bluuebunny/crossref_metadata_2025 huggingface dataset:
APPROXIMATING METRICS WITH PLANAR BOUNDARY-LABELED PHYLOGENETIC NETWORKS
Authors: SHENG RUOGU , BEREG SERGEY
Published: June 2012

Phylogenetic networks are useful for visualizing evolutionary relationships between species with reticulate events such as hybridizations and horizontal gene transfers. In this paper, we consider the problem of constructing undirected phylogenetic networks that (1) are planar graphs and (2) admit embeddings in the plane where the vertices labeling all taxa are on the boundary of the network. We develop a new algorithm for constructing phylogenetic networks satisfying these constraints. First, we show that only approximate networks can be constructed for some distance matrices with at least five taxa. Then we prove that any five-point metric can be represented approximately by a planar boundary-labeled network with guaranteed fit value of 94.79. We extend the networks constructed in the proof to design an algorithm for computing planar boundary-labeled networks for any number of taxa.
Processing flows of information
Authors: Cugola Gianpaolo , Margara Alessandro
Published: June 2012

A large number of distributed applications requires continuous and timely processing of information as it flows from the periphery to the center of the system. Examples include intrusion detection systems which analyze network traffic in real-time to identify possible attacks; environmental monitoring applications which process raw data coming from sensor networks to identify critical situations; or applications performing online analysis of stock prices to identify trends and forecast future values.

Traditional DBMSs, which need to store and index data before processing it, can hardly fulfill the requirements of timeliness coming from such domains. Accordingly, during the last decade, different research communities developed a number of tools, which we collectively call
Information flow processing (IFP) systems
, to support these scenarios. They differ in their system architecture, data model, rule model, and rule language. In this article, we survey these systems to help researchers, who often come from different backgrounds, in understanding how the various approaches they adopt may complement each other.

In particular, we propose a general, unifying model to capture the different aspects of an IFP system and use it to provide a complete and precise classification of the systems and mechanisms proposed so far.
Constraint Programming Approach to Reconfigurable Processor Extension Generation and Application Compilation
Authors: Martin Kevin , Wolinski Christophe , Kuchcinski Krzysztof , Floch Antoine , Charot François
Published: June 2012

In this article, we present a constraint programming approach for solving hard design problems present when automatically designing specialized processor extensions. Specifically, we discuss our approach for automatic selection and synthesis of processor extensions as well as efficient application compilation for these newly generated extensions. The discussed approach is implemented in our integrated design framework,
IFPEC
, built using Constraint Programming (CP). In our framework, custom instructions, implemented as processor extensions, are defined as computational patterns and represented as graphs. This, along with the graph representation of an application, provides a way to use our CP framework equipped with subgraph isomorphism and connected component constraints for identification of processor extensions as well as their selection, application scheduling, binding, and routing. All design steps assume architectures composed of runtime reconfigurable cells, implementing selected extensions, tightly connected to a processor. An advantage of our approach is the possibility of combining different heterogeneous constraints to represent and solve all our design problems. Moreover, the flexibility and expressiveness of the CP framework makes it possible to solve simultaneously extension selection, application scheduling, and binding and improve the quality of the generated results. The article is largely illustrated with experimental results.
Computational geometry column 53
Authors: Dumitrescu Adrian
Published: June 2012

This column is devoted to partitions of point-sets into convex subsets with interior-disjoint convex hulls. We review some partitioning problems and corresponding algorithms. At the end we list some open problems. For simplicity, in most cases we remain at the lowest possible interesting level, that is, in the plane.
Fluidization, resolidification, and reorientation of the endothelial cell in response to slow tidal stretches
Authors: Krishnan Ramaswamy , Canović Elizabeth Peruski , Iordan Andreea L. , Rajendran Kavitha , Manomohan Greeshma , Pirentis Athanassios P. , Smith Michael L. , Butler James P. , Fredberg Jeffrey J. , Stamenović Dimitrije
Published: June 2012

Mechanical stretch plays an important role in regulating shape and orientation of the vascular endothelial cell. This morphological response to stretch is basic to angiogenesis, neovascularization, and vascular homeostasis, but mechanism remains unclear. To elucidate mechanisms, we used cell mapping rheometry to measure traction forces in primary human umbilical vein endothelial cells subjected to periodic uniaxial stretches. Onset of periodic stretch of 10% strain amplitude caused a fluidization response typified by attenuation of traction forces almost to zero. As periodic stretch continued, the prompt fluidization response was followed by a slow resolidification response typified by recovery of the traction forces, but now aligned along the axis perpendicular to the imposed stretch. Reorientation of the cell body lagged reorientation of the traction forces, however. Together, these observations demonstrate that cellular reorientation in response to periodic stretch is preceded by traction attenuation by means of cytoskeletal fluidization and subsequent traction recovery transverse to the stretch direction by means of cytoskeletal resolidification.
The role of AMP-activated protein kinase in the coordination of skeletal muscle turnover and energy homeostasis
Authors: Sanchez Anthony M. J. , Candau Robin B. , Csibi Alfredo , Pagano Allan F. , Raibon Audrey , Bernardi Henri
Published: June 2012

The AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that acts as a sensor of cellular energy status switch regulating several systems including glucose and lipid metabolism. Recently, AMPK has been implicated in the control of skeletal muscle mass by decreasing mTORC1 activity and increasing protein degradation through regulation of ubiquitin-proteasome and autophagy pathways. In this review, we give an overview of the central role of AMPK in the control of skeletal muscle plasticity. We detail particularly its implication in the control of the hypertrophic and atrophic signaling pathways. In the light of these cumulative and attractive results, AMPK appears as a key player in regulating muscle homeostasis and the modulation of its activity may constitute a therapeutic potential in treating muscle wasting syndromes in humans.
A novel role of intestine epithelial GABAergic signaling in regulating intestinal fluid secretion
Authors: Li Yan , Xiang Yun-Yan , Lu Wei-Yang , Liu Chuanyong , Li Jingxin
Published: June 2012

γ-Aminobutyric acid (GABA) is the primary inhibitory neurotransmitter in the central nervous system, and it is produced via the enzymatic activity of glutamic acid decarboxylase (GAD). GABA generates fast biological signaling through type A receptors (GABAAR), an anionic channel. Intriguingly, GABA is found in the jejunum epithelium of rats. The present study intended to determine whether a functional GABA signaling system exists in the intestinal epithelium and if so whether the GABA signaling regulates intestinal epithelial functions. RT-PCR, Western blot, and immunohistochemical assays of small intestinal tissues of various species were performed to determine the expression of GABA-signaling proteins in intestinal epithelial cells. Perforated patch-clamp recording was used to measure GABA-induced transmembrane current in the small intestine epithelial cell line IEC-18. The fluid weight-to-intestine length ratio was measured in mice that were treated with GABAAR agonist and antagonist. The effect of GABAAR antagonist on allergic diarrhea was examined using a mouse model. GABA, GAD, and GABAAR subunits were identified in small intestine epithelial cells of mice, rats, pigs, and humans. GABAAR agonist induced an inward current and depolarized IEC-18. Both GABA and the GABAAR agonist muscimol increased intestinal fluid secretion of rats. The increased intestinal secretion was largely decreased by the GABAAR antagonist picrotoxin or gabazine, but not by tetrodotoxin. The expression levels of GABA-signaling proteins were increased in the intestinal epithelium of mice that were sensitized and challenged with ovalbumin (OVA). The OVA-treated mice exhibited diarrhea, which was alleviated by oral administration of gabazine or picrotoxin. An endogenous autocrine GABAergic signaling exists in the mammalian intestinal epithelium, which upregulates intestinal fluid secretion. The intestinal GABAergic signaling becomes intensified in allergic diarrhea, and inhibition of this GABA-signal system alleviates the allergic diarrhea.
Increased hepatic fibrosis and JNK2-dependent liver injury in mice exhibiting hepatocyte-specific deletion of cFLIP
Authors: Schattenberg Jörn M. , Nagel Michael , Kim Yong Ook , Kohl Tobias , Wörns Marcus A. , Zimmermann Tim , Schad Arno , Longerich Thomas , Schuppan Detlef , He You-Wen , Galle Peter R. , Schuchmann Marcus
Published: June 2012

Chronic liver disease promotes hepatocellular injury involving apoptosis and triggers compensatory regeneration that leads to the activation of quiescent stellate cells in the liver. The deposition of extracellular matrix from activated myofibroblasts promotes hepatic fibrosis and the progression to cirrhosis with deleterious effects on liver physiology. The role of apoptosis signaling pathways in the development of fibrosis remains undefined. The aim of the current study was to determine the involvement of the caspase-8 homologue cellular FLICE-inhibitory protein (cFLIP) during the initiation and progression of fibrosis. Liver injury and fibrosis from carbon tetrachloride (CCl4) and thioacetamide (TAA) were examined in mice exhibiting a hepatocyte-specific deletion of cFLIP ( flip −/−). Acute liver injury from CCl4 and TAA were enhanced in flip −/− mice. This was accompanied by increased activation of caspase-3 and -9, pronounced phosphorylation of JNK, and decreased phosphorylation of Erk. Deletion of the cJun NH2-terminal kinase 2 (JNK2) in flip −/− mice protected from injury. Hepatic fibrosis was increased at baseline in 12-wk-old flip −/− mice, and progression of fibrosis from TAA was accelerated compared with the wild type. In conclusion, deletion of cFLIP in hepatocytes leads to increased fibrosis and accelerated fibrosis progression. This is accompanied by increased injury involving the activation of caspases and JNK2. Thus predisposition to liver injury involving increased hepatocellular apoptosis is a critical mediator of accelerated fibrogenesis, and prevention of liver injury will be a most important measure for patients with chronic liver disease.
Antagonism of mmu-mir-106a attenuates asthma features in allergic murine model
Authors: Sharma Amit , Kumar Manish , Ahmad Tanveer , Mabalirajan Ulaganathan , Aich Jyotirmoi , Agrawal Anurag , Ghosh Balaram
Published: June 2012

MicroRNAs (miRs) regulate immunological pathways in health and disease, and a number of miRs have been shown to be altered in mouse models of asthma. The secretion of interleukin-10 (IL-10), an anti-inflammatory cytokine, has been shown to be defective in many inflammatory diseases including asthma. We recently demonstrated that miR-106a inhibits IL-10 in a post-transcriptional manner. In this study, we investigated the effect of inhibition of mmu-miR106a in asthmatic condition to find its possible role as a therapeutic target. Our in vitro experiments with mouse macrophage, RAW264.7, revealed that mmu-miR-106a potentially decreased IL-10 along with increase in proinflammatory cytokine. Furthermore, administration of mmu-miR-106a to naive mice reduced IL-10 levels in lungs in a dose-dependent manner without altering lung histology. Most interestingly, knockdown of mmu-miR-106a in an established allergic airway inflammation has significantly alleviated most of the features of asthma such as airway hyperresponsiveness, airway inflammation, increased Th2 response, goblet cell metaplasia, and subepithelial fibrosis along with increase in IL-10 levels in lung. This represents the first in vivo proof of a miRNA-mediated regulation of IL-10 with a potential to reverse an established asthmatic condition.
Differential expression and cellular localization of novel isoforms of the tendon biomarker tenomodulin
Authors: Qi J. , Dmochowski J. M. , Banes A. N. , Tsuzaki M. , Bynum D. , Patterson M. , Creighton A. , Gomez S. , Tech K. , Cederlund A. , Banes A. J.
Published: June 2012

Tenomodulin (Tnmd, also called Tendin) is classified as a type II transmembrane glycoprotein and is highly expressed in developing as well as in mature tendons. Along with scleraxis (scx), Tnmd is a candidate marker gene for tenocytes. Its function is unknown, but it has been reported to have anti-angiogenic properties. Results in a knockout mouse model did not substantiate that claim. It has homology to chondromodulin-I. Single nucleotide polymorphisms of TNMD have been associated with obesity, macular degeneration, and Alzheimer's disease in patients. In the present study, three Tnmd isoforms with deduced molecular weights of 20.3 (isoform II), 25.4 (isoform III), and 37.1 (isoform I) kDa were proposed and verified by Western blot from cells with green fluorescent protein-linked, overexpressed constructs, tissue, and by qPCR of isoforms from human tissues and cultured cells. Overexpression of each Tnmd isoform followed by immunofluorescence imaging showed that isoforms I and II had perinuclear localization while isoform III was cytoplasmic. Results of qPCR demonstrated differential expression of each Tnmd isoform in patient's specimens taken from flexor carpi radialis, biceps brachii, and flexor digitorum profundus tendons. Knockdown of Tnmd increased the expression of both scleraxis (scx) and myostatin, indicating a potential negative feedback loop between Tnmd and its regulators. Knockdown of all Tnmd isoforms simultaneously also reduced tenocyte proliferation. I-TASSER protein three-dimensional conformation modeling predictions indicated each Tnmd isoform had different structures and potential functions: isoform 1, modeled as a cytosine methyltransferase; isoform 2, a SUMO-1-like SENP-1 protease; and isoform 3, an α-syntrophin, plextrin homology domain scaffolding protein. Further functional studies with each Tnmd isoform may help us to better understand regulation of tenocyte proliferation, tendon development, response to injury and strain, as well as mechanisms in tendinoses. These results may indicate novel therapeutic targets in specific tenomodulin isoforms as well as treatments for tendon diseases.
Altered hemodynamics during muscle metaboreflex in young type 1 diabetes patients
Authors: Roberto Silvana , Marongiu Elisabetta , Pinna Marco , Angius Luca , Olla Sergio , Bassareo Pierpaolo , Tocco Filippo , Concu Alberto , Milia Raffaele , Crisafulli Antonio
Published: June 2012

A reduction in catecholamine levels during exercise has been described in young subjects with type 1 diabetes mellitus (DM1). It has been suggested that type 1 diabetes per se is associated with the loss of sympathetic response before any clinical evidence. Considering that an increase in sympathetic drive is required for normal cardiovascular response to muscle metaboreflex, the aim of this study was to assess the hemodynamics during metaboreflex in DM1 patients. Impedance cardiography was used to measure hemodynamics during metaboreflex activation, obtained through postexercise ischemia in 14 DM1 patients and in 11 healthy controls (CTL). Principal results were: 1) blunted blood pressure response during metaboreflex was observed in DM1 patients compared with the CTL; 2) reduced capacity to increase systemic vascular resistance was also witnessed in DM1 subjects; 3) DM1 subjects reported higher stroke volumes as a consequence of reduced cardiac afterload compared with the CTL, which led to a more evident cardiac output response, which partially compensated for the lack of vasoconstriction. These facts suggest that cardiovascular regulation was altered in DM1 patients and that there was a reduced capacity to increase sympathetic tone, even in the absence of any overt clinical sign. The metaboreflex test appears to be a valid tool to detect early signs of this cardiovascular dysregulation.
Cervical Cancers Require the Continuous Expression of the Human Papillomavirus Type 16 E7 Oncoprotein Even in the Presence of the Viral E6 Oncoprotein
Authors: Jabbar Sean F. , Park Soyeong , Schweizer Johannes , Berard-Bergery Marthe , Pitot Henry C. , Lee Denis , Lambert Paul F.
Published: June 2012

High-risk human papillomaviruses (HPV), such as HPV-16, are etiologic agents of a variety of anogenital and oral malignancies, including nearly all cases of cervical cancer. Cervical cancers arising in transgenic mice that express HPV-16 E7 in an inducible manner require the continuous expression of E7 for their maintenance. However, in HPV-associated cancers in vivo, E6 and E7 invariably are coexpressed. In this study, we investigated whether cervical cancers rely on the continuous expression of E7 in the context of constitutively expressed E6. We placed the inducible HPV-16 E7 transgene onto a background in which HPV-16 E6 was constitutively expressed. In transgenic mice with high-grade cervical dysplastic lesions and cervical cancer, repressing the expression of E7 led to the regression of all cancers and the vast majority of high-grade dysplastic lesions. In addition, cervical cancers were occasionally observed in transgenic mice in which E7 was repressed and then reexpressed. Our findings indicate that even in the presence of constitutively expressed E6, the continuous expression of E7 is required for the maintenance of cervical cancers and most precancerous lesions. These data have important implications for the potential clinical use of drugs designed to inhibit the expression and/or function of E7 to treat HPV-associated cancers. Cancer Res; 72(16); 4008–16. ©2012 AACR.
Immunogenic Tumor Cell Death Induced by Chemoradiotherapy in Patients with Esophageal Squamous Cell Carcinoma
Authors: Suzuki Yoshiyuki , Mimura Kousaku , Yoshimoto Yuya , Watanabe Mitsuaki , Ohkubo Yu , Izawa Shinichirou , Murata Kazutoshi , Fujii Hideki , Nakano Takashi , Kono Koji
Published: June 2012

Although it has been shown that chemoradiotherapy may induce immunogenic cell death, which could trigger T-cell immunity mediated by high-mobility group box 1 protein (HMGB1) and calreticulin, there is still limited information to support this theory directly in a clinical setting. In the present study, we evaluated antigen-specific T-cell responses against six cancer-testis antigens in peripheral blood lymphocytes from patients with esophageal squamous cell carcinoma (ESCC) receiving chemoradiation. Expression of HMGB1 and calreticulin within tumor microenvironment was also analyzed in resected samples with and without chemoradiotherapy in relation to patients survival. Tumor antigen–specific T-cell responses were confirmed in six (38%) of 16 patients with ESCC after chemoradiotherapy coexisting with elevated serum HMGB1. In addition, HMGB1 within tumor microenvironment was significantly upregulated in patients with ESCC with preoperative chemoradiotherapy, but not in those without chemoradiotherapy, and the degree of HMGB1 positively correlated with patient survival (n = 88). Both irradiation and chemotherapeutic drugs induced upregulation of HMGB1 and calreticulin in nine ESCC cell lines. Furthermore, HMGB1 was able to induce maturation of dendritic cells. Together, our findings indicate that chemoradiation induces tumor antigen–specific T-cell responses, and HMGB1 production is related to clinical outcome after chemoradiation. Cancer Res; 72(16); 3967–76. ©2012 AACR.
Predicting Post-Stroke Infections and Outcome with Blood-Based Immune and Stress Markers
Authors: Meisel Andreas , Meisel Christian , Harms Hendrik , Hartmann Oliver , Ulm Lena
Published: June 2012

About one third of early deaths and poor outcomes after acute stroke are caused by potentially preventable stroke-associated complications, especially infections. Early identification of patients at high risk of infections and poor prognosis with biomarkers might help to initiate adequate therapies and guide treatment decisions. Acute injury of the central nervous system, including stroke, disturbs the normally well-balanced interplay between the sympathetic nervous system and the immune system, thereby impairing the antibacterial immune response in stroke patients. Changes in immune and stress markers, for example a reduction in HLA-DR expression on monocytes or an increase in serum catecholamine levels, occur very early after stroke onset, explain the high susceptibility of stroke patients to bacterial infections, and are predictive of infectious complications occurring up to 2 weeks after stroke. Outcome prediction is of utmost importance for decision-making in stroke units as well as in neurological intensive care units. However, to date the accuracy of outcome prediction by physicians and clinical scoring systems is only moderate. So far, only two blood-based biomarkers have been identified as independent predictors of outcome and mortality after stroke: the stress marker copeptin and midregional pro-atrial natriuretic peptide. Careful evaluation of prognostic markers is needed to prevent the occurrence of self-fulfilling prophecy.
Effect of Parenteral Fish Oil Lipid Emulsion in Parenteral Nutrition Supplementation Combined With Enteral Nutrition Support in Patients Undergoing Pancreaticoduodenectomy
Authors: Zhu Xinhua , Wu Yafu , Qiu Yudong , Jiang Chunping , Ding Yitao
Published: June 2012

Background: The effect of parenteral fish oil lipid emulsion in parenteral nutrition (PN) supplementation combined with enteral nutrition (EN) support on pancreaticoduodenectomy (PD) was investigated with a randomized controlled clinical trial at the Affiliated Drum Tower Hospital. Materials and Methods: Seventy‐six patients who underwent PD in the Department of Hepatobiliary Surgery were randomly divided into 2 groups: the polyunsaturated fatty acid (PUFA) group (n = 38) and control group (n = 38). Patients in the PUFA group received parenteral fish oil lipid emulsion supplementation combined with early EN support for 5 days after PD. Venous blood samples were obtained for assay on the day before surgery and on day 6 after surgery. Results: Compared with the results of the control group, a significant difference was seen in the extent of the decrease in total protein and prealbumin in the PUFA group (P < .05). Alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) were significantly decreased on day 6 in the PUFA group (P < .01), and a significant difference was seen in the extent of decrease in ALT, AST, and LDH in the PUFA group (P < .05). The ratio of infectious complications in the PUFA group was significantly decreased, as well as the postoperative hospital stay (P < .05), and there was no hospital mortality in this study. Conclusion: Parenteral fish oil lipid emulsion in PN supplementation combined with EN support can greatly improve the nutrition state and liver function of patients, decrease the incidence of infectious morbidities, and shorten the postoperative hospital stay.
Microstructure and wear properties of laser processed Ni based amorphous matrix coatings
Authors: Li R F , Li Z G , Huang J , Zhu Y Y
Published: June 2012

Ni40·8Fe27·2B18Si10Nb4 (at-%) coating was deposited on mild steel substrate using high power diode laser cladding followed by laser remelting process. The phase composition and microstructures of the as cladded coating and remelted coating were analysed by X-ray diffraction, scanning electron microscopy and transmission electron microscopy. The microhardness and wear properties of the coatings were also tested and analysed. It was observed that the remelted coating has an amorphous matrix embedded with some dendrites. The remelting of the coating increased the hardness of as cladded coating by ∼25%. The remelted coating exhibited a characteristically lower friction coefficient (0·21) than the as cladded coating (0·27) and the substrate (0·31). Significant increase in wear resistance was found for the remelted coating compared with the as cladded coating and the substrate under identical conditions.
Economics of hematopoietic cell transplantation
Authors: Khera Nandita , Zeliadt Steven B. , Lee Stephanie J.
Published: June 2012

Given the rapidly rising healthcare costs, it is important to understand the economic costs of hematopoietic cell transplantation (HCT), a procedure that is being used more frequently in the treatment of various hematologic disorders. Studies have reported a wide range of costs for HCT, from $36 000 to $88 000 (USD) for a single autologous transplantation for the initial hospitalization, to $200 000 (USD) or more for a myeloablative allogeneic procedure involving an unrelated donor. Common posttransplantation complications, such as infections and GVHD, have been shown to be significant cost drivers. Comparisons across studies are limited by differences in patient populations, cost ascertainment methods, and length of follow-up. This article summarizes the current state of knowledge about costs and cost-effectiveness of HCT, highlighting the challenges in conducting these studies and identifying important areas for future research. We discuss the need for more value-based assessments of HCT using high-quality approaches to measuring costs and outcomes so that potential future efforts to contain costs are well informed and appropriate.
Identifying dysregulated pathways in cancers from pathway interaction networks
Authors: Liu Ke-Qin , Liu Zhi-Ping , Hao Jin-Kao , Chen Luonan , Zhao Xing-Ming
Published: June 2012

Background

Cancers, a group of multifactorial complex diseases, are generally caused by mutation of multiple genes or dysregulation of pathways. Identifying biomarkers that can characterize cancers would help to understand and diagnose cancers. Traditional computational methods that detect genes differentially expressed between cancer and normal samples fail to work due to small sample size and independent assumption among genes. On the other hand, genes work in concert to perform their functions. Therefore, it is expected that dysregulated pathways will serve as better biomarkers compared with single genes.

Results

In this paper, we propose a novel approach to identify dysregulated pathways in cancer based on a pathway interaction network. Our contribution is three-fold. Firstly, we present a new method to construct pathway interaction network based on gene expression, protein-protein interactions and cellular pathways. Secondly, the identification of dysregulated pathways in cancer is treated as a feature selection problem, which is biologically reasonable and easy to interpret. Thirdly, the dysregulated pathways are identified as subnetworks from the pathway interaction networks, where the subnetworks characterize very well the functional dependency or crosstalk between pathways. The benchmarking results on several distinct cancer datasets demonstrate that our method can obtain more reliable and accurate results compared with existing state of the art methods. Further functional analysis and independent literature evidence also confirm that our identified potential pathogenic pathways are biologically reasonable, indicating the effectiveness of our method.

Conclusions

Dysregulated pathways can serve as better biomarkers compared with single genes. In this work, by utilizing pathway interaction networks and gene expression data, we propose a novel approach that effectively identifies dysregulated pathways, which can not only be used as biomarkers to diagnose cancers but also serve as potential drug targets in the future.
Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb)
Authors: Hand Melanie L , Cogan Noel Oi , Forster John W
Published: June 2012

Background

Single nucleotide polymorphisms (SNPs) provide essential tools for the advancement of research in plant genomics, and the development of SNP resources for many species has been accelerated by the capabilities of second-generation sequencing technologies. The current study aimed to develop and use a novel bioinformatic pipeline to generate a comprehensive collection of SNP markers within the agriculturally important pasture grass tall fescue; an outbreeding allopolyploid species displaying three distinct morphotypes: Continental, Mediterranean and rhizomatous.

Results

A bioinformatic pipeline was developed that successfully identified SNPs within genotypes from distinct tall fescue morphotypes, following the sequencing of 414 polymerase chain reaction (PCR) – generated amplicons using 454 GS FLX technology. Equivalent amplicon sets were derived from representative genotypes of each morphotype, including six Continental, five Mediterranean and one rhizomatous. A total of 8,584 and 2,292 SNPs were identified with high confidence within the Continental and Mediterranean morphotypes respectively. The success of the bioinformatic approach was demonstrated through validation (at a rate of 70%) of a subset of 141 SNPs using both SNaPshot™ and GoldenGate™ assay chemistries. Furthermore, the quantitative genotyping capability of the GoldenGate™ assay revealed that approximately 30% of the putative SNPs were accessible to co-dominant scoring, despite the hexaploid genome structure. The sub-genome-specific origin of each SNP validated from Continental tall fescue was predicted using a phylogenetic approach based on comparison with orthologous sequences from predicted progenitor species.

Conclusions

Using the appropriate bioinformatic approach, amplicon resequencing based on 454 GS FLX technology is an effective method for the identification of polymorphic SNPs within the genomes of Continental and Mediterranean tall fescue. The GoldenGate™ assay is capable of high-throughput co-dominant SNP allele detection, and minimises the problems associated with SNP genotyping in a polyploid by effectively reducing the complexity to a diploid system. This SNP collection may now be refined and used in applications such as cultivar identification, genetic linkage map construction, genome-wide association studies and genomic selection in tall fescue. The bioinformatic pipeline described here represents an effective general method for SNP discovery within outbreeding allopolyploid species.
Deciphering the genomic structure, function and evolution of carotenogenesis related phytoene synthases in grasses
Authors: Dibari Bianca , Murat Florent , Chosson Audrey , Gautier Véronique , Poncet Charles , Lecomte Philippe , Mercier Ingrid , Bergès Hélène , Pont Caroline , Blanco Antonio , Salse Jérôme
Published: June 2012

Background

Carotenoids are isoprenoid pigments, essential for photosynthesis and photoprotection in plants. The enzyme phytoene synthase (PSY) plays an essential role in mediating condensation of two geranylgeranyl diphosphate molecules, the first committed step in carotenogenesis. PSY are nuclear enzymes encoded by a small gene family consisting of three paralogous genes (PSY 1-3) that have been widely characterized in rice, maize and sorghum.

Results

In wheat, for which yellow pigment content is extremely important for flour colour, only PSY 1 has been extensively studied because of its association with QTLs reported for yellow pigment whereas PSY 2 has been partially characterized. Here, we report the isolation of bread wheat PSY 3 genes from a Renan BAC library using Brachypodium as a model genome for the Triticeae to develop Conserved Orthologous Set markers prior to gene cloning and sequencing. Wheat PSY 3 homoeologous genes were sequenced and annotated, unravelling their novel structure associated with intron-loss events and consequent exonic fusions. A wheat PSY 3 promoter region was also investigated for the presence of cis-acting elements involved in the response to abscisic acid (ABA), since carotenoids also play an important role as precursors of signalling molecules devoted to plant development and biotic/abiotic stress responses. Expression of wheat PSYs in leaves and roots was investigated during ABA treatment to confirm the up-regulation of PSY 3 during abiotic stress.

Conclusions

We investigated the structural and functional determinisms of PSY genes in wheat. More generally, among eudicots and monocots, the PSY gene family was found to be associated with differences in gene copy numbers, allowing us to propose an evolutionary model for the entire PSY gene family in Grasses.
Association between the ABO blood group and the human intestinal microbiota composition
Authors: Mäkivuokko Harri , Lahtinen Sampo J , Wacklin Pirjo , Tuovinen Elina , Tenkanen Heli , Nikkilä Janne , Björklund Marika , Aranko Kari , Ouwehand Arthur C , Mättö Jaana
Published: June 2012

Background

The mucus layer covering the human intestinal epithelium forms a dynamic surface for host-microbial interactions. In addition to the environmental factors affecting the intestinal equilibrium, such as diet, it is well established that the microbiota composition is individually driven, but the host factors determining the composition have remained unresolved.

Results

In this study, we show that ABO blood group is involved in differences in relative proportion and overall profiles of intestinal microbiota. Specifically, the microbiota from the individuals harbouring the B antigen (secretor B and AB) differed from the non-B antigen groups and also showed higher diversity of the Eubacterium rectale-Clostridium coccoides (EREC) and Clostridium leptum (CLEPT) -groups in comparison with other blood groups.

Conclusions

Our novel finding indicates that the ABO blood group is one of the genetically determined host factors modulating the composition of the human intestinal microbiota, thus enabling new applications in the field of personalized nutrition and medicine.
The 5′UTR-intron of the Gladiolus polyubiquitin promoter GUBQ1 enhances translation efficiency in Gladiolus and Arabidopsis
Authors: Kamo Kathryn , Kim Ah-Young , Park Se Hee , Joung Young Hee
Published: June 2012

Background

There are many non-cereal monocots of agronomic, horticultural, and biofuel importance. Successful transformation of these species requires an understanding of factors controlling expression of their genes. Introns have been known to affect both the level and tissue-specific expression of genes in dicots and cereal monocots, but there have been no studies on an intron isolated from a non-cereal monocot. This study characterizes the levels of GUS expression and levels of uidA mRNA that code for β-glucuronidase (GUS) expression in leaves of Gladiolus and Arabidopsis using GUBQ1, a polyubiquitin promoter with a 1.234 kb intron, isolated from the non-cereal monocot Gladiolus, and an intronless version of this promoter.

Results

Gladiolus and Arabidopsis were verified by Southern hybridization to be transformed with the uidA gene that was under control of either the GUBQ1 promoter (1.9 kb), a 5′ GUBQ1 promoter missing its 1.234 kb intron (0.68 kb), or the CaMV 35 S promoter. Histochemical staining showed that GUS was expressed throughout leaves and roots of Gladiolus and Arabidopsis with the 1.9 kb GUBQ1 promoter. GUS expression was significantly decreased in Gladiolus and abolished in Arabidopsis when the 5′UTR-intron was absent. In Arabidopsis and Gladiolus, the presence of uidA mRNA was independent of the presence of the 5′UTR-intron. The 5′-UTR intron enhanced translation efficiency for both Gladiolus and Arabidopsis.

Conclusions

The GUBQ1 promoter directs high levels of GUS expression in young leaves of both Gladiolus and Arabidopsis. The 5′UTR-intron from GUBQ1 resulted in a similar pattern of β-glucuronidase translation efficiency for both species even though the intron resulted in different patterns of uidA mRNA accumulation for each species.
Burden of disease resulting from chronic mountain sickness among young Chinese male immigrants in Tibet
Authors: Pei Tao , Li Xiaoxiao , Tao Fasheng , Xu Haotong , You Haiyan , Zhou Linlin , Liu Yan , Gao Yuqi
Published: June 2012

Background

In young Chinese men of the highland immigrant population, chronic mountain sickness (CMS) is a major public health problem. The aim of this study was to measure the disease burden of CMS in this population.

Methods

We used disability-adjusted life years (DALYs) to estimate the disease burden of CMS. Disability weights were derived using the person trade-off methodology. CMS diagnoses, symptom severity, and individual characteristics were obtained from surveys collected in Tibet in 2009 and 2010. The DALYs of individual patients and the DALYs/1,000 were calculated.

Results

Disability weights were obtained for 21 CMS health stages. The results of the analyses of the two surveys were consistent with each other. At different altitudes, the CMS rates ranged from 2.1-37.4%; the individual DALYs of patients ranged from 0.13-0.33, and the DALYs/1,000 ranged from 3.60-52.78. The age, highland service years, blood pressure, heart rate, smoking rate, and proportion of the sample working in engineering or construction were significantly higher in the CMS group than in the non-CMS group (p < 0.05). These variables were also positively associated with the individual DALYs (p < 0.05). Among the symptoms, headaches caused the largest proportion of DALYs.

Conclusion

The results show that CMS imposes a considerable burden on Chinese immigrants to Tibet. Immigrants with characteristics such as a higher residential altitude, more advanced age, longer highland service years, being a smoker, and working in engineering or construction were more likely to develop CMS and to increase the disease burden. Higher blood pressure and heart rate as a result of CMS were also positively associated with the disease burden. The authorities should pay attention to the highland disease burden and support the development and application of DALYs studies of CMS and other highland diseases.
Analysis of medical expenditure and socio-economic status in patients with ocular chemical burns in East China: a retrospective study
Authors: Le Qihua , Chen Yan , Wang Xin , Hong Jiaxu , Sun Xinghuai , Xu Jianjiang
Published: June 2012

Background

Little has been known regarding the relationship between ocular chemical injury and victims’ medical expenditure, income loss and socio-economic status changes. So we conduct this retrospective cross-sectional study in patients with ocular chemical burns in East China.

Methods

Fifty-six patients were enrolled and required to complete a self-report questionnaire consisting of the following contents: entire expenditure on medical treatment; the victims’ personal and household per capita income, and income loss caused by the injury; and the changes of socioeconomic status as well.

Results

The median expense of medical treatment was CNY 40,000 (approximately US$5,900). The medical expenditure rose significantly with increased injury severity, prolonged hospital stay, and increased frequency of surgery. More than half victims (51.8 %, 29/56) paid all or the majority of medical expense by themselves. The expense of only 5 victims was mainly paid by medical insurance, accounting for less than ten percent (8.9 %, 5/56). The victims’ personal and household per capita income both decreased significantly after the injury, with the median reduction being CNY 24,000 and CNY 7,800 (approximately US$3600 and US$1200) per year respectively. The reduction amplitude of personal and household per capita income rose with increased injury severity and prolonged time of care required. The injury caused emotional depression or anxiety in 76.8 % (43/56) victims, and the relationship with their relatives got worse in 51.9 % (29/56) patients. Moreover, only 21.4 % (12/56) patients felt that the whole society gave them care and concern after the injury, whereas 46.4 % (26/56) and 28.6 % (16/56) felt indifference or discrimination from society as a whole (X2 = 16.916, P = 0.028).

Conclusions

The medical expense was a huge economic burden to most victims of ocular chemical burns, and personal and household per capita income of the victims decreased significantly after injury, both of which had a close relationship with the injury severity. Formal legislation was urgently needed to compel the employer to purchase injury or medical insurance and provide more compulsory protection to the population working in high risk occupations. In addition, psychological counseling and instruction shouldn’t be neglected in the aid and treatment of victims.
Inhibition of melanogenesis and antioxidant properties of Magnolia grandiflora L. flower extract
Authors: Huang Huey-Chun , Hsieh Wan-Yu , Niu Yu-Lin , Chang Tsong-Min
Published: June 2012

Background

Magnolia grandiflora L. flower is wildly used in Asian as a traditional herbal medication. The purpose of the study was to investigate the antimelanogenic and antioxidant properties of Magnolia grandiflora L. flower extract. In the study, the inhibitory effects of M. grandiflora L. flower extract on mushroom tyrosinase, B16F10 intracellular tyrosinase activity and melanin content were determined spectrophotometrically. Meanwhile, the antioxidative capacity of the flower extract was also investigated.

Results

Our results revealed that M. grandiflora L. flower extract inhibit mushroom tyrosinase activity (IC50 =11.1%; v/v), the flower extract also effectively suppressed intracellular tyrosinase activity (IC50 = 13.6%; v/v) and decreased the amount of melanin (IC50 = 25.6%; v/v) in a dose-dependent manner in B16F10 cells. Protein expression level of tyrosinase and tyrosinase-related protein 1 (TRP-1) were also decreased by the flower extract. Additionally, antioxidant capacities such as ABTS+ free radical scavenging activity, reducing capacity and total phenolic content of the flower extract were increased in a dose-dependent pattern.

Conclusions

Our results concluded that M. grandiflora L. flower extract decreased the expression of tyrosinase and TRP-1, and then inhibited melanogenesis in B16F10 cells. The flower extract also show antioxidant capacities and depleted cellular reactive oxygen species (ROS). Hence, M. grandiflora L. flower extract could be applied as a type of dermatological whitening agent in skin care products.
A stitch in time: a cross-sectional survey looking at long lasting insecticide-treated bed net ownership, utilization and attrition in SNNPR, Ethiopia
Authors: Batisso Esey , Habte Tedila , Tesfaye Gezahegn , Getachew Dawit , Tekalegne Agonafer , Kilian Albert , Mpeka Betty , Lynch Caroline
Published: June 2012

Background

Since 2002/03, an estimated 4.7 million nets have been distributed in the Southern Nations, Nationalities and Peoples Region (SNNPR) among an at risk population of approximately 10 million people. Evidence from the region suggests that large-scale net ownership rapidly increased over a relatively short period of time. However, little is known about how coverage is being maintained given that the last mass distribution was in 2006/2007. This study sought to determine the status of current net ownership, utilization and rate of long lasting insecticide-treated nets (LLIN) loss in the previous three years in the context of planning for future net distribution to try to achieve sustainable universal coverage.

Methods

A total of 750 household respondents were interviewed across malarious, rural kebeles of SNNPR. Households were randomly selected following a two-stage cluster sampling design where kebeles were defined as clusters. Kebeles were chosen using proportional population sampling (PPS), and 25 households within 30 kebeles randomly chosen.

Results

Approximately 67.5% (95%CI: 64.1–70.8) of households currently owned at least one net. An estimated 31.0% (95%CI 27.9–34.4) of all nets owned in the previous three years had been discarded by owners, the majority of whom considered the nets too torn, old or dirty (79.9%: 95%CI 75.8–84.0). Households reported that one-third of nets (33.7%) were less than one year old when they were discarded. The majority (58.8%) of currently owned nets had ‘good’ structural integrity according to a proportionate Hole Index. Nearly two-thirds of households (60.6%) reported using their nets the previous night. The overriding reason for not using nets was that they were too torn (45.7%, 95% CI 39.1–50.7). Yet, few households are making repairs to their nets (3.7%, 95% CI: 2.4–5.1).

Conclusions

Results suggest that the life span of nets may be shorter than previously thought, with little maintenance by their owners. With the global move towards malaria elimination it makes sense to aim for sustained high coverage of LLINs. However, in the current economic climate, it also makes sense to hark back to simple tools and messages on the importance of careful net maintenance, which could increase their lifespans.
Effect of 50 Hz electric field in diacylglycerol acyltransferase mRNA expression level and plasma concentration of triacylglycerol, free fatty acid, phospholipid and total cholesterol
Authors: Hori Takuya , Harakawa Shinji , Herbas Shirley M , Ueta Yoshiko Y , Inoue Noboru , Suzuki Hiroshi
Published: June 2012

Background

The effects of exposure to a 50 Hz electric field (EF) on plasma level of triacylglycerol, free fatty acids, total cholesterol and phospholipid and mRNA expression level of diacylglycerol acyltransferase (DGAT) 1 and 2 in liver and intestines from C57BL/6 J mice were studied.

Methods

The test was based on comparison between mice post treated with 50 Hz EF of 45 kV/m intensity for 30 min per day for 11 days or without EF. DGATs mRNA expression was analyzed by real-time quantitative polymerase chain reaction.

Results

There was no difference in the gene expression level of DGAT1 in liver and intestines. The DGAT2 gene expression level in liver derived from mice treated with EF was significantly lower than those in the control (P < 0.001). Both plasma total cholesterol (P < 0.01) and phospholipid (P < 0.05) in the group exposed to EF were lower than those in the control, but there was no difference in triacylglycerol or free fatty acid levels.

Conclusion

Exposure to 50 Hz EF decrease the plasma levels of total cholesterol and phospholipids, and downregulated DGAT2 mRNA expression in liver. The mechanisms for the effects of EF on lipid metabolism are not well understand yet, but altered DGAT2 activity may be involved.