ALBERT

Description: Sources and Transformations of Anthropogenic Nitrogen along an Urban River-Estuarine Continuum Michael J. Pennino, Sujay S. Kaushal, Sudhir Murthy, Joel Blomquist, Jeff Cornwell, and Lora Harris Biogeosciences Discuss., doi:10.5194/bg-2016-264,2016 Manuscript under review for BG (discussion: open, 0 comments) The results of this manuscript report the analysis of the fate and transport of wastewater and anthropogenic nitrogen along the Potomac River Estuary, from Washington D.C. to the Chesapeake Bay. In conjunction with a mass balance approach, nitrate isotopes were used to estimate fluxes and trace the sources and transformations N along the estuary. This study shows that estuaries have a large capacity to transform N inputs, but with large seasonal variability due to hydrological extremes.

Description: Boreal fire records in Northern Hemisphere ice cores: A review Michel Legrand, Joseph McConnell, Hubertus Fischer, Eric W. Wolff, Susanne Preunkert, Nathan Chellman, Daiana Leuenberger, Olivia Maselli, Michael Sigl, Simon Schüpbach, and Mike Flannigan Clim. Past Discuss., doi:10.5194/cp-2016-70,2016 Manuscript under review for CP (discussion: open, 0 comments) Here we review previous attempts made to reconstruct past forest fire using chemical signals recorded in Greenland ice. We showed that the Greenland ice records of ammonium, found to be a good fire proxy, consistently indicate changing fire activity in Canada in response to past climatic conditions that occurred since the last 15 000 years including the little ice age and the last large climatic transition.

Description: by Eva R. M. Joosten, Shihab A. Shamma, Christian Lorenzi, Peter Neri Sound waveforms convey information largely via amplitude modulations (AM). A large body of experimental evidence has provided support for a modulation (bandpass) filterbank. Details of this model have varied over time partly reflecting different experimental conditions and diverse datasets from distinct task strategies, contributing uncertainty to the bandwidth measurements and leaving important issues unresolved. We adopt here a solely data-driven measurement approach in which we first demonstrate how different models can be subsumed within a common ‘cascade’ framework, and then proceed to characterize the cascade via system identification analysis using a single stimulus/task specification and hence stable task rules largely unconstrained by any model or parameters. Observers were required to detect a brief change in level superimposed onto random level changes that served as AM noise; the relationship between trial-by-trial noisy fluctuations and corresponding human responses enables targeted identification of distinct cascade elements. The resulting measurements exhibit a dynamic complex picture in which human perception of auditory modulations appears adaptive in nature, evolving from an initial lowpass to bandpass modes (with broad tuning, Q∼1) following repeated stimulus exposure.

Description: by Bihai Shi, Cui Zhang, Caihuan Tian, Jin Wang, Quan Wang, Tengfei Xu, Yan Xu, Carolyn Ohno, Robert Sablowski, Marcus G. Heisler, Klaus Theres, Ying Wang, Yuling Jiao Shoot branching requires the establishment of new meristems harboring stem cells; this phenomenon raises questions about the precise regulation of meristematic fate. In seed plants, these new meristems initiate in leaf axils to enable lateral shoot branching. Using live-cell imaging of leaf axil cells, we show that the initiation of axillary meristems requires a meristematic cell population continuously expressing the meristem marker SHOOT MERISTEMLESS ( STM ). The maintenance of STM expression depends on the leaf axil auxin minimum. Ectopic expression of STM is insufficient to activate axillary buds formation from plants that have lost leaf axil STM expressing cells. This suggests that some cells undergo irreversible commitment to a developmental fate. In more mature leaves, REVOLUTA ( REV ) directly up-regulates STM expression in leaf axil meristematic cells, but not in differentiated cells, to establish axillary meristems. Cell type-specific binding of REV to the STM region correlates with epigenetic modifications. Our data favor a threshold model for axillary meristem initiation, in which low levels of STM maintain meristematic competence and high levels of STM lead to meristem initiation.

Description: by Lauren A. Richardson Our first ever Open Highlights explores recent Open Access research into the complex relationship between host and pathogen during the course of an infection, and the factors that determine its eventual outcome.

Description: by Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph Analyses of metagenome data (MG) and metatranscriptome data (MT) are often challenged by a paucity of complete reference genome sequences and the uneven/low sequencing depth of the constituent organisms in the microbial community, which respectively limit the power of reference-based alignment and de novo sequence assembly. These limitations make accurate protein family classification and abundance estimation challenging, which in turn hamper downstream analyses such as abundance profiling of metabolic pathways, identification of differentially encoded/expressed genes, and de novo reconstruction of complete gene and protein sequences from the protein family of interest. The profile hidden Markov model (HMM) framework enables the construction of very useful probabilistic models for protein families that allow for accurate modeling of position specific matches, insertions, and deletions. We present a novel homology detection algorithm that integrates banded Viterbi algorithm for profile HMM parsing with an iterative simultaneous alignment and assembly computational framework. The algorithm searches a given profile HMM of a protein family against a database of fragmentary MG/MT sequencing data and simultaneously assembles complete or near-complete gene and protein sequences of the protein family. The resulting program, HMM-GRASPx, demonstrates superior performance in aligning and assembling homologs when benchmarked on both simulated marine MG and real human saliva MG datasets. On real supragingival plaque and stool MG datasets that were generated from healthy individuals, HMM-GRASPx accurately estimates the abundances of the antimicrobial resistance (AMR) gene families and enables accurate characterization of the resistome profiles of these microbial communities. For real human oral microbiome MT datasets, using the HMM-GRASPx estimated transcript abundances significantly improves detection of differentially expressed (DE) genes. Finally, HMM-GRASPx was used to reconstruct comprehensive sets of complete or near-complete protein and nucleotide sequences for the query protein families. HMM-GRASPx is freely available online from http://sourceforge.net/projects/hmm-graspx.

Description: by Dazhe Meng, Manu Dubin, Pei Zhang, Edward J. Osborne, Oliver Stegle, Richard M. Clark, Magnus Nordborg The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis -methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs.

Description: by Minghua Nie, Emily Arner, John Prudden, Lana Schaffer, Steven Head, Michael N. Boddy Posttranslational modifications (PTMs) provide dynamic regulation of the cellular proteome, which is critical for both normal cell growth and for orchestrating rapid responses to environmental stresses, e.g. genotoxins. Key PTMs include ubiquitin, the Small Ubiquitin-like MOdifier SUMO, and phosphorylation. Recently, SUMO-targeted ubiquitin ligases (STUbLs) were found to integrate signaling through the SUMO and ubiquitin pathways. In general, STUbLs are recruited to target proteins decorated with poly-SUMO chains to ubiquitinate them and drive either their extraction from protein complexes, and/or their degradation at the proteasome. In fission yeast, reducing or preventing the formation of SUMO chains can circumvent the essential and DNA damage response functions of STUbL. This result indicates that whilst some STUbL "targets" have been identified, the crucial function of STUbL is to antagonize SUMO chain formation. Herein, by screening for additional STUbL suppressors, we reveal crosstalk between the serine/threonine phosphatase PP2A-Pab1 B55 and the SUMO pathway. A hypomorphic Pab1 B55 mutant not only suppresses STUbL dysfunction, but also mitigates the phenotypes associated with deletion of the SUMO protease Ulp2, or mutation of the STUbL cofactor Rad60. Together, our results reveal a novel role for PP2A-Pab1 B55 in modulating SUMO pathway output, acting in parallel to known critical regulators of SUMOylation homeostasis. Given the broad evolutionary functional conservation of the PP2A and SUMO pathways, our results could be relevant to the ongoing attempts to therapeutically target these factors.

Description: by Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus ) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the “healthy” microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly available at http://segatalab.cibio.unitn.it/tools/metaml.

Description: by Anja S. Ziegler, Simon J. McIlroy, Poul Larsen, Mads Albertsen, Aviaja A. Hansen, Nicolas Heinen, Per Halkjær Nielsen Membrane fouling presents the greatest challenge to the application of membrane bioreactor (MBR) technology. Formation of biofilms on the membrane surface is the suggested cause, yet little is known of the composition or dynamics of the microbial community responsible. To gain an insight into this important question, we applied 16S rRNA gene amplicon sequencing with a curated taxonomy and fluorescent in situ hybridization to monitor the community of a pilot-scale MBR carrying out enhanced biological nitrogen and phosphorus removal with municipal wastewater. In order to track the dynamics of the fouling process, we concurrently investigated the communities of the biofilm, MBR bulk sludge, and the conventional activated sludge system used to seed the MBR system over several weeks from start-up. As the biofilm matured the initially abundant betaproteobacterial genera Limnohabitans , Hydrogenophaga and Malikia were succeeded by filamentous Chloroflexi and Gordonia as the abundant species. This study indicates that, although putative pioneer species appear, the biofilm became increasingly similar to the bulk community with time. This suggests that the microbial population in bulk water will largely determine the community structure of the mature biofilm.

Description: by Petra E. Verburg, Graeme Tucker, Wendy Scheil, Jan Jaap H. M. Erwich, Gus A. Dekker, Claire Trelford Roberts Objectives Sexual inequality starts in utero . The contribution of biological sex to the developmental origins of health and disease is increasingly recognized. The aim of this study was to assess and interpret sexual dimorphisms for three major adverse pregnancy outcomes which affect the health of the neonate, child and potentially adult. Methods Retrospective population-based study of 574,358 South Australian singleton live births during 1981–2011. The incidence of three major adverse pregnancy outcomes [preterm birth (PTB), pregnancy induced hypertensive disorders (PIHD) and gestational diabetes mellitus (GDM)] in relation to fetal sex was compared according to traditional and fetus-at-risk (FAR) approaches. Results The traditional approach showed male predominance for PTB [20–24 weeks: Relative Risk (RR) M/F 1.351, 95%-CI 1.274–1.445], spontaneous PTB [25–29 weeks: RR M/F 1.118, 95%-CI 1.044–1.197%], GDM [RR M/F 1.042, 95%-CI 1.011–1.074], overall PIHD [RR M/F 1.053, 95%-CI 1.034–1.072] and PIHD with term birth [RR M/F 1.074, 95%-CI 1.044–1.105]. The FAR approach showed that males were at increased risk for PTB [20–24 weeks: RR M/F 1.273, 95%-CI 1.087–1.490], for spontaneous PTB [25–29 weeks: RR M/F 1.269, 95%-CI 1.143–1.410] and PIHD with term birth [RR M/F 1.074, 95%-CI 1.044–1.105%]. The traditional approach demonstrated female predominance for iatrogenic PTB [25–29 weeks: RR M/F 0.857, 95%-CI 0.780–0.941] and PIHD associated with PTB [25–29 weeks: RR M/F 0.686, 95%-CI 0.581–0.811]. The FAR approach showed that females were at increased risk for PIHD with PTB [25–29 weeks: RR M/F 0.779, 95%-CI 0.648–0.937]. Conclusions This study confirms the presence of sexual dimorphisms and presents a coherent framework based on two analytical approaches to assess and interpret the sexual dimorphisms for major adverse pregnancy outcomes. The mechanisms by which these occur remain elusive, but sex differences in placental gene expression and function are likely to play a key role. Further research on sex differences in placental function and maternal adaptation to pregnancy is required to delineate the causal molecular mechanisms in sex-specific pregnancy outcome. Identifying these mechanisms may inform fetal sex specific tailored antenatal and neonatal care.

Description: by Harald Schrem, Valentin Schneider, Marlene Kurok, Alon Goldis, Maren Dreier, Alexander Kaltenborn, Wilfried Gwinner, Marc Barthold, Jan Liebeneiner, Markus Winny, Jürgen Klempnauer, Moritz Kleine Background The aim of this study is to identify independent pre-transplant cancer risk factors after kidney transplantation and to assess the utility of G-chart analysis for clinical process control. This may contribute to the improvement of cancer surveillance processes in individual transplant centers. Patients and Methods 1655 patients after kidney transplantation at our institution with a total of 9,425 person-years of follow-up were compared retrospectively to the general German population using site-specific standardized-incidence-ratios (SIRs) of observed malignancies. Risk-adjusted multivariable Cox regression was used to identify independent pre-transplant cancer risk factors. G-chart analysis was applied to determine relevant differences in the frequency of cancer occurrences. Results Cancer incidence rates were almost three times higher as compared to the matched general population (SIR = 2.75; 95%-CI: 2.33–3.21). Significantly increased SIRs were observed for renal cell carcinoma (SIR = 22.46), post-transplant lymphoproliferative disorder (SIR = 8.36), prostate cancer (SIR = 2.22), bladder cancer (SIR = 3.24), thyroid cancer (SIR = 10.13) and melanoma (SIR = 3.08). Independent pre-transplant risk factors for cancer-free survival were age 62.6 years (p = 0.001, HR: 1.29), polycystic kidney disease other than autosomal dominant polycystic kidney disease (ADPKD) (p = 0.001, HR: 0.68), high body mass index in kg/m 2 (p

Description: by Prasamit Saurav Baruah, Myriam Beauchemin, Josée Hébert, Richard Bertrand Bcl-xL proteins undergo dynamic phosphorylation/dephosphorylation on Ser49 and Ser62 residues during mitosis. The expression of Bcl-xL(S49A), (S62A) and dual (S49/62A) phosphorylation mutants in tumor cells lead to severe mitotic defects associated with multipolar spindle, chromosome lagging and bridging, and micro-, bi- and multi-nucleated cells. Because the above observations were made in tumor cells which already display genomic instability, we now address the question: will similar effects occur in normal human diploid cells? We studied normal human diploid BJ foreskin fibroblast cells expressing Bcl-xL (wild type), (S49A), (S49D), (S62A), (S62D) and the dual-site (S49/62A) and (S49/62D) mutants. Cells expressing S49 and/or S62 phosphorylation mutants showed reduced kinetics of cell population doubling. These effects on cell population doubling kinetics correlated with early outbreak of senescence with no impact on the cell death rate. Senescent cells displayed typical senescence-associated phenotypes including high-level of senescence-associated β-galactosidase activity, interleukin-6 (IL-6) secretion, tumor suppressor p53 and cyclin-dependent kinase inhibitor p21Waf1/Cip1 activation as well as γH2A.X-associated nuclear chromatin foci. Fluorescence in situ hybridization analysis and Giemsa-banded karyotypes revealed that the expression of Bcl-xL phosphorylation mutants in normal diploid BJ cells provoked chromosome instability and aneuploidy. These findings suggest that dynamic Bcl-xL(S49) and (S62) phosphorylation/dephosphorylation cycles are important in the maintenance of chromosome integrity during mitosis in normal cells. They could impact future strategies aiming to develop and identify compounds that could target not only the anti-apoptotic domain of Bcl-xL protein, but also its mitotic domain for cancer therapy.

Description: by Vera Kloten, Martin Schlensog, Julian Eschenbruch, Janina Gasthaus, Janina Tiedemann, Jolein Mijnes, Timon Heide, Till Braunschweig, Ruth Knüchel, Edgar Dahl NDRG2 , a member of the N-myc downstream-regulated gene family, is thought to be a putative tumor suppressor gene with promising clinical impact in breast cancer. Since breast cancer comprises heterogeneous intrinsic subtypes with distinct clinical outcomes we investigated the pivotal role of NDRG2 in basal-type breast cancers. Based on subtype classified tumor (n = 45) and adjacent normal tissues (n = 17) we examined NDRG2 mRNA expression and CpG-hypermethylation, whose significance was further validated by independent data sets from The Cancer Genome Atlas (TCGA). In addition, NDRG2 protein expression was evaluated immunohistochemically using a tissue micro array (TMA, n = 211). In vitro , we investigated phenotypic effects caused by NDRG2 silencing in the basal A-like HCC1806 as well as NDRG2 over-expression in basal A-like BT20 compared to luminal-type MCF7 breast cancer cells. Our tissue collections demonstrated an overall low NDRG2 mRNA expression in breast cancer subtypes compared to normal breast tissue in line with an increased CpG-hypermethylation in breast cancer tissue. Independent TCGA data sets verified a significant (P

Description: by Viorica Ionut, Orison O. Woolcott, Hasmik J. Mkrtchyan, Darko Stefanovski, Morvarid Kabir, Malini S. Iyer, Huiwen Liu, Ana V. B. Castro, Qiang Wu, Josiane L. Broussard, Cathryn M. Kolka, Isaac Asare-Bediako, Richard N. Bergman Background Exenatide’s effects on glucose metabolism have been studied extensively in diabetes but not in pre-diabetes. Objective We examined the chronic effects of exenatide alone on glucose metabolism in pre-diabetic canines. Design and Methods After 10 weeks of high-fat diet (HFD), adult dogs received one injection of streptozotocin (STZ, 18.5 mg/kg). After induction of pre-diabetes, while maintained on HFD, animals were randomized to receive either exenatide (n = 7) or placebo (n = 7) for 12 weeks. β-Cell function was calculated from the intravenous glucose tolerance test (IVGTT, expressed as the acute insulin response, AIR G ), the oral glucose tolerance test (OGTT, insulinogenic index) and the graded-hyperglycemic clamp (clamp insulinogenic index). Whole-body insulin sensitivity was assessed by the IVGTT. At the end of the study, pancreatic islets were isolated to assess β-cell function in vitro . Results OGTT: STZ caused an increase in glycemia at 120 min by 22.0% (interquartile range, IQR, 31.5%) (P = 0.011). IVGTT: This protocol also showed a reduction in glucose tolerance by 48.8% (IQR, 36.9%) (P = 0.002). AIR G decreased by 54.0% (IQR, 40.7%) (P = 0.010), leading to mild fasting hyperglycemia (P = 0.039). Exenatide, compared with placebo, decreased body weight (P

Description: by Ha Young Kim, Eun Jin Jang, ByeongJu Park, Tae-Young Kim, Soon-Ae Shin, Yong-Chan Ha, Sunmee Jang Background Asian-specific prediction models for estimating individual risk of osteoporotic fractures are rare. We developed a Korean fracture risk prediction model using clinical risk factors and assessed validity of the final model. Methods A total of 718,306 Korean men and women aged 50–90 years were followed for 7 years in a national system-based cohort study. In total, 50% of the subjects were assigned randomly to the development dataset and 50% were assigned to the validation dataset. Clinical risk factors for osteoporotic fracture were assessed at the biennial health check. Data on osteoporotic fractures during the follow-up period were identified by ICD-10 codes and the nationwide database of the National Health Insurance Service (NHIS). Results During the follow-up period, 19,840 osteoporotic fractures were reported (4,889 in men and 14,951 in women) in the development dataset. The assessment tool called the Korean Fracture Risk Score (KFRS) is comprised of a set of nine variables, including age, body mass index, recent fragility fracture, current smoking, high alcohol intake, lack of regular exercise, recent use of oral glucocorticoid, rheumatoid arthritis, and other causes of secondary osteoporosis. The KFRS predicted osteoporotic fractures over the 7 years. This score was validated using an independent dataset. A close relationship with overall fracture rate was observed when we compared the mean predicted scores after applying the KFRS with the observed risks after 7 years within each 10th of predicted risk. Conclusion We developed a Korean specific prediction model for osteoporotic fractures. The KFRS was able to predict risk of fracture in the primary population without bone mineral density testing and is therefore suitable for use in both clinical setting and self-assessment. The website is available at http://www.nhis.or.kr.

Description: by Cecilia Ma, Eva Monsma This paper examines the factor structure and measurement invariance of the Task and Ego Orientation in Sport Questionnaire (TEOSQ) across American and Chinese samples. Results based on the mean and covariance structure analyses supported configural invariance, metric invariance and scalar invariance across groups. Latent means analyses revealed that American sample had significantly higher mean scores on task and ego orientations than the Chinese sample. The findings suggest that the TEOSQ is a valid and reliable instrument in assessing achievement motivation across these two diverse populations.

Description: by Lin Yang, Liangping Xia, Yan Wang, Shaodong Hong, Haiyang Chen, Shaobo Liang, Peijian Peng, Yong Chen Background Poor nutritional status is associated with progression and advanced disease in patients with cancer. The prognostic nutritional index (PNI) may represent a simple method of assessing host immunonutritional status. This study was designed to investigate the prognostic value of the PNI for distant metastasis-free survival (DMFS) in patients with nasopharyngeal carcinoma (NPC). Methods A training cohort of 1,168 patients with non-metastatic NPC from two institutions was retrospectively analyzed. The optimal PNI cutoff value for DMFS was identified using the online tool “Cutoff Finder”. DMFS was analyzed using stratified and adjusted analysis. Propensity score-matched analysis was performed to balance baseline characteristics between the high and low PNI groups. Subsequently, the prognostic value of the PNI for DMFS was validated in an external validation cohort of 756 patients with NPC. The area under the receiver operating characteristics curve (AUC) was calculated to compare the discriminatory ability of different prognostic scores. Results The optimal PNI cutoff value was determined to be 51. Low PNI was significantly associated with poorer DMFS than high PNI in univariate analysis (P

Description: by Hung Yuan Chen, Yen Ling Chiu, Shih Ping Hsu, Mei Fen Pai, Ju Yeh Yang, Yu Sen Peng Background Fractures are a common morbidity that lead to worse outcomes in dialysis patients. Fetuin A inhibits vascular calcification (VC), potentially promotes bone mineralization and its level positively correlates with bone mineral density in the general population. On the other hand, the presence of VC is associated with low bone volume in dialysis patients. Whether the fetuin A level and VC can predict the occurrence of fractures in dialysis patients remains unknown. Methods We performed this prospective, observational cohort study including 685 dialysis patients (629 hemodialysis and 56 peritoneal dialysis) from a single center in Taiwan for a median follow-up period of 3.4 years. The baseline fetuin A level and status of presence of aortic arch calcification (VC) and incidence of major fractures (hip, pelvis, humerus, proximal forearm, lower leg or vertebrae) were assessed using adjusted Cox proportional hazards models, recursive partitioning analysis and competing risk models. Results Overall, 177 of the patients had major fractures. The incidence rate of major fractures was 3.29 per 100 person-years. In adjusted analyses, the patients with higher baseline fetuin A levels had a lower incidence of fractures (adjusted hazard ratio (HR), 0.3; 95% CI, 0.18‒0.5, fetuin A tertile 3 vs . tertile 1 and HR, 0.52; 95% CI, 0.34‒0.78, tertile 2 vs . tertile 1). The presence of aortic arch calcification (VC) independently predicted the occurrence of fractures (adjusted HR, 1.95; 95% CI, 1.34‒2.84) as well. When accounting for death as an event in competing risk models, the patients with higher baseline fetuin A levels remained to have a lower incidence of fractures (SHR, 0.31; 95% CI, 0.17‒0.56, fetuin A tertile 3 vs . tertile 1 and 0.51; 95% CI, 0.32‒0.81, tertile 2 vs . tertile 1). Interpretations Lower baseline fetuin A levels and the presence of VC were independently linked to higher risk of incident fractures in prevalent dialysis patients.

Description: Tectonothermal evolution in the core of an arcuate fold and thrust belt: the south-eastern sector of the Cantabrian Zone (Variscan belt, north-western Spain) María Luz Valín, Susana García-López, Covadonga Brime, Fernando Bastida, and Jesús Aller Solid Earth, 7, 1003-1022, doi:10.5194/se-7-1003-2016, 2016 The tectonothermal evolution of an area located in the core of the Ibero-Armorican Arc (Variscan belt) has been determined by using the conodont colour alteration index (CAI), Kübler index of illite (KI), the Árkai index of chlorite (AI) and the analysis of clay minerals and rock cleavage. The area is part of the Cantabrian Zone (CZ), which represents the foreland fold and thrust belt of the orogen. It has been thrust by several large units of the CZ, what resulted in the generation of a large number of synorogenic Carboniferous sediments. CAI, KI and AI values show an irregular distribution of metamorphic grade, independent of stratigraphic position. Two tectonothermal events have been distinguished in the area. The first one, poorly defined, is mainly located in the northern part. It gave rise to very-low-grade metamorphism in some areas and it was associated with a deformation event that resulted in the emplacement of the last large thrust unit and development of upright folds and associated cleavage ( S 1 ). The second tectonothermal event gave rise to low-grade metamorphism and cleavage ( S 2 ) crosscutting earlier upright folds in the central, western and southern parts of the study area. The event continued with the intrusion of small igneous rock bodies, which gave rise to contact metamorphism and hydrothermal alteration. This event was linked to an extensional episode due to a gravitational instability at the end of the Variscan deformation. This tectonothermal evolution occurred during the Gzhelian–Sakmarian. Subsequently, several hydrothermal episodes took place and local crenulation cleavage developed during the Alpine deformation.

Description: Microstructures and deformation mechanisms in Opalinus Clay: insights from scaly clay from the Main Fault in the Mont Terri Rock Laboratory (CH) Ben Laurich, Janos L. Urai, and Christophe Nussbaum Solid Earth Discuss., doi:10.5194/se-2016-94,2016 Manuscript under review for SE (discussion: open, 0 comments) Scaly clay is a well-known rock fabric that can develop in tectonic systems and that can alter the physical rock properties of a formation. However, internal microstructure and evolution of this fabric remains poorly understood. We examined the scaly microstructure of progressively faulted Opalinus Clay using optical as well as scanning electron microscopy. We present an evolutionary model for scaly clay that is of interest in the evaluation of Opalinus Clay to host radioactive waste.

Description: Microstructures and deformation mechanisms in Opalinus Clay: insights from scaly clay from the Main Fault in the Mont Terri Rock Laboratory (CH) Ben Laurich, Janos L. Urai, and Christophe Nussbaum Solid Earth Discuss., doi:10.5194/se-2016-94,2016 Manuscript under review for SE (discussion: open, 0 comments) Scaly clay is a well-known rock fabric that can develop in tectonic systems and that can alter the physical rock properties of a formation. However, internal microstructure and evolution of this fabric remains poorly understood. We examined the scaly microstructure of progressively faulted Opalinus Clay using optical as well as scanning electron microscopy. We present an evolutionary model for scaly clay that is of interest in the evaluation of Opalinus Clay to host radioactive waste.

Description: Fixation kinetics of chelated and non-chelated zinc in semi-arid alkaline soils: application to zinc management Theophilus K. Udeigwe, Madeleine Eichmann, and Matthew C. Menkiti Solid Earth, 7, 1023-1031, doi:10.5194/se-7-1023-2016, 2016 Micronutrient fixation leads to the reduction of plant-available portions. This study examined the fixation kinetics of chelated and non-chelated zinc (Zn) in semi-arid soils. About 30 % more Zn was fixed in the non-chelated system in the first 14 days. Slope of change of Zn to Cu (i.e., Cu–Zn) was higher than other micronutrients. Zn fixation kinetics were better described by a power-function model. Tools developed from this study will be used to advance micronutrient management.

Description: Publication date: Available online 9 July 2016 Source: Geodesy and Geodynamics Author(s): Ruisha Li, Xi Zhang, Shouwen Gong, Hongtao Tang, Peng Jia The equation for determining cross-fault representative value is calculated based on hanging wall and foot wall reference level surfaces. The cross-fault data reliability are analyzed base on the stability of reference datum and observation points, thereby facilitating plotting of the representative value curves after removing interference. The spatial and temporal characteristics of fault deformation abnormalities before the 2016 Menyuan M s6.4 earthquake, as well as the fault-movement characteristics reflected by representative value, are summarized. The results show that many site trends had changed 1–3 years before the Menyuan M s6.4 earthquake in the Qilian Fault, reflecting certain background abnormalities. The short-term abnormalities centrally had appeared in the 6 months to 1 year period before the earthquake near and in the neighborhood of the source region, demonstrating a significantly increased number of short-term abnormalities. Many sites near and in the neighborhood of the source region had strengthened inverse activities or had changed from positive to inverse activities in the most recent 2–3 years, which reflect stress-field enhancements or adjustment features.

Description: Improved MODIS Dark Target Aerosol Optical Depth algorithm over land: Angular effect Correction Yerong Wu, Martin de Graaf, and Massimo Menenti Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-185,2016 Manuscript under review for AMT (discussion: open, 0 comments) In this paper, we developed a new algorithm to improve the retrieval of Aerosol Optical Depth (AOD) over land with satellite measurement, by refining the shape of the spectral surface reflectance to improve the estimated background reflectance in the channel used for AOD retrieval. The results show that the angular effects of the retrievals are largely reduced, including fewer occurrences of negative retrievals. This implies that the users can get more accurate data without angular bias.

Description: Investigation of processes controlling summertime gaseous elemental mercury oxidation at midlatitudinal marine, coastal, and inland sites Zhuyun Ye, Huiting Mao, Che-Jen Lin, and Su Youn Kim Atmos. Chem. Phys., 16, 8461-8478, doi:10.5194/acp-16-8461-2016, 2016 In this study, a state-of-the-art chemical mechanism was incorporated into a box model to investigate the atmospheric Hg cycling in different environments. As a result, for each of the three environments, GOM diurnal cycles of over half the selected cases were reasonably represented by the box model. A realistic model can be a powerful tool, providing important information on atmospheric Hg cycling and implications for policy makers.

Description: Effects of polar stratospheric clouds in the Nimbus 7 LIMS Version 6 data set Ellis Remsberg and V. Lynn Harvey Atmos. Meas. Tech., 9, 2927-2946, doi:10.5194/amt-9-2927-2016, 2016 Emissions from polar stratospheric cloud (PSC) particles affect the retrieved ozone and water vapor from the Limb Infrared Monitor of the Stratosphere (LIMS) satellite experiment. Threshold criteria are applied to the retrieved ozone for the detection and screening of those effects. The PSC effects correlate very well with regions of coldest temperatures (

Description: by Zhenyu Yuan, Heiko Praxenthaler, Nassif Tabaja, Rubben Torella, Anette Preiss, Dieter Maier, Rhett A. Kovall Notch is a conserved signaling pathway that specifies cell fates in metazoans. Receptor-ligand interactions induce changes in gene expression, which is regulated by the transcription factor CBF1/Su(H)/Lag-1 (CSL). CSL interacts with coregulators to repress and activate transcription from Notch target genes. While the molecular details of the activator complex are relatively well understood, the structure-function of CSL-mediated repressor complexes is poorly defined. In Drosophila , the antagonist Hairless directly binds Su(H) (the fly CSL ortholog) to repress transcription from Notch targets. Here, we determine the X-ray structure of the Su(H)-Hairless complex bound to DNA. Hairless binding produces a large conformational change in Su(H) by interacting with residues in the hydrophobic core of Su(H), illustrating the structural plasticity of CSL molecules to interact with different binding partners. Based on the structure, we designed mutants in Hairless and Su(H) that affect binding, but do not affect formation of the activator complex. These mutants were validated in vitro by isothermal titration calorimetry and yeast two- and three-hybrid assays. Moreover, these mutants allowed us to solely characterize the repressor function of Su(H) in vivo.

Description: The 1816 ‘year without a summer’ in an atmospheric reanalysis Philip Brohan, Gilbert P. Compo, Stefan Brönnimann, Robert J. Allan, Renate Auchmann, Yuri Brugnara, Prashant D. Sardeshmukh, and Jeffrey S. Whitaker Clim. Past Discuss., doi:10.5194/cp-2016-78,2016 Manuscript under review for CP (discussion: open, 0 comments) We have used modern weather forecasting tools to reconstruct the dreadful European weather of 200 years ago – 1816 was the ‘year without a summer’; harvests failed, and people starved. We can show that 1816’s extreme climate was caused by the eruption of the Tambora volcano the previous year. This means we have some chance of predicting such extreme summers if they occur in future, though this is still a challenge to today’s forecast models.

Description: Palynological evidence for late Miocene stepwise aridification on the northeastern Tibetan Plateau Jia Liu, Ji Jun Li, Chun Hui Song, Hao Yu, Ting Jiang Peng, Zheng Chuang Hui, and Xi Yan Ye Clim. Past, 12, 1473-1484, doi:10.5194/cp-12-1473-2016, 2016 The late Cenozoic basins in the northeastern Tibetan Plateau document both the tectonic uplift process and its associated environmental changes. Here, we investigated a late Miocene sporopollen record from the Tianshui Basin in the northeastern Tibetan Plateau. The results show that a persistent aridification trend parallels the global cooling of the late Miocene, and the stepwise vegetation succession is consistent with the major uplift events of the Tibetan Plateau.

Description: by Camille Attané, Marie-Line Peyot, Roxane Lussier, Dongwei Zhang, Erik Joly, S. R. Murthy Madiraju, Marc Prentki Many metabolic studies employ tissue-specific gene knockout mice, which requires breeding of floxed gene mice, available mostly on C57BL/6N (NN) genetic background, with cre or Flp recombinase-expressing mice, available on C57BL/6J (JJ) background, resulting in the generation of mixed C57BL/6NJ (NJ) genetic background mice. Recent awareness of many genetic differences between NN and JJ strains including the deletion of nicotinamide nucleotide transhydrogenase ( nnt ), necessitates examination of the consequence of mixed NJ background on glucose tolerance, beta cell function and other metabolic parameters. Male mice with NN and NJ genetic background were fed with normal or high fat diets (HFD) for 12 weeks and glucose and insulin homeostasis were studied. Genotype had no effect on body weight and food intake in mice fed normal or high fat diets. Insulinemia in the fed and fasted states and after a glucose challenge was lower in HFD-fed NJ mice, even though their glycemia and insulin sensitivity were similar to NN mice. NJ mice showed mild glucose intolerance. Moreover, glucose- but not KCl-stimulated insulin secretion in isolated islets was decreased in HFD-fed NJ vs NN mice without changes in insulin content and beta cell mass. Under normal diet, besides reduced fed insulinemia, NN and NJ mice presented similar metabolic parameters. However, HFD-fed NJ mice displayed lower fed and fasted insulinemia and glucose-induced insulin secretion in vivo and ex vivo , as compared to NN mice. These results strongly caution against using unmatched mixed genetic background C57BL/6 mice for comparisons, particularly under HFD conditions.

Description: by Jill A. Rahnert, Bin Zheng, Matthew B. Hudson, Myra E. Woodworth-Hobbs, S. Russ Price Muscle wasting associated with chronic diseases has been linked to decreased expression of PGC-1α and overexpression of PGC-1α counters muscle loss. CREB, in conjunction with the CREB-regulated transcription coactivator (CRTC2), is a positive modulator of PGC-1α transcription. We previously reported that PGC-1α expression is decreased in skeletal muscle of diabetic rats despite a high level of CREB phosphorylation (i.e., activation), suggesting that CRTC2-CREB signaling may be dysregulated. In this study, the relationship between CREB/CRTC signaling and PGC-1α expression was examined in L6 myotubes treated with dexamethasone (Dex, 48h) to induce atrophy. Dex decreased PGC-1α mRNA and protein as well as the levels of CRTC1 and CRTC2 in the nucleus. Dex also altered the nuclear levels of two known regulators of CRTC2 localization; the amount of calcinuerin catalytic A subunit (CnA) was decreased whereas SIK was increased. To assess PGC-1α transcription, muscle cells were transfected with a PGC-1α luciferase reporter plasmid (PGC-1α-Luc). Dex suppressed PGC-1α luciferase activity while both isobutylmethylxanthine (IBMX) and over-expression of CRTC1 or CRTC2 increased PGC-1α-Luc activity. Mutation of the CRE binding site from PGC-1α-Luc reporter attenuated the responses to both IBMX and the CRTC proteins. Consistent with the reporter gene results, overexpression of CRTC2 produced an increase in CRTC2 in the nucleus and in PGC-1α mRNA and PGC-1α protein. Overexpression of CRTC2 was not sufficient to prevent the decrease in PGC-1α mRNA or protein by Dex. In summary, these data suggest that attenuated CREB/CRTC signaling contributes to the decrease in PGC-1α expression during atrophy.

Description: by Fatima Ochoa-Gonzalez, Alberto R. Cervantes-Villagrana, Julio C. Fernandez-Ruiz, Hilda S. Nava-Ramirez, Adriana C. Hernandez-Correa, Jose A. Enciso-Moreno, Julio E. Castañeda-Delgado

Description: by Abdessamad Ababou, Vassilis Koronakis Gram-negative bacteria such as E . coli use tripartite efflux pumps such as AcrAB-TolC to expel antibiotics and noxious compounds. A key feature of the inner membrane transporter component, AcrB, is a short stretch of residues known as the gate/switch loop that divides the proximal and distal substrate binding pockets. Amino acid substitutions of the gate loop are known to decrease antibiotic resistance conferred by AcrB. Here we present two new AcrB gate loop variants, the first stripped of its bulky side chains, and a second in which the gate loop is removed entirely. By determining the crystal structures of the variant AcrB proteins in the presence and absence of erythromycin and assessing their ability to confer erythromycin tolerance, we demonstrate that the gate loop is important for AcrB export activity but is not required for erythromycin binding.

Description: by Shou-Chieh Wang, Chin-Chin Huang, Cheng-Huang Shen, Lei-Chen Lin, Pei-Wen Zhao, Shih-Ying Chen, Yu-Chiao Deng, Yi-Wen Liu Bladder cancer is highly recurrent after therapy, which has an enormous impact on the health and financial condition of the patient. It is worth developing diagnostic tools for bladder cancer. In our previous study, we found that the bladder carcinogen BBN increased urothelial global DNA CpG methylation and decreased GSTM1 protein expression in mice. Here, the correlation of BBN-decreased GSTM1 and GSTM gene CpG methylation status was analyzed in mice bladders. BBN treatment decreased the protein and mRNA expression of GSTM1, and the CpG methylation ratio of GSTM1 gene promoter was slightly increased in mice bladders. Unlike mouse GSTM1, the human GSTM1 gene tends to be deleted in bladder cancers. Among 7 human bladder cancer cell lines, GSTM1 gene is really null in 6 cell lines except one, T24 cells. The CpG methylation level of GSTM1 was 9.9% and 5-aza-dC did not significantly increase GSTM1 protein and mRNA expression in T24 cells; however, the GSTM5 gene was CpG hypermethylated (65.4%) and 5-aza-dC also did not affect the methylation ratio and mRNA expression. However, in other cell lines without GSTM1, 5-aza-dC increased GSTM5 expression and decreased its CpG DNA methylation ratio from 84.6% to 61.5% in 5637, and from 97.4% to 75% in J82 cells. In summary, two biomarkers of bladder tumor were provided. One is the GSTM1 gene which is down-regulated in mice bladder carcinogenesis and is usually deleted in human urothelial carcinoma, while the other is the GSTM5 gene, which is inactivated by DNA CpG methylation.

Description: by Anna Moretti, Michele Ghidini, Carmine De Angelis, Matteo Lambertini, Chiara Cremolini, Martina Imbimbo, Rossana Berardi, Massimo Di Maio, Stefano Cascinu, Nicla La Verde Background and objectives Relevant heterogeneity exists among Postgraduate Schools in Medical Oncology, also within the same country. In order to provide a comprehensive overview of the landscape of Italian Postgraduate Schools in Medical Oncology, the Italian Association of Medical Oncology (AIOM) undertook an online survey, inviting all the residents to describe their daily activities and to express their overall satisfaction about their programs. Methods A team composed of five residents and three consultants in medical oncology prepared a 38 items questionnaire that was published online in a reserved section, accessible through a link sent by e-mail. Residents were invited to anonymously fill in the questionnaire that included the following sub-sections: quality of teaching, clinical and research activity, overall satisfaction. Results Three-hundred and eleven (57%) out of 547 invited residents filled in the questionnaire. Two-hundred and twenty-three (72%) participants declared that attending lessons was frequently difficult and 153 (49%) declared they did not gain substantial improvement in their knowledge from them. Fifty-five percent stated that they did not receive lessons on palliative care. Their overall judgment about didactic activity was low in 63% of the interviewed. The satisfaction for clinical activity was in 86% of cases good: 84% recognized that, during the training period, they acquired a progressive independence on patients' management. About research activity, the majority (79%) of participants in the survey was actively engaged in managing patients included in clinical trials but the satisfaction level for the involvement in research activities was quite low (54%). Overall, 246 residents (79%) gave a positive global judgment of their Medical Oncology Schools. Conclusions The landscape of Italian Postgraduate Schools in Medical Oncology is quite heterogeneous across the country. Some improvements in the organization of teaching and in the access to research opportunity are needed; the perception about clinical activity and the overall judgment of the programs are quite satisfactory.

Description: by Jian Song, Zhangxiong Liu, Huilong Hong, Yansong Ma, Long Tian, Xinxiu Li, Ying-Hui Li, Rongxia Guan, Yong Guo, Li-Juan Qiu Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F 2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping.

Description: by Yuki Murai, Yuko Yotsumoto When individuals are asked to reproduce intervals of stimuli that are intermixedly presented at various times, longer intervals are often underestimated and shorter intervals overestimated. This phenomenon may be attributed to the central tendency of time perception, and suggests that our brain optimally encodes a stimulus interval based on current stimulus input and prior knowledge of the distribution of stimulus intervals. Two distinct systems are thought to be recruited in the perception of sub- and supra-second intervals. Sub-second timing is subject to local sensory processing, whereas supra-second timing depends on more centralized mechanisms. To clarify the factors that influence time perception, the present study investigated how both sensory modality and timescale affect the central tendency. In Experiment 1, participants were asked to reproduce sub- or supra-second intervals, defined by visual or auditory stimuli. In the sub-second range, the magnitude of the central tendency was significantly larger for visual intervals compared to auditory intervals, while visual and auditory intervals exhibited a correlated and comparable central tendency in the supra-second range. In Experiment 2, the ability to discriminate sub-second intervals in the reproduction task was controlled across modalities by using an interval discrimination task. Even when the ability to discriminate intervals was controlled, visual intervals exhibited a larger central tendency than auditory intervals in the sub-second range. In addition, the magnitude of the central tendency for visual and auditory sub-second intervals was significantly correlated. These results suggest that a common modality-independent mechanism is responsible for the supra-second central tendency, and that both the modality-dependent and modality-independent components of the timing system contribute to the central tendency in the sub-second range.

Description: by Martin W. von Websky, Koji Kitamura, Isis Ludwig-Portugall, Christian Kurts, Maximilian von Laffert, Joel LeMaoult, Edgardo D. Carosella, Kareem Abu-Elmagd, Joerg C. Kalff, Nico Schäfer The non-classical MHC I paralogue HLA-G is expressed by cytotrophoblast cells and implicated with fetomaternal tolerance by downregulating the maternal adaptive and innate immune response against the fetus. HLA-G expression correlates with favorable graft outcome in humans and recently promising immunosuppressive effects of therapeutic HLA-G in experimental transplantation (skin allograft acceptance) were shown. Consequently, we examined this novel therapeutic approach in solid organ transplantation. In this study, therapeutic recombinant HLA-G5 was evaluated for the first time in a solid organ model of acute rejection (ACR) after orthotopic intestinal transplantation (ITX). Allogenic ITX was performed in rats (Brown Norway to Lewis) with and without HLA-G treatment. It was found that HLA-G treatment significantly reduced histologically proven ACR at both an early and late postoperative timepoint (POD 4/7), concomitant to a functionally preserved graft contractility at POD 7. Interestingly, graft infiltration by myeloperoxidase+ cells was significantly reduced at POD7 by HLA-G treatment. Moreover, HLA-G treatment showed an effect on the allogenic T-cell immune response as assessed by flow cytometry: The influx of recipient-derived CD8 + T-cells into the graft mesenteric lymphnodes at POD7 was significantly reduced while CD4 + populations were not affected. As a potential mechanism of action, an induction of T-reg populations in the mesenteric lymphnodes was postulated, but flow cytometric analysis of classical CD4 + /CD25 + /FoxP3 + T reg -cells showed no significant alteration by HLA-G treatment. The novel therapeutic approach using recombinant HLA-G5 reported herein demonstrates a significant immunosuppressive effect in this model of allogenic experimental intestinal transplantation. This effect may be mediated via inhibition of recipient-derived CD8 + T-cell populations either directly or by induction of non-classical T reg populations.

Description: by Nayana Wijayathilaka, Madhava Meegaskumbura Vocalizing behavior of frogs and toads, once quantified, is useful for systematics, rapid species identification, behavioral experimentation and conservation monitoring. But yet, for many lineages vocalizations remain unknown or poorly quantified, especially in diversity rich tropical regions. Here we provide a quantitative acoustical analysis for all four Sri Lankan congeners of the genus Microhyla . Three of these species are endemic to the island, but Microhyla ornata is regionally widespread. Two of these endemics, M . karunaratnei (Critically Endangered) and M . zeylanica (Endangered), are highly threatened montane isolates; the other, M . mihintalei , is relatively common across the dry lowlands. We recorded and analyzed 100 advertisement calls from five calling males for each species, except for M . zeylanica , which only had 53 calls from three males suitable for analyses. All four species call in choruses and their vocal repertoires are simple compared to most frogs. Their calls contain multiple pulses and no frequency modulation. We quantified eight call characters. Call duration and number of pulses were higher for the two montane isolates (inhabiting cooler habitats at higher altitudes) compared to their lowland congeners. Microhyla zeylanica has the longest call duration (of 1.8 ± 0.12 s) and the highest number of pulses (of 61–92 pulses). The smallest of the species, Microhyla karunaratnei (16.2–18.3 mm), has the highest mean dominant frequency (3.3 ± 0.14 kHz) and pulse rate (77 ± 5.8 pulses per second). The calls separate well in the Principal Component space: PC1 axis is mostly explained by the number of pulses per call and call duration; PC2 is mostly explained by the pulse rate. A canonical means plot of a Discriminant Function analysis shows non-overlapping 95% confidence ellipses. This suggests that some call parameters can be used to distinguish these species effectively. We provide detailed descriptions for eight call properties and compare these with congeners for which data is available. This work provides a foundation for comparative bioacoustic analyses and species monitoring while facilitating the systematics of Microhyla across its range.

Description: by Rozalia Korbut, Foojan Mehrdana, Per Walter Kania, Marianne Halberg Larsen, Dorte Frees, Inger Dalsgaard, Louise von Gersdorff Jørgensen Immersion-vaccines (bacterins) are routinely used for aquacultured rainbow trout to protect against Yersinia ruckeri (Yr). During immersion vaccination, rainbow trout take up and process the antigens, which induce protection. The zebrafish was used as a model organism to study uptake mechanisms and subsequent antigen transport in fish. A genetically modified Yr was developed to constitutively express green fluorescent protein (GFP) and was used for bacterin production. Larval, juvenile and adult transparent zebrafish (tra:nac mutant) received a bath in the bacterin for up to 30 minutes. Samples were taken after 1 min, 15 min, 30 min, 2 h, 12 h and 24 h. At each sampling point fish were used for live imaging of the uptake using a fluorescence stereomicroscope and for immunohistochemistry (IHC). In adult fish, the bacterin could be traced within 30 min in scale pockets, skin, oesophagus, intestine and fins. Within two hours post bath (pb) Yr-antigens were visible in the spleen and at 24 h in liver and kidney. Bacteria were associated with the gills, but uptake at this location was limited. Antigens were rarely detected in the blood and never in the nares. In juvenile fish uptake of the bacterin was seen in the intestine 30 min pb and in the nares 2 hpb but never in scale pockets. Antigens were detected in the spleen 12 hpb. Zebrafish larvae exhibited major Yr uptake only in the mid-intestine enterocytes 24 hpb. The different life stages of zebrafish varied with regard to uptake locations, however the gut was consistently a major uptake site. Zebrafish and rainbow trout tend to have similar uptake mechanisms following immersion or bath vaccination, which points towards zebrafish as a suitable model organism for this aquacultured species.

Description: by Seema Thakur, Rajesh K. Grover, Sanjay Gupta, Ajay K. Yadav, Bhudev C. Das Of several subtypes of breast cancer, triple negative breast cancer (TNBC) is a highly aggressive tumor that lacks expression of hormone receptors for estrogen, progesterone and human epidermal growth factor receptor 2 and shows a worst prognosis. The small noncoding RNAs (miRNAs) considered as master regulator of gene expression play a key role in cancer initiation, progression and drug resistance and have emerged as attractive molecular biomarkers for diagnosis, prognosis and treatment targets in cancer. We have done expression profiling of selected miRNAs in paired serum and tissue samples of TNBC patients and corresponding cell lines and compared with that of other subtypes, in order to identify novel serum miRNA biomarkers for early detection and progression of TNBC. A total of 85 paired tumor tissues and sera with an equal number of adjacent normal tissue margins and normal sera from age matched healthy women including tissue and sera samples from 15 benign fibroadenomas were employed for the study. We report for the first time an extremely high prevalence (73.9%) of TNBC in premenopausal women below 35 years of age and a significant altered expression of a panel of three specific oncogenic miRNAs- miR-21, miR-221, miR-210, and three tumor suppressor miRNAs- miR-195, miR-145 and Let-7a in both tissues and corresponding sera of TNBC patients when compared with triple positive breast cancer (TPBC) patients. While miR-21, miR-221 and miR-210 showed significant over-expression, miR-195 and miR-145 were downregulated and well correlated with various clinicopathological and demographic risk factors, tumor grade, clinical stage and hormone receptor status. Interestingly, despite being a known tumor suppressor, Let-7a showed a significant overexpression in TNBCs. It is suggested that this panel of six miRNA signature may serve as a minimally invasive biomarker for an early detection of TNBC patients.

Description: by Martin G. Schwacha, Meenakshi Rani, Susannah E. Nicholson, Aaron M. Lewis, Travis L. Holloway, Salvador Sordo, Andrew P. Cap Background Gamma delta T-cells have been shown to be important to the early immunoinflammatory response to injury, independent of infection. This unique T-cell population acts to regulate cell trafficking and the release of cytokines and growth factors. We propose this sterile inflammatory response is in part associated with damage associated molecular patterns (DAMPs) generated by major injury, such as burn, and mediated via toll-like receptors (TLRs). It is unknown whether DAMPs can activate resident γδ T-cells that reside in skin. Methods Gamma delta T-cells were isolated from the skin of male C57BL/6 mice by enzymatic digestion. Mitochondrial DAMPs (MTDs) were generated from mitochondria isolated from mouse livers by sonication and centrifugation. Dermal γδ T-cells were incubated with MTDs (0–500 μg/ml) for 24 hr and cells and supernatants were collected for analysis. Results MTDs activated dermal γδ T-cells, as evidenced by increased TLR2 and TLR4 expression following in vitro exposure. MTDs also induced the production of inflammatory cytokines (IL-1β, IL-6), and growth factors (PDGF and VEGF) by γδ T-cells. Conclusions These findings herein support the concept that MTDs released after tissue/cellular injury are capable of activating dermal γδ T-cells. We propose that the activation of this unique T-cell population is central in the initiation of sterile inflammation and also contributes to the subsequent healing processes.

Description: by Tamaki Hayase Like various stressors, the addictive use of nicotine (NC) is associated with emotional symptoms such as anxiety and depression, although the underlying mechanisms have not yet been fully elucidated due to the complicated involvement of target neurotransmitter systems. In the elicitation of these emotional symptoms, the fundamental involvement of epigenetic mechanisms such as histone acetylation has recently been suggested. Furthermore, among the interacting neurotransmitter systems implicated in the effects of NC and stressors, the endocannabinoid (ECB) system is considered to contribute indispensably to anxiety and depression. In the present study, the epigenetic involvement of histone acetylation induced by histone deacetylase (HDAC) inhibitors was investigated in anxiety- and depression-related behavioral alterations caused by NC and/or immobilization stress (IM). Moreover, based on the contributing roles of the ECB system, the interacting influence of ECB ligands on the effects of HDAC inhibitors was evaluated in order to examine epigenetic therapeutic interventions. Anxiety-like (elevated plus-maze test) and depression-like (forced swimming test) behaviors, which were observed in mice treated with repeated (4 days) NC (subcutaneous 0.8 mg/kg) and/or IM (10 min), were blocked by the HDAC inhibitors sodium butyrate (SB) and valproic acid (VA). The cannabinoid type 1 (CB1) agonist ACPA (arachidonylcyclopropylamide; AC) also antagonized these behaviors. Conversely, the CB1 antagonist SR 141716A (SR), which counteracted the effects of AC, attenuated the anxiolytic-like effects of the HDAC inhibitors commonly in the NC and/or IM groups. SR also attenuated the antidepressant-like effects of the HDAC inhibitors, most notably in the IM group. From these results, the combined involvement of histone acetylation and ECB system was shown in anxiety- and depression-related behaviors. In the NC treatment groups, the limited influence of SR against the HDAC inhibitor-induced antidepressant-like effects may reflect the characteristic involvement of histone acetylation within the NC-related neurotransmitter systems other than the ECB system.

Description: Gone or just out of sight? The apparent disappearance of aromatic litter components in soils Thimo Klotzbücher, Karsten Kalbitz, Chiara Cerli, Peter J. Hernes, and Klaus Kaiser SOIL, 2, 325-335, doi:10.5194/soil-2-325-2016, 2016 Uncertainties concerning stabilization of organic compounds in soil limit our basic understanding on soil organic matter (SOM) formation and our ability to model and manage effects of global change on SOM stocks. One controversially debated aspect is the contribution of aromatic litter components, such as lignin and tannins, to stable SOM forms. Here, we summarize and discuss the inconsistencies and propose research options to clear them.

Description: Structure of Suasselkä Postglacial Fault in northern Finland obtained by analysis of local events and ambient seismic noise Nikita Afonin, Elena Kozlovskaya, Ilmo Kukkonen, and DAFNE/FINLAND Working Group Solid Earth Discuss., doi:10.5194/se-2016-90,2016 Manuscript under review for SE (discussion: open, 0 comments) Understanding inner structure of seismogenic faults and their ability to reactivate is particularly important in investigating continental intraplate seismicity regime. In our study we address this problem using analysis of local seismic events and ambient seismic noise recorded by the temporary DAFNE array in northern Fennoscandian Shield. The main purpose of the DAFNE/FINLAND passive seismic array experiment was to characterize the present-day seismicity of the Suasselkä post-glacial fault (SPGF) that was proposed as one potential target for the DAFNE (Drilling Active Faults in Northern Europe) project. The DAFNE/FINLAND array comprised the area of about 20 to 100 km and consisted of 8 short-period and 4 broad-band 3-component autonomous seismic stations installed in the close vicinity of the fault area. The array recorded continuous seismic data during September, 2011–May, 2013. Recordings of the array have being analyzed in order to identify and locate natural earthquakes from the fault area and to discriminate them from the blasts in the Kittilä Gold Mine. As a result, we found several dozens of natural seismic events originating from the fault area, which proves that the fault is still seismically active. In order to study the inner structure of the SPGF we use cross-correlation of ambient seismic noise recorded by the array. Analysis of azimuthal distribution of noise sources demonstrated that during the time interval under consideration the distribution of noise sources is close to the uniform one. The continuous data were processed in several steps including single station data analysis, instrument response removal and time-domain stacking. The data were used to estimate empirical Green’s functions between pairs of stations in the frequency band of 0.1–1 Hz and to calculate correspondent surface wave dispersion curves. The S-wave velocity models were obtained as a result of dispersion curves inversion. The results suggest that the area of the SPGF corresponds to a narrow region of low S-wave velocities surrounded by rocks with high S-wave velocities. We interpret this low velocity region as a non-healed mechanically weak fault damage zone (FDZ) that remained after the last major earthquake that occurred after the last glaciation.

Description: Structure of Suasselkä Postglacial Fault in northern Finland obtained by analysis of local events and ambient seismic noise Nikita Afonin, Elena Kozlovskaya, Ilmo Kukkonen, and DAFNE/FINLAND Working Group Solid Earth Discuss., doi:10.5194/se-2016-90,2016 Manuscript under review for SE (discussion: open, 0 comments) Understanding inner structure of seismogenic faults and their ability to reactivate is particularly important in investigating continental intraplate seismicity regime. In our study we address this problem using analysis of local seismic events and ambient seismic noise recorded by the temporary DAFNE array in northern Fennoscandian Shield. The main purpose of the DAFNE/FINLAND passive seismic array experiment was to characterize the present-day seismicity of the Suasselkä post-glacial fault (SPGF) that was proposed as one potential target for the DAFNE (Drilling Active Faults in Northern Europe) project. The DAFNE/FINLAND array comprised the area of about 20 to 100 km and consisted of 8 short-period and 4 broad-band 3-component autonomous seismic stations installed in the close vicinity of the fault area. The array recorded continuous seismic data during September, 2011–May, 2013. Recordings of the array have being analyzed in order to identify and locate natural earthquakes from the fault area and to discriminate them from the blasts in the Kittilä Gold Mine. As a result, we found several dozens of natural seismic events originating from the fault area, which proves that the fault is still seismically active. In order to study the inner structure of the SPGF we use cross-correlation of ambient seismic noise recorded by the array. Analysis of azimuthal distribution of noise sources demonstrated that during the time interval under consideration the distribution of noise sources is close to the uniform one. The continuous data were processed in several steps including single station data analysis, instrument response removal and time-domain stacking. The data were used to estimate empirical Green’s functions between pairs of stations in the frequency band of 0.1–1 Hz and to calculate correspondent surface wave dispersion curves. The S-wave velocity models were obtained as a result of dispersion curves inversion. The results suggest that the area of the SPGF corresponds to a narrow region of low S-wave velocities surrounded by rocks with high S-wave velocities. We interpret this low velocity region as a non-healed mechanically weak fault damage zone (FDZ) that remained after the last major earthquake that occurred after the last glaciation.

Description: Comparison of box counting and correlation dimension methods in well logging data analysis associate with the texture of volcanic rocks D. Mou and Z. W. Wang Nonlin. Processes Geophys. Discuss., doi:10.5194/npg-2014-85,2016 Manuscript under review for NPG (discussion: open, 0 comments) We have developed a fractal analysis method to estimate the dimension of well logging curves in Liaohe oil field, China. The box counting and correlation dimension are methods that can be applied to predict the texture of volcanic rocks with calculation the fractal dimension of well logging curves. The well logging curves are composed of gamma ray (GR), compensated neutron logs (CNL), acoustic (AC), density (DEN), Resistivity lateral log deep ( R LLD ), every curve contains a total of 6000 logging data. The dimension of well logging curves are calculated using box counting and correlation algorithms respectively. It is shown that two types of dimension of CNL, DEN and AC have the same average value. The box counting dimension of volcanic lava is lower than the pyroclastic rock obviously. The majority of correlation dimension of volcanic lava is lower than the pyroclastic rock, but a small amount of correlation dimension of volcanic lava is equal to the pyroclastic rock. It is demonstrated that the box counting dimension is more suitable for predicting the texture of volcanic rocks. Applications to logging data, A well show the relationship between the fractal dimension and the texture of volcanic rock in certain depth.

Description: First year of the new Arctic AWIPEV-COSYNA cabled Underwater Observatory in Kongsfjorden, Spitsbergen Philipp Fischer, Max Schwanitz, Reiner Loth, Uwe Posner, Markus Brand, and Friedhelm Schröder Ocean Sci. Discuss., doi:10.5194/os-2016-52,2016 Manuscript under review for OS (discussion: open, 0 comments) We observed oceanographic and community data from October 2013 to November 2014 in the shallow waters of Kongsfjorden on the west coast of Svalbard (Norway) using remote controlled hydrographic and optic sensors. Daily vertical profiles of temperature, salinity and turbidity were sampled together with stereo images of the macrobiotic community, including fish. A distinct seasonal cycle in total species abundances was found with surprisingly high animal counts during the polar winter.

Description: Landfast ice thickness in the Canadian Arctic Archipelago from observations and models Stephen E. L. Howell, Frédéric Laliberté, Ron Kwok, Chris Derksen, and Joshua King The Cryosphere, 10, 1463-1475, doi:10.5194/tc-10-1463-2016, 2016 The Canadian Ice Service record of observed landfast ice and snow thickness represents one of the longest in the Arctic that spans over 5 decades. We analyze this record to report on long-term trends and variability of ice and snow thickness within the Canadian Arctic Archipelago (CAA). Results indicate a thinning of ice at several sites in the CAA. State-of-the-art climate models still have difficultly capturing observed ice thickness values in the CAA and should be used with caution.

Description: Coastal dynamics and submarine permafrost in shallow water of the central Laptev Sea, East Siberia Pier Paul Overduin, Sebastian Wetterich, Frank Günther, Mikhail N. Grigoriev, Guido Grosse, Lutz Schirrmeister, Hans-Wolfgang Hubberten, and Aleksandr Makarov The Cryosphere, 10, 1449-1462, doi:10.5194/tc-10-1449-2016, 2016 How fast does permafrost warm up and thaw after it is covered by the sea? Ice-rich permafrost in the Laptev Sea, Siberia, is rapidly eroded by warm air and waves. We used a floating electrical technique to measure the depth of permafrost thaw below the sea, and compared it to 60 years of coastline retreat and permafrost depths from drilling 30 years ago. Thaw is rapid right after flooding of the land and slows over time. The depth of permafrost is related to how fast the coast retreats.

Description: Age of the Mt. Ortles ice cores, the Tyrolean Iceman and glaciation of the highest summit of South Tyrol since the Northern Hemisphere Climatic Optimum Paolo Gabrielli, Carlo Barbante, Giuliano Bertagna, Michele Bertó, Daniel Binder, Alberto Carton, Luca Carturan, Federico Cazorzi, Giulio Cozzi, Giancarlo Dalla Fontana, Mary Davis, Fabrizio De Blasi, Roberto Dinale, Gianfranco Dragà, Giuliano Dreossi, Daniela Festi, Massimo Frezzotti, Jacopo Gabrieli, Stephan Galos, Patrick Ginot, Petra Heidenwolf, Theo M. Jenk, Natalie Kehrwald, Donald Kenny, Olivier Magand, Volkmar Mair, Vladimir Mikhalenko, Ping Nan Lin, Klaus Oeggl, Gianni Piffer, Mirko Rinaldi, Ulrich Schotterer, Margit Schwikowski, Roberto Seppi, Andrea Spolaor, Barbara Stenni, Davdi Tonidandel, CChiara Uglietti, Victor Zagorodnov, Thomas Zanoner, and Piero Zennaro The Cryosphere Discuss., doi:10.5194/tc-2016-159,2016 Manuscript under review for TC (discussion: open, 0 comments) New ice cores were extracted from Alto dell'Ortles, the highest glacier of South Tyrol in the Italian Alps, to check whether prehistoric ice, that is coeval to the famous 5200 years old Tyrolean Iceman, is still preserved in this region. Dating of the ice cores confirms the hypothesis and indicates that the drilling site was glaciated since the end of the Northern Hemisphere Climatic Optimum (7000 BP). We also infer that an unprecedented acceleration of the glacier flow has just recently begun.

Description: Combined diurnal variations of discharge and hydrochemistry of the Isunnguata Sermia outlet of the Greenland Ice Sheet give in sight on sub glacial conditions Joseph Graly, Joel Harrington, and Neil Humphrey The Cryosphere Discuss., doi:10.5194/tc-2016-137,2016 Manuscript under review for TC (discussion: open, 0 comments) At a major outlet of the Greenland Ice Sheet in West Greenland, we find that the chemical solutes is the emerging subglacial waters are out of phase with water discharge and can spike in concentration during waning flow. This suggests that the subglacial waters are spreading out across a large area of the glacial bed throughout the day, stimulating chemical weathering beyond the major water distribution channels.

Description: Why did the storm ex-Gaston (2010) fail to redevelop during the PREDICT experiment? Thomas M. Freismuth, Blake Rutherford, Mark A. Boothe, and Michael T. Montgomery Atmos. Chem. Phys., 16, 8511-8519, doi:10.5194/acp-16-8511-2016, 2016 Numerical model analyses are used to investigate the role of dry, environmental air in the failed redevelopment of a tropical cyclone (ex-Gaston, 2010). As early as 12:00 UTC 2 September 2010, a dry layer at and above 600 hPa results in a decrease in the vertical mass flux and vertical, relative vorticity. The intrusion of dry air led to a reduction in vorticity and a compromised pouch at these middle levels. This study supports work looking at the role of dry air in moist convection.

Description: A comparative analysis of UV nadir-backscatter and infrared limb-emission ozone data assimilation Rossana Dragani Atmos. Chem. Phys., 16, 8539-8557, doi:10.5194/acp-16-8539-2016, 2016 We present an assessment of ultraviolet nadir-backscatter and infrared limb-emission ozone data assimilation. Understanding the differences in the impact produced by the assimilation of limb and nadir ozone data is relevant to many applications, including climate reanalysis and air quality. The results show the potential and limitations of each dataset and support the need for a more balanced long-term availability of both types of sensors than currently envisaged.

Description: Continuous measurements of isotopic composition of water vapour on the East Antarctic Plateau Mathieu Casado, Amaelle Landais, Valérie Masson-Delmotte, Christophe Genthon, Erik Kerstel, Samir Kassi, Laurent Arnaud, Ghislain Picard, Frederic Prie, Olivier Cattani, Hans-Christian Steen-Larsen, Etienne Vignon, and Peter Cermak Atmos. Chem. Phys., 16, 8521-8538, doi:10.5194/acp-16-8521-2016, 2016 Climatic conditions in Concordia are very cold (−55 °C in average) and very dry, imposing difficult conditions to measure the water vapour isotopic composition. New developments in infrared spectroscopy enable now the measurement of isotopic composition in water vapour traces (down to 20 ppmv). Here we present the results results of a first campaign of measurement of isotopic composition of water vapour in Concordia, the site where the 800 000 years long ice core was drilled.

Description: Surface Renewal as a Significant Mechanism for Dust Emission Jie Zhang, Zhenjiao Teng, Ning Huang, Lei Guo, and Yaping Shao Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-421,2016 Manuscript under review for ACP (discussion: open, 0 comments) In spite of the tremendous efforts, many questions remain unanswered regarding dust emission mechanisms. A series of wind-tunnel experiments are carried out on dust emissions from different soil surfaces to better understand relevant mechanisms. Here are some interesting results that demonstrate the importance of surface renewal mechanism which was normally neglected in previous researches and is strongly recommended to be considered in future dust models.

Description: Variations in O 3 , CO, and CH 4 over the Bay of Bengal during the summer monsoon season: Ship-borne measurements and model simulations Imran A. Girach, Narendra Ojha, Prabha R. Nair, Andrea Pozzer, Yogesh K. Tiwari, K. Ravi Kumar, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-595,2016 Manuscript under review for ACP (discussion: open, 0 comments) This study presents first ship-borne measurements of trace gases over the Bay of Bengal during summer monsoon. The observed variations in trace gases are shown to be due to dynamics/transport and en-route photochemistry. Analysis of meteorological and chemical fields shows that significantly lower ozone during rainfall is associated with the downdrafts. A regional model reproduces the observed variations and revealed the rapid transport of ozone across the Bay of Bengal during an event.

Description: Chemical Characteristics of Marine Fine Aerosols over Sea and at Offshore Islands during Three Cruise Sampling Campaigns in the Taiwan Strait– Sea Salts and Anthropogenic Particles Tsung-Chang Li, Chung-Shin Yuan, Chung-Hsuang Hung, Hsun-Yu Lin, Hu-Ching Huang, and Chon-Lin Lee Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-384,2016 Manuscript under review for ACP (discussion: open, 0 comments) This manuscript is significant because it is important to establish data on the background physicochemical characteristics of atmospheric fine particles, as well as their spatial distributions and seasonal variations given various meteorological conditions, and the results of this study will be very much valuable for clarifying the transportation PM 2.5 over sea and at the offshore islands at the Taiwan Strait, which can further fill the the important blank for the global atmospheric research.

Description: Continuous measurements of isotopic composition of water vapour on the East Antarctic Plateau Mathieu Casado, Amaelle Landais, Valérie Masson-Delmotte, Christophe Genthon, Erik Kerstel, Samir Kassi, Laurent Arnaud, Ghislain Picard, Frederic Prie, Olivier Cattani, Hans-Christian Steen-Larsen, Etienne Vignon, and Peter Cermak Atmos. Chem. Phys., 16, 8521-8538, doi:10.5194/acp-16-8521-2016, 2016 Climatic conditions in Concordia are very cold (−55 °C in average) and very dry, imposing difficult conditions to measure the water vapour isotopic composition. New developments in infrared spectroscopy enable now the measurement of isotopic composition in water vapour traces (down to 20 ppmv). Here we present the results results of a first campaign of measurement of isotopic composition of water vapour in Concordia, the site where the 800 000 years long ice core was drilled.

Description: On the role of tropopause folds in summertime tropospheric ozone over the eastern Mediterranean and the Middle East Dimitris Akritidis, Andrea Pozzer, Prodromos Zanis, Evangelos Tyrlis, Bojan Škerlak, Michael Sprenger, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-547,2016 Manuscript under review for ACP (discussion: open, 0 comments) We investigate the contribution of tropopause folds in the summertime tropospheric ozone pool over the eastern Mediterranean and the Middle East. For this purpose we use the EMAC atmospheric chemistry climate model and a fold identification algorithm. A clear increase of ozone is found in the middle troposphere due to fold activity. The interannual variability of near surface ozone over the eastern Mediterranean is related to that of both tropopause folds and ozone in the free troposphere.

Description: A Polarimetric Scattering Database for Non-spherical Ice Particles at MicrowaveWavelengths Yinghui Lu, Zhiyuan Jiang, Kultegin Aydin, Johannes Verlinde, Eugene E. Clothiaux, and Giovanni Botta Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-228,2016 Manuscript under review for AMT (discussion: open, 0 comments) The database contains the complete(polarimatric) scattering information for different types of ice particles at different incident and scattered radiation directions at 4 microwave wavelengths. These results are useful for understanding the dependence of ice-particle scattering properties on ice-particle orientation with respect to the incident and scattered radiation. It is also useful in ice property retrievals, radar forward simulation.

Description: Variations in O 3 , CO, and CH 4 over the Bay of Bengal during the summer monsoon season: Ship-borne measurements and model simulations Imran A. Girach, Narendra Ojha, Prabha R. Nair, Andrea Pozzer, Yogesh K. Tiwari, K. Ravi Kumar, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-595,2016 Manuscript under review for ACP (discussion: open, 0 comments) This study presents first ship-borne measurements of trace gases over the Bay of Bengal during summer monsoon. The observed variations in trace gases are shown to be due to dynamics/transport and en-route photochemistry. Analysis of meteorological and chemical fields shows that significantly lower ozone during rainfall is associated with the downdrafts. A regional model reproduces the observed variations and revealed the rapid transport of ozone across the Bay of Bengal during an event.

Description: A comparative analysis of UV nadir-backscatter and infrared limb-emission ozone data assimilation Rossana Dragani Atmos. Chem. Phys., 16, 8539-8557, doi:10.5194/acp-16-8539-2016, 2016 We present an assessment of ultraviolet nadir-backscatter and infrared limb-emission ozone data assimilation. Understanding the differences in the impact produced by the assimilation of limb and nadir ozone data is relevant to many applications, including climate reanalysis and air quality. The results show the potential and limitations of each dataset and support the need for a more balanced long-term availability of both types of sensors than currently envisaged.

Description: Why did the storm ex-Gaston (2010) fail to redevelop during the PREDICT experiment? Thomas M. Freismuth, Blake Rutherford, Mark A. Boothe, and Michael T. Montgomery Atmos. Chem. Phys., 16, 8511-8519, doi:10.5194/acp-16-8511-2016, 2016 Numerical model analyses are used to investigate the role of dry, environmental air in the failed redevelopment of a tropical cyclone (ex-Gaston, 2010). As early as 12:00 UTC 2 September 2010, a dry layer at and above 600 hPa results in a decrease in the vertical mass flux and vertical, relative vorticity. The intrusion of dry air led to a reduction in vorticity and a compromised pouch at these middle levels. This study supports work looking at the role of dry air in moist convection.

Description: Thermal infrared laser heterodyne spectro-radiometry for solar occultation atmospheric CO 2 measurements Alex Hoffmann, Neil A. Macleod, Marko Huebner, and Damien Weidmann Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-142,2016 Manuscript under review for AMT (discussion: open, 0 comments) This paper focuses on the demonstration and assessment of thermal infrared laser heterodyne spectro-radiometry for the remote sensing of carbon dioxide (CO 2 ). A research instrument has been developed and operated from the ground using direct sunlight to measure CO 2 to a high precision. This technology would enable the development of high-performance miniature ground-based sounders to complement existing measurement networks and contribute to the improvement of global carbon emission assessment.

Description: A Polarimetric Scattering Database for Non-spherical Ice Particles at MicrowaveWavelengths Yinghui Lu, Zhiyuan Jiang, Kultegin Aydin, Johannes Verlinde, Eugene E. Clothiaux, and Giovanni Botta Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-228,2016 Manuscript under review for AMT (discussion: open, 0 comments) The database contains the complete(polarimatric) scattering information for different types of ice particles at different incident and scattered radiation directions at 4 microwave wavelengths. These results are useful for understanding the dependence of ice-particle scattering properties on ice-particle orientation with respect to the incident and scattered radiation. It is also useful in ice property retrievals, radar forward simulation.

Description: Chemical Characteristics of Marine Fine Aerosols over Sea and at Offshore Islands during Three Cruise Sampling Campaigns in the Taiwan Strait– Sea Salts and Anthropogenic Particles Tsung-Chang Li, Chung-Shin Yuan, Chung-Hsuang Hung, Hsun-Yu Lin, Hu-Ching Huang, and Chon-Lin Lee Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-384,2016 Manuscript under review for ACP (discussion: open, 0 comments) This manuscript is significant because it is important to establish data on the background physicochemical characteristics of atmospheric fine particles, as well as their spatial distributions and seasonal variations given various meteorological conditions, and the results of this study will be very much valuable for clarifying the transportation PM 2.5 over sea and at the offshore islands at the Taiwan Strait, which can further fill the the important blank for the global atmospheric research.

Description: Evaluation of Machine Learning Algorithms for Classification of Primary Biological Aerosol using a new UV-LIF spectrometer Simon Ruske, David O. Topping, Virginia E. Foot, Paul H. Kaye, Warren R. Stanley, Ian Crawford, Andrew P. Morse, and Martin W. Gallagher Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-214,2016 Manuscript under review for AMT (discussion: open, 0 comments) Particles such as Bacteria, Pollen and Fungal spores have important implications within the environment and public health sectors. Here we evaluate the performance of various different methods for distinguishing between these different types of particles using a new instrument. We demonstrate that there may be better alternatives to the currently used methods which can be further investigated in future research.

Description: Identification of the cloud base height over the central Himalayan region: Intercomparison of Ceilometer and Doppler Lidar K. K. Shukla, K. Niranjan Kumar, D. V. Phanikumar, R. K. Newsom, V. R. Kotamarthi, T. B. M. J. Ouarda, and M. V. Ratnam Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-162,2016 Manuscript under review for AMT (discussion: open, 0 comments) Estimation of Cloud base height was carried out by using various ground based instruments (Doppler Lidar and Ceilometer) and satellite datasets (MODIS) over central Himalayan region for the first time. The present study demonstrates the potential of Doppler Lidar in precise estimation of cloud base height and updraft velocities. More such deployments will be invaluable inputs for regional weather prediction models over complex Himalayan terrains.

Description: On the role of tropopause folds in summertime tropospheric ozone over the eastern Mediterranean and the Middle East Dimitris Akritidis, Andrea Pozzer, Prodromos Zanis, Evangelos Tyrlis, Bojan Škerlak, Michael Sprenger, and Jos Lelieveld Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-547,2016 Manuscript under review for ACP (discussion: open, 0 comments) We investigate the contribution of tropopause folds in the summertime tropospheric ozone pool over the eastern Mediterranean and the Middle East. For this purpose we use the EMAC atmospheric chemistry climate model and a fold identification algorithm. A clear increase of ozone is found in the middle troposphere due to fold activity. The interannual variability of near surface ozone over the eastern Mediterranean is related to that of both tropopause folds and ozone in the free troposphere.

Description: Increased nitrate and decreased δ 15 N–NO 3 − in the Greenland Arctic after 1940 attributed to North American oil burning Nathan J. Chellman, Meredith G. Hastings, and Joseph R. McConnell The Cryosphere Discuss., doi:10.5194/tc-2016-163,2016 Manuscript under review for TC (discussion: open, 0 comments) This manuscript analyzes the changing sources of nitrate deposition to Greenland since 1760 CE using a dataset consisting of sub-seasonally resolved nitrogen isotopes of nitrate and source tracers. Correlations amongst ion concentration, source tracers, and the δ 15 N–NO 3 − provide evidence of the impact of biomass burning and fossil fuel combustion emissions of nitrogen oxides and suggest that oil combustion is the likely driver of increased nitrate concentration in Greenland ice since 1940 CE.

Description: Inversion of geothermal heat flux in a thermomechanically coupled nonlinear Stokes ice sheet model Hongyu Zhu, Noemi Petra, Georg Stadler, Tobin Isaac, Thomas J. R. Hughes, and Omar Ghattas The Cryosphere, 10, 1477-1494, doi:10.5194/tc-10-1477-2016, 2016 We study how well the basal geothermal heat flux can be inferred from surface velocity observations using a thermomechanically coupled nonlinear Stokes ice sheet model. The prospects and limitations of this inversion is studied in two and three dimensional model problems. We also argue that a one-way coupled approach for the adjoint equations motivated by staggered solvers for forward multiphysics problems can lead to an incorrect gradient and premature termination of the optimization iteration.

Description: Increased nitrate and decreased δ 15 N–NO 3 − in the Greenland Arctic after 1940 attributed to North American oil burning Nathan J. Chellman, Meredith G. Hastings, and Joseph R. McConnell The Cryosphere Discuss., doi:10.5194/tc-2016-163,2016 Manuscript under review for TC (discussion: open, 0 comments) This manuscript analyzes the changing sources of nitrate deposition to Greenland since 1760 CE using a dataset consisting of sub-seasonally resolved nitrogen isotopes of nitrate and source tracers. Correlations amongst ion concentration, source tracers, and the δ 15 N–NO 3 − provide evidence of the impact of biomass burning and fossil fuel combustion emissions of nitrogen oxides and suggest that oil combustion is the likely driver of increased nitrate concentration in Greenland ice since 1940 CE.

Description: Improving the inter-hemispheric gradient of total column atmospheric CO 2 and CH 4 in simulations with the ECMWF semi-Lagrangian atmospheric global model Anna Agusti-Panareda, Michail Diamantakis, Victor Bayona, Friedrich Klappenbach, and Andre Butz Geosci. Model Dev. Discuss., doi:10.5194/gmd-2016-143,2016 Manuscript under review for GMD (discussion: open, 0 comments) This paper demonstrates how important mass fixers can be in the simulation of long-lived greenhouse gases using transport models based on the highly efficient semi-lagrangian advection scheme. Mass fixers can have a large impact on the representation of the inter-hemispheric gradient of CO 2 and CH 4 , a crucial feature of their distribution. This work is relevant for models simulating atmospheric composition that use semi-lagrangian advection schemes both for climate and air quality applications.

Description: sUAS and their application in observing geomorphological processes Jozef Gallik and Lenka Bolešová Solid Earth, 7, 1033-1042, doi:10.5194/se-7-1033-2016, 2016 Technology is moving ahead very fast, and so researchers have new possibilities for their research. We tried to demonstrate benefits of using remote-sensing technology (Phantom 1 drone) such as its accuracy in the terrain, easy access to hardly accessible areas, and the possibility to collect data even during unfavourable weather conditions. The high mountainous environment provided us great conditions for testing the drone as a device for very easy and accurate mapping of natural phenomena.

Description: Response of seasonal soil freeze depth to climate change across China Xiaoqing Peng, Oliver W. Frauenfeld, Tingjun Zhang, Kang Wang, Bin Cao, Xinyue Zhong, Hang Su, and Cuicui Mu The Cryosphere Discuss., doi:10.5194/tc-2016-129,2016 Manuscript under review for TC (discussion: open, 0 comments) Previous researches paid more attention on the permafrost, e.g. active layer thickness, soil temperature, permafrost area extent, and associated with permafrost degradation leading other changes. However, seasonally frozen ground, vast area extent, did not focus by so much attention. Here, we combined more than 800 observation station data and gridded data to investigate soil freeze depth across China. The results indicate that soil freeze depth increase with climate warming.

Description: Slight glacier reduction over the northwestern Tibetan Plateau despite significant recent warming Yetang Wang, Shugui Hou, Wenling An, Hongxi Pang, and Yaping Liu The Cryosphere Discuss., doi:10.5194/tc-2016-165,2016 Manuscript under review for TC (discussion: open, 0 comments) This study further confirms "Pamir–Karakoram–Western-Kunlun-Mountain (northwestern Tibetan Plateau) Glacier Anomaly". Slight glacier reduction over the northwestern Tibetan Plateau may result from more accumulation from increased precipitation in winter which to great extent protects it from mass reductions under climate warming during 1961–2000. Warming slowdown since 2000 happening at this region may further mitigate glacier mass reduction.

Description: Response of seasonal soil freeze depth to climate change across China Xiaoqing Peng, Oliver W. Frauenfeld, Tingjun Zhang, Kang Wang, Bin Cao, Xinyue Zhong, Hang Su, and Cuicui Mu The Cryosphere Discuss., doi:10.5194/tc-2016-129,2016 Manuscript under review for TC (discussion: open, 0 comments) Previous researches paid more attention on the permafrost, e.g. active layer thickness, soil temperature, permafrost area extent, and associated with permafrost degradation leading other changes. However, seasonally frozen ground, vast area extent, did not focus by so much attention. Here, we combined more than 800 observation station data and gridded data to investigate soil freeze depth across China. The results indicate that soil freeze depth increase with climate warming.

Description: by Mario Novkovic, Lucas Onder, Jovana Cupovic, Jun Abe, David Bomze, Viviana Cremasco, Elke Scandella, Jens V. Stein, Gennady Bocharov, Shannon J. Turley, Burkhard Ludewig Fibroblastic reticular cells (FRCs) form the cellular scaffold of lymph nodes (LNs) and establish distinct microenvironmental niches to provide key molecules that drive innate and adaptive immune responses and control immune regulatory processes. Here, we have used a graph theory-based systems biology approach to determine topological properties and robustness of the LN FRC network in mice. We found that the FRC network exhibits an imprinted small-world topology that is fully regenerated within 4 wk after complete FRC ablation. Moreover, in silico perturbation analysis and in vivo validation revealed that LNs can tolerate a loss of approximately 50% of their FRCs without substantial impairment of immune cell recruitment, intranodal T cell migration, and dendritic cell-mediated activation of antiviral CD8 + T cells. Overall, our study reveals the high topological robustness of the FRC network and the critical role of the network integrity for the activation of adaptive immune responses.

Description: by Jose L. Herrera, Ravi Srinivasan, John S. Brownstein, Alison P. Galvani, Lauren Ancel Meyers As infectious disease surveillance systems expand to include digital, crowd-sourced, and social network data, public health agencies are gaining unprecedented access to high-resolution data and have an opportunity to selectively monitor informative individuals. Contact networks, which are the webs of interaction through which diseases spread, determine whether and when individuals become infected, and thus who might serve as early and accurate surveillance sensors. Here, we evaluate three strategies for selecting sensors—sampling the most connected, random, and friends of random individuals—in three complex social networks—a simple scale-free network, an empirical Venezuelan college student network, and an empirical Montreal wireless hotspot usage network. Across five different surveillance goals—early and accurate detection of epidemic emergence and peak, and general situational awareness—we find that the optimal choice of sensors depends on the public health goal, the underlying network and the reproduction number of the disease ( R 0 ). For diseases with a low R 0 , the most connected individuals provide the earliest and most accurate information about both the onset and peak of an outbreak. However, identifying network hubs is often impractical, and they can be misleading if monitored for general situational awareness, if the underlying network has significant community structure, or if R 0 is high or unknown. Taking a theoretical approach, we also derive the optimal surveillance system for early outbreak detection but find that real-world identification of such sensors would be nearly impossible. By contrast, the friends-of-random strategy offers a more practical and robust alternative. It can be readily implemented without prior knowledge of the network, and by identifying sensors with higher than average, but not the highest, epidemiological risk, it provides reasonably early and accurate information.

Description: by Liying Guan, Xuehua Ma, Jingyan Zhang, Jia-Jia Liu, Yingchun Wang, Mei Ding Eukaryotic cells extend a variety of surface protrusions to direct cell motility. Formation of protrusions is mediated by coordinated actions between the plasma membrane and the underlying actin cytoskeleton. Here, we found that the single calponin homology (CH) domain-containing protein CHDP-1 induces the formation of cell protrusions in C . elegans . CHDP-1 is anchored to the cortex through its amphipathic helix. CHDP-1 associates through its CH domain with the small GTPase Rac1/CED-10, which is a key regulator of the actin cytoskeleton. CHDP-1 preferentially binds to the GTP-bound active form of the CED-10 protein and preserves the membrane localization of GTP-CED-10. Hence, by coupling membrane expansion to Rac1-mediated actin dynamics, CHDP-1 promotes the formation of cellular protrusions in vivo .

Description: by Masashi Naito, Masaki Mori, Masayo Inagawa, Kohei Miyata, Naohiro Hashimoto, Sakae Tanaka, Hiroshi Asahara Cell differentiation status is defined by the gene expression profile, which is coordinately controlled by epigenetic mechanisms. Cell type-specific DNA methylation patterns are established by chromatin modifiers including de novo DNA methyltransferases, such as Dnmt3a and Dnmt3b . Since the discovery of the myogenic master gene MyoD , myogenic differentiation has been utilized as a model system to study tissue differentiation. Although knowledge about myogenic gene networks is accumulating, there is only a limited understanding of how DNA methylation controls the myogenic gene program. With an aim to elucidate the role of DNA methylation in muscle development and regeneration, we investigate the consequences of mutating Dnmt3a in muscle precursor cells in mice. Pax3 promoter-driven Dnmt3a -conditional knockout (cKO) mice exhibit decreased organ mass in the skeletal muscles, and attenuated regeneration after cardiotoxin-induced muscle injury. In addition, Dnmt3a -null satellite cells (SCs) exhibit a striking loss of proliferation in culture. Transcriptome analysis reveals dysregulated expression of p57Kip2 , a member of the Cip/Kip family of cyclin-dependent kinase inhibitors (CDKIs), in the Dnmt3a -KO SCs. Moreover, RNAi-mediated depletion of p57Kip2 replenishes the proliferation activity of the SCs, thus establishing a role for the Dnmt3a - p57Kip2 axis in the regulation of SC proliferation. Consistent with these findings, Dnmt3a -cKO muscles exhibit fewer Pax7 + SCs, which show increased expression of p57Kip2 protein. Thus, Dnmt3a is found to maintain muscle homeostasis by epigenetically regulating the proliferation of SCs through p57Kip2 .

Description: by William Zerges

Description: by Wenjun Ji, Zhou Shi, Jingyi Huang, Shuo Li

Description: by Sheetal Prakash Silal, Francesca Little, Karen Irma Barnes, Lisa Jane White

Description: Effect of tropical cyclones on the stratosphere–troposphere exchange observed using satellite observations over the north Indian Ocean M. Venkat Ratnam, S. Ravindra Babu, S. S. Das, G. Basha, B. V. Krishnamurthy, and B. Venkateswararao Atmos. Chem. Phys., 16, 8581-8591, doi:10.5194/acp-16-8581-2016, 2016 The impact of cyclones that occurred over the north Indian Ocean during 2007–2013 on the STE process is quantified using satellite observations. It is shown that cyclones have a significant impact on the tropopause structure, ozone and water vapour budget, and consequentially STE in the UTLS region. The cross-tropopause mass flux from the stratosphere to the troposphere for cyclonic storms is found to be 0.05 ± 0.29 × 10 −3  kg m −2 , and for very severe cyclonic storms it is 0.5 ± 1.07 × 10 −3  kg m −2 .

Description: by Christian Vinueza-Burgos, María Cevallos, Lenin Ron-Garrido, Sophie Bertrand, Lieven De Zutter Salmonella is frequently found in poultry and represent an important source for human gastrointestinal infections worldwide. The aim of this study was to investigate the prevalence, genotypes and antimicrobial resistance of Salmonella serotypes in broilers from Ecuador. Caeca content from 388 at random selected broiler batches were collected in 6 slaughterhouses during 1 year and analyzed by the ISO 6579/Amd1 protocol for the isolation for Salmonella . Isolates were serotyped and genotypic variation was acceded by pulsed field gel electrophoresis. MIC values for sulfamethoxazole, gentamicin, ciprofloxacin, ampicillin, cefotaxime, ceftazidime, tetracycline, streptomycin, trimethropim, chloramphenicol, colistin, florfenicol, kanamycin and nalidixic acid were obtained. Presence of bla CTX-M , bla TEM, bla SHV and bla CMY ; and mcr-1 plasmid genes was investigated in resistant strains to cefotaxime and colistin respectively. Prevalence at batch level was 16.0%. The most common serotype was S . Infantis (83.9%) followed by S . Enteritidis (14.5%) and S . Corvallis (1.6%). The pulsed field gel electrophoresis analysis showed that S . Corvallis, S . Enteritidis and S . Infantis isolates belonged to 1, 2 and 12 genotypes respectively. S . Infantis isolates showed high resistance rates to 12 antibiotics ranging from 57.7% (kanamycin) up to 98.1% (nalidixic acid and sulfamethoxazole). All S . Enteritidis isolates showed resistance to colistin. High multiresistant patterns were found for all the serotypes. The bla CTX-M gene was present in 33 S . Infantis isolates while mcr-1 was negative in 10 colistin resistant isolates. This study provides the first set of scientific data on prevalence and multidrug-resistant Salmonella coming from commercial poultry in Ecuador.

Description: by Chun-Ta Huang, Yu-Chung Chuang, Yi-Ju Tsai, Wen-Je Ko, Chong-Jen Yu Background Severe sepsis is a potentially deadly illness and always requires intensive care. Do-not-resuscitate (DNR) orders remain a debated issue in critical care and limited data exist about its impact on care of septic patients, particularly in East Asia. We sought to assess outcome of severe sepsis patients with regard to DNR status in Taiwan. Methods A retrospective cohort study was conducted in intensive care units (ICUs) between 2008 and 2010. All severe sepsis patients were included for analysis. Primary outcome was association between DNR orders and ICU mortality. Volume of interventions was used as proxy indicator to indicate aggressiveness of care. Results Sixty-seven (9.4%) of 712 patients had DNR orders on ICU admission, and these patients were older and had higher disease severity compared with patients without DNR orders. Notably, DNR patients experienced high ICU mortality (90%). Multivariate analysis revealed that the presence of DNR orders was independently associated with ICU mortality (odds ratio: 6.13; 95% confidence interval: 2.66–14.10). In propensity score-matched cohort, ICU mortality rate (91%) in the DNR group was statistically higher than that (62%) in the non-DNR group (p

Description: by Abbas Mirvakili, Mohammad Hossein Dadgarnia, Mohammad Hossein Baradaranfar, Saeid Atighechi, Vahid Zand, Abdollah Ansari

Description: by Julie M. Butler, Karen E. Field, Karen P. Maruska Fishes use multimodal signals during both inter- and intra-sexual displays to convey information about their sex, reproductive state, and social status. These complex behavioral displays can include visual, auditory, olfactory, tactile, and hydrodynamic signals, and the relative role of each sensory channel in these complex multi-sensory interactions is a common focus of neuroethology. The mechanosensory lateral line system of fishes detects near-body water movements and is implicated in a variety of behaviors including schooling, rheotaxis, social communication, and prey detection. Cobalt chloride is commonly used to chemically ablate lateral line neuromasts, thereby eliminating water-movement cues to test for mechanosensory-mediated behavioral functions. However, cobalt acts as a nonspecific calcium channel antagonist and could potentially disrupt function of all superficially located sensory receptor cells, including those for chemosensing. Here, we examined whether CoCl 2 treatment used to ablate the lateral line system also impairs olfaction in three freshwater fishes, the African cichlid fish Astatotilapia burtoni , goldfish Carassius auratus , and the Mexican blind cavefish Astyanax mexicanus . To examine the impact of CoCl 2 on the activity of peripheral receptors, we quantified DASPEI fluorescence intensity of the olfactory epithelium from fish exposed to control and CoCl 2 solutions. In addition, we examined brain activation in olfactory processing regions of A . burtoni immersed in either control or cobalt solutions. All three species exposed to CoCl 2 had decreased DASPEI staining of the olfactory epithelium, and in A . burtoni , cobalt treatment caused reduced neural activation in olfactory processing regions of the brain. To our knowledge this is the first empirical evidence demonstrating that the same CoCl 2 treatment used to ablate the lateral line system also impairs olfactory function. These data have important implications for the use of CoCl 2 in future research and suggest that previous studies using CoCl 2 should be reinterpreted in the context of both impaired mechanoreception and olfaction.

Description: by Tsugiko Kurita, Kotaro Sakurai, Youji Takeda, Toru Horinouchi, Ichiro Kusumi Objective Surgical intervention can result in complete seizure remission rates of up to 80% in patients with temporal lobe epilepsy with hippocampal sclerosis (TLE-HS). However, certain patients cannot be treated surgically for various reasons. We analyzed the very long-term clinical outcomes of patients with TLE-HS who could not be treated surgically. Methods Subjects were selected from among patients with TLE-HS who were actively followed up for 〉10 years and treated with medication without surgical treatment. Patient medical records were used to retrospectively study seizure frequency, various clinical factors, and social adjustment. Patients who were seizure-free or had only aura were classified into Group 1; the others were classified into Group 2. Clinical factors including both patient and disease-specific factors were compared between the two groups. Current social adjustment, including the education, work, and economic status of each patient, was also investigated. Results Forty-one (41) subjects met the criteria for analysis, of which 12 (29%) were classified into Group 1. The average age of patients in Group 1 was higher than that of Group 2 (p = 0.0468). Group 2 included a significantly higher rate of patients who had more than one seizure per week at the onset (p = 0.0328), as well as a greater mean number of anti-epileptic drugs taken (p = 0.0024). Regarding social adjustment, Group 2 contained significantly fewer current jobholders than Group 1 (p = 0.0288). Conclusions After very long-term follow-up periods, 29% of patients with TLE-HS had a good outcome through treatment with anticonvulsant medications. Older patients tended to have fewer seizures, and seizure frequency at the onset was the only factor that predicted outcome.

Description: Variation of CCN activity during new particle formation events in the North China Plain Nan Ma, Chunsheng Zhao, Jiangchuan Tao, Zhijun Wu, Simonas Kecorius, Zhibin Wang, Johannes Größ, Hongjian Liu, Yuxuan Bian, Ye Kuang, Monique Teich, Gerald Spindler, Konrad Müller, Dominik van Pinxteren, Hartmut Herrmann, Min Hu, and Alfred Wiedensohler Atmos. Chem. Phys., 16, 8593-8607, doi:10.5194/acp-16-8593-2016, 2016 New particle formation (NPF) is one of main sources of cloud condensation nuclei (CCN) in the atmosphere. Based on in situ measurements, we found that CCN activity of newly formed particles largely differs in different NPF events. It is therefore difficult to find a simple parameterization of CCN activity for NPF events. Using a fixed size-resolved activation ratio curve or critical diameter is very likely to result in large biases up to 50 % in the calculated N CCN during NPF events.

Description: Real time retrieval of volcanic cloud particles and SO 2 by satellite using an improved simplified approach Sergio Pugnaghi, Lorenzo Guerrieri, Stefano Corradini, and Luca Merucci Atmos. Meas. Tech., 9, 3053-3062, doi:10.5194/amt-9-3053-2016, 2016 Volcanic plume removal (VPR) is a procedure developed to retrieve the ash optical depth, effective radius and mass, and sulfur dioxide mass contained in a volcanic cloud from the thermal radiance at 8.7, 11, and 12 µm. It is based on an estimation of a virtual image representing what the sensor would have seen in a multispectral thermal image if the volcanic cloud were not present. Ash and sulfur dioxide were retrieved by the first version of the VPR using a very simple atmospheric model that ignored the layer above the volcanic cloud. This new version takes into account the layer of atmosphere above the cloud as well as thermal radiance scattering along the line of sight of the sensor. In addition to improved results, the new version also offers an easier and faster preliminary preparation and includes other types of volcanic particles (andesite, obsidian, pumice, ice crystals, and water droplets). As in the previous version, a set of parameters regarding the volcanic area, particle types, and sensor is required to run the procedure. However, in the new version, only the mean plume temperature is required as input data. In this work, a set of parameters to compute the volcanic cloud transmittance in the three quoted bands, for all the aforementioned particles, for both Mt. Etna (Italy) and Eyjafjallajökull (Iceland) volcanoes, and for the Terra and Aqua MODIS instruments is presented. Three types of tests are carried out to verify the results of the improved VPR. The first uses all the radiative transfer simulations performed to estimate the above mentioned parameters. The second one makes use of two synthetic images, one for Mt. Etna and one for Eyjafjallajökull volcanoes. The third one compares VPR and Look-Up Table (LUT) retrievals analyzing the true image of Eyjafjallajökull volcano acquired by MODIS aboard the Aqua satellite on 11 May 2010 at 14:05 GMT.

Description: Temperature-dependence of aerosol optical depth over the southeastern US Tero Mielonen, Anca Hienola, Thomas Kühn, Joonas Merikanto, Antti Lipponen, Tommi Bergman, Hannele Korhonen, Pekka Kolmonen, Larisa Sogacheva, Darren Ghent, Antti Arola, Gerrit de Leeuw, and Harri Kokkola Atmos. Chem. Phys. Discuss., doi:10.5194/acp-2016-625,2016 Manuscript under review for ACP (discussion: open, 0 comments) We studied the temperature dependence of AOD and its radiative effects over the southeastern US. We used spaceborne observations of AOD, LST and tropospheric NO 2 with simulations of ECHAM-HAMMOZ. The level of AOD in this region is governed by anthropogenic emissions but the temperature dependency is most likely caused by BVOC emissions. According to the observations and simulations, the regional clear-sky DRE for biogenic aerosols is −0.43 ± 0.88 W/m 2 /K and −0.86 ± 0.06 W/m 2 /K, respectively.

Description: Stratospheric Air Sub-sampler (SAS) and its application to analysis of Δ 17 O(CO 2 ) from small air samples collected with an AirCore Dorota Janina Mrozek, Carina van der Veen, Magdalena E. G. Hofmann, Huilin Chen, Rigel Kivi, Pauli Heikkinen, and Thomas Röckmann Atmos. Meas. Tech. Discuss., doi:10.5194/amt-2016-124,2016 Manuscript under review for AMT (discussion: open, 0 comments) Stratospheric Air Sub-sampler (SAS) is a device to collect and to store the stratospheric profile of air collected with an AirCore (Karion et al, 2010) in numerous sub-samples. The sub-samples (each of 25 mL at ambient temperature and pressure) can be later introduced to the continuous flow systems to measure for example the isotopic composition of CO 2 . The performance of the coupled system is demonstrated for a set of air samples from an AirCore flight in November 2014 near Sodankylä, Finland.

Description: Real time retrieval of volcanic cloud particles and SO 2 by satellite using an improved simplified approach Sergio Pugnaghi, Lorenzo Guerrieri, Stefano Corradini, and Luca Merucci Atmos. Meas. Tech., 9, 3053-3062, doi:10.5194/amt-9-3053-2016, 2016 Volcanic plume removal (VPR) is a procedure developed to retrieve the ash optical depth, effective radius and mass, and sulfur dioxide mass contained in a volcanic cloud from the thermal radiance at 8.7, 11, and 12 µm. It is based on an estimation of a virtual image representing what the sensor would have seen in a multispectral thermal image if the volcanic cloud were not present. Ash and sulfur dioxide were retrieved by the first version of the VPR using a very simple atmospheric model that ignored the layer above the volcanic cloud. This new version takes into account the layer of atmosphere above the cloud as well as thermal radiance scattering along the line of sight of the sensor. In addition to improved results, the new version also offers an easier and faster preliminary preparation and includes other types of volcanic particles (andesite, obsidian, pumice, ice crystals, and water droplets). As in the previous version, a set of parameters regarding the volcanic area, particle types, and sensor is required to run the procedure. However, in the new version, only the mean plume temperature is required as input data. In this work, a set of parameters to compute the volcanic cloud transmittance in the three quoted bands, for all the aforementioned particles, for both Mt. Etna (Italy) and Eyjafjallajökull (Iceland) volcanoes, and for the Terra and Aqua MODIS instruments is presented. Three types of tests are carried out to verify the results of the improved VPR. The first uses all the radiative transfer simulations performed to estimate the above mentioned parameters. The second one makes use of two synthetic images, one for Mt. Etna and one for Eyjafjallajökull volcanoes. The third one compares VPR and Look-Up Table (LUT) retrievals analyzing the true image of Eyjafjallajökull volcano acquired by MODIS aboard the Aqua satellite on 11 May 2010 at 14:05 GMT.

Description: by Ingebjørg Helena Nymo, Marit Seppola, Sascha Al Dahouk, Kathrine Ryvold Bakkemo, María Pilar Jiménez de Bagüés, Jacques Godfroid, Anett Kristin Larsen Pathology has not been observed in true seals infected with Brucella pinnipedialis . A lack of intracellular survival and multiplication of B . pinnipedialis in hooded seal ( Cystophora cristata ) macrophages in vitro indicates a lack of chronic infection in hooded seals. Both epidemiology and bacteriological patterns in the hooded seal point to a transient infection of environmental origin, possibly through the food chain. To analyse the potential role of fish in the transmission of B . pinnipedialis , Atlantic cod ( Gadus morhua ) were injected intraperitoneally with 7.5 x 10 7 bacteria of a hooded seal field isolate. Samples of blood, liver, spleen, muscle, heart, head kidney, female gonads and feces were collected on days 1, 7, 14 and 28 post infection to assess the bacterial load, and to determine the expression of immune genes and the specific antibody response. Challenged fish showed an extended period of bacteremia through day 14 and viable bacteria were observed in all organs sampled, except muscle, until day 28. Neither gross lesions nor mortality were recorded. Anti- Brucella antibodies were detected from day 14 onwards and the expression of hepcidin, cathelicidin, interleukin (IL)-1β, IL-10, and interferon (IFN)-γ genes were significantly increased in spleen at day 1 and 28. Primary mononuclear cells isolated from head kidneys of Atlantic cod were exposed to B . pinnipedialis reference (NCTC 12890) and hooded seal (17a-1) strain. Both bacterial strains invaded mononuclear cells and survived intracellularly without any major reduction in bacterial counts for at least 48 hours. Our study shows that the B . pinnipedialis strain isolated from hooded seal survives in Atlantic cod, and suggests that Atlantic cod could play a role in the transmission of B . pinnipedialis to hooded seals in the wild.

Description: by Muskan Jain, Rituraj Batth, Sumita Kumari, Ananda Mustafiz The glyoxalase pathway is ubiquitously found in all the organisms ranging from prokaryotes to eukaryotes. It acts as a major pathway for detoxification of methylglyoxal (MG), which deleteriously affects the biological system in stress conditions. The first important enzyme of this system is Glyoxalase I (GLYI). It is a metalloenzyme which requires divalent metal ions for its activity. This divalent metal ion can be either Zn 2+ as found in most of eukaryotes or Ni 2+ as seen in prokaryotes. In the present study, we have found three active GLYI enzymes (AtGLYI2, AtGLYI3 and AtGLYI6) belonging to different metal activation classes coexisting in Arabidopsis thaliana . These enzymes have been found to efficiently complement the GLYI yeast mutants. These three enzymes have been characterized in terms of their activity, metal dependency, kinetic parameters and their role in conferring tolerance to multiple abiotic stresses in E . coli and yeast. AtGLYI2 was found to be Zn 2+ dependent whereas AtGLYI3 and AtGLYI6 were Ni 2+ dependent. Enzyme activity of Zn 2+ dependent enzyme, AtGLYI2, was observed to be exceptionally high (~250–670 fold) as compared to Ni 2+ dependent enzymes, AtGLYI3 and AtGLYI6. The activity of these GLYI enzymes correlated well to their role in stress tolerance. Heterologous expression of these enzymes in E . coli led to better tolerance against various stress conditions. This is the first report of a higher eukaryotic species having multiple active GLYI enzymes belonging to different metal activation classes.

Description: by Tomohiko Kazama, Kinya Toriyama Nuclear genome substitutions between subspecies can lead to cytoplasmic male sterility (CMS) through incompatibility between nuclear and mitochondrial genomes. Boro-Taichung (BT)-type CMS rice was obtained by substituting the nuclear genome of Oryza sativa subsp. indica cultivar Chinsurah Boro II with that of Oryza sativa subsp. japonica cultivar Taichung 65. In BT-type CMS rice, the mitochondrial gene orf79 is associated with male sterility. A complete sequence of the Boro-type mitochondrial genome responsible for BT-type CMS has not been determined to date. Here, we used pyrosequencing to construct the Boro-type mitochondrial genome. The contiguous sequences were assembled into five circular DNA molecules, four of which could be connected into a single circle. The two resulting subgenomic circles were unable to form a reliable master circle, as recombination between them was scarcely detected. We also found an unequal abundance of DNA molecules for the two loci of atp6 . These results indicate the presence of multi-partite DNA molecules in the Boro-type mitochondrial genome. Expression patterns were investigated for Boro-type mitochondria-specific orf s, which were not found in the mitochondria from the standard japonica cultivar Nipponbare. Restorer of fertility 1 (RF1)-dependent RNA processing has been observed in orf79 -containing RNA but was not detected in other Boro-type mitochondria-specific orf s, supporting the conclusion that orf79 is a unique CMS-associated gene in Boro-type mitochondria.