Simulation of long-term fatigue damage in bioprosthetic heart valves: effects of leaflet and stent elastic properties

PubMed Central

Martin, Caitlin

2014-01-01

One of the major failure modes of bioprosthetic heart valves (BHVs) is noncalcific structural deterioration due to fatigue of the tissue leaflets; yet, the mechanisms of fatigue are not well understood. BHV durability is primarily assessed based on visual inspection of the leaflets following accelerated wear testing. In this study, we developed a computational framework to simulate BHV leaflet fatigue, which is both efficient and quantitative, making it an attractive alternative to traditional accelerated wear testing. We utilize a phenomenological soft tissue fatigue damage model developed previously to describe the stress softening and permanent set of the glutaraldehyde-treated bovine pericardium leaflets in BHVs subjected to cyclic loading. A parametric study was conducted to determine the effects of altered leaflet and stent elastic properties on the fatigue of the leaflets. The simulation results show that heterogeneity of the leaflet elastic properties, poor leaflet coaptation, and little stent-tip deflection may accelerate leaflet fatigue, which agrees with clinical findings. Therefore, the developed framework may be an invaluable tool for evaluating leaflet durability in new tissue valve designs, including traditional BHVs as well as new transcatheter valves. PMID:24092257

Content analysis of nutritional information in paediatric oral health education leaflets.

PubMed

Arora, Amit; Doan, Jenny; Martinez, Jessamine; Phan, Colin; Kolt, Gregory S; Bhole, Sameer; Harris, Mark Fort; Scott, Jane Anne; Hector, Debra

2017-02-20

The aim of this study was to determine if paediatric oral health education leaflets with a food and nutritional focus provide messages that are clear and consistent with the current Australian Dietary Guidelines and the Infant Feeding Guidelines. Forty-three leaflets aimed at parents were sourced from Australian state and territory Health Departments, oral health industry partners and commercial organisations, and a content analysis was performed. Recommendations on food and drink type, consumption frequency and general diet and nutrition advice were considered and cross-referenced with the Australian Dietary Guidelines and the Infant Feeding Guidelines to identify areas of consistency and discrepancy. Twenty leaflets recommended reducing the consumption of sugary and/or acidic food, while 23 leaflets recommended reducing the consumption of sugary and/or acidic drinks. The majority of the leaflets advised water (n = 35) and milk (n = 23) to drink. Although 33 leaflets encouraged a healthy diet, seven of these did not specify what a healthy diet was. Twenty-eight leaflets provided early childhood-related (0-2 years) feeding advice. Confusing messages were found in nine leaflets, with ambiguous recommendations that were open to individual interpretation. There were some inconsistencies between the leaflets and the dietary and infant feeding guidelines in Australia; and across the leaflets, as not all important messages were included in any one leaflet. Government Health Departments and other relevant agencies should ensure that advisory messages regarding diet, particularly those with dental implications, are clear, complete and consistent across all dental educational leaflets.

Crutches, confetti or useful tools? Professionals' views on and use of health education leaflets.

PubMed

Murphy, S; Smith, C

1993-06-01

This paper examines the views on and use of health education leaflets by a number of professional groups: health visitors, midwives, occupational health workers, pharmacists and school health education co-ordinators. Eighty nine percent currently obtain leaflets from health promotion units, with the exception of health visitors, professionals are largely satisfied with the units' service. Seventy six percent use commercial or sponsored leaflets primarily because of the large numbers and topics that are available. The numbers and type of leaflets used were found to vary across the professions. All professionals see an increasingly important role for leaflets in their work. A number of them, pharmacists and occupational health workers in particular, saw the numbers they use rising. These views were accompanied by lower levels of belief in a leaflets ability to increase knowledge and behaviour as well as lower levels of satisfaction with current leaflet use and a concern over the public's reception of leaflets. Methods of leaflet distribution to the public largely reflect the professionals' work contexts. Most popular were handing out leaflets with advice, leaving them in a public place and using them as a back-up to a meeting. A number of contradictions emerge between distribution practices and perceived effectiveness. Few professionals thought leaving leaflets in a public place was effective, and few health visitors and midwives believed giving leaflets to the family of a client was effective despite large numbers doing so. The implications of these findings for health promotion policy and practice are discussed.

Advertising, expectations and informed consent: the contents and functions of acupuncture leaflets.

PubMed

Bishop, Felicity L; Salmon, Cathy

2013-12-01

To evaluate the content of patient information leaflets about acupuncture. 401 patient information leaflets were obtained from practising UK acupuncturists and subjected to content and thematic analysis. 59% of included leaflets were from NHS physiotherapists. Almost all the leaflets defined acupuncture and the majority explained how it might work, described the treatment process and placed it in a historical context. Most described possible benefits and risks of acupuncture and discussed contraindications and safety. Just under a third of leaflets (120, 30%) suggested conditions that might be helped by acupuncture, most commonly musculoskeletal pain, arthritis and injuries. By emphasising differences between individuals in acupuncture treatments and responsiveness, the leaflets fostered hope for positive effects without making any guarantees. Information leaflets are broadly consistent with the evidence for acupuncture, but some claims are inconsistent with official advice from advertising regulators. An ethically sound, scientifically grounded and psychologically effective leaflet should accurately convey both benefits and risks of treatment, optimise patients' expectations and allay concerns about needling. This study suggests that acupuncture leaflets might achieve these multiple functions but care should be taken to ensure adequate coverage of risks.

Stent and leaflet stresses in a 26-mm first-generation balloon-expandable transcatheter aortic valve.

PubMed

Xuan, Yue; Krishnan, Kapil; Ye, Jian; Dvir, Danny; Guccione, Julius M; Ge, Liang; Tseng, Elaine E

2017-05-01

Transcatheter aortic valve replacement is established therapy for high-risk and inoperable patients with severe aortic stenosis, but questions remain regarding long-term durability. Valve design influences durability. Increased leaflet stresses in surgical bioprostheses have been correlated with degeneration; however, transcatheter valve leaflet stresses are unknown. From 2007 to 2014, a majority of US patients received first-generation balloon-expandable transcatheter valves. Our goal was to determine stent and leaflet stresses in this valve design using finite element analyses. A 26-mm Sapien Transcatheter Heart Valve (Edwards Lifesciences, Inc, Irvine, Calif) underwent high-resolution microcomputed tomography scanning to develop precise 3-dimensional geometry of the leaflets, the stent, and the polyethylene terephthalate elements. The stent was modeled using 3-dimensional elements and the leaflets were modeled using shell elements. Stent material properties were based on stainless steel, whereas those for leaflets were obtained from surgical bioprostheses. Noncylindrical Sapien valve geometry was also simulated. Pressure loading to 80 mm Hg and 120 mm Hg was performed using ABAQUS finite element software (Dassault Systèmes, Waltham, Mass). At 80 mm Hg, maximum principal stresses on Sapien leaflets were 1.31 megaspascals (MPa). Peak leaflet stress was observed at commissural tips where leaflets connected to the stent. Maximum principal stresses for the stent were 188.91 MPa and located at stent tips where leaflet commissures were attached. Noncylindrical geometry increased peak principal leaflet stresses by 16%. Using exact geometry from high-resolution scans, the 26-mm Sapien Transcatheter Heart Valve showed that peak stresses for both stent and leaflets were present at commissural tips where leaflets were attached. These regions would be prone to leaflet degeneration. Understanding stresses in first-generation transcatheter valves allows comparison to future designs for relative durability. Copyright © 2017 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

Regulation, overexpression, and target gene identification of Potato Homeobox 15 (POTH15) – a class-I KNOX gene in potato

PubMed Central

Mahajan, Ameya S.; Kondhare, Kirtikumar R.; Rajabhoj, Mohit P.; Kumar, Amit; Ghate, Tejashree; Ravindran, Nevedha; Habib, Farhat; Siddappa, Sundaresha; Banerjee, Anjan K.

2016-01-01

Potato Homeobox 15 (POTH15) is a KNOX-I (Knotted1-like homeobox) family gene in potato that is orthologous to Shoot Meristemless (STM) in Arabidopsis. Despite numerous reports on KNOX genes from different species, studies in potato are limited. Here, we describe photoperiodic regulation of POTH15, its overexpression phenotype, and identification of its potential targets in potato (Solanum tuberosum ssp. andigena). qRT-PCR analysis showed a higher abundance of POTH15 mRNA in shoot tips and stolons under tuber-inducing short-day conditions. POTH15 promoter activity was detected in apical and axillary meristems, stolon tips, tuber eyes, and meristems of tuber sprouts, indicating its role in meristem maintenance and leaf development. POTH15 overexpression altered multiple morphological traits including leaf and stem development, leaflet number, and number of nodes and branches. In particular, the rachis of the leaf was completely reduced and leaves appeared as a bouquet of leaflets. Comparative transcriptomic analysis of 35S::GUS and two POTH15 overexpression lines identified more than 6000 differentially expressed genes, including 2014 common genes between the two overexpression lines. Functional analysis of these genes revealed their involvement in responses to hormones, biotic/abiotic stresses, transcription regulation, and signal transduction. qRT-PCR of selected candidate target genes validated their differential expression in both overexpression lines. Out of 200 randomly chosen POTH15 targets, 173 were found to have at least one tandem TGAC core motif, characteristic of KNOX interaction, within 3.0kb in the upstream sequence of the transcription start site. Overall, this study provides insights to the role of POTH15 in controlling diverse developmental processes in potato. PMID:27217546

Compound Leaf Development and Evolution in the Legumes[W

PubMed Central

Champagne, Connie E.M.; Goliber, Thomas E.; Wojciechowski, Martin F.; Mei, Raymond W.; Townsley, Brad T.; Wang, Kan; Paz, Margie M.; Geeta, R.; Sinha, Neelima R.

2007-01-01

Across vascular plants, Class 1 KNOTTED1-like (KNOX1) genes appear to play a critical role in the development of compound leaves. An exception to this trend is found in the Fabaceae, where pea (Pisum sativum) uses UNIFOLIATA, an ortholog of the floral regulators FLORICAULA (FLO) and LEAFY (LFY), in place of KNOX1 genes to regulate compound leaf development. To assess the phylogenetic distribution of KNOX1-independent compound leaf development, a survey of KNOX1 protein expression across the Fabaceae was undertaken. The majority of compound-leafed Fabaceae have expression of KNOX1 proteins associated with developing compound leaves. However, in a large subclade of the Fabaceae, the inverted repeat–lacking clade (IRLC), of which pea is a member, KNOX1 expression is not associated with compound leaves. These data suggest that the FLO/LFY gene may function in place of KNOX1 genes in generating compound leaves throughout the IRLC. The contribution of FLO/LFY to leaf complexity in a member of the Fabaceae outside of the IRLC was examined by reducing expression of FLO/LFY orthologs in transgenic soybean (Glycine max). Transgenic plants with reduced FLO/LFY expression showed only slight reductions in leaflet number. Overexpression of a KNOX1 gene in alfalfa (Medicago sativa), a member of the IRLC, resulted in an increase in leaflet number. This implies that KNOX1 targets, which promote compound leaf development, are present in alfalfa and are still sensitive to KNOX1 regulation. These data suggest that KNOX1 genes and the FLO/LFY gene may have played partially overlapping roles in compound leaf development in ancestral Fabaceae but that the FLO/LFY gene took over this role in the IRLC. PMID:17993625

Plant glycosylphosphatidylinositol (GPI) anchored proteins at the plasma membrane-cell wall nexus.

PubMed

Yeats, Trevor H; Bacic, Antony; Johnson, Kim L

2018-04-18

Approximately 1% of plant proteins are predicted to be post-translationally modified with a glycosylphosphatidylinositol (GPI) anchor that tethers the polypeptide to the outer leaflet of the plasma membrane. While the synthesis and structure of GPI anchors is largely conserved across eukaryotes, the repertoire of functional domains present in the GPI-anchored proteome has diverged substantially. In plants, this includes a large fraction of the GPI-anchored proteome being further modified with plant-specific arabinogalactan (AG) O-glycans. The importance of the GPI-anchored proteome to plant development is underscored by the fact that GPI biosynthetic null mutants exhibit embryo lethality. Mutations in genes encoding specific GPI-anchored proteins (GAPs) further supports their contribution to diverse biological processes occurring at the interface of the plasma membrane and cell wall, including signaling, cell wall metabolism, cell wall polymer cross-linking, and plasmodesmatal transport. Here, we review the literature concerning plant GPI-anchored proteins in the context of their potential to act as molecular hubs that mediate interactions between the plasma membrane and the cell wall and their potential to transduce the signal into the protoplast and thereby activate signal transduction pathways. This article is protected by copyright. All rights reserved.

'What do patients want?' Tailoring medicines information to meet patients' needs.

PubMed

Young, Amber; Tordoff, June; Smith, Alesha

2017-11-01

Medicines information leaflets can equip patients to be in control of their own healthcare and support the safe and effective use of medicines. The design and content of leaflets influences patients' willingness to read them, and poor examples can cause patient confusion and anxiety. Researchers examined the literature over the past 8 years to determine the content and design of medicine information leaflets that patients prefer in order to read, understand, and use them effectively. It was found that existing leaflets do not meet patients' needs and appear ineffective. Leaflets lack the information patients seek and may contain non-essential material, affecting patients' perception of, and willingness to read them. Additionally, the acceptable leaflet length varies between patients. Application of good design principles improves readability, comprehension, and ability to locate information. Medicine information leaflets must meet patients' needs and be well designed. Tailoring information leaflets to patient characteristics and requirements would enhance effectiveness. Passive provision of pre-printed leaflets is outdated, unvalued and ineffective. Using automated computer systems for leaflet tailoring with the ability to further adapt patients' information might be the best way forward. Copyright © 2016 Elsevier Inc. All rights reserved.

Charged anaesthetics alter LM-fibroblast plasma-membrane enzymes by selective fluidization of inner or outer membrane leaflets.

PubMed Central

Sweet, W D; Schroeder, F

1986-01-01

The functional consequences of the differences in lipid composition and structure between the two leaflets of the plasma membrane were investigated. Fluorescence of 1,6-diphenylhexa-1,3,5-triene(DPH), quenching, and differential polarized phase fluorimetry demonstrated selective fluidization by local anaesthetics of individual leaflets in isolated LM-cell plasma membranes. As measured by decreased limiting anisotropy of DPH fluorescence, cationic (prilocaine) and anionic (phenobarbital and pentobarbital) amphipaths preferentially fluidized the cytofacial and exofacial leaflets respectively. Unlike prilocaine, procaine, also a cation, fluidized both leaflets of these membranes equally. Pentobarbital stimulated 5'-nucleotidase between 0.1 and 5 mM and inhibited at higher concentrations, whereas phenobarbital only inhibited, at higher concentrations. Cationic drugs were ineffective. Two maxima of (Na+ + K+)-ATPase activation were obtained with both anionic drugs. Only one activation maximum was obtained with both cationic drugs. The maximum in activity below 1 mM for all four drugs clustered about a single limiting anisotropy value in the cytofacial leaflet, whereas there was no correlation between activity and limiting anisotropy in the exofacial leaflets. Therefore, although phenobarbital and pentobarbital below 1 mM fluidized the exofacial leaflet more than the cytofacial leaflet, the smaller fluidization in the cytofacial leaflet was functionally significant for (Na+ + K+)-ATPase. Mg2+-ATPase was stimulated at 1 mM-phenobarbital, unaffected by pentobarbital and slightly stimulated by both cationic drugs at concentrations fluidizing both leaflets. Thus the activity of (Na+ + K+)-ATPase was highly sensitive to selective fluidization of the leaflet containing its active site, whereas the other enzymes examined were little affected by fluidization of either leaflet. PMID:3028369

Adaptation of child oral health education leaflets for Arabic migrants in Australia: a qualitative study.

PubMed

Arora, Amit; Al-Salti, Ibrahim; Murad, Hussam; Tran, Quang; Itaoui, Rhonda; Bhole, Sameer; Ajwani, Shilpi; Jones, Charlotte; Manohar, Narendar

2018-01-10

The purpose of this study was to gain an in-depth understanding of Arabic-speaking mothers views on the usefulness of existing oral health education leaflets aimed at young children and also to record their views on the tailored versions of these leaflets. This qualitative study was nested within a large ongoing birth cohort study in South Western Sydney, Australia. Arabic-speaking mothers (n = 19) with young children were purposively selected and approached for a semi-structured interview. Two original English leaflets giving advice on young children's oral health were sent to mother's prior to the interview. On the day of interview, mothers were given simplified-English and Arabic versions of both the leaflets and were asked to compare the three versions. Interviews were audio-recorded, subsequently transcribed verbatim and analysed by thematic analysis. Ethical approval was obtained from Human Research Ethics Committees of the former Sydney South West Area Health Service, University of Sydney and Western Sydney University. Mothers reported that simplified English together with the Arabic version of the leaflets were useful sources of information. Although many mothers favoured the simplified version over original English leaflets, the majority favoured the leaflets in Arabic. Ideally, a "dual Arabic - simplified English leaflet" was preferred. The understanding of key health messages was optimised through a simple layout and visual images. There is a need to tailor oral health education leaflets for Arabic-speaking migrants. Producers of dental leaflets should also consider a "dual Arabic - simplified English leaflet" to improve oral health knowledge of Arabic-speaking migrants. The use of simple layout and pictures assists Arabic-speaking migrants to understand the content of dental leaflets.

Simulated transcatheter aortic valve deformation: A parametric study on the impact of leaflet geometry on valve peak stress.

PubMed

Li, Kewei; Sun, Wei

2017-03-01

In this study, we developed a computational framework to investigate the impact of leaflet geometry of a transcatheter aortic valve (TAV) on the leaflet stress distribution, aiming at optimizing TAV leaflet design to reduce its peak stress. Utilizing a generic TAV model developed previously [Li and Sun, Annals of Biomedical Engineering, 2010. 38(8): 2690-2701], we first parameterized the 2D leaflet geometry by mathematical equations, then by perturbing the parameters of the equations, we could automatically generate a new leaflet design, remesh the 2D leaflet model and build a 3D leaflet model from the 2D design via a Python script. Approximately 500 different leaflet designs were investigated by simulating TAV closure under the nominal circular deployment and physiological loading conditions. From the simulation results, we identified a new leaflet design that could reduce the previously reported valve peak stress by about 5%. The parametric analysis also revealed that increasing the free edge width had the highest overall impact on decreasing the peak stress. A similar computational analysis was further performed for a TAV deployed in an abnormal, asymmetric elliptical configuration. We found that a minimal free edge height of 0.46 mm should be adopted to prevent central backflow leakage. This increase of the free edge height resulted in an increase of the leaflet peak stress. Furthermore, the parametric study revealed a complex response surface for the impact of the leaflet geometric parameters on the peak stress, underscoring the importance of performing a numerical optimization to obtain the optimal TAV leaflet design. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Determination of correlation between backflow volume and mitral valve leaflet young modulus from two dimensional echocardiogram images

NASA Astrophysics Data System (ADS)

Jong, Rudiyanto P.; Osman, Kahar; Adib, M. Azrul Hisham M.

2012-06-01

Mitral valve prolapse without proper monitoring might lead to a severe mitral valve failure which eventually leads to a sudden death. Additional information on the mitral valve leaflet condition against the backflow volume would be an added advantage to the medical practitioner for their decision on the patients' treatment. A study on two dimensional echocardiography images has been conducted and the correlations between the backflow volume of the mitral regurgitation and mitral valve leaflet Young modulus have been obtained. Echocardiogram images were analyzed on the aspect of backflow volume percentage and mitral valve leaflet dimensions on different rates of backflow volume. Young modulus values for the mitral valve leaflet were obtained by using the principle of elastic deflection and deformation on the mitral valve leaflet. The results show that the backflow volume increased with the decrease of the mitral valve leaflet Young modulus which also indicate the condition of the mitral valve leaflet approaching failure at high backflow volumes. Mitral valve leaflet Young modulus values obtained in this study agreed with the healthy mitral valve leaflet Young modulus from the literature. This is an initial overview of the trend on the prediction of the behaviour between the fluid and the structure of the blood and the mitral valve which is extendable to a larger system of prediction on the mitral valve leaflet condition based on the available echocardiogram images.

Effects of Leaflet Design on Transvalvular Gradients of Bioprosthetic Heart Valves.

PubMed

Dabiri, Yaghoub; Ronsky, Janet; Ali, Imtiaz; Basha, Ameen; Bhanji, Alisha; Narine, Kishan

2016-12-01

Bioprosthetic aortic valves (BAVs) are becoming the prostheses of choice in heart valve replacement. The objective of this paper is to assess the effects of leaflet geometry on the mechanics and hemodynamics of BAVs in a fluid structure interaction model. The curvature and angle of leaflets were varied in 10 case studies whereby the following design parameters were altered: a circular arch, a line, and a parabola for the radial curvature, and a circular arch, a spline, and a parabola for the circumferential curvature. Six different leaflet angles (representative of the inclination of the leaflets toward the surrounding aortic wall) were analyzed. The 3-dimensional geometry of the models were created using SolidWorks, Pointwise was used for meshing, and Comsol Multiphysics was used for implicit finite element calculations. Realistic loading was enforced by considering the time-dependent strongly-coupled interaction between blood flow and leaflets. Higher mean pressure gradients as well as von Mises stresses were obtained with a parabolic or circular curvature for radial curvature or a parabolic or spline curvature for the circumferential curvature. A smaller leaflet angle was associated with a lower pressure gradient, and, a lower von Mises stress. The leaflet curvature and angle noticeably affected the speed of valve opening, and closing. When a parabola was used for circumferential or radial curvature, leaflets displacements were asymmetric, and they opened and closed more slowly. A circular circumferential leaflet curvature, a linear leaflet radial curvature, and leaflet inclination toward the surrounding aortic wall were associated with superior BAVs mechanics.

Congenital uni-leaflet mitral valve with severe stenosis: A case report with literature review.

PubMed

Zhang, Weixin; Wang, Yonghuai; Ma, Chunyan; Zhang, Zhiwei; Yang, Jun

2017-03-01

Numerical abnormalities of mitral leaflets is a special entity in congenital mitral malformations. Previously reported cases of uni-leaflet mitral valve were primarily related to absence or dysplasia of certain leaflets. We present a case here with mitral leaflets that were not divided into anterior and posterior as usual, but developed as an integral structure instead, which is different from previously documented cases of uni-leaflet mitral valves. Real time three-dimensional echocardiography (RT3DE) provides a visual presentation of the abnormal mitral structure which was confirmed by surgical operation. To the best of our knowledge, this unusual form of uni-leaflet mitral valve has not been reported yet. © 2017, Wiley Periodicals, Inc.

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

PubMed Central

Wei, Hengling; Li, Wei; Sun, Xiwei; Zhu, Shuijin; Zhu, Jun

2013-01-01

Plant disease resistance genes are a key component of defending plants from a range of pathogens. The majority of these resistance genes belong to the super-family that harbors a Nucleotide-binding site (NBS). A number of studies have focused on NBS-encoding genes in disease resistant breeding programs for diverse plants. However, little information has been reported with an emphasis on systematic analysis and comparison of NBS-encoding genes in cotton. To fill this gap of knowledge, in this study, we identified and investigated the NBS-encoding resistance genes in cotton using the whole genome sequence information of Gossypium raimondii. Totally, 355 NBS-encoding resistance genes were identified. Analyses of the conserved motifs and structural diversity showed that the most two distinct features for these genes are the high proportion of non-regular NBS genes and the high diversity of N-termini domains. Analyses of the physical locations and duplications of NBS-encoding genes showed that gene duplication of disease resistance genes could play an important role in cotton by leading to an increase in the functional diversity of the cotton NBS-encoding genes. Analyses of phylogenetic comparisons indicated that, in cotton, the NBS-encoding genes with TIR domain not only have their own evolution pattern different from those of genes without TIR domain, but also have their own species-specific pattern that differs from those of TIR genes in other plants. Analyses of the correlation between disease resistance QTL and NBS-encoding resistance genes showed that there could be more than half of the disease resistance QTL associated to the NBS-encoding genes in cotton, which agrees with previous studies establishing that more than half of plant resistance genes are NBS-encoding genes. PMID:23936305

Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

PubMed

Yu, Jingyin; Tehrim, Sadia; Zhang, Fengqi; Tong, Chaobo; Huang, Junyan; Cheng, Xiaohui; Dong, Caihua; Zhou, Yanqiu; Qin, Rui; Hua, Wei; Liu, Shengyi

2014-01-03

Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome triplication analysis in B. oleracea, B. rapa and A. thaliana genomes, our study provides insight into the evolutionary history of NBS-encoding genes after divergence of A. thaliana and the Brassica lineage. These results together with expression pattern analysis of NBS-encoding orthologous genes provide useful resource for functional characterization of these genes and genetic improvement of relevant crops.

Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks.

PubMed

Lin, Wen-Hsien; Liu, Wei-Chung; Hwang, Ming-Jing

2009-03-11

Human cells of various tissue types differ greatly in morphology despite having the same set of genetic information. Some genes are expressed in all cell types to perform house-keeping functions, while some are selectively expressed to perform tissue-specific functions. In this study, we wished to elucidate how proteins encoded by human house-keeping genes and tissue-specific genes are organized in human protein-protein interaction networks. We constructed protein-protein interaction networks for different tissue types using two gene expression datasets and one protein-protein interaction database. We then calculated three network indices of topological importance, the degree, closeness, and betweenness centralities, to measure the network position of proteins encoded by house-keeping and tissue-specific genes, and quantified their local connectivity structure. Compared to a random selection of proteins, house-keeping gene-encoded proteins tended to have a greater number of directly interacting neighbors and occupy network positions in several shortest paths of interaction between protein pairs, whereas tissue-specific gene-encoded proteins did not. In addition, house-keeping gene-encoded proteins tended to connect with other house-keeping gene-encoded proteins in all tissue types, whereas tissue-specific gene-encoded proteins also tended to connect with other tissue-specific gene-encoded proteins, but only in approximately half of the tissue types examined. Our analysis showed that house-keeping gene-encoded proteins tend to occupy important network positions, while those encoded by tissue-specific genes do not. The biological implications of our findings were discussed and we proposed a hypothesis regarding how cells organize their protein tools in protein-protein interaction networks. Our results led us to speculate that house-keeping gene-encoded proteins might form a core in human protein-protein interaction networks, while clusters of tissue-specific gene-encoded proteins are attached to the core at more peripheral positions of the networks.

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence.

PubMed

Yassin, Atteyet F; Langenberg, Stefan; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Mukherjee, Supratim; Reddy, T B K; Daum, Chris; Shapiro, Nicole; Ivanova, Natalia; Woyke, Tanja; Kyrpides, Nikos C

2017-01-01

The permanent draft genome sequence of Actinotignum schaalii DSM 15541T is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that A. schaalii is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for de novo FAS biosynthesis. The plsY and plsX genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, A. schaalii harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. A. schaalii genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the tad genes encoding proteins required for pili assembly, the nanI gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the frxA gene, which encodes NADPH-flavin oxidoreductase.

Total ellipse of the heart valve: the impact of eccentric stent distortion on the regional dynamic deformation of pericardial tissue leaflets of a transcatheter aortic valve replacement

PubMed Central

Gunning, Paul S.; Saikrishnan, Neelakantan; Yoganathan, Ajit P.; McNamara, Laoise M.

2015-01-01

Transcatheter aortic valve replacements (TAVRs) are a percutaneous alternative to surgical aortic valve replacements and are used to treat patients with aortic valve stenosis. This minimally invasive procedure relies on expansion of the TAVR stent to radially displace calcified aortic valve leaflets against the aortic root wall. However, these calcium deposits can impede the expansion of the device causing distortion of the valve stent and pericardial tissue leaflets. The objective of this study was to elucidate the impact of eccentric TAVR stent distortion on the dynamic deformation of the tissue leaflets of the prosthesis in vitro. Dual-camera stereophotogrammetry was used to measure the regional variation in strain in a leaflet of a TAVR deployed in nominal circular and eccentric (eccentricity index = 28%) orifices, representative of deployed TAVRs in vivo. It was observed that (i) eccentric stent distortion caused incorrect coaptation of the leaflets at peak diastole resulting in a ‘peel-back’ leaflet geometry that was not present in the circular valve and (ii) adverse bending of the leaflet, arising in the eccentric valve at peak diastole, caused significantly higher commissure strains compared with the circular valve in both normotensive and hypertensive pressure conditions (normotension: eccentric = 13.76 ± 2.04% versus circular = 11.77 ± 1.61%, p = 0.0014, hypertension: eccentric = 15.07 ± 1.13% versus circular = 13.56 ± 0.87%, p = 0.0042). This study reveals that eccentric distortion of a TAVR stent can have a considerable impact on dynamic leaflet deformation, inducing deleterious bending of the leaflet and increasing commissures strains, which might expedite leaflet structural failure compared to leaflets in a circular deployed valve. PMID:26674192

Behavior of Bilayer Leaflets in Asymmetric Model Membranes: Atomistic Simulation Studies

DOE PAGES

Tian, Jianhui; Nickels, Jonathan; Katsaras, John; ...

2016-04-27

Spatial organization within lipid bilayers is an important feature for a range of biological processes. Leaflet compositional asymmetry and lateral lipid organization are just two of the ways in which membrane structure appears to be more complex than initially postulated by the fluid mosaic model. This raises the question of how the phase behavior in one bilayer leaflet may affect the apposing leaflet and how one begins to construct asymmetric model systems to investigate these interleaflet interactions. In this paper, we report on all-atom molecular dynamics simulations (a total of 4.1 μs) of symmetric and asymmetric bilayer systems composed ofmore » liquid-ordered (Lo) or liquid-disordered (Ld) leaflets, based on the nanodomain-forming POPC/DSPC/cholesterol system. We begin by analyzing an asymmetric bilayer with leaflets derived from simulations of symmetric Lo and Ld bilayers. In this system, we observe that the properties of the Lo and Ld leaflets are similar to those of the Lo and Ld leaflets in corresponding symmetric systems. However, it is not obvious that mixing the equilibrium structures of their symmetric counterparts is the most appropriate way to construct asymmetric bilayers nor that these structures will manifest interleaflet couplings that lead to domain registry/antiregistry. We therefore constructed and simulated four additional asymmetric bilayer systems by systematically adding or removing lipids in the Ld leaflet to mimic potential density fluctuations. We find that the number of lipids in the Ld leaflet affects its own properties, as well as those of the apposing Lo leaflet. Collectively, the simulations reveal the presence of weak acyl chain interdigitation across bilayer leaflets, suggesting that interdigitation alone does not contribute significantly to the interleaflet coupling in nonphase-separated bilayers of this chemical composition. Finally, however, the properties of both leaflets appear to be sensitive to changes in in-plane lipid packing, possibly providing a mechanism for interleaflet coupling by modulating local density and/or curvature fluctuations.« less

Preparation, validation and user-testing of pictogram-based patient information leaflets for hemodialysis patients.

PubMed

Mateti, Uday Venkat; Nagappa, Anantha Naik; Attur, Ravindra Prabhu; Bairy, Manohar; Nagaraju, Shankar Prasad; Mallayasamy, Surulivelrajan; Vilakkathala, Rajesh; Guddattu, Vasudev; Balkrishnan, Rajesh

2015-11-01

Patient information leaflets are universally-accepted resources to educate the patients/users about their medications, disease and lifestyle modification. The objective of the study was to prepare, validate and perform user-testing of pictogram-based patient information leaflets (P-PILs) among hemodialysis (HD) patients. The P-PILs are prepared by referring to the primary, secondary and tertiary resources. The content and pictograms of the leaflet have been validated by an expert committee consisting of three nephrologists and two academic pharmacists. The Baker Able Leaflet Design has been applied to develop the layout and design of the P-PILs. Quasi-experimental pre- and post-test design without control group was conducted on 81 HD patients for user-testing of P-PILs. The mean Baker Able Leaflet Design assessment score for English version of the leaflet was 28, and 26 for Kannada version. The overall user-testing knowledge assessment mean scores were observed to have significantly improved from 44.25 to 69.62 with p value <0.001. The overall user opinion of content and legibility of the leaflets was good. Pictogram-based patient information leaflets can be considered an effective educational tool for HD patients.

Nucleotide sequences of two genomic DNAs encoding peroxidase of Arabidopsis thaliana.

PubMed

Intapruk, C; Higashimura, N; Yamamoto, K; Okada, N; Shinmyo, A; Takano, M

1991-02-15

The peroxidase (EC 1.11.1.7)-encoding gene of Arabidopsis thaliana was screened from a genomic library using a cDNA encoding a neutral isozyme of horseradish, Armoracia rusticana, peroxidase (HRP) as a probe, and two positive clones were isolated. From the comparison with the sequences of the HRP-encoding genes, we concluded that two clones contained peroxidase-encoding genes, and they were named prxCa and prxEa. Both genes consisted of four exons and three introns; the introns had consensus nucleotides, GT and AG, at the 5' and 3' ends, respectively. The lengths of each putative exon of the prxEa gene were the same as those of the HRP-basic-isozyme-encoding gene, prxC3, and coded for 349 amino acids (aa) with a sequence homology of 89% to that encoded by prxC3. The prxCa gene was very close to the HRP-neutral-isozyme-encoding gene, prxC1b, and coded for 354 aa with 91% homology to that encoded by prxC1b. The aa sequence homology was 64% between the two peroxidases encoded by prxCa and prxEa.

Stress Analysis of Transcatheter Aortic Valve Leaflets Under Dynamic Loading: Effect of Reduced Tissue Thickness.

PubMed

Abbasi, Mostafa; Azadani, Ali N

2017-07-01

In order to accommodate transcatheter valves to miniaturized catheters, the leaflet thickness must be reduced to a value which is typically less than that of surgical bioprostheses. The study aim was to use finite-element simulations to determine the impact of the thickness reduction on stress and strain distribution. A 23 mm transcatheter aortic valve (TAV) was modelled based on the Edwards SAPIEN XT (Edwards Lifesciences, Irvine, CA, USA). Finite-element (FE) analysis was performed using the ABAQUS/Explicit solver. An ensemble-averaged transvalvular pressure waveform measured from in-vitro tests conducted in a pulse duplicator was applied to the leaflets. Through a parametric study, uniform TAV leaflet thickness was reduced from 0.5 to 0.18 mm. By reducing leaflet thickness, significantly higher stress values were found in the leaflet's fixed edge during systole, and in the commissures during diastole. Through dynamic FE simulations, the highest stress values were found during systole in the leaflet fixed edge. In contrast, at the peak of diastole high-stress regions were mainly observed in the commissures. The peak stress was increased by 178% and 507% within the leaflets after reducing the thickness of 0.5 mm to 0.18 mm at the peak of systole and diastole, respectively. The study results indicated that, the smaller the leaflet thickness, the higher the maximum principal stress. Increased mechanical stress on TAV leaflets may lead to accelerated tissue degeneration. By using a thinner leaflet, TAV durability may not atch with that of surgical bioprostheses.

Diet and Colorectal Cancer Risk: Evaluation of a Nutrition Education Leaflet

ERIC Educational Resources Information Center

Dyer, K. J.; Fearon, K. C. H.; Buckner, K.; Richardson, R. A.

2005-01-01

Objective: To evaluate the effect of a needs-based, nutrition education leaflet on nutritional knowledge. Design: Comparison of nutritional knowledge levels before and after exposure to a nutrition education leaflet. Setting: A regional colorectal out-patient clinic in Edinburgh. Method: A nutrition education leaflet, based on an earlier…

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters.

PubMed

de Lima-Morales, Daiana; Chaves-Moreno, Diego; Wos-Oxley, Melissa L; Jáuregui, Ruy; Vilchez-Vargas, Ramiro; Pieper, Dietmar H

2016-01-01

Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Promotion of family planning services in practice leaflets.

PubMed

Marshall, M N; Gray, D J; Pearson, V; Phillips, D R; Owen, M

1994-10-08

Providing 75% of family planning services in the United Kingdom, general practitioners are required to produce leaflets which describe the contraceptive services they provide. The authors analyzed information about family planning provided to clients through practice leaflets. 88% of practice leaflets from the 198 practices in Devon were available from the Devon Family Health Services Authority for analysis. It was determined that the leaflets are not being best used to advertise the range and potential of family planning services. Although all practices in Devon offer contraceptive services, only 90% of leaflets mentioned that the services are available. Reference to postcoital contraception and information about services outside the practice for people who might not want to see their family doctor are also sorely lacking. A clear need exists to provide patients with more information. Finally, the authors found that group practices and those with female partners are most likely to give high priority to family planning issues in their leaflets.

[Evaluation of a self-care leaflet].

PubMed

Lystad, N; Heian, F

1989-01-20

A self care leaflet of 50 pages was distributed in Tingvoll, a municipality with 3,500 inhabitants. The leaflet gives advice about self treatment and prevention of common health problems, and guidelines for contacting the health services. In surveys conducted just before and 10 months after the distribution, we documented -- how the leaflet was accepted and used --changes in knowledge about the health problems mentioned in the leaflet. The leaflet was well accepted. It was characterized as easy to read and to use. 10 months after distribution to read and to use. 10 months after distribution 90% found it within five minutes. 63% used the leaflet when they had a health problem. 90% of those using the leaflet felt more sure that they acted correctly after consulting it, and 60% changed their mind about consulting a general practitioner. We consider the level of knowledge about health problems to be low. The evaluation showed increased knowledge in all groups, except for persons "responsible for caring for elderly relatives". The increase was most marked for "men" and for "persons with health education".

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eicher, Barbara; Marquardt, Drew; Heberle, Frederick A.

We measured the effect of intrinsic lipid curvature, J 0, on structural properties of asymmetric vesicles made of palmitoyl-oleoyl-phosphatidylethanolamine (POPE; J 0 < 0) and palmitoyl-oleoyl-phosphatidylcholine (POPC; J 0 ~ 0). Electron microscopy and dynamic light scattering were used to determine vesicle size and morphology, and x-ray and neutron scattering, combined with calorimetric experiments and solution NMR, yielded insights into leaflet-specific lipid packing and melting processes. Below the lipid melting temperature we observed strong interleaflet coupling in asymmetric vesicles with POPE inner bilayer leaflets and outer leaflets enriched in POPC. This lipid arrangement manifested itself by lipids melting cooperatively inmore » both leaflets, and a rearrangement of lipid packing in both monolayers. On the other hand, no coupling was observed in vesicles with POPC inner bilayer leaflets and outer leaflets enriched in POPE. In this case, the leaflets melted independently and did not affect each other’s acyl chain packing. Furthermore, we found no evidence for transbilayer structural coupling above the melting temperature of either sample preparation. Our results are consistent with the energetically preferred location of POPE residing in the inner leaflet, where it also resides in natural membranes, most likely causing the coupling of both leaflets. The loss of this coupling in the fluid bilayers is most likely the result of entropic contributions.« less

Design and efficacy of a single-use bioreactor for heart valve tissue engineering.

PubMed

Converse, Gabriel L; Buse, Eric E; Neill, Kari R; McFall, Christopher R; Lewis, Holley N; VeDepo, Mitchell C; Quinn, Rachael W; Hopkins, Richard A

2017-02-01

Heart valve tissue engineering offers the promise of improved treatments for congenital heart disorders; however, widespread clinical availability of a tissue engineered heart valve (TEHV) has been hindered by scientific and regulatory concerns, including the lack of a disposable, bioreactor system for nondestructive valve seeding and mechanical conditioning. Here we report the design for manufacture and the production of full scale, functional prototypes of such a system. To evaluate the efficacy of this bioreactor as a tool for seeding, ovine aortic valves were decellularized and subjected to seeding with human mesenchymal stem cells (hMSC). The effects of pulsatile conditioning using cyclic waveforms tuned to various negative and positive chamber pressures were evaluated, with respect to the seeding of cells on the decellularized leaflet and the infiltration of seeded cells into the interstitium of the leaflet. Infiltration of hMSCs into the aortic valve leaflet was observed following 72 h of conditioning under negative chamber pressure. Additional conditioning under positive pressure improved cellular infiltration, while retaining gene expression within the MSC-valve interstitial cell phenotype lineage. This protocol resulted in a subsurface pilot population of cells, not full tissue recellularization. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 249-259, 2017. © 2015 Wiley Periodicals, Inc.

Randomised trial of mitral valve repair with leaflet resection versus leaflet preservation on functional mitral stenosis (The CAMRA CardioLink-2 Trial).

PubMed

Chan, Vincent; Chu, Michael W A; Leong-Poi, Howard; Latter, David A; Hall, Judith; Thorpe, Kevin E; de Varennes, Benoit E; Quan, Adrian; Tsang, Wendy; Dhingra, Natasha; Yared, Kibar; Teoh, Hwee; Chu, F Victor; Chan, Kwan-Leung; Mesana, Thierry G; Connelly, Kim A; Ruel, Marc; Jüni, Peter; Mazer, C David; Verma, Subodh

2017-05-30

The gold-standard treatment of severe mitral regurgitation (MR) due to degenerative disease is valve repair, which is surgically performed with either a leaflet resection or leaflet preservation approach. Recent data suggest that functional mitral stenosis (MS) may occur following valve repair using a leaflet resection strategy, which adversely affects patient prognosis. A randomised comparison of these two approaches to mitral repair on functional MS has not been conducted. This is a prospective, multicentre randomised controlled trial designed to test the hypothesis that leaflet preservation leads to better preservation of mitral valve geometry, and therefore, will be superior to leaflet resection for the primary outcome of functional MS as assessed by 12-month mean mitral valve gradient at peak exercise. Eighty-eight patients with posterior leaflet prolapse will be randomised intraoperatively once deemed by the operating surgeon to feasibly undergo mitral repair using either a leaflet resection or leaflet preservation approach. Secondary end points include comparison of repair strategies with regard to mitral valve orifice area, leaflet coaptation height, 6 min walk test and a composite major adverse event end point consisting of recurrent MR ≥2+, death or hospital readmission for congestive heart failure within 12 months of surgery. Institutional ethics approval has been obtained from all enrolling sites. Overall, there remains clinical equipoise regarding the mitral valve repair strategy that is associated with the least likelihood of functional MS. This trial hopes to introduce high-quality evidence to help surgical decision making in this context. NCT02552771. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Colposcopy information leaflets: what women want to know and when they want to receive this information.

PubMed

Byrom, J; Dunn, P D J; Hughes, G M; Lockett, J; Johnson, A; Neale, J; Redman, C W E

2003-01-01

To evaluate whether the information leaflets produced by UK colposcopy clinics provide women with the information they desire and to determine when they would like to receive this information. Questionnaire study and structured evaluation. The colposcopy clinic of a UK cancer centre. Forty-two women attending a pre-colposcopy counselling session and 100 consecutive women attending the colposcopy clinic. Thirty-eight standards derived from the concerns/questions asked by women attending a pre-colposcopy counselling session were used to assess locally produced colposcopy clinic leaflets from UK colposcopy clinics, the leaflets produced by the Royal College of Obstetricians and Gynaecologists and the National Health Service Cervical Screening Programme (NHSCSP), and two "leaflets" obtained from internet sites. The Gunning fog test was used to assess the leaflets' readability. A questionnaire survey of 100 women attending the colposcopy clinic was used to determine when women wanted to receive information about colposcopy. Percentage of questions answered by a given leaflet and Gunning fog scores for readability. The information leaflets of 128 colposcopy clinics were received and assessed. Thirty-two clinics only sent women the NHSCSP leaflet. No leaflet answered all 38 questions. Less than half (36/100) of the leaflets answered more than 50% of the questions. In addition to the lack of advice given, different leaflets frequently gave conflicting advice. The average Gunning fog score was 9.7 (range 5.5-15.5). The majority of women (70%) wanted to receive information about colposcopy at or prior to the time of receiving their abnormal smear test result, although only 42% of women actually received information at this time. Many UK colposcopy clinics do not appear to be providing women with the information they require to understand their condition and the procedure that they are about to undergo. Furthermore, this information is often not provided at the appropriate time in the screening process.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tian, Jianhui; Nickels, Jonathan; Katsaras, John

Spatial organization within lipid bilayers is an important feature for a range of biological processes. Leaflet compositional asymmetry and lateral lipid organization are just two of the ways in which membrane structure appears to be more complex than initially postulated by the fluid mosaic model. This raises the question of how the phase behavior in one bilayer leaflet may affect the apposing leaflet and how one begins to construct asymmetric model systems to investigate these interleaflet interactions. In this paper, we report on all-atom molecular dynamics simulations (a total of 4.1 μs) of symmetric and asymmetric bilayer systems composed ofmore » liquid-ordered (Lo) or liquid-disordered (Ld) leaflets, based on the nanodomain-forming POPC/DSPC/cholesterol system. We begin by analyzing an asymmetric bilayer with leaflets derived from simulations of symmetric Lo and Ld bilayers. In this system, we observe that the properties of the Lo and Ld leaflets are similar to those of the Lo and Ld leaflets in corresponding symmetric systems. However, it is not obvious that mixing the equilibrium structures of their symmetric counterparts is the most appropriate way to construct asymmetric bilayers nor that these structures will manifest interleaflet couplings that lead to domain registry/antiregistry. We therefore constructed and simulated four additional asymmetric bilayer systems by systematically adding or removing lipids in the Ld leaflet to mimic potential density fluctuations. We find that the number of lipids in the Ld leaflet affects its own properties, as well as those of the apposing Lo leaflet. Collectively, the simulations reveal the presence of weak acyl chain interdigitation across bilayer leaflets, suggesting that interdigitation alone does not contribute significantly to the interleaflet coupling in nonphase-separated bilayers of this chemical composition. Finally, however, the properties of both leaflets appear to be sensitive to changes in in-plane lipid packing, possibly providing a mechanism for interleaflet coupling by modulating local density and/or curvature fluctuations.« less

Overcoming the knowledge-behavior gap: The effect of evidence-based HPV vaccination leaflets on understanding, intention, and actual vaccination decision.

PubMed

Wegwarth, O; Kurzenhäuser-Carstens, S; Gigerenzer, G

2014-03-10

Informed decision making requires transparent and evidence-based (=balanced) information on the potential benefit and harms of medical preventions. An analysis of German HPV vaccination leaflets revealed, however, that none met the standards of balanced risk communication. We surveyed a sample of 225 girl-parent pairs in a before-after design on the effects of balanced and unbalanced risk communication on participants' knowledge about cervical cancer and the HPV vaccination, their perceived risk, their intention to have the vaccine, and their actual vaccination decision. The balanced leaflet increased the number of participants who were correctly informed about cervical cancer and the HPV vaccine by 33 to 66 absolute percentage points. In contrast, the unbalanced leaflet decreased the number of participants who were correctly informed about these facts by 0 to 18 absolute percentage points. Whereas the actual uptake of the HPV vaccination 14 months after the initial study did not differ between the two groups (22% balanced leaflet vs. 23% unbalanced leaflet; p=.93, r=.01), the originally stated intention to have the vaccine reliably predicted the actual vaccination decision for the balanced leaflet group only (concordance between intention and actual uptake: 97% in the balanced leaflet group, rs=.92, p=.00; 60% in the unbalanced leaflet group, rs=.37, p=.08). In contrast to a unbalanced leaflet, a balanced leaflet increased people's knowledge of the HPV vaccination, improved perceived risk judgments, and led to an actual vaccination uptake, which first was robustly predicted by people's intention and second did not differ from the uptake in the unbalanced leaflet group. These findings suggest that balanced reporting about HPV vaccination increases informed decisions about whether to be vaccinated and does not undermine actual uptake. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

A scanning electron microscopy study of the invasion of leaflets of a bloat-safe and a bloat-causing legume by rumen microorganisms.

PubMed

Fay, J P; Cheng, K J; Hanna, M R; Howarth, R E; Costerton, J W

1981-04-01

A newly developed technique using ruthenium red to detect foci of bacterial digestion in mounts of whole leaflets that had been incubated with rumen bacteria was used to compare the digestion of alfalfa, a bloat-causing legume, and sainfoin, a bloat-safe legume. When whole leaflets were suspended in an artificial rumen medium and inoculated with rumen bacteria, massive bacterial adhesion and proliferation were noted at the stomata of alfalfa leaflets after 6 h of incubation, whereas only a few isolated bacteria adhered near the stomata of sainfoin leaflets After 22 h of incubation, the epidermal layers of alfalfa leaflets had peeled away in many areas, revealing an extensive bacterial invasion of the underlying mesophyll tissue in which large bacterial microcolonies had formed in intercellular spaces, and in intracellular spaces in several areas where plant cell walls had broken down. After 22 h of incubation, the surface of sainfoin leaflets resembled that of alfalfa leaflets at 6 h, with bacterial microcolonies adhering to the area surrounding the stomata, but without sloughing of the epidermis. Uninoculated control leaflets of both species showed no surface alteration but part of their normal bacterial flora had proliferated to form microcolonies on the surface after 22 h incubation. Dry matter loss due to leaching or bacterial digestion when whole leaflets of legumes were suspended in an artificial rumen medium, alone or with rumen bacteria, was significantly higher in the bloat-causing group. Values of leaching and of bacterial digestion were positively correlated. We conclude that reported differences in plant anatomy, and in cell wall chemistry, produce distinct rates or organic nutrient release from legume leaflets, and that these same differences produce an equally distinct susceptibility of leaflets to bacterial invasion, plant cell rupture, and the consequent release of intracellular plant components. The rate of release of organic nutrients from legume leaflets may be important in the etiology of foamy pasture bloat. This technique of in vitro digestion of whole leaflets followed by ruthenium red staining shows some promise of providing a rapid and qualitative test to distinguish, within a species, cultivars that may differ in their bloat-related characteristics.

[Parenting Renewal. Leaflets and Lessons for Parents of Children Birth to Four.

ERIC Educational Resources Information Center

Clemson Univ., SC. Cooperative Extension Service.

Instructional materials on parenting skills for parents of newborn through 4-year-old children are provided, with teaching guides for extension service agents. Organized as a series of nine leaflets followed by nine corresponding lessons, leaflets for parents concern: (1) an overview of the leaflets; (2) readiness: guiding normal development; (3)…

Flow-induced Flutter of Heart Valves: Experiments with Canonical Models

NASA Astrophysics Data System (ADS)

Dou, Zhongwang; Seo, Jung-Hee; Mittal, Rajat

2017-11-01

For the better understanding of hemodynamics associated with valvular function in health and disease, the flow-induced flutter of heart valve leaflets is studied using benchtop experiments with canonical valve models. A simple experimental model with flexible leaflets is constructed and a pulsatile pump drives the flow through the leaflets. We quantify the leaflet dynamics using digital image analysis and also characterize the dynamics of the flow around the leaflets using particle imaging velocimetry. Experiments are conducted over a wide range of flow and leaflet parameters and data curated for use as a benchmark for validation of computational fluid-structure interaction models. The authors would like to acknowledge Supported from NSF Grants IIS-1344772, CBET-1511200 and NSF XSEDE Grant TG-CTS100002.

An uncommon cause of tricuspid regurgitation: three-dimensional echocardiographic incremental value, surgical and genetic insights.

PubMed

Theron, Alexis; Pinard, Amélie; Riberi, Alberto; Zaffran, Stéphane

2016-07-01

Congenital tricuspid valve disease is a rare defect that includes regurgitation, stenosis and Ebstein's anomaly. We report a case of severe tricuspid regurgitation associated with functional mitral regurgitation in a 47-year-old man with congestive heart failure. Transthoracic echocardiography (TTE) ruled out any Ebstein's anomaly. Three-dimensional TTE revealed a 'tricuspid hole' into the anterior leaflet that was only attached to the tricuspid annulus next to both anteroseptal and anteroposterior commissures. There was no sign of leaflet tear or perforation. The surgical repair of the tricuspid and mitral valves was performed with an optimal result. No sign of endocarditis or rheumatic disease was observed during the intervention. Sequence analysis of GATA4, HEY2 and ZFPM2 genes was performed, but no causative mutation was identified. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Pregnancy-induced remodeling of heart valves.

PubMed

Pierlot, Caitlin M; Moeller, Andrew D; Lee, J Michael; Wells, Sarah M

2015-11-01

Recent studies have demonstrated remodeling of aortic and mitral valves leaflets under the volume loading and cardiac expansion of pregnancy. Those valves' leaflets enlarge with altered collagen fiber architecture, content, and cross-linking and biphasic changes (decreases, then increases) in extensibility during gestation. This study extends our analyses to right-sided valves, with additional compositional measurements for all valves. Valve leaflets were harvested from nonpregnant heifers and pregnant cows. Leaflet structure was characterized by leaflet dimensions, and ECM composition was determined using standard biochemical assays. Histological studies assessed changes in cellular and ECM components. Leaflet mechanical properties were assessed using equibiaxial mechanical testing. Collagen thermal stability and cross-linking were assessed using denaturation and hydrothermal isometric tension tests. Pulmonary and tricuspid leaflet areas increased during pregnancy by 35 and 55%, respectively. Leaflet thickness increased by 20% only in the pulmonary valve and largely in the fibrosa (30% thickening). Collagen crimp length was reduced in both the tricuspid (61%) and pulmonary (42%) valves, with loss of crimped area in the pulmonary valve. Thermomechanics showed decreased collagen thermal stability with surprisingly maintained cross-link maturity. The pulmonary leaflet exhibited the biphasic change in extensibility seen in left side valves, whereas the tricuspid leaflet mechanics remained largely unchanged throughout pregnancy. The tricuspid valve exhibits a remodeling response during pregnancy that is significantly diminished from the other three valves. All valves of the heart remodel in pregnancy in a manner distinct from cardiac pathology, with much similarity valve to valve, but with interesting valve-specific responses in the aortic and tricuspid valves. Copyright © 2015 the American Physiological Society.

The contents of dental implant patient information leaflets available within the UK.

PubMed

Barber, J; Puryer, J; McNally, L; O'Sullivan, D

2015-02-01

Patient information leaflets are designed to provide easy to follow information summaries and first point of contact information about treatment options. This survey reviewed the content of dental implant patient information leaflets, produced by implant companies and available within the UK in 2011. Dental implant companies in the UK were asked to provide samples of their patient information leaflets. The information within the leaflets was then summarised, including the quantity and the types of images used and whether the source of the information was given. Quantitative data was obtained on the amount of information provided, size of images and number of references. A response rate of 71% was obtained and 23 leaflets were studied. Great variation was found between the leaflets, with the word counts ranging from 88 to 5,434, and 44 different topics were identified. The majority of the images used were decorative, and none of the leaflets gave any reference to the sources of their information. Implant treatment was generally described in a positive way, with an emphasis on describing the treatment and the advantages. Much less information was given about the potential disadvantages and risks of complications or failure, including the relevance of periodontal disease or smoking. Implant patient information leaflets provided by dental implant companies should not be solely relied upon to provide patients with all the information they need to give informed consent to treatment.

The development and testing of a brief ('gist-based') supplementary colorectal cancer screening information leaflet.

PubMed

Smith, Samuel G; Wolf, Michael S; Obichere, Austin; Raine, Rosalind; Wardle, Jane; von Wagner, Christian

2013-12-01

To design and user-test a 'gist-based' colorectal cancer screening information leaflet, which promotes comprehension of the screening offer. Twenty-eight individuals approaching screening age were recruited from organisations in deprived areas of England. Using a between-subjects design, we tested iterations of a newly-designed gist-based information leaflet. Participants read the leaflet and answered 8 'true' or 'false' comprehension statements. For the leaflet to be considered fit-for-purpose, all statements had to be answered correctly by at least 80% of participants in each round. Alterations were made if this threshold was not met and additional rounds of testing were undertaken. At round 1, answers to 2/8 statements did not meet the threshold. After changes, answers in round 2 did not reach the threshold for 1/8 statements. In round 3, all answers were adequate and the leaflet was deemed fit-for-purpose. Qualitative data offered solutions such as language and layout changes which led to improved comprehension of the leaflet. User-testing substantially improved the design and subsequent comprehensibility of a theory-driven gist-based colorectal cancer screening information leaflet. This leaflet will be evaluated as part of a large national randomised controlled trial designed to reduce socioeconomic inequalities in colorectal cancer screening participation. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Package leaflets of the most consumed medicines in Portugal: safety and regulatory compliance issues. A descriptive study.

PubMed

Pires, Carla; Vigário, Marina; Cavaco, Afonso

2015-01-01

Package leaflets are necessary for safe use of medicines. The aims of the present study were: 1) to assess the compliance between the content of the package leaflets and the specifications of the pharmaceutical regulations; and 2) to identify potential safety issues for patients. Qualitative descriptive study, involving all the package leaflets of branded medicines from the three most consumed therapeutic groups in Portugal, analyzed in the Department of Pharmacoepidemiology, School of Pharmacy, University of Lisbon. A checklist validated through an expert consensus process was used to gather the data. The content of each package leaflet in the sample was classified as compliant or non-compliant with compulsory regulatory issues (i.e. stated dosage and descriptions of adverse reactions) and optional regulatory issues (i.e. adverse reaction frequency, symptoms and procedures in cases of overdose). A total of 651 package leaflets were identified. Overall, the package leaflets were found to be compliant with the compulsory regulatory issues. However, the optional regulatory issues were only addressed in around half of the sample of package leaflets, which made it possible to identify some situations of potentially compromised drug safety. Ideally, the methodologies for package leaflet approval should be reviewed and optimized as a way of ensuring the inclusion of the minimum essential information for safe use of medicines.

Provision of tricuspid valve leaflets by septal papillary muscles in the right ventricle of human and other mammal hearts.

PubMed

Jezyk, Damian; Jerzemowski, Janusz; Grzybiak, Marek

2003-01-01

Leaflets of the tricuspid valve are provided by tendinous cords extending from the papillary muscles. The situation is complicated with the septal muscles, which generally occur in two groups, one as constant musculus coni arteriosi and the second as other variable septal muscles. We tested whether there is a variability in the provision of the tricuspid valve in different taxonomical groups of mammals. The material examined consisted of 299 hearts of mammals (Primates, Ungulata, Carnivora, Lagomorpha, Rodentia, Marsupialia). The musculus coni arteriosi in the majority of mammals provided only the front leaflet, but among Ungulata and Rodentia it provided simultaneously the front and septal leaflet. The other septal muscles provided the front, septal and even back leaflets. The following regularity was observed: in the hearts of Primates provision of the front leaflet and the front part of the septal leaflet predominated, among Ungulata the muscles provided the middle part of the septal leaflet, but among the other mammals the rest of the septal muscles provided, significantly, the back part of the septal leaflet. Such a provision was characteristic for predators, hares, rodents and marsupials. These circumstances may allow the conclusion to be drawn that there is a taxonomical dependence in the provision of the tricuspid valve in the hearts of the mammals under examination.

Intrinsic Curvature-Mediated Transbilayer Coupling in Asymmetric Lipid Vesicles

DOE PAGES

Eicher, Barbara; Marquardt, Drew; Heberle, Frederick A.; ...

2018-01-09

We measured the effect of intrinsic lipid curvature, J 0, on structural properties of asymmetric vesicles made of palmitoyl-oleoyl-phosphatidylethanolamine (POPE; J 0 < 0) and palmitoyl-oleoyl-phosphatidylcholine (POPC; J 0 ~ 0). Electron microscopy and dynamic light scattering were used to determine vesicle size and morphology, and x-ray and neutron scattering, combined with calorimetric experiments and solution NMR, yielded insights into leaflet-specific lipid packing and melting processes. Below the lipid melting temperature we observed strong interleaflet coupling in asymmetric vesicles with POPE inner bilayer leaflets and outer leaflets enriched in POPC. This lipid arrangement manifested itself by lipids melting cooperatively inmore » both leaflets, and a rearrangement of lipid packing in both monolayers. On the other hand, no coupling was observed in vesicles with POPC inner bilayer leaflets and outer leaflets enriched in POPE. In this case, the leaflets melted independently and did not affect each other’s acyl chain packing. Furthermore, we found no evidence for transbilayer structural coupling above the melting temperature of either sample preparation. Our results are consistent with the energetically preferred location of POPE residing in the inner leaflet, where it also resides in natural membranes, most likely causing the coupling of both leaflets. The loss of this coupling in the fluid bilayers is most likely the result of entropic contributions.« less

Patient assessment of medication information leaflets and validation of the Evaluative Linguistic Framework (ELF).

PubMed

Hirsh, Di; Clerehan, Rosemary; Staples, Margaret; Osborne, Richard H; Buchbinder, Rachelle

2009-11-01

To obtain patient feedback about the structure and quality of medication information leaflets and validate the usefulness of the Evaluative Linguistic Framework (ELF) for improving written communication with patients. Triangulated feedback about a set of rheumatoid arthritis (RA) medication leaflets, some developed with knowledge of the ELF, was obtained from 27 people with RA from interviews, focus group discussion and self-administered questionnaires. The principal elements of the framework were investigated: overall generic structure and functions of each stage, interpersonal relationship between writer and reader, technicality of language and density of information. Participant assessments of the leaflets aligned with the framework in terms of what constituted a good leaflet. While the main purpose of the leaflets was identified as being information provision, participants also wanted clear instructions, benefits to be highlighted and side effects to be comprehensively listed. For comprehensiveness and user-friendliness, leaflets developed with guidance of the ELF were consistently preferred. According to people with RA, leaflets generated from a linguistic framework are clearer and more effective in communicating information about medications. The ELF is a user-friendly, structured analytic system that can assist with the development of effective high quality patient information materials.

Optimal Elastomeric Scaffold Leaflet Shape for Pulmonary Heart Valve Leaflet Replacement

PubMed Central

Fan, Rong; Bayoumi, Ahmed S.; Chen, Peter; Hobson, Christopher M.; Wagner, William R.; Mayer, John E.; Sacks, Michael S.

2012-01-01

Surgical replacement of the pulmonary valve (PV) is a common treatment option for congenital pulmonary valve defects. Engineered tissue approaches to develop novel PV replacements are intrinsically complex, and will require methodical approaches for their development. Single leaflet replacement utilizing an ovine model is an attractive approach in that candidate materials can be evaluated under valve level stresses in blood contact without the confounding effects of a particular valve design. In the present study an approach for optimal leaflet shape design based on finite element (FE) simulation of a mechanically anisotropic, elastomeric scaffold for PV replacement is presented. The scaffold was modeled as an orthotropic hyperelastic material using a generalized Fung-type constitutive model. The optimal shape of the fully loaded PV replacement leaflet was systematically determined by minimizing the difference between the deformed shape obtained from FE simulation and an ex-vivo microCT scan of a native ovine PV leaflet. Effects of material anisotropy, dimensional changes of PV root, and fiber orientation on the resulting leaflet deformation were investigated. In-situ validation demonstrated that the approach could guide the design of the leaflet shape for PV replacement surgery. PMID:23294966

Meningioma of the superior leaflet of the velum interpositum: A case report

PubMed Central

Champagne, Pierre-Olivier; Bojanowski, Michel W.

2015-01-01

Background: Meningiomas of the velum interpositum in the roof of the third ventricle are rare. Knowing from which leaflet the meningioma originates and thus its relationships with the internal cerebral and Galen veins, may help in choosing the surgical approach. Case Description: We report the case of a 40-year-old male with a meningioma arising from the superior leaflet of the velum interpositum. The tumor was resected successfully using the infratentorial-supracerebellar approach. Reviewing the literature, of the 22 reported cases of velum interpositum meningiomas, sufficient information regarding the precise location of the origin of the tumor was provided in 14 cases, all of which were from the inferior leaflet. Conclusion: We report the first case of velum interpositum meningioma arising from the superior leaflet and give a potential explanation as to why meningiomas of the velum interpositum occur more commonly on the inferior leaflet. Distinguishing from which of the two leaflets the tumor originates may influence the surgical strategy. PMID:25949856

Curved butterfly bileaflet prosthetic cardiac valve

DOEpatents

McQueen, David M.; Peskin, Charles S.

1991-06-25

An annular valve body having a central passageway for the flow of blood therethrough with two curved leaflets each of which is pivotally supported on an accentric positioned axis in the central passageway for moving between a closed position and an open position. The leaflets are curved in a plane normal to the eccentric axis and positioned with the convex side of the leaflets facing each other when the leaflets are in the open position. Various parameters such as the curvature of the leaflets, the location of the eccentric axis, and the maximum opening angle of the leaflets are optimized according to the following performance criteria: maximize the minimum peak velocity through the valve, maximize the net stroke volume, and minimize the mean forward pressure difference, thereby reducing thrombosis and improving the hemodynamic performance.

Mollusk genes encoding lysine tRNA (UUU) contain introns.

PubMed

Matsuo, M; Abe, Y; Saruta, Y; Okada, N

1995-11-20

New intron-containing genes encoding tRNAs were discovered when genomic DNA isolated from various animal species was amplified by the polymerase chain reaction (PCR) with primers based on sequences of rabbit tRNA(Lys). From sequencing analysis of the products of PCR, we found that introns are present in several genes encoding tRNA(Lys) in mollusks, such as Loligo bleekeri (squid) and Octopus vulgaris (octopus). These introns were specific to genes encoding tRNA(Lys)(CUU) and were not present in genes encoding tRNA(Lys)(CUU). In addition, the sequences of the introns were different from one another. To confirm the results of our initial experiments, we isolated and sequenced genes encoding tRNA(Lys)(CUU) and tRNA(Lys)(UUU). The gene for tRNA(Lys)(UUU) from squid contained an intron, whose sequence was the same as that identified by PCR, and the gene formed a cluster with a corresponding pseudogene. Several DNA regions of 2.1 kb containing this cluster appeared to be tandemly arrayed in the squid genome. By contrast, the gene encoding tRNA(Lys)(CUU) did not contain an intron, as shown also by PCR. The tRNA(Lys)(UUU) that corresponded to the analyzed gene was isolated and characterized. The present study provides the first example of an intron-containing gene encoding a tRNA in mollusks and suggests the universality of introns in such genes in higher eukaryotes.

Human AZU-1 gene, variants thereof and expressed gene products

DOEpatents

Chen, Huei-Mei; Bissell, Mina

2004-06-22

A human AZU-1 gene, mutants, variants and fragments thereof. Protein products encoded by the AZU-1 gene and homologs encoded by the variants of AZU-1 gene acting as tumor suppressors or markers of malignancy progression and tumorigenicity reversion. Identification, isolation and characterization of AZU-1 and AZU-2 genes localized to a tumor suppressive locus at chromosome 10q26, highly expressed in nonmalignant and premalignant cells derived from a human breast tumor progression model. A recombinant full length protein sequences encoded by the AZU-1 gene and nucleotide sequences of AZU-1 and AZU-2 genes and variant and fragments thereof. Monoclonal or polyclonal antibodies specific to AZU-1, AZU-2 encoded protein and to AZU-1, or AZU-2 encoded protein homologs.

The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

PubMed Central

Grohmann, L; Brennicke, A; Schuster, W

1992-01-01

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed. Images PMID:1454526

Anaesthesia information--what patients want to know.

PubMed

Garden, A L; Merry, A F; Holland, R L; Petrie, K J

1996-10-01

We developed and introduced into clinical practice a leaflet to improve the delivery of information to patients before obtaining their consent to anaesthesia. The amount of information needs to be what a "reasonable" patient thinks appropriate; therefore we tested patients' responses to three levels of information: "full" disclosure, "standard" disclosure (as contained in our leaflet) and "minimal" disclosure. Forty-five patients scheduled to undergo cardiac surgery were enrolled in the study. None of the information sheets caused a significant change in state anxiety score and only the "full" disclosure significantly increased knowledge about anaesthesia (P = 0.016). All leaflets were easy to understand. When only one leaflet was provided 64-73% of patients thought the content was "just right", whereas when all three leaflets were viewed together, 63% of patients thought the "minimal" leaflet withheld too much information.

Effect of the Mitral Valve's Anterior Leaflet on Axisymmetry of Transmitral Vortex Ring.

PubMed

Falahatpisheh, Ahmad; Pahlevan, Niema M; Kheradvar, Arash

2015-10-01

The shape and formation of transmitral vortex ring are shown to be associated with diastolic function of the left ventricle (LV). Transmitral vortex ring is a flow feature that is observed to be non-axisymmetric in a healthy heart and its inherent asymmetry in the LV assists in efficient ejection of the blood during systole. This study is a first step towards understanding the effects of the mitral valve's anterior leaflet on transmitral flow. We experimentally study a single-leaflet model of the mitral valve to investigate the effect of the anterior leaflet on the axisymmetry of the generated vortex ring based on the three-dimensional data acquired using defocusing digital particle image velocimetry. Vortex rings form downstream of a D-shaped orifice in presence or absence of the anterior leaflet in various physiological stroke ratios. The results of the statistical analysis indicate that the formed vortex ring downstream of a D-shaped orifice is markedly non-axisymmetric, and presence of the anterior leaflet improves the ring's axisymmetry. This study suggests that the improvement of axisymmetry in presence of the anterior leaflet might be due to coupled dynamic interaction between rolling-up of the shear layer at the edges of the D-shaped orifice and the borders of the anterior leaflet. This interaction can reduce the non-uniformity in vorticity generation, which results in more axisymmetric behavior compared to the D-shaped orifice without the anterior leaflet.

Further insights into normal aortic valve function: role of a compliant aortic root on leaflet opening and valve orifice area.

PubMed

Sripathi, Vangipuram Canchi; Kumar, Ramarathnam Krishna; Balakrishnan, Komarakshi R

2004-03-01

This study aims to find the fundamental differences in the mechanism of opening and closing of a normal aortic valve and a valve with a stiff root, using a dynamic finite element model. A dynamic, finite element model with time varying pressure was used in this study. Shell elements with linear elastic properties for the leaflet and root were used. Two different cases were analyzed: (1) normal leaflets inside a compliant root, and (2) normal leaflets inside a stiff root. A compliant aortic root contributes substantially to the smooth and symmetrical leaflet opening with minimal gradients. In contrast, the leaflet opening inside a stiff root is delayed, asymmetric, and wrinkled. However, this wrinkling is not associated with increased leaflet stresses. In compliant roots, the effective valve orifice area can substantially increase because of increased root pressure and transvalvular gradients. In stiff roots this effect is strikingly absent. A compliant aortic root contributes substantially to smooth and symmetrical leaflet opening with minimal gradients. The compliance also contributes much to the ability of the normal aortic valve to increase its effective valve orifice in response to physiologic demands of exercise. This effect is strikingly absent in stiff roots.

Transcatheter valve underexpansion limits leaflet durability: implications for valve-in-valve procedures

PubMed Central

Martin, Caitlin; Sun, Wei

2016-01-01

Transcatheter aortic valve (TAV) implantation within a failed bioprosthetic valve is a growing trend for high-risk patients. The non-compliant stent of the previous prosthesis may prevent full expansion of the TAV, which has been shown to distort the leaflet configuration, and has been hypothesized to adversely affect durability. In this study, TAV leaflet fatigue damage under cyclic pressurization in the setting of stent underexpansion by 0 (fully expanded), 1, 2 and 3 mm was simulated using finite element analysis to test this hypothesis. In the 2 and 3 mm underexpanded devices, the TAV leaflets exhibited severe pin-wheeling during valve closure, which increased leaflet stresses dramatically, and resulted in accelerated fatigue damage of the leaflets. The leaflet fatigue damage in the 1 mm underexpanded case was similar to that in the fully expanded case. Clinically a range of 10% to 15% underexpansion is generally considered acceptable; however, it was observed in this study that ≥2 mm (≥9.1%) underexpansion, will significantly impact device durability. Further study is necessary to determine the impact of various deployment conditions, i.e. non-uniform and non-circular deployments and different implantation heights, on differing TAV devices, but it is clear that the normal TAV leaflet configuration must be preserved in order to preserve durability. PMID:27734178

Kangaroo versus porcine aortic valve tissue--valve geometry morphology, tensile strength and calcification potential.

PubMed

Neethling, W M; Papadimitriou, J M; Swarts, E; Hodge, A J

2000-06-01

Valve related factors and patient related factors are responsible for calcification of valvular bioprostheses. Recent studies showed different donor and recipient species have different influences on the total calcification rate of bioprostheses. This study was performed to evaluate and compare Kangaroo aortic valve leaflets with porcine aortic valve leaflets. Experimental design. Prospective study. Setting. Cardio-thoracic experimental research of a university department. Glutaraldehyde-fixed Kangaroo and porcine valve leaflets were evaluated in vitro according to valve geometry (internal diameter and leaflet thickness), morphology (light and electron microscopy) and tensile strength. In vivo evaluation consisted of implantation in a rat model for 8 weeks, Von Kossa stain for calcium and atomic absorption spectrophotometry for total extractable calcium content. Kangaroo valves indicated a smaller internal valve diameter as well as a thinner valve leaflet (p<0.01, ANOVA) at corresponding body weight, less proteoglycan spicules in the fibrosa, increased elasticity (p<0.05) and low calcification potential (p<0.01, confidence interval 95%). Kangaroo aortic valve leaflets have different valvular qualities compared to porcine valve tissue. Kangaroo valve leaflets are significantly superior to porcine valve leaflets as far as calcification is concerned. These results are encouraging and suggest further in vivo evaluation in a larger animal model before clinical application can be considered.

A novel biotinylated lipid raft reporter for electron microscopic imaging of plasma membrane microdomains[S

PubMed Central

Krager, Kimberly J.; Sarkar, Mitul; Twait, Erik C.; Lill, Nancy L.; Koland, John G.

2012-01-01

The submicroscopic spatial organization of cell surface receptors and plasma membrane signaling molecules is readily characterized by electron microscopy (EM) via immunogold labeling of plasma membrane sheets. Although various signaling molecules have been seen to segregate within plasma membrane microdomains, the biochemical identity of these microdomains and the factors affecting their formation are largely unknown. Lipid rafts are envisioned as submicron membrane subdomains of liquid ordered structure with differing lipid and protein constituents that define their specific varieties. To facilitate EM investigation of inner leaflet lipid rafts and the localization of membrane proteins therein, a unique genetically encoded reporter with the dually acylated raft-targeting motif of the Lck kinase was developed. This reporter, designated Lck-BAP-GFP, incorporates green fluorescent protein (GFP) and biotin acceptor peptide (BAP) modules, with the latter allowing its single-step labeling with streptavidin-gold. Lck-BAP-GFP was metabolically biotinylated in mammalian cells, distributed into low-density detergent-resistant membrane fractions, and was readily detected with avidin-based reagents. In EM images of plasma membrane sheets, the streptavidin-gold-labeled reporter was clustered in 20–50 nm microdomains, presumably representative of inner leaflet lipid rafts. The utility of the reporter was demonstrated in an investigation of the potential lipid raft localization of the epidermal growth factor receptor. PMID:22822037

Medication information leaflets for patients: the further validation of an analytic linguistic framework.

PubMed

Clerehan, Rosemary; Hirsh, Di; Buchbinder, Rachelle

2009-01-01

While clinicians may routinely use patient information leaflets about drug therapy, a poorly conceived leaflet has the potential to do harm. We previously developed a novel approach to analysing leaflets about a rheumatoid arthritis drug, using an analytic approach based on systemic functional linguistics. The aim of the present study was to verify the validity of the linguistic framework by applying it to two further arthritis drug leaflets. The findings confirmed the applicability of the framework and were used to refine it. A new stage or 'move' in the genre was identified. While the function of many of the moves appeared to be 'to instruct' the patient, the instruction was often unclear. The role relationships expressed in the text were critical to the meaning. As with our previous study, judged on their lexical density, the leaflets resembled academic text. The framework can provide specific tools to assess and produce medication information leaflets to support readers in taking medication. Future work could utilize the framework to evaluate information on other treatments and procedures or on healthcare information more widely.

Rapid pannus formation after few months of obstructing aortic mechanical prosthesis.

PubMed

Al-Alao, Bassel; Simoniuk, Urszula; Heron, Brian; Parissis, Haralabos

2015-11-01

We report a rare case of a prosthetic aortic valve obstruction due to pannus formation only 3 months following aortic and mitral valve replacement. Fragments of asymmetrical pannus formation affected one of the leaflets of the bi-leaflet mechanical valve; the leaflet appeared immobile due to pannus ingrowth into the mechanical skeleton resulting in encroachment of the leaflet, which in turn became immobile. The patient successfully underwent emergency redo-aortic valve replacement.

The organization of the fuc regulon specifying L-fucose dissimilation in Escherichia coli K12 as determined by gene cloning.

PubMed

Chen, Y M; Zhu, Y; Lin, E C

1987-12-01

In Escherichia coli the six known genes specifying the utilization of L-fucose as carbon and energy source cluster at 60.2 min and constitute a regulon. These genes include fucP (encoding L-fucose permease), fucI (encoding L-fucose isomerase), fucK (encoding L-fuculose kinase), fucA (encoding L-fuculose 1-phosphate aldolase), fucO (encoding L-1,2-propanediol oxidoreductase), and fucR (encoding the regulatory protein). In this study the fuc genes were cloned and their positions on the chromosome were established by restriction endonuclease and complementation analyses. Clockwise, the gene order is: fucO-fucA-fucP-fucI-fucK-fucR. The operons comprising the structural genes and the direction of transcription were determined by complementation analysis and Southern blot hybridization. The fucPIK and fucA operons are transcribed clockwise. The fucO operon is transcribed counterclockwise. The fucR gene product activates the three structural operons in trans.

Deformation Differences between Tricuspid and Bicuspid Aortic Valves in Vitro

NASA Astrophysics Data System (ADS)

Szeto, Kai; Rodriguez-Rodriguez, Javier; Pastuszko, Peter; Nigam, Vishal; Lasheras, Juan C.

2011-11-01

It has been shown in clinical studies that patients with congenital bicuspid aortic valves (CBAVs) develop degenerative calcification of the leaflets at young ages compared to patients with the normal tricuspid aortic valves (TAVs). It has been hypothesized that the asymmetrical geometry of the leaflets in CBAVs, flow shear stresses (SS), disturbed flow, and excessive strain rate levels are possible causes for the early calcification and stenosis. Central to the validation of this hypothesis is the need to quantify the differences in strain rate levels between the BAVs and TAVs. We simulate the CBAVs by surgically stitching two of the leaflets of a porcine aortic valve together. To quantify strain differences, we performed in-vitro experiments in both trileaflet and bileaflet valves by tracking the motion of small ink dots marked on each leaflet surface. We then used phase-locked stereo photogrammetry to reconstruct at each instant of time the 3D surface of the leaflets and measure the strain rates in both radial and circumferential directions during the whole cardiac cycle. Our results indicate that the total strain rate of the simulated BAVs is about 15 to 20% higher than the normal leaflets of TAVs at systole. In the BAVs' case, the fused leaflet stretches radially up to 25% higher than the reference length. The excessive stretching in both directions in the fused leaflet results in large changes in the flow patterns and associated wall SS.

Chemical Composition and Antioxidant Activity of Euterpe oleracea Roots and Leaflets.

PubMed

Brunschwig, Christel; Leba, Louis-Jérôme; Saout, Mona; Martial, Karine; Bereau, Didier; Robinson, Jean-Charles

2016-12-29

Euterpe oleracea (açaí) is a palm tree well known for the high antioxidant activity of its berries used as dietary supplements. Little is known about the biological activity and the composition of its vegetative organs. The objective of this study was to investigate the antioxidant activity of root and leaflet extracts of Euterpe oleracea ( E . oleracea ) and characterize their phytochemicals. E . oleracea roots and leaflets extracts were screened in different chemical antioxidant assays (DPPH-2,2-diphenyl-1-picrylhydrazyl, FRAP-ferric feducing antioxidant power, and ORAC-oxygen radical absorbance capacity), in a DNA nicking assay and in a cellular antioxidant activity assay. Their polyphenolic profiles were determined by UV and LC-MS/MS. E . oleracea leaflets had higher antioxidant activity than E . oleracea berries, and leaflets of Oenocarpus bacaba and Oenocarpus bataua , as well as similar antioxidant activity to green tea. E. oleracea leaflet extracts were more complex than root extracts, with fourteen compounds, including caffeoylquinic acids and C -glycosyl derivatives of apigenin and luteolin. In the roots, six caffeoylquinic and caffeoylshikimic acids were identified. Qualitative compositions of E. oleracea , Oenocarpus bacaba and Oenocarpus bataua leaflets were quite similar, whereas the quantitative compositions were quite different. These results provide new prospects for the valorization of roots and leaflets of E. oleracea in the pharmaceutical, food or cosmetic industry, as they are currently by-products of the açaí industry.

Chemical Composition and Antioxidant Activity of Euterpe oleracea Roots and Leaflets

PubMed Central

Brunschwig, Christel; Leba, Louis-Jérôme; Saout, Mona; Martial, Karine; Bereau, Didier; Robinson, Jean-Charles

2016-01-01

Euterpe oleracea (açaí) is a palm tree well known for the high antioxidant activity of its berries used as dietary supplements. Little is known about the biological activity and the composition of its vegetative organs. The objective of this study was to investigate the antioxidant activity of root and leaflet extracts of Euterpe oleracea (E. oleracea) and characterize their phytochemicals. E. oleracea roots and leaflets extracts were screened in different chemical antioxidant assays (DPPH—2,2-diphenyl-1-picrylhydrazyl, FRAP—ferric feducing antioxidant power, and ORAC—oxygen radical absorbance capacity), in a DNA nicking assay and in a cellular antioxidant activity assay. Their polyphenolic profiles were determined by UV and LC-MS/MS. E. oleracea leaflets had higher antioxidant activity than E. oleracea berries, and leaflets of Oenocarpus bacaba and Oenocarpus bataua, as well as similar antioxidant activity to green tea. E. oleracea leaflet extracts were more complex than root extracts, with fourteen compounds, including caffeoylquinic acids and C-glycosyl derivatives of apigenin and luteolin. In the roots, six caffeoylquinic and caffeoylshikimic acids were identified. Qualitative compositions of E. oleracea, Oenocarpus bacaba and Oenocarpus bataua leaflets were quite similar, whereas the quantitative compositions were quite different. These results provide new prospects for the valorization of roots and leaflets of E. oleracea in the pharmaceutical, food or cosmetic industry, as they are currently by-products of the açaí industry. PMID:28036089

Tricuspid leaflet resection in an open beating heart for the creation of a canine tricuspid regurgitation model.

PubMed

Xie, Xu-jing; Liao, Sheng-jie; Wu, Yue-heng; Lu, Cong; Zhu, Ping; Fei, Hong-wen; Xiao, Xue-jun; Huang, Huan-lei

2016-02-01

Outcomes of tricuspid valve replacement are poor, partly due to right heart remodelling. The research on its underlying mechanisms is hampered by a lack of animal models of tricuspid regurgitation (TR). Our objective was to create a reproducible and clinically compatible TR animal model to study right heart remodelling caused by TR. Fourteen juvenile male Beagle dogs were divided randomly into an intervention group (n = 11) and a sham-operated control group (n = 3). The intervention group underwent thoracotomy and right atrial incision following superior and inferior vena caval occlusion. The anterior leaflet, together with the chordae, of the tricuspid valve was resected in eight dogs ('one leaflet' group), whereas both anterior and posterior leaflets, together with the chordae, were resected in three dogs ('two leaflets' group). The right atrium and chest were then closed. The control group underwent the same procedure, except leaflet resection. One dog from the 'two leaflets' group and one control dog were sacrificed and autopsy was performed at 12 months post-surgery. All dogs survived over the 1-year observation period postoperatively. TR grade IV occurred immediately postoperatively in the 'one leaflet' group, and TR grade IV plus in the 'two leaflets' group. The overall procedure lasted 30-40 min, and the mean time of vena caval occlusion was 87 ± 10 s. Central venous pressure increased from 6 ± 1.2 at baseline to 13 ± 1.7 mmHg (P < 0.01). By 12 months after TR creation, both in the 'one leaflet' group and in the 'two leaflets' group, the right atrial area, tricuspid annular diameter and right ventricular index of myocardial performance increased significantly, right ventricular fractional area change and tricuspid annular plane systolic excursion decreased significantly. Autopsy of the intervention dog revealed oedema, ascites and cirrhosis. Our surgical technique to create a TR animal model was reproducible with high success and survival rates. This animal model would prove suitable to investigate the mechanisms of right heart remodelling. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Evolutionary Characteristics of Missing Proteins: Insights into the Evolution of Human Chromosomes Related to Missing-Protein-Encoding Genes.

PubMed

Xu, Aishi; Li, Guang; Yang, Dong; Wu, Songfeng; Ouyang, Hongsheng; Xu, Ping; He, Fuchu

2015-12-04

Although the "missing protein" is a temporary concept in C-HPP, the biological information for their "missing" could be an important clue in evolutionary studies. Here we classified missing-protein-encoding genes into two groups, the genes encoding PE2 proteins (with transcript evidence) and the genes encoding PE3/4 proteins (with no transcript evidence). These missing-protein-encoding genes distribute unevenly among different chromosomes, chromosomal regions, or gene clusters. In the view of evolutionary features, PE3/4 genes tend to be young, spreading at the nonhomology chromosomal regions and evolving at higher rates. Interestingly, there is a higher proportion of singletons in PE3/4 genes than the proportion of singletons in all genes (background) and OTCSGs (organ, tissue, cell type-specific genes). More importantly, most of the paralogous PE3/4 genes belong to the newly duplicated members of the paralogous gene groups, which mainly contribute to special biological functions, such as "smell perception". These functions are heavily restricted into specific type of cells, tissues, or specific developmental stages, acting as the new functional requirements that facilitated the emergence of the missing-protein-encoding genes during evolution. In addition, the criteria for the extremely special physical-chemical proteins were first set up based on the properties of PE2 proteins, and the evolutionary characteristics of those proteins were explored. Overall, the evolutionary analyses of missing-protein-encoding genes are expected to be highly instructive for proteomics and functional studies in the future.

[Genetic instability of probiotic characteristics in the Bifidobacterium longum subsp. longum B379M strain during cultivation and maintenance].

PubMed

Averina, O V; Nezametdinova, V Z; Alekseeva, M G; Danilenko, V N

2012-11-01

The stability of inheriting several genes in the Russian commercial strain Bifidobacterium longum subsp. longum B379M during cultivation and maintenance under laboratory conditions has been studied. The examined genes code for probiotic characteristics, such as utilization of several sugars (lacA2 gene, encoding beta-galactosidase; ara gene, encoding arabinosidase; and galA gene, encoding arabinogalactan endo-beta-galactosidase); synthesis of bacteriocins (lans gene, encoding lanthionine synthetase); and mobile gene tet(W), conferring resistance to the antibiotic tetracycline. The other gene families studied include the genes responsible for signal transduction and adaptation to stress conditions in the majority of bacteria (serine/threonine protein kinases and the toxin-antitoxin systems of MazEF and RelBE types) and transcription regulators (genes encoding WhiB family proteins). Genomic DNA was analyzed by PCR using specially selected primers. A loss of the genes galA and tet(W) has been shown. It is proposed to expand the requirements on probiotic strains, namely, to control retention of the key probiotic genes using molecular biological methods.

Isolated gene encoding an enzyme with UDP-glucose pyrophosphorylase and phosphoglucomutase activities from Cyclotella cryptica

DOEpatents

Jarvis, Eric E.; Roessler, Paul G.

1999-01-01

The present invention relates to a cloned gene which encodes an enzyme, the purified enzyme, and the applications and products resulting from the use of the gene and enzyme. The gene, isolated from Cyclotella cryptica, encodes a multifunctional enzyme that has both UDP-glucose pyrophosphorylase and phosphoglucomutase activities.

Human Genomic Signatures of Brain Oscillations During Memory Encoding.

PubMed

Berto, Stefano; Wang, Guang-Zhong; Germi, James; Lega, Bradley C; Konopka, Genevieve

2018-05-01

Memory encoding is an essential step for all learning. However, the genetic and molecular mechanisms underlying human memory encoding remain poorly understood, and how this molecular framework permits the emergence of specific patterns of brain oscillations observed during mnemonic processing is unknown. Here, we directly compare intracranial electroencephalography recordings from the neocortex in individuals performing an episodic memory task with human gene expression from the same areas. We identify genes correlated with oscillatory memory effects across 6 frequency bands. These genes are enriched for autism-related genes and have preferential expression in neurons, in particular genes encoding synaptic proteins and ion channels, supporting the idea that the genes regulating voltage gradients are involved in the modulation of oscillatory patterns during successful memory encoding across brain areas. Memory-related genes are distinct from those correlated with other forms of cognitive processing and resting state fMRI. These data are the first to identify correlations between gene expression and active human brain states as well as provide a molecular window into memory encoding oscillations in the human brain.

Subnanometer structure of an asymmetric model membrane: Interleaflet coupling influences domain properties

DOE PAGES

Heberle, Frederick A.; Marquardt, Drew; Doktorova, Milka; ...

2016-04-29

Cell membranes possess a complex three-dimensional architecture, including nonrandom lipid lateral organization within the plane of a bilayer leaflet, and compositional asymmetry between the two leaflets. As a result, delineating the membrane structure–function relationship has been a highly challenging task. Even in simplified model systems, the interactions between bilayer leaflets are poorly understood, due in part to the difficulty of preparing asymmetric model membranes that are free from the effects of residual organic solvent or osmotic stress. To address these problems, we have modified a technique for preparing asymmetric large unilamellar vesicles (aLUVs) via cyclodextrin-mediated lipid exchange in order tomore » produce tensionless, solvent-free aLUVs suitable for a range of biophysical studies. Leaflet composition and structure were characterized using isotopic labeling strategies, which allowed us to avoid the use of bulky labels. NMR and gas chromatography provided precise quantification of the extent of lipid exchange and bilayer asymmetry, while small-angle neutron scattering (SANS) was used to resolve bilayer structural features with subnanometer resolution. Isotopically asymmetric POPC vesicles were found to have the same bilayer thickness and area per lipid as symmetric POPC vesicles, demonstrating that the modified exchange protocol preserves native bilayer structure. Partial exchange of DPPC into the outer leaflet of POPC vesicles produced chemically asymmetric vesicles with a gel/fluid phase-separated outer leaflet and a uniform, POPC-rich inner leaflet. SANS was able to separately resolve the thicknesses and areas per lipid of coexisting domains, revealing reduced lipid packing density of the outer leaflet DPPC-rich phase compared to typical gel phases. Lastly, our finding that a disordered inner leaflet can partially fluidize ordered outer leaflet domains indicates some degree of interleaflet coupling, and invites speculation on a role for bilayer asymmetry in modulating membrane lateral organization.« less

An assessment of nutritional information in oral health education leaflets.

PubMed

Morgan, M Z; McFarlane, E; Stewart, K F; Hunter, M L; Fairchild, R M

2010-06-01

Dental caries prevalence in UK children remains high and obesity, closely linked to Type 2 diabetes, is rising. Literature suggests that dentists may not give dietary advice due to a lack of clear and consistent guidelines. The aim of the study was to determine whether oral health education leaflets with a food and nutritional focus conform to existing UK national nutritional guidelines from the Department of Health (DoH), the Food Standards Agency (FSA) and the Committee on Medical Aspects of Food and Nutrition Policy (COMA). A sample of 30 information leaflets, aimed at parents and children aged 3-16 years, was sourced during the winter of 2005-2006. A qualitative content analysis was carried out to identify key recommendations on type, frequency and quantity of food and drink and general diet-related health advice. Most leaflets (21) promoted milk and water in agreement with nutritional guidelines. Timing of sugary food and drink to mealtimes (25) and decreasing frequency of 'sugary' e.g. non-milk extrinsic (NME) sugar containing foods (22) and drinks (25) reflected guidelines. Inconsistencies were, however, recorded in the leaflets. Five leaflets advised that frequency of consumption rather than the amount of sugary food or drink was important for oral health. This conflicts with nutritional guidelines, aimed at tackling obesity, to decrease both amount and frequency. There was conflicting advice on healthy snacks. Crisps were presented as 'healthy' by two leaflets; another two advised against snacking on dried fruit, conflicting with FSA guidelines that dried fruit contributes to "5 a day". Sixteen leaflets promoted cheese as 'healthy' with no limits on portion size; this could conflict with nutritional guidelines associated with percentage energy contribution of saturated fat to the diet. While there was agreement between leaflet content and nutritional guidelines, there were inconsistencies. Dental professionals should acknowledge these when selecting leaflets for lay dissemination.

Consent information leaflets – readable or unreadable?

PubMed Central

Graham, Caroline; Reynard, John M; Turney, Benjamin W

2016-01-01

Objective The objective of this article is to assess the readability of leaflets about urological procedures provided by the British Association of Urological Surgeons (BAUS) to evaluate their suitability for providing information. Methods Information leaflets were assessed using three measures of readability: Flesch Reading Ease, Flesch-Kincaid and Simple Measure of Gobbledygook (SMOG) grade formulae. The scores were compared with national literacy statistics. Results Relatively good readability was demonstrated using the Flesch Reading Ease (53.4–60.1) and Flesch-Kincaid Grade Level (6.5–7.6) methods. However, the average SMOG index (14.0–15.0) for each category suggests that the majority of the leaflets are written above the reading level of an 18-year-old. Using national literacy statistics, at least 43% of the population will have significant difficultly understanding the majority of these leaflets. Conclusions The results suggest that comprehension of the leaflets provided by the BAUS is likely to be poor. These leaflets may be used as an adjunct to discussion but it is essential to ensure that all the information necessary to make an informed decision has been conveyed in a way that can be understood by the patient. PMID:27867520

Characterizing the Collagen Fiber Orientation in Pericardial Leaflets Under Mechanical Loading Conditions

PubMed Central

Alavi, S. Hamed; Ruiz, Victor; Krasieva, Tatiana; Botvinick, Elliot L.; Kheradvar, Arash

2014-01-01

When implanted inside the body, bioprosthetic heart valve leaflets experience a variety of cyclic mechanical stresses such as shear stress due to blood flow when the valve is open, flexural stress due to cyclic opening and closure of the valve, and tensile stress when the valve is closed. These types of stress lead to a variety of failure modes. In either a natural valve leaflet or a processed pericardial tissue leaflet, collagen fibers reinforce the tissue and provide structural integrity such that the very thin leaflet can stand enormous loads related to cyclic pressure changes. The mechanical response of the leaflet tissue greatly depends on collagen fiber concentration, characteristics, and orientation. Thus, understating the microstructure of pericardial tissue and its response to dynamic loading is crucial for the development of more durable heart valve, and computational models to predict heart valves’ behavior. In this work, we have characterized the 3D collagen fiber arrangement of bovine pericardial tissue leaflets in response to a variety of different loading conditions under Second-Harmonic Generation Microscopy. This real-time visualization method assists in better understanding of the effect of cyclic load on collagen fiber orientation in time and space. PMID:23180029

Iatrogenic Aortic Valve Perforation after Ventricular Septal Defect Repair

PubMed Central

Ren, Chonglei; Wang, Mingyan; Wang, Yao; Gao, Changqing

2017-01-01

Iatrogenic aortic valve (AV) perforation during non-aortic cardiac operations is a rare complication. The suture-related inadvertent injury to an AV leaflet can produce leaflet perforation with aortic regurgitation after ventricular septal defect repair (VSDR). We report three consecutive patients who had iatrogenic aortic leaflet perforation during VSDR in other hospitals and referred to our hospital for reoperation. In all three cases, the perforated AV leaflets were preserved and repaired by autologous pericardial patch or direct local closure. PMID:29057770

Development of Prescription Drug Information Leaflets: Impact of Cognitive Effort and Patient Involvement on Prescription Medication Information Processing.

PubMed

Patel, Harshali K; Bapat, Shweta S; Bhansali, Archita H; Sansgiry, Sujit S

2018-01-01

The objective of this study was to develop a one-page (1-page) prescription drug information leaflet (PILs) and assess their impact on the information processing variables, across 2 levels of patient involvement. One-page PILs were developed using cognitive principles to lower mental effort and improve comprehension. An experimental, 3 × 2 repeated measures study was conducted to determine the impact of cognitive effort, manipulated using leaflet type on comprehension across 2 levels (high/low) of patient involvement. Adults (≥18 years) in a university setting in Houston were recruited for the study. Each participant was exposed to 3 different types of prescription drug information leaflet (the current practice, preexisting 1-page text-only, and 1-page PILs) for the 3 drugs (Celebrex, Ventolin HFA, Prezista) for a given involvement scenario. A prevalidated survey instrument was used to measure product knowledge, attitude toward leaflet, and intention to read. Multivariate analysis of variance indicated significant positive effect of cognitive effort, involvement, and their interaction effect across all measured variables. Mean scores for product knowledge, attitude toward leaflet, and intention to read were highest for PILs ( P < .001), indicating that PILs exerted lowest cognitive effort. Univariate and post hoc analysis indicate that product knowledge significantly increases with high involvement. Patients reading PILs have higher comprehension compared with the current practice and text-only prototype leaflets evaluated. Higher levels of involvement further improve participant knowledge about the drug, increase their intention to read the leaflet, and change their attitude toward the leaflet. Implementation of PILs would improve information processing for consumers by reducing their cognitive effort.

Acute Mitral Valve Dysfunction Due to Escape of Prosthetic Mechanical Leaflet and Peripheral Leaftlet Embolization.

PubMed

Calik, Eyup Serhat; Limandal, Husnu Kamil; Arslan, Umit; Tort, Mehmet; Yildiz, Ziya; Bayram, Ednan; Dag, Ozgur; Kaygin, Mehmet Ali; Erkut, Bilgehan

2015-12-14

Leaflet escape of prosthetic valve is rare but potentially life threatening. Early diagnosis is essential on account of avoiding mortality, and emergency surgical correction is compulsory. This complication has previously been reported for both monoleaflet and bileaflet valve models. A 30-year-old man who had undergone mitral valve replacement with a bileaflet valve 8 years prior at another center was admitted with acute-onset with cardiogenic shock as an emergency case. Transthoracic echocardiograms showed acute-starting severe mitral regurgitation associated with prosthetic mitral valve. There was a suspicious finding of a single prosthetic mitral leaflet. But the problem related with the valve wasn't specifically determined. The patient underwent emergent surgery for replacement of the damaged prosthetic valves immediately. There was no tissue impingement and thrombosis, one of the two leaflets was absent, and there were no signs of endocarditis or pannus formation in the prosthetic valve. The missing leaflet could not be found within the cardiac cavity. The abdominal fluoroscopic study and plain radiography were unable to detect the escaped leaflet during surgery. The damaged valve was removed and a replacement 29 mm bileaflet mechanical valve was inserted by right lateral thoracotomy. After post-operative week one, the abdominal computed tomography scan and the ultrasound showed the escaped leaflet in the left femoral artery. Fifteen days after the surgery the escaped leaflet was removed safely from the left femoral artery and the patient made a complete recovery. The escaped leaflet showed a fracture of one of the pivot systems caused by structural failure. Early cardiac surgery should be applied because of life-threatening problems.

Readability Analysis of the Package Leaflets for Biological Medicines Available on the Internet Between 2007 and 2013: An Analytical Longitudinal Study

PubMed Central

2016-01-01

Background The package leaflet included in the packaging of all medicinal products plays an important role in the transmission of medicine-related information to patients. Therefore, in 2009, the European Commission published readability guidelines to try to ensure that the information contained in the package leaflet is understood by patients. Objective The main objective of this study was to calculate and compare the readability levels and length (number of words) of the package leaflets for biological medicines in 2007, 2010, and 2013. Methods The sample of this study included 36 biological medicine package leaflets that were downloaded from the European Medicines Agency website in three different years: 2007, 2010, and 2013. The readability of the selected package leaflets was obtained using the following readability formulas: SMOG grade, Flesch-Kincaid grade level, and Szigriszt’s perspicuity index. The length (number of words) of the package leaflets was also measured. Afterwards, the relationship between these quantitative variables (three readability indexes and length) and categorical (or qualitative) variables were analyzed. The categorical variables were the year when the package leaflet was downloaded, the package leaflet section, type of medicine, year of authorization of biological medicine, and marketing authorization holder. Results The readability values of all the package leaflets exceeded the sixth-grade reading level, which is the recommended value for health-related written materials. No statistically significant differences were found between the three years of study in the readability indexes, although differences were observed in the case of the length (P=.002), which increased over the study period. When the relationship between readability indexes and length and the other variables was analyzed, statistically significant differences were found between package leaflet sections (P<.001) and between the groups of medicine only with regard to the length over the three studied years (P=.002 in 2007, P=.007 in 2010, P=.009 in 2013). Linear correlation was observed between the readability indexes (SMOG grade and Flesch-Kincaid grade level: r2=.92; SMOG grade and Szigriszt’s perspicuity index: r2=.81; Flesch-Kincaid grade level and Szigriszt’s perspicuity index: r2=.95), but not between the readability indexes and the length (length and SMOG grade: r2=.05; length and Flesch-Kincaid grade level: r2=.03; length and Szigriszt’s perspicuity index: r2=.02). Conclusions There was no improvement in the readability of the package leaflets studied between 2007 and 2013 despite the European Commission’s 2009 guideline on the readability of package leaflets. The results obtained from the different readability formulas coincided from a qualitative point of view. Efforts to improve the readability of package leaflets for biological medicines are required to promote the understandability and accessibility of this online health information by patients and thereby contribute to the appropriate use of medicines and medicine safety. PMID:27226241

Readability Analysis of the Package Leaflets for Biological Medicines Available on the Internet Between 2007 and 2013: An Analytical Longitudinal Study.

PubMed

Piñero-López, María Ángeles; Modamio, Pilar; Lastra, Cecilia F; Mariño, Eduardo L

2016-05-25

The package leaflet included in the packaging of all medicinal products plays an important role in the transmission of medicine-related information to patients. Therefore, in 2009, the European Commission published readability guidelines to try to ensure that the information contained in the package leaflet is understood by patients. The main objective of this study was to calculate and compare the readability levels and length (number of words) of the package leaflets for biological medicines in 2007, 2010, and 2013. The sample of this study included 36 biological medicine package leaflets that were downloaded from the European Medicines Agency website in three different years: 2007, 2010, and 2013. The readability of the selected package leaflets was obtained using the following readability formulas: SMOG grade, Flesch-Kincaid grade level, and Szigriszt's perspicuity index. The length (number of words) of the package leaflets was also measured. Afterwards, the relationship between these quantitative variables (three readability indexes and length) and categorical (or qualitative) variables were analyzed. The categorical variables were the year when the package leaflet was downloaded, the package leaflet section, type of medicine, year of authorization of biological medicine, and marketing authorization holder. The readability values of all the package leaflets exceeded the sixth-grade reading level, which is the recommended value for health-related written materials. No statistically significant differences were found between the three years of study in the readability indexes, although differences were observed in the case of the length (P=.002), which increased over the study period. When the relationship between readability indexes and length and the other variables was analyzed, statistically significant differences were found between package leaflet sections (P<.001) and between the groups of medicine only with regard to the length over the three studied years (P=.002 in 2007, P=.007 in 2010, P=.009 in 2013). Linear correlation was observed between the readability indexes (SMOG grade and Flesch-Kincaid grade level: r(2)=.92; SMOG grade and Szigriszt's perspicuity index: r(2)=.81; Flesch-Kincaid grade level and Szigriszt's perspicuity index: r(2)=.95), but not between the readability indexes and the length (length and SMOG grade: r(2)=.05; length and Flesch-Kincaid grade level: r(2)=.03; length and Szigriszt's perspicuity index: r(2)=.02). There was no improvement in the readability of the package leaflets studied between 2007 and 2013 despite the European Commission's 2009 guideline on the readability of package leaflets. The results obtained from the different readability formulas coincided from a qualitative point of view. Efforts to improve the readability of package leaflets for biological medicines are required to promote the understandability and accessibility of this online health information by patients and thereby contribute to the appropriate use of medicines and medicine safety.

Melanocyte pigmentation stiffens murine cardiac tricuspid valve leaflet

PubMed Central

Balani, Kantesh; Brito, Flavia C.; Kos, Lidia; Agarwal, Arvind

2009-01-01

Pigmentation of murine cardiac tricuspid valve leaflet is associated with melanocyte concentration, which affects its stiffness. Owing to its biological and viscoelastic nature, estimation of the in situ stiffness measurement becomes a challenging task. Therefore, quasi-static and nanodynamic mechanical analysis of the leaflets of the mouse tricuspid valve is performed in the current work. The mechanical properties along the leaflet vary with the degree of pigmentation. Pigmented regions of the valve leaflet that contain melanocytes displayed higher storage modulus (7–10 GPa) than non-pigmented areas (2.5–4 GPa). These results suggest that the presence of melanocytes affects the viscoelastic properties of the mouse atrioventricular valves and are important for their proper functioning in the organism. PMID:19586956

Isolated gene encoding an enzyme with UDP-glucose pyrophosphorylase and phosphoglucomutase activities from Cyclotella cryptica

DOEpatents

Jarvis, E.E.; Roessler, P.G.

1999-07-27

The present invention relates to a cloned gene which encodes an enzyme, the purified enzyme, and the applications and products resulting from the use of the gene and enzyme. The gene, isolated from Cyclotella cryptica, encodes a multifunctional enzyme that has both UDP-glucose pyrophosphorylase and phosphoglucomutase activities. 8 figs.

Phototropic leaf movements and photosynthetic performance in an amphibious fern, Marsilea quadrifolia.

PubMed

Kao, Wen-Yuan; Lin, Bai-Ling

2010-09-01

Diurnal phototropism has not been reported in ferns. In this study we found that the four leaflets of the amphibious fern Marsilea quadrifolia are capable of adjusting their leaflet angle and leaflet azimuth in response to changes in the position of the sun's direct beam, exhibiting more diaphototropic movements (orienting the plane of the lamina perpendicular to incident light) in the morning and late afternoon, and more paraphototropic movements (orienting the plane of the lamina parallel to incident light) at noon. In addition, by cutting off the leaflet lamina and covering portions of leaflets with black tape, the junction between the leaflet and petiole was found to be responsible for light reception. Among the light spectrum investigated, blue light was the most effective at inducing diaphototropism. The role of diurnal phototropism in enhancing carbon return and ameliorating photoinhibition was also evaluated. It was concluded that diurnal phototropic leaf movement represents one of the plastic responses enabling this amphibious fern to grow under terrestrial conditions.

Late leaflet fracture and embolization of a Duromedics mitral prosthesis.

PubMed

Sudo, K; Sasagawa, N; Ide, H; Nunokawa, M; Fujiki, T; Tonari, K

2000-08-01

A case of leaflet fracture and embolization of a mitral prosthetic valve is described. A 54-year-old man had received mitral valve replacement with an Edwards-Duromedics 29M prosthetic valve, at 10 years ago. Emergency mitral valve replacement was performed because the patient had severe congestive left heart failure with severe acute mitral regurgitation caused by a fracture in one of the mitral valve leaflets. The leaflet, which was fractured into 2 pieces, was removed from the right common iliac artery at 3 months after valve replacement. Visual inspection revealed that the leaflet contained a midline fracture. The fracture originated within a cavitary erosion pit near the major radius of the leaflet. The patient recovered from acute renal failure, requiring hemodialysis for 80 days, and is currently without complaints. We have used a Duromedics mitral valve in 11 patients, from April 1987 to April 1988. No subsequent valve failure has occurred. The diagnosis, treatment and cause of a mechanical valve fracture are discussed.

Evolutionary analysis of hydrophobin gene family in two wood-degrading basidiomycetes, Phlebia brevispora and Heterobasidion annosum s.l.

PubMed Central

2013-01-01

Background Hydrophobins are small secreted cysteine-rich proteins that play diverse roles during different phases of fungal life cycle. In basidiomycetes, hydrophobin-encoding genes often form large multigene families with up to 40 members. The evolutionary forces driving hydrophobin gene expansion and diversification in basidiomycetes are poorly understood. The functional roles of individual genes within such gene families also remain unclear. The relationship between the hydrophobin gene number, the genome size and the lifestyle of respective fungal species has not yet been thoroughly investigated. Here, we present results of our survey of hydrophobin gene families in two species of wood-degrading basidiomycetes, Phlebia brevispora and Heterobasidion annosum s.l. We have also investigated the regulatory pattern of hydrophobin-encoding genes from H. annosum s.s. during saprotrophic growth on pine wood as well as on culture filtrate from Phlebiopsis gigantea using micro-arrays. These data are supplemented by results of the protein structure modeling for a representative set of hydrophobins. Results We have identified hydrophobin genes from the genomes of two wood-degrading species of basidiomycetes, Heterobasidion irregulare, representing one of the microspecies within the aggregate H. annosum s.l., and Phlebia brevispora. Although a high number of hydrophobin-encoding genes were observed in H. irregulare (16 copies), a remarkable expansion of these genes was recorded in P. brevispora (26 copies). A significant expansion of hydrophobin-encoding genes in other analyzed basidiomycetes was also documented (1–40 copies), whereas contraction through gene loss was observed among the analyzed ascomycetes (1–11 copies). Our phylogenetic analysis confirmed the important role of gene duplication events in the evolution of hydrophobins in basidiomycetes. Increased number of hydrophobin-encoding genes appears to have been linked to the species’ ecological strategy, with the non-pathogenic fungi having increased numbers of hydrophobins compared with their pathogenic counterparts. However, there was no significant relationship between the number of hydrophobin-encoding genes and genome size. Furthermore, our results revealed significant differences in the expression levels of the 16 H. annosum s.s. hydrophobin-encoding genes which suggest possible differences in their regulatory patterns. Conclusions A considerable expansion of the hydrophobin-encoding genes in basidiomycetes has been observed. The distribution and number of hydrophobin-encoding genes in the analyzed species may be connected to their ecological preferences. Results of our analysis also have shown that H. annosum s.l. hydrophobin-encoding genes may be under positive selection. Our gene expression analysis revealed differential expression of H. annosum s.s. hydrophobin genes under different growth conditions, indicating their possible functional diversification. PMID:24188142

Glutathione S-transferase-encoding gene as a potential probe for environmental bacterial isolates capable of degrading polycyclic aromatic hydrocarbons.

PubMed Central

Lloyd-Jones, G; Lau, P C

1997-01-01

Homologs of the glutathione S-transferase (GST)-encoding gene were identified in a collection of aromatic hydrocarbon-degrading Sphingomonas spp. isolated from New Zealand, Antarctica, and the United States by using PCR primers designed from the GST-encoding gene of Sphingomonas paucimobilis EPA505. Sequence analysis of PCR fragments generated from these isolates and of the GST gene amplified from DNA extracted from polycyclic aromatic hydrocarbon (PAH)-contaminated soil revealed a high degree of conservation, which may make the GST-encoding gene a potentially useful marker for PAH-degrading bacteria. PMID:9251217

Enterotoxin-encoding genes in Staphylococcus spp. from bulk goat milk.

PubMed

Lyra, Daniele G; Sousa, Francisca G C; Borges, Maria F; Givisiez, Patrícia E N; Queiroga, Rita C R E; Souza, Evandro L; Gebreyes, Wondwossen A; Oliveira, Celso J B

2013-02-01

Although Staphylococcus aureus has been implicated as the main Staphylococcus species causing human food poisoning, recent studies have shown that coagulase-negative Staphylococcus could also harbor enterotoxin-encoding genes. Such organisms are often present in goat milk and are the most important mastitis-causing agents. Therefore, this study aimed to investigate the occurrence of enterotoxin-encoding genes among coagulase-positive (CoPS) and coagulase-negative (CoNS) staphylococci isolated from raw goat milk produced in the semi-arid region of Paraiba, the most important region for goat milk production in Brazil. Enterotoxin-encoding genes were screened in 74 staphylococci isolates (30 CoPS and 44 CoNS) by polymerase chain reaction targeting the genes sea, seb, sec, sed, see, seg, seh, and sei. Enterotoxin-encoding genes were found in nine (12.2%) isolates, and four different genes (sea, sec, seg, and sei) were identified amongst the isolates. The most frequent genes were seg and sei, which were often found simultaneously in 44.5% of the isolates. The gene sec was the most frequent among the classical genes, and sea was found only in one isolate. All CoPS isolates (n=7) harboring enterotoxigenic genes were identified as S. aureus. The two coagulase-negative isolates were S. haemolyticus and S. hominis subsp. hominis and they harbored sei and sec genes, respectively. A higher frequency of enterotoxin-encoding genes was observed amongst CoPS (23.3%) than CoNS (4.5%) isolates (p<0.05), reinforcing the importance of S. aureus as a potential foodborne agent. However, the potential risk posed by CoNS in goat milk should not be ignored because it has a higher occurrence in goat milk and enterotoxin-encoding genes were detected in some isolates.

Developing leaflets to give dental health advice to Aboriginal families with young children.

PubMed

Blinkhorn, Fiona; Wallace, Janet; Smith, Leanne; Blinkhorn, Anthony S

2014-08-01

Dental caries (decay) is a serious problem for young Aboriginal children, causing pain and stress. Treatment often involves extraction of teeth under a general anaesthetic. However, dental caries can be prevented by reducing the frequency of sugar consumption and brushing teeth twice a day with fluoride toothpaste. Such straightforward advice could be given to families by Aboriginal Health Workers who are trusted by their communities and have an existing advisory role. This paper reports on the development of dental health advice leaflets for use in Aboriginal communities. An Aboriginal reference panel was recruited to comment on dental health advice leaflets prepared by an Aboriginal graphic designer. The panel was asked to consider the design, cultural appropriateness and practicality of the leaflets. Comments were collected through email and face-to-face discussions, which were collated and the leaflets altered accordingly. The advice from the panel resulted in greater use of pictures. For example large green ticks and red crosses highlighted healthy and unhealthy behaviours, respectively. The tooth brushing leaflet was amended to emphasise the safe storage of toothpaste in order to keep it out of reach of young children. The panel stated that all leaflets should incorporate the Aboriginal flag, and proposed that fridge magnets might be beneficial as all family members would benefit from seeing the messages every day. The consultation process refined dental advice leaflets to reflect the views of an Aboriginal Reference Panel, in terms of design, cultural competence and practicality. © 2014 FDI World Dental Federation.

Evaluation of written prescription information provided in community pharmacies: a study in eight states.

PubMed

Svarstad, Bonnie L; Bultman, Dara C; Mount, Jeanine K; Tabak, Ellen R

2003-01-01

To develop three tools for assessing the quality of written information provided with new prescriptions in community pharmacies and to identify pharmacy, pharmacist, and patient characteristics associated with the dissemination and quality of that information. Observational study. Regression techniques were used to analyze the influence of pharmacy, pharmacist, and shopper (acting as patient) characteristics on outcome measures. Trained shoppers (acting as patients) visited 306 randomly selected pharmacies in 8 states. Each shopper presented three prescriptions, answered questions according to a standard scenario, accepted the information offered, and paid for the prescriptions. Percentage of shoppers receiving any written information; quality of written information as judged by an expert panel using explicit criteria. Shoppers received an information leaflet with 87% of the 918 prescriptions dispensed. Although most leaflets provided unbiased information, leaflet length and quality of information varied greatly. A majority of leaflets did not include adequate information about contraindications, precautions, and how to avoid harm. Shoppers were more likely to receive leaflets in chain pharmacies and pharmacies with more staff. Information quality also was higher in chain pharmacies. Shopper and pharmacist demographic characteristics were unrelated to the level or quality of written information after controlling for other factors. The provision of patient leaflets is becoming a routine practice in the states studied. However, most leaflets do not meet quality criteria. It is important for pharmacists to become familiar with criteria for evaluating these leaflets and to take necessary action to improve their quality.

Three copies of a single protein II-encoding sequence in the genome of Neisseria gonorrhoeae JS3: evidence for gene conversion and gene duplication.

PubMed

van der Ley, P

1988-11-01

Gonococci express a family of related outer membrane proteins designated protein II (P.II). These surface proteins are subject to both phase variation and antigenic variation. The P.II gene repertoire of Neisseria gonorrhoeae strain JS3 was found to consist of at least ten genes, eight of which were cloned. Sequence analysis and DNA hybridization studies revealed that one particular P.II-encoding sequence is present in three distinct, but almost identical, copies in the JS3 genome. These genes encode the P.II protein that was previously identified as P.IIc. Comparison of their sequences shows that the multiple copies of this P.IIc-encoding gene might have been generated by both gene conversion and gene duplication.

Prosthetic Mitral Valve Leaflet Escape

PubMed Central

Kim, Darae; Hun, Sin Sang; Cho, In-Jeong; Shim, Chi-Young; Ha, Jong-Won; Chung, Namsik; Ju, Hyun Chul; Sohn, Jang Won

2013-01-01

Leaflet escape of prosthetic valve is rare but potentially life threatening. It is essential to make timely diagnosis in order to avoid mortality. Transesophageal echocardiography and cinefluoroscopy is usually diagnostic and the location of the missing leaflet can be identified by computed tomography (CT). Emergent surgical correction is mandatory. We report a case of fractured escape of Edward-Duromedics mitral valve 27 years after the surgery. The patient presented with symptoms of acute decompensated heart failure and cardiogenic shock. She was instantly intubated and mechanically ventilated. After prompt evaluation including transthoracic echocardiography and CT, the escape of the leaflet was confirmed. The patient underwent emergent surgery for replacement of the damaged prosthetic valves immediately. Eleven days after the surgery, the dislodged leaflet in iliac artery was removed safely and the patient recovered well. PMID:23837121

Aberrant tendinous chords with tethering of the tricuspid leaflets: a congenital anomaly causing severe tricuspid regurgitation.

PubMed

Kobza, R; Kurz, D J; Oechslin, E N; Prêtre, R; Zuber, M; Vogt, P; Jenni, R

2004-03-01

To define the entity of tricuspid regurgitation caused by tethering of the tricuspid valve leaflets by aberrant tendinous chords. Retrospective study. Tertiary care centre (university teaching hospital). 10 patients with unexplained severe tricuspid regurgitation. The last 13 500 echocardiographic studies from our facility were reviewed to identify patients with severe unexplained tricuspid regurgitation. Tethering was defined by the presence of aberrant tendinous chords to the tricuspid valve leaflets limiting the mobility of the tricuspid leaflet and resulting in incomplete coaptation and apical displacement of the regurgitant jet origin. Aberrant tendinous chords were defined as those inserting at the clear zone of the tricuspid leaflet and not originating from the papillary muscle. Patients fulfilling the diagnostic criteria for Ebstein's anomaly were excluded. 10 patients with aberrant tendinous chords tethering one or more tricuspid valve leaflets were identified. There were short non-aberrant tendinous chords in seven patients, five of whom also had right ventricular or tricuspid annulus dilatation. Tethering of the tricuspid valve leaflets by aberrant tendinous chords can be the sole mechanism of congenital tricuspid regurgitation. It is often associated with short non-aberrant tendinous chords, which may develop secondary to right ventricular or tricuspid annulus dilatation. Awareness of tethering as a cause of tricuspid regurgitation may be important in planning reconstructive surgery.

Promoting chlamydia screening with posters and leaflets in general practice--a qualitative study.

PubMed

Freeman, Elaine; Howell-Jones, Rebecca; Oliver, Isabel; Randall, Sarah; Ford-Young, William; Beckwith, Philippa; McNulty, Cliodna

2009-10-12

General practice staff are reluctant to discuss sexual health opportunistically in all consultations. Health promotion materials may help alleviate this barrier. Chlamydia screening promotion posters and leaflets, produced by the English National Chlamydia Screening Programme (NCSP), have been available to general practices, through local chlamydia screening offices, since its launch. In this study we explored the attitudes of general practice staff to these screening promotional materials, how they used them, and explored other promotional strategies to encourage chlamydia screening. Twenty-five general practices with a range of screening rates, were purposively selected from six NCSP areas in England. In focus groups doctors, nurses, administrative staff and receptionists were encouraged to discuss candidly their experiences about their use and opinions of posters, leaflets and advertising to promote chlamydia screening. Researchers observed whether posters and leaflets were on display in reception and/or waiting areas. Data were collected and analysed concurrently using a stepwise framework analytical approach. Although two-thirds of screening practices reported that they displayed posters and leaflets, they were not prominently displayed in most practices. Only a minority of practices reported actively using screening promotional materials on an ongoing basis. Most staff in all practices were not following up the advertising in posters and leaflets by routinely offering opportunistic screening to their target population. Some staff in many practices thought posters and leaflets would cause offence or embarrassment to their patients. Distribution of chlamydia leaflets by receptionists was thought to be inappropriate by some practices, as they thought patients would be offended when being offered a leaflet in a public area. Practice staff suggested the development of pocket-sized leaflets. The NCSP should consider developing a range of more discrete but eye catching posters and small leaflets specifically to promote chlamydia screening in different scenarios within general practice; coordinators should audit their use. Practice staff need to discuss, with their screening co-ordinator, how different practice staff can promote chlamydia screening most effectively using the NCSP promotional materials, and change them regularly so that they do not loose their impact. Education to change all practice staff's attitudes towards sexual health is needed to reduce their worries about displaying the chlamydia materials, and how they may follow up the advertising up with a verbal offer of screening opportunistically to 15-24 year olds whenever they visit the practice.

Promoting chlamydia screening with posters and leaflets in general practice - a qualitative study

PubMed Central

Freeman, Elaine; Howell-Jones, Rebecca; Oliver, Isabel; Randall, Sarah; Ford-Young, William; Beckwith, Philippa; McNulty, Cliodna

2009-01-01

Background General practice staff are reluctant to discuss sexual health opportunistically in all consultations. Health promotion materials may help alleviate this barrier. Chlamydia screening promotion posters and leaflets, produced by the English National Chlamydia Screening Programme (NCSP), have been available to general practices, through local chlamydia screening offices, since its launch. In this study we explored the attitudes of general practice staff to these screening promotional materials, how they used them, and explored other promotional strategies to encourage chlamydia screening. Methods Twenty-five general practices with a range of screening rates, were purposively selected from six NCSP areas in England. In focus groups doctors, nurses, administrative staff and receptionists were encouraged to discuss candidly their experiences about their use and opinions of posters, leaflets and advertising to promote chlamydia screening. Researchers observed whether posters and leaflets were on display in reception and/or waiting areas. Data were collected and analysed concurrently using a stepwise framework analytical approach. Results Although two-thirds of screening practices reported that they displayed posters and leaflets, they were not prominently displayed in most practices. Only a minority of practices reported actively using screening promotional materials on an ongoing basis. Most staff in all practices were not following up the advertising in posters and leaflets by routinely offering opportunistic screening to their target population. Some staff in many practices thought posters and leaflets would cause offence or embarrassment to their patients. Distribution of chlamydia leaflets by receptionists was thought to be inappropriate by some practices, as they thought patients would be offended when being offered a leaflet in a public area. Practice staff suggested the development of pocket-sized leaflets. Conclusion The NCSP should consider developing a range of more discrete but eye catching posters and small leaflets specifically to promote chlamydia screening in different scenarios within general practice; coordinators should audit their use. Practice staff need to discuss, with their screening co-ordinator, how different practice staff can promote chlamydia screening most effectively using the NCSP promotional materials, and change them regularly so that they do not loose their impact. Education to change all practice staff's attitudes towards sexual health is needed to reduce their worries about displaying the chlamydia materials, and how they may follow up the advertising up with a verbal offer of screening opportunistically to 15-24 year olds whenever they visit the practice. PMID:19821964

[Expression changes of major outer membrane protein antigens in Leptospira interrogans during infection and its mechanism].

PubMed

Zheng, Linli; Ge, Yumei; Hu, Weilin; Yan, Jie

2013-03-01

To determine expression changes of major outer membrane protein(OMP) antigens of Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai strain Lai during infection of human macrophages and its mechanism. OmpR encoding genes and OmpR-related histidine kinase (HK) encoding gene of L.interrogans strain Lai and their functional domains were predicted using bioinformatics technique. mRNA level changes of the leptospiral major OMP-encoding genes before and after infection of human THP-1 macrophages were detected by real-time fluorescence quantitative RT-PCR. Effects of the OmpR-encoding genes and HK-encoding gene on the expression of leptospiral OMPs during infection were determined by HK-peptide antiserum block assay and closantel inhibitive assays. The bioinformatics analysis indicated that LB015 and LB333 were referred to OmpR-encoding genes of the spirochete, while LB014 might act as a OmpR-related HK-encoding gene. After the spirochete infecting THP-1 cells, mRNA levels of leptospiral lipL21, lipL32 and lipL41 genes were rapidly and persistently down-regulated (P <0.01), whereas mRNA levels of leptospiral groEL, mce, loa22 and ligB genes were rapidly but transiently up-regulated (P<0.01). The treatment with closantel and HK-peptide antiserum partly reversed the infection-based down-regulated mRNA levels of lipL21 and lipL48 genes (P <0.01). Moreover, closantel caused a decrease of the infection-based up-regulated mRNA levels of groEL, mce, loa22 and ligB genes (P <0.01). Expression levels of L.interrogans strain Lai major OMP antigens present notable changes during infection of human macrophages. There is a group of OmpR-and HK-encoding genes which may play a major role in down-regulation of expression levels of partial OMP antigens during infection.

Low literacy and written drug information: information-seeking, leaflet evaluation and preferences, and roles for images.

PubMed

van Beusekom, Mara M; Grootens-Wiegers, Petronella; Bos, Mark J W; Guchelaar, Henk-Jan; van den Broek, Jos M

2016-12-01

Background Low-literate patients are at risk to misinterpret written drug information. For the (co-) design of targeted patient information, it is key to involve this group in determining their communication barriers and information needs. Objective To gain insight into how people with low literacy use and evaluate written drug information, and to identify ways in which they feel the patient leaflet can be improved, and in particular how images could be used. Setting Food banks and an education institution for Dutch language training in the Netherlands. Method Semi-structured focus groups and individual interviews were held with low-literate participants (n = 45). The thematic framework approach was used for analysis to identify themes in the data. Main outcome measure Low-literate people's experience with patient information leaflets, ideas for improvements, and perceptions on possible uses for visuals. Results Patient information leaflets were considered discouraging to use, and information difficult to find and understand. Many rely on alternative information sources. The leaflet should be shorter, and improved in terms of organisation, legibility and readability. Participants thought images could increase the leaflet's appeal, help ask questions, provide an overview, help understand textual information, aid recall, reassure, and even lead to increased confidence, empowerment and feeling of safety. Conclusion Already at the stages of paying attention to the leaflet and maintaining interest in the message, low-literate patients experience barriers in the communication process through written drug information. Short, structured, visual/textual explanations can lower the motivational threshold to use the leaflet, improve understanding, and empower the low-literate target group.

PN FOR CHILDREN - INFORMATION LEAFLET.

PubMed

Riddell, Rebecca; Lewis, Anthony; Tuthill, David

2016-09-01

To produce a leaflet for parents and carers of children receiving parenteral nutrition (PN) explaining:▸ What PN is▸ Why it is given▸ How it will be given▸ Risks & Complications▸ Other useful information▸ Nutrition team contact informationCurrent practice is for the nutrition team pharmacist to give a verbal account of the above information to parents/carers. It was felt that providing this information in a written format would introduce consisitency and allow parents/carers more time to take information on board. An internet search and discussions with other organisations with paediatric gastroenterology specialists was conduted to see if something similar was in existence. A similar information leaflet to what we hoped to produce was not found. Members of the paediatric nutrition team, which included consultants, nurse specialists, pharmacist and dietician, provided input to the type of information that should be included in the information leaflet. A first draft of the leaflet was produced and shown to the parents of current paediatric PN inpatients. Feedback was received and the leaflet updated following consultation with the nutrition team. Production of a very useful information leaflet for parents/carers, containing all the relevant information and detail. The leaflet uses colour and pictures to aid the transfer of information and makes it more attractive to read. The pharmacist is the main point of contact for the paediatric nutrition team and will be the individual responsible for distributing them. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Distribution of the microelastic properties within the human anterior mitral leaflet.

PubMed

Jensen, Anne Skakkebaek; Baandrup, Ulrik; Hasenkam, J Michael; Kundu, Tribikram; Jørgensen, Claus Schiøtt

2006-12-01

Knowledge of the biomechanical properties of the mitral valve leaflets and their relation to histologic structure is of importance for understanding the leaflet movement characteristics under normal and pathologic conditions, but such knowledge is not yet available. The aim of this study was to determine biomechanical properties of the human anterior mitral leaflet on a microscopic scale. We used scanning acoustic microscopy (SAM) to examine the human anterior mitral leaflet. Sections of fixed human anterior mitral leaflet tissue were obtained from postmortem human anterior mitral leaflets (n = 5). We measured the speed of sound (nu(L)) in each histologic layer in three regions-of-interest (ROIs): these were at the annular edge, at the valve midpoint and close to the free edge. nu(L) varied in the three histologic layers (p < 0.01). It was higher in the fibrous layer (1.76 km/s) compared with the atrial layer (1.75 km/s) and ventricular layer (1.73 km/s). Also, nu(L) differed between positions along the length of the annulus-free edge line (p < 0.01), showing a decline from the annular edge (1.76 km/s) to the free edge (1.73 km/s), both as a whole and also within the atrial and the fibrous layer. These results demonstrate that the fibrous layer is stiffer than the atrial and ventricular layer and that the leaflet as a whole and within the atrial and the fibrous layer is stiffer at the annulus part in comparison with those near the free edge. (E-mail: ).

Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes

PubMed Central

Minic, Zoran; Jamet, Elisabeth; San-Clemente, Hélène; Pelletier, Sandra; Renou, Jean-Pierre; Rihouey, Christophe; Okinyo, Denis PO; Proux, Caroline; Lerouge, Patrice; Jouanin, Lise

2009-01-01

Background Different strategies (genetics, biochemistry, and proteomics) can be used to study proteins involved in cell biogenesis. The availability of the complete sequences of several plant genomes allowed the development of transcriptomic studies. Although the expression patterns of some Arabidopsis thaliana genes involved in cell wall biogenesis were identified at different physiological stages, detailed microarray analysis of plant cell wall genes has not been performed on any plant tissues. Using transcriptomic and bioinformatic tools, we studied the regulation of cell wall genes in Arabidopsis stems, i.e. genes encoding proteins involved in cell wall biogenesis and genes encoding secreted proteins. Results Transcriptomic analyses of stems were performed at three different developmental stages, i.e., young stems, intermediate stage, and mature stems. Many genes involved in the synthesis of cell wall components such as polysaccharides and monolignols were identified. A total of 345 genes encoding predicted secreted proteins with moderate or high level of transcripts were analyzed in details. The encoded proteins were distributed into 8 classes, based on the presence of predicted functional domains. Proteins acting on carbohydrates and proteins of unknown function constituted the two most abundant classes. Other proteins were proteases, oxido-reductases, proteins with interacting domains, proteins involved in signalling, and structural proteins. Particularly high levels of expression were established for genes encoding pectin methylesterases, germin-like proteins, arabinogalactan proteins, fasciclin-like arabinogalactan proteins, and structural proteins. Finally, the results of this transcriptomic analyses were compared with those obtained through a cell wall proteomic analysis from the same material. Only a small proportion of genes identified by previous proteomic analyses were identified by transcriptomics. Conversely, only a few proteins encoded by genes having moderate or high level of transcripts were identified by proteomics. Conclusion Analysis of the genes predicted to encode cell wall proteins revealed that about 345 genes had moderate or high levels of transcripts. Among them, we identified many new genes possibly involved in cell wall biogenesis. The discrepancies observed between results of this transcriptomic study and a previous proteomic study on the same material revealed post-transcriptional mechanisms of regulation of expression of genes encoding cell wall proteins. PMID:19149885

[Parenting Renewal. Leaflet and Lessons for Parents of Adolescents.

ERIC Educational Resources Information Center

Clemson Univ., SC. Cooperative Extension Service.

Instructional materials on parenting skills for parents of adolescents are provided, with teaching guides for extension service agents. Organized as a series of five leaflets followed by five corresponding lessons, leaflets for parents concern: (1) a review of parenting skills and an overview of the course of instruction; (2) evolution:…

Diffusion in phospholipid bilayer membranes: dual-leaflet dynamics and the roles of tracer–leaflet and inter-leaflet coupling

PubMed Central

Hill, Reghan J.; Wang, Chih-Ying

2014-01-01

A variety of observations—sometimes controversial—have been made in recent decades when attempting to elucidate the roles of interfacial slip on tracer diffusion in phospholipid membranes. Evans–Sackmann theory (1988) has furnished membrane viscosities and lubrication-film thicknesses for supported membranes from experimentally measured lateral diffusion coefficients. Similar to the Saffman and Delbrück model, which is the well-known counterpart for freely supported membranes, the bilayer is modelled as a single two-dimensional fluid. However, the Evans–Sackman model cannot interpret the mobilities of monotopic tracers, such as individual lipids or rigidly bound lipid assemblies; neither does it account for tracer–leaflet and inter-leaflet slip. To address these limitations, we solve the model of Wang and Hill, in which two leaflets of a bilayer membrane, a circular tracer and supports are coupled by interfacial friction, using phenomenological friction/slip coefficients. This furnishes an exact solution that can be readily adopted to interpret the mobilities of a variety of mosaic elements—including lipids, integral monotopic and polytopic proteins, and lipid rafts—in supported bilayer membranes. PMID:25002822

Hydrothermal Pretreatment of Date Palm (Phoenix dactylifera L.) Leaflets and Rachis to Enhance Enzymatic Digestibility and Bioethanol Potential

PubMed Central

Fang, Chuanji; Cybulska, Iwona; Brudecki, Grzegorz P.; Frankær, Christian Grundahl; Thomsen, Mette Hedegaard

2015-01-01

Date palm residues are one of the most promising lignocellulosic biomass for bioethanol production in the Middle East. In this study, leaflets and rachis were subjected to hydrothermal pretreatment to overcome the recalcitrance of the biomass for enzymatic conversion. Evident morphological, structural, and chemical changes were observed by scanning electron microscopy, X-ray diffraction, and infrared spectroscopy after pretreatment. High glucan (>90% for both leaflets and rachis) and xylan (>75% for leaflets and >79% for rachis) recovery were achieved. Under the optimal condition of hydrothermal pretreatment (210°C/10 min) highly digestible (glucan convertibility, 100% to leaflets, 78% to rachis) and fermentable (ethanol yield, 96% to leaflets, 80% to rachis) solid fractions were obtained. Fermentability test of the liquid fractions proved that no considerable inhibitors to Saccharomyces cerevisiae were produced in hydrothermal pretreatment. Given the high sugar recovery, enzymatic digestibility, and ethanol yield, production of bioethanol by hydrothermal pretreatment could be a promising way of valorization of date palm residues in this region. PMID:26347878

[TECHNIQUES IN MITRAL VALVE REPAIR VIA A MINIMALLY INVASIVE APPROACH].

PubMed

Ito, Toshiaki

2016-03-01

In mitral valve repair via a minimally invasive approach, resection of the leaflet is technically demanding compared with that in the standard approach. For resection and suture repair of the posterior leaflet, premarking of incision lines is recommended for precise resection. As an alternative to resection and suture, the leaflet-folding technique is also recommended. For correction of prolapse of the anterior leaflet, neochordae placement with the loop technique is easy to perform. Premeasurement with transesophageal echocardiography or intraoperative measurement using a replica of artificial chordae is useful to determine the appropriate length of the loops. Fine-tuning of the length of neochordae is possible by adding a secondary fixation point on the leaflet if the loop is too long. If the loop is too short, a CV5 Gore-Tex suture can be passed through the loop and loosely tied several times to stack the knots, with subsequent fixation to the edge of the leaflet. Finally, skill in the mitral valve replacement technique is necessary as a back-up for surgeons who perform minimally invasive mitral valve repair.

Pannus overgrowth after mitral valve replacement with a Carpentier-Edwards pericardial bioprosthesis.

PubMed

Oda, Takeshi; Kato, Seiya; Tayama, Eiki; Fukunaga, Shuji; Akashi, Hidetoshi; Aoyagi, Shigeaki

2009-01-01

A Carpentier-Edwards pericardial (CEP) bioprosthesis was explanted from an 81-year-old woman due to nonstructural dysfunction 9 years after mitral valve replacement. The nonstructural dysfunction produced severe regurgitation in the mitral position. During the surgery, excessive pannus overgrowth was seen on the left ventricular side of the CEP bioprosthesis. Pannus overgrowth was prominent on one leaflet. That leaflet was stiff and shortened due to the excessive overgrowth of pannus. In this patient, the distortion of one leaflet was the main reason for transvalvular leakage of the CEP bioprosthesis in the mitral position. A new CEP bioprosthesis was implanted in the mitral position. Pathological analysis revealed fibrotic pannus with a small amount of cellular material over the leaflets of the resected CEP valve. This change was marked on the distorted leaflet.

The Ebola virus matrix protein VP40 selectively induces vesiculation from phosphatidylserine-enriched membranes.

PubMed

Soni, Smita P; Stahelin, Robert V

2014-11-28

Ebola virus is from the Filoviridae family of viruses and is one of the most virulent pathogens known with ∼ 60% clinical fatality. The Ebola virus negative sense RNA genome encodes seven proteins including viral matrix protein 40 (VP40), which is the most abundant protein found in the virions. Within infected cells VP40 localizes at the inner leaflet of the plasma membrane (PM), binds lipids, and regulates formation of new virus particles. Expression of VP40 in mammalian cells is sufficient to form virus-like particles that are nearly indistinguishable from the authentic virions. However, how VP40 interacts with the PM and forms virus-like particles is for the most part unknown. To investigate VP40 lipid specificity in a model of viral egress we employed giant unilamellar vesicles with different lipid compositions. The results demonstrate VP40 selectively induces vesiculation from membranes containing phosphatidylserine (PS) at concentrations of PS that are representative of the PM inner leaflet content. The formation of intraluminal vesicles was not significantly detected in the presence of other important PM lipids including cholesterol and polyvalent phosphoinositides, further demonstrating PS selectivity. Taken together, these studies suggest that PM phosphatidylserine may be an important component of Ebola virus budding and that VP40 may be able to mediate PM scission. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Regulation of Compound Leaf Development in Medicago truncatula by Fused Compound Leaf1, a Class M KNOX Gene[C][W

PubMed Central

Peng, Jianling; Yu, Jianbin; Wang, Hongliang; Guo, Yingqing; Li, Guangming; Bai, Guihua; Chen, Rujin

2011-01-01

Medicago truncatula is a legume species belonging to the inverted repeat lacking clade (IRLC) with trifoliolate compound leaves. However, the regulatory mechanisms underlying development of trifoliolate leaves in legumes remain largely unknown. Here, we report isolation and characterization of fused compound leaf1 (fcl1) mutants of M. truncatula. Phenotypic analysis suggests that FCL1 plays a positive role in boundary separation and proximal-distal axis development of compound leaves. Map-based cloning indicates that FCL1 encodes a class M KNOX protein that harbors the MEINOX domain but lacks the homeodomain. Yeast two-hybrid assays show that FCL1 interacts with a subset of Arabidopsis thaliana BEL1-like proteins with slightly different substrate specificities from the Arabidopsis homolog KNATM-B. Double mutant analyses with M. truncatula single leaflet1 (sgl1) and palmate-like pentafoliata1 (palm1) leaf mutants show that fcl1 is epistatic to palm1 and sgl1 is epistatic to fcl1 in terms of leaf complexity and that SGL1 and FCL1 act additively and are required for petiole development. Previous studies have shown that the canonical KNOX proteins are not involved in compound leaf development in IRLC legumes. The identification of FCL1 supports the role of a truncated KNOX protein in compound leaf development in M. truncatula. PMID:22080596

Trichoderma genes

DOEpatents

Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

2012-06-19

Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

The rice blast resistance gene Ptr encodes an atypical protein required for broad spectrum disease resistance

USDA-ARS?s Scientific Manuscript database

Plant resistance (R) genes typically encode proteins with nucleotide binding site-leucine rich repeat (NLR) domains. We identified a novel, broad-spectrum rice blast R gene, Ptr, encoding a non-NLR protein with four Armadillo repeats. Ptr was originally identified by fast neutron mutagenesis as a ...

Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface

PubMed Central

Cheng, Sara Y.; Chou, George; Buie, Creighton; Vaughn, Mark W.; Compton, Campbell; Cheng, Kwan H.

2016-01-01

We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein–lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein–protein but weaker protein–lipid interactions for a dimeric protein on membrane surfaces. PMID:26827904

Key facts. Leaflets.

PubMed

1998-01-01

Leaflets about HIV/AIDS are useful for distributing after talks or counseling sessions, leaving out in settings such as clinics, and mailing out in response to frequently asked questions or inquiries about an organization's services. As is the case with other educational materials, leaflet production involves identification of a target audience, careful planning and pretesting, and attention to design principles. Leaflets can be produced more quickly when adapted from existing materials distributed by other programs. Presented in this article are instructions that should be given to writers, designers, illustrators, or photographers when work is commissioned as well as guidelines for communicating with printers.

Partial hammock valve: surgical repair in adulthood.

PubMed

Aramendi, José I; Rodríguez, Miguel A; Voces, Roberto; Pérez, Pedro; Rodrigo, David

2006-09-01

We describe a forme frustrée of hammock valve involving only the posterior mitral leaflet. Three adult patients were referred to surgery with the diagnosis of severe mitral regurgitation due to fibrosis of the posterior mitral leaflet. The final diagnosis was done intraoperatively. In all of them the posterior leaflet was attached to some accessory papillary muscles arranged en palisade, with three to four fused muscle heads producing restrictive leaflet motion in systole. Repair consisted in division of the papillary muscles, patch augmentation, and ring annuloplasty. This previously unreported lesion is congenital but manifests itself in adulthood.

Selenium Pretreatment Alleviated LPS-Induced Immunological Stress Via Upregulation of Several Selenoprotein Encoding Genes in Murine RAW264.7 Cells.

PubMed

Wang, Longqiong; Jing, Jinzhong; Yan, Hui; Tang, Jiayong; Jia, Gang; Liu, Guangmang; Chen, Xiaoling; Tian, Gang; Cai, Jingyi; Shang, Haiying; Zhao, Hua

2018-04-18

This study was conducted to profile selenoprotein encoding genes in mouse RAW264.7 cells upon lipopolysaccharide (LPS) challenge and integrate their roles into immunological regulation in response to selenium (Se) pretreatment. LPS was used to develop immunological stress in macrophages. Cells were pretreated with different levels of Se (0, 0.5, 1.0, 1.5, 2.0 μmol Se/L) for 2 h, followed by LPS (100 ng/mL) stimulation for another 3 h. The mRNA expression of 24 selenoprotein encoding genes and 9 inflammation-related genes were investigated. The results showed that LPS (100 ng/mL) effectively induced immunological stress in RAW264.7 cells with induced inflammation cytokines, IL-6 and TNF-α, mRNA expression, and cellular secretion. LPS increased (P < 0.05) mRNA profiles of 9 inflammation-related genes in cells, while short-time Se pretreatment modestly reversed (P < 0.05) the LPS-induced upregulation of 7 genes (COX-2, ICAM-1, IL-1β, IL-6, IL-10, iNOS, and MCP-1) and further increased (P < 0.05) expression of IFN-β and TNF-α in stressed cells. Meanwhile, LPS decreased (P < 0.05) mRNA levels of 18 selenoprotein encoding genes and upregulated mRNA levels of TXNRD1 and TXNRD3 in cells. Se pretreatment recovered (P < 0.05) expression of 3 selenoprotein encoding genes (GPX1, SELENOH, and SELENOW) in a dose-dependent manner and increased (P < 0.05) expression of another 5 selenoprotein encoding genes (SELENOK, SELENOM, SELENOS, SELENOT, and TXNRD2) only at a high level (2.0 μmol Se/L). Taken together, LPS-induced immunological stress in RAW264.7 cells accompanied with the global downregulation of selenoprotein encoding genes and Se pretreatment alleviated immunological stress via upregulation of a subset of selenoprotein encoding genes.

Disruption of the psbA gene by the copy correction mechanism reveals that the expression of plastid-encoded genes is regulated by photosynthesis activity.

PubMed

Khan, Muhammad Sarwar; Hameed, Waqar; Nozoe, Mikio; Shiina, Takashi

2007-05-01

The functional analysis of genes encoded by the chloroplast genome of tobacco by reverse genetics is routine. Nevertheless, for a small number of genes their deletion generates heteroplasmic genotypes, complicating their analysis. There is thus the need for additional strategies to develop deletion mutants for these genes. We have developed a homologous copy correction-based strategy for deleting/mutating genes encoded on the chloroplast genome. This system was used to produce psbA knockouts. The resulting plants are homoplasmic and lack photosystem II (PSII) activity. Further, the deletion mutants exhibit a distinct phenotype; young leaves are green, whereas older leaves are bleached, irrespective of light conditions. This suggests that senescence is promoted by the absence of psbA. Analysis of the transcript levels indicates that NEP (nuclear-encoded plastid RNA polymerase)-dependent plastid genes are up regulated in the psbA deletion mutants, whereas the bleached leaves retain plastid-encoded plastid RNA polymerase activity. Hence, the expression of NEP-dependent plastid genes may be regulated by photosynthesis, either directly or indirectly.

Aberrant tendinous chords with tethering of the tricuspid leaflets: a congenital anomaly causing severe tricuspid regurgitation

PubMed Central

Kobza, R; Kurz, D J; Oechslin, E N; Prêtre, R; Zuber, M; Vogt, P; Jenni, R

2004-01-01

Objective: To define the entity of tricuspid regurgitation caused by tethering of the tricuspid valve leaflets by aberrant tendinous chords. Design: Retrospective study. Setting: Tertiary care centre (university teaching hospital). Patients: 10 patients with unexplained severe tricuspid regurgitation. Methods: The last 13 500 echocardiographic studies from our facility were reviewed to identify patients with severe unexplained tricuspid regurgitation. Tethering was defined by the presence of aberrant tendinous chords to the tricuspid valve leaflets limiting the mobility of the tricuspid leaflet and resulting in incomplete coaptation and apical displacement of the regurgitant jet origin. Aberrant tendinous chords were defined as those inserting at the clear zone of the tricuspid leaflet and not originating from the papillary muscle. Patients fulfilling the diagnostic criteria for Ebstein’s anomaly were excluded. Results: 10 patients with aberrant tendinous chords tethering one or more tricuspid valve leaflets were identified. There were short non-aberrant tendinous chords in seven patients, five of whom also had right ventricular or tricuspid annulus dilatation. Conclusions: Tethering of the tricuspid valve leaflets by aberrant tendinous chords can be the sole mechanism of congenital tricuspid regurgitation. It is often associated with short non-aberrant tendinous chords, which may develop secondary to right ventricular or tricuspid annulus dilatation. Awareness of tethering as a cause of tricuspid regurgitation may be important in planning reconstructive surgery. PMID:14966058

Bilayer registry in a multicomponent asymmetric membrane: Dependence on lipid composition and chain length

DOE Office of Scientific and Technical Information (OSTI.GOV)

Polley, Anirban; Mayor, Satyajit; Rao, Madan, E-mail: madan@rri.res.in, E-mail: madan@ncbs.res.in

2014-08-14

A question of considerable interest to cell membrane biology is whether phase segregated domains across an asymmetric bilayer are strongly correlated with each other and whether phase segregation in one leaflet can induce segregation in the other. We answer both these questions in the affirmative, using an atomistic molecular dynamics simulation to study the equilibrium statistical properties of a 3-component asymmetric lipid bilayer comprising an unsaturated palmitoyl-oleoyl-phosphatidyl-choline, a saturated sphingomyelin, and cholesterol with different composition ratios. Our simulations are done by fixing the composition of the upper leaflet to be at the coexistence of the liquid ordered (l{sub o})-liquid disorderedmore » (l{sub d}) phases, while the composition of the lower leaflet is varied from the phase coexistence regime to the mixed l{sub d} phase, across a first-order phase boundary. In the regime of phase coexistence in each leaflet, we find strong transbilayer correlations of the l{sub o} domains across the two leaflets, resulting in bilayer registry. This transbilayer correlation depends sensitively upon the chain length of the participating lipids and possibly other features of lipid chemistry, such as degree of saturation. We find that the l{sub o} domains in the upper leaflet can induce phase segregation in the lower leaflet, when the latter is nominally in the mixed (l{sub d}) phase.« less

Efficiency of printed materials in worksite health promotion.

PubMed

Kishchuk, N; Anbar, F; O'Loughlin, J; Masson, P; Sacks-Silver, G

1991-01-01

Printed health promotion materials are widely believed to be an efficient means of achieving basic health promotion objectives, such as increasing knowledge of risk factors. This study examined the efficiency of cardiovascular health promotion leaflets in reaching employees in a heterogeneous sample of worksites. Two types of distribution were used: copies of the leaflets were either made available centrally or distributed to each individual employee. Interviews were conducted with 272 employees in six worksites. Respondents were asked whether they recognized, had read, and had learned something from the leaflets. Only one-quarter of respondents recognized the leaflets and only 14% stated that they had learned something. The efficiency of the leaflets was therefore much lower than expected. Z-tests for proportions showed that recognition, reading, and learning were significantly greater among those employees who had been given individual copies of the material. Among those who had been given individual copies, 45% reported recognizing the leaflet, 36% reading it, and 23% learning something from it. Among those who had only central access, the respective scores were 11%, 7% and 6%. These results suggest that the potential cost-effectiveness of printed materials such as leaflets and brochures should be weighed against alternative forms of intervention, given specific program objectives and characteristics of the target population. They also suggest that the cost and effort required in organizing the distribution of individual copies may be recouped in greater penetration.

Readability Statistics of Patient Information Leaflets in a Speech and Language Therapy Department

ERIC Educational Resources Information Center

Pothier, Louise; Day, Rachael; Harris, Catherine; Pothier, David D.

2008-01-01

Background: Information leaflets are commonly used in Speech and Language Therapy Departments. Despite widespread use, they can be of variable quality. Aims: To revise current departmental leaflets using the National Health Service (NHS) Toolkit for Producing Patient Information and to test the effect that this has on the readability scores of the…

Genome-Wide Identification and Mapping of NBS-Encoding Resistance Genes in Solanum tuberosum Group Phureja

PubMed Central

Lozano, Roberto; Ponce, Olga; Ramirez, Manuel; Mostajo, Nelly; Orjeda, Gisella

2012-01-01

The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes. PMID:22493716

E-learning or educational leaflet: does it make a difference in oral health promotion? A clustered randomized trial.

PubMed

Al Bardaweel, Susan; Dashash, Mayssoon

2018-05-10

The early recognition of technology together with great ability to use computers and smart systems have promoted researchers to investigate the possibilities of utilizing technology for improving health care in children. The aim of this study was to compare between the traditional educational leaflets and E-applications in improving oral health knowledge, oral hygiene and gingival health in schoolchildren of Damascus city, Syria. A clustered randomized controlled trial at two public primary schools was performed. About 220 schoolchildren aged 10-11 years were included in this study and grouped into two clusters. Children in Leaflet cluster received oral health education through leaflets, while children in E-learning cluster received oral health education through an E-learning program. A questionnaire was designed to register information related to oral health knowledge and to record Plaque and Gingival indices. Questionnaire administration and clinical assessment were undertaken at baseline, 6 and at 12 weeks of oral health education. Data was analysed using one way repeated measures ANOVA, post hoc Bonferroni test and independent samples t-test. Leaflet cluster (107 participants) had statistically significant better oral health knowledge than E-learning cluster (104 participants) at 6 weeks (P < 0.05) and at 12 weeks (P < 0.05) (Leaflet cluster:100 participants, E-learning cluster:100 participants). The mean knowledge gain compared to baseline was higher in Leaflet cluster than in E-learning cluster. A significant reduction in the PI means at 6 weeks and 12 weeks was observed in both clusters (P < 0.05) when compared to baseline. Children in Leaflet cluster had significantly less plaque than those in E-learning cluster at 6 weeks (P < 0.05) and at 12 weeks (P < 0.05). Similarly, a significant reduction in the GI means at 6 weeks and 12 weeks was observed in both clusters when compared to baseline (P < 0.05). Children in Leaflet cluster had statistically significant better gingival health than E-learning cluster at 6 weeks (P < 0.05) and 12 weeks (P < 0.05). Traditional educational leaflets are an effective tool in the improvement of both oral health knowledge as well as clinical indices of oral hygiene and care among Syrian children. Leaflets can be used in school-based oral health education for a positive outcome. Australian New Zealand Clinical Trials Registry ( ACTRN12618000395235 ), Date registered: 16/03/2018, retrospectively registered.

Restoration of Tricuspid Valve Mechanism at the Level of Displaced Septal and Posterior Leaflets in Ebstein's Anomaly.

PubMed

Im, Yu-Mi; Park, Chun Soo; Park, Jeong-Jun; Yun, Tae-Jin

2016-03-01

Surgical techniques currently used for the repair of Ebstein's anomaly comprise reconstruction of the tricuspid valve mechanism at the level of the true annulus with or without plication of the atrialized right ventricle. However, performing this procedure for patients with a dysmorphic anterior leaflet (i.e., insufficient leaflet tissue and decreased mobility due to tethering) may necessitate technical modifications. A retrospective review was performed of 31 patients (seven males and 24 females, median age at operation 31 years) with Ebstein's anomaly, who underwent tricuspid valve repair between March 2002 and December 2014. The original Hetzer technique (annulus to annulus approximation) was employed for six patients with a well-formed anterior leaflet. In 25 patients, the tricuspid valve mechanism was restored at the displaced septal leaflet by approximating the anterior leaflet attachment in the true annulus to the displaced septal leaflet attachment in the mid-septum. A bidirectional superior cavopulmonary anastomosis was added in 27 of 31 (87%) patients. No early or late death occurred during the median follow-up of 66 months (1-138 months). Immediate postoperative tricuspid regurgitation was trivial to mild in 22 patients, and the median preoperative, immediate postoperative, and last follow-up tricuspid regurgitation jet areas in 21 adult patients were 23.3 cm2, 10.4 cm2, and 7.0 cm2, respectively. Two patients underwent reoperation at 81 and 119 months postoperatively. Five-year freedom from severe tricuspid regurgitation or reoperation was 93.2%. Restoration of the tricuspid valve mechanism at the level of displaced septal leaflet leads to excellent long-term outcomes. The addition of the bidirectional superior cavopulmonary anastomosis has contributed to the success of this technique. © 2016 Wiley Periodicals, Inc.

Practitioner and lay perspectives of the service provision of nutrition information leaflets in primary care.

PubMed

McClinchy, Jane; Dickinson, Angela; Barron, Duncan; Thomas, Hilary

2011-12-01

In primary care, leaflets are often used to communicate health information. Increasingly, primary healthcare practitioners need to provide dietary advice. There is limited research exploring how nutrition information leaflets are used in primary care. The present study explored practitioner and lay experiences with respect to providing and receiving nutrition information in primary care, focusing in particular on the use of leaflets for nutrition information. A qualitative design was used incorporating focus groups with 57 practitioners based at seven general practitioner practices and a purposive sample of 30 lay participants attending six Consumer Health Organisations within one primary care trust. Focus groups were taped and transcribed verbatim and data were analysed thematically, assisted by computer software n6® (QSR International Pty Ltd, Melbourne, Australia). Practitioners discussed barriers to giving nutritional advice, access to leaflets, lay receptiveness to advice and their perceptions about the value of leaflets to lay people. Food was not considered in terms of its nutritional components by lay participants and the need for nutritional information was not perceived to be relevant until they had received a medical diagnosis. Lay participants discussed the importance of receiving nutritional advice relating to their medical diagnosis and the altered status of written information that was delivered personally. Practitioner and lay groups suggested improvements to ensure that nutritional advice be supported by relevant and appropriate written information. This research has underlined the continuing importance of nutrition information leaflets and concludes that there is particular value in involving lay participants in the development of nutrition information leaflets. © 2011 The Authors. Journal of Human Nutrition and Dietetics © 2011 The British Dietetic Association Ltd.

The usefulness and scientific accuracy of private sector Arabic language patient drug information leaflets.

PubMed

Sukkari, Sana R; Al Humaidan, Abdullah S; Sasich, Larry D

2012-07-01

Inadequate access to useful scientifically accurate patient information is a major cause of the inappropriate use of drugs resulting in serious personal injury and related costs to the health care system. The definition of useful scientifically accurate patient information for prescription drugs was accepted by the US Secretary of the Department of Health and Human Services in 1996 as that derived from or consistent with the US FDA approved professional product label for a drug. Previous quality content studies found that English language patient drug information leaflets distributed by US pharmacies failed to meet minimum criteria defining useful and scientifically accurate information. Evaluation forms containing the explicit elements that define useful scientifically accurate information for three drugs with known serious adverse drug reactions were created based on the current US FDA approved professional product labels. The Arabic language patient drug information leaflets for celecoxib, paroxetine, and lamotrigine were obtained locally and evaluated using a methodology similar to that used in previous quality content patient drug information studies in the US. The Arabic leaflets failed to meet the definition of useful scientifically accurate information. The celecoxib leaflet contained 30% of the required information and the paroxetine and lamotrigine leaflets contained 24% and 20%, respectively. There are several limitations to this study. The Arabic leaflets from only one commercial North American vendor were evaluated and the evaluation included a limited number of drugs. A larger study is necessary to be able to generalize these results. The study results are consistent with those of previous quality content studies of commercially available English patient drug information leaflets. The results have important implications for patients as access to a reliable source of drug information may prevent harm or limit the suffering from serious adverse drug reactions.

Occluder closing behavior: a key factor in mechanical heart valve cavitation.

PubMed

Wu, Z J; Wang, Y; Hwang, N H

1994-04-01

A laser sweeping technique developed in this laboratory was found to be capable of monitoring the leaflet closing motion with microsecond precision. The leaflet closing velocity was measured inside the last three degrees before impact. Mechanical heart valve (MHV) leaflets were observed to close with a three-phase motion; the approaching phase, the decelerating phase, and the rebound phase, all of which take place within one to two milliseconds. The leaflet closing behavior depends mainly on the leaflet design and the hinge mechanism. Bileaflet and monoleaflet types of mechanical heart valves were tested in the mitral position in a physiologic mock circulatory flow loop, which incorporated a computer-controlled magnetic drive and an adjustable afterload system. The test loop was tuned to produce physiologic ventricular and aortic pressure wave forms at 70-120 beats/min, with the maximum ventricular dp/dt varying between 1500-5600 mmHg/sec. The experiments were conducted by controlling the cardiac output at a constant level between 2.0-9.0 liters/min. The measured time-displacement curve of each tested MHV leaflet and its geometry were taken as the input for computation of the squeeze flow field in the narrow gap space between the approaching leaflet and the valve housing. The results indicated rapid build-up of both the pressure and velocity in the gap field within microsecs before the impact. The pressure build-up in the gap space is apparently responsible for the leaflet deceleration before the impact. When the concurrent water hammer pressure reduction at closure was combined with the high energy squeeze jet ejected from the gap space, there were strong indications of the environment which favors micro cavitation inceptions in certain types of MHV.

A novel arthroscopic all-inside suture technique using the Fast-Fix 360 system for repairing horizontal meniscal tears in young athletes

PubMed Central

Atsumi, Satoru; Hara, Kunio; Arai, Yuji; Yamada, Manabu; Mizoshiri, Naoki; Kamitani, Aguri; Kubo, Toshikazu

2018-01-01

Abstract Rationale: Considering the risk of osteoarthritis following resection of a horizontally torn meniscus of the knee, repairing and preserving the meniscus as much as possible is preferred. We report 3 cases of restoration of horizontally torn menisci using a novel arthroscopic method we have called “all-inside interleaf vertical suture” that afforded preservation. Patient concerns: The 3 patients (aged 14, 17, and 21 years) had knee pain through sports activity. Diagnoses: All patients had horizontal tears in the posteromedial part of the meniscus. Interventions: The method uses Fast-Fix, whereby a first anchor is inserted from the tibial surface of the tear's superior leaflet and a second anchor is inserted from the femoral surface of the tear's inferior leaflet, and the 2 leaflets are closed using vertical suture. In all cases, the suture knots were embedded between the superior leaflet and inferior leaflet, avoiding contact with the articular cartilage, and superior leaflet and inferior leaflet crimping was good. Outcomes: All 3 were able to resume competing in sport and ≥ 1 year after surgery they had no pain and their postoperative mean Lysholm scores were 99.7. There were no complications or recurrence. On magnetic resonance imaging, the signal intensity of all the horizontal tears was high before surgery but low after surgery, suggesting that the repaired tear was healing. Lessons: The all-inside interleaf vertical suture procedure is a new surgical technique that can repair posteromedial horizontal meniscal tears of the knee of young people by easy crimping of the superior and inferior leaflets without the suture knots causing complications. PMID:29443758

Molecular analysis of interactions between dendrimers and asymmetric membranes at different transport stages.

PubMed

He, XiaoCong; Qu, ZhiGuo; Xu, Feng; Lin, Min; Wang, JiuLing; Shi, XingHua; Lu, TianJian

2014-01-07

Studying dendrimer-biomembrane interactions is important for understanding drug and gene delivery. In this study, coarse-grained molecular dynamics simulations were performed to investigate the behaviors of polyamidoamine (PAMAM) dendrimers (G4 and G5) as they interacted with asymmetric membranes from different sides of the bilayer, thus mimicking different dendrimer transport stages. The G4 dendrimer could insert into the membrane during an equilibrated state, and the G5 dendrimer could induce pore formation in the membrane when the dendrimers interacted with the outer side (outer interactions) of an asymmetric membrane [with 10% dipalmitoyl phosphatidylserine (DPPS) in the inner leaflet of the membrane]. During the interaction with the inner side of the asymmetric membrane (inner interactions), the G4 and G5 dendrimers only adsorbed onto the membrane. As the membrane asymmetry increased (e.g., increased DPPS percentage in the inner leaflet of the membrane), the G4 and G5 dendrimers penetrated deeper into the membrane during the outer interactions and the G4 and G5 dendrimers were adsorbed more tightly onto the membrane for the inner interactions. When the DPPS content reached 50%, the G4 dendrimer could completely penetrate through the membrane from the outer side to the inner side. Our study provides molecular understanding and reference information about different dendrimer transport stages during drug and gene delivery.

The candidate histocompatibility locus of a Basal chordate encodes two highly polymorphic proteins.

PubMed

Nydam, Marie L; Netuschil, Nikolai; Sanders, Erin; Langenbacher, Adam; Lewis, Daniel D; Taketa, Daryl A; Marimuthu, Arumugapradeep; Gracey, Andrew Y; De Tomaso, Anthony W

2013-01-01

The basal chordate Botryllus schlosseri undergoes a natural transplantation reaction governed by a single, highly polymorphic locus called the fuhc. Our initial characterization of this locus suggested it encoded a single gene alternatively spliced into two transcripts: a 555 amino acid-secreted form containing the first half of the gene, and a full-length, 1008 amino acid transmembrane form, with polymorphisms throughout the ectodomain determining outcome. We have now found that the locus encodes two highly polymorphic genes which are separated by a 227 bp intergenic region: first, the secreted form as previously described, and a second gene encoding a 531 amino acid membrane-bound gene containing three extracellular immunoglobulin domains. While northern blotting revealed only these two mRNAs, both PCR and mRNA-seq detect a single capped and polyadenylated transcript that encodes processed forms of both genes linked by the intergenic region, as well as other transcripts in which exons of the two genes are spliced together. These results might suggest that the two genes are expressed as an operon, during which both genes are co-transcribed and then trans-spliced into two separate messages. This type of transcriptional regulation has been described in tunicates previously; however, the membrane-bound gene does not encode a typical Splice Leader (SL) sequence at the 5' terminus that usually accompanies trans-splicing. Thus, the presence of stable transcripts encoding both genes may suggest a novel mechanism of regulation, or conversely may be rare but stable transcripts in which the two mRNAs are linked due to a small amount of read-through by RNA polymerase. Both genes are highly polymorphic and co-expressed on tissues involved in histocompatibility. In addition, polymorphisms on both genes correlate with outcome, although we have found a case in which it appears that the secreted form may be major allorecognition determinant.

Development of a gene synthesis platform for the efficient large scale production of small genes encoding animal toxins.

PubMed

Sequeira, Ana Filipa; Brás, Joana L A; Guerreiro, Catarina I P D; Vincentelli, Renaud; Fontes, Carlos M G A

2016-12-01

Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides. This improved gene synthesis method uses a PCR-based protocol to assemble synthetic DNA from pools of overlapping oligonucleotides and was developed to synthesise multiples genes simultaneously. This technology incorporates an accurate, automated and cost effective ligation independent cloning step to directly integrate the synthetic genes into an effective Escherichia coli expression vector. The robustness of this technology to generate large libraries of dozens to thousands of synthetic nucleic acids was demonstrated through the parallel and simultaneous synthesis of 96 genes encoding animal toxins. An automated platform was developed for the large-scale synthesis of small genes encoding eukaryotic toxins. Large scale recombinant expression of synthetic genes encoding eukaryotic toxins will allow exploring the extraordinary potency and pharmacological diversity of animal venoms, an increasingly valuable but unexplored source of lead molecules for drug discovery.

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families.

PubMed

Shah, Shiraz A; Alkhnbashi, Omer S; Behler, Juliane; Han, Wenyuan; She, Qunxin; Hess, Wolfgang R; Garrett, Roger A; Backofen, Rolf

2018-06-19

A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats - CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in Synechocystis confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk .

Modularity of Plant Metabolic Gene Clusters: A Trio of Linked Genes That Are Collectively Required for Acylation of Triterpenes in Oat[W][OA

PubMed Central

Mugford, Sam T.; Louveau, Thomas; Melton, Rachel; Qi, Xiaoquan; Bakht, Saleha; Hill, Lionel; Tsurushima, Tetsu; Honkanen, Suvi; Rosser, Susan J.; Lomonossoff, George P.; Osbourn, Anne

2013-01-01

Operon-like gene clusters are an emerging phenomenon in the field of plant natural products. The genes encoding some of the best-characterized plant secondary metabolite biosynthetic pathways are scattered across plant genomes. However, an increasing number of gene clusters encoding the synthesis of diverse natural products have recently been reported in plant genomes. These clusters have arisen through the neo-functionalization and relocation of existing genes within the genome, and not by horizontal gene transfer from microbes. The reasons for clustering are not yet clear, although this form of gene organization is likely to facilitate co-inheritance and co-regulation. Oats (Avena spp) synthesize antimicrobial triterpenoids (avenacins) that provide protection against disease. The synthesis of these compounds is encoded by a gene cluster. Here we show that a module of three adjacent genes within the wider biosynthetic gene cluster is required for avenacin acylation. Through the characterization of these genes and their encoded proteins we present a model of the subcellular organization of triterpenoid biosynthesis. PMID:23532069

Bicuspid aortic valve hemodynamics: a fluid-structure interaction study

NASA Astrophysics Data System (ADS)

Chandra, Santanu; Seaman, Clara; Sucosky, Philippe

2011-11-01

The bicuspid aortic valve (BAV) is a congenital defect in which the aortic valve forms with two leaflets instead of three. While calcific aortic valve disease (CAVD) also develops in the normal tricuspid aortic valve (TAV), its progression in the BAV is more rapid. Although studies have suggested a mechano-potential root for the disease, the native BAV hemodynamics remains largely unknown. This study aimed at characterizing BAV hemodynamics and quantifying the degree of wall-shear stress (WSS) abnormality on BAV leaflets. Fluid-structure interaction models validated with particle-image velocimetry were designed to predict the flow and leaflet dynamics in idealized TAV and BAV anatomies. Valvular function was quantified in terms of the effective orifice area. The regional leaflet WSS was characterized in terms of oscillatory shear index, temporal shear magnitude and temporal shear gradient. The predictions indicate the intrinsic degree of stenosis of the BAV anatomy, reveal drastic differences in shear stress magnitude and pulsatility on BAV and TAV leaflets and confirm the side- and site-specificity of the leaflet WSS. Given the ability of abnormal fluid shear stress to trigger valvular inflammation, these results support the existence of a mechano-etiology of CAVD in the BAV.

Creation New Patient Information Leaflets with Diabetes by Pharmacists and Assesment Conducted by Patients.

PubMed

Arai, Motoharu; Maeda, Kazuto; Satoh, Hiroki; Miki, Akiko; Sawada, Yasufumi

2016-10-01

We created a draft of new patient information leaflets to ensure patients' proper use of drugs and to highlight safety issues and improvement plans extracted and proposed by small group discussions (SGD) with pharmacists. A total of 3 SGDs (participants: 15 pharmacists) were conducted with the aim of improving patient information leaflets for oral diabetes drugs. First, the disadvantages and advantages of the current instructions as well as requests for ideal patient information leaflets were obtained from participants. Conventional patient information leaflets that could be improved were useful to understand drug efficacy, adverse effects, and instructions for daily consumption of medicines, and to encourage patients to re-check drugs at home and inform their family of the measures to be taken in the case of adverse effects from the standpoint of patients. However, some disadvantages arose; for example, the instructions were difficult to read because of small lettering and illustrations and too much text. It was not tailored for individual patients, and descriptions about serious adverse effects caused patients much anxiety. Therefore, we have created a draft of new patient information leaflets with diabetes that are simpler and easier to understand and use concise wording and illustrations that are impactful.

Oenocarpus bacaba and Oenocarpus bataua Leaflets and Roots: A New Source of Antioxidant Compounds

PubMed Central

Leba, Louis-Jérôme; Brunschwig, Christel; Saout, Mona; Martial, Karine; Bereau, Didier; Robinson, Jean-Charles

2016-01-01

Native palm trees fruit from the Amazonian rainforest, Oenocarpus bacaba and Oenocarpus bataua, are very often used in the diet of local communities, but the biological activities of their roots and leaflets remain poorly known. Total phenolic content (TPC) and antioxidant activity of root and leaflet extracts from Oenocarpus bacaba and Oenocarpus bataua were assessed by using different chemical assays, the oxygèn radical absorbance capacity (ORAC), the 2,2-diphenyl-l-picrylhydrazyl (DPPH) free radical-scavenging capacity and the ferric-reducing ability of plasma (FRAP). Cellular antioxidant activity and cytotoxicity were also measured in Normal Human Dermal Fibroblasts. The polyphenolic composition of Oenocarpus extracts was investigated by LC-MSn. Oenocarpus leaflet extracts were more antioxidant than root extracts, being at least as potent as Euterpe oleracea berries known as superfruit. Oenocarpus root extracts were characterized by hydroxycinnamic acids (caffeoylquinic and caffeoylshikimic acids), while leaflet extracts contained mainly caffeoylquinic acids and C-glycosyl flavones. These results suggest that leaflets of both Oenocarpus species could be valorized as a new non-cytotoxic source of antioxidants from Amazonia, containing hydroxycinnamic acids and flavonoids, in the pharmaceutical, cosmetic or agri-food industry. PMID:27355943

Automated segmentation and geometrical modeling of the tricuspid aortic valve in 3D echocardiographic images.

PubMed

Pouch, Alison M; Wang, Hongzhi; Takabe, Manabu; Jackson, Benjamin M; Sehgal, Chandra M; Gorman, Joseph H; Gorman, Robert C; Yushkevich, Paul A

2013-01-01

The aortic valve has been described with variable anatomical definitions, and the consistency of 2D manual measurement of valve dimensions in medical image data has been questionable. Given the importance of image-based morphological assessment in the diagnosis and surgical treatment of aortic valve disease, there is considerable need to develop a standardized framework for 3D valve segmentation and shape representation. Towards this goal, this work integrates template-based medial modeling and multi-atlas label fusion techniques to automatically delineate and quantitatively describe aortic leaflet geometry in 3D echocardiographic (3DE) images, a challenging task that has been explored only to a limited extent. The method makes use of expert knowledge of aortic leaflet image appearance, generates segmentations with consistent topology, and establishes a shape-based coordinate system on the aortic leaflets that enables standardized automated measurements. In this study, the algorithm is evaluated on 11 3DE images of normal human aortic leaflets acquired at mid systole. The clinical relevance of the method is its ability to capture leaflet geometry in 3DE image data with minimal user interaction while producing consistent measurements of 3D aortic leaflet geometry.

Retrieval of a leaflet escaped in a Tri-technologies bileaflet mechanical prosthetic valve.

PubMed

Cianciulli, Tomás F; Lax, Jorge A; Saccheri, María C; Guidoin, Robert; Salvado, César M; Fernández, Adrián J; Prezioso, Horacio A

2008-01-01

The escape of the prosthetic heart valve disc is one of the causes of prosthetic dysfunction that requires emergency surgery. The removal of the embolized disc should be carried out because of the risk of a progressive extrusion on the aortic wall. Several imaging techniques can be used for the detection of the missing disc localization. In this report we describe a 32-year-old man who underwent mitral valve replacement with a Tri-technologies bileaflet valve three years ago, and was admitted in cardiogenic shock. Transesophageal echocardiography showed acute-onset massive mitral regurgitation. The patient underwent emergency replacement of the prosthetic valve. Only one of the two leaflets remained in the removed prosthetic valve. The missing leaflet could not be found within the cardiac cavity. The abdominal fluoroscopic study and plain radiography were unable to detect the escaped leaflet. The abdominal computed tomography scan and the ultrasound showed the escaped leaflet in the terminal portion of the aortic bifurcation. To retrieve the embolized disc laparotomy and aortotomy were performed three months later. The escaped leaflet shows a fracture of one of the pivot systems caused by structural failure. This kind of failure mode is usually the result of high stress concentration.

Detection with synthetic oligonucleotide probes of nucleotide sequence variations in the genes encoding enterotoxins of Escherichia coli.

PubMed Central

Nishibuchi, M; Murakami, A; Arita, M; Jikuya, H; Takano, J; Honda, T; Miwatani, T

1989-01-01

We examined variations in the genes encoding heat-stable enterotoxin (ST) and heat-labile enterotoxin (LT) in 88 strains of Escherichia coli isolated from individuals with traveler's diarrhea to find suitable sequences for use as oligonucleotide probes. Four oligonucleotide probes of the gene encoding ST of human origin (STIb or STh), one oligonucleotide probe of the gene encoding ST of porcine origin (STIa or STp), and three oligonucleotide probes of the gene encoding LT of human origin (LTIh) were used in DNA colony hybridization tests. In 15 of 22 strains possessing the STh gene and 28 of 42 strains producing LT, the sequences of all regions tested were identical to the published sequences. One region in the STh gene examined with a 18-mer probe was relatively well conserved and was shown to be closely associated with the enterotoxicity of the E. coli strains in suckling mice. This oligonucleotide, however, hybridized with strains of Vibrio cholerae O1, V. parahaemolyticus, and Yersinia enterocolitica that gave negative results in the suckling mouse assay. PMID:2685027

Cyclic stretch-induced the cytoskeleton rearrangement and gene expression of cytoskeletal regulators in human periodontal ligament cells.

PubMed

Wu, Yaqin; Zhuang, Jiabao; Zhao, Dan; Zhang, Fuqiang; Ma, Jiayin; Xu, Chun

2017-10-01

This study aimed to explore the mechanism of the stretch-induced cell realignment and cytoskeletal rearrangement by identifying several mechanoresponsive genes related to cytoskeletal regulators in human PDL cells. After the cells were stretched by 1, 10 and 20% strains for 0.5, 1, 2, 4, 6, 12 or 24 h, the changes of the morphology and content of microfilaments were recorded and calculated. Meanwhile, the expression of 84 key genes encoding cytoskeletal regulators after 6 and 24 h stretches with 20% strain was detected by using real-time PCR array. Western blot was applied to identify the protein expression level of several cytoskeletal regulators encoded by these differentially expressed genes. The confocal fluorescent staining results confirmed that stretch-induced realignment of cells and rearrangement of microfilaments. Among the 84 genes screened, one gene was up-regulated while two genes were down-regulated after 6 h stretch. Meanwhile, three genes were up-regulated while two genes were down-regulated after 24 h stretch. These genes displaying differential expression included genes regulating polymerization/depolymerization of microfilaments (CDC42EP2, FNBP1L, NCK2, PIKFYVE, WASL), polymerization/depolymerization of microtubules (STMN1), interacting between microfilaments and microtubules (MACF1), as well as a phosphatase (PPP1R12B). Among the proteins encoded by these genes, the protein expression level of Cdc42 effector protein-2 (encoded by CDC42EP2) and Stathmin-1 (encoded by STMN1) was down-regulated, while the protein expression level of N-WASP (encoded by WASL) was up-regulated. The present study confirmed the cyclic stretch-induced cellular realignment and rearrangement of microfilaments in the human PDL cells and indicated several force-sensitive genes with regard to cytoskeletal regulators.

A High-Resolution Gene Map of the Chloroplast Genome of the Red Alga Porphyra purpurea.

PubMed Central

Reith, M; Munholland, J

1993-01-01

Extensive DNA sequencing of the chloroplast genome of the red alga Porphyra purpurea has resulted in the detection of more than 125 genes. Fifty-eight (approximately 46%) of these genes are not found on the chloroplast genomes of land plants. These include genes encoding 17 photosynthetic proteins, three tRNAs, and nine ribosomal proteins. In addition, nine genes encoding proteins related to biosynthetic functions, six genes encoding proteins involved in gene expression, and at least five genes encoding miscellaneous proteins are among those not known to be located on land plant chloroplast genomes. The increased coding capacity of the P. purpurea chloroplast genome, along with other characteristics such as the absence of introns and the conservation of ancestral operons, demonstrate the primitive nature of the P. purpurea chloroplast genome. In addition, evidence for a monophyletic origin of chloroplasts is suggested by the identification of two groups of genes that are clustered in chloroplast genomes but not in cyanobacteria. PMID:12271072

Genome-Wide Architecture of Disease Resistance Genes in Lettuce

PubMed Central

Christopoulou, Marilena; Wo, Sebastian Reyes-Chin; Kozik, Alex; McHale, Leah K.; Truco, Maria-Jose; Wroblewski, Tadeusz; Michelmore, Richard W.

2015-01-01

Genome-wide motif searches identified 1134 genes in the lettuce reference genome of cv. Salinas that are potentially involved in pathogen recognition, of which 385 were predicted to encode nucleotide binding-leucine rich repeat receptor (NLR) proteins. Using a maximum-likelihood approach, we grouped the NLRs into 25 multigene families and 17 singletons. Forty-one percent of these NLR-encoding genes belong to three families, the largest being RGC16 with 62 genes in cv. Salinas. The majority of NLR-encoding genes are located in five major resistance clusters (MRCs) on chromosomes 1, 2, 3, 4, and 8 and cosegregate with multiple disease resistance phenotypes. Most MRCs contain primarily members of a single NLR gene family but a few are more complex. MRC2 spans 73 Mb and contains 61 NLRs of six different gene families that cosegregate with nine disease resistance phenotypes. MRC3, which is 25 Mb, contains 22 RGC21 genes and colocates with Dm13. A library of 33 transgenic RNA interference tester stocks was generated for functional analysis of NLR-encoding genes that cosegregated with disease resistance phenotypes in each of the MRCs. Members of four NLR-encoding families, RGC1, RGC2, RGC21, and RGC12 were shown to be required for 16 disease resistance phenotypes in lettuce. The general composition of MRCs is conserved across different genotypes; however, the specific repertoire of NLR-encoding genes varied particularly of the rapidly evolving Type I genes. These tester stocks are valuable resources for future analyses of additional resistance phenotypes. PMID:26449254

Cloning, characterization, expression analysis and inhibition studies of a novel gene encoding Bowman-Birk type protease inhibitor from rice bean

USDA-ARS?s Scientific Manuscript database

This paper presents the first study describing the isolation, cloning and characterization of a full length gene encoding Bowman-Birk protease inhibitor (RbTI) from rice bean (Vigna umbellata). A full-length protease inhibitor gene with complete open reading frame of 327bp encoding 109 amino acids w...

Structural basis for maintenance of bacterial outer membrane lipid asymmetry.

PubMed

Abellón-Ruiz, Javier; Kaptan, Shreyas S; Baslé, Arnaud; Claudi, Beatrice; Bumann, Dirk; Kleinekathöfer, Ulrich; van den Berg, Bert

2017-12-01

The Gram-negative bacterial outer membrane (OM) is a unique bilayer that forms an efficient permeation barrier to protect the cell from noxious compounds 1 , 2 . The defining characteristic of the OM is lipid asymmetry, with phospholipids comprising the inner leaflet and lipopolysaccharides comprising the outer leaflet 1-3 . This asymmetry is maintained by the Mla pathway, a six-component system that is widespread in Gram-negative bacteria and is thought to mediate retrograde transport of misplaced phospholipids from the outer leaflet of the OM to the cytoplasmic membrane 4 . The OM lipoprotein MlaA performs the first step in this process via an unknown mechanism that does not require external energy input. Here we show, using X-ray crystallography, molecular dynamics simulations and in vitro and in vivo functional assays, that MlaA is a monomeric α-helical OM protein that functions as a phospholipid translocation channel, forming a ~20-Å-thick doughnut embedded in the inner leaflet of the OM with a central, amphipathic pore. This architecture prevents access of inner leaflet phospholipids to the pore, but allows outer leaflet phospholipids to bind to a pronounced ridge surrounding the channel, followed by diffusion towards the periplasmic space. Enterobacterial MlaA proteins form stable complexes with OmpF/C 5,6 , but the porins do not appear to play an active role in phospholipid transport. MlaA represents a lipid transport protein that selectively removes outer leaflet phospholipids to help maintain the essential barrier function of the bacterial OM.

Evaluating the application of research-based guidance to the design of an emergency preparedness leaflet.

PubMed

Hellier, E; Edworthy, J; Newbold, L; Titchener, K; Tucker, M; Gabe-Thomas, E

2014-09-01

Guidelines for the design of emergency communications were derived from primary research and interrogation of the literature. The guidelines were used to re-design a nuclear emergency preparedness leaflet routinely distributed to households in the local area. Pre-test measures of memory for, and self-reported understanding of, nuclear safety information were collected. The findings revealed high levels of non-receipt of the leaflet, and among those who did receive it, memory for safety advice was poor. Subjective evaluations of the trial leaflet suggested that it was preferred and judged easier to understand than the original. Objective measures of memory for the two leaflets were also recorded, once after the study period, and again one week or four weeks later. Memory for the advice was better, at all time periods, when participants studied the trial leaflet. The findings showcase evaluation of emergency preparedness literature and suggest that extant research findings can be applied to the design of communications to improve memory and understandability. Studies are described that showcase the use of research-based guidelines to design emergency communications and provide both subjective and objective data to support designing emergency communications in this way. In addition, the research evaluates the effectiveness of emergency preparedness leaflets that are routinely distributed to households. This work is of relevance to academics interested in risk communication and to practitioners involved in civil protection and emergency preparedness. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Isolated effect of geometry on mitral valve function for in silico model development.

PubMed

Siefert, Andrew William; Rabbah, Jean-Pierre Michel; Saikrishnan, Neelakantan; Kunzelman, Karyn Susanne; Yoganathan, Ajit Prithivaraj

2015-01-01

Computational models for the heart's mitral valve (MV) exhibit several uncertainties that may be reduced by further developing these models using ground-truth data-sets. This study generated a ground-truth data-set by quantifying the effects of isolated mitral annular flattening, symmetric annular dilatation, symmetric papillary muscle (PM) displacement and asymmetric PM displacement on leaflet coaptation, mitral regurgitation (MR) and anterior leaflet strain. MVs were mounted in an in vitro left heart simulator and tested under pulsatile haemodynamics. Mitral leaflet coaptation length, coaptation depth, tenting area, MR volume, MR jet direction and anterior leaflet strain in the radial and circumferential directions were successfully quantified at increasing levels of geometric distortion. From these data, increase in the levels of isolated PM displacement resulted in the greatest mean change in coaptation depth (70% increase), tenting area (150% increase) and radial leaflet strain (37% increase) while annular dilatation resulted in the largest mean change in coaptation length (50% decrease) and regurgitation volume (134% increase). Regurgitant jets were centrally located for symmetric annular dilatation and symmetric PM displacement. Asymmetric PM displacement resulted in asymmetrically directed jets. Peak changes in anterior leaflet strain in the circumferential direction were smaller and exhibited non-significant differences across the tested conditions. When used together, this ground-truth data-set may be used to parametrically evaluate and develop modelling assumptions for both the MV leaflets and subvalvular apparatus. This novel data may improve MV computational models and provide a platform for the development of future surgical planning tools.

Blistering of langmuir-blodgett bilayers containing anionic phospholipids as observed by atomic force microscopy.

PubMed Central

Rinia, H A; Demel, R A; van der Eerden, J P; de Kruijff, B

1999-01-01

Asymmetric bilayers of different phospholipid compositions have been prepared by the Langmuir-Blodgett (L-B) method, and imaged by atomic force microscopy (AFM). Such bilayers can function as a model for biological membranes. The first leaflet consisted of zwitterionic phospholipids phosphatidylcholine (PC) or phosphatidylethanolamine (PE). The second leaflet consisted of the anionic phospholipid phosphatidylglycerol (PG), in either the condensed or liquid phase or, for comparison, of PC. Different bilayers showed different morphology. In all bilayers defects in the form of holes were present. In some bilayers with a first leaflet consisting of PC, polygonal line-shaped defects were observed, whereas when the first leaflet consisted of PE, mainly round defects were seen. Not only the shape, but also the amount of defects varied, depending on the condition and the composition of the second leaflet. In most of the PG-containing systems the defects were surrounded by elevations, which reversibly disappeared in the presence of divalent cations. This is the first time that such elevations have been observed on phospholipid bilayers. We propose that they are induced by phospholipid exchange between the two leaflets around the defects, leading to the presence of negatively charged phospholipids in the first leaflet. Because the substrate is also negatively charged, the bilayer around the edges is repelled and lifted up. Since it was found that the elevations are indeed detached from the substrate, we refer to this effect as bilayer blistering. PMID:10465778

Systolic Anterior Motion of the Mitral Valve after Mitral Valve Repair

PubMed Central

Sternik, Leonid; Zehr, Kenton J.

2005-01-01

Factors predisposing patients to systolic anterior motion of the mitral valve (SAM) with left ventricular outflow tract (LVOT) obstruction after mitral valve repair are the presence of a myxomatous mitral valve with redundant leaflets, a nondilated hyperdynamic left ventricle, and a short distance between the mitral valve coaptation point and the ventricular septum after repair. From December 1999 through March 2000, we used our surgical method in 6 patients with severely myxomatous regurgitant mitral valves who were at risk of developing SAM. Leaflets were markedly redundant in all 6. Left ventricular function was hyperdynamic in 4 patients and normal in 2. Triangular or quadrangular resection of the midportion of the posterior leaflet and posterior band annuloplasty were performed. To prevent SAM and LVOT obstruction, extra, posteriorly directed, mid-posterior-leaflet secondary chordae tendineae, which would otherwise have been resected, were transferred to the underside of the middle of the mid-anterior leaflet with a small piece of associated valve as an anchoring pledget. This kept the redundant anterior leaflet edge, which extended below the coaptation point, away from the LVOT. No post-repair SAM or LVOT obstruction was observed on intraoperative or discharge echocardiography. All patients had no or trivial residual mitral regurgitation. We conclude that extra chordae tendineae, when available, can be used in mitral valve repair to tether the redundant anterior leaflet and thus prevent it from flipping into the LVOT. This will theoretically prevent SAM and LVOT obstruction in patients with risk factors for SAM. PMID:15902821

Cytochrome b5 gene and protein of Candida tropicalis and methods relating thereto

DOEpatents

Craft, David L.; Madduri, Krishna M.; Loper, John C.

2003-01-01

A novel gene has been isolated which encodes cytochrome b5 (CYTb5) protein of the .omega.-hydroxylase complex of C. tropicalis 20336. Vectors including this gene, and transformed host cells are provided. Methods of increasing the production of a CYTb5 protein are also provided which involve transforming a host cell with a gene encoding this protein and culturing the cells. Methods of increasing the production of a dicarboxylic acid are also provided which involve increasing in the host cell the number of genes encoding this protein.

Outlet strut fracture and leaflet escape of Bjork-Shiley convexo-concave valve.

PubMed

Uchino, Gaku; Yoshida, Hideo; Sakoda, Naoya; Hattori, Shigeru; Kawabata, Takuya; Saiki, Munehiro; Fujita, Yasufumi; Yunoki, Keiji; Hisamochi, Kunikazu; Mine, Yoshinari

2017-06-01

Prosthetic valve fracture is a serious complication and may arise in patient post-valve replacement. We experienced an outlet strut fracture and leaflet escape of a Bjork-Shiley convexo-concave valve. We performed an emergency redo mitral valve replacement and successfully retrieved the fractured strut and escaped leaflet from superficial femoral artery and the abdominal aorta. The patient showed an uneventful postoperative recovery.

Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface.

PubMed

Cheng, Sara Y; Chou, George; Buie, Creighton; Vaughn, Mark W; Compton, Campbell; Cheng, Kwan H

2016-03-01

We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein-lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein-protein but weaker protein-lipid interactions for a dimeric protein on membrane surfaces. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Computational fluid dynamics simulation of transcatheter aortic valve degeneration.

PubMed

Dwyer, Harry A; Matthews, Peter B; Azadani, Ali; Jaussaud, Nicolas; Ge, Liang; Guy, T Sloane; Tseng, Elaine E

2009-08-01

Studied under clinical trials, transcatheter aortic valves (TAV) have demonstrated good short-term feasibility and results in high-risk surgical patients with severe aortic stenosis. However, their long-term safety and durability are unknown. The objective of this study is to evaluate hemodynamic changes within TAV created by bioprosthetic leaflet degeneration. Computational fluid dynamics (CFD) simulations were performed to evaluate the hemodynamics through TAV sclerosis (35% orifice reduction) and stenosis (78% orifice reduction). A three-dimensional surface mesh of the TAV within the aortic root was generated for each simulation. Leaflets were contained within an open, cylindrical body without attachment to the sinus commissures representing the stent. A continuous surface between the annulus and TAV excluded the geometry of the native calcified leaflets and prevented paravalvular leak. Unsteady control volume analysis throughout systole was used to calculate leaflet shear stress and total force on the TAV. Sclerosis increased total force on the TAV by 63% (0.602-0.98 N). Advancement of degeneration from sclerosis to stenosis was accompanied by an 86% increase in total force (1.82 N) but only a 32% increase in peak wall shear stress on the leaflets. Of the total force exerted on the TAV, 99% was in the direction of axial flow. Shear stresses on the TAV were greatest during peak systolic flow with stress concentrations on the tips of the leaflets. In the normal TAV, the aortic root geometry and physiologic flow dominate location and magnitude of shear stress. Following leaflet degeneration, the specific geometry of the stenosis dictates the profile of axial velocity leaving the TAV and shear stress on the leaflets. A dramatic increase in peak leaflet shear stress was observed (115 Pa stenosis vs. 87 Pa sclerosis and 29 Pa normal). CFD simulations in this study provide the first of its kind data quantifying hemodynamics within stenosed TAV. Stenosis leads to significant forces of TAV during systole; however, diastolic forces predominate even with significant stenosis. Substantial changes in peak shear stress occur with TAV degeneration. As the first implanted TAV begin to stenose, the authors recommend watchful examination for device failure.

Genome complexity in the coelacanth is reflected in its adaptive immune system

USGS Publications Warehouse

Saha, Nil Ratan; Ota, Tatsuya; Litman, Gary W.; Hansen, John; Parra, Zuly; Hsu, Ellen; Buonocore, Francesco; Canapa, Adriana; Cheng, Jan-Fang; Amemiya, Chris T.

2014-01-01

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

The Bacillus subtilis ywjI (glpX) gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the class III Fbp enzyme.

PubMed

Jules, Matthieu; Le Chat, Ludovic; Aymerich, Stéphane; Le Coq, Dominique

2009-05-01

We present here experimental evidence that the Bacillus subtilis ywjI gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the fbp-encoded class III enzyme, and constitutes with the upstream gene, murAB, an operon transcribed at the same level under glycolytic or gluconeogenic conditions.

The Bacillus subtilis ywjI (glpX) Gene Encodes a Class II Fructose-1,6-Bisphosphatase, Functionally Equivalent to the Class III Fbp Enzyme▿

PubMed Central

Jules, Matthieu; Le Chat, Ludovic; Aymerich, Stéphane; Le Coq, Dominique

2009-01-01

We present here experimental evidence that the Bacillus subtilis ywjI gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the fbp-encoded class III enzyme, and constitutes with the upstream gene, murAB, an operon transcribed at the same level under glycolytic or gluconeogenic conditions. PMID:19270101

Three patients with signs of acute flail mitral leaflet seen on emergency department echo: a critical constellation within the focused cardiac exam

PubMed Central

Stephenson, George; Wallace, Craig; Mao, Pras; Moore, Chris

2015-01-01

Abstract Acute flail mitral leaflet is a time‐sensitive, reversible cause of cardiogenic shock. Transthoracic echocardiography (echo) is increasingly becoming a vital tool for non‐cardiologist physicians who treat patients with undifferentiated chest pain and dyspnoea. The sonographic abnormalities seen in acute flail mitral leaflet are within the boundaries of a focused echo. Individually, these findings are non‐specific. As a constellation, however, they are highly suggestive of this disease process. We present a case series of three patients with acute flail mitral leaflet seen on emergency department echo along with a discussion of the findings and the disease itself. PMID:28191212

Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages.

PubMed Central

Vasala, A; Dupont, L; Baumann, M; Ritzenthaler, P; Alatossava, T

1993-01-01

Virulent phage LL-H and temperate phage mv4 are two related bacteriophages of Lactobacillus delbrueckii. The gene clusters encoding structural proteins of these two phages have been sequenced and further analyzed. Six open reading frames (ORF-1 to ORF-6) were detected. Protein sequencing and Western immunoblotting experiments confirmed that ORF-3 (g34) encoded the main capsid protein Gp34. The presence of a putative late promoter in front of the phage LL-H g34 gene was suggested by primer extension experiments. Comparative sequence analysis between phage LL-H and phage mv4 revealed striking similarities in the structure and organization of this gene cluster, suggesting that the genes encoding phage structural proteins belong to a highly conservative module. Images PMID:8497043

Mechanism of valvular regurgitation.

PubMed

Khoo, Nee S; Smallhorn, Jeffery F

2011-10-01

Despite improvements in surgical techniques, valvular regurgitation results in major morbidity in children with heart disease. Functional anatomy, mechanisms of valve closure and adaptation to changing hemodynamic stress in normal mitral and tricuspid valves are complex and only partially understood. As well, pathology of atrioventricular valve regurgitation is further complicated by congenital valve abnormalities involving leaflet tissue, supporting chordal apparatus and displaced papillary muscles. This review provides a current understanding of the mechanisms that result in atrioventricular valve failure. Mitral valve leaflets have contractile elements, in addition to atrial muscle modulation of leaflet tension. When placed under mechanical tethering stress, the mitral valve adapts by leaflet expansion, which increases coaptation surface reserve and chordal thickening. Both pediatric and adult studies are increasingly reporting on the importance of subvalvar apparatus function in maintaining valve competency. The maintenance of efficient valve function is accomplished by a complex series of events involving atrial and annular contraction, annular deformation, active leaflet tension, chordal transmission of papillary muscle contractions and ventricular contraction.

Bacillus subtilis 168 Contains Two Differentially Regulated Genes Encoding l-Asparaginase

PubMed Central

Fisher, Susan H.; Wray, Lewis V.

2002-01-01

Expression of the two Bacillus subtilis genes encoding l-asparaginase is controlled by independent regulatory factors. The ansZ gene (formerly yccC) was shown by mutational analysis to encode a functional l-asparaginase, the expression of which is activated during nitrogen-limited growth by the TnrA transcription factor. Gel mobility shift and DNase I footprinting experiments indicate that TnrA regulates ansZ expression by binding to a DNA site located upstream of the ansZ promoter. The expression of the ansA gene, which encodes the second l-asparaginase, was found to be induced by asparagine. The ansA repressor, AnsR, was shown to negatively regulate its own expression. PMID:11914346

Bacillus subtilis 168 contains two differentially regulated genes encoding L-asparaginase.

PubMed

Fisher, Susan H; Wray, Lewis V

2002-04-01

Expression of the two Bacillus subtilis genes encoding L-asparaginase is controlled by independent regulatory factors. The ansZ gene (formerly yccC) was shown by mutational analysis to encode a functional L-asparaginase, the expression of which is activated during nitrogen-limited growth by the TnrA transcription factor. Gel mobility shift and DNase I footprinting experiments indicate that TnrA regulates ansZ expression by binding to a DNA site located upstream of the ansZ promoter. The expression of the ansA gene, which encodes the second L-asparaginase, was found to be induced by asparagine. The ansA repressor, AnsR, was shown to negatively regulate its own expression.

Recombinant DNA encoding a desulfurization biocatalyst

DOEpatents

Rambosek, John; Piddington, Chris S.; Kovacevich, Brian R.; Young, Kevin D.; Denome, Sylvia A.

1994-01-01

This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous.

Flail anterior tricuspid valve leaflet in a neonate: association with maternal antiphospholipid syndrome.

PubMed

Tarca, Adrian J; Eckersley, Luke; Kothari, Darshan

2017-10-01

This brief report describes a case of flail anterior tricuspid valve leaflet in a neonate associated with maternal antiphospholipid syndrome. Fetal echocardiography at 27 weeks of gestation showed competent atrioventricular valves with biventricular echogenic chordae. Fetal distress was noted at delivery, and echocardiography showed a flail anterior leaflet of the tricuspid valve with severe regurgitation. Possible causation and implications of maternal antiphospholipid syndrome are discussed.

Effect of a leaflet given to parents on knowledge of tooth avulsion.

PubMed

Ghaderi, F; Adl, A; Ranjbar, Z

2013-03-01

Parents can play an important role in improving the prognosis of avulsed permanent teeth if they are properly informed about the necessary dental first-aid steps at the time of an accident. The purpose of this study was to assess the knowledge of Shirazi parents in traumatic a simple leaflet on improving their knowledge about this topic. One hundred and fifty parents of children receiving dental care at the Shiraz Dental School participated in this study. Half of the participants received an informative leaflet with the possibility of asking questions about it to an operator, while the other half did not receive any leaflets and served as a control group. Using a questionnaire and a scoring system, the level of knowledge of parents was measured in the following categories: general knowledge of tooth avulsion, knowledge of replantation and primary/permanent teeth, knowledge of how to clean an avulsed tooth, knowledge of extra- oral time, and knowledge of storage, methods and transporting media. The results showed that knowledge level was low among Shirazi parents. Improvements were observed in all the categories of knowledge as a result of reading the leaflet and answering the questions. A simple leaflet is a suitable tool to impart knowledge to parents and improve awareness about tooth avulsion.

Comparison of transcatheter aortic valve and surgical bioprosthetic valve durability: a fatigue simulation study

PubMed Central

Martin, Caitlin; Sun, Wei

2015-01-01

Transcatheter aortic valve (TAV) intervention is now the standard-of-care treatment for inoperable patients and a viable alternative treatment option for high-risk patients with symptomatic aortic stenosis. While the procedure is associated with lower operative risk and shorter recovery times than traditional surgical aortic valve (SAV) replacement, TAV intervention is still not considered for lower-risk patients due in part to concerns about device durability. It is well known that bioprosthetic SAVs have limited durability, and TAVs are generally assumed to have even worse durability, yet there is little long-term data to confirm this suspicion. In this study, TAV and SAV leaflet fatigue due to cyclic loading was investigated through finite element analysis by implementing a computational soft tissue fatigue damage model to describe the behavior of the pericardial leaflets. Under identical loading conditions and with identical leaflet tissue properties, the TAV leaflets sustained higher stresses, strains, and fatigue damage compared to the SAV leaflets. The simulation results suggest that the durability of TAVs may be significantly reduced compared to SAVs to about 7.8 years. The developed computational framework may be useful in optimizing TAV design parameters to improve leaflet durability, and assessing the effects of underexpanded, elliptical, or non-uniformly expanded stent deployment on TAV durability. PMID:26294354

Opening and closing characteristics of the aortic valve after valve-sparing procedures using a new aortic root conduit.

PubMed

De Paulis, R; De Matteis, G M; Nardi, P; Scaffa, R; Buratta, M M; Chiariello, L

2001-08-01

The durability of aortic valve-sparing procedures is negatively affected by increased leaflet stress in the absence of normally shaped sinuses of Valsalva. We compared valve motion after remodeling procedures using a standard conduit and a specifically designed aortic root conduit. Echocardiographic studies of the aortic valve dynamics were performed in 14 patients after remodeling of the aortic root (7 standard conduits, group A; 7 new conduits, group B) and in 7 controls (group C). Opening and closing leaflet velocities and percent of slow closing leaflet displacement were measured. Root distensibility and the pressure strain of the elastic modulus were measured at all root levels. Root distensibility and the pressure strain of the elastic modulus were different in group A and B only at the sinuses (p < 0.001). Opening and closing leaflet velocities were not different among groups. Slow closing leaflet displacement was markedly more evident in group B patients (24.2%+/-1.9% versus 2.5%+/-1.9% in group A, p < 0.001) and similar to controls (22.1%+/-7.9%). The new conduit guarantees dynamic features of the aortic valve leaflets superior to those obtained with standard conduits and more similar to normal subjects.

Determination of the structures of small gold clusters on stepped magnesia by density functional calculations.

PubMed

Damianos, Konstantina; Ferrando, Riccardo

2012-02-21

The structural modifications of small supported gold clusters caused by realistic surface defects (steps) in the MgO(001) support are investigated by computational methods. The most stable gold cluster structures on a stepped MgO(001) surface are searched for in the size range up to 24 Au atoms, and locally optimized by density-functional calculations. Several structural motifs are found within energy differences of 1 eV: inclined leaflets, arched leaflets, pyramidal hollow cages and compact structures. We show that the interaction with the step clearly modifies the structures with respect to adsorption on the flat defect-free surface. We find that leaflet structures clearly dominate for smaller sizes. These leaflets are either inclined and quasi-horizontal, or arched, at variance with the case of the flat surface in which vertical leaflets prevail. With increasing cluster size pyramidal hollow cages begin to compete against leaflet structures. Cage structures become more and more favourable as size increases. The only exception is size 20, at which the tetrahedron is found as the most stable isomer. This tetrahedron is however quite distorted. The comparison of two different exchange-correlation functionals (Perdew-Burke-Ernzerhof and local density approximation) show the same qualitative trends. This journal is © The Royal Society of Chemistry 2012

Morphologic-echocardiographic correlates of Ebstein's malformation.

PubMed

Rusconi, P G; Zuberbuhler, J R; Anderson, R H; Rigby, M L

1991-07-01

The cross-sectional echocardiographic findings were analysed retrospectively in 26 patients with Ebstein's malformation in the light of studies of autopsied specimens from different patients showing this lesion. The salient anatomical feature in diagnosis is the finding of the hinge point of the septal and mural leaflets of the valve within the inlet component of the right ventricle rather than at the atrioventricular junction. The other important feature is the nature of the distal attachment of the leaflets, particularly the anterosuperior one, which can either be in focal or linear fashion. The hinge point of the septal leaflet was noted echocardiographically to be displaced in 19 patients but, significantly, the leaflet was absent in the other seven. Also significant was that the hinge point of the mural leaflet at the crux had been visualized in only 15 of the patients. The anterosuperior leaflet had a distal linear attachment in 20 of the patients, with the anteroseptal commissure becoming a keyhole in six of these through which blood passed to the functional right ventricle. The valve remained a competent structure, even though closing at the junction of atrialized and functional components of the right ventricle rather than at the atrioventricular junction. Cross-sectional echocardiography is the technique of choice with which to display the salient morphological features of Ebstein's malformation.

A highly divergent gene cluster in honey bees encodes a novel silk family.

PubMed

Sutherland, Tara D; Campbell, Peter M; Weisman, Sarah; Trueman, Holly E; Sriskantha, Alagacone; Wanjura, Wolfgang J; Haritos, Victoria S

2006-11-01

The pupal cocoon of the domesticated silk moth Bombyx mori is the best known and most extensively studied insect silk. It is not widely known that Apis mellifera larvae also produce silk. We have used a combination of genomic and proteomic techniques to identify four honey bee fiber genes (AmelFibroin1-4) and two silk-associated genes (AmelSA1 and 2). The four fiber genes are small, comprise a single exon each, and are clustered on a short genomic region where the open reading frames are GC-rich amid low GC intergenic regions. The genes encode similar proteins that are highly helical and predicted to form unusually tight coiled coils. Despite the similarity in size, structure, and composition of the encoded proteins, the genes have low primary sequence identity. We propose that the four fiber genes have arisen from gene duplication events but have subsequently diverged significantly. The silk-associated genes encode proteins likely to act as a glue (AmelSA1) and involved in silk processing (AmelSA2). Although the silks of honey bees and silkmoths both originate in larval labial glands, the silk proteins are completely different in their primary, secondary, and tertiary structures as well as the genomic arrangement of the genes encoding them. This implies independent evolutionary origins for these functionally related proteins.

Photocontrol of the expression of genes encoding chlorophyll a/b binding proteins and small subunit of ribulose-1,5-bisphosphate carboxylase in etiolated seedlings of Lycopersicon esculentum (L. ) and Nicotiana tabacum (L. )

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wehmeyer, B.; Cashmore, A.R.; Schaefer, E.

Phytochrome and the blue ultraviolet-A photoreceptor control light-induced expression of genes encoding the chlorophyll a/b binding protein of photosystem II and photosystem I and the genes for the small subunit of the ribulose-1,5-bisphosphate carboxylase in etiolated seedlings of Lycopersicon esculentum (tomato) and Nicotiana tabacum (tobacco). A high irradiance response also controls the induction of these genes. Genes encoding photosystem II- and I-associated chlorophyll a/b binding proteins both exhibit a transient rapid increase in expression in response to light pulse or to continuous irradiation. In contrast, genes encoding the small subunit exhibit a continuous increase in expression in response to light.more » These distinct expression characteristics are shown to reflect differences at the level of transcription.« less

The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus)

NASA Astrophysics Data System (ADS)

Yue, Jia-Xing; Holland, Nicholas D.; Holland, Linda Z.; Deheyn, Dimitri D.

2016-06-01

Green Fluorescent Protein (GFP) was originally found in cnidarians, and later in copepods and cephalochordates (amphioxus) (Branchiostoma spp). Here, we looked for GFP-encoding genes in Asymmetron, an early-diverged cephalochordate lineage, and found two such genes closely related to some of the Branchiostoma GFPs. Dim fluorescence was found throughout the body in adults of Asymmetron lucayanum, and, as in Branchiostoma floridae, was especially intense in the ripe ovaries. Spectra of the fluorescence were similar between Asymmetron and Branchiostoma. Lineage-specific expansion of GFP-encoding genes in the genus Branchiostoma was observed, largely driven by tandem duplications. Despite such expansion, purifying selection has strongly shaped the evolution of GFP-encoding genes in cephalochordates, with apparent relaxation for highly duplicated clades. All cephalochordate GFP-encoding genes are quite different from those of copepods and cnidarians. Thus, the ancestral cephalochordates probably had GFP, but since GFP appears to be lacking in more early-diverged deuterostomes (echinoderms, hemichordates), it is uncertain whether the ancestral cephalochordates (i.e. the common ancestor of Asymmetron and Branchiostoma) acquired GFP by horizontal gene transfer (HGT) from copepods or cnidarians or inherited it from the common ancestor of copepods and deuterostomes, i.e. the ancestral bilaterians.

Identification and characterization of the gltK gene encoding a membrane-associated glucose transport protein of pseudomonas aeruginosa.

PubMed

Adewoye, L O; Worobec, E A

2000-08-08

The Pseudomonas aeruginosa oprB gene encodes the carbohydrate-selective OprB porin, which translocates substrate molecules across the outer membrane to the periplasmic glucose-binding protein. We identified and cloned two open reading frames (ORFs) flanking the oprB gene but are not in operonic arrangement with the oprB gene. The downstream ORF encodes a putative polypeptide homologous to members of a family of transcriptional repressors, whereas the oprB gene is preceded by an ORF encoding a putative product, which exhibits strong homology to several carbohydrate transport ATP-binding cassette (ABC) proteins. The genomic copy of the upstream ORF was mutagenized by homologous recombination. Analysis of the deletion mutant in comparison with the wild type revealed a significant reduction in [14C] glucose transport activity in the mutant strain, suggesting that this ORF likely encodes the inner membrane component of the glucose ABC transporter. It is thus designated gltK gene to reflect its homology to the Pseudomona fluorescens mtlK and its involvement in the high-affinity glucose transport system. Multiple alignment analysis revealed that the P. aeruginosa gltK gene product is a member of the MalK subfamily of ABC proteins.

Consumer's Perception on Design and Layout of Consumer Medical Information Leaflets on Obesity and Lipid Lowering Drugs.

PubMed

Mathew, Elizabeth M; Rajiah, Kingston; Sharma, Krishana Kumar

2013-12-01

Printed education materials are often used to augment healthcare professional's verbal information to consumers so it serves as an important component of symptom management. They also enhance the teaching process and can be used by consumers as a home reference. This study was aimed to interpret consumers' perception on Consumer Medical Information Leaflets (CMILs) on obesity and lipid lowering drugs, on design and layout using the standard method such as Baker Able Leaflet Design (BALD). Convenience sampling was done. The study was conducted over a period of 3 years in community pharmacy settings in Tamil Nadu, India. The Consumer Medical Information Leaflets (CMILs) were randomly collected from different community pharmacies. Total of 19 CMILs which are commonly used by the consumers were collected and CMILs were assessed using BALD assessment tool Results: According to BALD assessment (46.28%) leaflets were rated as 'above standard' and (53.72) leaflets were rated as 'standard or poor' in layout and design since their scores were less than 25. This shows that this issue may be important from the patient's perspective, which may discourage patient from actually reading the CMILs. In India, generally CMILs are continued to be prepared in English and with higher proportion of consumers with English illiteracy. CMILs, which are prepared without taking consideration of reading level of consumers and proper layout and design, may not achieve the intended purpose. This is an important aspect that any company has to reckon while preparing leaflets and at least in some major local languages in which CMILs have to be prepared.

INTERLAYER MICROMECHANICS OF THE AORTIC HEART VALVE LEAFLET

PubMed Central

Buchanan, Rachel M.; Sacks, Michael S.

2014-01-01

While the mechanical behaviors of the fibrosa and ventricularis layers of the aortic valve (AV) leaflet are understood, little information exists on their mechanical interactions mediated by the GAG-rich central spongiosa layer. Parametric simulations of the interlayer interactions of the AV leaflets in flexure utilized a tri-layered finite element (FE) model of circumferentially oriented tissue sections to investigate inter-layer sliding hypothesized to occur. Simulation results indicated that the leaflet tissue functions as a tightly bonded structure when the spongiosa effective modulus was at least 25% that of the fibrosa and ventricularis layers. Novel studies that directly measured transmural strain in flexure of AV leaflet tissue specimens validated these findings. Interestingly, a smooth transmural strain distribution indicated that the layers of the leaflet indeed act as a bonded unit, consistent with our previous observations (Stella and Sacks, 2007) of a large number of transverse collagen fibers interconnecting the fibrosa and ventricularis layers. Additionally, when the tri-layered FE model was refined to match the transmural deformations, a layer-specific bimodular material model (resulting in four total moduli) accurately matched the transmural strain and moment-curvature relations simultaneously. Collectively, these results provide evidence, contrary to previous assumptions, that the valve layers function as a bonded structure in the low-strain flexure deformation mode. Most likely, this results directly from the transverse collagen fibers that bind the layers together to disable physical sliding and maintain layer residual stresses. Further, the spongiosa may function as a general dampening layer while the AV leaflets deforms as a homogenous structure despite its heterogeneous architecture. PMID:24292631

Neoseiulus californicus (Acari: Phytoseiidae) as a potential control agent of Tetranychus urticae (Acari: Tetranychidae): effect of pest/predator ratio on pest abundance on strawberry.

PubMed

Greco, Nancy M; Sánchez, Norma E; Liljesthröm, Gerardo G

2005-01-01

Neoseiulus californicus (McGregor) is a promising agent for successful Tetranychus urticae Koch control through conservation techniques, in strawberry crops in La Plata (Buenos Aires, Argentina). In prey-predator interaction, initial relative densities have an important effect on system dynamics. The economic threshold level (ETL) used for this pest in the present study was 50 active mites per leaflet. In our laboratory experiments, initial T. urticae to N. californicus ratio had a significant effect on the population abundance of T. urticae at a 7-day period. When pest/predator ratio was 5/1 (at initial pest densities from 5 to 15 females/leaflet) the final number of active T. urticae/leaflet was significantly lower than the ETL, while at 20 females/leaflet this number did not differ from the ETL. At 7.5/1 ratio, the final number of active T. urticae/leaflet, at initial pest densities from 5 to 15 females/leaflet, reached the ETL without surpassing it. At 10/1 and 15/1 ratios, pest densities exceeded the ETL only at 15 initial T. urticae/leaflet. Most greenhouse and field observations were consistent with the predictions of a graphical model based on experimental results. This predator was very effective in limiting pest densities at a 7-day period and within the range of pest-predator ratios and absolute densities used in this study. Conservation of N. californicus promoting favorable pest/predator ratios may result in early control of T. urticae.

Comprehensive 4-stage categorization of bicuspid aortic valve leaflet morphology by cardiac MRI in 386 patients.

PubMed

Murphy, I G; Collins, J; Powell, A; Markl, M; McCarthy, P; Malaisrie, S C; Carr, J C; Barker, A J

2017-08-01

Bicuspid aortic valve (BAV) disease is heterogeneous and related to valve dysfunction and aortopathy. Appropriate follow up and surveillance of patients with BAV may depend on correct phenotypic categorization. There are multiple classification schemes, however a need exists to comprehensively capture commissure fusion, leaflet asymmetry, and valve orifice orientation. Our aim was to develop a BAV classification scheme for use at MRI to ascertain the frequency of different phenotypes and the consistency of BAV classification. The BAV classification scheme builds on the Sievers surgical BAV classification, adding valve orifice orientation, partial leaflet fusion and leaflet asymmetry. A single observer successfully applied this classification to 386 of 398 Cardiac MRI studies. Repeatability of categorization was ascertained with intraobserver and interobserver kappa scores. Sensitivity and specificity of MRI findings was determined from operative reports, where available. Fusion of the right and left leaflets accounted for over half of all cases. Partial leaflet fusion was seen in 46% of patients. Good interobserver agreement was seen for orientation of the valve opening (κ = 0.90), type (κ = 0.72) and presence of partial fusion (κ = 0.83, p < 0.0001). Retrospective review of operative notes showed sensitivity and specificity for orientation (90, 93%) and for Sievers type (73, 87%). The proposed BAV classification schema was assessed by MRI for its reliability to classify valve morphology in addition to illustrating the wide heterogeneity of leaflet size, orifice orientation, and commissural fusion. The classification may be helpful in further understanding the relationship between valve morphology, flow derangement and aortopathy.

Randomised controlled trial using smartphone website vs leaflet to support antenatal perineal massage practice for pregnant women.

PubMed

Takeuchi, Shoko; Horiuchi, Shigeko

2016-10-01

In Japan, the rate of pregnant women who practice antenatal perineal massage was only 15.1%. The aim of this study was to develop and evaluate a smartphone website and a leaflet to support antenatal perineal massage practice for primiparous women. In a randomised control trial, 161 primiparous women were randomly assigned to a smartphone website group (n=81) or a leaflet group (n=80). Data analysis were by per protocol analysis and intention to treat analysis. Of the 161 women participants, 47 in the smartphone website group and 49 in the leaflet group completed all questionnaires. Primary outcome was continuance rate (three times a week over a three week period) of antenatal perineal massage practice. The rates by a per protocol analysis were 51.1% in the smartphone website group and 51.0% in the leaflet group, respectively. There was no significant difference between the groups. Moreover, the rates by an intention to treat analysis were 29.6% in the smartphone website group and 31.3% in the leaflet group, respectively. There was also no significant difference between the groups. There were no significant differences in the evaluation of perineal massage, childbirth self-efficacy, satisfaction with efforts towards childbirth, and perineal outcomes following childbirth which were measured as secondary outcomes between the groups. There was no significant difference in continuance rate of antenatal perineal massage practice between those using a smartphone website and those with a leaflet, however, the rate was better than no instructions. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Isolated Effect of Geometry on Mitral Valve Function for In-Silico Model Development

PubMed Central

Siefert, Andrew William; Rabbah, Jean-Pierre Michel; Saikrishnan, Neelakantan; Kunzelman, Karyn Susanne; Yoganathan, Ajit Prithivaraj

2013-01-01

Computational models for the heart’s mitral valve (MV) exhibit several uncertainties which may be reduced by further developing these models using ground-truth data sets. The present study generated a ground-truth data set by quantifying the effects of isolated mitral annular flattening, symmetric annular dilatation, symmetric papillary muscle displacement, and asymmetric papillary muscle displacement on leaflet coaptation, mitral regurgitation (MR), and anterior leaflet strain. MVs were mounted in an in vitro left heart simulator and tested under pulsatile hemodynamics. Mitral leaflet coaptation length, coaptation depth, tenting area, MR volume, MR jet direction, and anterior leaflet strain in the radial and circumferential directions were successfully quantified for increasing levels of geometric distortion. From these data, increasing levels of isolated papillary muscle displacement resulted in the greatest mean change in coaptation depth (70% increase), tenting area (150% increase), and radial leaflet strain (37% increase) while annular dilatation resulted in the largest mean change in coaptation length (50% decrease) and regurgitation volume (134% increase). Regurgitant jets were centrally located for symmetric annular dilatation and symmetric papillary muscle displacement. Asymmetric papillary muscle displacement resulted in asymmetrically directed jets. Peak changes in anterior leaflet strain in the circumferential direction were smaller and exhibited non-significant differences across the tested conditions. When used together, this ground-truth data may be used to parametrically evaluate and develop modeling assumptions for both the MV leaflets and subvalvular apparatus. This novel data may improve MV computational models and provide a platform for the development of future surgical planning tools. PMID:24059354

Fluid-structure interaction study of transcatheter aortic valve dynamics using smoothed particle hydrodynamics

PubMed Central

Mao, Wenbin; Li, Kewei; Sun, Wei

2016-01-01

Computational modeling of heart valve dynamics incorporating both fluid dynamics and valve structural responses has been challenging. In this study, we developed a novel fully-coupled fluid-structure interaction (FSI) model using smoothed particle hydrodynamics (SPH). A previously developed nonlinear finite element (FE) model of transcatheter aortic valves (TAV) was utilized to couple with SPH to simulate valve leaflet dynamics throughout the entire cardiac cycle. Comparative simulations were performed to investigate the impact of using FE-only models versus FSI models, as well as an isotropic versus an anisotropic leaflet material model in TAV simulations. From the results, substantial differences in leaflet kinematics between FE-only and FSI models were observed, and the FSI model could capture the realistic leaflet dynamic deformation due to its more accurate spatial and temporal loading conditions imposed on the leaflets. The stress and the strain distributions were similar between the FE and FSI simulations. However, the peak stresses were different due to the water hammer effect induced by the flow inertia in the FSI model during the closing phase, which led to 13%–28% lower peak stresses in the FE-only model compared to that of the FSI model. The simulation results also indicated that tissue anisotropy had a minor impact on hemodynamics of the valve. However, a lower tissue stiffness in the radial direction of the leaflets could reduce the leaflet peak stress caused by the water hammer effect. It is hoped that the developed FSI models can serve as an effective tool to better assess valve dynamics and optimize next generation TAV designs. PMID:27844463

Fluid-Structure Interaction Study of Transcatheter Aortic Valve Dynamics Using Smoothed Particle Hydrodynamics.

PubMed

Mao, Wenbin; Li, Kewei; Sun, Wei

2016-12-01

Computational modeling of heart valve dynamics incorporating both fluid dynamics and valve structural responses has been challenging. In this study, we developed a novel fully-coupled fluid-structure interaction (FSI) model using smoothed particle hydrodynamics (SPH). A previously developed nonlinear finite element (FE) model of transcatheter aortic valves (TAV) was utilized to couple with SPH to simulate valve leaflet dynamics throughout the entire cardiac cycle. Comparative simulations were performed to investigate the impact of using FE-only models vs. FSI models, as well as an isotropic vs. an anisotropic leaflet material model in TAV simulations. From the results, substantial differences in leaflet kinematics between FE-only and FSI models were observed, and the FSI model could capture the realistic leaflet dynamic deformation due to its more accurate spatial and temporal loading conditions imposed on the leaflets. The stress and the strain distributions were similar between the FE and FSI simulations. However, the peak stresses were different due to the water hammer effect induced by the fluid inertia in the FSI model during the closing phase, which led to 13-28% lower peak stresses in the FE-only model compared to that of the FSI model. The simulation results also indicated that tissue anisotropy had a minor impact on hemodynamics of the valve. However, a lower tissue stiffness in the radial direction of the leaflets could reduce the leaflet peak stress caused by the water hammer effect. It is hoped that the developed FSI models can serve as an effective tool to better assess valve dynamics and optimize next generation TAV designs.

Light-dependent changes in the leaflet movement rhythm of the plant Desmodium gyrans.

PubMed

Sharma, Vijay Kumar; Bardal, Tom Kristian; Johnsson, Anders

2003-01-01

The movements of the lateral leaflets of the Indian telegraph plant Desmodium gyrans (L. F.) DC, have earlier been studied in detail with regards to the effects of chemicals, DC currents, and static magnetic fields. In the present paper we have discussed the oscillation of the lateral leaflets under the influence of white light of various light levels (0-75 micromol x m(-2) x s(-1)), produced by an array of LEDs (light emitting diodes). LEDs were used in contrast to fluorescense tubes as in earlier studies in order to minimize changes of wavelength when light intensity was decreased or increased. Furthermore, care was taken to ensure that the temperature in the experimental chamber was constant. When the oscillations were first monitored in bright light, the oscillations were found to be very rapid and with decreasing light intensity the oscillations slowed down. For light levels lower than about 20 micromol x m(-2) x s(-1) the period of the oscillation of the lateral leaflets was almost constant (or even decreased slightly towards complete darkness). We also show that the oscillations could completely stop under prolonged darkness (for longer than about 6 h) and that such halted oscillations could be restarted in most of the leaflets when he light was turned back on. Such stopping of the oscillation of the lateral leaflets in prolonged darkness suggests that these short period oscillations of the lateral leaflets could have a daily component and in natural environment these oscillations could serve the purpose of optimising the amount of light falling on the leaflets or/and facilitating transpiration of water through stomata. Such a finding could have an implication for the answer to the long standing question of adaptive significance of short period oscillation of the Indian telegraph plant Desmodium gyrans (L. F.) DC.

Prediction of oxygen distribution in aortic valve leaflet considering diffusion and convection.

PubMed

Wang, Ling; Korossis, Sotirios; Fisher, John; Ingham, Eileen; Jin, Zhongmin

2011-07-01

Oxygen supply and transport is an important consideration in the development of tissue engineered constructs. Previous studies from our group have focused on the effect of tissue thickness on the oxygen diffusion within a three-dimensional aortic valve leaflet model, and highlighted the necessity for additional transport mechanisms such as oxygen convection. The aims of this study were to investigate the effect of interstitial fluid flow within the aortic valve leaflet, induced by the cyclic loading of the leaflet, on oxygen transport. Indentation testing and finite element modelings were employed to derive the biphasic properties of the leaflet tissue. The biphasic properties were subsequently used in the computational modeling of oxygen convection in the leaflet, which was based on the effective interstitial fluid velocity and the tissue deformation. Subsequently, the oxygen profile was predicted within the valve leaflet model by solving the diffusion and convection equation simultaneously utilizing the finite difference method. The compression modulus (E) and hydraulic permeability were determined by adapting a finite element model to the experimental indentation test on valvular tissue, E = 0.05MPa, and k =2.0 mm4/Ns. Finite element model of oxygen convection in valvular tissue incorporating the predicted biphasic properties was developed and the interstitial fluid flow rate was calculated falling in range of 0.025-0.25 mm/s depending on the tissue depth. Oxygen distribution within valvular tissue was predicted using one-dimensional oxygen diffusion model taking into consider the interstitial fluid effect. It was found that convection did enhance the oxygen transport in valvular tissue by up to 68% increase in the minimum oxygen tension within the tissue, depending on the strain level of the tissue as reaction of the magnitude and frequencies of the cardiac loading. The effective interstitial fluid velocity was found to play an important role in enhancing the oxygen transport within the valve leaflet. Such an understanding is important in the development of valvular tissue engineered constructs.

Measurement and reconstruction of the leaflet geometry for a pericardial artificial heart valve.

PubMed

Jiang, Hongjun; Campbell, Gord; Xi, Fengfeng

2005-03-01

This paper describes the measurement and reconstruction of the leaflet geometry for a pericardial heart valve. Tasks involved include mapping the leaflet geometries by laser digitizing and reconstructing the 3D freeform leaflet surface based on a laser scanned profile. The challenge is to design a prosthetic valve that maximizes the benefits offered to the recipient as compared to the normally operating naturally-occurring valve. This research was prompted by the fact that artificial heart valve bioprostheses do not provide long life durability comparable to the natural heart valve, together with the anticipated benefits associated with defining the valve geometries, especially the leaflet geometries for the bioprosthetic and human valves, in order to create a replicate valve fabricated from synthetic materials. Our method applies the concept of reverse engineering in order to reconstruct the freeform surface geometry. A Brown & Shape coordinate measuring machine (CMM) equipped with a HyMARC laser-digitizing system was used to measure the leaflet profiles of a Baxter Carpentier-Edwards pericardial heart valve. The computer software, Polyworks was used to pre-process the raw data obtained from the scanning, which included merging images, eliminating duplicate points, and adding interpolated points. Three methods, creating a mesh model from cloud points, creating a freeform surface from cloud points, and generating a freeform surface by B-splines are presented in this paper to reconstruct the freeform leaflet surface. The mesh model created using Polyworks can be used for rapid prototyping and visualization. To fit a freeform surface to cloud points is straightforward but the rendering of a smooth surface is usually unpredictable. A surface fitted by a group of B-splines fitted to cloud points was found to be much smoother. This method offers the possibility of manually adjusting the surface curvature, locally. However, the process is complex and requires additional manipulation. Finally, this paper presents a reverse engineered design for the pericardial heart valve which contains three identical leaflets with reconstructed geometry.

Participants' preference for type of leaflet used to feed back the results of a randomised trial: a survey.

PubMed

Brealey, Stephen; Andronis, Lazaros; Dennis, Laura; Atwell, Christine; Bryan, Stirling; Coulton, Simon; Cox, Helen; Cross, Ben; Fylan, Fiona; Garratt, Andrew; Gilbert, Fiona; Gillan, Maureen; Hendry, Maggie; Hood, Kerenza; Houston, Helen; King, David; Morton, Veronica; Robling, Michael; Russell, Ian; Wilkinson, Clare

2010-12-01

Hundreds of thousands of volunteers take part in medical research, but many will never hear from researchers about what the study revealed. There is a growing demand for the results of randomised trials to be fed back to research participants both for ethical research practice and for ensuring their co-operation in a trial. This study aims to determine participants' preferences for type of leaflet (short versus long) used to summarise the findings of a randomised trial; and to test whether certain characteristics explained participants' preferences. 553 participants in a randomised trial about General Practitioners' access to Magnetic Resonance Imaging for patients presenting with suspected internal derangement of the knee were asked in the final follow-up questionnaire whether they would like to be fed back the results of the trial. Participants who agreed to this were included in a postal questionnaire survey asking about their preference, if any, between a short and a long leaflet and what it was about the leaflet that they preferred. Multinomial logistic regression was used to test whether certain demographics of responding participants along with treatment group explained whether a participant had a preference for type of leaflet or no preference. Of the participants who returned the final follow-up questionnaire, 416 (88%) agreed to receive the results of the trial. Subsequently 132 (32%) participants responded to the survey. Most participants preferred the longer leaflet (55%) and the main reasons for this were the use of technical information (94%) and diagrams (89%). There was weak evidence to suggest that gender might explain whether participants have a preference for type of leaflet or not (P = 0.084). Trial participants want to receive feed back about the results and appear to prefer a longer leaflet. Males and females might require information to be communicated to them differently and should be the focus of further research. The trial is registered with http://www.isrctn.org/ and ID is ISRCTN76616358.

Planar biaxial testing of heart valve cusp replacement biomaterials: Experiments, theory and material constants.

PubMed

Labrosse, Michel R; Jafar, Reza; Ngu, Janet; Boodhwani, Munir

2016-11-01

Aortic valve (AV) repair has become an attractive option to correct aortic insufficiency. Yet, cusp reconstruction with various cusp replacement materials has been associated with greater long-term repair failures, and it is still unknown how such materials mechanically compare with native leaflets. We used planar biaxial testing to characterize six clinically relevant cusp replacement materials, along with native porcine AV leaflets, to ascertain which materials would be best suited for valve repair. We tested at least six samples of: 1) fresh autologous porcine pericardium (APP), 2) glutaraldehyde fixed porcine pericardium (GPP), 3) St Jude Medical pericardial patch (SJM), 4) CardioCel patch (CC), 5) PeriGuard (PG), 6) Supple PeriGuard (SPG) and 7) fresh porcine AV leaflets (PC). We introduced efficient displacement-controlled testing protocols and processing, as well as advanced convexity requirements on the strain energy functions used to describe the mechanical response of the materials under loading. The proposed experimental and data processing pipeline allowed for a robust in-plane characterization of all the materials tested, with constants determined for two Fung-like hyperelastic, anisotropic strain energy models. Overall, CC and SPG (respectively PG) patches ranked as the closest mechanical equivalents to young (respectively aged) AV leaflets. Because the native leaflets as well as CC, PG and SPG patches exhibit significant anisotropic behaviors, it is suggested that the fiber and cross-fiber directions of these replacement biomaterials be matched with those of the host AV leaflets. The long-term performance of cusp replacement materials would ideally be evaluated in large animal models for AV disease and cusp repair, and over several months or more. Given the unavailability and impracticality of such models, detailed information on stress-strain behavior, as studied herein, and investigations of durability and valve dynamics will be the best surrogates, as they have been for prosthetic valves. Overall, comparison with Fig. 3 suggests that CC and SPG (respectively PG) patches may be the closest mechanical equivalents to young (respectively aged) AV leaflets. Interestingly, the thicknesses of these materials are close to those reported for porcine and younger human AV leaflets, which may facilitate surgical implantation, by contrast to the thinner APP which has poor handling qualities. Because the native leaflets as well as CC, PG and SPG patches exhibit anisotropic behaviors, from a mechanistic perspective alone, it stands to reason that cardiac surgeons should seek to intraoperatively match the fiber and cross-fiber directions of these replacement biomaterials with those of the repaired AV leaflets. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Recombinant DNA encoding a desulfurization biocatalyst

DOEpatents

Rambosek, J.; Piddington, C.S.; Kovacevich, B.R.; Young, K.D.; Denome, S.A.

1994-10-18

This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous. 13 figs.

Structure, Function, Interaction, Co-evolution of Rice Blast Resistance Genes

USDA-ARS?s Scientific Manuscript database

Rice blast disease caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive rice diseases worldwide. Resistance (R) genes to blast encode proteins that detect pathogen signaling molecules encoded by M. oryzae avirulence (AVR) genes. R genes can be a single or a member of clu...

Molecular genetics of Erwinia amylovora involved in the development of fire blight.

PubMed

Oh, Chang-Sik; Beer, Steven V

2005-12-15

The bacterial plant pathogen, Erwinia amylovora, causes the devastating disease known as fire blight in some Rosaceous plants like apple, pear, quince, raspberry and several ornamentals. Knowledge of the factors affecting the development of fire blight has mushroomed in the last quarter century. On the molecular level, genes encoding a Hrp type III secretion system, genes encoding enzymes involved in synthesis of extracellular polysaccharides and genes facilitating the growth of E. amylovora in its host plants have been characterized. The Hrp pathogenicity island, delimited by genes suggesting horizontal gene transfer, is composed of four distinct regions, the hrp/hrc region, the HEE (Hrp effectors and elicitors) region, the HAE (Hrp-associated enzymes) region, and the IT (Island transfer) region. The Hrp pathogenicity island encodes a Hrp type III secretion system (TTSS), which delivers several proteins from bacteria to plant apoplasts or cytoplasm. E. amylovora produces two exopolysaccharides, amylovoran and levan, which cause the characteristic fire blight wilting symptom in host plants. In addition, other genes, and their encoded proteins, have been characterized as virulence factors of E. amylovora that encode enzymes facilitating sorbitol metabolism, proteolytic activity and iron harvesting. This review summarizes our understanding of the genes and gene products of E. amylovora that are involved in the development of the fire blight disease.

The Drosophila pigmentation gene pink (p) encodes a homologue of human Hermansky-Pudlak syndrome 5 (HPS5).

PubMed

Falcón-Pérez, Juan M; Romero-Calderón, Rafael; Brooks, Elizabeth S; Krantz, David E; Dell'Angelica, Esteban C

2007-02-01

Lysosome-related organelles comprise a group of specialized intracellular compartments that include melanosomes and platelet dense granules (in mammals) and eye pigment granules (in insects). In humans, the biogenesis of these organelles is defective in genetic disorders collectively known as Hermansky-Pudlak syndrome (HPS). Patients with HPS-2, and two murine HPS models, carry mutations in genes encoding subunits of adaptor protein (AP)-3. Other genes mutated in rodent models include those encoding VPS33A and Rab38. Orthologs of all of these genes in Drosophila melanogaster belong to the 'granule group' of eye pigmentation genes. Other genes associated with HPS encode subunits of three complexes of unknown function, named biogenesis of lysosome-related organelles complex (BLOC)-1, -2 and -3, for which the Drosophila counterparts had not been characterized. Here, we report that the gene encoding the Drosophila ortholog of the HPS5 subunit of BLOC-2 is identical to the granule group gene pink (p), which was first studied in 1910 but had not been identified at the molecular level. The phenotype of pink mutants was exacerbated by mutations in AP-3 subunits or in the orthologs of VPS33A and Rab38. These results validate D. melanogaster as a genetic model to study the function of the BLOCs.

Chlorella viruses contain genes encoding a complete polyamine biosynthetic pathway

PubMed Central

Baumann, Sascha; Sander, Adrianne; Gurnon, James R.; Yanai-Balser, Giane; VanEtten, James L.; Piotrowski, Markus

2007-01-01

Two genes encoding the putative polyamine biosynthetic enzymes agmatine iminohydrolase (AIH) and N-carbamoylputrescine amidohydrolase (CPA) were cloned from the chloroviruses PBCV-1, NY-2A and MT325. They were expressed in Escherichia coli to form C-terminal (His)6-tagged proteins and the recombinant proteins were purified by Ni2+- binding affinity chromatography. The biochemical properties of the two enzymes are similar to AIH and CPA enzymes from Arabidopsis thaliana and Pseudomonas aeruginosa. Together with the previously known virus genes encoding ornithine/arginine decarboxlyase (ODC/ADC) and homospermidine synthase, the chloroviruses have genes that encode a complete set of functional enzymes that synthesize the rare polyamine homospermidine from arginine via agmatine, N-carbamoylputrescine and putrescine. The PBCV-1 aih and cpa genes are expressed early during virus infection together with the odc/adc gene, suggesting that biosynthesis of putrescine is important in early stages of viral replication. The aih and cpa genes are widespread in the chlorella viruses. PMID:17101165

A Comprehensive Analysis of Nuclear-Encoded Mitochondrial Genes in Schizophrenia.

PubMed

Gonçalves, Vanessa F; Cappi, Carolina; Hagen, Christian M; Sequeira, Adolfo; Vawter, Marquis P; Derkach, Andriy; Zai, Clement C; Hedley, Paula L; Bybjerg-Grauholm, Jonas; Pouget, Jennie G; Cuperfain, Ari B; Sullivan, Patrick F; Christiansen, Michael; Kennedy, James L; Sun, Lei

2018-05-01

The genetic risk factors of schizophrenia (SCZ), a severe psychiatric disorder, are not yet fully understood. Multiple lines of evidence suggest that mitochondrial dysfunction may play a role in SCZ, but comprehensive association studies are lacking. We hypothesized that variants in nuclear-encoded mitochondrial genes influence susceptibility to SCZ. We conducted gene-based and gene-set analyses using summary association results from the Psychiatric Genomics Consortium Schizophrenia Phase 2 (PGC-SCZ2) genome-wide association study comprising 35,476 cases and 46,839 control subjects. We applied the MAGMA method to three sets of nuclear-encoded mitochondrial genes: oxidative phosphorylation genes, other nuclear-encoded mitochondrial genes, and genes involved in nucleus-mitochondria crosstalk. Furthermore, we conducted a replication study using the iPSYCH SCZ sample of 2290 cases and 21,621 control subjects. In the PGC-SCZ2 sample, 1186 mitochondrial genes were analyzed, among which 159 had p values < .05 and 19 remained significant after multiple testing correction. A meta-analysis of 818 genes combining the PGC-SCZ2 and iPSYCH samples resulted in 104 nominally significant and nine significant genes, suggesting a polygenic model for the nuclear-encoded mitochondrial genes. Gene-set analysis, however, did not show significant results. In an in silico protein-protein interaction network analysis, 14 mitochondrial genes interacted directly with 158 SCZ risk genes identified in PGC-SCZ2 (permutation p = .02), and aldosterone signaling in epithelial cells and mitochondrial dysfunction pathways appeared to be overrepresented in this network of mitochondrial and SCZ risk genes. This study provides evidence that specific aspects of mitochondrial function may play a role in SCZ, but we did not observe its broad involvement even using a large sample. Copyright © 2018 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

The ribosomal protein genes and Minute loci of Drosophila melanogaster

PubMed Central

Marygold, Steven J; Roote, John; Reuter, Gunter; Lambertsson, Andrew; Ashburner, Michael; Millburn, Gillian H; Harrison, Paul M; Yu, Zhan; Kenmochi, Naoya; Kaufman, Thomas C; Leevers, Sally J; Cook, Kevin R

2007-01-01

Background Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes. Results We combined bioinformatic and genetic approaches to conduct a systematic analysis of the relationship between RP genes and Minute loci. First, we identified 88 genes encoding 79 different cytoplasmic RPs (CRPs) and 75 genes encoding distinct mitochondrial RPs (MRPs). Interestingly, nine CRP genes are present as duplicates and, while all appear to be functional, one member of each gene pair has relatively limited expression. Next, we defined 65 discrete Minute loci by genetic criteria. Of these, 64 correspond to, or very likely correspond to, CRP genes; the single non-CRP-encoding Minute gene encodes a translation initiation factor subunit. Significantly, MRP genes and more than 20 CRP genes do not correspond to Minute loci. Conclusion This work answers a longstanding question about the molecular nature of Minute loci and suggests that Minute phenotypes arise from suboptimal protein synthesis resulting from reduced levels of cytoribosomes. Furthermore, by identifying the majority of haplolethal and haplosterile loci at the molecular level, our data will directly benefit efforts to attain complete deletion coverage of the D. melanogaster genome. PMID:17927810

Identifying metabolic enzymes with multiple types of association evidence

PubMed Central

Kharchenko, Peter; Chen, Lifeng; Freund, Yoav; Vitkup, Dennis; Church, George M

2006-01-01

Background Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes. Results We present a novel method for identifying genes encoding for a specific metabolic function based on a local structure of metabolic network and multiple types of functional association evidence, including clustering of genes on the chromosome, similarity of phylogenetic profiles, gene expression, protein fusion events and others. Using E. coli and S. cerevisiae metabolic networks, we illustrate predictive ability of each individual type of association evidence and show that significantly better predictions can be obtained based on the combination of all data. In this way our method is able to predict 60% of enzyme-encoding genes of E. coli metabolism within the top 10 (out of 3551) candidates for their enzymatic function, and as a top candidate within 43% of the cases. Conclusion We illustrate that a combination of genome context and other functional association evidence is effective in predicting genes encoding metabolic enzymes. Our approach does not rely on direct sequence homology to known enzyme-encoding genes, and can be used in conjunction with traditional homology-based metabolic reconstruction methods. The method can also be used to target orphan metabolic activities. PMID:16571130

[High gene conversion frequency between genes encoding 2-deoxyglucose-6-phosphate phosphatase in 3 Saccharomyces species].

PubMed

Piscopo, Sara-Pier; Drouin, Guy

2014-05-01

Gene conversions are nonreciprocal sequence exchanges between genes. They are relatively common in Saccharomyces cerevisiae, but few studies have investigated the evolutionary fate of gene conversions or their functional impacts. Here, we analyze the evolution and impact of gene conversions between the two genes encoding 2-deoxyglucose-6-phosphate phosphatase in S. cerevisiae, Saccharomyces paradoxus and Saccharomyces mikatae. Our results demonstrate that the last half of these genes are subject to gene conversions among these three species. The greater similarity and the greater percentage of GC nucleotides in the converted regions, as well as the absence of long regions of adjacent common converted sites, suggest that these gene conversions are frequent and occur independently in all three species. The high frequency of these conversions probably result from the fact that they have little impact on the protein sequences encoded by these genes.

Secretion Trap Tagging of Secreted and Membrane-Spanning Proteins Using Arabidopsis Gene Traps

Treesearch

Andrew T. Groover; Joseph R. Fontana; Juana M. Arroyo; Cristina Yordan; W. Richard McCombie; Robert A. Martienssen

2003-01-01

Secreted and membrane-spanning proteins play fundamental roles in plant development but pose challenges for genetic identification and characterization. We describe a "secretion trap" screen for gene trap insertions in genes encoding proteins routed through the secretory pathway. The gene trap transposon encodes a ß-glucuronidase reporter enzyme...

A deep auto-encoder model for gene expression prediction.

PubMed

Xie, Rui; Wen, Jia; Quitadamo, Andrew; Cheng, Jianlin; Shi, Xinghua

2017-11-17

Gene expression is a key intermediate level that genotypes lead to a particular trait. Gene expression is affected by various factors including genotypes of genetic variants. With an aim of delineating the genetic impact on gene expression, we build a deep auto-encoder model to assess how good genetic variants will contribute to gene expression changes. This new deep learning model is a regression-based predictive model based on the MultiLayer Perceptron and Stacked Denoising Auto-encoder (MLP-SAE). The model is trained using a stacked denoising auto-encoder for feature selection and a multilayer perceptron framework for backpropagation. We further improve the model by introducing dropout to prevent overfitting and improve performance. To demonstrate the usage of this model, we apply MLP-SAE to a real genomic datasets with genotypes and gene expression profiles measured in yeast. Our results show that the MLP-SAE model with dropout outperforms other models including Lasso, Random Forests and the MLP-SAE model without dropout. Using the MLP-SAE model with dropout, we show that gene expression quantifications predicted by the model solely based on genotypes, align well with true gene expression patterns. We provide a deep auto-encoder model for predicting gene expression from SNP genotypes. This study demonstrates that deep learning is appropriate for tackling another genomic problem, i.e., building predictive models to understand genotypes' contribution to gene expression. With the emerging availability of richer genomic data, we anticipate that deep learning models play a bigger role in modeling and interpreting genomics.

Educating adolescents about healthy sleep: experimental study of effectiveness of educational leaflet.

PubMed

Bakotić, Marija; Radosević-Vidacek, Biserka; Kosćec, Adrijana

2009-04-01

To evaluate how exposure to educational leaflet about healthy sleep affects knowledge about sleep in adolescents. The study included students aged 15-18 years from 12 high schools (1209 participants; 85% of eligible study population). Multistage sampling was used and the selected schools were randomly assigned into two intervention groups and two control groups, according to the Solomon experimental design. Intervention groups received educational leaflets and control groups did not. In one of the intervention groups and one of the control groups, pre-testing of knowledge about sleep was performed. Students answered the Sleep Knowledge Test, which was constructed in accordance with the information on the leaflet. Data were analyzed by four-way ANOVA and additional analyses of simple main effects were performed. Positive effect of educational leaflet was found in students aged 15 (F = 28.46; P < 0.001), 16 (F = 5.74; P = 0.017), and 17 (F = 17.17; P < 0.001), but there was no effect in students aged 18 (P = 0.467). In male students, positive effect of the leaflet was found only in the group that had not been pre-tested (F = 6.29; P = 0.012), while in female students, it was found in both pre-tested (F = 26.24; P < 0.001) and not pre-tested group (F = 17.36; P < 0.001), with greater effect in pre-tested group (F = 5.70; P = 0.017). Female students generally showed better knowledge about sleep than male students (F = 95.95; P < 0.001). Educational leaflets can be an effective first step in educating younger high school students about healthy sleep, with the method being more effective in female adolescents.

Model of an asymmetric DPPC/DPPS membrane: effect of asymmetry on the lipid properties. A molecular dynamics simulation study.

PubMed

López Cascales, J J; Otero, T F; Smith, Bradley D; González, Carlos; Márquez, M

2006-02-09

The study of asymmetric lipid bilayers is of a crucial importance due to the great number of biological process in which they are involved such as exocytosis, intracellular fusion processes, phospholipid-protein interactions, and signal transduction pathway. In addition, the loss of this asymmetry is a hallmark of the early stages of apoptosis. In this regard, a model of an asymmetric lipid bilayer composed of DPPC and DPPS was simulated by molecular dynamics simulation. Thus, the asymmetric membrane was modeled by 264 lipids, of which 48 corresponded to DPPS- randomly distributed in the same leaflet with 96 DPPC. In the other leaflet, 120 DPPC were placed without DPPS-. Due to the presence of a net charge of -1 for the DPPS- in physiological conditions, 48 Na+ were introduced into the system to balance the charge. To ascertain whether the presence of the DPPS- in only one of the two leaflets perturbs the properties of the DPPC in the other leaflet composed only of DPPC, different properties were studied, such as the atomic density of the different components across the membrane, the electrostatic potential across the membrane, the translational diffusion of DPPC and DPPS, the deuterium order parameters, lipid hydration, and lipid-lipid charge bridges. Thus, we obtained that certain properties such as the surface area lipid molecule, lipid head orientation, order parameter, translational diffusion coefficient, or lipid hydration of DPPC in the leaflet without DPPS remain unperturbed by the presence of DPPS in the other leaflet, compared with a DPPC bilayer. On the other hand, in the leaflet containing DPPS, some of the DPPC properties were strongly affected by the presence of DPPS such as the order parameter or electrostatic potential.

Consumer’s Perception on Design and Layout of Consumer Medical Information Leaflets on Obesity and Lipid Lowering Drugs

PubMed Central

Mathew, Elizabeth M.; Rajiah, Kingston; Sharma, Krishana Kumar

2013-01-01

Background: Printed education materials are often used to augment healthcare professional’s verbal information to consumers so it serves as an important component of symptom management. They also enhance the teaching process and can be used by consumers as a home reference. Objective: This study was aimed to interpret consumers’ perception on Consumer Medical Information Leaflets (CMILs) on obesity and lipid lowering drugs, on design and layout using the standard method such as Baker Able Leaflet Design (BALD). Material and Methods: Convenience sampling was done. The study was conducted over a period of 3 years in community pharmacy settings in Tamil Nadu, India. The Consumer Medical Information Leaflets (CMILs) were randomly collected from different community pharmacies. Total of 19 CMILs which are commonly used by the consumers were collected and CMILs were assessed using BALD assessment tool Results: According to BALD assessment (46.28%) leaflets were rated as ‘above standard’ and (53.72) leaflets were rated as ‘standard or poor’ in layout and design since their scores were less than 25. This shows that this issue may be important from the patient’s perspective, which may discourage patient from actually reading the CMILs. Conclusion: In India, generally CMILs are continued to be prepared in English and with higher proportion of consumers with English illiteracy. CMILs, which are prepared without taking consideration of reading level of consumers and proper layout and design, may not achieve the intended purpose. This is an important aspect that any company has to reckon while preparing leaflets and at least in some major local languages in which CMILs have to be prepared. PMID:24551641

Evolving Techniques for Mitral Valve Reconstruction

PubMed Central

Galloway, Aubrey C.; Grossi, Eugene A.; Bizekis, Costas S.; Ribakove, Greg; Ursomanno, Patricia; Delianides, Julie; Baumann, F. Gregory; Spencer, Frank C.; Colvin, Stephen B.

2002-01-01

Objective To analyze the effectiveness of new techniques of mitral valve reconstruction (MVR) that have evolved over the last decade, such as aggressive anterior leaflet repair and minimally invasive surgery using an endoaortic balloon occluder. Summary Background Data MVR via conventional sternotomy has been an established treatment for mitral insufficiency for over 20 years, primarily for the treatment of patients with posterior leaflet prolapse. Methods Between June 1980 and June 2001, 1,195 consecutive patients had MVR with ring annuloplasty. Conventional sternotomy was used in 843 patients, minimally invasive surgery in 352 (since June 1996). Anterior leaflet repair was performed in 374 patients, with increasing use over the last 10 years. Follow-up was 100% complete (mean 4.6 years, range 0.5–20.5). Results Hospital mortality was 4.7% overall and 1.4% for isolated MVR (1.1% for minimally invasive surgery vs. 1.6% for conventional sternotomy;P = .4). Multivariate analysis showed the factors predictive of increased operative risk to be age, NYHA functional class, concomitant procedures, and previous cardiac surgery. The 5-year results for freedom from cardiac death, reoperation, and valve-related complications among the 782 patients with degenerative etiology are, respectively, as follows (P > .05 for all end points): for anterior leaflet repair, 93%, 94%, 90%; for no anterior leaflet repair, 91%, 92%, 91%; for minimally invasive surgery, 97%, 89%, 93%; and for conventional sternotomy, 93%, 94%, 90%. Conclusions These findings indicate that late results of MVR after minimally invasive surgery and after anterior leaflet repair are equivalent to those achievable with conventional sternotomy and posterior leaflet repair. These options significantly expand the range of patients suitable for mitral valve repair surgery and give further evidence to support wider use of minimally invasive techniques. PMID:12192315

Biomechanical and ultrastructural comparison of cryopreservation and a novel cellular extraction of porcine aortic valve leaflets.

PubMed

Courtman, D W; Pereira, C A; Omar, S; Langdon, S E; Lee, J M; Wilson, G J

1995-12-01

Heart valve substitutes of biological origin often fail by degenerative mechanisms. Many authors have hypothesized that mechanical fatigue and structural degradation are instrumental to in vivo failure. Since the properties of the structural matrix at implantation may predetermine failure, we have examined the ultrastructure, fracture, mechanics, and uniaxial high-strain-rate viscoelastic properties of: (1) fresh, (2) cryopreserved, and (3) cellular extracted porcine aortic valve leaflets. The cellular extraction process is being developed in order to reduce immunological attack and calcification. Cryopreservation causes cellular disruption and necrotic changes throughout the tissue, whereas extraction removes all cells and lipid membranes. Both processes leave an intact collagen and elastin structural matrix and preserve the high-strain-rate viscoelastic characteristics of the fresh leaflets. Extraction does cause a 20% reduction in the fracture tension and increases tissue extensibility, with the percent strain at fracture rising to 45.3 +/- 4 (mean +/- SEM) from 31.5 +/- 3 for fresh leaflets. However, extraction does preserve matrix structure and mechanics over the physiological loading range. Glutaraldehyde fixation produces increased extensibility, increased elastic behavior, and, when applied to extracted leaflets, it causes a marked drop in fracture tension, to 50% of that for fresh leaflets. The combination of extraction and fixation may lead to early degenerative failure. The cellular extraction technique alone may be a useful alternative to glutaraldehyde fixation in preparing bioprosthetic heart valves.

Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes.

PubMed

Ghoshroy, Sohini; Robertson, Deborah L

2015-01-01

Nitrogen assimilation is a highly regulated process requiring metabolic coordination of enzymes and pathways in the cytosol, chloroplast, and mitochondria. Previous studies of prasinophyte genomes revealed that genes encoding nitrate and ammonium transporters have a complex evolutionary history involving both vertical and horizontal transmission. Here we examine the evolutionary history of well-conserved nitrogen-assimilating enzymes to determine if a similar complex history is observed. Phylogenetic analyses suggest that genes encoding glutamine synthetase (GS) III in the prasinophytes evolved by horizontal gene transfer from a member of the heterokonts. In contrast, genes encoding GSIIE, a canonical vascular plant and green algal enzyme, were found in the Micromonas genomes but have been lost from Ostreococcus. Phylogenetic analyses placed the Micromonas GSIIs in a larger chlorophyte/vascular plant clade; a similar topology was observed for ferredoxin-dependent nitrite reductase (Fd-NiR), indicating the genes encoding GSII and Fd-NiR in these prasinophytes evolved via vertical transmission. Our results show that genes encoding the nitrogen-assimilating enzymes in Micromonas and Ostreococcus have been differentially lost and as well as recruited from different evolutionary lineages, suggesting that the regulation of nitrogen assimilation in prasinophytes will differ from other green algae.

Living colors in the gray mold pathogen Botrytis cinerea: codon-optimized genes encoding green fluorescent protein and mCherry, which exhibit bright fluorescence.

PubMed

Leroch, Michaela; Mernke, Dennis; Koppenhoefer, Dieter; Schneider, Prisca; Mosbach, Andreas; Doehlemann, Gunther; Hahn, Matthias

2011-05-01

The green fluorescent protein (GFP) and its variants have been widely used in modern biology as reporters that allow a variety of live-cell imaging techniques. So far, GFP has rarely been used in the gray mold fungus Botrytis cinerea because of low fluorescence intensity. The codon usage of B. cinerea genes strongly deviates from that of commonly used GFP-encoding genes and reveals a lower GC content than other fungi. In this study, we report the development and use of a codon-optimized version of the B. cinerea enhanced GFP (eGFP)-encoding gene (Bcgfp) for improved expression in B. cinerea. Both the codon optimization and, to a smaller extent, the insertion of an intron resulted in higher mRNA levels and increased fluorescence. Bcgfp was used for localization of nuclei in germinating spores and for visualizing host penetration. We further demonstrate the use of promoter-Bcgfp fusions for quantitative evaluation of various toxic compounds as inducers of the atrB gene encoding an ABC-type drug efflux transporter of B. cinerea. In addition, a codon-optimized mCherry-encoding gene was constructed which yielded bright red fluorescence in B. cinerea.

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones

PubMed Central

Glass, Jennifer B.; Kretz, Cecilia B.; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L.; Buck, Kristen N.; Landing, William M.; Morton, Peter L.; Moffett, James W.; Giovannoni, Stephen J.; Vergin, Kevin L.; Stewart, Frank J.

2015-01-01

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO3−, NO2−, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu. PMID:26441925

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones.

PubMed

Glass, Jennifer B; Kretz, Cecilia B; Ganesh, Sangita; Ranjan, Piyush; Seston, Sherry L; Buck, Kristen N; Landing, William M; Morton, Peter L; Moffett, James W; Giovannoni, Stephen J; Vergin, Kevin L; Stewart, Frank J

2015-01-01

Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O2, NO[Formula: see text], NO[Formula: see text], Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding proteins in 21 metagenomes and 9 metatranscriptomes from Eastern Tropical North and South Pacific oxygen minimum zones and 7 metagenomes from the Bermuda Atlantic Time-series Station. Dissolved Fe concentrations increased sharply at upper oxic-anoxic transition zones, with the highest Fe:Cu molar ratio (1.8) occurring at the anoxic core of the Eastern Tropical North Pacific oxygen minimum zone and matching the predicted maximum ratio based on data from diverse ocean sites. The relative abundance of genes encoding Fe-binding proteins was negatively correlated with O2, driven by significant increases in genes encoding Fe-proteins involved in dissimilatory nitrogen metabolisms under anoxia. Transcripts encoding cytochrome c oxidase, the Fe- and Cu-containing terminal reductase in aerobic respiration, were positively correlated with O2 content. A comparison of the taxonomy of genes encoding Fe- and Cu-binding vs. bulk proteins in OMZs revealed that Planctomycetes represented a higher percentage of Fe genes while Thaumarchaeota represented a higher percentage of Cu genes, particularly at oxyclines. These results are broadly consistent with higher relative abundance of genes encoding Fe-proteins in the genome of a marine planctomycete vs. higher relative abundance of genes encoding Cu-proteins in the genome of a marine thaumarchaeote. These findings highlight the importance of metalloenzymes for microbial processes in oxygen minimum zones and suggest preferential Cu use in oxic habitats with Cu > Fe vs. preferential Fe use in anoxic niches with Fe > Cu.

Microstructured Nickel-Titanium Thin Film Leaflets for Hybrid Tissue Engineered Heart Valves Fabricated by Magnetron Sputter Deposition.

PubMed

Loger, K; Engel, A; Haupt, J; Lima de Miranda, R; Lutter, G; Quandt, E

2016-03-01

Heart valves are constantly exposed to high dynamic loading and are prone to degeneration. Therefore, it is a challenge to develop a durable heart valve substitute. A promising approach in heart valve engineering is the development of hybrid scaffolds which are composed of a mechanically strong inorganic mesh enclosed by valvular tissue. In order to engineer an efficient, durable and very thin heart valve for transcatheter implantations, we developed a fabrication process for microstructured heart valve leaflets made from a nickel-titanium (NiTi) thin film shape memory alloy. To examine the capability of microstructured NiTi thin film as a matrix scaffold for tissue engineered hybrid heart valves, leaflets were successfully seeded with smooth muscle cells (SMCs). In vitro pulsatile hydrodynamic testing of the NiTi thin film valve leaflets demonstrated that the SMC layer significantly improved the diastolic sufficiency of the microstructured leaflets, without affecting the systolic efficiency. Compared to an established porcine reference valve model, magnetron sputtered NiTi thin film material demonstrated its suitability for hybrid tissue engineered heart valves.

Flow-Induced Mitral Leaflet Motion in Hypertrophic Cardiomyopathy

NASA Astrophysics Data System (ADS)

Meschini, Valentina; Mittal, Rajat; Verzicco, Roberto

2017-11-01

Hypertrophic cardiomyopathy (HCM) is considered the cause of sudden cardiac death in developed countries. Clinically it is found to be related to the thickening of the intra-ventricular septum combined with elongated mitral leaflets. During systole the low pressure, induced by the abnormal velocities in the narrowed aortic channel, can attract one or both the mitral leaflets causing the aortic obstruction and sometimes instantaneous death. In this paper a fluid structure interaction model for the flow in the left ventricle with a native mitral valve is employed to investigate the physio-pathology of HCM. The problem is studied using direct numerical simulations of the Navier-Stokes equations with a two-way coupled structural solver based on interaction potential approach for the structure dynamics. Simulations are performed for two different degrees of hypertrophy, and two values of pumping efficiency. The leaflets dynamics and the ventricle deformation resulting from the echocardiography of patients affected by HCM are well captured by the simulations. Moreover, the procedures of leaflets plication and septum myectomy are simulated in order to get insights into the efficiency and reliability of such surgery.

Efficient replacement of plasma membrane outer leaflet phospholipids and sphingolipids in cells with exogenous lipids

PubMed Central

Kim, JiHyun; Huang, Zhen; St. Clair, Johnna R.; Brown, Deborah A.; London, Erwin

2016-01-01

Our understanding of membranes and membrane lipid function has lagged far behind that of nucleic acids and proteins, largely because it is difficult to manipulate cellular membrane lipid composition. To help solve this problem, we show that methyl-α-cyclodextrin (MαCD)-catalyzed lipid exchange can be used to maximally replace the sphingolipids and phospholipids in the outer leaflet of the plasma membrane of living mammalian cells with exogenous lipids, including unnatural lipids. In addition, lipid exchange experiments revealed that 70–80% of cell sphingomyelin resided in the plasma membrane outer leaflet; the asymmetry of metabolically active cells was similar to that previously defined for erythrocytes, as judged by outer leaflet lipid composition; and plasma membrane outer leaflet phosphatidylcholine had a significantly lower level of unsaturation than phosphatidylcholine in the remainder of the cell. The data also provided a rough estimate for the total cellular lipids residing in the plasma membrane (about half). In addition to such lipidomics applications, the exchange method should have wide potential for investigations of lipid function and modification of cellular behavior by modification of lipids. PMID:27872310

Efficient replacement of plasma membrane outer leaflet phospholipids and sphingolipids in cells with exogenous lipids.

PubMed

Li, Guangtao; Kim, JiHyun; Huang, Zhen; St Clair, Johnna R; Brown, Deborah A; London, Erwin

2016-12-06

Our understanding of membranes and membrane lipid function has lagged far behind that of nucleic acids and proteins, largely because it is difficult to manipulate cellular membrane lipid composition. To help solve this problem, we show that methyl-α-cyclodextrin (MαCD)-catalyzed lipid exchange can be used to maximally replace the sphingolipids and phospholipids in the outer leaflet of the plasma membrane of living mammalian cells with exogenous lipids, including unnatural lipids. In addition, lipid exchange experiments revealed that 70-80% of cell sphingomyelin resided in the plasma membrane outer leaflet; the asymmetry of metabolically active cells was similar to that previously defined for erythrocytes, as judged by outer leaflet lipid composition; and plasma membrane outer leaflet phosphatidylcholine had a significantly lower level of unsaturation than phosphatidylcholine in the remainder of the cell. The data also provided a rough estimate for the total cellular lipids residing in the plasma membrane (about half). In addition to such lipidomics applications, the exchange method should have wide potential for investigations of lipid function and modification of cellular behavior by modification of lipids.

Photosynthetic carbon metabolism in leaflets, stipules and tendrils of Pisum sativum L

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cote, R.; Grodzinski, B.

1990-05-01

Gas exchange and photosynthetic carbon metabolism have been investigated for each of the dominant parts of the pea leaf (P. sativum) in a normal and a semi-leafless phenotype (cv. Improved Laxton's Progress, and cv. Curly, respectively). On a fresh weight basis, net photosynthesis of leaflets and stipules have similar rates, while in tendrils the rte is 40% lower. However, on a surface area basis, tendrils are only 5-10% less efficient photosynthetically when the area is corrected by a factor {pi}/2. Transpiration rates are similar for leaflets and stipules, but double for tendrils even though stomatal frequency on tendrils is reducedmore » by 50%. Dark respiration is higher in tendrils than leaflets and stipules. Gas exchange is comparable in both cultivars. The early {sup 14}C-labelled products of stipules, leaflets and tendrils are similar in both phenotypes, however the tendrils clearly partition about 2-3 times more of the newly fixed {sup 14}CO{sub 2} into the amino acid fraction. These data will be discussed in relation to the anatomy and function of pea tendrils.« less

Design and ergonomics of package inserts of drugs in Brazil: a reality in construction.

PubMed

da Silva, Charles Ricardo Leite; Soares, Marcelo Marcio

2012-01-01

This research deals with the design of leaflets of medicines, evidencing the problems resulting from the lack of Brazilian normalization to promote the use of the graphical representation of instructional texts warnings. It approaches studies related to the effectiveness and efficiency of information systems, highlighting the semiotics and the cultural and informational ergonomics. The analysis of the context uses as method, an analytical study on selected warnings of thirty leaflets of medicines, followed by interviews lead with the public managers involved with the regulation of the pharmaceutical companies, and two experiments with users performed in city of Recife, in State of Pernambuco: one aiming at to identify how they interact with the leaflets of medicines, and the second one testing their understanding concerning standardized illustrations in the United States and the South Africa. The results show the need for improvements in presentation and graphic representation of leaflets of medicines, powering them to the role of communication, to ensure the consumption of medicine safely by its users. The conclusion congregates parameters and recommendations for the graphic representation of warnings in leaflets of medicines in Brazil.

The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules

PubMed Central

McArthur, Sarah D; Pulvermacher, Sarah C; Stauffer, George V

2006-01-01

Background In recent years it has become clear that small non-coding RNAs function as regulatory elements in bacterial virulence and bacterial stress responses. We tested for the presence of the small non-coding GcvB RNAs in Y. pestis as possible regulators of gene expression in this organism. Results In this study, we report that the Yersinia pestis KIM6 gcvB gene encodes two small RNAs. Transcription of gcvB is activated by the GcvA protein and repressed by the GcvR protein. The gcvB-encoded RNAs are required for repression of the Y. pestis dppA gene, encoding the periplasmic-binding protein component of the dipeptide transport system, showing that the GcvB RNAs have regulatory activity. A deletion of the gcvB gene from the Y. pestis KIM6 chromosome results in a decrease in the generation time of the organism as well as a change in colony morphology. Conclusion The results of this study indicate that the Y. pestis gcvB gene encodes two small non-coding regulatory RNAs that repress dppA expression. A gcvB deletion is pleiotropic, suggesting that the sRNAs are likely involved in controlling genes in addition to dppA. PMID:16768793

The Ebola virus matrix protein penetrates into the plasma membrane: a key step in viral protein 40 (VP40) oligomerization and viral egress.

PubMed

Adu-Gyamfi, Emmanuel; Soni, Smita P; Xue, Yi; Digman, Michelle A; Gratton, Enrico; Stahelin, Robert V

2013-02-22

Ebola, a fatal virus in humans and non-human primates, has no Food and Drug Administration-approved vaccines or therapeutics. The virus from the Filoviridae family causes hemorrhagic fever, which rapidly progresses and in some cases has a fatality rate near 90%. The Ebola genome encodes seven genes, the most abundantly expressed of which is viral protein 40 (VP40), the major Ebola matrix protein that regulates assembly and egress of the virus. It is well established that VP40 assembles on the inner leaflet of the plasma membrane; however, the mechanistic details of plasma membrane association by VP40 are not well understood. In this study, we used an array of biophysical experiments and cellular assays along with mutagenesis of VP40 to investigate the role of membrane penetration in VP40 assembly and egress. Here we demonstrate that VP40 is able to penetrate specifically into the plasma membrane through an interface enriched in hydrophobic residues in its C-terminal domain. Mutagenesis of this hydrophobic region consisting of Leu(213), Ile(293), Leu(295), and Val(298) demonstrated that membrane penetration is critical to plasma membrane localization, VP40 oligomerization, and viral particle egress. Taken together, VP40 membrane penetration is an important step in the plasma membrane localization of the matrix protein where oligomerization and budding are defective in the absence of key hydrophobic interactions with the membrane.

Screening for ATM Mutations in an African-American Population to Identify a Predictor of Breast Cancer Susceptibility

DTIC Science & Technology

2006-07-01

ATM genetic variant identified affects radiosensitivity and levels of the protein encoded by the ATM gene for each mutation examined. 15. SUBJECT...women without breast cancer. An additional objective is to determine the functional impact upon the protein encoded by the ATM gene for each mutation ...each ATM variant identified affects radiosensitivity and levels of the protein encoded by the ATM gene for mutations identified. Body STATEMENT

Isolation of a gene encoding a novel spectinomycin phosphotransferase from Legionella pneumophila.

PubMed

Suter, T M; Viswanathan, V K; Cianciotto, N P

1997-06-01

A gene capable of conferring spectinomycin resistance was isolated from Legionella pneumophila, the agent of Legionnaires' disease. The gene (aph) encoded a 36-kDa protein which has similarity to aminoglycoside phosphotransferases. Biochemical analysis confirmed that aph encodes a phosphotransferase which modifies spectinomycin but not hygromycin, kanamycin, or streptomycin. The strain that was the source of aph demonstrated resistance to spectinomycin, and Southern hybridizations determined that aph also exists in other legionellae.

Isolation of a gene encoding a novel spectinomycin phosphotransferase from Legionella pneumophila.

PubMed Central

Suter, T M; Viswanathan, V K; Cianciotto, N P

1997-01-01

A gene capable of conferring spectinomycin resistance was isolated from Legionella pneumophila, the agent of Legionnaires' disease. The gene (aph) encoded a 36-kDa protein which has similarity to aminoglycoside phosphotransferases. Biochemical analysis confirmed that aph encodes a phosphotransferase which modifies spectinomycin but not hygromycin, kanamycin, or streptomycin. The strain that was the source of aph demonstrated resistance to spectinomycin, and Southern hybridizations determined that aph also exists in other legionellae. PMID:9174205

Escherichia coli yjjPB genes encode a succinate transporter important for succinate production.

PubMed

Fukui, Keita; Nanatani, Kei; Hara, Yoshihiko; Yamakami, Suguru; Yahagi, Daiki; Chinen, Akito; Tokura, Mitsunori; Abe, Keietsu

2017-09-01

Under anaerobic conditions, Escherichia coli produces succinate from glucose via the reductive tricarboxylic acid cycle. To date, however, no genes encoding succinate exporters have been established in E. coli. Therefore, we attempted to identify genes encoding succinate exporters by screening an E. coli MG1655 genome library. We identified the yjjPB genes as candidates encoding a succinate transporter, which enhanced succinate production in Pantoea ananatis under aerobic conditions. A complementation assay conducted in Corynebacterium glutamicum strain AJ110655ΔsucE1 demonstrated that both YjjP and YjjB are required for the restoration of succinate production. Furthermore, deletion of yjjPB decreased succinate production in E. coli by 70% under anaerobic conditions. Taken together, these results suggest that YjjPB constitutes a succinate transporter in E. coli and that the products of both genes are required for succinate export.

Molecular cloning and expression of the gene encoding the kinetoplast-associated type II DNA topoisomerase of Crithidia fasciculata.

PubMed

Pasion, S G; Hines, J C; Aebersold, R; Ray, D S

1992-01-01

A type II DNA topoisomerase, topoIImt, was shown previously to be associated with the kinetoplast DNA of the trypanosomatid Crithidia fasciculata. The gene encoding this kinetoplast-associated topoisomerase has been cloned by immunological screening of a Crithidia genomic expression library with monoclonal antibodies raised against the purified enzyme. The gene CfaTOP2 is a single copy gene and is expressed as a 4.8-kb polyadenylated transcript. The nucleotide sequence of CfaTOP2 has been determined and encodes a predicted polypeptide of 1239 amino acids with a molecular mass of 138,445. The identification of the cloned gene is supported by immunoblot analysis of the beta-galactosidase-CfaTOP2 fusion protein expressed in Escherichia coli and by analysis of tryptic peptide sequences derived from purified topoIImt. CfaTOP2 shares significant homology with nuclear type II DNA topoisomerases of other eukaryotes suggesting that in Crithidia both nuclear and mitochondrial forms of topoisomerase II are encoded by the same gene.

Two pheromone precursor genes are transcriptionally expressed in the homothallic ascomycete Sordaria macrospora.

PubMed

Pöggeler, S

2000-06-01

In order to analyze the involvement of pheromones in cell recognition and mating in a homothallic fungus, two putative pheromone precursor genes, named ppg1 and ppg2, were isolated from a genomic library of Sordaria macrospora. The ppg1 gene is predicted to encode a precursor pheromone that is processed by a Kex2-like protease to yield a pheromone that is structurally similar to the alpha-factor of the yeast Saccharomyces cerevisiae. The ppg2 gene encodes a 24-amino-acid polypeptide that contains a putative farnesylated and carboxy methylated C-terminal cysteine residue. The sequences of the predicted pheromones display strong structural similarity to those encoded by putative pheromones of heterothallic filamentous ascomycetes. Both genes are expressed during the life cycle of S. macrospora. This is the first description of pheromone precursor genes encoded by a homothallic fungus. Southern-hybridization experiments indicated that ppg1 and ppg2 homologues are also present in other homothallic ascomycetes.

Arxula adeninivorans (Blastobotrys adeninivorans) — A Dimorphic Yeast of Great Biotechnological Potential

NASA Astrophysics Data System (ADS)

Böer, Erik; Steinborn, Gerhard; Florschütz, Kristina; Körner, Martina; Gellissen, Gerd; Kunze, Gotthard

The dimorphic ascomycetous yeast Arxula adeninivorans exhibits some unusual properties. Being a thermo- and halotolerant species it is able to assimilate and ferment many compounds as sole carbon and/or nitrogen source. It utilises n-alkanes and is capable of degrading starch. Due to these unusual biochemical properties A. adeninivorans can be exploited as a gene donor for the production of enzymes with attractive biotechnological characteristics. Examples of A. adeninivorans-derived genes that are overexpressed include the ALIP1 gene encoding a secretory lipase, the AINV encoding invertase, the AXDH encoding xylitol dehydrogenase and the APHY encoding a secretory phosphatase with phytase activity.

Quantification and comparison of the mechanical properties of four human cardiac valves.

PubMed

Pham, Thuy; Sulejmani, Fatiesa; Shin, Erica; Wang, Di; Sun, Wei

2017-05-01

Although having the same ability to permit unidirectional flow within the heart, the four main valves-the mitral valve (MV), aortic (AV), tricuspid (TV) and pulmonary (PV) valves-experience different loading conditions; thus, they exhibit different structural integrity from one another. Most research on heart valve mechanics have been conducted mainly on MV and AV or an individual valve, but none quantify and compare the mechanical and structural properties among the four valves from the same aged patient population whose death was unrelated to cardiovascular disease. A total of 114 valve leaflet samples were excised from 12 human cadavers whose death was unrelated to cardiovascular disease (70.1±3.7years old). Tissue mechanical and structural properties were characterized by planar biaxial mechanical testing and histological methods. The experimental data were then fitted with a Fung-type constitutive model. The four valves differed substantially in thickness, degree of anisotropy, and stiffness. The leaflets of the left heart (the AV leaflets and the anterior mitral leaflets, AML) were significantly stiffer and less compliant than their counterparts in the right heart. TV leaflets were the most extensible and isotropic, while AML and AV leaflets were the least extensible and the most anisotropic. Age plays a significant role in the reduction of leaflet stiffness and extensibility with nearly straightened collagen fibers observed in the leaflet samples from elderly groups (65years and older). Results from 114 human leaflet samples not only provided a baseline quantification of the mechanical properties of aged human cardiac valves, but also offered a better understanding of the age-dependent differences among the four valves. It is hoped that the experimental data collected and the associated constitutive models in this study can facilitate future studies of valve diseases, treatments and the development of interventional devices. Most research on heart valve mechanics have been conducted mainly on mitral and aortic valves or an individual valve, but none quantify and compare the mechanical and structural properties among the four valves from the same relatively healthy elderly patient population. In this study, the mechanical and microstructural properties of 114 leaflets of aortic, mitral, pulmonary and tricuspid valves from 12 human cadaver hearts were mechanically tested, analyzed and compared. Our results not only provided a baseline quantification of the mechanical properties of aged human valves, but a age range between patients (51-87years) also offers a better understanding of the age-dependent differences among the four valves. It is hoped that the obtained experimental data and associated constitutive parameters can facilitate studies of valve diseases, treatments and the development of interventional devices. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Structure of the Elastin-Contractile Units in the Thoracic Aorta and How Genes That Cause Thoracic Aortic Aneurysms and Dissections Disrupt This Structure.

PubMed

Karimi, Ashkan; Milewicz, Dianna M

2016-01-01

The medial layer of the aorta confers elasticity and strength to the aortic wall and is composed of alternating layers of smooth muscle cells (SMCs) and elastic fibres. The SMC elastin-contractile unit is a structural unit that links the elastin fibres to the SMCs and is characterized by the following: (1) layers of elastin fibres that are surrounded by microfibrils; (2) microfibrils that bind to the integrin receptors in focal adhesions on the cell surface of the SMCs; and (3) SMC contractile filaments that are linked to the focal adhesions on the inner side of the membrane. The genes that are altered to cause thoracic aortic aneurysms and aortic dissections encode proteins involved in the structure or function of the SMC elastin-contractile unit. Included in this gene list are the genes encoding protein that are structural components of elastin fibres and microfibrils, FBN1, MFAP5, ELN, and FBLN4. Also included are genes that encode structural proteins in the SMC contractile unit, including ACTA2, which encodes SMC-specific α-actin and MYH11, which encodes SMC-specific myosin heavy chain, along with MYLK and PRKG1, which encode kinases that control SMC contraction. Finally, mutations in the gene encoding the protein linking integrin receptors to the contractile filaments, FLNA, also predispose to thoracic aortic disease. Thus, these data suggest that functional SMC elastin-contractile units are important for maintaining the structural integrity of the aorta. Copyright © 2016 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

Medicago truncatula contains a second gene encoding a plastid located glutamine synthetase exclusively expressed in developing seeds.

PubMed

Seabra, Ana R; Vieira, Cristina P; Cullimore, Julie V; Carvalho, Helena G

2010-08-19

Nitrogen is a crucial nutrient that is both essential and rate limiting for plant growth and seed production. Glutamine synthetase (GS), occupies a central position in nitrogen assimilation and recycling, justifying the extensive number of studies that have been dedicated to this enzyme from several plant sources. All plants species studied to date have been reported as containing a single, nuclear gene encoding a plastid located GS isoenzyme per haploid genome. This study reports the existence of a second nuclear gene encoding a plastid located GS in Medicago truncatula. This study characterizes a new, second gene encoding a plastid located glutamine synthetase (GS2) in M. truncatula. The gene encodes a functional GS isoenzyme with unique kinetic properties, which is exclusively expressed in developing seeds. Based on molecular data and the assumption of a molecular clock, it is estimated that the gene arose from a duplication event that occurred about 10 My ago, after legume speciation and that duplicated sequences are also present in closely related species of the Vicioide subclade. Expression analysis by RT-PCR and western blot indicate that the gene is exclusively expressed in developing seeds and its expression is related to seed filling, suggesting a specific function of the enzyme associated to legume seed metabolism. Interestingly, the gene was found to be subjected to alternative splicing over the first intron, leading to the formation of two transcripts with similar open reading frames but varying 5' UTR lengths, due to retention of the first intron. To our knowledge, this is the first report of alternative splicing on a plant GS gene. This study shows that Medicago truncatula contains an additional GS gene encoding a plastid located isoenzyme, which is functional and exclusively expressed during seed development. Legumes produce protein-rich seeds requiring high amounts of nitrogen, we postulate that this gene duplication represents a functional innovation of plastid located GS related to storage protein accumulation exclusive to legume seed metabolism.

Molecular cloning and expression of heteromeric ACCase subunit genes from Jatropha curcas.

PubMed

Gu, Keyu; Chiam, Huihui; Tian, Dongsheng; Yin, Zhongchao

2011-04-01

Acetyl-CoA carboxylase (ACCase) catalyzes the biotin-dependent carboxylation of acetyl-CoA to produce malonyl-CoA, which is the essential first step in the biosynthesis of long-chain fatty acids. ACCase exists as a multi-subunit enzyme in most prokaryotes and the chloroplasts of most plants and algae, while it is present as a multi-domain enzyme in the endoplasmic reticulum of most eukaryotes. The heteromeric ACCase of higher plants consists of four subunits: an α-subunit of carboxyltransferase (α-CT, encoded by accA gene), a biotin carboxyl carrier protein (BCCP, encoded by accB gene), a biotin carboxylase (BC, encoded by accC gene) and a β-subunit of carboxyltransferase (β-CT, encoded by accD gene). In this study, we cloned and characterized the genes accA, accB1, accC and accD that encode the subunits of heteromeric ACCase in Jatropha (Jatropha curcas), a potential biofuel plant. The full-length cDNAs of the four subunit genes were isolated from a Jatropha cDNA library and by using 5' RACE, whereas the genomic clones were obtained from a Jatropha BAC library. They encode a 771 amino acid (aa) α-CT, a 286-aa BCCP1, a 537-aa BC and a 494-aa β-CT, respectively. The single-copy accA, accB1 and accC genes are nuclear genes, while the accD gene is located in chloroplast genome. Jatropha α-CT, BCCP1, BC and β-CT show high identity to their homologues in other higher plants at amino acid level and contain all conserved domains for ACCase activity. The accA, accB1, accC and accD genes are temporally and spatially expressed in the leaves and endosperm of Jatropha plants, which are regulated by plant development and environmental factors. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Gene Cluster Encoding Cholate Catabolism in Rhodococcus spp.

PubMed Central

Wilbrink, Maarten H.; Casabon, Israël; Stewart, Gordon R.; Liu, Jie; van der Geize, Robert; Eltis, Lindsay D.

2012-01-01

Bile acids are highly abundant steroids with important functions in vertebrate digestion. Their catabolism by bacteria is an important component of the carbon cycle, contributes to gut ecology, and has potential commercial applications. We found that Rhodococcus jostii RHA1 grows well on cholate, as well as on its conjugates, taurocholate and glycocholate. The transcriptome of RHA1 growing on cholate revealed 39 genes upregulated on cholate, occurring in a single gene cluster. Reverse transcriptase quantitative PCR confirmed that selected genes in the cluster were upregulated 10-fold on cholate versus on cholesterol. One of these genes, kshA3, encoding a putative 3-ketosteroid-9α-hydroxylase, was deleted and found essential for growth on cholate. Two coenzyme A (CoA) synthetases encoded in the cluster, CasG and CasI, were heterologously expressed. CasG was shown to transform cholate to cholyl-CoA, thus initiating side chain degradation. CasI was shown to form CoA derivatives of steroids with isopropanoyl side chains, likely occurring as degradation intermediates. Orthologous gene clusters were identified in all available Rhodococcus genomes, as well as that of Thermomonospora curvata. Moreover, Rhodococcus equi 103S, Rhodococcus ruber Chol-4 and Rhodococcus erythropolis SQ1 each grew on cholate. In contrast, several mycolic acid bacteria lacking the gene cluster were unable to grow on cholate. Our results demonstrate that the above-mentioned gene cluster encodes cholate catabolism and is distinct from a more widely occurring gene cluster encoding cholesterol catabolism. PMID:23024343

The prrF-Encoded Small Regulatory RNAs Are Required for Iron Homeostasis and Virulence of Pseudomonas aeruginosa

PubMed Central

Reinhart, Alexandria A.; Powell, Daniel A.; Nguyen, Angela T.; O'Neill, Maura; Djapgne, Louise; Wilks, Angela; Ernst, Robert K.

2014-01-01

Pseudomonas aeruginosa is an opportunistic pathogen that requires iron to cause infection, but it also must regulate the uptake of iron to avoid iron toxicity. The iron-responsive PrrF1 and PrrF2 small regulatory RNAs (sRNAs) are part of P. aeruginosa's iron regulatory network and affect the expression of at least 50 genes encoding iron-containing proteins. The genes encoding the PrrF1 and PrrF2 sRNAs are encoded in tandem in P. aeruginosa, allowing for the expression of a distinct, heme-responsive sRNA named PrrH that appears to regulate genes involved in heme metabolism. Using a combination of growth, mass spectrometry, and gene expression analysis, we showed that the ΔprrF1,2 mutant, which lacks expression of the PrrF and PrrH sRNAs, is defective for both iron and heme homeostasis. We also identified phuS, encoding a heme binding protein involved in heme acquisition, and vreR, encoding a previously identified regulator of P. aeruginosa virulence genes, as novel targets of prrF-mediated heme regulation. Finally, we showed that the prrF locus encoding the PrrF and PrrH sRNAs is required for P. aeruginosa virulence in a murine model of acute lung infection. Moreover, we showed that inoculation with a ΔprrF1,2 deletion mutant protects against future challenge with wild-type P. aeruginosa. Combined, these data demonstrate that the prrF-encoded sRNAs are critical regulators of P. aeruginosa virulence. PMID:25510881

3D echocardiographic location of implantable device leads and mechanism of associated tricuspid regurgitation.

PubMed

Mediratta, Anuj; Addetia, Karima; Yamat, Megan; Moss, Joshua D; Nayak, Hemal M; Burke, Martin C; Weinert, Lynn; Maffessanti, Francesco; Jeevanandam, Valluvan; Mor-Avi, Victor; Lang, Roberto M

2014-04-01

This study sought to: 1) determine the feasibility of using 3-dimensional transthoracic echocardiography (3D TTE) in patients with implantable cardiac resynchronization devices, pacemakers, and defibrillators to visualize the device leads in the right heart and their position relative to the tricuspid valve leaflets; 2) determine the prevalence of different lead positions; and 3) study the relationship between lead location and tricuspid regurgitation (TR) severity. Pacemaker, defibrillator, and cardiac resynchronization device implantation is currently guided by fluoroscopy, not allowing targeted lead positioning relative to the tricuspid valve leaflets. These leads have been reported to cause TR of variable degrees, but echocardiography is not routinely used to elucidate the mechanisms of lead interference with tricuspid valve leaflets in individual patients. 3D TTE full-volume images of the right ventricle and/or zoomed images of the tricuspid valve were obtained in 121 patients with implanted devices. Images were viewed offline to determine the position of the device-lead relative to the tricuspid valve leaflets. Severity of TR was estimated on the basis of vena contracta measurements. 3D TTE clearly depicted lead position in 90% of patients. The right ventricular lead was impinging on either the posterior (20%) or septal (23%) leaflet or was not interfering with leaflet motion (53%) when positioned near the posteroseptal commissure or in the central portion of the tricuspid valve orifice. In the remaining patients, leads were impinging on the anterior leaflet (4%) or positioned in either the anteroposterior or anteroseptal commissure (3%). Leads interfering with normal leaflet mobility were associated with more TR than nonimpinging leads (vena contracta: median 0.62 cm [1st and 3rd quartiles: 0.51, 0.84 cm] vs. 0.27 cm [1st and 3rd quartiles: 0.00, 0.48 cm]; p < 0.001). 3D TTE showed a clear association between device lead position and TR. To minimize TR induced by device-leads, 3D TTE guidance should be considered for placement in a commissural position. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

CIP1 polypeptides and their uses

DOEpatents

Foreman, Pamela [Los Altos, CA; Van Solingen, Pieter [Naaldwijk, NL; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA

2011-04-12

Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

Paralogous ALT1 and ALT2 Retention and Diversification Have Generated Catalytically Active and Inactive Aminotransferases in Saccharomyces cerevisiae

PubMed Central

Peñalosa-Ruiz, Georgina; Aranda, Cristina; Ongay-Larios, Laura; Colon, Maritrini; Quezada, Hector; Gonzalez, Alicia

2012-01-01

Background Gene duplication and the subsequent divergence of paralogous pairs play a central role in the evolution of novel gene functions. S. cerevisiae possesses two paralogous genes (ALT1/ALT2) which presumably encode alanine aminotransferases. It has been previously shown that Alt1 encodes an alanine aminotransferase, involved in alanine metabolism; however the physiological role of Alt2 is not known. Here we investigate whether ALT2 encodes an active alanine aminotransferase. Principal Findings Our results show that although ALT1 and ALT2 encode 65% identical proteins, only Alt1 displays alanine aminotransferase activity; in contrast ALT2 encodes a catalytically inert protein. ALT1 and ALT2 expression is modulated by Nrg1 and by the intracellular alanine pool. ALT1 is alanine-induced showing a regulatory profile of a gene encoding an enzyme involved in amino acid catabolism, in agreement with the fact that Alt1 is the sole pathway for alanine catabolism present in S. cerevisiae. Conversely, ALT2 expression is alanine-repressed, indicating a role in alanine biosynthesis, although the encoded-protein has no alanine aminotransferase enzymatic activity. In the ancestral-like yeast L. kluyveri, the alanine aminotransferase activity was higher in the presence of alanine than in the presence of ammonium, suggesting that as for ALT1, LkALT1 expression could be alanine-induced. ALT2 retention poses the questions of whether the encoded protein plays a particular function, and if this function was present in the ancestral gene. It could be hypotesized that ALT2 diverged after duplication, through neo-functionalization or that ALT2 function was present in the ancestral gene, with a yet undiscovered function. Conclusions ALT1 and ALT2 divergence has resulted in delegation of alanine aminotransferase activity to Alt1. These genes display opposed regulatory profiles: ALT1 is alanine-induced, while ALT2 is alanine repressed. Both genes are negatively regulated by the Nrg1 repressor. Presented results indicate that alanine could act as ALT2 Nrg1-co-repressor. PMID:23049841

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

PubMed

Auerbach, Raymond K; Chen, Bin; Butte, Atul J

2013-08-01

Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses. The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu. abutte@stanford.edu Supplementary material is available at Bioinformatics online.

Antibodies to a novel leptospiral protein, LruC, in the eye fluids and sera of horses with Leptospira-associated uveitis.

PubMed

Verma, Ashutosh; Matsunaga, James; Artiushin, Sergey; Pinne, Marija; Houwers, Dirk J; Haake, David A; Stevenson, Brian; Timoney, John F

2012-03-01

Screening of an expression library of Leptospira interrogans with eye fluids from uveitic horses resulted in identification of a novel protein, LruC. LruC is located in the inner leaflet of the leptospiral outer membrane, and an lruC gene was detected in all tested pathogenic L. interrogans strains. LruC-specific antibody levels were significantly higher in eye fluids and sera of uveitic horses than healthy horses. These findings suggest that LruC may play a role in equine leptospiral uveitis.

Rudimentary expression of RYamide in Drosophila melanogaster relative to other Drosophila species points to a functional decline of this neuropeptide gene.

PubMed

Veenstra, Jan A; Khammassi, Hela

2017-04-01

RYamides are arthropod neuropeptides with unknown function. In 2011 two RYamides were isolated from D. melanogaster as the ligands for the G-protein coupled receptor CG5811. The D. melanogaster gene encoding these neuropeptides is highly unusual, as there are four RYamide encoding exons in the current genome assembly, but an exon encoding a signal peptide is absent. Comparing the D. melanogaster gene structure with those from other species, including D. virilis, suggests that the gene is degenerating. RNAseq data from 1634 short sequence read archives at NCBI containing more than 34 billion spots yielded numerous individual spots that correspond to the RYamide encoding exons, of which a large number include the intron-exon boundary at the start of this exon. Although 72 different sequences have been spliced onto this RYamide encoding exon, none codes for the signal peptide of this gene. Thus, the RNAseq data for this gene reveal only noise and no signal. The very small quantities of peptide recovered during isolation and the absence of credible RNAseq data, indicates that the gene is very little expressed, while the RYamide gene structure in D. melanogaster suggests that it might be evolving into a pseudogene. Yet, the identification of the peptides it encodes clearly shows it is still functional. Using region specific antisera, we could localize numerous neurons and enteroendocrine cells in D. willistoni, D. virilis and D. pseudoobscura, but only two adult abdominal neurons in D. melanogaster. Those two neurons project to and innervate the rectal papillae, suggesting that RYamides may be involved in the regulation of water homeostasis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis and Manipulation of Aspartate Pathway Genes for l-Lysine Overproduction from Methanol by Bacillus methanolicus▿

PubMed Central

Nærdal, Ingemar; Netzer, Roman; Ellingsen, Trond E.; Brautaset, Trygve

2011-01-01

We investigated the regulation and roles of six aspartate pathway genes in l-lysine overproduction in Bacillus methanolicus: dapG, encoding aspartokinase I (AKI); lysC, encoding AKII; yclM, encoding AKIII; asd, encoding aspartate semialdehyde dehydrogenase; dapA, encoding dihydrodipicolinate synthase; and lysA, encoding meso-diaminopimelate decarboxylase. Analysis of the wild-type strain revealed that in vivo lysC transcription was repressed 5-fold by l-lysine and induced 2-fold by dl-methionine added to the growth medium. Surprisingly, yclM transcription was repressed 5-fold by dl-methionine, while the dapG, asd, dapA, and lysA genes were not significantly repressed by any of the aspartate pathway amino acids. We show that the l-lysine-overproducing classical B. methanolicus mutant NOA2#13A52-8A66 has—in addition to a hom-1 mutation—chromosomal mutations in the dapG coding region and in the lysA promoter region. No mutations were found in its dapA, lysC, asd, and yclM genes. The mutant dapG gene product had abolished feedback inhibition by meso-diaminopimelate in vitro, and the lysA mutation was accompanied by an elevated (6-fold) lysA transcription level in vivo. Moreover, yclM transcription was increased 16-fold in mutant strain NOA2#13A52-8A66 compared to the wild-type strain. Overexpression of wild-type and mutant aspartate pathway genes demonstrated that all six genes are important for l-lysine overproduction as tested in shake flasks, and the effects were dependent on the genetic background tested. Coupled overexpression of up to three genes resulted in additive (above 80-fold) increased l-lysine production levels. PMID:21724876

Analysis and manipulation of aspartate pathway genes for L-lysine overproduction from methanol by Bacillus methanolicus.

PubMed

Nærdal, Ingemar; Netzer, Roman; Ellingsen, Trond E; Brautaset, Trygve

2011-09-01

We investigated the regulation and roles of six aspartate pathway genes in L-lysine overproduction in Bacillus methanolicus: dapG, encoding aspartokinase I (AKI); lysC, encoding AKII; yclM, encoding AKIII; asd, encoding aspartate semialdehyde dehydrogenase; dapA, encoding dihydrodipicolinate synthase; and lysA, encoding meso-diaminopimelate decarboxylase. Analysis of the wild-type strain revealed that in vivo lysC transcription was repressed 5-fold by L-lysine and induced 2-fold by dl-methionine added to the growth medium. Surprisingly, yclM transcription was repressed 5-fold by dl-methionine, while the dapG, asd, dapA, and lysA genes were not significantly repressed by any of the aspartate pathway amino acids. We show that the L-lysine-overproducing classical B. methanolicus mutant NOA2#13A52-8A66 has-in addition to a hom-1 mutation-chromosomal mutations in the dapG coding region and in the lysA promoter region. No mutations were found in its dapA, lysC, asd, and yclM genes. The mutant dapG gene product had abolished feedback inhibition by meso-diaminopimelate in vitro, and the lysA mutation was accompanied by an elevated (6-fold) lysA transcription level in vivo. Moreover, yclM transcription was increased 16-fold in mutant strain NOA2#13A52-8A66 compared to the wild-type strain. Overexpression of wild-type and mutant aspartate pathway genes demonstrated that all six genes are important for L-lysine overproduction as tested in shake flasks, and the effects were dependent on the genetic background tested. Coupled overexpression of up to three genes resulted in additive (above 80-fold) increased L-lysine production levels.

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

PubMed Central

Gillis, Jesse; Pavlidis, Paul

2012-01-01

Gene networks are commonly interpreted as encoding functional information in their connections. An extensively validated principle called guilt by association states that genes which are associated or interacting are more likely to share function. Guilt by association provides the central top-down principle for analyzing gene networks in functional terms or assessing their quality in encoding functional information. In this work, we show that functional information within gene networks is typically concentrated in only a very few interactions whose properties cannot be reliably related to the rest of the network. In effect, the apparent encoding of function within networks has been largely driven by outliers whose behaviour cannot even be generalized to individual genes, let alone to the network at large. While experimentalist-driven analysis of interactions may use prior expert knowledge to focus on the small fraction of critically important data, large-scale computational analyses have typically assumed that high-performance cross-validation in a network is due to a generalizable encoding of function. Because we find that gene function is not systemically encoded in networks, but dependent on specific and critical interactions, we conclude it is necessary to focus on the details of how networks encode function and what information computational analyses use to extract functional meaning. We explore a number of consequences of this and find that network structure itself provides clues as to which connections are critical and that systemic properties, such as scale-free-like behaviour, do not map onto the functional connectivity within networks. PMID:22479173

Sensing Phosphatidylserine in Cellular Membranes

PubMed Central

Kay, Jason G.; Grinstein, Sergio

2011-01-01

Phosphatidylserine, a phospholipid with a negatively charged head-group, is an important constituent of eukaryotic cellular membranes. On the plasma membrane, rather than being evenly distributed, phosphatidylserine is found preferentially in the inner leaflet. Disruption of this asymmetry, leading to the appearance of phosphatidylserine on the surface of the cell, is known to play a central role in both apoptosis and blood clotting. Despite its importance, comparatively little is known about phosphatidylserine in cells: its precise subcellular localization, transmembrane topology and intracellular dynamics are poorly characterized. The recent development of new, genetically-encoded probes able to detect phosphatidylserine within live cells, however, is leading to a more in-depth understanding of the biology of this phospholipid. This review aims to give an overview of the current methods for phosphatidylserine detection within cells, and some of the recent realizations derived from their use. PMID:22319379

Sensing phosphatidylserine in cellular membranes.

PubMed

Kay, Jason G; Grinstein, Sergio

2011-01-01

Phosphatidylserine, a phospholipid with a negatively charged head-group, is an important constituent of eukaryotic cellular membranes. On the plasma membrane, rather than being evenly distributed, phosphatidylserine is found preferentially in the inner leaflet. Disruption of this asymmetry, leading to the appearance of phosphatidylserine on the surface of the cell, is known to play a central role in both apoptosis and blood clotting. Despite its importance, comparatively little is known about phosphatidylserine in cells: its precise subcellular localization, transmembrane topology and intracellular dynamics are poorly characterized. The recent development of new, genetically-encoded probes able to detect phosphatidylserine within live cells, however, is leading to a more in-depth understanding of the biology of this phospholipid. This review aims to give an overview of the current methods for phosphatidylserine detection within cells, and some of the recent realizations derived from their use.

Mobile genetic element-encoded cytolysin connects virulence to methicillin resistance in MRSA.

PubMed

Queck, Shu Y; Khan, Burhan A; Wang, Rong; Bach, Thanh-Huy L; Kretschmer, Dorothee; Chen, Liang; Kreiswirth, Barry N; Peschel, Andreas; Deleo, Frank R; Otto, Michael

2009-07-01

Bacterial virulence and antibiotic resistance have a significant influence on disease severity and treatment options during bacterial infections. Frequently, the underlying genetic determinants are encoded on mobile genetic elements (MGEs). In the leading human pathogen Staphylococcus aureus, MGEs that contain antibiotic resistance genes commonly do not contain genes for virulence determinants. The phenol-soluble modulins (PSMs) are staphylococcal cytolytic toxins with a crucial role in immune evasion. While all known PSMs are core genome-encoded, we here describe a previously unidentified psm gene, psm-mec, within the staphylococcal methicillin resistance-encoding MGE SCCmec. PSM-mec was strongly expressed in many strains and showed the physico-chemical, pro-inflammatory, and cytolytic characteristics typical of PSMs. Notably, in an S. aureus strain with low production of core genome-encoded PSMs, expression of PSM-mec had a significant impact on immune evasion and disease. In addition to providing high-level resistance to methicillin, acquisition of SCCmec elements encoding PSM-mec by horizontal gene transfer may therefore contribute to staphylococcal virulence by substituting for the lack of expression of core genome-encoded PSMs. Thus, our study reveals a previously unknown role of methicillin resistance clusters in staphylococcal pathogenesis and shows that important virulence and antibiotic resistance determinants may be combined in staphylococcal MGEs.

Vent-induced prosthetic leaflet thrombosis treated by open-heart valve-in-valve implantation.

PubMed

Stamm, Christof; Pasic, Miralem; Buz, Semih; Hetzer, Roland

2015-09-01

A patient required emergency mitral valve replacement and extracorporeal membrane oxygenation (ECMO) support for acute biventricular failure. The left ventricular (LV) vent inserted via the left upper pulmonary vein induced thrombotic immobilization of a prosthetic valve leaflet, with significant intra-prosthesis regurgitation after ECMO explantation. Therefore, the left atrium was opened on the beating heart during conventional extracorporeal circulation, all prosthesis leaflets were excised and a 29-mm expandable Edwards Sapien prosthesis was inserted within the scaffold of the original prosthesis under direct vision. This case illustrates the benefits and potential problems of LV venting on ECMO support, and a rapid and safe way of replacing the prosthesis leaflets in a critical situation. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Juvenile Rhus glabra leaves have higher temperatures and lower gas exchange rates than mature leaves when compared in the field during periods of high irradiance.

PubMed

Snider, John L; Choinski, John S; Wise, Robert R

2009-05-01

We sought to test the hypothesis that stomatal development determines the timing of gas exchange competency, which then influences leaf temperature through transpirationally driven leaf cooling. To test this idea, daily patterns of gas exchange and leaflet temperature were obtained from leaves of two distinctively different developmental stages of smooth sumac (Rhus glabra) grown in its native habitat. Juvenile and mature leaves were also sampled for ultrastructural studies of stomatal development. When plants were sampled in May-June, the hypothesis was supported: juvenile leaflets were (for part of the day) from 1.4 to 6.0 degrees C warmer than mature leaflets and as much as 2.0 degrees C above ambient air temperature with lower stomatal conductance and photosynthetic rates than mature leaflets. When measurements were taken from July to October, no significant differences were observed, although mature leaflet gas exchange rates declined to the levels of the juvenile leaves. The gas exchange data were supported by the observations that juvenile leaves had approximately half the number of functional stomata on a leaf surface area basis as did mature leaves. It was concluded that leaf temperature and stage of leaf development in sumac are strongly linked with the higher surface temperatures observed in juvenile leaflets in the early spring possibly being involved in promoting photosynthesis and leaf expansion when air temperatures are cooler.

Leaflet escape in a new bileaflet mechanical valve: TRI technologies.

PubMed

Bottio, Tomaso; Casarotto, Dino; Thiene, Gaetano; Caprili, Luca; Angelini, Annalisa; Gerosa, Gino

2003-05-13

Leaflet escape is a mode of structural valve failure for mechanical prostheses. This complication previously has been reported for both monoleaflet and bileaflet valve models. We report 2 leaflet escape occurrences observed in 2 patients who underwent valve replacement with a TRI Technologies valve prosthesis. At the University of Padua, between November 2000 and February 2002, 36 TRI Technologies valve prostheses (26 aortic and 10 mitral) were implanted in 34 patients (12 women and 22 men) with a mean age of 59.9+/-10.3 years (range, 30 to 75 years). There were 5 deaths: 3 in hospital, 1 early after discharge, and 1 late. Two patients experienced a catastrophic prosthetic leaflet escape; the first patient was a 52-year-old man who died 10 days after aortic valve and ascending aorta replacement, and the second was a 58-year-old man who underwent a successful emergency reoperation 20 months after mitral valve replacement. Examination of the explanted prostheses showed in both cases a leaflet escape caused by a leaflet's pivoting system fracture. Prophylactic replacement was then successfully accomplished so far in 12 patients, without evidence of structural valve failure in any of them. Among other significant postoperative complications, we observed 3 major thromboembolisms, 1 hemorrhage, and 1 paravalvular leak. These catastrophes prompted us to interrupt the implantation program, and they cast a shadow on the durability of the TRI Technologies valve prosthesis because of its high risk of structural failure.

Robotic Posterior Mitral Leaflet Repair: Neochordal versus Resectional Techniques

PubMed Central

Mihaljevic, Tomislav; Pattakos, Gregory; Gillinov, A. Marc; Bajwa, Gurjyot; Planinc, Mislav; Williams, Sarah J.; Blackstone, Eugene H.

2013-01-01

Background Resectional techniques are the established method of posterior mitral valve leaflet repair for degenerative disease; however, use of neochordae in a robotically assisted approach is gaining acceptance because of its versatility for difficult multi-segment disease. The purposes of this study were to compare the versatility, safety, and effectiveness of neochordal vs. resectional techniques for robotic posterior mitral leaflet repair. Methods From 12/2007 to 7/2010, 334 patients underwent robotic posterior mitral leaflet repair for degenerative disease by a resectional (n=248) or neochordal (n=86) technique. Outcomes were compared unadjusted and after propensity score matching. Results Neochordae were more likely to be used than resection in patients with two (28% vs. 13%, P=.002) or three (3.7% vs. 0.87%, P=.08) diseased posterior leaflet segments. Three resection patients (0.98%) but no neochordal patient required reoperation for hemodynamically significant systolic anterior motion (SAM). Residual mitral regurgitation (MR) at hospital discharge was similar for matched neochordal vs. resection patients (P=.14) (MR 0+, 82% vs. 89%; MR 1+, 14% vs. 8.2%; MR 2+, 2.3% vs. 2.6%; one neochordal patient had 4+ MR and was reoperated). Among matched patients, postoperative mortality and morbidity were similarly low. Conclusion Compared with a resectional technique, robotic posterior mitral leaflet repair with neochordae is associated with shorter operative times and no occurrence of SAM. The versatility, effectiveness, and safety of this repair make it a good choice for patients with advanced multi-segment disease. PMID:23103008

Staphylococcus aureus nasal carriage in Ukraine: antibacterial resistance and virulence factor encoding genes.

PubMed

Netsvyetayeva, Irina; Fraczek, Mariusz; Piskorska, Katarzyna; Golas, Marlena; Sikora, Magdalena; Mlynarczyk, Andrzej; Swoboda-Kopec, Ewa; Marusza, Wojciech; Palmieri, Beniamino; Iannitti, Tommaso

2014-03-05

The number of studies regarding the incidence of multidrug resistant strains and distribution of genes encoding virulence factors, which have colonized the post-Soviet states, is considerably limited. The aim of the study was (1) to assess the Staphylococcus (S.) aureus nasal carriage rate, including Methicillin Resistant S. aureus (MRSA) strains in adult Ukrainian population, (2) to determine antibiotic resistant pattern and (3) the occurrence of Panton Valentine Leukocidine (PVL)-, Fibronectin-Binding Protein A (FnBPA)- and Exfoliative Toxin (ET)-encoding genes. Nasal samples for S. aureus culture were obtained from 245 adults. The susceptibility pattern for several classes of antibiotics was determined by disk diffusion method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The virulence factor encoding genes, mecA, lukS-lukF, eta, etb, etd, fnbA, were detected by Polymerase Chain Reaction (PCR). The S. aureus nasal carriage rate was 40%. The prevalence of nasal MRSA carriage in adults was 3.7%. LukS-lukF genes were detected in over 58% of the strains. ET-encoding genes were detected in over 39% of the strains and the most prevalent was etd. The fnbA gene was detected in over 59% of the strains. All MRSA isolates tested were positive for the mecA gene. LukS-lukF genes and the etd gene were commonly co-present in MRSA, while lukS-lukF genes and the fnbA gene were commonly co-present in Methicillin Sensitive S. aureus (MSSA) isolates. No significant difference was detected between the occurrence of lukS-lukF genes (P > 0.05) and the etd gene (P > 0.05) when comparing MRSA and MSSA. The occurrence of the fnbA gene was significantly more frequent in MSSA strains (P < 0.05). In Ukraine, S. aureus is a common cause of infection. The prevalence of S. aureus nasal carriage in our cohort of patients from Ukraine was 40.4%. We found that 9.1% of the strains were classified as MRSA and all MRSA isolates tested positive for the mecA gene. We also observed a high prevalence of PVL- and ET- encoding genes among S. aureus nasal carriage strains. A systematic surveillance system can help prevent transmission and spread of drug resistant toxin producing S. aureus strains.

Carbohydrate metabolism genes and pathways in insects: insights from the honey bee genome

PubMed Central

Kunieda, T; Fujiyuki, T; Kucharski, R; Foret, S; Ament, S A; Toth, A L; Ohashi, K; Takeuchi, H; Kamikouchi, A; Kage, E; Morioka, M; Beye, M; Kubo, T; Robinson, G E; Maleszka, R

2006-01-01

Carbohydrate-metabolizing enzymes may have particularly interesting roles in the honey bee, Apis mellifera, because this social insect has an extremely carbohydrate-rich diet, and nutrition plays important roles in caste determination and socially mediated behavioural plasticity. We annotated a total of 174 genes encoding carbohydrate-metabolizing enzymes and 28 genes encoding lipid-metabolizing enzymes, based on orthology to their counterparts in the fly, Drosophila melanogaster, and the mosquito, Anopheles gambiae. We found that the number of genes for carbohydrate metabolism appears to be more evolutionarily labile than for lipid metabolism. In particular, we identified striking changes in gene number or genomic organization for genes encoding glycolytic enzymes, cellulase, glucose oxidase and glucose dehydrogenases, glucose-methanol-choline (GMC) oxidoreductases, fucosyltransferases, and lysozymes. PMID:17069632

Novel Type V Staphylococcal Cassette Chromosome mec Driven by a Novel Cassette Chromosome Recombinase, ccrC

PubMed Central

Ito, Teruyo; Ma, Xiao Xue; Takeuchi, Fumihiko; Okuma, Keiko; Yuzawa, Harumi; Hiramatsu, Keiichi

2004-01-01

Staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element composed of the mec gene complex, which encodes methicillin resistance, and the ccr gene complex, which encodes the recombinases responsible for its mobility. The mec gene complex has been classified into four classes, and the ccr gene complex has been classified into three allotypes. Different combinations of mec gene complex classes and ccr gene complex types have so far defined four types of SCCmec elements. Now we introduce the fifth allotype of SCCmec, which was found on the chromosome of a community-acquired methicillin-resistant Staphylococcus aureus strain (strain WIS [WBG8318]) isolated in Australia. The element shared the same chromosomal integration site with the four extant types of SCCmec and the characteristic nucleotide sequences at the chromosome-SCCmec junction regions. The novel SCCmec carried mecA bracketed by IS431 (IS431-mecA-ΔmecR1-IS431), which is designated the class C2 mec gene complex; and instead of ccrA and ccrB genes, it carried a single copy of a gene homologue that encoded cassette chromosome recombinase. Since the open reading frame (ORF) was found to encode an enzyme which catalyzes the precise excision as well as site- and orientation-specific integration of the element, we designated the ORF cassette chromosome recombinase C (ccrC), and we designated the element type V SCCmec. Type V SCCmec is a small SCCmec element (28 kb) and does not carry any antibiotic resistance genes besides mecA. Unlike the extant SCCmec types, it carries a set of foreign genes encoding a restriction-modification system that might play a role in the stabilization of the element on the chromosome. PMID:15215121

Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norton, Jeanette M.; Klotz, Martin G; Stein, Lisa Y

2008-01-01

The complete genome of the ammonia-oxidizing bacterium, Nitrosospira multiformis (ATCC 25196T), consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2827 putative proteins. Of these, 2026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and N. eutropha were the best match for 42% of the predicted genes in N. multiformis. The genome contains three nearly identical copies of amo and hao gene clusters as large repeats. Distinguishing features compared to N. europaea include: the presencemore » of gene clusters encoding urease and hydrogenase, a RuBisCO-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced AOB genomes. Gene clusters encoding proteins associated with outer membrane and cell envelope functions including transporters, porins, exopolysaccharide synthesis, capsule formation and protein sorting/export were abundant. Numerous sensory transduction and response regulator gene systems directed towards sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate and cyanophycin storage and utilization were identified providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.« less

Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media

PubMed Central

Hottes, Alison K.; Meewan, Maliwan; Yang, Desiree; Arana, Naomi; Romero, Pedro; McAdams, Harley H.; Stephens, Craig

2004-01-01

Microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium Caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (PYE) and minimal salts medium with glucose or xylose as the carbon source. Nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. The differentially expressed genes included many encoding transport systems, most notably diverse TonB-dependent outer membrane channels of unknown substrate specificity. Amino acid degradation pathways constituted the largest class of genes induced in PYE. In contrast, many of the genes upregulated in minimal media encoded enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induced expression of genes encoding enzymes of the Entner-Doudoroff pathway, which was demonstrated here through mutational analysis to be essential in C. crescentus for growth on glucose. Xylose induced expression of genes encoding several hydrolytic exoenzymes as well as an operon that may encode a novel pathway for xylose catabolism. A conserved DNA motif upstream of many xylose-induced genes was identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggest that in addition to serving as a carbon source for growth of C. crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation. PMID:14973021

Assessment of the quality of medication information for patients in Spain.

PubMed

Mira, José Joaquín; Lorenzo, Susana; Pérez-Jover, Virtudes; Navarro, Isabel; Martín de Rosales, Ana María; Lara, Catalina

2013-01-01

To analyze the extent to which Spanish leaflets and drug information on the Net met quality criteria. A descriptive study was conducted comparing readability (REA) and comprehensibility (COM) criteria of a random sample of 77 marketed products of the 12 active ingredients most frequently sold in 2010 in Spain. Leaflets were approved by the Spanish Agency for Medication (AEMPS). Flesch index, DISCERN, ELF, MIDAS and CIRF scales were used to evaluate quality criteria. COM assessment yielded between 63 and 77% of the maximum possible scores on the scales. None of the websites or leaflets met all the quality criteria of the DISCERN, CIRF or MIDAS scales. Four (3%) leaflets met all the 22 quality criteria of ELF. The leaflets showed shortcomings regarding: medication benefits (17 required substantial improvements, 31.5%), correct forms of storage (13, 24.1%), contraindications (12, 22.2%), side effects (11, 20.4%) and precautions to be taken (9, 16.7%). The quality of the information approved by the AEMPS is superior to that which can be found by surfing the Net. More specific information on precautions, complications and how to avoid common patient errors would allow patients the best chance to contribute to their own clinical safety.

Absence of posterior tricuspid valve leaflet and valve reconstruction

PubMed Central

Komoda, Takeshi; Stamm, Christof; Fleck, Eckart; Hetzer, Roland

2012-01-01

We report a rare case of the absence of a posterior tricuspid valve leaflet. A male patient, aged 46, suffering from severe tricuspid valve regurgitation (TR) of unknown aetiology and atrial septal aneurysm was referred to our hospital for surgery. On surgical inspection, the posterior tricuspid valve leaflet and its subvalvular apparatus were completely absent and only the valve annulus was seen in the corresponding position. The anterior and septal leaflets were normal. We successfully reconstructed the tricuspid valve as follows: the head of an anterior papillary muscle was approximated to the ventricular septum (Sebening stitch). After the approximation of the centre of the tricuspid annulus of the anterior leaflet to the tricuspid annulus on the opposite side, a sizer of 29 mm in diameter was easily passed through the anterior orifice. The posterior orifice was closed with running sutures (posterior annulorrhaphy after Hetzer). Before these procedures, we attempted to reconstruct the tricuspid valve with a posterior annulorrhaphy alone; however, valve competence was insufficient. A Sebening stitch was necessary to improve the valve competence. Echocardiography showed TR grade 1 at the patient's discharge from hospital and TR grade 1 to 2 at the follow-up, 10 months after the operation. PMID:22419794

Multi-physics 3D computational study of leaflet thrombus formation following surgical and transcatheter aortic valve replacement

NASA Astrophysics Data System (ADS)

Vahidkhah, Koohyar; Abbasi, Mostafa; Barakat, Mohammed; Dvir, Danny; Azadani, Ali

2017-11-01

An increasingly recognized complication following surgical/transcatheter aortic valve replacement is thrombosis or blood clot formation on replacement valve leaflets. A predisposing factor in thrombus formation on biomaterial surfaces of a bioprosthetic heart valve is blood stasis. Longer residence time of blood provides an opportunity for platelets and agonists to accumulate to critical concentrations that leads to platelet activation and then thrombosis. In this study, we have developed a fluid-solid interaction (FSI) modeling approach, to quantify blood stasis on the leaflets of bioprosthetic aortic valves with different design operating in a patient-specific geometry. We have validated our FSI model against experimental measurements of valve opening/closing as well as in-vitro particle image velocimetry. We have also embedded in our method a model for transport of platelets and agonists (ADP, TxA2, and thrombin) and their interactions that result in platelets activation and adhesion to biomaterial bioprosthetic surfaces. We have provided quantitative evidence for the correlation between long residence of blood on bioprosthetic aortic valve leaflets and formation of high thrombogenicity risk regions on the leaflets that are characterized by accumulation of activated platelet.

Effect of the mitral valve on diastolic flow patterns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seo, Jung Hee; Vedula, Vijay; Mittal, Rajat, E-mail: mittal@jhu.edu

2014-12-15

The leaflets of the mitral valve interact with the mitral jet and significantly impact diastolic flow patterns, but the effect of mitral valve morphology and kinematics on diastolic flow and its implications for left ventricular function have not been clearly delineated. In the present study, we employ computational hemodynamic simulations to understand the effect of mitral valve leaflets on diastolic flow. A computational model of the left ventricle is constructed based on a high-resolution contrast computed-tomography scan, and a physiological inspired model of the mitral valve leaflets is synthesized from morphological and echocardiographic data. Simulations are performed with a diodemore » type valve model as well as the physiological mitral valve model in order to delineate the effect of mitral-valve leaflets on the intraventricular flow. The study suggests that a normal physiological mitral valve promotes the formation of a circulatory (or “looped”) flow pattern in the ventricle. The mitral valve leaflets also increase the strength of the apical flow, thereby enhancing apical washout and mixing of ventricular blood. The implications of these findings on ventricular function as well as ventricular flow models are discussed.« less

Mitral Valve Stenosis after Open Repair Surgery for Non-rheumatic Mitral Valve Regurgitation: A Review.

PubMed

Shabsigh, Muhammad; Lawrence, Cassidy; Rosero-Britton, Byron R; Kumar, Nicolas; Kimura, Satoshi; Durda, Michael Andrew; Essandoh, Michael

2016-01-01

Mitral stenosis (MS) after mitral valve (MV) repair is a slowly progressive condition, usually detected many years after the index MV surgery. It is defined as a mean transmitral pressure gradient (TMPG) >5 mmHg or a mitral valve area (MVA) <1.5 cm(2). Pannus formation around the mitral annulus or extending to the mitral leaflets is suggested as the main mechanism for developing delayed MS after MV repair. On the other hand, early stenosis is thought to be a direct result of an undersized annuloplasty ring. Furthermore, in MS following ischemic mitral regurgitation (MR) repair, subvalvular tethering is the hypothesized pathophysiology. MS after MV repair has an incidence of 9-54%. Several factors have been associated with a higher risk for developing MS after MV repair, including the use of flexible Duran annuloplasty rings versus rigid Carpentier-Edwards rings, complete annuloplasty rings versus partial bands, small versus large anterior leaflet opening angle, and anterior leaflet tip opening length. Intraoperative echocardiography can measure the anterior leaflet opening angle, the anterior leaflet tip opening dimension, the MVA and the mean TMPG, and may help identify patients at risk for developing MS after MV repair.

Mitral Valve Stenosis after Open Repair Surgery for Non-rheumatic Mitral Valve Regurgitation: A Review

PubMed Central

Shabsigh, Muhammad; Lawrence, Cassidy; Rosero-Britton, Byron R.; Kumar, Nicolas; Kimura, Satoshi; Durda, Michael Andrew; Essandoh, Michael

2016-01-01

Mitral stenosis (MS) after mitral valve (MV) repair is a slowly progressive condition, usually detected many years after the index MV surgery. It is defined as a mean transmitral pressure gradient (TMPG) >5 mmHg or a mitral valve area (MVA) <1.5 cm2. Pannus formation around the mitral annulus or extending to the mitral leaflets is suggested as the main mechanism for developing delayed MS after MV repair. On the other hand, early stenosis is thought to be a direct result of an undersized annuloplasty ring. Furthermore, in MS following ischemic mitral regurgitation (MR) repair, subvalvular tethering is the hypothesized pathophysiology. MS after MV repair has an incidence of 9–54%. Several factors have been associated with a higher risk for developing MS after MV repair, including the use of flexible Duran annuloplasty rings versus rigid Carpentier–Edwards rings, complete annuloplasty rings versus partial bands, small versus large anterior leaflet opening angle, and anterior leaflet tip opening length. Intraoperative echocardiography can measure the anterior leaflet opening angle, the anterior leaflet tip opening dimension, the MVA and the mean TMPG, and may help identify patients at risk for developing MS after MV repair. PMID:27148540

Mitral valve repair using ePTFE sutures for ruptured mitral chordae tendineae: a computational simulation study.

PubMed

Rim, Yonghoon; Laing, Susan T; McPherson, David D; Kim, Hyunggun

2014-01-01

Mitral valve (MV) repair using expanded polytetrafluoroethylene sutures is an established and preferred interventional method to resolve the complex pathophysiologic problems associated with chordal rupture. We developed a novel computational evaluation protocol to determine the effect of the artificial sutures on restoring MV function following valve repair. A virtual MV was created using three-dimensional echocardiographic data in a patient with ruptured mitral chordae tendineae (RMCT). Virtual repairs were designed by adding artificial sutures between the papillary muscles and the posterior leaflet where the native chordae were ruptured. Dynamic finite element simulations were performed to evaluate pre- and post-repair MV function. Abnormal posterior leaflet prolapse and mitral regurgitation was clearly demonstrated in the MV with ruptured chordae. Following virtual repair to reconstruct ruptured chordae, the severity of the posterior leaflet prolapse decreased and stress concentration was markedly reduced both in the leaflet tissue and the intact native chordae. Complete leaflet coaptation was restored when four or six sutures were utilized. Computational simulations provided quantitative information of functional improvement following MV repair. This novel simulation strategy may provide a powerful tool for evaluation and prediction of interventional treatment for RMCT.

Molecular cloning and characterization of alpha - galactosidase gene from Glaciozyma antarctica

NASA Astrophysics Data System (ADS)

Moheer, Reyad Qaed Al; Bakar, Farah Diba Abu; Murad, Abdul Munir Abdul

2015-09-01

Psychrophilic enzymes are proteins produced by psychrophilic organisms which recently are the limelight for industrial applications. A gene encoding α-galactosidase from a psychrophilic yeast, Glaciozyma antarctica PI12 which belongs to glycoside hydrolase family 27, was isolated and analyzed using several bioinformatic tools. The cDNA of the gene with the size of 1,404-bp encodes a protein with 467 amino acid residues. Predicted molecular weight of protein was 48.59 kDa and hence we name the gene encoding α-galactosidase as GAL48. We found that the predicted protein sequences possessed signal peptide sequence and are highly conserved among other fungal α-galactosidase.

Isolation of Nicotiana plumbaginifolia cDNAs encoding isoforms of serine acetyltransferase and O-acetylserine (thiol) lyase in a yeast two-hybrid system with Escherichia coli cysE and cysK genes as baits.

PubMed

Liszewska, Frantz; Gaganidze, Dali; Sirko, Agnieszka

2005-01-01

We applied the yeast two-hybrid system for screening of a cDNA library of Nicotiana plumbaginifolia for clones encoding plant proteins interacting with two proteins of Escherichia coli: serine acetyltransferase (SAT, the product of cysE gene) and O-acetylserine (thiol)lyase A, also termed cysteine synthase (OASTL-A, the product of cysK gene). Two plant cDNA clones were identified when using the cysE gene as a bait. These clones encode a probable cytosolic isoform of OASTL and an organellar isoform of SAT, respectively, as indicated by evolutionary trees. The second clone, encoding SAT, was identified independently also as a "prey" when using cysK as a bait. Our results reveal the possibility of applying the two-hybrid system for cloning of plant cDNAs encoding enzymes of the cysteine synthase complex in the two-hybrid system. Additionally, using genome walking sequences located upstream of the sat1 cDNA were identified. Subsequently, in silico analyses were performed aiming towards identification of the potential signal peptide and possible location of the deduced mature protein encoded by sat1.

Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments.

PubMed

Nunoura, Takuro; Hirayama, Hisako; Takami, Hideto; Oida, Hanako; Nishi, Shinro; Shimamura, Shigeru; Suzuki, Yohey; Inagaki, Fumio; Takai, Ken; Nealson, Kenneth H; Horikoshi, Koki

2005-12-01

Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota.

The genomic structure of the human Charcot-Leyden crystal protein gene is analogous to those of the galectin genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dyer, K.D.; Handen, J.S.; Rosenberg, H.F.

The Charcot-Leyden crystal (CLC) protein, or eosinophil lysophospholipase, is a characteristic protein of human eosinophils and basophils; recent work has demonstrated that the CLC protein is both structurally and functionally related to the galectin family of {beta}-galactoside binding proteins. The galectins as a group share a number of features in common, including a linear ligand binding site encoded on a single exon. In this work, we demonstrate that the intron-exon structure of the gene encoding CLC is analogous to those encoding the galectins. The coding sequence of the CLC gene is divided into four exons, with the entire {beta}-galactoside bindingmore » site encoded by exon III. We have isolated CLC {beta}-galactoside binding sites from both orangutan (Pongo pygmaeus) and murine (Mus musculus) genomic DNAs, both encoded on single exons, and noted conservation of the amino acids shown to interact directly with the {beta}-galactoside ligand. The most likely interpretation of these results suggests the occurrence of one or more exon duplication and insertion events, resulting in the distribution of this lectin domain to CLC as well as to the multiple galectin genes. 35 refs., 3 figs.« less

Recombination and mutation of class II histocompatibility genes in wild mice.

PubMed

Wakeland, E K; Darby, B R

1983-12-01

We have compared the tryptic peptide fingerprints of the A alpha, A beta, E alpha, and E beta subunits encoded by four wild-derived H-2 complexes expressing A molecules closely related to Ak. The A molecules encoded by these Ak-related mice have A alpha and A beta subunits that differ from A alpha k and A beta k by less than 10% of their tryptic peptides. Comparisons among the four wild-derived A molecules suggested that these contemporary A alpha and A beta alleles arose by sequential mutational events from common ancestor A alpha and A beta alleles. These results suggest that A alpha and A beta may co-evolve as an A beta A alpha gene duplex in wild mice. Tryptic peptide fingerprint comparisons of the E beta gene linked to these Ak-related A beta A alpha gene duplexes indicate that two encode E beta d-like subunits, whereas another encodes an E beta s-like subunit. These results strongly suggest that the A beta A alpha duplex and E beta recombine in wild mouse populations. The significantly different evolutionary patterns exhibited by the class II genes encoding A vs E molecules are discussed.

Cross sectional echocardiographic feature in carcinoid heart disease. A mechanism for tricuspid regurgitation in this syndrome.

PubMed

Davies, M K; Lowry, P J; Littler, W A

1984-03-01

In a patient with severe tricuspid regurgitation and mild pulmonary stenosis due to carcinoid heart disease cross sectional echocardiography showed nodular thickening and coaptation of the tricuspid leaflets at the beginning of systole. The leaflets were, however, seen to be increasingly pulled apart as right ventricular systole proceeded. This finding, which is probably due to traction on the leaflets by the thickened chordae tendineae, is therefore a mechanism of valvular incompetence, perhaps accounting for the particularly severe tricuspid regurgitation seen in carcinoid heart disease.

Catheter Entrapment During Posterior Mitral Leaflet Pushing Maneuver for MitraClip Implantation.

PubMed

Castrodeza, Javier; Amat-Santos, Ignacio J; Tobar, Javier; Varela-Falcón, Luis H

2016-06-01

MitraClip (Abbott Vascular) therapy has been reported to be an effective procedure for mitral regurgitation, especially in high-risk patients. Recently, the novel pushing maneuver technique has been described for approaching restricted and short posterior leaflets with a pigtail catheter in order to facilitate grasping of the clip. However, complications or unexpected situations may occur. We report the case of an 84-year-old patient who underwent MitraClip implantation wherein the pushing maneuver was complicated by the clip accidentally gripping the pigtail catheter along with the two leaflets.

Multi-functional acetyl-CoA carboxylase from Brassica napus is encoded by a multi-gene family: indication for plastidic localization of at least one isoform.

PubMed

Schulte, W; Töpfer, R; Stracke, R; Schell, J; Martini, N

1997-04-01

Three genes coding for different multifunctional acetyl-CoA carboxylase (ACCase; EC 6.4.1.2) isoenzymes from Brassica napus were isolated and divided into two major classes according to structural features in their 5' regions: class I comprises two genes with an additional coding exon of approximately 300 bp at the 5' end, and class II is represented by one gene carrying an intron of 586 bp in its 5' untranslated region. Fusion of the peptide sequence encoded by the additional first exon of a class I ACCase gene to the jellyfish Aequorea victoria green fluorescent protein (GFP) and transient expression in tobacco protoplasts targeted GFP to the chloroplasts. In contrast to the deduced primary structure of the biotin carboxylase domain encoded by the class I gene, the corresponding amino acid sequence of the class II ACCase shows higher identity with that of the Arabidopsis ACCase, both lacking a transit peptide. The Arabidopsis ACCase has been proposed to be a cytosolic isoenzyme. These observations indicate that the two classes of ACCase genes encode plastidic and cytosolic isoforms of multi-functional, eukaryotic type, respectively, and that B. napus contains at least one multi-functional ACCase besides the multi-subunit, prokaryotic type located in plastids. Southern blot analysis of genomic DNA from B. napus, Brassica rapa, and Brassica oleracea, the ancestors of amphidiploid rapeseed, using a fragment of a multi-functional ACCase gene as a probe revealed that ACCase is encoded by a multi-gene family of at least five members.

Characterization of GM-CSF-inhibitory factor and Uracil DNA glycosylase encoding genes from camel pseudocowpoxvirus.

PubMed

Nagarajan, G; Swami, Shelesh Kumar; Dahiya, Shyam Singh; Narnaware, S D; Mehta, S C; Singh, P K; Singh, Raghvendar; Tuteja, F C; Patil, N V

2015-06-01

The present study describes the PCR amplification of GM-CSF-inhibitory factor (GIF) and Uracil DNA glycosylase (UDG) encoding genes of pseudocowpoxvirus (PCPV) from the Indian Dromedaries (Camelus dromedarius) infected with contagious ecthyma using the primers based on the corresponding gene sequences of human PCPV and reindeer PCPV, respectively. The length of GIF gene of PCPV obtained from camel is 795 bp and due to the addition of one cytosine residue at position 374 and one adenine residue at position 516, the open reading frame (ORF) got altered, resulting in the production of truncated polypeptide. The ORF of UDG encoding gene of camel PCPV is 696 bp encoding a polypeptide of 26.0 kDa. Comparison of amino acid sequence homologies of GIF and UDG of camel PCPV revealed that the camel PCPV is closer to ORFV and PCPV (reference stains of both human and reindeer), respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

A mutation in a new gene bglJ, activates the bgl operon in Escherichia coli K-12

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giel, M.; Desnoyer, M.; Lopilato, J.

1996-06-01

A new mutation , bglJ4, has been characterized that results in the expression of the silent bgl operon. The bgl operon encodes proteins necessary for the transport and utilization of the aromatic {beta}-glucosides arbutin and salicin. A variety of mutations activate the operon and result in a Bgl{sup +} phenotype. Activating mutations are located upstream of the bgl promoter and in genes located elsewhere on the chromosome. Mutations outside of the bgl operon occur in the genes encoding DNA gyrase and in the gene encoding the nucleoid associated protein H-NS. The mutation described here, bglJ4, has been mapped to amore » new locus at min 99 on the Escherichia coli K-12 genetic map. The putative protein encoded by the bglJ gene has homology to a family of transcriptional activators. Evidence is presented that increased expression of the bglJ product is needed for activation of the bgl operon. 56 refs., 3 figs., 3 tabs.« less

Two Closely Related Genes of Arabidopsis Encode Plastidial Cytidinediphosphate Diacylglycerol Synthases Essential for Photoautotrophic Growth1[C

PubMed Central

Haselier, André; Akbari, Hana; Weth, Agnes; Baumgartner, Werner; Frentzen, Margrit

2010-01-01

Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the formation of cytidinediphosphate diacylglycerol, an essential precursor of anionic phosphoglycerolipids like phosphatidylglycerol or -inositol. In plant cells, CDS isozymes are located in plastids, mitochondria, and microsomes. Here, we show that these isozymes are encoded by five genes in Arabidopsis (Arabidopsis thaliana). Alternative translation initiation or alternative splicing of CDS2 and CDS4 transcripts can result in up to 10 isoforms. Most of the cDNAs encoding the various plant isoforms were functionally expressed in yeast and rescued the nonviable phenotype of the mutant strain lacking CDS activity. The closely related genes CDS4 and CDS5 were found to encode plastidial isozymes with similar catalytic properties. Inactivation of both genes was required to obtain Arabidopsis mutant lines with a visible phenotype, suggesting that the genes have redundant functions. Analysis of these Arabidopsis mutants provided further independent evidence for the importance of plastidial phosphatidylglycerol for structure and function of thylakoid membranes and, hence, for photoautotrophic growth. PMID:20442275

The rgg0182 gene encodes a transcriptional regulator required for the full Streptococcus thermophilus LMG18311 thermal adaptation.

PubMed

Henry, Romain; Bruneau, Emmanuelle; Gardan, Rozenn; Bertin, Stéphane; Fleuchot, Betty; Decaris, Bernard; Leblond-Bourget, Nathalie

2011-10-07

Streptococcus thermophilus is an important starter strain for the production of yogurt and cheeses. The analysis of sequenced genomes of four strains of S. thermophilus indicates that they contain several genes of the rgg familly potentially encoding transcriptional regulators. Some of the Rgg proteins are known to be involved in bacterial stress adaptation. In this study, we demonstrated that Streptococcus thermophilus thermal stress adaptation required the rgg0182 gene which transcription depends on the culture medium and the growth temperature. This gene encoded a protein showing similarity with members of the Rgg family transcriptional regulator. Our data confirmed that Rgg0182 is a transcriptional regulator controlling the expression of its neighboring genes as well as chaperones and proteases encoding genes. Therefore, analysis of a Δrgg0182 mutant revealed that this protein played a role in the heat shock adaptation of Streptococcus thermophilus LMG18311. These data showed the importance of the Rgg0182 transcriptional regulator on the survival of S. thermophilus during dairy processes and more specifically during changes in temperature.

Identification of an opd (organophosphate degradation) gene in an Agrobacterium isolate.

PubMed

Horne, Irene; Sutherland, Tara D; Harcourt, Rebecca L; Russell, Robyn J; Oakeshott, John G

2002-07-01

We isolated a bacterial strain, Agrobacterium radiobacter P230, which can hydrolyze a wide range of organophosphate (OP) insecticides. A gene encoding a protein involved in OP hydrolysis was cloned from A. radiobacter P230 and sequenced. This gene (called opdA) had sequence similarity to opd, a gene previously shown to encode an OP-hydrolyzing enzyme in Flavobacterium sp. strain ATCC 27551 and Brevundimonas diminuta MG. Insertional mutation of the opdA gene produced a strain lacking the ability to hydrolyze OPs, suggesting that this is the only gene encoding an OP-hydrolyzing enzyme in A. radiobacter P230. The OPH and OpdA proteins, encoded by opd and opdA, respectively, were overexpressed and purified as maltose-binding proteins, and the maltose-binding protein moiety was cleaved and removed. Neither protein was able to hydrolyze the aliphatic OP malathion. The kinetics of the two proteins for diethyl OPs were comparable. For dimethyl OPs, OpdA had a higher k(cat) than OPH. It was also capable of hydrolyzing the dimethyl OPs phosmet and fenthion, which were not hydrolyzed at detectable levels by OPH.

Detection of β-lactamase encoding genes in feces, soil and water from a Brazilian pig farm.

PubMed

Furlan, João Pedro Rueda; Stehling, Eliana Guedes

2018-01-10

β-lactam antibiotics are widely used for the treatment of different types of infections worldwide and the resistance to these antibiotics has grown sharply, which is of great concern. Resistance to β-lactams in gram-negative bacteria is mainly due to the production of β-lactamases, which are classified according to their functional activities. The aim of this study was to verify the presence of β-lactamases encoding genes in feces, soil, and water from a Brazilian pig farm. Different β-lactamases encoding genes were found, including bla CTX-M-Gp1 , bla CTX-M-Gp9 , bla SHV , bla OXA-1-like , bla GES , and bla VEB . The bla SHV and bla CTX-M-Gp1 genes have been detected in all types of samples, indicating the spread of β-lactam resistant bacteria among farm pigs and the environment around them. These results indicate that β-lactamase encoding genes belonging to the cloxacillinase, ESBL, and carbapenemase and they have high potential to spread in different sources, due to the fact that genes are closely related to mobile genetic elements, especially plasmids.

Impact of Implantable Transvenous Device Lead Location on Severity of Tricuspid Regurgitation

PubMed Central

Addetia, Karima; Maffessanti, Francesco; Mediratta, Anuj; Yamat, Megan; Weinert, Lynn; Moss, Joshua D.; Nayak, Hemal M.; Burke, Martin C.; Patel, Amit R.; Kruse, Eric; Jeevanandam, Valluvan; Mor-Avi, Victor; Lang, Roberto M.

2015-01-01

Background Implantable device leads can cause tricuspid regurgitation (TR) when they interfere with leaflet motion. The aim of this study was to determine whether lead-leaflet interference is associated with TR severity, independent of other causative factors of functional TR. Methods A total of 100 patients who underwent transthoracic two-dimensional and three-dimensional (3D) echocardiography of the tricuspid valve before and after lead placement were studied. Lead position was classified on 3D echocardiography as leaflet-interfering or noninterfering. TR severity was estimated by vena contracta (VC) width. Logistic regression analysis was used to identify factors associated with postdevice TR, including predevice VC width, right ventricular end-diastolic and end-systolic areas, fractional area change, right atrial size, tricuspid annular diameter, TR gradient, device lead age, and presence or absence of lead interference. Odds ratios were used to describe the association with moderate (VC width ≥ 0.5 cm) or severe (VC width ≥ 0.7 cm) TR, separately, using bivariate and stepwise multivariate logistic regression analysis. Results Forty-five of 100 patients showed device lead tricuspid valve leaflet interference. The septal leaflet was the most commonly affected (23 patients). On bivariate analysis, preimplantation VC width, right atrial size, tricuspid annular diameter, and lead-leaflet interference were significantly associated with postdevice TR. On multivariate analysis, preimplantation VC width and the presence of an interfering lead were independently associated with postdevice TR. Furthermore, the presence of an interfering lead was the only factor associated with TR worsening, increasing the likelihood of developing moderate or severe TR by 15- and 11-fold, respectively. Conclusion Lead-leaflet interference as seen on 3D echocardiography is associated with TR after device lead placement, suggesting that 3D echocardiography should be used to assess for lead interference in patients with significant TR. PMID:25129393

Crimping and deployment of balloon-expandable valved stents are responsible for the increase in the hydraulic conductance of leaflets.

PubMed

Convelbo, Channing; Guetat, Pierre; Cambillau, Michèle; Allam, Bachir; Bruneval, Patrick; Lafont, Antoine; Zegdi, Rachid

2013-12-01

Leaflet injury has been documented to occur during the deployment of valved stents (VSs). The pathological aspects, however, of this injury are difficult to quantify. Conversely, the hydraulic conductance of a (pericardial) membrane may be easily determined. The impact of crimping and deployment of VS on this parameter was therefore investigated. Bovine pericardial square (25 × 25 mm) patches were placed within a pressure chamber and their hydraulic conductance was determined. The influence of the pressure gradient and tissue thickness on this parameter was analysed. Six balloon-expandable VS were constructed. The hydraulic conductance of their bovine pericardial leaflets was determined before and after VS crimping and deployment in four of them. Pericardial leaflets of non-crimped VS were used as controls. Hydraulic conductance increased insignificantly with the pressure level within the chamber: from 128 ± 26.9 ml/h/m(2)/mmHg at a pressure of 50 mmHg to 232.3 ± 51.9 ml/h/m(2)/mmHg at a pressure of 250 mmHg (P = 0.117). Hydraulic conductance was not correlated to pericardial thickness, for thickness measurements ranging from 0.34 to 0.76 mm. The hydraulic conductance of VS leaflets significantly increased immediately after crimping from 45.2 ± 7.6 to 667.9.0 ± 527.2 ml/h/m(2)/mmHg (P < 0.001). This increase was still observed 24 h after VS deployment. No change in hydraulic conductance occurred in the control group. The determination of the hydraulic conductance of pericardial patches was easy to perform, reproducible and not influenced by tissue thickness. The hydraulic conductance of pericardial leaflets dramatically increased after VS crimping and deployment. This parameter might be, in the future, a useful noninvasive tool in studying leaflet trauma.

The molecular genetics of Usher syndrome.

PubMed

Ahmed, Z M; Riazuddin, S; Riazuddin, S; Wilcox, E R

2003-06-01

Association of sensorineural deafness and progressive retinitis pigmentosa with and without a vestibular abnormality is the hallmark of Usher syndrome and involves at least 12 loci among three different clinical subtypes. Genes identified for the more commonly inherited loci are USH2A (encoding usherin), MYO7A (encoding myosin VIIa), CDH23 (encoding cadherin 23), PCDH15 (encoding protocadherin 15), USH1C (encoding harmonin), USH3A (encoding clarin 1), and USH1G (encoding SANS). Transcripts from all these genes are found in many tissues/cell types other than the inner ear and retina, but all are uniquely critical for retinal and cochlear cell function. Many of these protein products have been demonstrated to have direct interactions with each other and perform an essential role in stereocilia homeostasis.

Finite element modeling of mitral leaflet tissue using a layered shell approximation

PubMed Central

Ratcliffe, Mark B.; Guccione, Julius M.

2012-01-01

The current study presents a finite element model of mitral leaflet tissue, which incorporates the anisotropic material response and approximates the layered structure. First, continuum mechanics and the theory of layered composites are used to develop an analytical representation of membrane stress in the leaflet material. This is done with an existing anisotropic constitutive law from literature. Then, the concept is implemented in a finite element (FE) model by overlapping and merging two layers of transversely isotropic membrane elements in LS-DYNA, which homogenizes the response. The FE model is then used to simulate various biaxial extension tests and out-of-plane pressure loading. Both the analytical and FE model show good agreement with experimental biaxial extension data, and show good mutual agreement. This confirms that the layered composite approximation presented in the current study is able to capture the exponential stiffening seen in both the circumferential and radial directions of mitral leaflets. PMID:22971896

Severe mitral regurgitation due to mitral leaflet aneurysm diagnosed by three-dimensional transesophageal echocardiography: a case report.

PubMed

Konishi, Takao; Funayama, Naohiro; Yamamoto, Tadashi; Hotta, Daisuke; Kikuchi, Kenjiro; Ohori, Katsumi; Nishihara, Hiroshi; Tanaka, Shinya

2016-11-22

A small mitral valve aneurysm (MVA) presenting as severe mitral regurgitation (MR) is uncommon. A 47-year-old man with a history of hypertension complained of exertional chest discomfort. A transthoracic echocardiogram (TTE) revealed the presence of MR and prolapse of the posterior leaflet. A 6-mm in diameter MVA, not clearly visualized by TTE, was detected on the posterior leaflet on a three-dimensional (3D) transesophageal echocardiography (TEE). The patient underwent uncomplicated triangular resection of P2 and mitral valve annuloplasty, and was discharged from postoperative rehabilitation, 2 weeks after the operation. Histopathology of the excised leaflet showed myxomatous changes without infective vegetation or signs of rheumatic heart disease. A small, isolated MVA is a cause of severe MR, which might be overlooked and, therefore, managed belatedly. 3D TEE was helpful in imaging its morphologic details.

Cloning of the Pichia anomala SEC61 gene and its expression in a Saccharomyces cerevisiae sec61 mutant.

PubMed

Ruíz, Teresa; De la Rosa, José M; Domínguez, Angel; Rodríguez, Luis

2003-05-01

In several organisms, including Saccharomyces cerevisiae and other yeast species, the product encoded by the SEC61 gene is considered to be the core element of the translocation apparatus within the endoplasmic reticulum membrane through which translocation of secretory and membrane proteins occurs. In this study, we have cloned and characterized the homolog of the SEC61 gene from the yeast Pichia anomala. The cloned gene includes an ORF, interrupted after the first ten nucleotides by an intron of 131 bp, encoding a 479-amino acid putative polypeptide exhibiting homology to the products encoded by different eukaryotic SEC61 genes, particularly to those from other yeast species. We show that the P. anomala SEC61 gene is correctly processed (intron splicing) when expressed in S. cerevisiae and that it is able to complement the thermosensitive phenotype associated with a mutation in the S. cerevisiae SEC61 gene.

Identification of the gene for fly non-muscle myosin heavy chain: Drosophila myosin heavy chains are encoded by a gene family.

PubMed Central

Kiehart, D P; Lutz, M S; Chan, D; Ketchum, A S; Laymon, R A; Nguyen, B; Goldstein, L S

1989-01-01

In contrast to vertebrate species Drosophila has a single myosin heavy chain gene that apparently encodes all sarcomeric heavy chain polypeptides. Flies also contain a cytoplasmic myosin heavy chain polypeptide that by immunological and peptide mapping criteria is clearly different from the major thoracic muscle isoform. Here, we identify the gene that encodes this cytoplasmic isoform and demonstrate that it is distinct from the muscle myosin heavy chain gene. Thus, fly myosin heavy chains are the products of a gene family. Our data suggest that the contractile function required to power myosin based movement in non-muscle cells requires myosin diversity beyond that available in a single heavy chain gene. In addition, we show, that accumulation of cytoplasmic myosin transcripts is regulated in a developmental stage specific fashion, consistent with a key role for this protein in the movements of early embryogenesis. Images PMID:2498088

A novel chlorophyll a/b binding (Cab) protein gene from petunia which encodes the lower molecular weight Cab precursor protein.

PubMed

Stayton, M M; Black, M; Bedbrook, J; Dunsmuir, P

1986-12-22

The 16 petunia Cab genes which have been characterized are all closely related at the nucleotide sequence level and they encode Cab precursor polypeptides which are similar in sequence and length. Here we describe a novel petunia Cab gene which encodes a unique Cab precursor protein. This protein is a member of the smallest class of Cab precursor proteins for which no gene has previously been assigned in petunia or any other species. The features of this Cab precursor protein are that it is shorter by 2-3 amino acids than the formerly characterized Cab precursors, its transit peptide sequence is unrelated, and the mature polypeptide is significantly diverged at the functionally important N terminus from other petunia Cab proteins. Gene structure also discriminates this gene which is the only intron containing Cab gene in petunia genomic DNA.

Identification of chitinolytic bacteria isolated from shrimp pond sediment and characterization of their chitinase encoding gene

NASA Astrophysics Data System (ADS)

Triwijayani, A. U.; Puspita, I. D.; Murwantoko; Ustadi

2018-03-01

Chitinolytic bacteria are a group of bacteria owning enzymes that able to hydrolyze chitin. Previously, we isolated chitinolytic bacteria from shrimp pond sediment in Bantul, Yogyakarta, and obtained five isolates showing high chitinolytic index named as isolate PT1, PT2, PT5, PT6 and PB2. The aims of this study were to identify chitinolytic bacteria isolated from shrimp pond sediment and to characterize the chitinase encoding gene from each isolate. The molecular technique was performed by amplification of 16S rDNA, amplification of chitinase encoding gene and sequence analysis. Two chitinolytic bacteria of PT1 and PT2 were similar to Aeromonas bivalvium strain D15, PT5 to Pseudomonas stutzeri strain BD-2.2.1, PT6 to Serratia marcescens strain FZSF02 and PB2 to Streptomyces misionensis strain OsiRt-1. The comparison of chitinase encoding gene between three isolates with those in Gen Bank shows that PT1 had similar sequences with the chi1 gene in Aeromonas sp. 17m, PT2 with chi1 gene in A. caviae (CB101) and PT6 with chiB gene in S. Marcescens (BJL200).

Characterization of EhaJ, a New Autotransporter Protein from Enterohemorrhagic and Enteropathogenic Escherichia coli

PubMed Central

Easton, Donna M.; Totsika, Makrina; Allsopp, Luke P.; Phan, Minh-Duy; Idris, Adi; Wurpel, Daniël J.; Sherlock, Orla; Zhang, Bing; Venturini, Carola; Beatson, Scott A.; Mahony, Timothy J.; Cobbold, Rowland N.; Schembri, Mark A.

2011-01-01

Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC) are diarrheagenic pathotypes of E. coli that cause gastrointestinal disease with the potential for life-threatening sequelae. While certain EHEC and EPEC virulence mechanisms have been extensively studied, the factors that mediate host colonization remain to be properly defined. Previously, we identified four genes (ehaA, ehaB, ehaC, and ehaD) from the prototypic EHEC strain EDL933 that encode for proteins that belong to the autotransporter (AT) family. Here we have examined the prevalence of these genes, as well as several other AT-encoding genes, in a collection of EHEC and EPEC strains. We show that the complement of AT-encoding genes in EHEC and EPEC strains is variable, with some AT-encoding genes being highly prevalent. One previously uncharacterized AT-encoding gene, which we have termed ehaJ, was identified in 12/44 (27%) of EHEC and 2/20 (10%) of EPEC strains. The ehaJ gene lies immediately adjacent to a gene encoding a putative glycosyltransferase (referred to as egtA). Western blot analysis using an EhaJ-specific antibody indicated that EhaJ is glycosylated by EgtA. Expression of EhaJ in a recombinant E. coli strain, revealed EhaJ is located at the cell surface and in the presence of the egtA glycosyltransferase gene mediates strong biofilm formation in microtiter plate and flow cell assays. EhaJ also mediated adherence to a range of extracellular matrix proteins, however this occurred independent of glycosylation. We also demonstrate that EhaJ is expressed in a wild-type EPEC strain following in vitro growth. However, deletion of ehaJ did not significantly alter its adherence or biofilm properties. In summary, EhaJ is a new glycosylated AT protein from EPEC and EHEC. Further studies are required to elucidate the function of EhaJ in colonization and virulence. PMID:21687429

Targeted next-generation sequencing helps to decipher the genetic and phenotypic heterogeneity of hypertrophic cardiomyopathy

PubMed Central

Cecconi, Massimiliano; Parodi, Maria I.; Formisano, Francesco; Spirito, Paolo; Autore, Camillo; Musumeci, Maria B.; Favale, Stefano; Forleo, Cinzia; Rapezzi, Claudio; Biagini, Elena; Davì, Sabrina; Canepa, Elisabetta; Pennese, Loredana; Castagnetta, Mauro; Degiorgio, Dario; Coviello, Domenico A.

2016-01-01

Hypertrophic cardiomyopathy (HCM) is mainly associated with myosin, heavy chain 7 (MYH7) and myosin binding protein C, cardiac (MYBPC3) mutations. In order to better explain the clinical and genetic heterogeneity in HCM patients, in this study, we implemented a target-next generation sequencing (NGS) assay. An Ion AmpliSeq™ Custom Panel for the enrichment of 19 genes, of which 9 of these did not encode thick/intermediate and thin myofilament (TTm) proteins and, among them, 3 responsible of HCM phenocopy, was created. Ninety-two DNA samples were analyzed by the Ion Personal Genome Machine: 73 DNA samples (training set), previously genotyped in some of the genes by Sanger sequencing, were used to optimize the NGS strategy, whereas 19 DNA samples (discovery set) allowed the evaluation of NGS performance. In the training set, we identified 72 out of 73 expected mutations and 15 additional mutations: the molecular diagnosis was achieved in one patient with a previously wild-type status and the pre-excitation syndrome was explained in another. In the discovery set, we identified 20 mutations, 5 of which were in genes encoding non-TTm proteins, increasing the diagnostic yield by approximately 20%: a single mutation in genes encoding non-TTm proteins was identified in 2 out of 3 borderline HCM patients, whereas co-occuring mutations in genes encoding TTm and galactosidase alpha (GLA) altered proteins were characterized in a male with HCM and multiorgan dysfunction. Our combined targeted NGS-Sanger sequencing-based strategy allowed the molecular diagnosis of HCM with greater efficiency than using the conventional (Sanger) sequencing alone. Mutant alleles encoding non-TTm proteins may aid in the complete understanding of the genetic and phenotypic heterogeneity of HCM: co-occuring mutations of genes encoding TTm and non-TTm proteins could explain the wide variability of the HCM phenotype, whereas mutations in genes encoding only the non-TTm proteins are identifiable in patients with a milder HCM status. PMID:27600940

Characterization of two genes encoding the Mycobacterium tuberculosis ribonucleotide reductase small subunit.

PubMed Central

Yang, F; Curran, S C; Li, L S; Avarbock, D; Graf, J D; Chua, M M; Lu, G; Salem, J; Rubin, H

1997-01-01

Two nrdF genes, nrdF1 and nrdF2, encoding the small subunit (R2) of ribonucleotide reductase (RR) from Mycobacterium tuberculosis have 71% identity at the amino acid level and are both highly homologous with Salmonella typhimurium R2F. The calculated molecular masses of R2-1 and R2-2 are 36,588 (322 amino acids [aa]) and 36,957 (324 aa) Da, respectively. Western blot analysis of crude M. tuberculosis extracts indicates that both R2s are expressed in vivo. Recombinant R2-2 is enzymatically active when assayed with pure recombinant M. tuberculosis R1 subunit. Both ATP and dATP are activators for CDP reduction up to 2 and 1 mM, respectively. The gene encoding M. tuberculosis R2-1, nrdF1, is not linked to nrdF2, nor is either gene linked to the gene encoding the large subunit, M. tuberculosis nrdE. The gene encoding MTP64 was found downstream from nrdF1, and the gene encoding alcohol dehydrogenase was found downstream from nrdF2. A nrdA(Ts) strain of E. coli (E101) could be complemented by simultaneous transformation with M. tuberculosis nrdE and nrdF2. An M. tuberculosis nrdF2 variant in which the codon for the catalytically necessary tyrosine was replaced by the phenylalanine codon did not complement E101 when cotransformed with M. tuberculosis nrdE. Similarly, M. tuberculosis nrdF1 and nrdE did not complement E101. Activity of recombinant M. tuberculosis RR was inhibited by incubating the enzyme with a peptide corresponding to the 7 C-terminal amino acid residues of the R2-2 subunit. M. tuberculosis is a species in which a nrdEF system appears to encode the biologically active species of RR and also the only bacterial species identified so far in which class I RR subunits are not arranged on an operon. PMID:9335290

Randomly organized lipids and marginally stable proteins: a coupling of weak interactions to optimize membrane signaling.

PubMed

Rice, Anne M; Mahling, Ryan; Fealey, Michael E; Rannikko, Anika; Dunleavy, Katie; Hendrickson, Troy; Lohese, K Jean; Kruggel, Spencer; Heiling, Hillary; Harren, Daniel; Sutton, R Bryan; Pastor, John; Hinderliter, Anne

2014-09-01

Eukaryotic lipids in a bilayer are dominated by weak cooperative interactions. These interactions impart highly dynamic and pliable properties to the membrane. C2 domain-containing proteins in the membrane also interact weakly and cooperatively giving rise to a high degree of conformational plasticity. We propose that this feature of weak energetics and plasticity shared by lipids and C2 domain-containing proteins enhance a cell's ability to transduce information across the membrane. We explored this hypothesis using information theory to assess the information storage capacity of model and mast cell membranes, as well as differential scanning calorimetry, carboxyfluorescein release assays, and tryptophan fluorescence to assess protein and membrane stability. The distribution of lipids in mast cell membranes encoded 5.6-5.8bits of information. More information resided in the acyl chains than the head groups and in the inner leaflet of the plasma membrane than the outer leaflet. When the lipid composition and information content of model membranes were varied, the associated C2 domains underwent large changes in stability and denaturation profile. The C2 domain-containing proteins are therefore acutely sensitive to the composition and information content of their associated lipids. Together, these findings suggest that the maximum flow of signaling information through the membrane and into the cell is optimized by the cooperation of near-random distributions of membrane lipids and proteins. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014 Elsevier B.V. All rights reserved.

Cloning and sequence analysis of the LEU2 homologue gene from Pichia anomala.

PubMed

De la Rosa, J M; Pérez, J A; Gutiérrez, F; González, J M; Ruiz, T; Rodríguez, L

2001-11-01

The Pichia anomala LEU2 gene (PaLEU2) was isolated by complementation of a leu2 Saccharomyces cerevisiae mutant. The cloned gene also allowed growth of a Escherichia coli leuB mutant in leucine-lacking medium, indicating that it encodes a product able to complement the beta-isopropylmalate dehydrogenase deficiency of the mutants. The sequenced DNA fragment contains a complete ORF of 1092 bp, and the deduced polypeptide shares significant homologies with the products of the LEU2 genes from S. cerevisiae (84% identity) and other yeast species. A sequence resembling the GC-rich palindrome motif identified in the 5' region of S. cerevisiae LEU2 gene as the binding site for the transcription activating factor encoded by the LEU3 gene was found at the promoter region. In addition, upstream of the PaLEU2 the 3'-terminal half of a gene of the same orientation, encoding a homologue of the S. cerevisiae NFS1/SPL1 gene that encodes a mitochondrial cysteine desulphurase involved in both tRNA processing and mitochondrial metabolism, was found. The genomic organization of the PaNFS1-PaLEU2 gene pair is similar to that found in several other yeast species, including S. cerevisiae and Candida albicans, except that in some of them the LEU2 gene appears in the reverse orientation. Copyright 2001 John Wiley & Sons, Ltd.

Mitral valve coaptation and its relationship to late diastolic flow: A color Doppler and vector flow map echocardiographic study in normal subjects.

PubMed

Sherrid, Mark V; Kushner, Josef; Yang, Georgiana; Ro, Richard

2017-04-01

Three competing theories about the mechanism of mitral coaptation in normal subjects were evaluated by color Doppler and vector flow mapping (VFM): (1) beginning of ventricular (LV) ejection, (2) "breaking of the jet" of diastolic LV inflow, and (3) returning diastolic vortices impacting the leaflets on their LV surfaces. We analyzed 80 color Doppler frames and 320 VFM measurements. In all 20 normal subjects, coaptation occurred before LV ejection, 78±16 ms before onset. On color Doppler frames the larger anterior, and smaller posterior vortices circle back and, in all cases, strike the ventricular surfaces of the leaflets. On the first closing-begins frame, for the first time, vortex velocity normal to the ventricular surface of the anterior leaflet (AML) is greater than that in the mitral orifice, and the angle of attack of LV vortical flow onto the AML is twice as high as the angle of flow onto the valve in orifice. Thus, at the moment coaptation begins, vortical flow strikes the mitral leaflet with higher velocity, and higher angle of attack than orifice flow, and thus with greater force. According to the "breaking of the jet" theory, one would expect to see de novo LV flow perpendicular to the leaflets beginning after transmitral flow terminates. Instead, the returning continuous LV vortical flow that impacts the valve builds continuously after the P-wave. Late diastolic vortices strike the ventricular surfaces of the mitral leaflets and contribute to valve coaptation, permitted by concomitant decline in transmitral flow. © 2017, Wiley Periodicals, Inc.

An inverse modeling approach for semilunar heart valve leaflet mechanics: exploitation of tissue structure.

PubMed

Aggarwal, Ankush; Sacks, Michael S

2016-08-01

Determining the biomechanical behavior of heart valve leaflet tissues in a noninvasive manner remains an important clinical goal. While advances in 3D imaging modalities have made in vivo valve geometric data available, optimal methods to exploit such information in order to obtain functional information remain to be established. Herein we present and evaluate a novel leaflet shape-based framework to estimate the biomechanical behavior of heart valves from surface deformations by exploiting tissue structure. We determined accuracy levels using an "ideal" in vitro dataset, in which the leaflet geometry, strains, mechanical behavior, and fibrous structure were known to a high level of precision. By utilizing a simplified structural model for the leaflet mechanical behavior, we were able to limit the number of parameters to be determined per leaflet to only two. This approach allowed us to dramatically reduce the computational time and easily visualize the cost function to guide the minimization process. We determined that the image resolution and the number of available imaging frames were important components in the accuracy of our framework. Furthermore, our results suggest that it is possible to detect differences in fiber structure using our framework, thus allowing an opportunity to diagnose asymptomatic valve diseases and begin treatment at their early stages. Lastly, we observed good agreement of the final resulting stress-strain response when an averaged fiber architecture was used. This suggests that population-averaged fiber structural data may be sufficient for the application of the present framework to in vivo studies, although clearly much work remains to extend the present approach to in vivo problems.

Transapical endovascular implantation of neochordae using a suction and suture device.

PubMed

Maisano, Francesco; Michev, Iassen; Rowe, Stanton; Addis, Alessandro; Campagnol, Marino; Guidotti, Andrea; Colombo, Antonio; Alfieri, Ottavio

2009-07-01

Neochordae implantation is a standard method for treatment of mitral valve prolapse. We describe a transcatheter technology enabling transapical endovascular chordal implantation. Six adult pigs were anesthetized. Two 10F sheaths were introduced in the femoral vessels for monitoring and intracardiac echo. After midline sternotomy, the pericardium was opened, the apex was punctured inside two 2-0 polypropylene purse strings. A 0.035 in J tipped guidewire was introduced in the left ventricle and an ultra stiff 14F sheath (guide catheter) inserted through the apex. A suction-and-suture device was introduced in the left ventricle. The mitral valve was crossed under echo guidance. Using suction, either the anterior (two cases) or posterior (four cases) leaflet was captured and a loop of 4-0 polypropylene was thrown at the edge of the leaflet. The loop, with a pledget, was exteriorized through the introducer. The introducer was removed and the purse-string tied. Under echo guidance, the neochordae suture was pulled and tied over a pledget to evoke leaflet tethering. The animals were sacrificed and gross anatomy reviewed. Leaflet capture was feasible in the intended location in all cases. Following suture tethering, variable degrees of MR were obtained. At gross anatomy, the neochordae were positioned at 1-4mm from the leaflet free edge, and were firmly attached to the leaflets. Transcatheter endovascular neochordae implantation is feasible. A prolapse model is needed to further demonstrate feasibility under pathologic conditions. The apical approach allows easy and direct route to transcatheter beating heart minimally invasive mitral repair.

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease

PubMed Central

Bacci, Giovanni; Fiscarelli, Ersilia; Taccetti, Giovanni; Dolce, Daniela; Paganin, Patrizia; Morelli, Patrizia; Tuccio, Vanessa; De Alessandri, Alessandra; Lucidi, Vincenzina

2017-01-01

In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease. PMID:28758937

Activation of Pathogenesis-related Genes by the Rhizobacterium, Bacillus sp. JS, Which Induces Systemic Resistance in Tobacco Plants.

PubMed

Kim, Ji-Seong; Lee, Jeongeun; Lee, Chan-Hui; Woo, Su Young; Kang, Hoduck; Seo, Sang-Gyu; Kim, Sun-Hyung

2015-06-01

Plant growth promoting rhizobacteria (PGPR) are known to confer disease resistance to plants. Bacillus sp. JS demonstrated antifungal activities against five fungal pathogens in in vitro assays. To verify whether the volatiles of Bacillus sp. JS confer disease resistance, tobacco leaves pre-treated with the volatiles were damaged by the fungal pathogen, Rhizoctonia solani and oomycete Phytophthora nicotianae. Pre-treated tobacco leaves had smaller lesion than the control plant leaves. In pathogenesis-related (PR) gene expression analysis, volatiles of Bacillus sp. JS caused the up-regulation of PR-2 encoding β-1,3-glucanase and acidic PR-3 encoding chitinase. Expression of acidic PR-4 encoding chitinase and acidic PR-9 encoding peroxidase increased gradually after exposure of the volatiles to Bacillus sp. JS. Basic PR-14 encoding lipid transfer protein was also increased. However, PR-1 genes, as markers of salicylic acid (SA) induced resistance, were not expressed. These results suggested that the volatiles of Bacillus sp. JS confer disease resistance against fungal and oomycete pathogens through PR genes expression.

Fusagene vectors: a novel strategy for the expression of multiple genes from a single cistron.

PubMed

Gäken, J; Jiang, J; Daniel, K; van Berkel, E; Hughes, C; Kuiper, M; Darling, D; Tavassoli, M; Galea-Lauri, J; Ford, K; Kemeny, M; Russell, S; Farzaneh, F

2000-12-01

Transduction of cells with multiple genes, allowing their stable and co-ordinated expression, is difficult with the available methodologies. A method has been developed for expression of multiple gene products, as fusion proteins, from a single cistron. The encoded proteins are post-synthetically cleaved and processed into each of their constituent proteins as individual, biologically active factors. Specifically, linkers encoding cleavage sites for the Golgi expressed endoprotease, furin, have been incorporated between in-frame cDNA sequences encoding different secreted or membrane bound proteins. With this strategy we have developed expression vectors encoding multiple proteins (IL-2 and B7.1, IL-4 and B7.1, IL-4 and IL-2, IL-12 p40 and p35, and IL-12 p40, p35 and IL-2 ). Transduction and analysis of over 100 individual clones, derived from murine and human tumour cell lines, demonstrate the efficient expression and biological activity of each of the encoded proteins. Fusagene vectors enable the co-ordinated expression of multiple gene products from a single, monocistronic, expression cassette.

Physiotherapy Post Lumbar Discectomy: Prospective Feasibility and Pilot Randomised Controlled Trial

PubMed Central

Rushton, Alison; Goodwin, Peter C.

2015-01-01

Objectives To evaluate: acceptability and feasibility of trial procedures; distribution of scores on the Roland Morris Disability Questionnaire (RMDQ, planned primary outcome); and efficient working of trial components. Design and Setting A feasibility and external pilot randomised controlled trial (ISRCTN33808269, assigned 10/12/2012) was conducted across 2 UK secondary care outpatient physiotherapy departments associated with regional spinal surgery centres. Participants Consecutive consenting patients aged >18 years; post primary, single level, lumbar discectomy. Interventions Participants were randomised to either 1:1 physiotherapy outpatient management including patient leaflet, or patient leaflet alone. Main Outcome Measures Blinded assessments were made at 4 weeks post surgery (baseline) and 12 weeks post baseline (proposed primary end point). Secondary outcomes included: Global Perceived Effect, back/leg pain, straight leg raise, return to work/function, quality of life, fear avoidance, range of movement, medication, re-operation. Results At discharge, 110 (44%) eligible patients gave consent to be contacted. 59 (54%) patients were recruited. Loss to follow up was 39% at 12 weeks, with one site contributing 83% losses. Mean (SD) RMDQ was 10.07 (5.58) leaflet and 10.52 (5.94) physiotherapy/leaflet at baseline; and 5.37 (4.91) leaflet and 5.53 (4.49) physiotherapy/leaflet at 12 weeks. 5.1% zero scores at 12 weeks illustrated no floor effect. Sensitivity to change was assessed at 12 weeks with mean (SD) change -4.53 (6.41), 95%CI -7.61 to -1.44 for leaflet; and -6.18 (5.59), 95%CI -9.01 to -3.30 for physiotherapy/leaflet. RMDQ mean difference (95%CI) between change from baseline to twelve weeks was 1.65(-2.46 to 5.75). Mean difference (95%CI) between groups at 12 weeks was -0.16 (-3.36 to 3.04). Participant adherence with treatment was good. No adverse events were reported. Conclusions Both interventions were acceptable, and it is promising that they both demonstrated a trend in reducing disability in this population. A randomised controlled trial, using a different trial design, is needed to ascertain the effectiveness of combining the interventions into a stepped care intervention and comparing to a no intervention arm. Findings will guide design changes for an adequately powered randomised controlled trial, using RMDQ as the primary outcome. Trial Registration ISRCTN registry 33808269 PMID:26562660

Structure, Expression, Chromosomal Location and Product of the Gene Encoding Adh2 in Petunia

PubMed Central

Gregerson, R. G.; Cameron, L.; McLean, M.; Dennis, P.; Strommer, J.

1993-01-01

In most higher plants the genes encoding alcohol dehydrogenase comprise a small gene family, usually with two members. The Adh1 gene of Petunia has been cloned and analyzed, but a second identifiable gene was not recovered from any of three genomic libraries. We have therefore employed the polymerase chain reaction to obtain the major portion of a second Adh gene. From sequence, mapping and northern data we conclude this gene encodes ADH2, the major anaerobically inducible Adh gene of Petunia. The availability of both Adh1 and Adh2 from Petunia has permitted us to compare their structures and patterns of expression to those of the well-studied Adh genes of maize, of which one is highly expressed developmentally, while both are induced in response to hypoxia. Despite their evolutionary distance, evidenced by deduced amino acid sequence as well as taxonomic classification, the pairs of genes are regulated in strikingly similar ways in maize and Petunia. Our findings suggest a significant biological basis for the regulatory strategy employed by these distant species for differential expression of multiple Adh genes. PMID:8096485

Regulation of Bacteriocin Production in Streptococcus mutans by the Quorum-Sensing System Required for Development of Genetic Competence

PubMed Central

van der Ploeg, Jan R.

2005-01-01

In Streptococcus mutans, competence for genetic transformation and biofilm formation are dependent on the two-component signal transduction system ComDE together with the inducer peptide pheromone competence-stimulating peptide (CSP) (encoded by comC). Here, it is shown that the same system is also required for expression of the nlmAB genes, which encode a two-peptide nonlantibiotic bacteriocin. Expression from a transcriptional nlmAB′-lacZ fusion was highest at high cell density and was increased up to 60-fold following addition of CSP, but it was abolished when the comDE genes were interrupted. Two more genes, encoding another putative bacteriocin and a putative bacteriocin immunity protein, were also regulated by this system. The regions upstream of these genes and of two further putative bacteriocin-encoding genes and a gene encoding a putative bacteriocin immunity protein contained a conserved 9-bp repeat element just upstream of the transcription start, which suggests that expression of these genes is also dependent on the ComCDE regulatory system. Mutations in the repeat element of the nlmAB promoter region led to a decrease in CSP-dependent expression of nlmAB′-lacZ. In agreement with these results, a comDE mutant and mutants unable to synthesize or export CSP did not produce bacteriocins. It is speculated that, at high cell density, bacteriocin production is induced to liberate DNA from competing streptococci. PMID:15937160

Functional characterization of an apple (Malus x domestica) LysM domain receptor encoding gene for its role in defense response

USDA-ARS?s Scientific Manuscript database

Apple gene MDP0000136494 was identified as the only LysM containing protein encoding gene which was specifically up-regulated in P. ultimum infected apple root by a previous transcriptome analysis. In current study, the functional identity of MDP0000136494 was investigated using combined genomic, tr...

Cloning and sequencing the genes encoding goldfish and carp ependymin.

PubMed

Adams, D S; Shashoua, V E

1994-04-20

Ependymins (EPNs) are brain glycoproteins thought to function in optic nerve regeneration and long-term memory consolidation. To date, epn genes have been characterized in two orders of teleost fish. In this study, polymerase chain reactions (PCR) were used to amplify the complete 1.6-kb epn genes, gf-I and cc-I, from genomic DNA of Cypriniformes, goldfish and carp, respectively. Amplified bands were cloned and sequenced. Each gene consists of six exons and five introns. The exon portion of gf-I encodes a predicted 215-amino-acid (aa) protein previously characterized as GF-I, while cc-I encodes a predicted 215-aa protein 95% homologous to GF-I.

The complete mitochondrial genome sequence of Eimeria innocua (Eimeriidae, Coccidia, Apicomplexa).

PubMed

Hafeez, Mian Abdul; Vrba, Vladimir; Barta, John Robert

2016-07-01

The complete mitochondrial genome of Eimeria innocua KR strain (Eimeriidae, Coccidia, Apicomplexa) was sequenced. This coccidium infects turkeys (Meleagris gallopavo), Bobwhite quails (Colinus virginianus), and Grey partridges (Perdix perdix). Genome organization and gene contents were comparable with other Eimeria spp. infecting galliform birds. The circular-mapping mt genome of E. innocua is 6247 bp in length with three protein-coding genes (cox1, cox3, and cytb), 19 gene fragments encoding large subunit (LSU) rRNA and 14 gene fragments encoding small subunit (SSU) rRNA. Like other Apicomplexa, no tRNA was encoded. The mitochondrial genome of E. innocua confirms its close phylogenetic affinities to Eimeria dispersa.

Genes encoding novel lipid transporters and their use to increase oil production in vegetative tissues of plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Changcheng; Fan, Jilian; Yan, Chengshi

The present invention discloses a novel gene encoding a transporter protein trigalactosyldiacylglycerol-5 (TGD5), mutations thereof and their use to enhance TAG production and retention in plant vegetative tissue.

Isolation and characterization of polygalacturonase genes (pecA and pecB) from Aspergillus flavus.

PubMed Central

Whitehead, M P; Shieh, M T; Cleveland, T E; Cary, J W; Dean, R A

1995-01-01

Two genes, pecA and pecB, encoding endopolyglacturonases were cloned from a highly aggressive strain of Aspergillus flavus. The pecA gene consisted of 1,228 bp encoding a protein of 363 amino acids with a predicted molecular mass of 37.6 kDa, interrupted by two introns of 58 and 81 bp in length. Accumulation of pecA mRNA in both pectin- or glucose-grown mycelia in the highly aggressive strain matched the activity profile of a pectinase previously identified as P2c. Transformants of a weakly aggressive strain containing a functional copy of the pecA gene produced P2c in vitro, confirming that pecA encodes P2c. The coding region of pecB was determined to be 1,217 bp in length interrupted by two introns of 65 and 54 bp in length. The predicted protein of 366 amino acids had an estimated molecular mass of 38 kDa. Transcripts of this gene accumulated in mycelia grown in medium containing pectin alone, never in mycelia grown in glucose-containing medium, for both highly and weakly aggressive strains. Thus, pecB encodes the activity previously identified as P1 or P3. pecA and pecB share a high degree of sequence identity with polygalacturonase genes from Aspergillus parasiticus and Aspergillus oryzae, further establishing the close relationships between members of the A. flavus group. Conservation of intron positions in these genes also indicates that they share a common ancestor with genes encoding endopolyglacturonases of Aspergillus niger. PMID:7574642

Draft Genome Sequence of Ezakiella peruensis Strain M6.X2, a Human Gut Gram-Positive Anaerobic Coccus.

PubMed

Diop, Awa; Diop, Khoudia; Tomei, Enora; Raoult, Didier; Fenollar, Florence; Fournier, Pierre-Edouard

2018-03-01

We report here the draft genome sequence of Ezakiella peruensis strain M6.X2 T The draft genome is 1,672,788 bp long and harbors 1,589 predicted protein-encoding genes, including 26 antibiotic resistance genes with 1 gene encoding vancomycin resistance. The genome also exhibits 1 clustered regularly interspaced short palindromic repeat region and 333 genes acquired by horizontal gene transfer. Copyright © 2018 Diop et al.

Deregulation of Rab and Rab Effector Genes in Bladder Cancer

PubMed Central

Ho, Joel R.; Chapeaublanc, Elodie; Kirkwood, Lisa; Nicolle, Remy; Benhamou, Simone; Lebret, Thierry; Allory, Yves; Southgate, Jennifer; Radvanyi, François; Goud, Bruno

2012-01-01

Growing evidence indicates that Rab GTPases, key regulators of intracellular transport in eukaryotic cells, play an important role in cancer. We analysed the deregulation at the transcriptional level of the genes encoding Rab proteins and Rab-interacting proteins in bladder cancer pathogenesis, distinguishing between the two main progression pathways so far identified in bladder cancer: the Ta pathway characterized by a high frequency of FGFR3 mutation and the carcinoma in situ pathway where no or infrequent FGFR3 mutations have been identified. A systematic literature search identified 61 genes encoding Rab proteins and 223 genes encoding Rab-interacting proteins. Transcriptomic data were obtained for normal urothelium samples and for two independent bladder cancer data sets corresponding to 152 and 75 tumors. Gene deregulation was analysed with the SAM (significant analysis of microarray) test or the binomial test. Overall, 30 genes were down-regulated, and 13 were up-regulated in the tumor samples. Five of these deregulated genes (LEPRE1, MICAL2, RAB23, STXBP1, SYTL1) were specifically deregulated in FGFR3-non-mutated muscle-invasive tumors. No gene encoding a Rab or Rab-interacting protein was found to be specifically deregulated in FGFR3-mutated tumors. Cluster analysis showed that the RAB27 gene cluster (comprising the genes encoding RAB27 and its interacting partners) was deregulated and that this deregulation was associated with both pathways of bladder cancer pathogenesis. Finally, we found that the expression of KIF20A and ZWINT was associated with that of proliferation markers and that the expression of MLPH, MYO5B, RAB11A, RAB11FIP1, RAB20 and SYTL2 was associated with that of urothelial cell differentiation markers. This systematic analysis of Rab and Rab effector gene deregulation in bladder cancer, taking relevant tumor subgroups into account, provides insight into the possible roles of Rab proteins and their effectors in bladder cancer pathogenesis. This approach is applicable to other group of genes and types of cancer. PMID:22724020

The inner side of T cell lipid rafts.

PubMed

Gri, Giorgia; Molon, Barbara; Manes, Santos; Pozzan, Tullio; Viola, Antonella

2004-07-15

A key question in understanding the functional role of lipid rafts is whether lipid microdomains at the plasma membrane outer leaflet are coupled to lipid microdomains at the inner leaflet. By using a cyan-fluorescent protein (CFP) targeted to inner plasma membrane rafts of Jurkat T cells, we found that raft domains at the outer and inner leaflets are physically coupled and that this coupling requires cholesterol. Interestingly, TCR/CD3 cross-linking induces co-capping of the raft bilayer independently of cholesterol or signaling events, indicating that cholesterol-extracting drugs are unable to destroy TCR-lipid rafts interaction.

Mitral valve stenosis caused by abnormal pannus extension over the prosthetic ring and leaflets after Duran ring mitral annuloplasty.

PubMed

Yunoki, Junji; Minato, Naoki; Katayama, Yuji; Sato, Hisashi

2009-01-01

We treated a 61-year-old woman with mitral stenosis caused by pannus formation after Duran ring annuloplasty. Pannus overgrowth on the ring with extension onto both leaflets narrowed the mitral orifice and severely restricted the mobility of the valve leaflets. Mitral valve replacement with a St. Jude Medical mechanical heart valve prosthesis was successfully performed, and the postoperative course was uneventful. Patients undergoing Duran ring annuloplasty should be followed up with the consideration of possible mitral stenosis caused by pannus extension, as the cause for pannus formation remains unclear.

Premeasured Chordal Loops for Mitral Valve Repair.

PubMed

Gillinov, Marc; Quinn, Reed; Kerendi, Faraz; Gaudiani, Vince; Shemin, Richard; Barnhart, Glenn; Raines, Edward; Gerdisch, Marc W; Banbury, Michael

2016-09-01

Premeasured expanded polytetrafluoroethylene chordal loops with integrated sutures for attachment to the papillary muscle and leaflet edges facilitate correction of mitral valve prolapse. Configured as a group of 3 loops (length range 12 to 24 mm), the loops are attached to a pledget that is passed through the papillary muscle and tied. Each of the loops has 2 sutures with attached needles; these needles are passed through the free edge of the leaflet and then the sutures are tied to each other, securing the chordal loop to the leaflet. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

A study of the pulsatile flow and its interaction with rectangular leaflets

NASA Astrophysics Data System (ADS)

Ledesma, Rene; Zenit, Roberto; Pulos, Guillermo

2009-11-01

To avoid the complexity and limited understanding of the 3D pulsatile flow field through heart valves, a cardiac-like flow circuit and a test channel were designed to study the behavior of bidimensional leaflets made of hyperelastic materials. We study a simple 2D arrangement to understand the basic physics of the flow-leaflet interaction. Creating a periodic pressure gradient, measurements of leaflet deflection were obtained for different flow conditions, geometries and materials. Using PIV and Phase Locking techniques, we have obtained the leaflet motion and the time-dependent flow velocity fields. The results show that two dimensionless parameters determine the performance of a simple bi-dimensional valve, in accordance with the flow conditions applied: π1=f(sw)^1/2(E/ρ)^1/2 and π2=V/(2slw), where f is the pulsation frequency, V is the stroke volume, s, w and l are the dimensions on the leaftlet and E and ρ are the elastic modulus and density of the material, respectively. Furthermore, we have identified the conditions for which the fluid stresses can be minimized. With these results we propose a new set of parameters to improve the performance of prosthetic heart valves and, in consequence, to reduce blood damage.

A descriptive study of the readability of patient information leaflets designed by nurses.

PubMed

Mumford, M E

1997-11-01

Written patient information materials can be valuable communication tools for teaching and reinforcing the verbal message, especially in the present climate of today's health service where patients are in hospital for such short times. They are only useful if the patient is able to read and understand them, otherwise they become an expensive waste of resources. Various studies have shown that many healthcare information leaflets are written at university or postgraduate level and would cause problems with understanding for many people reading them. This study set out to examine the readability of nurse-designed written information leaflets using the Flesch Reading Ease score and the FOG and SMOG readability formulae. This descriptive study used a sample of 24 leaflets designed by trained nurses in a large teaching hospital. The results produced a mean grade of 11.3 with a range of 8.9 to 14.8. This was similar to the results of other studies and meant that patients may have difficulty comprehending the information. It would appear that little progress has been made in 40 years in this area and potential reasons are discussed. Advantages and disadvantages of readability formulae and other guidelines available for developing information leaflets are explored. Recommendations for further research are made.

How to improve the readability of the patient package leaflet: a survey on the use of colour, print size and layout.

PubMed

Bernardini, C; Ambrogi, V; Fardella, G; Perioli, L; Grandolini, G

2001-05-01

This paper displays the results of the second part of a survey about patient information and the use of the patient package leaflet. The aim of this research is to investigate the consumers' attitude towards written information. As the formal aspects of the written message are very important in communication, we prepared a questionnaire in order to evaluate the attitude of patients towards some typographical modifications. Patients were invited to give indications about which colours could be used in the different paragraphs of the package leaflet and which print size could be easily read. All people interviewed were asked to choose a colour, from six proposed by us, to be used for 'therapeutic indications', 'side effects', 'how to use', 'paediatric use', 'contraindications', 'use in pregnancy' and 'warnings'. Clear suggestions for the choice of colours for therapeutic indications, side effects and contraindications arose from the survey. In the other cases there was no uniformity of answers. All people complained that the print size used in the package leaflet is too small and suggested 10 and 11 points Didot. Finally, from the survey it emerged that people would appreciate a more detailed package leaflet but information should be given in a schematic and concise way. Copyright 2001 Academic Press.

Mitral Valve Repair Using ePTFE Sutures for Ruptured Mitral Chordae Tendineae: A Computational Simulation Study

PubMed Central

Rim, Yonghoon; Laing, Susan T.; McPherson, David D.; Kim, Hyunggun

2013-01-01

Mitral valve repair using expanded polytetrafluoroethylene (ePTFE) sutures is an established and preferred interventional method to resolve the complex pathophysiologic problems associated with chordal rupture. We developed a novel computational evaluation protocol to determine the effect of the artificial sutures on restoring mitral valve function following valve repair. A virtual mitral valve was created using three-dimensional echocardiographic data in a patient with ruptured mitral chordae tendineae. Virtual repairs were designed by adding artificial sutures between the papillary muscles and the posterior leaflet where the native chordae were ruptured. Dynamic finite element simulations were performed to evaluate pre- and post-repair mitral valve function. Abnormal posterior leaflet prolapse and mitral regurgitation was clearly demonstrated in the mitral valve with ruptured chordae. Following virtual repair to reconstruct ruptured chordae, the severity of the posterior leaflet prolapse decreased and stress concentration was markedly reduced both in the leaflet tissue and the intact native chordae. Complete leaflet coaptation was restored when four or six sutures were utilized. Computational simulations provided quantitative information of functional improvement following mitral valve repair. This novel simulation strategy may provide a powerful tool for evaluation and prediction of interventional treatment for ruptured mitral chordae tendineae. PMID:24072489

Differences in virulence genes and genome patterns of mastitis-associated Staphylococcus aureus among goat, cow, and human isolates in Taiwan.

PubMed

Chu, Chishih; Wei, Yajiun; Chuang, Shih-Te; Yu, Changyou; Changchien, Chih-Hsuan; Su, Yaochi

2013-03-01

A total of 117 mastitis-associated Staphylococcus aureus isolates from cow, goat, and human patients were analyzed for differences in antibiotic susceptibility, virulence genes, and genotypes using accessory gene regulator (agr) typing, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Multidrug-resistant (MDR) S. aureus were commonly found in all sources, though they were predominantly found in human and goat isolates. Almost 70% of the isolates were resistant to ampicillin and penicillin. Host-associated virulence genes were identified as follows: tst, a gene encoding toxic shock syndrome toxin, was found in goat isolates; lukED and lukM, genes encoding leukocidin, found in cow isolates; lukPV, a gene encoding leukocidin, found in human isolates; and eta, a gene encoding for exfoliative toxin, found in both human and cow isolates. All four types of hemolysin, α, β, γ, and δ, were identified in human isolates, three types (α, γ, and δ), were identified in cow isolates, and two types (α and δ) were identified in goat isolates. Agr-typing determined agr1 to be the main subtype in human and cow isolates. PFGE and MLST analysis revealed the presence of diverse genotypes among the three sources. In conclusion, mastitis-associated, genetically diverse strains of MDR S. aureus differed in virulence genes among human, cow, and goat isolates.

Functions of the Magnaporthe oryzae Flb3p and Flb4p transcription factors in the regulation of conidiation.

PubMed

Matheis, S; Yemelin, A; Scheps, D; Andresen, K; Jacob, S; Thines, E; Foster, A J

2017-03-01

The Magnaporthe oryzae genes FLB3 and FLB4, orthologues of the Aspergillus nidulans regulators of conidiation FlbC and FlbD, were inactivated. These genes encode C2H2 zinc finger and Myb-like transcription factors, respectively, in A. nidulans. Analysis of the resultant mutants demonstrated that FLB4 is essential for spore formation and that strains lacking this gene are fluffy in their colony morphology due to an inability to complete conidiophore formation. Meanwhile, FLB3 is required for normal levels of aerial mycelium formation. We identified genes dependent on both transcription factors using microarray analysis. This analysis revealed that the transcription of several genes encoding proteins implicated in sporulation in Magnaporthe oryzae and other filamentous fungi are affected by FLB3 or FLB4 inactivation. Furthermore, the microarray analysis indicates that Flb3p may effectively reprogramme the cell metabolically by repressing transcription of genes encoding biosynthetic enzymes and inducing transcription of genes encoding catabolic enzymes. Additionally, qRT-PCR was employed and showed that FLB3 and FLB4 transcripts are enriched in synchronously sporulating cultures, as were the transcripts of other genes that are necessary for normal conidiation, consistent with a role for their gene products in this process. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Ornithorhynchus anatinus (platypus) links the evolution of immunoglobulin genes in eutherian mammals and nonmammalian tetrapods.

PubMed

Zhao, Yaofeng; Cui, Huiting; Whittington, Camilla M; Wei, Zhiguo; Zhang, Xiaofeng; Zhang, Ziding; Yu, Li; Ren, Liming; Hu, Xiaoxiang; Zhang, Yaping; Hellman, Lars; Belov, Katherine; Li, Ning; Hammarström, Lennart

2009-09-01

The evolutionary origins of mammalian immunoglobulin H chain isotypes (IgM, IgD, IgG, IgE, and IgA) are still incompletely understood as these isotypes differ considerably in structure and number from their counterparts in nonmammalian tetrapods. We report in this study that the platypus (Ornithorhynchus anatinus) Ig H chain constant region gene locus contains eight Ig encoding genes, which are arranged in an mu-delta-omicron-gamma2-gamma1-alpha1-epsilon-alpha2 order, spanning a total of approximately 200 kb DNA, encoding six distinct isotypes. The omicron (omicron for Ornithorhynchus) gene encodes a novel Ig H chain isotype that consists of four constant region domains and a hinge, and is structurally different from any of the five known mammalian Ig classes. This gene is phylogenetically related to upsilon (epsilon) and gamma, and thus appears to be a structural intermediate between these two genes. The platypus delta gene encodes ten heavy chain constant region domains, lacks a hinge region and is similar to IgD in amphibians and fish, but strikingly different from that in eutherian mammals. The platypus Ig H chain isotype repertoire thus shows a unique combination of genes that share similarity both to those of nonmammalian tetrapods and eutherian animals and demonstrates how phylogenetically informative species can be used to reconstruct the evolutionary history of functionally important genes.

The bglA Gene of Aspergillus kawachii Encodes Both Extracellular and Cell Wall-Bound β-Glucosidases

PubMed Central

Iwashita, Kazuhiro; Nagahara, Tatsuya; Kimura, Hitoshi; Takano, Makoto; Shimoi, Hitoshi; Ito, Kiyoshi

1999-01-01

We cloned the genomic DNA and cDNA of bglA, which encodes β-glucosidase in Aspergillus kawachii, based on a partial amino acid sequence of purified cell wall-bound β-glucosidase CB-1. The nucleotide sequence of the cloned bglA gene revealed a 2,933-bp open reading frame with six introns that encodes an 860-amino-acid protein. Based on the deduced amino acid sequence, we concluded that the bglA gene encodes cell wall-bound β-glucosidase CB-1. The amino acid sequence exhibited high levels of homology with the amino acid sequences of fungal β-glucosidases classified in subfamily B. We expressed the bglA cDNA in Saccharomyces cerevisiae and detected the recombinant β-glucosidase in the periplasm fraction of the recombinant yeast. A. kawachii can produce two extracellular β-glucosidases (EX-1 and EX-2) in addition to the cell wall-bound β-glucosidase. A. kawachii in which the bglA gene was disrupted produced none of the three β-glucosidases, as determined by enzyme assays and a Western blot analysis. Thus, we concluded that the bglA gene encodes both extracellular and cell wall-bound β-glucosidases in A. kawachii. PMID:10584016

Microarray analysis of toxicogenomic effects of Ortho-phenylphenol in Staphylococcus aureus

PubMed Central

Jang, Hyeung-Jin; Nde, Chantal; Toghrol, Freshteh; Bentley, William E

2008-01-01

Background Staphylococcus aureus (S. aureus), is responsible for many infectious diseases, ranging from benign skin infections to life-threatening endocarditis and toxic shock syndrome. Ortho-phenylphenol (OPP) is an antimicrobial agent and an active ingredient of EPA-registered disinfectants with wide human exposure in various agricultural, hospital and veterinary disinfectant products. Despite many uses, an understanding of a cellular response to OPP and it's mechanism of action, targeted genes, and the connectivity between targeted genes and the rest of cell metabolism remains obscure. Results Herein, we performed a genome-wide transcriptome analysis of the cellular responses of S. aureus when exposed to 0.82 mM of OPP for 20 and 60 min. Our data indicated that OPP downregulated the biosynthesis of many amino acids, which are required for protein synthesis. In particular, the genes encoding the enzymes of the diaminopimelate (DAP) pathway which results in lysine biosynthesis were significantly downregualted. Intriguingly, we revealed that the transcription of genes encoding ribosomal proteins was upregulated by OPP and at the same time, the genes encoding iron acquisition and transport were downregulated. The genes encoding virulence factors were upregulated and genes encoding phospholipids were downregulated upon 20 min exposure to OPP. Conclusion By using microarray analysis that enables us to simultaneously and globally examine the complete transcriptome during cellular responses, we have revealed novel information regarding the mode of action of OPP on Staphylococcus: OPP inhibits anabolism of many amino acids and highly downregulates the genes that encode the enzymes involved in the DAP pathway. Lysine and DAP are essential for building up the peptidoglycan cell wall. It was concluded that the mode of action of OPP is similar to the mechanism of action of some antibiotics. The discovery of this phenomenon provides useful information that will benefit further antimicrobial research on S. aureus. PMID:18793396

Degradation of triglycerides by a pseudomonad isolated from milk: molecular analysis of a lipase-encoding gene and its expression in Escherichia coli.

PubMed Central

Johnson, L A; Beacham, I R; MacRae, I C; Free, M L

1992-01-01

Psychrotrophic lipolytic bacteria represent a significant problem in the storage of refrigerated dairy products. A lipase-encoding gene has been cloned and characterized from a highly lipolytic strain of Pseudomonas. The nucleotide sequence of the gene predicts a polypeptide of M(r) 49,905, which was identified when the gene was expressed in Escherichia coli. Images PMID:1622251

Genes encoding giant danio and golden shiner ependymin.

PubMed

Adams, D S; Kiyokawa, M; Getman, M E; Shashoua, V E

1996-03-01

Ependymin (EPN) is a brain glycoprotein that functions as a neurotrophic factor in optic nerve regeneration and long-term memory consolidation in goldfish. To date, true epn genes have been characterized in one order of teleost fish, Cypriniformes. In the study presented here, polymerase chain reactions were used to analyze the complete epn genes, gd (1480 bp), and sh (2071 bp), from Cypriniformes giant danio and shiner, respectively. Southern hybridizations demonstrated the existence of one copy of each gene per corresponding haploid genome. Each gene was found to contain six exons and five introns. Gene gd encodes a predicted 218-amino acid (aa) protein GD 93 percent conserved to goldfish EPN, while sh encodes a predicted 214-aa protein SH 91 percent homologous to goldfish. Evidence is presented classifying proteins previously termed "EPNs" into two major categories: true EPNs and non-EPN cerebrospinal fluid glycoproteins. Proteins GD and SH contain all the hallmark, features of true EPNs.

Ti plasmid-encoded genes responsible for catabolism of the crown gall opine mannopine by Agrobacterium tumefaciens are homologs of the T-region genes responsible for synthesis of this opine by the plant tumor.

PubMed

Kim, K S; Farrand, S K

1996-06-01

Agrobacterium tumefaciens NT1 harboring pSaB4, which contains the 14-kb BamHI fragment 4 from the octopine/mannityl opine-type Ti plasmid pTi15955, grew well with agropine (AGR) but slowly with mannopine (MOP) as the sole carbon source. When a second plasmid encoding a dedicated transport system for MOP was introduced, these cells grew well with both AGR and MOP. Transposon insertion mutagenesis and subcloning identified a 5.7-kb region of BamHI fragment 4 that encodes functions required for the degradation of MOP. DNA sequence analysis revealed seven putative genes in this region: mocD (moc for mannityl opine catabolism) and mocE, oriented from right to left, and mocRCBAS, oriented from left to right. Significant identities exist at the nucleotide and derived amino acid sequence levels between these moc genes and the mas genes that are responsible for opine biosynthesis in crown gall tumors. MocD is a homolog of Mas2, the anabolic conjugase encoded by mas2'. MocE and MocC are related to the amino half and the carboxyl half, respectively, of Mas1 (MOP reductase), the second enzyme for MOP biosynthesis. These results indicate that the moc and mas genes evolved from a common origin. MocR and MocS are related to each other and to a putative repressor for the AGR degradation system encoded by the rhizogenic plasmid pRiA4. MocB and MocA are homologs of 6-phosphogluconate dehydratase and glucose-6-phosphate dehydrogenase, respectively. Mutations in mocD and mocE, but not mocC, are suppressed by functions encoded by the chromosome or the 450-kb megaplasmid present in many Agrobacterium isolates. We propose that moc genes derived from genes located elsewhere in the bacterial genome and that the tumor-expressed mas genes evolved from the bacterial moc genes.

Ti plasmid-encoded genes responsible for catabolism of the crown gall opine mannopine by Agrobacterium tumefaciens are homologs of the T-region genes responsible for synthesis of this opine by the plant tumor.

PubMed Central

Kim, K S; Farrand, S K

1996-01-01

Agrobacterium tumefaciens NT1 harboring pSaB4, which contains the 14-kb BamHI fragment 4 from the octopine/mannityl opine-type Ti plasmid pTi15955, grew well with agropine (AGR) but slowly with mannopine (MOP) as the sole carbon source. When a second plasmid encoding a dedicated transport system for MOP was introduced, these cells grew well with both AGR and MOP. Transposon insertion mutagenesis and subcloning identified a 5.7-kb region of BamHI fragment 4 that encodes functions required for the degradation of MOP. DNA sequence analysis revealed seven putative genes in this region: mocD (moc for mannityl opine catabolism) and mocE, oriented from right to left, and mocRCBAS, oriented from left to right. Significant identities exist at the nucleotide and derived amino acid sequence levels between these moc genes and the mas genes that are responsible for opine biosynthesis in crown gall tumors. MocD is a homolog of Mas2, the anabolic conjugase encoded by mas2'. MocE and MocC are related to the amino half and the carboxyl half, respectively, of Mas1 (MOP reductase), the second enzyme for MOP biosynthesis. These results indicate that the moc and mas genes evolved from a common origin. MocR and MocS are related to each other and to a putative repressor for the AGR degradation system encoded by the rhizogenic plasmid pRiA4. MocB and MocA are homologs of 6-phosphogluconate dehydratase and glucose-6-phosphate dehydrogenase, respectively. Mutations in mocD and mocE, but not mocC, are suppressed by functions encoded by the chromosome or the 450-kb megaplasmid present in many Agrobacterium isolates. We propose that moc genes derived from genes located elsewhere in the bacterial genome and that the tumor-expressed mas genes evolved from the bacterial moc genes. PMID:8655509

24 CFR 245.115 - Protected activities.

Code of Federal Regulations, 2010 CFR

2010-04-01

... operation of a tenant organization: (1) Distributing leaflets in lobby areas; (2) Placing leaflets at or... management representatives. In order to preserve the independence of tenant organizations, management... discuss a specific issue or issues; and (9) Formulating responses to owner's requests for: (i) Rent...

Hypoplasia or Absence of Posterior Leaflet: A Rare Congenital Anomaly of The Mitral Valve in Adulthood - Case Series.

PubMed

Parato, Vito Maurizio; Masia, Stefano Lucio

2018-01-01

We present a case series of two adult patients with almost complete absence of the posterior mitral valve leaflet and who are asymptomatic or mildly symptomatic, with two different degrees of mitral regurgitation.

Systematic Identification and Characterization of Novel Human Skin-Associated Genes Encoding Membrane and Secreted Proteins

PubMed Central

Buhren, Bettina Alexandra; Martinez, Cynthia; Schrumpf, Holger; Gasis, Marcia; Grether-Beck, Susanne; Krutmann, Jean

2013-01-01

Through bioinformatics analyses of a human gene expression database representing 105 different tissues and cell types, we identified 687 skin-associated genes that are selectively and highly expressed in human skin. Over 50 of these represent uncharacterized genes not previously associated with skin and include a subset that encode novel secreted and plasma membrane proteins. The high levels of skin-associated expression for eight of these novel therapeutic target genes were confirmed by semi-quantitative real time PCR, western blot and immunohistochemical analyses of normal skin and skin-derived cell lines. Four of these are expressed specifically by epidermal keratinocytes; two that encode G-protein-coupled receptors (GPR87 and GPR115), and two that encode secreted proteins (WFDC5 and SERPINB7). Further analyses using cytokine-activated and terminally differentiated human primary keratinocytes or a panel of common inflammatory, autoimmune or malignant skin diseases revealed distinct patterns of regulation as well as disease associations that point to important roles in cutaneous homeostasis and disease. Some of these novel uncharacterized skin genes may represent potential biomarkers or drug targets for the development of future diagnostics or therapeutics. PMID:23840300

Transgenic tomatoes express an antigenic polypeptide containing epitopes of the diphtheria, pertussis and tetanus exotoxins, encoded by a synthetic gene.

PubMed

Soria-Guerra, Ruth Elena; Rosales-Mendoza, Sergio; Márquez-Mercado, Crisóforo; López-Revilla, Rubén; Castillo-Collazo, Rosalba; Alpuche-Solís, Angel Gabriel

2007-07-01

A current priority of vaccinology is the development of multicomponent vaccines that protect against several pathogens. The diphtheria-pertussis-tetanus (DPT) vaccine prevents the symptoms of three serious and often fatal diseases due to the exotoxins produced by Corynebacterium diphteriae, Bordetella pertussis and Clostridium tetani. We are attempting to develop an edible DPT multicomponent vaccine in plants, based on the fusion of protective exotoxin epitopes encoded by synthetic genes. By means of Agrobacterium mediated transformation we generated transgenic tomatoes with a plant-optimised synthetic gene encoding a novel polypeptide containing two adjuvant and six DPT immunoprotective exotoxin epitopes joined by peptide linkers. In transformed tomato plants, integration of the synthetic DPT (sDPT) gene detected by PCR was confirmed by Southern blot, and specific transcripts of the expected molecular size were detected by RT-PCR. Expression of the putative polypeptide encoded by the sDPT gene was detected by immunoassay with specific antibodies to the diphtheria, pertussis and tetanus exotoxins. The sDPT gene is therefore integrated, transcribed and translated as the expected recombinant sDPT multiepitope polypeptide in transgenic tomatoes that constitute a potential edible vaccine.

Ubiquitin--conserved protein or selfish gene?

PubMed

Catic, André; Ploegh, Hidde L

2005-11-01

The posttranslational modifier ubiquitin is encoded by a multigene family containing three primary members, which yield the precursor protein polyubiquitin and two ubiquitin moieties, Ub(L40) and Ub(S27), that are fused to the ribosomal proteins L40 and S27, respectively. The gene encoding polyubiquitin is highly conserved and, until now, those encoding Ub(L40) and Ub(S27) have been generally considered to be equally invariant. The evolution of the ribosomal ubiquitin moieties is, however, proving to be more dynamic. It seems that the genes encoding Ub(L40) and Ub(S27) are actively maintained by homologous recombination with the invariant polyubiquitin locus. Failure to recombine leads to deterioration of the sequence of the ribosomal ubiquitin moieties in several phyla, although this deterioration is evidently constrained by the structural requirements of the ubiquitin fold. Only a few amino acids in ubiquitin are vital for its function, and we propose that conservation of all three ubiquitin genes is driven not only by functional properties of the ubiquitin protein, but also by the propensity of the polyubiquitin locus to act as a 'selfish gene'.

Alternative intronic promoters in development and disease.

PubMed

Vacik, Tomas; Raska, Ivan

2017-05-01

Approximately 20,000 mammalian genes are estimated to encode between 250 thousand and 1 million different proteins. This enormous diversity of the mammalian proteome is caused by the ability of a single-gene locus to encode multiple protein isoforms. Protein isoforms encoded by one gene locus can be functionally distinct, and they can even have antagonistic functions. One of the mechanisms involved in creating this proteome complexity is alternative promoter usage. Alternative intronic promoters are located downstream from their canonical counterparts and drive the expression of alternative RNA isoforms that lack upstream exons. These upstream exons can encode some important functional domains, and proteins encoded by alternative mRNA isoforms can be thus functionally distinct from the full-length protein encoded by canonical mRNA isoforms. Since any misbalance of functionally distinct protein isoforms is likely to have detrimental consequences for the cell and the whole organism, their expression must be precisely regulated. Misregulation of alternative intronic promoters is frequently associated with various developmental defects and diseases including cancer, and it is becoming increasingly clear that this phenomenon deserves more attention.

Amplification of Chromosome 1q Genes Encoding the Phosphoinositide Signalling Enzymes PI4KB, AKT3, PIP5K1A and PI3KC2B in Breast Cancer

PubMed Central

Waugh, Mark G.

2014-01-01

Little is known about the possible oncogenic roles of genes encoding for the phosphatidylinositol 4-kinases, a family of enzymes that regulate an early step in phosphoinositide signalling. To address this issue, the mutational status of all four human phosphatidylinositol 4-kinases genes was analyzed across 852 breast cancer samples using the COSMIC data resource. Point mutations in the phosphatidylinositol 4-kinase genes were uncommon and appeared in less than 1% of the patient samples however, 62% of the tumours had increases in gene copy number for PI4KB which encodes the phosphatidylinositol 4-kinase IIIbeta isozyme. Extending this analysis to subsequent enzymes in the phosphoinositide signalling cascades revealed that the only PIP5K1A, PI3KC2B and AKT3 genes exhibited similar patterns of gene copy number variation. By comparison, gene copy number increases for established oncogenes such as EGFR and HER2/Neu were only evident in 20% of the samples. The PI4KB, PIP5K1A, PI3KC2B and AKT3 genes are related in that they all localize to chromosome 1q which is often structurally and numerically abnormal in breast cancer. These results demonstrate that a gene quartet encoding a potential phosphoinositide signalling pathway is amplified in a subset of breast cancers. PMID:25368680

Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

NASA Astrophysics Data System (ADS)

Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

2016-11-01

In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

Role and Regulation of the Flp/Tad Pilus in the Virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193

PubMed Central

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E. Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers. PMID:24040039

Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193.

PubMed

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.

Antibodies to a Novel Leptospiral Protein, LruC, in the Eye Fluids and Sera of Horses with Leptospira-Associated Uveitis

PubMed Central

Matsunaga, James; Artiushin, Sergey; Pinne, Marija; Houwers, Dirk J.; Haake, David A.; Stevenson, Brian; Timoney, John F.

2012-01-01

Screening of an expression library of Leptospira interrogans with eye fluids from uveitic horses resulted in identification of a novel protein, LruC. LruC is located in the inner leaflet of the leptospiral outer membrane, and an lruC gene was detected in all tested pathogenic L. interrogans strains. LruC-specific antibody levels were significantly higher in eye fluids and sera of uveitic horses than healthy horses. These findings suggest that LruC may play a role in equine leptospiral uveitis. PMID:22237897

Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

PubMed Central

Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P.

2016-01-01

Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

Characterization of the Genes Encoding the Cytosolic and Plastidial Forms of ADP-Glucose Pyrophosphorylase in Wheat Endosperm1

PubMed Central

Burton, Rachel A.; Johnson, Philip E.; Beckles, Diane M.; Fincher, Geoffrey B.; Jenner, Helen L.; Naldrett, Mike J.; Denyer, Kay

2002-01-01

In most species, the synthesis of ADP-glucose (Glc) by the enzyme ADP-Glc pyrophosphorylase (AGPase) occurs entirely within the plastids in all tissues so far examined. However, in the endosperm of many, if not all grasses, a second form of AGPase synthesizes ADP-Glc outside the plastid, presumably in the cytosol. In this paper, we show that in the endosperm of wheat (Triticum aestivum), the cytosolic form accounts for most of the AGPase activity. Using a combination of molecular and biochemical approaches to identify the cytosolic and plastidial protein components of wheat endosperm AGPase we show that the large and small subunits of the cytosolic enzyme are encoded by genes previously thought to encode plastidial subunits, and that a gene, Ta.AGP.S.1, which encodes the small subunit of the cytosolic form of AGPase, also gives rise to a second transcript by the use of an alternate first exon. This second transcript encodes an AGPase small subunit with a transit peptide. However, we could not find a plastidial small subunit protein corresponding to this transcript. The protein sequence of the purified plastidial small subunit does not match precisely to that encoded by Ta.AGP.S.1 or to the predicted sequences of any other known gene from wheat or barley (Hordeum vulgare). Instead, the protein sequence is most similar to those of the plastidial small subunits from chickpea (Cicer arietinum) and maize (Zea mays) and rice (Oryza sativa) seeds. These data suggest that the gene encoding the major plastidial small subunit of AGPase in wheat endosperm has yet to be identified. PMID:12428011

The complex leaves of the monkey's comb (Amphilophium crucigerum, Bignoniaceae): a climbing strategy without glue.

PubMed

Seidelmann, Katrin; Melzer, Björn; Speck, Thomas

2012-11-01

Monkey's comb (Amphilophium crucigerum) is a widely spread neotropical leaf climber that develops attachment pads for anchorage. A single complex leaf of the species comprises a basal pair of foliate, assimilating leaflets and apical, attaching leaflet tendrils. This study aims to analyze these leaves and their ontogenetic development for a better understanding of the attachment process, the form-structure-function relationships involved, and the overall maturation of the leaves. Thorough morphometrical, morphological, and anatomical analyses incorporated high-resolution microscopy, various staining techniques, SEM, and photographic recordings over the entire ontogenetic course of leaf development. The foliate, assimilating leaflets and the anchorage of the more apical leaflet tendrils acted independently of each other. Attachment was achieved by coiling of the leaflet tendrils and/or development of attachment pads at the tendril apices that grow opportunistically into gaps and fissures of the substrate. In contact zones with the substrate, the cells of the pads differentiate into a vessel element-like tissue. During the entire attachment process of the plant, no glue was excreted. The complex leaves of monkey's comb are highly differentiated organs with specialized leaf parts whose functions-photosynthesis or attachment-work independently of each other. The function of attachment includes coiling and maturation process of the leaflet tendrils and the formation of attachment pads, resulting in a biomechanically sound and persistent anchorage of the plant without the need of glue excretion. This kind of glue-less attachment is not only of interest in the framework of analyzing the functional variety of attachment structures evolved in climbing plants, but also for the development of innovative biomimetic attachment structures for manifold technical applications.

Reproducibility of a novel echocardiographic 3D automated software for the assessment of mitral valve anatomy.

PubMed

Aquila, Iolanda; González, Ariana; Fernández-Golfín, Covadonga; Rincón, Luis Miguel; Casas, Eduardo; García, Ana; Hinojar, Rocio; Jiménez-Nacher, José Julio; Zamorano, José Luis

2016-05-17

3D transesophageal echocardiography (TEE) is superior to 2D TEE in quantitative anatomic evaluation of the mitral valve (MV) but it shows limitations regarding automatic quantification. Here, we tested the inter-/intra-observer reproducibility of a novel full-automated software in the evaluation of MV anatomy compared to manual 3D assessment. Thirty-six out of 61 screened patients referred to our Cardiac Imaging Unit for TEE were retrospectively included. 3D TEE analysis was performed both manually and with the automated software by two independent operators. Mitral annular area, intercommissural distance, anterior leaflet length and posterior leaflet length were assessed. A significant correlation between both methods was found for all variables: intercommissural diameter (r = 0.84, p < 0.01), mitral annular area (r = 0.94, p > 0, 01), anterior leaflet length (r = 0.83, p < 0.01) and posterior leaflet length (r = 0.67, p < 0.01). Interobserver variability assessed by the intraclass correlation coefficient was superior for the automatic software: intercommisural distance 0.997 vs. 0.76; mitral annular area 0.957 vs. 0.858; anterior leaflet length 0.963 vs. 0.734 and posterior leaflet length 0.936 vs. 0.838. Intraobserver variability was good for both methods with a better level of agreement with the automatic software. The novel 3D automated software is reproducible in MV anatomy assessment. The incorporation of this new tool in clinical MV assessment may improve patient selection and outcomes for MV interventions as well as patient diagnosis and prognosis stratification. Yet, high-quality 3D images are indispensable.

Home delivery of medication - the role of a patient information leaflet on maximising service uptake.

PubMed

Watson, L; Ahmed, N; Mccall, H; Minton, J; Benn, P; Edwards, S; Waters, L

2014-12-01

There are currently over 30,000 HIV-positive individuals in London and over 25,000 on anti-retroviral therapy. In 2009/2010, this equated to £170m spent by London's NHS on anti-retroviral drugs. Ways employed to reduce this cost include standardising the drugs patients are on and delivering medication to patients at home. Home delivery (HD) medication is exempt from value-added tax. The savings made from 10 patients using the home delivery service would free up resources to provide anti-retroviral therapy to one further patient. Studies have shown that concerns surrounding potential breaches of confidentiality are a potential barrier to some people using the home delivery service. In order to challenge these concerns, a leaflet was devised highlighting the major benefits to both the patient and the NHS of home delivery and addressing concerns over confidentiality. The leaflet was handed out to patients at the Mortimer Market Centre who were currently on anti-retroviral medication but not on home delivery. They were asked to complete a survey on their views of the service before and after reading the leaflet, whether they had been previously aware of the service and whether their concerns had been addressed. Some 79% felt that the patient information leaflet addressed all of their concerns, and it helped 11% decide whether to consider using home delivery. However, as more patients were opposed to the service after reading the patient information leaflet than those considering it, more work needs to be done to explore patients' concerns and other factors influencing home delivery service uptake. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Readability of medicinal package leaflets: a systematic review.

PubMed

Pires, Carla; Vigário, Marina; Cavaco, Afonso

2015-01-01

OBJECTIVE To review studies on the readability of package leaflets of medicinal products for human use. METHODS We conducted a systematic literature review between 2008 and 2013 using the keywords "Readability and Package Leaflet" and "Readability and Package Insert" in the academic search engine Biblioteca do Conhecimento Online, comprising different bibliographic resources/databases. The preferred reporting items for systematic reviews and meta-analyses criteria were applied to prepare the draft of the report. Quantitative and qualitative original studies were included. Opinion or review studies not written in English, Portuguese, Italian, French, or Spanish were excluded. RESULTS We identified 202 studies, of which 180 were excluded and 22 were enrolled [two enrolling healthcare professionals, 10 enrolling other type of participants (including patients), three focused on adverse reactions, and 7 descriptive studies]. The package leaflets presented various readability problems, such as complex and difficult to understand texts, small font size, or few illustrations. The main methods to assess the readability of the package leaflet were usability tests or legibility formulae. Limitations with these methods included reduced number of participants; lack of readability formulas specifically validated for specific languages (e.g., Portuguese); and absence of an assessment on patients literacy, health knowledge, cognitive skills, levels of satisfaction, and opinions. CONCLUSIONS Overall, the package leaflets presented various readability problems. In this review, some methodological limitations were identified, including the participation of a limited number of patients and healthcare professionals, the absence of prior assessments of participant literacy, humor or sense of satisfaction, or the predominance of studies not based on role-plays about the use of medicines. These limitations should be avoided in future studies and be considered when interpreting the results.

Fluid-Structure Interaction and Structural Analyses using a Comprehensive Mitral Valve Model with 3D Chordal Structure

PubMed Central

Toma, Milan; Einstein, Daniel R.; Bloodworth, Charles H.; Cochran, Richard P.; Yoganathan, Ajit P.; Kunzelman, Karyn S.

2016-01-01

Over the years, three-dimensional models of the mitral valve have generally been organized around a simplified anatomy. Leaflets have been typically modeled as membranes, tethered to discrete chordae typically modeled as one-dimensional, non-linear cables. Yet, recent, high-resolution medical images have revealed that there is no clear boundary between the chordae and the leaflets. In fact, the mitral valve has been revealed to be more of a webbed structure whose architecture is continuous with the chordae and their extensions into the leaflets. Such detailed images can serve as the basis of anatomically accurate, subject-specific models, wherein the entire valve is modeled with solid elements that more faithfully represent the chordae, the leaflets, and the transition between the two. These models have the potential to enhance our understanding of mitral valve mechanics, and to re-examine the role of the mitral valve chordae, which heretofore have been considered to be “invisible” to the fluid and to be of secondary importance to the leaflets. However, these new models also require a rethinking of modeling assumptions. In this study, we examine the conventional practice of loading the leaflets only and not the chordae in order to study the structural response of the mitral valve apparatus. Specifically, we demonstrate that fully resolved 3D models of the mitral valve require a fluid-structure interaction analysis to correctly load the valve even in the case of quasi-static mechanics. While a fluid-structure interaction mode is still more computationally expensive than a structural-only model, we also show that advances in GPU computing have made such models tractable. PMID:27342229

Fluid-structure interaction and structural analyses using a comprehensive mitral valve model with 3D chordal structure.

PubMed

Toma, Milan; Einstein, Daniel R; Bloodworth, Charles H; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

2017-04-01

Over the years, three-dimensional models of the mitral valve have generally been organized around a simplified anatomy. Leaflets have been typically modeled as membranes, tethered to discrete chordae typically modeled as one-dimensional, non-linear cables. Yet, recent, high-resolution medical images have revealed that there is no clear boundary between the chordae and the leaflets. In fact, the mitral valve has been revealed to be more of a webbed structure whose architecture is continuous with the chordae and their extensions into the leaflets. Such detailed images can serve as the basis of anatomically accurate, subject-specific models, wherein the entire valve is modeled with solid elements that more faithfully represent the chordae, the leaflets, and the transition between the two. These models have the potential to enhance our understanding of mitral valve mechanics and to re-examine the role of the mitral valve chordae, which heretofore have been considered to be 'invisible' to the fluid and to be of secondary importance to the leaflets. However, these new models also require a rethinking of modeling assumptions. In this study, we examine the conventional practice of loading the leaflets only and not the chordae in order to study the structural response of the mitral valve apparatus. Specifically, we demonstrate that fully resolved 3D models of the mitral valve require a fluid-structure interaction analysis to correctly load the valve even in the case of quasi-static mechanics. While a fluid-structure interaction mode is still more computationally expensive than a structural-only model, we also show that advances in GPU computing have made such models tractable. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Annular dilatation and loss of sino-tubular junction in aneurysmatic aorta: implications on leaflet quality at the time of surgery. A finite element study†

PubMed Central

Weltert, Luca; de Tullio, Marco D.; Afferrante, Luciano; Salica, Andrea; Scaffa, Raffaele; Maselli, Daniele; Verzicco, Roberto; De Paulis, Ruggero

2013-01-01

OBJECTIVES In the belief that stress is the main determinant of leaflet quality deterioration, we sought to evaluate the effect of annular and/or sino-tubular junction dilatation on leaflet stress. A finite element computer-assisted stress analysis was used to model four different anatomic conditions and analyse the consequent stress pattern on the aortic valve. METHODS Theoretical models of four aortic root configurations (normal, with dilated annulus, with loss of sino-tubular junction and with both dilatation simultaneously) were created with computer-aided design technique. The pattern of stress and strain was then analysed by means of finite elements analysis, when a uniform pressure of 100 mmHg was applied to the model. Analysis produced von Mises charts (colour-coded, computational, three-dimensional stress-pattern graphics) and bidimensional plots of compared stress on arc-linear line, which allowed direct comparison of stress in the four different conditions. RESULTS Stresses both on the free margin and on the ‘belly’ of the leaflet rose from 0.28 MPa (normal conditions) to 0.32 MPa (+14%) in case of isolated dilatation of the sino-tubular junction, while increased to 0.42 MPa (+67%) in case of isolated annular dilatation, with no substantial difference whether sino-tubular junction dilatation was present or not. CONCLUSIONS Annular dilatation is the key element determining an increased stress on aortic leaflets independently from an associated sino-tubular junction dilatation. The presence of annular dilatation associated with root aneurysm greatly decreases the chance of performing a valve sparing procedure without the need for additional manoeuvres on leaflet tissue. This information may lead to a refinement in the optimal surgical strategy. PMID:23536020

Epicardially-derived Fibroblasts Preferentially Contribute to the Parietal Leaflets of the Atrioventricular Valves in the Murine Heart

PubMed Central

Wessels, Andy; van den Hoff, Maurice J. B.; Adamo, Richard F.; Phelps, Aimee L.; Lockhart, Marie M.; Sauls, Kimberly; Briggs, Laura E.; Norris, Russell A.; van Wijk, Bram; Perez-Pomares, Jose M.; Dettman, Robert W.; Burch, John B. E.

2012-01-01

The importance of the epicardium for myocardial and valvuloseptal development has been well established; perturbation of epicardial development results in cardiac abnormalities, including thinning of the ventricular myocardial wall and malformations of the atrioventricular valvuloseptal complex. To determine the spatiotemporal contribution of epicardially derived cells to the developing fibroblast population in the heart we have used a mWt1/IRES/GFP-Cre mouse to trace the fate of EPDCs from embryonic day (ED)10 until birth. EPDCs begin to populate the compact ventricular myocardium around ED12. The migration of epicardially-derived fibroblasts toward the interface between compact and trabecular myocardium is completed around ED14. Remarkably, epicardially-derived fibroblasts do not migrate into the trabecular myocardium until after ED17. Migration of EPDCs into the atrioventricular cushion mesenchyme commences around ED12. As development progresses, the number of EPDCs increases significantly, specifically in the leaflets which derive from the lateral atrioventricular cushions. In these developing leaflets the epicardially-derived fibroblasts eventually largely replace the endocardially-derived cells. Importantly, the contribution of EPDCs to the leaflets derived from the major AV cushions is very limited. The differential contribution of EPDCs to the various leaflets of the atrioventricular valves provides a new paradigm in valve development and could lead to new insights into the pathogenesis of abnormalities that preferentially affect individual components of this region of the heart. The notion that there is a significant difference in the contribution of epicardially and endocardially derived cells to the individual leaflets of the atrioventricular valves has also important pragmatic consequences for the use of endocardial and epicardial cre-mouse models in studies of heart development. PMID:22546693

Posterior leaflet preservation during mitral valve replacement for rheumatic mitral stenosis.

PubMed

Djukić, P L; Obrenović-Kirćanski, B B; Vranes, M R; Kocica, M J; Mikić, A Dj; Velinović, M M; Kacar, S M; Kovacević, N S; Parapid, B J

2006-01-01

Mitral valve replacement with posterior leaflet preservation was shown beneficial for postoperative left vetricular (LV) performance in patients with mitral regurgitation. Some authors find it beneficial even for the long term LV function. We investigated a long term effect of this technique in patients with rheumatic mitral stenosis. We studied 20 patents with mitral valve replacement due to rheumatic mitral stenosis, in the period from January 1988 to December 1989. In group A (10 patients) both leaflets and coresponding chordal excision was performed, while in group B (10 patients) the posterior leaflet was preserved. In all patients a Carbomedics valve was inserted. We compared clinical pre and postoperative status, as well as hemodynamic characteristics of the valve and left ventricle in both groups. Control echocardiographyc analysis included: maximal (PG) and mean (MG) gradients; effective valve area (AREA); telediastolic (TDV) and telesystolic (TSV) LV volume; stroke volume (SV); ejection fraction (EF); fractional shortening (FS) and segmental LV motion. The mean size of inserted valve was 26.6 in group A and 27.2 in group B. Hemodynamic data: PG (10.12 vs 11.1); MG (3.57 vs 3.87); AREA (2.35 vs 2.30); TDV 126.0 vs 114.5); TSV (42.2 vs 36.62); SV (83.7 vs 77.75); EF (63.66 vs 67.12); FS (32.66 vs 38.25). Diaphragmal segmental hypokinesis was evident in one patient from group A and in two patients from group B. In patients with rheumatic stenosis, posterior leaflet preservation did not have increased beneficial effect on left ventricular performance during long-term follow-up. An adequate posterior leaflet preservation does not change hemodynamic valvular characteristics even after long-term follow-up.

Structural and transcriptional characterization of a novel member of the soybean urease gene family.

PubMed

Wiebke-Strohm, Beatriz; Ligabue-Braun, Rodrigo; Rechenmacher, Ciliana; De Oliveira-Busatto, Luisa Abruzzi; Carlini, Célia Regina; Bodanese-Zanettini, Maria Helena

2016-04-01

In plants, ureases have been related to urea degradation, to defense against pathogenic fungi and phytophagous insects, and to the soybean-Bradyrhizobium japonicum symbiosis. Two urease isoforms have been described for soybean: the embryo-specific, encoded by Eu1 gene, and the ubiquitous urease, encoded by Eu4. A third urease-encoding locus exists in the completed soybean genome. The gene was designated Eu5 and the putative product of its ORF as SBU-III. Phylogenetic analysis shows that 41 plant, moss and algal ureases have diverged from a common ancestor protein, but ureases from monocots, eudicots and ancient species have evolved independently. Genomes of ancient organisms present a single urease-encoding gene and urease-encoding gene duplication has occurred independently along the evolution of some eudicot species. SBU-III has a shorter amino acid sequence, since many gaps are found when compared to other sequences. A mutation in a highly conserved amino acid residue suggests absence of ureolytic activity, but the overall protein architecture remains very similar to the other ureases. The expression profile of urease-encoding genes in different organs and developmental stages was determined by RT-qPCR. Eu5 transcripts were detected in seeds one day after dormancy break, roots of young plants and embryos of developing seeds. Eu1 and Eu4 transcripts were found in all analyzed organs, but Eu4 expression was more prominent in seeds one day after dormancy break whereas Eu1 predominated in developing seeds. The evidence suggests that SBU-III may not be involved in nitrogen availability to plants, but it could be involved in other biological role(s). Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Systems-level analysis of risk genes reveals the modular nature of schizophrenia.

PubMed

Liu, Jiewei; Li, Ming; Luo, Xiong-Jian; Su, Bing

2018-05-19

Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10 -31 ). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10 -11 ), closeness centrality (P = 7.56 × 10 -11 ), betweeness centrality (P = 1.29 × 10 -11 ), clustering coefficient (P = 2.22 × 10 -2 ), and shorter average shortest path length (P = 7.56 × 10 -11 ). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia. Copyright © 2018 Elsevier B.V. All rights reserved.

Multiphoton microscopy of ECM proteins in baboon aortic leaflet

NASA Astrophysics Data System (ADS)

Gonzalez, Mariacarla; Saytashev, Ilyas; Luna, Camila; Gonzalez, Brittany; Pinero, Alejandro; Perez, Manuel; Ramaswamy, Sharan; Ramella-Roman, Jessica

2018-02-01

The extracellular matrix (ECM) plays crucial role in defining mechanical properties of a heart valve yet the mechanobiological role of the ECM proteins - collagen and elastin - in living heart valve leaflets is still poorly understood. In this study, non-linear microscopy was used to obtain three dimensional images of collagen and elastin arrangement in aortic leaflets under combined steady flow (850 ml/min) and cyclic flexure (1 Hz) mechanical (dynamic) training. A novel bioreactor capable of mimicking the flow conditions in a living heart was used in this study and was optimized for microscopic imagery. A custom made non-linear microscope was used in this study to provide Second Harmonic Generation (SHG) imaging of collagen arrangement and two-photon imaging of elastin. Two control and three trained leaflet samples from static and dynamic tissue culture were imaged to observe protein changes in the tissue for a period of seven days. Dynamic training led to a decrease in alignment index of the protein fibers compared to the static treatment.

Simulation of Blood flow in Different Configurations Design of Bi-leaflet Mechanical Heart Valve

NASA Astrophysics Data System (ADS)

Hafizah Mokhtar, N.; Abas, Aizat

2018-05-01

In this work, two different designs of artificial heart valve were devised and then compared by considering the thrombosis, wear and valve orifice to anatomical orifice ratio of each mechanical heart valve. These different design configurations of bi-leaflet mechanical heart valves model are created through the use of Computer-aided design (CAD) modelling and simulated using Computational fluid dynamic (CFD) software. Design 1 is based on existing conventional bi-leaflet valve and design 2 based on modified bi-leaflet respectively. The flow pattern, velocity, vorticity and stress analysis have been done to justify the best design. Based on results, both of the designs show a Doppler velocity index of less than the allowable standard of 2.2 which is safe to be used as replacement of the human heart valve. However, design 2 shows that it has a lower possibility of cavitation issue which will lead to lower thrombosis and provide good central flow area of blood as compared to design 1.

[A philosophical information leaflet to accompany a DSM classification].

PubMed

Kraaijenbrink, J; Kuipers, T; van der Laan, B; Kremer, S

2016-01-01

The introduction of the dsm-5 has re-ignited discussion about the classification of mental disorders. The public may have misconceptions with regard to the nature of the information contained in a dsm-classification. To bring about a conceptual switch so that the professional user of a classification sees it as an aid to diagnosis rather than as a definition of a problem or illness. We devised a 'thought experiment' to serve as a support for dsm classifications. The 'thought experiment' led us to devise a medicine package containing a 'philosophical' information leaflet. This 'thought-experiment', the information leaflet and the medicine package were presented to both students and trainee doctors at the ucp in Groningen and to clinicians at the fpc dr. S. van Mesdag Clinic. Students and trainee doctors were able to make the desired conceptual switch as a result of 'the thought experiment' and with the help they received from the medicine packaging containing the 'philosophical' information leaflet.

Nonlinear solid finite element analysis of mitral valves with heterogeneous leaflet layers

NASA Astrophysics Data System (ADS)

Prot, V.; Skallerud, B.

2009-02-01

An incompressible transversely isotropic hyperelastic material for solid finite element analysis of a porcine mitral valve response is described. The material model implementation is checked in single element tests and compared with a membrane implementation in an out-of-plane loading test to study how the layered structures modify the stress response for a simple geometry. Three different collagen layer arrangements are used in finite element analysis of the mitral valve. When the leaflets are arranged in two layers with the collagen on the ventricular side, the stress in the fibre direction through the thickness in the central part of the anterior leaflet is homogenized and the peak stress is reduced. A simulation using membrane elements is also carried out for comparison with the solid finite element results. Compared to echocardiographic measurements, the finite element models bulge too much in the left atrium. This may be due to evidence of active muscle fibres in some parts of the anterior leaflet, whereas our constitutive modelling is based on passive material.

Correlation of two-dimensional echocardiography and pathologic findings in porcine valve dysfunction.

PubMed

Forman, M B; Phelan, B K; Robertson, R M; Virmani, R

1985-02-01

Two-dimensional echocardiographic findings in porcine valve dysfunction were compared with pathologic findings in 10 patients (12 valves). Three specific echocardiographic findings were identified in patients with regurgitant lesions: prolapse, fracture and flail leaflets. Prolapse was associated pathologically with thinning of the leaflets, longitudinal tears close to the ring margin and acid mucopolysaccharide accumulation. Valve fracture was seen with and without prolapse and was accompanied pathologically by small pinpoint perforations or tears of the leaflet. A flail leaflet was seen with a linear tear of the free margin and was associated with calcific deposits. Mild degrees of fracture seen pathologically were missed on the echocardiographic study in five patients. Thickening or calcification, when present in moderate or severe amounts, was correctly identified by echocardiography. When all abnormal features were considered collectively, two-dimensional echocardiography correctly identified at least one of them in all patients. Therefore, two-dimensional echocardiography may prove useful in assessing the source of valvular regurgitation in patients with bioprosthetic valves.

Treatment of severe mitral regurgitation caused by lesions in both leaflets using multiple mitral valve plasty techniques in a small dog

PubMed Central

Yokoyama, Satoko; Kanemoto, Isamu; Mihara, Kippei; Ando, Takanori; Kawase, Koudai; Sahashi, Yasuaki; Iguchi, Kazuhito

2017-01-01

Mitral valve plasty (MVP) is preferred over mitral valve replacement (MVR) for mitral regurgitation in humans because of its favorable effect on quality of life. In small dogs, it is difficult to repair multiple lesions in both leaflets using MVP. Herein, we report a case of severe mitral regurgitation caused by multiple severe lesions in the posterior leaflet (PL) in a mixed Chihuahua. Initially, we had planned MVR with an artificial valve. However, MVP combined with artificial chordal reconstruction of both leaflets, semicircular suture annuloplasty, and valvuloplasty using a newly devised direct scallop suture for the PL was attempted in this dog. The dog recovered well and showed no adverse cardiac signs, surviving two major operations. The dog died 4 years and 10 months after the MVP due to non-cardiovascular disease. Our additional technique of using a direct scallop suture seemed useful for PL repair involving multiple scallops in a small dog. PMID:29201662

Cloning and expression of prion protein encoding gene of flounder ( Paralichthys olivaceus)

NASA Astrophysics Data System (ADS)

Zhang, Zhiwen; Sun, Xiuqin; Zhang, Jinxing; Zan, Jindong

2008-02-01

The prion protein (PrP) encoding gene of flounder ( Paralichthys olivaceus) was cloned. It was not interrupted by an intron. This gene has two promoters in its 5' upstream, indicating that its transcription may be intensive, and should have an important function. It was expressed in all 14 tissues tested, demonstrating that it is a house-keeping gene. Its expression in digestion and reproduction systems implies that the possible prions of fish may transfer horizontally.

Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485

DOE PAGES

Zhou, Jilai; Olson, Daniel G.; Lanahan, Anthony A.; ...

2015-09-15

We report that Thermoanaerobacter saccharolyticum is a thermophilic microorganism that has been engineered to produce ethanol at high titer (30–70 g/L) and greater than 90 % theoretical yield. However, few genes involved in pyruvate to ethanol production pathway have been unambiguously identified. In T. saccharolyticum, the products of six putative pfor gene clusters and one pfl gene may be responsible for the conversion of pyruvate to acetyl-CoA. To gain insights into the physiological roles of PFOR and PFL, we studied the effect of deletions of several genes thought to encode these activities. We found that that pyruvate ferredoxin oxidoreductase enzymemore » (PFOR) is encoded by the pforA gene and plays a key role in pyruvate dissimilation. We further demonstrated that pyruvate formate-lyase activity (PFL) is encoded by the pfl gene. Although the pfl gene is normally expressed at low levels, it is crucial for biosynthesis in T. saccharolyticum. In pforA deletion strains, pfl expression increased and was able to partially compensate for the loss of PFOR activity. Deletion of both pforA and pfl resulted in a strain that required acetate and formate for growth and produced lactate as the primary fermentation product, achieving 88 % theoretical lactate yield. PFOR encoded by Tsac_0046 and PFL encoded by Tsac_0628 are only two routes for converting pyruvate to acetyl-CoA in T. saccharolyticum. The physiological role of PFOR is pyruvate dissimilation, whereas that of PFL is supplying C1 units for biosynthesis.« less

Identification and Characterization of Three Differentially Expressed Genes, Encoding S-Adenosylhomocysteine Hydrolase, Methionine Aminopeptidase, and a Histone-Like Protein, in the Toxic Dinoflagellate Alexandrium fundyense†

PubMed Central

Taroncher-Oldenburg, Gaspar; Anderson, Donald M.

2000-01-01

Genes showing differential expression related to the early G1 phase of the cell cycle during synchronized circadian growth of the toxic dinoflagellate Alexandrium fundyense were identified and characterized by differential display (DD). The determination in our previous work that toxin production in Alexandrium is relegated to a narrow time frame in early G1 led to the hypothesis that transcriptionally up- or downregulated genes during this subphase of the cell cycle might be related to toxin biosynthesis. Three genes, encoding S-adenosylhomocysteine hydrolase (Sahh), methionine aminopeptidase (Map), and a histone-like protein (HAf), were isolated. Sahh was downregulated, while Map and HAf were upregulated, during the early G1 phase of the cell cycle. Sahh and Map encoded amino acid sequences with about 90 and 70% similarity to those encoded by several eukaryotic and prokaryotic Sahh and Map genes, respectively. The partial Map sequence also contained three cobalt binding motifs characteristic of all Map genes. HAf encoded an amino acid sequence with 60% similarity to those of two histone-like proteins from the dinoflagellate Crypthecodinium cohnii Biecheler. This study documents the potential of applying DD to the identification of genes that are related to physiological processes or cell cycle events in phytoplankton under conditions where small sample volumes represent an experimental constraint. The identification of an additional 21 genes with various cell cycle-related DD patterns also provides evidence for the importance of pretranslational or transcriptional regulation in dinoflagellates, contrary to previous reports suggesting the possibility that translational mechanisms are the primary means of circadian regulation in this group of organisms. PMID:10788388

Identification of a Novel Dioxygenase Involved in Metabolism of o-Xylene, Toluene, and Ethylbenzene by Rhodococcus sp. Strain DK17

PubMed Central

Kim, Dockyu; Chae, Jong-Chan; Zylstra, Gerben J.; Kim, Young-Soo; Kim, Seong-Ki; Nam, Myung Hee; Kim, Young Min; Kim, Eungbin

2004-01-01

Rhodococcus sp. strain DK17 is able to grow on o-xylene, benzene, toluene, and ethylbenzene. DK17 harbors at least two megaplasmids, and the genes encoding the initial steps in alkylbenzene metabolism are present on the 330-kb pDK2. The genes encoding alkylbenzene degradation were cloned in a cosmid clone and sequenced completely to reveal 35 open reading frames (ORFs). Among the ORFs, we identified two nearly exact copies (one base difference) of genes encoding large and small subunits of an iron sulfur protein terminal oxygenase that are 6 kb apart from each other. Immediately downstream of one copy of the dioxygenase genes (akbA1a and akbA2a) is a gene encoding a dioxygenase ferredoxin component (akbA3), and downstream of the other copy (akbA1b and akbA2b) are genes putatively encoding a meta-cleavage pathway. RT-PCR experiments show that the two copies of the dioxygenase genes are operonic with the downstream putative catabolic genes and that both operons are induced by o-xylene. When expressed in Escherichia coli, AkbA1a-AkbA2a-AkbA3 transformed o-xylene into 2,3- and 3,4-dimethylphenol. These were apparently derived from an unstable o-xylene cis-3,4-dihydrodiol, which readily dehydrates. This indicates a single point of attack of the dioxygenase on the aromatic ring. In contrast, attack of AkbA1a-AkbA2a-AkbA3 on ethylbenzene resulted in the formation of two different cis-dihydrodiols resulting from an oxidation at the 2,3 and the 3,4 positions on the aromatic ring, respectively. PMID:15574904

Discovery of Herpes B Virus-Encoded MicroRNAs▿

PubMed Central

Besecker, Michael I.; Harden, Mallory E.; Li, Guanglin; Wang, Xiu-Jie; Griffiths, Anthony

2009-01-01

Herpes B virus (BV) naturally infects macaque monkeys and is a close relative of herpes simplex virus. BV can zoonotically infect humans to cause a rapidly ascending encephalitis with ∼80% mortality. Therefore, BV is a serious danger to those who come into contact with these monkeys or their tissues and cells. MicroRNAs are regulators of gene expression, and there have been reports of virus-encoded microRNAs. We hypothesize that BV-encoded microRNAs are important for the regulation of viral and cellular genes. Herein, we report the discovery of three herpes B virus-encoded microRNAs. PMID:19144716

Engineering tissue constructs to mimic native aortic and pulmonary valve leaflets' structures and mechanics

NASA Astrophysics Data System (ADS)

Masoumi, Nafiseh

There are several disadvantages correlated with current heart valve replacement, including anticoagulation therapy for patients with mechanical valves and the low durability of bioprosthetic valves. The non-viable nature of such devices is a critical drawback especially for pediatric cases due to the inability of the graft to grow in vivo with the patients. A tissue engineered heart valve (TEHV) with remodeling and growth ability, is conceptually appealing to use in the surgical repair and could serve as a permanent replacements when operating for pediatric valvular lesions. It is critical that scaffolds for functional heart valve tissue engineering, be capable of mimicking the native leaflet's structure and mechanical properties at the time of implantation. Meanwhile, the scaffolds should be able to support cellular proliferation and native-like tissue formation as the TEHV remodels toward a scaffold-free state. Our overall hypothesis is that an "ideal" engineered construct, designed based on native leaflet's structure and mechanics, will complement a native heart valve leaflet in providing benchmarks for use in the design of clinically-applicable TEHV. This hypothesis was addressed through several experiments conducted in the present study. To establish a functional biomimetic TEHV, we developed scaffolds capable of matching the anisotropic stiffness of native leaflet while promoting native-like cell and collagen content and supporting the ECM generation. Scaffolds with various polymer contents (e.g., poly (glycerol sebacate) (PGS) and poly (epsilon-caprolactone) (PCL)) and structural designs (e.g., microfabricated and microfibrous scaffolds), were fabricated based on native leaflet's structure and mechanics. It was found that the tri-layered scaffold, designed with assembly of microfabricated PGS and microfibrous PGS/PCL was a functional leaflet capable of promoting tissue formation. Furthermore, to investigate the effect of cyclic stress and flexure individually on the TEHV development, we designed a simple and novel stretch-flexure bioreactor in which samples were subjected to well-defined stimulations with a controlled strain-rate. The stretch and flexure was found to accelerate and increase tissue formation on the microfabricated PGS scaffolds cultivated in the bioreactors.

Gene encoding acetyl-coenzyme A carboxylase

DOEpatents

Roessler, Paul G.; Ohlrogge, John B.

1996-01-01

A DNA encoding an acetyl-coenzyme A carboxylase (ACCase) from a photosynthetic organism and functional derivatives thereof which are resistant to inhibition from certain herbicides. This gene can be placed in organisms to increase their fatty acid content or to render them resistant to certain herbicides.

Oxidative dearomatisation: the key step of sorbicillinoid biosynthesis† †Electronic supplementary information (ESI) available: Containing all experimental details. See DOI: 10.1039/c3sc52911h Click here for additional data file.

PubMed Central

Fahad, Ahmed al; Abood, Amira; Fisch, Katja M.; Osipow, Anna; Davison, Jack; Avramović, Marija; Butts, Craig P.; Piel, Jörn; Simpson, Thomas J.

2014-01-01

An FAD-dependent monooxygenase encoding gene (SorbC) was cloned from Penicillium chrysogenum E01-10/3 and expressed as a soluble protein in Escherichia coli. The enzyme efficiently performed the oxidative dearomatisation of sorbicillin and dihydrosorbicillin to give sorbicillinol and dihydrosorbicillinol respectively. Bioinformatic examination of the gene cluster surrounding SorbC indicated the presence of two polyketide synthase (PKS) encoding genes designated sorbA and sorbB. The gene sorbA-encodes a highly reducing iterative PKS while SorbB encodes a non-reducing iterative PKS which features a reductive release domain usually involved in the production of polyketide aldehydes. Using these observations and previously reported results from isotopic feeding experiments a new and simpler biosynthetic route to the sorbicillin class of secondary metabolites is proposed which is consistent with all reported experimental results. PMID:25580210

A gene encoding the plant-like alternative oxidase is present in Phytomonas but absent in Leishmania spp.

PubMed

Van Hellemond, J J; Simons, B; Millenaar, F F; Tielens, A G

1998-01-01

The constituents of the respiratory chain are believed to differ among the trypanosomatids; bloodstream stages of African trypanosomes and Phytomonas promastigotes oxidize ubiquinol by a ubiquinol:oxygen oxidoreductase, also known as alternative oxidase, whereas Leishmania spp. oxidize ubiquinol via a classic cytochrome-containing respiratory chain. The molecular basis for this elementary difference in ubiquinol oxidation by the mitochondrial electron-transport chain in distinct trypanosomatids was investigated. The presence of a gene encoding the plant-like alternative oxidase could be demonstrated in Phytomonas and Trypanosoma brucei, trypanosomatids that are known to contain alternative oxidase activity. Our results further demonstrated that Leishmania spp. lack a gene encoding the plant-like alternative oxidase, and therefore, all stages of Leishmania spp. will lack the alternative oxidase protein. The observed fundamental differences between the respiratory chains of distinct members of the trypanosomatid family are thus caused by the presence or absence of a gene encoding the plant-like alternative oxidase.

Cloning of gene-encoded stem bromelain on system coming from Pichia pastoris as therapeutic protein candidate

NASA Astrophysics Data System (ADS)

Yusuf, Y.; Hidayati, W.

2018-01-01

The process of identifying bacterial recombination using PCR, and restriction, and then sequencing process was done after identifying the bacteria. This research aimed to get a yeast cell of Pichia pastoris which has an encoder gene of stem bromelain enzyme. The production of recombinant stem bromelain enzymes using yeast cells of P. pastoris can produce pure bromelain rod enzymes and have the same conformation with the enzyme’s conformation in pineapple plants. This recombinant stem bromelain enzyme can be used as a therapeutic protein in inflammatory, cancer and degenerative diseases. This study was an early stage of a step series to obtain bromelain rod protein derived from pineapple made with genetic engineering techniques. This research was started by isolating the RNA of pineapple stem which was continued with constructing cDNA using reserve transcriptase-PCR technique (RT-PCR), doing the amplification of bromelain enzyme encoder gene with PCR technique using a specific premiere couple which was designed. The process was continued by cloning into bacterium cells of Escherichia coli. A vector which brought the encoder gene of stem bromelain enzyme was inserted into the yeast cell of P. pastoris and was continued by identifying the yeast cell of P. pastoris which brought the encoder gene of stem bromelain enzyme. The research has not found enzyme gene of stem bromelain in yeast cell of P. pastoris yet. The next step is repeating the process by buying new reagent; RNase inhibitor, and buying liquid nitrogen.

Cloning and sequencing of a gene encoding a novel extracellular neutral proteinase from Streptomyces sp. strain C5 and expression of the gene in Streptomyces lividans 1326.

PubMed Central

Lampel, J S; Aphale, J S; Lampel, K A; Strohl, W R

1992-01-01

The gene encoding a novel milk protein-hydrolyzing proteinase was cloned on a 6.56-kb SstI fragment from Streptomyces sp. strain C5 genomic DNA into Streptomyces lividans 1326 by using the plasmid vector pIJ702. The gene encoding the small neutral proteinase (snpA) was located within a 2.6-kb BamHI-SstI restriction fragment that was partially sequenced. The molecular mass of the deduced amino acid sequence of the mature protein was determined to be 15,740, which corresponds very closely with the relative molecular mass of the purified protein (15,500) determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The N-terminal amino acid sequence of the purified neutral proteinase was determined, and the DNA encoding this sequence was found to be located within the sequenced DNA. The deduced amino acid sequence contains a conserved zinc binding site, although secondary ligand binding and active sites typical of thermolysinlike metalloproteinases are absent. The combination of its small size, deduced amino acid sequence, and substrate and inhibition profile indicate that snpA encodes a novel neutral proteinase. Images PMID:1569011

Structure of a gene encoding a murine thymus leukemia antigen, and organization of Tla genes in the BALB/c mouse

PubMed Central

1985-01-01

We have determined the DNA sequence of a gene encoding a thymus leukemia (TL) antigen in the BALB/c mouse, and have more definitively mapped the cloned BALB/c Tla-region class I gene clusters. Analysis of the sequence shows that the Tla gene is less closely related to the H-2 genes than H-2 genes are to one another or to a Qa-2,3-region genes. The Tla gene, 17.3A, contains an apparent gene conversion. Comparison of the BALB/c Tla genes with those from C57BL shows that BALB/c has more Tla-region class I genes, and that one of the genes absent in C57BL is gene 17.3A. PMID:3894562

Genome-Wide Identification and Expression Analysis of Homeodomain Leucine Zipper Subfamily IV (HDZ IV) Gene Family from Musa accuminata

PubMed Central

Pandey, Ashutosh; Misra, Prashant; Alok, Anshu; Kaur, Navneet; Sharma, Shivani; Lakhwani, Deepika; Asif, Mehar H.; Tiwari, Siddharth; Trivedi, Prabodh K.

2016-01-01

The homeodomain zipper family (HD-ZIP) of transcription factors is present only in plants and plays important role in the regulation of plant-specific processes. The subfamily IV of HDZ transcription factors (HD-ZIP IV) has primarily been implicated in the regulation of epidermal structure development. Though this gene family is present in all lineages of land plants, members of this gene family have not been identified in banana, which is one of the major staple fruit crops. In the present work, we identified 21 HDZIV encoding genes in banana by the computational analysis of banana genome resource. Our analysis suggested that these genes putatively encode proteins having all the characteristic domains of HDZIV transcription factors. The phylogenetic analysis of the banana HDZIV family genes further confirmed that after separation from a common ancestor, the banana, and poales lineages might have followed distinct evolutionary paths. Further, we conclude that segmental duplication played a major role in the evolution of banana HDZIV encoding genes. All the identified banana HDZIV genes expresses in different banana tissue, however at varying levels. The transcript levels of some of the banana HDZIV genes were also detected in banana fruit pulp, suggesting their putative role in fruit attributes. A large number of genes of this family showed modulated expression under drought and salinity stress. Taken together, the present work lays a foundation for elucidation of functional aspects of the banana HDZIV encoding genes and for their possible use in the banana improvement programs. PMID:26870050

Microarray Analyses of Gene Expression during Adventitious Root Development in Pinus contorta1[w

PubMed Central

Brinker, Monika; van Zyl, Leonel; Liu, Wenbin; Craig, Deborah; Sederoff, Ronald R.; Clapham, David H.; von Arnold, Sara

2004-01-01

In order to investigate the gene expression pattern during adventitious root development, RNA of Pinus contorta hypocotyls, pulse-treated with the auxin indole-3-butyric acid and harvested at distinct developmental time points of root development, was hybridized to microarrays containing 2,178 cDNAs from Pinus taeda. Over the period of observation of root development, the transcript levels of 220 genes changed significantly. During the root initiation phase, genes involved in cell replication and cell wall weakening and a transcript encoding a PINHEAD/ZWILLE-like protein were up-regulated, while genes related to auxin transport, photosynthesis, and cell wall synthesis were down-regulated. In addition, there were changes in transcript abundance of genes related to water stress. During the root meristem formation phase the transcript abundances of genes involved in auxin transport, auxin responsive transcription, and cell wall synthesis, and of a gene encoding a B-box zinc finger-like protein, increased, while those encoding proteins involved in cell wall weakening decreased. Changes of transcript abundance of genes related to water stress during the root meristem formation and root formation phase indicate that the plant roots had become functional in water transport. Simultaneously, genes involved in auxin transport were up-regulated, while genes related to cell wall modification were down-regulated. Finally, during the root elongation phase down-regulation of transcripts encoding proteins involved in cell replication and stress occurred. Based on the observed changes in transcript abundances, we suggest hypotheses about the relative importance of various physiological processes during the auxin-induced development of roots in P. contorta. PMID:15247392

Surgical repair of tricuspid valve leaflet tear following percutaneous closure of perimembranous ventricular septal defect using Amplatzer duct occluder I: Report of two cases

PubMed Central

Kuwelker, Saatchi Mahesh; Shetty, Devi Prasad; Dalvi, Bharat

2017-01-01

Tricuspid valve (TV) injury following transcatheter closure of perimembranous ventricular septal defect (PMVSD) with Amplatzer ductal occluder I (ADO I), requiring surgical repair, is rare. We report two cases of TV tear involving the anterior and septal leaflets following PMVSD closure using ADO I. In both the patients, the subvalvular apparatus remained unaffected. The patients presented with severe tricuspid regurgitation (TR) 6 weeks and 3 months following the device closure. They underwent surgical repair with patch augmentation of the TV leaflets. Postoperatively, both are asymptomatic with a mild residual TR. PMID:28163430

Identification of a Linked Set of Genes in Serpulina hyodysenteriae (B204) Predicted To Encode Closely Related 39-Kilodalton Extracytoplasmic Proteins

PubMed Central

Gabe, Jeffrey D.; Dragon, Elizabeth; Chang, Ray-Jen; McCaman, Michael T.

1998-01-01

A tandem pair of nearly identical genes from Serpulina hyodysenteriae (B204) were cloned and sequenced. The full open reading frame of one gene and the partial open reading frame of the neighboring gene appear to encode secreted proteins which are homologous to, yet distinct from, the 39-kDa extracytoplasmic protein purified from the membrane fraction of S. hyodysenteriae. We have designated these newly identified genes vspA and vspB (for variable surface protein). PMID:9440540

Direct cloning of the trxB gene that encodes thioredoxin reductase.

PubMed Central

Russel, M; Model, P

1985-01-01

A strain was constructed which contains mutations in the genes encoding thioredoxin (trxA) and thioredoxin reductase (trxB) such that filamentous phage f1 cannot grow. The complementation of either mutation with its wild-type allele permits phage growth. We used this strain to select f1 phage which contain a cloned trxB gene. The location of the gene on the cloned fragment was determined, and its protein product was identified. Plasmid subclones that contain this gene overproduce thioredoxin reductase. Images PMID:2989245

Wound induced Beta vulgaris polygalacturonase-inhibiting protein genes encode a longer leucine-rich repeat domain and inhibit fungal polygalacturonases

USDA-ARS?s Scientific Manuscript database

Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defense. Sugar beet (Beta vulgaris L.) PGIP genes, BvPGIP1, BvPGIP2 and BvPGIP3, were isolated from two breeding lines, F1016 and F1010. Full-length cDNA sequences of the three BvPGIP genes encod...

Innate responses to gene knockouts impact overlapping gene networks and vary with respect to resistance to viral infection.

PubMed

Liu, Yonghong; Liu, Yuanyuan; Wu, Jiaming; Roizman, Bernard; Zhou, Grace Guoying

2018-04-03

Analyses of the levels of mRNAs encoding IFIT1, IFI16, RIG-1, MDA5, CXCL10, LGP2, PUM1, LSD1, STING, and IFNβ in cell lines from which the gene encoding LGP2, LSD1, PML, HDAC4, IFI16, PUM1, STING, MDA5, IRF3, or HDAC 1 had been knocked out, as well as the ability of these cell lines to support the replication of HSV-1, revealed the following: ( i ) Cell lines lacking the gene encoding LGP2, PML, or HDAC4 (cluster 1) exhibited increased levels of expression of partially overlapping gene networks. Concurrently, these cell lines produced from 5 fold to 12 fold lower yields of HSV-1 than the parental cells. ( ii ) Cell lines lacking the genes encoding STING, LSD1, MDA5, IRF3, or HDAC 1 (cluster 2) exhibited decreased levels of mRNAs of partially overlapping gene networks. Concurrently, these cell lines produced virus yields that did not differ from those produced by the parental cell line. The genes up-regulated in cell lines forming cluster 1, overlapped in part with genes down-regulated in cluster 2. The key conclusions are that gene knockouts and subsequent selection for growth causes changes in expression of multiple genes, and hence the phenotype of the cell lines cannot be ascribed to a single gene; the patterns of gene expression may be shared by multiple knockouts; and the enhanced immunity to viral replication by cluster 1 knockout cell lines but not by cluster 2 cell lines suggests that in parental cells, the expression of innate resistance to infection is specifically repressed.

Hypoplasia or Absence of Posterior Leaflet: A Rare Congenital Anomaly of The Mitral Valve in Adulthood – Case Series

PubMed Central

Parato, Vito Maurizio; Masia, Stefano Lucio

2018-01-01

We present a case series of two adult patients with almost complete absence of the posterior mitral valve leaflet and who are asymptomatic or mildly symptomatic, with two different degrees of mitral regurgitation. PMID:29629259

Genomic characterization of an extensively-drug resistance Salmonella enterica serotype Indiana strain harboring blaNDM-1 gene isolated from a chicken carcass in China.

PubMed

Wang, Wei; Peng, Zixin; Baloch, Zulqarnain; Hu, Yujie; Xu, Jin; Zhang, Wenhui; Fanning, Séamus; Li, Fengqin

2017-11-01

The objective of this study was to genetically characterize the antimicrobial resistance mechanisms of Salmonella enterica serotype Indiana C629 isolated from a chicken carcass in China in 2014. Antimicrobial susceptibility against a panel of 23 antimicrobial agents was carried out on Salmonella enterica serotype Indiana C629 and assessed according to CLSI standards. Whole-genome sequencing of this isolate was conducted to obtain the complete genome of S. Indiana. Salmonella Indiana C629 expressed an XDR phenotype being resistant to more than 20 antimicrobial agents, including imipenem and meropenem. From the analysis of the resistance mechanisms, two mutations were identified in subunit A of DNA gyrase within the quinolone resistance determining region, in addition to the acquisition of mobile efflux pumps encoding oqxA/B/R. Additionally, four beta-lactamases resistance genes (bla CTX-M-65 , bla TEM-1 , bla OXA-1 , and bla NDM-1 ), five aminoglycosides resistance genes (aac(3)-IV, aac(6')-Ib-cr, aadA2, aadA5, and aph(4)-Ia), two phenicol resistance genes (catB3 and floR), and five trimethoprim/sulfamethoxazole resistance genes (sul1/2/3 and dfrA12/17) were also identified. A total of 191 virulence genes were identified. Among them, 57 belonged to type-three secretion system (T3SS) encoding genes, 55 belonged to fimbrial adherence encoding genes, and 39 belonged to flagella-encoding genes CONCLUSIONS: This study demonstrated that multi-resistance mechanisms consistent with an XDR-phenotype, along with various virulence encoding genes of a S. Indiana strain in China These findings highlight the importance of cooperation among different sectors in order to monitor the spread of resistant pathogens among food animal, foods of animal origin and human beings that might further take measures to protect consumers' health. Copyright © 2017 Elsevier GmbH. All rights reserved.

Molecular and functional characterization of novel fructosyltransferases and invertases from Agave tequilana.

PubMed

Cortés-Romero, Celso; Martínez-Hernández, Aída; Mellado-Mojica, Erika; López, Mercedes G; Simpson, June

2012-01-01

Fructans are the main storage polysaccharides found in Agave species. The synthesis of these complex carbohydrates relies on the activities of specific fructosyltransferase enzymes closely related to the hydrolytic invertases. Analysis of Agave tequilana transcriptome data led to the identification of ESTs encoding putative fructosyltransferases and invertases. Based on sequence alignments and structure/function relationships, two different genes were predicted to encode 1-SST and 6G-FFT type fructosyltransferases, in addition, 4 genes encoding putative cell wall invertases and 4 genes encoding putative vacuolar invertases were also identified. Probable functions for each gene, were assigned based on conserved amino acid sequences and confirmed for 2 fructosyltransferases and one invertase by analyzing the enzymatic activity of recombinant Agave protein s expressed and purified from Pichia pastoris. The genome organization of the fructosyltransferase/invertase genes, for which the corresponding cDNA contained the complete open reading frame, was found to be well conserved since all genes were shown to carry a 9 bp mini-exon and all showed a similar structure of 8 exons/7 introns with the exception of a cell wall invertase gene which has 7 exons and 6 introns. Fructosyltransferase genes were strongly expressed in the storage organs of the plants, especially in vegetative stages of development and to lower levels in photosynthetic tissues, in contrast to the invertase genes where higher levels of expression were observed in leaf tissues and in mature plants.

Molecular and Functional Characterization of Novel Fructosyltransferases and Invertases from Agave tequilana

PubMed Central

Cortés-Romero, Celso; Martínez-Hernández, Aída; Mellado-Mojica, Erika; López, Mercedes G.; Simpson, June

2012-01-01

Fructans are the main storage polysaccharides found in Agave species. The synthesis of these complex carbohydrates relies on the activities of specific fructosyltransferase enzymes closely related to the hydrolytic invertases. Analysis of Agave tequilana transcriptome data led to the identification of ESTs encoding putative fructosyltransferases and invertases. Based on sequence alignments and structure/function relationships, two different genes were predicted to encode 1-SST and 6G-FFT type fructosyltransferases, in addition, 4 genes encoding putative cell wall invertases and 4 genes encoding putative vacuolar invertases were also identified. Probable functions for each gene, were assigned based on conserved amino acid sequences and confirmed for 2 fructosyltransferases and one invertase by analyzing the enzymatic activity of recombinant Agave protein s expressed and purified from Pichia pastoris. The genome organization of the fructosyltransferase/invertase genes, for which the corresponding cDNA contained the complete open reading frame, was found to be well conserved since all genes were shown to carry a 9 bp mini-exon and all showed a similar structure of 8 exons/7 introns with the exception of a cell wall invertase gene which has 7 exons and 6 introns. Fructosyltransferase genes were strongly expressed in the storage organs of the plants, especially in vegetative stages of development and to lower levels in photosynthetic tissues, in contrast to the invertase genes where higher levels of expression were observed in leaf tissues and in mature plants. PMID:22558253

Impact assessment of bisphenol A on lignin-modifying enzymes by basidiomycete Trametes versicolor.

PubMed

Takamiya, Minako; Magan, Naresh; Warner, Philip J

2008-06-15

The impact of different concentrations of bisphenol A (BPA) was evaluated on growth of the white-rot basidiomycete, Trametes versicolor, and on the expression of genes encoding lignin-modifying enzyme (LME) activities. Effective doses (EDs) were obtained from fungal growth rate to monitor LME activities and the expression levels of their encoding genes. The fungus showed mycelial growth at concentrations of up to 300 microg ml(-1) of BPA with an ED50 value of 185 microg ml(-1). The LME activities were stimulated by BPA concentrations up to 300 microg ml(-1). The lignin peroxidase (LIP) encoding gene may be sensitive to BPA stress.

Characterization of three-dimensional anisotropic heart valve tissue mechanical properties using inverse finite element analysis.

PubMed

Abbasi, Mostafa; Barakat, Mohammed S; Vahidkhah, Koohyar; Azadani, Ali N

2016-09-01

Computational modeling has an important role in design and assessment of medical devices. In computational simulations, considering accurate constitutive models is of the utmost importance to capture mechanical response of soft tissue and biomedical materials under physiological loading conditions. Lack of comprehensive three-dimensional constitutive models for soft tissue limits the effectiveness of computational modeling in research and development of medical devices. The aim of this study was to use inverse finite element (FE) analysis to determine three-dimensional mechanical properties of bovine pericardial leaflets of a surgical bioprosthesis under dynamic loading condition. Using inverse parameter estimation, 3D anisotropic Fung model parameters were estimated for the leaflets. The FE simulations were validated using experimental in-vitro measurements, and the impact of different constitutive material models was investigated on leaflet stress distribution. The results of this study showed that the anisotropic Fung model accurately simulated the leaflet deformation and coaptation during valve opening and closing. During systole, the peak stress reached to 3.17MPa at the leaflet boundary while during diastole high stress regions were primarily observed in the commissures with the peak stress of 1.17MPa. In addition, the Rayleigh damping coefficient that was introduced to FE simulations to simulate viscous damping effects of surrounding fluid was determined. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of the effects of sdiA, a luxR homologue, on adherence and motility of Escherichia coli O157 : H7.

PubMed

Sharma, Vijay K; Bearson, Shawn M D; Bearson, Bradley L

2010-05-01

Quorum-sensing (QS) signalling pathways are important regulatory networks for controlling the expression of genes promoting adherence of enterohaemorrhagic Escherichia coli (EHEC) O157 : H7 to epithelial cells. A recent study has shown that EHEC O157 : H7 encodes a luxR homologue, called sdiA, which upon overexpression reduces the expression of genes encoding flagellar and locus of enterocyte effacement (LEE) proteins, thus negatively impacting on the motility and intimate adherence phenotypes, respectively. Here, we show that the deletion of sdiA from EHEC O157 : H7 strain 86-24, and from a hha (a negative regulator of ler) mutant of this strain, enhanced bacterial adherence to HEp-2 epithelial cells of the sdiA mutant strains relative to the strains containing a wild-type copy of sdiA. Quantitative reverse transcription PCR showed that the expression of LEE-encoded genes ler, espA and eae in strains with the sdiA deletions was not significantly different from that of the strains wild-type for sdiA. Similarly, no additional increases in the expression of LEE genes were observed in a sdiA hha double mutant strain relative to that observed in the hha deletion mutant. While the expression of fliC, which encodes flagellin, was enhanced in the sdiA mutant strain, the expression of fliC was reduced by several fold in the hha mutant strain, irrespective of the presence or absence of sdiA, indicating that the genes sdiA and hha exert opposing effects on the expression of fliC. The strains with deletions in sdiA or hha showed enhanced expression of csgA, encoding curlin of the curli fimbriae, with the expression of csgA highest in the sdiA hha double mutant, suggesting an additive effect of these two gene deletions on the expression of csgA. No significant differences were observed in the expression of the genes lpfA and fimA of the operons encoding long polar and type 1 fimbriae in the sdiA mutant strain. These data indicate that SdiA has no significant effect on the expression of LEE genes, but that it appears to act as a strong repressor of genes encoding flagella and curli fimbriae, and the alleviation of the SdiA-mediated repression of these genes in an EHEC O157 : H7 sdiA mutant strain contributes to enhanced bacterial motility and increased adherence to HEp-2 epithelial cells.

Molecular characterization and expression of the M6 gene of grass carp hemorrhage virus (GCHV), an aquareovirus.

PubMed

Qiu, T; Lu, R H; Zhang, J; Zhu, Z Y

2001-07-01

The complete nucleotide sequence of M6 gene of grass carp hemorrhage virus (GCHV) was determined. It is 2039 nucleotides in length and contains a single large open reading frame that could encode a protein of 648 amino acids with predicted molecular mass of 68.7 kDa. Amino acid sequence comparison revealed that the protein encoded by GCHV M6 is closely related to the protein mu1 of mammalian reovirus. The M6 gene, encoding the major outer-capsid protein, was expressed using the pET fusion protein vector in Escherichia coli and detected by Western blotting using chicken anti-GCHV immunoglobulin (IgY). The result indicates that the protein encoded by M6 may share a putative Asn-42-Pro-43 proteolytic cleavage site with mu1.

A [Cu]rious Ribosomal Profiling Pattern Leads to the Discovery of Ribosomal Frameshifting in the Synthesis of a Copper Chaperone.

PubMed

Atkins, John F; Loughran, Gary; Baranov, Pavel V

2017-01-19

In many bacteria, separate genes encode a copper binding chaperone and a copper efflux pump, but in some the chaperone encoding gene has been elusive. In this issue of Molecular Cell, Meydan et al. (2017) report that ribosomes translating the ORF that encodes the copper pump frequently frameshift and terminate to produce the copper chaperone. Copyright © 2017 Elsevier Inc. All rights reserved.

Transcriptome analysis of Neisseria meningitidis in human whole blood and mutagenesis studies identify virulence factors involved in blood survival.

PubMed

Echenique-Rivera, Hebert; Muzzi, Alessandro; Del Tordello, Elena; Seib, Kate L; Francois, Patrice; Rappuoli, Rino; Pizza, Mariagrazia; Serruto, Davide

2011-05-01

During infection Neisseria meningitidis (Nm) encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expression of ≈30% of ORFs of the genome and major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. In particular, we found that the gene encoding the regulator Fur, as well as all genes encoding iron uptake systems, were significantly up-regulated. Analysis of regulated genes encoding for surface-exposed proteins involved in Nm pathogenesis allowed us to better understand mechanisms used to circumvent host defenses. During blood infection, Nm activates genes encoding for the factor H binding proteins, fHbp and NspA, genes encoding for detoxifying enzymes such as SodC, Kat and AniA, as well as several less characterized surface-exposed proteins that might have a role in blood survival. Through mutagenesis studies of a subset of up-regulated genes we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. Nm mutant strains lacking the genes encoding the hypothetical protein NMB1483 and the surface-exposed proteins NalP, Mip and NspA, the Fur regulator, the transferrin binding protein TbpB, and the L-lactate permease LctP were sensitive to killing by human blood. This increased knowledge of how Nm responds to adaptation in blood could also be helpful to develop diagnostic and therapeutic strategies to control the devastating disease cause by this microorganism.

Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival

PubMed Central

Del Tordello, Elena; Seib, Kate L.; Francois, Patrice; Rappuoli, Rino; Pizza, Mariagrazia; Serruto, Davide

2011-01-01

During infection Neisseria meningitidis (Nm) encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expression of ≈30% of ORFs of the genome and major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. In particular, we found that the gene encoding the regulator Fur, as well as all genes encoding iron uptake systems, were significantly up-regulated. Analysis of regulated genes encoding for surface-exposed proteins involved in Nm pathogenesis allowed us to better understand mechanisms used to circumvent host defenses. During blood infection, Nm activates genes encoding for the factor H binding proteins, fHbp and NspA, genes encoding for detoxifying enzymes such as SodC, Kat and AniA, as well as several less characterized surface-exposed proteins that might have a role in blood survival. Through mutagenesis studies of a subset of up-regulated genes we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. Nm mutant strains lacking the genes encoding the hypothetical protein NMB1483 and the surface-exposed proteins NalP, Mip and NspA, the Fur regulator, the transferrin binding protein TbpB, and the L-lactate permease LctP were sensitive to killing by human blood. This increased knowledge of how Nm responds to adaptation in blood could also be helpful to develop diagnostic and therapeutic strategies to control the devastating disease cause by this microorganism. PMID:21589640

Gene encoding acetyl-coenzyme A carboxylase

DOEpatents

Roessler, P.G.; Ohlrogge, J.B.

1996-09-24

A DNA encoding an acetyl-coenzyme A carboxylase (ACCase) from a photosynthetic organism and functional derivatives are disclosed which are resistant to inhibition from certain herbicides. This gene can be placed in organisms to increase their fatty acid content or to render them resistant to certain herbicides. 5 figs.

Mutations in iron-sulfur cluster proteins that improve xylose utilization

DOEpatents

Froehlich, Allan; Henningsen, Brooks; Covalla, Sean; Zelle, Rintze M.

2018-03-20

There is provided an engineered host cells comprising (a) one or more mutations in one or more endogenous genes encoding a protein associated with iron metabolism; and (b) at least one gene encoding a polypeptide having xylose isomerase activity, and methods of their use thereof.

Heterologous production and characterization of two glyoxal oxidases from Pycnoporus cinnabarinus

Treesearch

Marianne Daou; François Piumi; Daniel Cullen; Eric Record; Craig B. Faulds

2016-01-01

The genome of the white rot fungus Pycnoporus cinnabarinus includes a large number of genes encoding enzymes implicated in lignin degradation. Among these, three genes are predicted to encode glyoxal oxidase, an enzyme previously isolated from Phanerochaete chrysosporium. The glyoxal oxidase of P. chrysosporium...

Genomic polymorphism, recombination, and linkage disequilibrium in human major histocompatibility complex-encoded antigen-processing genes.

PubMed Central

van Endert, P M; Lopez, M T; Patel, S D; Monaco, J J; McDevitt, H O

1992-01-01

Recently, two subunits of a large cytosolic protease and two putative peptide transporter proteins were found to be encoded by genes within the class II region of the major histocompatibility complex (MHC). These genes have been suggested to be involved in the processing of antigenic proteins for presentation by MHC class I molecules. Because of the high degree of polymorphism in MHC genes, and previous evidence for both functional and polypeptide sequence polymorphism in the proteins encoded by the antigen-processing genes, we tested DNA from 27 consanguineous human cell lines for genomic polymorphism by restriction fragment length polymorphism (RFLP) analysis. These studies demonstrate a strong linkage disequilibrium between TAP1 and LMP2 RFLPs. Moreover, RFLPs, as well as a polymorphic stop codon in the telomeric TAP2 gene, appear to be in linkage disequilibrium with HLA-DR alleles and RFLPs in the HLA-DO gene. A high rate of recombination, however, seems to occur in the center of the complex, between the TAP1 and TAP2 genes. Images PMID:1360671

Functional differentiation and spatial-temporal co-expression networks of the NBS-encoding gene family in Jilin ginseng, Panax ginseng C.A. Meyer.

PubMed

Yin, Rui; Zhao, Mingzhu; Wang, Kangyu; Lin, Yanping; Wang, Yanfang; Sun, Chunyu; Wang, Yi; Zhang, Meiping

2017-01-01

Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes). Four hundred twelve PgNBS gene transcripts, derived from 284 gene models, were identified from the transcriptomes of 14 ginseng tissues. These genes were classified into eight types, including TNL, TN, CNL, CN, NL, N, RPW8-NL and RPW8-N. Seven conserved motifs were identified in both the Toll/interleukine-1 receptor (TIR) and coiled-coil (CC) typed genes whereas six were identified in the RPW8 typed genes. Phylogenetic analysis showed that the PgNBS gene family is an ancient family, with a vast majority of its genes originated before ginseng originated. In spite of their belonging to a family, the PgNBS genes have functionally dramatically differentiated and been categorized into numerous functional categories. The expressions of the across tissues, different aged roots and the roots of different genotypes. However, they are coordinating in expression, forming a single co-expression network. These results provide a deeper understanding of the origin, evolution and functional differentiation and expression dynamics of the NBS-encoding gene family in plants in general and in ginseng particularly, and a NBS gene toolkit useful for isolation and characterization of disease resistance genes and for enhanced disease resistance breeding in ginseng and related species.

Functional differentiation and spatial-temporal co-expression networks of the NBS-encoding gene family in Jilin ginseng, Panax ginseng C.A. Meyer

PubMed Central

Wang, Kangyu; Lin, Yanping; Wang, Yanfang; Sun, Chunyu; Wang, Yi

2017-01-01

Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes). Four hundred twelve PgNBS gene transcripts, derived from 284 gene models, were identified from the transcriptomes of 14 ginseng tissues. These genes were classified into eight types, including TNL, TN, CNL, CN, NL, N, RPW8-NL and RPW8-N. Seven conserved motifs were identified in both the Toll/interleukine-1 receptor (TIR) and coiled-coil (CC) typed genes whereas six were identified in the RPW8 typed genes. Phylogenetic analysis showed that the PgNBS gene family is an ancient family, with a vast majority of its genes originated before ginseng originated. In spite of their belonging to a family, the PgNBS genes have functionally dramatically differentiated and been categorized into numerous functional categories. The expressions of the across tissues, different aged roots and the roots of different genotypes. However, they are coordinating in expression, forming a single co-expression network. These results provide a deeper understanding of the origin, evolution and functional differentiation and expression dynamics of the NBS-encoding gene family in plants in general and in ginseng particularly, and a NBS gene toolkit useful for isolation and characterization of disease resistance genes and for enhanced disease resistance breeding in ginseng and related species. PMID:28727829

Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome.

PubMed

Pauchet, Y; Saski, C A; Feltus, F A; Luyten, I; Quesneville, H; Heckel, D G

2014-06-01

The ability of herbivorous beetles from the superfamilies Chrysomeloidea and Curculionoidea to degrade plant cell wall polysaccharides has only recently begun to be appreciated. The presence of plant cell wall degrading enzymes (PCWDEs) in the beetle's digestive tract makes this degradation possible. Sequences encoding these beetle-derived PCWDEs were originally identified from transcriptomes and strikingly resemble those of saprophytic and phytopathogenic microorganisms, raising questions about their origin; e.g. are they insect- or microorganism-derived? To demonstrate unambiguously that the genes encoding PCWDEs found in beetle transcriptomes are indeed of insect origin, we generated a bacterial artificial chromosome library from the genome of the leaf beetle Chrysomela tremula, containing 18 432 clones with an average size of 143 kb. After hybridizing this library with probes derived from 12 C. tremula PCWDE-encoding genes and sequencing the positive clones, we demonstrated that the latter genes are encoded by the insect's genome and are surrounded by genes possessing orthologues in the genome of Tribolium castaneum as well as in three other beetle genomes. Our analyses showed that although the level of overall synteny between C. tremula and T. castaneum seems high, the degree of microsynteny between both species is relatively low, in contrast to the more closely related Colorado potato beetle. © 2014 The Royal Entomological Society.

Identification of a Polymorphic Gene, BCL2A1, Encoding Two Novel Hematopoietic Lineage-specific Minor Histocompatibility Antigens

PubMed Central

Akatsuka, Yoshiki; Nishida, Tetsuya; Kondo, Eisei; Miyazaki, Mikinori; Taji, Hirohumi; Iida, Hiroatsu; Tsujimura, Kunio; Yazaki, Makoto; Naoe, Tomoki; Morishima, Yasuo; Kodera, Yoshihisa; Kuzushima, Kiyotaka; Takahashi, Toshitada

2003-01-01

We report the identification of two novel minor histocompatibility antigens (mHAgs), encoded by two separate single nucleotide polymorphisms on a single gene, BCL2A1, and restricted by human histocompatibility leukocyte antigen (HLA)-A*2402 (the most common HLA-A allele in Japanese) and B*4403, respectively. Two cytotoxic T lymphocyte (CTL) clones specific for these mHAgs were first isolated from two distinct recipients after hematopoietic cell transplantation. Both clones lyse only normal and malignant cells within the hematopoietic lineage. To localize the gene encoding the mHAgs, two-point linkage analysis was performed on the CTL lytic patterns of restricting HLA-transfected B lymphoblastoid cell lines obtained from Centre d'Etude du Polymorphisme Humain. Both CTL clones showed a completely identical lytic pattern for 4 pedigrees and the gene was localized within a 3.6-cM interval of 15q24.3–25.1 region that encodes at least 46 genes. Of those, only BCL2A1 has been reported to be expressed in hematopoietic cells and possess three nonsynonymous nucleotide changes. Minigene transfection and epitope reconstitution assays with synthetic peptides identified both HLA-A*2402– and B*4403-restricted mHAg epitopes to be encoded by distinct polymorphisms within BCL2A1. PMID:12771180

A Shigella flexneri Virulence Plasmid Encoded Factor Controls Production of Outer Membrane Vesicles

PubMed Central

Sidik, Saima; Kottwitz, Haila; Benjamin, Jeremy; Ryu, Julie; Jarrar, Ameer; Garduno, Rafael; Rohde, John R.

2014-01-01

Shigella spp. use a repertoire of virulence plasmid-encoded factors to cause shigellosis. These include components of a Type III Secretion Apparatus (T3SA) that is required for invasion of epithelial cells and many genes of unknown function. We constructed an array of 99 deletion mutants comprising all genes encoded by the virulence plasmid (excluding those known to be required for plasmid maintenance) of Shigella flexneri. We screened these mutants for their ability to bind the dye Congo red: an indicator of T3SA function. This screen focused our attention on an operon encoding genes that modify the cell envelope including virK, a gene of partially characterized function. We discovered that virK is required for controlled release of proteins to the culture supernatant. Mutations in virK result in a temperature-dependent overproduction of outer membrane vesicles (OMVs). The periplasmic chaperone/protease DegP, a known regulator of OMV production in Escherichia coli (encoded by a chromosomal gene), was found to similarly control OMV production in S. flexneri. Both virK and degP show genetic interactions with mxiD, a structural component of the T3SA. Our results are consistent with a model in which VirK and DegP relieve the periplasmic stress that accompanies assembly of the T3SA. PMID:25378474

A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene

PubMed Central

Farrugia, Daniel N.; Elbourne, Liam D. H.; Mabbutt, Bridget C.; Paulsen, Ian T.

2015-01-01

Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5′ end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature. PMID:25883135

Gene disruption in Trichoderma atroviride via Agrobacterium-mediated transformation.

PubMed

Zeilinger, Susanne

2004-02-01

A modified Agrobacterium-mediated transformation method for the efficient disruption of two genes encoding signaling compounds of the mycoparasite Trichoderma atroviride is described, using the hph gene of Escherichia coli as selection marker. The transformation vectors contained about 1 kb of 5' and 3' non-coding regions from the tmk1 (encoding a MAP kinase) or tga3 (encoding an alpha-subunit of a heterotrimeric G protein) target loci flanking a selection marker. Transformation of fungal conidia and selection on hygromycin-containing media applying an overlay-based procedure, which overcomes the lack of formation of distinct single colonies by the fungus, led to stable clones for both disruption constructs. Southern and PCR analyses proved gene disruption by single-copy homologous integration with a frequency of approximately 60% for both genes; and the loss of tmk1 and tga3 transcript formation in the disruptants was demonstrated by RT-PCR.

Overexpression of the gene encoding HMG-CoA reductase in Saccharomyces cerevisiae for production of prenyl alcohols.

PubMed

Ohto, Chikara; Muramatsu, Masayoshi; Obata, Shusei; Sakuradani, Eiji; Shimizu, Sakayu

2009-04-01

To develop microbial production method for prenyl alcohols (e.g., (E,E)-farnesol (FOH), (E)-nerolidol (NOH), and (E,E,E)-geranylgeraniol (GGOH)), the genes encoding enzymes in the mevalonate and prenyl diphosphate pathways were overexpressed in Saccharomyces cerevisiae, and the resultant transformants were evaluated as to the production of these alcohols. Overexpression of the gene encoding hydroxymethylglutaryl (HMG)-CoA reductase was most effective among the genes tested. A derivative of S. cerevisiae ATCC 200589, which was selected through screening, was found to be the most suitable host for the production. On cultivation of the resultant transformant, in which the HMG-CoA reductase gene was overexpressed, in a 5-liter bench-scale jar fermenter for 7 d, the production of FOH, NOH, and GGOH reached 145.7, 98.8, and 2.46 mg/l, respectively.

Caring: Information for Family Day-Care Providers.

ERIC Educational Resources Information Center

California Univ., Berkeley. Cooperative Extension Service.

This series of leaflets provides information for family day care providers on nine topics. Age differences and developmental stages are emphasized. The first topic concerns ways to help young children get along with others. Self-esteem is emphasized, and methods for helping children develop self-esteem are listed. The second leaflet discusses…

[SAFE: Making Your Children Safer on Public Playgrounds.

ERIC Educational Resources Information Center

Thompson, Donna; Hudson, Susan D.

This collection of nine leaflets from the National Program for Playground Safety addresses the active role parents and other adults should take in ensuring playground safety for children. Four leaflets, each focusing on a topic related to a letter in the word "safe," provide suggestions to ensure playground safety. Leaflet…

Nuclear Energy and the Environment.

ERIC Educational Resources Information Center

International Atomic Energy Agency, Vienna (Austria).

"Nuclear Energy and the Environment" is a pocket folder of removable leaflets concerned with two major topics: Nuclear energy and Nuclear Techniques. Under Nuclear Energy, leaflets concerning the topics of "Radiation--A Fact of Life,""The Impact of a Fact: 1963 Test Ban Treaty,""Energy Needs and Nuclear Power,""Power Reactor Safety,""Transport,"…

prtH2, Not prtH, Is the Ubiquitous Cell Wall Proteinase Gene in Lactobacillus helveticus▿

PubMed Central

Genay, M.; Sadat, L.; Gagnaire, V.; Lortal, S.

2009-01-01

Lactobacillus helveticus strains possess an efficient proteolytic system that releases peptides which are essential for lactobacillus growth in various fermented dairy products and also affect textural properties or biological activities. Cell envelope proteinases (CEPs) are bacterial enzymes that hydrolyze milk proteins. In the case of L. helveticus, two CEPs with low percentages of amino acid identity have been described, i.e., PrtH and PrtH2. However, the distribution of the genes that encode CEPs still remains unclear, rendering it difficult to further control the formation of particular peptides. This study evaluated the diversity of genes that encode CEPs in a collection of strains of L. helveticus isolated from various biotopes, both in terms of the presence or absence of these genes and in terms of nucleotide sequence, and studied their transcription in dairy matrices. After defining three sets of primers for both the prtH and prtH2 genes, we studied the distribution of the genes by using PCR and Southern blotting experiments. The prtH2 gene was ubiquitous in the 29 strains of L. helveticus studied, whereas only 18 of them also exhibited the prtH gene. Sequencing of a 350-bp internal fragment of these genes revealed the existence of intraspecific diversity. Finally, expression of these two CEP-encoding genes was followed during the growth in dairy matrices of two strains, ITG LH77 and CNRZ32, which possess one and two CEP-encoding genes, respectively. Both genes were shown to be expressed by L. helveticus at each stage of growth in milk and at different stages of mini-Swiss-type cheese making and ripening. PMID:19286786

The Aquilegia JAGGED homolog promotes proliferation of adaxial cell types in both leaves and stems.

PubMed

Min, Ya; Kramer, Elena M

2017-10-01

In order to explore the functional conservation of JAGGED, a key gene involved in the sculpting of lateral organs in several model species, we identified its ortholog AqJAG in the lower eudicot species Aquilegia coerulea. We analyzed the expression patterns of AqJAG in various tissues and developmental stages, and used RNAi-based methods to generate knockdown phenotypes of AqJAG. AqJAG was strongly expressed in shoot apices, floral meristems, lateral root primordia and all lateral organ primordia. Silencing of AqJAG revealed a wide range of defects in the developing stems, leaves and flowers; strongest phenotypes include severe reduction of leaflet laminae due to a decrease in cell size and number, change of adaxial cell identity, outgrowth of laminar-like tissue on the inflorescence stem, and early arrest of floral meristems and floral organ primordia. Our results indicate that AqJAG plays a critical role in controlling primordia initiation and distal growth of floral organs, and laminar development of leaflets. Most strikingly, we demonstrated that AqJAG disproportionally controls the behavior of cells with adaxial identity in vegetative tissues, providing evidence of how cell proliferation is controlled in an identity-specific manner. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

The Arabidopsis thaliana ortholog of a purported maize cholinesterase gene encodes a GDSL-lipase

PubMed Central

Muralidharan, Mrinalini; Buss, Kristina; Larrimore, Katherine E.; Segerson, Nicholas A.; Kannan, Latha

2013-01-01

Acetylcholinesterase is an enzyme that is intimately associated with regulation of synaptic transmission in the cholinergic nervous system and in neuromuscular junctions of animals. However the presence of cholinesterase activity has been described also in non-metazoan organisms such as slime molds, fungi and plants. More recently, a gene purportedly encoding for acetylcholinesterase was cloned from maize. We have cloned the Arabidopsis thaliana homolog of the Zea mays gene, At3g26430, and studied its biochemical properties. Our results indicate that the protein encoded by the gene exhibited lipase activity with preference to long chain substrates but did not hydrolyze choline esters. The At3g26430 protein belongs to the SGNH clan of serine hydrolases, and more specifically to the GDS(L) lipase family. PMID:23430565

Genetic analysis reveals the identity of the photoreceptor for phototaxis in hormogonium filaments of Nostoc punctiforme.

PubMed

Campbell, Elsie L; Hagen, Kari D; Chen, Rui; Risser, Douglas D; Ferreira, Daniela P; Meeks, John C

2015-02-15

In cyanobacterial Nostoc species, substratum-dependent gliding motility is confined to specialized nongrowing filaments called hormogonia, which differentiate from vegetative filaments as part of a conditional life cycle and function as dispersal units. Here we confirm that Nostoc punctiforme hormogonia are positively phototactic to white light over a wide range of intensities. N. punctiforme contains two gene clusters (clusters 2 and 2i), each of which encodes modular cyanobacteriochrome-methyl-accepting chemotaxis proteins (MCPs) and other proteins that putatively constitute a basic chemotaxis-like signal transduction complex. Transcriptional analysis established that all genes in clusters 2 and 2i, plus two additional clusters (clusters 1 and 3) with genes encoding MCPs lacking cyanobacteriochrome sensory domains, are upregulated during the differentiation of hormogonia. Mutational analysis determined that only genes in cluster 2i are essential for positive phototaxis in N. punctiforme hormogonia; here these genes are designated ptx (for phototaxis) genes. The cluster is unusual in containing complete or partial duplicates of genes encoding proteins homologous to the well-described chemotaxis elements CheY, CheW, MCP, and CheA. The cyanobacteriochrome-MCP gene (ptxD) lacks transmembrane domains and has 7 potential binding sites for bilins. The transcriptional start site of the ptx genes does not resemble a sigma 70 consensus recognition sequence; moreover, it is upstream of two genes encoding gas vesicle proteins (gvpA and gvpC), which also are expressed only in the hormogonium filaments of N. punctiforme. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

A Disease-causing Mutation Illuminates the Protein Membrane Topology of the Kidney-expressed Prohibitin Homology (PHB) Domain Protein Podocin*

PubMed Central

Schurek, Eva-Maria; Völker, Linus A.; Tax, Judit; Lamkemeyer, Tobias; Rinschen, Markus M.; Ungrue, Denise; Kratz, John E.; Sirianant, Lalida; Kunzelmann, Karl; Chalfie, Martin; Schermer, Bernhard; Benzing, Thomas; Höhne, Martin

2014-01-01

Mutations in the NPHS2 gene are a major cause of steroid-resistant nephrotic syndrome, a severe human kidney disorder. The NPHS2 gene product podocin is a key component of the slit diaphragm cell junction at the kidney filtration barrier and part of a multiprotein-lipid supercomplex. A similar complex with the podocin ortholog MEC-2 is required for touch sensation in Caenorhabditis elegans. Although podocin and MEC-2 are membrane-associated proteins with a predicted hairpin-like structure and amino and carboxyl termini facing the cytoplasm, this membrane topology has not been convincingly confirmed. One particular mutation that causes kidney disease in humans (podocinP118L) has also been identified in C. elegans in genetic screens for touch insensitivity (MEC-2P134S). Here we show that both mutant proteins, in contrast to the wild-type variants, are N-glycosylated because of the fact that the mutant C termini project extracellularly. PodocinP118L and MEC-2P134S did not fractionate in detergent-resistant membrane domains. Moreover, mutant podocin failed to activate the ion channel TRPC6, which is part of the multiprotein-lipid supercomplex, indicative of the fact that cholesterol recruitment to the ion channels, an intrinsic function of both proteins, requires C termini facing the cytoplasmic leaflet of the plasma membrane. Taken together, this study demonstrates that the carboxyl terminus of podocin/MEC-2 has to be placed at the inner leaflet of the plasma membrane to mediate cholesterol binding and contribute to ion channel activity, a prerequisite for mechanosensation and the integrity of the kidney filtration barrier. PMID:24596097

Identification of an Amino Acid Domain Encoded by the Capsid Protein Gene of Porcine Circovirus Type 2 that Modulates Viral Protein Distribution During Replication

USDA-ARS?s Scientific Manuscript database

Previous work showed that distinct amino acid motifs are encoded by the Rep, Cap and ORF3 genes of two subgroups of porcine circoviruses (PCV), PCV2a and PCV2b. At a specific location of the gene, a certain amino acid residue or sequence is preferred. Specifically, two amino acid domains located in ...

Generation of α1,3-galactosyltransferase and cytidine monophospho-N-acetylneuraminic acid hydroxylase gene double-knockout pigs

PubMed Central

MIYAGAWA, Shuji; MATSUNARI, Hitomi; WATANABE, Masahito; NAKANO, Kazuaki; UMEYAMA, Kazuhiro; SAKAI, Rieko; TAKAYANAGI, Shuko; TAKEISHI, Toki; FUKUDA, Tooru; YASHIMA, Sayaka; MAEDA, Akira; EGUCHI, Hiroshi; OKUYAMA, Hiroomi; NAGAYA, Masaki; NAGASHIMA, Hiroshi

2015-01-01

Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) are new tools for producing gene knockout (KO) animals. The current study reports produced genetically modified pigs, in which two endogenous genes were knocked out. Porcine fibroblast cell lines were derived from homozygous α1,3-galactosyltransferase (GalT) KO pigs. These cells were subjected to an additional KO for the cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) gene. A pair of ZFN-encoding mRNAs targeting exon 8 of the CMAH gene was used to generate the heterozygous CMAH KO cells, from which cloned pigs were produced by somatic cell nuclear transfer (SCNT). One of the cloned pigs obtained was re-cloned after additional KO of the remaining CMAH allele using the same ZFN-encoding mRNAs to generate GalT/CMAH-double homozygous KO pigs. On the other hand, the use of TALEN-encoding mRNAs targeting exon 7 of the CMAH gene resulted in efficient generation of homozygous CMAH KO cells. These cells were used for SCNT to produce cloned pigs homozygous for a double GalT/CMAH KO. These results demonstrate that the combination of TALEN-encoding mRNA, in vitro selection of the nuclear donor cells and SCNT provides a robust method for generating KO pigs. PMID:26227017

Generation of α1,3-galactosyltransferase and cytidine monophospho-N-acetylneuraminic acid hydroxylase gene double-knockout pigs.

PubMed

Miyagawa, Shuji; Matsunari, Hitomi; Watanabe, Masahito; Nakano, Kazuaki; Umeyama, Kazuhiro; Sakai, Rieko; Takayanagi, Shuko; Takeishi, Toki; Fukuda, Tooru; Yashima, Sayaka; Maeda, Akira; Eguchi, Hiroshi; Okuyama, Hiroomi; Nagaya, Masaki; Nagashima, Hiroshi

2015-01-01

Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) are new tools for producing gene knockout (KO) animals. The current study reports produced genetically modified pigs, in which two endogenous genes were knocked out. Porcine fibroblast cell lines were derived from homozygous α1,3-galactosyltransferase (GalT) KO pigs. These cells were subjected to an additional KO for the cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) gene. A pair of ZFN-encoding mRNAs targeting exon 8 of the CMAH gene was used to generate the heterozygous CMAH KO cells, from which cloned pigs were produced by somatic cell nuclear transfer (SCNT). One of the cloned pigs obtained was re-cloned after additional KO of the remaining CMAH allele using the same ZFN-encoding mRNAs to generate GalT/CMAH-double homozygous KO pigs. On the other hand, the use of TALEN-encoding mRNAs targeting exon 7 of the CMAH gene resulted in efficient generation of homozygous CMAH KO cells. These cells were used for SCNT to produce cloned pigs homozygous for a double GalT/CMAH KO. These results demonstrate that the combination of TALEN-encoding mRNA, in vitro selection of the nuclear donor cells and SCNT provides a robust method for generating KO pigs.

Effect of sypQ gene on poly-N-acetylglucosamine biosynthesis in Vibrio parahaemolyticus and its role in infection process.

PubMed

Ye, Libin; Zheng, Xiaolin; Zheng, Hongjian

2014-04-01

The syp locus includes four genes encoding putative regulators, six genes encoding glycosyltransferases, two encoding export proteins, and six other genes encoding unidentified functional proteins associated with biofilm formation and symbiotic colonization. However, the individual functions of the respective genes remain unclear. Amino acid alignment indicates that sypQ is presumably involved in biosynthesizing poly-N-acetylglucosamine (PNAG), which is proposed to be a critical virulence factor in pathogen infection and is regarded as a target for protective immunity against a variety of Gram-negative/positive pathogens. However, no evidence showing that Vibrio parahaemolyticus also produces PNAG has been reported. Herein, the V. parahaemolyticus is confirmed to possess potential for producing PNAG for the first time. Our results indicated that gene sypQ is associated with PNAG biosynthesis and PNAG is involved in pathogen colonization. We propose that the function of pgaC in Escherichia coli could be taken over by sypQ from V. parahaemolyticus. We also tested whether PNAG can be used as a target against V. parahaemolyticus when it infects Pseudosciaena crocea. Our results showed that PNAG isolated from V. parahaemolyticus is an effective agent for decreasing V. parahaemolyticus invasion, implying that PNAG could be used to develop an effective vaccine against V. parahaemolyticus infection.

Development of a polymerase chain reaction to distinguish monocellate cobra (Naja khouthia) bites from other common Thai snake species, using both venom extracts and bite-site swabs.

PubMed

Suntrarachun, S; Pakmanee, N; Tirawatnapong, T; Chanhome, L; Sitprija, V

2001-07-01

A PCR technique was used in this study to identify and distinguish monocellate cobra snake bites using snake venoms and swab specimens from snake bite-sites in mice from bites by other common Thai snakes. The sequences of nucleotide primers were selected for the cobrotoxin-encoding gene from the Chinese cobra (Naja atra) since the sequences of monocellate cobra (Naja kaouthia) venom are still unknown. However, the 113-bp fragment of cDNA of the cobrotoxin-encoding gene was detected in the monocellate cobra venom using RT-PCR. This gene was not found in the venoms of Ophiophagus hannah (king cobra), Bungarus fasciatus (banded krait), Daboia russelii siamensis (Siamese Russell's Viper, and Calloselasma rhodostoma (Malayan pit viper). Moreover, direct PCR could detect a 665-bp fragment of the cobrotoxin-encoding gene in the monocellate cobra venom but not the other snake venoms. Likewise, this gene was only observed in swab specimens from cobra snake bite-sites in mice. This is the first report demonstrating the ability of PCR to detect the cobrotoxin-encoding gene from snake venoms and swab specimens. Further studies are required for identification of this and other snakes from the bite-sites on human skin.

Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate in Alcaligenes eutrophus JMP134(pJP4).

PubMed Central

Don, R H; Weightman, A J; Knackmuss, H J; Timmis, K N

1985-01-01

Plasmid pJP4 permits its host bacterium, strain JMP134, to degrade and utilize as sole sources of carbon and energy 3-chlorobenzoate and 2,4-dichlorophenoxyacetic acid (R. H. Don and J. M. Pemberton, J. Bacteriol. 145:681-686, 1981). Mutagenesis of pJP4 by transposons Tn5 and Tn1771 enabled localization of five genes for enzymes involved in these catabolic pathways. Four of the genes, tfdB, tfdC, tfdD, and tfdE, encoded 2,4-dichlorophenol hydroxylase, dichlorocatechol 1,2-dioxygenase, chloromuconate cycloisomerase, and chlorodienelactone hydrolase, respectively. No function has been assigned to the fifth gene, tfdF, although it may encode a trans-chlorodiene-lactone isomerase. Inactivation of genes tfdC, tfdD, and tfdE, which encode the transformation of dichlorocatechol to chloromaleylacetic acid, prevented host strain JMP134 from degrading both 3-chlorobenzoate and 2,4-dichlorophenoxyacetic acid, which indicates that the pathways for these two substrates utilize common enzymes for the dissimilation of chlorocatechols. Studies with cloned catabolic genes from pJP4 indicated that whereas all essential steps in the degradation of 2,4-dichlorophenoxyacetic acid are plasmid encoded, the conversion of 3-chlorobenzoate to chlorocatechol is specified by chromosomal genes. PMID:2981813

Parallel loss of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases and mtDNA-encoded tRNAs in Cnidaria.

PubMed

Haen, Karri M; Pett, Walker; Lavrov, Dennis V

2010-10-01

Unlike most animal mitochondrial (mt) genomes, which encode a set of 22 transfer RNAs (tRNAs) sufficient for mt protein synthesis, those of cnidarians have only retained one or two tRNA genes. Whether the missing cnidarian mt-tRNA genes relocated outside the main mt chromosome or were lost remains unclear. It is also unknown what impact the loss of tRNA genes had on other components of the mt translational machinery. Here, we explored the nuclear genome of the cnidarian Nematostella vectensis for the presence of mt-tRNA genes and their corresponding mt aminoacyl-tRNA synthetases (mt-aaRS). We detected no candidates for mt-tRNA genes and only two mt-aaRS orthologs. At the same time, we found that all but one cytosolic aaRS appear to be targeted to mitochondria. These results indicate that the loss of mt-tRNAs in Cnidaria is genuine and occurred in parallel with the loss of nuclear-encoded mt-aaRS. Our phylogenetic analyses of individual aaRS revealed that although the nearly total loss of mt-aaRS is rare, aaRS gene deletion and replacement have occurred throughout the evolution of Metazoa.

Expression and characterization of hyperthermostable exo-polygalacturonase RmGH28 from Rhodothermus marinus

USDA-ARS?s Scientific Manuscript database

The gene RmGH28 from the organism Rhodothermus marinus putatively encoding a glycosyl hydrolase family 28 polygalacturonase was expressed in E. coli, and the enzyme purified and biochemically characterized. The gene was found to encode an exo- polygalacturonase, with galacturonic acid monomer and th...

Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

USDA-ARS?s Scientific Manuscript database

Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants. The availability of genomic data of the two diploid cotton species, Gossypium arboreum and Gossypium raimondii, and the two allotetraploid cotton species, Gossypium hirsutum (TM-1) and Gossypium ...

The pine Pschi4 promoter directs wound-induced transcription

Treesearch

Haiguo Wu; Charles H. Michler; Liborio LaRussa; John M. Davis

1999-01-01

Mechanical wounding stimulates the accumulation of Pschi4 transcripts (encoding a putative extracellular chitinase) in pine trees. To gain insight into the transcriptional regulatory region(s) in this gymnosperm defense gene, the 5'-flanking region of Pschi4 was fused to the uidA reporter gene encoding -...

Amino acid substitutions in the VanS sensor of the VanA-type vancomycin-resistant Enterococcus strains result in high-level vancomycin resistance and low-level teicoplanin resistance.

PubMed

Hashimoto, Y; Tanimoto, K; Ozawa, Y; Murata, T; Ike, Y

2000-04-15

The vancomycin-resistant enterococci GV1, GV2 and GV3, which were isolated from droppings from broiler farms in Japan have been characterized as VanA-type VRE, which express high-level vancomycin resistance (256 or 512 microg ml(-1), MIC) and low-level teicoplanin resistance (1 or 2 microg ml(-1), MIC). The vancomycin resistances were encoded on plasmids. The vancomycin resistance conjugative plasmid pMG2 was isolated from the GV2 strain. The VanA determinant of pMG2 showed the same genetic organization as that of the VanA genes encoded on the representative transposon Tn1546, which comprises vanRSHAXYZ. The nucleotide sequences of all the genes, except the gene related to the vanS gene on Tn1546, were completely identical to the genes encoded on Tn1546. Three amino acid substitutions in the N-terminal region of the deduced VanS were detected in the nucleotide sequence of vanS encoded on pMG2. There were also three amino acid substitutions in the vanS gene of the GV1 and GV3 strains in the same positions as in the vanS gene of pMG2. Vancomycin induced the increased teicoplanin resistance in these strains.

[Cloning, mutagenesis and symbiotic phenotype of three lipid transfer protein encoding genes from Mesorhizobium huakuii 7653R].

PubMed

Li, Yanan; Zeng, Xiaobo; Zhou, Xuejuan; Li, Youguo

2016-12-04

Lipid transfer protein superfamily is involved in lipid transport and metabolism. This study aimed to construct mutants of three lipid transfer protein encoding genes in Mesorhizobium huakuii 7653R, and to study the phenotypes and function of mutations during symbiosis with Astragalus sinicus. We used bioinformatics to predict structure characteristics and biological functions of lipid transfer proteins, and conducted semi-quantitative and fluorescent quantitative real-time PCR to analyze the expression levels of target genes in free-living and symbiotic conditions. Using pK19mob insertion mutagenesis to construct mutants, we carried out pot plant experiments to observe symbiotic phenotypes. MCHK-5577, MCHK-2172 and MCHK-2779 genes encoding proteins belonged to START/RHO alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) superfamily, involved in lipid transport or metabolism, and were identical to M. loti at 95% level. Gene relative transcription level of the three genes all increased compared to free-living condition. We obtained three mutants. Compared with wild-type 7653R, above-ground biomass of plants and nodulenitrogenase activity induced by the three mutants significantly decreased. Results indicated that lipid transfer protein encoding genes of Mesorhizobium huakuii 7653R may play important roles in symbiotic nitrogen fixation, and the mutations significantly affected the symbiotic phenotypes. The present work provided a basis to study further symbiotic function mechanism associated with lipid transfer proteins from rhizobia.

Molecular characterization and analysis of the acrB gene of Aspergillus nidulans: a gene identified by genetic interaction as a component of the regulatory network that includes the CreB deubiquitination enzyme.

PubMed Central

Boase, Natasha A; Lockington, Robin A; Adams, Julian R J; Rodbourn, Louise; Kelly, Joan M

2003-01-01

Mutations in the acrB gene, which were originally selected through their resistance to acriflavine, also result in reduced growth on a range of sole carbon sources, including fructose, cellobiose, raffinose, and starch, and reduced utilization of omega-amino acids, including GABA and beta-alanine, as sole carbon and nitrogen sources. The acrB2 mutation suppresses the phenotypic effects of mutations in the creB gene that encodes a regulatory deubiquitinating enzyme, and in the creC gene that encodes a WD40-repeat-containing protein. Thus AcrB interacts with a regulatory network controlling carbon source utilization that involves ubiquitination and deubiquitination. The acrB gene was cloned and physically analyzed, and it encodes a novel protein that contains three putative transmembrane domains and a coiled-coil region. AcrB may play a role in the ubiquitination aspect of this regulatory network. PMID:12750323

Cloning and characterization of the nagA gene that encodes beta-n-acetylglucosaminidase from Aspergillus nidulans and its expression in Aspergillus oryzae.

PubMed

Kim, Sunhwa; Matsuo, Ichiro; Ajisaka, Katsumi; Nakajima, Harushi; Kitamoto, Katsuhiko

2002-10-01

We isolated a beta-N-acetylglucosaminidase encoding gene and its cDNA from the filamentous fungus Aspergillus nidulans, and designated it nagA. The nagA gene contained no intron and encoded a polypeptide of 603 amino acids with a putative 19-amino acid signal sequence. The deduced amino acid sequence was very similar to the sequence of Candida albicans Hex1 and Trichoderma harzianum Nag1. Yeast cells containing the nagA cDNA under the control of the GAL1 promoter expressed beta-N-acetylglucosaminidase activity. The chromosomal nagA gene of A. nidulans was disrupted by replacement with the argB marker gene. The disruptant strains expressed low levels of beta-N-acetylglucosaminidase activity and showed poor growth on a medium containing chitobiose as a carbon source. Aspergillus oryzae strain carrying the nagA gene under the control of the improved glaA promoter produced large amounts of beta-N-acetylglucosaminidase in a wheat bran solid culture.

Cloning and heterologous expression of the antibiotic peptide (ABP) genes from Rhizopus oligosporus NBRC 8631.

PubMed

Yamada, Osamu; Sakamoto, Kazutoshi; Tominaga, Mihoko; Nakayama, Tasuku; Koseki, Takuya; Fujita, Akiko; Akita, Osamu

2005-03-01

We carried out protein sequencing of purified Antibiotic Peptide (ABP), and cloned two genes encoding this peptide as abp1 and abp2, from Rhizopus oligosporus NBRC 8631. Both genes contain an almost identical 231-bp segment, with only 3 nucleotide substitutions, encoding a 77 amino acid peptide. The abp gene product comprises a 28 amino acid signal sequence and a 49 amino acid mature peptide. Northern blot analysis showed that at least one of the abp genes is transcribed in R. oligosporus NBRC 8631. A truncated form of abp1 encoding only the mature peptide was fused with the alpha-factor signal peptide and engineered for expression in Pichia pastoris SMD1168H. Culture broth of the recombinant Pichia displayed ABP activity against Bacillus subtilis NBRC 3335 after induction of heterologous gene expression. This result indicates that mature ABP formed the active structure without the aid of other factors from R. oligosporus, and was secreted.

Capturing novel mouse genes encoding chromosomal and other nuclear proteins.

PubMed

Tate, P; Lee, M; Tweedie, S; Skarnes, W C; Bickmore, W A

1998-09-01

The burgeoning wealth of gene sequences contrasts with our ignorance of gene function. One route to assigning function is by determining the sub-cellular location of proteins. We describe the identification of mouse genes encoding proteins that are confined to nuclear compartments by splicing endogeneous gene sequences to a promoterless betageo reporter, using a gene trap approach. Mouse ES (embryonic stem) cell lines were identified that express betageo fusions located within sub-nuclear compartments, including chromosomes, the nucleolus and foci containing splicing factors. The sequences of 11 trapped genes were ascertained, and characterisation of endogenous protein distribution in two cases confirmed the validity of the approach. Three novel proteins concentrated within distinct chromosomal domains were identified, one of which appears to be a serine/threonine kinase. The sequence of a gene whose product co-localises with splicesome components suggests that this protein may be an E3 ubiquitin-protein ligase. The majority of the other genes isolated represent novel genes. This approach is shown to be a powerful tool for identifying genes encoding novel proteins with specific sub-nuclear localisations and exposes our ignorance of the protein composition of the nucleus. Motifs in two of the isolated genes suggest new links between cellular regulatory mechanisms (ubiquitination and phosphorylation) and mRNA splicing and chromosome structure/function.

Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters

PubMed Central

WANG, JIACHEN; DASGUPTA, INDRANI; FOX, GEORGE E.

2009-01-01

The genomic associations of the archaeal ribosomal proteins, (r-proteins), were examined in detail. The archaeal versions of the universal r-protein genes are typically in clusters similar or identical and to those found in bacteria. Of the 35 nonuniversal archaeal r-protein genes examined, the gene encoding L18e was found to be associated with the conserved L13 cluster, whereas the genes for S4e, L32e and L19e were found in the archaeal version of the spc operon. Eleven nonuniversal protein genes were not associated with any common genomic context. Of the remaining 19 protein genes, 17 were convincingly assigned to one of 10 previously unrecognized gene clusters. Examination of the gene content of these clusters revealed multiple associations with genes involved in the initiation of protein synthesis, transcription or other cellular processes. The lack of such associations in the universal clusters suggests that initially the ribosome evolved largely independently of other processes. More recently it likely has evolved in concert with other cellular systems. It was also verified that a second copy of the gene encoding L7ae found in some bacteria is actually a homolog of the gene encoding L30e and should be annotated as such. PMID:19478915

Identification of candidate transmission-blocking antigen genes in Theileria annulata and related vector-borne apicomplexan parasites.

PubMed

Lempereur, Laetitia; Larcombe, Stephen D; Durrani, Zeeshan; Karagenc, Tulin; Bilgic, Huseyin Bilgin; Bakirci, Serkan; Hacilarlioglu, Selin; Kinnaird, Jane; Thompson, Joanne; Weir, William; Shiels, Brian

2017-06-05

Vector-borne apicomplexan parasites are a major cause of mortality and morbidity to humans and livestock globally. The most important disease syndromes caused by these parasites are malaria, babesiosis and theileriosis. Strategies for control often target parasite stages in the mammalian host that cause disease, but this can result in reservoir infections that promote pathogen transmission and generate economic loss. Optimal control strategies should protect against clinical disease, block transmission and be applicable across related genera of parasites. We have used bioinformatics and transcriptomics to screen for transmission-blocking candidate antigens in the tick-borne apicomplexan parasite, Theileria annulata. A number of candidate antigen genes were identified which encoded amino acid domains that are conserved across vector-borne Apicomplexa (Babesia, Plasmodium and Theileria), including the Pfs48/45 6-cys domain and a novel cysteine-rich domain. Expression profiling confirmed that selected candidate genes are expressed by life cycle stages within infected ticks. Additionally, putative B cell epitopes were identified in the T. annulata gene sequences encoding the 6-cys and cysteine rich domains, in a gene encoding a putative papain-family cysteine peptidase, with similarity to the Plasmodium SERA family, and the gene encoding the T. annulata major merozoite/piroplasm surface antigen, Tams1. Candidate genes were identified that encode proteins with similarity to known transmission blocking candidates in related parasites, while one is a novel candidate conserved across vector-borne apicomplexans and has a potential role in the sexual phase of the life cycle. The results indicate that a 'One Health' approach could be utilised to develop a transmission-blocking strategy effective against vector-borne apicomplexan parasites of animals and humans.

Identification of β-propeller phytase-encoding genes in culturable Paenibacillus and Bacillus spp. from the rhizosphere of pasture plants on volcanic soils.

PubMed

Jorquera, Milko A; Crowley, David E; Marschner, Petra; Greiner, Ralf; Fernández, María Teresa; Romero, Daniela; Menezes-Blackburn, Daniel; De La Luz Mora, María

2011-01-01

Phytate is one of the most abundant sources of organic phosphorus (P) in soils, but must be mineralized by phytase-producing bacteria to release P for plant uptake. Microbial inoculants based on Bacillus spp. have been developed commercially, but few studies have evaluated the ecology of these bacteria in the rhizosphere or the types of enzymes that they produce. Here, we studied the diversity of aerobic endospore-forming bacteria (EFB) with the ability to mineralize phytate in the rhizosphere of pasture plants grown in volcanic soils of southern Chile. PCR methods were used to detect candidate phytase-encoding genes and to identify EFB bacteria that carry these genes. This study revealed that the phytate-degrading EFB populations of pasture plants included species of Paenibacillus and Bacillus, which carried genes encoding β-propeller phytase (BPP). Assays of enzymatic activity confirmed the ability of these rhizosphere isolates to degrade phytate. The phytase-encoding genes described here may prove valuable as molecular markers to evaluate the role of EFB in organic P mobilization in the rhizosphere. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Isolation and characterization of major histocompatibility complex class IIB genes from the nurse shark.

PubMed

Bartl, S; Weissman, I L

1994-01-04

The major histocompatibility complex (MHC) contains a set of linked genes which encode cell surface proteins involved in the binding of small peptide antigens for their subsequent recognition by T lymphocytes. MHC proteins share structural features and the presence and location of polymorphic residues which play a role in the binding of antigens. In order to compare the structure of these molecules and gain insights into their evolution, we have isolated two MHC class IIB genes from the nurse shark, Ginglymostoma cirratum. Two clones, most probably alleles, encode proteins which differ by 13 amino acids located in the putative antigen-binding cleft. The protein structure and the location of polymorphic residues are similar to their mammalian counterparts. Although these genes appear to encode a typical MHC protein, no T-cell-mediated responses have been demonstrated in cartilaginous fish. The nurse shark represents the most phylogenetically primitive organism in which both class IIA [Kasahara, M., Vazquez, M., Sato, K., McKinney, E.C. & Flajnik, M.F. (1992) Proc. Natl. Acad. Sci USA 89, 6688-6692] and class IIB genes, presumably encoding the alpha/beta heterodimer, have been isolated.

The Retrovirus pol Gene Encodes a Product Required for DNA Integration: Identification of a Retrovirus int Locus

NASA Astrophysics Data System (ADS)

Panganiban, Antonito T.; Temin, Howard M.

1984-12-01

We mutagenized cloned spleen necrosis virus DNA to identify a region of the retrovirus genome encoding a polypeptide required for integration of viral DNA. Five plasmids bearing different lesions in the 3' end of the pol gene were examined for the ability to integrate or replicate following transfection of chicken embryo fibroblasts. Transfection with one of these DNAs resulted in the generation of mutant virus incapable of integrating but able to replicate at low levels; this phenotype is identical to that of mutants bearing alterations in the cis-acting region, att. To determine whether the 3' end of the pol gene encodes a protein that interacts with att, we did a complementation experiment. Cells were first infected with an att- virus and then superinfected with the integration-deficient virus containing a lesion in the pol gene and a wild-type att site. The results showed that the att- virus provided a trans-acting function allowing integration of viral DNA derived from the mutant bearing a wild-type att site. Thus, the 3' end of the pol gene serves as an ``int'' locus and encodes a protein mediating integration of retrovirus DNA through interaction with att.

Cloning and characterization of largemouth bass ( Micropterus salmoides) myostatin encoding gene and its promoter

NASA Astrophysics Data System (ADS)

Li, Shengjie; Bai, Junjie; Wang, Lin

2008-08-01

Myostatin or GDF-8, a member of the transforming growth factor-β (TGF-β) superfamily, has been demonstrated to be a negative regulator of skeletal muscle mass in mammals. In the present study, we obtained a 5.64 kb sequence of myostatin encoding gene and its promoter from largemouth bass ( Micropterus salmoides). The myostatin encoding gene consisted of three exons (488 bp, 371 bp and 1779 bp, respectively) and two introns (390 bp and 855 bp, respectively). The intron-exon boundaries were conservative in comparison with those of mammalian myostatin encoding genes, whereas the size of introns was smaller than that of mammals. Sequence analysis of 1.569 kb of the largemouth bass myostatin gene promoter region revealed that it contained two TATA boxes, one CAAT box and nine putative E-boxes. Putative muscle growth response elements for myocyte enhancer factor 2 (MEF2), serum response factor (SRF), activator protein 1 (AP1), etc., and muscle-specific Mt binding site (MTBF) were also detected. Some of the transcription factor binding sites were conserved among five teleost species. This information will be useful for studying the transcriptional regulation of myostatin in fish.

A member of a new plant gene family encoding a meprin and TRAF homology (MATH) domain-containing protein is involved in restriction of long distance movement of plant viruses

PubMed Central

Cosson, Patrick; Sofer, Luc; Schurdi-Levraud, Valérie

2010-01-01

Restriction of long distance movement of several potyviruses in Arabidopsis thaliana is controlled by at least three dominant restricted TEV movement (RTM) genes, named RTM1, RTM2 and RTM3 and acts as a non-conventional resistance. RTM1 encodes a protein belonging to the jacalin family and RTM2 encodes a protein which has similarities to small heat shock proteins. The recent cloning of RTM3 which encodes a protein belonging to an unknown protein family of 29 members that has a meprin and TRAF homology (MATH) domain in its N-terminal region and a coiled-coil (CC) domain at its C-terminal end is an important breakthrough for a better understanding of this resistance process. Not only the third gene involved in this resistance has been identified and has allowed revealing a new gene family in plant but the discovery that the RTM3 protein interacts directly with RTM1 strongly suggests that the RTM proteins form a multimeric complex. However, these data also highlight striking similarities of the RTM resistance with the well known R-gene mediated resistance. PMID:20930558

Characterization of Urtica dioica agglutinin isolectins and the encoding gene family.

PubMed

Does, M P; Ng, D K; Dekker, H L; Peumans, W J; Houterman, P M; Van Damme, E J; Cornelissen, B J

1999-01-01

Urtica dioica agglutinin (UDA) has previously been found in roots and rhizomes of stinging nettles as a mixture of UDA-isolectins. Protein and cDNA sequencing have shown that mature UDA is composed of two hevein domains and is processed from a precursor protein. The precursor contains a signal peptide, two in-tandem hevein domains, a hinge region and a carboxyl-terminal chitinase domain. Genomic fragments encoding precursors for UDA-isolectins have been amplified by five independent polymerase chain reactions on genomic DNA from stinging nettle ecotype Weerselo. One amplified gene was completely sequenced. As compared to the published cDNA sequence, the genomic sequence contains, besides two basepair substitutions, two introns located at the same positions as in other plant chitinases. By partial sequence analysis of 40 amplified genes, 16 different genes were identified which encode seven putative UDA-isolectins. The deduced amino acid sequences share 78.9-98.9% identity. In extracts of roots and rhizomes of stinging nettle ecotype Weerselo six out of these seven isolectins were detected by mass spectrometry. One of them is an acidic form, which has not been identified before. Our results demonstrate that UDA is encoded by a large gene family.

The Elicitor Protein AsES Induces a Systemic Acquired Resistance Response Accompanied by Systemic Microbursts and Micro-Hypersensitive Responses in Fragaria ananassa.

PubMed

Hael-Conrad, Verónica; Perato, Silvia Marisa; Arias, Marta Eugenia; Martínez-Zamora, Martín Gustavo; Di Peto, Pía de Los Ángeles; Martos, Gustavo Gabriel; Castagnaro, Atilio Pedro; Díaz-Ricci, Juan Carlos; Chalfoun, Nadia Regina

2018-01-01

The elicitor AsES (Acremonium strictum elicitor subtilisin) is a 34-kDa subtilisin-like protein secreted by the opportunistic fungus Acremonium strictum. AsES activates innate immunity and confers resistance against anthracnose and gray mold diseases in strawberry plants (Fragaria × ananassa Duch.) and the last disease also in Arabidopsis. In the present work, we show that, upon AsES recognition, a cascade of defense responses is activated, including: calcium influx, biphasic oxidative burst (O 2 ⋅- and H 2 O 2 ), hypersensitive cell-death response (HR), accumulation of autofluorescent compounds, cell-wall reinforcement with callose and lignin deposition, salicylic acid accumulation, and expression of defense-related genes, such as FaPR1, FaPG1, FaMYB30, FaRBOH-D, FaRBOH-F, FaCHI23, and FaFLS. All these responses occurred following a spatial and temporal program, first induced in infiltrated leaflets (local acquired resistance), spreading out to untreated lateral leaflets, and later, to distal leaves (systemic acquired resistance). After AsES treatment, macro-HR and macro-oxidative bursts were localized in infiltrated leaflets, while micro-HRs and microbursts occurred later in untreated leaves, being confined to a single cell or a cluster of a few epidermal cells that differentiated from the surrounding ones. The differentiated cells initiated a time-dependent series of physiological and anatomical changes, evolving to idioblasts accumulating H 2 O 2 and autofluorescent compounds that blast, delivering its content into surrounding cells. This kind of systemic cell-death process in plants is described for the first time in response to a single elicitor. All data presented in this study suggest that AsES has the potential to activate a wide spectrum of biochemical and molecular defense responses in F. ananassa that may explain the induced protection toward pathogens of opposite lifestyle, like hemibiotrophic and necrotrophic fungi.

Host Cell Plasma Membrane Phosphatidylserine Regulates the Assembly and Budding of Ebola Virus

PubMed Central

Adu-Gyamfi, Emmanuel; Johnson, Kristen A.; Fraser, Mark E.; Scott, Jordan L.; Soni, Smita P.; Jones, Keaton R.; Digman, Michelle A.; Gratton, Enrico; Tessier, Charles R.

2015-01-01

ABSTRACT Lipid-enveloped viruses replicate and bud from the host cell where they acquire their lipid coat. Ebola virus, which buds from the plasma membrane of the host cell, causes viral hemorrhagic fever and has a high fatality rate. To date, little has been known about how budding and egress of Ebola virus are mediated at the plasma membrane. We have found that the lipid phosphatidylserine (PS) regulates the assembly of Ebola virus matrix protein VP40. VP40 binds PS-containing membranes with nanomolar affinity, and binding of PS regulates VP40 localization and oligomerization on the plasma membrane inner leaflet. Further, alteration of PS levels in mammalian cells inhibits assembly and egress of VP40. Notably, interactions of VP40 with the plasma membrane induced exposure of PS on the outer leaflet of the plasma membrane at sites of egress, whereas PS is typically found only on the inner leaflet. Taking the data together, we present a model accounting for the role of plasma membrane PS in assembly of Ebola virus-like particles. IMPORTANCE The lipid-enveloped Ebola virus causes severe infection with a high mortality rate and currently lacks FDA-approved therapeutics or vaccines. Ebola virus harbors just seven genes in its genome, and there is a critical requirement for acquisition of its lipid envelope from the plasma membrane of the human cell that it infects during the replication process. There is, however, a dearth of information available on the required contents of this envelope for egress and subsequent attachment and entry. Here we demonstrate that plasma membrane phosphatidylserine is critical for Ebola virus budding from the host cell plasma membrane. This report, to our knowledge, is the first to highlight the role of lipids in human cell membranes in the Ebola virus replication cycle and draws a clear link between selective binding and transport of a lipid across the membrane of the human cell and use of that lipid for subsequent viral entry. PMID:26136573

L-rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake.

PubMed

Tamayo-Ramos, Juan A; Flipphi, Michel; Pardo, Ester; Manzanares, Paloma; Orejas, Margarita

2012-02-21

Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus Aspergillus nidulans growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (rhaE) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/rhaA). Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (rhaE). The cDNA of rhaE was expressed in Saccharomyces cerevisiae and yielded pNP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse A. nidulans strains cultivated under different growth conditions indicate that rhaA and rhaE are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these rha genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression. The A. nidulans rhaE gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of rhaE and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, A. nidulans α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR.

L-Rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake

PubMed Central

2012-01-01

Background Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus Aspergillus nidulans growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (rhaE) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/rhaA). Results Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (rhaE). The cDNA of rhaE was expressed in Saccharomyces cerevisiae and yielded pNP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse A. nidulans strains cultivated under different growth conditions indicate that rhaA and rhaE are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these rha genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression. Conclusions The A. nidulans rhaE gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of rhaE and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, A. nidulans α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR. PMID:22353731

Typing of Panton-Valentine Leukocidin-Encoding Phages and lukSF-PV Gene Sequence Variation in Staphylococcus aureus from China.

PubMed

Zhao, Huanqiang; Hu, Fupin; Jin, Shu; Xu, Xiaogang; Zou, Yuhan; Ding, Baixing; He, Chunyan; Gong, Fang; Liu, Qingzhong

2016-01-01

Panton-Valentine leukocidin (PVL, encoded by lukSF-PV genes), a bi-component and pore-forming toxin, is carried by different staphylococcal bacteriophages. The prevalence of PVL in Staphylococcus aureus has been reported around the globe. However, the data on PVL-encoding phage types, lukSF-PV gene variation and chromosomal phage insertion sites for PVL-positive S. aureus are limited, especially in China. In order to obtain a more complete understanding of the molecular epidemiology of PVL-positive S. aureus, an integrated and modified PCR-based scheme was applied to detect the PVL-encoding phage types. Phage insertion locus and the lukSF-PV variant were determined by PCR and sequencing. Meanwhile, the genetic background was characterized by staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) gene polymorphisms typing, pulsed-field gel electrophoresis (PFGE) typing, accessory gene regulator (agr) locus typing and multilocus sequence typing (MLST). Seventy eight (78/1175, 6.6%) isolates possessed the lukSF-PV genes and 59.0% (46/78) of PVL-positive strains belonged to CC59 lineage. Eight known different PVL-encoding phage types were detected, and Φ7247PVL/ΦST5967PVL (n = 13) and ΦPVL (n = 12) were the most prevalent among them. While 25 (25/78, 32.1%) isolates, belonging to ST30, and ST59 clones, were unable to be typed by the modified PCR-based scheme. Single nucleotide polymorphisms (SNPs) were identified at five locations in the lukSF-PV genes, two of which were non-synonymous. Maximum-likelihood tree analysis of attachment sites sequences detected six SNP profiles for attR and eight for attL, respectively. In conclusion, the PVL-positive S. aureus mainly harbored Φ7247PVL/ΦST5967PVL and ΦPVL in the regions studied. lukSF-PV gene sequences, PVL-encoding phages, and phage insertion locus generally varied with lineages. Moreover, PVL-positive clones that have emerged worldwide likely carry distinct phages.

The vacuolar ATPase from Entamoeba histolytica: molecular cloning of the gene encoding for the B subunit and subcellular localization of the protein.

PubMed

Meléndez-Hernández, Mayra Gisela; Barrios, María Luisa Labra; Orozco, Esther; Luna-Arias, Juan Pedro

2008-12-23

Entamoeba histolytica is a professional phagocytic cell where the vacuolar ATPase plays a key role. This enzyme is a multisubunit complex that regulates pH in many subcellular compartments, even in those that are not measurably acidic. It participates in a wide variety of cellular processes such as endocytosis, intracellular transport and membrane fusion. The presence of a vacuolar type H+-ATPase in E. histolytica trophozoites has been inferred previously from inhibition assays of its activity, the isolation of the Ehvma1 and Ehvma3 genes, and by proteomic analysis of purified phagosomes. We report the isolation and characterization of the Ehvma2 gene, which encodes for the subunit B of the vacuolar ATPase. This polypeptide is a 55.3 kDa highly conserved protein with 34 to 80% identity to orthologous proteins from other species. Particularly, in silico studies showed that EhV-ATPase subunit B displays 78% identity and 90% similarity to its Dictyostelium ortholog. A 462 bp DNA fragment of the Ehvma2 gene was expressed in bacteria and recombinant polypeptide was used to raise mouse polyclonal antibodies. EhV-ATPase subunit B antibodies detected a 55 kDa band in whole cell extracts and in an enriched fraction of DNA-containing organelles named EhkOs. The V-ATPase subunit B was located by immunofluorescence and confocal microscopy in many vesicles, in phagosomes, plasma membrane and in EhkOs. We also identified the genes encoding for the majority of the V-ATPase subunits in the E. histolytica genome, and proposed a putative model for this proton pump. We have isolated the Ehvma2 gene which encodes for the V-ATPase subunit B from the E. histolytica clone A. This gene has a 154 bp intron and encodes for a highly conserved polypeptide. Specific antibodies localized EhV-ATPase subunit B in many vesicles, phagosomes, plasma membrane and in EhkOs. Most of the orthologous genes encoding for the EhV-ATPase subunits were found in the E. histolytica genome, indicating the conserved nature of V-ATPase in this parasite.

The complete chloroplast genome sequence of Dianthus superbus var. longicalycinus.

PubMed

Gurusamy, Raman; Lee, Do-Hyung; Park, SeonJoo

2016-05-01

The complete chloroplast genome (cpDNA) sequence of Dianthus superbus var. longicalycinus is an economically important traditional Chinese medicine was reported and characterized. The cpDNA of Dianthus superbus var. longicalycinus is 149,539 bp, with 36.3% GC content. A pair of inverted repeats (IRs) of 24,803 bp is separated by a large single-copy region (LSC, 82,805 bp) and a small single-copy region (SSC, 17,128 bp). It encodes 85 protein-coding genes, 36 tRNA genes and 8 rRNA genes. Of 129 individual genes, 13 genes encoded one intron and three genes have two introns.

Repressed expression of a gene for a basic helix-loop-helix protein causes a white flower phenotype in carnation

PubMed Central

Totsuka, Akane; Okamoto, Emi; Miyahara, Taira; Kouno, Takanobu; Cano, Emilio A.; Sasaki, Nobuhiro; Watanabe, Aiko; Tasaki, Keisuke; Nishihara, Masahiro; Ozeki, Yoshihiro

2018-01-01

In a previous study, two genes responsible for white flower phenotypes in carnation were identified. These genes encoded enzymes involved in anthocyanin synthesis, namely, flavanone 3-hydroxylase (F3H) and dihydroflavonol 4-reductase (DFR), and showed reduced expression in the white flower phenotypes. Here, we identify another candidate gene for white phenotype in carnation flowers using an RNA-seq analysis followed by RT-PCR. This candidate gene encodes a transcriptional regulatory factor of the basic helix-loop-helix (bHLH) type. In the cultivar examined here, both F3H and DFR genes produced active enzyme proteins; however, expression of DFR and of genes for enzymes involved in the downstream anthocyanin synthetic pathway from DFR was repressed in the absence of bHLH expression. Occasionally, flowers of the white flowered cultivar used here have red speckles and stripes on the white petals. We found that expression of bHLH occurred in these red petal segments and induced expression of DFR and the following downstream enzymes. Our results indicate that a member of the bHLH superfamily is another gene involved in anthocyanin synthesis in addition to structural genes encoding enzymes. PMID:29681756

Distribution of Suicin Gene Clusters in Streptococcus suis Serotype 2 Belonging to Sequence Types 25 and 28.

PubMed

Athey, Taryn B T; Vaillancourt, Katy; Frenette, Michel; Fittipaldi, Nahuel; Gottschalk, Marcelo; Grenier, Daniel

2016-01-01

Recently, we reported the purification and characterization of three distinct lantibiotics (named suicin 90-1330, suicin 3908, and suicin 65) produced by Streptococcus suis . In this study, we investigated the distribution of the three suicin lantibiotic gene clusters among serotype 2 S. suis strains belonging to sequence type (ST) 25 and ST28, the two dominant STs identified in North America. The genomes of 102 strains were interrogated for the presence of suicin gene clusters encoding suicins 90-1330, 3908, and 65. The gene cluster encoding suicin 65 was the most prevalent and mainly found among ST25 strains. In contrast, none of the genes related to suicin 90-1330 production were identified in 51 ST25 strains nor in 35/51 ST28 strains. However, the complete suicin 90-1330 gene cluster was found in ten ST28 strains, although some genes in the cluster were truncated in three of these isolates. The vast majority (101/102) of S. suis strains did not possess any of the genes encoding suicin 3908. In conclusion, this study indicates heterogeneous distribution of suicin genes in S. suis .

Screening of the Enterocin-Encoding Genes and Antimicrobial Activity in Enterococcus Species.

PubMed

Ogaki, Mayara Baptistucci; Rocha, Katia Real; Terra, MÁrcia Regina; Furlaneto, MÁrcia Cristina; Maia, Luciana Furlaneto

2016-06-28

In the current study, a total of 135 enterococci strains from different sources were screened for the presence of the enterocin-encoding genes entA, entP, entB, entL50A, and entL50B. The enterocin genes were present at different frequencies, with entA occurring the most frequently, followed by entP and entB; entL50A and L50B were not detected. The occurrence of single enterocin genes was higher than the occurrence of multiple enterocin gene combinations. The 80 isolates that harbor at least one enterocin-encoding gene (denoted "Gene(+) strains") were screened for antimicrobial activity. A total of 82.5% of the Gene(+) strains inhibited at least one of the indicator strains, and the isolates harboring multiple enterocin-encoding genes inhibited a larger number of indicator strains than isolates harboring a single gene. The indicator strains that exhibited growth inhibition included Listeria innocua strain CLIP 12612 (ATCC BAA-680), Listeria monocytogenes strain CDC 4555, Enterococcus faecalis ATCC 29212, Staphylococcus aureus ATCC 25923, S. aureus ATCC 29213, S. aureus ATCC 6538, Salmonella enteritidis ATCC 13076, Salmonella typhimurium strain UK-1 (ATCC 68169), and Escherichia coli BAC 49LT ETEC. Inhibition due to either bacteriophage lysis or cytolysin activity was excluded. The growth inhibition of antilisterial Gene+ strains was further tested under different culture conditions. Among the culture media formulations, the MRS agar medium supplemented with 2% (w/v) yeast extract was the best solidified medium for enterocin production. Our findings extend the current knowledge of enterocin-producing enterococci, which may have potential applications as biopreservatives in the food industry due to their capability of controlling food spoilage pathogens.

Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia

PubMed Central

2012-01-01

Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs) and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Findings Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. Conclusion To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants. PMID:22883984

Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia.

PubMed

Zuiter, Afnan Saeid; Sawwan, Jammal; Al Abdallat, Ayed

2012-08-10

Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs) and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants.

The euryhaline yeast Debaryomyces hansenii has two catalase genes encoding enzymes with differential activity profile.

PubMed

Segal-Kischinevzky, Claudia; Rodarte-Murguía, Beatriz; Valdés-López, Victor; Mendoza-Hernández, Guillermo; González, Alicia; Alba-Lois, Luisa

2011-03-01

Debaryomyces hansenii is a spoilage yeast able to grow in a variety of ecological niches, from seawater to dairy products. Results presented in this article show that (i) D. hansenii has an inherent resistance to H2O2 which could be attributed to the fact that this yeast has a basal catalase activity which is several-fold higher than that observed in Saccharomyces cerevisiae under the same culture conditions, (ii) D. hansenii has two genes (DhCTA1 and DhCTT1) encoding two catalase isozymes with a differential enzymatic activity profile which is not strictly correlated with a differential expression profile of the encoding genes.

Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in the southern United States.

PubMed

Sharma, Sandeep; Zaccaron, Alex Z; Ridenour, John B; Allen, Tom W; Conner, Kassie; Doyle, Vinson P; Price, Trey; Sikora, Edward; Singh, Raghuwinder; Spurlock, Terry; Tomaso-Peterson, Maria; Wilkerson, Tessie; Bluhm, Burton H

2018-04-01

The draft genome of Xylaria sp. isolate MSU_SB201401, causal agent of taproot decline of soybean in the southern U.S., is presented here. The genome assembly was 56.7 Mb in size with an L50 of 246. A total of 10,880 putative protein-encoding genes were predicted, including 647 genes encoding carbohydrate-active enzymes and 1053 genes encoding secreted proteins. This is the first draft genome of a plant-pathogenic Xylaria sp. associated with soybean. The draft genome of Xylaria sp. isolate MSU_SB201401 will provide an important resource for future experiments to determine the molecular basis of pathogenesis.

Cloning and characterization of a mouse gene with homology to the human von Hippel-Lindau disease tumor suppressor gene: implications for the potential organization of the human von Hippel-Lindau disease gene.

PubMed

Gao, J; Naglich, J G; Laidlaw, J; Whaley, J M; Seizinger, B R; Kley, N

1995-02-15

The human von Hippel-Lindau disease (VHL) gene has recently been identified and, based on the nucleotide sequence of a partial cDNA clone, has been predicted to encode a novel protein with as yet unknown functions [F. Latif et al., Science (Washington DC), 260: 1317-1320, 1993]. The length of the encoded protein and the characteristics of the cellular expressed protein are as yet unclear. Here we report the cloning and characterization of a mouse gene (mVHLh1) that is widely expressed in different mouse tissues and shares high homology with the human VHL gene. It predicts a protein 181 residues long (and/or 162 amino acids, considering a potential alternative start codon), which across a core region of approximately 140 residues displays a high degree of sequence identity (98%) to the predicted human VHL protein. High stringency DNA and RNA hybridization experiments and protein expression analyses indicate that this gene is the most highly VHL-related mouse gene, suggesting that it represents the mouse VHL gene homologue rather than a related gene sharing a conserved functional domain. These findings provide new insights into the potential organization of the VHL gene and nature of its encoded protein.

Plasmid-Encoded Tetracycline Efflux Pump Protein Alters Bacterial Stress Responses and Ecological Fitness of Acinetobacter oleivorans

PubMed Central

Hong, Hyerim; Jung, Jaejoon; Park, Woojun

2014-01-01

Acquisition of the extracellular tetracycline (TC) resistance plasmid pAST2 affected host gene expression and phenotype in the oil-degrading soil bacterium, Acinetobacter oleivorans DR1. Whole-transcriptome profiling of DR1 cells harboring pAST2 revealed that all the plasmid genes were highly expressed under TC conditions, and the expression levels of many host chromosomal genes were modulated by the presence of pAST2. The host energy burden imposed by replication of pAST2 led to (i) lowered ATP concentrations, (ii) downregulated expression of many genes involved in cellular growth, and (iii) reduced growth rate. Interestingly, some phenotypes were restored by deleting the plasmid-encoded efflux pump gene tetH, suggesting that the membrane integrity changes resulting from the incorporation of efflux pump proteins also resulted in altered host response under the tested conditions. Alteration of membrane integrity by tetH deletion was shown by measuring permeability of fluorescent probe and membrane hydrophobicity. The presence of the plasmid conferred peroxide and superoxide resistance to cells, but only peroxide resistance was diminished by tetH gene deletion, suggesting that the plasmid-encoded membrane-bound efflux pump protein provided peroxide resistance. The downregulation of fimbriae-related genes presumably led to reduced swimming motility, but this phenotype was recovered by tetH gene deletion. Our data suggest that not only the plasmid replication burden, but also its encoded efflux pump protein altered host chromosomal gene expression and phenotype, which also alters the ecological fitness of the host in the environment. PMID:25229538

Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster.

PubMed

Robertson, Hugh M; Warr, Coral G; Carlson, John R

2003-11-25

The insect chemoreceptor superfamily in Drosophila melanogaster is predicted to consist of 62 odorant receptor (Or) and 68 gustatory receptor (Gr) proteins, encoded by families of 60 Or and 60 Gr genes through alternative splicing. We include two previously undescribed Or genes and two previously undescribed Gr genes; two previously predicted Or genes are shown to be alternative splice forms. Three polymorphic pseudogenes and one highly defective pseudogene are recognized. Phylogenetic analysis reveals deep branches connecting multiple highly divergent clades within the Gr family, and the Or family appears to be a single highly expanded lineage within the superfamily. The genes are spread throughout the Drosophila genome, with some relatively recently diverged genes still clustered in the genome. The Gr5a gene on the X chromosome, which encodes a receptor for the sugar trehalose, has transposed from one such tandem cluster of six genes at cytological location 64, as has Gr61a, and all eight of these receptors might bind sugars. Analysis of intron evolution suggests that the common ancestor consisted of a long N-terminal exon encoding transmembrane domains 1-5 followed by three exons encoding transmembrane domains 6-7. As many as 57 additional introns have been acquired idiosyncratically during the evolution of the superfamily, whereas the ancestral introns and some of the older idiosyncratic introns have been lost at least 48 times independently. Altogether, these patterns of molecular evolution suggest that this is an ancient superfamily of chemoreceptors, probably dating back at least to the origin of the arthropods.

Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster

PubMed Central

Robertson, Hugh M.; Warr, Coral G.; Carlson, John R.

2003-01-01

The insect chemoreceptor superfamily in Drosophila melanogaster is predicted to consist of 62 odorant receptor (Or) and 68 gustatory receptor (Gr) proteins, encoded by families of 60 Or and 60 Gr genes through alternative splicing. We include two previously undescribed Or genes and two previously undescribed Gr genes; two previously predicted Or genes are shown to be alternative splice forms. Three polymorphic pseudogenes and one highly defective pseudogene are recognized. Phylogenetic analysis reveals deep branches connecting multiple highly divergent clades within the Gr family, and the Or family appears to be a single highly expanded lineage within the superfamily. The genes are spread throughout the Drosophila genome, with some relatively recently diverged genes still clustered in the genome. The Gr5a gene on the X chromosome, which encodes a receptor for the sugar trehalose, has transposed from one such tandem cluster of six genes at cytological location 64, as has Gr61a, and all eight of these receptors might bind sugars. Analysis of intron evolution suggests that the common ancestor consisted of a long N-terminal exon encoding transmembrane domains 1-5 followed by three exons encoding transmembrane domains 6-7. As many as 57 additional introns have been acquired idiosyncratically during the evolution of the superfamily, whereas the ancestral introns and some of the older idiosyncratic introns have been lost at least 48 times independently. Altogether, these patterns of molecular evolution suggest that this is an ancient superfamily of chemoreceptors, probably dating back at least to the origin of the arthropods. PMID:14608037

Plasmid-encoded tetracycline efflux pump protein alters bacterial stress responses and ecological fitness of Acinetobacter oleivorans.

PubMed

Hong, Hyerim; Jung, Jaejoon; Park, Woojun

2014-01-01

Acquisition of the extracellular tetracycline (TC) resistance plasmid pAST2 affected host gene expression and phenotype in the oil-degrading soil bacterium, Acinetobacter oleivorans DR1. Whole-transcriptome profiling of DR1 cells harboring pAST2 revealed that all the plasmid genes were highly expressed under TC conditions, and the expression levels of many host chromosomal genes were modulated by the presence of pAST2. The host energy burden imposed by replication of pAST2 led to (i) lowered ATP concentrations, (ii) downregulated expression of many genes involved in cellular growth, and (iii) reduced growth rate. Interestingly, some phenotypes were restored by deleting the plasmid-encoded efflux pump gene tetH, suggesting that the membrane integrity changes resulting from the incorporation of efflux pump proteins also resulted in altered host response under the tested conditions. Alteration of membrane integrity by tetH deletion was shown by measuring permeability of fluorescent probe and membrane hydrophobicity. The presence of the plasmid conferred peroxide and superoxide resistance to cells, but only peroxide resistance was diminished by tetH gene deletion, suggesting that the plasmid-encoded membrane-bound efflux pump protein provided peroxide resistance. The downregulation of fimbriae-related genes presumably led to reduced swimming motility, but this phenotype was recovered by tetH gene deletion. Our data suggest that not only the plasmid replication burden, but also its encoded efflux pump protein altered host chromosomal gene expression and phenotype, which also alters the ecological fitness of the host in the environment.

Why Organizations Continue to Create Patient Information Leaflets with Readability and Usability Problems: An Exploratory Study

ERIC Educational Resources Information Center

Gal, Iddo; Prigat, Ayelet

2005-01-01

Readability and usability problems with patient information leaflets continue to be reported despite long-standing recognition of their existence and the availability of guidelines for developing health education materials. This exploratory study examined possible causes for such problems, based on interviews with professionals who developed…

Transmembrane protein diffusion in gel-supported dual-leaflet membranes.

PubMed

Wang, Chih-Ying; Hill, Reghan J

2014-11-18

Tools to measure transmembrane-protein diffusion in lipid bilayer membranes have advanced in recent decades, providing a need for predictive theoretical models that account for interleaflet leaflet friction on tracer mobility. Here we address the fully three-dimensional flows driven by a (nonprotruding) transmembrane protein embedded in a dual-leaflet membrane that is supported above and below by soft porous supports (e.g., hydrogel or extracellular matrix), each of which has a prescribed permeability and solvent viscosity. For asymmetric configurations, i.e., supports with contrasting permeability, as realized for cells in contact with hydrogel scaffolds or culture media, the diffusion coefficient can reflect interleaflet friction. Reasonable approximations, for sufficiently large tracers on low-permeability supports, are furnished by a recent phenomenological theory from the literature. Interpreting literature data, albeit for hard-supported membranes, provides a theoretical basis for the phenomenological Stokes drag law as well as strengthening assertions that nonhydrodynamic interactions are important in supported bilayer systems, possibly leading to overestimates of the membrane/leaflet viscosity. Our theory provides a theoretical foundation for future experimental studies of tracer diffusion in gel-supported membranes.

Enhancement of Phloem Exudation from Fraxinus uhdei Wenz. (Evergreen Ash) using Ethylenediaminetetraacetic Acid 1

PubMed Central

Costello, L. R.; Bassham, James A.; Calvin, Melvin

1982-01-01

Ethylenediaminetetraacetic acid (EDTA) enhanced the exudation of 14C-labeled assimilates from excised leaflets and whole plant specimens of Fraxinus uhdei Wenz. A 2 millimolar EDTA concentration was found to be most effective in promoting exudation from excised leaflets, while 10 millimolar EDTA was most effective in whole plants experiments. Exudation rate reached a maximum after 24 hours in both experiments. The continuous presence of EDTA throughout the treatment period was required for maximum exudation from excised leaflets. Stachyose, raffinose, verbascose, and sucrose were the principal compounds found to occur in exudate samples. These compounds are typically transported in sieve elements of various Fraxinus species suggesting the exudate was of phloem origin. Electron microscope studies of petiolule sieve plate pores from excised leaflets showed substantially less callose appearing after treatment with EDTA than after H2O treatment. It is suggested that EDTA enhances phloem exudation by inhibiting or reducing callose formation in sieve plate pores. The exudation enhancement technique described for whole plant specimens is suggested as a useful means of collecting phloem sap and studying translocation in woody plants. Images PMID:16662189

Joint small-angle X-ray and neutron scattering data analysis of asymmetric lipid vesicles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eicher, Barbara; Heberle, Frederick A.; Marquardt, Drew T.

2017-02-28

Low- and high-resolution models describing the internal transbilayer structure of asymmetric lipid vesicles have been developed. These models can be used for the joint analysis of small-angle neutron and X-ray scattering data. The models describe the underlying scattering length density/electron density profiles either in terms of slabs or through the so-called scattering density profile, previously applied to symmetric lipid vesicles. Both models yield structural details of asymmetric membranes, such as the individual area per lipid, and the hydrocarbon thickness of the inner and outer bilayer leaflets. The scattering density profile model, however, comes at a cost of increased computational effortmore » but results in greater structural resolution, showing a slightly lower packing of lipids in the outer bilayer leaflet of ~120 nm diameter palmitoyloleoyl phosphatidylcholine (POPC) vesicles, compared to the inner leaflet. Here, analysis of asymmetric dipalmitoyl phosphatidylcholine/POPC vesicles did not reveal evidence of transbilayer coupling between the inner and outer leaflets at 323 K, i.e.above the melting transition temperature of the two lipids.« less

The Streptococcus pyogenes serotype M49 Nra-Ralp3 transcriptional regulatory network and its control of virulence factor expression from the novel eno ralp3 epf sagA pathogenicity region.

PubMed

Kreikemeyer, Bernd; Nakata, Masanobu; Köller, Thomas; Hildisch, Hendrikje; Kourakos, Vassilios; Standar, Kerstin; Kawabata, Shigetada; Glocker, Michael O; Podbielski, Andreas

2007-12-01

Many Streptococcus pyogenes (group A streptococcus [GAS]) virulence factor- and transcriptional regulator-encoding genes cluster together in discrete genomic regions. Nra is a central regulator of the FCT region. Previous studies exclusively described Nra as a transcriptional repressor of adhesin and toxin genes. Here transcriptome and proteome analysis of a serotype M49 GAS strain and an isogenic Nra mutant of this strain revealed the complete Nra regulon profile. Nra is active in all growth phases tested, with the largest regulon in the transition phase. Almost exclusively, virulence factor-encoding genes are repressed by Nra; these genes include the GAS pilus operon, the capsule synthesis operon, the cytolysin-mediated translocation system genes, all Mga region core virulence genes, and genes encoding other regulators, like the Ihk/Irr system, Rgg, and two additional RofA-like protein family regulators. Surprisingly, our experiments revealed that Nra additionally acts as a positive regulator, mostly for genes encoding proteins and enzymes with metabolic functions. Epidemiological investigations revealed strong genetic linkage of one particular Nra-repressed regulator, Ralp3 (SPy0735), with a gene encoding Epf (extracellular protein factor from Streptococcus suis). In a serotype-specific fashion, this ralp3 epf gene block is integrated, most likely via transposition, into the eno sagA virulence gene block, which is present in all GAS serotypes. In GAS serotypes M1, M4, M12, M28, and M49 this novel discrete genetic region is therefore designated the eno ralp3 epf sagA (ERES) pathogenicity region. Functional experiments showed that Epf is a novel GAS plasminogen-binding protein and revealed that Ralp3 activity counteracts Nra and MsmR regulatory activity. In addition to the Mga and FCT regions, the ERES region is the third discrete chromosomal pathogenicity region. All of these regions are transcriptionally linked, adding another level of complexity to the known GAS growth phase-dependent regulatory network.

The Streptococcus pyogenes Serotype M49 Nra-Ralp3 Transcriptional Regulatory Network and Its Control of Virulence Factor Expression from the Novel eno ralp3 epf sagA Pathogenicity Region▿ †

PubMed Central

Kreikemeyer, Bernd; Nakata, Masanobu; Köller, Thomas; Hildisch, Hendrikje; Kourakos, Vassilios; Standar, Kerstin; Kawabata, Shigetada; Glocker, Michael O.; Podbielski, Andreas

2007-01-01

Many Streptococcus pyogenes (group A streptococcus [GAS]) virulence factor- and transcriptional regulator-encoding genes cluster together in discrete genomic regions. Nra is a central regulator of the FCT region. Previous studies exclusively described Nra as a transcriptional repressor of adhesin and toxin genes. Here transcriptome and proteome analysis of a serotype M49 GAS strain and an isogenic Nra mutant of this strain revealed the complete Nra regulon profile. Nra is active in all growth phases tested, with the largest regulon in the transition phase. Almost exclusively, virulence factor-encoding genes are repressed by Nra; these genes include the GAS pilus operon, the capsule synthesis operon, the cytolysin-mediated translocation system genes, all Mga region core virulence genes, and genes encoding other regulators, like the Ihk/Irr system, Rgg, and two additional RofA-like protein family regulators. Surprisingly, our experiments revealed that Nra additionally acts as a positive regulator, mostly for genes encoding proteins and enzymes with metabolic functions. Epidemiological investigations revealed strong genetic linkage of one particular Nra-repressed regulator, Ralp3 (SPy0735), with a gene encoding Epf (extracellular protein factor from Streptococcus suis). In a serotype-specific fashion, this ralp3 epf gene block is integrated, most likely via transposition, into the eno sagA virulence gene block, which is present in all GAS serotypes. In GAS serotypes M1, M4, M12, M28, and M49 this novel discrete genetic region is therefore designated the eno ralp3 epf sagA (ERES) pathogenicity region. Functional experiments showed that Epf is a novel GAS plasminogen-binding protein and revealed that Ralp3 activity counteracts Nra and MsmR regulatory activity. In addition to the Mga and FCT regions, the ERES region is the third discrete chromosomal pathogenicity region. All of these regions are transcriptionally linked, adding another level of complexity to the known GAS growth phase-dependent regulatory network. PMID:17893125

Molecular cloning and characterization of two novel genes from hexaploid wheat that encode double PR-1 domains coupled with a receptor-like protein kinase

USDA-ARS?s Scientific Manuscript database

Hexaploid wheat (Triticum aestivum L.) contains at least 23 TaPr-1 genes encoding the group 1 pathogenesis-related (PR-1) proteins as identified in our previous work. Here we report the cloning and characterization of TaPr-1-rk1 and TaPr-1-rk2, two novel genes closely related to the wheat PR-1 famil...

Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France

PubMed Central

Auffret, Pauline; Segura, Audrey; Klopp, Christophe; Bouchez, Olivier; Kérourédan, Monique; Bibbal, Delphine; Brugère, Hubert; Forano, Evelyne

2017-01-01

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) with serotype O157:H7 is a major foodborne pathogen. Here, we report the draft genome sequence of EHEC O157:H7 strain MC2 isolated from cattle in France. The assembly contains 5,400,376 bp that encoded 5,914 predicted genes (5,805 protein-encoding genes and 109 RNA genes). PMID:28983004

Evolution of Prdm Genes in Animals: Insights from Comparative Genomics

PubMed Central

Vervoort, Michel; Meulemeester, David; Béhague, Julien; Kerner, Pierre

2016-01-01

Prdm genes encode transcription factors with a subtype of SET domain known as the PRDF1-RIZ (PR) homology domain and a variable number of zinc finger motifs. These genes are involved in a wide variety of functions during animal development. As most Prdm genes have been studied in vertebrates, especially in mice, little is known about the evolution of this gene family. We searched for Prdm genes in the fully sequenced genomes of 93 different species representative of all the main metazoan lineages. A total of 976 Prdm genes were identified in these species. The number of Prdm genes per species ranges from 2 to 19. To better understand how the Prdm gene family has evolved in metazoans, we performed phylogenetic analyses using this large set of identified Prdm genes. These analyses allowed us to define 14 different subfamilies of Prdm genes and to establish, through ancestral state reconstruction, that 11 of them are ancestral to bilaterian animals. Three additional subfamilies were acquired during early vertebrate evolution (Prdm5, Prdm11, and Prdm17). Several gene duplication and gene loss events were identified and mapped onto the metazoan phylogenetic tree. By studying a large number of nonmetazoan genomes, we confirmed that Prdm genes likely constitute a metazoan-specific gene family. Our data also suggest that Prdm genes originated before the diversification of animals through the association of a single ancestral SET domain encoding gene with one or several zinc finger encoding genes. PMID:26560352

The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation and is specifically induced in the presence of aromatic compounds.

PubMed

de Vries, Ronald P; vanKuyk, Patricia A; Kester, Harry C M; Visser, Jaap

2002-04-15

The faeB gene encoding a second feruloyl esterase from Aspergillus niger has been cloned and characterized. It consists of an open reading frame of 1644 bp containing one intron. The gene encodes a protein of 521 amino acids that has sequence similarity to that of an Aspergillus oryzae tannase. However, the encoded enzyme, feruloyl esterase B (FAEB), does not have tannase activity. Comparison of the physical characteristics and substrate specificity of FAEB with those of a cinnamoyl esterase from A. niger [Kroon, Faulds and Williamson (1996) Biotechnol. Appl. Biochem. 23, 255-262] suggests that they are in fact the same enzyme. The expression of faeB is specifically induced in the presence of certain aromatic compounds, but not in the presence of other constituents present in plant-cell-wall polysaccharides such as arabinoxylan or pectin. The expression profile of faeB in the presence of aromatic compounds was compared with the expression of A. niger faeA, encoding feruloyl esterase A (FAEA), and A. niger bphA, the gene encoding a benzoate-p-hydroxylase. All three genes have different subsets of aromatic compounds that induce their expression, indicating the presence of different transcription activating systems in A. niger that respond to aromatic compounds. Comparison of the activity of FAEA and FAEB on sugar-beet pectin and wheat arabinoxylan demonstrated that they are both involved in the degradation of both polysaccharides, but have opposite preferences for these substrates. FAEA is more active than FAEB towards wheat arabinoxylan, whereas FAEB is more active than FAEA towards sugar-beet pectin.

The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation and is specifically induced in the presence of aromatic compounds.

PubMed Central

de Vries, Ronald P; vanKuyk, Patricia A; Kester, Harry C M; Visser, Jaap

2002-01-01

The faeB gene encoding a second feruloyl esterase from Aspergillus niger has been cloned and characterized. It consists of an open reading frame of 1644 bp containing one intron. The gene encodes a protein of 521 amino acids that has sequence similarity to that of an Aspergillus oryzae tannase. However, the encoded enzyme, feruloyl esterase B (FAEB), does not have tannase activity. Comparison of the physical characteristics and substrate specificity of FAEB with those of a cinnamoyl esterase from A. niger [Kroon, Faulds and Williamson (1996) Biotechnol. Appl. Biochem. 23, 255-262] suggests that they are in fact the same enzyme. The expression of faeB is specifically induced in the presence of certain aromatic compounds, but not in the presence of other constituents present in plant-cell-wall polysaccharides such as arabinoxylan or pectin. The expression profile of faeB in the presence of aromatic compounds was compared with the expression of A. niger faeA, encoding feruloyl esterase A (FAEA), and A. niger bphA, the gene encoding a benzoate-p-hydroxylase. All three genes have different subsets of aromatic compounds that induce their expression, indicating the presence of different transcription activating systems in A. niger that respond to aromatic compounds. Comparison of the activity of FAEA and FAEB on sugar-beet pectin and wheat arabinoxylan demonstrated that they are both involved in the degradation of both polysaccharides, but have opposite preferences for these substrates. FAEA is more active than FAEB towards wheat arabinoxylan, whereas FAEB is more active than FAEA towards sugar-beet pectin. PMID:11931668

Impact of written information on control and adherence in type 2 diabetes.

PubMed

Caetano, Inês Rosendo Carvalho E Silva; Santiago, Luiz Miguel; Marques, Margarida

2018-02-01

Diabetes therapeutic education and information by leaflets is important. This study aimed to understand the effectiveness of written information to diabetic patients, after six months, in the control of diabetes and medication adherence. Non-pharmacological clinical trial. Randomized sample of diabetic patients of 65 volunteer doctors, distributed among the five health regions in Portugal. At the first appointment, patients were randomized in four groups (three intervention with validated leaflets and one control), leaflet reading being reinforced at the follow-up appointments in a 6-months period. Variables collected: HbA1c, home blood glucose, weight, waist circumference, blood pressure, cigarettes smoked, physical activity level, adherence to medication, medication, height, diabetes progression, age, sex and educational background. Descriptive and inferential statistics. From the 709 patients recruited, 702 were studied in this 6-months period with no statistical differences in the baseline variables studied. After six months of intervention, the adherence to medication improved in the leaflet group (p=0.034). This was noticed in those under 65 years of age (p=0.027), with diabetes for ≤ 5 years (p=0.010), with educational background up to 4 years (p=0.030) and 9 years (p=0.006) and with HbA1c ≥ 7% at the beginning of the study. Interventions with leaflets handed in primary healthcare to people with diabetes type 2 can bring benefits in what concerns adherence to therapeutics, namely in younger people with a less studies.

Architecture of an in vivo-tissue engineered autologous conduit "Biovalve".

PubMed

Hayashida, Kyoko; Kanda, Keiichi; Oie, Tomonori; Okamoto, Yoshihiro; Ishibashi-Ueda, Hatsue; Onoyama, Masaaki; Tajikawa, Tsutomu; Ohba, Kenkichi; Yaku, Hitoshi; Nakayama, Yasuhide

2008-07-01

As a practical concept of regenerative medicine, we have focused on in vivo tissue engineering utilizing the foreign body reaction. Plastic substrates for valvular leaflet organization, consisting of two pieces assembled with a small aperture were inserted into a microporous polyurethane conduit scaffold. The assembly was placed in the subcutaneous spaces of Japanese white rabbits for 1 month. After the substrates were pulled out from the harvested implant, valve leaflet-shaped membranous tissue was formed inside the tubular scaffold as designed. The valve leaflet was composed of the same collagen-rich tissue, with the absence of any elastic fiber, as that which had ingrown or covered the scaffold. No abnormal collection or infiltration of inflammatory cells in the leaflet and the scaffold could be demonstrated. According to the immunohistochemical staining, the leaflet was comprised of numerous vimentin- or alpha-SMA-positive cells, corresponding to fibroblasts or myofibroblats, but contained no desmin-positive cells. The analysis of the video data of the valve movement showed that, in synchronization with the backward flow in the diastolic phase, the valve closed rapidly and tightly and, in the transition phase of the flow direction, the valve opened smoothly without flapping or hitting the scaffold wall. Using mold designs, consisting of two different plastic substrates and the tubular scaffold, in conjunction with "in body tissue architecture," the complex 3-dimensional autologous conduit-typed Biovalve was developed for the first time. 2007 Wiley Periodicals, Inc.

Echocardiographic assessment of mitral valve morphology and performance after triangular resection of the prolapsing posterior leaflet for degenerative myxomatous disease.

PubMed

Chiappini, Bruno; Gregorini, Renato; De Remigis, Franco; Petrella, Licia; Villani, Carmine; Di Pietrantonio, Fabrizio; Pavicevic, Srdan; Mazzola, Alessandro

2009-08-01

The gold standard for the surgical treatment of prolapse of the posterior leaflet of the mitral valve (MV) for degenerative myxomatous disease has been represented by the quadrangular resection of the leaflet, according to the Carpentier technique. Since 2006 we performed a triangular resection of the prolapsing leaflet in 20 patients with myxomatous mitral regurgitation (MR). Seventeen patients (85%) underwent the triangular resection of P2; one patient (5%) had a triple scallops triangular resection (P1, P2, P3) and two (10%) a double scallops (P2, P3) resection. In this study, we report the immediate and mid-term clinical and echocardiographic results of a cohort of 20 patients, who underwent this technique. Thirty-day mortality was 0. Acute renal failure occurred in three patients (15%) and they resolved with conservative management. One patient (5%) required re-exploration for bleeding. At the mean follow-up of 13.1+/-4.2 months survival was 95%; one patient died of lymphoma during the follow-up time. All the cases were in New York Heart Association (NYHA) class I. Nineteen survivors underwent transthoracic echocardiography (TTE) (5), or transesophageal echocardiography (TEE) (13), performed by two skilled cardiologists. All patients showed no or trivial MV regurgitation. We believe that triangular resection of posterior MV leaflet (PMVL) provides excellent mid-term results providing the surgeon with a reliable and reproducible surgical option for myxomatous degenerative MV regurgitation.

Mitral stenosis and hypertrophic obstructive cardiomyopathy: An unusual combination.

PubMed

Hong, Joonhwa; Schaff, Hartzell V; Ommen, Steve R; Abel, Martin D; Dearani, Joseph A; Nishimura, Rick A

2016-04-01

Systolic anterior motion of mitral valve (MV) leaflets is a main pathophysiologic feature of left ventricular outflow tract (LVOT) obstruction in hypertrophic obstructive cardiomyopathy. Thus, restricted leaflet motion that occurs with MV stenosis might be expected to minimize outflow tract obstruction related to systolic anterior motion. From January 1993 through February 2015, we performed MV replacement and septal myectomy in 12 patients with mitral stenosis and hypertrophic obstructive cardiomyopathy at Mayo Clinic Hospital in Rochester, Minn. Preoperative data, echocardiographic images, operative records, and postoperative outcomes were reviewed. Mean (standard deviation) age was 70 (7.6) years. Preoperative mean (standard deviation) maximal LVOT pressure gradient was 75.0 (35.0) mm Hg; MV gradient was 13.7 (2.8) mm Hg. From echocardiographic images, 4 mechanisms of outflow tract obstruction were identified: systolic anterior motion without severe limitation in MV leaflet excursion, severe limitation in MV leaflet mobility with systolic anterior motion at the tip of the MV anterior leaflet, septal encroachment toward the LVOT, and MV displacement toward the LVOT by calcification. Mitral valve replacement and extended septal myectomy relieved outflow gradients in all patients, with no death or serious morbidity. Patients with mitral stenosis and hypertrophic obstructive cardiomyopathy have multiple LVOT obstruction mechanisms, and MV replacement may not be adequate treatment. We favor septal myectomy and MV replacement in this complex subset of hypertrophic obstructive cardiomyopathy. Copyright © 2016 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

Tricuspid valve repair for severe tricuspid regurgitation due to pacemaker leads.

PubMed

Uehara, Kyokun; Minakata, Kenji; Watanabe, Kentaro; Sakaguchi, Hisashi; Yamazaki, Kazuhiro; Ikeda, Tadashi; Sakata, Ryuzo

2016-07-01

Tricuspid valve regurgitation due to pacemaker leads is a well-known complication. Although some reports have suggested that pacemaker leads should be surgically explanted, strongly adhered leads cannot always be removed. The aim of this study was to describe our tricuspid valve repair techniques with pacemaker leads left in situ. Our retrospective study investigated 6 consecutive patients who required tricuspid valve surgery for severe regurgitation induced by pacemaker leads. From the operative findings, we identified 3 patterns of tricuspid valve and pacemaker lead involvement. In 3 patients, the leads were caught in the chordae, in 2 patients, tricuspid regurgitation was caused by lead impingement on the septal leaflet, and in 3 patients, tricuspid valve leaflets had been perforated by the pacemaker leads. During surgery, all leads were left in situ after being separated from the leaflet or valvular apparatus. In addition, suture annuloplasty was performed for annular dilatation in all cases. In one patient, the lead was reaffixed to the annulus after the posterior leaflet was cut back towards the annulus, and the leaflet was then closed. There was one hospital death due to sepsis. The degree of tricuspid regurgitation was trivial in all surviving patients at discharge. During a mean follow-up of 21 months, one patient died from pneumonia 20 months after tricuspid valve repair. In patients undergoing tricuspid valve surgery due to severe tricuspid regurgitation caused by pacemaker leads, the leads can be left in situ after proper repair with annuloplasty. © The Author(s) 2016.

Cloning and characterization of the metE gene encoding S-adenosylmethionine synthetase from Bacillus subtilis.

PubMed Central

Yocum, R R; Perkins, J B; Howitt, C L; Pero, J

1996-01-01

The metE gene, encoding S-adenosylmethionine synthetase (EC 2.5.1.6) from Bacillus subtilis, was cloned in two steps by normal and inverse PCR. The DNA sequence of the metE gene contains an open reading frame which encodes a 400-amino-acid sequence that is homologous to other known S-adenosylmethionine synthetases. The cloned gene complements the metE1 mutation and integrates at or near the chromosomal site of metE1. Expression of S-adenosylmethionine synthetase is reduced by only a factor of about 2 by exogenous methioinine. Overproduction of S-adenosylmethionine synthetase from a strong constitutive promoter leads to methionine auxotrophy in B. subtilis, suggesting that S-adenosylmethionine is a corepressor of methionine biosynthesis in B. subtilis, as others have already shown for Escherichia coli. PMID:8755891

Cloning and characterization of the metE gene encoding S-adenosylmethionine synthetase from Bacillus subtilis.

PubMed

Yocum, R R; Perkins, J B; Howitt, C L; Pero, J

1996-08-01

The metE gene, encoding S-adenosylmethionine synthetase (EC 2.5.1.6) from Bacillus subtilis, was cloned in two steps by normal and inverse PCR. The DNA sequence of the metE gene contains an open reading frame which encodes a 400-amino-acid sequence that is homologous to other known S-adenosylmethionine synthetases. The cloned gene complements the metE1 mutation and integrates at or near the chromosomal site of metE1. Expression of S-adenosylmethionine synthetase is reduced by only a factor of about 2 by exogenous methioinine. Overproduction of S-adenosylmethionine synthetase from a strong constitutive promoter leads to methionine auxotrophy in B. subtilis, suggesting that S-adenosylmethionine is a corepressor of methionine biosynthesis in B. subtilis, as others have already shown for Escherichia coli.

GDP-L-fucose: {beta}-D-galactoside 2-{alpha}-Lfucosyltransferases, DNA sequences encoding the same, method for producing the same and a method of genotyping a person

DOEpatents

Lowe, J.B.; Lennon, G.; Rouquier, S.; Giorgi, D.; Kelly, R.J.

1998-09-15

The gene encoding GDP-L-fucose: {beta}-D-Galactoside 2-{alpha}-Lfucosyltransferase has been cloned, and a mutation in this gene has been found to be responsible for an individual being a non-secretor. 30 figs.

Similarity and functional analyses of expressed parasitism genes in Heterodera schachtii and Heterodera glycines

USDA-ARS?s Scientific Manuscript database

The secreted proteins encoded by “parasitism genes” expressed within the esophageal glands cells of cyst nematodes play important roles in plant parasitism. Homologous transcripts and encoded proteins of the Heterodera glycines pioneer parasitism genes Hgsyv46, Hg4e02 and Hg5d08 were identified and ...

Two Bombyx mori acetylcholinesterase genes influence motor control and development in different ways

USDA-ARS?s Scientific Manuscript database

Among its other biological roles, acetylcholinesterase (AChE, EC 3.1.1.7), encoded by two ace genes in most insects, catalyses the breakdown of acetylcholine, thereby terminating synaptic transmission. ace1 encodes the synaptic enzyme and ace2 has other essential actions in many insect species, such...

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

USDA-ARS?s Scientific Manuscript database

Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation....

Influence of energy supply on expression of genes encoding for lipogenic enzymes and regulatory proteins in growing beef steers

USDA-ARS?s Scientific Manuscript database

Forty crossbred beef steers were used to determine the effects metabolizable energy (ME) intake and of site and complexity of carbohydrate (CHO) infusion on expression of genes encoding lipogenic enzymes and regulatory proteins in subcutaneous (SC), mesenteric (MES) and omental (OM) adipose. Treatm...

GDP-L-fucose: .beta.-D-galactoside 2-.alpha.-L-fucosyltransferases, DNA sequences encoding the same, method for producing the same and a method of genotyping a person

DOEpatents

Lowe, John B.; Lennon, Gregory; Rouquier, Sylvie; Giorgi, Dominique; Kelly, Robert J.

1998-01-01

The gene encoding GDP-L-fucose: .beta.-D-Galactoside 2-.alpha.-L-fucosyltransferase has been cloned, and a mutation in this gene has been found to be responsible for an individual being a non-secretor.

Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity.

PubMed

Murphy, James; Klumpp, Jochen; Mahony, Jennifer; O'Connell-Motherway, Mary; Nauta, Arjen; van Sinderen, Douwe

2014-10-01

So-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control phage proliferation and decades of research, these phages continue to negatively impact cheese production in terms of the final product quality and consequently, monetary return. Whole genome sequencing and in silico analysis of three 936-type phage genomes identified several putative (orphan) methyltransferase (MTase)-encoding genes located within the packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis was performed on all three phages, allowing the identification of adenine modifications consistent with N-6 methyladenine sequence methylation, which in some cases could be attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.Phi145I/M.Phi93I and M.Phi93DAM, encoded by genes located within the packaging module, provide protection against the restriction enzymes HphI and DpnII, respectively, representing the first functional MTases identified in members of 936-type phages. SMRT sequencing technology enabled the identification of the target motifs of MTases encoded by the genomes of three lytic 936-type phages and these MTases represent the first functional MTases identified in this species of phage. The presence of these MTase-encoding genes on 936-type phage genomes is assumed to represent an adaptive response to circumvent host encoded restriction-modification systems thereby increasing the fitness of the phages in a dynamic dairy environment.

The clover technique for the treatment of complex tricuspid valve insufficiency: midterm clinical and echocardiographic results in 66 patients.

PubMed

Lapenna, Elisabetta; De Bonis, Michele; Verzini, Alessandro; La Canna, Giovanni; Ferrara, David; Calabrese, Maria Chiara; Taramasso, Maurizio; Alfieri, Ottavio

2010-06-01

This study assesses the results of the 'clover technique' (suturing together the middle point of the free edges of the tricuspid leaflets) for the treatment of tricuspid regurgitation (TR) due to severe prolapse or tethering. From 2001, 66 patients with severe TR due to prolapsing or tethered leaflets underwent 'clover repair'. Annuloplasty was associated in 64 patients (97%). The aetiology of TR was degenerative in 52 cases (79%), post-traumatic in eight (12%) and secondary to dilated cardiomyopathy (DCM) in six (9%). The main mechanism of TR was prolapse/flail of one leaflet in 15 patients (23%), of two leaflets in 31 (47%) and of all three leaflets in 14 (21%). The remaining six patients (9%) presented with severe leaflets' tethering. Four deaths (6%) occurred during hospitalisation and one patient died 3.6 years after surgery. Survival was 91 + or - 4.1% at 5 years. Follow-up of the 62 hospital survivors was 100% complete (mean length 3.5 + or - 1.6 years, range 13 months-7.1 years). At the last echocardiogram, no or mild TR was detected in 55 (88.7%) patients, moderate (2+/4+) in six (9.6%) and severe (4+/4+) in one patient (1.6%). Mean tricuspid valve area and gradient were 4.3 + or - 0.6 cm(2) and 2.8 + or -1.4 mmHg. In six patients, stress echocardiography was performed and no signs of tricuspid stenosis were detected. At the multivariable analysis, the degree of TR at hospital discharge was identified as the only predictor of TR > or = 2+ at follow-up. Midterm clinical and echocardiographic results confirm the role of the 'clover technique' in the surgical treatment of TR due to lesions, which are unlikely to be effectively treatable by annuloplasty alone. Copyright 2010 European Association for Cardio-Thoracic Surgery. Published by Elsevier B.V. All rights reserved.

Virtual reality 3D echocardiography in the assessment of tricuspid valve function after surgical closure of ventricular septal defect.

PubMed

Bol Raap, Goris; Koning, Anton H J; Scohy, Thierry V; ten Harkel, A Derk-Jan; Meijboom, Folkert J; Kappetein, A Pieter; van der Spek, Peter J; Bogers, Ad J J C

2007-02-16

This study was done to investigate the potential additional role of virtual reality, using three-dimensional (3D) echocardiographic holograms, in the postoperative assessment of tricuspid valve function after surgical closure of ventricular septal defect (VSD). 12 data sets from intraoperative epicardial echocardiographic studies in 5 operations (patient age at operation 3 weeks to 4 years and bodyweight at operation 3.8 to 17.2 kg) after surgical closure of VSD were included in the study. The data sets were analysed as two-dimensional (2D) images on the screen of the ultrasound system as well as holograms in an I-space virtual reality (VR) system. The 2D images were assessed for tricuspid valve function. In the I-Space, a 6 degrees-of-freedom controller was used to create the necessary projectory positions and cutting planes in the hologram. The holograms were used for additional assessment of tricuspid valve leaflet mobility. All data sets could be used for 2D as well as holographic analysis. In all data sets the area of interest could be identified. The 2D analysis showed no tricuspid valve stenosis or regurgitation. Leaflet mobility was considered normal. In the virtual reality of the I-Space, all data sets allowed to assess the tricuspid leaflet level in a single holographic representation. In 3 holograms the septal leaflet showed restricted mobility that was not appreciated in the 2D echocardiogram. In 4 data sets the posterior leaflet and the tricuspid papillary apparatus were not completely included. This report shows that dynamic holographic imaging of intraoperative postoperative echocardiographic data regarding tricuspid valve function after VSD closure is feasible. Holographic analysis allows for additional tricuspid valve leaflet mobility analysis. The large size of the probe, in relation to small size of the patient, may preclude a complete data set. At the moment the requirement of an I-Space VR system limits the applicability in virtual reality 3D echocardiography in clinical practice.

Functional mitral stenosis after surgical annuloplasty for ischemic mitral regurgitation: Importance of subvalvular tethering in the mechanism and dynamic deterioration during exertion

PubMed Central

Kubota, Kayoko; Otsuji, Yutaka; Ueno, Tetsuya; Koriyama, Chihaya; Levine, Robert A.; Sakata, Ryuzo; Tei, Chuwa

2010-01-01

Objective Diastolic subvalvular mitral leaflet tethering by left ventricular remodeling that restricts leaflet opening in the presence of annular size reduction by surgery for ischemic mitral regurgitation potentially causes functional mitral stenosis in the absence of organic leaflet lesions. Exercise, known to worsen systolic tethering and ischemic mitral regurgitation, might also dynamically exacerbate such mitral stenosis by increasing tethering. This study evaluates the mechanism and response of such mitral stenosis to exercise. Methods We measured the diastolic mitral valve area, annular area, and peak and mean transmitral pressure gradient by echocardiography in 20 healthy individuals and 31 patients who underwent surgical annuloplasty for ischemic mitral regurgitation. Results Although the mitral valve area and annular area did not significantly differ in healthy individuals (4.7 ± 0.6 cm2 vs 5.2 ± 0.6 cm2, not significant), mitral valve area was significantly smaller than the annular area in patients after annuloplasty (1.6 ± 0.2 cm2 vs 3.3 ± 0.5 cm2, P < .01). The mitral valve area was less than 1.5 cm2 only after the surgery (P < .01) and was significantly correlated with restricted leaflet opening (r2 = 0.74, P <.001), left ventricular dilatation (r2 = 0.17, P <.05), and New York Heart Association functional class (P <. 05). Exercise stress echocardiography of 12 patients demonstrated dynamic worsening in functional mitral stenosis (mitral valve area: 2.0 ± 0.5 cm2 to 1.4 ± 0.2 cm2, P < .01; mean pressure gradient: 1.5 ± 0.9 mm Hg to 6.0 ± 2.2 mm Hg, P < .01). Conclusions Persistent subvalvular leaflet tethering in the presence of annular size reduction by surgery in ischemic mitral regurgitation frequently causes functional mitral stenosis at the leaflet tip level, which is related to heart failure symptoms and can be dynamic with significant exercise-induced worsening. PMID:20122701

Quantity and location of aortic valve complex calcification predicts severity and location of paravalvular regurgitation and frequency of post-dilation after balloon-expandable transcatheter aortic valve replacement.

PubMed

Khalique, Omar K; Hahn, Rebecca T; Gada, Hemal; Nazif, Tamim M; Vahl, Torsten P; George, Isaac; Kalesan, Bindu; Forster, Molly; Williams, Mathew B; Leon, Martin B; Einstein, Andrew J; Pulerwitz, Todd C; Pearson, Gregory D N; Kodali, Susheel K

2014-08-01

This study sought to determine the impact of quantity and location of aortic valve calcification (AVC) on paravalvular regurgitation (PVR) and rates of post-dilation (PD) immediately after transcatheter aortic valve replacement (TAVR). The impact of AVC in different locations within the aortic valve complex is incompletely understood. This study analyzed 150 patients with severe, symptomatic aortic stenosis who underwent TAVR. Total AVC volume scores were calculated from contrast-enhanced multidetector row computed tomography imaging. AVC was divided by leaflet sector and region (Leaflet, Annulus, left ventricular outflow tract [LVOT]), and a combination of LVOT and Annulus (AnnulusLVOT). Asymmetry was assessed. Receiver-operating characteristic analysis was performed with greater than or equal to mild PVR and PD as classification variables. Logistic regression was performed. Quantity of and asymmetry of AVC for all regions of the aortic valve complex predicted greater than or equal to mild PVR by receiver-operating characteristic analysis (area under the curve = 0.635 to 0.689), except Leaflet asymmetry. Receiver-operating characteristic analysis for PD was significant for quantity and asymmetry of AVC in all regions, with higher area under the curve values than for PVR (area under the curve = 0.648 to 0.741). On multivariable analysis, Leaflet and AnnulusLVOT calcification were independent predictors of both PVR and PD regardless of multidetector row computed tomography area cover index. Quantity and asymmetry of AVC in all regions of the aortic valve complex predict greater than or equal to mild PVR and performance of PD, with the exception of Leaflet asymmetry. Quantity of AnnulusLVOT and Leaflet calcification independently predict PVR and PD when taking into account multidetector row computed tomography area cover index. Copyright © 2014 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Diel Variation in Population Size and Ice Nucleation Activity of Pseudomonas syringae on Snap Bean Leaflets.

PubMed

Hirano, S S; Upper, C D

1989-03-01

The extent to which diel changes in the physical environment affect changes in population size and ice nucleation activity of Pseudomonas syringae on snap bean leaflets was determined under field conditions. To estimate bacterial population size and ice nucleation activity, bean leaflets were harvested at 2-h intervals during each of three 26-h periods. A tube nucleation test was used to assay individual leaflets for ice nuclei. Population sizes of P. syringae were determined by dilution plating of leaflet homogenates. The overall diel changes in P. syringae population sizes differed during each of the 26-h periods. In one 26-h period, there was a continuous increase in the logarithm of P. syringae population size despite intense solar radiation, absence of free moisture on leaf surfaces, and low relative humidity during the day. A mean doubling time of approximately 4.9 h was estimated for the 28-fold increase in P. syringae population size that occurred from 0900 to 0900 h during the 26-h period. However, doubling times of 3.3 and 1.9 h occurred briefly during this period from 1700 to 2300 h and from 0100 to 0700 h, respectively. Thus, growth rates of P. syringae in association with leaves in the field were of the same order of magnitude as optimal rates measured in the laboratory. The frequency with which leaflets bore ice nuclei active at -2.0, -2.2, and -2.5 degrees C varied greatly within each 26-h period. These large diel changes were inversely correlated primarily with the diel changes in air temperature and reflected changes in nucleation frequency rather than changes in population size of P. syringae. Thus, the response of bacterial ice nucleation activity to the physical environment was distinct from the changes in population size of ice nucleation-active P. syringae.

Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum bicolor.

PubMed

McKinley, Brian; Rooney, William; Wilkerson, Curtis; Mullet, John

2016-11-01

Biomass accumulated preferentially in leaves of the sweet sorghum Della until floral initiation, then stems until anthesis, followed by panicles until grain maturity, and apical tillers. Sorghum stem RNA-seq transcriptome profiles and composition data were collected for approximately 100 days of development beginning at floral initiation. The analysis identified >200 differentially expressed genes involved in stem growth, cell wall biology, and sucrose accumulation. Genes encoding expansins and xyloglucan endotransglucosylase/hydrolases were differentially expressed in growing stem internodes. Genes encoding enzymes involved in the synthesis of cellulose, lignin, and glucuronoarabinoxylan were expressed at elevated levels in stems until approximately 7 days before anthesis and then down-regulated. CESA genes involved in primary and secondary cell wall synthesis showed different temporal patterns of expression. Following floral initiation, the level of sucrose and other non-structural carbohydrates increased to approximately 50% of the stem's dry weight. Stem sucrose accumulation was inversely correlated with >100-fold down-regulation of SbVIN1, a gene encoding a vacuolar invertase. Accumulation of stem sucrose was also correlated with cessation of leaf and stem growth at anthesis, decreased expression of genes involved in stem cell wall synthesis, and approximately 10-fold lower expression of SbSUS4, a gene encoding sucrose synthase that generates UDP-glucose from sucrose for cell wall biosynthesis. Genes for mixed linkage glucan synthesis (CSLF) and turnover were expressed at high levels in stems throughout development. Overall, the stem transcription profile resource and the genes and regulatory dynamics identified in this study will be useful for engineering sorghum stem composition for improved conversion to biofuels and bio-products. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

The restriction-modification genes of Escherichia coli K-12 may not be selfish: they do not resist loss and are readily replaced by alleles conferring different specificities.

PubMed

O'Neill, M; Chen, A; Murray, N E

1997-12-23

Type II restriction and modification (R-M) genes have been described as selfish because they have been shown to impose selection for the maintenance of the plasmid that encodes them. In our experiments, the type I R-M system EcoKI does not behave in the same way. The genes specifying EcoKI are, however, normally residents of the chromosome and therefore our analyses were extended to monitor the deletion of chromosomal genes rather than loss of plasmid vector. If EcoKI were to behave in the same way as the plasmid-encoded type II R-M systems, the loss of the relevant chromosomal genes by mutation or recombination should lead to cell death because the cell would become deficient in modification enzyme and the bacterial chromosome would be vulnerable to the restriction endonuclease. Our data contradict this prediction; they reveal that functional type I R-M genes in the chromosome are readily replaced by mutant alleles and by alleles encoding a type I R-M system of different specificity. The acquisition of allelic genes conferring a new sequence specificity, but not the loss of the resident genes, is dependent on the product of an unlinked gene, one predicted [Prakash-Cheng, A., Chung, S. S. & Ryu, J. (1993) Mol. Gen. Genet. 241, 491-496] to be relevant to control of expression of the genes that encode EcoKI. Our evidence suggests that not all R-M systems are evolving as "selfish" units; rather, the diversity and distribution of the family of type I enzymes we have investigated require an alternative selective pressure.

Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System.

PubMed

Sharma, Akanksha; Sharma, Niharika; Bhalla, Prem; Singh, Mohan

2017-01-01

Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional characterization in related grass species.

Molecular cloning, sequence identification and tissue expression profile of three novel sheep (Ovis aries) genes - BCKDHA, NAGA and HEXA.

PubMed

Liu, G Y; Gao, S Z

2009-01-01

The complete coding sequences of three sheep genes- BCKDHA, NAGA and HEXA were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR), based on the conserved sequence information of the mouse or other mammals. The nucleotide sequences of these three genes revealed that the sheep BCKDHA gene encodes a protein of 313 amino acids which has high homology with the BCKDHA gene that encodes a protein of 447 amino acids that has high homology with the Branched chain keto acid dehydrogenase El, alpha polypeptide (BCKDHA) of five species chimpanzee (93%), human (96%), crab-eating macaque (93%), bovine (98%) and mouse (91%). The sheep NAGA gene encodes a protein of 411 amino acids that has high homology with the alpha-N-acetylgalactosaminidase (NAGA) of five species human (85%), bovine (94%), mouse (91%), rat (83%) and chicken (74%). The sheep HEXA gene encodes a protein of 529 amino acids that has high homology with the hexosaminidase A(HEXA) of five species bovine (98%), human (84%), Bornean orangután (84%), rat (80%) and mouse (81%). Finally these three novel sheep genes were assigned to GenelDs: 100145857, 100145858 and 100145856. The phylogenetic tree analysis revealed that the sheep BCKDHA, NAGA, and HEXA all have closer genetic relationships to the BCKDHA, NAGA, and HEXA of bovine. Tissue expression profile analysis was also carried out and results revealed that sheep BCKDHA, NAGA and HEXA genes were differentially expressed in tissues including muscle, heart, liver, fat, kidney, lung, small and large intestine. Our experiment is the first to establish the primary foundation for further research on these three sheep genes.

Sexual selection, genetic conflict, selfish genes, and the atypical patterns of gene expression in spermatogenic cells.

PubMed

Kleene, Kenneth C

2005-01-01

This review proposes that the peculiar patterns of gene expression in spermatogenic cells are the consequence of powerful evolutionary forces known as sexual selection. Sexual selection is generally characterized by intense competition of males for females, an enormous variety of the strategies to maximize male reproductive success, exaggerated male traits at all levels of biological organization, co-evolution of sexual traits in males and females, and conflict between the sexual advantage of the male trait and the reproductive fitness of females and the individual fitness of both sexes. In addition, spermatogenesis is afflicted by selfish genes that promote their transmission to progeny while causing deleterious effects. Sexual selection, selfish genes, and genetic conflict provide compelling explanations for many atypical features of gene expression in spermatogenic cells including the gross overexpression of certain mRNAs, transcripts encoding truncated proteins that cannot carry out basic functions of the proteins encoded by the same genes in somatic cells, the large number of gene families containing paralogous genes encoding spermatogenic cell-specific isoforms, the large number of testis-cancer-associated genes that are expressed only in spermatogenic cells and malignant cells, and the overbearing role of Sertoli cells in regulating the number and quality of spermatozoa.

A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans.

PubMed

Eshghi, Azad; Becam, Jérôme; Lambert, Ambroise; Sismeiro, Odile; Dillies, Marie-Agnès; Jagla, Bernd; Wunder, Elsio A; Ko, Albert I; Coppee, Jean-Yves; Goarant, Cyrille; Picardeau, Mathieu

2014-06-01

Limited research has been conducted on the role of transcriptional regulators in relation to virulence in Leptospira interrogans, the etiological agent of leptospirosis. Here, we identify an L. interrogans locus that encodes a sensor protein, an anti-sigma factor antagonist, and two genes encoding proteins of unknown function. Transposon insertion into the gene encoding the sensor protein led to dampened transcription of the other 3 genes in this locus. This lb139 insertion mutant (the lb139(-) mutant) displayed attenuated virulence in the hamster model of infection and reduced motility in vitro. Whole-transcriptome analyses using RNA sequencing revealed the downregulation of 115 genes and the upregulation of 28 genes, with an overrepresentation of gene products functioning in motility and signal transduction and numerous gene products with unknown functions, predicted to be localized to the extracellular space. Another significant finding encompassed suppressed expression of the majority of the genes previously demonstrated to be upregulated at physiological osmolarity, including the sphingomyelinase C precursor Sph2 and LigB. We provide insight into a possible requirement for transcriptional regulation as it relates to leptospiral virulence and suggest various biological processes that are affected due to the loss of native expression of this genetic locus.

Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants

PubMed Central

Ngaki, Micheline N.; Wang, Bing; Sahu, Binod B.; Srivastava, Subodh K.; Farooqi, Mohammad S.; Kambakam, Sekhar; Swaminathan, Sivakumar

2016-01-01

Fusarium virguliforme causes the serious disease sudden death syndrome (SDS) in soybean. Host resistance to this pathogen is partial and is encoded by a large number of quantitative trait loci, each conditioning small effects. Breeding SDS resistance is therefore challenging and identification of single-gene encoded novel resistance mechanisms is becoming a priority to fight this devastating this fungal pathogen. In this transcriptomic study we identified a few putative soybean defense genes, expression of which is suppressed during F. virguliforme infection. The F. virguliforme infection-suppressed genes were broadly classified into four major classes. The steady state transcript levels of many of these genes were suppressed to undetectable levels immediately following F. virguliforme infection. One of these classes contains two novel genes encoding ankyrin repeat-containing proteins. Expression of one of these genes, GmARP1, during F. virguliforme infection enhances SDS resistance among the transgenic soybean plants. Our data suggest that GmARP1 is a novel defense gene and the pathogen presumably suppress its expression to establish compatible interaction. PMID:27760122

Screening of Metagenomic and Genomic Libraries Reveals Three Classes of Bacterial Enzymes That Overcome the Toxicity of Acrylate

PubMed Central

Curson, Andrew R. J.; Burns, Oliver J.; Voget, Sonja; Daniel, Rolf; Todd, Jonathan D.; McInnis, Kathryn; Wexler, Margaret; Johnston, Andrew W. B.

2014-01-01

Acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. Acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-CoA. Previous work identified an acrylyl-CoA reductase, encoded by the gene acuI, as being important for conferring on bacteria the ability to grow in the presence of acrylate. However, some bacteria lack acuI, and, conversely, many bacteria that may not encounter acrylate in their regular environments do contain this gene. We therefore sought to identify new genes that might confer tolerance to acrylate. To do this, we used functional screening of metagenomic and genomic libraries to identify novel genes that corrected an E. coli mutant that was defective in acuI, and was therefore hyper-sensitive to acrylate. The metagenomic libraries yielded two types of genes that overcame this toxicity. The majority encoded enzymes resembling AcuI, but with significant sequence divergence among each other and previously ratified AcuI enzymes. One other metagenomic gene, arkA, had very close relatives in Bacillus and related bacteria, and is predicted to encode an enoyl-acyl carrier protein reductase, in the same family as FabK, which catalyses the final step in fatty-acid biosynthesis in some pathogenic Firmicute bacteria. A genomic library of Novosphingobium, a metabolically versatile alphaproteobacterium that lacks both acuI and arkA, yielded vutD and vutE, two genes that, together, conferred acrylate resistance. These encode sequential steps in the oxidative catabolism of valine in a pathway in which, significantly, methacrylyl-CoA is a toxic intermediate. These findings expand the range of bacteria for which the acuI gene encodes a functional acrylyl-CoA reductase, and also identify novel enzymes that can similarly function in conferring acrylate resistance, likely, again, through the removal of the toxic product acrylyl-CoA. PMID:24848004

Spreading of genes encoding enterotoxins, haemolysins, adhesin and biofilm among methicillin resistant Staphylococcus aureus strains with staphylococcal cassette chromosome mec type IIIA isolated from burn patients.

PubMed

Motallebi, Mitra; Jabalameli, Fereshteh; Asadollahi, Kheirollah; Taherikalani, Morovat; Emaneini, Mohammad

2016-08-01

The emergence of antibiotic-resistant Staphylococcus aureus in particular methicillin-resistant S. aureus (MRSA) is an important concern in burn medical centers either in Iran or worldwide. A total of 128 S. aureus isolates were collected from wound infection of burn patients during June 2013 to June 2014. Multiplex-polymerase chain reaction (MPCR) assay was performed for the characterization of the staphylococcal cassette chromosome mec (SCCmec). Genes encoding virulence factors and biofilm were targeted by PCR. Of 128 S. aureus isolates, 77 (60.1%) isolates were MRSA. Fifty four (70.1%) isolates were identified as SCCmec type IIIA. The most frequently detected toxin genes among MRSA isolates with SCCmec type IIIA were sea (64.1%) and hla (51.8%). The rate of coexistence of sea with hla and sea with hla and hlb was 37% and12.9%, respectively. The sec, eta, tst, pvl, hla and hlb genes were not detected in any of the MRSA isolates. The most prevalent genes encoding biofilm was eno, found in 61.1% of isolates, followed by fib and icaA found in 48.1% and 38.8% of the isolates, respectively. The rate of coexistence of fib + eno + icaA + icaD and fib + eno was 20.3% and 9.2%, respectively. The ebps gene was not detected in any of the isolates. In conclusion, our study indicated that the sea, hla, fib and icaA were most frequent genes encoding virulence factors among MRSA with SCCmec type IIIA isolated from burn wound infection. Moreover, the results of this study shows that the rate of coexistence of genes encoding different virulence factor were high. Copyright © 2016 Elsevier Ltd. All rights reserved.

Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response

PubMed Central

Lamacchia, Marina; Dyrka, Witold; Breton, Annick; Saupe, Sven J.; Paoletti, Mathieu

2016-01-01

Recognition and response to non self is essential to development and survival of all organisms. It can occur between individuals of the same species or between different organisms. Fungi are established models for conspecific non self recognition in the form of vegetative incompatibility (VI), a genetically controlled process initiating a programmed cell death (PCD) leading to the rejection of a fusion cell between genetically different isolates of the same species. In Podospora anserina VI is controlled by members of the hnwd gene family encoding for proteins analogous to NOD Like Receptors (NLR) immune receptors in eukaryotes. It was hypothesized that the hnwd controlled VI reaction was derived from the fungal innate immune response. Here we analyze the P. anserina transcriptional responses to two bacterial species, Serratia fonticola to which P. anserina survives and S. marcescens to which P. anserina succumbs, and compare these to the transcriptional response induced under VI conditions. Transcriptional responses to both bacteria largely overlap, however the number of genes regulated and magnitude of regulation is more important when P. anserina survives. Transcriptional responses to bacteria also overlap with the VI reaction for both up or down regulated gene sets. Genes up regulated tend to be clustered in the genome, and display limited phylogenetic distribution. In all three responses we observed genes related to autophagy to be up-regulated. Autophagy contributes to the fungal survival in all three conditions. Genes encoding for secondary metabolites and histidine kinase signaling are also up regulated in all three conditions. Transcriptional responses also display differences. Genes involved in response to oxidative stress, or encoding small secreted proteins are essentially expressed in response to bacteria, while genes encoding NLR proteins are expressed during VI. Most functions encoded in response to bacteria favor survival of the fungus while most functions up regulated during VI would lead to cell death. These differences are discussed in the frame of a multilayered response to non self in fungi. PMID:27148175

Comparative differential gene expression analysis of nucleus-encoded proteins for Rafflesia cantleyi against Arabidopsis thaliana

NASA Astrophysics Data System (ADS)

Ng, Siuk-Mun; Lee, Xin-Wei; Wan, Kiew-Lian; Firdaus-Raih, Mohd

2015-09-01

Regulation of functional nucleus-encoded proteins targeting the plastidial functions was comparatively studied for a plant parasite, Rafflesia cantleyi versus a photosynthetic plant, Arabidopsis thaliana. This study involved two species of different feeding modes and different developmental stages. A total of 30 nucleus-encoded proteins were found to be differentially-regulated during two stages in the parasite; whereas 17 nucleus-encoded proteins were differentially-expressed during two developmental stages in Arabidopsis thaliana. One notable finding observed for the two plants was the identification of genes involved in the regulation of photosynthesis-related processes where these processes, as expected, seem to be present only in the autotroph.

DNA methylation of miRNA-encoding genes in non-small cell lung cancer patients.

PubMed

Heller, Gerwin; Altenberger, Corinna; Steiner, Irene; Topakian, Thais; Ziegler, Barbara; Tomasich, Erwin; Lang, György; End-Pfützenreuter, Adelheid; Zehetmayer, Sonja; Döme, Balazs; Arns, Britt-Madeleine; Klepetko, Walter; Zielinski, Christoph C; Zöchbauer-Müller, Sabine

2018-03-23

De-regulated DNA methylation leading to transcriptional inactivation of certain genes occurs frequently in non-small cell lung cancers (NSCLC). Besides protein-encoding genes also microRNA (miRNA)-encoding genes may be targets for methylation in NSCLCs, however, the number of known methylated miRNA genes is still small. Thus, we investigated methylation of miRNA genes in primary tumours (TU) and corresponding non-malignant lung tissue samples (NL) of 50 NSCLC patients using methylated DNA immunoprecipitation followed by custom designed tiling microarray analyses (MeDIP-chip) and 252 differentially methylated probes between TU and NL samples were identified. These probes were annotated which resulted in the identification of 34 miRNA-encoding genes with increased methylation in TU specimens. While some of these miRNA-encoding genes were already known to be methylated in NSCLCs (e.g. miR-9-3, miR-124), methylation of the vast majority of them was unknown so far. We selected six miRNA genes (miR-10b, miR-1179, miR-137, miR-572, miR-3150b and miR-129-2) for gene-specific methylation analyses in TU and corresponding NL samples of 104 NSCLC patients and observed a statistically significant increase of methylation of these miRNA genes in TU samples (p<0.0001, respectively). In silico target prediction of the six miRNAs identified several oncogenic/cell proliferation promoting factors (e.g. CCNE1 as miR-1179 target). To investigate if miR-1179 indeed targets CCNE1, we transfected miR-1179 mimics into CCNE1 expressing NSCLC cells and observed down-regulated CCNE1 mRNA expression in these cells compared to control cells. Similar effects on Cyclin E1 expression were seen in Western blot analyses. In addition, we found a statistically significant growth reduction of NSCLC cells transfected with miR-1179 mimics compared to control cells. In conclusion, we identified many methylated miRNA genes in NSCLC patients and found that miR-1179 is a potential tumour cell growth suppressor in NSCLCs. Overall, our findings emphasize the impact of miRNA gene methylation on the pathogenesis of NSCLCs. This article is protected by copyright. All rights reserved.

Characterization of the Tupaia rhabdovirus genome reveals a long open reading frame overlapping with P and a novel gene encoding a small hydrophobic protein.

PubMed

Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

2005-06-01

Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses.

Bacteriophage-based vectors for site-specific insertion of DNA in the chromosome of Corynebacteria.

PubMed

Oram, Mark; Woolston, Joelle E; Jacobson, Andrew D; Holmes, Randall K; Oram, Diana M

2007-04-15

In Corynebacterium diphtheriae, diphtheria toxin is encoded by the tox gene of some temperate corynephages such as beta. beta-like corynephages are capable of inserting into the C. diphtheriae chromosome at two specific sites, attB1 and attB2. Transcription of the phage-encoded tox gene, and many chromosomally encoded genes, is regulated by the DtxR protein in response to Fe(2+) levels. Characterizing DtxR-dependent gene regulation is pivotal in understanding diphtheria pathogenesis and mechanisms of iron-dependent gene expression; although this has been hampered by a lack of molecular genetic tools in C. diphtheriae and related Coryneform species. To expand the systems for genetic manipulation of C. diphtheriae, we constructed plasmid vectors capable of integrating into the chromosome. These plasmids contain the beta-encoded attP site and the DIP0182 integrase gene of C. diphtheriae NCTC13129. When these vectors were delivered to the cytoplasm of non-lysogenic C. diphtheriae, they integrated into either the attB1 or attB2 sites with comparable frequency. Lysogens were also transformed with these vectors, by virtue of the second attB site. An integrated vector carrying an intact dtxR gene complemented the mutant phenotypes of a C. diphtheriae DeltadtxR strain. Additionally, strains of beta-susceptible C. ulcerans, and C. glutamicum, a species non-permissive for beta, were each transformed with these vectors. This work significantly extends the tools available for targeted transformation of both pathogenic and non-pathogenic Corynebacterium species.

Characterization of the Tupaia Rhabdovirus Genome Reveals a Long Open Reading Frame Overlapping with P and a Novel Gene Encoding a Small Hydrophobic Protein

PubMed Central

Springfeld, Christoph; Darai, Gholamreza; Cattaneo, Roberto

2005-01-01

Rhabdoviruses are negative-stranded RNA viruses of the order Mononegavirales and have been isolated from vertebrates, insects, and plants. Members of the genus Lyssavirus cause the invariably fatal disease rabies, and a member of the genus Vesiculovirus, Chandipura virus, has recently been associated with acute encephalitis in children. We present here the complete genome sequence and transcription map of a rhabdovirus isolated from cultivated cells of hepatocellular carcinoma tissue from a moribund tree shrew. The negative-strand genome of tupaia rhabdovirus is composed of 11,440 nucleotides and encodes six genes that are separated by one or two intergenic nucleotides. In addition to the typical rhabdovirus genes in the order N-P-M-G-L, a gene encoding a small hydrophobic putative type I transmembrane protein of approximately 11 kDa was identified between the M and G genes, and the corresponding transcript was detected in infected cells. Similar to some Vesiculoviruses and many Paramyxovirinae, the P gene has a second overlapping reading frame that can be accessed by ribosomal choice and encodes a protein of 26 kDa, predicted to be the largest C protein of these virus families. Phylogenetic analyses of the tupaia rhabdovirus N and L genes show that the virus is distantly related to the Vesiculoviruses, Ephemeroviruses, and the recently characterized Flanders virus and Oita virus and further extends the sequence territory occupied by animal rhabdoviruses. PMID:15890917

Detection of virulence and β-lactamase encoding genes in Enterobacter aerogenes and Enterobacter cloacae clinical isolates from Brazil.

PubMed

Azevedo, Paola Aparecida Alves; Furlan, João Pedro Rueda; Oliveira-Silva, Mariana; Nakamura-Silva, Rafael; Gomes, Carolina Nogueira; Costa, Karen Regina Carim; Stehling, Eliana Guedes; Pitondo-Silva, André

2018-05-21

Enterobacter cloacae and E. aerogenes have been increasingly reported as important opportunistic pathogens. In this study, a high prevalence of multi-drug resistant isolates from Brazil, harboring several β-lactamase encoding genes was found. Several virulence genes were observed in E. aerogenes, contrasting with the E. cloacae isolates which presented none. Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Regulation of Sulfur Assimilation Pathways in Burkholderia cenocepacia through Control of Genes by the SsuR Transcription Factor▿

PubMed Central

Łochowska, Anna; Iwanicka-Nowicka, Roksana; Zielak, Agata; Modelewska, Anna; Thomas, Mark S.; Hryniewicz, Monika M.

2011-01-01

The genome of Burkholderia cenocepacia contains two genes encoding closely related LysR-type transcriptional regulators, CysB and SsuR, involved in control of sulfur assimilation processes. In this study we show that the function of SsuR is essential for the utilization of a number of organic sulfur sources of either environmental or human origin. Among the genes upregulated by SsuR identified here are the tauABC operon encoding a predicted taurine transporter, three tauD-type genes encoding putative taurine dioxygenases, and atsA encoding a putative arylsulfatase. The role of SsuR in expression of these genes/operons was characterized through (i) construction of transcriptional reporter fusions to candidate promoter regions and analysis of their expression in the presence/absence of SsuR and (ii) testing the ability of SsuR to bind SsuR-responsive promoter regions. We also demonstrate that expression of SsuR-activated genes is not repressed in the presence of inorganic sulfate. A more detailed analysis of four SsuR-responsive promoter regions indicated that ∼44 bp of the DNA sequence preceding and/or overlapping the predicted −35 element of such promoters is sufficient for SsuR binding. The DNA sequence homology among SsuR “recognition motifs” at different responsive promoters appears to be limited. PMID:21317335

Molecular and genomic basis of volatile-mediated indirect defense against insects in rice.

PubMed

Yuan, Joshua S; Köllner, Tobias G; Wiggins, Greg; Grant, Jerome; Degenhardt, Jörg; Chen, Feng

2008-08-01

Rice plants fed on by fall armyworm (Spodoptera frugiperda, FAW) caterpillars emit a blend of volatiles dominated by terpenoids. These volatiles were highly attractive to females of the parasitoid Cotesia marginiventris. Microarray analysis identified 196 rice genes whose expression was significantly upregulated by FAW feeding, 18 of which encode metabolic enzymes potentially involved in volatile biosynthesis. Significant induction of expression of seven of the 11 terpene synthase (TPS) genes identified through the microarray experiments was confirmd using real-time RT-PCR. Enzymes encoded by three TPS genes, Os02g02930, Os08g07100 and Os08g04500, were biochemically characterized. Os02g02930 was found to encode a monoterpene synthase producing the single product S-linalool, which is the most abundant volatile emitted from FAW-damaged rice plants. Both Os08g07100 and Os08g04500 were found to encode sesquiterpene synthases, each producing multiple products. These three enzymes are responsible for production of the majority of the terpenes released from FAW-damaged rice plants. In addition to TPS genes, several key genes in the upstream terpenoid pathways were also found to be upregulated by FAW feeding. This paper provides a comprehensive analysis of FAW-induced volatiles and the corresponding volatile biosynthetic genes potentially involved in indirect defense in rice. Evolution of the genetic basis governing volatile terpenoid biosynthesis for indirect defense is discussed.

Involvement of the ornithine decarboxylase gene in acid stress response in probiotic Lactobacillus delbrueckii UFV H2b20.

PubMed

Ferreira, A B; Oliveira, M N V de; Freitas, F S; Paiva, A D; Alfenas-Zerbini, P; Silva, D F da; Queiroz, M V de; Borges, A C; Moraes, C A de

2015-01-01

Amino acid decarboxylation is important for the maintenance of intracellular pH under acid stress. This study aims to carry out phylogenetic and expression analysis by real-time PCR of two genes that encode proteins involved in ornithine decarboxylation in Lactobacillus delbrueckii UFV H2b20 exposed to acid stress. Sequencing and phylogeny analysis of genes encoding ornithine decarboxylase and amino acid permease in L. delbrueckii UFV H2b20 showed their high sequence identity (99%) and grouping with those of L. delbrueckii subsp. bulgaricus ATCC 11842. Exposure of L. delbrueckii UFV H2b20 cells in MRS pH 3.5 for 30 and 60 min caused a significant increase in expression of the gene encoding ornithine decarboxylase (up to 8.1 times higher when compared to the control treatment). Increased expression of the ornithine decarboxylase gene demonstrates its involvement in acid stress response in L. delbrueckii UFV H2b20, evidencing that the protein encoded by that gene could be involved in intracellular pH regulation. The results obtained show ornithine decarboxylation as a possible mechanism of adaptation to an acidic environmental condition, a desirable and necessary characteristic for probiotic cultures and certainly important to the survival and persistence of the L. delbrueckii UFV H2b20 in the human gastrointestinal tract.

Increased mitochondrial-encoded gene transcription in immortal DF-1 cells.

PubMed

Kim, H; You, S; Kim, I J; Farris, J; Foster, L K; Foster, D N

2001-05-01

We have established, in continuous cell culture, a spontaneously immortalized chicken embryo fibroblast (CEF) cell line (DF-1) as well as several other immortal CEF cell lines. The immortal DF-1 cells divided more rapidly than primary and other immortal CEF cells. To identify the genes involved in rapidly dividing DF-1 cells, we have used differential display RT-PCR. Of the numerous genes analyzed, three mitochondrial-encoded genes (ATPase 8/6, 16S rRNA, and cytochrome b) were shown to express at higher levels in DF-1 cells compared to primary and other immortal CEF cells. The inhibition of mitochondrial translation by treatment with chloramphenicol markedly decreased ATP production and cell proliferation in DF-1 cells, while not affecting growth in either primary or other immortal CEF cells. This result suggests a correlation between rapid cell proliferation and the increased mitochondrial respiratory functions. We also determined that the increased transcription of mitochondrial-encoded genes in DF-1 cells is due to increased de novo transcript synthesis as shown by mitochondrial run-on assays, and not the result of either increased mitochondrial biogenesis or mitochondrial transcript half-lives. Together, the present studies suggest that the transcriptional activation of mitochondrial-encoded genes and the elevated respiratory function should be one of the characteristics of rapidly dividing immortal cells. Copyright 2001 Academic Press.

Insight into the expression variation of metal-responsive genes in the seedling of date palm (Phoenix dactylifera).

PubMed

Chaâbene, Zayneb; Rorat, Agnieszka; Rekik Hakim, Imen; Bernard, Fabien; Douglas, Grubb C; Elleuch, Amine; Vandenbulcke, Franck; Mejdoub, Hafedh

2018-04-01

Phytochelatin synthase and metallothionein gene expressions were monitored via qPCR in order to investigate the molecular mechanisms involved in Cd and Cr detoxification in date palm (Phoenix dactylifera). A specific reference gene validation procedure using BestKeeper, NormFinder and geNorm programs allowed selection of the three most stable reference genes in a context of Cd or Cr contamination among six reference gene candidates, namely elongation factor α1, actin, aldehyde dehydrogenase, SAND family, tubulin 6 and TaTa box binding protein. Phytochelatin synthase (pcs) and metallothionein (mt) encoding gene expression were induced from the first days of exposure. At low Cd stress (0.02 mM), genes were still up-regulated until 60th day of exposure. At the highest metal concentrations, however, pcs and mt gene expressions decreased. pcs encoding gene was significantly up-regulated under Cr exposure, and was more responsive to increasing Cr concentration than mt encoding gene. Moreover, exposure to Cd or Cr influenced clearly seed germination and hypocotyls elongation. Thus, the results have proved that both analyzed genes participate in metal detoxification and their expression is regulated at transcriptional level in date palm subjected to Cr and Cd stress. Consequently, variations of expression of mt and pcs genes may serve as early-warning biomarkers of metal stress in this species. Copyright © 2018 Elsevier Ltd. All rights reserved.