors: Davis James J. , Xia Fangfang , Overbeek Ross A. , Olsen Gary J.
Published: April 2013

The tree of life is paramount for achieving an integrated understanding of microbial evolution and the relationships between physiology, genealogy and genomics. It provides the framework for interpreting environmental sequence data, whether applied to microbial ecology or to human health. However, there remain many instances where there is ambiguity in our understanding of the phylogeny of major lineages, and/or confounding nomenclature. Here we apply recent genomic sequence data to examine the evolutionary history of members of the classes

Mollicutes

(phylum

Tenericutes

) and

Erysipelotrichia

(phylum

Firmicutes

). Consistent with previous analyses, we find evidence of a specific relationship between them in molecular phylogenies and signatures of the 16S rRNA, 23S rRNA, ribosomal proteins and aminoacyl-tRNA synthetase proteins. Furthermore, by mapping functions over the phylogenetic tree we find that the erysipelotrichia lineages are involved in various stages of genomic reduction, having lost (often repeatedly) a variety of metabolic functions and the ability to form endospores. Although molecular phylogeny has driven numerous taxonomic revisions, we find it puzzling that the most recent taxonomic revision of the phyla

Firmicutes

and

Tenericutes

has further separated them into distinct phyla, rather than reflecting their common roots.
Frischella perrara gen. nov., sp. nov., a gammaproteobacterium isolated from the gut of the honeybee, Apis mellifera
Authors: Engel Philipp , Kwong Waldan K. , Moran Nancy A.
Published: April 2013

The gut of the Western honeybee, Apis mellifera, is colonized by a characteristic set of bacteria. Two distinct gammaproteobacteria are consistent members of this unique microbial community, and one has recently been described in a new genus and species with the name

Gilliamella apicola

. Here, we present the isolation and characterization of PEB0191T, a strain belonging to the second gammaproteobacterial species present in the honeybee gut microbiota, formerly referred to as ‘Gammaproteobacterium-2’. Cells of strain PEB0191T were mesophilic and had a mean length of around 2 µm, and optimal growth was achieved under anaerobic conditions. Growth was not obtained under aerobic conditions and was reduced in a microaerophilic environment. Based on 16S rRNA gene sequence analysis, strain PEB0191T belongs to the family

Orbaceae

, and its closest relatives, with around 95 % sequence similarity, are species of the genera

Orbus

and

Gilliamella

. Phylogenetic analyses suggest that PEB0191T is more closely related to the genus

Orbus

than to the genus

Gilliamella

. In accordance with its evolutionary relationship, further similarities between strain PEB0191T and other members of the family

Orbaceae

were revealed based on the respiratory quinone type (ubiquinone 8), the fatty acid profile and the DNA G+C content. Interestingly, like strains of the genus

Gilliamella

, PEB0191T exhibited a high level of resistance to oxytetracycline. The similar levels of sequence divergence from the genera

Gilliamella

and

Orbus

and its uncertain phylogenetic position within the family

Orbaceae

indicate that strain PEB0191T represents a novel species of a new genus, with the proposed name Frischella perrara gen. nov., sp. nov. The type strain of Frischella perrara is PEB0191T ( = NCIMB 14821T = ATCC BAA-2450T).
Albimonas pacifica sp. nov., isolated from seawater of the Pacific, and emended description of the genus

Albimonas
Authors: Li Guo-Wei , Zhang Xi-Ying , Wang Chun-Sheng , Zhang Yan-Jiao , Xu Xue-Wei , Liu Chang , Li Hai , Liu Ang , Xu Zhong , Song Xiao-Yan , Chen Xiu-Lan , Zhou Bai-Cheng , Zhang Yu-Zhong
Published: April 2013

A Gram-stain-negative, aerobic, catalase- and oxidase-positive, non-flagellated, rod-shaped bacterium, designated strain P-50-3T, was isolated from seawater of the Pacific. The strain grew at 10–40 °C (optimum at 30 °C) and with 0–12 % (w/v, optimum 2 %) NaCl. It reduced nitrate to nitrite but did not hydrolyse gelatin, starch or Tween 80. Analysis of 16S rRNA gene sequences showed that strain P-50-3T clustered tightly with the genus

Albimonas

and shared the highest 16S rRNA gene sequence similarity (94.3 %) with the type strain of

Albimonas donghaensis

. The major respiratory quinone was Q-10 and the major cellular fatty acids were C18 : 1ω7c, C18 : 0, 11-methyl C18 : 1ω7c and C16 : 0. Polar lipids included phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids and an unidentified lipid. The genomic DNA G+C content of strain P-50-3T was 69.0 mol%. On the basis of the data obtained in this polyphasic study, strain P-50-3T represents a novel species within the genus

Albimonas

, for which the name Albimonas pacifica sp. nov. is proposed. The type strain of Albimonas pacifica is P-50-3T ( = KACC 16527T = CGMCC 1.11030T). An emended description of the genus

Albimonas

Lim et al. 2008 is also proposed.
Francisella

guangzhouensis sp. nov., isolated from air-conditioning systems
Authors: Qu Ping-Hua , Chen Shou-Yi , Scholz Holger C. , Busse Hans-Jürgen , Gu Quan , Kämpfer Peter , Foster Jeffrey T. , Glaeser Stefanie P. , Chen Cha , Yang Zhi-Chong
Published: April 2013

Four strains (08HL01032T, 09HG994, 10HP82-6 and 10HL1960) were isolated from water of air-conditioning systems of various cooling towers in Guangzhou city, China. Cells were Gram-stain-negative coccobacilli without flagella, catalase-positive and oxidase-negative, showing no reduction of nitrate, no hydrolysis of urea and no production of H2S. Growth was characteristically enhanced in the presence of l-cysteine, which was consistent with the properties of members of the genus

Francisella

. The quinone system was composed of ubiquinone Q-8 with minor amounts of Q-9. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids (PL2, PL3), an unidentified aminophospholipid and an unidentified glycolipid (GL2). The polyamine pattern consisted of the major compounds spermidine, cadaverine and spermine. The major cellular fatty acids were C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 1 3-OH. A draft whole-genome sequence of the proposed type strain 08HL01032T was generated. Comparative sequence analysis of the complete 16S and 23S rRNA genes confirmed affiliation to the genus

Francisella

, with 95 % sequence identity to the closest relatives in the database, the type strains of

Francisella philomiragia

and

Francisella noatunensis subsp. orientalis

. Full-length deduced amino acid sequences of various housekeeping genes, recA, gyrB, groEL, dnaK, rpoA, rpoB, rpoD, rpoH, fopA and sdhA, exhibited similarities of 67–92 % to strains of other species of the genus

Francisella

. Strains 08HL01032T, 09HG994, 10HP82-6 and 10HL1960 exhibited highly similar pan-genome PCR profiles. Both the phenotypic and molecular data support the conclusion that the four strains belong to the genus

Francisella

but exhibit considerable divergence from all recognized

Francisella

species. Therefore, we propose the name

Francisella

guangzhouensis sp. nov., with the type strain 08HL01032T ( = CCUG 60119T = NCTC 13503T).
Dyadobacter

tibetensis sp. nov., isolated from glacial ice core
Authors: Shen Liang , Liu Yongqin , Yao Tandong , Wang Ninglian , Xu Baiqing , Jiao Nianzhi , Liu Hongcan , Zhou Yuguang , Liu Xiaobo , Wang Yanan
Published: April 2013

A Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, designated Y620-1T, was isolated from a glacier on the Tibetan Plateau, China. The 16S rRNA gene sequence of the novel isolate shared 93.6–95.1 % similarity with type strains of species of the genus

Dyadobacter

. The major fatty acids of strain Y620-1T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone and polar lipid were MK-7 and phosphatidylethanolamine (PE), respectively. The DNA G+C content was 44.4±0.3 mol% (T
m). Flexirubin-type pigment was produced. The novel isolate was classified in the genus

Dyadobacter

, but a number of phenotypic characteristics distinguished the novel isolate from type strains of species of the genus

Dyadobacter

. From these genotypic and phenotypic data, it is evident that strain Y620-1T represents a novel species of the genus

Dyadobacter

, for which the name

Dyadobacter

tibetensis sp. nov. is proposed. The type strain is Y620-1T ( = JCM 18589T = CGMCC 1.12215T).
A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera
Authors: Yoneda Yasuko , Yoshida Takashi , Yasuda Hisato , Imada Chiaki , Sako Yoshihiko
Published: April 2013

A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1T, was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0–3.0 µm straight rods, often observed with round endospores. Strain KKC1Tgrew at 55–68 °C, pH 5.2–9.2 and 0.8–14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0–7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1Tgrew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1Twas most closely related to those of members of the genusMoorellawith similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the nameCalderihabitans maritimusgen. nov., sp. nov.; the type strain of the type species is KKC1T( = DSM 26464T = NBRC 109353T).
The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains
Authors: Takada Toyoyuki , Ebata Toshinobu , Noguchi Hideki , Keane Thomas M. , Adams David J. , Narita Takanori , Shin-I Tadasu , Fujisawa Hironori , Toyoda Atsushi , Abe Kuniya , Obata Yuichi , Sakaki Yoshiyuki , Moriwaki Kazuo , Fujiyama Asao , Kohara Yuji , Shiroishi Toshihiko
Published: April 2013

Commonly used classical inbred mouse strains have mosaic genomes with sequences from different subspecific origins. Their genomes are derived predominantly from the Western European subspecies Mus musculus domesticus, with the remaining sequences derived mostly from the Japanese subspecies Mus musculus molossinus. However, it remains unknown how this intersubspecific genome introgression occurred during the establishment of classical inbred strains. In this study, we resequenced the genomes of two M. m. molossinus–derived inbred strains, MSM/Ms and JF1/Ms. MSM/Ms originated from Japanese wild mice, and the ancestry of JF1/Ms was originally found in Europe and then transferred to Japan. We compared the characteristics of these sequences to those of the C57BL/6J reference sequence and the recent data sets from the resequencing of 17 inbred strains in the Mouse Genome Project (MGP), and the results unequivocally show that genome introgression from M. m. molossinus into M. m. domesticus provided the primary framework for the mosaic genomes of classical inbred strains. Furthermore, the genomes of C57BL/6J and other classical inbred strains have long consecutive segments with extremely high similarity (>99.998%) to the JF1/Ms strain. In the early 20th century, Japanese waltzing mice with a morphological phenotype resembling that of JF1/Ms mice were often crossed with European fancy mice for early studies of “Mendelism,” which suggests that the ancestor of the extant JF1/Ms strain provided the origin of the M. m. molossinus genome in classical inbred strains and largely contributed to its intersubspecific genome diversity.
Identifying Genotype-by-Environment Interactions in the Metabolism of Germinating Arabidopsis Seeds Using Generalized Genetical Genomics
Authors: Joosen Ronny Viktor Louis , Arends Danny , Li Yang , Willems Leo A.J. , Keurentjes Joost J.B. , Ligterink Wilco , Jansen Ritsert C. , Hilhorst Henk W.M.
Published: April 2013

A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with “omics” analysis can help to disentangle the genetic basis of such quantitative traits. This so-called genetical genomics approach can effectively capture both genetic and epistatic interactions. However, to understand how the environment interacts with genomic-encoded information, a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup, this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated quantitative trait loci mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. In addition, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis (Arabidopsis thaliana) seeds. In the metabolome, many changes were observed that were under both environmental and genetic controls and their interaction. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics, which requires a broad understanding of both plasticity and dynamic regulation.
Brain and retinal microglia in health and disease: An unrecognized target of the renin–angiotensin system
Authors: McCarthy Claudia A , Widdop Robert E , Deliyanti Devy , Wilkinson‐Berka Jennifer L
Published: April 2013

Microglia are the resident immune cells within the brain and retina, commonly known as the macrophages of the central nervous system (CNS). Microglia survey the surrounding milieu to eliminate invading microbes, clear cellular debris and enforce programmed cell death by removing apoptotic cells. Complementary to their ‘house‐keeping’ role, microglia are capable of releasing brain‐derived neurotrophic factor (BDNF), as well as various anti‐inflammatory cytokines that sustain and support neuronal survival.

Although microglia are essential for maintaining a healthy CNS, paradoxically they may undergo phenotypic changes to influence numerous neurodegenerative disorders, including Parkinson's disease and Alzheimer's disease. Understanding the underlying mechanisms that determine whether microglia are supportive or toxic could elucidate novel and more effective therapeutic targets to treat an array of neurological and retinal diseases.

Although relatively little is known about the influences that evoke phenotypic changes in the microglial population, there is accumulating evidence illustrating an interaction with the renin‐angiotensin system (RAS). The angiotensin AT1 and AT2 receptors may have differential roles in mediating the activity of microglia. Understanding the actions of these angiotensin receptors will be important in defining whether microglia are an important therapeutic target for RAS blockade in brain and ocular diseases.
Expression of catalytically active matrix metalloproteinase‐1 in dermal fibroblasts induces collagen fragmentation and functional alterations that resemble aged human skin
Authors: Xia Wei , Hammerberg Craig , Li Yong , He Tianyuan , Quan Taihao , Voorhees John J. , Fisher Gary J.
Published: April 2013

Increased expression of matrix metalloproteinase‐1 (MMP‐1) and reduced production of type I collagen by dermal fibroblasts are prominent features of aged human skin. We have proposed that MMP‐1‐mediated collagen fibril fragmentation is a key driver of age‐related decline of skin function. To investigate this hypothesis, we constructed, characterized, and expressed constitutively active MMP‐1 mutant (MMP‐1 V94G) in adult human skin in organ culture and fibroblasts in three‐dimensional collagen lattice cultures. Expression of MMP‐1 V94G in young skin in organ culture caused fragmentation and ultrastructural alterations of collagen fibrils similar to those observed in aged human skin in vivo. Expression of MMP‐1 V94G in dermal fibroblasts cultured in three‐dimensional collagen lattices caused substantial collagen fragmentation, which was markedly reduced by MMP‐1 siRNA‐mediated knockdown or MMP inhibitor MMI270. Importantly, fibroblasts cultured in MMP‐1 V94G‐fragmented collagen lattices displayed many alterations observed in fibroblasts in aged human skin, including reduced cytoplasmic area, disassembled actin cytoskeleton, impaired TGF‐β pathway, and reduced collagen production. These results support the concept that MMP‐1‐mediated fragmentation of dermal collagen fibrils alters the morphology and function of dermal fibroblasts and provide a foundation for understanding specific mechanisms that link collagen fibril fragmentation to age‐related decline of fibroblast function.