bluuebunny/crossref_metadata_2025 huggingface dataset:
TIPIN depletion leads to apoptosis in breast cancer cells
Authors: Baldeyron Céline , Brisson Amélie , Tesson Bruno , Némati Fariba , Koundrioukoff Stéphane , Saliba Elie , De Koning Leanne , Martel Elise , Ye Mengliang , Rigaill Guillem , Meseure Didier , Nicolas André , Gentien David , Decaudin Didier , Debatisse Michelle , Depil Stéphane , Cruzalegui Francisco , Pierré Alain , Roman-Roman Sergio , Tucker Gordon C. , Dubois Thierry
Published: May 2015

Triple‐negative breast cancer (TNBC) is the breast cancer subgroup with the most aggressive clinical behavior. Alternatives to conventional chemotherapy are required to improve the survival of TNBC patients. Gene‐expression analyses for different breast cancer subtypes revealed significant overexpression of the Timeless‐interacting protein (TIPIN), which is involved in the stability of DNA replication forks, in the highly proliferative associated TNBC samples. Immunohistochemistry analysis showed higher expression of TIPIN in the most proliferative and aggressive breast cancer subtypes including TNBC, and no TIPIN expression in healthy breast tissues. The depletion of TIPIN by RNA interference impairs the proliferation of both human breast cancer and non‐tumorigenic cell lines. However, this effect may be specifically associated with apoptosis in breast cancer cells. TIPIN silencing results in higher levels of single‐stranded DNA (ssDNA), indicative of replicative stress (RS), in TNBC compared to non‐tumorigenic cells. Upon TIPIN depletion, the speed of DNA replication fork was significantly decreased in all BC cells. However, TIPIN‐depleted TNBC cells are unable to fire additional replication origins in response to RS and therefore undergo apoptosis. TIPIN knockdown in TNBC cells decreases tumorigenicity in vitro and delays tumor growth in vivo. Our findings suggest that TIPIN is important for the maintenance of DNA replication and represents a potential treatment target for the worst prognosis associated breast cancers, such as TNBC.
Electron-ion plasma dynamics in the presence of highly charged dust-clusters
Authors: Djebli Mourad , Benkhelifa El-Amine
Published: May 2015

Electron-ion plasma expansion is studied in the presence of positively (negatively) highly charged uniformly distributed dust particles, considered as impurities. For that purpose, a multi-fluid model is used, where the charged impurities characteristics are included in Poisson's equation. We found that ion acceleration is enhanced by the presence of positively charged dust. The latter leads to spiky structures in the ion front which have a higher amplitude as the charge increases. The charged impurities have a significant effect when the combination of their charge and density is greater than a critical value which depends on ion to electron temperature ratio.
Analysis of shock-wave propagation in aqueous foams using shock tube experiments
Authors: Jourdan G. , Mariani C. , Houas L. , Chinnayya A. , Hadjadj A. , Del Prete E. , Haas J.-F. , Rambert N. , Counilh D. , Faure S.
Published: May 2015

This paper reports experimental results of planar shock waves interacting with aqueous foams in a horizontal conventional shock tube. Four incident shock wave Mach numbers are considered, ranging from 1.07 to 1.8, with two different foam columns of one meter thickness and expansion ratios of 30 and 80. High-speed flow visualizations are used along with pressure measurements to analyse the main physical mechanisms that govern shock wave mitigation in foams. During the shock/foam interaction, a precursor leading pressure jump was identified as the trace of the liquid film destruction stage in the foam fragmentation process. The corresponding pressure threshold is found to be invariant for a given foam. Regarding the mitigation effect, the results show that the speed of the shock is drastically reduced and that wetter is the foam, slower are the transmitted waves. The presence of the foam barrier attenuates the induced pressure impulse behind the transmitted shock, while the driest foam appears to be more effective, as it limits the pressure induced by the reflected shock off the foam front. Finally, it was found that the pressure histories in the two-phase gas-liquid mixture are different from those previously obtained within a cloud of droplets. The observed behavior is attributed to the process of foam fragmentation and to the modification of the flow topology past the shock. These physical phenomena occurring during the shock/foam interaction should be properly accounted for when elaborating new physical models.
Space charge limited current emission for a sharp tip
Authors: Zhu Y. B. , Ang L. K.
Published: May 2015

In this paper, we formulate a self-consistent model to study the space charge limited current emission from a sharp tip in a dc gap. The tip is assumed to have a radius in the order of 10s nanometer. The electrons are emitted from the tip due to field emission process. It is found that the localized current density J at the apex of the tip can be much higher than the classical Child Langmuir law (flat surface). A scaling of J ∝ Vg3/2/Dm, where Vg is the gap bias, D is the gap size, and m = 1.1–1.2 (depending on the emission area or radius) is proposed. The effects of non-uniform emission and the spatial dependence of work function are presented.
Irregular-regular-irregular mixed mode oscillations in a glow discharge plasma
Authors: Ghosh Sabuj , Shaw Pankaj Kumar , Saha Debajyoti , Janaki M. S. , Iyengar A. N. Sekar
Published: May 2015

Floating potential fluctuations of a glow discharge plasma are found to exhibit different kinds of mixed mode oscillations. Power spectrum analysis reveals that with change in the nature of the mixed mode oscillation (MMO), there occurs a transfer of power between the different harmonics and subharmonics. The variation in the chaoticity of different types of mmo was observed with the study of Lyapunov exponents. Estimates of correlation dimension and the Hurst exponent suggest that these MMOs are of low dimensional nature with an anti persistent character. Numerical modeling also reflects the experimentally found transitions between the different MMOs.
Numerical investigation on transverse heat transfer properties in cross section of full size Nb3Sn CICC ITER conductor
Authors: Jia Shuming , Wang Dengming , Zheng Xiaojing
Published: May 2015

The contact mechanical characteristics in the cross section of the Nb3Sn cable are sensitive to the cryogenic cooling and cyclic transverse electromagnetic loads, which may affect the cable’s performance. In this paper, based on a proposed discrete dynamic model (DEM), where the contact heat transfer among strands and the convective heat transfer in liquid helium are taken into account, the cooling process under two heat transfer mechanisms is performed. Simulation results show that the temperature variation of Poloidal Field Insert Sample (PFIS) cable with time agrees well with the existing experimental results, and the role of contact heat transfer cannot be neglected during cryogenic cooling. It is obtained from the further analysis that the effect of contact heat transfer becomes more prominent with the decrease of mass flow rate of liquid helium, which leads to the stress status within cable changed significantly. With the temperature boundary condition imposed on the cable radial direction, the effective thermal conductivity (ETC) of cable can be obtained. It can be found that the ETC increases with increasing the transverse loads and is sensitive to the low temperature environment, while it is not affected by load cycles basically. These results may provide the guide for the design and application of the future CICC conductors.
Mechanism for resistive switching in chalcogenide-based electrochemical metallization memory cells
Authors: Zhuge Fei , Li Kang , Fu Bing , Zhang Hongliang , Li Jun , Chen Hao , Liang Lingyan , Gao Junhua , Cao Hongtao , Liu Zhimin , Luo Hao
Published: May 2015

It has been reported that in chalcogenide-based electrochemical metallization (ECM) memory cells (e.g., As2S3:Ag, GeS:Cu, and Ag2S), the metal filament grows from the cathode (e.g., Pt and W) towards the anode (e.g., Cu and Ag), whereas filament growth along the opposite direction has been observed in oxide-based ECM cells (e.g., ZnO, ZrO2, and SiO2). The growth direction difference has been ascribed to a high ion diffusion coefficient in chalcogenides in comparison with oxides. In this paper, upon analysis of OFF state I–V characteristics of ZnS-based ECM cells, we find that the metal filament grows from the anode towards the cathode and the filament rupture and rejuvenation occur at the cathodic interface, similar to the case of oxide-based ECM cells. It is inferred that in ECM cells based on the chalcogenides such as As2S3:Ag, GeS:Cu, and Ag2S, the filament growth from the cathode towards the anode is due to the existence of an abundance of ready-made mobile metal ions in the chalcogenides rather than to the high ion diffusion coefficient.
Gener: a minimal programming module for chemical controllers based on DNA strand displacement
Authors: Kahramanoğulları Ozan , Cardelli Luca
Published: May 2015

Summary: Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX.

Availability and implementation: Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono.

Contact: ozan@cosbi.eu
INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments
Authors: de Pretis Stefano , Kress Theresia , Morelli Marco J. , Melloni Giorgio E. M. , Riva Laura , Amati Bruno , Pelizzola Mattia
Published: May 2015

Motivation: Cellular mRNA levels originate from the combined action of multiple regulatory processes, which can be recapitulated by the rates of pre-mRNA synthesis, pre-mRNA processing and mRNA degradation. Recent experimental and computational advances set the basis to study these intertwined levels of regulation. Nevertheless, software for the comprehensive quantification of RNA dynamics is still lacking.

Results: INSPEcT is an R package for the integrative analysis of RNA- and 4sU-seq data to study the dynamics of transcriptional regulation. INSPEcT provides gene-level quantification of these rates, and a modeling framework to identify which of these regulatory processes are most likely to explain the observed mRNA and pre-mRNA concentrations. Software performance is tested on a synthetic dataset, instrumental to guide the choice of the modeling parameters and the experimental design.

Availability and implementation: INSPEcT is submitted to Bioconductor and is currently available as Supplementary Additional File S1.

Contact:  mattia.pelizzola@iit.it

Supplementary Information:  Supplementary data are available at Bioinformatics online.
INPS: predicting the impact of non-synonymous variations on protein stability from sequence
Authors: Fariselli Piero , Martelli Pier Luigi , Savojardo Castrense , Casadio Rita
Published: May 2015

Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for understanding the effects of Mendelian and somatic mutations in the genome. Next Generation Sequencing studies are constantly increasing the number of protein sequences. Given the huge disproportion between protein sequences and structures, there is a need for tools suited to annotate the effect of mutations starting from protein sequence without relying on the structure. Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on SVM regression and it is trained to predict the thermodynamic free energy change upon single-point variations in protein sequences.

Results: We show that INPS performs similarly to the state-of-the-art methods based on protein structure when tested in cross-validation on a non-redundant dataset. INPS performs very well also on a newly generated dataset consisting of a number of variations occurring in the tumor suppressor protein p53. Our results suggest that INPS is a tool suited for computing the effect of non-synonymous polymorphisms on protein stability when the protein structure is not available. We also show that INPS predictions are complementary to those of the state-of-the-art, structure-based method mCSM. When the two methods are combined, the overall prediction on the p53 set scores significantly higher than those of the single methods.

Availability and implementation: The presented method is available as web server at http://inps.biocomp.unibo.it.

Contact:  piero.fariselli@unibo.it

Supplementary information:  Supplementary Materials are available at Bioinformatics online.
Using combined evidence from replicates to evaluate ChIP-seq peaks
Authors: Jalili Vahid , Matteucci Matteo , Masseroli Marco , Morelli Marco J
Published: May 2015

Motivation

Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) detects genome-wide DNA–protein interactions and chromatin modifications, returning enriched regions (ERs), usually associated with a significance score. Moderately significant interactions can correspond to true, weak interactions, or to false positives; replicates of a ChIP-seq experiment can provide co-localised evidence to decide between the two cases. We designed a general methodological framework to rigorously combine the evidence of ERs in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a minimum number of samples bearing this evidence.

Results

We applied our method to Myc transcription factor ChIP-seq datasets in K562 cells available in the ENCODE project. Using replicates, we could extend up to 3 times the ER number with respect to single-sample analysis with equivalent significance threshold. We validated the ‘rescued’ ERs by checking for the overlap with open chromatin regions and for the enrichment of the motif that Myc binds with strongest affinity; we compared our results with alternative methods (IDR and jMOSAiCS), obtaining more validated peaks than the former and less peaks than latter, but with a better validation.

Availability and implementation

An implementation of the proposed method and its source code under GPLv3 license are freely available at http://www.bioinformatics.deib.polimi.it/MSPC/ and https://github.com/Genometric/MSPC, respectively.

Contact

marco.morelli@iit.it

Supplementary information

Supplementary Material are available at Bioinformatics online.
Report on a characteristic oscillation about 38 mHz (26 s) in northeastern Japan following surface wave of the 2011 Tohoku megathrust earthquake
Authors: Mitsui Yuta , Heki Kosuke
Published: May 2015

We try to detect an unidentified signal from the surface motion at northeastern Japan immediately after the 2011 Tohoku earthquake. A focused frequency range is 10–100 mHz (10–100 s). We find a peaky signal with frequency of about 38 mHz (26 s) based on the horizontal-to-vertical (H/V) spectral ratio using the high-rate GNSS data at 382 GEONET stations. We are not able to identify locality of the signal. The signal appears several minutes after the passing of surface wave fronts. The duration of the signal is about 2 min. Since the origin of the 38 mHz signal is unlikely to be local hydrologic tremors, tectonic tremors, or the tsunami, we speculate that the 38 mHz signal originates from a kind of a characteristic oscillation of Northeastern Japan triggered by the 2011 Tohoku earthquake. A normal-mode simulation implies that high-order radial overtones could create the signal with a spherically-layered velocity structure, however, the detailed mechanism of the signal still remains a mystery.
Examining the functional role of current area closures used for the conservation of an overexploited and highly mobile fishery species
Authors: McAllister Jaime D. , Barnett Adam , Lyle Jeremy M. , Semmens Jayson M.
Published: May 2015

Protecting essential habitats through the implementation of area closures has been recognized as a useful management tool for rebuilding overfished populations and minimizing habitat degradation. School shark (Galeorhinus galeus) have suffered significant stock declines in Australia; however, recent stock assessments suggest the population may have stabilized and the protection of closed nursery areas has been identified as a key management strategy to rebuilding their numbers. Young-of-the-year (YOY) and juvenile G. galeus were acoustically tagged and monitored to determine ontogenetic differences in residency and seasonal use of an important protected nursery area (Shark Refuge Area or SRA) in southeastern Tasmania. Both YOY and juvenile G. galeus showed a distinct seasonal pattern of occurrence in the SRA with most departing the area during winter and only a small proportion of YOY (33%) and no juveniles returning the following spring, suggesting areas outside the SRA may also be important during these early life-history stages. While these behaviors confirm SRAs continue to function as essential habitat during G. galeus early life history, evidence of YOY and juveniles emigrating from these areas within their first 1–2 years and the fact that few YOY return suggest that these areas may only afford protection for a more limited amount of time than previously thought. Determining the importance of neighbouring coastal waters and maintaining the use of traditional fisheries management tools are therefore required to ensure effective conservation of G. galeus during early life history.
The cell surface receptor Slamf6 modulates innate immune responses during Citrobacter rodentium-induced colitis
Authors: van Driel Boaz , Wang Guoxing , Liao Gongxian , Halibozek Peter J. , Keszei Marton , O’Keeffe Michael S. , Bhan Atul K. , Wang Ninghai , Terhorst Cox
Published: May 2015

The homophilic cell surface receptors CD150 (Slamf1) and CD352 (Slamf6) are known to modulate adaptive immune responses. Although the Th17 response was enhanced in Slamf6−/− C57BL/6 mice upon oral infection with Citrobacter rodentium, the pathologic consequences are indistinguishable from an infection of wild-type C57BL/6 mice. Using a reporter-based binding assay, we show that Slamf6 can engage structures on the outer cell membrane of several Gram− bacteria. Therefore, we examined whether Slamf6, like Slamf1, is also involved in innate responses to bacteria and regulates peripheral inflammation by assessing the outcome of C. rodentium infections in Rag−/− mice. Surprisingly, the pathology and immune responses in the lamina propria of C. rodentium-infected Slamf6−/−Rag−/− mice were markedly reduced as compared with those of Rag−/− mice. Infiltration of inflammatory phagocytes into the lamina propria was consistently lower in Slamf6−/−Rag−/− mice than in Rag−/− animals. Concomitant with the reduced systemic translocation of the bacteria was an enhanced production of IL-22, suggesting that Slamf6 suppresses a mucosal protective program. Furthermore, administering a mAb (330) that inhibits bacterial interactions with Slamf6 to Rag−/− mice ameliorated the infection compared with a control antibody. We conclude that Slamf6-mediated interactions of colonic innate immune cells with specific Gram− bacteria reduce mucosal protection and enhance inflammation, contributing to lethal colitis that is caused by C. rodentium infections in Rag−/− mice.
Rheinheimera aestuari sp. nov., a marine bacterium isolated from coastal sediment
Authors: Baek Kyunghwa , Jeon Che Ok
Published: May 2015

A Gram-stain-negative, strictly aerobic, non-pigmented, motile bacterium with a single polar flagellum, designated H29T, was isolated from coastal sediment of Jeju Island, South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain H29T was observed at 10–40 °C (optimum, 20–25 °C) and pH 6.0–9.0 (optimum, pH 7.0–8.0), and in the presence of 1–4 % (w/v) NaCl (optimum, 2–3 %). Strain H29T contained C16 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids and ubiquinone-8 (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 46.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H29T formed a phyletic lineage with Rheinheimera hassiensis E48T within the genus Rheinheimera of the family Chromatiaceae. Strain H29T was most closely related to Rheinheimera pacifica KMM 1406T, Rheinheimera muenzenbergensis E49T, Rheinheimera hassiensis E48T and Rheinheimera baltica OSBAC1T with 97.8 %, 97.6 %, 97.4 % and 97.2 % 16S rRNA gene sequence similarities, respectively. However, DNA–DNA hybridization values of strain H29T with type strains of these species were lower than 70 %. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain H29T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera
aestuarii sp. nov. is proposed. The type strain is H29T ( = KACC 18251T = JCM 30404T).
Shewanella mangrovi sp. nov., an acetaldehyde-degrading bacterium isolated from mangrove sediment
Authors: Liu Yang , Shang Xie-Xie , Yi Zhi-Wei , Gu Li , Zeng Run-Ying
Published: May 2015

A taxonomic study was carried out on strain YQH10T, which was isolated from mangrove sediment collected from Zhangzhou, China during the screening of acetaldehyde-degrading bacteria. Cells of strain YQH10T were Gram-stain-negative rods and pale brown-pigmented. Growth was observed at salinities from 0 to 11 % and at temperatures from 4 to 42 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YQH10T is affiliated to the genus Shewanella, showing the highest similarity with Shewanella haliotis DW01T (95.7 %) and other species of the genus Shewanella (91.4–95.6 %). The principal fatty acids were iso-C15 : 0 and C17 : 1ω8c. The major respiratory quinone was Q-8. The polar lipids comprised phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA had a G+C content of 48.3 mol%. Strain YQH10T can completely degrade 0.02 % (w/v) acetaldehyde on 2216E at 28 °C within 48 h. Based on these phenotypic and genotypic data, strain YQH10T represents a novel species of the genus Shewanella, for which the name Shewanella mangrovi sp. nov. is proposed. The type strain is YQH10T ( = MCCC 1A00830T = JCM 30121T).
Marinithermofilum abyssi gen. nov., sp. nov. and Desmospora profundinema sp. nov., isolated from a deep-sea sediment, and emended description of the genus Desmospora

Yassin et al. 2009
Authors: Zhang Yi , Li Jie , Tian Xinpeng , Zhang Si
Published: May 2015

Two novel filamentous bacteria, strains SCSIO 11157T and SCSIO 11154T, were isolated from a deep-sea sediment sample. Strain SCSIO 11157T grew optimally at 55–60 °C, while strain SCSIO 11154T grew optimally at 40 °C. Both strains produced aerial and substrate mycelia. Phylogenetic analysis of the 16S rRNA gene sequences of strains SCSIO 11157T and SCSIO 11154T showed that the isolates were affiliated to the family Thermoactinomycetaceae. The two isolates contained ll-diaminopimelic acid as the cell-wall diamino acid, and did not have diagnostic sugars. The major polar lipids of strain SCSIO 11157T were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol, and the major polar lipids of SCSIO 11154T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant menaquinone of both strains was MK-7. The major cellular fatty acids of strain SCSIO 11157T were iso-C15 : 0, C18 : 1ω9c and iso-C17 : 0, and strain SCSIO 11154T contained iso-C15 : 0 and iso-C17 : 0 as major fatty acids. The DNA G+C contents of strains SCSIO 11157T and SCSIO 11154T were 54.2 and 51.8 mol %, respectively. On the basis of its phenotypic and phylogenetic properties, strain SCSIO 11157T represents a novel species in the new genus, for which we propose the name Marinithermofilum abyssi gen. nov., sp. nov. The type strain of Marinithermofilum abyssi is SCSIO 11157T ( = CGMCC 1.15179T = NBRC 109939T). Strain SCSIO 11154T represents a novel species of the genus Desmospora, for which we propose the name Desmospora profundinema sp. nov. The type strain is SCSIO 11154T ( = DSM 45903T = NBRC 109626T).
Latent infection of myeloid progenitors by human cytomegalovirus protects cells from FAS-mediated apoptosis through the cellular IL-10/PEA-15 pathway
Authors: Poole Emma , Lau Jonathan C. H. , Sinclair John
Published: May 2015

Latent infection of primary CD34+ progenitor cells by human cytomegalovirus (HCMV) results in their increased survival in the face of pro-apoptotic signals. For instance, we have shown previously that primary myeloid cells are refractory to FAS-mediated killing and that cellular IL-10 (cIL-10) is an important survival factor for this effect. However, how cIL-10 mediates this protection is unclear. Here, we have shown that cIL-10 signalling leading to upregulation of the cellular factor PEA-15 mediates latency-associated protection of CD34+ progenitor cells from the extrinsic death pathway.
Integration of experiments across diverse environments identifies the genetic determinants of variation inSorghum bicolorseed element composition
Authors: Shakoor Nadia , Ziegler Greg , Dilkes Brian P. , Brenton Zachary , Boyles Richard , Connolly Erin L. , Kresovich Stephen , Baxter Ivan
Published: May 2015

Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. Identification of genes and alleles that modify element content in the grains of cereals, includingSorghum bicolor, is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high throughput workflow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel (SAP), representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome wide association was demonstrated by implementing rank transformation and a multilocus mixed model (MLMM) to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc (Zn) manganese (Mn), nickel (Ni), calcium (Ca) and cadmium (Cd) in sorghum seed. In addition to strong candidates for these four elements, we provide a list of candidate loci for several other elements. Our approach enabled identification of SNPs in strong LD with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.

One sentence summary

High-throughput measurements of element accumulation and genome-wide association analysis across multiple environments identified novel alleles controlling seed element accumulation inSorghum bicolor.

This project was partially funded by the iHUB Visiting Scientist Program (http://www.ionomicshub.org), Chromatin, Inc., NSF EAGER (1450341) to I.B. and BPD, NSF IOS 1126950 to IB, NSF IOS-0919739 to EC, and BMGF (OPP 1052924) to B.P.D.
Improving the Power of Structural Variation Detection by Augmenting the Reference
Authors: Schröder Jan , Girirajan Santhosh , Papenfuss Anthony T. , Medvedev Paul
Published: May 2015

The uses of the Genome Reference Consortium’s human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and limits their accuracy. We show how decoupling these two references and developing a separate alignment reference can significantly improve the accuracy of structural variation detection, lead to improved genotyping of disease related genes, and decrease the cost of studying polymorphism in a population.
Open science resources for the discovery and analysis ofTaraOceans Data
Authors: Pesant Stéphane , Not Fabrice , Picheral Marc , Kandels-Lewis Stefanie , Bescot Noan Le , Gorsky Gabriel , Iudicone Daniele , Karsenti Eric , Speich Sabrina , Troublé Romain , Dimier Céline , Searson Sarah ,   Tara Oceans Consortium Coordinators
Published: May 2015

TheTaraOceans expedition (2009-2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.
Mitochondria, mutations and sex: a new hypothesis for the evolution of sex based on mitochondrial mutational erosion
Authors: Havird Justin C. , Hall Matthew D. , Dowling Damian K.
Published: May 2015

The evolution of sex in eukaryotes represents a paradox, given the “two-fold” fitness cost it incurs. We hypothesize that the mutational dynamics of the mitochondrial genome would have favoured the evolution of sexual reproduction. Mitochondrial DNA (mtDNA) exhibits a high mutation rate across most eukaryote taxa, and several lines of evidence suggest this high rate is an ancestral character. This seems inexplicable given mtDNA-encoded genes underlie the expression of life’s most salient functions, including energy conversion. We propose that negative metabolic effects linked to mitochondrial mutation accumulation would have invoked selection for sexual recombination between divergent host nuclear genomes in early eukaryote lineages. This would provide a mechanism by which recombinant host genotypes could be rapidly shuffled and screened for the presence of compensatory modifiers that offset mtDNA-induced harm. Under this hypothesis, recombination provides the genetic variation necessary for compensatory nuclear coadaptation to keep pace with mitochondrial mutation accumulation.
Two-Dimensional Mapping of 3D Data from Confocal Microscopy
Authors: Fan Anthony , Cassidy Justin , Carthew Richard W. , Hilgenfeldt Sascha
Published: May 2015

Confocal microscopy has been experimentally proven for decades to provide high-quality images for biological research. Its unique property of blocking out-of-focus light enables 3D rendering from planar stacks and visualization of internal features. However, visualizing 3D data on a flat display is not intuitive, and would lead to occasional distortion. In this study, a novel, easy-to-implement, and computationally fast solution is provided to reconstruct a confocal stack to true 3D data and subsequently map the information correctly with size and shape consistency to a 2D space for visualization and image analysis purposes.
LIN28 cooperates with WNT signaling to drive invasive intestinal and colorectal adenocarcinoma in mice and humans
Authors: Tu Ho-Chou , Schwitalla Sarah , Qian Zhirong , LaPier Grace S. , Yermalovich Alena , Ku Yuan-Chieh , Chen Shann-Ching , Viswanathan Srinivas R. , Zhu Hao , Nishihara Reiko , Inamura Kentaro , Kim Sun A. , Morikawa Teppei , Mima Kosuke , Sukawa Yasutaka , Yang Juhong , Meredith Gavin , Fuchs Charles S. , Ogino Shuji , Daley George Q.
Published: May 2015

Colorectal cancer (CRC) remains a major contributor to cancer-related mortality. LIN28A and LIN28B are highly related RNA-binding protein paralogs that regulate biogenesis of let-7 microRNAs and influence development, metabolism, tissue regeneration, and oncogenesis. Here we demonstrate that overexpression of either LIN28 paralog cooperates with the Wnt pathway to promote invasive intestinal adenocarcinoma in murine models. When LIN28 alone is induced genetically, half of the resulting tumors harbor Ctnnb1 (β-catenin) mutation. When overexpressed in ApcMin/+ mice, LIN28 accelerates tumor formation and enhances proliferation and invasiveness. In conditional genetic models, enforced expression of a LIN28-resistant form of the let-7 microRNA reduces LIN28-induced tumor burden, while silencing of LIN28 expression reduces tumor volume and increases tumor differentiation, indicating that LIN28 contributes to tumor maintenance. We detected aberrant expression of LIN28A and/or LIN28B in 38% of a large series of human CRC samples (n = 595), where LIN28 expression levels were associated with invasive tumor growth. Our late-stage CRC murine models and analysis of primary human tumors demonstrate prominent roles for both LIN28 paralogs in promoting CRC growth and progression and implicate the LIN28/let-7 pathway as a therapeutic target.
Selective modulation of the functions of a conserved DNA motor by a histone fold complex
Authors: Xue Xiaoyu , Choi Koyi , Bonner Jacob N. , Szakal Barnabas , Chen Yu-Hung , Papusha Alma , Saro Dorina , Niu Hengyao , Ira Grzegorz , Branzei Dana , Sung Patrick , Zhao Xiaolan
Published: May 2015

Budding yeast Mph1 helicase and its orthologs drive multiple DNA transactions. Elucidating the mechanisms that regulate these motor proteins is central to understanding genome maintenance processes. Here, we show that the conserved histone fold MHF complex promotes Mph1-mediated repair of damaged replication forks but does not influence the outcome of DNA double-strand break repair. Mechanistically, scMHF relieves the inhibition imposed by the structural maintenance of chromosome protein Smc5 on Mph1 activities relevant to replication-associated repair through binding to Mph1 but not DNA. Thus, scMHF is a function-specific enhancer of Mph1 that enables flexible response to different genome repair situations.
Replacement of bovine milk with vegetable milk: Effects on the survival of probiotics and rheological and physicochemical properties of frozen fermented dessert
Authors: Aboulfazli Fatemeh , Baba Ahmad Salihin , Misran Misni
Published: May 2015

In this study, frozen fermented desserts containing Lactobacillus acidophilus (La‐05; L) and Bifidobacterium bifidum (Bb‐12; B), were made from bovine (W), soya (S), coconut (C) and composite (i.e. combinations of coconut or bovine milks with soya milk) milks. The changes in frozen dessert eating qualities and the survival of added microbes were evaluated. The highest viscosity and melting resistance, and the lowest total sensory scores, were found in the products made using soya milk. After 90‐day storage at −20 °C, the highest survival percentage of La‐05 was found in the products made using coconut milk (CL); and for Bb‐12, it was found in the products made using soya milk, coconut milk and a 25:75 blend of soya milk and coconut milk respectively ( samples SB, CB and SC3B) SB, SCB and CB samples.
Isolation and characterisation of a Lactobacillus delbrueckii subsp. bulgaricus mutant with low H+‐ATPase activity
Authors: Dan Tong , Chen Yongfu , Chen Xia , Sun Chunling , Wang Xueni , Wang Junguo , Zhang Heping
Published: May 2015

Lactobacillus delbrueckii subsp. bulgaricus is an acid‐tolerant species used in yoghurt production and considered important in postacidification reductions in palatability of yoghurt during storage. In this study, a variant (ND06‐2) of L. delbrueckii subsp. bulgaricus ND06 was selected using neomycin sulphate. ND06‐2 exhibited sensitivity to acids and lower H+‐ATPase activity compared with ND06. High‐pressure liquid chromatography (HPLC) was used to demonstrate that the capacity of ND06‐2 to produce lactic acid was significantly lower than for ND06 during fermentation or storage. These results suggest that the L. delbrueckii subsp. bulgaricus variant could be used in yoghurt starters and have a lower tendency to cause postacidification.
Direct determination of lactulose in heat‐treated milk using diffuse reflectance infrared Fourier transform spectroscopy and partial least squares regression
Authors: Pappas Christos S , Sakkas Lambros , Moschopoulou Ekaterini , Moatsou Golfo
Published: May 2015

The aim of this work was the direct determination of lactulose (LCT) concentration in freeze‐dried heat‐treated milks using diffuse reflectance Fourier transform infrared spectroscopy (DRIFTS) without any chemical pretreatment of the milk. The ‘actual’ lactulose concentrations estimated by means of high‐performance liquid chromatography (HPLC) were correlated with the spectral region 1286–754 cm−1 of DRIFTS spectra in the second‐derivative form of the milk samples using partial least squares (PLS) regression. A linear relationship was established between the ‘actual’ and the concentrations recalculated using the built model. The proposed DRIFTS method is simple, rapid and low cost.
Soil application ofBeauveria bassianaGHA against apple sawfly,Hoplocampa testudinea(Hymenoptera: Tenthredinidae): Field mortality and fungal persistence
Authors: Świergiel Weronika , Meyling Nicolai V. , Porcel Mario , Rämert Birgitta
Published: May 2015

Low impact alternatives to synthetic insecticides for the control of apple sawfly (Hoplocampa testudineaKlug) are scarce encumbering pest management in organic apple orchards. We investigated the soil persistence and field efficacy of the entomopathogenic fungusBeauveria bassiana(Balsamo) Vuillemin (BotaniGard) against apple sawfly under common organic orchard practices. We also assessed the efficacy ofB. bassianaGHA andMetarhizium brunneumPetch (indigenous strain) against sawfly in the laboratory. Larvae treated with either fungus in the laboratory died faster than control larvae and displayed 49.4%–68.4% mycosis. In the field,B. bassianadensity remained high in the week after application, during larval descent to the soil. Fungal density decreased to 25% at 49 d after application and to 0.4% after 55 weeks. Molecular markers revealed that the majority of fungal isolates recovered comprised the appliedB. bassianastrain GHA. Larvae pupating in soil cages in the orchard for 49 d displayed 17% mycosis. The high efficacy under laboratory conditions was not seen in the field.B. bassianaapplication resulted in densities above the upper natural background level during the growing season, but reversion to background levels occurred within a year. It remains to be investigated whether this has a detrimental effect on nontarget organisms. Additional work is needed to bridge the knowledge gap between laboratory and field efficacy in orchards.
obitools: a unix‐inspired software package for DNA metabarcoding
Authors: Boyer Frédéric , Mercier Céline , Bonin Aurélie , Le Bras Yvan , Taberlet Pierre , Coissac Eric
Published: May 2015

DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next‐generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor‐made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.
Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly
Authors: Feng Yan‐Jie , Liu Qing‐Feng , Chen Meng‐Yun , Liang Dan , Zhang Peng
Published: May 2015

In phylogenetics and population genetics, a large number of loci are often needed to accurately resolve species relationships. Normally, loci are enriched by PCR and sequenced by Sanger sequencing, which is expensive when the number of amplicons is large. Next‐generation sequencing (NGS) techniques are increasingly used for parallel amplicon sequencing, which reduces sequencing costs tremendously, but has not reduced preparation costs very much. Moreover, for most current NGS methods, amplicons need to be purified and quantified before sequencing and their lengths are also restricted (normally <700 bp). Here, we describe an approach to sequence pooled amplicons of any length using the Illumina platform. Using this method, amplicons are pooled at equal volume rather than at equal concentration, thus eliminating the laborious purification and quantification steps. We then shear the pooled amplicons, repair the ends, add sample identifying linkers and pool multiple samples prior to Illumina library preparation. Data are then assembled using the transcriptome assembly program trinity, which is optimized to deal with templates of highly varying quantities. We demonstrated the utility of our approach by recovering 93.5% of the target amplicons (size up to 1650 bp) in full length for a 16 taxa × 101 loci project, using ~2.0 GB of Illumina HiSeq paired‐end 90‐bp data. Overall, we validate a rapid, cost‐effective and scalable approach to sequence a large number of targeted loci from a large number of samples that is particularly suitable for both phylogenetics and population genetics studies that require a modest scale of data.
Delayed Enrichment for c‐kit and Inducing Cardiac Differentiation Attenuated Protective Effects of BMSCs’ Transplantation in Pig Model of Acute Myocardial Ischemia
Authors: Zhang Guang‐Wei , Gu Tian‐Xiang , Guan Xiao‐Yu , Sun Xue‐Jun , Jiang Da‐Qing , Tang Rui , Qi Xun , Li Xue‐Yuan
Published: May 2015

Objective

To investigate the effects of immature cardiomyocytes differentiated from c‐kit+ bone marrow mesenchymal stem cells (BMSCs) against acute myocardial infarction (AMI).

Methods

Miniswine passage 8 BMSCs were enriched for c‐kit and induced by 5 μM 5‐azacytidine (AZA) for 14 days, and a second enrichment for the dihydropyridine receptor subunit α2δ1 was performed (enriched BMSCs). Thereafter, enriched BMSCs were analyzed by determining cardiac differentiation, secretion function, and the effects of these secreted factors on cardiac stem cells (CSCs). Miniswine with AMI were divided into control, primary BMSCs’ (PB), and enriched BMSCs’ (EB) groups. Autologous BMSCs were intramyocardially injected into the ischemic regions in PB and EB groups. The following indices were evaluated at different time points, including paracrine of implanted BMSCs, histological and morphological analysis, myocardial perfusion, and cardiac function.

Results

As shown by in vitro study, enrichment + AZA significantly promoted BMSCs to express cardiac‐specific markers and format action potential, but down‐regulated the expression of VEGF and bFGF, consequently attenuated BMSCs‐inducing CSCs proliferation, migration, and differentiation. The in vivo experiments revealed similar results like the in vitro 6 weeks postoperatively. And in EB group, there were decreased angiogenesis and myocardial perfusion, attenuated resident CSCs‐mediated myocardial regeneration, and consequently impaired cardiac function compared with PB group.

Conclusions

This pretreatment promoted BMSCs to differentiate into myocardiocytes both in vitro and in vivo, but impaired their paracrine function and effects on resident CSCs, suggesting that inducing cardiac differentiation alone may not improve protective effects of BMSCs transplantation on AMI.
Levosimendan Improves Hemodynamic Status in Critically Ill Patients with Severe Aortic Stenosis and Left Ventricular Dysfunction: An Interventional Study
Authors: García‐González Martín J. , Jorge‐Pérez Pablo , Jiménez‐Sosa Alejandro , Acea Antonio Barragán , Lacalzada Almeida Juan B. , Ferrer Hita Julio J.
Published: May 2015

Aims

To study the hemodynamic effect of levosimendan administration in acute heart failure patients with severe aortic stenosis (AS) and reduced left ventricular ejection fraction (LVEF).

Methods

Hemodynamic response to 24 h intravenous levosimendan infusion (0.1 μg/kg/min without a loading dose) in patients with severe AS (aortic valve area ≤1 cm2, time‐velocity integral between left ventricular out‐flow tract and aortic valve <0.25), reduced LVEF (≤40%), and a depressed cardiac index (CI) <2.2 L/min/m2 was determined in a sequential group of nine patients aged 76 ± 10 years (5 men).

Results

Baseline mean ejection fraction was 33 ± 0.7%; mean aortic valve area was 0.37 ±0.11 cm2/m2; peak and mean gradients of 63.6 ± 20.53 and 36.7 ± 12.62 mmHg, respectively; and mean CI was 1.65 ± 0.20 L/min/m2. At 6 and 12 h of levosimendan therapy, mean CI had increased to 2.00 ± 0.41 L/min/m2 (P = 0.02) and 2.17 ± 0.40 L/min/m2 (P = 0.01), respectively. At 24 h, mean CI had increased further to 2.37 ± 0.49 L/min/m2 (P = 0.01). A significant beneficial effect was also observed in pulmonary capillary wedge pressure, pulmonary artery mean pressure, central venous pressure, systemic vascular resistances, pulmonary vascular resistances, stroke volume index, left ventricular stroke work index. NTproBNP levels decreased at 24 h of levosimendan treatment. Levosimendan infusion was also well tolerated. Five patients subsequently underwent aortic valve surgery replacement. One died (of postoperative multiorgan failure). At 30 days, overall survival was 75%.

Conclusions

Levosimendan administration improves hemodynamic parameters in critically ill patients with severe AS and reduced LVEF. In our study, it provides a safe and effective bridge to aortic‐valve replacement or oral vasodilator therapy in surgical contraindicated patients. A controlled study is needed to confirm these preliminary findings.
Growing Halal Meat Demand: Does Australia Miss Out A Potential Trade Opportunity?
Authors: Kabir Shahriar
Published: May 2015

With growing number of Muslim population and improved purchasing power of Muslim community in Asia‐pacific zone, Halal food market appears as a potential opportunity for meat producers. The strict requirement of Halal standard, however, makes the entry to this potential market often challenging. This study analyses trade potential in Halal Bovine meat industry; and finds that India and Brazil have successfully entered the market and grabbed a substantial segment of the market. Australia, being a leader in global Bovine meat supply, stays far behind in the race. Collaboration with Muslim countries (that have advanced in developing acceptable Halal standard) would help Australia to take a lead in the Global Halal Bovine meat market.