bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

AbstractBackgroundRubber 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.ResultsThe 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.ConclusionsHeveahas 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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

AbstractIn 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

AbstractBackgroundCancer-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.ResultsUsing 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.ConclusionsWe 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.
Structural, optical and fluorescence properties of wet chemically synthesized ZnO:Pd2+ nanocrystals
Authors: Kaur Jasmeet , Kumar Praveen , Sathiaraj Thangaiah Stephen , Thangaraj Rengasamy 
Published: January 2013

Abstract
This paper presents the structural, optical and photoluminescence properties of wet chemically synthesized ZnO:Pd2+ colloidal nanocrystals characterised by X-ray diffraction, scanning electron microscopy/energy-dispersive X-ray spectroscopy (EDS) and Fourier transform infrared spectroscopic techniques. Increase in lattice parameters from diffraction data indicates the incorporation of Pd2+ in the ZnO crystal lattice. A small amount of dopant favours the formation of stoichiometric ZnO nanoparticles; otherwise, non-stoichiometric nanocrystal formation was observed from the EDS data. The optical gap was found to decrease with the doping concentration, except for the small dopant level of 0.05% of Pd2+ where an increase in the optical gap was observed. Intensities of characteristic luminescence bands for pure ZnO nanocrystals (357, 387 and 420 nm) were found to decrease with the increasing Pd2+ concentration, and two new bands centred at 528 and 581 nm for 0.5% Pd2+ concentration were observed. These results have been explained on the basis of change in the oxygen vacancy-related defects and/or formation of new trap states which in turn affect the luminescence properties of ZnO:Pd2+ nanocrystals, which are important in the realisation of visible light-emitting solid-state devices.
Disease severity in K/BxN serum transfer-induced arthritis is not affected by IL-33 deficiency
Authors: Martin Praxedis , Talabot-Ayer Dominique , Seemayer Christian Alexander , Vigne Solenne , Lamacchia Céline , Rodriguez Emiliana , Finckh Axel , Smith Dirk E , Gabay Cem , Palmer Gaby 
Published: January 2013

Abstract
Introduction
Interleukin (IL)-33 is a cytokine of the IL-1 family, which signals through the ST2 receptor. Previous work suggested implication of the IL-33/ST2 axis in the pathogenesis of human and mouse arthritis. Here, we directly investigated the role of endogenous IL-33 in K/BxN serum transfer-induced arthritis by using IL-33 knockout (KO) mice.

Methods
Arthritis was induced by injection of complete K/BxN serum or purified IgG. Disease severity was monitored by clinical and histological scoring.

Results
K/BxN serum transfer induced pronounced arthritis with similar incidence and severity in IL-33 KO and wild-type (WT) mice. In contrast, disease development was significantly reduced in ST2 KO mice. IL-33 expression in synovial tissue was comparable in arthritic WT and ST2 KO mice, and absent in IL-33 KO mice. Transfer of purified arthritogenic IgG instead of complete K/BxN serum also resulted in similar arthritis severity in IL-33 KO and WT mice, excluding a contribution of IL-33 contained in the serum of donor mice to explain this result. We investigated additional potential confounding factors, including purity of genetic background, but the mechanisms underlying reduced arthritis in ST2 KO mice remained unclear.

Conclusions
The data obtained with IL-33 KO mice indicate that endogenous IL-33 is not required for the development of joint inflammation in K/BxN serum transfer-induced arthritis. On the contrary, arthritis severity was reduced in ST2 KO mice. This observation might relate to IL-33 independent effects of ST2, and/or reveal the existence of confounding variables affecting the severity of joint inflammation in these KO strains.