WorldWideScience

Sample records for scar sequence characterized

  1. Using a sequence characterized amplified region (SCAR) marker for ...

    African Journals Online (AJOL)

    GREGORY

    2010-09-13

    Sep 13, 2010 ... This work used sequence characterized amplified region (SCAR) marker to detect the Bacillus cereus strain in strawberry fields. The purpose was to develop an effective molecular method for detecting the functional target microorganisms applied in agricultural fields. A 3×109. CFU/ml vegetative cell.

  2. Sequence characterized amplified region (SCAR) markers-based ...

    African Journals Online (AJOL)

    ajl yemi

    2011-12-19

    Dec 19, 2011 ... reverse transcription polymerase chain reaction (RT-PCR), differential-display .... were synthesized by Sangon Biological Engineering Technology and. Services ..... to cold tolerance to scar markers in common carp. J. Dalian.

  3. [Study on sequence characterized amplified region (SCAR) markers of Cornus officinalis].

    Science.gov (United States)

    Chen, Suiqing; Lu, Xiaolei; Wang, Lili

    2011-05-01

    To establish sequence characterized amplified region markers of Cornus officinalis and provide a scientific basis for molecular identification of C. officinalis. The random primer was screened through RAPD to obtain specific RAPD marker bands. The RAPD marker bands were separated, extracted, cloned and sequenced. Both ends of the sequence of RAPD marker bands were determined. A pair of specific primers was designed for conventional PCR reaction, and SCAR marker was acquired. Four pairs of primers were designed based on the sequence of RAPD marker bands. The DNA of the seven varieties of C. officinalis was amplified by using YST38 and YST43 primer. The results showed that seven varieties of C. officinalis were able to produce a single PCR product. It was an effective way to identify C. officinalis. The varieties with cylindrical and long-pear shape fruits amplified by YST38 showed a specific band, which could be used as the evidence of variety identification. Seven varieties of C. oficinalis were amplified by using primer YST39. But the size of band of the variety with spindly shape fruit (35,0400 bp) was about 300 bp, which was shorter than those of the variety with the other shape fruits of C. officinalis (650-700 bp). The variety with the spindly shape fruit could be identified through this difference. The primer YST92 could produce a fragment from 600-700 bp in the varieties with cylindrical and long-pear shape fruits, a fragment from 200-300 bp in the varieties with oval and short-cylindrical shape fruits and had no fragment in the varieties with long cylindrical, elliptic and short-pear shape fruits, which could be used to select the different shapes of C. officinalis. SCAR mark is established and can be used as the basis for breeding and distinguishing the verieties of C. officinalis.

  4. A modification to the SCAR (Sequence Characterized Amplified Region method provides phylogenetic insights within Ceratozamia (Zamiaceae Una modificación al método SCAR (Sequence Characterized Amplified Region aporta entendimiento filogenético en Ceratozamia (Zamiaceae

    Directory of Open Access Journals (Sweden)

    Dolores González

    2012-12-01

    Full Text Available Phylogenetic relationships among closely related plant species are still problematic. DNA intergenic regions often are insufficiently variable to provide desired resolution or support. In this study, a modification to the Sequence Characterized Amplified Region (SCAR method was used to find polymorphic loci for phylogenetic analyses within Ceratozamia. RAPD markers were first used to detect variation in 5 species. Then, equal length fragments found in 2 or more species were excised from the gel, purified and digested with frequent cutter restriction enzymes for isolating both ends, which have the same primer site. Digested fragments were sequenced with the RAPD primer. Variable sequences were used to design specific primers for amplifying and sequencing in all species for phylogenetic analyses. Our results confirmed the previously known high genome sequence resemblance within this genus that contrasts with its high morphological variation. Only 7 parsimony informative characters were found with this approach. Nonetheless, the Digested-SCAR (D-SCAR method provided some phylogenetic insights. Four main clades consistent with distribution ranges of the species were detected. The approach presented here was effective to solve some relationships within the genus and can potentially be implemented in other organisms to find polymorphic loci for phylogenetic studies at any taxonomic level.Las relaciones filogenéticas entre especies de plantas cercanamente relacionadas es aún problemático. Las regiones intergénicas del ADN son a menudo insuficientemente variables para proveer los niveles de resolución y soporte deseados. En este estudio, se usó una modificación al método Sequence Characterized Amplified Region (SCAR para encontrar loci polimórficos para análisis filogenéticos en Ceratozamia. Primero se usaron marcadores RAPD para detectar variación en 5 especies; luego, se cortaron del gel los fragmentos de la misma longitud en 2 o m

  5. Development of SCAR (sequence-characterized amplified region) markers as a complementary tool for identification of ginger (Zingiber officinale Roscoe) from crude drugs and multicomponent formulations.

    Science.gov (United States)

    Chavan, Preeti; Warude, Dnyaneshwar; Joshi, Kalpana; Patwardhan, Bhushan

    2008-05-01

    Zingiber officinale Roscoe (common or culinary ginger) is an official drug in Ayurvedic, Indian herbal, Chinese, Japanese, African and British Pharmacopoeias. The objective of the present study was to develop DNA-based markers that can be applied for the identification and differentiation of the commercially important plant Z. officinale Roscoe from the closely related species Zingiber zerumbet (pinecone, bitter or 'shampoo' ginger) and Zingiber cassumunar [cassumunar or plai (Thai) ginger]. The rhizomes of the other two Zingiber species used in the present study are morphologically similar to that of Z. officinale Roscoe and can be used as its adulterants or contaminants. Various methods, including macroscopy, microscopy and chemoprofiling, have been reported for the quality control of crude ginger and its products. These methods are reported to have limitations in distinguishing Z. officinale from closely related species. Hence, newer complementary methods for correct identification of ginger are useful. In the present study, RAPD (random amplification of polymorphic DNA) analysis was used to identify putative species-specific amplicons for Z. officinale. These were further cloned and sequenced to develop SCAR (sequence-characterized amplified region) markers. The developed SCAR markers were tested in several non-Zingiber species commonly used in ginger-containing formulations. One of the markers, P3, was found to be specific for Z. officinale and was successfully applied for detection of Z. officinale from Trikatu, a multicomponent formulation.

  6. Development of dominant sequence characterized amplified region (SCAR marker linked with plume moth (Exelastis atomosa Walsingham 1886 resistance in pigeon-pea

    Directory of Open Access Journals (Sweden)

    Ramya R Mishra

    2015-12-01

    Full Text Available The mode of gene action governing resistance to plume moth (Exelastis atomosa Walsingham 1886 derived from pigeon-pea (Cajanus scarabaeoides (L. Thouars accession ICPW-94 has been determined and the resistance alleles have been designated as PPM1. The progenies of F2 population and F3 families derived from an interspecific cross C. cajan (L. Huth ('ICP-26' x C. scarabaeoides (accession ICPW-94 revealed monogenic gene action for resistance to plume moth, and the dominant control by single locus or cluster of tightly linked alleles. Bulked segregant analysis (BSA of 116 F2 progenies by using 143 parental polymorphic RAPD primers could identify a fragment OPA09(910 associated with plume moth resistance in coupling phase of linkage. Further single plant analysis of the 116 F2 mapping population revealed OPA09(910 was linked to PPMi locus conferring host resistance to plume moth with recombination fraction (rf value of 0.125 (12.7 cM of Kosambi function. The resistance specific fragment OPA09(910 was cloned, sequenced and converted into a sequence characterized amplified region (SCAR marker, SCOPA09(942, which was also closely associated (10.3 cM with the locus PPMl with rf value 0.102. BLAST analysis with pigeon-pea genome sequence also confirmed its occurrence in CcLG02 (Scafseq.LG_V5.0fa and contig 01597 (AFSP01.fsa1. This SCAR marker showed reasonable screening efficiency in the F2, F3, and BC1F1 lines, thus it can be used as genetic handle in marker-assisted introgression of the genomic fragment conferring plume moth resistance and screening of breeding lines in pigeon-pea.

  7. Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF): a case study in the Phoma exigua species complex.

    Science.gov (United States)

    Aveskamp, Maikel M; Woudenberg, Joyce H C; de Gruyter, Johannes; Turco, Elena; Groenewald, Johannes Z; Crous, Pedro W

    2009-05-01

    Phoma exigua is considered to be an assemblage of at least nine varieties that are mainly distinguished on the basis of host specificity and pathogenicity. However, these varieties are also reported to be weak pathogens and secondary invaders on non-host tissue. In practice, it is difficult to distinguish P. exigua from its close relatives and to correctly identify isolates up to the variety level, because of their low genetic variation and high morphological similarity. Because of quarantine issues and phytosanitary measures, a robust DNA-based tool is required for accurate and rapid identification of the separate taxa in this species complex. The present study therefore aims to develop such a tool based on unique nucleotide sequence identifiers. More than 60 strains of P. exigua and related species were compared in terms of partial actin gene sequences, or analysed using DNA amplification fingerprinting (DAF) with short, arbitrary, mini-hairpin primers. Fragments in the fingerprint unique to a single taxon were identified, purified and sequenced. Alignment of the sequence data and subsequent primer trials led to the identification of taxon-specific sequence characterized amplified regions (SCARs), and to a set of specific oligonucleotide combinations that can be used to identify these organisms in plant quarantine inspections.

  8. Differentiating Authentic Adenophorae Radix from Its Adulterants in Commercially-Processed Samples Using Multiplexed ITS Sequence-Based SCAR Markers

    Directory of Open Access Journals (Sweden)

    Byeong Cheol Moon

    2017-06-01

    Full Text Available Determining the precise botanical origin of a traditional herbal medicine is important for basic quality control. In both the Chinese and Korean herbal pharmacopoeia, authentic Adenophorae Radix is defined as the roots of Adenophora stricta and Adenophora triphylla. However, the roots of Codonopsis lanceolata, Codonopsis pilosula, and Glehnia littoralis are frequently distributed as Adenophorae Radix in Korean herbal markets. Unfortunately, correctly identifying dried roots is difficult using conventional methods because the roots of those species are morphologically similar. Therefore, we developed DNA-based markers for the identification of authentic Adenophorae Radix and its common adulterants in commercially-processed samples. To develop a reliable method to discriminate between Adenophorae Radix and its adulterants, we sequenced the nuclear ribosomal DNA internal transcribed spacers (nrDNA-ITS and designed sequence-characterized amplified region (SCAR primers specific to the authentic and adulterant species. Using these primers, we developed SCAR markers for each species and established a multiplex-PCR method that can authenticate the four herbal medicines in a single PCR reaction. Furthermore, we confirmed that commercially-processed herbal medicines, which often have degraded DNA, could be assessed with our method. Therefore, our method is a reliable genetic tool to protect against adulteration and to standardize the quality of Adenophorae Radix.

  9. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

    DEFF Research Database (Denmark)

    Mirzadeh, Kiavash; Martinez, Virginia; Toddo, Stephen

    2015-01-01

    are poorly expressed even when they are codon-optimized and expressed from vectors with powerful genetic elements. In this study, we show that poor expression can be caused by certain nucleotide sequences (e.g., cloning scars) at the junction between the vector and the coding sequence. Since these sequences...

  10. MRI in differentiation between recurrent disk herniation and postoperative scar. Value of FLAIR sequences

    International Nuclear Information System (INIS)

    Capiel, Carlos A. h; Bouzas, Carlos A.; Porto, Viviana G.

    2000-01-01

    The differential diagnosis between epidural fibrosis and recurrent or residual disk herniation in symptomatic patients who have been operated is often difficult. The MRI with Spin Echo T1 sequences before and after i.v. gadolinium plays and important role in the differentiation of these two entities. The signal characteristics in T1 and T2 sequences are not reliable to distinguish between herniated disk and scar. In order to evaluate the use of the FLAIR technique in the differentiation between herniated disk and epidural fibrosis we used MRI to study 37 symptomatic patients who had been operated of lumbar disk herniation, with FSE-T2 sequences in axial and sagittal planes, FLAIR in axial sections and SE-T1 in sagittal and axial sections before and after i.v. gadolinium. This sequence was used as gold standard for the final diagnosis. We conclude that the FLAIR technique is a reliable alternative in the differential diagnosis between epidural fibrosis and herniated disk, providing a positive correlation to the SE-T1-weighted images with i.v. gadolinium in 100% of the patients. (author)

  11. Development of a sequence characterized amplified region (SCAR ...

    African Journals Online (AJOL)

    The varieties of rice are difficult to be distinguished because of their similar morphological characters, therefore rice variety identification or differentiation is very important. The authentication by using molecular marker or DNA fingerprinting is the most accurate method. In this study, random amplified polymorphic DNA ...

  12. Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn.

    Science.gov (United States)

    Cha, Thye San; Anne-Marie, Kaben; Chuah, Tse Seng

    2014-02-01

    Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.

  13. Acne Scars

    Science.gov (United States)

    ... or scrubbing scarred areas can further reduce skin elasticity and heighten the appearance of the scar. Pick ... technique or procedure is appropriate for my skin type? Did the doctor show me before-and-after ...

  14. Roentgenodiagnosis of stomach postulcer scar

    International Nuclear Information System (INIS)

    Strunin, A.E.

    1985-01-01

    A study was made of the X-ray picture of the stomach postulcer scar in correlation with fibrogastroscopy in 39 patients. The X-ray picture was characterized by considerable polymorphism and at the same time it was difficult to single out pathognomonic features. For specified diagnosis and differentiation the detection of the postulcer scar must become a multifaceted roentgenoendoscopic problem. Stomach ulcers may scar, sometimes with the complete regeneration of the mucosa relief, however their recurrences can develop in the zone of the postulcer scar

  15. Development and detection efficiency of sequence characterized amplified region markers for authentication of medicinal plant Ruta graveolens and its adulterant Euphorbia dracunculoides

    Directory of Open Access Journals (Sweden)

    Irum Gul

    2016-01-01

    Full Text Available Background: With the increase in demand of herbal medicines, adulteration in these drugs is also gaining momentum and remains an indispensable problem in domestic and export markets. Correct identification is the first step toward assuring quality, safety, and efficacy of indigenous herbal medicines. Materials and Methods: In this study, sequence characterized amplified region (SCAR markers were developed to discriminate Ruta graveolens from its adulterant Euphorbia dracunculoides. Random amplified polymorphic DNA (RAPD was performed and subsequently converted into SCAR markers. Results: After performing RAPD, SCAR primers were designed from the selected unique RAPD amplicons of the genuine drug as well as its adulterant. These primers produced 670 bp and 750 bp SCAR markers with genomic DNA sample of R. graveolens and E. dracunculoides, respectively. Conclusion: Development of these markers will help in the quality control of herbal drugs and monitoring widespread adulteration of these drugs by pharmaceutical industries and government agencies.

  16. SCAR marker specific to detect Magnaporthe grisea infecting finger millets (Eleusine coracana).

    Science.gov (United States)

    Gnanasing Jesumaharaja, L; Manikandan, R; Raguchander, T

    2016-09-01

    To determine the molecular variability and develop specific Sequence Characterized Amplified Region (SCAR) marker for the detection of Magnaporthe grisea causing blast disease in finger millet. Random amplified polymorphic DNA (RAPD) was performed with 14 isolates of M. grisea using 20 random primers. SCAR marker was developed for accurate and specific detection of M. grisea infecting only finger millets. The genetic similarity coefficient within each group and variation between the groups was observed. Among the primers, OPF-08 generated a RAPD polymorphic profile that showed common fragment of 478 bp in all the isolates. This fragment was cloned and sequenced. SCAR primers, Mg-SCAR-FP and Mg-SCAR-RP, were designed using sequence of the cloned product. The specificity of the SCAR primers was evaluated using purified DNA from M. grisea isolates from finger millets and other pathogens viz., Pyricularia oryzae, Colletotrichum gloeosporioides, Colletotrichum falcatum and Colletotrichum capcisi infecting different crops. The SCAR primers amplified only specific 460 bp fragment from DNA of M. grisea isolates and this fragment was not amplified in other pathogens tested. SCAR primers distinguish blast disease of finger millet from rice as there is no amplification in the rice blast pathogen. PCR-based SCAR marker is a convenient tool for specific and rapid detection of M. grisea in finger millets. Genetic diversity in fungal population helps in developing a suitable SCAR marker to identify the blast pathogen at the early stage of infection. © 2016 The Society for Applied Microbiology.

  17. Scars of the Wigner Function.

    Science.gov (United States)

    Toscano; de Aguiar MA; Ozorio De Almeida AM

    2001-01-01

    We propose a picture of Wigner function scars as a sequence of concentric rings along a two-dimensional surface inside a periodic orbit. This is verified for a two-dimensional plane that contains a classical hyperbolic orbit of a Hamiltonian system with 2 degrees of freedom. The stationary wave functions are the familiar mixture of scarred and random waves, but the spectral average of the Wigner functions in part of the plane is nearly that of a harmonic oscillator and individual states are also remarkably regular. These results are interpreted in terms of the semiclassical picture of chords and centers.

  18. Characterizing leader sequences of CRISPR loci

    DEFF Research Database (Denmark)

    Alkhnbashi, Omer; Shah, Shiraz Ali; Garrett, Roger Antony

    2016-01-01

    The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR...... array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs...... sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from...

  19. Post-burn scars and scar contractures

    Directory of Open Access Journals (Sweden)

    Goel Arun

    2010-10-01

    Full Text Available The mortality and morbidity from burns have diminished tremendously over the last six to seven decades. However, these do not truly reflect whether the victim could go back to society as a useful person or not and lead a normal life because of the inevitable post-burn scars, contractures and other deformities which collectively have aesthetic and functional considerations. This article gives an overview of the post-burn scars and scar contractures, especially their prevention, minimisation and principles of management.

  20. The characterization of twenty sequenced human genomes.

    Directory of Open Access Journals (Sweden)

    Kimberly Pelak

    2010-09-01

    Full Text Available We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals with severe hemophilia A and ten "control" genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.

  1. Computation Sequences: A Way to Characterize Classes of Attribute Grammars

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis

    1983-01-01

    A computation sequence for a derivation tree specifies a way of walking through the tree evaluating all the attributes of all nodes. By requiring that each derivation tree has a computation sequence with a certain property, it is possible to give simple characterizations of well-known subclasses ...

  2. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Science.gov (United States)

    Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  3. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    Directory of Open Access Journals (Sweden)

    Satish K Guttikonda

    Full Text Available Demand for the commercial use of genetically modified (GM crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

  4. [Physical therapy for scars].

    Science.gov (United States)

    Masanovic, Marguerite Guillot

    2013-01-01

    Physical therapy consists notably of hand or mechanical massages, pressure therapy using various fabrics or splints, cryotherapy, laser therapy, etc. It forms part of the range of therapies used to treat pathological scars, including medical and surgical treatment. While the results are often satisfactory for hypertrophic scars, they remain uncertain for major keloids.

  5. Facial Scar Revision: Understanding Facial Scar Treatment

    Science.gov (United States)

    ... keep the head elevated when lying down, to use cold compresses to reduce swelling, and to avoid any activity that places undue stress on the area of the incision. Depending on the surgery performed and the site of the scar, the facial plastic surgeon will explain the types of activities to ...

  6. Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays.

    Science.gov (United States)

    Roy, Neha Samir; Park, Kyong-Cheul; Lee, Sung-Il; Im, Min-Ji; Ramekar, Rahul Vasudeo; Kim, Nam-Soo

    2018-02-01

    Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population. A total of 108 dominant SCAR markers were designed out of which, 32 were successfully integrated in to the linkage map of maize RIL population and the remaining were added to a physical map for references to check the distribution throughout all chromosomes. Moreover, 76 polymorphic SCARs were used for diversity analysis of corn accessions being used in Korean corn breeding program. The overall average polymorphic information content (PIC) was 0.34, expected heterozygosity was 0.324 and Shannon's information index was 0.491 with a percentage of polymorphism of 98.67%. Further analysis by associating with desirable traits may also provide some accurate trait specific tagged SCAR markers. TE linked SCARs can provide an added level of polymorphism as well as improved discriminating ability and therefore can be useful in further breeding programs to develop high yielding germplasm.

  7. Pathological mechanism for delayed hyperenhancement of chronic scarred myocardium in contrast agent enhanced magnetic resonance imaging.

    Directory of Open Access Journals (Sweden)

    Jian Wang

    Full Text Available OBJECTIVES: To evaluate possible mechanism for delayed hyperenhancement of scarred myocardium by investigating the relationship of contrast agent (CA first pass and delayed enhancement patterns with histopathological changes. MATERIALS AND METHODS: Eighteen pigs underwent 4 weeks ligation of 1 or 2 diagonal coronary arteries to induce chronic infarction. The hearts were then removed and perfused in a Langendorff apparatus. The hearts firstly experienced phosphorus 31 MR spectroscopy. The hearts in group I (n = 9 and II (n = 9 then received the bolus injection of Gadolinium diethylenetriamine pentaacetic acid (0.05 mmol/kg and gadolinium-based macromolecular agent (P792, 15 µmol/kg, respectively. First pass T2* MRI was acquired using a gradient echo sequence. Delayed enhanced T1 MRI was acquired with an inversion recovery sequence. Masson's trichrome and anti- von Willebrand Factor (vWF staining were performed for infarct characterization. RESULTS: Wash-in of both kinds of CA caused the sharp and dramatic T2* signal decrease of scarred myocardium similar to that of normal myocardium. Myocardial blood flow and microvessel density were significantly recovered in 4-week-old scar tissue. Steady state distribution volume (ΔR1 relaxation rate of Gd-DTPA was markedly higher in scarred myocardium than in normal myocardium, whereas ΔR1 relaxation rate of P792 did not differ significantly between scarred and normal myocardium. The ratio of extracellular volume to the total water volume was significantly greater in scarred myocardium than in normal myocardium. Scarred myocardium contained massive residual capillaries and dilated vessels. Histological stains indicated the extensively discrete matrix deposition and lack of cellular structure in scarred myocardium. CONCLUSIONS: Collateral circulation formation and residual vessel effectively delivered CA into scarred myocardium. However, residual vessel without abnormal hyperpermeability allowed Gd

  8. Keloids and Hypertrophic Scars

    Science.gov (United States)

    ... to the skin both skin cells and connective tissue cells (fibroblasts) begin multiplying to repair the damage. A scar is made up of 'connective tissue', gristle-like fibers deposited in the skin by ...

  9. Radiation scars on mammograms

    International Nuclear Information System (INIS)

    Otto, H.; Breining, H.; Knappschafts-Krankenhaus Essen

    1985-01-01

    Six patients with radiation scars are described. In each case the diagnosis was confirmed histologically in five cases corresponding mammograms were available. The histological appearances of radiation scars are described and the radiological features are presented. These lesions can be diagnosed mammographically in vivo. Macroscopically differentiation from a scirrhous carcinoma is not possible and therefore a radiation scar must always be excised; this also leads to definitive cure. On mammographic screening the incidence is 0.5 to 0.9 per thousand. The significance of radiation scars depends on the fact that they are pre-cancerous and therefore are equivalent to the early diagnosis of a carcinoma with the possibility of a complete cure. (orig.) [de

  10. A study on scar revision

    Directory of Open Access Journals (Sweden)

    Ashutosh Talwar

    2016-04-01

    Full Text Available Introduction: Scars are psychologically distressing for the patients and have an impact on the quality of life and self esteem of the patients. Scar revision is an aesthetic skill which is mastered by plastic surgeons and encroached now by dermatosurgeons. Scars on the face are aesthetically unacceptable and various techniques have been improvised for making a scar aesthetically acceptable. Various types of techniques are used for scar revision like W plasty, Z plasty and VY plasty. Aims: To see the efficacy of various scar revision techniques including Z plasty, VY plasty and W plasty in 30 patients with disfiguring scars. Methods: We selected twenty patients of disfiguring scars for the study. The scars from various causes including trauma and burns were included in our study. Various techniques of scar revision include Z plasty, W plasty and VY plasty were performed according to the type and site of scar. Results: Male: female was 1.5: 1. The scar revision surgery yielded excellent results with minimal complications including haematoma formation, secondary infection and delayed healing seen in 5% patients each. Regarding the efficacy of scar revision, excellent improvement was seen in 60% patients, moderate improvement was seen in 30% patients and mild improvement was seen in 10% patients. Conclusions: Dermatologists can employ a number of surgical scar revision techniques. While some are better suited to treat specific types of scars, they can be used in combination with each other or with adjunctive therapies to achieve optimal results.

  11. Characterizing the D2 statistic: word matches in biological sequences.

    Science.gov (United States)

    Forêt, Sylvain; Wilson, Susan R; Burden, Conrad J

    2009-01-01

    Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between two sequences. Recent advances have been made in the characterization of this statistic and in the approximation of its distribution. Here, these results are extended to the case of approximate word matches. We compute the exact value of the variance of the D2 statistic for the case of a uniform letter distribution, and introduce a method to provide accurate approximations of the variance in the remaining cases. This enables the distribution of D2 to be approximated for typical situations arising in biological research. We apply these results to the identification of cis-regulatory modules, and show that this method detects such sequences with a high accuracy. The ability to approximate the distribution of D2 for both exact and approximate word matches will enable the use of this statistic in a more precise manner for sequence comparison, database searches, and identification of transcription factor binding sites.

  12. Keratinocyte-derived growth factors play a role in the formation of hypertrophic scars

    NARCIS (Netherlands)

    Niessen, FB; Andriessen, MP; Schalkwijk, J; Visser, L; Timens, W

    In predisposed individuals, wound healing can lead to hypertrophic scar or keloid formation, characterized by an overabundant extracellular matrix. It has recently been shown that hypertrophic scars are accompanied by abnormal keratinocyte differentiation and proliferation, and significantly

  13. Cesarean scar pregnancy

    DEFF Research Database (Denmark)

    Petersen, Kathrine Birch; Hoffmann, Elise; Rifbjerg Larsen, Christian

    2016-01-01

    OBJECTIVE: To study treatment modalities for cesarean scar pregnancies (CSPs), focusing on efficacy and complications in relation to study quality. DESIGN: Systematic review. SETTING: Not applicable. PATIENT(S): A total of 2,037 women with CSP. INTERVENTION(S): Review of MEDLINE, EMBASE, and Coch......OBJECTIVE: To study treatment modalities for cesarean scar pregnancies (CSPs), focusing on efficacy and complications in relation to study quality. DESIGN: Systematic review. SETTING: Not applicable. PATIENT(S): A total of 2,037 women with CSP. INTERVENTION(S): Review of MEDLINE, EMBASE...

  14. Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

    Science.gov (United States)

    Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A

    2015-05-25

    The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

  15. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants

    NARCIS (Netherlands)

    Ho, Cynthia K. Y.; Welkers, Matthijs R. A.; Thomas, Xiomara V.; Sullivan, James C.; Kieffer, Tara L.; Reesink, Henk W.; Rebers, Sjoerd P. H.; de Jong, Menno D.; Schinkel, Janke; Molenkamp, Richard

    2015-01-01

    We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were

  16. Characterization and perturbation of Gabor frame sequences with rational parameters

    DEFF Research Database (Denmark)

    Bownik, M.; Christensen, Ole

    2007-01-01

    Let A c L-2(R) be at most countable, and E N. We characterize various frame-properties for Gabor systems of the form G(l. p/q . A) = {e(2 pi imx) g (x-np/q) : m, n epsilon Z, g epsilon A} in terms of the corresponding frame properties for the row vectors in the Zibulski-Zeevi matrix. This extends...... work by [Ron and Shen, Weyl-Heisenherg systenis and Riesz bases in L-2(R-d). Duke Math. J. 89 (1997) 237-282]. who considered the case where A is finite. As a consequence of the results, we obtain results concerning stability of Gabor frames under perturbation of the generators. We also introduce...... the concept of rigid frame sequences, which have the property that all Sufficiently small perturbations with a lower frame bound above some threshold value, automatically generate the same closed linear span. Finally, we characterize rigid Gabor frame sequences in terms of their Zibulski-Zeevi matrix....

  17. Elastin Is Differentially Regulated by Pressure Therapy in a Porcine Model of Hypertrophic Scar.

    Science.gov (United States)

    Carney, Bonnie C; Liu, Zekun; Alkhalil, Abdulnaser; Travis, Taryn E; Ramella-Roman, Jessica; Moffatt, Lauren T; Shupp, Jeffrey W

    Beneficial effects of pressure therapy for hypertrophic scars have been reported, but the mechanisms of action are not fully understood. This study evaluated elastin and its contribution to scar pliability. The relationship between changes in Vancouver Scar Scale (VSS) scores of pressure-treated scars and differential regulation of elastin was assessed. Hypertrophic scars were created and assessed weekly using VSS and biopsy procurement. Pressure treatment began on day 70 postinjury. Treated scars were compared with untreated shams. Treatment lasted 2 weeks, through day 84, and scars were assessed weekly through day 126. Transcript and protein levels of elastin were quantified. Pressure treatment resulted in lower VSS scores compared with sham-treated scars. Pliability (VSSP) was a key contributor to this difference. At day 70 pretreatment, VSSP = 2. Without treatment, sham-treated scars became less pliable, while pressure-treated scars became more pliable. The percentage of elastin in scars at day 70 was higher than in uninjured skin. Following treatment, the percentage of elastin increased and continued to increase through day 126. Untreated sham scars did not show a similar increase. Quantification of Verhoeff-Van Gieson staining corroborated the findings and immunofluorescence revealed the alignment of elastin fibers. Pressure treatment results in increased protein level expression of elastin compared with sham-untreated scars. These findings further characterize the extracellular matrix's response to the application of pressure as a scar treatment, which will contribute to the refinement of rehabilitation practices and ultimately improvements in functional and psychosocial outcomes for patients.

  18. Acne Scar Treatment: A Multimodality Approach Tailored to Scar Type.

    Science.gov (United States)

    Zaleski-Larsen, Lisa A; Fabi, Sabrina G; McGraw, Timothy; Taylor, Mark

    2016-05-01

    Acne scarring can be classified into atrophic icepick, boxcar, and rolling scars in addition to keloidal and hypertrophic scars. Additionally, these scars can be erythematous, hyperpigmented, and/or hypopigmented. Each scar type has a different structural cause warranting a customized approach. Many cosmetic options exist to address these changes individually, but little literature exists about the safety and efficacy of combining such procedures and devices. A Medline search was performed on combination treatments because it relates to facial acne scarring, and results are summarized. Practical applications for these combinations of procedures are also discussed. Studies examining the efficacy and safety of ablative, nonablative, fractionated, and nonfractionated lasers, dermabrasion, chemical peels, needling, subcision, radiofrequency, stem cell therapy, fat transplantation, platelet-rich plasma, and hyaluronic acid dermal fillers for acne scars were found. The authors review their experience in combining these techniques. Review of the literature revealed multiple single options for facial acne scarring treatment with minimal evidence in the literature found on the safety and efficacy of combining such procedures and devices. The authors' experience is that combining acne scar treatment techniques can be performed safely and synergistically with optimal patient outcomes.

  19. Comparison of next generation sequencing technologies for transcriptome characterization

    Directory of Open Access Journals (Sweden)

    Soltis Douglas E

    2009-08-01

    Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

  20. Characterization and sequence analysis of cysteine and glycine-rich ...

    African Journals Online (AJOL)

    Primers specific for CSRP3 were designed using known cDNA sequences of Bos taurus published in database with different accession numbers. Polymerase chain reaction (PCR) was performed and products were purified and sequenced. Sequence analysis and alignment were carried out using CLUSTAL W (1.83).

  1. Can Acne Scars Be Removed?

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Can Acne Scars Be Removed? KidsHealth / For Teens / Can Acne ... eliminar las cicatrices del acné? Different Types of Acne Scars from acne can seem like double punishment — ...

  2. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

    Directory of Open Access Journals (Sweden)

    Takeru Nakazato

    Full Text Available High-throughput sequencing technology, also called next-generation sequencing (NGS, has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA. As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/. This service will improve accessibility to high-quality data from SRA.

  3. Tuberculin reaction and BCG scar

    DEFF Research Database (Denmark)

    Timmermann, Clara Amalie Gade; Biering-Sørensen, Sofie; Aaby, Peter

    2015-01-01

    rate ratio (MRR) comparing children with a BCG scar with those without was 0.42 (95% CI = 0.19; 0.93). There was a similar tendency for TST positivity: MRR = 0.47 (95% CI = 0.14; 1.54). For LBW children who had both a positive TST reaction and a scar, the MRR was 0.22 (95% CI = 0.05; 0.87). For NBW...

  4. Molecular characterization of Giardia psittaci by multilocus sequence analysis.

    Science.gov (United States)

    Abe, Niichiro; Makino, Ikuko; Kojima, Atsushi

    2012-12-01

    Multilocus sequence analyses targeting small subunit ribosomal DNA (SSU rDNA), elongation factor 1 alpha (ef1α), glutamate dehydrogenase (gdh), and beta giardin (β-giardin) were performed on Giardia psittaci isolates from three Budgerigars (Melopsittacus undulates) and four Barred parakeets (Bolborhynchus lineola) kept in individual households or imported from overseas. Nucleotide differences and phylogenetic analyses at four loci indicate the distinction of G. psittaci from the other known Giardia species: Giardia muris, Giardia microti, Giardia ardeae, and Giardia duodenalis assemblages. Furthermore, G. psittaci was related more closely to G. duodenalis than to the other known Giardia species, except for G. microti. Conflicting signals regarded as "double peaks" were found at the same nucleotide positions of the ef1α in all isolates. However, the sequences of the other three loci, including gdh and β-giardin, which are known to be highly variable, from all isolates were also mutually identical at every locus. They showed no double peaks. These results suggest that double peaks found in the ef1α sequences are caused not by mixed infection with genetically different G. psittaci isolates but by allelic sequence heterogeneity (ASH), which is observed in diplomonad lineages including G. duodenalis. No sequence difference was found in any G. psittaci isolates at the gdh and β-giardin, suggesting that G. psittaci is indeed not more diverse genetically than other Giardia species. This report is the first to provide evidence related to the genetic characteristics of G. psittaci obtained using multilocus sequence analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Southern-by-Sequencing: A Robust Screening Approach for Molecular Characterization of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Gina M. Zastrow-Hayes

    2015-03-01

    Full Text Available Molecular characterization of events is an integral part of the advancement process during genetically modified (GM crop product development. Assessment of these events is traditionally accomplished by polymerase chain reaction (PCR and Southern blot analyses. Southern blot analysis can be time-consuming and comparatively expensive and does not provide sequence-level detail. We have developed a sequence-based application, Southern-by-Sequencing (SbS, utilizing sequence capture coupled with next-generation sequencing (NGS technology to replace Southern blot analysis for event selection in a high-throughput molecular characterization environment. SbS is accomplished by hybridizing indexed and pooled whole-genome DNA libraries from GM plants to biotinylated probes designed to target the sequence of transformation plasmids used to generate events within the pool. This sequence capture process enriches the sequence data obtained for targeted regions of interest (transformation plasmid DNA. Taking advantage of the DNA adjacent to the targeted bases (referred to as next-to-target sequence that accompanies the targeted transformation plasmid sequence, the data analysis detects plasmid-to-genome and plasmid-to-plasmid junctions introduced during insertion into the plant genome. Analysis of these junction sequences provides sequence-level information as to the following: the number of insertion loci including detection of unlinked, independently segregating, small DNA fragments; copy number; rearrangements, truncations, or deletions of the intended insertion DNA; and the presence of transformation plasmid backbone sequences. This molecular evidence from SbS analysis is used to characterize and select GM plants meeting optimal molecular characterization criteria. SbS technology has proven to be a robust event screening tool for use in a high-throughput molecular characterization environment.

  6. RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).

    Science.gov (United States)

    Zhao, Ya-E; Wu, Li-Ping

    2012-06-01

    For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.

  7. Characterization and sequence analysis of cysteine and glycine-rich ...

    African Journals Online (AJOL)

    Tarek

    2011-04-18

    Apr 18, 2011 ... nucleotide alignment of both native buffalo and cattle CSRP3 cDNAs sequences ..... Exon III, Identities = 71/75 (94%), Gaps = 1/75 (1%) Strand=Plus/Plus ... Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J,.

  8. Time course of epidural scar enhancement with Gd-DTPA in an animal model

    International Nuclear Information System (INIS)

    Blaser, S.I.; Ross, J.S.; Berridge, M.; Emery, S.; Bolesta, M.J.; Modic, M.T.; Masaryk, T.J.; Bohlman, H.

    1988-01-01

    In eight beagles following laminectomies, dynamic contrast enhancement of posterior epidural scar was assessed sequentially over 4 months by means of FLASH sequence (20/10/50) following Gd-DTPA. A consistent pattern of enhancement was apparent in all dogs. Maximum enhancement occurred after 1 month (80%-130%), with peak enhancement at 7-10 minutes. There was decreased enhancement each succeeding month with a similar time to peak. Time curves were obtained for blood, muscle, and scar following injection of 40 μCi Gd-153 DTPA and correlated well with in vivo MR image intensities. Histology showed granulation tissue early following surgery, which matured to scar by 4 months. These findings are in contrast to reports of enhancement of anterior scar in humans irrespective of age. The difference may be secondary to location in that posterior scar does not receive the trauma and stress acting on anterior scar associated with a degenerative disk

  9. Molecular mapping of the Pinus monticola Cr2 gene using AFLP and SCAR markers

    Directory of Open Access Journals (Sweden)

    A.K.M. Ekramoddoullah

    2013-12-01

    Full Text Available White pine blister rust (WPBR, caused by Cronartium ribicola, is a devastating disease in five-needle pines. Genetic resistance is an important component of integrated strategies to control WPBR. The major resistance gene Cr2, discovered by Kinloch etal.(1999, is also effective against British Columbia (BC isolates of WPBR (Hunt et al. 2004. Pyramiding Cr2 gene with other resistancegenes is being pursued as a strategy in BC white pine breeding. To facilitate this strategy, we have recently identified a few RAPD markerslinked to Cr2 at one side (Liu et al. 2006. The objective of the present study was to identify amplified fragment length polymorphism(AFLP markers linked to both sides of Cr2 for its more precise apping. Use of the AFLP technique combined with bulked segregant analysis (BSA and haploid segregation analysis allowed the identification of five AFLP markers. Of these five AFLP markers in the Cr2 linkage, markers EacccMccgat-365, EactgMcccac- 290, and EacagEacag-750 werelinked in coupling and EacagMcccag-160r and EacccMccgat-180r in repulsion. Following cloning and sequencing of the AFLP andRAPD markers, specific PCR primers were designed and used in the amplification of sequence characterized amplified region(SCAR markers at both sides of Cr2. EacccMccgat- 365 and RAPD marker U570-843 reported previously were converted into SCARmarkers. These two SCARs segregated in a 1:1 (presence:absence ratio and the scoring cosegregated with their respective AFLP orRAPD marker. The SCAR marker EacccMccgat- 365-scar was positioned at 3.1 Kosambi cM from one side of Cr2 and U570-843-scarlocalized at 1.4 Kosambi cM from other side. Both SCAR markers can be useful in breeding programs with marker-assisted selection procedureto screen for resistance. This study represents the first report of the development of PCR-based sequence-specific markers linkedto blister rust resistance in five-needle pines. These findings may

  10. Sequencing and characterization of the guppy (Poecilia reticulata transcriptome

    Directory of Open Access Journals (Sweden)

    Rodd F Helen

    2011-04-01

    Full Text Available Abstract Background Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs, and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in

  11. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Neumann, Pavel; Macas, Jiří

    2010-01-01

    Roč. 11, č. 1 (2010), s. 378-389 ISSN 1471-2105 R&D Projects: GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : repetitive DNA * plant genome * next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.028, year: 2010

  12. Characterization of a desert soil sequence at Yucca Mountain, NV

    International Nuclear Information System (INIS)

    Guertal, W.R.; Hofmann, L.L. Hudson, D.B.; Flint, A.L.

    1994-01-01

    Yucca Mountain, Nevada, is currently being evaluated as a potential site for a geologic repository for high level radioactive waste. Hydrologic evaluation of the unsaturated zone of Yucca Mountain is being conducted as an integrated set of surface and subsurface-based activities with a common objective to characterize the temporal and spatial distribution of water flux through the potential repository. Yucca Mountain is covered with a thin to thick layer of colluvial/alluvial materials, where there are not bedrock outcrops. It is across this surface boundary that all infiltration and all exfiltration occurs. This surface boundary effects water movement through the unsaturated zone. Characterization of the hydrologic properties of surficial materials is then a necessary step for short term characterization goals and for long term modeling

  13. Characterization of methicillin-resistant Staphylococcus aureus Sequence Type 398

    DEFF Research Database (Denmark)

    Christiansen, Mette Theilgaard

    Staphylococcus aureus is an opportunistic pathogen that colonizes the nares and skin surfaces of several animal species, including man. S. aureus can cause a wide variety of infections ranging from superficial soft tissue and skin infections to severe and deadly systemic infections. Traditionally S....... aureus and methicillin-resistant Staphylococcus aureus (MRSA) have been associated with hospitals, but during the past decades MRSA has emerged in the community and now a new branch of MRSA has been found in association with livestock (LA-MRSA). A specific lineage (multilocus sequence type 398 (ST398...

  14. Development of new strains and related SCAR markers for an edible mushroom, Hypsizygus marmoreus.

    Science.gov (United States)

    Lee, Chang Y; Park, Jeong-Eun; Lee, Jia; Kim, Jong-Kuk; Ro, Hyeon-Su

    2012-02-01

    New fast-growing and less bitter varieties of Hypsizygus marmoreus were developed by crossing monokaryotic mycelia from a commercial strain (Hm1-1) and a wild strain (Hm3-10). Six of the better tasting new strains with a shorter cultivation period were selected from 400 crosses in a large-scale cultivation experiment. We attempted to develop sequence characterized amplified region (SCAR) markers to identify the new strain from other commercial strains. For the SCAR markers, we conducted molecular genetic analysis on a wild strain and the eight most cultivated H. marmoreus strains collected from various areas in East Asia by randomly amplified polymorphic DNA. Ten unique DNA bands for a commercial Hm1-1 strain and the Hm3-10 strain were extracted and their sequences were determined. Primer sets were designed based on the determined sequences. PCR reactions with the primer sets revealed that four primer sets successfully discriminated the new strains from other commercial strains and are thus suitable for commercial purposes. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  15. Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

    Directory of Open Access Journals (Sweden)

    Ma Bi

    2017-10-01

    Full Text Available Copia and Gypsy play important roles in structural, functional and evolutionary dynamics of plant genomes. In this study, a total of 106 and 101, Copia and Gypsy reverse transcriptase (rt were amplified respectively in the Morus notabilis genome using degenerate primers. All sequences exhibited high levels of heterogeneity, were rich in AT and possessed higher sequence divergence of Copia rt in comparison to Gypsy rt. Two reasons are likely to account for this phenomenon: a these elements often experience deletions or fragmentation by illegitimate or unequal homologous recombination in the transposition process; b strong purifying selective pressure drives the evolution of these elements through “selective silencing” with random mutation and eventual deletion from the host genome. Interestingly, mulberry rt clustered with other rt from distantly related taxa according to the phylogenetic analysis. This phenomenon did not result from horizontal transposable element transfer. Results obtained from fluorescence in situ hybridization revealed that most of the hybridization signals were preferentially concentrated in pericentromeric and distal regions of chromosomes, and these elements may play important roles in the regions in which they are found. Results of this study support the continued pursuit of further functional studies of Copia and Gypsy in the mulberry genome.

  16. Potential utility of MRI in the evaluation of children at risk of renal scarring

    International Nuclear Information System (INIS)

    Chan Yuleung; Chan Kamwing; Roebuck, D.J.; Chu, W.C.W.; Metreweli, C.; Yeung Chungkwong; Lee Kimhung

    1999-01-01

    Background. Gadolinium-enhanced MRI has recently been employed in the diagnosis of acute pyelonephritis. Its potential utility in the diagnosis of renal scars in children is unknown. Objective. To evaluate the potential utility of MRI using fat-saturated T1-weighted (T1-W) and post-gadolinium, short-tau inversion-recovery (STIR) sequences in detecting renal scarring by comparison with technetium dimercaptosuccinic acid ( 99 m Tc-DMSA) renal scintigraphy in children at risk of renal scarring. Materials and methods. A group of 24 children with spina bifida and neurogenic bladder or anorectal anomaly was studied. No patient had a history of acute pyelonephritis. Documented urinary tract infection (UTI) was present in 10 children (42 %). The remaining 14 (58 %) children had a history of asymptomatic bacteriuria. None had clinical signs or symptoms of acute UTI at the time of the study. 99 m Tc-DMSA and MRI were performed to detect renal scarring. 99 m Tc-DMSA scans were supplemented with pinhole imaging. MRI of the kidneys employed a fat-saturated T1-W sequence and a post-gadolinium STIR sequence employing a short echo time. Results. Of the kidneys studied, 33 % (n = 16) had evidence of a renal parenchymal defect suggestive of scarring on 99 m Tc-DMSA. The concordance in the detection of a scarred kidney by post-gadolinium STIR sequence and 99 m Tc-DMSA is 94 %; that by fat-saturated T1-W sequence and 99 m Tc-DMSA is 82 %; that by both sequences (positive result on either sequence) and 99 m Tc-DMSA is 100 %. Using 99 m Tc-DMSA as the gold standard, MRI had a sensitivity of 100 % and a specificity of 78 % in the diagnosis of a scarred kidney. The concordance in the detection of a scarred zone by post-gadolinium STIR sequence and 99 m Tc-DMSA is 68 %; that by fat-saturated T1-W sequence and DMSA is 44 %; that by both sequences (positive result on either sequence) and 99 m Tc-DMSA is 84 %. MRI had a sensitivity of 84 % and a specificity of 86 % in the diagnosis of a

  17. Rare complications of cesarean scar

    International Nuclear Information System (INIS)

    Mahajan, Divyesh; Kang, Mandeep; Sandhu, Manavjit Singh; Jain, Vanita; Kalra, Naveen; Khandelwal, Niranjan

    2013-01-01

    Cesarean scar pregnancy (CSP) and cesarean scar dehiscence (CSD) are the most dreaded complications of cesarean scar (CS). As the incidence of CS is increasing worldwide, so is the incidence of CSP, especially in cases with assisted reproduction techniques. It is of utmost importance to diagnose CSP in the early first trimester, as it can lead to myometrial rupture with fatal outcome. On the other hand, CSD may be encountered during pregnancy or in the postpartum period. CSD in the postpartum period is very rare and can cause secondary postpartum hemorrhage (PPH) leading to increased maternal morbidity or even death if not diagnosed and managed promptly. Both complications can be diagnosed on ultrasonography (USG) and confirmed on magnetic resonance imaging (MRI). These two conditions carry high morbidity and mortality. In this article, we highlight the role of imaging in the early diagnosis and management of these conditions

  18. Rare complications of cesarean scar

    Directory of Open Access Journals (Sweden)

    Divyesh Mahajan

    2013-01-01

    Full Text Available Cesarean scar pregnancy (CSP and cesarean scar dehiscence (CSD are the most dreaded complications of cesarean scar (CS. As the incidence of CS is increasing worldwide, so is the incidence of CSP, especially in cases with assisted reproduction techniques. It is of utmost importance to diagnose CSP in the early first trimester, as it can lead to myometrial rupture with fatal outcome. On the other hand, CSD may be encountered during pregnancy or in the postpartum period. CSD in the postpartum period is very rare and can cause secondary postpartum hemorrhage (PPH leading to increased maternal morbidity or even death if not diagnosed and managed promptly. Both complications can be diagnosed on ultrasonography (USG and confirmed on magnetic resonance imaging (MRI. These two conditions carry high morbidity and mortality. In this article, we highlight the role of imaging in the early diagnosis and management of these conditions.

  19. Diversity of black Aspergilli isolated from raisins in Argentina: Polyphasic approach to species identification and development of SCAR markers for Aspergillus ibericus.

    Science.gov (United States)

    Giaj Merlera, G; Muñoz, S; Coelho, I; Cavaglieri, L R; Torres, A M; Reynoso, M M

    2015-10-01

    Aspergillus section Nigri is a heterogeneous fungal group including some ochratoxin A producer species that usually contaminate raisins. The section contains the Series Carbonaria which includes the toxigenic species Aspergillus carbonarius and nontoxigenic Aspergillus ibericus that are phenotypically undistinguishable. The aim of this study was to examine the diversity of black aspergilli isolated from raisins and to develop a specific genetic marker to distinguish A. ibericus from A. carbonarius. The species most frequently found in raisins in this study were Aspergillus tubingensis (35.4%) and A. carbonarius (32.3%), followed by Aspergillus luchuensis (10.7%), Aspergillus japonicus (7.7%), Aspergillus niger (6.2%), Aspergillus welwitschiae (4.6%) and A. ibericus (3.1%). Based on inter-simple sequence repeat (ISSR) fingerprinting profiles of major Aspergillus section Nigri members, a sequence-characterized amplified region (SCAR) marker was identified. Primers were designed based on the conserved regions of the SCAR marker and were utilized in a PCR for simultaneous identification of A. carbonarius and A. ibericus. The detection level of the SCAR-PCR was found to be 0.01 ng of purified DNA. The present SCAR-PCR is rapid and less cumbersome than conventional identification techniques and could be a supplementary strategy and a reliable tool for high-throughput sample analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Classical resonances and quantum scarring

    International Nuclear Information System (INIS)

    Manderfeld, Christopher

    2003-01-01

    We study the correspondence between phase-space localization of quantum (quasi-)energy eigenstates and classical correlation decay, given by Ruelle-Pollicott resonances of the Frobenius-Perron operator. It will be shown that scarred (quasi-)energy eigenstates are correlated: pairs of eigenstates strongly overlap in phase space (scar in same phase-space regions) if the difference of their eigenenergies is close to the phase of a leading classical resonance. Phase-space localization of quantum states will be measured by L 2 norms of their Husimi functions

  1. A Prospective Study of Ripple Mapping the Post-Infarct Ventricular Scar to Guide Substrate Ablation for Ventricular Tachycardia.

    Science.gov (United States)

    Luther, Vishal; Linton, Nick W F; Jamil-Copley, Shahnaz; Koa-Wing, Michael; Lim, Phang Boon; Qureshi, Norman; Ng, Fu Siong; Hayat, Sajad; Whinnett, Zachary; Davies, D Wyn; Peters, Nicholas S; Kanagaratnam, Prapa

    2016-06-01

    Post-infarct ventricular tachycardia is associated with channels of surviving myocardium within scar characterized by fractionated and low-amplitude signals usually occurring late during sinus rhythm. Conventional automated algorithms for 3-dimensional electro-anatomic mapping cannot differentiate the delayed local signal of conduction within the scar from the initial far-field signal generated by surrounding healthy tissue. Ripple mapping displays every deflection of an electrogram, thereby providing fully informative activation sequences. We prospectively used CARTO-based ripple maps to identify conducting channels as a target for ablation. High-density bipolar left ventricular endocardial electrograms were collected using CARTO3v4 in sinus rhythm or ventricular pacing and reviewed for ripple mapping conducting channel identification. Fifteen consecutive patients (median age 68 years, left ventricular ejection fraction 30%) were studied (6 month preprocedural implantable cardioverter defibrillator therapies: median 19 ATP events [Q1-Q3=4-93] and 1 shock [Q1-Q3=0-3]). Scar (ripple mapping conducting channels were seen within each scar (length 60 mm; initial component 0.44 mV; delayed component 0.20 mV; conduction 55 cm/s). Ablation was performed along all identified ripple mapping conducting channels (median 18 lesions) and any presumed interconnected late-activating sites (median 6 lesions; Q1-Q3=2-12). The diastolic isthmus in ventricular tachycardia was mapped in 3 patients and colocated within the ripple mapping conducting channels identified. Ventricular tachycardia was noninducible in 85% of patients post ablation, and 71% remain free of ventricular tachycardia recurrence at 6-month median follow-up. Ripple mapping can be used to identify conduction channels within scar to guide functional substrate ablation. © 2016 American Heart Association, Inc.

  2. Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury

    Science.gov (United States)

    Dutta, Suhrid R.; Kar, Prasanta K.; Srivastava, Ashok K.; Sinha, Manoj K.; Shankar, Jai; Ghosh, Ananta K.

    2012-01-01

    The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and low (LCSW) cocoon and shell weights, and the F2 progeny of a cross between these two groups were obtained. DNA from these silkworms was screened by PCR using 34 random primers and the resulting RAPD fragments were used for cluster analysis and discriminant function analysis (DFA). The clustering pattern in a UPGMA-based dendogram and DFA clearly distinguished the HCSW and LCSW groups. Multiple regression analysis identified five markers associated with cocoon and shell weights. The marker OPW16905 bp showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F2 progeny. Cloning and sequencing of this 905 bp fragment showed 88% identity between its 134 nucleotides and the Bmc-1/Yamato-like retroposon of A. mylitta. This marker was further converted into a diagnostic SCAR marker (SCOPW 16826 bp). The SCAR marker developed here may be useful in identifying the right parental stock of tasar silk-worms for high cocoon and shell weights in breeding programs designed to enhance the productivity of tasar silk. PMID:23271934

  3. Isolation and characterization of gene sequences expressed in cotton fiber

    Directory of Open Access Journals (Sweden)

    Taciana de Carvalho Coutinho

    2016-06-01

    Full Text Available ABSTRACT Cotton fiber are tubular cells which develop from the differentiation of ovule epidermis. In addition to being one of the most important natural fiber of the textile group, cotton fiber afford an excellent experimental system for studying the cell wall. The aim of this work was to isolate and characterise the genes expressed in cotton fiber (Gossypium hirsutum L. to be used in future work in cotton breeding. Fiber of the cotton cultivar CNPA ITA 90 II were used to extract RNA for the subsequent generation of a cDNA library. Seventeen sequences were obtained, of which 14 were already described in the NCBI database (National Centre for Biotechnology Information, such as those encoding the lipid transfer proteins (LTPs and arabinogalactans (AGP. However, other cDNAs such as the B05 clone, which displays homology with the glycosyltransferases, have still not been described for this crop. Nevertheless, results showed that several clones obtained in this study are associated with cell wall proteins, wall-modifying enzymes and lipid transfer proteins directly involved in fiber development.

  4. Human liver cell trafficking mutants: characterization and whole exome sequencing.

    Directory of Open Access Journals (Sweden)

    Fei Yuan

    Full Text Available The HuH7 liver cell mutant Trf1 is defective in membrane trafficking and is complemented by the casein kinase 2α subunit CK2α''. Here we identify characteristic morphologies, trafficking and mutational changes in six additional HuH7 mutants Trf2-Trf7. Trf1 cells were previously shown to be severely defective in gap junction functions. Using a Lucifer yellow transfer assay, remarkable attenuation of gap junction communication was revealed in each of the mutants Trf2-Trf7. Electron microscopy and light microscopy of thiamine pyrophosphatase showed that several mutants exhibited fragmented Golgi apparatus cisternae compared to parental HuH7 cells. Intracellular trafficking was investigated using assays of transferrin endocytosis and recycling and VSV G secretion. Surface binding of transferrin was reduced in all six Trf2-Trf7 mutants, which generally correlated with the degree of reduced expression of the transferrin receptor at the cell surface. The mutants displayed the same transferrin influx rates as HuH7, and for efflux rate, only Trf6 differed, having a slower transferrin efflux rate than HuH7. The kinetics of VSV G transport along the exocytic pathway were altered in Trf2 and Trf5 mutants. Genetic changes unique to particular Trf mutants were identified by exome sequencing, and one was investigated in depth. The novel mutation Ile34Phe in the GTPase RAB22A was identified in Trf4. RNA interference knockdown of RAB22A or overexpression of RAB22AI34F in HuH7 cells caused phenotypic changes characteristic of the Trf4 mutant. In addition, the Ile34Phe mutation reduced both guanine nucleotide binding and hydrolysis activities of RAB22A. Thus, the RAB22A Ile34Phe mutation appears to contribute to the Trf4 mutant phenotype.

  5. Simple sequence repeat (SSR) vs. sequence-related amplified polymorphism (SRAP) markers for Cynara cardunculus characterization

    Energy Technology Data Exchange (ETDEWEB)

    Casadevall, R.; Martin, E.; Cravero, V.

    2011-07-01

    A little is known about the genetic variability present in globe artichoke, cultivated and wild cardoons. This knowledge is very important for efficient genetic resources utilization, and to gain a better understanding of genetic structure of this botanical varieties. With the aims to determine genetic distances between Cynara cardunculus accessions and to compare two molecular markers systems for their efficiency to differ between botanical varieties, a molecular characterization of sixteen accessions from different geographical origins was performed. Seven SSR and seven SRAP markers were used for varieties characterization and to calculate genetic distances between them. Both distance matrices were subjected to cluster analysis. Exclusive SSR alleles were found for globe artichoke and for wild cardoon, but non exclusive alleles were found for cultivated cardoon. For both markers systems two major groups were identified, one of them included mostly globe artichoke accessions and the other one grouped mainly cardoons. The differences observed in the sub-cluster conformation with each marker systems may be due to intrinsic characteristics of the markers. Concluding, both kind of molecular markers are valuable tools for studying genetic distances between C. cardunculus accessions although they give different information. Nevertheless, SSR electrophoretic profiles are simpler to score than SRAP markers because they consist of just a few bands. As well, bands are highly informative because of the great number of alleles existing in population and they are codominant markers. In addition, SSRs use would reduce time and costs. (Author) 31 refs.

  6. Endometriosis in an episiotomy scar

    Directory of Open Access Journals (Sweden)

    Mine islimye Taskin

    2016-03-01

    Full Text Available Endometriosis that is defined as the presence of functional endometrial tissue outside the uterine cavity is seen 5-10% of reproductive age women. Endometriosis can be seen any other site of the body; but the most frequently affected areas are ovaries, pelvic peritoneum, uterosacral ligament and Douglas pouche. Several teories exist for the development of endometriosis including retrograde menstruation, venous or lymphatic metastasis and immun dysfunction. Endometriosis of the perineum and vulva are extremely rare with the most common sites being episiotomy scars. Scar endometriosis is likely to be caused by mechanical transplantation of endometrium from the uterine cavity into the wound at the time of the surgery. The primary treatment for scar endometriosis is total surgical excision of the lesion. It is important not to leave residual tissue during surgery to prevent the recurrence. Here we present a patient who had her vaginal delivery 5 years ago, have a complaint of painful vulvar lump at the right mediolateral episiotomy scar since 1 year during her every menstruation period and whose final diagnosis was endometriosis after surgical removal and histopathologic examination. Althought vulvar endometrosis is rare, it should be considered in the patients who had a vaginal delivery and complaining painful vulvar lump with swelling in her mestrual cycle. [Cukurova Med J 2016; 41(1.000: 164-166

  7. Episiotomy scar endometriosis diagnosed on cytology - a case report

    African Journals Online (AJOL)

    Endometriosis, the presence of functioning endometrial tissue outside the uterus, is a common gynaecological condition. Perineal endometriosis is a rare disease characterized by the presence of ectopic endometrial stroma and glands in the perineum. Most commonly observed in the episiotomy scar after normal vaginal ...

  8. Skin cancer full-grown from scar

    International Nuclear Information System (INIS)

    Zikiryakhodjaev, D.Z.; Sanginov, D.R.

    2001-01-01

    In this chapter authors investigate the peculiarities of skin cancer full-grown from scar, the theory of it's descent, quote some statistical data on skin cancer full-grown from scar and variety clinical forms of skin cancer full-grown from scar was shown, quote some methods of treatment

  9. Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing.

    Science.gov (United States)

    Zhou, Wei; Hu, Yiyi; Sui, Zhenghong; Fu, Feng; Wang, Jinguo; Chang, Lianpeng; Guo, Weihua; Li, Binbin

    2013-01-01

    Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon.

  10. Genome Survey Sequencing and Genetic Background Characterization of Gracilariopsis lemaneiformis (Rhodophyta) Based on Next-Generation Sequencing

    Science.gov (United States)

    Sui, Zhenghong; Fu, Feng; Wang, Jinguo; Chang, Lianpeng; Guo, Weihua; Li, Binbin

    2013-01-01

    Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon. PMID:23875008

  11. Techniques for Optimizing Surgical Scars, Part 2: Hypertrophic Scars and Keloids.

    Science.gov (United States)

    Potter, Kathryn; Konda, Sailesh; Ren, Vicky Zhen; Wang, Apphia Lihan; Srinivasan, Aditya; Chilukuri, Suneel

    2017-01-01

    Surgical management of benign or malignant cutaneous tumors may result in noticeable scars that are of great concern to patients, regardless of sex, age, or ethnicity. Techniques to optimize surgical scars are discussed in this three-part review. Part 2 focuses on scar revision for hypertrophic and keloids scars. Scar revision options for hypertrophic and keloid scars include corticosteroids, bleomycin, fluorouracil, verapamil, avotermin, hydrogel scaffold, nonablative fractional lasers, ablative and fractional ablative lasers, pulsed dye laser (PDL), flurandrenolide tape, imiquimod, onion extract, silicone, and scar massage.

  12. Phylogenetic characterization of Canine Parvovirus VP2 partial sequences from symptomatic dogs samples.

    Science.gov (United States)

    Zienius, D; Lelešius, R; Kavaliauskis, H; Stankevičius, A; Šalomskas, A

    2016-01-01

    The aim of the present study was to detect canine parvovirus (CPV) from faecal samples of clinically ill domestic dogs by polymerase chain reaction (PCR) followed by VP2 gene partial sequencing and molecular characterization of circulating strains in Lithuania. Eleven clinically and antigen-tested positive dog faecal samples, collected during the period of 2014-2015, were investigated by using PCR. The phylogenetic investigations indicated that the Lithuanian CPV VP2 partial sequences (3025-3706 cds) were closely related and showed 99.0-99.9% identity. All Lithuanian sequences were associated with one phylogroup, but grouped in different clusters. Ten of investigated Lithuanian CPV VP2 sequences were closely associated with CPV 2a antigenic variant (99.4% nt identity). Five CPV VP2 sequences from Lithuania were related to CPV-2a, but were rather divergent (6.8 nt differences). Only one CPV VP2 sequence from Lithuania was associated (99.3% nt identity) with CPV-2b VP2 sequences from France, Italy, USA and Korea. The four of eleven investigated Lithuanian dogs with CPV infection symptoms were vaccinated with CPV-2 vaccine, but their VP2 sequences were phylogenetically distantly associated with CPV vaccine strains VP2 sequences (11.5-15.8 nt differences). Ten Lithuanian CPV VP2 sequences had monophyletic relations among the close geographically associated samples, but five of them were rather divergent (1.0% less sequence similarity). The one Lithuanian CPV VP2 sequence was closely related with CPV-2b antigenic variant. All the Lithuanian CPV VP2 partial sequences were conservative and phylogenetically low associated with most commonly used CPV vaccine strains.

  13. Characterization of GM events by insert knowledge adapted re-sequencing approaches

    OpenAIRE

    Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

    2013-01-01

    Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-ad...

  14. Forensic analysis of rockfall scars

    Science.gov (United States)

    de Vilder, Saskia J.; Rosser, Nick J.; Brain, Matthew J.

    2017-10-01

    We characterise and analyse the detachment (scar) surfaces of rockfalls to understand the mechanisms that underpin their failure. Rockfall scars are variously weathered and comprised of both discontinuity release surfaces and surfaces indicative of fracturing through zones of previously intact rock, known as rock bridges. The presence of rock bridges and pre-existing discontinuities is challenging to quantify due to the difficulty in determining discontinuity persistence below the surface of a rock slope. Rock bridges form an important control in holding blocks onto rockslopes, with their frequency, extent and location commonly modelled from the surface exposure of daylighting discontinuities. We explore an alternative approach to assessing their role, by characterising failure scars. We analyse a database of multiple rockfall scar surfaces detailing the areal extent, shape, and location of broken rock bridges and weathered surfaces. Terrestrial laser scanning and gigapixel imagery were combined to record the detailed texture and surface morphology. From this, scar surfaces were mapped via automated classification based on RGB pixel values. Our analysis of the resulting data from scars on the North Yorkshire coast (UK) indicates a wide variation in both weathering and rock bridge properties, controlled by lithology and associated rock mass structure. Importantly, the proportion of rock bridges in a rockfall failure surface does not increase with failure size. Rather larger failures display fracturing through multiple rock bridges, and in contrast smaller failures fracture occurs only through a single critical rock bridge. This holds implications for how failure mechanisms change with rockfall size and shape. Additionally, the location of rock bridges with respect to the geometry of an incipient rockfall is shown to determine failure mode. Weathering can occur both along discontinuity surfaces and previously broken rock bridges, indicating the sequential stages of

  15. Applicability of SCAR markers to food genomics: olive oil traceability.

    Science.gov (United States)

    Pafundo, Simona; Agrimonti, Caterina; Maestri, Elena; Marmiroli, Nelson

    2007-07-25

    DNA analysis with molecular markers has opened a shortcut toward a genomic comprehension of complex organisms. The availability of micro-DNA extraction methods, coupled with selective amplification of the smallest extracted fragments with molecular markers, could equally bring a breakthrough in food genomics: the identification of original components in food. Amplified fragment length polymorphisms (AFLPs) have been instrumental in plant genomics because they may allow rapid and reliable analysis of multiple and potentially polymorphic sites. Nevertheless, their direct application to the analysis of DNA extracted from food matrixes is complicated by the low quality of DNA extracted: its high degradation and the presence of inhibitors of enzymatic reactions. The conversion of an AFLP fragment to a robust and specific single-locus PCR-based marker, therefore, could extend the use of molecular markers to large-scale analysis of complex agro-food matrixes. In the present study is reported the development of sequence characterized amplified regions (SCARs) starting from AFLP profiles of monovarietal olive oils analyzed on agarose gel; one of these was used to identify differences among 56 olive cultivars. All the developed markers were purposefully amplified in olive oils to apply them to olive oil traceability.

  16. Two dimensional unstable scar statistics.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Kotulski, Joseph Daniel; Lee, Kelvin S. H. (ITT Industries/AES Los Angeles, CA)

    2006-12-01

    This report examines the localization of time harmonic high frequency modal fields in two dimensional cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This paper examines the enhancements for these unstable orbits when the opposing mirrors are both convex and concave. In the latter case the construction includes the treatment of interior foci.

  17. Characterization of Satellite DNA Sequences from the Commercially Important Marine Rotifers Brachionus rotundiformis and Brachionus plicatilis.

    Science.gov (United States)

    Boehm; Gibson; Lubzens

    2000-01-01

    This study was initiated to search for species-specific and strain-specific satellite DNA sequences for which oligonucleotide primers could be designed to differentiate between various commercially important strains of the marine monogonont rotifers Brachionus rotundiformis and Brachionus plicatilis. Two unrelated, highly reiterated satellite sequences were cloned and characterized. The eight sequenced monomers from B. rotundiformis and six from B. plicatilis had low intrarepeat variability and were similar in their overall lengths, A + T compositions, and high degrees of repeated motif substructure. However, hybridizations to 19 representative strains, sequence characterizations, and GenBank searches indicated that these two satellites are morphotype-specific and population-specific, respectively, and share little homology to each other or to other characterized sequences in the database. Primer pairs designed for the B. rotundiformis satellite confirmed hybridization specificities on polymerase chain reaction and could serve as a useful molecular diagnostic tool to identify strains belonging to the SS morphotype, which are gaining widespread usage as first feeds for marine fish in commercial production.

  18. Sulfates, Clouds and Radiation Brazil (SCAR-B) AERONET (AErosol RObotic NETwork) Data

    Data.gov (United States)

    National Aeronautics and Space Administration — SCAR_B_AERONET data are Smoke, Clouds and Radiation Brazil (SCARB) Aerosol Robotic Network (AERONET) data for aerosol characterization.Smoke/Sulfates, Clouds and...

  19. Rickettsia asembonensis Characterization by Multilocus Sequence Typing of Complete Genes, Peru.

    Science.gov (United States)

    Loyola, Steev; Flores-Mendoza, Carmen; Torre, Armando; Kocher, Claudine; Melendrez, Melanie; Luce-Fedrow, Alison; Maina, Alice N; Richards, Allen L; Leguia, Mariana

    2018-05-01

    While studying rickettsial infections in Peru, we detected Rickettsia asembonensis in fleas from domestic animals. We characterized 5 complete genomic regions (17kDa, gltA, ompA, ompB, and sca4) and conducted multilocus sequence typing and phylogenetic analyses. The molecular isolate from Peru is distinct from the original R. asembonensis strain from Kenya.

  20. Characterization of GM events by insert knowledge adapted re-sequencing approaches.

    Science.gov (United States)

    Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

    2013-10-03

    Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

  1. Sequence Ready Characterization of the Pericentromeric Region of 19p12

    Energy Technology Data Exchange (ETDEWEB)

    Evan E. Eichler

    2006-08-31

    Current mapping and sequencing strategies have been inadequate within the proximal portion of 19p12 due, in part, to the presence of a recently expanded ZNF (zinc-finger) gene family and the presence of large (25-50 kb) inverted beta-satellite repeat structures which bracket this tandemly duplicated gene family. The virtual of absence of classically defined “unique” sequence within the region has hampered efforts to identify and characterize a suitable minimal tiling path of clones which can be used as templates required for finished sequencing of the region. The goal of this proposal is to develop and implement a novel sequence-anchor strategy to generate a contiguous BAC map of the most proximal portion of chromosome 19p12 for the purpose of complete sequence characterization. The target region will be an estimated 4.5 Mb of DNA extending from STS marker D19S450 (the beginning of the ZNF gene cluster) to the centromeric (alpha-satellite) junction of 19p11. The approach will entail 1) pre-selection of 19p12 BAC and cosmid clones (NIH approved library) utilizing both 19p12 -unique and 19p12-SPECIFIC repeat probes (Eichler et al., 1998); 2) the generation of a BAC/cosmid end-sequence map across the region with a density of one marker every 8kb; 3) the development of a second-generation of STS (sequence tagged sites) which will be used to identify and verify clonal overlap at the level of the sequence; 4) incorporation of these sequence-anchored overlapping clones into existing cosmid/BAC restriction maps developed at Livermore National Laboratory; and 5) validation of the organization of this region utilizing high-resolution FISH techniques (extended chromatin analysis) on monochromosomal 19 somatic cell hybrids and parental cell lines of source material. The data generated will be used in the selection of the most parsimonious tiling path of BAC clones to be sequenced as part of the JGI effort on chromosome 19 and should serve as a model for the sequence

  2. Structural characterization of HDPE/LLDPE blend-based nano composites obtained by different blending sequence

    International Nuclear Information System (INIS)

    Passador, Fabio R.; Ruvolo Filho, Adhemar; Pessan, Luiz A.

    2011-01-01

    The blending sequence affects the morphology formation of the nanocomposites. In this work, the blending sequences were explored to determine its influence in the rheological behavior of HDPE/LLDPE/OMMT nanocomposites. The nanocomposites were obtained by melt-intercalation using a mixture of LLDPE-g-MA and HDPE-g-MA as compatibilizer system in a torque rheometer at 180 deg C and five blending sequences were studied. The materials structures were characterized by wide angle X-ray diffraction (WAXD) and by rheological properties. The nanoclay's addition increased the shear viscosity at low shear rates, changing the behavior of HDPE/LLDPE matrix to a Bingham model behavior with an apparent yield stress. Intense interactions were obtained for the blending sequence where LLDPE and/or LLDPE-g-MA were first reinforced with organoclay since the intercalation process occurs preferentially in the amorphous phase. (author)

  3. Comparative effect and safety of verapamil in keloid and hypertrophic scar treatment: a meta-analysis

    OpenAIRE

    Li ZN; Jin ZH

    2016-01-01

    Zhouna Li, Zhehu Jin Department of Dermatology, Yanbian University Affiliated hospital, Yanji, Jilin, People’s Republic of China Background: Keloids and hypertrophic scars are the most common types of pathological scarring. Traditionally, keloids have been considered as a result of aberrant wound healing, involving excessive fibroblast participation that is characterized by hyalinized collagen bundles. However, the usefulness of this characterization has been questioned. In recent yea...

  4. Comparative effect and safety of verapamil in keloid and hypertrophic scar treatment: a meta-analysis

    OpenAIRE

    Li,Zhouna; Jin,Zhehu

    2016-01-01

    Zhouna Li, Zhehu Jin Department of Dermatology, Yanbian University Affiliated hospital, Yanji, Jilin, People’s Republic of China Background: Keloids and hypertrophic scars are the most common types of pathological scarring. Traditionally, keloids have been considered as a result of aberrant wound healing, involving excessive fibroblast participation that is characterized by hyalinized collagen bundles. However, the usefulness of this characterization has been questioned. In recent...

  5. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  6. Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.

    Directory of Open Access Journals (Sweden)

    Fan Gao

    Full Text Available In human immune system, V(DJ recombination produces an enormously large repertoire of immunoglobulins (Ig so that they can tackle different antigens from bacteria, viruses and tumor cells. Several studies have demonstrated the utility of next-generation sequencers such as Roche 454 and Illumina Genome Analyzer to characterize the repertoire of immunoglobulins. However, these techniques typically require separation of B cell population from whole blood and require a few weeks for running the sequencers, so it may not be practical to implement them in clinical settings. Recently, the Ion Torrent personal genome sequencer has emerged as a tabletop personal genome sequencer that can be operated in a time-efficient and cost-effective manner. In this study, we explored the technical feasibility to use multiplex PCR for amplifying V(DJ recombination for IgH, directly from whole blood, then sequence the amplicons by the Ion Torrent sequencer. The whole process including data generation and analysis can be completed in one day. We tested the method in a pilot study on patients with benign, atypical and malignant meningiomas. Despite the noisy data, we were able to compare the samples by their usage frequencies of the V segment, as well as their somatic hypermutation rates. In summary, our study suggested that it is technically feasible to perform clinical monitoring of V(DJ recombination within a day by personal genome sequencers.

  7. Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques

    Science.gov (United States)

    Campbell, Kevin J.; Detmer, Ann M.; Karl, Julie A.; Wiseman, Roger W.; Blasky, Alex J.; Hughes, Austin L.; Bimber, Benjamin N.; O’Connor, Shelby L.; O’Connor, David H.

    2009-01-01

    Cynomolgus macaques (Macaca fascicularis) provide increasingly common models for infectious disease research. Several geographically distinct populations of these macaques from Southeast Asia and the Indian Ocean island of Mauritius are available for pathogenesis studies. Though host genetics may profoundly impact results of such studies, similarities and differences between populations are often overlooked. In this study we identified 47 full-length MHC class I nucleotide sequences in 16 cynomolgus macaques of Filipino origin. The majority of MHC class I sequences characterized (39 of 47) were unique to this regional population. However, we discovered eight sequences with perfect identity and six sequences with close similarity to previously defined MHC class I sequences from other macaque populations. We identified two ancestral MHC haplotypes that appear to be shared between Filipino and Mauritian cynomolgus macaques, notably a Mafa-B haplotype that has previously been shown to protect Mauritian cynomolgus macaques against challenge with a simian/human immunodeficiency virus, SHIV89.6P. We also identified a Filipino cynomolgus macaque MHC class I sequence for which the predicted protein sequence differs from Mamu-B*17 by a single amino acid. This is important because Mamu-B*17 is strongly associated with protection against simian immunodeficiency virus (SIV) challenge in Indian rhesus macaques. These findings have implications for the evolutionary history of Filipino cynomolgus macaques as well as for the use of this model in SIV/SHIV research protocols. PMID:19107381

  8. Scar-free wound healing and regeneration following tail loss in the leopard gecko, Eublepharis macularius.

    Science.gov (United States)

    Delorme, Stephanie Lynn; Lungu, Ilinca Mihaela; Vickaryous, Matthew Kenneth

    2012-10-01

    Many lizards are able to undergo scar-free wound healing and regeneration following loss of the tail. In most instances, lizard tail loss is facilitated by autotomy, an evolved mechanism that permits the tail to be self-detached at pre-existing fracture planes. However, it has also been reported that the tail can regenerate following surgical amputation outside the fracture plane. In this study, we used the leopard gecko, Eublepharis macularius, to investigate and compare wound healing and regeneration following autotomy at a fracture plane and amputation outside the fracture plane. Both forms of tail loss undergo a nearly identical sequence of events leading to scar-free wound healing and regeneration. Early wound healing is characterized by transient myofibroblasts and the formation of a highly proliferative wound epithelium immunoreactive for the wound keratin marker WE6. The new tail forms from what is commonly referred to as a blastema, a mass of proliferating mesenchymal-like cells. Blastema cells express the protease matrix metalloproteinase-9. Apoptosis (demonstrated by activated caspase 3 immunostaining) is largely restricted to isolated cells of the original and regenerating tail tissues, although cell death also occurs within dermal structures at the original-regenerated tissue interface and among clusters of newly formed myocytes. Furthermore, the autotomized tail is unique in demonstrating apoptosis among cells adjacent to the fracture planes. Unlike mammals, transforming growth factor-β3 is not involved in wound healing. We demonstrate that scar-free wound healing and regeneration are intrinsic properties of the tail, unrelated to the location or mode of tail detachment. Copyright © 2012 Wiley Periodicals, Inc.

  9. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

    Directory of Open Access Journals (Sweden)

    Yandell Mark

    2010-07-01

    Full Text Available Abstract Background In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24. The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. Results We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity elsewhere in the genome, but only 23% have identical copies (99% identity. The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. Conclusions This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is

  10. A Case of Multiple Spontaneous Keloid Scars

    Directory of Open Access Journals (Sweden)

    Abdulhadi Jfri

    2015-07-01

    Full Text Available Keloid scars result from an abnormal healing response to cutaneous injury or inflammation that extends beyond the borders of the original wound. Spontaneous keloid scars forming in the absence of any previous trauma or surgical procedure are rare. Certain syndromes have been associated with this phenomenon, and few reports have discussed the evidence of single spontaneous keloid scar, which raises the question whether they are really spontaneous. Here, we present a 27-year-old mentally retarded single female with orbital hypertelorism, broad nasal bridge, repaired cleft lip and high-arched palate who presented with progressive multiple spontaneous keloid scars in different parts of her body which were confirmed histologically by the presence of typical keloidal collagen. This report supports the fact that keloid scars can appear spontaneously and are possibly linked to a genetic factor. Furthermore, it describes a new presentation of spontaneous keloid scars in the form of multiple large lesions in different sites of the body.

  11. Molecular characterization of Fasciola gigantica from Mauritania based on mitochondrial and nuclear ribosomal DNA sequences.

    Science.gov (United States)

    Amor, Nabil; Farjallah, Sarra; Salem, Mohamed; Lamine, Dia Mamadou; Merella, Paolo; Said, Khaled; Ben Slimane, Badreddine

    2011-10-01

    Fasciolosis caused by Fasciola hepatica and Fasciola gigantica (Platyhelminthes: Trematoda: Digenea) is considered the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. From Africa, F. gigantica has been previously characterized from Burkina Faso, Senegal, Kenya, Zambia and Mali, while F. hepatica has been reported from Morocco and Tunisia, and both species have been observed from Ethiopia and Egypt on the basis of morphometric differences, while the use of molecular markers is necessary to distinguish exactly between species. Samples identified morphologically as F. gigantica (n=60) from sheep and cattle from different geographical localities of Mauritania were genetically characterized by sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes and the mitochondrial Cytochrome c Oxidase I (COI) gene. Comparison of the sequences of the Mauritanian samples with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. gigantica. The nucleotide sequencing of ITS rDNA of F. gigantica showed no nucleotide variation in the ITS-1, 5.8S, and ITS-2 rDNA sequences among all samples examined and those from Burkina Faso, Kenya, Egypt and Iran. The phylogenetic trees based on the ITS-1 and ITS-2 sequences showed a close relationship of the Mauritanian samples with isolates of F. gigantica from different localities of Africa and Asia. The COI genotypes of the Mauritanian specimens of F. gigantica had a high level of diversity, and they belonged to the F. gigantica phylogenically distinguishable clade. The present study is the first molecular characterization of F. gigantica in sheep and cattle from Mauritania, allowing a reliable approach for the genetic differentiation of Fasciola spp. and providing basis for further studies on liver flukes in the African countries. Copyright © 2011 Elsevier Inc. All

  12. Mammographic scar for stereotaxic biopsy

    International Nuclear Information System (INIS)

    Guzman Tattis; Hincapie U, Ana Lucia; Patino P, Jairo Hernando

    1997-01-01

    It is reported the case of 56 years old woman who underwent a stereotactic biopsy because of having a circumscribed breast nodule. The histologic diagnosis was benign. After six months, during the mammographic control, it was noticed that the nodule showed irregular contours, because of that a surgical biopsy was performed. The histopathology was reported as benign. it is considered then, that the mammographic changes observed in the mammographic control are due to scar phenomenon after stereotactic biopsy. This findings has not been reported previously

  13. Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis

    Directory of Open Access Journals (Sweden)

    Roodt-Wilding Rouvay

    2011-03-01

    Full Text Available Abstract Background Worldwide, the genus Haliotis is represented by 56 extant species and several of these are commercially cultured. Among the six abalone species found in South Africa, Haliotis midae is the only aquacultured species. Despite its economic importance, genomic sequence resources for H. midae, and for abalone in general, are still scarce. Next generation sequencing technologies provide a fast and efficient tool to generate large sequence collections that can be used to characterize the transcriptome and identify expressed genes associated with economically important traits like growth and disease resistance. Results More than 25 million short reads generated by the Illumina Genome Analyzer were de novo assembled in 22,761 contigs with an average size of 260 bp. With a stringent E-value threshold of 10-10, 3,841 contigs (16.8% had a BLAST homologous match against the Genbank non-redundant (NR protein database. Most of these sequences were annotated using the gene ontology (GO and eukaryotic orthologous groups of proteins (KOG databases and assigned to various functional categories. According to annotation results, many gene families involved in immune response were identified. Thousands of simple sequence repeats (SSR and single nucleotide polymorphisms (SNP were detected. Setting stringent parameters to ensure a high probability of amplification, 420 primer pairs in 181 contigs containing SSR loci were designed. Conclusion This data represents the most comprehensive genomic resource for the South African abalone H. midae to date. The amount of assembled sequences demonstrated the utility of the Illumina sequencing technology in the transcriptome characterization of a non-model species. It allowed the development of several markers and the identification of promising candidate genes for future studies on population and functional genomics in H. midae and in other abalone species.

  14. The Use of Next Generation Sequencing and Junction Sequence Analysis Bioinformatics to Achieve Molecular Characterization of Crops Improved Through Modern Biotechnology

    Directory of Open Access Journals (Sweden)

    David Kovalic

    2012-11-01

    Full Text Available The assessment of genetically modified (GM crops for regulatory approval currently requires a detailed molecular characterization of the DNA sequence and integrity of the transgene locus. In addition, molecular characterization is a critical component of event selection and advancement during product development. Typically, molecular characterization has relied on Southern blot analysis to establish locus and copy number along with targeted sequencing of polymerase chain reaction products spanning any inserted DNA to complete the characterization process. Here we describe the use of next generation (NexGen sequencing and junction sequence analysis bioinformatics in a new method for achieving full molecular characterization of a GM event without the need for Southern blot analysis. In this study, we examine a typical GM soybean [ (L. Merr.] line and demonstrate that this new method provides molecular characterization equivalent to the current Southern blot-based method. We also examine an event containing in vivo DNA rearrangement of multiple transfer DNA inserts to demonstrate that the new method is effective at identifying complex cases. Next generation sequencing and bioinformatics offers certain advantages over current approaches, most notably the simplicity, efficiency, and consistency of the method, and provides a viable alternative for efficiently and robustly achieving molecular characterization of GM crops.

  15. DWI in breast MRI: Role of ADC value to determine diagnosis between recurrent tumor and surgical scar in operated patients

    Energy Technology Data Exchange (ETDEWEB)

    Rinaldi, Pierluigi, E-mail: pierluigi.rinaldi@rm.unicatt.i [Department of Bio-Imaging and Radiological Sciences, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Giuliani, Michela, E-mail: micgiuli@yahoo.i [Department of Bio-Imaging and Radiological Sciences, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Belli, Paolo, E-mail: pbelli@rm.unicatt.i [Department of Bio-Imaging and Radiological Sciences, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Costantini, Melania, E-mail: mcostantini@rm.unicatt.i [Department of Bio-Imaging and Radiological Sciences, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Romani, Maurizio, E-mail: mromani@rm.unicatt.i [Department of Bio-Imaging and Radiological Sciences, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Distefano, Daniela, E-mail: daniela_distefano@hotmail.i [Department of Bio-Imaging and Radiological Sciences, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Bufi, Enida, E-mail: reagandus@alice.i [Department of Bio-Imaging and Radiological Sciences, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Mule, Antonino, E-mail: amule@rm.unicatt.i [Division of Pathology and Histology, Catholic University - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Magno, Stefano, E-mail: smagno@rm.unicatt.i [Department of Surgery, Breast Unit, Catholic University Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Masetti, Riccardo, E-mail: riccardo.masetti@rm.unicatt.i [Department of Surgery, Breast Unit, Catholic University Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy); Bonomo, Lorenzo, E-mail: lbonomo@rm.unicatt.i [Dept. of Bio-Imaging and Radiological Sciences, Catholic Univ. - Policlinic A. Gemelli, L.go A. Gemelli 8, 00168 Rome (Italy)

    2010-08-15

    Introduction: Purpose of our study is to evaluate the role of the apparent diffusion coefficient (ADC) in the diagnosis of recurrent tumor on the scar in patients operated for breast cancer. Assess, therefore, the weight of diagnostic diffusion echo-planar sequence, in association with the morphological and dynamic sequences in the diagnosis of tumor recurrence versus surgical scar. Materials and methods: From September 2007 to March 2009, 72 patients operated for breast cancer with suspected recurrence on the scar were consecutively subjected to magnetic resonance imaging (MRI), including use of a diffusion sequence. All patients with pathological enhancement in the scar were then subjected to histological typing. MRI was considered negative in the absence of areas of suspicious enhancement. In all cases it was measured the ADC value in the scar area or in the area with pathological enhancement. The ADC values were compared with MRI findings and histological results obtained. Results: 26 cases were positive/doubtful at MRI and then subjected to histological typing: of these recurrences were 20 and benign were 6. 46 cases were judged negative at MRI and therefore not sent to cyto-histology. The average ADC value of recurrences was statistically lower of scarring (p < 0.001). Conclusions: ADC value can be a specific parameter in differential diagnosis between recurrence and scar. The diffusion sequence, in association with the morphological and dynamic sequences, can be considered a promising tool for the surgical indication in suspected recurrence of breast cancer.

  16. DWI in breast MRI: Role of ADC value to determine diagnosis between recurrent tumor and surgical scar in operated patients

    International Nuclear Information System (INIS)

    Rinaldi, Pierluigi; Giuliani, Michela; Belli, Paolo; Costantini, Melania; Romani, Maurizio; Distefano, Daniela; Bufi, Enida; Mule, Antonino; Magno, Stefano; Masetti, Riccardo; Bonomo, Lorenzo

    2010-01-01

    Introduction: Purpose of our study is to evaluate the role of the apparent diffusion coefficient (ADC) in the diagnosis of recurrent tumor on the scar in patients operated for breast cancer. Assess, therefore, the weight of diagnostic diffusion echo-planar sequence, in association with the morphological and dynamic sequences in the diagnosis of tumor recurrence versus surgical scar. Materials and methods: From September 2007 to March 2009, 72 patients operated for breast cancer with suspected recurrence on the scar were consecutively subjected to magnetic resonance imaging (MRI), including use of a diffusion sequence. All patients with pathological enhancement in the scar were then subjected to histological typing. MRI was considered negative in the absence of areas of suspicious enhancement. In all cases it was measured the ADC value in the scar area or in the area with pathological enhancement. The ADC values were compared with MRI findings and histological results obtained. Results: 26 cases were positive/doubtful at MRI and then subjected to histological typing: of these recurrences were 20 and benign were 6. 46 cases were judged negative at MRI and therefore not sent to cyto-histology. The average ADC value of recurrences was statistically lower of scarring (p < 0.001). Conclusions: ADC value can be a specific parameter in differential diagnosis between recurrence and scar. The diffusion sequence, in association with the morphological and dynamic sequences, can be considered a promising tool for the surgical indication in suspected recurrence of breast cancer.

  17. Cutaneous osteosarcoma arising from a burn scar

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Min A.; Yi, Jaehyuck [Kyungpook National University, Department of Radiology, College of Medicine, Daegu (Korea, Republic of); Kyungpook National University Hospital, Department of Radiology, Daegu (Korea, Republic of); Chae, Jong Min [Kyungpook National University, Department of Pathology, College of Medicine, Daegu (Korea, Republic of)

    2017-04-15

    Tumors that develop in old burn scars are usually squamous cell carcinomas. Sarcomas have also been reported, albeit rarely. To our knowledge, there has been only one case report of an extraskeletal osteosarcoma arising in a prior burn scar reported in the English-language literature, mainly discussing the clinicopathological features. Herein, we present a case of cutaneous osteosarcoma visualized as a mineralized soft-tissue mass arising from the scar associated with a previous skin burn over the back. This seems to be the first report describing the imaging features of a cutaneous osteosarcoma from an old burn scar. (orig.)

  18. Characterization of full-length sequenced cDNA inserts (FLIcs from Atlantic salmon (Salmo salar

    Directory of Open Access Journals (Sweden)

    Lunner Sigbjørn

    2009-10-01

    Full Text Available Abstract Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP, the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91% of the transcripts were annotated using Gene Ontology (GO terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS. The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS. This

  19. Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)

    Science.gov (United States)

    Andreassen, Rune; Lunner, Sigbjørn; Høyheim, Bjørn

    2009-01-01

    Background Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small. Results High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences. Conclusion This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining c

  20. Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus.

    Science.gov (United States)

    Collart, F R; Osipiuk, J; Trent, J; Olsen, G J; Huberman, E

    1996-10-03

    We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Pyrococcus furiosus (Pf), a hyperthermophillic archeon. Sequence analysis of the Pf gene indicated an open reading frame specifying a protein of 485 amino acids (aa) with a calculated M(r) of 52900. Canonical Archaea promoter elements, Box A and Box B, are located -49 and -17 nucleotides (nt), respectively, upstream of the putative start codon. The sequence of the putative active-site region conforms to the IMPDH signature motif and contains a putative active-site cysteine. Phylogenetic relationships derived by using all available IMPDH sequences are consistent with trees developed for other molecules; they do not precisely resolve the history of Pf IMPDH but indicate a close similarity to bacterial IMPDH proteins. The phylogenetic analysis indicates that a gene duplication occurred prior to the division between rodents and humans, accounting for the Type I and II isoforms identified in mice and humans.

  1. Outcome after burns: An observational study on burn scar maturation and predictors for severe scarring

    NARCIS (Netherlands)

    van der Wal, M.B.A.; Vloemans, J.F.P.M.; Tuinebreijer, W.E.; van de Ven, P.M.; van Unen, E.; van Zuijlen, P.P.M.; Middelkoop, E.

    2012-01-01

    Long-term outcome of burn scars as well as the relation with clinically relevant parameters has not been studied quantitatively. Therefore, we conducted a detailed analysis on the clinical changes of burn scars in a longitudinal setup. In addition, we focused on the differences in scar quality in

  2. Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867.

    Directory of Open Access Journals (Sweden)

    Huixia Du

    Full Text Available BACKGROUND: Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus. RESULTS: In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs and 54,000 single nucleotide polymorphisms (SNPs were detected in the A. japonicus transcriptome. CONCLUSION: Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic

  3. Immunohistochemical Analysis of Scarring Trachoma Indicates Infiltration by Natural Killer and Undefined CD45 Negative Cells.

    Science.gov (United States)

    Hu, Victor H; Luthert, Philip J; Derrick, Tamsyn; Pullin, James; Weiss, Helen A; Massae, Patrick; Mtuy, Tara; Makupa, William; Essex, David; Mabey, David C W; Bailey, Robin L; Holland, Martin J; Burton, Matthew J

    2016-05-01

    The phenotype and function of immune cells infiltrating the conjunctiva in scarring trachoma have yet to be fully characterized. We assessed tissue morphology and immunophenotype of cellular infiltrates found in trachomatous scarring compared to control participants. Clinical assessments and conjunctival biopsy samples were obtained from 34 individuals with trachomatous scarring undergoing trichiasis surgery and 33 control subjects undergoing cataract or retinal detachment surgery. Biopsy samples were fixed in buffered formalin and embedded in paraffin wax. Hematoxylin and eosin (H&E) staining was performed for assessment of the inflammatory cell infiltrate. Immunohistochemical staining of single markers on individual sections was performed to identify cells expressing CD3 (T-cells), CD4 (helper T-cells), CD8 (suppressor/cytotoxic T-cells and Natural Killer, NK, cells), NCR1 (NK cells), CD20 (B-cells), CD45 (nucleated hematopoietic cells), CD56 (NK and T-cells), CD68 (macrophages/monocytes) and CD83 (mature dendritic cells). The degree of scarring was assessed histologically using cross-polarized light to visualize collagen fibres. Scarring, regardless of clinical inflammation, was associated with increased inflammatory cell infiltrates on H&E and CD45 staining. Scarring was also associated with increased CD8+ and CD56+ cells, but not CD3+ cells, suggestive of a NK cell infiltrate. This was supported by the presence of NCR1+ cells. There was some increase in CD20+ cells, but no evidence for increased CD4+, CD68+ or CD83+ cells. Numerous CD45 negative cells were also seen in the population of infiltrating inflammatory cells in scarred conjunctiva. Disorganization of the normal collagen architecture was strongly associated with clinical scarring. These data point to the infiltration of immune cells with a phenotype suggestive of NK cells in conjunctival trachomatous scarring. A large proportion of CD45 negative inflammatory cells were also present. Future work should

  4. Biological characterization and complete nucleotide sequence of a Tunisian isolate of Moroccan watermelon mosaic virus.

    Science.gov (United States)

    Yakoubi, S; Desbiez, C; Fakhfakh, H; Wipf-Scheibel, C; Marrakchi, M; Lecoq, H

    2008-01-01

    During a survey conducted in October 2005, cucurbit leaf samples showing virus-like symptoms were collected from the major cucurbit-growing areas in Tunisia. DAS-ELISA showed the presence of Moroccan watermelon mosaic virus (MWMV, Potyvirus), detected for the first time in Tunisia, in samples from the region of Cap Bon (Northern Tunisia). MWMV isolate TN05-76 (MWMV-Tn) was characterized biologically and its full-length genome sequence was established. MWMV-Tn was found to have biological properties similar to those reported for the MWMV type strain from Morocco. Phylogenetic analysis including the comparison of complete amino-acid sequences of 42 potyviruses confirmed that MWMV-Tn is related (65% amino-acid sequence identity) to Papaya ringspot virus (PRSV) isolates but is a member of a distinct virus species. Sequence analysis on parts of the CP gene of MWMV isolates from different geographical origins revealed some geographic structure of MWMV variability, with three different clusters: one cluster including isolates from the Mediterranean region, a second including isolates from western and central Africa, and a third one including isolates from the southern part of Africa. A significant correlation was observed between geographic and genetic distances between isolates. Isolates from countries in the Mediterranean region where MWMV has recently emerged (France, Spain, Portugal) have highly conserved sequences, suggesting that they may have a common and recent origin. MWMV from Sudan, a highly divergent variant, may be considered an evolutionary intermediate between MWMV and PRSV.

  5. Mapping and characterizing N6-methyladenine in eukaryotic genomes using single molecule real-time sequencing.

    Science.gov (United States)

    Zhu, Shijia; Beaulaurier, John; Deikus, Gintaras; Wu, Tao; Strahl, Maya; Hao, Ziyang; Luo, Guanzheng; Gregory, James A; Chess, Andrew; He, Chuan; Xiao, Andrew; Sebra, Robert; Schadt, Eric E; Fang, Gang

    2018-05-15

    N6-methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes, however, methods for high resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic genomes, but its application to detecting m6dA in eukaryotic genomes has not been rigorously examined. Herein, we identified unique characteristics of eukaryotic m6dA methylomes that fundamentally differ from those of prokaryotes. Based on these differences, we describe the first approach for mapping m6dA events using SMRT sequencing specifically designed for the study of eukaryotic genomes, and provide appropriate strategies for designing experiments and carrying out sequencing in future studies. We apply the novel approach to study two eukaryotic genomes. For green algae, we construct the first complete genome-wide map of m6dA at single nucleotide and single molecule resolution. For human lymphoblastoid cells (hLCLs), joint analyses of SMRT sequencing and independent sequencing data suggest that putative m6dA events are enriched in the promoters of young, full length LINE-1 elements (L1s). These analyses demonstrate a general method for rigorous mapping and characterization of m6dA events in eukaryotic genomes. Published by Cold Spring Harbor Laboratory Press.

  6. Context based computational analysis and characterization of ARS consensus sequences (ACS of Saccharomyces cerevisiae genome

    Directory of Open Access Journals (Sweden)

    Vinod Kumar Singh

    2016-09-01

    Full Text Available Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS requires an essential consensus sequence (ACS for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC denoted as ORC-ACS and non-replicating ACS sequences (nrACS, that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.

  7. Formation of hypertrophic scars: Evolution and susceptibility

    NARCIS (Netherlands)

    Mahdavian Delavary, B.; van der Veer, W.M.; Ferreira, J.A.; Niessen, F.B.

    2012-01-01

    Formation of hypertrophic scars is a common complication of wound healing, and at present little is known about the incidence and risk factors. Our aim was to analyse the incidence, progression, and regression of postoperative hypertrophic scars over time and to identify risk factors of hypertrophic

  8. Cutaneous leiomyosarcoma arising in a smallpox scar

    NARCIS (Netherlands)

    Pol, Robert A.; Dannenberg, Hilde; Robertus, Jan-Lukas; van Ginkel, Robert J.

    2012-01-01

    Background: Cutaneous leiomyosarcoma (CLM) is a very rare smooth muscle tumour that accounts for about 2-3% of all superficial soft tissue sarcomas. Although the development of various malignancies in scar tissue is well known, we report the first case of a CLM developing in a small pox scar. Case

  9. SCAR/WAVE: A complex issue.

    Science.gov (United States)

    Davidson, Andrew J; Insall, Robert H

    2013-11-01

    The SCAR/WAVE complex drives the actin polymerisation that underlies protrusion of the front of the cell and thus drives migration. However, it is not understood how the activity of SCAR/WAVE is regulated to generate the infinite range of cellular shape changes observed during cell motility. What are the relative roles of the subunits of the SCAR/WAVE complex? What signaling molecules do they interact with? And how does the complex integrate all this information in order to control the temporal and spatial polymerisation of actin during protrusion formation? Unfortunately, the interdependence of SCAR complex members has made genetic dissection hard. In our recent paper,(1) we describe stabilization of the Dictyostelium SCAR complex by a small fragment of Abi. Here we summarize the main findings and discuss how this approach can help reveal the inner workings of this impenetrable complex.

  10. Strong quantum scarring by local impurities

    Science.gov (United States)

    Luukko, Perttu J. J.; Drury, Byron; Klales, Anna; Kaplan, Lev; Heller, Eric J.; Räsänen, Esa

    2016-11-01

    We discover and characterise strong quantum scars, or quantum eigenstates resembling classical periodic orbits, in two-dimensional quantum wells perturbed by local impurities. These scars are not explained by ordinary scar theory, which would require the existence of short, moderately unstable periodic orbits in the perturbed system. Instead, they are supported by classical resonances in the unperturbed system and the resulting quantum near-degeneracy. Even in the case of a large number of randomly scattered impurities, the scars prefer distinct orientations that extremise the overlap with the impurities. We demonstrate that these preferred orientations can be used for highly efficient transport of quantum wave packets across the perturbed potential landscape. Assisted by the scars, wave-packet recurrences are significantly stronger than in the unperturbed system. Together with the controllability of the preferred orientations, this property may be very useful for quantum transport applications.

  11. Prevention and curative management of hypertrophic scar formation

    NARCIS (Netherlands)

    Bloemen, M.C.; Veer, van der W.M.; Ulrich, M.; Zuijlen, van P.P.; Niessen, F.B.; Middelkoop, E.

    2009-01-01

    Although hypertrophic scarring commonly occurs following burns, many aspects such as incidence of and optimal treatment for scar hypertrophy remain unclear. This review will focus on hypertrophic scar formation after burn in particular, exploring multiple treatment options and describing their

  12. Outcome after burns: an observational study on burn scar maturation and predictors for severe scarring.

    Science.gov (United States)

    van der Wal, Martijn B A; Vloemans, Jos F P M; Tuinebreijer, Wim E; van de Ven, Peter; van Unen, Ella; van Zuijlen, Paul P M; Middelkoop, Esther

    2012-01-01

    Long-term outcome of burn scars as well as the relation with clinically relevant parameters has not been studied quantitatively. Therefore, we conducted a detailed analysis on the clinical changes of burn scars in a longitudinal setup. In addition, we focused on the differences in scar quality in relation to the depth, etiology of the burn wound and age of the patient. Burn scars of 474 patients were subjected to a scar assessment protocol 3, 6, and 12 months postburn. Three different age groups were defined (≤5, 5-18, and ≥18 years). The observer part of the patient and observer scar assessment scale revealed a significant (p burned (p  0.230) have no significant influence on scar quality when corrected for sex, total body surface area burned, time, and age or etiology, respectively. © 2012 by the Wound Healing Society.

  13. [Characterization of Black and Dichothrix Cyanobacteria Based on the 16S Ribosomal RNA Gene Sequence

    Science.gov (United States)

    Ortega, Maya

    2010-01-01

    My project focuses on characterizing different cyanobacteria in thrombolitic mats found on the island of Highborn Cay, Bahamas. Thrombolites are interesting ecosystems because of the ability of bacteria in these mats to remove carbon dioxide from the atmosphere and mineralize it as calcium carbonate. In the future they may be used as models to develop carbon sequestration technologies, which could be used as part of regenerative life systems in space. These thrombolitic communities are also significant because of their similarities to early communities of life on Earth. I targeted two cyanobacteria in my research, Dichothrix spp. and whatever black is, since they are believed to be important to carbon sequestration in these thrombolitic mats. The goal of my summer research project was to molecularly identify these two cyanobacteria. DNA was isolated from each organism through mat dissections and DNA extractions. I ran Polymerase Chain Reactions (PCR) to amplify the 16S ribosomal RNA (rRNA) gene in each cyanobacteria. This specific gene is found in almost all bacteria and is highly conserved, meaning any changes in the sequence are most likely due to evolution. As a result, the 16S rRNA gene can be used for bacterial identification of different species based on the sequence of their 16S rRNA gene. Since the exact sequence of the Dichothrix gene was unknown, I designed different primers that flanked the gene based on the known sequences from other taxonomically similar cyanobacteria. Once the 16S rRNA gene was amplified, I cloned the gene into specialized Escherichia coli cells and sent the gene products for sequencing. Once the sequence is obtained, it will be added to a genetic database for future reference to and classification of other Dichothrix sp.

  14. De novo sequencing, assembly and characterization of antennal transcriptome of Anomala corpulenta Motschulsky (Coleoptera: Rutelidae.

    Directory of Open Access Journals (Sweden)

    Haoliang Chen

    Full Text Available Anomala corpulenta is an important insect pest and can cause enormous economic losses in agriculture, horticulture and forestry. It is widely distributed in China, and both larvae and adults can cause serious damage. It is difficult to control this pest because the larvae live underground. Any new control strategy should exploit alternatives to heavily and frequently used chemical insecticides. However, little genetic research has been carried out on A. corpulenta due to the lack of genomic resources. Genomic resources could be produced by next generation sequencing technologies with low cost and in a short time. In this study, we performed de novo sequencing, assembly and characterization of the antennal transcriptome of A. corpulenta.Illumina sequencing technology was used to sequence the antennal transcriptome of A. corpulenta. Approximately 76.7 million total raw reads and about 68.9 million total clean reads were obtained, and then 35,656 unigenes were assembled. Of these unigenes, 21,463 of them could be annotated in the NCBI nr database, and, among the annotated unigenes, 11,154 and 6,625 unigenes could be assigned to GO and COG, respectively. Additionally, 16,350 unigenes could be annotated in the Swiss-Prot database, and 14,499 unigenes could map onto 258 pathways in the KEGG Pathway database. We also found 24 unigenes related to OBPs, 6 to CSPs, and in total 167 unigenes related to chemodetection. We analyzed 4 OBPs and 3CSPs sequences and their RT-qPCR results agreed well with their FPKM values.We produced the first large-scale antennal transcriptome of A. corpulenta, which is a species that has little genomic information in public databases. The identified chemodetection unigenes can promote the molecular mechanistic study of behavior in A. corpulenta. These findings provide a general sequence resource for molecular genetics research on A. corpulenta.

  15. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

    Directory of Open Access Journals (Sweden)

    Muhammad Naveed

    2014-09-01

    Full Text Available In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ. Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

  16. Characterizing ncRNAs in human pathogenic protists using high-throughput sequencing technology

    Directory of Open Access Journals (Sweden)

    Lesley Joan Collins

    2011-12-01

    Full Text Available ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, snoRNAs and long ncRNAs on a genomic scale making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.

  17. Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology

    Science.gov (United States)

    Collins, Lesley Joan

    2011-01-01

    ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases. PMID:22303390

  18. Characterization of Aftershock Sequences from Large Strike-Slip Earthquakes Along Geometrically Complex Faults

    Science.gov (United States)

    Sexton, E.; Thomas, A.; Delbridge, B. G.

    2017-12-01

    Large earthquakes often exhibit complex slip distributions and occur along non-planar fault geometries, resulting in variable stress changes throughout the region of the fault hosting aftershocks. To better discern the role of geometric discontinuities on aftershock sequences, we compare areas of enhanced and reduced Coulomb failure stress and mean stress for systematic differences in the time dependence and productivity of these aftershock sequences. In strike-slip faults, releasing structures, including stepovers and bends, experience an increase in both Coulomb failure stress and mean stress during an earthquake, promoting fluid diffusion into the region and further failure. Conversely, Coulomb failure stress and mean stress decrease in restraining bends and stepovers in strike-slip faults, and fluids diffuse away from these areas, discouraging failure. We examine spatial differences in seismicity patterns along structurally complex strike-slip faults which have hosted large earthquakes, such as the 1992 Mw 7.3 Landers, the 2010 Mw 7.2 El-Mayor Cucapah, the 2014 Mw 6.0 South Napa, and the 2016 Mw 7.0 Kumamoto events. We characterize the behavior of these aftershock sequences with the Epidemic Type Aftershock-Sequence Model (ETAS). In this statistical model, the total occurrence rate of aftershocks induced by an earthquake is λ(t) = λ_0 + \\sum_{i:t_i

  19. Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.

    Science.gov (United States)

    Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2014-02-01

    Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

  20. Characterization of race 65 of Colletotrichum lindemuthianum by sequencing ITS regions

    Directory of Open Access Journals (Sweden)

    Marcela Coelho

    2016-09-01

    Full Text Available The present work aimed characterize isolates of C. lindemuthianum race 65 from different regions in Brazil by ITS sequencing. A total of 17 isolates of race 65, collected in the states of Mato Grosso, Minas Gerais, Paraná, Santa Catarina and São Paulo, were studied. Analysis of the sequences of isolates 8, 9, 12, 14 and 15 revealed the presence of two single nucleotide polymorphisms (SNPs in the ITS1 region at the same positions. These isolates, when analyzed together with the sequence of isolate 17, revealed a SNP in the ITS2 region. The highest genetic dissimilarity, observed between isolates 11 and  3 and between isolates 11 and 10, was 0.772. In turn, isolates 7 and 2 were the most similar, with a value of 0.002 for genetic distance. The phylogenetic tree obtained based on the sequences of the ITS1 and ITS2 regions revealed the formation of two groups, one with a subgroup. The results reveal high molecular variability among isolates of race 65 of C. lindemuthianum.

  1. Characterization of sequence diversity in Plasmodium falciparum SERA5 from Indian isolates

    Directory of Open Access Journals (Sweden)

    Rahul C.N

    2015-06-01

    Full Text Available Objective: To characterize the sequence diversity of blood-stage Plasmodium falciparum serine repeat antigen-5 (PfSERA5 which is lacking in a malaria-endemic country like India. Methods: In this study, parasitic DNA was obtained from field isolates collected from various geographic regions. Subsequently, PfSERA5 gene sequence was PCR amplified and DNA sequenced. Results: We reported the existence of unique repeat polymorphisms and novel haplotypes for both the octamer repeat (OR and serine repeat (SR regions of the N-terminal fragment of PfSERA5 from Indian isolates. Several isolates from India were identical to low-frequency African haplotypes. Unique finding of our study was an Indian isolate showing deletion in a perfectly conserved 14 mer sequence within octamer repeat. Indian haplotypes reported in this study were found to be distributed into the three earlier classified allelic clusters of FCR3, K1 and Honduras showcasing broad diversity as compared to worldwide haplotypes. Conclusions: This study is the first report on genetic diversity of PfSERA5 antigen from India. Further evaluation of these haplotypes by serotyping would provide useful information for investigating variant-specific immunity and aid in malaria vaccine research.

  2. A Retrospective Examination of Feline Leukemia Subgroup Characterization: Viral Interference Assays to Deep Sequencing

    Directory of Open Access Journals (Sweden)

    Elliott S. Chiu

    2018-01-01

    Full Text Available Feline leukemia virus (FeLV was the first feline retrovirus discovered, and is associated with multiple fatal disease syndromes in cats, including lymphoma. The original research conducted on FeLV employed classical virological techniques. As methods have evolved to allow FeLV genetic characterization, investigators have continued to unravel the molecular pathology associated with this fascinating agent. In this review, we discuss how FeLV classification, transmission, and disease-inducing potential have been defined sequentially by viral interference assays, Sanger sequencing, PCR, and next-generation sequencing. In particular, we highlight the influences of endogenous FeLV and host genetics that represent FeLV research opportunities on the near horizon.

  3. A Retrospective Examination of Feline Leukemia Subgroup Characterization: Viral Interference Assays to Deep Sequencing.

    Science.gov (United States)

    Chiu, Elliott S; Hoover, Edward A; VandeWoude, Sue

    2018-01-10

    Feline leukemia virus (FeLV) was the first feline retrovirus discovered, and is associated with multiple fatal disease syndromes in cats, including lymphoma. The original research conducted on FeLV employed classical virological techniques. As methods have evolved to allow FeLV genetic characterization, investigators have continued to unravel the molecular pathology associated with this fascinating agent. In this review, we discuss how FeLV classification, transmission, and disease-inducing potential have been defined sequentially by viral interference assays, Sanger sequencing, PCR, and next-generation sequencing. In particular, we highlight the influences of endogenous FeLV and host genetics that represent FeLV research opportunities on the near horizon.

  4. Cutaneous leiomyosarcoma arising in a smallpox scar.

    Science.gov (United States)

    Pol, Robert A; Dannenberg, Hilde; Robertus, Jan-Lukas; van Ginkel, Robert J

    2012-07-16

    Cutaneous leiomyosarcoma (CLM) is a very rare smooth muscle tumour that accounts for about 2-3% of all superficial soft tissue sarcomas. Although the development of various malignancies in scar tissue is well known, we report the first case of a CLM developing in a small pox scar. A 66-year-old man presented with a painless, slow-growing lump in a small pox scar on his left shoulder. Histological biopsies showed the lesion to be a primary, well-differentiated cutaneous leiomyosarcoma. A CT scan of the thorax was conducted, which showed no signs of metastases. The complete lesion was then surgically excised, and histopathological examination revealed a radically excised cutaneous type leiomyosarcoma After 13 months' review the patient was doing well with no evidence of tumour recurrence. This is the first report of a CLM arising in a small pox scar. Although the extended time interval between scarring and malignant changes makes it difficult to advise strict follow-up for patients with small pox scars, one should be aware that atypical changes and/or symptoms occurring in a small pox scar could potentially mean malignant transformation.

  5. Cutaneous leiomyosarcoma arising in a smallpox scar

    Directory of Open Access Journals (Sweden)

    Pol Robert A

    2012-07-01

    Full Text Available Abstract Background Cutaneous leiomyosarcoma (CLM is a very rare smooth muscle tumour that accounts for about 2–3% of all superficial soft tissue sarcomas. Although the development of various malignancies in scar tissue is well known, we report the first case of a CLM developing in a small pox scar. Case presentation A 66-year-old man presented with a painless, slow-growing lump in a small pox scar on his left shoulder. Histological biopsies showed the lesion to be a primary, well-differentiated cutaneous leiomyosarcoma. A CT scan of the thorax was conducted, which showed no signs of metastases. The complete lesion was then surgically excised, and histopathological examination revealed a radically excised cutaneous type leiomyosarcoma After 13 months’ review the patient was doing well with no evidence of tumour recurrence. Conclusions This is the first report of a CLM arising in a small pox scar. Although the extended time interval between scarring and malignant changes makes it difficult to advise strict follow-up for patients with small pox scars, one should be aware that atypical changes and/or symptoms occurring in a small pox scar could potentially mean malignant transformation.

  6. Values of a Patient and Observer Scar Assessment Scale to Evaluate the Facial Skin Graft Scar.

    Science.gov (United States)

    Chae, Jin Kyung; Kim, Jeong Hee; Kim, Eun Jung; Park, Kun

    2016-10-01

    The patient and observer scar assessment scale (POSAS) recently emerged as a promising method, reflecting both observer's and patient's opinions in evaluating scar. This tool was shown to be consistent and reliable in burn scar assessment, but it has not been tested in the setting of skin graft scar in skin cancer patients. To evaluate facial skin graft scar applied to POSAS and to compare with objective scar assessment tools. Twenty three patients, who diagnosed with facial cutaneous malignancy and transplanted skin after Mohs micrographic surgery, were recruited. Observer assessment was performed by three independent rates using the observer component of the POSAS and Vancouver scar scale (VSS). Patient self-assessment was performed using the patient component of the POSAS. To quantify scar color and scar thickness more objectively, spectrophotometer and ultrasonography was applied. Inter-observer reliability was substantial with both VSS and the observer component of the POSAS (average measure intraclass coefficient correlation, 0.76 and 0.80, respectively). The observer component consistently showed significant correlations with patients' ratings for the parameters of the POSAS (all p -valuesskin graft scar assessment in skin cancer patients, the POSAS showed acceptable inter-observer reliability. This tool was more comprehensive and had higher correlation with patient's opinion.

  7. Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities* #

    Science.gov (United States)

    Pérez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Carú, Margarita

    2014-01-01

    Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20–23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community. PMID:25367789

  8. Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities.

    Science.gov (United States)

    Pérez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Carú, Margarita

    2014-11-01

    Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20-23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community.

  9. Molecular detection and sequence characterization of diverse rhabdoviruses in bats, China.

    Science.gov (United States)

    Xu, Lin; Wu, Jianmin; Jiang, Tinglei; Qin, Shaomin; Xia, Lele; Li, Xingyu; He, Biao; Tu, Changchun

    2018-01-15

    The Rhabdoviridae is among the most diverse families of RNA viruses and currently classified into 18 genera with some rhabdoviruses lethal to humans and other animals. Herein, we describe genetic characterization of three novel rhabdoviruses from bats in China. Of these, two viruses (Jinghong bat virus and Benxi bat virus) found in Rhinolophus bats showed a phylogenetic relationship with vesiculoviruses, and sequence analyses indicate that they represent two new species within the genus Vesiculovirus. The remaining Yangjiang bat virus found in Hipposideros larvatus bats were only distantly related to currently known rhabdoviruses. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Characterization and sequence analysis of the F2 promoter from corynephage BFK20

    International Nuclear Information System (INIS)

    Koptides, M.; Ugorcakova, J.; Baloghova, E.; Bukovska, G.; Timko, J.

    1994-01-01

    F2 promoter from corynephage BFK20 was isolated and characterized. It was functional in Escherichia coli and Corynebacterium glutamicum. Cloning of the F2 promoter into the pJUP05 promoter probe vector caused an increase of the neomycin phosphotransferase II specific activity. According to the Northern blot hybridization the nptII gene was expressed from the cloned F2 promoter. The apparent transcription start point in E. coli and C. glutamicum was determined. The-35 region of F2 promoter showed high similarity to that of E. coli promoter consensus sequence, but its - 10 region was G+C rich and had no significant homology to that. (author)

  11. Potential utility of MRI in the evaluation of children at risk of renal scarring

    Energy Technology Data Exchange (ETDEWEB)

    Chan Yuleung; Chan Kamwing; Roebuck, D.J.; Chu, W.C.W.; Metreweli, C. [Dept. of Diagnostic Radiology and Organ Imaging, Chinese Univ. of Hong Kong, Shatin (China); Yeung Chungkwong; Lee Kimhung [Dept. of Surgery, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong (China)

    1999-11-01

    Background. Gadolinium-enhanced MRI has recently been employed in the diagnosis of acute pyelonephritis. Its potential utility in the diagnosis of renal scars in children is unknown. Objective. To evaluate the potential utility of MRI using fat-saturated T1-weighted (T1-W) and post-gadolinium, short-tau inversion-recovery (STIR) sequences in detecting renal scarring by comparison with technetium dimercaptosuccinic acid ({sup 99} {sup m}Tc-DMSA) renal scintigraphy in children at risk of renal scarring. Materials and methods. A group of 24 children with spina bifida and neurogenic bladder or anorectal anomaly was studied. No patient had a history of acute pyelonephritis. Documented urinary tract infection (UTI) was present in 10 children (42 %). The remaining 14 (58 %) children had a history of asymptomatic bacteriuria. None had clinical signs or symptoms of acute UTI at the time of the study. {sup 99} {sup m}Tc-DMSA and MRI were performed to detect renal scarring. {sup 99} {sup m}Tc-DMSA scans were supplemented with pinhole imaging. MRI of the kidneys employed a fat-saturated T1-W sequence and a post-gadolinium STIR sequence employing a short echo time. Results. Of the kidneys studied, 33 % (n = 16) had evidence of a renal parenchymal defect suggestive of scarring on {sup 99} {sup m}Tc-DMSA. The concordance in the detection of a scarred kidney by post-gadolinium STIR sequence and {sup 99} {sup m}Tc-DMSA is 94 %; that by fat-saturated T1-W sequence and {sup 99} {sup m}Tc-DMSA is 82 %; that by both sequences (positive result on either sequence) and {sup 99} {sup m}Tc-DMSA is 100 %. Using {sup 99} {sup m}Tc-DMSA as the gold standard, MRI had a sensitivity of 100 % and a specificity of 78 % in the diagnosis of a scarred kidney. The concordance in the detection of a scarred zone by post-gadolinium STIR sequence and {sup 99} {sup m}Tc-DMSA is 68 %; that by fat-saturated T1-W sequence and DMSA is 44 %; that by both sequences (positive result on either sequence) and {sup 99

  12. Assessment of left ventricular myocardial scar with three-dimensional MRI

    International Nuclear Information System (INIS)

    Yin Gang; Zhao Shihua; Lu Minjie

    2011-01-01

    Objective: To assess the value of free-breathing 3D phase sensitive inversion recovery (PSIR) turbo FLASH for demonstrating the left ventricular myocardial scar in patients with myocardial infarction. Methods: Twenty-three patients with myocardial infarction underwent 2D and 3D phase sensitive inversion recovery (PSIR) Turbo FLASH sequences 10-15 minutes after injection of dimeglumine gadopentetate. The image quality, the area, location and volume of hyperenhanced scar were independently assessed by two experienced radiologists. Student's t test or rank sum test and Pearson linear correlation were used for the statistics. Results: There were no significant differences in the overall image quality (2.57± 0.59 vs 2.39±0.66, Z=-0.93, P=0.35), the area (24.48±10.83 vs 29.00±11.56, Z=-1.41, P=0.16) and location (16.78±6.51 vs 18.87±6.76, Z=-1.17, P=0.24) of hyperenhanced scar between 2D and 3D PSIR sequences. The mean volume of hyperenhanced scar was significantly greater in 3D PSIR sequence than that in 2D PSIR sequence [(23.46±10.61) vs (31.65±13.86) cm 3 , t=-2.25, P= 0.03]. There was a good correlation in the volume of hyperenhanced scar between 2D PSIR and 3D PSIR sequences (r=0.940, P 2 =0.883). Conclusion: Free-breathing 3D PSIR Turbo FLASH is a promising new imaging technique for accurate assessment of myocardial scar. (authors)

  13. The soft mechanical signature of glial scars in the central nervous system

    Science.gov (United States)

    Moeendarbary, Emad; Weber, Isabell P.; Sheridan, Graham K.; Koser, David E.; Soleman, Sara; Haenzi, Barbara; Bradbury, Elizabeth J.; Fawcett, James; Franze, Kristian

    2017-03-01

    Injury to the central nervous system (CNS) alters the molecular and cellular composition of neural tissue and leads to glial scarring, which inhibits the regrowth of damaged axons. Mammalian glial scars supposedly form a chemical and mechanical barrier to neuronal regeneration. While tremendous effort has been devoted to identifying molecular characteristics of the scar, very little is known about its mechanical properties. Here we characterize spatiotemporal changes of the elastic stiffness of the injured rat neocortex and spinal cord at 1.5 and three weeks post-injury using atomic force microscopy. In contrast to scars in other mammalian tissues, CNS tissue significantly softens after injury. Expression levels of glial intermediate filaments (GFAP, vimentin) and extracellular matrix components (laminin, collagen IV) correlate with tissue softening. As tissue stiffness is a regulator of neuronal growth, our results may help to understand why mammalian neurons do not regenerate after injury.

  14. Characterization of some sedimentary sequences from Cambay basin, India, by pyrolysis-GC

    Science.gov (United States)

    Philp, R. P.; Garg, A. K.

    Pyrolysis-gas chromatography of sedimentary sequences from a key exploratory well of the southern Cambay Basin, India, has been performed to characterize the nature of the source material and its maturity. In samples from the Eocene-Paleocene section (2960-3407 m), the pyrolysate is dominated by hydrocarbons in the lower molecular weight region indicating a significant input algal source material. The presence of various xylenes and phenols in the pyrograms is indicative of a significant input from higher plant material. The organic material in this section is interpreted to have been derived from marine-terrestrial source inputs deposited under swampy to marine and reducing environments. Good mature source rocks with type III kerogens which are wet gas/gas condensate-prone have been identified in this region. This paper intends to discuss the characterization of source rocks using the pyrolysis-gas chromatography approach and the significance of the distribution of the pyrolysis product.

  15. Sequence characterization of heat shock protein gene of Cyclospora cayetanensis isolates from Nepal, Mexico, and Peru.

    Science.gov (United States)

    Sulaiman, Irshad M; Torres, Patricia; Simpson, Steven; Kerdahi, Khalil; Ortega, Ynes

    2013-04-01

    We have described the development of a 2-step nested PCR protocol based on the characterization of the 70-kDa heat shock protein (HSP70) gene for rapid detection of the human-pathogenic Cyclospora cayetanensis parasite. We tested and validated these newly designed primer sets by PCR amplification followed by nucleotide sequencing of PCR-amplified HSP70 fragments belonging to 16 human C. cayetanensis isolates from 3 different endemic regions that include Nepal, Mexico, and Peru. No genetic polymorphism was observed among the isolates at the characterized regions of the HSP70 locus. This newly developed HSP70 gene-based nested PCR protocol provides another useful genetic marker for the rapid detection of C. cayetanensis in the future.

  16. [Multilocus sequence-typing for characterization of Moscow strains of Haemophilus influenzae type b].

    Science.gov (United States)

    Platonov, A E; Mironov, K O; Iatsyshina, S B; Koroleva, I S; Platonova, O V; Gushchin, A E; Shipulin, G A

    2003-01-01

    Haemophilius influenzae, type b (Hib) bacteria, were genotyped by multilocus sequence typing (MLST) using 5 loci (adk, fucK, mdh, pgi, recA). 42 Moscow Hib strains (including 38 isolates form cerebrospinal fluid of children, who had purulent meningitis in 1999-2001, and 4 strains isolated from healthy carriers of Hib), as well as 2 strains from Yekaterinburg were studied. In MLST a strain is characterized, by alleles and their combinations (an allele profile) referred to also as sequence-type (ST). 9 Sts were identified within the Russian Hib bacteria: ST-1 was found in 25 strains (57%), ST-12 was found in 8 strains (18%), ST-11 was found in 4 strains (9%) and ST-15 was found in 2 strains (4.5%); all other STs strains (13, 14, 16, 17, 51) were found in isolated cases (2.3%). A comparison of allelic profiles and of nucleotide sequences showed that 93% of Russian isolates, i.e. strain with ST-1, 11, 12, 13, 15 and 17, belong to one and the same clonal complex. 2 isolates from Norway and Sweden from among 7 foreign Hib strains studied up to now can be described as belonging to the same clonal complex; 5 Hib strains were different from the Russian ones.

  17. Medical makeup for concealing facial scars.

    Science.gov (United States)

    Mee, Donna; Wong, Brian J F

    2012-10-01

    Surgical, laser, and pharmacological therapies are all used to correct scars and surgical incisions, though have limits with respect to how well facial skin can be restored or enhanced. The use of cosmetics has long been a relevant adjunct to all scar treatment modalities. In recent years, technical advancements in the chemistry and composition of cosmetic products have provided the patient with a broader range of products to employ for concealing scars. This review will provide an overview of contemporary methods for concealing facial scars, birthmarks, and pigmentary changes without the use of traditional/dated, heavy appearing camouflage products. Additionally, general guidelines and information will be provided with respect to identifying competent makeup artists for care of the medical patient. The article by no means is meant to be a tutorial, but rather serves as a starting point in this allied field of medicine. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  18. Characterization of platelet adhesion under flow using microscopic image sequence analysis.

    Science.gov (United States)

    Machin, M; Santomaso, A; Cozzi, M R; Battiston, M; Mazzuccato, M; De Marco, L; Canu, P

    2005-07-01

    A method for quantitative analysis of platelet deposition under flow is discussed here. The model system is based upon perfusion of blood platelets over an adhesive substrate immobilized on a glass coverslip acting as the lower surface of a rectangular flow chamber. The perfusion apparatus is mounted onto an inverted microscope equipped with epifluorescent illumination and intensified CCD video camera. Characterization is based on information obtained from a specific image analysis method applied to continuous sequences of microscopical images. Platelet recognition across the sequence of images is based on a time-dependent, bidimensional, gaussian-like pdf. Once a platelet is located,the variation of its position and shape as a function of time (i.e., the platelet history) can be determined. Analyzing the history we can establish if the platelet is moving on the surface, the frequency of this movement and the distance traveled before its resumes the velocity of a non-interacting cell. Therefore, we can determine how long the adhesion would last which is correlated to the resistance of the platelet-substrate bond. This algorithm enables the dynamic quantification of trajectories, as well as residence times, arrest and release frequencies for a high numbers of platelets at the same time. Statistically significant conclusions on platelet-surface interactions can then be obtained. An image analysis tool of this kind can dramatically help the investigation and characterization of the thrombogenic properties of artificial surfaces such as those used in artificial organs and biomedical devices.

  19. Characterizing Aftershock Sequences of the Recent Strong Earthquakes in Central Italy

    Science.gov (United States)

    Kossobokov, Vladimir G.; Nekrasova, Anastasia K.

    2017-10-01

    The recent strong earthquakes in Central Italy allow for a comparative analysis of their aftershocks from the viewpoint of the Unified Scaling Law for Earthquakes, USLE, which generalizes the Gutenberg-Richter relationship making use of naturally fractal distribution of earthquake sources of different size in a seismic region. In particular, we consider aftershocks as a sequence of avalanches in self-organized system of blocks-and-faults of the Earth lithosphere, each aftershock series characterized with the distribution of the USLE control parameter, η. We found the existence, in a long-term, of different, intermittent levels of rather steady seismic activity characterized with a near constant value of η, which switch, in mid-term, at times of transition associated with catastrophic events. On such a transition, seismic activity may follow different scenarios with inter-event time scaling of different kind, including constant, logarithmic, power law, exponential rise/decay or a mixture of those as observed in the case of the ongoing one associated with the three strong earthquakes in 2016. Evidently, our results do not support the presence of universality of seismic energy release, while providing constraints on modelling seismic sequences for earthquake physicists and supplying decision makers with information for improving local seismic hazard assessments.

  20. Molecular characterization of Taenia multiceps isolates from Gansu Province, China by sequencing of mitochondrial cytochrome C oxidase subunit 1.

    Science.gov (United States)

    Li, Wen Hui; Jia, Wan Zhong; Qu, Zi Gang; Xie, Zhi Zhou; Luo, Jian Xun; Yin, Hong; Sun, Xiao Lin; Blaga, Radu; Fu, Bao Quan

    2013-04-01

    A total of 16 Taenia multiceps isolates collected from naturally infected sheep or goats in Gansu Province, China were characterized by sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The complete cox1 gene was amplified for individual T. multiceps isolates by PCR, ligated to pMD18T vector, and sequenced. Sequence analysis indicated that out of 16 T. multiceps isolates 10 unique cox1 gene sequences of 1,623 bp were obtained with sequence variation of 0.12-0.68%. The results showed that the cox1 gene sequences were highly conserved among the examined T. multiceps isolates. However, they were quite different from those of the other Taenia species. Phylogenetic analysis based on complete cox1 gene sequences revealed that T. multiceps isolates were composed of 3 genotypes and distinguished from the other Taenia species.

  1. Phylogenetic Analysis of Apple scar skin viroid Isolates in Korea

    Directory of Open Access Journals (Sweden)

    Kang Hee Cho

    2015-12-01

    Full Text Available To identify genome sequences of Apple scar skin viroid (ASSVd isolates in Korea, the field survey was performed from ‘Hongro’ apple orchards located in eight sites in South Korea (Bongwha, Cheongsong, Dangjin, Gimchoen, Muju, Mungyeong, Suwon, and Yeongwol. ASSVd was detected by RT-PCR and PCR fragments were cloned into cloning vector. Full-length viral genomes of eight ASSVd isolates were sequenced and compared with 21 isolates reported previously from Korea, India, China, Japan and Greece. Eight isolates in this study showed 92.2-99.7% nucleotide sequence identities with those reported previously. Phylogenetic analysis showed that seven isolates reported in this study belong to the same group distinct from other groups.

  2. Assessment of scar quality after cleft lip closure

    NARCIS (Netherlands)

    Frans, Franceline A.; van Zuijlen, Paul P. M.; Griot, J. P. W. Don; van der Horst, Chantal M. A. M.

    2012-01-01

    To assess scar quality after cleft lip repair. The linear scars of patients with cleft lip with or without cleft palate were evaluated in a prospective study using the Patient and Observer Scar Assessment Scale. Linear regression was performed to identify which scar characteristics were important

  3. [How to optimize scarring in dermatologic surgery?

    Science.gov (United States)

    Amici, J M; Chaussade, V

    2016-12-01

    Scarring is the response elicited by the skin surface to injury and loss of tissue material. Wound healing takes place through a complex natural repair system consisting of vascular, inflammatory and proliferative phenomena, followed by a remodelling and cell apoptosis phase. This incredible repair system is inevitable, but sometimes unpredictable due to individual differences based on multiple factors. The scar is the objective criterion of a skin surgery, both for the patient and the dermsurgeon. It is therefore crucial to establish with the patient during the preoperative consultation, the size and positioning of the expected scar, taking into account the oncologic, anatomic and surgical constraints. Scars can ideally blend into normal skin, but may also give rise to various abnormalities. We can manage and prevent these abnormalities by mastering initial inflammation, that may induce hyperpigmentation and hypertrophy. Early massage using cortocosteroid topic or anti-inflammatory moisturizers may be effective. Random individual scarring may be minimized by a dynamic personalized accompanying scarring. © 2016 Elsevier Masson SAS. Tous droits réservés.

  4. Overview of surgical scar prevention and management.

    Science.gov (United States)

    Son, Daegu; Harijan, Aram

    2014-06-01

    Management of incisional scar is intimately connected to stages of wound healing. The management of an elective surgery patient begins with a thorough informed consent process in which the patient is made aware of personal and clinical circumstances that cannot be modified, such as age, ethnicity, and previous history of hypertrophic scars. In scar prevention, the single most important modifiable factor is wound tension during the proliferative and remodeling phases, and this is determined by the choice of incision design. Traditional incisions most often follow relaxed skin tension lines, but no such lines exist in high surface tension areas. If such incisions are unavoidable, the patient must be informed of this ahead of time. The management of a surgical incision does not end when the sutures are removed. Surgical scar care should be continued for one year. Patient participation is paramount in obtaining the optimal outcome. Postoperative visits should screen for signs of scar hypertrophy and has a dual purpose of continued patient education and reinforcement of proper care. Early intervention is a key to control hyperplastic response. Hypertrophic scars that do not improve by 6 months are keloids and should be managed aggressively with intralesional steroid injections and alternate modalities.

  5. Scar modification. Techniques for revision and camouflage.

    Science.gov (United States)

    Horswell, B B

    1998-09-01

    The surgery and management of scars is a protracted and staged process that includes preparation of the skin through hygienic measures, scar softening (if indicated) with steroids, massage and pressure dressings, skilled execution of the surgical plan, and thorough postoperative wound care. This process generally covers a 1-year period for the various stages mentioned. Many general host and local skin factors will directly affect the final revision result. The two most important indirect factors that the surgeon must endeavor to control are optimal patient preparation and cutaneous health, and patient compliance with, and an ability to carry out, those wound care measures that the surgeon prescribes. Keloid and burn contracture scars represent two entities that are complicated and challenging to treat owing to their abnormal morphophysiologic features. Management of these scars is prolonged, and the patient must understand that the ultimate result will usually be a compromise. New grafting techniques, such as cultured autodermal grafts, offer improved initial management of burn wounds that may subsequently optimize scar revision in these patients. Keloids, and to a lesser extent hypertrophic scars, require steroid injections, pressure treatment, careful surgery, and protracted wound support and pressure treatment (exceeding 6 months) after surgery.

  6. Molecular characterization, tissue expression and sequence variability of the barramundi (Lates calcarifer myostatin gene

    Directory of Open Access Journals (Sweden)

    Smith-Keune Carolyn

    2008-02-01

    Full Text Available Abstract Background Myostatin (MSTN is a member of the transforming growth factor-β superfamily that negatively regulates growth of skeletal muscle tissue. The gene encoding for the MSTN peptide is a consolidate candidate for the enhancement of productivity in terrestrial livestock. This gene potentially represents an important target for growth improvement of cultured finfish. Results Here we report molecular characterization, tissue expression and sequence variability of the barramundi (Lates calcarifer MSTN-1 gene. The barramundi MSTN-1 was encoded by three exons 379, 371 and 381 bp in length and translated into a 376-amino acid peptide. Intron 1 and 2 were 412 and 819 bp in length and presented typical GT...AG splicing sites. The upstream region contained cis-regulatory elements such as TATA-box and E-boxes. A first assessment of sequence variability suggested that higher mutation rates are found in the 5' flanking region with several SNP's present in this species. A putative micro RNA target site has also been observed in the 3'UTR (untranslated region and is highly conserved across teleost fish. The deduced amino acid sequence was conserved across vertebrates and exhibited characteristic conserved putative functional residues including a cleavage motif of proteolysis (RXXR, nine cysteines and two glycosilation sites. A qualitative analysis of the barramundi MSTN-1 expression pattern revealed that, in adult fish, transcripts are differentially expressed in various tissues other than skeletal muscles including gill, heart, kidney, intestine, liver, spleen, eye, gonad and brain. Conclusion Our findings provide valuable insights such as sequence variation and genomic information which will aid the further investigation of the barramundi MSTN-1 gene in association with growth. The finding for the first time in finfish MSTN of a miRNA target site in the 3'UTR provides an opportunity for the identification of regulatory mutations on the

  7. Development of a thematic collection of Musa spp accessions using SCAR markers for preventive breeding against Fusarium oxysporum f. sp cubense tropical race 4.

    Science.gov (United States)

    Silva, P R O; de Jesus, O N; Bragança, C A D; Haddad, F; Amorim, E P; Ferreira, C F

    2016-03-11

    Bananas are one of the most consumed fruits worldwide, but are affected by many pests and diseases. One of the most devastating diseases is Fusarium wilt, caused by Fusarium oxysporum f. sp cubense (Foc). Recently, Fusarium tropical race 4 (Foc TR4) has been causing irreparable damage, especially in Asia and Africa where it has devastated entire plantations, including areas with Cavendish, which is known to be resistant to Foc race 1. Although this race is not yet present in Brazil, results obtained by Embrapa in partnership with the University of Wageningen, The Netherlands, indicate that 100% of the cultivars used by Brazilian growers are susceptible to Foc TR 4. In our study, 276 banana accessions were screened with sequence characterized amplified region (SCAR) markers that have been linked to the resistance of Foc TR 4. Two SCAR primers were tested and the results revealed that SCAR ScaU1001 was efficient at discriminating accessions with possible resistance in 36.6% of the evaluated accessions. This is the first attempt to develop a thematic collection of possible Foc TR 4 resistant banana accessions in Brazil, which could be tested in Asian or African countries to validate marker-assisted selection (MAS), and for use in the preventive breeding of the crop to safeguard our banana plantations against Foc TR 4. We believe that this is an important step towards the prevention of this devastating disease, especially considering that our banana plantations are at risk.

  8. Assessment of SCAR markers to design real-time PCR primers for rhizosphere quantification of Azospirillum brasilense phytostimulatory inoculants of maize.

    Science.gov (United States)

    Couillerot, O; Poirier, M-A; Prigent-Combaret, C; Mavingui, P; Caballero-Mellado, J; Moënne-Loccoz, Y

    2010-08-01

    To assess the applicability of sequence characterized amplified region (SCAR) markers obtained from BOX, ERIC and RAPD fragments to design primers for real-time PCR quantification of the phytostimulatory maize inoculants Azospirillum brasilense UAP-154 and CFN-535 in the rhizosphere. Primers were designed based on strain-specific SCAR markers and were screened for successful amplification of target strain and absence of cross-reaction with other Azospirillum strains. The specificity of primers thus selected was verified under real-time PCR conditions using genomic DNA from strain collection and DNA from rhizosphere samples. The detection limit was 60 fg DNA with pure cultures and 4 x 10(3) (for UAP-154) and 4 x 10(4) CFU g(-1) (for CFN-535) in the maize rhizosphere. Inoculant quantification was effective from 10(4) to 10(8) CFU g(-1) soil. BOX-based SCAR markers were useful to find primers for strain-specific real-time PCR quantification of each A. brasilense inoculant in the maize rhizosphere. Effective root colonization is a prerequisite for successful Azospirillum phytostimulation, but cultivation-independent monitoring methods were lacking. The real-time PCR methods developed here will help understand the effect of environmental conditions on root colonization and phytostimulation by A. brasilense UAP-154 and CFN-535.

  9. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.

    Science.gov (United States)

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-07-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.

  10. Identification and characterization of earthquake clusters: a comparative analysis for selected sequences in Italy

    Science.gov (United States)

    Peresan, Antonella; Gentili, Stefania

    2017-04-01

    Identification and statistical characterization of seismic clusters may provide useful insights about the features of seismic energy release and their relation to physical properties of the crust within a given region. Moreover, a number of studies based on spatio-temporal analysis of main-shocks occurrence require preliminary declustering of the earthquake catalogs. Since various methods, relying on different physical/statistical assumptions, may lead to diverse classifications of earthquakes into main events and related events, we aim to investigate the classification differences among different declustering techniques. Accordingly, a formal selection and comparative analysis of earthquake clusters is carried out for the most relevant earthquakes in North-Eastern Italy, as reported in the local OGS-CRS bulletins, compiled at the National Institute of Oceanography and Experimental Geophysics since 1977. The comparison is then extended to selected earthquake sequences associated with a different seismotectonic setting, namely to events that occurred in the region struck by the recent Central Italy destructive earthquakes, making use of INGV data. Various techniques, ranging from classical space-time windows methods to ad hoc manual identification of aftershocks, are applied for detection of earthquake clusters. In particular, a statistical method based on nearest-neighbor distances of events in space-time-energy domain, is considered. Results from clusters identification by the nearest-neighbor method turn out quite robust with respect to the time span of the input catalogue, as well as to minimum magnitude cutoff. The identified clusters for the largest events reported in North-Eastern Italy since 1977 are well consistent with those reported in earlier studies, which were aimed at detailed manual aftershocks identification. The study shows that the data-driven approach, based on the nearest-neighbor distances, can be satisfactorily applied to decompose the seismic

  11. Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF): a case study in the Phoma exigua species complex

    NARCIS (Netherlands)

    Aveskamp, M.M.; Woudenberg, J.H.C.; Gruyter, de J.; Turco, E.; Groenewald, J.Z.; Crous, P.W.

    2009-01-01

    Phoma exigua is considered to be an assemblage of at least nine varieties that are mainly distinguished on the basis of host specificity and pathogenicity. However, these varieties are also reported to be weak pathogens and secondary invaders on non-host tissue. In practice, it is difficult to

  12. Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF) : a case study in the Phoma exigua species complex

    NARCIS (Netherlands)

    Aveskamp, M.M.; Woudenberg, J.H.C.; de Gruyter, J.; Turco, E.; Groenewald, J.Z.; Crous, P.W.

    2009-01-01

    Phoma exigua is considered to be an assemblage of at least nine varieties that are mainly distinguished on the basis of host specificity and pathogenicity. However, these varieties are also reported to be weak pathogens and secondary invaders on non-host tissue. In practice, it is difficult to

  13. Enhanced secretion of TIMP-1 by human hypertrophic scar keratinocytes could contribute to fibrosis.

    Science.gov (United States)

    Simon, Franck; Bergeron, Daniele; Larochelle, Sébastien; Lopez-Vallé, Carlos A; Genest, Hervé; Armour, Alexis; Moulin, Véronique J

    2012-05-01

    Hypertrophic scars are a pathological process characterized by an excessive deposition of extracellular matrix components. Using a tissue-engineered reconstructed human skin (RHS) method, we previously reported that pathological keratinocytes induce formation of a fibrotic dermal matrix. We further investigated keratinocyte action using conditioned media. Results showed that conditioned media induce a similar action on dermal thickness similar to when an epidermis is present. Using a two-dimensional electrophoresis technique, we then compared conditioned media from normal or hypertrophic scar keratinocytes and determined that TIMP-1 was increased in conditioned media from hypertrophic scar keratinocytes. This differential profile was confirmed using ELISA, assaying TIMP-1 presence on media from monolayer cultured keratinocytes and from RHS. The dermal matrix of these RHS was recreated using mesenchymal cells from three different origins (skin, wound and hypertrophic scar). The effect of increased TIMP-1 levels on dermal fibrosis was also validated independently from the mesenchymal cell origin. Immunodetection of TIMP-1 showed that this protein was increased in the epidermis of hypertrophic scar biopsies. The findings of this study represent an important advance in understanding the role of keratinocytes as a direct potent modulator for matrix degradation and scar tissue remodeling, possibly through inactivation of MMPs. Copyright © 2011 Elsevier Ltd and ISBI. All rights reserved.

  14. Enhanced in Vivo Delivery of 5-Fluorouracil by Ethosomal Gels in Rabbit Ear Hypertrophic Scar Model

    Directory of Open Access Journals (Sweden)

    Yan Wo

    2014-12-01

    Full Text Available Applying Ethosomal Gels (EGs in transdermal drug delivery systems has evoked considerable interest because of their good water-solubility and biocompatibility. However, there has not been an explicit description of applying EGs as a vehicle for hypertrophic scars treatment. Here, a novel transdermal EGs loaded with 5-fluorouracil (5-FU EGs was successfully prepared and characterized. The stability assay in vitro revealed that 5-FU EGs stored for a period of 30 days at 4 ± 1 °C had a better size stability than that at 25 ± 1 °C. Furthermore, using confocal laser scanning microscopy, EGs labeled with Rhodamine 6 G penetrated into the deep dermis of the hypertrophic scar within 24 h in the rabbit ear hypertrophic model suggested that the EGs were an optional delivery carrier through scar tissues. In addition, the value of the Scar Elevation Index (SEI of 5-FU EGs group in the rabbit ear scar model was lower than that of 5-FU Phosphate Buffered Saline gel and Control groups. To conclude, these results suggest that EGs delivery system loaded 5-fluorouracil is a perfect candidate drug for hypertrophic scars therapy in future.

  15. Multimodal imaging of vocal fold scarring in a rabbit model by multiphoton microscopy

    Science.gov (United States)

    Kazarine, Alexei; Bouhabel, Sarah; Douillette, Annie H.; Kost, Karen; Li-Jessen, Nicole Y. K.; Mongeau, Luc; Wiseman, Paul W.

    2017-02-01

    Vocal fold scarring as a result of injury or disease can lead to voice disorders which can significantly affect the quality of life. During the scarring process, the normally elastic tissue of the vocal fold lamina propria is replaced by a much stiffer collagen-based fibrotic tissue, which impacts the fold's ability to vibrate. Surgical removal of this tissue is often ineffective and can result in further scarring. Injectable biomaterials, a form of tissue engineering, have been proposed as a potential solution to reduce existing scars or prevent scarring altogether. In order to properly evaluate the effectiveness of these new materials, multiphoton microscopy emerges as an effective tool due to its intrinsic multiple label free contrast mechanisms that highlight extracellular matrix elements. In this study, we evaluate the spatial distribution of collagen and elastin fibers in a rabbit model using second harmonic generation (SHG), third harmonic generation (THG) and two photon autofluorescence (TPAF) applied to unlabeled tissue sections. In comparison to traditional methods that rely on histological staining or immunohistochemistry, SHG, THG and TPAF provide a more reliable detection of these native proteins. The evaluation of collagen levels allows us to follow the extent of scarring, while the presence of elastin fibers is thought to be indicative of the level of healing of the injured fold. Using these imaging modalities, we characterize the outcome of injectable biomaterial treatments in order to direct future treatments for tissue engineering.

  16. Collagen cross-linking by adipose-derived mesenchymal stromal cells and scar-derived mesenchymal cells: Are mesenchymal stromal cells involved in scar formation?

    NARCIS (Netherlands)

    Bogaerdt, van den A.J.; Veen, van der A.G.; Zuijlen, van P.P.; Reijnen, L.; Verkerk, M.; Bank, R.A.; Middelkoop, E.; Ulrich, M.

    2009-01-01

    In this work, different fibroblast-like (mesenchymal) cell populations that might be involved in wound healing were characterized and their involvement in scar formation was studied by determining collagen synthesis and processing. Depending on the physical and mechanical properties of the tissues,

  17. Collagen cross-linking by adipose-derived mesenchymal stromal cells and scar-derived mesenchymal cells : Are mesenchymal stromal cells involved in scar formation?

    NARCIS (Netherlands)

    van den Bogaerdt, Antoon J.; van der Veen, Vincent C.; van Zuijlen, Paul P. M.; Reijnen, Linda; Verkerk, Michelle; Bank, Ruud A.; Middelkoop, Esther; Ulrich, Magda M. W.

    2009-01-01

    In this work, different fibroblast-like (mesenchymal) cell populations that might be involved in wound healing were characterized and their involvement in scar formation was studied by determining collagen synthesis and processing. Depending on the physical and mechanical properties of the tissues,

  18. The role of massage in scar management: a literature review.

    Science.gov (United States)

    Shin, Thuzar M; Bordeaux, Jeremy S

    2012-03-01

    Many surgeons recommend postoperative scar massage to improve aesthetic outcome, although scar massage regimens vary greatly. To review the regimens and efficacy of scar massage. PubMed was searched using the following key words: "massage" in combination with "scar," or "linear," "hypertrophic," "keloid," "diasta*," "atrophic." Information on study type, scar type, number of patients, scar location, time to onset of massage therapy, treatment protocol, treatment duration, outcomes measured, and response to treatment was tabulated. Ten publications including 144 patients who received scar massage were examined in this review. Time to treatment onset ranged from after suture removal to longer than 2 years. Treatment protocols ranged from 10 minutes twice daily to 30 minutes twice weekly. Treatment duration varied from one treatment to 6 months. Overall, 65 patients (45.7%) experienced clinical improvement based on Patient Observer Scar Assessment Scale score, Vancouver Scar Scale score, range of motion, pruritus, pain, mood, depression, or anxiety. Of 30 surgical scars treated with massage, 27 (90%) had improved appearance or Patient Observer Scar Assessment Scale score. The evidence for the use of scar massage is weak, regimens used are varied, and outcomes measured are neither standardized nor reliably objective, although its efficacy appears to be greater in postsurgical scars than traumatic or postburn scars. Although scar massage is anecdotally effective, there is scarce scientific data in the literature to support it. © 2011 by the American Society for Dermatologic Surgery, Inc. Published by Wiley Periodicals, Inc.

  19. Effectiveness of Onion Extract Gel on Surgical Scars in Asians

    Directory of Open Access Journals (Sweden)

    Kumutnart Chanprapaph

    2012-01-01

    Full Text Available Background. Onion extracts have been shown in vitro to accelerate wound healing. Results from clinical studies on surgical scars in Caucasians were disappointing. The aim of this study is to evaluate the effectiveness of onion extract gel in improving the cosmetic and symptoms of surgical scars in Asians. Patients/Methods. Twenty Asians who had new Pfannenstiel’s cesarean section scars were recruited in this prospective double-blinded, split-scar study. Each side was randomly assigned treatment with onion extract gel or placebo at 7 days after surgery. The product was applied three times daily for 12 weeks. Subjects were evaluated at baseline and 4th and 12th weeks. Scar redness was assessed by calorimeter, scar height and pliability were assessed by blinded investigators, and scar symptoms and overall cosmetic improvement were assessed by subjects. Results. Sixteen subjects completed the study. A statistically significant difference between two sides of scar in terms of scar height and scar symptoms was found. There was no statistically significant difference in scar redness, scar pliability, and overall cosmetic appearance between two sides. Conclusions. The early use of topical 12% onion extract gel on Pfannenstiel’s cesarean section scar in Asians resulted in the improvement of scar height and scar symptoms.

  20. Characterization of Campylobacter jejuni applying flaA short variable region sequencing, multilocus sequencing and Fourier transform infrared spectroscopy

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Bonnichsen, Lise; Larsson, Jonas

    flaA short variable region sequencing and phenetic Fourier transform infrared (FTIR) spectroscopy was applied on a collection of 102 Campylobacter jejuni isolated from continuous sampling of organic, free range geese and chickens. FTIR has been shown to serve as a valuable tool in typing...

  1. Vertical scar versus the inverted-T scar reduction mammaplasty : A 10-year follow-up

    NARCIS (Netherlands)

    Bouwer, Lesley R.; van der Biezen, Jan Jaap; Spronk, Cees A.; van der Lei, Berend

    2012-01-01

    A retrospective study was undertaken to evaluate whether the initial outcome of two types of reduction mammaplasty techniques (vertical scar reduction mammaplasty vs. the inverted-T scar reduction mammaplasty) remains stable in the long term: Sixty-nine patients who had undergone breast reduction

  2. In silico characterization of boron transporter (BOR1 protein sequences in Poaceae species

    Directory of Open Access Journals (Sweden)

    Ertuğrul Filiz

    2013-01-01

    Full Text Available Boron (B is essential for the plant growth and development, and its primary function is connected with formation of the cell wall. Moreover, boron toxicity is a shared problem in semiarid and arid regions. In this study, boron transporter protein (BOR1 sequences from some Poaceae species (Hordeum vulgare subsp. vulgare, Zea mays, Brachypodium distachyon, Oryza sativa subsp. japonica, Oryza sativa subsp. indica, Sorghum bicolor, Triticum aestivum were evaluated by bioinformatics tools. Physicochemical analyses revealed that most of BOR1 proteins were basic character and had generally aliphatic amino acids. Analysis of the domains showed that transmembrane domains were identified constantly and three motifs were detected with 50 amino acids length. Also, the motif SPNPWEPGSYDHWTVAKDMFNVPPAYIFGAFIPATMVAGLYYFDHSVASQ was found most frequently with 25 repeats. The phylogenetic tree showed divergence into two main clusters. B. distachyon species were clustered separately. Finally, this study contributes to the new BOR1 protein characterization in grasses and create scientific base for in silico analysis in future.

  3. Classification and characterization of species within the genus lens using genotyping-by-sequencing (GBS.

    Directory of Open Access Journals (Sweden)

    Melissa M L Wong

    Full Text Available Lentil (Lens culinaris ssp. culinaris is a nutritious and affordable pulse with an ancient crop domestication history. The genus Lens consists of seven taxa, however, there are many discrepancies in the taxon and gene pool classification of lentil and its wild relatives. Due to the narrow genetic basis of cultivated lentil, there is a need towards better understanding of the relationships amongst wild germplasm to assist introgression of favourable genes into lentil breeding programs. Genotyping-by-sequencing (GBS is an easy and affordable method that allows multiplexing of up to 384 samples or more per library to generate genome-wide single nucleotide Polymorphism (SNP markers. In this study, we aimed to characterize our lentil germplasm collection using a two-enzyme GBS approach. We constructed two 96-plex GBS libraries with a total of 60 accessions where some accessions had several samples and each sample was sequenced in two technical replicates. We developed an automated GBS pipeline and detected a total of 266,356 genome-wide SNPs. After filtering low quality and redundant SNPs based on haplotype information, we constructed a maximum-likelihood tree using 5,389 SNPs. The phylogenetic tree grouped the germplasm collection into their respective taxa with strong support. Based on phylogenetic tree and STRUCTURE analysis, we identified four gene pools, namely L. culinaris/L. orientalis/L. tomentosus, L. lamottei/L. odemensis, L. ervoides and L. nigricans which form primary, secondary, tertiary and quaternary gene pools, respectively. We discovered sequencing bias problems likely due to DNA quality and observed severe run-to-run variation in the wild lentils. We examined the authenticity of the germplasm collection and identified 17% misclassified samples. Our study demonstrated that GBS is a promising and affordable tool for screening by plant breeders interested in crop wild relatives.

  4. Discovery and characterization of 3000+ main-sequence binaries from APOGEE spectra

    Science.gov (United States)

    El-Badry, Kareem; Ting, Yuan-Sen; Rix, Hans-Walter; Quataert, Eliot; Weisz, Daniel R.; Cargile, Phillip; Conroy, Charlie; Hogg, David W.; Bergemann, Maria; Liu, Chao

    2018-05-01

    We develop a data-driven spectral model for identifying and characterizing spatially unresolved multiple-star systems and apply it to APOGEE DR13 spectra of main-sequence stars. Binaries and triples are identified as targets whose spectra can be significantly better fit by a superposition of two or three model spectra, drawn from the same isochrone, than any single-star model. From an initial sample of ˜20 000 main-sequence targets, we identify ˜2500 binaries in which both the primary and secondary stars contribute detectably to the spectrum, simultaneously fitting for the velocities and stellar parameters of both components. We additionally identify and fit ˜200 triple systems, as well as ˜700 velocity-variable systems in which the secondary does not contribute detectably to the spectrum. Our model simplifies the process of simultaneously fitting single- or multi-epoch spectra with composite models and does not depend on a velocity offset between the two components of a binary, making it sensitive to traditionally undetectable systems with periods of hundreds or thousands of years. In agreement with conventional expectations, almost all the spectrally identified binaries with measured parallaxes fall above the main sequence in the colour-magnitude diagram. We find excellent agreement between spectrally and dynamically inferred mass ratios for the ˜600 binaries in which a dynamical mass ratio can be measured from multi-epoch radial velocities. We obtain full orbital solutions for 64 systems, including 14 close binaries within hierarchical triples. We make available catalogues of stellar parameters, abundances, mass ratios, and orbital parameters.

  5. CLONING, SEQUENCE ANALYSIS, AND CHARACTERIZATION OF PUTATIVE BETA-LACTAMASE OF STENOTROPHOMONAS MALTOPHILIA

    Directory of Open Access Journals (Sweden)

    Chong Seng Shueh

    2012-10-01

    Full Text Available The main objective of current study was to explore the function of chromosomal putative beta-lactamase gene (smlt 0115 in clinical Stenotrophomonas maltophilia. Antibiotic susceptibility test (AST screening for current antimicrobial drugs was done and Minimum Inhibitory Concentration (MIC level towards beta-lactams was determined by E-test. Putative beta-lactamase gene of S. maltophilia was amplified via PCR, with specific primers, then cloned into pET-15 expression plasmid and transformed into Escherichia coli BL21. The gene was sequenced and analyzed. The expressed protein was purified by affinity chromatography and the kinetic assay was performed. S. maltophilia ATCC 13637 was included in this experiment. Besides, a hospital strain which exhibited resistant to a series of beta-lactams including cefepime was identified via AST and MIC, hence it was named as S2 strain and was considered in this study. Sequencing result showed that putative beta-lactamase gene obtained from ATCC 13637 and S2 strains were predicted to have cephalosporinase activity by National Center for Biotechnology Information (NCBI blast program. Differences in the sequences of both ATCC 13637 and S2 strains were found via ClustalW alignment software. Kinetic assay proved a cephalosporinase characteristic produced by E. coli BL21 clone that overexpressed the putative beta-lactamase gene cloned under the control of an external promoter. Yet, expressed protein purified from S2 strain had high catalytic activity against beta-lactam antibiotics which was 14-fold higher than expressed protein purified from ATCC 13637 strain. This study represents the characterization analysis of putative beta-lactamase gene (smlt 0115 of S. maltophilia. The presence of the respective gene in the chromosome of S. maltophilia suggested that putative beta-lactamase gene (smlt 0115 of S. maltophilia plays a role in beta-lactamase resistance.

  6. Purification and sequence characterization of chondroitin sulfate and dermatan sulfate from fishes.

    Science.gov (United States)

    Lin, Na; Mo, Xiaoli; Yang, Yang; Zhang, Hong

    2017-04-01

    Chondroitin sulfate (CS) and dermatan sulfate (DS) were extracted and purified from skins or bones of salmon (Salmo salar), snakehead (Channa argus), monkfish (Lophius litulon) and skipjack tuna (Katsuwonus pelamis). Size, structural sequences and sulfate groups of oligosaccharides in the purified CS and DS could be characterized and identified using high performance liquid chromatography (HPLC) combined with Orbitrap mass spectrometry. CS and DS chain structure varies depending on origin, but motif structure appears consistent. Structures of CS and DS oligosaccharides with different size and sulfate groups were compared between fishes and other animals, and results showed that some minor differences of special structures could be identified by hydrophilic interaction chromatography-liquid chromatography-fourier transform-mass/mass spectrometry (HILIC-LC-FT-MS/MS). For example, data showed that salmon and skipjack CS had a higher percentage content of high-level sulfated oligosaccharides than that porcine CS. In addition, structural information of different origins of CS and DS was analyzed by principal component analysis (PCA) and results showed that CS and DS samples could be differentiated according to their molecular conformation and oligosaccharide fragments information. Understanding CS and DS structure derived from different origins may lead to the production of CS or DS with unique disaccharides or oligosaccharides sequence composition and biological functions.

  7. High- and ultrahigh-field magnetic resonance imaging of naïve, injured and scarred vocal fold mucosae in rats

    Science.gov (United States)

    Kishimoto, Ayami Ohno; Kishimoto, Yo; Young, David L.; Zhang, Jinjin

    2016-01-01

    ABSTRACT Subepithelial changes to the vocal fold mucosa, such as fibrosis, are difficult to identify using visual assessment of the tissue surface. Moreover, without suspicion of neoplasm, mucosal biopsy is not a viable clinical option, as it carries its own risk of iatrogenic injury and scar formation. Given these challenges, we assessed the ability of high- (4.7 T) and ultrahigh-field (9.4 T) magnetic resonance imaging to resolve key vocal fold subepithelial tissue structures in the rat, an important and widely used preclinical model in vocal fold biology. We conducted serial in vivo and ex vivo imaging, evaluated an array of acquisition sequences and contrast agents, and successfully resolved key anatomic features of naïve, acutely injured, and chronically scarred vocal fold mucosae on the ex vivo scans. Naïve lamina propria was hyperintense on T1-weighted imaging with gadobenate dimeglumine contrast enhancement, whereas chronic scar was characterized by reduced lamina propria T1 signal intensity and mucosal volume. Acutely injured mucosa was hypointense on T2-weighted imaging; lesion volume steadily increased, peaked at 5 days post-injury, and then decreased – consistent with the physiology of acute, followed by subacute, hemorrhage and associated changes in the magnetic state of hemoglobin and its degradation products. Intravenous administration of superparamagnetic iron oxide conferred no T2 contrast enhancement during the acute injury period. These findings confirm that magnetic resonance imaging can resolve anatomic substructures within naïve vocal fold mucosa, qualitative and quantitative features of acute injury, and the presence of chronic scar. PMID:27638667

  8. High- and ultrahigh-field magnetic resonance imaging of naïve, injured and scarred vocal fold mucosae in rats.

    Science.gov (United States)

    Kishimoto, Ayami Ohno; Kishimoto, Yo; Young, David L; Zhang, Jinjin; Rowland, Ian J; Welham, Nathan V

    2016-11-01

    Subepithelial changes to the vocal fold mucosa, such as fibrosis, are difficult to identify using visual assessment of the tissue surface. Moreover, without suspicion of neoplasm, mucosal biopsy is not a viable clinical option, as it carries its own risk of iatrogenic injury and scar formation. Given these challenges, we assessed the ability of high- (4.7 T) and ultrahigh-field (9.4 T) magnetic resonance imaging to resolve key vocal fold subepithelial tissue structures in the rat, an important and widely used preclinical model in vocal fold biology. We conducted serial in vivo and ex vivo imaging, evaluated an array of acquisition sequences and contrast agents, and successfully resolved key anatomic features of naïve, acutely injured, and chronically scarred vocal fold mucosae on the ex vivo scans. Naïve lamina propria was hyperintense on T1-weighted imaging with gadobenate dimeglumine contrast enhancement, whereas chronic scar was characterized by reduced lamina propria T1 signal intensity and mucosal volume. Acutely injured mucosa was hypointense on T2-weighted imaging; lesion volume steadily increased, peaked at 5 days post-injury, and then decreased - consistent with the physiology of acute, followed by subacute, hemorrhage and associated changes in the magnetic state of hemoglobin and its degradation products. Intravenous administration of superparamagnetic iron oxide conferred no T2 contrast enhancement during the acute injury period. These findings confirm that magnetic resonance imaging can resolve anatomic substructures within naïve vocal fold mucosa, qualitative and quantitative features of acute injury, and the presence of chronic scar. © 2016. Published by The Company of Biologists Ltd.

  9. High- and ultrahigh-field magnetic resonance imaging of naïve, injured and scarred vocal fold mucosae in rats

    Directory of Open Access Journals (Sweden)

    Ayami Ohno Kishimoto

    2016-11-01

    Full Text Available Subepithelial changes to the vocal fold mucosa, such as fibrosis, are difficult to identify using visual assessment of the tissue surface. Moreover, without suspicion of neoplasm, mucosal biopsy is not a viable clinical option, as it carries its own risk of iatrogenic injury and scar formation. Given these challenges, we assessed the ability of high- (4.7 T and ultrahigh-field (9.4 T magnetic resonance imaging to resolve key vocal fold subepithelial tissue structures in the rat, an important and widely used preclinical model in vocal fold biology. We conducted serial in vivo and ex vivo imaging, evaluated an array of acquisition sequences and contrast agents, and successfully resolved key anatomic features of naïve, acutely injured, and chronically scarred vocal fold mucosae on the ex vivo scans. Naïve lamina propria was hyperintense on T1-weighted imaging with gadobenate dimeglumine contrast enhancement, whereas chronic scar was characterized by reduced lamina propria T1 signal intensity and mucosal volume. Acutely injured mucosa was hypointense on T2-weighted imaging; lesion volume steadily increased, peaked at 5 days post-injury, and then decreased – consistent with the physiology of acute, followed by subacute, hemorrhage and associated changes in the magnetic state of hemoglobin and its degradation products. Intravenous administration of superparamagnetic iron oxide conferred no T2 contrast enhancement during the acute injury period. These findings confirm that magnetic resonance imaging can resolve anatomic substructures within naïve vocal fold mucosa, qualitative and quantitative features of acute injury, and the presence of chronic scar.

  10. The Subunit Principle in Scar Face Revision.

    Science.gov (United States)

    Elshahat, Ahmed; Lashin, Riham

    2017-06-01

    Facial scaring is considered one of the most difficult cosmetic problems for any plastic surgeon to solve. The condition is more difficult if the direction of the scar is not parallel to relaxed skin tension lines. Attempts to manage this difficult situation included revisions using geometric designs, Z plasties or W plasties to camouflage the straight line visible scaring. The use of long-lasting resorbable sutures was tried too. Recently, the use of botulinum toxin during revision improved the results. Fractional CO2 lasers, microfat grafts, and platelet-rich plasma were added to the armamentarium. The scar is least visible if placed in the junction between the facial subunits. The aim of this study is to investigate the use of the subunit principle to improve the results of scar revision. Four patients were included in this study. Tissue expansion of the intact part of the subunit allowed shifting the scar to the junction between the affected subunit and the adjacent one. Tissue expansion, delivery of the expanders, and advancement of the flaps were successful in all patients. The fact that this is a 2-stage procedure and sacrifices some of the intact skin from the affected facial subunit, makes this technique reserved to patients with ugly facial scars who are ambitious to improve their appearance.

  11. In search of scar seeking radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Salehi, N.; Lawlor, J.M.; Lichtenstein, M.; Allaway, M.; Barencevic, A. [Royal Melbourne Hospital, Melbourne, VIC (Australia). Department of Nuclear Medicine]|[University of Melbourne, VIC (Australia)

    1998-03-01

    Full text: Sensitive detection of acute peri-osseous scar tissue should be valuable for detection of partial ligamentous, tears and other common rheumatological conditions including back pain and ligamentous scars. Our aim was to investigate acute scar uptake of {sup 99m}Tc(V)-DMSA (dimercapto-succinic-acid), {sup 99m}Tc-DMAD (di- methyl-aminodiphosphonate) compared to {sup 99m}Tc-MDP (methylen-diphosphonate), the standard bone-scanning radiopharmaceutical. New Zealand white rabbits were anaesthetised and had 5-7cm of their mid-line abdominal wall surgically incised. At 24, 48, 72, 96 and 240 hours post surgery, 74 MBq (2 mCi) of the above radiopharmaceuticals were injected intravenously and scintigraphy performed 2.5 hours later. Relative count rate in scar is tabulated. In conclusion, the increased activity in the acute surgical site and lesser bone uptake confirmed that Tc (V)-DMSA and Tc-DMAD are superior to Tc- MDP for detection of new scar tissue in the region of bone. 1 tab.

  12. Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR Markers

    Directory of Open Access Journals (Sweden)

    Yongming Yu

    2012-05-01

    Full Text Available Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84% were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard’s similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA-based clustering and the principal coordinate analysis (PCoA, distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well.

  13. Characterization of CG6178 gene product with high sequence similarity to firefly luciferase in Drosophila melanogaster.

    Science.gov (United States)

    Oba, Yuichi; Ojika, Makoto; Inouye, Satoshi

    2004-03-31

    This is the first identification of a long-chain fatty acyl-CoA synthetase in Drosophila by enzymatic characterization. The gene product of CG6178 (CG6178) in Drosophila melanogaster genome, which has a high sequence similarity to firefly luciferase, has been expressed and characterized. CG6178 showed long-chain fatty acyl-CoA synthetic activity in the presence of ATP, CoA and Mg(2+), suggesting a fatty acyl adenylate is an intermediate. Recently, it was revealed that firefly luciferase has two catalytic functions, monooxygenase (luciferase) and AMP-mediated CoA ligase (fatty acyl-CoA synthetase). However, unlike firefly luciferase, CG6178 did not show luminescence activity in the presence of firefly luciferin, ATP, CoA and Mg(2+). The enzymatic properties of CG6178 including substrate specificity, pH dependency and optimal temperature were close to those of firefly luciferase and rat fatty acyl-CoA synthetase. Further, phylogenic analyses strongly suggest that the firefly luciferase gene may have evolved from a fatty acyl-CoA synthetase gene as a common ancestral gene.

  14. Fraxelated radiofrequency device for acne scars

    Science.gov (United States)

    Rao, Babar K.; Khokher, Sairah

    2012-09-01

    Acne scars can be improved with various treatments such as topical creams, chemical peels, dermal fillers, microdermabrasion, laser, and radiofrequency devices. Some of these treatments especially lasers and deep chemical peels can have significant side effects such as post inflammatory hyperpigmentation in darker skin types. Fraxelated RF Laser devices have been reported to have lower incidence of side effects in all skin phototypes. Nine patients between ages 18 and 35 of various skin phototypes were selected from a private practice and treated with a RF fraxelated device (E-matrix) for acne scars. Outcomes were measured by physician observation, subjective feedback received by patients, and comparison of before and after photographs. In this small group of patients with various skin phototypes, fraxelated radiofrequency device improved acne scars with minimal side effects and downtime.

  15. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

    Science.gov (United States)

    Konkel, Miriam K; Walker, Jerilyn A; Hotard, Ashley B; Ranck, Megan C; Fontenot, Catherine C; Storer, Jessica; Stewart, Chip; Marth, Gabor T; Batzer, Mark A

    2015-08-29

    The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization

    Directory of Open Access Journals (Sweden)

    Ranjan Akash

    2007-08-01

    Full Text Available Abstract Background Mycobacterium smegmatis is fast growing non-pathogenic mycobacteria. This organism has been widely used as a model organism to study the biology of other virulent and extremely slow growing species like Mycobacterium tuberculosis. Based on the homology of the N-terminal DNA binding domain, the recently sequenced genome of M. smegmatis has been shown to possess several putative GntR regulators. A striking characteristic feature of this family of regulators is that they possess a conserved N-terminal DNA binding domain and a diverse C-terminal domain involved in the effector binding and/or oligomerization. Since the physiological role of these regulators is critically dependent upon effector binding and operator sites, we have analysed and classified these regulators into their specific subfamilies and identified their potential binding sites. Results The sequence analysis of M. smegmatis putative GntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators are encoded by 45, 8, 8 and 1 genes respectively. Further out of 45 FadR-like regulators, 19 were classified into the FadR group and 26 into the VanR group. All these proteins showed similar secondary structural elements specific to their respective subfamilies except MSMEG_3959, which showed additional secondary structural elements. Using the reciprocal BLAST searches, we further identified the orthologs of these regulators in Bacillus subtilis and other mycobacteria. Since the expression of many regulators is auto-regulatory, we have identified potential operator sites for a number of these GntR regulators by analyzing the upstream sequences. Conclusion This study helps in extending the annotation of M. smegmatis GntR proteins. It identifies the GntR regulators of M. smegmatis that could serve as a model for studying orthologous regulators from virulent as well as other saprophytic mycobacteria. This study also sheds some light on the nucleotide preferences in the

  17. Identification and characterization of plastid-type proteins from sequence-attributed features using machine learning

    Science.gov (United States)

    2013-01-01

    Background Plastids are an important component of plant cells, being the site of manufacture and storage of chemical compounds used by the cell, and contain pigments such as those used in photosynthesis, starch synthesis/storage, cell color etc. They are essential organelles of the plant cell, also present in algae. Recent advances in genomic technology and sequencing efforts is generating a huge amount of DNA sequence data every day. The predicted proteome of these genomes needs annotation at a faster pace. In view of this, one such annotation need is to develop an automated system that can distinguish between plastid and non-plastid proteins accurately, and further classify plastid-types based on their functionality. We compared the amino acid compositions of plastid proteins with those of non-plastid ones and found significant differences, which were used as a basis to develop various feature-based prediction models using similarity-search and machine learning. Results In this study, we developed separate Support Vector Machine (SVM) trained classifiers for characterizing the plastids in two steps: first distinguishing the plastid vs. non-plastid proteins, and then classifying the identified plastids into their various types based on their function (chloroplast, chromoplast, etioplast, and amyloplast). Five diverse protein features: amino acid composition, dipeptide composition, the pseudo amino acid composition, Nterminal-Center-Cterminal composition and the protein physicochemical properties are used to develop SVM models. Overall, the dipeptide composition-based module shows the best performance with an accuracy of 86.80% and Matthews Correlation Coefficient (MCC) of 0.74 in phase-I and 78.60% with a MCC of 0.44 in phase-II. On independent test data, this model also performs better with an overall accuracy of 76.58% and 74.97% in phase-I and phase-II, respectively. The similarity-based PSI-BLAST module shows very low performance with about 50% prediction

  18. The clinical outcome of cesarean scar pregnancies implanted "on the scar" versus "in the niche".

    Science.gov (United States)

    Kaelin Agten, Andrea; Cali, Giuseppe; Monteagudo, Ana; Oviedo, Johana; Ramos, Joanne; Timor-Tritsch, Ilan

    2017-05-01

    The term cesarean scar pregnancy refers to placental implantation within the scar of a previous cesarean delivery. The rising numbers of cesarean deliveries in the last decades have led to an increased incidence of cesarean scar pregnancy. Complications of cesarean scar pregnancy include morbidly adherent placenta, uterine rupture, severe hemorrhage, and preterm labor. It is suspected that cesarean scar pregnancies that are implanted within a dehiscent scar ("niche") behave differently compared with those implanted on top of a well-healed scar. To date there are no studies that have compared pregnancy outcomes between cesarean scar pregnancies implanted either "on the scar" or "in the niche." The purpose of this study was to determine the pregnancy outcome of cesarean scar pregnancy implanted either "on the scar" or "in the niche." This was a retrospective 2-center study of 17 patients with cesarean scar pregnancy that was diagnosed from 5-9 weeks gestation (median, 8 weeks). All cesarean scar pregnancies were categorized as either implanted or "on the scar" (group A) or "in the niche" (group B), based on their first-trimester transvaginal ultrasound examination. Clinical outcomes based on gestational age at delivery, mode of delivery, blood loss at delivery, neonate weight and placental histopathologic condition were compared between the groups with the use of the Mann-Whitney U test. Myometrial thickness overlying the placenta was compared among all the patients who required hysterectomy and those who did not with the use of the Mann-Whitney U test. Myometrial thickness was also correlated with gestational age at delivery with the use of Spearman's correlation. Group A consisted of 6 patients; group B consisted of 11 patients. Gestational age at delivery was lower in group B (median, 34 weeks; range, 20-36 weeks) than in group A (median, 38 weeks; range, 37-39 weeks; P=.001). In group A, 5 patients were delivered via cesarean delivery (with normal placenta), and

  19. Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L. Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic–Physical Map Integration

    Directory of Open Access Journals (Sweden)

    Juana M. Córdoba

    2010-11-01

    Full Text Available Microsatellite markers or simple sequence repeat (SSR loci are useful for diversity characterization and genetic–physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs from the G19833 common bean ( L. library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]. Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-, and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.

  20. "Scars" connect classical and quantum theory

    CERN Multimedia

    Monteiro, T

    1990-01-01

    Chaotic systems are unstable and extremely sensitive to initial condititions. So far, scientists have been unable to demonstrate that the same kind of behaviour exists in quantum or microscopic systems. New connections have been discovered though between classical and quantum theory. One is the phenomena of 'scars' which cut through the wave function of a particle (1 page).

  1. Recombinant human endostatin reduces hypertrophic scar ...

    African Journals Online (AJOL)

    Methods: Sixteen New Zealand white rabbits were used to establish HS models. Then, rabbit ears containing HS were randomly assigned to either the Endostar group or the control group. The changes of appearance and histology were evaluated using the naked eye, hematoxylin eosin staining, and a scar elevation index.

  2. 9 CFR 11.3 - Scar rule.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Scar rule. 11.3 Section 11.3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE ANIMAL... inflammation, and, other bilateral evidence of abuse indicative of soring including, but not limited to...

  3. Sequence analysis and molecular characterization of Wnt4 gene in metacestodes of Taenia solium.

    Science.gov (United States)

    Hou, Junling; Luo, Xuenong; Wang, Shuai; Yin, Cai; Zhang, Shaohua; Zhu, Xueliang; Dou, Yongxi; Cai, Xuepeng

    2014-04-01

    Wnt proteins are a family of secreted glycoproteins that are evolutionarily conserved and considered to be involved in extensive developmental processes in metazoan organisms. The characterization of wnt genes may improve understanding the parasite's development. In the present study, a wnt4 gene encoding 491amino acids was amplified from cDNA of metacestodes of Taenia solium using reverse transcription PCR (RT-PCR). Bioinformatics tools were used for sequence analysis. The conserved domain of the wnt gene family was predicted. The expression profile of Wnt4 was investigated using real-time PCR. Wnt4 expression was found to be dramatically increased in scolex evaginated cysticerci when compared to invaginated cysticerci. In situ hybridization showed that wnt4 gene was distributed in the posterior end of the worm along the primary body axis in evaginated cysticerci. These findings indicated that wnt4 may take part in the process of cysticerci evagination and play a role in scolex/bladder development of cysticerci of T. solium.

  4. Deep sequencing and ecological characterization of gut microbial communities of diverse bumble bee species.

    Directory of Open Access Journals (Sweden)

    Haw Chuan Lim

    Full Text Available Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5% bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera.

  5. Genetic characterization of autochthonous grapevine cultivars from Eastern Turkey by simple sequence repeats (SSRs

    Directory of Open Access Journals (Sweden)

    Sadiye Peral Eyduran

    2016-01-01

    Full Text Available In this research, two well-recognized standard grape cultivars, Cabernet Sauvignon and Merlot, together with eight historical autochthonous grapevine cultivars from Eastern Anatolia in Turkey, were genetically characterized by using 12 pairs of simple sequence repeat (SSR primers in order to evaluate their genetic diversity and relatedness. All of the used SSR primers produced successful amplifications and revealed DNA polymorphisms, which were subsequently utilized to evaluate the genetic relatedness of the grapevine cultivars. Allele richness was implied by the identification of 69 alleles in 8 autochthonous cultivars with a mean value of 5.75 alleles per locus. The average expected heterozygosity and observed heterozygosity were found to be 0.749 and 0.739, respectively. Taking into account the generated alleles, the highest number was recorded in VVC2C3 and VVS2 loci (nine and eight alleles per locus, respectively, whereas the lowest number was recorded in VrZAG83 (three alleles per locus. Two main clusters were produced by using the unweighted pair-group method with arithmetic mean dendrogram constructed on the basis of the SSR data. Only Cabernet Sauvignon and Merlot cultivars were included in the first cluster. The second cluster involved the rest of the autochthonous cultivars. The results obtained during the study illustrated clearly that SSR markers have verified to be an effective tool for fingerprinting grapevine cultivars and carrying out grapevine biodiversity studies. The obtained data are also meaningful references for grapevine domestication.

  6. Characterization of promoter sequence of toll-like receptor genes in Vechur cattle

    Directory of Open Access Journals (Sweden)

    R. Lakshmi

    2016-06-01

    Full Text Available Aim: To analyze the promoter sequence of toll-like receptor (TLR genes in Vechur cattle, an indigenous breed of Kerala with the sequence of Bos taurus and access the differences that could be attributed to innate immune responses against bovine mastitis. Materials and Methods: Blood samples were collected from Jugular vein of Vechur cattle, maintained at Vechur cattle conservation center of Kerala Veterinary and Animal Sciences University, using an acid-citrate-dextrose anticoagulant. The genomic DNA was extracted, and polymerase chain reaction was carried out to amplify the promoter region of TLRs. The amplified product of TLR2, 4, and 9 promoter regions was sequenced by Sanger enzymatic DNA sequencing technique. Results: The sequence of promoter region of TLR2 of Vechur cattle with the B. taurus sequence present in GenBank showed 98% similarity and revealed variants for four sequence motifs. The sequence of the promoter region of TLR4 of Vechur cattle revealed 99% similarity with that of B. taurus sequence but not reveals significant variant in motifregions. However, two heterozygous loci were observed from the chromatogram. Promoter sequence of TLR9 gene also showed 99% similarity to B. taurus sequence and revealed variants for four sequence motifs. Conclusion: The results of this study indicate that significant variation in the promoter of TLR2 and 9 genes in Vechur cattle breed and may potentially link the influence the innate immunity response against mastitis diseases.

  7. Generation and Characterization of HIV-1 Transmitted and Founder Virus Consensus Sequence from Intravenous Drug Users in Xinjiang, China.

    Science.gov (United States)

    Li, Fan; Ma, Liying; Feng, Yi; Hu, Jing; Ni, Na; Ruan, Yuhua; Shao, Yiming

    2017-06-01

    HIV-1 transmission in intravenous drug users (IDUs) has been characterized by high genetic multiplicity and suggests a greater challenge for HIV-1 infection blocking. We investigated a total of 749 sequences of full-length gp160 gene obtained by single genome sequencing (SGS) from 22 HIV-1 early infected IDUs in Xinjiang province, northwest China, and generated a transmitted and founder virus (T/F virus) consensus sequence (IDU.CON). The T/F virus was classified as subtype CRF07_BC and predicted to be CCR5-tropic virus. The variable region (V1, V2, and V4 loop) of IDU.CON showed length variation compared with the heterosexual T/F virus consensus sequence (HSX.CON) and homosexual T/F virus consensus sequence (MSM.CON). A total of 26 N-linked glycosylation sites were discovered in the IDU.CON sequence, which is less than that of MSM.CON and HSX.CON. Characterization of T/F virus from IDUs highlights the genetic make-up and complexity of virus near the moment of transmission or in early infection preceding systemic dissemination and is important toward the development of an effective HIV-1 preventive methods, including vaccines.

  8. Characterization and Sequencing of a Genotype XII Newcastle Disease Virus Isolated from a Peacock (Pavo cristatus) in Peru.

    Science.gov (United States)

    Chumbe, Ana; Izquierdo-Lara, Ray; Tataje-Lavanda, Luis; Figueroa, Aling; Segovia, Karen; Gonzalez, Rosa; Cribillero, Giovana; Montalvan, Angela; Fernández-Díaz, Manolo; Icochea, Eliana

    2015-07-30

    Here, we report the first complete sequence and biological characterization of a Newcastle disease virus (NDV) isolated from a peacock in South America (NDV/peacock/Peru/2011). This isolate, classified as genotype XII in class II, highlights the need for increased surveillance of noncommercial avian species. Copyright © 2015 Chumbe et al.

  9. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization

    CSIR Research Space (South Africa)

    Gcebe, N

    2017-04-01

    Full Text Available Journal of Systematic and Evolutionary Microbiology: DOI 10.1099/ijsem.0.001678 Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization Gcebe N Rutten V Gey...

  10. Perioperative interstitial brachytherapy for recurrent keloid scars

    International Nuclear Information System (INIS)

    Rio, E.; Bardet, E.; Peuvrel, P.; Martinet, L.; Perrot, P.; Baraer, F.; Loirat, Y.; Sartre, J.Y.; Malard, O.; Ferron, C.; Dreno, B.

    2010-01-01

    Purpose: Evaluation of the results of perioperative interstitial brachytherapy with low dose-rate (L.D.R.) Ir-192 in the treatment of keloid scars. Patients and methods: We performed a retrospective analysis of 73 histologically confirmed keloids (from 58 patients) resistant to medico surgical treated by surgical excision plus early perioperative brachytherapy. All lesions were initially symptomatic. Local control was evaluated by clinical evaluation. Functional and cosmetic results were assessed in terms of patient responses to a self-administered questionnaire. Results: Median age was 28 years (range 13-71 years). Scars were located as follows: 37% on the face, 32% on the trunk or abdomen, 16% on the neck, and 15% on the arms or legs. The mean delay before loading was four hours (range, 1-6 h). The median dose was 20 Gy (range, 15-40 Gy). Sixty-four scars (from 53 patients) were evaluated. Local control was 86% (follow-up, 44.5 months; range, 14-150 months). All relapses occurred early within 2 years posttreatment. At 20 months, survival without recurrence was significantly lower when treated lengths were more than 6 cm long. The rate was 100% for treated scars below 4.5 cm in length, 95% (95% CI: 55-96) for those 4.5-6 cm long, and 75% (95% CI: 56-88) beyond 6 cm (p = 0.038). Of the 35 scars (28 patients) whose results were reassessed, six remained symptomatic and the esthetic results were considered to be good in 51% (18/35) and average in 37% (13/35) (median follow-up, 70 months; range, 16-181 months). Conclusion: Early perioperative L.D.R. brachytherapy delivering 20 Gy at 5 mm reduced the rate of recurrent keloids resistant to other treatments and gave good functional results. (authors)

  11. MR imaging findings in cesarean scar pregnancy

    International Nuclear Information System (INIS)

    Zhang Xiangqun; Xu Yikai; Luo Xiaoqin

    2012-01-01

    Objective: To analyze MRI findings of cesarean scar pregnancy (CSP). Methods: The MR findings in 18 patients who were diagnosed as CSP by surgery from March 2010 to November 2011 were retrospectively analyzed, and comparison was made between the MRI findings and surgical results. Results: All Gestational sacs (18) were clearly detected by MRI. Among the 18 cases,gestational sac presented as cystic mass with smooth margin located within the scar of uterine wall at the lower anterior uterus in 16 cases. In 2 of the 16 cases, gestational sac was found within the myometrium, whereas in the remaining 14 cases, gestational sac was found partially within the myometrium with extension into the uterine cavity. The anterior wall of isthmus uteri became thinner. In the remaining 2 of the 18 cases, gestational sac presented as irregular, multilobolated mass, growing deep into the myometrium as well as into the uterine cavity. On T 2 WI, the mass showed heterogeneous signal intensity. A small amount of hemorrhage within the mass and uterine cavity could be seen on T 1 WI. An enhancing solid component with a heterogeneous mass could be seen. All gestational sacs in 18 cases were located at or adjacent to the previous cesarean scar. In the area of cesarean scar,the signal of the uterine wall was disconnected, with focal indentation or thinning and the previous cesarean scar exhibited hypointensity on both T 1 WI and T 2 WI. Conclusion: CSP has its unique findings on MRI, these specific features can provide useful information in the management of CSP. (authors)

  12. Combination therapy in the management of atrophic acne scars

    Directory of Open Access Journals (Sweden)

    Shilpa Garg

    2014-01-01

    Full Text Available Background: Atrophic acne scars are difficult to treat. The demand for less invasive but highly effective treatment for scars is growing. Objective: To assess the efficacy of combination therapy using subcision, microneedling and 15% trichloroacetic acid (TCA peel in the management of atrophic scars. Materials and Methods: Fifty patients with atrophic acne scars were graded using Goodman and Baron Qualitative grading. After subcision, dermaroller and 15% TCA peel were performed alternatively at 2-weeks interval for a total of 6 sessions of each. Grading of acne scar photographs was done pretreatment and 1 month after last procedure. Patients own evaluation of improvement was assessed. Results: Out of 16 patients with Grade 4 scars, 10 (62.5% patients improved to Grade 2 and 6 (37.5% patients improved to Grade 3 scars. Out of 22 patients with Grade 3 scars, 5 (22.7% patients were left with no scars, 2 (9.1% patients improved to Grade 1and 15 (68.2% patients improved to Grade 2. All 11 (100% patients with Grade 2 scars were left with no scars. There was high level of patient satisfaction. Conclusion: This combination has shown good results in treating not only Grade 2 but also severe Grade 4 and 3 scars.

  13. A Rat Excised Larynx Model of Vocal Fold Scar

    Science.gov (United States)

    Welham, Nathan V.; Montequin, Douglas W.; Tateya, Ichiro; Tateya, Tomoko; Choi, Seong Hee; Bless, Diane M.

    2009-01-01

    Purpose: To develop and evaluate a rat excised larynx model for the measurement of acoustic, aerodynamic, and vocal fold vibratory changes resulting from vocal fold scar. Method: Twenty-four 4-month-old male Sprague-Dawley rats were assigned to 1 of 4 experimental groups: chronic vocal fold scar, chronic vocal fold scar treated with 100-ng basic…

  14. Prevalence of scar contractures after burn : A systematic review

    NARCIS (Netherlands)

    Oosterwijk, Anouk M; Mouton, Leonora J; Schouten, Hennie; Disseldorp, Laurien M; van der Schans, Cees P.; Nieuwenhuis, Marianne K

    OBJECTIVE: Burn scar contractures are the pathological outcome of excessive scarring and ongoing scar contraction. Impairment of joint range of motion is a threat to performing activities in daily living. To direct treatment strategies to prevent and/or correct such contractures, insight into the

  15. Pulmonary scar carcinoma in South Africa | Jenkins | South African ...

    African Journals Online (AJOL)

    Post-obstructive bronchiectasis and other changes secondary to cancer were considered not to represent scarring. Results. We identified 435 cases of primary lung cancer. In total, 95 patients (21.8%) had CT evidence of pulmonary scarring. Eighty-three of 85 patients (97.6%) had focal scarring in the same lobe as the ...

  16. Analysis of genetic diversity of Brassica rapa var. chinensis using ISSR markers and development of SCAR marker specific for Fragrant Bok Choy, a product of geographic indication.

    Science.gov (United States)

    Shen, X L; Zhang, Y M; Xue, J Y; Li, M M; Lin, Y B; Sun, X Q; Hang, Y Y

    2016-04-25

    Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource.

  17. Sequence characterization of cotton leaf curl virus from Rajasthan: phylogenetic relationship with other members of geminiviruses and detection of recombination.

    Science.gov (United States)

    Kumar, A; Kumar, J; Khan, J A

    2010-04-01

    Diseased cotton plants showing typical leaf curl symptoms were collected from experimental plot of Agriculture Research Station-Sriganganagar, Rajasthan. Complete DNA-A component from samples taken from two areas were amplified through rolling circle amplification (RCA) using templiphi kit (GE Healthcare) and characterized. DNA-A of one isolate consists of 2751 nucleotides and second isolate of 2759 nucleotide. Both sequences comprised six ORF's. Genome organization of DNA-A of one isolate shows high sequence similarity with other characterized local begomovirus isolates of Rajasthan, while other isolate shows high sequence similarity with CLCuV reported from Pakistan. The maximum similarity of first isolate, CLCuV-SG01, shows highest sequence identity with Cotton leaf curl Abohar (Rajasthan) virus, and second isolate, CLCuV-SG02, shows highest sequence identity with cotton leaf curl virus from Pakistan. Both isolates showed 85% similarities with each other. The sequence data revealed probable infiltration of some strains of Cotton leaf curl virus from Pakistan to India, or co-existence of different isolates under similar geographical conditions. While CLCuV-SG01 shows highest nt sequence similarity with CLCuV Rajasthan (Abohar), nt identity of V1 ORF (encoding coat protein) of SG01 shows the highest nt identity (100%) with CLCuV Multan (Bhatinda) and Abohar virus while AC1 region also showed difference. Complete nucleotide sequence of SG01 shows only 86% similarity with CLCuV Multan virus. Similarity search revealed significant difference in AV1 and AC1 regions with respect to DNA-A suggesting an evolutionary history of recombination. Computer based analysis, recombination detection Program (RDP) supports the recombination hypothesis, indicated that recombination with other begomoviruses had taken place within V1 ORF and AC1 ORF of CLCuV-SG01 and AC1 ORF of CLCuV-SG02 and also in noncoding intergenic region (IR).

  18. Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

    KAUST Repository

    Ali, Asho; Hasan, Zahra; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant A.; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G.; Hasan, Rumina

    2015-01-01

    Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91-94 codons in 81% of strains; four strains had only gyr B mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded

  19. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    International Nuclear Information System (INIS)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank

    2013-01-01

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  20. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank, E-mail: fkempken@bot.uni-kiel.de

    2013-08-30

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  1. Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

    KAUST Repository

    Ali, Asho

    2015-02-26

    Improved molecular diagnostic methods for detection drug resistance in Mycobacterium tuberculosis (MTB) strains are required. Resistance to first- and second- line anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, these SNPs can vary between MTB lineages therefore local data is required to describe different strain populations. We used whole genome sequencing (WGS) to characterize 37 extensively drug-resistant (XDR) MTB isolates from Pakistan and investigated 40 genes associated with drug resistance. Rifampicin resistance was attributable to SNPs in the rpoB hot-spot region. Isoniazid resistance was most commonly associated with the katG codon 315 (92%) mutation followed by inhA S94A (8%) however, one strain did not have SNPs in katG, inhA or oxyR-ahpC. All strains were pyrazimamide resistant but only 43% had pncA SNPs. Ethambutol resistant strains predominantly had embB codon 306 (62%) mutations, but additional SNPs at embB codons 406, 378 and 328 were also present. Fluoroquinolone resistance was associated with gyrA 91-94 codons in 81% of strains; four strains had only gyr B mutations, while others did not have SNPs in either gyrA or gyrB. Streptomycin resistant strains had mutations in ribosomal RNA genes; rpsL codon 43 (42%); rrs 500 region (16%), and gidB (34%) while six strains did not have mutations in any of these genes. Amikacin/kanamycin/capreomycin resistance was associated with SNPs in rrs at nt1401 (78%) and nt1484 (3%), except in seven (19%) strains. We estimate that if only the common hot-spot region targets of current commercial assays were used, the concordance between phenotypic and genotypic testing for these XDR strains would vary between rifampicin (100%), isoniazid (92%), flouroquinolones (81%), aminoglycoside (78%) and ethambutol (62%); while pncA sequencing would provide genotypic resistance in less than half the isolates. This work highlights the importance of expanded

  2. Comparative effect and safety of verapamil in keloid and hypertrophic scar treatment: a meta-analysis.

    Science.gov (United States)

    Li, Zhouna; Jin, Zhehu

    2016-01-01

    Keloids and hypertrophic scars are the most common types of pathological scarring. Traditionally, keloids have been considered as a result of aberrant wound healing, involving excessive fibroblast participation that is characterized by hyalinized collagen bundles. However, the usefulness of this characterization has been questioned. In recent years, studies have reported the appropriate use of verapamil for keloids and hypertrophic scars. Searches were conducted on the databases Medline, Embase, Cochrane, PubMed, and China National Knowledge Infrastructure from 2006 to July 2016. State12.0 was used for literature review, data extraction, and meta-analysis. Treatment groups were divided into verapamil and nonverapamil group. Nonverapamil group includes steroids and intense pulsed light (IPL) therapy. Total effective rates include cure rate and effective rate. Cure: skin lesions were completely flattened, became soft and symptoms disappeared. Efficacy: skin lesions subsided, patient significantly reduced symptoms. Inefficient definition of skin was progression free or became worse. Random-effects model was used for the meta-analysis. Six studies that included 331 patients with keloids and hypertrophic scars were analyzed. Analysis of the total effective rate of skin healing was performed. The total effective rates in the two groups were 54.07% (verapamil) and 53.18% (nonverapamil), respectively. The meta-analysis showed that there was no difference between the two groups. We also compared the adverse reactions between the verapamil treatment group and the steroids treatment group in two studies, and the result indicated that the verapamil group showed less adverse reactions. There were no differences between the application of verapamil and nonverapamil group in keloids and hypertrophic scars treatment. Verapamil could act as an effective alternative modality in the prevention and treatment of keloid and hypertrophic scars. A larger number of studies are required to

  3. In Silico Characterization of Pectate Lyase Protein Sequences from Different Source Organisms

    Directory of Open Access Journals (Sweden)

    Amit Kumar Dubey

    2010-01-01

    Full Text Available A total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. The multiple sequence alignment of these pectate lyase protein sequences from different source organisms showed conserved regions at different stretches with maximum homology from amino acid residues 439–467, 715–816, and 829–910 which could be used for designing degenerate primers or probes specific for pectate lyases. The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

  4. Systematic characterization of Bacillus Genetic Stock Center Bacillus thuringiensis strains using Multi-Locus Sequence Typing.

    Science.gov (United States)

    Wang, Kui; Shu, Changlong; Soberón, Mario; Bravo, Alejandra; Zhang, Jie

    2018-04-30

    The goal of this work was to perform a systematic characterization of Bacillus thuringiensis (Bt) strains from the Bacillus Genetic Stock Center (BGSC) collection using Multi-Locus Sequence Typing (MLST). Different genetic markers of 158 Bacillus thuringiensis (Bt) strains from 73 different serovars stored in the BGSC, that represented 92% of the different Bt serovars of the BGSC were analyzed, the 8% that were not analyzed were not available. In addition, we analyzed 72 Bt strains from 18 serovars available at the pubMLST bcereus database, and Bt strains G03, HBF18 and Bt185, with no H serovars provided by our laboratory. We performed a systematic MLST analysis using seven housekeeping genes (glpF, gmK, ilvD, pta, pur, pycA and tpi) and analyzed correlation of the results of this analysis with strain serovars. The 233 Bt strains analyzed were assigned to 119 STs from which 19 STs were new. Genetic relationships were established by phylogenetic analysis and showed that STs could be grouped in two major Clusters containing 21 sub-groups. We found that a significant number of STs (101 in total) correlated with specific serovars, such as ST13 that corresponded to nine Bt isolates from B. thuringiensis serovar kenyae. However, other serovars showed high genetic variability and correlated with multiple STs; for example, B. thuringiensis serovar morrisoni correlated with 11 different STs. In addition, we found that 16 different STs correlated with multiple serovars (2-4 different serovars); for example, ST12 correlated with B. thuringiensis serovar alesti, dakota, palmanyolensis and sotto/dendrolimus. These data indicated that only partial correspondence between MLST and serotyping can be established. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Characterization of the Burkholderia thailandensis SOS response by using whole-transcriptome shotgun sequencing.

    Science.gov (United States)

    Ulrich, Ricky L; Deshazer, David; Kenny, Tara A; Ulrich, Melanie P; Moravusova, Anna; Opperman, Timothy; Bavari, Sina; Bowlin, Terry L; Moir, Donald T; Panchal, Rekha G

    2013-10-01

    The bacterial SOS response is a well-characterized regulatory network encoded by most prokaryotic bacterial species and is involved in DNA repair. In addition to nucleic acid repair, the SOS response is involved in pathogenicity, stress-induced mutagenesis, and the emergence and dissemination of antibiotic resistance. Using high-throughput sequencing technology (SOLiD RNA-Seq), we analyzed the Burkholderia thailandensis global SOS response to the fluoroquinolone antibiotic, ciprofloxacin (CIP), and the DNA-damaging chemical, mitomycin C (MMC). We demonstrate that a B. thailandensis recA mutant (RU0643) is ∼4-fold more sensitive to CIP in contrast to the parental strain B. thailandensis DW503. Our RNA-Seq results show that CIP and MMC treatment (P SOS response were induced and include lexA, uvrA, dnaE, dinB, recX, and recA. At the genome-wide level, we found an overall decrease in gene expression, especially for genes involved in amino acid and carbohydrate transport and metabolism, following both CIP and MMC exposure. Interestingly, we observed the upregulation of several genes involved in bacterial motility and enhanced transcription of a B. thailandensis genomic island encoding a Siphoviridae bacteriophage designated E264. Using B. thailandensis plaque assays and PCR with B. mallei ATCC 23344 as the host, we demonstrate that CIP and MMC exposure in B. thailandensis DW503 induces the transcription and translation of viable bacteriophage in a RecA-dependent manner. This is the first report of the SOS response in Burkholderia spp. to DNA-damaging agents. We have identified both common and unique adaptive responses of B. thailandensis to chemical stress and DNA damage.

  6. Identification and characterization of Highlands J virus from a Mississippi sandhill crane using unbiased next-generation sequencing

    Science.gov (United States)

    Ip, Hon S.; Wiley, Michael R.; Long, Renee; Gustavo, Palacios; Shearn-Bochsler, Valerie; Whitehouse, Chris A.

    2014-01-01

    Advances in massively parallel DNA sequencing platforms, commonly termed next-generation sequencing (NGS) technologies, have greatly reduced time, labor, and cost associated with DNA sequencing. Thus, NGS has become a routine tool for new viral pathogen discovery and will likely become the standard for routine laboratory diagnostics of infectious diseases in the near future. This study demonstrated the application of NGS for the rapid identification and characterization of a virus isolated from the brain of an endangered Mississippi sandhill crane. This bird was part of a population restoration effort and was found in an emaciated state several days after Hurricane Isaac passed over the refuge in Mississippi in 2012. Post-mortem examination had identified trichostrongyliasis as the possible cause of death, but because a virus with morphology consistent with a togavirus was isolated from the brain of the bird, an arboviral etiology was strongly suspected. Because individual molecular assays for several known arboviruses were negative, unbiased NGS by Illumina MiSeq was used to definitively identify and characterize the causative viral agent. Whole genome sequencing and phylogenetic analysis revealed the viral isolate to be the Highlands J virus, a known avian pathogen. This study demonstrates the use of unbiased NGS for the rapid detection and characterization of an unidentified viral pathogen and the application of this technology to wildlife disease diagnostics and conservation medicine.

  7. Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads

    DEFF Research Database (Denmark)

    Mourier, Tobias; Mollerup, Sarah; Vinner, Lasse

    2015-01-01

    From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs...... to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads...

  8. Molecular characterizations of somatic hybrids developed between Pleurotus florida and Lentinus squarrosulus through inter-simple sequence repeat markers and sequencing of ribosomal RNA-ITS gene.

    Science.gov (United States)

    Mallick, Pijush; Chattaraj, Shruti; Sikdar, Samir Ranjan

    2017-10-01

    The 12 pfls somatic hybrids and 2 parents of Pleurotus florida and Lentinus s quarrosulus were characterized by ISSR and sequencing of rRNA-ITS genes. Five ISSR primers were used and amplified a total of 54 reproducible fragments with 98.14% polymorphism among all the pfls hybrid populations and parental strains. UPGMA-based cluster exhibited a dendrogram with three major groups between the parents and pfls hybrids. Parent P . florida and L . squarrosulus showed different degrees of genetic distance with all the hybrid lines and they showed closeness to hybrid pfls 1m and pfls 1h , respectively. ITS1(F) and ITS4(R) amplified the rRNA-ITS gene with 611-867 bp sequence length. The nucleotide polymorphisms were found in the ITS1, ITS2 and 5.8S rRNA region with different number of bases. Based on rRNA-ITS sequence, UPGMA cluster exhibited three distinct groups between L. squarrosulus and pfls 1p , pfls 1m and pfls 1s , and pfls 1e and P. florida .

  9. Strategies in protein sequencing and characterization: Multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Nardiello, Donatella; Palermo, Carmen, E-mail: carmen.palermo@unifg.it; Natale, Anna; Quinto, Maurizio; Centonze, Diego

    2015-01-07

    Highlights: • Multi-enzyme digestion for protein sequencing and characterization by CID/ETD. • Simultaneous use of trypsin/chymotrypsin for the maximization of sequence. • Identification of PTMs, sequence variants and species-specific residues. • Increase of accuracy in sequence assignments by orthogonal fragmentation techniques. - Abstract: A strategy based on a simultaneous multi-enzyme digestion coupled with electron transfer dissociation (ETD) and collision-induced dissociation (CID) was developed for protein sequencing and characterization, as a valid alternative platform in ion-trap based proteomics. The effect of different proteolytic procedures using chymotrypsin, trypsin, a combination of both, and Lys-C, was carefully evaluated in terms of number of identified peptides, protein coverage, and score distribution. A systematic comparison between CID and ETD is shown for the analysis of peptides originating from the in-solution digestion of standard caseins. The best results were achieved with a trypsin/chymotrypsin mix combined with CID and ETD operating in alternating mode. A post-database search validation of MS/MS dataset was performed, then, the matched peptides were cross checked by the evaluation of ion scores, rank, number of experimental product ions, and their relative abundances in the MS/MS spectrum. By integrated CID/ETD experiments, high quality-spectra have been obtained, thus allowing a confirmation of spectral information and an increase of accuracy in peptide sequence assignments. Overlapping peptides, produced throughout the proteins, reduce the ambiguity in mapping modifications between natural variants and animal species, and allow the characterization of post translational modifications. The advantages of using the enzymatic mix trypsin/chymotrypsin were confirmed by the nanoLC and CID/ETD tandem mass spectrometry of goat milk proteins, previously separated by two-dimensional gel electrophoresis.

  10. Combination laser treatment for immediate post-surgical scars: a retrospective analysis of 33 immature scars.

    Science.gov (United States)

    Lee, Yongsoo; Kim, Wooram

    2017-07-01

    The application of laser treatments beginning on the day of stitch removal has been demonstrated to improve scar quality. However, there are few guidelines for the treatment of immature scars (ISs), which are defined as "scars whose features are not yet expressed." The purpose of this study was to extract information about early combination laser treatment (CLT) beyond what is currently known by analyzing 33 pairs of pre-treatment and post-treatment photographs of ISs. Two hundred fifty medical records of patients with scars were reviewed, and 33 scars were included in the study. The included scars were treated with vascular lasers (585 or 532 nm) followed by 1550-nm fractional lasers from May 2014 to July 2015 (fewer than 52 days after stitch removal, Fitzpatrick's skin types III-IV, mean age = 16.0 years). Blinded evaluators (one plastic surgeon and two dermatologists) evaluated the pre-treatment and post-treatment photographs. The pre-treatment photographs were scored on a spectrum from "0," when no difference with the surrounding unaffected skin was observed, to "100," when the worst scarring was present. The pre-treatment and post-treatment photographs were compared, and the results were graded on a spectrum from 0, when no difference between the pre-treatment and post-treatment photographs was observed, to 100, when no difference was observed between the post-treatment skin and the surrounding unaffected skin. Statistical analyses were performed with PASW 17.0, SPSS Korea, Seoul, Korea (p laser groups. Patient age and Wtd score were negatively correlated, and a significant difference was observed in the Wtd scores between the age groups (≥15 and lasers are equally effective for CLT of ISs.

  11. Current options for the treatment of pathological scarring.

    Science.gov (United States)

    Poetschke, Julian; Gauglitz, Gerd G

    2016-05-01

    Scarring is the consequence of surgery, trauma or different skin diseases. Apart from fresh, immature scars,that transform into mature scars over the course of would healing and that do not require further treatment,linear hypertrophic scars, widespread hypertrophic scars, keloids and atrophic scars exist. Symptoms like pruritusand pain, stigmatization as well as functional and aesthetic impairments that are very disturbing for the affected patients can bethe basis for the desire for treatment. Today, a multitude of options for the treatment and prevention of scars exists. Topical agents based on silicone or onion extract, intralesional injections of cristalline glucocorticoids (oftentimes in combinationwith cryotherapy) or 5-Fluorouracil as well as ablative and nonablative laser treatment are used. Current guidelines summarize the multitude of available treatment options and the currently available datafor the treating physicians, allowing them to make clear therapy recommendations for every single scar type. Relieving patients of their discomfort and doing their aesthetic demands justice is thus possible. Apart from scar prevention becoming more and more important, the increased use of modernlaser treatment options constitutes a key point in clinical scar treatment. At the same time the attention is turned to evaluating current therapeutic options with the help of contemporary study designs so as to graduallyimprove the level of evidence in scar treatment. © 2016 Deutsche Dermatologische Gesellschaft (DDG). Published by John Wiley & Sons Ltd.

  12. Umbilical scarring in hatchling American alligators

    Science.gov (United States)

    Wiebe, J.J.; Sepulveda, M.S.; Buckland, J.E.; Anderson, S.R.; Gross, T.S.

    2004-01-01

    Umbilical scarring is the presence of excess scar tissue deposited between abdominal dermal layers at the site of yolk sac absorption in hatchling American alligators (Alligator mississippiensis). The presence of this dermal condition plays a key evaluatory role in the overall quality and subsequent value for various commercial leather products. Despite the prevalent nature of this condition, currently the industry has no standardized protocols for its quantification. The objectives of this study were to examine the relationship between hatchling weight and age and incidence of umbilical scarring and to develop a quantifiable and reproducible technique to measure this dermal condition in hatchling American alligators. Thirty eggs from each of nine clutches were incubated in two separate incubators at different facilities and hatchling umbilical scarring was measured at 2 and 10 days of age using digital calipers. Umbilical area was calculated by multiplying umbilical length times umbilical width. There was a significant effect of both age and clutch on umbilical area (overall decline of 64%) by 10 days post-hatch. However, only five of the nine clutches utilized expressed a noticeable decline in the size of this dermal condition (range 67-74%). We had hypothesized that larger hatchlings would have larger umbilical areas and a slower rate of improvement in this condition during the first few days post-hatch. The differences in umbilical area and percent decline with age across clutches, however, were not associated with differences in initial hatchling weights. Within clutches and time periods, hatchling weight had no significant effect on the size and/or rate of decline of this condition. ?? 2004 Published by Elsevier B.V.

  13. Sequence characterization and glycosylation sites identification of donkey milk lactoferrin by multiple enzyme digestions and mass spectrometry

    DEFF Research Database (Denmark)

    Gallina, Serafina; Cunsolo, Vincenzo; Saletti, Rosaria

    2016-01-01

    Lactoferrin, a protein showing an array of biochemical properties, including immuno-modulation, iron-binding ability, as well as antioxidant, antibacterial and antiviral activities, but which may also represent a potential milk allergen, was isolated from donkey milk by ion exchange chromatography...... characterization of donkey lactoferrin sequence, that, at least for the covered sequence, differs from the horse genomic deduced sequence (UniProtKB Acc. Nr. O77811) by five point substitutions located at positions 91 (Arg → His), 328 (Thr → Ile/Leu), 466 (Ala → Gly), 642 (Asn → Ser) and 668 (Ser → Ala). Analysis...... of the glycosylated protein showed that glycans in donkey lactoferrin are linked to the protein backbone via an amide bond to asparagine residues located at the positions 137, 281 and 476....

  14. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.

    Directory of Open Access Journals (Sweden)

    Hongliang Liu

    Full Text Available Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology.Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51% unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17% unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes.The transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

  15. Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA–microRNA regulatory network in nasopharyngeal carcinoma model systems

    Directory of Open Access Journals (Sweden)

    Carol Ying-Ying Szeto

    2014-01-01

    Full Text Available Nasopharyngeal carcinoma (NPC is a prevalent malignancy in Southeast Asia among the Chinese population. Aberrant regulation of transcripts has been implicated in many types of cancers including NPC. Herein, we characterized mRNA and miRNA transcriptomes by RNA sequencing (RNASeq of NPC model systems. Matched total mRNA and small RNA of undifferentiated Epstein–Barr virus (EBV-positive NPC xenograft X666 and its derived cell line C666, well-differentiated NPC cell line HK1, and the immortalized nasopharyngeal epithelial cell line NP460 were sequenced by Solexa technology. We found 2812 genes and 149 miRNAs (human and EBV to be differentially expressed in NP460, HK1, C666 and X666 with RNASeq; 533 miRNA–mRNA target pairs were inversely regulated in the three NPC cell lines compared to NP460. Integrated mRNA/miRNA expression profiling and pathway analysis show extracellular matrix organization, Beta-1 integrin cell surface interactions, and the PI3K/AKT, EGFR, ErbB, and Wnt pathways were potentially deregulated in NPC. Real-time quantitative PCR was performed on selected mRNA/miRNAs in order to validate their expression. Transcript sequence variants such as short insertions and deletions (INDEL, single nucleotide variant (SNV, and isomiRs were characterized in the NPC model systems. A novel TP53 transcript variant was identified in NP460, HK1, and C666. Detection of three previously reported novel EBV-encoded BART miRNAs and their isomiRs were also observed. Meta-analysis of a model system to a clinical system aids the choice of different cell lines in NPC studies. This comprehensive characterization of mRNA and miRNA transcriptomes in NPC cell lines and the xenograft provides insights on miRNA regulation of mRNA and valuable resources on transcript variation and regulation in NPC, which are potentially useful for mechanistic and preclinical studies.

  16. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis

    Directory of Open Access Journals (Sweden)

    Qian Ding

    2015-01-01

    Full Text Available Simple sequence repeats (SSRs are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%, amplicons were successfully generated with high quality. Seventeen (89.5% showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.

  17. Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

    Science.gov (United States)

    Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

    2013-08-01

    Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

  18. Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

    NARCIS (Netherlands)

    Sanders, Ashley D; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Lansdorp, Peter M.

    The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange

  19. Characterization of upstream sequences of the LIM2 gene that bind developmentally regulated and lens-specific proteins

    Institute of Scientific and Technical Information of China (English)

    HSU Heng; Robert L. CHURCH

    2004-01-01

    During lens development, lens epithelial cells differentiate into fiber cells. To date, four major lens fiber cell intrinsic membrane proteins (MIP) ranging in size from 70 kD to 19 kD have been characterized. The second most abundant lens fiber cell intrinsic membrane protein is MP19. This protein probably is involved with lens cell communication and relates with cataractogenesis. The aim of this research is to characterize upstream sequences of the MP19 (also called LIM2) gene that bind developmentally regulated and lens-specific proteins. We have used the gel mobility assays and corresponding competition experiments to identify and characterize cis elements within approximately 500 bases of LIM2 upstream sequences. Our studies locate the positions of some cis elements, including a "CA" repeat, a methylation Hha I island, an FnuD II site, an Ap1 and an Ap2 consensus sequences, and identify some specific cis elements which relate to lens-specific transcription of LIM2. Our experiments also preliminarily identify trans factors which bind to specific cis elements of the LIM2 promoter and/or regulate transcription of LIM2. We conclude that developmental regulation and coordination of the MP 19 gene in ocular lens fiber cells is controlled by the presence of specific cis elements that bind regulatory trans factors that affect LIM2 gene expression. DNA methylation is one mechanism of controlling LIM2 gene expression during lens development.

  20. The Efficacy of a Silicone Sheet in Postoperative Scar Management.

    Science.gov (United States)

    Kim, Jin Sam; Hong, Joon Pio; Choi, Jong Woo; Seo, Dong Kyo; Lee, Eun Sook; Lee, Ho Seong

    2016-09-01

    Silicone gel sheeting has been introduced to prevent scarring, but objective evidence for its usefulness in scar healing is limited. Therefore, the authors' objective was to examine the effectiveness of silicone gel sheeting by randomly applying it to only unilateral scars from a bilateral hallux valgus surgery with symmetrical closure. In a prospective randomized, blinded, intraindividual comparison study, the silicone gel sheeting was applied to 1 foot of a hallux valgus incision scar (an experiment group) for 12 weeks upon removal of the stitches, whereas the symmetrical scar from the other foot was left untreated (a control group). The scars were evaluated at 4 and 12 weeks after the silicon sheet application. The Vancouver Scar Scale was used to measure the vascularity, pigmentation, pliability, height, and length of the scars. Adverse effects were also evaluated, and they included pain, itchiness, rash, erythema, and skin softening. At weeks 4 and 12, the experiment group scored significantly better on the Vancouver Scar Scale in all items, except length (P sheet does not cause adverse effects (P sheet application did show a significant improvement in prevention of postoperative scarring.

  1. Sonographic evaluation of surgical repair of uterine cesarean scar defects.

    Science.gov (United States)

    Pomorski, Michal; Fuchs, Tomasz; Rosner-Tenerowicz, Anna; Zimmer, Mariusz

    2017-10-01

    The aim of the study was to assess the clinical outcomes of surgical repair of uterine cesarean scar defects with sonography (US). Seven nonpregnant women with history of cesarean section and a large uterine scar defect were enrolled. The surgical repair was performed by minilaparotomy. The US assessment of the uterine scar was performed using a standardized approach at baseline, then at a first visit 2-3 days following the surgical intervention (V1) and at a follow-up visit 3 months later (V2). Residual myometrial thickness (RMT), width, and depth of the scar defect were measured. The mean RMT increased significantly from 1.9 mm at baseline to 8.8 mm at V1 and 8.0 mm at V2. No intraoperative complications were observed. Postmenstrual spotting and abdominal pain reported preoperatively resolved after the operation. A surgical repair procedure for an incompletely healed uterine cesarean scar is effective in increasing RMT thickness, decreasing the depth of the scar, and reducing symptoms related to the cesarean section scar defect. Further studies on post-repair pregnancy outcomes are required to evaluate whether the procedure affects the rate of cesarean scar pregnancy, morbidly adherent placenta, and/or uterine scar dehiscence and rupture. The repair of a cesarean scar defect is recommended only for symptomatic women. © 2017 Wiley Periodicals, Inc. J Clin Ultrasound 45:455-460, 2017. © 2017 Wiley Periodicals, Inc.

  2. RNA-ID, a Powerful Tool for Identifying and Characterizing Regulatory Sequences.

    Science.gov (United States)

    Brule, C E; Dean, K M; Grayhack, E J

    2016-01-01

    The identification and analysis of sequences that regulate gene expression is critical because regulated gene expression underlies biology. RNA-ID is an efficient and sensitive method to discover and investigate regulatory sequences in the yeast Saccharomyces cerevisiae, using fluorescence-based assays to detect green fluorescent protein (GFP) relative to a red fluorescent protein (RFP) control in individual cells. Putative regulatory sequences can be inserted either in-frame or upstream of a superfolder GFP fusion protein whose expression, like that of RFP, is driven by the bidirectional GAL1,10 promoter. In this chapter, we describe the methodology to identify and study cis-regulatory sequences in the RNA-ID system, explaining features and variations of the RNA-ID reporter, as well as some applications of this system. We describe in detail the methods to analyze a single regulatory sequence, from construction of a single GFP variant to assay of variants by flow cytometry, as well as modifications required to screen libraries of different strains simultaneously. We also describe subsequent analyses of regulatory sequences. © 2016 Elsevier Inc. All rights reserved.

  3. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

    Directory of Open Access Journals (Sweden)

    Claire eBertelli

    2015-02-01

    Full Text Available With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by embedded bioinformaticians, i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the Sequence a genome class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2,233 putative proteins. Estrella also possesses a 9,136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

  4. Treatment of facial atrophic scars with Esthélis, a hyaluronic acid filler with polydense cohesive matrix (CPM).

    Science.gov (United States)

    Hasson, Ariel; Romero, William A

    2010-12-01

    The treatment of atrophic scars is difficult and dermal filler materials provide a simple alternative with immediate results. Esthélis® is an injectable non-animal crosslinked hyaluronic acid of Swiss origin characterized by a polydense cohesive matrix (CPM®) which produces a gel of uniform consistency with better biointegration to the tissues and a longer duration. To evaluate Esthélis in the treatment of atrophic scars. Twelve patients aged 18-56 years with facial atrophic scars caused by acne vulgaris, dog bite, piercing, basal cell carcinoma and leishmaniasis were treated with Esthélis. The injection technique was linear threading, serial puncture or a combination of both. Clinical efficacy was assessed independently by the authors and by patients immediately, one week and one month after the injection. Adverse events were registered. Authors described the results as moderate (27%), good (57%) and excellent (17%), immediately, one week and one month after the injection. Patients evaluated the cosmetic improvement as good (42%) or excellent (58%) one month after the treatment. Pain during the injection was described as slight or moderate. Only mild erythema was observed immediately after injection, which spontaneously resolved within few hours. Esthélis showed good or excellent results in most patients with atrophic scars, and these were perceived as even better when patients evaluated the cosmetic improvement. The best results were observed in patients with more deforming scars such as surgical scars or trauma.

  5. Molecular genetic characterization of the RD-114 gene family of endogenous feline retroviral sequences.

    Science.gov (United States)

    Reeves, R H; O'Brien, S J

    1984-01-01

    RD-114 is a replication-competent, xenotropic retrovirus which is homologous to a family of moderately repetitive DNA sequences present at ca. 20 copies in the normal cellular genome of domestic cats. To examine the extent and character of genomic divergence of the RD-114 gene family as well as to assess their positional association within the cat genome, we have prepared a series of molecular clones of endogenous RD-114 DNA segments from a genomic library of cat cellular DNA. Their restriction endonuclease maps were compared with each other as well as to that of the prototype-inducible RD-114 which was molecularly cloned from a chronically infected human cell line. The endogenous sequences analyzed were similar to each other in that they were colinear with RD-114 proviral DNA, were bounded by long terminal redundancies, and conserved many restriction sites in the gag and pol regions. However, the env regions of many of the sequences examined were substantially deleted. Several of the endogenous RD-114 genomes contained a novel envelope sequence which was unrelated to the env gene of the prototype RD-114 env gene but which, like RD-114 and endogenous feline leukemia virus provirus, was found only in species of the genus Felis, and not in other closely related Felidae genera. The endogenous RD-114 sequences each had a distinct cellular flank which indicates that these sequences are not tandem but dispersed nonspecifically throughout the genome. Southern analysis of cat cellular DNA confirmed the conclusions about conserved restriction sites in endogenous sequences and indicated that a single locus may be responsible for the production of the major inducible form of RD-114. Images PMID:6090693

  6. Improvement of Atrophic Acne Scars in Skin of Color Using Topical Synthetic Epidermal Growth Factor (EGF) Serum: A Pilot Study.

    Science.gov (United States)

    Stoddard, Marie Alexia; Herrmann, Jennifer; Moy, Lauren; Moy, Ronald

    2017-04-01

    BACKGROUND: Atrophic scarring in skin of color is a common, permanent, and distressing result of uncontrolled acne vulgaris. Ablative lasers and chemical peels are frequently used to improve the appearance of atrophic scars, primarily through the stimulation of collagen and elastin; however, these treatment modalities are associated with risks, such as dyspigmentation and hypertrophic scarring, especially in patients with darker skin. OBJECTIVE: We evaluated the efficacy of topically applied synthetic epidermal growth factor (EGF) serum in reducing the appearance of atrophic acne scars in skin of color. METHODS: A single-center clinical trial was performed on twelve healthy men and women (average age 32.5) with Fitzpatrick Type IV-V skin and evidence of facial grade II-IV atrophic acne scars. Subjects applied topical EGF serum to the full-face twice daily for 12 weeks. Scar improvement was investigated at each visit using an Investigator Global Assessment (IGA), a Goodman grade, clinical photography, and patient self-assessment. RESULTS: Eleven subjects completed the trial. Compared to baseline, there was an improvement in mean IGA score from 3.36 (SEM = 0.15) to 2.18 (SEM = 0.33). Mean Goodman grade was reduced from 2.73 (SEM = 0.19) to 2.55 (SEM = 0.21). Of the eleven pairs of before and after photographs, nine were correctly chosen as the post-treatment image by a blind investigator. On self-assessment, 81% reported a "good" to "excellent" improvement in their scars compared to baseline (P = 0.004). CONCLUSION: Topical EGF may improve the appearance of atrophic acne scars in skin of color. Additional, larger studies should be conducted to better characterize improvement. J Drugs Dermatol. 2017;16(4):322-326..

  7. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization.

    Science.gov (United States)

    Gcebe, Nomakorinte; Rutten, Victor; Pittius, Nicolaas Gey van; Naicker, Brendon; Michel, Anita

    2017-04-01

    Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment, and an increasing number of NTM species have been isolated and characterized from both humans and animals, highlighting the zoonotic potential of these bacteria. Host exposure to NTM may impact on cross-reactive immune responsiveness, which may affect diagnosis of bovine tuberculosis and may also play a role in the variability of the efficacy of Mycobacterium bovis BCG vaccination against tuberculosis. In this study we characterized 10 NTM isolates originating from water, soil, nasal swabs of cattle and African buffalo as well as bovine tissue samples. These isolates were previously identified during an NTM survey and were all found, using 16S rRNA gene sequence analysis to be closely related to Mycobacterium moriokaense. A polyphasic approach that included phenotypic characterization, antibiotic susceptibility profiling, mycolic acid profiling and phylogenetic analysis of four gene loci, 16S rRNA, hsp65, sodA and rpoB, was employed to characterize these isolates. Sequence data analysis of the four gene loci revealed that these isolates belong to a unique species of the genus Mycobacterium. This evidence was further supported by several differences in phenotypic characteristics between the isolates and the closely related species. We propose the name Mycobacterium malmesburyense sp. nov. for this novel species. The type strain is WCM 7299T (=ATCC BAA-2759T=CIP 110822T).

  8. Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils.

    Science.gov (United States)

    Duan, Y P; Castro, H F; Hewlett, T E; White, J H; Ogram, A V

    2003-01-01

    Various bacterial species in the genus Pasteuria have great potential as biocontrol agents against plant-parasitic nematodes, although study of this important genus is hampered by the current inability to cultivate Pasteuria species outside their host. To aid in the study of this genus, an extensive 16S rRNA gene sequence phylogeny was constructed and this information was used to develop cultivation-independent methods for detection of Pasteuria in soils and nematodes. Thirty new clones of Pasteuria 16S rRNA genes were obtained directly from nematodes and soil samples. These were sequenced and used to construct an extensive phylogeny of this genus. These sequences were divided into two deeply branching clades within the low-G + C, Gram-positive division; some sequences appear to represent novel species within the genus Pasteuria. In addition, a surprising degree of 16S rRNA gene sequence diversity was observed within what had previously been designated a single strain of Pasteuria penetrans (P-20). PCR primers specific to Pasteuria 16S rRNA for detection of Pasteuria in soils were also designed and evaluated. Detection limits for soil DNA were 100-10,000 Pasteuria endospores (g soil)(-1).

  9. Molecular characterization, sequence analysis and tissue expression of a porcine gene – MOSPD2

    Directory of Open Access Journals (Sweden)

    Yang Jie

    2017-01-01

    Full Text Available The full-length cDNA sequence of a porcine gene, MOSPD2, was amplified using the rapid amplification of cDNA ends method based on a pig expressed sequence tag sequence which was highly homologous to the coding sequence of the human MOSPD2 gene. Sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 491 amino acids that has high homology with the motile sperm domain-containing protein 2 (MOSPD2 of five species: horse (89%, human (90%, chimpanzee (89%, rhesus monkey (89% and mouse (85%; thus, it could be defined as a porcine MOSPD2 gene. This novel porcine gene was assigned GeneID: 100153601. This gene is structured in 15 exons and 14 introns as revealed by computer-assisted analysis. The phylogenetic analysis revealed that the porcine MOSPD2 gene has a closer genetic relationship with the MOSPD2 gene of horse. Tissue expression analysis indicated that the porcine MOSPD2 gene is generally and differentially expressed in the spleen, muscle, skin, kidney, lung, liver, fat and heart. Our experiment is the first to establish the primary foundation for further research on the porcine MOSPD2 gene.

  10. Impact of sequencing depth on the characterization of the microbiome and resistome.

    Science.gov (United States)

    Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E; Morley, Paul S; McAllister, Tim A

    2018-04-12

    Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

  11. Cesarean Scar Ectopic Pregnancy: Laparoscopic Resection and Total Scar Dehiscence Repair.

    Science.gov (United States)

    Mahgoub, Sara; Gabriele, Victor; Faller, Emilie; Langer, Bruno; Wattiez, Arnaud; Lecointre, Lise; Akladios, Cherif

    2018-02-01

    To illustrate a laparoscopic technique for the resection of cesarean scar ectopic pregnancy, associated with isthmocele repair. Case report (Canadian Task Force classification III). A tertiary referral center in Strasbourg, France. Cesarean scar pregnancy is a rare form of ectopic pregnancy. The major risk of this type of pregnancy is the early uterine rupture with massive, sometimes life-threatening, bleeding. Thus, active management of these pregnancies starting immediately after diagnosis is crucial. Therapeutic options can be medical, surgical, or a combination. Numerous case reports or case series can be found in the literature, but there are few clinical studies, which are difficult to conduct because of case rarity and inconclusiveness. A 2016 meta-analysis that included 194 articles published between 1978 and 2014 (126 case reports, 45 cases series, and 23 clinical studies) concluded that hysteroscopy or laparoscopic hysterotomy seems to be the best first-line approach to treating cesarean scar ectopic pregnancy, with uterine artery embolization reserved for significant bleeding and/or a high suspicion index for arteriovenous malformation [1]. There is no consensus on the treatment of reference, however. The case involves a 38-year-old primiparous women who underwent a cesarean section delivery in 2010 and who was diagnosed by ultrasound scan at 7 weeks gestation with cesarean scar ectopic pregnancy, which was confirmed by pelvic magnetic resonance imaging. The patient initially received medical treatment with 2 intramuscular injections of methotrexate and one local intragestational injection of KCl. Her initial human chorionic gonadotropin (hCG) level was 82 000 IU/L. Rigorous weekly biological and ultrasound monitoring revealed an involution of the ectopic pregnancy associated with decreasing hCG. No bleeding or infectious complications occurred during this period. After 10 weeks of monitoring, her hCG had stabilized at 300 IU/L, and a residual image

  12. Analysis of multilocus sequence typing and virulence characterization of Listeria monocytogenes isolates from Chinese retail ready-to-eat food

    Directory of Open Access Journals (Sweden)

    Shi eWu

    2016-02-01

    Full Text Available Eighty Listeria monocytogenes isolates were obtained from Chinese retail ready-to-eat (RTE food and were previously characterized with serotyping and antibiotic susceptibility tests. The aim of this study was to characterize the subtype and virulence potential of these L. monocytogenes isolates by multilocus sequence typing (MLST, virulence-associate genes, epidemic clones (ECs and sequence analysis of the important virulence factor: internalin A (inlA. The result of MLST revealed that these L. monocytogenes isolates belonged to 14 different sequence types (STs. With the exception of four new STs (ST804, ST805, ST806 and ST807, all other STs observed in this study have been associated with human listeriosis and outbreaks to varying extents. Six virulence-associate genes (inlA, inlB, inlC, inlJ, hly and llsX were selected and their presence was investigated using PCR. All strains carried inlA, inlB, inlC, inlJ, and hly, whereas 38.8% (31/80 of strains harbored the listeriolysin S genes (llsX. A multiplex PCR assay was used to evaluate the presence of markers specific to epidemic clones of L. monocytogenes and identified 26.3% (21/80 of ECI in the 4b-4d-4e strains. Further study of inlA sequencing revealed that most strains contained the full-length InlA required for host cell invasion, whereas three mutations lead to premature stop codons (PMSC within a novel PMSCs at position 326 (GAA→TAA. MLST and inlA sequence analysis results were concordant, and different virulence potentials within isolates were observed. These findings suggest that L. monocytogenes isolates from RTE food in China could be virulent and be capable of causing human illness. Furthermore, the STs and virulence profiles of L. monocytogenes isolates have significant implications for epidemiological and public health studies of this pathogen.

  13. Analysis of Multilocus Sequence Typing and Virulence Characterization of Listeria monocytogenes Isolates from Chinese Retail Ready-to-Eat Food.

    Science.gov (United States)

    Wu, Shi; Wu, Qingping; Zhang, Jumei; Chen, Moutong; Guo, Weipeng

    2016-01-01

    Eighty Listeria monocytogenes isolates were obtained from Chinese retail ready-to-eat (RTE) food and were previously characterized with serotyping and antibiotic susceptibility tests. The aim of this study was to characterize the subtype and virulence potential of these L. monocytogenes isolates by multilocus sequence typing (MLST), virulence-associate genes, epidemic clones (ECs), and sequence analysis of the important virulence factor: internalin A (inlA). The result of MLST revealed that these L. monocytogenes isolates belonged to 14 different sequence types (STs). With the exception of four new STs (ST804, ST805, ST806, and ST807), all other STs observed in this study have been associated with human listeriosis and outbreaks to varying extents. Six virulence-associate genes (inlA, inlB, inlC, inlJ, hly, and llsX) were selected and their presence was investigated using PCR. All strains carried inlA, inlB, inlC, inlJ, and hly, whereas 38.8% (31/80) of strains harbored the listeriolysin S genes (llsX). A multiplex PCR assay was used to evaluate the presence of markers specific to epidemic clones of L. monocytogenes and identified 26.3% (21/80) of ECI in the 4b-4d-4e strains. Further study of inlA sequencing revealed that most strains contained the full-length InlA required for host cell invasion, whereas three mutations lead to premature stop codons (PMSC) within a novel PMSCs at position 326 (GAA → TAA). MLST and inlA sequence analysis results were concordant, and different virulence potentials within isolates were observed. These findings suggest that L. monocytogenes isolates from RTE food in China could be virulent and be capable of causing human illness. Furthermore, the STs and virulence profiles of L. monocytogenes isolates have significant implications for epidemiological and public health studies of this pathogen.

  14. Prosthodontist contribution in treating post-burn hypertrophic facial scars

    Directory of Open Access Journals (Sweden)

    Padmanabhan T

    2010-01-01

    Full Text Available The formation of hypertrophic scars is common following healing of the burn wound, particularly in children. The face is one of the areas of the body most frequently affected by burns. Scar formation as a result of burn wounds leads to contraction of the formed granulation tissue, which causes both aesthetic and functional impairment for the patient. Scarring has major psychological and physical repercussions. Scarring on the face and visible regions of the body can be very distressing for the patient. Prevention of scars involves early and continuous use of a compressive orthesis. However, their efficacy is often limited to the facial region because of the contours of this area of body. This paper describes a clinical case of post-burn hypertrophic scars treated with silicone gel sheeting applied with pressure under custom made auto-polymerizing resin stent.

  15. Cutaneous Scar Prevention and Management; Overview of current therapies

    Directory of Open Access Journals (Sweden)

    Sultan Al-Shaqsi

    2016-02-01

    Full Text Available Cutaneous scarring is common after trauma, surgery and infection and occurs when normal skin tissue is replaced by fibroblastic tissue during the healing process. The pathophysiology of scar formation is not yet fully understood, although the degree of tension across the wound edges and the speed of cell growth are believed to play central roles. Prevention of scars is essential and can be achieved by attention to surgical techniques and the use of measures to reduce cell growth. Grading and classifying scars is important to determine available treatment strategies. This article presents an overview of the current therapies available for the prevention and treatment of scars. It is intended to be a practical guide for surgeons and other health professionals involved with and interested in scar management.

  16. Sequence characterization of 5S ribosomal RNA from eight gram positive procaryotes

    Science.gov (United States)

    Woese, C. R.; Luehrsen, K. R.; Pribula, C. D.; Fox, G. E.

    1976-01-01

    Complete nucleotide sequences are presented for 5S rRNA from Bacillus subtilis, B. firmus, B. pasteurii, B. brevis, Lactobacillus brevis, and Streptococcus faecalis, and 5S rRNA oligonucleotide catalogs and partial sequence data are given for B. cereus and Sporosarcina ureae. These data demonstrate a striking consistency of 5S rRNA primary and secondary structure within a given bacterial grouping. An exception is B. brevis, in which the 5S rRNA sequence varies significantly from that of other bacilli in the tuned helix and the procaryotic loop. The localization of these variations suggests that B. brevis occupies an ecological niche that selects such changes. It is noted that this organism produces antibiotics which affect ribosome function.

  17. Identification and functional characterization of a novel bipartite nuclear localization sequence in ARID1A

    Energy Technology Data Exchange (ETDEWEB)

    Bateman, Nicholas W. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Shoji, Yutaka [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids 49503, MI (United States); Conrads, Kelly A.; Stroop, Kevin D. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); Hamilton, Chad A. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, 8901 Wisconsin Ave, MD, Bethesda, 20889 (United States); Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda 20814, MD (United States); Darcy, Kathleen M. [Women' s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale 22003, VA (United States); The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD (United States); Maxwell, George L. [Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA 22042 (United States); Risinger, John I. [Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids 49503, MI (United States); and others

    2016-01-01

    AT-rich interactive domain-containing protein 1A (ARID1A) is a recently identified nuclear tumor suppressor frequently altered in solid tumor malignancies. We have identified a bipartite-like nuclear localization sequence (NLS) that contributes to nuclear import of ARID1A not previously described. We functionally confirm activity using GFP constructs fused with wild-type or mutant NLS sequences. We further show that cyto-nuclear localized, bipartite NLS mutant ARID1A exhibits greater stability than nuclear-localized, wild-type ARID1A. Identification of this undescribed functional NLS within ARID1A contributes vital insights to rationalize the impact of ARID1A missense mutations observed in patient tumors. - Highlights: • We have identified a bipartite nuclear localization sequence (NLS) in ARID1A. • Confirmation of the NLS was performed using GFP constructs. • NLS mutant ARID1A exhibits greater stability than wild-type ARID1A.

  18. Characterization of Request Sequences for List Accessing Problem and New Theoretical Results for MTF Algorithm

    OpenAIRE

    Mohanty, Rakesh; Sharma, Burle; Tripathy, Sasmita

    2011-01-01

    List Accessing Problem is a well studied research problem in the context of linear search. Input to the list accessing problem is an unsorted linear list of distinct elements along with a sequence of requests, where each request is an access operation on an element of the list. A list accessing algorithm reorganizes the list while processing a request sequence on the list in order to minimize the access cost. Move-To-Front algorithm has been proved to be the best performing list accessing onl...

  19. Microneedle physical contact as a therapeutic for abnormal scars

    OpenAIRE

    Yeo, David C.; Balmayor, Elizabeth R.; Schantz, Jan-Thorsten; Xu, Chenjie

    2017-01-01

    Background Abnormal (keloid and hypertrophic) scars are a significant affliction with no satisfactory single modality therapy to-date. Available options are often ineffective, painful, potentially hazardous, and require healthcare personnel involvement. Herein a self-administered microneedle device based on drug-free physical contact for inhibiting abnormal scars is reported. Its therapeutic activity through microneedle contact eliminates hazards associated with toxic anti-scarring drugs whil...

  20. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA.

    Science.gov (United States)

    Chandrananda, Dineika; Thorne, Natalie P; Bahlo, Melanie

    2015-06-17

    High-throughput sequencing of cell-free DNA fragments found in human plasma has been used to non-invasively detect fetal aneuploidy, monitor organ transplants and investigate tumor DNA. However, many biological properties of this extracellular genetic material remain unknown. Research that further characterizes circulating DNA could substantially increase its diagnostic value by allowing the application of more sophisticated bioinformatics tools that lead to an improved signal to noise ratio in the sequencing data. In this study, we investigate various features of cell-free DNA in plasma using deep-sequencing data from two pregnant women (>70X, >50X) and compare them with matched cellular DNA. We utilize a descriptive approach to examine how the biological cleavage of cell-free DNA affects different sequence signatures such as fragment lengths, sequence motifs at fragment ends and the distribution of cleavage sites along the genome. We show that the size distributions of these cell-free DNA molecules are dependent on their autosomal and mitochondrial origin as well as the genomic location within chromosomes. DNA mapping to particular microsatellites and alpha repeat elements display unique size signatures. We show how cell-free fragments occur in clusters along the genome, localizing to nucleosomal arrays and are preferentially cleaved at linker regions by correlating the mapping locations of these fragments with ENCODE annotation of chromatin organization. Our work further demonstrates that cell-free autosomal DNA cleavage is sequence dependent. The region spanning up to 10 positions on either side of the DNA cleavage site show a consistent pattern of preference for specific nucleotides. This sequence motif is present in cleavage sites localized to nucleosomal cores and linker regions but is absent in nucleosome-free mitochondrial DNA. These background signals in cell-free DNA sequencing data stem from the non-random biological cleavage of these fragments. This

  1. Characterization and Sequencing of MT-Cox1 Gene in Khorasan ...

    African Journals Online (AJOL)

    The aim of this study was to investigate the nucleotide sequence of COX1 gene in mitochondrial genome of Khorasan native chicken and detect the possible mutations in the genome. For this purpose, after sampling and extracting DNA from the whole blood samples, the COX1 gene was amplified using specific primers and ...

  2. De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing.

    Science.gov (United States)

    Sun, Xiudong; Zhou, Shumei; Meng, Fanlu; Liu, Shiqi

    2012-10-01

    Garlic is widely used as a spice throughout the world for the culinary value of its flavor and aroma, which are created by the chemical transformation of a series of organic sulfur compounds. To analyze the transcriptome of Allium sativum and discover the genes involved in sulfur metabolism, cDNAs derived from the total RNA of Allium sativum buds were analyzed by Illumina sequencing. Approximately 26.67 million 90 bp paired-end clean reads were achieved in two libraries. A total of 127,933 unigenes were generated by de novo assembly and were compared with the sequences in public databases. Of these, 45,286 unigenes had significant hits to the sequences in the Nr database, 29,514 showed significant similarity to known proteins in the Swiss-Prot database and, 20,706 and 21,952 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Moreover, genes involved in organic sulfur biosynthesis were identified. These unigenes data will provide the foundation for research on gene expression, genomics and functional genomics in Allium sativum. Key message The obtained unigenes will provide the foundation for research on functional genomics in Allium sativum and its closely related species, and fill the gap of the existing plant EST database.

  3. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.

    Directory of Open Access Journals (Sweden)

    Margaret Staton

    Full Text Available Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

  4. Nucleotide Sequence and Characterization of the Broad-Host-Range Lactococcal Plasmid pWVO1

    NARCIS (Netherlands)

    Leenhouts, Cornelis; Tolner, Berend; Bron, Sierd; Kok, Jan; Venema, Gerhardus; Seegers, Jozef

    The nucleotide sequence of the Lactococcus lactis broad-host-range plasmid pWVO1, replicating in both gram-positive and gram-negative bacteria, was determined. This analysis revealed four open reading frames (ORFs). ORF A appeared to encode a trans-acting 26.8-kDa protein (RepA), necessary for

  5. Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

    Directory of Open Access Journals (Sweden)

    Mei Jiang

    2018-05-01

    Full Text Available To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

  6. Cloning, sequence analysis, and characterization of the genes involved in isoprimeverose metabolism in Lactobacillus pentosus

    NARCIS (Netherlands)

    Chaillou, S.; Lokman, B.C.; Leer, R.J.; Posthuma, C.; Postma, P.W.; Pouwels, P.H.

    1998-01-01

    Two genes, xylP and xylQ, from the xylose regulon of Lactobacillus pentosus were cloned and sequenced. Together with the repressor gene of the regulon, xylR, the xylPQ genes form an operon which is inducible by xylose and which is transcribed from a promoter located 145 bp upstream of xylP. A

  7. Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples

    DEFF Research Database (Denmark)

    Hasman, Henrik; Saputra, Dhany; Sicheritz-Pontén, Thomas

    2014-01-01

    Whole genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples this could further reduce diagnostic time and thereby improve control and treatment. A major bottle-neck is the availability of fast and reliable bioinformatics...

  8. First-time characterization of JY-1-like sequence in goats

    African Journals Online (AJOL)

    2015-07-11

    Jul 11, 2015 ... Material and Methods. Nine well-recognized .... available, the bovine JY-1 gene sequence (GenBank accession no. .... Since no phenotypes on fecundity and sexual precocity are currently available for goats, it may not be ...

  9. Molecular characterization of Fasciola spp. from the endemic area of northern Iran based on nuclear ribosomal DNA sequences.

    Science.gov (United States)

    Amor, Nabil; Halajian, Ali; Farjallah, Sarra; Merella, Paolo; Said, Khaled; Ben Slimane, Badreddine

    2011-07-01

    Fasciolosis caused by Fasciola spp. (Platyhelminthes: Trematoda: Digenea) is considered as the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. In the endemic regions of the North of Iran, Fasciola hepatica and Fasciola gigantica have been previously characterized on the basis of morphometric differences, but the use of molecular markers is necessary to distinguish exactly between species and intermediate forms. Samples from buffaloes and goats from different localities of northern Iran were identified morphologically and then genetically characterized by sequences of the first (ITS-1) and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA). Comparison of the ITS of the northern Iranian samples with sequences of Fasciola spp. from GenBank showed that the examined specimens had sequences identical to those of the most frequent haplotypes of F. hepatica (n=25, 48.1%) and F. gigantica (n=20, 38.45%), which differed from each other in different variable nucleotide positions of ITS region sequences, and their intermediate forms (n=7, 13.45%), which had nucleotides overlapped between the two Fasciola species in all the positions. The ITS sequences from populations of Fasciola isolates in buffaloes and goats had experienced introgression/hybridization as previously reported in isolates from other ruminants and humans. Based on ITS-1 and ITS-2 sequences, flukes are scattered in pure F. hepatica, F. gigantica and intermediate Fasciola clades, revealing that multiple genotypes of Fasciola are able to infect goats and buffaloes in North of Iran. Furthermore, the phylogenetic trees based upon the ITS-1 and ITS-2 sequences showed a close relationship of the Iranian samples with isolates of F. hepatica and F. gigantica from different localities of Africa and Asia. In the present study, the intergenic transcribed spacers ITS-1 and ITS-2 showed to be reliable approaches for the genetic

  10. Scarred resonances and steady probability distribution in a chaotic microcavity

    International Nuclear Information System (INIS)

    Lee, Soo-Young; Rim, Sunghwan; Kim, Chil-Min; Ryu, Jung-Wan; Kwon, Tae-Yoon

    2005-01-01

    We investigate scarred resonances of a stadium-shaped chaotic microcavity. It is shown that two components with different chirality of the scarring pattern are slightly rotated in opposite ways from the underlying unstable periodic orbit, when the incident angles of the scarring pattern are close to the critical angle for total internal reflection. In addition, the correspondence of emission pattern with the scarring pattern disappears when the incident angles are much larger than the critical angle. The steady probability distribution gives a consistent explanation about these interesting phenomena and makes it possible to expect the emission pattern in the latter case

  11. NEW MOLECULAR MEDICINE-BASED SCAR MANAGEMENT STRATEGIES

    Science.gov (United States)

    Arno, Anna I; Gauglitz, Gerd G; Barret, Juan P; Jeschke, Marc G

    2014-01-01

    Keloids and hypertrophic scars are prevalent disabling conditions with still suboptimal treatments. Basic science and molecular-based medicine research has contributed to unravel new bench-to-bedside scar therapies, and to dissect the complex signaling pathways involved. Peptides such as transforming growth factor beta (TGF-β) superfamily, with SMADs, Ski, SnoN, Fussels, endoglin, DS-Sily, Cav-1p, AZX100, thymosin-β4 and other related molecules may emerge as targets to prevent and treat keloids and hypertrophic scars. The aim of this review is to describe the basic complexity of these new molecular scar management strategies, and point out new fibrosis research lines. PMID:24438742

  12. Abnormal pigmentation within cutaneous scars: A complication of wound healing

    Directory of Open Access Journals (Sweden)

    Sarah Chadwick

    2012-01-01

    Full Text Available Abnormally pigmented scars are an undesirable consequence of cutaneous wound healing and are a complication every single individual worldwide is at risk of. They present a challenge for clinicians, as there are currently no definitive treatment options available, and render scars much more noticeable making them highly distressing for patients. Despite extensive research into both wound healing and the pigment cell, there remains a scarcity of knowledge surrounding the repigmentation of cutaneous scars. Pigment production is complex and under the control of many extrinsic and intrinsic factors and patterns of scar repigmentation are unpredictable. This article gives an overview of human skin pigmentation, repigmentation following wounding and current treatment options.

  13. Molecular Characterization of Five Potyviruses Infecting Korean Sweet Potatoes Based on Analyses of Complete Genome Sequences

    Directory of Open Access Journals (Sweden)

    Hae-Ryun Kwak

    2015-12-01

    Full Text Available Sweet potatoes (Ipomea batatas L. are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle virus (SPFMV, Sweet potato virus C (SPVC, Sweet potato virus G (SPVG, Sweet potato virus 2 (SPV2, and Sweet potato latent virus (SPLV, have been detected in sweet potato fields at a high (~95% incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88% nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.

  14. Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing.

    Science.gov (United States)

    Meason-Smith, Courtney; Diesel, Alison; Patterson, Adam P; Older, Caitlin E; Johnson, Timothy J; Mansell, Joanne M; Suchodolski, Jan S; Rodrigues Hoffmann, Aline

    2017-02-01

    Next generation sequencing (NGS) studies have demonstrated a diverse skin-associated microbiota and microbial dysbiosis associated with atopic dermatitis in people and in dogs. The skin of cats has yet to be investigated using NGS techniques. We hypothesized that the fungal microbiota of healthy feline skin would be similar to that of dogs, with a predominance of environmental fungi, and that fungal dysbiosis would be present on the skin of allergic cats. Eleven healthy cats and nine cats diagnosed with one or more cutaneous hypersensitivity disorders, including flea bite, food-induced and nonflea nonfood-induced hypersensitivity. Healthy cats were sampled at twelve body sites and allergic cats at six sites. DNA was isolated and Illumina sequencing was performed targeting the internal transcribed spacer region of fungi. Sequences were processed using the bioinformatics software QIIME. The most abundant fungal sequences from the skin of all cats were classified as Cladosporium and Alternaria. The mucosal sites, including nostril, conjunctiva and reproductive tracts, had the fewest number of fungi, whereas the pre-aural space had the most. Allergic feline skin had significantly greater amounts of Agaricomycetes and Sordariomycetes, and significantly less Epicoccum compared to healthy feline skin. The skin of healthy cats appears to have a more diverse fungal microbiota compared to previous studies, and a fungal dysbiosis is noted in the skin of allergic cats. Future studies assessing the temporal stability of the skin microbiota in cats will be useful in determining whether the microbiota sequenced using NGS are colonizers or transient microbes. © 2016 ESVD and ACVD.

  15. Comparative effect and safety of verapamil in keloid and hypertrophic scar treatment: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Li ZN

    2016-11-01

    Full Text Available Zhouna Li, Zhehu Jin Department of Dermatology, Yanbian University Affiliated hospital, Yanji, Jilin, People’s Republic of China Background: Keloids and hypertrophic scars are the most common types of pathological scarring. Traditionally, keloids have been considered as a result of aberrant wound healing, involving excessive fibroblast participation that is characterized by hyalinized collagen bundles. However, the usefulness of this characterization has been questioned. In recent years, studies have reported the appropriate use of verapamil for keloids and hypertrophic scars.Methods: Searches were conducted on the databases Medline, Embase, Cochrane, PubMed, and China National Knowledge Infrastructure from 2006 to July 2016. State12.0 was used for literature review, data extraction, and meta-analysis. Treatment groups were divided into verapamil and nonverapamil group. Nonverapamil group includes steroids and intense pulsed light (IPL therapy. Total effective rates include cure rate and effective rate. Cure: skin lesions were completely flattened, became soft and symptoms disappeared. Efficacy: skin lesions subsided, patient significantly reduced symptoms. Inefficient definition of skin was progression free or became worse. Random-effects model was used for the meta-analysis.Results: Six studies that included 331 patients with keloids and hypertrophic scars were analyzed. Analysis of the total effective rate of skin healing was performed. The total effective rates in the two groups were 54.07% (verapamil and 53.18% (nonverapamil, respectively. The meta-analysis showed that there was no difference between the two groups. We also compared the adverse reactions between the verapamil treatment group and the steroids treatment group in two studies, and the result indicated that the verapamil group showed less adverse reactions.Conclusion: There were no differences between the application of verapamil and nonverapamil group in keloids and

  16. Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

    Science.gov (United States)

    Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

    2018-01-01

    Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

  17. Rapid Characterization of Insulin Modifications and Sequence Variations by Proteinase K Digestion and UHPLC-ESI-MS

    Science.gov (United States)

    Yang, Rong-Sheng; Tang, Weijuan; Sheng, Huaming; Meng, Fanyu

    2018-05-01

    Discovery of novel insulin analogs as therapeutics has remained an active area of research. Compared with native human insulin, insulin analog molecules normally incorporate either covalent modifications or amino acid sequence variations. From the drug discovery and development perspective, methods for efficient and detailed characterization of these primary structural changes are very important. In this report, we demonstrate that proteinase K digestion coupled with UPLC-ESI-MS analysis provides a simple and rapid approach to characterize the modifications and sequence variations of insulin molecules. A commercially available proteinase K digestion kit was used to process recombinant human insulin (RHI), insulin glargine, and fluorescein isothiocynate-labeled recombinant human insulin (FITC-RHI) samples. The LC-MS data clearly showed that RHI and insulin glargine samples can be differentiated, and the FITC modifications in all three amine sites of the RHI molecule are well characterized. The end-to-end experiment and data interpretation was achieved within 60 min. This approach is fast and simple, and can be easily implemented in early drug discovery laboratories to facilitate research on more advanced insulin therapeutics. [Figure not available: see fulltext.

  18. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

  19. Sequence and structural characterization of Trx-Grx type of monothiol glutaredoxins from Ashbya gossypii.

    Science.gov (United States)

    Yadav, Saurabh; Kumari, Pragati; Kushwaha, Hemant Ritturaj

    2013-01-01

    Glutaredoxins are enzymatic antioxidants which are small, ubiquitous, glutathione dependent and essentially classified under thioredoxin-fold superfamily. Glutaredoxins are classified into two types: dithiol and monothiol. Monothiol glutaredoxins which carry the signature "CGFS" as a redox active motif is known for its role in oxidative stress, inside the cell. In the present analysis, the 138 amino acid long monothiol glutaredoxin, AgGRX1 from Ashbya gossypii was identified and has been used for the analysis. The multiple sequence alignment of the AgGRX1 protein sequence revealed the characteristic motif of typical monothiol glutaredoxin as observed in various other organisms. The proposed structure of the AgGRX1 protein was used to analyze signature folds related to the thioredoxin superfamily. Further, the study highlighted the structural features pertaining to the complex mechanism of glutathione docking and interacting residues.

  20. Molecular cloning, sequence characterization and expression pattern of Rab18 gene from watermelon (Citrullus lanatus).

    Science.gov (United States)

    Xinli, Xiao; Lei, Peng

    2015-03-04

    The complete mRNA sequence of watermelon Rab18 gene was amplified through the rapid amplification of cDNA ends (RACE) method. The full-length mRNA was 1010 bp containing a 645 bp open reading frame, which encodes a protein of 214 amino acids. Sequence analysis revealed that watermelon Rab18 protein shares high homology with the Rab18 of cucumber (99%), muskmelon (98%), Morus notabilis (90%), tomato (89%), wine grape (89%) and potato (88%). Phylogenetic analysis revealed that watermelon Rab18 gene has a closer genetic relationship with Rab18 gene of cucumber and muskmelon. Tissue expression profile analysis indicated that watermelon Rab18 gene was highly expressed in root, stem and leaf, moderately expressed in flower and weakly expressed in fruit.

  1. Sequencing and Characterization of the Invasive Sycamore Lace Bug Corythucha ciliata (Hemiptera: Tingidae) Transcriptome

    Science.gov (United States)

    Qu, Cheng; Fu, Ningning; Xu, Yihua

    2016-01-01

    The sycamore lace bug, Corythucha ciliata (Hemiptera: Tingidae), is an invasive forestry pest rapidly expanding in many countries. This pest poses a considerable threat to the urban forestry ecosystem, especially to Platanus spp. However, its molecular biology and biochemistry are poorly understood. This study reports the first C. ciliata transcriptome, encompassing three different life stages (Nymphs, adults female (AF) and adults male (AM)). In total, 26.53 GB of clean data and 60,879 unigenes were obtained from three RNA-seq libraries. These unigenes were annotated and classified by Nr (NCBI non-redundant protein sequences), Nt (NCBI non-redundant nucleotide sequences), Pfam (Protein family), KOG/COG (Clusters of Orthologous Groups of proteins), Swiss-Prot (A manually annotated and reviewed protein sequence database), and KO (KEGG Ortholog database). After all pairwise comparisons between these three different samples, a large number of differentially expressed genes were revealed. The dramatic differences in global gene expression profiles were found between distinct life stages (nymphs and AF, nymphs and AM) and sex difference (AF and AM), with some of the significantly differentially expressed genes (DEGs) being related to metamorphosis, digestion, immune and sex difference. The different express of unigenes were validated through quantitative Real-Time PCR (qRT-PCR) for 16 randomly selected unigenes. In addition, 17,462 potential simple sequence repeat molecular markers were identified in these transcriptome resources. These comprehensive C. ciliata transcriptomic information can be utilized to promote the development of environmentally friendly methodologies to disrupt the processes of metamorphosis, digestion, immune and sex differences. PMID:27494615

  2. Characterization of Rous sarcoma virus-related sequences in the Japanese quail.

    Science.gov (United States)

    Chambers, J A; Cywinski, A; Chen, P J; Taylor, J M

    1986-08-01

    We detected sequences related to the avian retrovirus Rous sarcoma virus within the genome of the Japanese quail, a species previously considered to be free of endogenous avian leukosis virus elements. Using low-stringency conditions of hybridization, we screened a quail genomic library for clones containing retrovirus-related information. Of five clones so selected, one, lambda Q48, contained sequence information related to the gag, pol, and env genes of Rous sarcoma virus arranged in a contiguous fashion and spanning a distance of approximately 5.8 kilobases. This organization is consistent with the presence of an endogenous retroviral element within the Japanese quail genome. Use of this element as a high-stringency probe on Southern blots of genomic digests of several quail DNA demonstrated hybridization to a series of high-molecular-weight bands. By slot hybridization to quail DNA with a cloned probe, it was deduced that there were approximately 300 copies per diploid cell. In addition, the quail element also hybridized at low stringency to the DNA of the White Leghorn chicken and at high stringency to the DNAs of several species of jungle fowl and both true and ruffed pheasants. Limited nucleotide sequencing analysis of lambda Q48 revealed homologies of 65, 52, and 46% compared with the sequence of Rous sarcoma virus strain Prague C for the endonuclease domain of pol, the pol-env junction, and the 3'-terminal region of env, respectively. Comparisons at the amino acid level were also significant, thus confirming the retrovirus relatedness of the cloned quail element.

  3. A tapping device for recording and quantitative characterization of rhythmic/auditory sequences.

    Science.gov (United States)

    Piazza, Caterina; Cesareo, Ambra; Caccia, Martina; Reni, Gianluigi; Lorusso, Maria L

    2017-07-01

    The processing of auditory stimuli is essential for the correct perception of language and deficits in this ability are often related to the presence or development of language disorders. The motor imitation (e.g. tapping or beating) of rhythmic sequences can be a very sensitive correlate of deficits in auditory processing. Thus, the study of the tapping performance, with the investigation of both temporal and intensity information, might be very useful. The present work is aimed at the development and preliminary testing of a tapping device to be used for the imitation and/or the production of rhythmic sequences, allowing the recording of both tapping duration and intensity. The device is essentially made up of a Force Sensing Resistor and an Arduino UNO board. It was validated using different sampling frequencies (f s ) in a group of 10 young healthy adults investigating its efficacy in terms of touch and intensity detection by means of two testing procedures. Results demonstrated a good performance of the device when programmed with fs equal to 50 and 100Hz. Moreover, both temporal and intensity parameters were extracted, thus supporting the potential use of the device for the analysis of the imitation or production of rhythmic sequences. This work represents a first step for the development of a useful, low cost tool to support the diagnosis, training and rehabilitation of language disorders.

  4. De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing.

    Science.gov (United States)

    Ong, Wen Dee; Voo, Lok-Yung Christopher; Kumar, Vijay Subbiah

    2012-01-01

    Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the mechanism and processes underlying fruit ripening would enable scientists to enhance the improvement of quality traits such as, flavor, texture, appearance and fruit sweetness. Although, the pineapple is an important fruit, there is insufficient transcriptomic or genomic information that is available in public databases. Application of high throughput transcriptome sequencing to profile the pineapple fruit transcripts is therefore needed. To facilitate this, we have performed transcriptome sequencing of ripe yellow pineapple fruit flesh using Illumina technology. About 4.7 millions Illumina paired-end reads were generated and assembled using the Velvet de novo assembler. The assembly produced 28,728 unique transcripts with a mean length of approximately 200 bp. Sequence similarity search against non-redundant NCBI database identified a total of 16,932 unique transcripts (58.93%) with significant hits. Out of these, 15,507 unique transcripts were assigned to gene ontology terms. Functional annotation against Kyoto Encyclopedia of Genes and Genomes pathway database identified 13,598 unique transcripts (47.33%) which were mapped to 126 pathways. The assembly revealed many transcripts that were previously unknown. The unique transcripts derived from this work have rapidly increased of the number of the pineapple fruit mRNA transcripts as it is now available in public databases. This information can be further utilized in gene expression, genomics and other functional genomics studies in pineapple.

  5. Characterization of genic microsatellite markers derived from expressed sequence tags in Pacific abalone ( Haliotis discus hannai)

    Science.gov (United States)

    Li, Qi; Shu, Jing; Zhao, Cui; Liu, Shikai; Kong, Lingfeng; Zheng, Xiaodong

    2010-01-01

    Simple sequence repeat (SSR) markers were developed from the expressed sequence tags (ESTs) of Pacific abalone ( Haliotis discus hannai). Repeat motifs were found in 4.95% of the ESTs at a frequency of one repeat every 10.04 kb of EST sequences, after redundancy elimination. Seventeen polymorphic EST-SSRs were developed. The number of alleles per locus varied from 2-17, with an average of 6.8 alleles per locus. The expected and observed heterozygosities ranged from 0.159 to 0.928 and from 0.132 to 0.922, respectively. Twelve of the 17 loci (70.6%) were successfully amplified in H. diversicolor. Seventeen loci segregated in three families, with three showing the presence of null alleles (17.6%). The adequate level of variability and low frequency of null alleles observed in H. discus hannai, together with the high rate of transportability across Haliotis species, make this set of EST-SSR markers an important tool for comparative mapping, marker-assisted selection, and evolutionary studies, not only in the Pacific abalone, but also in related species.

  6. Reliable scar scoring system to assess photographs of burn patients.

    Science.gov (United States)

    Mecott, Gabriel A; Finnerty, Celeste C; Herndon, David N; Al-Mousawi, Ahmed M; Branski, Ludwik K; Hegde, Sachin; Kraft, Robert; Williams, Felicia N; Maldonado, Susana A; Rivero, Haidy G; Rodriguez-Escobar, Noe; Jeschke, Marc G

    2015-12-01

    Several scar-scoring scales exist to clinically monitor burn scar development and maturation. Although scoring scars through direct clinical examination is ideal, scars must sometimes be scored from photographs. No scar scale currently exists for the latter purpose. We modified a previously described scar scale (Yeong et al., J Burn Care Rehabil 1997) and tested the reliability of this new scale in assessing burn scars from photographs. The new scale consisted of three parameters as follows: scar height, surface appearance, and color mismatch. Each parameter was assigned a score of 1 (best) to 4 (worst), generating a total score of 3-12. Five physicians with burns training scored 120 representative photographs using the original and modified scales. Reliability was analyzed using coefficient of agreement, Cronbach alpha, intraclass correlation coefficient, variance, and coefficient of variance. Analysis of variance was performed using the Kruskal-Wallis test. Color mismatch and scar height scores were validated by analyzing actual height and color differences. The intraclass correlation coefficient, the coefficient of agreement, and Cronbach alpha were higher for the modified scale than those of the original scale. The original scale produced more variance than that in the modified scale. Subanalysis demonstrated that, for all categories, the modified scale had greater correlation and reliability than the original scale. The correlation between color mismatch scores and actual color differences was 0.84 and between scar height scores and actual height was 0.81. The modified scar scale is a simple, reliable, and useful scale for evaluating photographs of burn patients. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

    Science.gov (United States)

    Fitzpatrick, Margaret A.; Hauser, Alan R.

    2015-01-01

    Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts. PMID:26699703

  8. Characterization and sequencing of the active site of 1-aminocyclopropane-1-carboxylate synthase

    International Nuclear Information System (INIS)

    Yip, Wing-Kin; Dong, Jian-Guo; Yang, S.F.; Kenny, J.W.; Thompson, G.A.

    1990-01-01

    The pyridoxal phosphate (PLP)-dependent 1-aminocyclopropane-1-carboxylic acid (ACC) synthase the key enzyme in ethylene biosynthesis, is inactivated by its substrate S-adenosylmethionine (AdoMet). Apple ACC synthase was purified with an immunoaffinity gel, and its active site was probed with NaB 3 H 4 or Ado[ 14 C]Met. Peptide sequencing of both 3 H- and 14 C-labeled peptides revealed a common dodecapeptide of Ser-Leu-Ser-Xaa-Asp-Leu-Gly-Leu-Pro-Gly-Phe-Arg, where Xaa was the modified, radioactive residue in each case. Acid hydrolysis of the 3 H-labeled enzyme released radioactive N-pyridoxyllysine, indicating that the active-site peptide contained lysine at position 4. Mass spectrometry of the 14 C-labeled peptide indicated a protonated molecular ion at m/z 1390.6, from which the mass of Xaa was calculated to be 229, a number that is equivalent to the mass of a lysine residue alkylated by the 2-aminobutyrate portion of AdoMet, as we previously proposed. These results indicate that the same active-site lysine binds the PLP and convalently links to the 2-aminobutyrate portion of AdoMet during inactivation. The active site of tomato ACC synthase was probed in the same manner with Ado [ 14 C]Met. Sequencing of the tomato active-site peptide revealed two highly conserved dodecapeptides; the minor peptide possessed a sequence identical to that of the apple enzyme, whereas the major peptide differed from the minor peptide in that methionine replaced leucine at position 6

  9. External charring and fire scarring in three western conifers

    Science.gov (United States)

    E. K. Sutherland; Josh Farella; David K Wright; Ian Hyp; K. T. Smith; Donald A. Falk; Estelle Arbellay; Markus Stoffel

    2013-01-01

    Fires that injure but do not kill trees cause scars used as proxies for the reconstruction of wildfire history. Understanding about these wildfires - and their relationship to vegetation dynamics and climate - has profoundly affected wildfire and land management policy globally. To better understand scarring in the context of wildfire behavior, landscape and biological...

  10. Macroanatomy of compartmentalization in fire scars of three western conifers

    Science.gov (United States)

    Kevin T. Smith; Elaine Sutherland; Estelle Arbellay; Markus Stoffel; Donald. Falk

    2013-01-01

    Fire scars are visible evidence of compartmentalization and closure processes that contribute to tree survival after fire injury. Preliminary observations of dissected fire scars from trees injured within the last decade showed centripetal development of wound-initiated discoloration (WID) through 2-3 decades of former sapwood in Larix occidentalis and Pseudotsuga...

  11. Fractional CO2 laser resurfacing for atrophic acne scars

    DEFF Research Database (Denmark)

    Hedelund, Lene; Haak, Christina Skovbølling; Togsverd-Bo, Katrine

    2012-01-01

    The treatment of acne scars with fractional CO(2) lasers is gaining increasing impact, but has so far not been compared side-by-side to untreated control skin.......The treatment of acne scars with fractional CO(2) lasers is gaining increasing impact, but has so far not been compared side-by-side to untreated control skin....

  12. Relationship between tuberculous scar and carcinomas of the lung

    International Nuclear Information System (INIS)

    Richardson, S.; Hirsch, A.; Bickel, M.

    1987-01-01

    Results of a transversal case-control study are reported which shows that there is a statistically significant association between tuberculous scars and carcinoma of the lung. Accordingly the possibility of malignancy has to be kept in mind when radiological or scintigraphic scanning reveal the presence of lung scars. (orig.)

  13. Trachomatous Scar Ranking: A Novel Outcome for Trachoma Studies.

    Science.gov (United States)

    Baldwin, Angela; Ryner, Alexander M; Tadesse, Zerihun; Shiferaw, Ayalew; Callahan, Kelly; Fry, Dionna M; Zhou, Zhaoxia; Lietman, Thomas M; Keenan, Jeremy D

    2017-06-01

    AbstractWe evaluated a new trachoma scarring ranking system with potential use in clinical research. The upper right tarsal conjunctivas of 427 individuals from Ethiopian villages with hyperendemic trachoma were photographed. An expert grader first assigned a scar grade to each photograph using the 1981 World Health Organization (WHO) grading system. Then, all photographs were ranked from least (rank = 1) to most scarring (rank = 427). Photographic grading found 79 (18.5%) conjunctivae without scarring (C0), 191 (44.7%) with minimal scarring (C1), 105 (24.6%) with moderate scarring (C2), and 52 (12.2%) with severe scarring (C3). The ranking method demonstrated good internal validity, exhibiting a monotonic increase in the median rank across the levels of the 1981 WHO grading system. Intrarater repeatability was better for the ranking method (intraclass correlation coefficient = 0.84, 95% CI = 0.74-0.94). Exhibiting better internal and external validity, this ranking method may be useful for evaluating the difference in scarring between groups of individuals.

  14. Intralesional Cryotherapy for Treatment of Keloid Scars: A Prospective Study

    NARCIS (Netherlands)

    van Leeuwen, M.C.E.; van der Wal, M.B.A.; Bulstra, A.E.J.; Galindo Garre, F.; Molier, J.; van Zuijlen, P.P.M.; van Leeuwen, P.A.M.; Niessen, F.B.

    2015-01-01

    Background: Intralesional cryotherapy is a novel treatment for keloid scars in which the scar is frozen from inside. Published results are promising, but the treatment has only been tested in a Caucasian patient population. Therefore, the authors evaluated intralesional cryotherapy in a patient

  15. Patient reported facial scar assessment: directions for the professional

    NARCIS (Netherlands)

    Hoogewerf, C.J.; van Baar, M.E.; Middelkoop, E.; van Loey, N.E.

    2014-01-01

    Background The face is central to our identity and provides our most expressive means of communication. Currently, the role of facial scarring in relation to self-esteem is unclear and the value of self-reported scar assessment is insufficiently understood. The aim of this study was twofold: (1) to

  16. Patient reported facial scar assessment : directions for the professional

    NARCIS (Netherlands)

    Hoogewerf, Cornelis J; van Baar, Margriet E; Middelkoop, Esther; Van Loey, N.E.E.

    BACKGROUND: The face is central to our identity and provides our most expressive means of communication. Currently, the role of facial scarring in relation to self-esteem is unclear and the value of self-reported scar assessment is insufficiently understood. The aim of this study was twofold: (1) to

  17. Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles.

    Science.gov (United States)

    Guo, Shaogui; Liu, Jingan; Zheng, Yi; Huang, Mingyun; Zhang, Haiying; Gong, Guoyi; He, Hongju; Ren, Yi; Zhong, Silin; Fei, Zhangjun; Xu, Yong

    2011-09-21

    Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and molecular basis of these changes and significantly expand the watermelon transcript catalog, we have selected four critical stages of watermelon fruit development and used Roche/454 next-generation sequencing technology to generate a large expressed sequence tag (EST) dataset and a comprehensive transcriptome profile for watermelon fruit flesh tissues. We performed half Roche/454 GS-FLX run for each of the four watermelon fruit developmental stages (immature white, white-pink flesh, red flesh and over-ripe) and obtained 577,023 high quality ESTs with an average length of 302.8 bp. De novo assembly of these ESTs together with 11,786 watermelon ESTs collected from GenBank produced 75,068 unigenes with a total length of approximately 31.8 Mb. Overall 54.9% of the unigenes showed significant similarities to known sequences in GenBank non-redundant (nr) protein database and around two-thirds of them matched proteins of cucumber, the most closely-related species with a sequenced genome. The unigenes were further assigned with gene ontology (GO) terms and mapped to biochemical pathways. More than 5,000 SSRs were identified from the EST collection. Furthermore we carried out digital gene expression analysis of these ESTs and identified 3,023 genes that were differentially expressed during watermelon fruit development and ripening, which provided novel insights into watermelon fruit biology and a comprehensive resource of candidate genes for future functional analysis. We then generated profiles of several interesting metabolites that are important to fruit quality including pigmentation and sweetness. Integrative analysis of metabolite and digital gene expression

  18. Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis.

    Science.gov (United States)

    Schweitzer, Mary H; Zheng, Wenxia; Organ, Chris L; Avci, Recep; Suo, Zhiyong; Freimark, Lisa M; Lebleu, Valerie S; Duncan, Michael B; Vander Heiden, Matthew G; Neveu, John M; Lane, William S; Cottrell, John S; Horner, John R; Cantley, Lewis C; Kalluri, Raghu; Asara, John M

    2009-05-01

    Molecular preservation in non-avian dinosaurs is controversial. We present multiple lines of evidence that endogenous proteinaceous material is preserved in bone fragments and soft tissues from an 80-million-year-old Campanian hadrosaur, Brachylophosaurus canadensis [Museum of the Rockies (MOR) 2598]. Microstructural and immunological data are consistent with preservation of multiple bone matrix and vessel proteins, and phylogenetic analyses of Brachylophosaurus collagen sequenced by mass spectrometry robustly support the bird-dinosaur clade, consistent with an endogenous source for these collagen peptides. These data complement earlier results from Tyrannosaurus rex (MOR 1125) and confirm that molecular preservation in Cretaceous dinosaurs is not a unique event.

  19. Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

    OpenAIRE

    Zhu, Ke-Cheng; Liang, Yin-Yin; Wu, Na; Guo, Hua-Yang; Zhang, Nan; Jiang, Shi-Gui; Zhang, Dian-Chang

    2017-01-01

    To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PC...

  20. Characterization of the promoter and upstream activating sequence from the Pseudomonas alcaligenes lipase gene

    NARCIS (Netherlands)

    Cox, M; Gerritse, G; Dankmeyer, L; Quax, W.J.

    2001-01-01

    Pseudomonas alcaligenes secretes a lipase with a high pH optimum, which has interesting properties for application in detergents. The expression of the lipase is strongly dependent on the presence of lipids in the growth medium such as soybean oil. The promoter of the gene was characterized and

  1. Purification and Characterization of Enzymes from Yeast: An Extended Undergraduate Laboratory Sequence for Large Classes

    Science.gov (United States)

    Johanson, Kelly E.; Watt, Terry J.; McIntyre, Neil R.; Thompson, Marleesa

    2013-01-01

    Providing a project-based experience in an undergraduate biochemistry laboratory class can be complex with large class sizes and limited resources. We have designed a 6-week curriculum during which students purify and characterize the enzymes invertase and phosphatase from bakers yeast. Purification is performed in two stages via ethanol…

  2. Genomic Characterization for Parasitic Weeds of the Genus Striga by Sample Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Matt C. Estep

    2012-03-01

    Full Text Available Generation of ∼2200 Sanger sequence reads or ∼10,000 454 reads for seven Lour. DNA samples (five species allowed identification of the highly repetitive DNA content in these genomes. The 14 most abundant repeats in these species were identified and partially assembled. Annotation indicated that they represent nine long terminal repeat (LTR retrotransposon families, three tandem satellite repeats, one long interspersed element (LINE retroelement, and one DNA transposon. All of these repeats are most closely related to repetitive elements in other closely related plants and are not products of horizontal transfer from their host species. These repeats were differentially abundant in each species, with the LTR retrotransposons and satellite repeats most responsible for variation in genome size. Each species had some repetitive elements that were more abundant and some less abundant than the other species examined, indicating that no single element or any unilateral growth or decrease trend in genome behavior was responsible for variation in genome size and composition. Genome sizes were determined by flow sorting, and the values of 615 Mb [ (L. Kuntze], 1330 Mb [ (Willd. Vatke], 1425 Mb [ (Delile Benth.] and 2460 Mb ( Benth. suggest a ploidy series, a prediction supported by repetitive DNA sequence analysis. Phylogenetic analysis using six chloroplast loci indicated the ancestral relationships of the five most agriculturally important species, with the unexpected result that the one parasite of dicotyledonous plants ( was found to be more closely related to some of the grass parasites than many of the grass parasites are to each other.

  3. High levels of diversity characterize mandrill (Mandrillus sphinx) Mhc-DRB sequences.

    Science.gov (United States)

    Abbott, Kristin M; Wickings, E Jean; Knapp, Leslie A

    2006-08-01

    The major histocompatibility complex (MHC) is highly polymorphic in most primate species studied thus far. The rhesus macaque (Macaca mulatta) has been studied extensively and the Mhc-DRB region demonstrates variability similar to humans. The extent of MHC diversity is relatively unknown for other Old World monkeys (OWM), especially among genera other than Macaca. A molecular survey of the Mhc-DRB region in mandrills (Mandrillus sphinx) revealed extensive variability, suggesting that other OWMs may also possess high levels of Mhc-DRB polymorphism. In the present study, 33 Mhc-DRB loci were identified from only 13 animals. Eleven were wild-born and presumed to be unrelated and two were captive-born twins. Two to seven different sequences were identified for each individual, suggesting that some mandrills may have as many as four Mhc-DRB loci on a single haplotype. From these sequences, representatives of at least six Mhc-DRB loci or lineages were identified. As observed in other primates, some new lineages may have arisen through the process of gene conversion. These findings indicate that mandrills have Mhc-DRB diversity not unlike rhesus macaques and humans.

  4. Characterization of Sri Lanka rabies virus isolates using nucleotide sequence analysis of nucleoprotein gene.

    Science.gov (United States)

    Arai, Y T; Takahashi, H; Kameoka, Y; Shiino, T; Wimalaratne, O; Lodmell, D L

    2001-01-01

    Thirty-four suspected rabid brain samples from 2 humans, 24 dogs, 4 cats, 2 mongooses, I jackal and I water buffalo were collected in 1995-1996 in Sri Lanka. Total RNA was extracted directly from brain suspensions and examined using a one-step reverse transcription-polymerase chain reaction (RT-PCR) for the rabies virus nucleoprotein (N) gene. Twenty-eight samples were found positive for the virus N gene by RT-PCR and also for the virus antigens by fluorescent antibody (FA) test. Rabies virus isolates obtained from different animal species in different regions of Sri Lanka were genetically homogenous. Sequences of 203 nucleotides (nt)-long RT-PCR products obtained from 16 of 27 samples were found identical. Sequences of 1350 nt of N genes of 14 RT-PCR products were determined. The Sri Lanka isolates under study formed a specific cluster that included also an earlier isolate from India but did not include the known isolates from China, Thailand, Malaysia, Israel, Iran, Oman, Saudi Arabia, Russia, Nepal, Philippines, Japan and from several other countries. These results suggest that one type of rabies virus is circulating among human, dog, cat, mongoose, jackal and water buffalo living near Colombo City and in other five remote regions in Sri Lanka.

  5. Characterization of unknown genetic modifications using high throughput sequencing and computational subtraction

    Directory of Open Access Journals (Sweden)

    Butenko Melinka A

    2009-10-01

    Full Text Available Abstract Background When generating a genetically modified organism (GMO, the primary goal is to give a target organism one or several novel traits by using biotechnology techniques. A GMO will differ from its parental strain in that its pool of transcripts will be altered. Currently, there are no methods that are reliably able to determine if an organism has been genetically altered if the nature of the modification is unknown. Results We show that the concept of computational subtraction can be used to identify transgenic cDNA sequences from genetically modified plants. Our datasets include 454-type sequences from a transgenic line of Arabidopsis thaliana and published EST datasets from commercially relevant species (rice and papaya. Conclusion We believe that computational subtraction represents a powerful new strategy for determining if an organism has been genetically modified as well as to define the nature of the modification. Fewer assumptions have to be made compared to methods currently in use and this is an advantage particularly when working with unknown GMOs.

  6. Transcriptomic characterization of soybean (Glycine max) roots in response to rhizobium infection by RNA sequencing

    International Nuclear Information System (INIS)

    He, Q.; Li, Z.; Wang, S.; Huang, S.; Yang, H.

    2018-01-01

    Legumes interacting with rhizobium to convert N2 into ammonia for plant use has attracted worldwide interest. However, the plant basal nitrogen fixation mechanisms induced in response to Rhizobium, giving differential gene expression of plants, have not yet been fully realized. The differential expressed genes of soybean between inoculated and mock-inoculated were analyzed by a RNA-Seq. The results of the sequencing were aligned against the Williams 82 genome sequence, which contain 55787 transcripts; 280 and 316 transcripts were found to be up- and down-regulated, respectively, for inoculated and mock-inoculated soybean roots at stage V1. Gene ontology (GO) analyses detected 104, 182 and 178 genes associated with the cell component category, molecular function category and biological process category, respectively. Pathway analysis revealed that 98 differentially expressed genes (115 transcripts) were involved in 169 biological pathways. We selected 19 differentially expressed genes and analyzed their expressions in mock-inoculated, inoculated USDA110 and CCBAU45436 using qRT-PCR. The results were in accordance with those obtained from rhizobia infected RNA-Seq data. These showed that the results of RNA-Seq had reliability and universality. Additionally, this study showed some novel genes associated with the nitrogen fixation process in comparison to previously identified QTLs. (author)

  7. Characterizing Intermediate-Mass, Pre-Main-Sequence Stars via X-Ray Emision

    Science.gov (United States)

    Haze Nunez, Evan; Povich, Matthew Samuel; Binder, Breanna Arlene; Broos, Patrick; Townsley, Leisa K.

    2018-01-01

    The X-ray emission from intermediate-mass, pre-main-sequence stars (IMPS) can provide useful constraints on the ages of very young (${getting power from the gravitational contraction of the star. Main-sequence late-B and A-type stars are not expected to be strong X-ray emitters, because they lack the both strong winds of more massive stars and the magneto-coronal activity of lower-mass stars. There is, however, mounting evidence that IMPS are powerful intrinsic x-ray emitters during their convection-dominated early evolution, before the development and rapid growth of a radiation zone. We present our prime candidates for intrinsic, coronal X-ray emission from IMPS identified in the Chandra Carina Complex Project. The Carina massive star-forming complex is of special interest due to the wide variation of star formation stages within the region. Candidate IMPS were identified using infrared spectral energy distribution (SED) models. X-ray properties, including thermal plasma temperatures and absorption-corrected fluxes, were derived from XSPEC fits performed using absorption ($N_{H}$) constrained by the extinction values returned by the infrared SED fits. We find that IMPS have systematically higher X-ray luminosities compared to their lower-mass cousins, the TTauri stars.This work is supported by the National Science Foundation under grant CAREER-1454334 and by NASA through Chandra Award 18200040.

  8. Sequence and Genetic Characterization of etrA, an fnr Analog that Regulates Anaerobic Respiration in Shewanella putrefaciens MR-1

    Science.gov (United States)

    Saffarini, Daad A.; Nelson, Kenneth H.

    1993-01-01

    An electron transport regulatory gene, etrA, has been isolated and characterized from the obligate respiratory bacterium Shewanella putrefaciens MR-l. The deduced amino acid sequence of etrA (EtrA) shows a high degree of identity to both the Fnr of Escherichia coli (73.6%) and the analogous protein (ANR) of Pseudomonas aeruginosa (50.8%). The four active cysteine residues of Fnr are conserved in EtrA, and the amino acid sequence of the DNA-binding domains of the two proteins are identical. Further, S.putrefaciens etrA is able to complement an fnr mutant of E.coli. In contrast to fnr, there is no recognizable Fnr box upstream of the etrA sequence. Gene replacement etr.A mutants of MR-1 were deficient in growth on nitrite, thiosulfate, sulfite, trimethylamine-N-oxide, dimethyl sulfoxide, Fe(III), and fumarate, suggesting that EtrA is involved in the regulation of the corresponding reductase genes. However, the mutants were all positive for reduction of and growth on nitrate and Mn(IV), indicating that EtrA is not involved in the regulation of these two systems. Southern blots of S.putrefaciens DNA with use of etrA as a probe revealed the expected etrA bands and a second set of hybridization signals whose genetic and functional properties remain to be determined.

  9. Sedimentology, Sequence Stratigraphy and Reservoir Characterization of Samana Suk Formation Exposed in Namal Gorge Section, Salt Range, Mianwali, Punjab, Pakistan

    Directory of Open Access Journals (Sweden)

    Muhammad Hayat

    2016-06-01

    Full Text Available Samana Suk Formation of Bathonian-callovain age, exposed in Nammal Gorge Salt Range, has been studied for microfacies and sequence stratigraphic investigation. The formation is mainly composed of limestone, with minor beds of sandstone and marl. The limestone is grey, yellowish and purple in color. Limestone is fine grained, thin to medium bedded and inter-bedded with algal laminations. The sandstone is light yellowish brown, brick red in color, calcareous and quartzose. Within Samana Suk Formation one 2ndorder sequence and two 3rdorder sequences have been identified. Their regional correlation through fine-tuned dating helped to develop basin fill model and to understand facies dynamics. A facie belt comprising a wide belt of carbonate facies characterized by Peloidal Packstone microfacies represents inner ramp setting and Pelletal/ Peloidal Wackstone, Mud-Wackstone and Mudstone microfacies represent the low energy lagoonal environment. The sandstone lithofacies represents high energy beach environment which indicates aggrading to pro-grading pattern. The porosity analysis has been done on different samples of limestone and sandstone. For the porosity analysis the Image J software is used. In limestone the porosity ranges up to 6% while in sandstone the porosity ranging up to 18%. From the field and porosity analysis it is concluded that Samana Suk Formation in study area is good reservoir.

  10. Semiclassical scar functions in phase space

    International Nuclear Information System (INIS)

    Rivas, Alejandro M F

    2007-01-01

    We develop a semiclassical approximation for the scar function in the Weyl-Wigner representation in the neighborhood of a classically unstable periodic orbit of chaotic two-dimensional systems. The prediction of hyperbolic fringes, asymptotic to the stable and unstable manifolds, is verified computationally for a (linear) cat map, after the theory is adapted to a discrete phase space appropriate to a quantized torus. Characteristic fringe patterns can be distinguished even for quasi-energies where the fixed point is not Bohr-quantized. Also the patterns are highly localized in the neighborhood of the periodic orbit and along its stable and unstable manifolds without any long distance patterns that appear for the case of the spectral Wigner function

  11. Breast Cancer from the Excisional Scar of a Benign Mass

    International Nuclear Information System (INIS)

    Kim, Min Jung; Kim, Eun Kyung; Lee, Ji Young; Youk, Ji Hyun; Park, Byeong Woo; Kim, Hae Ryoung; Oh, Ki Keun

    2007-01-01

    Burns and chronic inflammation are well-known circumstances in which malignant transformation may occur during wound healing. There are many reports of malignancies developing from a burn scar; however, there are only a few reports of malignancy arising from chronic inflammation or from the skin of a surgical scar following excision of a benign mass, in any part of the body. There are only twelve reported cases of breast cancer developing from a surgical scar, moreover, there have been no reports in the last 30 years. This case is a recent example of breast cancer developing in a surgical scar that showed subtle changes on sequential sonograms. The imaging findings of this case were subtle but the mass that had been shrinking developed an angular margin in one region. These findings, along with the penetrating vascularity revealed on Doppler, prompted us to proceed to a biopsy of the lesion. It was of critical importance to compare the size and the shape of the lesion with previous ultrasounds in order to exclude malignancy in any iatrogenically altered lesion. Based on this case, we conclude that whenever a subtle change is detected, at a surgical site, a biopsy should be performed. Breast cancer developing from a surgical scar is rare; this type of malignancy has been reported in only 12 cases to date. Herein, we report on a 52-year-old female who developed infiltrating ductal carcinoma in a surgical scar following excision of a benign mass. Two years previously, the patient underwent surgery and radiotherapy for invasive ductal carcinoma of the contralateral breast. The initial appearance of the scar was similar to fat necrosis; it was observed to be progressively shrinking on follow-up sonography. On the two year follow-up ultrasound, the appearance changed, an angular margin and vascularity at the periphery of the scar were noted. A biopsy and subsequent excision of the scar were performed; the diagnosis of infiltrating ductal carcinoma of the scar was

  12. Fibromodulin reduces scar size and increases scar tensile strength in normal and excessive-mechanical-loading porcine cutaneous wounds.

    Science.gov (United States)

    Jiang, Wenlu; Ting, Kang; Lee, Soonchul; Zara, Janette N; Song, Richard; Li, Chenshuang; Chen, Eric; Zhang, Xinli; Zhao, Zhihe; Soo, Chia; Zheng, Zhong

    2018-04-01

    Hypertrophic scarring is a major postoperative complication which leads to severe disfigurement and dysfunction in patients and usually requires multiple surgical revisions due to its high recurrence rates. Excessive-mechanical-loading across wounds is an important initiator of hypertrophic scarring formation. In this study, we demonstrate that intradermal administration of a single extracellular matrix (ECM) molecule-fibromodulin (FMOD) protein-can significantly reduce scar size, increase tensile strength, and improve dermal collagen architecture organization in the normal and even excessive-mechanical-loading red Duroc pig wound models. Since pig skin is recognized by the Food and Drug Administration as the closest animal equivalent to human skin, and because red Duroc pigs show scarring that closely resembles human proliferative scarring and hypertrophic scarring, FMOD-based technologies hold high translational potential and applicability to human patients suffering from scarring-especially hypertrophic scarring. © 2018 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  13. Oligo-Miocene reservoir sequence characterization and structuring in the Sisseb El Alem-Kalaa Kebira regions (Northeastern Tunisia)

    Science.gov (United States)

    Houatmia, Faten; Khomsi, Sami; Bédir, Mourad

    2015-11-01

    The Sisseb El Alem-Enfidha basin is located in the northeastern Tunisia, It is borded by Nadhour - Saouaf syncline to the north, Kairouan plain to the south, the Mediterranean Sea to the east and Tunisian Atlassic "dorsale" to the west. Oligocene and Miocene deltaic deposits present the main potential deep aquifers in this basin with high porosity (25%-30%). The interpretation of twenty seismic reflection profiles, calibrated by wire line logging data of twelve oil wells, hydraulic wells and geologic field sections highlighted the impact of tectonics on the structuring geometry of Oligo-Miocene sandstones reservoirs and their distribution in raised structures and subsurface depressions. Miocene seismostratigraphy analysis from Ain Ghrab Formation (Langhian) to the Segui Formation (Quaternary) showed five third-order seismic sequence deposits and nine extended lenticular sandy bodies reservoirs limited by toplap and downlap surfaces unconformities, Oligocene deposits presented also five third- order seismic sequences with five extended lenticular sandy bodies reservoirs. The Depth and the thickness maps of these sequence reservoir packages exhibited the structuring of this basin in sub-basins characterized by important lateral and vertical geometric and thichness variations. Petroleum wells wire line logging correlation with clay volume calculation showed an heterogeneous multilayer reservoirs of Oligocene and Miocene formed by the arrangement of fourteen sandstone bodies being able to be good reservoirs, separated by impermeable clay packages and affected by faults. Reservoirs levels correspond mainly to the lower system tract (LST) of sequences. Intensive fracturing by deep seated faults bounding the different sub-basins play a great role for water surface recharge and inter-layer circulations between affected reservoirs. The total pore volume of the Oligo-Miocene reservoir sandy bodies in the study area, is estimated to about 4 × 1012 m3 and equivalent to 4

  14. Identification and characterization of microRNAs from peanut (Arachis hypogaea L. by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Xiaoyuan Chi

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are noncoding RNAs of approximately 21 nt that regulate gene expression in plants post-transcriptionally by endonucleolytic cleavage or translational inhibition. miRNAs play essential roles in numerous developmental and physiological processes and many of them are conserved across species. Extensive studies of miRNAs have been done in a few model plants; however, less is known about the diversity of these regulatory RNAs in peanut (Arachis hypogaea L., one of the most important oilseed crops cultivated worldwide. RESULTS: A library of small RNA from peanut was constructed for deep sequencing. In addition to 126 known miRNAs from 33 families, 25 novel peanut miRNAs were identified. The miRNA* sequences of four novel miRNAs were discovered, providing additional evidence for the existence of miRNAs. Twenty of the novel miRNAs were considered to be species-specific because no homolog has been found for other plant species. qRT-PCR was used to analyze the expression of seven miRNAs in different tissues and in seed at different developmental stages and some showed tissue- and/or growth stage-specific expression. Furthermore, potential targets of these putative miRNAs were predicted on the basis of the sequence homology search. CONCLUSIONS: We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library. This study of the identification and characterization of miRNAs in peanut can initiate further study on peanut miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in peanut.

  15. Sequencing and Characterization of Divergent Marbling Levels in the Beef Cattle ( Muscle Transcriptome

    Directory of Open Access Journals (Sweden)

    Dong Chen

    2015-02-01

    Full Text Available Marbling is an important trait regarding the quality of beef. Analysis of beef cattle transcriptome and its expression profile data are essential to extend the genetic information resources and would support further studies on beef cattle. RNA sequencing was performed in beef cattle using the Illumina High-Seq2000 platform. Approximately 251.58 million clean reads were generated from a high marbling (H group and low marbling (L group. Approximately 80.12% of the 19,994 bovine genes (protein coding were detected in all samples, and 749 genes exhibited differential expression between the H and L groups based on fold change (>1.5-fold, p<0.05. Multiple gene ontology terms and biological pathways were found significantly enriched among the differentially expressed genes. The transcriptome data will facilitate future functional studies on marbling formation in beef cattle and may be applied to improve breeding programs for cattle and closely related mammals.

  16. Vocal fold scars : current concepts and future directions. Consensus report of the phonosurgery committee of the European laryngological society

    NARCIS (Netherlands)

    Friedrich, G.; Dikkers, F. G.; Arens, C.; Remacle, M.; Hess, M.; Giovanni, A.; Duflo, S.; Hantzakos, A.; Bachy, V.; Gugatschka, M.

    Scarring of the vocal folds leads to a deterioration of the highly complex micro-structure with consecutively impaired vibratory pattern and glottic insufficiency. The resulting dysphonia is predominantly characterized by a reduced vocal capacity. Despite the considerable progress in understanding

  17. Murine mammary tumor virus pol-related sequences in human DNA: characterization and sequence comparison with the complete murine mammary tumor virus pol gene

    International Nuclear Information System (INIS)

    Deen, K.C.; Sweet, R.W.

    1986-01-01

    Sequences in the human genome with homology to the murine mammary tumor virus (MMTV) pol gene were isolated from a human phage library. Ten clones with extensive pol homology were shown to define five separate loci. These loci share common sequences immediately adjacent to the pol-like segments and, in addition, contain a related repeat element which bounds this region. This organization is suggestive of a proviral structure. The authors estimate that the human genome contains 30 to 40 copies of these pol-related sequences. The pol region of one of the cloned segments (HM16) and the complete MMTV pol gene were sequenced and compared. The nucleotide homology between these pol sequences is 52% and is concentrated in the terminal regions. The MMTV pol gene contains a single long open reading frame encoding 899 amino acids and is demarcated from the partially overlapping putative gag gene by termination codons and a shift in translational reading frame. The pol sequence of HM16 is multiply terminated but does contain open reading frames which encode 370, 105, and 112 amino acids residues in separate reading frames. The authors deduced a composite pol protein sequence for HM16 by aligning it to the MMTV pol gene and then compared these sequences with other retroviral pol protein sequences. Conserved sequences occur in both the amino and carboxyl regions which lie within the polymerase and endonuclease domains of pol, respectively

  18. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.

    Science.gov (United States)

    Kröber, Magdalena; Bekel, Thomas; Diaz, Naryttza N; Goesmann, Alexander; Jaenicke, Sebastian; Krause, Lutz; Miller, Dimitri; Runte, Kai J; Viehöver, Prisca; Pühler, Alfred; Schlüter, Andreas

    2009-06-01

    The phylogenetic structure of the microbial community residing in a fermentation sample from a production-scale biogas plant fed with maize silage, green rye and liquid manure was analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Sequencing of 109 clones from a bacterial and an archaeal 16S-rDNA amplicon library revealed that the obtained nucleotide sequences are similar but not identical to 16S-rDNA database sequences derived from different anaerobic environments including digestors and bioreactors. Most of the bacterial 16S-rDNA sequences could be assigned to the phylum Firmicutes with the most abundant class Clostridia and to the class Bacteroidetes, whereas most archaeal 16S-rDNA sequences cluster close to the methanogen Methanoculleus bourgensis. Further sequences of the archaeal library most probably represent so far non-characterised species within the genus Methanoculleus. A similar result derived from phylogenetic analysis of mcrA clone sequences. The mcrA gene product encodes the alpha-subunit of methyl-coenzyme-M reductase involved in the final step of methanogenesis. BLASTn analysis applying stringent settings resulted in assignment of 16S-rDNA metagenome sequence reads to 62 16S-rDNA amplicon sequences thus enabling frequency of abundance estimations for 16S-rDNA clone library sequences. Ribosomal Database Project (RDP) Classifier processing of metagenome 16S-rDNA reads revealed abundance of the phyla Firmicutes, Bacteroidetes and Euryarchaeota and the orders Clostridiales, Bacteroidales and Methanomicrobiales. Moreover, a large fraction of 16S-rDNA metagenome reads could not be assigned to lower taxonomic ranks, demonstrating that numerous microorganisms in the analysed fermentation sample of the biogas plant are still unclassified or unknown.

  19. Characterization of microflora in Latin-style cheeses by next-generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Lusk Tina S

    2012-11-01

    Full Text Available Abstract Background Cheese contamination can occur at numerous stages in the manufacturing process including the use of improperly pasteurized or raw milk. Of concern is the potential contamination by Listeria monocytogenes and other pathogenic bacteria that find the high moisture levels and moderate pH of popular Latin-style cheeses like queso fresco a hospitable environment. In the investigation of a foodborne outbreak, samples typically undergo enrichment in broth for 24 hours followed by selective agar plating to isolate bacterial colonies for confirmatory testing. The broth enrichment step may also enable background microflora to proliferate, which can confound subsequent analysis if not inhibited by effective broth or agar additives. We used 16S rRNA gene sequencing to provide a preliminary survey of bacterial species associated with three brands of Latin-style cheeses after 24-hour broth enrichment. Results Brand A showed a greater diversity than the other two cheese brands (Brands B and C at nearly every taxonomic level except phylum. Brand B showed the least diversity and was dominated by a single bacterial taxon, Exiguobacterium, not previously reported in cheese. This genus was also found in Brand C, although Lactococcus was prominent, an expected finding since this bacteria belongs to the group of lactic acid bacteria (LAB commonly found in fermented foods. Conclusions The contrasting diversity observed in Latin-style cheese was surprising, demonstrating that despite similarity of cheese type, raw materials and cheese making conditions appear to play a critical role in the microflora composition of the final product. The high bacterial diversity associated with Brand A suggests it may have been prepared with raw materials of high bacterial diversity or influenced by the ecology of the processing environment. Additionally, the presence of Exiguobacterium in high proportions (96% in Brand B and, to a lesser extent, Brand C (46%, may

  20. Cloning, sequence analysis, expression of Cyathus bulleri laccase in Pichia pastoris and characterization of recombinant laccase

    Directory of Open Access Journals (Sweden)

    Garg Neha

    2012-10-01

    Full Text Available Abstract Background Laccases are blue multi-copper oxidases and catalyze the oxidation of phenolic and non-phenolic compounds. There is considerable interest in using these enzymes for dye degradation as well as for synthesis of aromatic compounds. Laccases are produced at relatively low levels and, sometimes, as isozymes in the native fungi. The investigation of properties of individual enzymes therefore becomes difficult. The goal of this study was to over-produce a previously reported laccase from Cyathus bulleri using the well-established expression system of Pichia pastoris and examine and compare the properties of the recombinant enzyme with that of the native laccase. Results In this study, complete cDNA encoding laccase (Lac from white rot fungus Cyathus bulleri was amplified by RACE-PCR, cloned and expressed in the culture supernatant of Pichia pastoris under the control of the alcohol oxidase (AOX1 promoter. The coding region consisted of 1,542 bp and encodes a protein of 513 amino acids with a signal peptide of 16 amino acids. The deduced amino acid sequence of the matured protein displayed high homology with laccases from Trametes versicolor and Coprinus cinereus. The sequence analysis indicated the presence of Glu 460 and Ser 113 and LEL tripeptide at the position known to influence redox potential of laccases placing this enzyme as a high redox enzyme. Addition of copper sulfate to the production medium enhanced the level of laccase by about 12-fold to a final activity of 7200 U L-1. The recombinant laccase (rLac was purified by ~4-fold to a specific activity of ~85 U mg-1 protein. A detailed study of thermostability, chloride and solvent tolerance of the rLac indicated improvement in the first two properties when compared to the native laccase (nLac. Altered glycosylation pattern, identified by peptide mass finger printing, was proposed to contribute to altered properties of the rLac. Conclusion Laccase of C. bulleri was

  1. Cloning, sequence analysis, expression of Cyathus bulleri laccase in Pichia pastoris and characterization of recombinant laccase.

    Science.gov (United States)

    Garg, Neha; Bieler, Nora; Kenzom, Tenzin; Chhabra, Meenu; Ansorge-Schumacher, Marion; Mishra, Saroj

    2012-10-23

    Laccases are blue multi-copper oxidases and catalyze the oxidation of phenolic and non-phenolic compounds. There is considerable interest in using these enzymes for dye degradation as well as for synthesis of aromatic compounds. Laccases are produced at relatively low levels and, sometimes, as isozymes in the native fungi. The investigation of properties of individual enzymes therefore becomes difficult. The goal of this study was to over-produce a previously reported laccase from Cyathus bulleri using the well-established expression system of Pichia pastoris and examine and compare the properties of the recombinant enzyme with that of the native laccase. In this study, complete cDNA encoding laccase (Lac) from white rot fungus Cyathus bulleri was amplified by RACE-PCR, cloned and expressed in the culture supernatant of Pichia pastoris under the control of the alcohol oxidase (AOX)1 promoter. The coding region consisted of 1,542 bp and encodes a protein of 513 amino acids with a signal peptide of 16 amino acids. The deduced amino acid sequence of the matured protein displayed high homology with laccases from Trametes versicolor and Coprinus cinereus. The sequence analysis indicated the presence of Glu 460 and Ser 113 and LEL tripeptide at the position known to influence redox potential of laccases placing this enzyme as a high redox enzyme. Addition of copper sulfate to the production medium enhanced the level of laccase by about 12-fold to a final activity of 7200 U L-1. The recombinant laccase (rLac) was purified by ~4-fold to a specific activity of ~85 U mg(-1) protein. A detailed study of thermostability, chloride and solvent tolerance of the rLac indicated improvement in the first two properties when compared to the native laccase (nLac). Altered glycosylation pattern, identified by peptide mass finger printing, was proposed to contribute to altered properties of the rLac. Laccase of C. bulleri was successfully produced extra-cellularly to a high level of 7200

  2. Deep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence.

    Science.gov (United States)

    Clark, Shaunna L; McClay, Joseph L; Adkins, Daniel E; Kumar, Gaurav; Aberg, Karolina A; Nerella, Srilaxmi; Xie, Linying; Collins, Ann L; Crowley, James J; Quackenbush, Corey R; Hilliard, Christopher E; Shabalin, Andrey A; Vrieze, Scott I; Peterson, Roseann E; Copeland, William E; Silberg, Judy L; McGue, Matt; Maes, Hermine; Iacono, William G; Sullivan, Patrick F; Costello, Elizabeth J; van den Oord, Edwin J

    2017-04-01

    Previous genomewide association studies (GWASs) have identified a number of putative risk loci for alcohol dependence (AD). However, only a few loci have replicated and these replicated variants only explain a small proportion of AD risk. Using an innovative approach, the goal of this study was to generate hypotheses about potentially causal variants for AD that can be explored further through functional studies. We employed targeted capture of 71 candidate loci and flanking regions followed by next-generation deep sequencing (mean coverage 78X) in 806 European Americans. Regions included in our targeted capture library were genes identified through published GWAS of alcohol, all human alcohol and aldehyde dehydrogenases, reward system genes including dopaminergic and opioid receptors, prioritized candidate genes based on previous associations, and genes involved in the absorption, distribution, metabolism, and excretion of drugs. We performed single-locus tests to determine if any single variant was associated with AD symptom count. Sets of variants that overlapped with biologically meaningful annotations were tested for association in aggregate. No single, common variant was significantly associated with AD in our study. We did, however, find evidence for association with several variant sets. Two variant sets were significant at the q-value <0.10 level: a genic enhancer for ADHFE1 (p = 1.47 × 10 -5 ; q = 0.019), an alcohol dehydrogenase, and ADORA1 (p = 5.29 × 10 -5 ; q = 0.035), an adenosine receptor that belongs to a G-protein-coupled receptor gene family. To our knowledge, this is the first sequencing study of AD to examine variants in entire genes, including flanking and regulatory regions. We found that in addition to protein coding variant sets, regulatory variant sets may play a role in AD. From these findings, we have generated initial functional hypotheses about how these sets may influence AD. Copyright © 2017 by the Research Society on

  3. Short Communication Phylogenetic Characterization of HIV Type 1 CRF01_AE V3 Envelope Sequences in Pregnant Women in Northern Vietnam

    Science.gov (United States)

    Caridha, Rozina; Ha, Tran Thi Thanh; Gaseitsiwe, Simani; Hung, Pham Viet; Anh, Nguyen Mai; Bao, Nguyen Huy; Khang, Dinh Duy; Hien, Nguyen Tran; Cam, Phung Dac; Chiodi, Francesca

    2012-01-01

    Abstract Characterization of HIV-1 strains is important for surveillance of the HIV-1 epidemic. In Vietnam HIV-1-infected pregnant women often fail to receive the care they are entitled to. Here, we analyzed phylogenetically HIV-1 env sequences from 37 HIV-1-infected pregnant women from Ha Noi (n=22) and Hai Phong (n=15), where they delivered in 2005–2007. All carried CRF01_AE in the gp120 V3 region. In 21 women CRF01_AE was also found in the reverse transcriptase gene. We compared their env gp120 V3 sequences phylogenetically in a maximum likelihood tree to those of 198 other CRF01_AE sequences in Vietnam and 229 from neighboring countries, predominantly Thailand, from the HIV-1 database. Altogether 464 sequences were analyzed. All but one of the maternal sequences colocalized with sequences from northern Vietnam. The maternal sequences had evolved the least when compared to sequences collected in Ha Noi in 2002, as shown by analysis of synonymous and nonsynonymous changes, than to other Vietnamese sequences collected earlier and/or elsewhere. Since the HIV-1 epidemic in women in Vietnam may still be underestimated, characterization of HIV-1 in pregnant women is important to observe how HIV-1 has evolved and follow its molecular epidemiology. PMID:21936713

  4. Characterizing the Genetic Basis for Nicotine Induced Cancer Development: A Transcriptome Sequencing Study.

    Directory of Open Access Journals (Sweden)

    Jasmin H Bavarva

    Full Text Available Nicotine is a known risk factor for cancer development and has been shown to alter gene expression in cells and tissue upon exposure. We used Illumina® Next Generation Sequencing (NGS technology to gain unbiased biological insight into the transcriptome of normal epithelial cells (MCF-10A to nicotine exposure. We generated expression data from 54,699 transcripts using triplicates of control and nicotine stressed cells. As a result, we identified 138 differentially expressed transcripts, including 39 uncharacterized genes. Additionally, 173 transcripts that are primarily associated with DNA replication, recombination, and repair showed evidence for alternative splicing. We discovered the greatest nicotine stress response by HPCAL4 (up-regulated by 4.71 fold and NPAS3 (down-regulated by -2.73 fold; both are genes that have not been previously implicated in nicotine exposure but are linked to cancer. We also discovered significant down-regulation (-2.3 fold and alternative splicing of NEAT1 (lncRNA that may have an important, yet undiscovered regulatory role. Gene ontology analysis revealed nicotine exposure influenced genes involved in cellular and metabolic processes. This study reveals previously unknown consequences of nicotine stress on the transcriptome of normal breast epithelial cells and provides insight into the underlying biological influence of nicotine on normal cells, marking the foundation for future studies.

  5. Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.

    Science.gov (United States)

    Rademacher, Antje; Zakrzewski, Martha; Schlüter, Andreas; Schönberg, Mandy; Szczepanowski, Rafael; Goesmann, Alexander; Pühler, Alfred; Klocke, Michael

    2012-03-01

    DNAs of two biofilms of a thermophilic two-phase leach-bed biogas reactor fed with rye silage and winter barley straw were sequenced by 454-pyrosequencing technology to assess the biofilm-based microbial community and their genetic potential for anaerobic digestion. The studied biofilms matured on the surface of the substrates in the hydrolysis reactor (HR) and on the packing in the anaerobic filter reactor (AF). The classification of metagenome reads showed Clostridium as most prevalent bacteria in the HR, indicating a predominant role for plant material digestion. Notably, insights into the genetic potential of plant-degrading bacteria were determined as well as further bacterial groups, which may assist Clostridium in carbohydrate degradation. Methanosarcina and Methanothermobacter were determined as most prevalent methanogenic archaea. In consequence, the biofilm-based methanogenesis in this system might be driven by the hydrogenotrophic pathway but also by the aceticlastic methanogenesis depending on metabolite concentrations such as the acetic acid concentration. Moreover, bacteria, which are capable of acetate oxidation in syntrophic interaction with methanogens, were also predicted. Finally, the metagenome analysis unveiled a large number of reads with unidentified microbial origin, indicating that the anaerobic degradation process may also be conducted by up to now unknown species. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  6. A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.

    Science.gov (United States)

    Schlecht, Ulrich; Liu, Zhimin; Blundell, Jamie R; St Onge, Robert P; Levy, Sasha F

    2017-05-25

    Several large-scale efforts have systematically catalogued protein-protein interactions (PPIs) of a cell in a single environment. However, little is known about how the protein interactome changes across environmental perturbations. Current technologies, which assay one PPI at a time, are too low throughput to make it practical to study protein interactome dynamics. Here, we develop a highly parallel protein-protein interaction sequencing (PPiSeq) platform that uses a novel double barcoding system in conjunction with the dihydrofolate reductase protein-fragment complementation assay in Saccharomyces cerevisiae. PPiSeq detects PPIs at a rate that is on par with current assays and, in contrast with current methods, quantitatively scores PPIs with enough accuracy and sensitivity to detect changes across environments. Both PPI scoring and the bulk of strain construction can be performed with cell pools, making the assay scalable and easily reproduced across environments. PPiSeq is therefore a powerful new tool for large-scale investigations of dynamic PPIs.

  7. Isolation and characterization of microsatellite markers for Dendranthema morifolium (Asteraceae) using next-generation sequencing.

    Science.gov (United States)

    Yuan, W-J; Ye, S; Du, L-H; Li, S-M; Miao, X; Shang, F-D

    2016-10-05

    Dendranthema morifolium (Asteraceae) is a perennial herbaceous plant native to China. A long history of artificial crossings may have resulted in complex genetic background and decreased genetic diversity. To protect the genetic diversity of D. morifolium and enabling breeding of new D. morifolium cultivars, we developed a set of molecular markers. We used pyrosequencing of an enriched microsatellite library by Roche 454 FLX+ platform, to isolate D. morifolium simple sequence repeats (SSRs). A total of 32,863 raw reads containing 2251 SSRs were obtained. To test the effectiveness of these SSR markers, we designed primers by randomly selecting 100 novel SSRs, and amplified them across 60 cultivars representing five different petal shape groups. Sixteen SSRs were polymorphic with the number of alleles ranging from 6 to 19, and their expected and observed heterozygosities ranging from 0.477 to 0.848, and 0.250 to 0.804, respectively. The polymorphism information content ranged from 0.459 to 0.854 and the inbreeding coefficient ranged from -0.119 to 0.759. An unweighted pair-group method arithmetic average analysis was performed to survey the phylogenetic relationships of these 60 cultivars and five clusters were identified. These markers can be used for investigating genetic relationships and identifying elite alleles through linkage and association analyses.

  8. High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs.

    Directory of Open Access Journals (Sweden)

    Germán Martínez

    Full Text Available Micro RNAS (miRNAs are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance. Here we report a combined approach of bioinformatics prediction, high-throughput sequencing data and molecular methods to analyze miRNAs populations in cucumber (Cucumis sativus plants. A set of 19 conserved and 6 known but non-conserved miRNA families were found in our cucumber small RNA dataset. We also identified 7 (3 with their miRNA* strand not previously described miRNAs, candidates to be cucumber-specific. To validate their description these new C. sativus miRNAs were detected by northern blot hybridization. Additionally, potential targets for most conserved and new miRNAs were identified in cucumber genome.In summary, in this study we have identified, by first time, conserved, known non-conserved and new miRNAs arising from an agronomically important species such as C. sativus. The detection of this complex population of regulatory small RNAs suggests that similarly to that observe in other plant species, cucumber miRNAs may possibly play an important role in diverse biological and metabolic processes.

  9. Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.

    Science.gov (United States)

    Das, Sarbashis; Pettersson, B M Fredrik; Behra, Phani Rama Krishna; Ramesh, Malavika; Dasgupta, Santanu; Bhattacharya, Alok; Kirsebom, Leif A

    2015-06-16

    We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  10. Sequencing and Characterization of Novel PII Signaling Protein Gene in Microalga Haematococcus pluvialis

    Directory of Open Access Journals (Sweden)

    Ruijuan Ma

    2017-10-01

    Full Text Available The PII signaling protein is a key protein for controlling nitrogen assimilatory reactions in most organisms, but little information is reported on PII proteins of green microalga Haematococcus pluvialis. Since H. pluvialis cells can produce a large amount of astaxanthin upon nitrogen starvation, its PII protein may represent an important factor on elevated production of Haematococcus astaxanthin. This study identified and isolated the coding gene (HpGLB1 from this microalga. The full-length of HpGLB1 was 1222 bp, including 621 bp coding sequence (CDS, 103 bp 5′ untranslated region (5′ UTR, and 498 bp 3′ untranslated region (3′ UTR. The CDS could encode a protein with 206 amino acids (HpPII. Its calculated molecular weight (Mw was 22.4 kDa and the theoretical isoelectric point was 9.53. When H. pluvialis cells were exposed to nitrogen starvation, the HpGLB1 expression was increased 2.46 times in 48 h, concomitant with the raise of astaxanthin content. This study also used phylogenetic analysis to prove that HpPII was homogeneous to the PII proteins of other green microalgae. The results formed a fundamental basis for the future study on HpPII, for its potential physiological function in Haematococcus astaxanthin biosysthesis.

  11. Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile).

    Science.gov (United States)

    Zhu, Ke-Cheng; Liang, Yin-Yin; Wu, Na; Guo, Hua-Yang; Zhang, Nan; Jiang, Shi-Gui; Zhang, Dian-Chang

    2017-11-10

    To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.

  12. Sequencing and characterization of Varicella-Zoster virus vaccine strain SuduVax

    Directory of Open Access Journals (Sweden)

    Kim Jong

    2011-12-01

    Full Text Available Abstract Background Varicella-zoster virus (VZV causes chickenpox in children and shingles in older people. Currently, live attenuated vaccines based on the Oka strain are available worldwide. In Korea, an attenuated VZV vaccine has been developed from a Korean isolate and has been commercially available since 1994. Despite this long history of use, the mechanism for the attenuation of the vaccine strain is still elusive. We attempted to understand the molecular basis of attenuation mechanism by full genome sequencing and comparative genomic analyses of the Korean vaccine strain SuduVax. Results SuduVax was found to contain a genome that was 124,759 bp and possessed 74 open reading frames (ORFs. SuduVax was genetically most close to Oka strains and these Korean-Japanese strains formed a strong clade in phylogenetic trees. SuduVax, similar to the Oka vaccine strains, underwent T- > C substitution at the stop codon of ORF0, resulting in a read-through mutation to code for an extended form of ORF0 protein. SuduVax also shared certain deletion and insertion mutations in ORFs 17, 29, 56 and 60 with Oka vaccine strains and some clinical strains. Conclusions The Korean VZV vaccine strain SuduVax is genetically similar to the Oka vaccine strains. Further comparative genomic and bioinformatics analyses will help to elucidate the molecular basis of the attenuation of the VZV vaccine strains.

  13. Medicinal Plants for the Treatment of Hypertrophic Scars

    Directory of Open Access Journals (Sweden)

    Qi Ye

    2015-01-01

    Full Text Available Hypertrophic scar is a complication of wound healing and has a high recurrence rate which can lead to significant abnormity in aesthetics and functions. To date, no ideal treatment method has been established. Meanwhile, the underlying mechanism of hypertrophic scarring has not been clearly defined. Although a large amount of scientific research has been reported on the use of medicinal plants as a natural source of treatment for hypertrophic scarring, it is currently scattered across a wide range of publications. Therefore, a systematic summary and knowledge for future prospects are necessary to facilitate further medicinal plant research for their potential use as antihypertrophic scar agents. A bibliographic investigation was accomplished by focusing on medicinal plants which have been scientifically tested in vitro and/or in vivo and proved as potential agents for the treatment of hypertrophic scars. Although the chemical components and mechanisms of action of medicinal plants with antihypertrophic scarring potential have been investigated, many others remain unknown. More investigations and clinical trials are necessary to make use of these medical plants reasonably and phytotherapy is a promising therapeutic approach against hypertrophic scars.

  14. External rhinoplasty for the Arabian nose: a columellar scar analysis.

    Science.gov (United States)

    Foda, Hossam M T

    2004-01-01

    This study aimed to evaluate columellar scar problems after external rhinoplasty in the Arabian population, and to analyze the technical factors that help prevent such problems and maximize the scar cosmesis. The investigation was conducted in university and private practice settings of the author in Alexandria, Egypt. A total of 600 Arab patients who underwent external rhinoplasty were included in the study. All the patients underwent surgery using the external rhinoplasty approach, in which bilateral alar marginal incisions were connected by an inverted V-shaped transcolumellar incision. At completion of the procedure, a two-layer closure of the columellar incision was performed. At a minimum of 1 year postoperatively, the columellar scar was evaluated subjectively by means of a patient questionnaire, and objectively by clinical examination and comparison of the close-up pre- and postoperative basal view photographs. Objectively, anything less than a barely visible, leveled, thin, linear scar was considered unsatisfactory. Subjectively, 95.5% of the patients rated the scar as unnoticeable, 3% as noticeable but acceptable, and 1.5% as unacceptable. Objectively, the scar was unsatisfactory in 7% of the cases. This was because of scar widening with or without depression (5%), hyperpigmentation (1.5%), and columellar rim notching (0.5%). The use of a deep 6/0 polydioxanon (PDS) suture significantly decreased the incidence of scar widening (p < 0.005).The columellar incision can be used safely in the Arab population regardless of their thick, dark, and oily skin. Technical factors that contributed to the favorable outcome of the columellar scar included proper planning of location and design of the incision used, precise execution, meticulous multilayered closure, and good postoperative care.

  15. Nonlinear optics for the study of human scar tissue

    Science.gov (United States)

    Ferro, D. P.; Vieira-Damiani, G.; Adam, R. L.; Cesar, C. L.; Metze, Konradin

    2012-03-01

    Collagen fibers are an essential component of the dynamic process of scarring, which accompanies various diseases. Scar tissue may reveal different morphologic expressions, such as hypertrophic scars or keloids. Collagen fibers can be visualized by fluorescent light when stained with eosin. Second Harmonic Generation (SHG) creates a non linear signal that occurs only in molecules without inversion symmetry and is particularly strong in the collagen fibers arranged in triple helices. The aim of this study was to describe the methodology for the analysis of the density and texture of collagen in keloids, hypertrophic scars and conventional scars. Samples were examined in the National Institute of Science and Technology on Photonics Applied to Cell Biology (INFABIC) at the State University of Campinas. The images were acquired in a multiphoton microscopy LSM 780-NLO Zeiss 40X. Both signals, two-photon fluorescence (TPEF) and SHG, were excited by a Mai-Tai Ti:Sapphire laser at 940 nm. We used a LP490/SP485 NDD filter for SHG, and a BP565-610 NDD filter for fluorescence In each case, ten images were acquired serially (512×512 μm) in Z-stack and joined together to one patchwork-image . Image analysis was performed by a gliding-box-system with in-house made software. Keloids, hypertrophic scars and normal scar tissue show different collagen architecture. Inside an individual case differences of the scar process may be found between central and peripheral parts. In summary, the use of nonlinear optics is a helpful tool for the study of scars tissue.

  16. Microneedle physical contact as a therapeutic for abnormal scars.

    Science.gov (United States)

    Yeo, David C; Balmayor, Elizabeth R; Schantz, Jan-Thorsten; Xu, Chenjie

    2017-08-14

    Abnormal (keloid and hypertrophic) scars are a significant affliction with no satisfactory single modality therapy to-date. Available options are often ineffective, painful, potentially hazardous, and require healthcare personnel involvement. Herein a self-administered microneedle device based on drug-free physical contact for inhibiting abnormal scars is reported. Its therapeutic activity through microneedle contact eliminates hazards associated with toxic anti-scarring drugs while self-treatment enables administration flexibility. The microneedle patch was fabricated with FDA-approved liquid crystalline polymer under good manufacturing practice. It was first tested to ascertain its ability to inhibit (keloid) fibroblast proliferation. Later the microneedle patch was examined on the rabbit ear hypertrophic scar model to explore its potential in inhibiting the generation of abnormal scars post-injury. Finally, the microneedle patch was applied to the caudal region of a hypertrophic scar located on a female patient's dorsum to verify clinical efficacy. On untreated control cultures, barely any non-viable fibroblasts could be seen. After 12-h treatment with the microneedle patch, the non-viable proportion increased to 83.8 ± 11.96%. In rabbit ear hypertrophic scar model, 100% of the control wounds without the presence of patches on rabbit ears generated regions of raised dermis originating from the wound site (3/3), whereas microneedle treatment prevented dermis tissue thickening in 83.33% of the wounds (15/18). In the clinical test, the microneedle patch was well tolerated by the patient. Compared to the untreated region, microneedle treatment decreased the number of infiltrated inflammatory cells, with less disrupted dermis tissue architecture and more flattened appearance. A self-administered, drug-free microneedle patch appears highly promising in reducing abnormal scarring as observed from in vitro, in vivo and clinical experiments. Larger cohort clinical

  17. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

    Science.gov (United States)

    Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

    2016-08-05

    Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis

  18. Cathepsin L of Triatoma brasiliensis (Reduviidae, Triatominae): sequence characterization, expression pattern and zymography.

    Science.gov (United States)

    Waniek, Peter J; Pacheco Costa, Juliana E; Jansen, Ana M; Costa, Jane; Araújo, Catarina A C

    2012-01-01

    Triatoma brasiliensis is considered one of the main vectors of Chagas disease commonly found in semi-arid areas of northeastern Brazil. These insects use proteases, such as carboxypeptidase B, aminopeptidases and different cathepsins for blood digestion. In the present study, two genes encoding cathepsin L from the midgut of T. brasiliensis were identified and characterized. Mature T. brasiliensis cathepsin L-like proteinases (TBCATL-1, TBCATL-2) showed a high level of identity to the cathepsin L-like proteinases of other insects, with highest similarity to Rhodnius prolixus. Both cathepsin L transcripts were highly abundant in the posterior midgut region, the main region of the blood digestion. Determination of the pH in the whole intestine of unfed T. brasiliensis revealed alkaline conditions in the anterior midgut region (stomach) and acidic conditions in the posterior midgut region (small intestine). Gelatine in-gel zymography showed the activity of at least four distinct proteinases in the small intestine and the cysteine proteinase inhibitors transepoxysuccinyl-l-leucylamido-(4-guanidino)butane (E-64) and cathepsin B inhibitor and N-(l-3-trans-propylcarbamoyl-oxirane-2-carbonyl)-l-isoleucyl-l-proline (CA-074) were employed to characterize enzymatic activity. E-64 fully inhibited cysteine proteinase activity, whereas in the samples treated with CA-074 residual proteinase activity was detectable. Thus, proteolytic activity could at least partially be ascribed to cathepsin L. Western blot analysis using specific anti cathepsin L antibodies confirmed the presence of cathepsin L in the lumen of the small intestine of the insects. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

    Science.gov (United States)

    Feng, Yue; Feng, Yue-Mei; Feng, Yang; Lu, Caixia; Liu, Li; Sun, Xiaomei; Dai, Jiejie; Xia, Xueshan

    2015-10-01

    Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection. This study aimed to construct a liver microRNA (miRNA) data of the tree shrew. Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing. A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction. According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

  20. De novo Assembly and Characterization of Cajanus scarabaeoides (L. Thouars Transcriptome by Paired-End Sequencing

    Directory of Open Access Journals (Sweden)

    Deepti Nigam

    2017-07-01

    Full Text Available Pigeonpea [Cajanus cajan (L. Millsp.] is a heat and drought resilient legume crop grown mostly in Asia and Africa. Pigeonpea is affected by various biotic (diseases and insect pests and abiotic stresses (salinity and water logging which limit the yield potential of this crop. However, resistance to all these constraints is not readily available in the cultivated genotypes and some of the wild relatives have been found to withstand these resistances. Thus, the utilization of crop wild relatives (CWR in pigeonpea breeding has been effective in conferring resistance, quality and breeding efficiency traits to this crop. Bud and leaf tissue of Cajanus scarabaeoides, a wild relative of pigeon pea were used for transcriptome profiling. Approximately 30 million clean reads filtered from raw reads by removal of adaptors, ambiguous reads and low-quality reads (3.02 gigabase pairs were generated by Illumina paired-end RNA-seq technology. All of these clean reads were pooled and assembled de novo into 1,17,007 transcripts using the Trinity. Finally, a total of 98,664 unigenes were derived with mean length of 396 bp and N50 values of 1393. The assembly produced significant mapping results (73.68% in BLASTN searches of the Glycine max CDS sequence database (Ensembl. Further, uniprot database of Viridiplantae was used for unigene annotation; 81,799 of 98,664 (82.90% unigenes were finally annotated with gene descriptions or conserved protein domains. Further, a total of 23,475 SSRs were identified in 27,321 unigenes. This data will provide useful information for mining of functionally important genes and SSR markers for pigeonpea improvement.

  1. Identification, sequence analysis, and characterization of serine/threonine protein kinase 17A from Clonorchis sinensis.

    Science.gov (United States)

    Huang, Lisi; Lv, Xiaoli; Huang, Yan; Hu, Yue; Yan, Haiyan; Zheng, Minghui; Zeng, Hua; Li, Xuerong; Liang, Chi; Wu, Zhongdao; Yu, Xinbing

    2014-05-01

    This is the first report of a novel protein from Clonorchis sinensis (C. sinensis), serine/threonine protein kinase 17A (CsSTK17A), which belongs to a member of the death-associated protein kinase (DAPK) family known to regulate diverse biological processes. The full-length sequence encoding CsSTK17A was isolated from C. sinensis adult cDNA plasmid library. Two transcribed isoforms of the gene were identified from the genome of C. sinensis. CsSTK17A contains a kinase domain at the N-terminus that shares a degree of conservation with the DAPK families. Besides, the catalytic domain contains 11 subdomains conserved among STKs and shares the highest identity with STK from Schistosoma mansoni (55.9%). Three-dimensional structure of CsSTK17A displays the canonical STK fold, including the helix C, P-loop, and the activation loop. We obtained recombinant CsSTK17A (rCsSTK17A) and anti-rCsSTK17A IgG. The rCsSTK17A could be probed by anti-rCsSTK17A rat serum, C. sinensis-infected rat serum and the sera from rats immunized with C. sinensis excretory-secretory products, indicating that it is a circulating antigen possessing a strong immunocompetence. Moreover, quantitative RT-PCR and western blotting analyses revealed that CsSTK17A exhibited the highest mRNA and protein expression level in eggs, followed by metacercariae and adult worms. Intriguingly, in the immunolocalization assay, CsSTK17A was intensively localized to the operculum region of eggs in uterus, as well as the vitelline gland of both adult worm and metacercaria, implying that the protein was associated with the reproduction and development of C. sinensis. Overall, these fundamental studies might contribute to further researches on signaling systems of the parasite.

  2. Extracorporeal shock wave therapy with low-energy flux density inhibits hypertrophic scar formation in an animal model.

    Science.gov (United States)

    Zhao, Jing-Chun; Zhang, Bo-Ru; Hong, Lei; Shi, Kai; Wu, Wei-Wei; Yu, Jia-Ao

    2018-04-01

    Hypertrophic scar is characterized by excessive deposits of collagen during skin wound healing, which could become a challenge to clinicians. This study assessed the effects of the extracorporeal shock wave therapy (ESWT) on hypertrophic scar formation and the underlying gene regu-lation. A rabbit ear hypertrophic scar model was generated and randomly divided into three groups: L-ESWT group to receive L-ESWT (energy flux density of 0.1 mJ/mm2), H-ESWT (energy flux density of 0.2 mJ/mm2) and sham ESWT group (S-ESWT). Hypertrophic scar tissues were then collected and stained with hematoxylin and eosin (H&E) and Masson's trichrome staining, respectively, to assess scar elevation index (SEI), fibroblast density and collagen fiber arrangement. Expression of cell proliferation marker proliferating cell nuclear antigen (PCNA) and α-smooth muscle actin (α-SMA) were assessed using RT-PCR and immunohistochemistry in hypertrophic scar tissues. H&E staining sections showed significant reduction of SEI and fibroblast density in both ESWT treatment groups compared to S-ESWT, but there was no dramatic difference between L-ESWT and H-ESWT groups. Masson's trichrome staining showed that collagen fibers were more slender and broader and oriented in parallel to skin surface after administration of ESWT compared to control tissues. At the gene level, PCNA‑positive fibroblasts and α-SMA-positive myofibroblasts were significantly decreased after L-ESWT or H-ESWT compared to the controls. Furthermore, there was no significant difference in expression of PCNA mRNA between L-ESWT or H-ESWT and S-ESWT, whereas expression of α-SMA mRNA significantly decreased in L-ESWT compared to that of H-ESWT and S-ESWT (P=0.002 and P=0.030, respectively). In conclusion, L-ESWT could be effective on suppression of hypertrophic scar formation by inhibition of scar elevation index and fibroblast density as well as α-SMA expression in hypertrophic scar tissues of the rabbit model.

  3. Study of performances, stability and microbial characterization of a Sequencing Batch Biofilter Granular Reactor working at low recirculation flow.

    Science.gov (United States)

    De Sanctis, Marco; Beccari, Mario; Di Iaconi, Claudio; Majone, Mauro; Rossetti, Simona; Tandoi, Valter

    2013-02-01

    The Sequencing Batch Biofilter Granular Reactor (SBBGR) is a promising wastewater treatment technology characterized by high biomass concentration in the system, good depuration performance and low sludge production. Its main drawback is the high energy consumption required for wastewater recirculation through the reactor bed to ensure both shear stress and oxygen supply. Therefore, the effect of low recirculation flow on the long-term (38 months) performance of a laboratory scale SBBGR was studied. Both the microbial components of the granules, and their main metabolic activities were evaluated (heterotrophic oxidation, nitrification, denitrification, fermentation, sulphate reduction and methanogenesis). The results indicate that despite reduced recirculation, the SBBGR system maintained many of its advantageous characteristics. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

    DEFF Research Database (Denmark)

    Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis

    2016-01-01

    Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which...... performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel...... on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways...

  5. Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758

    Directory of Open Access Journals (Sweden)

    Christine Ewers-Saucedo

    2016-05-01

    Full Text Available Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758. Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria.

  6. Microsatellite loci discovery from next-generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

    Science.gov (United States)

    Zardus, John D.; Wares, John P.

    2016-01-01

    Microsatellite markers remain an important tool for ecological and evolutionary research, but are unavailable for many non-model organisms. One such organism with rare ecological and evolutionary features is the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758). Chelonibia testudinaria appears to be a host generalist, and has an unusual sexual system, androdioecy. Genetic studies on host specificity and mating behavior are impeded by the lack of fine-scale, highly variable markers, such as microsatellite markers. In the present study, we discovered thousands of new microsatellite loci from next-generation sequencing data, and characterized 12 loci thoroughly. We conclude that 11 of these loci will be useful markers in future ecological and evolutionary studies on C. testudinaria. PMID:27231653

  7. Characterization of a polymorphism in the coding sequence of FCN3 resulting in a Ficolin-3 (Hakata antigen) deficiency state

    DEFF Research Database (Denmark)

    Munthe-Fog, Lea; Hummelshøj, Tina; Ma, Ying Jie

    2008-01-01

    Ficolin-3 (Hakata antigen or H-ficolin) is a soluble pattern recognition molecule in the lectin complement pathway. We speculated whether common genetic variations in the FCN3 gene contribute to deficiency of Ficolin-3. The FCN3 gene was sequenced in 237 healthy Danish Caucasians. The relevance...... of polymorphisms was assessed with antibodies against Ficolin-3 in a novel ELISA system and by production of recombinant Ficolin-3 variants. Ficolin-3 serum profiles were analyzed by SDS-PAGE and western blotting. Ficolin-3 serum concentration varied 10-fold (median, 24microg/ml; range, 3-54microg/ml). Out.......025). SDS-PAGE and western blotting of serum revealed a weak band corresponding to the truncated molecule in addition to the normal Ficolin-3 pattern. Characterization of recombinant Ficolin-3 derived from FCN3+1637delC showed that in the homozygous situation this allelic variant would lead to Ficolin-3...

  8. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.

    Science.gov (United States)

    Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis G; De Francisci, Davide; Valle, Giorgio; Angelidaki, Irini

    2016-01-01

    Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge. In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway. This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the

  9. Full genome sequences and molecular characterization of tick-borne encephalitis virus strains isolated from human patients.

    Science.gov (United States)

    Formanová, Petra; Černý, Jiří; Bolfíková, Barbora Černá; Valdés, James J; Kozlova, Irina; Dzhioev, Yuri; Růžek, Daniel

    2015-02-01

    Tick-borne encephalitis virus (TBEV) causes tick-borne encephalitis (TBE), one of the most important human neuroinfections across Eurasia. Up to date, only three full genome sequences of human European TBEV isolates are available, mostly due to difficulties with isolation of the virus from human patients. Here we present full genome characterization of an additional five low-passage TBEV strains isolated from human patients with severe forms of TBE. These strains were isolated in 1953 within Central Bohemia in the former Czechoslovakia, and belong to the historically oldest human TBEV isolates in Europe. We demonstrate here that all analyzed isolates are distantly phylogenetically related, indicating that the emergence of TBE in Central Europe was not caused by one predominant strain, but rather a pool of distantly related TBEV strains. Nucleotide identity between individual sequenced TBEV strains ranged from 97.5% to 99.6% and all strains shared large deletions in the 3' non-coding region, which has been recently suggested to be an important determinant of virulence. The number of unique amino acid substitutions varied from 3 to 9 in individual isolates, but no characteristic amino acid substitution typical exclusively for all human TBEV isolates was identified when compared to the isolates from ticks. We did, however, correlate that the exploration of the TBEV envelope glycoprotein by specific antibodies were in close proximity to these unique amino acid substitutions. Taken together, we report here the largest number of patient-derived European TBEV full genome sequences to date and provide a platform for further studies on evolution of TBEV since the first emergence of human TBE in Europe. Copyright © 2014 Elsevier GmbH. All rights reserved.

  10. Identification and characterization of novel serum microRNA candidates from deep sequencing in cervical cancer patients.

    Science.gov (United States)

    Juan, Li; Tong, Hong-li; Zhang, Pengjun; Guo, Guanghong; Wang, Zi; Wen, Xinyu; Dong, Zhennan; Tian, Ya-ping

    2014-09-03

    Small non-coding microRNAs (miRNAs) are involved in cancer development and progression, and serum profiles of cervical cancer patients may be useful for identifying novel miRNAs. We performed deep sequencing on serum pools of cervical cancer patients and healthy controls with 3 replicates and constructed a small RNA library. We used MIREAP to predict novel miRNAs and identified 2 putative novel miRNAs between serum pools of cervical cancer patients and healthy controls after filtering out pseudo-pre-miRNAs using Triplet-SVM analysis. The 2 putative novel miRNAs were validated by real time PCR and were significantly decreased in cervical cancer patients compared with healthy controls. One novel miRNA had an area under curve (AUC) of 0.921 (95% CI: 0.883, 0.959) with a sensitivity of 85.7% and a specificity of 88.2% when discriminating between cervical cancer patients and healthy controls. Our results suggest that characterizing serum profiles of cervical cancers by Solexa sequencing may be a good method for identifying novel miRNAs and that the validated novel miRNAs described here may be cervical cancer-associated biomarkers.

  11. Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils.

    Directory of Open Access Journals (Sweden)

    Zewei Song

    Full Text Available Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS. The following treatments were considered: 1 the amount of soil used in DNA extraction, 2 the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation in the extraction procedure, 3 the amount of DNA template used in PCR, and 4 the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.

  12. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.

    Science.gov (United States)

    Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F; Li, Shuaicheng; Hu, Kailin

    2016-01-07

    The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

  13. BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.

    Science.gov (United States)

    Kanehisa, Minoru; Sato, Yoko; Morishima, Kanae

    2016-02-22

    BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site (http://www.kegg.jp/blastkoala/). In BlastKOALA, the KO assignment is performed by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with Cd-hit clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Sequence analysis and characterization of rolling-circle replicating plasmid pVCM01 from Salmonella enterica

    Directory of Open Access Journals (Sweden)

    Penido, A. F. B.

    2013-12-01

    Full Text Available Aims: Characterization of cryptic plasmid pVCM01 (accession number JX133088 isolated from Salmonella enterica Enteritidis. Methodology and results: The complete sequence of pVCM01 was obtained. This plasmid possesses 1981 bp, with G+C content of 57% in agreement of the range of Salmonella genomic DNA. pVCM01 has a high degree of similarity to pB and pJ plasmids. It possesses six main open reading frames, only one have a very high degree of amino acid identity with protein involved in the rolling-circle-like replication (RCR. Based on the sequence similarities, pVCM01 plasmid belonged to the pC194/pUB110 rolling-circle replicating plasmid family. The Rep pVCM01 possesses the motifs: FLTLTVRN, HPHFHTL, SGDGYVKHERW, which were present in all Rep proteins. Conclusion, significance and impact of study: The small size of pVCM01 plasmid and its stability in E. coli cells, make it an attractive candidate to develop new vectors, such as cloning and/or expression vector.

  15. Characterization of European Yersinia enterocolitica 1A strains using restriction fragment length polymorphism and multilocus sequence analysis.

    Science.gov (United States)

    Murros, A; Säde, E; Johansson, P; Korkeala, H; Fredriksson-Ahomaa, M; Björkroth, J

    2016-10-01

    Yersinia enterocolitica is currently divided into two subspecies: subsp. enterocolitica including highly pathogenic strains of biotype 1B and subsp. palearctica including nonpathogenic strains of biotype 1A and moderately pathogenic strains of biotypes 2-5. In this work, we characterized 162 Y. enterocolitica strains of biotype 1A and 50 strains of biotypes 2-4 isolated from human, animal and food samples by restriction fragment length polymorphism using the HindIII restriction enzyme. Phylogenetic relatedness of 20 representative Y. enterocolitica strains including 15 biotype 1A strains was further studied by the multilocus sequence analysis of four housekeeping genes (glnA, gyrB, recA and HSP60). In all the analyses, biotype 1A strains formed a separate genomic group, which differed from Y. enterocolitica subsp. enterocolitica and from the strains of biotypes 2-4 of Y. enterocolitica subsp. palearctica. Based on these results, biotype 1A strains considered nonpathogenic should not be included in subspecies palearctica containing pathogenic strains of biotypes 2-5. Yersinia enterocolitica strains are currently divided into six biotypes and two subspecies. Strains of biotype 1A, which are phenotypically and genotypically very heterogeneous, are classified as subspecies palearctica. In this study, European Y. enterocolitica 1A strains isolated from both human and nonhuman sources were characterized using restriction fragment length polymorphism and multilocus sequence analysis. The European biotype 1A strains formed a separate group, which differed from strains belonging to subspecies enterocolitica and palearctica. This may indicate that the current division between the two subspecies is not sufficient considering the strain diversity within Y. enterocolitica. © 2016 The Society for Applied Microbiology.

  16. Evolutive and regressive soil sequences for characterization of soils in laurel forest (Tenerife, Canary Islands

    Directory of Open Access Journals (Sweden)

    José Asterio Guerra-García

    2014-03-01

    Full Text Available Soil degradation processes have achieved the recognition of a global environmental problem in recent years. It has been suggested by various international forums and organizations that in order to adequately establish methods to combat land degradation, it is necessary to evaluate this degradation locally and at a detailed scale. The evaluation of soil degradation of natural ecosystems at a detailed scale requires the definition of standards to which to compare this degradation. To define these standards and properly handle the processes that give rise to variations in soil quality and degradation, it is necessary to establish in some detail the pedogenic processes that have or have not taken place in a particular area and which lead to the formation of a mature soil. A mature soil should be considered as standard in these situations and, therefore, a non-degraded soil. This paper presents the possible evolutive and regressive sequences of soil, and provides some examples of using this methodology to evaluate the degradation of the same in the Monteverde of the island of Tenerife. It also presents some physical, chemical and mineralogical properties of climacic mature soils, degraded soils and low quality soils, and examines their similarities and differences in this bioclimatic environment and on different parent materials. Thus it is observed that the main processes of degradation in these areas are related to plant cover modifications that lead to the decreasing protection of the soil surface, which results in the long term, in the onset of degradation processes such as water erosion, biological degradation, loss of andic properties, compaction and sealing and crusting surface, loss of water retention capacity, illuviation, etc. Climacic soils that can be found in areas of steep lava flows are Leptosols, while gently sloping areas are Cambisols and Andosols. On pyroclastic materials there are vitric Andosols and andic Andosols according to

  17. Surgical correction of gynecomastia with minimal scarring.

    Science.gov (United States)

    Lee, Jun-Ho; Kim, Il-Kug; Kim, Tae-Gon; Kim, Yong-Ha

    2012-12-01

    Gynecomastia is a benign, excessive development of the male breast that occurs at an overall incidence of 32-36 %. The authors effectively removed peripheral fat tissues with power-assisted liposuction (PAL) and periareolar glandular tissues with a cartilage shaver in a series of patients. The small periareolar incisions were not easily recognized. Between February 2010 and April 2012, the charts of 15 patients (28 breasts) treated with PAL and a cartilage shaver were retrospectively reviewed. The mean volume of fat tissue removed with liposuction was 319 mL, and the mean volume of glandular tissue removed with the cartilage shaver was 70 mL. The mean follow-up period was 11.2 months. No infection, nipple-areola complex necrosis, nipple retraction, or saucer deformity was encountered in this series. Intraoperative bleeding occurred in one patient. Mild asymmetries developed in three patients. Use of PAL and a cartilage shaver for the treatment of gynecomastia allows for effective removal of both the fat and the glandular tissue of the breast through a minimal periareolar incision. This technique can achieve excellent aesthetic results with inconspicuous scarring. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

  18. Pyelonephritis, renal scarring, and reflux nephropathy: a pediatric urologist's perspective

    International Nuclear Information System (INIS)

    Smith, Edwin A.

    2008-01-01

    Imaging of children with a clinical diagnosis of pyelonephritis is performed to characterize the extent of the infection, to identify associated renal injury and to uncover risk factors for future infections and renal damage. Although there is general agreement regarding the need for parenchymal imaging and the need to exclude processes that are either functionally or anatomically obstructive, there is controversy regarding the need for routine cystography, especially when parenchymal involvement has not been documented. A protocol that limits the use of cystography for evaluation of urinary tract infections must assume that the diagnosis of reflux is at least of variable clinical significance. It is now clear that vesicoureteral reflux and reflux nephropathy represent a diverse population that includes both congenital and acquired processes. MR imaging will improve our understanding of vesicoureteral reflux, pyelonephritis and renal scarring and might help us to identify and manage those patients most at risk for recurrent infections and renal injury. To recognize the potential contributions of this newer imaging technique it is helpful to look at our understanding of the pathophysiology of pyelonephritis, reflux and reflux nephropathy. (orig.)

  19. Managing Caesarean Scar Pregnancy in low Resource Settings: 2 ...

    African Journals Online (AJOL)

    AJRH Managing Editor

    ultrasound guided approach with dilatation of uterine cervix and subsequent evacuation of uterine ... Keywords: caesarean scar pregnancy, transrectal ultrasound guided surgical approach. ... a viable embryo with a crown rump length (CRL).

  20. Before and After Photos: Treatment of Hypertrophic Scars

    Science.gov (United States)

    ... for Every Season How to Choose the Best Skin Care Products In This Section Dermatologic Surgery What is dermatologic ... for Every Season How to Choose the Best Skin Care Products Before and after photos: Treatment of hypertrophic scars ...

  1. Before and After Photos: Treatment of Hypertrophic Scars

    Science.gov (United States)

    ... Back Injectable Deoxycholic Acid Injectable Hyaluronic Acid Injectable Poly-l-lactic Acid Injectable Polymethylmethacrylate + Bovine Collagen Filler ... Does acne scar removal hurt? What are my pain management and anesthesia options? How long is the ...

  2. Quantitative measurement of hypertrophic scar: interrater reliability and concurrent validity.

    Science.gov (United States)

    Nedelec, Bernadette; Correa, José A; Rachelska, Grazyna; Armour, Alexis; LaSalle, Léo

    2008-01-01

    Research into the pathophysiology and treatment of hypertrophic scar (HSc) remains limited by the heterogeneity of scar and the imprecision with which its severity is measured. The objective of this study was to test the interrater reliability and concurrent validity of the Cutometer measurement of elasticity, the Mexameter measurement of erythema and pigmentation, and total thickness measure of the DermaScan C relative to the modified Vancouver Scar Scale (mVSS) in patient-matched normal skin, normal scar, and HSc. Three independent investigators evaluated 128 sites (severe HSc, moderate or mild HSc, donor site, and normal skin) on 32 burn survivors using all of the above measurement tools. The intraclass correlation coefficient, which was used to measure interrater reliability, reflects the inherent amount of error in the measure and is considered acceptable when it is >0.75. Interrater reliability of the totals of the height, pliability, and vascularity subscales of the mVSS fell below the acceptable limit ( congruent with0.50). The individual subscales of the mVSS fell well below the acceptable level (0.89) for each study site with the exception of severe scar. Mexameter and DermaScan C reliability measurements were acceptable for all sites (>0.82). Concurrent validity correlations with the mVSS were significant except for the comparison of the mVSS pliability subscale and the Cutometer maximum deformation measure comparison in severe scar. In conclusion, the Mexameter and DermaScan C measurements of scar color and thickness of all sites, as well as the Cutometer measurement of elasticity in all but the most severe scars shows high interrater reliability. Their significant concurrent validity with the mVSS confirms that these tools are measuring the same traits as the mVSS, and in a more objective way.

  3. Do Preexisting Abdominal Scars Threaten Wound Healing in Abdominoplasty?

    OpenAIRE

    Shermak, Michele A.; Mallalieu, Jessie; Chang, David

    2010-01-01

    Purpose: Abdominal scars may impair healing after abdominoplasty. We aimed to determine whether right subcostal or upper midline scars led to increased wound healing problems. Methods and Materials: Review of all patients who had abdominoplasty from March 1998 to February 2008 was performed. Variables studied included age, gender, body mass index (BMI), medical history, and postoperative complications. Statistical analysis was performed in Stata SE, version 10. Results: Of 420 abdominoplasty ...

  4. Characterizing spatial heterogeneity based on the b-value and fractal analyses of the 2015 Nepal earthquake sequence

    Science.gov (United States)

    Nampally, Subhadra; Padhy, Simanchal; Dimri, Vijay P.

    2018-01-01

    The nature of spatial distribution of heterogeneities in the source area of the 2015 Nepal earthquake is characterized based on the seismic b-value and fractal analysis of its aftershocks. The earthquake size distribution of aftershocks gives a b-value of 1.11 ± 0.08, possibly representing the highly heterogeneous and low stress state of the region. The aftershocks exhibit a fractal structure characterized by a spectrum of generalized dimensions, Dq varying from D2 = 1.66 to D22 = 0.11. The existence of a fractal structure suggests that the spatial distribution of aftershocks is not a random phenomenon, but it self-organizes into a critical state, exhibiting a scale-independent structure governed by a power-law scaling, where a small perturbation in stress is sufficient enough to trigger aftershocks. In order to obtain the bias in fractal dimensions resulting from finite data size, we compared the multifractal spectrum for the real data and random simulations. On comparison, we found that the lower limit of bias in D2 is 0.44. The similarity in their multifractal spectra suggests the lack of long-range correlation in the data, with an only weakly multifractal or a monofractal with a single correlation dimension D2 characterizing the data. The minimum number of events required for a multifractal process with an acceptable error is discussed. We also tested for a possible correlation between changes in D2 and energy released during the earthquakes. The values of D2 rise during the two largest earthquakes (M > 7.0) in the sequence. The b- and D2 values are related by D2 = 1.45 b that corresponds to the intermediate to large earthquakes. Our results provide useful constraints on the spatial distribution of b- and D2-values, which are useful for seismic hazard assessment in the aftershock area of a large earthquake.

  5. Integra artificial skin dermal regeneration templates in burn scar surgery

    International Nuclear Information System (INIS)

    Rexon Ngim

    1999-01-01

    Integra artificial skin is a porous matrix used as a permanent dermal replacement. Developed in the 1970's, it has been used successfully in the treatment of acute bums requiring full or deep partial thickness skin replacement. Three patients with burn scars received Integra Artificial Skin to resurface various areas of burn scars and also contractures. The first was a 24-year-old woman who had two pieces of Integra to resurface a forearm/elbow/wrist defect. The second was a 28-year-old woman who had two pieces of Integra to resurface a neck contracture. The third was a 44 year-old woman who had two pieces to correct severe burn contractures/ scars of her hands. The results of these three patients, probably the first time Integra was used for bum scar and contracture revision, indicate that there is a place for Integra in Burn Scar surgery. However, the basic principle of its application must be adhered to. These include excision to remove the complete scar, recreation of original size of skin defect and meticulous application of the Artificial Skin and its care post-operatively. Details of its application will be highlighted

  6. Renal scar formation after urinary tract infection in children

    Directory of Open Access Journals (Sweden)

    Young Seo Park

    2012-10-01

    Full Text Available Urinary tract infection (UTI is a common bacterial illness in children. Acute pyelonephritis in children may lead to renal scarring with the risk of later hypertension, preeclampsia during pregnancy, proteinuria, and renal insufficiency. Until now, vesicoureteral reflux (VUR has been considered the most important risk factor for post-UTI renal scar formation in children. VUR predisposes children with UTI to pyelonephritis, and both are associated with renal scarring. However, reflux nephropathy is not always acquired; rather, it reflects refluxassociated congenital dysplastic kidneys. The viewpoint that chronic kidney disease results from renal maldevelopment-associated VUR has led to questioning the utility of any regimen directed at identifying or treating VUR. Despite the recognition that underlying renal anomalies may be the cause of renal scarring that was previously attributed to infection, the prevention of renal scarring remains the goal of all therapies for childhood UTI. Therefore, children at high risk of renal scar formation after UTI should be treated and investigated until a large clinical study and basic research give us more information.

  7. Up-to-date approach to manage keloids and hypertrophic scars: a useful guide.

    Science.gov (United States)

    Arno, Anna I; Gauglitz, Gerd G; Barret, Juan P; Jeschke, Marc G

    2014-11-01

    Keloids and hypertrophic scars occur anywhere from 30 to 90% of patients, and are characterized by pathologically excessive dermal fibrosis and aberrant wound healing. Both entities have different clinical and histochemical characteristics, and unfortunately still represent a great challenge for clinicians due to lack of efficacious treatments. Current advances in molecular biology and genetics reveal new preventive and therapeutical options which represent a hope to manage this highly prevalent, chronic and disabling problem, with long-term beneficial outcomes and improvement of quality of life. While we wait for these translational clinical products to be marketed, however, it is imperative to know the basics of the currently existing wide array of strategies to deal with excessive scars: from the classical corticotherapy, to the most recent botulinum toxin and lasers. The main aim of this review paper is to offer a useful up-to-date guideline to prevent and treat keloids and hypertrophic scars. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

  8. Matrix Metalloproteinases Are Differentially Regulated and Responsive to Compression Therapy in a Red Duroc Model of Hypertrophic Scar.

    Science.gov (United States)

    Travis, Taryn E; Ghassemi, Pejhman; Prindeze, Nicholas J; Moffatt, Lauren T; Carney, Bonnie C; Alkhalil, Abdulnaser; Ramella-Roman, Jessica C; Shupp, Jeffrey W

    2018-01-01

    Objective: Proteins of the matrix metalloproteinases family play a vital role in extracellular matrix maintenance and basic physiological processes in tissue homeostasis. The function and activities of matrix metalloproteinases in response to compression therapies have yet to be defined. Here, a swine model of hypertrophic scar was used to profile the transcription of all known 26 matrix metalloproteinases in scars treated with a precise compression dose. Methods: Full-thickness excisional wounds were created. Wounds underwent healing and scar formation. A subset of scars underwent 2 weeks of compression therapy. Biopsy specimens were preserved, and microarrays, reverse transcription-polymerase chain reaction, Western blotting, and immunohistochemistry were performed to characterize the transcription and expression of various matrix metalloproteinase family members. Results: Microarray results showed that 13 of the known 26 matrix metalloproteinases were differentially transcribed in wounds relative to the preinjury skin. The predominant upregulation of these matrix metalloproteinases during early wound-healing stages declined gradually in later stages of wound healing. The use of compression therapy reduced this decline in 10 of the 13 differentially regulated matrix metalloproteinases. Further investigation of MMP7 using reverse transcription-polymerase chain reaction confirmed the effect of compression on transcript levels. Assessment of MMP7 at the protein level using Western blotting and immunohistochemistry was concordant. Conclusions: In a swine model of hypertrophic scar, the application of compression to hypertrophic scar attenuated a trend of decreasing levels of matrix metalloproteinases during the process of hypertrophic wound healing, including MMP7, whose enzyme regulation was confirmed at the protein level.

  9. Molecular Characterization of Fasciola Samples Using Sequences of Second Internal Transcribed Spacer-rDNA in Different Geographical Localities of Sistan and Balouchestan Province, Iran

    Directory of Open Access Journals (Sweden)

    Mahsa Shahbakhsh

    2016-02-01

    Full Text Available Background: The Fasciola trematodes are the most common liver flukes, living in a range of animals with global distribution and resulting in profound economic loss and public health challenges. Previous studies have indicated that the sequences of the second internal transcribed spacer (ITS-2 of ribosomal DNA (rDNA provide reliable genetic markers for molecular systemic studies of Fasciola. Objectives: The objective of the present study was to characterize Fasciola samples from different geographical regions of Sistan and Balouchestan province using sequences of second internal transcribed spacer (ITS-2 of ribosomal DNA (rDNA. Materials and Methods: Twenty adult trematodes were collected from the livers of slaughtered infected cattle. Total genomic DNA was extracted and ITS-2 rDNA targets were amplified by polymerase chain reaction (PCR. All samples were sequenced and investigated using the ClustalW2 sequence alignment tool and MEGA software. The sequences of some Iranian and non-Iranian isolates were used for comparison, in order to evaluate the variation in sequence homology between geographically different trematode populations. Results: The results of comparing the ITS-2 sequences with the BLAST GenBank database showed one type of sequence for F. hepatica and three different types of sequences for F. gigantica in the specimens. Conclusions: The present study demonstrated that Fasciola samples from cattle in two geographical locations in Sistan and Balouchestan province represented no genetic diversity in F. hepatica and high genetic variation in F. gigantica.

  10. Clinical characterization and diagnosis of cystic fibrosis through exome sequencing in Chinese infants with Bartter-syndrome-like hypokalemia alkalosis.

    Science.gov (United States)

    Qiu, Liru; Yang, Fengjie; He, Yonghua; Yuan, Huiqing; Zhou, Jianhua

    2018-03-09

    Cystic fibrosis (CF) is a fatal autosomal-recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. CF is characterized by recurrent pulmonary infection with obstructive pulmonary disease. CF is common in the Caucasian population but is rare in the Chinese population. The symptoms of early-stage CF are often untypical and may sometimes manifest as Bartter syndrome (BS)-like hypokalemic alkalosis. Therefore, the ability of doctors to differentiate CF from BS-like hypokalemic alkalosis in Chinese infants is a great challenge in the timely and accurate diagnosis of CF. In China, sporadic CF has not been diagnosed in children younger than three years of age to date. Three infants, who were initially admitted to our hospital over the period of June 2013 to September 2014 with BS-like hypokalemic alkalosis, were diagnosed with CF through exome sequencing and sweat chloride measurement. The compound heterozygous mutations of the CFTR gene were detected in two infants, and a homozygous missense mutation was found in one infant. Among the six identified mutations, two are novel point mutations (c.1526G > C and c.3062C > T) that are possibly pathogenic. The three infants are the youngest Chinese patients to have been diagnosed with sporadic CF at a very early stage. Follow-up examination showed that all of the cases remained symptom-free after early intervention, indicating the potential benefit of very early diagnosis and timely intervention in children with CF. Our results demonstrate the necessity of distinguishing CF from BS in Chinese infants with hypokalemic alkalosis and the significant diagnostic value of powerful exome sequencing for rare genetic diseases. Furthermore, our findings expand the CFTR mutation spectrum associated with CF.

  11. De novo assembly and characterization of the spleen transcriptome of common carp (Cyprinus carpio) using Illumina paired-end sequencing.

    Science.gov (United States)

    Li, Guoxi; Zhao, Yinli; Liu, Zhonghu; Gao, Chunsheng; Yan, Fengbin; Liu, Bianzhi; Feng, Jianxin

    2015-06-01

    Common carp (Cyprinus carpio) is one of the most important aquacultured species of the family Cyprinidae, and breeding this species for disease resistance is becoming more and more important. However, at the genome or transcriptome levels, study of the immunogenetics of disease resistance in the common carp is lacking. In this study, 60,316,906 and 75,200,328 paired-end clean reads were obtained from two cDNA libraries of the common carp spleen by Illumina paired-end sequencing technology. Totally, 130,293 unique transcript fragments (unigenes) were assembled, with an average length of 1400.57 bp. Approximately 105,612 (81.06%) unigenes could be annotated according to their homology with matches in the Nr, Nt, Swiss-Prot, COG, GO, or KEGG databases, and they were found to represent 46,747 non-redundant genes. Comparative analysis showed that 59.82% of the unigenes have significant similarity to zebrafish Refseq proteins. Gene expression comparison revealed that 10,432 and 6889 annotated unigenes were, respectively, up- and down-regulated with at least twofold changes between two developmental stages of the common carp spleen. Gene ontology and KEGG analysis were performed to classify all unigenes into functional categories for understanding gene functions and regulation pathways. In addition, 46,847 simple sequence repeats (SSRs) were detected from 35,618 unigenes, and a large number of single nucleotide polymorphism (SNP) and insertion/deletion (INDEL) sites were identified in the spleen transcriptome of common carp. This study has characterized the spleen transcriptome of the common carp for the first time, providing a valuable resource for a better understanding of the common carp immune system and defense mechanisms. This knowledge will also facilitate future functional studies on common carp immunogenetics that may eventually be applied in breeding programs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis.

    Science.gov (United States)

    Goettel, Wolfgang; Ramirez, Martha; Upchurch, Robert G; An, Yong-Qiang Charles

    2016-08-01

    Identification and characterization of a 254-kb genomic deletion on a duplicated chromosome segment that resulted in a low level of palmitic acid in soybean seeds using transcriptome sequencing. A large number of soybean genotypes varying in seed oil composition and content have been identified. Understanding the molecular mechanisms underlying these variations is important for breeders to effectively utilize them as a genetic resource. Through design and application of a bioinformatics approach, we identified nine co-regulated gene clusters by comparing seed transcriptomes of nine soybean genotypes varying in oil composition and content. We demonstrated that four gene clusters in the genotypes M23, Jack and N0304-303-3 coincided with large-scale genome rearrangements. The co-regulated gene clusters in M23 and Jack mapped to a previously described 164-kb deletion and a copy number amplification of the Rhg1 locus, respectively. The coordinately down-regulated gene clusters in N0304-303-3 were caused by a 254-kb deletion containing 19 genes including a fatty acyl-ACP thioesterase B gene (FATB1a). This deletion was associated with reduced palmitic acid content in seeds and was the molecular cause of a previously reported nonfunctional FATB1a allele, fap nc . The M23 and N0304-304-3 deletions were located in duplicated genome segments retained from the Glycine-specific whole genome duplication that occurred 13 million years ago. The homoeologous genes in these duplicated regions shared a strong similarity in both their encoded protein sequences and transcript accumulation levels, suggesting that they may have conserved and important functions in seeds. The functional conservation of homoeologous genes may result in genetic redundancy and gene dosage effects for their associated seed traits, explaining why the large deletion did not cause lethal effects or completely eliminate palmitic acid in N0304-303-3.

  13. Quantitative measurement of hypertrophic scar: intrarater reliability, sensitivity, and specificity.

    Science.gov (United States)

    Nedelec, Bernadette; Correa, José A; Rachelska, Grazyna; Armour, Alexis; LaSalle, Léo

    2008-01-01

    The comparison of scar evaluation over time requires measurement tools with acceptable intrarater reliability and the ability to discriminate skin characteristics of interest. The objective of this study was to evaluate the intrarater reliability and sensitivity and specificity of the Cutometer, the Mexameter, and the DermaScan C relative to the modified Vancouver Scar Scale (mVSS) in patient-matched normal skin, normal scar (donor sites), and hypertrophic scar (HSc). A single investigator evaluated four tissue types (severe HSc, less severe HSc, donor site, and normal skin) in 30 burn survivors with all four measurement tools. The intraclass correlation coefficient (ICC) for the Cutometer was acceptable (> or =0.75) for the maximum deformation measure for the donor site and normal skin (>0.78) but was below the acceptable range for the HSc sites and all other parameters. The ICC for the Mexameter erythema (>0.75) and melanin index (>0.89) and the DermaScan C total thickness measurement (>0.82) were acceptable for all sites. The ICC for the total of the height, pliability, and vascularity subscales of the mVSS was acceptable (0.81) for normal scar but below the acceptable range for the scar sites. The DermaScan C was clearly able to discriminate HSc from normal scar and normal skin based on the total thickness measure. The Cutometer was less discriminating but was still able to discriminate HSc from normal scar and normal skin. The Mexameter erythema index was not a good discriminator of HSc and normal scar. Receiver operating characteristic curves were generated to establish the best cutoff point for the DermaScan C total thickness and the Cutometer maximum deformation, which were 2.034 and 0.387 mm, respectively. This study showed that although the Cutometer, the DermaScan C, and the Mexameter have measurement properties that make them attractive substitutes for the mVSS, caution must be used when interpreting results since the Cutometer has a ceiling effect when

  14. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

    Science.gov (United States)

    2012-01-01

    Background Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation. Conclusions This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding

  15. Development and Characterization of Simple Sequence Repeat (SSR) Markers Based on RNA-Sequencing of Medicago sativa and In silico Mapping onto the M. truncatula Genome

    Science.gov (United States)

    Wang, Zan; Yu, Guohui; Shi, Binbin; Wang, Xuemin; Qiang, Haiping; Gao, Hongwen

    2014-01-01

    Sufficient codominant genetic markers are needed for various genetic investigations in alfalfa since the species is an outcrossing autotetraploid. With the newly developed next generation sequencing technology, a large amount of transcribed sequences of alfalfa have been generated and are available for identifying SSR markers by data mining. A total of 54,278 alfalfa non-redundant unigenes were assembled through the Illumina HiSeqTM 2000 sequencing technology. Based on 3,903 unigene sequences, 4,493 SSRs were identified. Tri-nucleotide repeats (56.71%) were the most abundant motif class while AG/CT (21.7%), AGG/CCT (19.8%), AAC/GTT (10.3%), ATC/ATG (8.8%), and ACC/GGT (6.3%) were the subsequent top five nucleotide repeat motifs. Eight hundred and thirty- seven EST-SSR primer pairs were successfully designed. Of these, 527 (63%) primer pairs yielded clear and scored PCR products and 372 (70.6%) exhibited polymorphisms. High transferability was observed for ssp falcata at 99.2% (523) and 71.7% (378) in M. truncatula. In addition, 313 of 527 SSR marker sequences were in silico mapped onto the eight M. truncatula chromosomes. Thirty-six polymorphic SSR primer pairs were used in the genetic relatedness analysis of 30 Chinese alfalfa cultivated accessions generating a total of 199 scored alleles. The mean observed heterozygosity and polymorphic information content were 0.767 and 0.635, respectively. The codominant markers not only enriched the current resources of molecular markers in alfalfa, but also would facilitate targeted investigations in marker-trait association, QTL mapping, and genetic diversity analysis in alfalfa. PMID:24642969

  16. Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.

    Science.gov (United States)

    Shen, Peter S; Domek, Matthew J; Sanz-García, Eduardo; Makaju, Aman; Taylor, Ryan M; Hoggan, Ryan; Culumber, Michele D; Oberg, Craig J; Breakwell, Donald P; Prince, John T; Belnap, David M

    2012-08-01

    Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpD-like densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.

  17. Sequencing and characterization of asclepain f: the first cysteine peptidase cDNA cloned and expressed from Asclepias fruticosa latex.

    Science.gov (United States)

    Trejo, Sebastián A; López, Laura M I; Caffini, Néstor O; Natalucci, Claudia L; Canals, Francesc; Avilés, Francesc X

    2009-07-01

    Asclepain f is a papain-like protease previously isolated and characterized from latex of Asclepias fruticosa. This enzyme is a member of the C1 family of cysteine proteases that are synthesized as preproenzymes. The enzyme belongs to the alpha + beta class of proteins, with two disulfide bridges (Cys22-Cys63 and Cys56-Cys95) in the alpha domain, and another one (Cys150-Cys201) in the beta domain, as was determined by molecular modeling. A full-length 1,152 bp cDNA was cloned by RT-RACE-PCR from latex mRNA. The sequence was predicted as an open reading frame of 340 amino acid residues, of which 16 residues belong to the signal peptide, 113 to the propeptide and 211 to the mature enzyme. The full-length cDNA was ligated to pPICZalpha vector and expressed in Pichia pastoris. Recombinant asclepain f showed endopeptidase activity on pGlu-Phe-Leu-p-nitroanilide and was identified by PMF-MALDI-TOF MS. Asclepain f is the first peptidase cloned and expressed from mRNA isolated from plant latex, confirming the presence of the preprocysteine peptidase in the latex.

  18. Copolymers of N-cyclohexylacrylamide and n-butyl acrylate: synthesis, characterization, monomer reactivity ratios and mean sequence length

    Directory of Open Access Journals (Sweden)

    2007-06-01

    Full Text Available Copolymerization of N-cyclohexylacrylamide (NCHA and n-butyl acrylate (BA was carried out in dimethylformamide at 55±1°C using azobisisobutyronitrile as a free radical initiator. The copolymers were characterized by 1H-NMR spectroscopy and the copolymer compositions were determined by 1H-NMR analysis. The reactivity ratios of the monomers were determined by both linear and non-linear methods. The reactivity ratios of monomers determined using linear methods like Fineman-Ross (r1 = 0.37 and r2 = 1.77 , Kelen-Tudos (r1 = 0.38 and r2 = 1.77, ext. Kelen-Tudos (r1 = 0.37 and r2 = 1.75 Yezrieler-Brokhina-Roskin (r1 = 0.37 and r2 = 1.77 and non-linear methods like Tidwell-Mortimer (r1 = 0.37 and r2 = 1.76, ProCop (r1 = 0.36 and r2 = 1.82. The Q and e values for NCHA are 0.67 and 0.68 respectively. Mean sequence lengths of copolymers are estimated from r1 and r2 values. It shows that the BA units increases in a linear fashion in the polymer chain as the concentration of BA increases in the monomer feed.

  19. Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

    Directory of Open Access Journals (Sweden)

    Matthew D. MacManes

    2014-10-01

    Full Text Available As a direct result of intense heat and aridity, deserts are thought to be among the most harsh of environments, particularly for their mammalian inhabitants. Given that osmoregulation can be challenging for these animals, with failure resulting in death, strong selection should be observed on genes related to the maintenance of water and solute balance. One such animal, Peromyscus eremicus, is native to the desert regions of the southwest United States and may live its entire life without oral fluid intake. As a first step toward understanding the genetics that underlie this phenotype, we present a characterization of the P. eremicus transcriptome. We assay four tissues (kidney, liver, brain, testes from a single individual and supplement this with population level renal transcriptome sequencing from 15 additional animals. We identified a set of transcripts undergoing both purifying and balancing selection based on estimates of Tajima’s D. In addition, we used the branch-site test to identify a transcript—Slc2a9, likely related to desert osmoregulation—undergoing enhanced selection in P. eremicus relative to a set of related non-desert rodents.

  20. Fully automatic segmentation of left atrium and pulmonary veins in late gadolinium-enhanced MRI: Towards objective atrial scar assessment.

    Science.gov (United States)

    Tao, Qian; Ipek, Esra Gucuk; Shahzad, Rahil; Berendsen, Floris F; Nazarian, Saman; van der Geest, Rob J

    2016-08-01

    To realize objective atrial scar assessment, this study aimed to develop a fully automatic method to segment the left atrium (LA) and pulmonary veins (PV) from late gadolinium-enhanced (LGE) magnetic resonance imaging (MRI). The extent and distribution of atrial scar, visualized by LGE-MRI, provides important information for clinical treatment of atrial fibrillation (AF) patients. Forty-six AF patients (age 62 ± 8, 14 female) who underwent cardiac MRI prior to RF ablation were included. A contrast-enhanced MR angiography (MRA) sequence was acquired for anatomy assessment followed by an LGE sequence for LA scar assessment. A fully automatic segmentation method was proposed consisting of two stages: 1) global segmentation by multiatlas registration; and 2) local refinement by 3D level-set. These automatic segmentation results were compared with manual segmentation. The LA and PVs were automatically segmented in all subjects. Compared with manual segmentation, the method yielded a surface-to-surface distance of 1.49 ± 0.65 mm in the LA region when using both MRA and LGE, and 1.80 ± 0.93 mm when using LGE alone (P automatic and manual segmentation was comparable to the interobserver difference (P = 0.8 in LA region and P = 0.7 in PV region). We developed a fully automatic method for LA and PV segmentation from LGE-MRI, with comparable performance to a human observer. Inclusion of an MRA sequence further improves the segmentation accuracy. The method leads to automatic generation of a patient-specific model, and potentially enables objective atrial scar assessment for AF patients. J. Magn. Reson. Imaging 2016;44:346-354. © 2016 Wiley Periodicals, Inc.

  1. Hypertrophic scars and keloids in surgery: current concepts.

    Science.gov (United States)

    Song, Colin

    2014-09-01

    Hypertrophic scars and keloids remain a challenge in surgery. We appreciate that our understanding of the process at cellular and molecular level, profound as it is, when it comes to the clinical evidence much is left to be desired. Although the bench to bedside conundrum remains, the science of translational research calls for an even higher level of cooperation between the scientist and the clinician for the impetus to succeed.The clinicians alerted us to the possible theories in the pathogenesis of keloid formation, inter alia, the ischemia theory, mast cell theory, immune theory, transforming growth factor β interaction, mechanical theory, and the melanocyte stimulating hormone theory. All of the above presupposed a stimulus that would result in an uncontrolled upregulation of collagen and extracellular matrix expression in the pathogenesis of the keloid. This bedside to bench initiative, as in true science, realized more ponderables than possibilities.By the same token, research into the epidermal-mesenchymal signaling, molecular biology, genomics, and stem cell research holds much promise in the bench top arena. To assess efficacy, many scar assessment scores exist in the literature. The clinical measurement of scar maturity can aid in determining end points for therapeutics. Tissue oxygen tension and color assessment of scars by standardized photography proved to be useful.In surgery, the use of dermal substitutes holds some promise as we surmise that quality scars that arise from dermal elements, molecular and enzyme behavior, and balance. Although a systematic review shows some benefit for earlier closure and healing of wounds, no such review exists at this point in time for the use of dermal substitutes in scars.Adipose-derived stem cell, as it pertains to scars, will hopefully realize the potential of skin regeneration rather than by repair in which we are familiar with as well as the undesirable scarring as a result of healing through the inflammatory

  2. ["Palimpsest scar" lesions in a context of torture (Darfur, Sudan)].

    Science.gov (United States)

    Charlier, P; Bou Abdallah, F; Mostefai Dulac, Y; Deo, S; Jacqueline, S; Brun, L; Hervé, C

    2017-11-01

    As a result of the current exponentially growing refugee population from the Middle-East and East Africa (Sudan, Darfur, Eritrea), clinicians (including forensic pathologists) are seeing atypical skin lesions, mainly of a traumatic nature, but in some cases associated with long-standing lesions related to ethnic practices. A case of torture sequelae is presented herein in a patient originally from Darfur (Sudan): cutaneous incisions were made on old scars several times using a knife. The clinical presentation of scarification lesions and that of atypically healed wounds (presumably an effect of inflammation induced by the introduction of irritating foreign bodies such as sand, salt, etc.) are completely different: in all cases they indicate a relative timeframe of the facts, which the clinician should not overlook in reconstructing the patient's course and the injuries to which he has been subjected (hence the proposed designation of "palimpsest scar", in the sense that a palimpsest is a manuscript on a parchment that previously contained writing but has been scratched clean to be overwritten). Thus, a "palimpsest scar" constitutes a fresh scar on top of and hiding another (ritual) scar in a context of ethnic cleansing. The diagnostic and clinical significance comes from the importance of differentiating between ethnic-type lesions and those induced by physical violence and abuse in a context of war. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  3. [Comparision of Different Methods of Area Measurement in Irregular Scar].

    Science.gov (United States)

    Ran, D; Li, W J; Sun, Q G; Li, J Q; Xia, Q

    2016-10-01

    To determine a measurement standard of irregular scar area by comparing the advantages and disadvantages of different measurement methods in measuring same irregular scar area. Irregular scar area was scanned by digital scanning and measured by coordinate reading method, AutoCAD pixel method, Photoshop lasso pixel method, Photoshop magic bar filled pixel method and Foxit PDF reading software, and some aspects of these methods such as measurement time, repeatability, whether could be recorded and whether could be traced were compared and analyzed. There was no significant difference in the scar areas by the measurement methods above. However, there was statistical difference in the measurement time and repeatability by one or multi performers and only Foxit PDF reading software could be traced back. The methods above can be used for measuring scar area, but each one has its advantages and disadvantages. It is necessary to develop new measurement software for forensic identification. Copyright© by the Editorial Department of Journal of Forensic Medicine

  4. Caesarean section greatly increases risk of scar endometriosis.

    Science.gov (United States)

    Nominato, Nilo Sérgio; Prates, Luis Felipe Victor Spyer; Lauar, Isabela; Morais, Jaqueline; Maia, Laura; Geber, Selmo

    2010-09-01

    To estimate the incidence of scar endometriosis after different surgical procedures. A retrospective study of 72 patients diagnosed with scar endometriosis between 1978 and 2003 was performed. Patient age, site of endometriosis, previous operations, time-gap between last surgery and onset of symptoms, nodule characteristics, and recurrence were evaluated. Age ranged from 16 to 48 years. Location varied according to the previous surgery: 46 caesarean section, one hysterectomy, one in abdominal surgery, 19 episiotomy, one was a relapse and two pelvic floor procedures, two women with no previous surgery. The incidence of scar endometriosis after caesarean section was significantly higher than after episiotomy (0.2 and 0.06%, respectively: p<0.00001) with a relative risk of 3.3. Pain was the most frequent symptom. The mean time between surgery and onset of symptoms was 3.7 years. Our findings confirm that scar endometriosis is a rare condition and indicate, probably for the first time, that caesarean section greatly increases the risk of developing scar endometriosis. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

  5. Emergent scar lines in chaotic advection of passive directors

    Science.gov (United States)

    Hejazi, Bardia; Mehlig, Bernhard; Voth, Greg A.

    2017-12-01

    We examine the spatial field of orientations of slender fibers that are advected by a two-dimensional fluid flow. The orientation field of these passive directors are important in a wide range of industrial and geophysical flows. We introduce emergent scar lines as the dominant coherent structures in the orientation field of passive directors in chaotic flows. Previous work has identified the existence of scar lines where the orientation rotates by π over short distances, but the lines that were identified disappeared as time progressed. As a result, earlier work focused on topological singularities in the orientation field, which we find to play a negligible role at long times. We use the standard map as a simple time-periodic two-dimensional flow that produces Lagrangian chaos. This class of flows produces persistent patterns in passive scalar advection and we find that a different kind of persistent pattern develops in the passive director orientation field. We identify the mechanism by which emergent scar lines grow to dominate these patterns at long times in complex flows. Emergent scar lines form where the recent stretching of the fluid element is perpendicular to earlier stretching. Thus these scar lines can be labeled by their age, defined as the time since their stretching reached a maximum.

  6. Understanding the NG2 glial scar after spinal cord injury

    Directory of Open Access Journals (Sweden)

    Amber R Hackett

    2016-11-01

    Full Text Available NG2 cells, also known as oligodendrocyte progenitor cells, are located throughout the central nervous system and serve as a pool of progenitors to differentiate into oligodendrocytes. In response to spinal cord injury, NG2 cells increase their proliferation and differentiation into remyelinating oligodendrocytes. While astrocytes are typically associated with being the major cell type in the glial scar, many NG2 cells also accumulate within the glial scar but their function remains poorly understood. Similar to astrocytes, these cells hypertrophy, upregulate expression of chondroitin sulfate proteoglycans, inhibit axon regeneration, contribute to the glial-fibrotic scar border, and some even differentiate into astrocytes. Whether NG2 cells also have a role in other astrocyte functions, such as preventing the spread of infiltrating leukocytes and expression of inflammatory cytokines, is not yet known. Thus, NG2 cells are not only important for remyelination after spinal cord injury, but are also a major component of the glial scar with functions that overlap with astrocytes in this region. In this review, we describe the signaling pathways important for the proliferation and differentiation of NG2 cells, as well as the role of NG2 cells in scar formation and tissue repair.

  7. Lactic acid peeling in superficial acne scarring in Indian skin.

    Science.gov (United States)

    Sachdeva, Silonie

    2010-09-01

    Chemical peeling with both alpha and beta hydroxy acids has been used to improve acne scarring with pigmentation. Lactic acid, a mild alpha hydroxy acid, has been used in the treatment of various dermatological indications but no study is reported in acne scarring with pigmentation. To evaluate the efficacy and safety of full strength pure lactic acid 92% (pH 2.0) chemical peel in superficial acne scarring in Indian skin. Seven patients, Fitzpatrick skin type IV-V, in age group 20-30 years with superficial acne scarring were enrolled in the study. Chemical peeling was done with lactic acid at an interval of 2 weeks to a maximum of four peels. Pre- and post-peel clinical photographs were taken at every session. Patients were followed every month for 3 months after the last peel to evaluate the effects. At the end of 3 months, there was definite improvement in the texture, pigmentation, and appearance of the treated skin, with lightening of scars. Significant improvement (greater than 75% clearance of lesions) occurred in one patient (14.28%), good improvement (51-75% clearance) in three patients (42.84%), moderate improvement (26-50% clearance) in two patients (28.57%), and mild improvement (1-25% clearance) in one patient (14.28%). © 2010 Wiley Periodicals, Inc.

  8. Characterization of expressed sequence tag-derived simple sequence repeat markers for Aspergillus flavus: emphasis on variability of isolates from the southern United States.

    Science.gov (United States)

    Wang, Xinwang; Wadl, Phillip A; Wood-Jones, Alicia; Windham, Gary; Trigiano, Robert N; Scruggs, Mary; Pilgrim, Candace; Baird, Richard

    2012-12-01

    Simple sequence repeat (SSR) markers were developed from Aspergillus flavus expressed sequence tag (EST) database to conduct an analysis of genetic relationships of Aspergillus isolates from numerous host species and geographical regions, but primarily from the United States. Twenty-nine primers were designed from 362 tri-nucleotide EST-SSR sequences. Eighteen polymorphic loci were used to genotype 96 Aspergillus species isolates. The number of alleles detected per locus ranged from 2 to 24 with a mean of 8.2 alleles. Haploid diversity ranged from 0.28 to 0.91. Genetic distance matrix was used to perform principal coordinates analysis (PCA) and to generate dendrograms using unweighted pair group method with arithmetic mean (UPGMA). Two principal coordinates explained more than 75 % of the total variation among the isolates. One clade was identified for A. flavus isolates (n = 87) with the other Aspergillus species (n = 7) using PCA, but five distinct clusters were present when the others taxa were excluded from the analysis. Six groups were noted when the EST-SSR data were compared using UPGMA. However, the latter PCA or UPGMA comparison resulted in no direct associations with host species, geographical region or aflatoxin production. Furthermore, there was no direct correlation to visible morphological features such as sclerotial types. The isolates from Mississippi Delta region, which contained the largest percentage of isolates, did not show any unusual clustering except for isolates K32, K55, and 199. Further studies of these three isolates are warranted to evaluate their pathogenicity, aflatoxin production potential, additional gene sequences (e.g., RPB2), and morphological comparisons.

  9. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.

    Directory of Open Access Journals (Sweden)

    Binhua Liang

    Full Text Available BACKGROUND: Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS: HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE: Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.

  10. Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

    Science.gov (United States)

    Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

    2016-05-23

    Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family.

  11. Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale

    DEFF Research Database (Denmark)

    Liu, Siyang; Huang, Shujia; Rao, Junhua

    2015-01-01

    present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome......) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. We...... assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction...

  12. A Study Of 7 Cases Of Depressed Facial Scars Corrected By Subcision

    Directory of Open Access Journals (Sweden)

    Malakar Subrata

    1997-01-01

    Full Text Available Seven (7 cases of depressed facial scars which included depressed distensile acne scars, depressed bound down scars of acne excluding deep ice pick scars, and scars of varicella constituted the study group. The scars were treated with a new method named subcuticular undermining. A tri-bevelled hypodermic needle was inserted through a puncture in the skin surface and its sharp edges were manouevered under the scar. The depression was lifted by the releasing action of the needle maneuevere and from connective tissue that forms in course of normal wound healing. Approximately 50% to 80% improvement of all the scars were noticed. Patient’s compliance was highly satisfactory. Subcision is an appropriate, option in depressed scars of black skin (Type IV-Type VI where dermabrasion and medium-depth and deep chemical peeling are contraindicated.

  13. Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan

    KAUST Repository

    Hasan, Zahra; Ali, Asho; McNerney, Ruth; Mallard, Kim; Hill-Cawthorne, Grant A.; Coll, Francesc; Nair, Mridul; Pain, Arnab; Clark, Taane G.; Hasan, Rumina

    2015-01-01

    Objectives: The global increase in drug resistance in Mycobacterium tuberculosis (MTB) strains increases the focus on improved molecular diagnostics for MTB. Extensively drug-resistant (XDR) - TB is caused by MTB strains resistant to rifampicin, isoniazid, fluoroquinolone and aminoglycoside antibiotics. Resistance to anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs), in particular MTB genes. However, there is regional variation between MTB lineages and the SNPs associated with resistance. Therefore, there is a need to identify common resistance conferring SNPs so that effective molecular-based diagnostic tests for MTB can be developed. This study investigated used whole genome sequencing (WGS) to characterize 37 XDR MTB isolates from Pakistan and investigated SNPs related to drug resistance. Methods: XDR-TB strains were selected. DNA was extracted from MTB strains, and samples underwent WGS with 76-base-paired end fragment sizes using Illumina paired end HiSeq2000 technology. Raw sequence data were mapped uniquely to H37Rv reference genome. The mappings allowed SNPs and small indels to be called using SAMtools/BCFtools. Results: This study found that in all XDR strains, rifampicin resistance was attributable to SNPs in the rpoB RDR region. Isoniazid resistance-associated mutations were primarily related to katG codon 315 followed by inhA S94A. Fluoroquinolone resistance was attributable to gyrA 91-94 codons in most strains, while one did not have SNPs in either gyrA or gyrB. Aminoglycoside resistance was mostly associated with SNPs in rrs, except in 6 strains. Ethambutol resistant strains had embB codon 306 mutations, but many strains did not have this present. The SNPs were compared with those present in commercial assays such as LiPA Hain MDRTBsl, and the sensitivity of the assays for these strains was evaluated. Conclusions: If common drug resistance associated with SNPs evaluated the concordance between phenotypic and

  14. Whole genome sequencing-based characterization of extensively drug resistant (XDR) strains of Mycobacterium tuberculosis from Pakistan

    KAUST Repository

    Hasan, Zahra

    2015-03-01

    Objectives: The global increase in drug resistance in Mycobacterium tuberculosis (MTB) strains increases the focus on improved molecular diagnostics for MTB. Extensively drug-resistant (XDR) - TB is caused by MTB strains resistant to rifampicin, isoniazid, fluoroquinolone and aminoglycoside antibiotics. Resistance to anti-tuberculous drugs has been associated with single nucleotide polymorphisms (SNPs), in particular MTB genes. However, there is regional variation between MTB lineages and the SNPs associated with resistance. Therefore, there is a need to identify common resistance conferring SNPs so that effective molecular-based diagnostic tests for MTB can be developed. This study investigated used whole genome sequencing (WGS) to characterize 37 XDR MTB isolates from Pakistan and investigated SNPs related to drug resistance. Methods: XDR-TB strains were selected. DNA was extracted from MTB strains, and samples underwent WGS with 76-base-paired end fragment sizes using Illumina paired end HiSeq2000 technology. Raw sequence data were mapped uniquely to H37Rv reference genome. The mappings allowed SNPs and small indels to be called using SAMtools/BCFtools. Results: This study found that in all XDR strains, rifampicin resistance was attributable to SNPs in the rpoB RDR region. Isoniazid resistance-associated mutations were primarily related to katG codon 315 followed by inhA S94A. Fluoroquinolone resistance was attributable to gyrA 91-94 codons in most strains, while one did not have SNPs in either gyrA or gyrB. Aminoglycoside resistance was mostly associated with SNPs in rrs, except in 6 strains. Ethambutol resistant strains had embB codon 306 mutations, but many strains did not have this present. The SNPs were compared with those present in commercial assays such as LiPA Hain MDRTBsl, and the sensitivity of the assays for these strains was evaluated. Conclusions: If common drug resistance associated with SNPs evaluated the concordance between phenotypic and

  15. RAPD-SCAR Markers for Genetically Improved NEW GIFT Nile Tilapia (Oreochromis niloticus niloticus L.) and Their Application in Strain Identification.

    Science.gov (United States)

    Li, Si-Fa; Tang, Shou-Jie; Cai, Wan-Qi

    2010-04-01

    The NEW GIFT Nile tilapia (Oreochromis niloticus niloticus L.) is a nationally certificated new strain selected over 14 years and 9 generations from the base strain of GIFT Nile tilapia, introduced in 1994. This new variety has been extended in most of areas of China. The management of genetically improved strains, including the genetic markers for identification is needed urgently. RAPD analysis was conducted and their conversion to SCAR markers was developed. From NEW GIFT Nile tilapia, two strain-specific RAPD bands, S(304 )(624 bp ) and S(36 )(568 bp ) were identified. The strain-specific RAPD bands were gel-purified, cloned, and sequenced. Locus-specific primers were then designed to amplify the strain-specific bands. PCR amplification was conducted to test the variations in allele frequencies of two converted SCAR markers among the NEW GIFT Nile tilapia and its base strains, as well as 7 additional farmed strains worldwide. The frequency of SCAR marker I (553 bp) was 85.7% in NEW GIFT Nile tilapia, but 16.7% in the base strain. The frequency of SCAR marker II (558 bp) was 91.4% in NEW GIFT Nile tilapia, but 0% - 70% in the 7 other strains. In order to confirm the utility of these two markers, an examination was conducted for a wild population from Egypt, resulted the frequency of SCAR I and II was 10% and 70%, respectively, much lower than that of New GIFT strain. The increase in allele frequency of these two SCAR markers suggests that these markers might be genetically linked to the quantitative trait loci (QTL) underlining the performance traits by long term selection, and indicate the bright potential of SCAR marker technology for tracking generations during selection progress and for distinguishing among genetically improved strain and other strains.

  16. Etiopathogenesis of Post-endodontic Periapical Scar Formation

    Directory of Open Access Journals (Sweden)

    Edita Horká

    2012-01-01

    Full Text Available Introduction: A periapical scar represents a clinically asymptomatic, non-progressive, small, periapical radiolucency in patients with a previously well-performed root canal treatment.The hypothesis: We introduce a hypothesis that periapical scar formation is caused by osseoinhibitory molecular signaling from the epithelial cell rests of Malassez.Evaluation of the hypothesis: When epithelial cell rests of Malassez are present in teeth with an infected root canal system, a periapical cyst develops, whereas in the case of a treated root canal system infection, periapical inflammation is diminished and the periapical leasion heals until the regeneration process reaches the apical part of the tooth where epithelial cell rests of Malassez are present. Cytokines cause rapidly progressive defensive fibroproduction and scar formation, in which osteoblasts cannot differentiate into

  17. Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene.

    Science.gov (United States)

    Yohda, Masafumi; Yagi, Osami; Takechi, Ayane; Kitajima, Mizuki; Matsuda, Hisashi; Miyamura, Naoaki; Aizawa, Tomoko; Nakajima, Mutsuyasu; Sunairi, Michio; Daiba, Akito; Miyajima, Takashi; Teruya, Morimi; Teruya, Kuniko; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Juan, Ayaka; Nakano, Kazuma; Aoyama, Misako; Terabayashi, Yasunobu; Satou, Kazuhito; Hirano, Takashi

    2015-07-01

    A Dehalococcoides-containing bacterial consortium that performed dechlorination of 0.20 mM cis-1,2-dichloroethene to ethene in 14 days was obtained from the sediment mud of the lotus field. To obtain detailed information of the consortium, the metagenome was analyzed using the short-read next-generation sequencer SOLiD 3. Matching the obtained sequence tags with the reference genome sequences indicated that the Dehalococcoides sp. in the consortium was highly homologous to Dehalococcoides mccartyi CBDB1 and BAV1. Sequence comparison with the reference sequence constructed from 16S rRNA gene sequences in a public database showed the presence of Sedimentibacter, Sulfurospirillum, Clostridium, Desulfovibrio, Parabacteroides, Alistipes, Eubacterium, Peptostreptococcus and Proteocatella in addition to Dehalococcoides sp. After further enrichment, the members of the consortium were narrowed down to almost three species. Finally, the full-length circular genome sequence of the Dehalococcoides sp. in the consortium, D. mccartyi IBARAKI, was determined by analyzing the metagenome with the single-molecule DNA sequencer PacBio RS. The accuracy of the sequence was confirmed by matching it to the tag sequences obtained by SOLiD 3. The genome is 1,451,062 nt and the number of CDS is 1566, which includes 3 rRNA genes and 47 tRNA genes. There exist twenty-eight RDase genes that are accompanied by the genes for anchor proteins. The genome exhibits significant sequence identity with other Dehalococcoides spp. throughout the genome, but there exists significant difference in the distribution RDase genes. The combination of a short-read next-generation DNA sequencer and a long-read single-molecule DNA sequencer gives detailed information of a bacterial consortium. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  18. Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.

    Science.gov (United States)

    Tkavc, Rok; Matrosova, Vera Y; Grichenko, Olga E; Gostinčar, Cene; Volpe, Robert P; Klimenkova, Polina; Gaidamakova, Elena K; Zhou, Carol E; Stewart, Benjamin J; Lyman, Mathew G; Malfatti, Stephanie A; Rubinfeld, Bonnee; Courtot, Melanie; Singh, Jatinder; Dalgard, Clifton L; Hamilton, Theron; Frey, Kenneth G; Gunde-Cimerman, Nina; Dugan, Lawrence; Daly, Michael J

    2017-01-01

    Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans . However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

  19. Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015

    Directory of Open Access Journals (Sweden)

    Sopio Chochua

    2017-09-01

    Full Text Available Group A streptococci (GAS are genetically diverse. Determination of strain features can reveal associations with disease and resistance and assist in vaccine formulation. We employed whole-genome sequence (WGS-based characterization of 1,454 invasive GAS isolates recovered in 2015 by Active Bacterial Core Surveillance and performed conventional antimicrobial susceptibility testing. Predictions were made for genotype, GAS carbohydrate, antimicrobial resistance, surface proteins (M family, fibronectin binding, T, R28, secreted virulence proteins (Sda1, Sic, exotoxins, hyaluronate capsule, and an upregulated nga operon (encodes NADase and streptolysin O promoter (Pnga3. Sixty-four M protein gene (emm types were identified among 69 clonal complexes (CCs, including one CC of Streptococcus dysgalactiae subsp. equisimilis. emm types predicted the presence or absence of active sof determinants and were segregated into sof-positive or sof-negative genetic complexes. Only one “emm type switch” between strains was apparent. sof-negative strains showed a propensity to cause infections in the first quarter of the year, while sof+ strain infections were more likely in summer. Of 1,454 isolates, 808 (55.6% were Pnga3 positive and 637 (78.9% were accounted for by types emm1, emm89, and emm12. Theoretical coverage of a 30-valent M vaccine combined with an M-related protein (Mrp vaccine encompassed 98% of the isolates. WGS data predicted that 15.3, 13.8, 12.7, and 0.6% of the isolates were nonsusceptible to tetracycline, erythromycin plus clindamycin, erythromycin, and fluoroquinolones, respectively, with only 19 discordant phenotypic results. Close phylogenetic clustering of emm59 isolates was consistent with recent regional emergence. This study revealed strain traits informative for GAS disease incidence tracking, outbreak detection, vaccine strategy, and antimicrobial therapy.

  20. Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149

    Directory of Open Access Journals (Sweden)

    Rok Tkavc

    2018-01-01

    Full Text Available Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute, heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

  1. Disfiguring scarring following mesotherapy-associated Mycobacterium cosmeticum infection.

    Science.gov (United States)

    Beer, Kenneth; Waibel, Jill

    2009-04-01

    Mesotherapy is a popular procedure that poses risks that include scarring, contour changes and bacterial infections. The benefits of the procedure remain to be objectively delineated in a placebo-controlled, blinded study. Despite the lack of evidence to support its use, it is marketed as a "nonsurgical and safe" way to remove fat. The authors report a case of mycobacterial infection resulting from mesotherapy. This infection should be considered when a patient presents with a mesotherapy complication and should be discussed with the patient prior to the procedure. Options for treatment of the scarring are considered.

  2. Isolation and sequence characterization of DNA-A genome of a new begomovirus strain associated with severe leaf curling symptoms of Jatropha curcas L.

    KAUST Repository

    Chauhan, Sushma

    2018-04-22

    Begomoviruses belong to the family Geminiviridae are associated with several disease symptoms, such as mosaic and leaf curling in Jatropha curcas. The molecular characterization of these viral strains will help in developing management strategies to control the disease. In this study, J. curcas that was infected with begomovirus and showed acute leaf curling symptoms were identified. DNA-A segment from pathogenic viral strain was isolated and sequenced. The sequenced genome was assembled and characterized in detail. The full-length DNA-A sequence was covered by primer walking. The genome sequence showed the general organization of DNA-A from begomovirus by the distribution of ORFs in both viral and anti-viral strands. The genome size ranged from 2844 bp–2852 bp. Three strains with minor nucleotide variations were identified, and a phylogenetic analysis was performed by comparing the DNA-A segments from other reported begomovirus isolates. The maximum sequence similarity was observed with Euphorbia yellow mosaic virus (FN435995). In the phylogenetic tree, no clustering was observed with previously reported begomovirus strains isolated from J. curcas host. The strains isolated in this study belong to new begomoviral strain that elicits symptoms of leaf curling in J. curcas. The results indicate that the probable origin of the strains is from Jatropha mosaic virus infecting J. gassypifolia. The strains isolated in this study are referred as Jatropha curcas leaf curl India virus (JCLCIV) based on the major symptoms exhibited by host J. curcas.

  3. Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus.

    Science.gov (United States)

    Nakano, Michiharu; Shimada, Takehiko; Endo, Tomoko; Fujii, Hiroshi; Nesumi, Hirohisa; Kita, Masayuki; Ebina, Masumi; Shimizu, Tokurou; Omura, Mitsuo

    2012-02-01

    Polyembryony, in which multiple somatic nucellar cell-derived embryos develop in addition to the zygotic embryo in a seed, is common in the genus Citrus. Previous genetic studies indicated polyembryony is mainly determined by a single locus, but the underlying molecular mechanism is still unclear. As a step towards identification and characterization of the gene or genes responsible for nucellar embryogenesis in Citrus, haplotype-specific physical maps around the polyembryony locus were constructed. By sequencing three BAC clones aligned on the polyembryony haplotype, a single contiguous draft sequence consisting of 380 kb containing 70 predicted open reading frames (ORFs) was reconstructed. Single nucleotide polymorphism genotypes detected in the sequenced genomic region showed strong association with embryo type in Citrus, indicating a common polyembryony locus is shared among widely diverse Citrus cultivars and species. The arrangement of the predicted ORFs in the characterized genomic region showed high collinearity to the genomic sequence of chromosome 4 of Vitis vinifera and linkage group VI of Populus trichocarpa, suggesting that the syntenic relationship among these species is conserved even though V. vinifera and P. trichocarpa are non-apomictic species. This is the first study to characterize in detail the genomic structure of an apomixis locus determining adventitious embryony. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  4. A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.

    Directory of Open Access Journals (Sweden)

    Wayne Aubrey

    Full Text Available Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed number of times. Deletion methods that recycle markers generally are either imprecise (remove untargeted sequences, or leave scar sequences which can cause genome instability and rearrangements. No existing marker recycling method is automation-friendly. We have developed a novel openly available deletion tool that consists of: 1 a method for deleting genomic elements that can be repeatedly used without limit, is precise, scar-free, and suitable for automation; and 2 software to design the method's primers. Our tool is sequence agnostic and could be used to delete large numbers of coding sequences, promoter regions, transcription factor binding sites, terminators, etc in a single genome. We have validated our tool on the deletion of non-essential open reading frames (ORFs from S. cerevisiae. The tool is applicable to arbitrary genomes, and we provide primer sequences for the deletion of: 90% of the ORFs from the S. cerevisiae genome, 88% of the ORFs from S. pombe genome, and 85% of the ORFs from the L. lactis genome.

  5. Scar-free cutaneous wound healing in the leopard gecko, Eublepharis macularius.

    Science.gov (United States)

    Peacock, Hanna M; Gilbert, Emily A B; Vickaryous, Matthew K

    2015-11-01

    Cutaneous wounds heal with two possible outcomes: scarification or near-perfect integumentary restoration. Whereas scar formation has been intensively investigated, less is known about the tissue-level events characterising wounds that spontaneously heal scar-free, particularly in non-foetal amniotes. Here, a spatiotemporal investigation of scar-free cutaneous wound healing following full-thickness excisional biopsies to the tail and body of leopard geckos (Eublepharis macularius) is provided. All injuries healed without scarring. Cutaneous repair involves the development of a cell-rich aggregate within the wound bed, similar to scarring wounds. Unlike scar formation, scar-free healing involves a more rapid closure of the wound epithelium, and a delay in blood vessel development and collagen deposition within the wound bed. It was found that, while granulation tissue of scarring wounds is hypervascular, scar-free wound healing conspicuously does not involve a period of exuberant blood vessel formation. In addition, during scar-free wound healing the newly formed blood vessels are typically perivascular cell-supported. Immunohistochemistry revealed widespread expression of both the pro-angiogenic factor vascular endothelial growth factor A and the anti-angiogenic factor thrombospondin-1 within the healing wound. It was found that scar-free wound healing is an intrinsic property of leopard gecko integument, and involves a modulation of the cutaneous scar repair program. This proportional revascularisation is an important factor in scar-free wound healing. © 2015 Anatomical Society.

  6. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  7. The persistence to slaughter age of scars resulting from damage ...

    African Journals Online (AJOL)

    Cut wounds were persistent to slaughter as were scratch marks, with only a small percentage of scratch wounds incurred at a young age not persisting to slaughter age. Mean scar size at slaughter became smaller with an increase in age at which the wounds were inflicted, except at 13 months of age where it was assumed ...

  8. Macular scar secondary to congenital toxoplasmosis | El Hamichi ...

    African Journals Online (AJOL)

    A 8 years old girl suffers from strabismus since her first months of life. Her visual acuity was very low and could only see fingers moving in her left eye. Her left eye fundus showed a chorioretinal scar in the macula due to congenital toxoplasmosis. The biological findings proved the diagnosis of congenital toxoplasmosis.

  9. Basal Cell Carcinoma Arising in a Breast Augmentation Scar.

    Science.gov (United States)

    Edwards, Lisa R; Cresce, Nicole D; Russell, Mark A

    2017-04-01

    We report a case of a 46-year-old female who presented with a persistent lesion on the inferior right breast. The lesion was located within the scar from a breast augmentation procedure 12 years ago. The lesion had been treated as several conditions with no improvement. Biopsy revealed a superficial and nodular basal cell carcinoma, and the lesion was successfully removed with Mohs micrographic surgery. Basal cell carcinoma arising in a surgical scar is exceedingly rare with only 13 reported cases to date. This is the first reported case of basal cell carcinoma arising in a breast augmentation scar. We emphasize the importance of biopsy for suspicious lesions or those refractory to treatment, particularly those lesions that form within a scar. Level of Evidence V This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

  10. Episiotomy Scar Endometriosis Diagnosed on Cytology - A Case ...

    African Journals Online (AJOL)

    2017-06-30

    Jun 30, 2017 ... Dnyanada Kokode*, Anne Wilkinson, Sadhana Mahore and Trupti Dongre ... Endometriosis, the presence of functioning endometrial tissue outside the ... examination, a tender, irregular, raised nodule measuring .... hematoma, hypertrophic scar tissue, traumatic neuroma, ... CT and MRI seem to be useful in.

  11. The Purse-String Reinforced SMASectomy Short Scar Facelift

    NARCIS (Netherlands)

    van der Lei, Berend; Cromheecke, Michel; Hofer, Stefan O. P.

    Background: Over the last two decades, short scar facelifts, often referred to as "mini'' facelifts, have gained popularity. We use a purse-string reinforced (PRS) superficial musculoaponeurotic system rhytidectomy (SMASectomy) shortscar facelift that combines a SMASectomy in the vertical direction

  12. Terminology and biology of fire scars in selected central hardwoods

    Science.gov (United States)

    Kevin T. Smith; Elaine Kennedy Sutherland

    2001-01-01

    Dendrochronological analysis of fire scars requires tree survival of fire exposure. Trees survive fire exposure by: (1) avoidance of injury through constitutive protection and (2) induced defense. Induced defenses include (a) compartmentalization processes that resist the spread of injury and infection and (b) closure processes that restore the continuity of the...

  13. Triterpenes for Well-Balanced Scar Formation in Superficial Wounds

    Directory of Open Access Journals (Sweden)

    Stefan Kindler

    2016-08-01

    Full Text Available Triterpenes are demonstrably effective for accelerating re-epithelialisation of wounds and known to improve scar formation for superficial lesions. Among the variety of triterpenes, betuline is of particular medical interest. Topical betuline gel (TBG received drug approval in 2016 from the European Commission as the first topical therapeutic agent with the proven clinical benefit of accelerating wound healing. Two self-conducted randomized intra-individual comparison clinical studies with a total of 220 patients involved in TBG treatment of skin graft surgical wounds have been screened for data concerning the aesthetic aspect of wound healing. Three months after surgery wound treatment with TBG resulted in about 30% of cases with more discreet scars, and standard of care in about 10%. Patients themselves appreciate the results of TBG after 3 months even more (about 50% compared to standard of care (about 10%. One year after surgery, the superiority of TBG counts for about 25% in comparison with about 10%, and from the patients’ point of view, for 25% compared to 4% under standard of care. In the majority of wound treatment cases, there is no difference visible between TBG treatment and standard of care after 1 year of scar formation. However, in comparison, TBG still offers a better chance for discreet scars and therefore happens to be superior in good care of wounds.

  14. Histologic features of alopecias: part II: scarring alopecias.

    Science.gov (United States)

    Bernárdez, C; Molina-Ruiz, A M; Requena, L

    2015-05-01

    The diagnosis of disorders of the hair and scalp can generally be made on clinical grounds, but clinical signs are not always diagnostic and in some cases more invasive techniques, such as a biopsy, may be necessary. This 2-part article is a detailed review of the histologic features of the main types of alopecia based on the traditional classification of these disorders into 2 major groups: scarring and nonscarring alopecias. Scarring alopecias are disorders in which the hair follicle is replaced by fibrous scar tissue, a process that leads to permanent hair loss. In nonscarring alopecias, the follicles are preserved and hair growth can resume when the cause of the problem is eliminated. In the second part of this review, we describe the histologic features of the main forms of scarring alopecia. Since a close clinical-pathological correlation is essential for making a correct histopathologic diagnosis of alopecia, we also include a brief description of the clinical features of the principal forms of this disorder. Copyright © 2014 Elsevier España, S.L.U. and AEDV. All rights reserved.

  15. The cosmetic outcome of the scar formation after cesarean section

    DEFF Research Database (Denmark)

    Lindholt, Jes Sanddal; Möller-Christensen, T; Steele, R E

    1994-01-01

    Three methods of skin closure after cesarean section were tested and compared in a prospective trial. Eighty-nine (82.5%) appeared for follow-up investigation 4-5 months after delivery. The mean scar width was significantly narrower after phannenstiel incision compared with percutaneous nylon sut...

  16. 5-Fluorouracil-Loaded Transfer some as Theranostics in Dermal Tumor of Hypertrophic Scar Tissue

    International Nuclear Information System (INIS)

    Zhang, Z.; Wang, X.; Chen, X.; Wo, Y.; Zhang, Y.; Biskup, E.

    2015-01-01

    To investigate the ability of transfersomal gel carrying the anti scarring agent (5-FU) to permeate hypertrophic scars in vivo and in vitro, scar permeation studies were performed after the agent was labeled with the fluorescent agent, rhodamine 6GO. Laser con focal microscope was employed to dynamically observe the effects of transfersomal gel carrying 5-FU at different time points. High-performance liquid chromatography (HPLC) was used to analyze the contents of the agent in the scar tissues at different hours after administration. Scar elevation index (SEI) was used to evaluate the changes of the ear scar models in rabbits. Compared with the PBS gel of 5-FU, the transfers omal gel displayed greater permeation rate and depth, as well as a higher content retention of the agent in scar tissues. Local administrations of the agent for some certain periods effectively inhibited the hyperplasia of ear scars in rabbits. Transfersomes can be chosen as a potential transdermal drug delivery system

  17. Fractional CO2 laser treatment of caesarean section scars

    DEFF Research Database (Denmark)

    Karmisholt, Katrine E; Taudorf, Elisabeth H; Wulff, Camilla B

    2017-01-01

    BACKGROUND AND OBJECTIVES: Caesarean section (c-section) scars can be pose functional and cosmetic challenges and ablative fractional laser (AFXL) treatment may offer benefit to patients. We evaluated textural and color changes over time in AFXL-treated versus untreated control scars. MATERIALS...... AND METHODS: A randomized, controlled, intra-individual split-scar trial with three sessions of AFXL-treatments for mature c-section scars. Settings of AFXL were adjusted to each individual scar. End-points were blinded on-site clinical evaluations at 1, 3, and 6 months follow-up (Patient and Observer Scar...... Assessment Scale [POSAS] and Vancouver Scar Scale [VSS]), blinded photo-evaluations, reflectance measurements, tissue histology, and patients satisfaction. RESULTS: Eleven of 12 patients completed the study. At 1 month follow-up, AFXL-treated scars were significantly improved in pliability (POSAS P = 0...

  18. An objective device for measuring surface roughness of skin and scars

    NARCIS (Netherlands)

    Bloemen, Monica C. T.; van Gerven, Maaike S.; van der Wal, Martijn B. A.; Verhaegen, Pauline D. H. M.; Middelkoop, Esther

    2011-01-01

    Scar formation remains a major clinical problem; therefore, various therapies have been developed to improve scar quality. To evaluate the effectiveness of these therapies, objective measurement tools are necessary. An appropriate, objective measuring instrument for assessment of surface roughness

  19. An objective device for measuring surface roughness of skin and scars

    NARCIS (Netherlands)

    Bloemen, M.C.T.; van Gerven, M.S.; van der Wal, M.B.A.; Verhaegen, P.D.H.M.; Middelkoop, E.

    2011-01-01

    Background: Scar formation remains a major clinical problem; therefore, various therapies have been developed to improve scar quality. To evaluate the effectiveness of these therapies, objective measurement tools are necessary. An appropriate, objective measuring instrument for assessment of surface

  20. Postmastectomy radiotherapy with integrated scar boost using helical tomotherapy

    International Nuclear Information System (INIS)

    Rong Yi; Yadav, Poonam; Welsh, James S.; Fahner, Tasha; Paliwal, Bhudatt

    2012-01-01

    The purpose of this study was to evaluate helical tomotherapy dosimetry in postmastectomy patients undergoing treatment for chest wall and positive nodal regions with simultaneous integrated boost (SIB) in the scar region using strip bolus. Six postmastectomy patients were scanned with a 5-mm-thick strip bolus covering the scar planning target volume (PTV) plus 2-cm margin. For all 6 cases, the chest wall received a total cumulative dose of 49.3–50.4 Gy with daily fraction size of 1.7–2.0 Gy. Total dose to the scar PTV was prescribed to 58.0–60.2 Gy at 2.0–2.5 Gy per fraction. The supraclavicular PTV and mammary nodal PTV received 1.7–1.9 dose per fraction. Two plans (with and without bolus) were generated for all 6 cases. To generate no-bolus plans, strip bolus was contoured and overrode to air density before planning. The setup reproducibility and delivered dose accuracy were evaluated for all 6 cases. Dose-volume histograms were used to evaluate dose-volume coverage of targets and critical structures. We observed reduced air cavities with the strip bolus setup compared with what we normally see with the full bolus. The thermoluminescence dosimeters (TLD) in vivo dosimetry confirmed accurate dose delivery beneath the bolus. The verification plans performed on the first day megavoltage computed tomography (MVCT) image verified that the daily setup and overall dose delivery was within 2% accuracy compared with the planned dose. The hotspot of the scar PTV in no-bolus plans was 111.4% of the prescribed dose averaged over 6 cases compared with 106.6% with strip bolus. With a strip bolus only covering the postmastectomy scar region, we observed increased dose uniformity to the scar PTV, higher setup reproducibility, and accurate dose delivered beneath the bolus. This study demonstrates the feasibility of using a strip bolus over the scar using tomotherapy for SIB dosimetry in postmastectomy treatments.

  1. Characterization of four species of Trichuris (Nematoda: Enoplida) by their second internal transcribed spacer ribosomal DNA sequence.

    Science.gov (United States)

    Oliveros, R; Cutillas, C; De Rojas, M; Arias, P

    2000-12-01

    Adult worms of Trichuris ovis and T. globulosa were collected from Ovis aries (sheep) and Capra hircus (goats). T. suis was isolated from Sus scrofa domestica (swine) and T. leporis was isolated from Lepus europaeus (rabbits) in Spain. Genomic DNA was isolated and a ribosomal internal transcribed spacer (ITS2) was amplified and sequenced using polymerase-chain-reaction (PCR) techniques. The ITS2 of T. ovis and T. globulosa was 407 nucleotides in length and had a GC content of about 62%. Furthermore, the ITS2 of T. suis and T. leporis was 534 and 418 nucleotides in length and had a GC content of about 64.8% and 62.4%, respectively. There was evidence of slight variation in the sequence within individuals of all species analyzed, indicating intraindividual variation in the sequence of different copies of the ribosomal DNA. Furthermore, low-level intraspecific variation was detected. Sequence analyses of ITS2 products of T. ovis and T. globulosa demonstrated no sequence difference between them. Nevertheless, differences were detected between the ITS2 sequences of T. suis, T. leporis, and T. ovis, indicating that Trichuris species can reliably be differentiated by their ITS2 sequences and PCR-linked restriction-fragment-length polymorphism (RFLP).

  2. Early treatment using fractional CO2 laser before skin suture during scar revision surgery in Asians.

    Science.gov (United States)

    Du, Feiya; Yu, Yusheng; Zhou, Zhiqin; Wang, Liujia; Zheng, Shusen

    2018-04-01

    Fractional CO 2 laser is one of the most effective treatment options used to resurface scars. However, most previous studies have been performed on mature scars at least 2 months after surgery. Recent studies have emphasized the importance of early treatment to reduce scar formation. In the present study, we described our experience with fractional CO 2 laser intervention before skin suture during scar revision surgery in Asians, and found the treatment was safe and effective.

  3. Genetic Characterization of Fasciola Isolates from West Azerbaijan Province Iran Based on ITS1 and ITS2 Sequence of Ribosomal DNA

    Science.gov (United States)

    GALAVANI, Hossein; GHOLIZADEH, Saber; HAZRATI TAPPEH, Khosrow

    2016-01-01

    Background: Fascioliasis, caused by Fasciola hepatica and F. gigantica, has medical and economic importance in the world. Molecular approaches comparing traditional methods using for identification and characterization of Fasciola spp. are precise and reliable. The aims of current study were molecular characterization of Fasciola spp. in West Azerbaijan Province, Iran and then comparative analysis of them using GenBank sequences. Methods: A total number of 580 isolates were collected from different hosts in five cities of West Azerbaijan Province, in 2014 from 90 slaughtered cattle (n=50) and sheep (n=40). After morphological identification and DNA extraction, designing specific primer were used to amplification of ITS1, 5.8s and ITS2 regions, 50 samples were conducted to sequence, randomly. Result: Using morphometric characters 99.14% and 0.86% of isolates identified as F. hepatica and F. gigantica, respectively. PCR amplification of 1081 bp fragment and sequencing result showed 100% similarity with F. hepatica in ITS1 (428 bp), 5.8s (158 bp), and ITS2 (366 bp) regions. Sequence comparison among current study sequences and GenBank data showed 98% identity with 11 nucleotide mismatches. However, in phylogenetic tree F. hepatica sequences of West Azerbaijan Province, Iran, were in a close relationship with Iranian, Asian, and African isolates. Conclusions: Only F. hepatica species is distributed among sheep and cattle in West Azerbaijan Province Iran. However, 5 and 6 bp variation in ITS1 and ITS2 regions, respectively, is not enough to separate of Fasciola spp. Therefore, more studies are essential for designing new molecular markers to correct species identification. PMID:27095969

  4. Radial scars detected mammographically in a breast cancer screening programme

    International Nuclear Information System (INIS)

    Azavedo, E.; Svane, G.

    1992-01-01

    Radial scars are getting more and more common since implementation of mammography as diagnostic tool in screening women for breast cancer. At Karolinska Hospital, 18987 asymptomatic women, aged 50-69, were screened for breast cancer through mammography during August 1989-May 1991. A total of 735 (3.87%) were recalled for additional views after initial mammograms and 463 (2.44%) were assessed with help of cytology. In all 175 women (0.92%) were selected for surgery and 146 (0.77%) had histologically verified cancers. The remaining 29 (0.15%) had non- malignant lesions of which 11 (0.06%) were radial scars. All radial scars were diagnosed on mammograms and later confirmed with histology. The radiologic characteristics were found to be a) rather thick and long radiating structures accompanied by radiolucent linear structures parallel to some of the spicules, b) absence of calcifications, c) radiolucent areas in the body of the lesion, d) an average mean size of 6 mm and e) changing image in different views. Most of the lesions, 73% (8/11), were in moderately dense breasts and there was no specific relation to the right or left breast. A majority of radial scars, 64% (7/11), were found in the upper outer quadrants, 3/11 in the lower outer quadrants and 1/11 in the lower inner quadrant. Literature shows that histology uses many synonyms for radial scars and therefore team work between radiologists and pathologists is suggested for better conformity of the diagnosis. (author). 32 refs.; 1 fig

  5. Blockade of mast cell activation reduces cutaneous scar formation.

    Directory of Open Access Journals (Sweden)

    Lin Chen

    Full Text Available Damage to the skin initiates a cascade of well-orchestrated events that ultimately leads to repair of the wound. The inflammatory response is key to wound healing both through preventing infection and stimulating proliferation and remodeling of the skin. Mast cells within the tissue are one of the first immune cells to respond to trauma, and upon activation they release pro-inflammatory molecules to initiate recruitment of leukocytes and promote a vascular response in the tissue. Additionally, mast cells stimulate collagen synthesis by dermal fibroblasts, suggesting they may also influence scar formation. To examine the contribution of mast cells in tissue repair, we determined the effects the mast cell inhibitor, disodium cromoglycate (DSCG, on several parameters of dermal repair including, inflammation, re-epithelialization, collagen fiber organization, collagen ultrastructure, scar width and wound breaking strength. Mice treated with DSCG had significantly reduced levels of the inflammatory cytokines IL-1α, IL-1β, and CXCL1. Although DSCG treatment reduced the production of inflammatory mediators, the rate of re-epithelialization was not affected. Compared to control, inhibition of mast cell activity caused a significant decrease in scar width along with accelerated collagen re-organization. Despite the reduced scar width, DSCG treatment did not affect the breaking strength of the healed tissue. Tryptase β1 exclusively produced by mast cells was found to increase significantly in the course of wound healing. However, DSCG treatment did not change its level in the wounds. These results indicate that blockade of mast cell activation reduces scar formation and inflammation without further weakening the healed wound.

  6. Molecular Cloning and Sequencing of AlkalophilicCellulosimicrobium cellulans CKMX1 Xylanase Gene Isolated from Mushroom Compost and Characterization of the Gene Product

    Directory of Open Access Journals (Sweden)

    Abhishek Walia

    2015-12-01

    Full Text Available ABSTRACT A xylanolytic bacterium was isolated from mushroom compost by using enrichment technique. Results from the metabolic fingerprinting, whole-cell fatty acids methyl ester analysis and 16S rDNA sequencing suggested the bacterium to be Cellulosimicrobium cellulans CKMX1. Due to the xylanolytic activity of this bacterium, isolation and characterization of the xylanase gene were attempted. A distinct fragment of about 1671 bp was successfully amplified using PCR and cloned into Escherichia coli DH5α. A BLAST search confirmed that the DNA sequence from the amplified fragment was endo-1, 4-beta-xylanase, which was a member of glycoside hydrolase family 11. It showed 98% homology withCellulosimicrobium sp. xylanase gene (Accession no. FJ859907.1 reported from the gut of Eisenia fetida in Korea. In silicophysico-chemical characterization of amino acid sequence of xylanase showed an open reading frame encoding a 556 amino acid sequence with a molecular weight of 58 kDa and theoretical isolectric point (pI of 4.46 was computed using Expasy's ProtParam server. Secondary and homology based 3D structure of xylanase was analysed using SOPMA and Swiss-Prot software.

  7. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  8. Macroanatomy and compartmentalization of recent fire scars in three North American conifers

    Science.gov (United States)

    Kevin T. Smith; Estelle Arbellay; Donald A. Falk; Elaine Kennedy Sutherland

    2016-01-01

    Fire scars are initiated by cambial necrosis caused by localized lethal heating of the tree stem. Scars develop as part of the linked survival processes of compartmentalization and wound closure. The position of scars within dated tree ring series is the basis for dendrochronological reconstruction of fire history. Macroanatomical features were described for western...

  9. Epithelioid sarcoma and squamous cell carcinoma arising in a burn scar

    Directory of Open Access Journals (Sweden)

    Kusum D Jashnani

    2011-01-01

    Full Text Available Development of a malignant tumor is a well known complication of a chronic burn scar. Most of these tumors are squamous cell carcinomas and only 28 cases of burn scar sarcomas have been reported in literature. We report the first occurrence of the combination of squamous cell carcinoma and epithelioid sarcoma arising in a burn scar.

  10. Evidence-Based Scar Management: How to Improve Results with Technique and Technology.

    Science.gov (United States)

    Khansa, Ibrahim; Harrison, Bridget; Janis, Jeffrey E

    2016-09-01

    Scars represent the visible sequelae of trauma, injury, burn, or surgery. They may induce distress in the patient because of their aesthetically unpleasant appearance, especially if they are excessively raised, depressed, wide, or erythematous. They may also cause the patient symptoms of pain, tightness, and pruritus. Numerous products are marketed for scar prevention or improvement, but their efficacy is unclear. A literature review of high-level studies analyzing methods to prevent or improve hypertrophic scars, keloids, and striae distensae was performed. The evidence from these articles was analyzed to generate recommendations. Each intervention's effectiveness at preventing or reducing scars was rated as none, low, or high, depending on the strength of the evidence for that intervention. For the prevention of hypertrophic scars, silicone, tension reduction, and wound edge eversion seem to have high efficacy, whereas onion extract, pulsed-dye laser, pressure garments, and scar massage have low efficacy. For the treatment of existing hypertrophic scars, silicone, pulsed-dye laser, CO2 laser, corticosteroids, 5-fluorouracil, bleomycin, and scar massage have high efficacy, whereas onion extract and fat grafting seem to have low efficacy. For keloid scars, effective adjuncts to excision include corticosteroids, mitomycin C, bleomycin, and radiation therapy. No intervention seems to have significant efficacy in the prevention or treatment of striae distensae. Although scars can never be completely eliminated in an adult, this article presents the most commonly used, evidence-based methods to improve the quality and symptoms of hypertrophic scars, as well as keloid scars and striae distensae.

  11. Weather, logging, and tree growth associated with fir engraver attack scars in white fir

    Science.gov (United States)

    George T. Ferrell

    1973-01-01

    The boles of 32 recently killed, and 41 living, white fir were examined for embedded fir engraver (Scolytus ventralis) attack scars. Of 287 scars found in annual rings for the years 1934-69, only 2 to 3 percent represented reproductively successful attacks. Trends in scar abundance were directly correlated with trends in white fir killed by ...

  12. Comparative genome analysis and characterization of the Salmonella Typhimurium strain CCRJ_26 isolated from swine carcasses using whole-genome sequencing approach.

    Science.gov (United States)

    Panzenhagen, P H N; Cabral, C C; Suffys, P N; Franco, R M; Rodrigues, D P; Conte-Junior, C A

    2018-04-01

    Salmonella pathogenicity relies on virulence factors many of which are clustered within the Salmonella pathogenicity islands. Salmonella also harbours mobile genetic elements such as virulence plasmids, prophage-like elements and antimicrobial resistance genes which can contribute to increase its pathogenicity. Here, we have genetically characterized a selected S. Typhimurium strain (CCRJ_26) from our previous study with Multiple Drugs Resistant profile and high-frequency PFGE clonal profile which apparently persists in the pork production centre of Rio de Janeiro State, Brazil. By whole-genome sequencing, we described the strain's genome virulent content and characterized the repertoire of bacterial plasmids, antibiotic resistance genes and prophage-like elements. Here, we have shown evidence that strain CCRJ_26 genome possible represent a virulence-associated phenotype which may be potentially virulent in human infection. Whole-genome sequencing technologies are still costly and remain underexplored for applied microbiology in Brazil. Hence, this genomic description of S. Typhimurium strain CCRJ_26 will provide help in future molecular epidemiological studies. The analysis described here reveals a quick and useful pipeline for bacterial virulence characterization using whole-genome sequencing approach. © 2018 The Society for Applied Microbiology.

  13. Whole-genome characterization in pedigreed non-human primates using Genotyping-By-Sequencing and imputation.

    OpenAIRE

    Cervera-Juanes, Rita; Vinson, Amanda; Ferguson, Betsy; Carbone, Lucia; Spindel, Eliot; Mccouch, Susan; Spindel, Jennifer; Nevonen, Kimberly; Letaw, John; Raboin, Michael; Bimber, Ben

    2016-01-01

    Background: Rhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still undeveloped. Whole-genome sequence (WGS) data in pedigreed macaque colonies could provide substantial experimental power, but the collection of WGS data in large cohorts remains a formidable expense. Here, we describe a cost-effective approach that selects the most informative macaques in a pedigree for whole-genome sequenci...

  14. Characterization of cereal cyst nematodes (Heterodera spp. in Morocco based on morphology, morphometrics and rDNA-ITS sequence analysis

    Directory of Open Access Journals (Sweden)

    Mokrini Fouad

    2017-09-01

    Full Text Available Morphological and molecular diversity among 11 populations of cereal cyst nematodes from different wheat production areas in Morocco was investigated using light microscopy, species-specific primers, complemented by the ITS-rDNA sequences. Morphometrics of cysts and second-stage juveniles (J2s were generally within the expected ranges for Heterodera avenae; only the isolate from Aïn Jmaa showed morphometrics conforming to those of H. latipons. When using species-specific primers for H. avenae and H. latipons, the specific bands of 109 bp and 204 bp, respectively, confirmed the morphological identification. In addition, the internal transcribed spacer (ITS regions were sequenced to study the diversity of the 11 populations. These sequences were compared with those of Heterodera species available in the GenBank database (www.ncbi.nlm.nih.gov and confirmed again the identity of the species. Ten sequences of the ITS-rDNA were similar (99–100% to the sequences of H. avenae published in GenBank and three sequences, corresponding with one population, were similar (97–99% to H. latipons.

  15. Characterization of the first complete genome sequence of an Impatiens necrotic spot orthotospovirus isolate from the United States and worldwide phylogenetic analyses of INSV isolates.

    Science.gov (United States)

    Zhao, Kaixi; Margaria, Paolo; Rosa, Cristina

    2018-05-10

    Impatiens necrotic spot orthotospovirus (INSV) can impact economically important ornamental plants and vegetables worldwide. Characterization studies on INSV are limited. For most INSV isolates, there are no complete genome sequences available. This lack of genomic information has a negative impact on the understanding of the INSV genetic diversity and evolution. Here we report the first complete nucleotide sequence of a US INSV isolate. INSV-UP01 was isolated from an impatiens in Pennsylvania, US. RT-PCR was used to clone its full-length genome and Vector NTI to assemble overlapping sequences. Phylogenetic trees were constructed by using MEGA7 software to show the phylogenetic relationships with other available INSV sequences worldwide. This US isolate has genome and biological features classical of INSV species and clusters in the Western Hemisphere clade, but its origin appears to be recent. Furthermore, INSV-UP01 might have been involved in a recombination event with an Italian isolate belonging to the Asian clade. Our analyses support that INSV isolates infect a broad plant-host range they group by geographic origin and not by host, and are subjected to frequent recombination events. These results justify the need to generate and analyze complete genome sequences of orthotospoviruses in general and INSV in particular.

  16. Characterization of Fasciola samples by ITS of rDNA sequences revealed the existence of Fasciola hepatica and Fasciola gigantica in Yunnan Province, China.

    Science.gov (United States)

    Shu, Fan-Fan; Lv, Rui-Qing; Zhang, Yi-Fang; Duan, Gang; Wu, Ding-Yu; Li, Bi-Feng; Yang, Jian-Fa; Zou, Feng-Cai

    2012-08-01

    On mainland China, liver flukes of Fasciola spp. (Digenea: Fasciolidae) can cause serious acute and chronic morbidity in numerous species of mammals such as sheep, goats, cattle, and humans. The objective of the present study was to examine the taxonomic identity of Fasciola species in Yunnan province by sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA). The ITS rDNA was amplified from 10 samples representing Fasciola species in cattle from 2 geographical locations in Yunnan Province, by polymerase chain reaction (PCR), and the products were sequenced directly. The lengths of the ITS-1 and ITS-2 sequences were 422 and 361-362 base pairs, respectively, for all samples sequenced. Using ITS sequences, 2 Fasciola species were revealed, namely Fasciola hepatica and Fasciola gigantica. This is the first demonstration of F. gigantica in cattle in Yunnan Province, China using a molecular approach; our findings have implications for studying the population genetic characterization of the Chinese Fasciola species and for the prevention and control of Fasciola spp. in this province.

  17. Isolation and characterization of antigen-specific alpaca (Lama pacos) VHH antibodies by biopanning followed by high-throughput sequencing.

    Science.gov (United States)

    Miyazaki, Nobuo; Kiyose, Norihiko; Akazawa, Yoko; Takashima, Mizuki; Hagihara, Yosihisa; Inoue, Naokazu; Matsuda, Tomonari; Ogawa, Ryu; Inoue, Seiya; Ito, Yuji

    2015-09-01

    The antigen-binding domain of camelid dimeric heavy chain antibodies, known as VHH or Nanobody, has much potential in pharmaceutical and industrial applications. To establish the isolation process of antigen-specific VHH, a VHH phage library was constructed with a diversity of 8.4 × 10(7) from cDNA of peripheral blood mononuclear cells of an alpaca (Lama pacos) immunized with a fragment of IZUMO1 (IZUMO1PFF) as a model antigen. By conventional biopanning, 13 antigen-specific VHHs were isolated. The amino acid sequences of these VHHs, designated as N-group VHHs, were very similar to each other (>93% identity). To find more diverse antibodies, we performed high-throughput sequencing (HTS) of VHH genes. By comparing the frequencies of each sequence between before and after biopanning, we found the sequences whose frequencies were increased by biopanning. The top 100 sequences of them were supplied for phylogenic tree analysis. In total 75% of them belonged to N-group VHHs, but the other were phylogenically apart from N-group VHHs (Non N-group). Two of three VHHs selected from non N-group VHHs showed sufficient antigen binding ability. These results suggested that biopanning followed by HTS provided a useful method for finding minor and diverse antigen-specific clones that could not be identified by conventional biopanning. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  18. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.

    Science.gov (United States)

    Keinath, Melissa C; Timoshevskiy, Vladimir A; Timoshevskaya, Nataliya Y; Tsonis, Panagiotis A; Voss, S Randal; Smith, Jeramiah J

    2015-11-10

    Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes.

  19. Genetic characterization of the Pacific sheath-tailed bat (Emballonura semicaudata rotensis) using mitochondrial DNA sequence data

    Science.gov (United States)

    Oyler-McCance, Sara J.; Valdez, Ernest W.; O'Shea, Thomas J.; Fike, Jennifer A.

    2013-01-01

    Emballonura semicaudata occurs in the southwestern Pacific and populations on many islands have declined or disappeared. One subspecies (E. semicaudata rotensis) occurs in the Northern Mariana Islands, where it has been extirpated from all but 1 island (Aguiguan). We assessed genetic similarity between the last population of E. s. rotensis and 2 other subspecies, and examined genetic diversity on Aguiguan. We sampled 12 E. s. rotensis, sequenced them at 3 mitochondrial loci, and compared them with published sequences from 2 other subspecies. All 12 E. s. rotensis had identical sequences in each of the 3 regions. Using cytochrome-b (Cytb) data E. s. rotensis was sister to E. s. palauensis in a clade separate from E. s. semicaudata. 12S ribosomal RNA (12S) sequences grouped all E. s. semicaudata in 1 clade with E. s. rotensis in a clade by itself. Genetic distances among the 3 subspecies at Cytb were smallest between E. s. palauensis and E. s. rotensis. Distance between E. s. semicaudata and the other 2 subspecies was not different from the distance between E. s. semicaudata and the full species E. raffrayana. A similar relationship was found using the 12S data. These distances are larger than those typically reported for mammalian subspecies using Cytb sequence and within the range of sister species.

  20. Characterization of Human Cytomegalovirus Genome Diversity in Immunocompromised Hosts by Whole-Genome Sequencing Directly From Clinical Specimens.

    Science.gov (United States)

    Hage, Elias; Wilkie, Gavin S; Linnenweber-Held, Silvia; Dhingra, Akshay; Suárez, Nicolás M; Schmidt, Julius J; Kay-Fedorov, Penelope C; Mischak-Weissinger, Eva; Heim, Albert; Schwarz, Anke; Schulz, Thomas F; Davison, Andrew J; Ganzenmueller, Tina

    2017-06-01

    Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Next-generation sequencing was performed on target enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast milk, respiratory samples, biopsies, and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients, and congenitally infected children). De novo-assembled HCMV genome sequences were obtained for 57 of 68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intraindividual blood samples from 9 of 15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in 6 individuals with sequential blood samples and upon compartmental analysis of 1 patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral-resistance mutations. In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  1. Scar evaluation of split thickness skin graft donor site

    Directory of Open Access Journals (Sweden)

    Jani Muha

    2014-12-01

    Full Text Available BACKGROUND. Split thickness skin graft harvesting causes a certain degree of scaring on the donor site. Donor site scar can cause aesthetic and functional sequelae on the patient's body. Our goal was to study the process of donor site selection, and then evaluate donor site scars and their impact on patients. PATIENTS AND METHODS. This retrospective study included 45 patients aged 5 to 61 years (in average 36, who have been treated with STSG in the 2004–2010 period. 57.8% of them were men. On a follow-up visit, we photographed healed skin defects and donor sites. We then determined and compared the surface areas of skin defect and the donor site using the Adobe® Illustrator® CS5 computer program. Donor site scars were assessed according to the Vancouver scar scale (VSS. We examined scar’s light touch sensitivity with monofilaments and skin colouring compared to adjacent healthy skin using colorimeter. Patients were also interviewed about their treatment course in a form of a standardized questionnaire. RESULTS. Our research has revealed that 20.0% of patients participated in the decision making process of choosing the donor site, while in 80.0% the donor site was chosen by the surgeon himself. 6.7% of patients were not satisfied with their donor site. Most of the patients (37/45 had donor sites on their thighs. In average, the donor site surface area was 94% bigger than the skin defect area. We found statistically significant differences in VSS values, light touch sensitivity and skin colouring between donor site scaring and adjacent healthy skin. CONCLUSIONS. Donor site scar can represent a lasting aesthetic and functional disability for patients. Our research has shown that most of the patients do not participate in the donor site selection process, but are satisfied with their donor site. In most cases, STGSs are harvested from the thigh, other anatomical regions, where scarring would be aesthetically less obtrusive, are underused

  2. Incidence of stunned, hibernating and scarred myocardium in ischaemic cardiomyopathy

    International Nuclear Information System (INIS)

    Hernandez-Pampaloni, Miguel; Morita, Koichi; Dutka, David P.; Camici, Paolo G.; Bax, Jeroen J.

    2005-01-01

    Different criteria to identify residual viability in chronically dysfunctioning myocardium in patients with coronary artery disease (CAD) can be derived by the combined assessment of myocardial blood flow (MBF) and glucose utilisation (MRG) using positron emission tomography (PET). The aim of this study was to evaluate, in a large number of patients, the prevalence of these different patterns by purely quantitative means. One hundred and sixteen consecutive patients with ischaemic cardiomyopathy (LVEF ≤40%) underwent resting 2D echocardiography to assess regional contractile function (16-segment model). PET with 15 O-labelled water (H 2 15 O) and 18 F-fluorodeoxyglucose (FDG) was used to quantify MBF and MRG during hyperinsulinaemic euglycaemic clamp. Dysfunctional segments with normal MBF (≥0.6 ml min -1 g -1 ) were classified as stunned, and segments with reduced MBF ( -1 g -1 ) as hibernating if MRG was ≥0.25 μmol min -1 g -1 . Segments with reduced MBF and MRG -1 g -1 were classified as transmural scars and segments with reduced MBF and MRG between 0.20 and 0.25 μmol min -1 g -1 as non-transmural scars. Eight hundred and thirty-four (46%) segments were dysfunctional. Of these, 601 (72%) were chronically stunned, with 368 (61%) having normal MRG (0.47±0.20 μmol min -1 g -1 ) and 233 (39%) reduced MRG (0.16±0.05 μmol min -1 g -1 ). Seventy-four (9%) segments with reduced MBF had preserved MRG (0.40±0.18 μmol min -1 g -1 ) and were classified as hibernating myocardium. In addition, 15% of segments were classified as transmural and 4% as non-transmural scar. The mean MBF was highest in stunned myocardium (0.95±0.32 ml min -1 g -1 ), intermediate in hibernating myocardium and non-transmural scars (0.47±0.09 ml min -1 g -1 and 0.48±0.08 ml min -1 g -1 , respectively), and lowest in transmural scars (0.40±0.14 ml min -1 g -1 , P -1 g -1 vs 0.46±0.20 μmol min -1 g -1 , NS), and lowest in stunned myocardium with reduced MRG and transmural scars

  3. Fractional ablative CO2 laser treatment versus scar subcision and autologous fat transfer in the treatment of atrophic acne scars: New technique

    Directory of Open Access Journals (Sweden)

    Laila Mohammad

    2016-04-01

    Full Text Available There are different modalities for management of atrophic acne scars which include lasers. Ablative fractional CO2 laser was developed to address the shortcomings of traditional ablative lasers, with superior results to non-ablative fractional lasers. Autologous fat transfer has been utilized for nearly a decade in tissue augmentation and reconstruction.Present studies were designed to compare ablative fractional CO2 laser treatment with scar subcision and autologous fat transfer in the treatment of atrophic acne scars. 20 patients with atrophic acne scars were recruited: 10 patients were treated by three sessions of ablative fractional CO2 laser therapy, and 10 patients treated by subcision and autologous fat transfer. All patients were followed up for three months, and were assessed by digital photograph before and after treatment through the application of Goodman and Baron quantitative and qualitative grading systems, in addition to reports by three physicians committees and reports of patients’ satisfaction. Analysis of both groups showed significant improvements in all types of atrophic acne scars. The mean percentage of total quantitative improvement was more significant in the case of autologous fat transfer with regard to ice-pick and total number of scars. Therefore, scar subcision with autologous fat transfer proved to be as effective as, or even more effective than, ablative fractional CO2 laser in the treatment of atrophic acne scars with regard to the total number of scars as well as ice-pick type.

  4. Isolation and sequence characterization of DNA-A genome of a new begomovirus strain associated with severe leaf curling symptoms of Jatropha curcas L.

    Science.gov (United States)

    Chauhan, Sushma; Rahman, Hifzur; Mastan, Shaik G; Pamidimarri, D V N Sudheer; Reddy, Muppala P

    2018-07-20

    Begomoviruses belong to the family Geminiviridae are associated with several disease symptoms, such as mosaic and leaf curling in Jatropha curcas. The molecular characterization of these viral strains will help in developing management strategies to control the disease. In this study, J. curcas that was infected with begomovirus and showed acute leaf curling symptoms were identified. DNA-A segment from pathogenic viral strain was isolated and sequenced. The sequenced genome was assembled and characterized in detail. The full-length DNA-A sequence was covered by primer walking. The genome sequence showed the general organization of DNA-A from begomovirus by the distribution of ORFs in both viral and anti-viral strands. The genome size ranged from 2844 bp-2852 bp. Three strains with minor nucleotide variations were identified, and a phylogenetic analysis was performed by comparing the DNA-A segments from other reported begomovirus isolates. The maximum sequence similarity was observed with Euphorbia yellow mosaic virus (FN435995). In the phylogenetic tree, no clustering was observed with previously reported begomovirus strains isolated from J. curcas host. The strains isolated in this study belong to new begomoviral strain that elicits symptoms of leaf curling in J. curcas. The results indicate that the probable origin of the strains is from Jatropha mosaic virus infecting J. gassypifolia. The strains isolated in this study are referred as Jatropha curcas leaf curl India virus (JCLCIV) based on the major symptoms exhibited by host J. curcas. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Use of makeup, hairstyles, glasses, and prosthetics as adjuncts to scar camouflage.

    Science.gov (United States)

    Sidle, Douglas M; Decker, Jennifer R

    2011-08-01

    Scars after facial trauma or surgery can be a source of distress for patients, and facial plastic surgeons are frequently called upon to help manage them. Although no technique can remove a scar, numerous treatment modalities have been developed to improve facial scar appearance with varying levels of invasiveness. This article reviews techniques that camouflage scars without surgical intervention. Topical scar treatments, camouflage cosmetics, use of hairstyling and glasses, and facial prosthetics are discussed. In addition, professional counseling is provided on selection and application of topical cosmetics for use as part of an office practice. 2011 Elsevier Inc. All rights reserved.

  6. Characterization of the haloacid dehalogenase from Xanthobacter autotrophicus GJ10 and sequencing of the dhlB gene

    DEFF Research Database (Denmark)

    van der Ploeg, J; Van Hall, Gerrit; Janssen, D B

    1991-01-01

    B) was cloned and could be allocated to a 6.5-kb EcoRI-BglII fragment. Part of this fragment was sequenced, and the dhlB open reading frame was identified by comparison with the N-terminal amino acid sequence of the protein. The gene was found to encode a protein of 27,433 Da that showed considerable homology...... chromatography. The enzyme was active with 2-halogenated carboxylic acids and converted only the L-isomer of 2-chloropropionic acid with inversion of configuration to produce D-lactate. The activity of the enzyme was not readily influenced by thiol reagents. The gene encoding the haloacid dehalogenase (dhl...... (60.5 and 61.0% similarity) with the two other haloacid dehalogenases sequenced to date but not with the haloalkane dehalogenase from X. autotrophicus GJ10....

  7. Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

    Science.gov (United States)

    Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

    2010-02-01

    Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

  8. In Silico Mining of Microsatellites in Coding Sequences of the Date Palm (Arecaceae Genome, Characterization, and Transferability

    Directory of Open Access Journals (Sweden)

    Frédérique Aberlenc-Bertossi

    2014-01-01

    Full Text Available Premise of the study: To complement existing sets of primarily dinucleotide microsatellite loci from noncoding sequences of date palm, we developed primers for tri- and hexanucleotide microsatellite loci identified within genes. Due to their conserved genomic locations, the primers should be useful in other palm taxa, and their utility was tested in seven other Phoenix species and in Chamaerops, Livistona, and Hyphaene. Methods and Results: Tandem repeat motifs of 3–6 bp were searched using a simple sequence repeat (SSR–pipeline package in coding portions of the date palm draft genome sequence. Fifteen loci produced highly consistent amplification, intraspecific polymorphisms, and stepwise mutation patterns. Conclusions: These microsatellite loci showed sufficient levels of variability and transferability to make them useful for population genetic, selection signature, and interspecific gene flow studies in Phoenix and other Coryphoideae genera.

  9. Characterization of shark complement factor I gene(s): genomic analysis of a novel shark-specific sequence.

    Science.gov (United States)

    Shin, Dong-Ho; Webb, Barbara M; Nakao, Miki; Smith, Sylvia L

    2009-07-01

    Complement factor I is a crucial regulator of mammalian complement activity. Very little is known of complement regulators in non-mammalian species. We isolated and sequenced four highly similar complement factor I cDNAs from the liver of the nurse shark (Ginglymostoma cirratum), designated as GcIf-1, GcIf-2, GcIf-3 and GcIf-4 (previously referred to as nsFI-a, -b, -c and -d) which encode 689, 673, 673 and 657 amino acid residues, respectively. They share 95% (shark-specific sequence between the leader peptide (LP) and the factor I membrane attack complex (FIMAC) domain. The cDNA sequences differ only in the size and composition of the shark-specific region (SSR). Sequence analysis of each SSR has identified within the region two novel short sequences (SS1 and SS2) and three repeat sequences (RS1-3). Genomic analysis has revealed the existence of three introns between the leader peptide and the FIMAC domain, tentatively designated intron 1, intron 2, and intron 3 which span 4067, 2293 and 2082bp, respectively. Southern blot analysis suggests the presence of a single gene copy for each cDNA type. Phylogenetic analysis suggests that complement factor I of cartilaginous fish diverged prior to the emergence of mammals. All four GcIf cDNA species are expressed in four different tissues and the liver is the main tissue in which expression level of all four is high. This suggests that the expression of GcIf isotypes is tissue-dependent.

  10. The effect of burn rehabilitation massage therapy on hypertrophic scar after burn: a randomized controlled trial.

    Science.gov (United States)

    Cho, Yoon Soo; Jeon, Jong Hyun; Hong, Aram; Yang, Hyeong Tae; Yim, Haejun; Cho, Yong Suk; Kim, Do-Hern; Hur, Jun; Kim, Jong Hyun; Chun, Wook; Lee, Boung Chul; Seo, Cheong Hoon

    2014-12-01

    To evaluate the effect of burn rehabilitation massage therapy on hypertrophic scar after burn. One hundred and forty-six burn patients with hypertrophic scar(s) were randomly divided into an experimental group and a control group. All patients received standard rehabilitation therapy for hypertrophic scars and 76 patients (massage group) additionally received burn scar rehabilitation massage therapy. Both before and after the treatment, we determined the scores of visual analog scale (VAS) and itching scale and assessed the scar characteristics of thickness, melanin, erythema, transepidermal water loss (TEWL), sebum, and elasticity by using ultrasonography, Mexameter(®), Tewameter(®), Sebumeter(®), and Cutometer(®), respectively. The scores of both VAS and itching scale decreased significantly in both groups, indicating a significant intragroup difference. With regard to the scar characteristics, the massage group showed a significant decrease after treatment in scar thickness, melanin, erythema, TEWL and a significant intergroup difference. In terms of scar elasticity, a significant intergroup difference was noted in immediate distension and gross skin elasticity, while the massage group significant improvement in skin distensibility, immediate distension, immediate retraction, and delayed distension. Our results suggest that burn rehabilitation massage therapy is effective in improving pain, pruritus, and scar characteristics in hypertrophic scars after burn. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

  11. Predictors of renal scar in children with urinary infection and vesicoureteral reflux.

    Science.gov (United States)

    Soylu, Alper; Demir, Belde Kasap; Türkmen, Mehmet; Bekem, Ozlem; Saygi, Murat; Cakmakçi, Handan; Kavukçu, Salih

    2008-12-01

    We evaluated the predictors of renal scar in children with urinary tract infections (UTIs) having primary vesicoureteral reflux (VUR). Data of patients who were examined by dimercaptosuccinic acid (DMSA) scintigraphy between 1995 and 2005 were evaluated retrospectively. Gender, age, reflux grade, presence/development of scarring, breakthrough UTIs, and resolution of reflux, were recorded. The relation of gender, age and VUR grade to preformed scarring and the relation of gender, age, VUR grade, presence of preformed scarring, number of breakthrough UTIs and reflux resolution to new scarring were assessed. There were 138 patients [male/female (M/F) 53/85]. Multivariate analysis showed that male gender [odds ratio (OR) 2.5], age > or = 27 months in girls (OR 4.2) and grades IV-V reflux (OR 12.4) were independent indicators of renal scarring. On the other hand, only the presence of previous renal scarring was found to be an independent indicator for the development of new renal scar (OR 13.4). In conclusion, while the most predictive variables for the presence of renal scarring among children presenting with a UTI were male gender, age > or = 27 months in girls, and grades IV-V reflux, the best predictor of new scar formation was presence of previous renal scarring.

  12. Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

    Directory of Open Access Journals (Sweden)

    Rodrigo Pessôa

    Full Text Available BACKGROUND: Here, we report on the partial and full-length genomic (FLG variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs, 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP and 7 adult T-cell leukemia/lymphoma (ATLL patients, using an Illumina paired-end protocol. METHODS: Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. RESULTS: A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14 and FLG (n = 76 data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5% individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA and that 4 individuals (4.5% were infected with the Japanese sub-subtypes (aB. A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. CONCLUSIONS: This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data

  13. Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology.

    Science.gov (United States)

    Pessôa, Rodrigo; Watanabe, Jaqueline Tomoko; Nukui, Youko; Pereira, Juliana; Casseb, Jorge; Kasseb, Jorge; de Oliveira, Augusto César Penalva; Segurado, Aluisio Cotrim; Sanabani, Sabri Saeed

    2014-01-01

    Here, we report on the partial and full-length genomic (FLG) variability of HTLV-1 sequences from 90 well-characterized subjects, including 48 HTLV-1 asymptomatic carriers (ACs), 35 HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and 7 adult T-cell leukemia/lymphoma (ATLL) patients, using an Illumina paired-end protocol. Blood samples were collected from 90 individuals, and DNA was extracted from the PBMCs to measure the proviral load and to amplify the HTLV-1 FLG from two overlapping fragments. The amplified PCR products were subjected to deep sequencing. The sequencing data were assembled, aligned, and mapped against the HTLV-1 genome with sufficient genetic resemblance and utilized for further phylogenetic analysis. A high-throughput sequencing-by-synthesis instrument was used to obtain an average of 3210- and 5200-fold coverage of the partial (n = 14) and FLG (n = 76) data from the HTLV-1 strains, respectively. The results based on the phylogenetic trees of consensus sequences from partial and FLGs revealed that 86 (95.5%) individuals were infected with the transcontinental sub-subtypes of the cosmopolitan subtype (aA) and that 4 individuals (4.5%) were infected with the Japanese sub-subtypes (aB). A comparison of the nucleotide and amino acids of the FLG between the three clinical settings yielded no correlation between the sequenced genotype and clinical outcomes. The evolutionary relationships among the HTLV sequences were inferred from nucleotide sequence, and the results are consistent with the hypothesis that there were multiple introductions of the transcontinental subtype in Brazil. This study has increased the number of subtype aA full-length genomes from 8 to 81 and HTLV-1 aB from 2 to 5 sequences. The overall data confirmed that the cosmopolitan transcontinental sub-subtypes were the most prevalent in the Brazilian population. It is hoped that this valuable genomic data will add to our current understanding of the

  14. Ectopic pregnancy in a Caesarean section scar: a case study

    Directory of Open Access Journals (Sweden)

    Piotr Niziurski

    2013-08-01

    Full Text Available Implantation of a pregnancy in a scar after Caesarean section is one of the rarest locations of ectopic pregnancies. A diagnosis and/or treatment which is too late may lead to a uterine rupture, the necessity to remove the uterus and a significant increase in morbidity among mothers. The study presents a diagnostically difficult case of a 29-year-old woman, who was diagnosed with pregnancy in its seventh week, located in a scar after a Caesarean section, with highly increased values of human chorionic gonadotropin (β-HCG concentration in blood serum. The pregnancy was removed and the wound was stitched during laparotomy, without a need to remove the uterus.

  15. Molecular and phylogenetic characterizations of an Eimeria krijgsmanni Yakimoff & Gouseff, 1938 (Apicomplexa: Eimeriidae) mouse intestinal protozoan parasite by partial 18S ribosomal RNA gene sequence analysis.

    Science.gov (United States)

    Takeo, Toshinori; Tanaka, Tetsuya; Matsubayashi, Makoto; Maeda, Hiroki; Kusakisako, Kodai; Matsui, Toshihiro; Mochizuki, Masami; Matsuo, Tomohide

    2014-08-01

    Previously, we characterized an undocumented strain of Eimeria krijgsmanni by morphological and biological features. Here, we present a detailed molecular phylogenetic analysis of this organism. Namely, 18S ribosomal RNA gene (rDNA) sequences of E. krijgsmanni were analyzed to incorporate this species into a comprehensive Eimeria phylogeny. As a result, partial 18S rDNA sequence from E. krijgsmanni was successfully determined, and two different types, Type A and Type B, that differed by 1 base pair were identified. E. krijgsmanni was originally isolated from a single oocyst, and thus the result show that the two types might have allelic sequence heterogeneity in the 18S rDNA. Based on phylogenetic analyses, the two types of E. krijgsmanni 18S rDNA formed one of two clades among murine Eimeria spp.; these Eimeria clades reflected morphological similarity among the Eimeria spp. This is the third molecular phylogenetic characterization of a murine Eimeria spp. in addition to E. falciformis and E. papillata. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products

    NARCIS (Netherlands)

    Holst-Jensen, Arne; Spilsberg, Bjørn; Arulandhu, Alfred J.; Kok, Esther; Shi, Jianxin; Zel, Jana

    2016-01-01

    The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however,

  17. Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, Mia; Skov, Marianne N.; Sandvang, Dorthe

    2005-01-01

    subspecies enterica isolates. A total of 25 serotypes were investigated that had been isolated from humans or veterinary sources in Denmark between 1995 and 2001. All isolates were genotyped by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and amplified fragment length...

  18. Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease.

    Science.gov (United States)

    Zhang, Peipei; Liu, Yan; Liu, Wenwen; Cao, Mengji; Massart, Sebastien; Wang, Xifeng

    2017-01-01

    To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae . Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90%) in the family Luteoviridae . Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

  19. Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease

    Directory of Open Access Journals (Sweden)

    Peipei Zhang

    2017-09-01

    Full Text Available To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV (most likely pathogens using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV. The full genome of WLYaV corresponds to 5,772 nucleotides (nt, with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame, and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV, but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP were 64.9 and 86.2%, respectively, below the species demarcation thresholds (90% in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study adds a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat.

  20. Characterization of novel precursor miRNAs using next generation sequencing and prediction of miRNA targets in Atlantic halibut.

    Directory of Open Access Journals (Sweden)

    Teshome Tilahun Bizuayehu

    Full Text Available BACKGROUND: microRNAs (miRNAs are implicated in regulation of many cellular processes. miRNAs are processed to their mature functional form in a step-wise manner by multiple proteins and cofactors in the nucleus and cytoplasm. Many miRNAs are conserved across vertebrates. Mature miRNAs have recently been characterized in Atlantic halibut (Hippoglossus hippoglossus L.. The aim of this study was to identify and characterize precursor miRNA (pre-miRNAs and miRNA targets in this non-model flatfish. Discovery of miRNA precursor forms and targets in non-model organisms is difficult because of limited source information available. Therefore, we have developed a methodology to overcome this limitation. METHODS: Genomic DNA and small transcriptome of Atlantic halibut were sequenced using Roche 454 pyrosequencing and SOLiD next generation sequencing (NGS, respectively. Identified pre- miRNAs were further validated with reverse-transcription PCR. miRNA targets were identified using miRanda and RNAhybrid target prediction tools using sequences from public databases. Some of miRNA targets were also identified using RACE-PCR. miRNA binding sites were validated with luciferase assay using the RTS34st cell line. RESULTS: We obtained more than 1.3 M and 92 M sequence reads from 454 genomic DNA sequencing and SOLiD small RNA sequencing, respectively. We identified 34 known and 9 novel pre-miRNAs. We predicted a number of miRNA target genes involved in various biological pathways. miR-24 binding to kisspeptin 1 receptor-2 (kiss1-r2 was confirmed using luciferase assay. CONCLUSION: This study demonstrates that identification of conserved and novel pre-miRNAs in a non-model vertebrate lacking substantial genomic resources can be performed by combining different next generation sequencing technologies. Our results indicate a wide conservation of miRNA precursors and involvement of miRNA in multiple regulatory pathways, and provide resources for further research on mi

  1. Etiopathogenesis of post-endodontic periapical scar formation

    Czech Academy of Sciences Publication Activity Database

    Horká, E.; Foltán, R.; Hanzelka, T.; Pavlíková, G.; Klíma, K.; Šedý, Jiří

    2012-01-01

    Roč. 3, č. 1 (2012), s. 5-15 ISSN 2155-8213 R&D Projects: GA MŠk 1M0538; GA MŠk(CZ) LC554; GA ČR GAP304/10/0320 Grant - others:UK(CZ) UNCE 204021 Institutional research plan: CEZ:AV0Z50390703 Keywords : postendodontic scar * endodontics * tooth Subject RIV: FH - Neurology

  2. Moisturisers in scar management following burn: A survey report.

    Science.gov (United States)

    Klotz, Tanja; Kurmis, Rochelle; Munn, Zachary; Heath, Kathryn; Greenwood, John

    2017-08-01

    Scar management is a recognised key component of rehabilitation following burn. Moisturising often combined with massage is commenced once healing tissue has gained sufficient strength to tolerate surface friction, with the aim being to hydrate the dry scar. The studies on various moisturisers and creams provide some guidance on moisturiser selection, but many are inconclusive. This survey aimed to determine the current expert opinion regarding moisturiser recommendations, including the basis for these recommendations, across the burns community. A brief web-based survey was distributed to burn therapists via mailing lists of the Australian and New Zealand Burn Association (ANZBA), and American Burn Association (ABA) 'Occupational and Physical Therapist Burn Special Interest Group'. The fifty three respondents indicated that there were 29 different moisturisers commonly recommended in practice. Three main themes were indicated as influencing recommendations for moisturiser: the perceived effects on the scar/skin (48%); the general properties of the moisturiser (38%); the ingredients (14%). Therapists reported that the principle stimuli determining their recommendations were patient feedback and the choice of the previous burn therapist in their service. Many were also guided by medical staff, pharmacists and sales representatives. Only three respondents were able to provide citations for published evidence supporting their recommendations. There is a paucity of evidence currently to support optimal moisturiser choice. This survey demonstrates that conflicting opinions are held on the ideal moisturiser brand, properties and ingredients. The recommendations made are based on low level evidence. Further research is required to inform clinicians which moisturiser to recommend to their clients. An ideal moisturiser should be one that is conducive to scar maturation, non- or minimally irritant, prevent skin drying, minimise transepidermal water loss and have no negative

  3. Lumican alleviates hypertrophic scarring by suppressing integrin-FAK signaling

    International Nuclear Information System (INIS)

    Zhao, Yuqian; Li, Xueyong; Xu, Xiaoli; He, Zhi; Cui, Lei; Lv, Xiaoxing

    2016-01-01

    Hypertrophic scarring (HS) is an overcompensation of wound healing that increases the risk of cosmetic disfigurement and functional impairment. No gold standard has been established for the treatment or prevention of HS. Our study aims to elucidate the expression and function of lumican in the pathogenesis of HS as well as the underlying mechanism involved in this procedure. An animal model of HS (rabbit ear) was established, and the Ad-lumican vectors were locally injected. Primary fibroblasts isolated from patients with hypertrophic burn scars were used in vitro. Histological and molecular changes in HS pathogenesis were evaluated. The results showed that lumican is significantly reduced in HS tissues and fibroblasts from HS patients as compared to normal skin or cells. Lumican levels were further suppressed in response to TGF-β stimulation. However, lumican upregulation effectively thinned the scar area and inhibited fibroblast proliferation and the cell cycle. Meanwhile, Ad-lumican administration suppressed the deposition of extracellular matrix, such as collagen and CTGF. Ad-lumican injected animals or fibroblasts presented comparable integrin α 2 β 1 expression while greatly reduced phosphorylation of FAK compared to the negative control. Moreover, Ad-lumican administration largely enhanced the binding of lumican to integrin α 2 β 1 and may thus inhibit the signaling propagation of collagen-integrin α 2 β 1 . Overall, the restoration of lumican levels contributed to suppressing the HS progression by inhibiting collagen-integrin α 2 β 1 -FAK signaling. - Highlights: • Lumican is downregulated during hypertrophic scar formation. • Lumican inhibits fibroblast proliferation. • Lumican inhibits extracellular matrix deposition. • Lumican suppresses collagen-integrin-FAK signaling.

  4. The use of chemotherapeutics for the treatment of keloid scars

    Directory of Open Access Journals (Sweden)

    Christopher David Jones

    2015-05-01

    Full Text Available Keloid scars are pathological scars, which develop as a result of exaggerated dermal tissue proliferation following cutaneous injury and often cause physical, psychological and cosmetic problems. Various theories regarding keloidogenesis exist, however the precise pathophysiological events remain unclear. Many different treatment modalities have been implicated in their management, but currently there is no entirely satisfactory method for treating all keloid lesions. We review a number of different chemotherapeutic agents which have been proposed for the treatment of keloid and hypertrophic scars while giving insight into some of the novel chemotherapeutic drugs which are currently being investigated. Non-randomized trials evaluating the influence of different chemotherapeutic agents, such as 5-fluorouracil (5-FU; mitomycin C; bleomycin and steroid injection, either alone or in combination with other chemotherapeutic agents or alternative treatment modalities, for the treatment of keloids were identified using a predefined PubMed search strategy. Twenty seven papers were identified. Scar improvement ≥50% was found in the majority of cases treated with 5-FU, with similar results found for mitomycin C, bleomycin and steroid injection. Combined intralesional 5-FU and steroid injection produced statistically significant improvements when compared to monotherapy. Monotherapy recurrence rates ranged from 0-47% for 5-FU, 0-15% for bleomycin and 0-50% for steroid injection. However, combined therapy in the form of surgical excision and adjuvant 5-FU or steroid injections demonstrated lower recurrence rates; 19% and 6% respectively. Currently, most of the literature supports the use of combination therapy (usually surgery and adjuvant chemotherapy as the mainstay treatment of keloids, however further investigation is necessary to determine success rates over longer time frames. Furthermore, there is the potential for novel therapies, but further

  5. Risk Factors for Recurrent Urinary Tract Infection and Renal Scarring.

    Science.gov (United States)

    Keren, Ron; Shaikh, Nader; Pohl, Hans; Gravens-Mueller, Lisa; Ivanova, Anastasia; Zaoutis, Lisa; Patel, Melissa; deBerardinis, Rachel; Parker, Allison; Bhatnagar, Sonika; Haralam, Mary Ann; Pope, Marcia; Kearney, Diana; Sprague, Bruce; Barrera, Raquel; Viteri, Bernarda; Egigueron, Martina; Shah, Neha; Hoberman, Alejandro

    2015-07-01

    To identify risk factors for recurrent urinary tract infection (UTI) and renal scarring in children who have had 1 or 2 febrile or symptomatic UTIs and received no antimicrobial prophylaxis. This 2-year, multisite prospective cohort study included 305 children aged 2 to 71 months with vesicoureteral reflux (VUR) receiving placebo in the RIVUR (Randomized Intervention for Vesicoureteral Reflux) study and 195 children with no VUR observed in the CUTIE (Careful Urinary Tract Infection Evaluation) study. Primary exposure was presence of VUR; secondary exposures included bladder and bowel dysfunction (BBD), age, and race. Outcomes were recurrent febrile or symptomatic urinary tract infection (F/SUTI) and renal scarring. Children with VUR had higher 2-year rates of recurrent F/SUTI (Kaplan-Meier estimate 25.4% compared with 17.3% for VUR and no VUR, respectively). Other factors associated with recurrent F/SUTI included presence of BBD at baseline (adjusted hazard ratio: 2.07 [95% confidence interval (CI): 1.09-3.93]) and presence of renal scarring on the baseline (99m)Tc-labeled dimercaptosuccinic acid scan (adjusted hazard ratio: 2.88 [95% CI: 1.22-6.80]). Children with BBD and any degree of VUR had the highest risk of recurrent F/SUTI (56%). At the end of the 2-year follow-up period, 8 (5.6%) children in the no VUR group and 24 (10.2%) in the VUR group had renal scars, but the difference was not statistically significant (adjusted odds ratio: 2.05 [95% CI: 0.86-4.87]). VUR and BBD are risk factors for recurrent UTI, especially when they appear in combination. Strategies for preventing recurrent UTI include antimicrobial prophylaxis and treatment of BBD. Copyright © 2015 by the American Academy of Pediatrics.

  6. Color doppler ultrasound diagonosis in cesarean scar pregnancy

    International Nuclear Information System (INIS)

    Chen Shanshan; Xia Fei; Shen Zongji; Xu Jianyin; Gu Xinxian

    2010-01-01

    Objective: To study the sonographic characteristics of cesarean scar pregnancy(CSP), and the value of color Doppler in the diagnosis of CSP. Methods: Twelve cases of CSP were all confirmed by transabdominal and transvaginal ultrasound. Results: The ultrasonogram of CSP could be divided into gestational sac type and mixed mass type. Conclusion: Color Doppler can give guidance to the early diagnosis, treatment and following-up of CSP because of the sonographic specifity of CSP. (authors)

  7. MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

    Directory of Open Access Journals (Sweden)

    Kuczmarski Thomas A

    2006-10-01

    Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

  8. A picorna-like virus from the red imported fire ant, Solenopsis invicta: initial discovery, genome sequence, and characterization

    International Nuclear Information System (INIS)

    Valles, Steven M.; Strong, Charles A.; Dang, Phat M.; Hunter, Wayne B.; Pereira, Roberto M.; Oi, David H.; Shapiro, Alexandra M.; Williams, David F.

    2004-01-01

    We report the first discovery and genome sequence of a virus infecting the red imported fire ant, Solenopsis invicta. The 8026 nucleotide, polyadenylated, RNA genome encoded two large open reading frames (ORF1 and ORF2), flanked and separated by 27, 223, and 171 nucleotide untranslated regions, respectively. The predicted amino acid sequence of the 5' proximal ORF1 (nucleotides 28 to 4218) exhibited significant identity and possessed consensus sequences characteristic of the helicase, cysteine protease, and RNA-dependent RNA polymerase sequence motifs from picornaviruses, picorna-like viruses, comoviruses, caliciviruses, and sequiviruses. The predicted amino acid sequence of the 3' proximal ORF2 (nucleotides 4390-7803) showed similarity to structural proteins in picorna-like viruses, especially the acute bee paralysis virus. Electron microscopic examination of negatively stained samples from virus-infected fire ants revealed isometric particles with a diameter of 31 nm, consistent with Picornaviridae. A survey for the fire ant virus from areas around Florida revealed a pattern of fairly widespread distribution. Among 168 nests surveyed, 22.9% were infected. The virus was found to infect all fire ant caste members and developmental stages, including eggs, early (1st-2nd) and late (3rd-4th) instars, worker pupae, workers, sexual pupae, alates ( male and female ), and queens. The virus, tentatively named S. invicta virus (SINV-1), appears to belong to the picorna-like viruses. We did not observe any perceptible symptoms among infected nests in the field. However, in every case where an SINV-1-infected colony was excavated from the field with an inseminated queen and held in the laboratory, all of the brood in these colonies died within 3 months

  9. Outcome measures and scar aesthetics in minimally invasive video-assisted parathyroidectomy.

    LENUS (Irish Health Repository)

    Casserly, Paula

    2012-02-01

    OBJECTIVES: To compare the scar outcome of video-assisted parathyroidectomy (VAP) with traditional bilateral cervical exploration (BCE) using previously validated scar assessment scales, and to examine the feasibility of introducing VAP into a general otolaryngology-head and neck practice. DESIGN: A retrospective review of medical records from a prospectively obtained database of patients and long-term follow-up of scar analysis. PATIENTS: The records of 60 patients undergoing parathyroidectomy were reviewed: 29 patients underwent VAP and 31 patients underwent an open procedure with BCE. The groups were matched for age and sex. A total of 46 patients were followed up to assess scar outcome. MAIN OUTCOME MEASURES: The primary outcome was a comparison of patient and observer scar satisfaction between VAP and traditional BCE using validated scar assessment tools: the Patient Scar Assessment Scale and the Manchester Scar Scale. The secondary outcomes were to retrospectively evaluate our results with VAP and to assess the suitability of introducing this technique into a general otolaryngology-head and neck practice. RESULTS: The average scar length in the VAP group was 1.7 cm, and the average scar length in the BCE group was 4.3 cm. The patients in the BCE group scored higher than the patients in the VAP group on the Manchester Scar Scale (P < .01) and on the Patient and Observer Scar Scales (P = .02), indicating a worse scar outcome. The mean operative time in the VAP group was 41 minutes compared with 115 minutes in the open procedure BCE group. There was no difference between the 2 groups in terms of postoperative complications. CONCLUSIONS: Video-assisted parathyroidectomy is a safe and feasible procedure in the setting of a general otolaryngology-head and neck practice, with outcomes and complication rates that are comparable to those of traditional bilateral neck exploration. Both patient and observer analysis demonstrated that VAP was associated with a more

  10. Retrospective analysis of factors affecting the efficacy of surgical treatment of the scar.

    Science.gov (United States)

    Yang, Z; Shi, X; Zhang, Y; Wang, S; Lei, Z; Liu, X; Fan, D

    2014-04-01

    The scar is a major problem in the medical profession. Its timely treatment is very important for the better outcome of the scar treatment and for the improvement of the life quality of the patients. The aim of this study was retrospectively analyzed the epidemiological characteristics affecting the efficacy of the scar surgical treatment of the people in the western part of China. Total 414 scar cases were retrospectively analyzed to clarify the epidemiological characteristics and the factors affecting the scar surgical treatment efficacy. The factors included were sex, age, area distribution, treatment seasons, injury sites, injury causes, and the time from scarring to the surgical treatment. All scar cases were surgically treated with the repairing technology including skin graft, flap and soft tissue dilation. There were 206 males and 208 females with the average age 20.53±12.9 years (age range 1-68 years). The patient proportions in the age groups of 0-20, 21-40 and >40 years were 61.4% (254 cases), 29.2% (121 cases), and 9.4% (39 cases) respectively. The patient's attendance rate reached the highest during the summer and winter. Most patients were from the rural areas with an increasing tendency each year. The burn scars were the most abundant and the injury sites were mostly the head and face. Univariate analysis showed that the time from scarring to the surgical treatment and the injury sites were significantly influenced the scar surgical treatment efficacy. Logistic regression analysis demonstrated that the injured sites of the head and face significantly influenced the scar surgical treatment efficacy. With the development of economy in China, more scar patients especially younger and children visit doctors predominantely from the rural areas. Usually, they get their scars in the exposed area of their bodies (head and face) which seriously affect the patient's appearance and function. Factors influencing the scar surgical treatment efficacy has

  11. Three-Dimensional Electromagnetic High Frequency Axisymmetric Cavity Scars.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Jorgenson, Roy Eberhardt

    2014-10-01

    This report examines the localization of high frequency electromagnetic fi elds in three-dimensional axisymmetric cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This report treats both the case where the opposing sides, or mirrors, are convex, where there are no interior foci, and the case where they are concave, leading to interior foci. The scalar problem is treated fi rst but the approximations required to treat the vector fi eld components are also examined. Particular att ention is focused on the normalization through the electromagnetic energy theorem. Both projections of the fi eld along the scarred orbit as well as point statistics are examined. Statistical comparisons are m ade with a numerical calculation of the scars run with an axisymmetric simulation. This axisymmetric cas eformstheoppositeextreme(wherethetwomirror radii at each end of the ray orbit are equal) from the two -dimensional solution examined previously (where one mirror radius is vastly di ff erent from the other). The enhancement of the fi eldontheorbitaxiscanbe larger here than in the two-dimensional case. Intentionally Left Blank

  12. Characterizing colonic motility in children with chronic intractable constipation: a look beyond high-amplitude propagating sequences

    NARCIS (Netherlands)

    Wessel, S.; Koppen, I. J. N.; Wiklendt, L.; Costa, M.; Benninga, M. A.; Dinning, P. G.

    2016-01-01

    Children with chronic intractable constipation experience severe and long-lasting symptoms, which respond poorly to conventional therapeutic strategies. Detailed characterization of colonic motor patterns in such children has not yet been obtained. In 18 children with chronic intractable

  13. Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage

    Directory of Open Access Journals (Sweden)

    Maugel Timothy K

    2007-07-01

    Full Text Available Abstract Background Bioinformatic analysis of the genome sequence of Neisseria gonorrhoeae revealed the presence of nine probable prophage islands. The distribution, conservation and function of many of these sequences, and their ability to produce bacteriophage particles are unknown. Results Our analysis of the genomic sequence of FA1090 identified five genomic regions (NgoΦ1 – 5 that are related to dsDNA lysogenic phage. The genetic content of the dsDNA prophage sequences were examined in detail and found to contain blocks of genes encoding for proteins homologous to proteins responsible for phage DNA replication, structural proteins and proteins responsible for phage assembly. The DNA sequences from NgoΦ1, NgoΦ2 and NgoΦ3 contain some significant regions of identity. A unique region of NgoΦ2 showed very high similarity with the Pseudomonas aeruginosa generalized transducing phage F116. Comparative analysis at the nucleotide and protein levels suggests that the sequences of NgoΦ1 and NgoΦ2 encode functionally active phages, while NgoΦ3, NgoΦ4 and NgoΦ5 encode incomplete genomes. Expression of the NgoΦ1 and NgoΦ2 repressors in Escherichia coli inhibit the growth of E. coli and the propagation of phage λ. The NgoΦ2 repressor was able to inhibit transcription of N. gonorrhoeae genes and Haemophilus influenzae HP1 phage promoters. The holin gene of NgoΦ1 (identical to that encoded by NgoΦ2, when expressed in E. coli, could serve as substitute for the phage λ s gene. We were able to detect the presence of the DNA derived from NgoΦ1 in the cultures of N. gonorrhoeae. Electron microscopy analysis of culture supernatants revealed the presence of multiple forms of bacteriophage particles. Conclusion These data suggest that the genes similar to dsDNA lysogenic phage present in the gonococcus are generally conserved in this pathogen and that they are able to regulate the expression of other neisserial genes. Since phage particles were

  14. Repetitive DNA in the pea (Pisum sativum L. genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Navrátilová Alice

    2007-11-01

    Full Text Available Abstract Background Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum. Results Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. Conclusion We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data

  15. Molecular detection and characterization of Hop stunt viroid sequence variants from naturally infected pomegranate (Punica granatum L. in Tunisia

    Directory of Open Access Journals (Sweden)

    Faten GORSANE

    2010-09-01

    Full Text Available Tunisian pomegranate Hop stunt viroid (HSVd variants are described. Dot-blot hybridization, S-Page, and reverse transcription polymerase chain reaction (RT-PCR of RNA extracts from infected tissues were carried out. Results obtained by these techniques were confirmed by cDNA sequencing. The genetic diversity among the Tunisian variants was investigated, which also involved analysis of sequences of previously described HSVd variants from Tunisian citrus var. clementine and fig, and from fruit trees from other Mediterranean countries. Phylogenetic analysis showed that Tunisian pomegranate HSVd variants were clustered into two groups: a cachexia strain within the citrus type group and a recombinant citrus-plum type group. Results also showed a high haplotype diversity which was not related either to the host or to the geographical origin. Selective neutrality and genetic network tests suggest that the HSVd isolates have spread rapidly.

  16. Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110.

    Science.gov (United States)

    Fomukong, N G; Tang, T H; al-Maamary, S; Ibrahim, W A; Ramayah, S; Yates, M; Zainuddin, Z F; Dale, J W

    1994-12-01

    DNA fingerprinting with the insertion sequence IS6110 (also known as IS986) has become established as a major tool for investigating the spread of tuberculosis. Most strains of Mycobacterium tuberculosis have multiple copies of IS6110, but a small minority carry a single copy only. We have examined selected strains from Malaysia, Tanzania and Oman, in comparison with M. bovis isolates and BCG strains carrying one or two copies of IS6110. The insertion sequence appears to be present in the same position in all these strains, which suggests that in these organisms the element is defective in transposition and that the loss of transposability may have occurred at an early stage in the evolution of the M. tuberculosis complex.

  17. Data-driven model comparing the effects of glial scarring and interface interactions on chronic neural recordings in non-human primates

    Science.gov (United States)

    Malaga, Karlo A.; Schroeder, Karen E.; Patel, Paras R.; Irwin, Zachary T.; Thompson, David E.; Bentley, J. Nicole; Lempka, Scott F.; Chestek, Cynthia A.; Patil, Parag G.

    2016-02-01

    Objective. We characterized electrode stability over twelve weeks of impedance and neural recording data from four chronically-implanted Utah arrays in two rhesus macaques, and investigated the effects of glial scarring and interface interactions at the electrode recording site on signal quality using a computational model. Approach. A finite-element model of a Utah array microelectrode in neural tissue was coupled with a multi-compartmental model of a neuron to quantify the effects of encapsulation thickness, encapsulation resistivity, and interface resistivity on electrode impedance and waveform amplitude. The coupled model was then reconciled with the in vivo data. Histology was obtained seventeen weeks post-implantation to measure gliosis. Main results. From week 1-3, mean impedance and amplitude increased at rates of 115.8 kΩ/week and 23.1 μV/week, respectively. This initial ramp up in impedance and amplitude was observed across all arrays, and is consistent with biofouling (increasing interface resistivity) and edema clearing (increasing tissue resistivity), respectively, in the model. Beyond week 3, the trends leveled out. Histology showed that thin scars formed around the electrodes. In the model, scarring could not match the in vivo data. However, a thin interface layer at the electrode tip could. Despite having a large effect on impedance, interface resistivity did not have a noticeable effect on amplitude. Significance. This study suggests that scarring does not cause an electrical problem with regard to signal quality since it does not appear to be the main contributor to increasing impedance or significantly affect amplitude unless it displaces neurons. This, in turn, suggests that neural signals can be obtained reliably despite scarring as long as the recording site has sufficiently low impedance after accumulating a thin layer of biofouling. Therefore, advancements in microelectrode technology may be expedited by focusing on improvements to the

  18. Identification and characterization of two novel bla(KLUC resistance genes through large-scale resistance plasmids sequencing.

    Directory of Open Access Journals (Sweden)

    Teng Xu

    Full Text Available Plasmids are important antibiotic resistance determinant carriers that can disseminate various drug resistance genes among species or genera. By using a high throughput sequencing approach, two groups of plasmids of Escherichia coli (named E1 and E2, each consisting of 160 clinical E. coli strains isolated from different periods of time were sequenced and analyzed. A total of 20 million reads were obtained and mapped onto the known resistance gene sequences. As a result, a total of 9 classes, including 36 types of antibiotic resistant genes, were identified. Among these genes, 25 and 27 single nucleotide polymorphisms (SNPs appeared, of which 9 and 12 SNPs are nonsynonymous substitutions in the E1 and E2 samples. It is interesting to find that a novel genotype of bla(KLUC, whose close relatives, bla(KLUC-1 and bla(KLUC-2, have been previously reported as carried on the Kluyvera cryocrescens chromosome and Enterobacter cloacae plasmid, was identified. It shares 99% and 98% amino acid identities with Kluc-1 and Kluc-2, respectively. Further PCR screening of 608 Enterobacteriaceae family isolates yielded a second variant (named bla(KLUC-4. It was interesting to find that Kluc-3 showed resistance to several cephalosporins including cefotaxime, whereas bla(KLUC-4 did not show any resistance to the antibiotics tested. This may be due to a positively charged residue, Arg, replaced by a neutral residue, Leu, at position 167, which is located within an omega-loop. This work represents large-scale studies on resistance gene distribution, diversification and genetic variation in pooled multi-drug resistance plasmids, and provides insight into the use of high throughput sequencing technology for microbial resistance gene detection.

  19. Characterization of the Complete Mitochondrial Genome Sequence of the Globose Head Whiptail Cetonurus globiceps (Gadiformes: Macrouridae and Its Phylogenetic Analysis.

    Directory of Open Access Journals (Sweden)

    Xiaofeng Shi

    Full Text Available The particular environmental characteristics of deep water such as its immense scale and high pressure systems, presents technological problems that have prevented research to broaden our knowledge of deep-sea fish. Here, we described the mitogenome sequence of a deep-sea fish, Cetonurus globiceps. The genome is 17,137 bp in length, with a standard set of 22 transfer RNA genes (tRNAs, two ribosomal RNA genes, 13 protein-coding genes, and two typical non-coding control regions. Additionally, a 70 bp tRNA(Thr-tRNA(Pro intergenic spacer is present. The C. globiceps mitogenome exhibited strand-specific asymmetry in nucleotide composition. The AT-skew and GC-skew values in the whole genome of C. globiceps were 0 and -0.2877, respectively, revealing that the H-strand had equal amounts of A and T and that the overall nucleotide composition was C skewed. All of the tRNA genes could be folded into cloverleaf secondary structures, while the secondary structure of tRNA(Ser(AGY lacked a discernible dihydrouridine stem. By comparing this genome sequence with the recognition sites in teleost species, several conserved sequence blocks were identified in the control region. However, the GTGGG-box, the typical characteristic of conserved sequence block E (CSB-E, was absent. Notably, tandem repeats were identified in the 3' portion of the control region. No similar repetitive motifs are present in most of other gadiform species. Phylogenetic analysis based on 12 protein coding genes provided strong support that C. globiceps was the most derived in the clade. Some relationships however, are in contrast with those presented in previous studies. This study enriches our knowledge of mitogenomes of the genus Cetonurus and provides valuable information on the evolution of Macrouridae mtDNA and deep-sea fish.

  20. Transcriptome Characterization and Sequencing-Based Identification of Salt-Responsive Genes in Millettia pinnata, a Semi-Mangrove Plant

    OpenAIRE

    Huang, Jianzi; Lu, Xiang; Yan, Hao; Chen, Shouyi; Zhang, Wanke; Huang, Rongfeng; Zheng, Yizhi

    2012-01-01

    Semi-mangroves form a group of transitional species between glycophytes and halophytes, and hold unique potential for learning molecular mechanisms underlying plant salt tolerance. Millettia pinnata is a semi-mangrove plant that can survive a wide range of saline conditions in the absence of specialized morphological and physiological traits. By employing the Illumina sequencing platform, we generated ∼192 million short reads from four cDNA libraries of M. pinnata and processed them into 108 ...

  1. Implementation of Whole Genome Sequencing (WGS for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC in the United States

    Directory of Open Access Journals (Sweden)

    Rebecca L Lindsey

    2016-05-01

    Full Text Available Shiga toxin-producing Escherichia coli (STEC is an important foodborne pathogen capable of causing severe disease in humans. Rapid and accurate identification and characterization techniques are essential during outbreak investigations. Current methods for characterization of STEC are expensive and time-consuming. With the advent of rapid and cheap whole genome sequencing (WGS benchtop sequencers, the potential exists to replace traditional workflows with WGS. The aim of this study was to validate tools to do reference identification and characterization from WGS for STEC in a single workflow within an easy to use commercially available software platform. Publically available serotype, virulence, and antimicrobial resistance databases were downloaded from the Center for Genomic Epidemiology (CGE (www.genomicepidemiology.org and integrated into a genotyping plug-in with in silico PCR tools to confirm some of the virulence genes detected from WGS data. Additionally, down sampling experiments on the WGS sequence data were performed to determine a threshold for sequence coverage needed to accurately predict serotype and virulence genes using the established workflow. The serotype database was tested on a total of 228 genomes and correctly predicted from WGS for 96.1% of O serogroups and 96.5% of H serogroups identified by conventional testing techniques. A total of 59 genomes were evaluated to determine the threshold of coverage to detect the different WGS targets, 40 were evaluated for serotype and virulence gene detection and 19 for the stx gene subtypes. For serotype, 95% of the O and 100% of the H serogroups were detected at > 40x and ≥ 30x coverage, respectively. For virulence targets and stx gene subtypes, nearly all genes were detected at > 40x, though some targets were 100% detectable from genomes with coverage ≥20x. The resistance detection tool was 97% concordant with phenotypic testing results. With isolates sequenced to > 40x

  2. Implementation of Whole Genome Sequencing (WGS) for Identification and Characterization of Shiga Toxin-Producing Escherichia coli (STEC) in the United States

    Science.gov (United States)

    Lindsey, Rebecca L.; Pouseele, Hannes; Chen, Jessica C.; Strockbine, Nancy A.; Carleton, Heather A.

    2016-01-01

    Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe disease in humans. Rapid and accurate identification and characterization techniques are essential during outbreak investigations. Current methods for characterization of STEC are expensive and time-consuming. With the advent of rapid and cheap whole genome sequencing (WGS) benchtop sequencers, the potential exists to replace traditional workflows with WGS. The aim of this study was to validate tools to do reference identification and characterization from WGS for STEC in a single workflow within an easy to use commercially available software platform. Publically available serotype, virulence, and antimicrobial resistance databases were downloaded from the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org) and integrated into a genotyping plug-in with in silico PCR tools to confirm some of the virulence genes detected from WGS data. Additionally, down sampling experiments on the WGS sequence data were performed to determine a threshold for sequence coverage needed to accurately predict serotype and virulence genes using the established workflow. The serotype database was tested on a total of 228 genomes and correctly predicted from WGS for 96.1% of O serogroups and 96.5% of H serogroups identified by conventional testing techniques. A total of 59 genomes were evaluated to determine the threshold of coverage to detect the different WGS targets, 40 were evaluated for serotype and virulence gene detection and 19 for the stx gene subtypes. For serotype, 95% of the O and 100% of the H serogroups were detected at > 40x and ≥ 30x coverage, respectively. For virulence targets and stx gene subtypes, nearly all genes were detected at > 40x, though some targets were 100% detectable from genomes with coverage ≥20x. The resistance detection tool was 97% concordant with phenotypic testing results. With isolates sequenced to > 40x coverage, the different

  3. Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing.

    Science.gov (United States)

    Silar, Philippe; Barreau, Christian; Debuchy, Robert; Kicka, Sébastien; Turcq, Béatrice; Sainsard-Chanet, Annie; Sellem, Carole H; Billault, Alain; Cattolico, Laurence; Duprat, Simone; Weissenbach, Jean

    2003-08-01

    A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.

  4. Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples

    Directory of Open Access Journals (Sweden)

    I. Fernández-Natal

    2016-03-01

    Full Text Available During a 12-year period we isolated five Corynebacterium argentoratense strains identified by phenotypic methods, including the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF and 16S rRNA gene sequencing. In addition, antimicrobial susceptibility was determined, and genome sequencing for the detection of antibiotic resistance genes was performed. The organisms were isolated from blood and throat cultures and could be identified by all methods used. All strains were resistant to cotrimoxazole, and resistance to β-lactams was partly present. Two strains were resistant to erythromycin and clindamycin. The draft genome sequences of theses isolates revealed the presence of the erm(X resistance gene that is embedded in the genetic structure of the transposable element Tn5423. Although rarely reported as a human pathogen, C. argentoratense can be involved in bacteraemia and probably in other infections. Our results also show that horizontal transfer of genes responsible for antibiotic resistance is occurring in this species.

  5. Genome-wide identification and characterization of Notch transcription complex-binding sequence paired sites in leukemia cells

    Science.gov (United States)

    Severson, Eric; Arnett, Kelly L.; Wang, Hongfang; Zang, Chongzhi; Taing, Len; Liu, Hudan; Pear, Warren S.; Liu, X. Shirley; Blacklow, Stephen C.; Aster, Jon C.

    2018-01-01

    Notch transcription complexes (NTCs) drive target gene expression by binding to two distinct types of genomic response elements, NTC monomer-binding sites and sequence-paired sites (SPSs) that bind NTC dimers. SPSs are conserved and are linked to the Notch-responsiveness of a few genes, but their overall contribution to Notch-dependent gene regulation is unknown. To address this issue, we determined the DNA sequence requirements for NTC dimerization using a fluorescence resonance energy transfer (FRET) assay, and applied insights from these in vitro studies to Notch-“addicted” leukemia cells. We find that SPSs contribute to the regulation of approximately a third of direct Notch target genes. While originally described in promoters, SPSs are present mainly in long-range enhancers, including an enhancer containing a newly described SPS that regulates HES5. Our work provides a general method for identifying sequence-paired sites in genome-wide data sets and highlights the widespread role of NTC dimerization in Notch-transformed leukemia cells. PMID:28465412

  6. m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveals the census and complexity of the m6A epitranscriptome

    OpenAIRE

    Molinie, Benoit; Wang, Jinkai; Lim, Kok-Seong; Hillebrand, Roman; Lu, Zhi-xiang; Van Wittenberghe, Nicholas; Howard, Benjamin D.; Daneshvar, Kaveh; Mullen, Alan C.; Dedon, Peter; Xing, Yi; Giallourakis, Cosmas C.

    2016-01-01

    N6-Methyladenosine (m6A) is a widespread, reversible chemical modification of RNA molecules, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (‘m6A levels’) or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A-level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad...

  7. Isolation and characterization of human glycophorin A cDNA clones by a synthetic oligonucleotide approach: nucleotide sequence and mRNA structure

    International Nuclear Information System (INIS)

    Siebert, P.D.; Fukuda, M.

    1986-01-01

    In an effort to understand the relationships among and the regulation of human glycophorins, the authors have isolated and characterized several glycophorin A-specific cDNA clones obtained from a human erythroleukemic K562 cell cDNA library. This was accomplished by using mixed synthetic oligonucleotides, corresponding to various regions of the known amino acid sequence, to prime the synthesis of the cDNA as well as to screen the cDNA library. They also used synthetic oligonucleotides to sequence the largest of the glycophorin cDNAs. The nucleotide sequence obtained suggests the presence of a potential leader peptide, consistent with the membrane localization of this glycoprotein. Examination of the structure of glycophorin mRNA by blot hybridization revealed the existence of several electrophoretically distinct mRNAs numbering three or four, depending on the size of the glycophorin cDNA used as a hybridization probe. The smaller cDNA hybridized to three mRNAs of approximately 2.8, 1.7, and 1.0 kilobases. In contrast, the larger cDNA hybridized to an additional mRNA of approximately 0.6 kilobases. Further examination of the relationships between these multiple mRNAs by blot hybridization was conducted with the use of exact-sequence oligonucleotide probes constructed from various regions of the cDNA representing portions of the amino acid sequence of glycophorin A with or without known homology with glycophorin B. In total, the results obtained are consistent with the hypothesis that the three larger mRNAs represent glycophorin A gene transcripts and that the smallest (0.6 kilobase) mRNA may be specific for glycophorin B

  8. A prospective study of time to healing and hypertrophic scarring in paediatric burns: every day counts.

    Science.gov (United States)

    Chipp, Elizabeth; Charles, Lisa; Thomas, Clare; Whiting, Kate; Moiemen, Naiem; Wilson, Yvonne

    2017-01-01

    It is commonly accepted that burns taking longer than 3 weeks to heal have a much higher rate of hypertrophic scarring than those which heal more quickly. However, some of our patients develop hypertrophic scars despite healing within this 3-week period. We performed a prospective study of 383 paediatric burns treated non-operatively at a regional burns centre over a 2-year period from May 2011 to April 2013. Scar assessment was performed by a senior burns therapist using the Vancouver Scar Scale. Overall rates of hypertrophic scarring were 17.2%. Time to healing was the strongest predictor of developing hypertrophic scarring, and the earliest hypertrophic scar developed in a patient who was healed after 8 days. The risk of hypertrophic scarring was multiplied by 1.138 for every additional day taken for the burn wound to heal. There was a trend towards higher rates of hypertrophic scarring in non-white skin types but this did not reach statistical significance. The risk of hypertrophic scarring increases with every day and, therefore, every effort should be made to get the wound healed as quickly as possible, even within the traditional 3-week period usually allowed for healing. We believe that the traditional dogma of aiming for healing within 3 weeks is overly simplistic and should be abandoned: in paediatric burns, every day counts. Not applicable.

  9. Probability mapping of scarred myocardium using texture and intensity features in CMR images

    Science.gov (United States)

    2013-01-01

    Background The myocardium exhibits heterogeneous nature due to scarring after Myocardial Infarction (MI). In Cardiac Magnetic Resonance (CMR) imaging, Late Gadolinium (LG) contrast agent enhances the intensity of scarred area in the myocardium. Methods In this paper, we propose a probability mapping technique using Texture and Intensity features to describe heterogeneous nature of the scarred myocardium in Cardiac Magnetic Resonance (CMR) images after Myocardial Infarction (MI). Scarred tissue and non-scarred tissue are represented with high and low probabilities, respectively. Intermediate values possibly indicate areas where the scarred and healthy tissues are interwoven. The probability map of scarred myocardium is calculated by using a probability function based on Bayes rule. Any set of features can be used in the probability function. Results In the present study, we demonstrate the use of two different types of features. One is based on the mean intensity of pixel and the other on underlying texture information of the scarred and non-scarred myocardium. Examples of probability maps computed using the mean intensity of pixel and the underlying texture information are presented. We hypothesize that the probability mapping of myocardium offers alternate visualization, possibly showing the details with physiological significance difficult to detect visually in the original CMR image. Conclusion The probability mapping obtained from the two features provides a way to define different cardiac segments which offer a way to identify areas in the myocardium of diagnostic importance (like core and border areas in scarred myocardium). PMID:24053280

  10. A clinical study and the diagnosis in magnetic resonance imaging of renal scarring

    International Nuclear Information System (INIS)

    Tsugaya, Masayuki; Hirao, Noriaki; Ohtaguro, Kazuo; Kato, Jiro.

    1989-01-01

    Twenty-nine kidneys of seventeen patients (nine boys and eight girls) with vesicoureteral reflux and repeated urinary tract infection were studied by magnetic resonance imaging for diagnosis of renal scarring and correlation between clinical data and the degree renal scarring. Renal scarring is classified into three types according to findings in magnetic resonance imaging. The degree of renal scarring are classified into five grades according to traditional grading of intravenous pyelogram. If a fine deformity of calyx is shown on intravenous pyelogram, magnetic resonance imaging demonstrates renal scarring. Magnetic resonance imaging without irradiation is exceedingly valuable for the diagnosis of renal scarring. The appearances of magnetic resonance imaging were supported by X-ray computed tomography. There is a substantial correlation between serum creatinine and the grades of renal scarring by magnetic resonance imaging. There is a substantial correlation between fever attacks and the grade of renal scarring, and there is a significant reverse correlation between the age of the onset of upper urinary tract infection and the grade of renal scarring. It is suggested that upper urinary tract infection is the most significant factor in scar formation. (author)

  11. A second pectin lyase gene (pel2) from Aspergillus oryzae KBN616: its sequence analysis and overexpression, and characterization of the gene products.

    Science.gov (United States)

    Kitamoto, N; Yoshino-Yasuda, S; Ohmiya, K; Tsukagoshi, N

    2001-01-01

    A second pectin lyase gene, designated pel2, was isolated from a shoyu koji mold Aspergillus oryzae KBN616 and characterized. The structural gene comprised 1306 bp with three introns. The ORF encoded 375 amino acids with a signal peptide of 19 amino acids. The deduced amino acid sequence showed high similarity to those of A. oryzae Pel1, Aspergillus niger pectin lyases and Glomerella cingulata Pn1A. The pel2 gene was overexpressed under the control of the promoter of the A. oryzae TEF1 gene for purification and enzymatic characterization of its gene product. The gene product exhibited two molecular masses of 48 and 44 kDa due to different degrees of glycosylation. Both proteins had the same pH optimum of 6.0 and temperature optimum of 50 degrees C.

  12. Cloning and characterization of cDNAs encoding the complete sequence of decay-accelerating factor of human complement

    International Nuclear Information System (INIS)

    Medof, M.E.; Lublin, D.M.; Holers, V.M.; Ayers, D.J.; Getty, R.R.; Leykam, J.F.; Atkinson, J.P.; Tykocinski, M.L.

    1987-01-01

    cDNAs encoding the complement decay-accelerating factor (DAF) were isolated from HeLa and differentiated HL-60 λgt cDNA libraries by screening with a codon preference oligonucleotide corresponding to DAF NH 2 -terminal amino acids 3-14. The composite cDNA sequence showed a 347-amino acid protein preceded by an NH 2 -terminal leader peptide sequence. The translated sequence beginning at the DAF NH 2 terminus encodes four contiguous ≅ 61-amino acid long repetitive units of internal homology. The repetitive regions contain four conserved cysteines, one proline, one glycine, one glycine/alanine, four leucines/isoleucines/valines, one serine, three tyrosines/phenylalanines, and on tryptophan and show striking homology to similar regions previously identified in factor B, C2, C4 binding protein, factor H, C1r, factor XIII, interleukin 2 receptor, and serum β 2 -glycoprotein I. The consensus repeats are attached to a 70-amino acid long segment rich in serine and threonine (potential O-glycosylation sites), which is in turn followed by a stretch of hydrophobic amino acids. RNA blot analysis of HeLa and HL-60 RNA revealed three DAF mRNA species of 3.1, 2.7, and 2.0 kilobases. The results indicate that portions of the DAF gene may have evolved from a DNA element common to the above proteins, that DAF cDNA predicts a COOH-terminal anchoring polypeptide, and that distinct species of DAF message are elaborated in cells

  13. Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon.

    Directory of Open Access Journals (Sweden)

    Sathishkumar Natarajan

    Full Text Available Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L. and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, 'SCNU1154', 'Edisto47', 'MR-1', and 'PMR5'. To investigate the genetic variation of these accessions, whole genome re-sequencing using the Illumina HiSeq 2000 platform was performed. A total of 754,759,704 quality-filtered reads were generated, with an average of 82.64% coverage relative to the reference genome. Comparisons of the sequences for the melon accessions revealed around 7.4 million single nucleotide polymorphisms (SNPs, 1.9 million InDels, and 182,398 putative structural variations (SVs. Functional enrichment analysis of detected variations classified them into biological process, cellular component and molecular function categories. Further, a disease-associated QTL map was constructed for 390 SNPs and 45 InDels identified as related to defense-response genes. Among them 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes. Accordingly, this whole genome re-sequencing study identified SNPs and InDels associated with defense genes that will serve as candidate polymorphisms in the search for sources of resistance against powdery mildew disease and could accelerate marker-assisted breeding in melon.

  14. Browning in Annona cherimola fruit: role of polyphenol oxidase and characterization of a coding sequence of the enzyme.

    Science.gov (United States)

    Prieto, Humberto; Utz, Daniella; Castro, Alvaro; Aguirre, Carlos; González-Agüero, Mauricio; Valdés, Héctor; Cifuentes, Nicolas; Defilippi, Bruno G; Zamora, Pablo; Zúñiga, Gustavo; Campos-Vargas, Reinaldo

    2007-10-31

    Cherimoya (Annona cherimola Mill.) fruit is an attractive candidate for food processing applications as fresh cut. However, along with its desirable delicate taste, cherimoya shows a marked susceptibility to browning. This condition is mainly attributed to polyphenol oxidase activity (PPO). A general lack of knowledge regarding PPO and its role in the oxidative loss of quality in processed cherimoya fruit requires a better understanding of the mechanisms involved. The work carried out included the cloning of a full-length cDNA, an analysis of its properties in the deduced amino sequence, and linkage of its mRNA levels with enzyme activity in mature and ripe fruits after wounding. The results showed one gene different at the nucleotide level when compared with previously reported genes, but a well-conserved protein, either in functional and in structural terms. Cherimoya PPO gene (Ac-ppo, GenBank DQ990911) showed to be present apparently in one copy of the genome, and its transcripts could be significantly detected in leaves and less abundantly in flowers and fruits. Analysis of wounded matured and ripened fruits revealed an inductive behavior for mRNA levels in the flesh of mature cherimoya after 16 h. Although the highest enzymatic activity was observed on rind, a consistent PPO activity was detected on flesh samples. A lack of correlation between PPO mRNA level and PPO activity was observed, especially in flesh tissue. This is probably due to the presence of monophenolic substrates inducing a lag period, enzyme inhibitors and/or diphenolic substrates causing suicide inactivation, and proenzyme or latent isoforms of PPO. To our knowledge this is the first report of a complete PPO sequence in cherimoya. Furthermore, the gene is highly divergent from known nucleotide sequences but shows a well conserved protein in terms of its function, deduced structure, and physiological role.

  15. Sequence analysis-based characterization and identification of neurovirulence-associated variants of 36 EV71 strains from China.

    Science.gov (United States)

    Xu, Jun; Wang, Fang; Zhao, Desheng; Liu, Jiang; Su, Hong; Wang, Baolong

    2018-03-30

    Enterovirus 71 (EV71) is the main pathogen of hand-foot-mouth disease (HFMD) and causes several neurological complications. As new strains of EV71 are constantly discovered, it is important to understand the genomic characteristics of the viruses and the mechanism of virulence. Herein, we isolated five strains of EV71 from HFMD patients with or without neurovirulence and sequenced their whole genomes. We then performed whole genome sequence analysis of totally 36 EV71 strains. The phylogenetic analysis of the VP1 region revealed all five isolated strains are clustered into C4a of C4 subgenotype. In addition, by comparing the complete genome sequences of 36 strains, 253 variable amino acid positions were found, 14 of which were identified to be associated with neurovirulence (P < 0.05). Moreover, a similar pattern of amino acid variants combination was identified in four strains without neurovirulence, indicating this type of variant pattern might be associated with avirulence. The strains with neurovirulence appeared to be distinguished from those without neurovirulence by the variants in VP1 and P2 regions, implying VP1 and P2 are the important regions associated with neurovirulence. Indeed, 3-D modeling of VP1 and P2 regions of non-neurovirulent and neurovirulent strains revealed that the different variants resulted in different protein structures and amino acid composition of ligand binding site, which might account for their difference in neurovirulence. In summary, our study reveals 14 variable amino acid positions of VP1, P2 and P3 regions are related to the virulence and that mutations in the capsid proteins of EV71 might contribute to neurovirulence. © 2018 Wiley Periodicals, Inc.

  16. SSH analysis of endosperm transcripts and characterization of heat stress regulated expressed sequence tags in bread wheat

    Directory of Open Access Journals (Sweden)

    Suneha Goswami

    2016-08-01

    Full Text Available Heat stress is one of the major problems in agriculturally important cereal crops, especially wheat. Here, we have constructed a subtracted cDNA library from the endosperm of HS-treated (42°C for 2 h wheat cv. HD2985 by suppression subtractive hybridization (SSH. We identified ~550 recombinant clones ranging from 200 to 500 bp with an average size of 300 bp. Sanger’s sequencing was performed with 205 positive clones to generate the differentially expressed sequence tags (ESTs. Most of the ESTs were observed to be localized on the long arm of chromosome 2A and associated with heat stress tolerance and metabolic pathways. Identified ESTs were BLAST search using Ensemble, TriFLD and TIGR databases and the predicted CDS were translated and aligned with the protein sequences available in pfam and InterProScan 5 databases to predict the differentially expressed proteins (DEPs. We observed eight different types of post-translational modifications (PTMs in the DEPs corresponds to the cloned ESTs—147 sites with phosphorylation, 21 sites with sumoylation, 237 with palmitoylation, 96 sites with S-nitrosylation, 3066 calpain cleavage sites, and 103 tyrosine nitration sites, predicted to sense the heat stress and regulate the expression of stress genes. Twelve DEPs were observed to have transmembrane helixes (TMH in their structure, predicted to play the role of sensors of HS. Quantitative Real-Time PCR of randomly selected ESTs showed very high relative expression of HSP17 under HS; up-regulation was observed more in wheat cv. HD2985 (thermotolerant, as compared to HD2329 (thermosusceptible during grain-filling. The abundance of transcripts was further validated through northern blot analysis. The ESTs and their corresponding DEPs can be used as molecular marker for screening or targeted precision breeding program. PTMs identified in the DEPs can be used to elucidate the thermotolerance mechanism of wheat – a novel step towards the development of

  17. Transcriptome Characterization for Non-Model Endangered Lycaenids, Protantigius superans and Spindasis takanosis, Using Illumina HiSeq 2500 Sequencing

    Directory of Open Access Journals (Sweden)

    Bharat Bhusan Patnaik

    2015-12-01

    Full Text Available The Lycaenidae butterflies, Protantigius superans and Spindasis takanosis, are endangered insects in Korea known for their symbiotic association with ants. However, necessary genomic and transcriptomics data are lacking in these species, limiting conservation efforts. In this study, the P. superans and S. takanosis transcriptomes were deciphered using Illumina HiSeq 2500 sequencing. The P. superans and S. takanosis transcriptome data included a total of 254,340,693 and 245,110,582 clean reads assembled into 159,074 and 170,449 contigs and 107,950 and 121,140 unigenes, respectively. BLASTX hits (E-value of 1.0 × 10−5 against the known protein databases annotated a total of 46,754 and 51,908 transcripts for P. superans and S. takanosis. Approximately 41.25% and 38.68% of the unigenes for P. superans and S. takanosis found homologous sequences in Protostome DB (PANM-DB. BLAST2GO analysis confirmed 18,611 unigenes representing Gene Ontology (GO terms and a total of 5259 unigenes assigned to 116 pathways for P. superans. For S. takanosis, a total of 6697 unigenes were assigned to 119 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG pathway database. Additionally, 382,164 and 390,516 Simple Sequence Repeats (SSRs were compiled from the unigenes of P. superans and S. takanosis, respectively. This is the first report to record new genes and their utilization for conservation of lycaenid species population and as a reference information for closely related species.

  18. Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases

    Directory of Open Access Journals (Sweden)

    Edoardo Piombo

    2018-04-01

    Full Text Available The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product “Shemer.” Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M. fructicola using PacBio and Illumina shotgun sequencing technologies. Using the PacBio, a high-quality draft genome consisting of 93 contigs, with an estimated genome size of approximately 26 Mb, was obtained. Comparative analysis of M. fructicola proteins with the other three available closely related genomes revealed a shared core of homologous proteins coded by 5,776 genes. Comparing the genomes of the two M. fructicola strains using a SNP calling approach resulted in the identification of 564,302 homologous SNPs with 2,004 predicted high impact mutations. The size of the genome is exceptionally high when compared with those of available closely related organisms, and the high rate of homology among M. fructicola genes points toward a recent whole-genome duplication event as the cause of this large genome. Based on the assembled genome, sequences were annotated with a gene description and gene ontology (GO term and clustered in functional groups. Analysis of CAZymes family genes revealed 1,145 putative genes, and transcriptomic analysis of CAZyme expression levels in M. fructicola during its interaction with either grapefruit peel tissue or Penicillium digitatum revealed a high level of CAZyme gene expression when the yeast was placed in wounded fruit tissue.

  19. Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon.

    Science.gov (United States)

    Natarajan, Sathishkumar; Kim, Hoy-Taek; Thamilarasan, Senthil Kumar; Veerappan, Karpagam; Park, Jong-In; Nou, Ill-Sup

    2016-01-01

    Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L.) and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, 'SCNU1154', 'Edisto47', 'MR-1', and 'PMR5'. To investigate the genetic variation of these accessions, whole genome re-sequenc