bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of residual stresses in dissimilar steel surfacing layers during process of post-weld heat treatment
Authors: Wang K Y , Lu H , Gong L
Published: January 2013

Residual stress relaxation during post-weld heat treatment (PWHT) is a thermodynamic process, which is affected not only by the heat treatment process, but also by the welding residual stress. In this study, the residual stresses in as welded and heat treated surfacing metal were measured using blind hole and X-ray method. The results reveal that the welding residual stresses are compressive at the surface of the weld and tensile at inner weld. However, after PWHT, the residual stresses at surface and inner weld change to the opposite state. Finite element simulations show that the differences of expansion coefficients between base metal and filler material are the main factor to the changes of stress state. The experimental results verify that the expansion coefficients of base metal and filler materials have been changed greatly after long soaking at high temperature.
Investigation of heat affected zone softening in armour steels Part 1 – Phase transformation kinetics
Authors: Hanhold B , Babu S S , Cola G
Published: January 2013

Heat affected zone (HAZ) softening in two armour steels (high hard and flash processed) was investigated by monitoring phase transformations during simulated welding thermal cycles. The high hard steel was produced by conventional thermomechanical processing followed by quench and tempering. Flash processed steel was produced by rapid heating and cooling of a spheroidised steel to produce a mixed microstructure. Heat affected zone softening in high hard steel was observed on heating to a peak temperature below Ac1 due to overtempering of the original microstructure. In flash processed steel, the softening was associated with allotriomorphic ferrite formation when heated to a peak temperature between Ac1 and Ac3. The above results demonstrate the importance of initial microstructure on HAZ on phase transformation transients and associated softening in armour steels.
Hydroxyapatite/Al2O3/diopside ceramic composites and their behaviour in simulated body fluid
Authors: Zhang M F , Zhang X H , Liu C X , Sun J L
Published: January 2013

In the present work, alumina and diopside were introduced in hydroxyapatite matrix, and hydroxyapatite/Al2O3/diopside ceramic composites with good mechanical properties were fabricated by uniaxial hot pressing. The behaviours of hydroxyapatite/Al2O3/diopside ceramic composites in simulated body fluid were studied by SEM, Fourier transform infrared spectroscopy and electron probe microanalyser. Scanning electron microscopy images showed an obvious mineral layer formed on the soaked composite surface, which indicated that the introduction of Al2O3 and diopside in hydroxyapatite matrix could not only improve the strength and toughness of the composites but also maintain its ability to precipitate an apatite layer.
Thermal stability of retained austenite in Cr–Ni weld metals at low temperatures
Authors: Qiu H , Qi J G , Wang L N , Yin F X , Hiraoka K
Published: January 2013

As environmental temperature decreases, the amount of retained austenite is more likely to greatly reduce due to the thermal austenite–martensite transformation caused by the decreased thermal stability of retained austenite, probably making its amount lower than the required content. In the present study, the thermal stability of retained austenite in Cr–Ni weld metals was investigated to see whether sufficient retained austenite can be maintained at low temperatures. The specific experimental procedure is as follows: briefly, the samples were cooled in turn from room temperature to 0, −20, −40, −60, −80, −100 and −196°C; the amount of retained austenite at the above temperatures was measured using X-ray diffraction. Through investigating the dependence of the content of retained austenite on temperature, it was revealed that when the content of retained austenite is <20, retained austenite can be maintained until −196°C.
Development of artificial black patina on Mycenaean metal finds
Authors: Giumlia-Mair A R G
Published: January 2013

Artificially black patinated finds from Mycenaean contexts are among the most interesting Bronze Age metal objects. They come from several contexts in the Eastern Mediterranean and are important because of their technology and as indication of trade and cultural connections. Regrettably only few examples of items of this material have been scientifically examined. Archaeologists without a scientific background are still not aware of the true nature of the black material with precious metal inlays. This paper presents a research on the development of the patina on a Mycenaean dagger and on the famous silver cup from Enkomi in Cyprus. The alloys employed for the black inlays, analysed up to now, consist of Cu containing low amounts of Au that was artificially patinated by different methods: either the red hot object was plunged into an aqueous solution containing copper salts and alum or it was heated in the boiling solution.
Non-destructive characterisation of fourteenth century painting by means of molecular spectroscopy and unilateral NMR
Authors: Marchettini N , Atrei A , Benetti F , Proietti N , Di Tullio V , Mascalchi M , Osticioli I , Siano S , Turbanti Memmi I
Published: January 2013

The present work was aimed at characterising the materials and assessing the state of conservation of the ‘Adorazione dei Magi’, a wooden panel painted by Bartolo di Fredi in the second half of fourteenth century. To this goal, innovative non-destructive investigation techniques such as portable Raman spectroscopy, visible reflectance spectroscopy and unilateral nuclear magnetic resonance, were used in situ in order to achieve surface and bulk compositional data. The former allowed the identification of the artist's palette including cinnabar, red ochre, minium, carbon black, lead white, ultramarine blue, malachite and phthalocyanine green, while the latter provided information on the stratigraphic structure and state of conservation of the wooden panel.
Surface treatments of wood by chemically modified shellac
Authors: Licchelli M , Malagodi M , Somaini M , Weththimuni M , Zanchi C
Published: January 2013

Shellac is an animal resin, which has been widely used as a decorative lacquer for wooden handicrafts in the last centuries. It still finds application as wood sealer and finisher because of its peculiar properties. However, there are also some limitations, such as sensitivity to alcoholic solvents and to pH variations and considerable tendency to chromatic variations upon ageing. The aim of this work is to improve some features of shellac by inducing a cross-linking in its structure. Two new materials were obtained by addition of a polyamine and a polyaziridine to shellac, and their performance were studied by different experiments. The varnish obtained by addition of polyaziridine shows a considerably improved performance when compared to plain shellac. In particular, it preserves almost unaltered the chromatic properties of shellac varnish and it shows an increased resistance to alcohols, to basic agents and to artificial ageing caused by a long lasting UV irradiation.
Thermostability of S30432 shot peened surface layer
Authors: Zhan K , Xie L C , Jiang C H , Ji V
Published: January 2013

The recrystallisation behaviour of S30432 shot peened deformation surface layer during isothermal annealing has been investigated by X-ray diffraction line profile analysis method. The results revealed that annealing time and temperature were two key parameters for isothermal annealing process of S30432 steel. With higher annealing temperature, the recrystallisation behaviour in the shot peened deformed layer was more obvious. Based on the results of line profile analysis, the recrystallisation activation energy and microstrain relaxation energy were calculated. In addition, after isothermal annealing, the depth distribution of domain size in the deformed layer was also investigated and discussed in details. According to the analysis, the results showed that the thermostability of S30432 shot peened surface layer was relatively stable when the annealing temperature was below 650°C.
Nanotribological properties of silicon with silane derived surface modification
Authors: Peng Y , Ni Z , Bu H , Wang Y
Published: January 2013

Silicon substrates were modified with octadecyltrichlorosilane and 3-Aminopropyl-triethoxysilane molecules by chemical adsorption process. The surface properties, morphology and composition were characterised by means of contact angle measurement, atomic force microscopic (AFM) analysis and X-ray photoelectron spectroscopy. To achieve quantitative results, it is important to implement the proper force calibration in AFMs. Both the lateral and the normal spring constants of the AFM cantilever were calibrated. The nanotribological properties including adhesion, friction and antiwear of silane derived surface modification are comparatively studied with the calibrated AFM cantilever. The results demonstrated that the silane derived surface modification reduces adhesion and friction. Hydrophobic methyl terminated modification possesses better friction reduction and antiwear capacity than hydrophilic amine terminated surface.
Laser cladding of rail steel with Co–Cr
Authors: Clare A. T. , Oyelola O. , Abioye T. E. , Farayibi P. K.
Published: January 2013

Degradation and subsequent failure of rail tracks are commonly caused by rolling contact fatigue among other mechanisms of wear. Rail crossings are known to exhibit more of these failures due to increased localised traffic and environmental conditions. A high proportion of the costs associated with the repair of rail tracks was due to the rolling contact fatigue phenomenon. In order to mitigate these costs, laser cladding of worn regions has been proposed for the repair of used tracks in situ to limit the need for them to be replaced and for the preservice protection of newly rolled rails and cast crossings. A Co–Cr, Stellite 6, alloy is chosen to demonstrate repair and also surface coating/protection of R260 rail steel. Results showed that cladded Stellite 6 possessed improved hardness, good tribological performance and excellent workhardening ability when compared with rail steel. These demonstrate laser cladding as a viable solution for repair worn rail track.
Properties of TiO2 thin films prepared using sol–gel process
Authors: Rojviroon T , Sirivithayapakorn S
Published: January 2013

Titanium dioxide (TiO2) thin films were prepared using a sol–gel process and applying between two and five coating layers onto the surface of borosilicate glass slides and 304 stainless steel sheets. The physical properties of the multilayer TiO2 thin films on both of the substrates under the same fabrication process were systematically compared. Our results indicate that the crystalline phase structure of the prepared TiO2 thin film was entirely composed of anatase with an optical band gap of 3·27 eV. The grain sizes of the TiO2 crystals in the films on the glass slides and the stainless steel sheets were in the ranges of 15–100 nm and 20–250 nm respectively. The results suggested that at least three layers of coating were required to produce the TiO2 thin film with the desired range of properties.
Effect of electroplating parameters on properties of Zn–nano-TiO2 composite coatings
Authors: Mokabber T , Rastegari S , Razavizadeh H
Published: January 2013

In this paper, Zn–nano-TiO2 composite coatings were deposited on the mild steel substrate. Coatings were produced by electroplating method from sulphate bath in which nanosized TiO2 particles were suspended. The chemical composition and surface morphology of coatings were investigated using energy dispersive spectroscopy and scanning electron microscopy respectively. Corrosion behaviour of the coatings was studied in 3·5 wt-% NaCl solutions, and their microhardness was evaluated through Vickers microhardness test. According to the results, the parameters of current density, particle concentration in the solution and temperature were optimised with respect to TiO2 content in the composite coatings. The optimised current density, particle concentration and temperature of the bath were found to be 3 A dm−2, 5 g L−1 and 40°C respectively. Accordingly, an increase in the amount of TiO2 particles in the composite coatings increases the hardness of composite coatings but did not have harmful effects on corrosion resistance.
Under the surface: silvering in Adrian Athenaeum
Authors: Anguilano L
Published: January 2013

The recovery of a metal workshop dated to the sixth century AD, superimposed to the Hadrian's Athenaeum in Piazza Madonna di Loreto, Rome, provided the opportunity to identify a series of metallurgical processes linked to the two chaînes opératoires related to copper, bronze, silver and lead productions. Some analysed fragments presented superficial treatment identified as silvering, the focus of this paper. The main aim is to investigate the signs of the surface treatment on the artefacts and discuss what methods would be best employed to analyse and interpret them in order to identify the process to which they relate. Different analytical techniques were used to obtain information on the superficial layer, and their pros and cons are presented so as to discuss how analytical limits can affect the interpretation of a process and the identification of an object. The conclusions reached here are necessarily limited because of the scarce number of samples analysed and the techniques used.
Electrochemically aged arc-sprayed zinc coating to concrete: bond strength study
Authors: Shi X M , Soltesz S , Li Y X , Cross J D , Ewan L
Published: January 2013

This research was conducted to preliminarily investigate the anode removal process that could affect the interface of electrochemically aged arc sprayed zinc coating to concrete using experimental and artificial neural network methodologies. Experimental results showed that the bond strength of newly sprayed zinc to concrete was influenced by the presence of the old reaction layer and dependent on the electrochemical age of the layer. Artificial neural networks were used to achieve better understanding of the complex cause-and-effect relationships inherent in the zinc/concrete system and was successful in finding meaningful, logical results from the bond strength data.
Microstructure characterisation of alumina coating on steel by PEO
Authors: Wang Y L , Wang M , Zhou M , Li B J , Amoako G , Jiang Z H
Published: January 2013

Alumina ceramic coating was prepared on Q235 carbon steel by plasma electrolytic oxidation. The discharge process was analysed according to the voltage–time curve. The microstructure of the ceramic coating was investigated by scanning electron microscopy, X-ray diffractometry and energy dispersive X-ray spectroscopy. The bonding strength, thickness, hardness, surface roughness and corrosion properties of the coatings were studied. The results indicated that coating on Q235 carbon steel mainly consisted of α-Al2O3 and γ-A12O3. The coating showed coarse and porous surface. The surface roughness of the coating was 1·8 μm, and the average diameter of the pores was 3–4 μm. The hardness of the coating was 1854 HV. The thickness of the coating was ∼28 μm, and the bonding strength was 23 MPa. The corrosion tests indicated that the corrosion current density of alumina coated Q235 in 3·5%NaCl was 8·289×10−7 A cm−2, which was decreased by two orders of magnitude compared with the uncoated one. The corrosion potential was increased to −0·379 V, which shifted positively by 0·303 V compared to the uncoated one.
Markedly additive antitumor activity with the combination of a selective survivin suppressant YM155 and alemtuzumab in adult T-cell leukemia
Authors: Chen Jing , Pise-Masison Cynthia A. , Shih Joanna H. , Morris John C. , Janik John E. , Conlon Kevin C. , Keating Anne , Waldmann Thomas A.
Published: January 2013

Key Points

Markedly additive antitumor activity with the combination of a selective survivin suppressant (YM155) and alemtuzumab in adult T-cell leukemia.
Tumor-promoting immune-suppressive myeloid-derived suppressor cells in the multiple myeloma microenvironment in humans
Authors: Görgün Güllü Topal , Whitehill Gregory , Anderson Jennifer L. , Hideshima Teru , Maguire Craig , Laubach Jacob , Raje Noopur , Munshi Nikhil C. , Richardson Paul G. , Anderson Kenneth C.
Published: January 2013

Key Points

MDSCs are increased in patients with MM and have bidirectional interaction with tumors in the MM microenvironment. MM-MDSCs promote MM growth and induce immune suppression; conversely, MM cells induce MDSC development.
MYD88 L265P in Waldenström macroglobulinemia, immunoglobulin M monoclonal gammopathy, and other B-cell lymphoproliferative disorders using conventional and quantitative allele-specific polymerase chain reaction
Authors: Xu Lian , Hunter Zachary R. , Yang Guang , Zhou Yangsheng , Cao Yang , Liu Xia , Morra Enrica , Trojani Alessandra , Greco Antonino , Arcaini Luca , Varettoni Marzia , Brown Jennifer R. , Tai Yu-Tzu , Anderson Kenneth C. , Munshi Nikhil C. , Patterson Christopher J. , Manning Robert J. , Tripsas Christina K. , Lindeman Neal I. , Treon Steven P.
Published: January 2013

Key Points

MYD88 L265P is expressed in WM and IgM MGUS patients using AS-PCR assays with potential use in diagnostic discrimination and response assessment.
Failure-free survival after second-line systemic treatment of chronic graft-versus-host disease
Authors: Inamoto Yoshihiro , Storer Barry E. , Lee Stephanie J. , Carpenter Paul A. , Sandmaier Brenda M. , Flowers Mary E. D. , Martin Paul J.
Published: January 2013

Key Points

Relapse-free survival without treatment change can form the basis of the primary end point in studies of chronic graft-versus-host disease. Steroid doses at the time of assessment should be taken into account in treatment studies of chronic graft-versus-host disease.
Applications of Kato’s inequality for n-tuples of operators in Hilbert spaces, (I)
Authors: Dragomir Sever S , Cho Yeol Je , Kim Young-Ho
Published: January 2013

In this paper, by the use of the famous Kato’s inequality for bounded linear operators, we establish some inequalities for n-tuples of operators and apply them for functions of normal operators defined by power series as well as for some norms and numerical radii that arise in multivariate operator theory.

MSC:47A63, 47A99.
xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data
Authors: Uppal Karan , Soltow Quinlyn A , Strobel Frederick H , Pittard W Stephen , Gernert Kim M , Yu Tianwei , Jones Dean P
Published: January 2013

Background

Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation.

Results

xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites.

Conclusions

xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.
Saccharopolyspora erythraea’sgenome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch
Authors: Marcellin Esteban , Mercer Tim R , Licona-Cassani Cuauhtemoc , Palfreyman Robin W , Dinger Marcel E , Steen Jennifer A , Mattick John S , Nielsen Lars K
Published: January 2013

Background

Actinobacteria form a major bacterial phylum that includes numerous human pathogens. Actinobacteria are primary contributors to carbon cycling and also represent a primary source of industrial high value products such as antibiotics and biopesticides. Consistent with other members of the actinobacterial phylum, Saccharopolyspora erythraea undergo a transitional switch. This switch is characterized by numerous metabolic and morphological changes.

Results

We performed RNA sequencing to analyze the transcriptional changes that occur during growth of Saccharopolyspora erythraea in batch culture. By sequencing RNA across the fermentation time course, at a mean coverage of 4000X, we found the vast majority of genes to be prominently expressed, showing that we attained close to saturating sequencing coverage of the transcriptome. During the metabolic switch, global changes in gene expression influence the metabolic machinery of Saccharopolyspora erythraea, resetting an entirely novel gene expression program. After the switch, global changes include the broad repression of half the genes regulated by complex transcriptional mechanisms. Paralogous transposon clusters, delineate these transcriptional programs. The new transcriptional program is orchestrated by a bottleneck event during which mRNA levels are severely restricted by targeted mRNA degradation.

Conclusions

Our results, which attained close to saturating sequencing coverage of the transcriptome, revealed unanticipated transcriptional complexity with almost one third of transcriptional content originating from un-annotated sequences. We showed that the metabolic switch is a sophisticated mechanism of transcriptional regulation capable of resetting and re-synchronizing gene expression programs at extraordinary speed and scale.
Effect of the myostatin locus on muscle mass and intramuscular fat content in a cross between mouse lines selected for hypermuscularity
Authors: Kärst Stefan , Strucken Eva M , Schmitt Armin O , Weyrich Alexandra , de Villena Fernando PM , Yang Hyuna , Brockmann Gudrun A
Published: January 2013

Background

This study is aimed at the analysis of genetic and physiological effects of myostatin on economically relevant meat quality traits in a genetic background of high muscularity. For this purpose, we generated G3 populations of reciprocal crosses between the two hypermuscular mouse lines BMMI866, which carries a myostatin mutation and is lean, and BMMI806, which has high intramuscular and body fat content. To assess the relationship between muscle mass, body composition and muscle quality traits, we also analysed intramuscular fat content (IMF), water holding capacity (WHC), and additional physiological parameters in M. quadriceps and M. longissimus in 308 G3-animals.

Results

We found that individuals with larger muscles have significantly lower total body fat (r = −0.28) and IMF (r = −0.64), and in females, a lower WHC (r = −0.35). In males, higher muscle mass was also significantly correlated with higher glycogen contents (r = 0.2) and lower carcass pH-values 24 hours after dissection (r = −0.19). Linkage analyses confirmed the influence of the myostatin mutation on higher lean mass (1.35 g), reduced body fat content (−1.15%), and lower IMF in M. longissimus (−0.13%) and M. quadriceps (−0.07%). No effect was found for WHC. A large proportion of variation of intramuscular fat content of the M. longissimus at the myostatin locus could be explained by sex (23%) and direction-of-cross effects (26%). The effects were higher in males (+0.41%). An additional locus with negative over-dominance effects on total fat mass (−0.55 g) was identified on chromosome 16 at 94 Mb (86–94 Mb) which concurs with fat related QTL in syntenic regions on SSC13 in pigs and BTA1 in cattle.

Conclusion

The data shows QTL effects on mouse muscle that are similar to those previously observed in livestock, supporting the mouse model. New information from the mouse model helps to describe variation in meat quantity and quality, and thus contribute to research in livestock.
Transcriptome analysis of rice root heterosis by RNA-Seq
Authors: Zhai Rongrong , Feng Yue , Wang Huimin , Zhan Xiaodeng , Shen Xihong , Wu Weiming , Zhang Yingxin , Chen Daibo , Dai Gaoxing , Yang Zhanlie , Cao Liyong , Cheng Shihua
Published: January 2013

Background

Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focused, root heterosis is also an indispensable component of heterosis in the entire plant and of major importance to plant breeding. Consequently, systematic investigations of root heterosis, particularly in reproductive-stage rice, are needed. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis studies.

Results

Using the Illumina HiSeq 2000 platform, the root transcriptomes of the super-hybrid rice variety Xieyou 9308 and its parents were analyzed at tillering and heading stages. Approximately 391 million high-quality paired-end reads (100-bp in size) were generated and aligned against the Nipponbare reference genome. We found that 38,872 of 42,081 (92.4%) annotated transcripts were represented by at least one sequence read. A total of 829 and 4186 transcripts that were differentially expressed between the hybrid and its parents (DGHP) were identified at tillering and heading stages, respectively. Out of the DGHP, 66.59% were down-regulated at the tillering stage and 64.41% were up-regulated at the heading stage. At the heading stage, the DGHP were significantly enriched in pathways related to processes such as carbohydrate metabolism and plant hormone signal transduction, with most of the key genes that are involved in the two pathways being up-regulated in the hybrid. Several significant DGHP that could be mapped to quantitative trait loci (QTLs) for yield and root traits are also involved in carbohydrate metabolism and plant hormone signal transduction pathways.

Conclusions

An extensive transcriptome dataset was obtained by RNA-Seq, giving a comprehensive overview of the root transcriptomes at tillering and heading stages in a heterotic rice cross and providing a useful resource for the rice research community. Using comparative transcriptome analysis, we detected DGHP and identified a group of potential candidate transcripts. The changes in the expression of the candidate transcripts may lay a foundation for future studies on molecular mechanisms underlying root heterosis.
Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna
Authors: Dang Zhen-hua , Zheng Lin-lin , Wang Jia , Gao Zhe , Wu Shu-biao , Qi Zhi , Wang Ying-chun
Published: January 2013

Background

Reaumuria trigyna is an endangered small shrub endemic to desert regions in Inner Mongolia. This dicotyledonous recretohalophyte has unique morphological characteristics that allow it to tolerate the stress imposed by semi-desert saline soil. However, it is impossible to explore the mechanisms underlying this tolerance without detailed genomic information. Fortunately, newly developed high-throughput sequencing technologies are powerful tools for de novo sequencing to gain such information for this species.

Results

Two sequencing libraries prepared from control (C21) and NaCl-treated samples (T43) were sequenced using short reads sequencing technology (Illumina) to investigate changes in the R. trigyna transcriptome in response to salt stress. Among 65340 unigenes, 35495 (52.27%) were annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic pathways with a cut-off E-value of 10-5. These included 44 Gene Ontology (GO) terms, 119 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 25 Clusters of Orthologous Groups families. By comparing the transcriptomes from control and NaCl-treated plants, 5032 genes showed significantly differences in transcript abundance under salt stress (false discovery rate ≤ 0.001 and |log2Ratio| ≥ 1). These genes were significantly enriched in 29 KEGG pathways and 26 GO terms. The transcription profiles indicated that genes related to ion transport and the reactive oxygen species scavenging system were relevant to the morphological and physiological characteristics of this species. The expression patterns of 30 randomly selected genes resulted from quantitative real-time PCR were basically consistent with their transcript abundance changes identified by RNA-seq.

Conclusions

The present study identified potential genes involved in salt tolerance of R. trigyna. The globally sequenced genes covered a considerable proportion of the R. trigyna transcriptome. These data represent a genetic resource for the discovery of genes related to salt tolerance in this species, and may be a useful source of reference sequences for closely related taxa. These results can also further our understanding of salt tolerance in other halophytes surviving under sodic stress.
Identification of the Hevea brasiliensisAP2/ERF superfamily by RNA sequencing
Authors: Duan Cuifang , Argout Xavier , Gébelin Virginie , Summo Marilyne , Dufayard Jean-François , Leclercq Julie , Kuswanhadi  , Piyatrakul Piyanuch , Pirrello Julien , Rio Maryannick , Champion Antony , Montoro Pascal
Published: January 2013

Background

Rubber tree (Hevea brasiliensis) laticifers are the source of natural rubber. Rubber production depends on endogenous and exogenous ethylene (ethephon). AP2/ERF transcription factors, and especially Ethylene-Response Factors, play a crucial role in plant development and response to biotic and abiotic stresses. This study set out to sequence transcript expressed in various tissues using next-generation sequencing and to identify AP2/ERF superfamily in the rubber tree.

Results

The 454 sequencing technique was used to produce five tissue-type transcript libraries (leaf, bark, latex, embryogenic tissues and root). Reads from all libraries were pooled and reassembled to improve mRNA lengths and produce a global library. One hundred and seventy-three AP2/ERF contigs were identified byin silicoanalysis based on the amino acid sequence of the conserved AP2 domain from the global library. The 142 contigs with the full AP2 domain were classified into three main families (20 AP2 members, 115 ERF members divided into 11 groups, and 4 RAV members) and 3 soloist members. Fifty-nine AP2/ERF transcripts were found in latex. Alongside the microRNA172 already described in plants, eleven additional microRNAs were predicted to inhibitHeveaAP2/ERF transcripts.

Conclusions

Heveahas a similar number ofAP2/ERFgenes to that of other dicot species. We adapted the alignment and classification methods to data from next-generation sequencing techniques to provide reliable information. We observed several specific features for the ERF family. Three HbSoloist members form a group inHevea. SeveralAP2/ERFgenes highly expressed in latex suggest they have a specific function inHevea. The analysis of AP2/ERF transcripts inHeveapresented here provides the basis for studying the molecular regulation of latex production in response to abiotic stresses and latex cell differentiation.
Comparative gene expression between two yeast species
Authors: Guan Yuanfang , Dunham Maitreya J , Troyanskaya Olga G , Caudy Amy A
Published: January 2013

Background

Comparative genomics brings insight into sequence evolution, but even more may be learned by coupling sequence analyses with experimental tests of gene function and regulation. However, the reliability of such comparisons is often limited by biased sampling of expression conditions and incomplete knowledge of gene functions across species. To address these challenges, we previously systematically generated expression profiles in Saccharomyces bayanus to maximize functional coverage as compared to an existing Saccharomyces cerevisiae data repository.

Results

In this paper, we take advantage of these two data repositories to compare patterns of ortholog expression in a wide variety of conditions. First, we developed a scalable metric for expression divergence that enabled us to detect a significant correlation between sequence and expression conservation on the global level, which previous smaller-scale expression studies failed to detect. Despite this global conservation trend, between-species gene expression neighborhoods were less well-conserved than within-species comparisons across different environmental perturbations, and approximately 4% of orthologs exhibited a significant change in co-expression partners. Furthermore, our analysis of matched perturbations collected in both species (such as diauxic shift and cell cycle synchrony) demonstrated that approximately a quarter of orthologs exhibit condition-specific expression pattern differences.

Conclusions

Taken together, these analyses provide a global view of gene expression patterns between two species, both in terms of the conditions and timing of a gene's expression as well as co-expression partners. Our results provide testable hypotheses that will direct future experiments to determine how these changes may be specified in the genome.
Developmentally regulated expression and complex processing of barley pri-microRNAs
Authors: Kruszka Katarzyna , Pacak Andrzej , Swida-Barteczka Aleksandra , Stefaniak Agnieszka K , Kaja Elzbieta , Sierocka Izabela , Karlowski Wojciech , Jarmolowski Artur , Szweykowska-Kulinska Zofia
Published: January 2013

Background

MicroRNAs (miRNAs) regulate gene expression via mRNA cleavage or translation inhibition. In spite of barley being a cereal of great economic importance, very little data is available concerning its miRNA biogenesis. There are 69 barley miRNA and 67 pre-miRNA sequences available in the miRBase (release 19). However, no barley pri-miRNA and MIR gene structures have been shown experimentally. In the present paper, we examine the biogenesis of selected barley miRNAs and the developmental regulation of their pri-miRNA processing to learn more about miRNA maturation in barely.

Results

To investigate the organization of barley microRNA genes, nine microRNAs - 156g, 159b, 166n, 168a-5p/168a-3p, 171e, 397b-3p, 1120, and 1126 - were selected. Two of the studied miRNAs originate from one MIR168a-5p/168a-3p gene. The presence of all miRNAs was confirmed using a Northern blot approach. The miRNAs are encoded by genes with diverse organizations, representing mostly independent transcription units with or without introns. The intron-containing miRNA transcripts undergo complex splicing events to generate various spliced isoforms. We identified miRNAs that were encoded within introns of the noncoding genes MIR156g and MIR1126. Interestingly, the intron that encodes miR156g is spliced less efficiently than the intron encoding miR1126 from their specific precursors. miR397b-3p was detected in barley as a most probable functional miRNA, in contrast to rice where it has been identified as a complementary partner miRNA*. In the case of miR168a-5p/168a-3p, we found the generation of stable, mature molecules from both pre-miRNA arms, confirming evolutionary conservation of the stability of both species, as shown in rice and maize. We suggest that miR1120, located within the 3′ UTR of a protein-coding gene and described as a functional miRNA in wheat, may represent a siRNA generated from a mariner-like transposable element.

Conclusions

Seven of the eight barley miRNA genes characterized in this study contain introns with their respective transcripts undergoing developmentally specific processing events prior to the dicing out of pre-miRNA species from their pri-miRNA precursors. The observed tendency to maintain the intron encoding miR156g within the transcript, and preferences in splicing the miR1126-harboring intron, may suggest the existence of specific regulation of the levels of intron-derived miRNAs in barley.
POLG1 mutations and stroke like episodes: a distinct clinical entity rather than an atypical MELAS syndrome
Authors: Cheldi Antonella , Ronchi Dario , Bordoni Andreina , Bordo Bianca , Lanfranconi Silvia , Bellotti Maria Grazia , Corti Stefania , Lucchini Valeria , Sciacco Monica , Moggio Maurizio , Baron Pierluigi , Comi Giacomo Pietro , Colombo Antonio , Bersano Anna
Published: January 2013

Background

POLG1 mutations have been associated with MELAS-like phenotypes. However given several clinical differences it is unknown whether POLG1 mutations are possible causes of MELAS or give raise to a distinct clinical and genetic entity, named POLG1-associated encephalopathy.

Case presentation

We describe a 74 years old man carrying POLG1 mutations presenting with strokes, myopathy and ragged red fibers with some atypical aspects for MELAS such as late onset, lack of cerebral calcification and presence of frontal and occipital MRI lesions better consistent with the POLG associated-encephalopathy spectrum.

Conclusion

The lack of available data hampers a definite diagnosis in our patient as well as makes it difficult to compare MELAS, which is a clearly defined clinical syndrome, with POLG1-associated encephalopathy, which is so far a purely molecularly defined syndrome with a quite heterogeneous clinical picture. However, the present report contributes to expand the phenotypic spectrum of POLG1 mutations underlining the importance of searching POLG1 mutations in patients with mitochondrial signs and MELAS like phenotypes but negative for common mtDNA mutations.
Increased MiR-221 expression in hepatocellular carcinoma tissues and its role in enhancing cell growth and inhibiting apoptosis in vitro
Authors: Rong Minhua , Chen Gang , Dang Yiwu
Published: January 2013

Background

MiR-221 is over-expressed in human hepatocellular carcinoma (HCC), but its clinical significance and function in HCC remains uncertain. The aim of the study was to investigate the relationship between miR-221 overexpression and clinicopathological parameters in HCC formalin-fixed paraffin-embedded (FFPE) tissues, and the effect of miR-221 inhibitor and mimic on different HCC cell lines in vitro.

Methods

MiR-221 expression was detected using real time RT-qPCR in FFPE HCC and the adjacent noncancerous liver tissues. The relationship between miR-221 level and clinicopathological features was also analyzed. Furthermore, miR-221 inhibitor and mimic were transfected into HCC cell lines HepB3, HepG2 and SNU449. The effects of miR-221 on cell growth, cell cycle, caspase activity and apoptosis were also investigated by spectrophotometry, fluorimetry, fluorescence microscopy and flow cytometry, respectively.

Results

The relative expression of miR-221 in clinical TNM stages III and IV was significantly higher than that in the stages I and II. The miR-221 level was also upregulated in the metastatic group compared to the nonmetastatic group. Furthermore, miR-221 over-expression was related to the status of tumor capsular infiltration in HCC clinical samples. Functionally, cell growth was inhibited, cell cycle was arrested in G1/S-phase and apoptosis was increased by miR-221 inhibitor in vitro. Likewise, miR-221 mimic accelerated the cell growth.

Conclusions

Expression of miR-221 in FFPE tissues could provide predictive significance for prognosis of HCC patients. Moreover, miR-221 inhibitor could be useful to suppress proliferation and induce apoptosis in HCC cells. Thus miR-221 might be a critical targeted therapy strategy for HCC.
Lipoprotein lipase links vitamin D, insulin resistance, and type 2 diabetes: a cross-sectional epidemiological study
Authors: Huang Yifan , Li Xiaoxia , Wang Maoqing , Ning Hua , A Lima , Li Ying , Sun Changhao
Published: January 2013

Background

Lipoprotein lipase (LPL) and serum 25-hydroxyvitamin D [25(OH)D] play important roles in the regulation of lipid metabolism. Although dyslipidemia is associated with insulin resistance (IR) and type 2 diabetes (T2D), there are limited data available regarding the relationship of LPL and 25(OH)D to IR and T2D at a population level. The objective of the present study is to investigate the associations of LPL and 25(OH)D with IR and T2D in a Chinese population.

Methods

The study cohort consisted of 2708 subjects (1326 males, 1382 females; mean age 48.5 ± 12.6 years) in main communities of Harbin, China. Serum 25(OH)D, LPL, free fatty acids (FFAs), fasting glucose (FG), fasting insulin, lipid profile, apoA and apoB concentrations were measured.

Results

Serum 25(OH)D concentration was positively associated with LPL (β = 0.168, P < 0.001). LPL was inversely associated with IR and T2D. Subjects in the lowest quartile of LPL had the highest risk of IR [odds ratio (OR) = 1.85, 95% CI = 1.22-2.68] and T2D (OR = 1.65, 95% CI = 1.14-2.38). Serum 25(OH)D was also inversely associated with IR and T2D. Vitamin D deficiency [25(OH)D < 20 ng/ml] was associated with an increasing risk of IR (OR = 1.91, 95% CI = 1.23-2.76) and T2D (OR = 2.06, 95% CI = 1.37-3.24). The associations of 25(OH)D with IR and T2D were attenuated by further adjustment for LPL.

Conclusions

LPL is associated with serum 25(OH)D, IR and T2D in the Chinese population. These results suggest a potential mediating role of LPL in the associations of 25(OH)D with IR and T2D.
Multivariable analysis of host amino acids in plasma and liver during infection of malaria parasite Plasmodium yoelii
Authors: Saiki Erisha , Nagao Kenji , Aonuma Hiroka , Fukumoto Shinya , Xuan Xuenan , Bannai Makoto , Kanuka Hirotaka
Published: January 2013

Background

Malaria is the most significant human parasitic disease, and yet understanding of the energy metabolism of the principle pathogen, Plasmodium falciparum, remains to be fully elucidated. Amino acids were shown to be essential nutritional requirements since early times and much of the current knowledge of Plasmodium energy metabolism is based on early biochemical work, performed using basic analytical techniques, carried out almost exclusively on human plasma with considerable inter-individual variability.

Methods

In order to further characterize the fate of amino acid metabolism in malaria parasite, multivariate analysis using statistical modelling of amino acid concentrations (aminogram) of plasma and liver were determined in host infected with rodent malaria parasite, Plasmodium yoelii.

Results and conclusion

Comprehensive and statistical aminogram analysis revealed that P. yoelii infection caused drastic change of plasma and liver aminogram, and altered intra- and inter-correlation of amino acid concentration in plasma and liver. These findings of the interactions between amino acids and Plasmodium infection may provide insight to reveal the interaction between nutrients and parasites.
Ethno-entomological observations from North Korea (officially known as the “Democratic People’s Republic of Korea”)
Authors: Meyer-Rochow V Benno
Published: January 2013

In terms of scientific activities generally and ethnobiological pursuits in particular, North Korea, officially known as the Democratic People’s Republic of Korea, is an almost blank entity on the quilt of global research. During a sabbatical semester at Pyongyang University of Science and Technology the author used this opportunity to gather some information on the uses of insect and other terrestrial arthropods as human food and components of traditional healing methods in that country. Despite the widely publicised shortcomings in the supply of food stuffs to the population of North Korea, insects are not generally seen as a source of food worthy of exploitation. However, the therapeutic use of insects, centipedes and scorpions to treat illnesses as diverse as the common cold, skin rashes, constipation, dysentery, nervous prostration, whooping cough, osteomyelitis, tetanus, and various forms of cancer is apparently still popular. The arthropods used therapeutically are credited with anti-inflammatory, immunological and other health-promoting effects, because they are said to contain hormones, steroids, lipids and plant-derived alkaloids, all of which capable of exerting their effects on the human body.
BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
Authors: van Roon Eddy H , Boot Arnoud , Dihal Ashwin A , Ernst Robert F , van Wezel Tom , Morreau Hans , Boer Judith M
Published: January 2013

Background

Cancer-specific hypermethylation of (promoter) CpG islands is common during the tumorigenesis of colon cancer. Although associations between certain genetic aberrations, such asBRAFmutation and microsatellite instability, and the CpG island methylator phenotype (CIMP), have been found, the mechanisms by which these associations are established are still unclear. We studied genome-wide DNA methylation differences between colorectal tumors carrying aBRAFmutation andBRAFwildtype tumors.

Results

Using differential methylation hybridization on oligonucleotide microarrays representing 32,171 CpG-rich regions, we identified 1,770 regions with differential methylation between colorectal tumor and paired normal colon. Next, we compared the tumor/normal methylation ratios between different groups of patients. Related to CIMP, we identified 749 differentially methylated regions, of which 86% had a higher tumor/normal methylation ratio in the CIMP-positive group. We identified 758 regions with aBRAFmutation-specific methylation change, of which 96% had a higher tumor/normal methylation ratio in theBRAFmutant group. Among the genes affected byBRAFmutation-specific methylation changes, we found enrichment of several cancer-related pathways, including the PI3 kinase and Wnt signaling pathways. To focus on genes that are silenced in a tumor-specific rather than a lineage-specific manner, we used information on the epigenetic silencing mark H3K27me3in embryonic stem (ES) cells. Among the genes showingBRAFmutation-specific promoter methylation but no H3K27me3mark in ES cells were forkhead box (FOX) transcription factors associated with the PI3 kinase pathway, as well asMLH1andSMO. Repression ofFOXD3gene expression in tumors could be related to its promoter hypermethylation.

Conclusions

We identified newBRAFmutation-specific methylation changes in colorectal cancer. Epigenetic downregulation of these targets may contribute to mutationally activeBRAF-driven tumorigenesis, explaining its association with aberrant DNA methylation.