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Sample records for molecular cytogenetic techniques

  1. Novel cytogenetic and molecular techniques in the diagnosis of congenital anomalies in newborns.

    PubMed

    Szczałuba, Krzysztof; Śmigiel, Robert

    2015-01-01

    Knowledge of what causes developmental disorders, including congenital structural defects/anomalies, in the newborn population, facilitates the choice of further investigations, therapy and rehabilitation, allows the use of appropriate prophylaxis against comorbidities, makes it possible to specify prognosis, as well as provide reliable family counselling (both pre- and postnatal). Attempting to formulate a clinical diagnosis of a specific congenital anomaly syndrome, with or without dysmorphic features, based on history and detailed physical examination, remains crucial for the selection of the right genetic testing. Modern methods of molecular cytogenetics and molecular biology are targeted in nature (microdeletion MLPA, single gene sequencing) or are capable of analyzing the genome as a whole (array CGH, newgeneration sequencing). Especially the latter techniques are now causing a rapid increase of diagnostic efficacy across different age groups, including newborns.

  2. Human molecular cytogenetics: From cells to nucleotides.

    PubMed

    Riegel, Mariluce

    2014-03-01

    The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.

  3. Karyotype analysis of seven species of the tribe Lophiohylini (Hylinae, Hylidae, Anura), with conventional and molecular cytogenetic techniques

    PubMed Central

    Gruber, Simone Lilian; Haddad, Célio Fernando Baptista; Kasahara, Sanae

    2012-01-01

    Abstract Few species of the tribe Lophiohylini have been karyotyped so far, and earlier analyses were performed mainly with standard staining. Based on the analysis of seven species with use of routine banding and molecular cytogenetic techniques, the karyotypes were compared and the cytogenetic data were evaluated in the light of the current phylogenies. A karyotype with 2n = 24 and NOR in the chromosome 10 detected by Ag-impregnation and FISH with an rDNA probe was shared by Aparasphenodon bokermanni Miranda-Ribeiro, 1920, Itapotihyla langsdorffii (Duméril and Bibron, 1841), Trachycephalus sp., Trachycephalus mesophaeus (Hensel, 1867), and Trachycephalus typhonius (Linnaeus, 1758). Phyllodytes edelmoi Peixoto, Caramaschi et Freire, 2003 and Phyllodytes luteolus (Wied-Neuwied, 1824) had reduced the diploid number from 2n = 24 to 2n = 22 with one of the small-sized pairs clearly missing, and NOR in the large chromosome 2, but the karyotypes were distinct regarding the morphology of chromosome pairs 4 and 6. Based on the cytogenetic and phylogenetic data, it was presumed that the chromosome evolution occurred from an ancestral type with 2n = 24, in which a small chromosome had been translocated to one or more unidentified chromosomes. Whichever hypothesis is more probable, other rearrangements should have occurred later, to explain the karyotype differences between the two species of Phyllodytes Wagler, 1830. The majority of the species presented a small amount of centromeric C-banded heterochromatin and these regions were GC-rich. The FISH technique using a telomeric probe identified the chromosome ends and possibly (TTAGGG)n-like sequences in the repetitive DNA out of the telomeres in Itapotihyla langsdorffii and Phyllodytes edelmoi. The data herein obtained represent an important contribution for characterizing the karyotype variability within the tribe Lophiohylini scarcely analysed so far. PMID:24260681

  4. Genomic imbalances in esophageal squamous cell carcinoma identified by molecular cytogenetic techniques

    PubMed Central

    2010-01-01

    This review summarizes the chromosomal changes detected by molecular cytogenetic approaches in esophageal squamous cell carcinoma (ESCC), the ninth most common malignancy in the world. Whole genome analyses of ESCC cell lines and tumors indicated that the most frequent genomic gains occurred at 1, 2q, 3q, 5p, 6p, 7, 8q, 9q, 11q, 12p, 14q, 15q, 16, 17, 18p, 19q, 20q, 22q and X, with focal amplifications at 1q32, 2p16-22, 3q25-28, 5p13-15.3, 7p12-22, 7q21-22, 8q23-24.2, 9q34, 10q21, 11p11.2, 11q13, 13q32, 14q13-14, 14q21, 14q31-32, 15q22-26, 17p11.2, 18p11.2-11.3 and 20p11.2. Recurrent losses involved 3p, 4, 5q, 6q, 7q, 8p, 9, 10p, 12p, 13, 14p, 15p, 18, 19p, 20, 22, Xp and Y. Gains at 5p and 7q, and deletions at 4p, 9p, and 11q were significant prognostic factors for patients with ESCC. Gains at 6p and 20p, and losses at 10p and 10q were the most significant imbalances, both in primary carcinoma and in metastases, which suggested that these regions may harbor oncogenes and tumor suppressor genes. Gains at 12p and losses at 3p may be associated with poor relapse-free survival. The clinical applicability of these changes as markers for the diagnosis and prognosis of ESCC, or as molecular targets for personalized therapy should be evaluated. PMID:21637470

  5. Diagnosis of Familial Wolf-Hirschhorn Syndrome due to a Paternal Cryptic Chromosomal Rearrangement by Conventional and Molecular Cytogenetic Techniques

    PubMed Central

    Venegas-Vega, Carlos A.; Zepeda, Luis M.; Garduño-Zarazúa, Luz M.; Berumen, Jaime; Kofman, Susana; Cervantes, Alicia

    2013-01-01

    The use of conventional cytogenetic techniques in combination with fluorescent in situ hybridization (FISH) and single-nucleotide polymorphism (SNP) microarrays is necessary for the identification of cryptic rearrangements in the diagnosis of chromosomal syndromes. We report two siblings, a boy of 9 years and 9 months of age and his 7-years- and 5-month-old sister, with the classic Wolf-Hirschhorn syndrome (WHS) phenotype. Using high-resolution GTG- and NOR-banding karyotypes, as well as FISH analysis, we characterized a pure 4p deletion in both sibs and a balanced rearrangement in their father, consisting in an insertion of 4p material within a nucleolar organizing region of chromosome 15. Copy number variant (CNV) analysis using SNP arrays showed that both siblings have a similar size of 4p deletion (~6.5 Mb). Our results strongly support the need for conventional cytogenetic and FISH analysis, as well as high-density microarray mapping for the optimal characterization of the genetic imbalance in patients with WHS; parents must always be studied for recognizing cryptic balanced chromosomal rearrangements for an adequate genetic counseling. PMID:23484094

  6. Molecular cytogenetics using fluorescence in situ hybridization

    SciTech Connect

    Gray, J.W.; Kuo, Wen-Lin; Lucas, J.; Pinkel, D.; Weier, H-U.; Yu, Loh-Chung.

    1990-12-07

    Fluorescence in situ hybridization (FISH) with chromosome-specific probes enables several new areas of cytogenetic investigation by allowing visual determination of the presence and normality of specific genetic sequences in single metaphase or interphase cells. in this approach, termed molecular cytogenetics, the genetic loci to be analyzed are made microscopically visible in single cells using in situ hybridization with nucleic acid probes specific to these loci. To accomplish this, the DNA in the target cells is made single stranded by thermal denaturation and incubated with single-stranded, chemically modified probe under conditions where the probe will anneal only with DNA sequences to which it has high DNA sequence homology. The bound probe is then made visible by treatment with a fluorescent reagent such as fluorescein that binds to the chemical modification carried by the probe. The DNA to which the probe does not bind is made visible by staining with a dye such as propidium iodide that fluoresces at a wavelength different from that of the reagent used for probe visualization. We show in this report that probes are now available that make this technique useful for biological dosimetry, prenatal diagnosis and cancer biology. 31 refs., 3 figs.

  7. Application of molecular cytogenetic techniques to clarify apparently balanced complex chromosomal rearrangements in two patients with an abnormal phenotype: case report

    PubMed Central

    de Vree, Paula JP; Simon, Marleen EH; van Dooren, Marieke F; Stoevelaar, Gerda HT; Hilkmann, José TW; Rongen, Michel A; Huijbregts, Gido CM; Verkerk, Annemieke JMH; Poddighe, Pino J

    2009-01-01

    Background Complex chromosomal rearrangements (CCR) are rare cytogenetic findings that are difficult to karyotype by conventional cytogenetic analysis partially because of the relative low resolution of this technique. High resolution genotyping is necessary in order to identify cryptic imbalances, for instance near the multiple breakpoints, to explain the abnormal phenotype in these patients. We applied several molecular techniques to elucidate the complexity of the CCRs of two adult patients with abnormal phenotypes. Results Multicolour fluorescence in situ hybridization (M-FISH) showed that in patient 1 the chromosomes 1, 10, 15 and 18 were involved in the rearrangement whereas for patient 2 the chromosomes 5, 9, 11 and 13 were involved. A 250 k Nsp1 SNP-array analysis uncovered a deletion in chromosome region 10p13 for patient 1, harbouring 17 genes, while patient 2 showed no pathogenic gains or losses. Additional FISH analysis with locus specific BAC-probes was performed, leading to the identification of cryptic interstitial structural rearrangements in both patients. Conclusion Application of M-FISH and SNP-array analysis to apparently balanced CCRs is useful to delineate the complex chromosomal rearrangement in detail. However, it does not always identify cryptic imbalances as an explanation for the abnormal phenotype in patients with a CCR. PMID:19594915

  8. Cytogenetic and molecular findings in patients with Turner's syndrome stigmata.

    PubMed Central

    Kuznetzova, T; Baranov, A; Schwed, N; Ivaschenko, T; Malet, P; Giollant, M; Savitsky, G A; Baranov, V

    1995-01-01

    Cytogenetic and DNA analysis in 12 people with stigmata of Turner's syndrome was carried out. Cytogenetic analysis of these patients showed two subjects with 46,X, i(Xq) karyotypes, one with 45,X/46,X, i(Xq), one with 46,X,t(X;Y), and eight with 45,X/46,X,mar. Molecular analysis of DNA samples was performed in nine out of 12 patients with marker chromosomes. PCR analysis with oligoprimers specific for SRY, DYZ1, or DYZ3 loci identified Y chromosome material in five patients in the latter group. The X chromosome origin of the marker chromosome was proved by FISH technique with biotin labelled pericentromeric X chromosome specific probe in four other patients. These results show that patients with a number of Turner's syndrome stigmata usually do not have a typical XO karyotype but have some structural chromosomal aberrations involving the X or Y chromosomes. Combined application of cytogenetic, molecular cytogenetic (FISH), and PCR techniques significantly improves the precision of marker chromosome identification and thus might be of practical importance for the proper management and treatment of affected patients. Peculiarities of pathological manifestations of different karyotypes bearing structural abnormalities of the X or Y chromosomes in patients with Turner's syndrome stigmata, as well as feasible genetic mechanisms of sex determination and differentiation abnormalities in these subjects, are briefly discussed. Images PMID:8825925

  9. Updates on the cytogenetics and molecular cytogenetics of benign and intermediate soft tissue tumors

    PubMed Central

    NISHIO, JUN

    2013-01-01

    Soft tissue tumors are classified according to their histological resemblance to normal adult tissues and can be grouped into the following categories based on metastatic potential: benign, intermediate (locally aggressive), intermediate (rarely metastasizing) and malignant. Over the past two decades, considerable progress has been made in our understanding of the genetic background of soft tissue tumors. Traditional laboratory techniques, such as cytogenetic analysis and fluorescence in situ hybridization (FISH), can be used for diagnostic purposes in soft tissue pathology practice. Moreover, cytogenetic and molecular studies are often necessary for prognostics and follow-up of soft tissue sarcoma patients. This review provides updated information on the applicability of laboratory genetic testing in the diagnosis of benign and intermediate soft tissue tumors. These tumors include nodular fasciitis, chondroid lipoma, collagenous fibroma (desmoplastic fibroblastoma), giant cell tumor of tendon sheath (GCTTS)/pigmented villonodular synovitis (PVNS), angiofibroma of soft tissue, myxoinflammatory fibroblastic sarcoma (MIFS) and ossifying fibromyxoid tumor (OFMT). PMID:23255885

  10. Precision in chromosome identification with leads in molecular cytogenetics: An illustrated review

    PubMed Central

    Dutta, Usha R.

    2014-01-01

    Chromosomal aberrations are a major cause of human genetic diseases. Conventional cytogenetic banding techniques are the method of identification for both numerical and structural chromosomal abnormalities but with limited resolution. However, precise identification and characterization of the chromosomal abnormalities can only be achieved by advanced molecular cytogenetic techniques. These techniques are based mainly on fluorescence in situ hybridization, which have become an invaluable tool in the field of diagnostics. The advent of these molecular cytogenetic techniques has helped in the identification of chromosomal abnormalities to its minutest level. Apparently, the leads in molecular cytogenetic techniques have paved way for advanced molecular diagnosis, which now plays a significant role in both diagnostics and clinical research. These advances have led to the increased knowledge of the possible molecular mechanism involved in the chromosomal rearrangements and the genotype-phenotype correlation thus helping the patients towards better diagnosis and genetic counseling. This article highlights the advances in molecular cytogenetic techniques emphasizing the precision in identification of chromosomal rearrangements, and also illustrates few chromosomal abnormalities pediatric cases identified using these molecular cytogenetic techniques. PMID:27625861

  11. Precision in chromosome identification with leads in molecular cytogenetics: An illustrated review.

    PubMed

    Dutta, Usha R

    2014-03-01

    Chromosomal aberrations are a major cause of human genetic diseases. Conventional cytogenetic banding techniques are the method of identification for both numerical and structural chromosomal abnormalities but with limited resolution. However, precise identification and characterization of the chromosomal abnormalities can only be achieved by advanced molecular cytogenetic techniques. These techniques are based mainly on fluorescence in situ hybridization, which have become an invaluable tool in the field of diagnostics. The advent of these molecular cytogenetic techniques has helped in the identification of chromosomal abnormalities to its minutest level. Apparently, the leads in molecular cytogenetic techniques have paved way for advanced molecular diagnosis, which now plays a significant role in both diagnostics and clinical research. These advances have led to the increased knowledge of the possible molecular mechanism involved in the chromosomal rearrangements and the genotype-phenotype correlation thus helping the patients towards better diagnosis and genetic counseling. This article highlights the advances in molecular cytogenetic techniques emphasizing the precision in identification of chromosomal rearrangements, and also illustrates few chromosomal abnormalities pediatric cases identified using these molecular cytogenetic techniques. PMID:27625861

  12. Nanotechnology and molecular cytogenetics: the future has not yet arrived

    PubMed Central

    Ioannou, Dimitris; Griffin, Darren K.

    2010-01-01

    Quantum dots (QDs) are a novel class of inorganic fluorochromes composed of nanometer-scale crystals made of a semiconductor material. They are resistant to photo-bleaching, have narrow excitation and emission wavelengths that can be controlled by particle size and thus have the potential for multiplexing experiments. Given the remarkable optical properties that quantum dots possess, they have been proposed as an ideal material for use in molecular cytogenetics, specifically the technique of fluorescent in situ hybridisation (FISH). In this review, we provide an account of the current QD-FISH literature, and speculate as to why QDs are not yet optimised for FISH in their current form. PMID:22110858

  13. Nanotechnology and molecular cytogenetics: the future has not yet arrived.

    PubMed

    Ioannou, Dimitris; Griffin, Darren K

    2010-01-01

    Quantum dots (QDs) are a novel class of inorganic fluorochromes composed of nanometer-scale crystals made of a semiconductor material. They are resistant to photo-bleaching, have narrow excitation and emission wavelengths that can be controlled by particle size and thus have the potential for multiplexing experiments. Given the remarkable optical properties that quantum dots possess, they have been proposed as an ideal material for use in molecular cytogenetics, specifically the technique of fluorescent in situ hybridisation (FISH). In this review, we provide an account of the current QD-FISH literature, and speculate as to why QDs are not yet optimised for FISH in their current form.

  14. Evolutionary molecular cytogenetics of catarrhine primates: past, present and future.

    PubMed

    Stanyon, R; Rocchi, M; Bigoni, F; Archidiacono, N

    2012-01-01

    The catarrhine primates were the first group of species studied with comparative molecular cytogenetics. Many of the fundamental techniques and principles of analysis were initially applied to comparisons in these primates, including interspecific chromosome painting, reciprocal chromosome painting and the extensive use of cloned DNA probes for evolutionary analysis. The definition and importance of chromosome syntenies and associations for a correct cladistics analysis of phylogenomic relationships were first applied to catarrhines. These early chromosome painting studies vividly illustrated a striking conservation of the genome between humans and macaques. Contemporarily, it also revealed profound differences between humans and gibbons, a group of species more closely related to humans, making it clear that chromosome evolution did not follow a molecular clock. Chromosome painting has now been applied to more that 60 primate species and the translocation history has been mapped onto the major taxonomic divisions in the tree of primate evolution. In situ hybridization of cloned DNA probes, primarily BAC-FISH, also made it possible to more precisely map breakpoints with spanning and flanking BACs. These studies established marker order and disclosed intrachromosomal rearrangements. When applied comparatively to a range of primate species, they led to the discovery of evolutionary new centromeres as an important new category of chromosome evolution. BAC-FISH studies are intimately connected to genome sequencing, and probes can usually be assigned to a precise location in the genome assembly. This connection ties molecular cytogenetics securely to genome sequencing, assuring that molecular cytogenetics will continue to have a productive future in the multidisciplinary science of phylogenomics. PMID:22710640

  15. Molecular Cytogenetics and Cytogenomics of Brain Diseases

    PubMed Central

    Iourov, I.Y; Vorsanova, S.G; Yurov, Y.B

    2008-01-01

    Molecular cytogenetics is a promising field of biomedical research that has recently revolutionized our thinking on genome structure and behavior. This is in part due to discoveries of human genomic variations and their contribution to biodiversity and disease. Since these studies were primarily targeted at variation of the genome structure, it appears apposite to cover them by molecular cytogenomics. Human brain diseases, which encompass pathogenic conditions from severe neurodegenerative diseases and major psychiatric disorders to brain tumors, are a heavy burden for the patients and their relatives. It has been suggested that most of them, if not all, are of genetic nature and several recent studies have supported the hypothesis assuming them to be associated with genomic instabilities (i.e. single-gene mutations, gross and subtle chromosome imbalances, aneuploidy). The present review is focused on the intriguing relationship between genomic instability and human brain diseases. Looking through the data, we were able to conclude that both interindividual and intercellular genomic variations could be pathogenic representing, therefore, a possible mechanism for human brain malfunctioning. Nevertheless, there are still numerous gaps in our knowledge concerning the link between genomic variations and brain diseases, which, hopefully, will be filled by forthcoming studies. In this light, the present review considers perspectives of this dynamically developing field of neurogenetics and genomics. PMID:19506734

  16. Methods in molecular biology: plant cytogenetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cytogenetic studies have contributed greatly to our understanding of genetics, biology, reproduction, and evolution. From early studies in basic chromosome behavior the field has expanded enabling whole genome analysis to the manipulation of chromosomes and their organization. This book covers a ran...

  17. Cytogenetic and molecular abnormalities in chronic myelomonocytic leukemia

    PubMed Central

    Patnaik, M M; Tefferi, A

    2016-01-01

    Chronic myelomonocytic leukemia (CMML) is a clonal stem cell disorder associated with peripheral blood monocytosis and an inherent tendency to transform to acute myeloid leukemia. CMML has overlapping features of myelodysplastic syndromes and myeloproliferative neoplasms. Clonal cytogenetic changes are seen in ~30%, whereas gene mutations are seen in >90% of patients. Common cytogenetic abnormalities include; trisomy 8, -Y, -7/del(7q), trisomy 21 and del(20q), with the Mayo–French risk stratification effectively risk stratifying patients based on cytogenetic abnormalities. Gene mutations frequently involve epigenetic regulators (TET2 ~60%), modulators of chromatin (ASXL1 ~40%), spliceosome components (SRSF2 ~50%), transcription factors (RUNX1 ~15%) and signal pathways (RAS ~30%, CBL ~15%). Of these, thus far, only nonsense and frameshift ASXL1 mutations have been shown to negatively impact overall survival. This has resulted in the development of contemporary, molecularly integrated (inclusive of ASXL1 mutations) CMML prognostic models, including Molecular Mayo Model and the Groupe Français des Myélodysplasies model. Better understanding of the prevalent genetic and epigenetic dysregulation has resulted in emerging targeted treatment options for some patients. The development of an integrated (cytogenetic and molecular) prognostic model along with CMML-specific response assessment criteria are much needed future goals. PMID:26849014

  18. Molecular cytogenetic characterization of a human thyroid cancercell line

    SciTech Connect

    Weier, Heinz-Ulrich G.; Tuton, Tiffany B.; Ito, Yuko; Chu, LisaW.; Lu, Chung-Mei; Baumgartner, Adolf; Zitzelsberger, Horst F.; Weier,Jingly F.

    2006-01-04

    The incidence of papillary thyroid carcinoma (PTC) increases significantly after exposure of the head and neck region to ionizing radiation, yet we know neither the steps involved in malignant transformation of thyroid epithelium nor the specific carcinogenic mode of action of radiation. Such increased tumor frequency became most evident in children after the 1986 nuclear accident in Chernobyl, Ukraine. In the twelve years following the accident, the average incidence of childhood PTCs (chPTC) increased over one hundred-fold compared to the rate of about 1 tumor incidence per 10{sup 6} children per year prior to 1986. To study the etiology of radiation-induced thyroid cancer, we formed an international consortium to investigate chromosomal changes and altered gene expression in cases of post-Chernobyl chPTC. Our approach is based on karyotyping of primary cultures established from chPTC specimens, establishment of cell lines and studies of genotype-phenotype relationships through high resolution chromosome analysis, DNA/cDNA micro-array studies, and mouse xenografts that test for tumorigenicity. Here, we report the application of fluorescence in situ hybridization (FISH)-based techniques for the molecular cytogenetic characterization of a highly tumorigenic chPTC cell line, S48TK, and its subclones. Using chromosome 9 rearrangements as an example, we describe a new approach termed ''BAC-FISH'' to rapidly delineate chromosomal breakpoints, an important step towards a better understanding of the formation of translocations and their functional consequences.

  19. Cytogenetic characterization by in situ hybridization techniques and molecular analysis of 5S rRNA genes of the European hazelnut (Corylus avellana).

    PubMed

    Falistocco, E; Marconi, G

    2013-03-01

    The European hazelnut (Corylus avellana L.) is widespread in Europe, where it has been cultivated for centuries. Despite progress in genetics, most of the cytogenetic aspects of this species have been overlooked. The aim of this study was to fill in this gap and obtain basic information on the chromosome structure of this species. Karyomorphological analysis confirmed the chromosome number 2n = 22 and showed that, despite their apparent uniformity, the chromosomes could be separated into three groups of different size: large (L), medium (M), and small (S). As a first step towards the physical mapping of the hazelnut chromosomes, we applied FISH to localize the position of rRNA genes (rDNA). The sites of 45S and 5S rDNA enabled us to identify two chromosome pairs belonging, respectively, to the L and S groups. The self-GISH procedure revealed that repetitive DNA is concentrated in the pericentromeric regions of the chromosomes, as with other species with rather small genomes. The analysis of 5S rDNA repeats offered additional information on the hazelnut genome by obtaining the whole sequence of the transcribed region so far unpublished. The overall results constitute a substantial advance in hazelnut cytogenetics. Further investigation of other species of Corylus could be an effective approach to understanding the phylogenesis of the genus and resolving taxonomic problems.

  20. Molecular cytogenetic diagnosis of Williams syndrome

    SciTech Connect

    Hirota, Hamao; Matsuoka, Rumiko; Kimura, Misa

    1996-08-23

    Williams syndrome (WS) is characterized by distinct facial changes, growth deficiency, mental retardation, and congenital heart defect (particularly supravalvular aortic stenosis), associated at times with infantile hypercalcemia. Molecular genetic studies have indicated that hemizygosity at the elastin locus (7q11.23) causes WS. The purpose of this study was to confirm that this regional deletion, involving the elastin locus, is the cause of WS in Japan, and to clarify the correlation between the phenotype and the elastin locus. Thirty-two patients with WS and thirty of their relatives were examined by fluorescent in situ hybridization (FISH), using the WS chromosome region (WSCR) probe. All patients had cardiovascular disease (100%), 30 had typical WS facial changes (94%), 31 had mental retardation or developmental delay (97%), 16 were small-for-date at birth (50%), 14 had short stature (44%), and 13 had dental anomalies (41%). No relatives showed any manifestation of WS. Hemizygosity for a region of 7q11.23, involving the elastin locus, was found in all WS patients, but was not found in the 30 relatives. 22 refs., 4 figs., 1 tab.

  1. [Dicentric Y chromosomes. First part: cytogenetic and molecular aspects].

    PubMed

    Bouayed Abdelmoula, N; Amouri, A

    2005-01-01

    Dicentric Y chromosomes have been reviewed twice in 1994 by Hsu et al. and in 1995 by Tuck-Muller et al. who showed that dic(Y) are the most common Y structural abnormalities and that their influence on gonadal and somatic development is extremely variable. The prediction of their phenotypic consequences is often difficult because of the variety of genomic sequences concerned by duplications and deletions, because of the variable degrees of mosaicism (cell line 45,X in particular) and at the end, because of identification and analysis technical difficulties of the structure of the rearranged Y chromosome. The clinical specter of this cytogenetic abnormality is rather wide going from almost-normal or infertile males, to females with or without stigmas of Turner syndrome. Middle phenotypes consist of various degrees of genital ambiguities. However, clinical expression seems to be related to the genomic capital of the Y chromosome, mainly the Y genes involved in the control of the process of the determination of gonads (Yp) and spermatogenesis (Yq) as well as control of the growth and the skeletal development (Yp). Here, we report a third comprehensive review of the literature concerning dicentric Y chromosomes reported since 1994. In the light of previous reviews as well as the recent data of the genetic cartography of the Y chromosome, we try, in this first part, to determine characteristics of reported dicentric Y chromosomes as well as their chromosomal mechanics, their mitotic stability and finally their cytogenetic and molecular investigations.

  2. Molecular Cytogenetic Analysis of Deschampsia antarctica Desv. (Poaceae), Maritime Antarctic.

    PubMed

    Amosova, Alexandra V; Bolsheva, Nadezhda L; Samatadze, Tatiana E; Twardovska, Maryana O; Zoshchuk, Svyatoslav A; Andreev, Igor O; Badaeva, Ekaterina D; Kunakh, Viktor A; Muravenko, Olga V

    2015-01-01

    Deschampsia antarctica Desv. (Poaceae) (2n = 26) is one of the two vascular plants adapted to the harshest environment of the Antarctic. Although the species is a valuable model for study of environmental stress tolerance in plants, its karyotype is still poorly investigated. We firstly conducted a comprehensive molecular cytogenetic analysis of D. antarctica collected on four islands of the Maritime Antarctic. D. antarctica karyotypes were studied by Giemsa C- and DAPI/C-banding, Ag-NOR staining, multicolour fluorescence in situ hybridization with repeated DNA probes (pTa71, pTa794, telomere repeats, pSc119.2, pAs1) and the GAA simple sequence repeat probe. We also performed sequential rapid in situ hybridization with genomic DNA of D. caespitosa. Two chromosome pairs bearing transcriptionally active 45S rDNA loci and five pairs with 5S rDNA sites were detected. A weak intercalary site of telomere repeats was revealed on the largest chromosome in addition to telomere hybridization signals at terminal positions. This fact confirms indirectly the hypothesis that chromosome fusion might have been the cause of the unusual for cereals chromosome number in this species. Based on patterns of distribution of the examined molecular cytogenetic markers, all chromosomes in karyotypes were identified, and chromosome idiograms of D. antarctica were constructed. B chromosomes were found in most karyotypes of plants from Darboux Island. A mixoploid plant with mainly triploid cells bearing a Robertsonian rearrangement was detected among typical diploid specimens from Great Jalour Island. The karyotype variability found in D. antarctica is probably an expression of genome instability induced by environmental stress factors. The differences in C-banding patterns and in chromosome distribution of rDNA loci as well as homologous highly repeated DNA sequences detected between genomes of D. antarctica and its related species D. caespitosa indicate that genome reorganization involving

  3. Molecular Cytogenetic Analysis of Deschampsia antarctica Desv. (Poaceae), Maritime Antarctic.

    PubMed

    Amosova, Alexandra V; Bolsheva, Nadezhda L; Samatadze, Tatiana E; Twardovska, Maryana O; Zoshchuk, Svyatoslav A; Andreev, Igor O; Badaeva, Ekaterina D; Kunakh, Viktor A; Muravenko, Olga V

    2015-01-01

    Deschampsia antarctica Desv. (Poaceae) (2n = 26) is one of the two vascular plants adapted to the harshest environment of the Antarctic. Although the species is a valuable model for study of environmental stress tolerance in plants, its karyotype is still poorly investigated. We firstly conducted a comprehensive molecular cytogenetic analysis of D. antarctica collected on four islands of the Maritime Antarctic. D. antarctica karyotypes were studied by Giemsa C- and DAPI/C-banding, Ag-NOR staining, multicolour fluorescence in situ hybridization with repeated DNA probes (pTa71, pTa794, telomere repeats, pSc119.2, pAs1) and the GAA simple sequence repeat probe. We also performed sequential rapid in situ hybridization with genomic DNA of D. caespitosa. Two chromosome pairs bearing transcriptionally active 45S rDNA loci and five pairs with 5S rDNA sites were detected. A weak intercalary site of telomere repeats was revealed on the largest chromosome in addition to telomere hybridization signals at terminal positions. This fact confirms indirectly the hypothesis that chromosome fusion might have been the cause of the unusual for cereals chromosome number in this species. Based on patterns of distribution of the examined molecular cytogenetic markers, all chromosomes in karyotypes were identified, and chromosome idiograms of D. antarctica were constructed. B chromosomes were found in most karyotypes of plants from Darboux Island. A mixoploid plant with mainly triploid cells bearing a Robertsonian rearrangement was detected among typical diploid specimens from Great Jalour Island. The karyotype variability found in D. antarctica is probably an expression of genome instability induced by environmental stress factors. The differences in C-banding patterns and in chromosome distribution of rDNA loci as well as homologous highly repeated DNA sequences detected between genomes of D. antarctica and its related species D. caespitosa indicate that genome reorganization involving

  4. Molecular Cytogenetic Analysis of Deschampsia antarctica Desv. (Poaceae), Maritime Antarctic

    PubMed Central

    Amosova, Alexandra V.; Bolsheva, Nadezhda L.; Samatadze, Tatiana E.; Twardovska, Maryana O.; Zoshchuk, Svyatoslav A.; Andreev, Igor O.; Badaeva, Ekaterina D.; Kunakh, Viktor A.; Muravenko, Olga V.

    2015-01-01

    Deschampsia antarctica Desv. (Poaceae) (2n = 26) is one of the two vascular plants adapted to the harshest environment of the Antarctic. Although the species is a valuable model for study of environmental stress tolerance in plants, its karyotype is still poorly investigated. We firstly conducted a comprehensive molecular cytogenetic analysis of D. antarctica collected on four islands of the Maritime Antarctic. D. antarctica karyotypes were studied by Giemsa C- and DAPI/C-banding, Ag-NOR staining, multicolour fluorescence in situ hybridization with repeated DNA probes (pTa71, pTa794, telomere repeats, pSc119.2, pAs1) and the GAA simple sequence repeat probe. We also performed sequential rapid in situ hybridization with genomic DNA of D. caespitosa. Two chromosome pairs bearing transcriptionally active 45S rDNA loci and five pairs with 5S rDNA sites were detected. A weak intercalary site of telomere repeats was revealed on the largest chromosome in addition to telomere hybridization signals at terminal positions. This fact confirms indirectly the hypothesis that chromosome fusion might have been the cause of the unusual for cereals chromosome number in this species. Based on patterns of distribution of the examined molecular cytogenetic markers, all chromosomes in karyotypes were identified, and chromosome idiograms of D. antarctica were constructed. B chromosomes were found in most karyotypes of plants from Darboux Island. A mixoploid plant with mainly triploid cells bearing a Robertsonian rearrangement was detected among typical diploid specimens from Great Jalour Island. The karyotype variability found in D. antarctica is probably an expression of genome instability induced by environmental stress factors. The differences in C-banding patterns and in chromosome distribution of rDNA loci as well as homologous highly repeated DNA sequences detected between genomes of D. antarctica and its related species D. caespitosa indicate that genome reorganization involving

  5. Molecular prognostic markers for adult acute myeloid leukemia with normal cytogenetics

    PubMed Central

    Gregory, Tara K; Wald, David; Chen, Yichu; Vermaat, Johanna M; Xiong, Yin; Tse, William

    2009-01-01

    Acute myeloid leukemia (AML) is a heterogenous disorder that results from a block in the differentiation of hematopoietic progenitor cells along with uncontrolled proliferation. In approximately 60% of cases, specific recurrent chromosomal aberrations can be identified by modern cytogenetic techniques. This cytogenetic information is the single most important tool to classify patients at their initial diagnosis into three prognostic categories: favorable, intermediate, and poor risk. Currently, favorable risk AML patients are usually treated with contemporary chemotherapy while poor risk AML patients receive allogeneic stem cell transplantation if suitable stem cell donors exist. The largest subgroup of AML patients (~40%) have no identifiable cytogenetic abnormalities and are classified as intermediate risk. The optimal therapeutic strategies for these patients are still largely unclear. Recently, it is becoming increasingly evident that it is possible to identify a subgroup of poorer risk patients among those with normal cytogenic AML (NC-AML). Molecular risk stratification for NC-AML patients may be possible due to mutations of NPM1, FLT3, MLL, and CEBPα as well as alterations in expression levels of BAALC, MN1, ERG, and AF1q. Further prospective studies are needed to confirm if poorer risk NC-AML patients have improved clinical outcomes after more aggressive therapy. PMID:19490647

  6. Molecular cytogenetic analysis of Xq critical regions in premature ovarian failure

    PubMed Central

    2013-01-01

    Background One of the frequent reasons for unsuccessful conception is premature ovarian failure/primary ovarian insufficiency (POF/POI) that is defined as the loss of functional follicles below the age of 40 years. Among the genetic causes the most common one involves the X chromosome, as in Turner syndrome, partial X deletion and X-autosome translocations. Here we report a case of a 27-year-old female patient referred to genetic counselling because of premature ovarian failure. The aim of this case study to perform molecular genetic and cytogenetic analyses in order to identify the exact genetic background of the pathogenic phenotype. Results For premature ovarian failure disease diagnostics we performed the Fragile mental retardation 1 gene analysis using Southern blot technique and Repeat Primed PCR in order to identify the relationship between the Fragile mental retardation 1 gene premutation status and the premature ovarion failure disease. At this early onset, the premature ovarian failure affected patient we detected one normal allele of Fragile mental retardation 1 gene and we couldn’t verify the methylated allele, therefore we performed the cytogenetic analyses using G-banding and fluorescent in situ hybridization methods and a high resolution molecular cytogenetic method, the array comparative genomic hybridization technique. For this patient applying the G-banding, we identified a large deletion on the X chromosome at the critical region (ChrX q21.31-q28) which is associated with the premature ovarian failure phenotype. In order to detect the exact breakpoints, we used a special cytogenetic array ISCA plus CGH array and we verified a 67.355 Mb size loss at the critical region which include total 795 genes. Conclusions We conclude for this case study that the karyotyping is definitely helpful in the evaluation of premature ovarian failure patients, to identify the non submicroscopic chromosomal rearrangement, and using the array CGH technique we can

  7. Cytogenetic and molecular studies of down syndrome individual with leukemia

    SciTech Connect

    Shen, J.J.; Hassold, T.J.; Williams, B.J.; Zupursky, A.; Doyle, J.; Sherman, S.L.; Jacobs, P.A.; Shugar, A.L.; Soukup, S.W.

    1995-04-01

    There is an increased risk of leukemia in Down syndrome (DS) patients, with estimates ranging from 14 to 30 times the incidence rate observed for chromosomally normal children. Furthermore, one type of leukemia, called {open_quotes}transient leukemia{close_quotes} (TL), occurs almost exclusively in DS infants. The basis of the association between DS and leukemia is unknown, but we and others have hypothesized that it may be influenced by the mechanism of origin of the extra chromosome. Therefore, we initiated a cytogenetic and molecular study of nondisjunction in leukemic DS individuals. To date, we have obtained blood and/or tissue samples from 55 individuals consisting of 17 cases with TL, 7 cases of acute nonlymphocytic leukemia subtype M7 (ANLL-M7, or acute megakaryoblastic leukemia, postulated to be related to TL), and 31 cases of other forms of leukemia. Analysis of these cases suggests differences between DS children with TL and those with other types of leukemia or DS individuals with no history of leukemia. Specifically, the TL and ANLL-M7 cases have a highly significant increase in the frequency of {open_quotes}atypical{close_quotes} constitutional karyotypes (i.e., mosaic trisomies, rings, and/or isochromosomes) and are almost always male. Additionally, genetic mapping studies suggest an increase in the frequency of disomic homozygosity, especially in proximal 21q, in DS individuals with TL and ANLL-M7. 19 refs., 3 figs., 4 tabs.

  8. Molecular cytogenetic characterization of the Amazon River dolphin Inia geoffrensis.

    PubMed

    Bonifácio, Heidi L; da Silva, Vera M F; Martin, Anthony R; Feldberg, Eliana

    2012-09-01

    Classical and molecular cytogenetic (18S rDNA, telomeric sequence, and LINE-1 retrotransposon probes) studies were carried out to contribute to an understanding of the organization of repeated DNA elements in the Amazon River dolphin (boto, Inia geoffrensis). Twenty-seven specimens were examined, each presenting 2n = 44 chromosomes, the karyotype formula 12m + 14sm + 6st + 10t + XX/XY, and fundamental number (FN) = 74. C-positive heterochromatin was observed in terminal and interstitial positions, with the occurrence of polymorphism. Interstitial telomeric sequences were not observed. The nucleolar organizer region (NOR) was located at a single site on a smallest autosomal pair. LINE-1 was preferentially distributed in the euchromatin regions, with the greatest accumulation on the X chromosome. Although the karyotype structure in cetaceans is considered to be conserved, the boto karyotype demonstrated significant variations in its formula, heterochromatin distribution, and the location of the NOR compared to other cetacean species. These results contribute to knowledge of the chromosome organization in boto and to a better understanding of karyoevolution in cetaceans.

  9. Prenatal identification of i(Yp) by molecular cytogenetic analysis

    SciTech Connect

    Wang, B.T.; Peng, W.; Williams, J. III

    1994-09-01

    An isochromosome derived from the short arm of the Y chromosome, i(Yp), is a rare marker chromosome. Its de novo presence prenatally represents a diagnostic dilemna since its impact on fetal development is difficult to predict. We present a case of 46,X,+i(Yp) de novo detected in an amniotic fluid specimen received for karyotype analysis. Fluorescence in situ hybridization (FISH) studies using a panel of Y-specific biotinylated DNA probes including a Y-centromere probe, a Y whole chromosome painting probe, and a lambda HAM2 probe containing 19 kb of AMG-Y sequence, located to Yp11.2, have identified the marker chromosome as i(Yp). The breakpoint on this marker chromosome is tentatively assigned to Yq11.1 which is close to the centromere. The present report illustrates the importance of FISH techniques as a complement to cytogenetic methods for accurate identification of chromosome rearrangements in prenatal diagnosis and genetic counseling.

  10. Nondisjunction of chromosome 21: Comparisons of cytogenetic and molecular studies of the meiotic stage and parent of origin

    SciTech Connect

    Lorber, B.J.; Grantham, M.; Peters, J.; Hassold, T.J. ); Willard, H.F. )

    1992-12-01

    In the present report, the authors summarize studies aimed at examining the reliability of chromosome heteromorphisms in analyses of chromosome 21, nondisjunction. They used two cytogenetic approaches - fluorescent in sity hybridization (FISH) to repetitive sequences on 21p and traditional Q-banding - to distinguish chromosome 21 homologues and then compared the results of these studies with those obtained by DNA markers. Using a conservative scoring system for Q-banding and FISH heteromorphisms, they were able to specify the parental origin of trisomy in 10% of cases, in contrast, DNA marker studies were informative for parental origin in almost all cases. The results of the molecular and cytogenetic studies of parental origin concurred in all cases in which assignments were made independently using both techniques. However, in 4 of 13 cases in which the molecular studies contributed to the interpretation of the cytogenetic findings, the two results did not agree with respect to the meiotic stage of nondisjunction. A relatively high frequency of crossing-over on either the short arm or proximal long arm of chromosome 21 could explain these results and may be a mechanism leading to nondisjunction. 20 refs., 2 figs., 4 tabs.

  11. [Comparative molecular cytogenetic characterization of partial wheat-wheatgrass hybrids].

    PubMed

    Krupin, P Yu; Divashuk, M G; Belov, V I; Glukhova, L I; Aleksandrov, O S; Karlov, G I

    2011-04-01

    The chromosomal composition of the Zernokormovaya 169, Istra 1, Ostankinskaya, and Otrastayushchaya 38 cultivars of octoploid partial wheat-wheatgrass hybrids was studied using genomic in situ hybridization (GISH). Differentiation of wheatgrass chromosomes by the distribution of the GISH signal along the chromosome was revealed. The wheatgrass chromosomes of the hybrid cultivars studied in the work differed in the type of differentiation, centromeric index, and absolute size. The cytogenetic distinctions of these chromosomes revealed by us can be used in making crosses and in studying the transmission through gametes of additional wheatgrass chromosomes.

  12. Molecular and cytogenetic assessment of Dipterygium glaucum genotoxicity.

    PubMed

    Altwaty, Nada H; El-Sayed, Osama E; Aly, Nariman A H; Baeshen, Mohamed N; Baeshen, Nabih A

    2016-01-01

    The aim of the present study is to assess the genotoxicity of Dipterygium glaucum grows widely in Saudi Arabia desert to produce safety herbal products. This work is considered the first and pioneer report so far due to the lack and poor evaluated reports of the plant species for their mutagensity, genotoxicity and cytogenetics effects. Cytogenetic effects of D. glaucum on mitotic in roots of Vicia faba showed reduction in mitotic activity using three extracts; water, ethanol and ethyl acetate. Chromosomal abnormalities were recorded that included stickiness of chromosomes, chromatin bridge, fragments, lagging chromosome and micronuclei. Protein bands and RAPD analyses of V. faba treated with three D. glaucum extracts revealed some newly induced proteins and DNA fragments and other disappeared. Chemical constitution of the plant species should be identified with their biological activities against human and animal cells like HeLa cancer cell line. We are recommending using additional genotoxicity tests and other toxicity tests on animal culture with different concentrations and also utilizing several drought and heat tolerant genes of the plant species in gene cloning to develop and improve other economical crop plants instead of using the species as oral herbal remedy. PMID:27142548

  13. Molecular and cytogenetic assessment of Dipterygium glaucum genotoxicity.

    PubMed

    Altwaty, Nada H; El-Sayed, Osama E; Aly, Nariman A H; Baeshen, Mohamed N; Baeshen, Nabih A

    2016-01-01

    The aim of the present study is to assess the genotoxicity of Dipterygium glaucum grows widely in Saudi Arabia desert to produce safety herbal products. This work is considered the first and pioneer report so far due to the lack and poor evaluated reports of the plant species for their mutagensity, genotoxicity and cytogenetics effects. Cytogenetic effects of D. glaucum on mitotic in roots of Vicia faba showed reduction in mitotic activity using three extracts; water, ethanol and ethyl acetate. Chromosomal abnormalities were recorded that included stickiness of chromosomes, chromatin bridge, fragments, lagging chromosome and micronuclei. Protein bands and RAPD analyses of V. faba treated with three D. glaucum extracts revealed some newly induced proteins and DNA fragments and other disappeared. Chemical constitution of the plant species should be identified with their biological activities against human and animal cells like HeLa cancer cell line. We are recommending using additional genotoxicity tests and other toxicity tests on animal culture with different concentrations and also utilizing several drought and heat tolerant genes of the plant species in gene cloning to develop and improve other economical crop plants instead of using the species as oral herbal remedy.

  14. Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics

    PubMed Central

    Artoni, Roberto Ferreira; Castro, Jonathan Pena; Jacobina, Uedson Pereira; Lima-Filho, Paulo Augusto; Félix da Costa, Gideão Wagner Werneck; Molina, Wagner Franco

    2015-01-01

    Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features. PMID:26345638

  15. Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics.

    PubMed

    Artoni, Roberto Ferreira; Castro, Jonathan Pena; Jacobina, Uedson Pereira; Lima-Filho, Paulo Augusto; da Costa, Gideão Wagner Werneck Félix; Molina, Wagner Franco

    2015-01-01

    Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

  16. Combined Use of Cytogenetic and Molecular Methods in Prenatal Diagnostics of Chromosomal Abnormalities

    PubMed Central

    Stomornjak-Vukadin, Meliha; Kurtovic-Basic, Ilvana; Mehinovic, Lejla; Konjhodzic, Rijad

    2015-01-01

    Aim: The aim of prenatal diagnostics is to provide information of the genetic abnormalities of the fetus early enough for the termination of pregnancy to be possible. Chromosomal abnormalities can be detected in an unborn child through the use of cytogenetic, molecular- cytogenetic and molecular methods. In between them, central spot is still occupied by cytogenetic methods. In cases where use of such methods is not informative enough, one or more molecular cytogenetic methods can be used for further clarification. Combined use of the mentioned methods improves the quality of the final findings in the diagnostics of chromosomal abnormalities, with classical cytogenetic methods still occupying the central spot. Material and methods: Conducted research represent retrospective-prospective study of a four year period, from 2008 through 2011. In the period stated, 1319 karyotyping from amniotic fluid were conducted, along with 146 FISH analysis. Results: Karyotyping had detected 20 numerical and 18 structural aberrations in that period. Most common observed numerical aberration were Down syndrome (75%), Klinefelter syndrome (10%), Edwards syndrome, double Y syndrome and triploidy (5% each). Within observed structural aberrations more common were balanced chromosomal aberrations then non balanced ones. Most common balanced structural aberrations were as follows: reciprocal translocations (60%), Robertson translocations (13.3%), chromosomal inversions, duplications and balanced de novo chromosomal rearrangements (6.6% each). Conclusion: With non- balanced aberrations observed in the samples of amniotic fluid, non- balanced translocations, deletions and derived chromosomes were equally represented. Number of detected aneuploidies with FISH, prior to obtaining results with karyotyping, were 6. PMID:26005269

  17. Molecular cytogenetic mapping of Humulus lupulus sex chromosomes.

    PubMed

    Divashuk, M G; Alexandrov, O S; Kroupin, P Yu; Karlov, G I

    2011-01-01

    Dioecy is relatively rare in plants and sex determination systems vary among such species. A good example of a plant with heteromorphic sex chromosomes is hop (Humulus lupulus). The genotypes carrying XX or XY chromosomes correspond to female and male plants, respectively. Until now no clear cytogenetic markers for the sex chromosomes of hop have been established. Here, for the first time the sex chromosomes of hop are clearly identified and characterized. The high copy sequence of hop (HSR1) has been cloned and localized on chromosomes by fluorescence in situ hybridization. The HSR1 repeat has shown subtelomeric location on autosomes with the same intensity of the signal. The signal has been present in the subtelomeric region of the long arm and in the near-centromeric region but absent in the telomeric region of the short arm of the X chromosome. At the same time the signal has been found in the telomeric region only of the long arm of the Y chromosome. This finding indicates that the sex chromosomes of hop have evolved from a pair of autosomes via ancient translocation or inversion. The observation of the meiotic configuration of the sex bivalents shows the location of a pseudoautosomal region on the long arms of X and Y chromosomes. PMID:21709414

  18. Molecular cytogenetics of the california condor: evolutionary and conservation implications.

    PubMed

    Modi, W S; Romanov, M; Green, E D; Ryder, O

    2009-01-01

    Evolutionary cytogenetic comparisons involved 5 species of birds (California condor, chicken, zebra finch, collared flycatcher and black stork) belonging to divergent taxonomic orders. Seventy-four clones from a condor BAC library containing 80 genes were mapped to condor chromosomes using FISH, and 15 clones containing 16 genes were mapped to the stork Z chromosome. Maps for chicken and finch were derived from genome sequence databases, and that for flycatcher from the published literature. Gene content and gene order were highly conserved when individual condor, chicken, and zebra finch autosomes were compared, confirming that these species largely retain karyotypes close to the ancestral condition for neognathous birds. However, several differences were noted: zebra finch chromosomes 1 and 1A are homologous to condor and chicken chromosomes 1, the CHUNK1 gene appears to have transposed on condor chromosome 1, condor chromosomes 4 and 9 and zebra finch chromosomes 4 and 4A are homologous to chicken chromosome arms 4q and 4p, and novel inversions on chromosomes 4, 12 and 13 were found. Condor and stork Z chromosome gene orders are collinear and differentiated by a series of inversions/transpositions when compared to chicken, zebra finch, or flycatcher; phylogenetic analyses suggest independent rearrangement along the chicken, finch, and flycatcher lineages.

  19. Molecular cytogenetics of the california condor: evolutionary and conservation implications.

    PubMed

    Modi, W S; Romanov, M; Green, E D; Ryder, O

    2009-01-01

    Evolutionary cytogenetic comparisons involved 5 species of birds (California condor, chicken, zebra finch, collared flycatcher and black stork) belonging to divergent taxonomic orders. Seventy-four clones from a condor BAC library containing 80 genes were mapped to condor chromosomes using FISH, and 15 clones containing 16 genes were mapped to the stork Z chromosome. Maps for chicken and finch were derived from genome sequence databases, and that for flycatcher from the published literature. Gene content and gene order were highly conserved when individual condor, chicken, and zebra finch autosomes were compared, confirming that these species largely retain karyotypes close to the ancestral condition for neognathous birds. However, several differences were noted: zebra finch chromosomes 1 and 1A are homologous to condor and chicken chromosomes 1, the CHUNK1 gene appears to have transposed on condor chromosome 1, condor chromosomes 4 and 9 and zebra finch chromosomes 4 and 4A are homologous to chicken chromosome arms 4q and 4p, and novel inversions on chromosomes 4, 12 and 13 were found. Condor and stork Z chromosome gene orders are collinear and differentiated by a series of inversions/transpositions when compared to chicken, zebra finch, or flycatcher; phylogenetic analyses suggest independent rearrangement along the chicken, finch, and flycatcher lineages. PMID:20051671

  20. Basic Concepts in Molecular Cytogenetics of Soft Tissue Tumors for the Clinician.

    PubMed

    Rubin, Brian P.; Fetcher, Jonathan A.

    1999-01-01

    Over the past several years, cytogenetic and molecular analyses have played a growing adjunct role in the clinicopathological evaluation of soft tissue tumors. Recent technological advances, especially in fluorescence in situ hybridization and polymerase chain reaction, have enabled the analysis of frozen and paraffin-embedded tissue as well as fresh tumor samples. Many characteristic genetic abnormalities have been identified that are of diagnostic utility in the analysis of soft tissue tumors. Additionally, certain genetic aberrations have been found to be of potential prognostic value. With the abundance of useful tools that are available, molecular cytogenetic analyses are likely to become an integral part of the analysis of soft tissue tumors. These analyses can be performed readily using small amounts of tumor (e.g., from sonographically or computed tomographic guided percutaneous biopsy specimens).

  1. Molecular cytogenetic study of the European bitterling Rhodeus amarus (Teleostei: Cyprinidae: Acheilognathinae).

    PubMed

    Kirtiklis, Lech; Ocalewicz, Konrad; Wiechowska, Marzena; Boroń, Alicja; Hliwa, Piotr

    2014-04-01

    The European bitterlings (Rhodeus amarus) from the Eastern locations were cytogenetically examined by conventional and molecular techniques. All analyzed individuals presented invariably the same chromosomal constitution of 2n = 48, with 8 metacentrics + 20 submetacentrics + 20 subtelo-acrocentrics and C-banding positive heterochromatin at the pericentromeric regions in most of the chromosomes. Moreover, some of the chromosomes had short arms entirely built with heterochromatin. GC-rich Ag-NORs (nucleolus organizer regions) were located at the short arms of two submetacentric chromosomes, and the length polymorphism of these regions was found. Multiple location of 28S rDNA sequences with fluorescence in situ hybridization signals was observed on the long and/or short arms of three submetacentric chromosomes including NOR regions and short arms of three to five acrocentric chromosomes in the studied fish. 5S rDNA sites were found on the short arms of two subtelocentric chromosomes, and telomeric repeats were localized at the ends of all chromosomes. Provided results have expanded our knowledge concerning genetic characteristics of the European bitterlings that may be profitable in the conservation programs of this endangered species.

  2. Molecular cytogenetic and phenotypic characterization of ring chromosome 13 in three unrelated patients.

    PubMed

    Abdallah-Bouhjar, Inesse B; Mougou-Zerelli, Soumaya; Hannachi, Hanene; Gmidène, Abir; Labalme, Audrey; Soyah, Najla; Sanlaville, Damien; Saad, Ali; Elghezal, Hatem

    2013-09-01

    We report on the cytogenetic and molecular investigations of constitutional de-novo ring chromosome 13s in three unrelated patients for better understanding and delineation of the phenotypic variability characterizing this genomic rearrangement. The patient's karyotypes were as follows: 46,XY,r(13)(p11q34) dn for patients 1 and 2 and 46,XY,r(13)(p11q14) dn for patient 3, as a result of the deletion in the telomeric regions of chromosome 13. The patients were, therefore, monosomic for the segment 13q34 → 13qter; in addition, for patient 3, the deletion was larger, encompassing the segment 13q14 → 13qter. Fluorescence in situ hybridization confirmed these rearrangement and array CGH technique showed the loss of at least 2.9 Mb on the short arm and 4.7 Mb on the long arm of the chromosome 13 in patient 2. Ring chromosome 13 (r(13)) is associated with several phenotypic features like intellectual disability, marked short stature, brain and heart defects, microcephaly and genital malformations in males, including undescended testes and hypospadias. However, the hearing loss and speech delay that were found in our three patients have rarely been reported with ring chromosome 13. Although little is known about its etiology, there is interesting evidence for a genetic cause for the ring chromosome 13. We thus performed a genotype-phenotype correlation analysis to ascertain the contribution of ring chromosome 13 to the clinical features of our three cases. PMID:27625853

  3. Molecular cytogenetic analyses of Epinephelus bruneus and Epinephelus moara (Perciformes, Epinephelidae).

    PubMed

    Guo, Minglan; Wang, Shifeng; Su, Yongquan; Zhou, Yongcan; Liu, Min; Wang, Jun

    2014-01-01

    Genus Epinephelus (Perciformes, Epinephelidae), commonly known as groupers, are usually difficult in species identification for the lack and/or change of morphological specialization. In this study, molecular cytogenetic analyses were firstly performed to identify the closely related species Epinephelus bruneus and E. moara in this genus. The species-specific differences of both fish species showed in karyotype, chromosomal distribution of nucleolar organizer regions (NORs) and localization of 18S rDNA. The heterochromatin (interstitial C-bands) and distribution pattern of telomere (TTAGGG) n in E. bruneus revealed the chromosomal rearrangements and different karyotypic evolutionary characteristics compared to those in E. moara. The cytogenetic data suggested that the lineages of E. bruneus and E. moara were recently derived within the genus Epinephelus, and E. moara exhibited more plesiomorphic features than E. bruneus. All results confirmed that E. moara, which has long been considered a synonym of E. bruneus, is a distinct species in the family Epinephelidae. In addition, molecular cytogenetic analyses are useful in species differentiation and phylogenetic reconstruction in groupers. PMID:24949234

  4. Molecular cytogenetic analyses of Epinephelus bruneus and Epinephelus moara (Perciformes, Epinephelidae).

    PubMed

    Guo, Minglan; Wang, Shifeng; Su, Yongquan; Zhou, Yongcan; Liu, Min; Wang, Jun

    2014-01-01

    Genus Epinephelus (Perciformes, Epinephelidae), commonly known as groupers, are usually difficult in species identification for the lack and/or change of morphological specialization. In this study, molecular cytogenetic analyses were firstly performed to identify the closely related species Epinephelus bruneus and E. moara in this genus. The species-specific differences of both fish species showed in karyotype, chromosomal distribution of nucleolar organizer regions (NORs) and localization of 18S rDNA. The heterochromatin (interstitial C-bands) and distribution pattern of telomere (TTAGGG) n in E. bruneus revealed the chromosomal rearrangements and different karyotypic evolutionary characteristics compared to those in E. moara. The cytogenetic data suggested that the lineages of E. bruneus and E. moara were recently derived within the genus Epinephelus, and E. moara exhibited more plesiomorphic features than E. bruneus. All results confirmed that E. moara, which has long been considered a synonym of E. bruneus, is a distinct species in the family Epinephelidae. In addition, molecular cytogenetic analyses are useful in species differentiation and phylogenetic reconstruction in groupers.

  5. The Bactrocera dorsalis species complex: comparative cytogenetic analysis in support of Sterile Insect Technique applications

    PubMed Central

    2014-01-01

    Background The Bactrocera dorsalis species complex currently harbors approximately 90 different members. The species complex has undergone many revisions in the past decades, and there is still an ongoing debate about the species limits. The availability of a variety of tools and approaches, such as molecular-genomic and cytogenetic analyses, are expected to shed light on the rather complicated issues of species complexes and incipient speciation. The clarification of genetic relationships among the different members of this complex is a prerequisite for the rational application of sterile insect technique (SIT) approaches for population control. Results Colonies established in the Insect Pest Control Laboratory (IPCL) (Seibersdorf, Vienna), representing five of the main economic important members of the Bactrocera dorsalis complex were cytologically characterized. The taxa under study were B. dorsalis s.s., B. philippinensis, B. papayae, B. invadens and B. carambolae. Mitotic and polytene chromosome analyses did not reveal any chromosomal characteristics that could be used to distinguish between the investigated members of the B. dorsalis complex. Therefore, their polytene chromosomes can be regarded as homosequential with the reference maps of B. dorsalis s.s.. In situ hybridization of six genes further supported the proposed homosequentiallity of the chromosomes of these specific members of the complex. Conclusions The present analysis supports that the polytene chromosomes of the five taxa under study are homosequential. Therefore, the use of the available polytene chromosome maps for B. dorsalis s.s. as reference maps for all these five biological entities is proposed. Present data provide important insight in the genetic relationships among the different members of the B. dorsalis complex, and, along with other studies in the field, can facilitate SIT applications targeting this complex. Moreover, the availability of 'universal' reference polytene chromosome

  6. The history of human cytogenetics in India-A review.

    PubMed

    Dutta, Usha R

    2016-09-10

    It is 60years since the discovery of the correct number of chromosomes in 1956; the field of cytogenetics had evolved. The late evolution of this field with respect to other fields is primarily due to the underdevelopment of lenses and imaging techniques. With the advent of the new technologies, especially automation and evolution of advanced compound microscopes, cytogenetics drastically leaped further to greater heights. This review describes the historic events that had led to the development of human cytogenetics with a special attention about the history of cytogenetics in India, its present status, and future. Apparently, this review provides a brief account into the insights of the early laboratory establishments, funding, and the German collaborations. The details of the Indian cytogeneticists establishing their labs, promoting the field, and offering the chromosomal diagnostic services are described. The detailed study of chromosomes helps in increasing the knowledge of the chromosome structure and function. The delineation of the chromosomal rearrangements using cytogenetics and molecular cytogenetic techniques pays way in identifying the molecular mechanisms involved in the chromosomal rearrangement. Although molecular cytogenetics is greatly developing, the conventional cytogenetics still remains the gold standard in the diagnosis of various numerical chromosomal aberrations and a few structural aberrations. The history of cytogenetics and its importance even in the era of molecular cytogenetics are discussed. PMID:26850130

  7. The history of human cytogenetics in India-A review.

    PubMed

    Dutta, Usha R

    2016-09-10

    It is 60years since the discovery of the correct number of chromosomes in 1956; the field of cytogenetics had evolved. The late evolution of this field with respect to other fields is primarily due to the underdevelopment of lenses and imaging techniques. With the advent of the new technologies, especially automation and evolution of advanced compound microscopes, cytogenetics drastically leaped further to greater heights. This review describes the historic events that had led to the development of human cytogenetics with a special attention about the history of cytogenetics in India, its present status, and future. Apparently, this review provides a brief account into the insights of the early laboratory establishments, funding, and the German collaborations. The details of the Indian cytogeneticists establishing their labs, promoting the field, and offering the chromosomal diagnostic services are described. The detailed study of chromosomes helps in increasing the knowledge of the chromosome structure and function. The delineation of the chromosomal rearrangements using cytogenetics and molecular cytogenetic techniques pays way in identifying the molecular mechanisms involved in the chromosomal rearrangement. Although molecular cytogenetics is greatly developing, the conventional cytogenetics still remains the gold standard in the diagnosis of various numerical chromosomal aberrations and a few structural aberrations. The history of cytogenetics and its importance even in the era of molecular cytogenetics are discussed.

  8. Molecular cytogenetic and phenotypic characterization of ring chromosome 13 in three unrelated patients

    PubMed Central

    Abdallah-Bouhjar, Inesse B.; Mougou-Zerelli, Soumaya; Hannachi, Hanene; Gmidène, Abir; Labalme, Audrey; Soyah, Najla; Sanlaville, Damien; Saad, Ali; Elghezal, Hatem

    2013-01-01

    We report on the cytogenetic and molecular investigations of constitutional de-novo ring chromosome 13s in three unrelated patients for better understanding and delineation of the phenotypic variability characterizing this genomic rearrangement. The patient’s karyotypes were as follows: 46,XY,r(13)(p11q34) dn for patients 1 and 2 and 46,XY,r(13)(p11q14) dn for patient 3, as a result of the deletion in the telomeric regions of chromosome 13. The patients were, therefore, monosomic for the segment 13q34 → 13qter; in addition, for patient 3, the deletion was larger, encompassing the segment 13q14 → 13qter. Fluorescence in situ hybridization confirmed these rearrangement and array CGH technique showed the loss of at least 2.9 Mb on the short arm and 4.7 Mb on the long arm of the chromosome 13 in patient 2. Ring chromosome 13 (r(13)) is associated with several phenotypic features like intellectual disability, marked short stature, brain and heart defects, microcephaly and genital malformations in males, including undescended testes and hypospadias. However, the hearing loss and speech delay that were found in our three patients have rarely been reported with ring chromosome 13. Although little is known about its etiology, there is interesting evidence for a genetic cause for the ring chromosome 13. We thus performed a genotype-phenotype correlation analysis to ascertain the contribution of ring chromosome 13 to the clinical features of our three cases. PMID:27625853

  9. Clinical, cytogenetic, and molecular diagnosis of Angelman syndrome: Estimated prevalence rate in a Danish country

    SciTech Connect

    Petersen, M.B.; Brondum-Nielsen, K.; Hansen, L.K.; Wulff, K.

    1995-06-19

    Angelman syndrome (AS) was initially considered a rather rare abnormality, but in later years, with the possibilities for cytogenetic and molecular diagnosis an increasing number of patients have been reported. The incidence is quoted to be around 1:20,000. The etiology of AS is associated with the lack of maternal allele(s) of one or more loci at 15q11-q13, and is considered an effect of parental imprinting of that region, since a similar deficiency of paternal alleles leads to Prader-Willi syndrome. 9 refs., 1 tab.

  10. Molecular and Cytogenetic Characterization of Wild Musa Species

    PubMed Central

    Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Doležel, Jaroslav

    2015-01-01

    The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region

  11. Molecular and Cytogenetic Characterization of Wild Musa Species.

    PubMed

    Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Doležel, Jaroslav

    2015-01-01

    The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region

  12. Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background.

    PubMed

    Gong, Wenping; Li, Guangrong; Zhou, Jianping; Li, Genying; Liu, Cheng; Huang, Chengyan; Zhao, Zhendong; Yang, Zujun

    2014-09-01

    Aegilops uniaristata has many agronomically useful traits that can be used for wheat breeding. So far, a Triticum turgidum - Ae. uniaristata amphiploid and one set of Chinese Spring (CS) - Ae. uniaristata addition lines have been produced. To guide Ae. uniaristata chromatin transformation from these lines into cultivated wheat through chromosome engineering, reliable cytogenetic and molecular markers specific for Ae. uniaristata chromosomes need to be developed. Standard C-banding shows that C-bands mainly exist in the centromeric regions of Ae. uniaristata but rarely at the distal ends. Fluorescence in situ hybridization (FISH) using (GAA)8 as a probe showed that the hybridization signal of chromosomes 1N-7N are different, thus (GAA)8 can be used to identify all Ae. uniaristata chromosomes in wheat background simultaneously. Moreover, a total of 42 molecular markers specific for Ae. uniaristata chromosomes were developed by screening expressed sequence tag - sequence tagged site (EST-STS), expressed sequence tag - simple sequence repeat (EST-SSR), and PCR-based landmark unique gene (PLUG) primers. The markers were subsequently localized using the CS - Ae. uniaristata addition lines and different wheat cultivars as controls. The cytogenetic and molecular markers developed herein will be helpful for screening and identifying wheat - Ae. uniaristata progeny.

  13. Cytogenetic and molecular characterization of 57 individuals with the Parder-Willi syndrome

    SciTech Connect

    Butler, M.G.; Forrest, K.B.; Miller, L.K.

    1994-09-01

    Prader-Willi syndrome (PWS) is characterized by hypotonia, early childhood obesity, mental deficiency, hypogonadism and an interstitial deletion of 15q11q13 of paternal origin in 50-70% of patients. The remaining patients have either submicroscopic deletions, maternal disomy or other anomalies of chromosome 15. We have undertaken cytogenetic and molecular genetic studies of 57 individuals presenting with features consistent with PWS (28 males and 29 females; age range of 3 months to 38 years), 25 with recognizable 15q11q13 deletions (44%), 28 with normal appearing chromosomes (49%), and four patients with other chromosome 15 anomalies (7%). High resolution chromosome analysis and PCR amplification were performed utilizing 17 STRs from 15q11q13 region, quantitative Southern hybridization using seven 15q11q13 probes, and fluorescence in situ hybridization (FISH) using four 15q11q13 probes (4-3R, SNRPN, 3-21, and GABRB3). The cytogenetic deletion was paternal in all PWS families studied but the deletion varied in size in 10 patients. Parental DNA studies from 20 of 28 non-deletion patients showed maternal disomy in 7 patients and biparental inheritance in 13 non-deletion patients. In order to evaluate for submicroscopic deletions, PCR amplification with several loci in the area of the PWS minimal critical region, FISH using SNRPN and quantitative hybridization using a PCR product generated from primers of exons E and H of the SNRPN gene were undertaken on the non-deletion patients. Quantitative hybridization and FISH using SNRPN from 3 of 11 non-deletion patients (excluding maternal disomy cases) showed a submicroscopic deletion. One of these patients also showed a paternal deletion of D15S128 and MN1. We furthur support the use of both cytogenetic and molecular genetic methods for determining the genetic status of PWS patients.

  14. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    PubMed

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies. PMID:26758200

  15. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    PubMed

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  16. Clinical characteristics, cytogenetic and molecular findings in patients with disorders of sex development.

    PubMed

    Tian, Li; Chen, Ming; Peng, Jian-hong; Zhang, Jian-wu; Li, Li

    2014-02-01

    The clinical characteristics of patients with disorders of sex development (DSD), and the diagnostic values of classic cytogenetic and molecular genetic assays for DSD were investigated. In the enrolled 56 cases, there were 9 cases of 46,XY DSD, 6 cases of Turner syndrome (TS), one case of Super female syndrome, 25 cases of Klinefelter syndrome, 14 cases of 46,XX DSD, and one case of autosomal balanced rearrangements with hypospadias. The diagnosis of sex was made through physical examination, cytogenetic assay, ultrasonography, gonadal biopsy and hormonal analysis. PCR was used to detect SRY, ZFX, ZFY, DYZ3 and DYZ1 loci on Y and X chromosomes respectively. The DSD patients with the same category had similar clinical characteristics. The karyotypes in peripheral blood lymphocytes of all patients were identified. PCR-based analysis showed presence or absence of the X/Y-linked loci in several cases. Of the 9 cases of 46,XY DSD, 6 were positive for SRY, 9 for ZFX/ZFY, 9 for DYZ3 and 8 for DYZ1 loci. Of the 6 cases of TS, only 1 case with the karyotype of 45,X,/46,XX/46,XY was positive for all 5 loci. Of the 25 cases of Klinefelter syndrome, all were positive for all 5 loci. In one case of rare Klinefelter syndrome variants azoospermia factor (AZF) gene detection revealed the loss of the AZFa+AZFb region. In 14 cases of 46,XX DSD, 7 cases were positive for SRY, 14 for ZFX, 7 for ZFY, 7 for ZYZ3, and 5 for DYZ1. PCR can complement and also confirm cytogenetic studies in the diagnosis of sex in cases of DSD.

  17. Particular aspects in the cytogenetics and molecular biology of salivary gland tumours - current review of reports.

    PubMed

    Ochal-Choińska, Aleksandra J; Osuch-Wójcikiewicz, Ewa

    2016-01-01

    Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours. The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours. PMID:27688723

  18. Molecular cytogenetic analysis and genomic organization of major DNA repeats in castor bean (Ricinus communis L.).

    PubMed

    Alexandrov, O S; Karlov, G I

    2016-04-01

    This article addresses the bioinformatic, molecular genetic, and cytogenetic study of castor bean (Ricinus communis, 2n = 20), which belongs to the monotypic Ricinus genus within the Euphorbiaceae family. Because castor bean chromosomes are small, karyotypic studies are difficult. However, the use of DNA repeats has yielded new prospects for karyotypic research and genome characterization. In the present study, major DNA repeat sequences were identified, characterized and localized on mitotic metaphase and meiotic pachytene chromosomes. Analyses of the nucleotide composition, curvature models, and FISH localization of the rcsat39 repeat suggest that this repeat plays a key role in building heterochromatic arrays in castor bean. Additionally, the rcsat390 sequences were determined to be chromosome-specific repeats located in the pericentromeric region of mitotic chromosome A (pachytene chromosome 1). The localization of rcsat39, rcsat390, 45S and 5S rDNA genes allowed for the development of cytogenetic landmarks for chromosome identification. General questions linked to heterochromatin formation, DNA repeat distribution, and the evolutionary emergence of the genome are discussed. The article may be of interest to biologists studying small genome organization and short monomer DNA repeats. PMID:26589420

  19. A somatic cell hybrid panel for pig regional gene mapping characterized by molecular cytogenetics.

    PubMed

    Yerle, M; Echard, G; Robic, A; Mairal, A; Dubut-Fontana, C; Riquet, J; Pinton, P; Milan, D; Lahbib-Mansais, Y; Gellin, J

    1996-01-01

    A panel of 27 pig x rodent somatic cell hybrids was produced and characterized cytogenetically. The first step of this study consisted of hybridizing a SINE probe to GTG-banded metaphases of each hybrid clone in order to count and identify the normal pig chromosomes and to detect rearranged ones. The second step consisted of using the DNA of each clone as a probe after pIRS-PCR (porcine interspersed repetitive sequence-polymerase chain reaction) amplification to highly enrich it in pig sequences. These probes, hybridized to normal pig metaphase chromosomes, enabled the identification of the complete porcine complement in the hybrid lines. Whole chromosomes and fragments were characterized quickly and precisely, and results were compared. In addition to this cytogenetic characterization, molecular verification was also carried out by using primers specific to six microsatellites and to one gene previously mapped to pig chromosomes. The results obtained allow us to conclude that we have produced a panel that is informative for all porcine chromosomes. This panel constitutes a highly efficient tool to establish not only assignments of genes and markers but also regional localizations on pig chromosomes. PMID:8697807

  20. Molecular cytogenetic analysis and genomic organization of major DNA repeats in castor bean (Ricinus communis L.).

    PubMed

    Alexandrov, O S; Karlov, G I

    2016-04-01

    This article addresses the bioinformatic, molecular genetic, and cytogenetic study of castor bean (Ricinus communis, 2n = 20), which belongs to the monotypic Ricinus genus within the Euphorbiaceae family. Because castor bean chromosomes are small, karyotypic studies are difficult. However, the use of DNA repeats has yielded new prospects for karyotypic research and genome characterization. In the present study, major DNA repeat sequences were identified, characterized and localized on mitotic metaphase and meiotic pachytene chromosomes. Analyses of the nucleotide composition, curvature models, and FISH localization of the rcsat39 repeat suggest that this repeat plays a key role in building heterochromatic arrays in castor bean. Additionally, the rcsat390 sequences were determined to be chromosome-specific repeats located in the pericentromeric region of mitotic chromosome A (pachytene chromosome 1). The localization of rcsat39, rcsat390, 45S and 5S rDNA genes allowed for the development of cytogenetic landmarks for chromosome identification. General questions linked to heterochromatin formation, DNA repeat distribution, and the evolutionary emergence of the genome are discussed. The article may be of interest to biologists studying small genome organization and short monomer DNA repeats.

  1. Molecular cytogenetic characterization of a case of primary amenorrhea with intrachromosomal triplication of the X chromosome q arm.

    PubMed

    Ocak, Z; Surucu, R

    2012-01-01

    This is a unique case of intrachromosomal triplication of the X chromosome q arm detected with cytogenetic and spectral karyotyping in a 21-year-old woman with primary amenorrhea, who had been referred because of primary hypergonadotropic hypogonadism and Mullerian hypoplasia. Intrachromosomal triplications are rare rearrangements resulting in partial tetrasomy. Since 1993, at least 34 cases of intrachromosomal triplications involving 9 different chromosomes have been reported. The vast majority of the reported triplications are on the 15th chromosome, arised de novo and had middle inverted repetitions. In this report the genotype-fenotype correlation in a case of primary amenorrhea associated with triplication of the X chromosome q arm and the possible mechanisms of this rearrangement are discussed. Further the clinical usability of SKY analysis as a molecular cytogenetic tool in searching for genomic instability arising from cytogenetic rearrangements is highlighted. PMID:22876590

  2. Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic).

    PubMed

    Claustres, Mireille; Kožich, Viktor; Dequeker, Els; Fowler, Brain; Hehir-Kwa, Jayne Y; Miller, Konstantin; Oosterwijk, Cor; Peterlin, Borut; van Ravenswaaij-Arts, Conny; Zimmermann, Uwe; Zuffardi, Orsetta; Hastings, Ros J; Barton, David E

    2014-02-01

    Genetic test results can have considerable importance for patients, their parents and more remote family members. Clinical therapy and surveillance, reproductive decisions and genetic diagnostics in family members, including prenatal diagnosis, are based on these results. The genetic test report should therefore provide a clear, concise, accurate, fully interpretative and authoritative answer to the clinical question. The need for harmonizing reporting practice of genetic tests has been recognised by the External Quality Assessment (EQA), providers and laboratories. The ESHG Genetic Services Quality Committee has produced reporting guidelines for the genetic disciplines (biochemical, cytogenetic and molecular genetic). These guidelines give assistance on report content, including the interpretation of results. Selected examples of genetic test reports for all three disciplines are provided in an annexe.

  3. Molecular cytogenetic detection of chromosome 15 deletions in patients with Prader-Willi and Angelman syndromes

    SciTech Connect

    Chadwick, D.E.; Weksberg, R.; Shuman, C.

    1994-09-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are clinically distinct genetic disorders involving alterations of chromosome 15q11-q13. Approximately 75% of individuals with PWS and AS have deletions within 15q11-q13 by molecular analysis. We have evaluated fluorescence in situ hybridization (FISH) for the clinical laboratory detection of del(15)(q11q13) using the cosmid probes D15S11 and GABRB3 (ONCOR, Gaithersburg, NY). 4/4 PWS and 1/1 AS patients previously identified as having cytogenetic deletions were deleted for both probes. In a prospectively ascertained series of 54 patient samples referred to rule out either PWS or AS, 8 were deleted for D15S11 and GABRB3. In addition, an atypical deletion patient with PWS was also identified who was found to be deleted for GABRB3 but not D15S11. The SNRPN locus was also deleted in this patient. Only 4 of the 9 patient samples having molecular cytogenetic deletions were clearly deleted by high resolution banding (HRB) analysis. The microscopic and submicroscopic deletions have been confirmed by dinucleotide (CA) repeat analysis. Microsatellite polymorphism analysis was also used to demonstrate that five non-deletion patients in this series had biparental inheritance of chromosome 15, including region q11-q13. Deletions were not detected by either HRB, FISH or microsatellite polymorphism analysis in samples obtained from parents of the deletion patients. Methylation studies of chromosome 15q11-q13 are in progress for this series of PWS and AS families. FISH analysis of chromosome 15q11-q13 in patients with PWS and AS is a rapid, sensitive and reliable method for deletion detection.

  4. Serial assessment of suspected myelodysplastic syndromes: significance of flow cytometric findings validated by cytomorphology, cytogenetics, and molecular genetics

    PubMed Central

    Kern, Wolfgang; Haferlach, Claudia; Schnittger, Susanne; Alpermann, Tamara; Haferlach, Torsten

    2013-01-01

    The significance of flow cytometry indicating myelodysplasia without proof of myelodysplasia by cytomorphology remains to be clarified. We evaluated follow-up analyses in 142 patients analyzed in parallel by flow cytometry, cytomorphology and cytogenetics for suspected myelodysplasia without proof of myelodysplasia by cytomorphology. At initial assessment, flow cytometry indicated myelodysplasia in 64 of 142 (45.1%) patients. In 9 of 142 (6.3%) patients, cytogenetics revealed aberrant karyotypes at first evaluation that were found in 5 of 64 (7.8%) patients rated with myelodysplasia by flow cytometry. The remaining 133 patients without proof of myelodysplasia by cytomorphology and with normal karyotype underwent follow-up analyses that confirmed myelodysplasia by cytomorphology, cytogenetics or molecular genetics in 47 (35.3%) after a median interval of nine months (range 1-53 months). As far as initial flow cytometry results are concerned, this applied to 30 of 59 (50.1%) with myelodysplasia, 10 of 42 (23.8%) with “possible myelodysplasia” (minor antigen aberrancies only) and 7 of 32 (21.9%) without myelodysplasia (P=0.004). Notably, in these latter 7 patients, flow cytometry results changed at follow up to “possible myelodysplasia” (n=4) and “myelodysplasia” (n=2). These data argue in favor of including flow cytometry along with cytomorphology, cytogenetics and molecular genetics to diagnose myelodysplasia, and suggest a closer monitoring of patients with myelodysplasia-typical aberrant antigen expression found by flow cytometry. PMID:22929975

  5. A first generation cytogenetic ideogram for the Florida manatee (Trichechus manatus latirostris) based on multiple chromosome banding techniques

    USGS Publications Warehouse

    Gray, B.A.; Zori, Roberto T.; McGuire, P.M.; Bonde, R.K.

    2002-01-01

    Detailed chromosome studies were conducted for the Florida manatee (Trichechus manatus latirostris) utilizing primary chromosome banding techniques (G- and Q-banding). Digital microscopic imaging methods were employed and a standard G-banded karyotype was constructed for both sexes. Based on chromosome banding patterns and measurements obtained in these studies, a standard karyotype and ideogram are proposed. Characterization of additional cytogenetic features of this species by supplemental chromosome banding techniques, C-banding (constitutive heterochromatin), Ag-NOR staining (nucleolar organizer regions), and DA/DAPI staining, was also performed. These studies provide detailed cytogenetic data for T. manatus latirostris, which could enhance future genetic mapping projects and interspecific and intraspecific genomic comparisons by techniques such as zoo-FISH.

  6. Microphthalmia with linear skin defects (MLS) syndrome: Clinical, cytogenetic, and molecular characterization

    SciTech Connect

    Lindsay, E.A.; Grillo, A.; Ferrero, G.B.; Baldini, A.; Ballabio, A.; Zoghbi, H.Y.; Roth, E.J.; Magenis, E.; Grompe, M.; Hulten, M.

    1994-01-15

    The microphthalmia with linear skin defects (MLS) syndrome (MIM309801) is a severe developmental disorder observed in XX individuals with distal Xp segmental monosomy. The phenotype of this syndrome overlaps with that of both Aicardi (MIM 305050) and Goltz (MIM 305600) syndromes, two X-linked dominant, male-lethal disorders. Here the authors report the clinical, cytogenetic, and molecular characterization of 3 patients with this syndrome. Two of these patients are females with a terminal Xpter-p22.2 deletion. One of these 2 patients had an aborted fetus with anencephaly and the same chromosome abnormality. The third patient is an XX male with Xp/Yp exchange spanning the SRY gene which results in distal Xp monosomy. The extensive clinical variability observed in these patients and the results of the molecular analysis suggest that X-inactivation plays an important role in determining the phenotype of the MLS syndrome. The authors propose that the MLS, Aicardi, and Goltz syndromes are due to the involvement of the same gene(s), and that different patterns of X-inactivation are responsible for the phenotypic differences observed in these 3 disorders. However, they cannot rule out that each component of the MLS phenotype is caused by deletion of a different gene (a contiguous gene syndrome). 24 refs., 4 figs., 1 tab.

  7. Molecular cytogenetic characterisation of partial trisomy 9q in a case with pyloric stenosis and a review

    PubMed Central

    Heller, A.; Seidel, J; Hubler, A; Starke, H; Beensen, V; Senger, G; Rocchi, M; Wirth, J; Chudoba, I; Claussen, U; Liehr, T

    2000-01-01

    Partial trisomy 9q represents a rare and heterogeneous group of chromosomal aberrations characterised by various clinical features including pyloric stenosis. Here, we describe the case of a 1 year old female patient with different dysmorphic features including pyloric stenosis and prenatally detected partial trisomy 9q. This partial trisomy 9q has been analysed in detail to determine the size of the duplication and to characterise the chromosomal breakpoints. According to the data gained by different molecular cytogenetic techniques, such as fluorescence in situ hybridisation (FISH) with whole and partial chromosome painting probes, yeast artificial chromosome (YAC) probes, and comparative genomic hybridisation (CGH), the derivative chromosome 9 can be described as dup(9)(pter→q22.1::q31.1→q22.1::q31.1→ q22.1::q31.1→qter). Four breakpoint spanning YACs have been identified (y806f02, y906g6, y945f5, and y747b3) for the proximal breakpoint. According to this new case and previously published data, the recently postulated putative critical region for pyloric stenosis can be narrowed down to the subbands 9q22.1-q31.1 and is the result of either partial trisomy of gene(s) located in this region or a gene disrupted in 9q31.


Keywords: partial trisomy 9q; pyloric stenosis; FISH; CGH PMID:10882757

  8. Molecular cytogenetic characterization of the dioecious Cannabis sativa with an XY chromosome sex determination system.

    PubMed

    Divashuk, Mikhail G; Alexandrov, Oleg S; Razumova, Olga V; Kirov, Ilya V; Karlov, Gennady I

    2014-01-01

    Hemp (Cannabis sativa L.) was karyotyped using by DAPI/C-banding staining to provide chromosome measurements, and by fluorescence in situ hybridization with probes for 45 rDNA (pTa71), 5S rDNA (pCT4.2), a subtelomeric repeat (CS-1) and the Arabidopsis telomere probes. The karyotype has 18 autosomes plus a sex chromosome pair (XX in female and XY in male plants). The autosomes are difficult to distinguish morphologically, but three pairs could be distinguished using the probes. The Y chromosome is larger than the autosomes, and carries a fully heterochromatic DAPI positive arm and CS-1 repeats only on the less intensely DAPI-stained, euchromatic arm. The X is the largest chromosome of all, and carries CS-1 subtelomeric repeats on both arms. The meiotic configuration of the sex bivalent locates a pseudoautosomal region of the Y chromosome at the end of the euchromatic CS-1-carrying arm. Our molecular cytogenetic study of the C. sativa sex chromosomes is a starting point for helping to make C. sativa a promising model to study sex chromosome evolution. PMID:24465491

  9. Molecular Cytogenetics in Trough Shells (Mactridae, Bivalvia): Divergent GC-Rich Heterochromatin Content.

    PubMed

    García-Souto, Daniel; Pérez-García, Concepción; Kendall, Jack; Pasantes, Juan J

    2016-01-01

    The family Mactridae is composed of a diverse group of marine organisms, commonly known as trough shells or surf clams, which illustrate a global distribution. Although this family includes some of the most fished and cultured bivalve species, their chromosomes are poorly studied. In this work, we analyzed the chromosomes of Spisula solida, Spisula subtruncata and Mactra stultorum by means of fluorochrome staining, C-banding and fluorescent in situ hybridization using 28S ribosomal DNA (rDNA), 5S rDNA, H3 histone gene and telomeric probes. All three trough shells presented 2n = 38 chromosomes but different karyotype compositions. As happens in most bivalves, GC-rich regions were limited to the nucleolus organizing regions in Spisula solida. In contrast, many GC-rich heterochromatic bands were detected in both Spisula subtruncata and Mactra stultorum. Although the three trough shells presented single 5S rDNA and H3 histone gene clusters, their chromosomal locations differed. Regarding major rDNA clusters, while Spisula subtruncata presented a single cluster, both Spisula solida and Mactra stultorum showed two. No evidence of intercalary telomeric signals was detected in these species. The molecular cytogenetic characterization of these taxa will contribute to understanding the role played by chromosome changes in the evolution of trough shells. PMID:27537915

  10. Molecular Cytogenetics in Trough Shells (Mactridae, Bivalvia): Divergent GC-Rich Heterochromatin Content

    PubMed Central

    García-Souto, Daniel; Pérez-García, Concepción; Kendall, Jack; Pasantes, Juan J.

    2016-01-01

    The family Mactridae is composed of a diverse group of marine organisms, commonly known as trough shells or surf clams, which illustrate a global distribution. Although this family includes some of the most fished and cultured bivalve species, their chromosomes are poorly studied. In this work, we analyzed the chromosomes of Spisula solida, Spisula subtruncata and Mactra stultorum by means of fluorochrome staining, C-banding and fluorescent in situ hybridization using 28S ribosomal DNA (rDNA), 5S rDNA, H3 histone gene and telomeric probes. All three trough shells presented 2n = 38 chromosomes but different karyotype compositions. As happens in most bivalves, GC-rich regions were limited to the nucleolus organizing regions in Spisula solida. In contrast, many GC-rich heterochromatic bands were detected in both Spisula subtruncata and Mactra stultorum. Although the three trough shells presented single 5S rDNA and H3 histone gene clusters, their chromosomal locations differed. Regarding major rDNA clusters, while Spisula subtruncata presented a single cluster, both Spisula solida and Mactra stultorum showed two. No evidence of intercalary telomeric signals was detected in these species. The molecular cytogenetic characterization of these taxa will contribute to understanding the role played by chromosome changes in the evolution of trough shells. PMID:27537915

  11. Molecular cytogenetics of tragelaphine and alcelaphine interspecies hybrids: hybridization, introgression and speciation in some African antelope

    PubMed Central

    Robinson, T. J.; Cernohorska, H.; Schulze, E.; Duran-Puig, A.

    2015-01-01

    Hybridization can occur naturally among diverging lineages as part of the evolutionary process leading to complete reproductive isolation, or it can result from range shifts and habitat alteration through global warming and/or other anthropogenic influences. Here we report a molecular cytogenetic investigation of hybridization between taxonomically distinct species of the Alcelaphini (Alcelaphus buselaphus 2n = 40 × Damaliscus lunatus 2n = 36) and the Tragelaphini (Tragelaphus strepsiceros 2n = 31/32 × Tragelaphus angasii 2n = 55/56). Cross-species fluorescence in situ hybridization provides unequivocal evidence of the scale of karyotypic difference distinguishing parental species. The findings suggest that although hybrid meiosis of the former cross would necessitate the formation of a chain of seven, a ring of four and one trivalent, the progeny follow Haldane's rule showing F1 male sterility and female fertility. The tragelaphine F1 hybrid, a male, was similarly sterile and, given the 11 trivalents and chain of five anticipated in its meiosis, not unexpectedly so. We discuss these findings within the context of the broader evolutionary significance of hybridization in African antelope, and reflect on what these hold for our views of antelope species and their conservation. PMID:26582842

  12. Molecular cytogenetic analysis of human blastocysts andcytotrophoblasts by multi-color FISH and Spectra Imaging analyses

    SciTech Connect

    Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf; Jung,Christine J.; Nguyen, Ha-Nam; Chu, Lisa W.; Pedersen, Roger A.; Fisher,Susan J.; Weier, Heinz-Ulrich G.

    2006-02-08

    Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failed to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.

  13. Cytogenetic and molecular studies of Down syndrome individuals with transient leukemia

    SciTech Connect

    Shen, J.J.; Hassold, T.J.; Zipursky, A.

    1994-09-01

    There is an increased risk of leukemia in Down syndrome (DS) patients with estimates ranging from 14 to 30 times the incidence rate observed for normal children. Furthermore, one subtype of leukemia, called transient myeloproliferative disorder, or transient leukemia (TL), occurs almost exclusively in DS infants. The basis of the association between DS and leukemia is unknown but we and others have hypothesized that it may be attributable to the mechanism of origin of the extra chromosome. Therefore, we have initiated a cytogenetic and molecular study of nondisjunction in leukemic DS individuals. To date, we have obtained blood and/or tissue samples from 54 individuals, consisting of 16 cases with TL and 6 with acute megakaryoblastic leukemia (postulated to be related to TL), and 32 cases of other forms of leukemia (15 ALL, 10 AML, 7 others). Our preliminary data suggest significant differences between DS children with TL and those with other types of leukemia or DS individuals with no history of leukemia. For example, the TL cases have a highly significant increase in the frequency of {open_quotes}atypical{close_quotes} constitutional karyotypes (i.e. mosaic trisomies, rings, isochromosomes) and are almost always male. Initial gene mapping studies of these cases aimed at identifying loci important in the genesis of TL will be presented and compared to similar data from DS individuals with other forms of leukemia and those without leukemia.

  14. Molecular Cytogenetic Characterization of the Dioecious Cannabis sativa with an XY Chromosome Sex Determination System

    PubMed Central

    Divashuk, Mikhail G.; Alexandrov, Oleg S.; Razumova, Olga V.; Kirov, Ilya V.; Karlov, Gennady I.

    2014-01-01

    Hemp (Cannabis sativa L.) was karyotyped using by DAPI/C-banding staining to provide chromosome measurements, and by fluorescence in situ hybridization with probes for 45 rDNA (pTa71), 5S rDNA (pCT4.2), a subtelomeric repeat (CS-1) and the Arabidopsis telomere probes. The karyotype has 18 autosomes plus a sex chromosome pair (XX in female and XY in male plants). The autosomes are difficult to distinguish morphologically, but three pairs could be distinguished using the probes. The Y chromosome is larger than the autosomes, and carries a fully heterochromatic DAPI positive arm and CS-1 repeats only on the less intensely DAPI-stained, euchromatic arm. The X is the largest chromosome of all, and carries CS-1 subtelomeric repeats on both arms. The meiotic configuration of the sex bivalent locates a pseudoautosomal region of the Y chromosome at the end of the euchromatic CS-1-carrying arm. Our molecular cytogenetic study of the C. sativa sex chromosomes is a starting point for helping to make C. sativa a promising model to study sex chromosome evolution. PMID:24465491

  15. De novo proximal interstitial deletions of 14q: Cytogenetic and molecular investigations

    SciTech Connect

    Shapira, S.K.; Anderson, K.L.; Orr-Urtregar, A.; Craigen, W.J.; Lupski, J.R.; Shaffer, L.G.

    1994-08-01

    We report on 2 unrelated patients who had chromosome analysis performed because of psychomotor delay, failure to thrive, and minor anomalies. Each patient had a novel proximal 14q deletion (q11.2 to q21.1 in patient 737 and q12 to q22 in patient 777). Polymorphic (C-A){sub n} microsatellite markers distributed along the length of chromosome 14q were examined in both patients and their parents in order to determine which marker loci were deleted. The deletion in patient 737 was found to be paternal in origin, based on the analysis of 2 marker loci (D14S54 and D14S70), thus assigning these loci to the deleted interval q11.2 q21.1. Furthermore, 3 loci were not deleted (TCRD, D14S50, and D14S80), suggesting that they are within or proximal to 14q11.2. In the other family (patient 777), none of the markers were fully informative, but the deleted chromosome was determined to be paternally derived based on cytogenetic heteromorphisms. Despite having overlapping proximal 14q deletions, these 2 patients shared few phenotypic similarities except for failure to thrive, micrognathia, and hypoplasia of the corpus callosum. Therefore, a distinct proximal 14q deletion syndrome is not yet apparent. However, the molecular analyses facilitated the localization of several 14q DNA markers to the deletion regions in these 2 patients, while excluding other markers from each deletion. 24 refs., 4 figs.

  16. Molecular cytogenetic characterization of the dioecious Cannabis sativa with an XY chromosome sex determination system.

    PubMed

    Divashuk, Mikhail G; Alexandrov, Oleg S; Razumova, Olga V; Kirov, Ilya V; Karlov, Gennady I

    2014-01-01

    Hemp (Cannabis sativa L.) was karyotyped using by DAPI/C-banding staining to provide chromosome measurements, and by fluorescence in situ hybridization with probes for 45 rDNA (pTa71), 5S rDNA (pCT4.2), a subtelomeric repeat (CS-1) and the Arabidopsis telomere probes. The karyotype has 18 autosomes plus a sex chromosome pair (XX in female and XY in male plants). The autosomes are difficult to distinguish morphologically, but three pairs could be distinguished using the probes. The Y chromosome is larger than the autosomes, and carries a fully heterochromatic DAPI positive arm and CS-1 repeats only on the less intensely DAPI-stained, euchromatic arm. The X is the largest chromosome of all, and carries CS-1 subtelomeric repeats on both arms. The meiotic configuration of the sex bivalent locates a pseudoautosomal region of the Y chromosome at the end of the euchromatic CS-1-carrying arm. Our molecular cytogenetic study of the C. sativa sex chromosomes is a starting point for helping to make C. sativa a promising model to study sex chromosome evolution.

  17. Molecular cytogenetic characterization of a familial pericentric inversion 3 associated with short stature.

    PubMed

    Dutta, Usha R; Hansmann, Ingo; Schlote, Dietmar

    2015-03-01

    Short stature refers to the height of an individual which is below expected. The causes are heterogenous and influenced by several genetic and environmental factors. Chromosomal abnormalities are a major cause of diseases and cytogenetic mapping is one of the powerful tools for the identification of novel disease genes. Here we report a three generation family with a heterozygous pericentric inversion of 46, XX, inv(3) (p24.1q26.1) associated with Short stature. Positional cloning strategy was used to physically map the breakpoint regions by Fluorescence in situ hybridization (FISH). Fine mapping was performed with Bacterial Artificial Chromosome (BAC) clones spanning the breakpoint regions. In order to further characterize the breakpoint regions extensive molecular mapping was carried out with the breakpoint spanning BACs which narrowed down the breakpoint region to 2.9 kb and 5.3 kb regions on p and q arm respectively. Although these breakpoints did not disrupt any validated genes, we had identified a novel putative gene in the vicinity of 3q26.1 breakpoint region by in silico analysis. Trying to find the presence of any transcripts of this putative gene we analyzed human total RNA by RT-PCR and identified transcripts containing three new exons confirming the existence of a so far unknown gene close to the 3q breakpoint.

  18. Relationships of the Woody Medicago Species (Section Dendrotelis) Assessed by Molecular Cytogenetic Analyses

    PubMed Central

    Rosato, Marcela; Castro, Mercedes; Rosselló, Josep A.

    2008-01-01

    Background and Aims The organization of rDNA genes in the woody medic species from the agronomically important Medicago section Dendrotelis was analysed to gain insight into their taxonomic relationships, to assess the levels of infraspecific variation concerning ribosomal loci in a restricted and fragmented insular species (M. citrina) and to assess the nature of its polyploidy. Methods Fluorescence in situ hybridization (FISH) was used for physical mapping of 5S and 45S ribosomal DNA genes in the three species of section Dendrotelis (M. arborea, M. citrina, M. strasseri) and the related M. marina from section Medicago. Genomic in situ hybridization (GISH) was used to assess the genomic relationships of the polyploid M. citrina with the putatively related species from section Dendrotelis. Key Results The diploid (2n = 16) M. marina has a single 45S and two 5S rDNA loci, a pattern usually detected in previous studies of Medicago diploid species. However, polyploid species from section Dendrotelis depart from expectations. The tetraploid species (2n = 32) M. arborea and M. strasseri have one 45S rDNA locus and two 5S rDNA loci, whereas in the hexaploid (2n = 48) M. citrina four 45S rDNA and five 5S rDNA loci have been detected. No single chromosome of M. citrina was uniformly labelled after using genomic probes from M. arborea and M. strasseri. Instead, cross-hybridization signals in M. citrina were restricted to terminal chromosome arms and NOR regions. Conclusions FISH results support the close taxonomic interrelationship between M. arborea and M. strasseri. In these tetraploid species, NOR loci have experienced a diploidization event through physical loss of sequences, a cytogenetic feature so far not reported in other species of the genus. The high number of rDNA loci and GISH results support the specific status for the hexaploid M. citrina, and it is suggested that this species is not an autopolyploid derivative of M. arborea or M. strasseri. Further, molecular

  19. Molecular cytogenetic studies in the ladybird beetle Henosepilachnaargus Geoffroy, 1762 (Coleoptera, Coccinellidae, Epilachninae).

    PubMed

    Mora, Pablo; Vela, Jesús; Sanllorente, Olivia; Palomeque, Teresa; Lorite, Pedro

    2015-01-01

    The ladybird Henosepilachnaargus Geoffroy, 1762 has been cytogenetically studied. In addition we have conducted a review of chromosome numbers and the chromosomal system of sex determination available in the literature in species belonging to the genus Henosepilachna and in its closely related genus Epilachna. Chromosome number of Henosepilachnaargus was 2n=18, including the sex chromosome pair, a common diploid chromosome number within the tribe Epilachnini. The study of prophase I meiotic chromosomes showed the typical Xyp "parachute" bivalent as in the majority of species of Coccinellidae. C-banding and fluorescent staining with AT-specific DAPI fluorochrome dye have been carried out for the first time in H. argus. C-banding technique revealed that heterochromatic blocks are pericentromerically located and DAPI staining showed that this heterochromatin is AT rich. Fluorescence in situ hybridizations using rDNA and the telomeric TTAGG sequence as probes have been carried out. FISH using rDNA showed that the nucleolar organizing region is located on the short arm of the X chromosome. FISH with the telomeric sequence revealed that in this species telomeres of chromosomes are composed of the pentanucleotide TTAGG repeats. This is the first study on the telomeric sequences in Coccinellidae. PMID:26312131

  20. Molecular cytogenetic studies in the ladybird beetle Henosepilachna argus Geoffroy, 1762 (Coleoptera, Coccinellidae, Epilachninae)

    PubMed Central

    Mora, Pablo; Vela, Jesús; Sanllorente, Olivia; Palomeque, Teresa; Lorite, Pedro

    2015-01-01

    Abstract The ladybird Henosepilachna argus Geoffroy, 1762 has been cytogenetically studied. In addition we have conducted a review of chromosome numbers and the chromosomal system of sex determination available in the literature in species belonging to the genus Henosepilachna and in its closely related genus Epilachna. Chromosome number of Henosepilachna argus was 2n=18, including the sex chromosome pair, a common diploid chromosome number within the tribe Epilachnini. The study of prophase I meiotic chromosomes showed the typical Xyp “parachute” bivalent as in the majority of species of Coccinellidae. C-banding and fluorescent staining with AT-specific DAPI fluorochrome dye have been carried out for the first time in H. argus. C-banding technique revealed that heterochromatic blocks are pericentromerically located and DAPI staining showed that this heterochromatin is AT rich. Fluorescence in situ hybridizations using rDNA and the telomeric TTAGG sequence as probes have been carried out. FISH using rDNA showed that the nucleolar organizing region is located on the short arm of the X chromosome. FISH with the telomeric sequence revealed that in this species telomeres of chromosomes are composed of the pentanucleotide TTAGG repeats. This is the first study on the telomeric sequences in Coccinellidae. PMID:26312131

  1. Molecular cytogenetic studies in the ladybird beetle Henosepilachnaargus Geoffroy, 1762 (Coleoptera, Coccinellidae, Epilachninae).

    PubMed

    Mora, Pablo; Vela, Jesús; Sanllorente, Olivia; Palomeque, Teresa; Lorite, Pedro

    2015-01-01

    The ladybird Henosepilachnaargus Geoffroy, 1762 has been cytogenetically studied. In addition we have conducted a review of chromosome numbers and the chromosomal system of sex determination available in the literature in species belonging to the genus Henosepilachna and in its closely related genus Epilachna. Chromosome number of Henosepilachnaargus was 2n=18, including the sex chromosome pair, a common diploid chromosome number within the tribe Epilachnini. The study of prophase I meiotic chromosomes showed the typical Xyp "parachute" bivalent as in the majority of species of Coccinellidae. C-banding and fluorescent staining with AT-specific DAPI fluorochrome dye have been carried out for the first time in H. argus. C-banding technique revealed that heterochromatic blocks are pericentromerically located and DAPI staining showed that this heterochromatin is AT rich. Fluorescence in situ hybridizations using rDNA and the telomeric TTAGG sequence as probes have been carried out. FISH using rDNA showed that the nucleolar organizing region is located on the short arm of the X chromosome. FISH with the telomeric sequence revealed that in this species telomeres of chromosomes are composed of the pentanucleotide TTAGG repeats. This is the first study on the telomeric sequences in Coccinellidae.

  2. Molecular and cytogenetic characterization of expanded B-cell clones from multiclonal versus monoclonal B-cell chronic lymphoproliferative disorders

    PubMed Central

    Henriques, Ana; Rodríguez-Caballero, Arancha; Criado, Ignacio; Langerak, Anton W.; Nieto, Wendy G.; Lécrevisse, Quentin; González, Marcos; Cortesão, Emília; Paiva, Artur; Almeida, Julia; Orfao, Alberto

    2014-01-01

    Chronic antigen-stimulation has been recurrently involved in the earlier stages of monoclonal B-cell lymphocytosis, chronic lymphocytic leukemia and other B-cell chronic lymphoproliferative disorders. The expansion of two or more B-cell clones has frequently been reported in individuals with these conditions; potentially, such coexisting clones have a greater probability of interaction with common immunological determinants. Here, we analyzed the B-cell receptor repertoire and molecular profile, as well as the phenotypic, cytogenetic and hematologic features, of 228 chronic lymphocytic leukemia-like and non-chronic lymphocytic leukemia-like clones comparing multiclonal (n=85 clones from 41 cases) versus monoclonal (n=143 clones) monoclonal B-cell lymphocytosis, chronic lymphocytic leukemia and other B-cell chronic lymphoproliferative disorders. The B-cell receptor of B-cell clones from multiclonal cases showed a slightly higher degree of HCDR3 homology than B-cell clones from mono clonal cases, in association with unique hematologic (e.g. lower B-lymphocyte counts) and cytogenetic (e.g. lower frequency of cytogenetically altered clones) features usually related to earlier stages of the disease. Moreover, a subgroup of coexisting B-cell clones from individual multiclonal cases which were found to be phylogenetically related showed unique molecular and cytogenetic features: they more frequently shared IGHV3 gene usage, shorter HCDR3 sequences with a greater proportion of IGHV mutations and del(13q14.3), than other unrelated B-cell clones. These results would support the antigen-driven nature of such multiclonal B-cell expansions, with potential involvement of multiple antigens/epitopes. PMID:24488564

  3. Molecular and cytogenetic studies in a case of XX SRY-negative sex reversal in an Arabian horse.

    PubMed

    Ciotola, F; Albarella, S; Pasolini, M P; Auletta, L; Esposito, L; Iannuzzi, L; Peretti, V

    2012-01-01

    An 18-month-old Arabian foal characterized by a stallion-like appearance was submitted for cytogenetic and molecular genetics examinations due to abnormalities of external genitalia and the presence of ovotestis-like structures in the abdominal cavity. By RB-banding the animal showed the normal female equine karyotype (2n = 64,XX). Molecular analysis revealed the absence of the SRY and ZFY genes and the presence of ZFX, a typical female equine condition. The entire RSPO1 coding region was examined to exclude its involvement. Although a SNP was found in exon 3, it was not responsible for an amino acid substitution.

  4. Molecular and cytogenetic studies in a case of XX SRY-negative sex reversal in an Arabian horse.

    PubMed

    Ciotola, F; Albarella, S; Pasolini, M P; Auletta, L; Esposito, L; Iannuzzi, L; Peretti, V

    2012-01-01

    An 18-month-old Arabian foal characterized by a stallion-like appearance was submitted for cytogenetic and molecular genetics examinations due to abnormalities of external genitalia and the presence of ovotestis-like structures in the abdominal cavity. By RB-banding the animal showed the normal female equine karyotype (2n = 64,XX). Molecular analysis revealed the absence of the SRY and ZFY genes and the presence of ZFX, a typical female equine condition. The entire RSPO1 coding region was examined to exclude its involvement. Although a SNP was found in exon 3, it was not responsible for an amino acid substitution. PMID:22025175

  5. Cytogenetic and molecular evidence suggest multiple origins and geographical parthenogenesis in Nothoscordum gracile (Alliaceae)

    PubMed Central

    Souza, Luiz Gustavo Rodrigues; Crosa, Orfeo; Speranza, Pablo; Guerra, Marcelo

    2012-01-01

    Background and Aims Nothoscordum gracile is an apomitic tetraploid widely distributed throughout the Americas and naturalized in many temperate regions of other continents. It has been suggested to form a species complex with sexual and apomictic N. nudicaule and N. macrostemon. Tetraploids of these species also share a structurally heterozygous chromosome complement 2n = 19 (13M + 6A). In this work, the origin of N. gracile and its relationships with its related species was investigated based on cytological and molecular data. Methods Cytogenetic analyses were based on meiotic behaviour, CMA bands, localization of 5S and 45S rDNA sites, and genomic in situ hybridization (GISH). Nuclear ITS and plastidial trnL-trnF sequences were also obtained for most individuals. Key Results Proximal CMA bands were observed in the long arms of all acrocentrics of 2x and 4x N. macrostemon but not in diploid and some tetraploid cytotypes of N. nudicaule. Samples of N. gracile showed a variable number of CMA bands in the long arms of acrocentrics. Analysis of ITS sequences, dot-blot, GISH, and 5S and 45S rDNA sites, revealed no differentiation among the three species. The trnL-trnF cpDNA fragment showed variation with a trend to geographical structuring irrespective of morphospecies and fully congruent with karyotype variation. Conclusions The 2n = 19 karyotype was probably formed by a centric fusion event occurring in N. nudicaule and later transmitted to tetraploid cytotypes of N. macrostemon. Diploids of N. nudicaule and N. macrostemon appeared as consistent recently diverged species, whereas tetraploid apomicts seem to constitute an assemblage of polyploid hybrids originating from multiple independent hybridization events between them, part of which are morphologically recognizable as N. gracile. PMID:22362660

  6. Molecular cytogenetic characterisation of Salix viminalis L. using repetitive DNA sequences.

    PubMed

    Németh, Anna Viktória; Dudits, Dénes; Molnár-Láng, Márta; Linc, Gabriella

    2013-08-01

    Salix viminalis L. (2n = 38) is a diploid dicot species belonging to the Salix genus of the Salicaceae family. This short-rotation woody crop is one of the most important renewable bioenergy resources worldwide. In breeding for high biomass productivity, limited knowledge is available on the molecular cytogenetics of willow, which could be combined with genetic linkage mapping. The present paper describes the adaptation of a fluorescence in situ hybridisation (FISH) protocol as a new approach to analyse the genomic constitution of Salix viminalis using the heterologous DNA clones pSc119.2, pTa71, pTa794, pAs1, Afa-family, pAl1, HT100.3, ZCF1 and the GAA microsatellite marker. Three of the nine probes showed unambiguous signals on the metaphase chromosomes. FISH analysis with the pTa71 probe detected one major 18S-5.8S-26S rDNA locus on the short arm of one chromosome pair; however, the pTa794 rDNA site was not visible. One chromosome pair showed a distinct signal around the centromeric region after FISH with the telomere-specific DNA clone HT100.3. Two chromosome pairs were found to have pAs1 FISH signals, which represent a D-genome-specific insert from Aegilops tauschii. Based on the FISH study, a set of chromosomes with characteristic patterns is presented, which could be used to establish the karyotype of willow species.

  7. Cytogenetic and Molecular Analyses Reveal a Divergence between Acromyrmex striatus (Roger, 1863) and Other Congeneric Species: Taxonomic Implications

    PubMed Central

    Cristiano, Maykon Passos; Cardoso, Danon Clemes; Fernandes-Salomão, Tânia Maria

    2013-01-01

    The leafcutter ants, which consist of Acromyrmex and Atta genera, are restricted to the New World and they are considered the main herbivores in the neotropics. Cytogenetic studies of leafcutter ants are available for five species of Atta and 14 species of Acromyrmex, both including subspecies. These two ant genera have a constant karyotype with a diploid number of 22 and 38 chromosomes, respectively. The most distinct Acromyrmex species from Brazil is A. striatus, which is restricted to the southern states of Santa Catarina and Rio Grande do Sul. Several cytogenetic and phylogenetic studies have been conducted with ants, but the karyotypic characterization and phylogenetic position of this species relative to leafcutter ants remains unknown. In this study, we report a diploid number of 22 chromosomes for A. striatus. The phylogenetic relationship between A. striatus and other leafcutter ants was estimated based on the four nuclear genes. A. striatus shared the same chromosome number as Atta species and the majority of metacentric chromosomes. Nuclear data generated a phylogenetic tree with a well-supported cluster, where A. striatus formed a different clade from other Acromyrmex spp. This combination of cytogenetic and molecular approaches provided interesting insights into the phylogenetic position of A. striatus among the leafcutter ants and the tribe Attini. PMID:23527267

  8. Branchio-otic syndrome caused by a genomic rearrangement: clinical findings and molecular cytogenetic studies in a patient with a pericentric inversion of chromosome 8.

    PubMed

    Schmidt, T; Bierhals, T; Kortüm, F; Bartels, I; Liehr, T; Burfeind, P; Shoukier, M; Frank, V; Bergmann, C; Kutsche, K

    2014-01-01

    Branchio-oto-renal (BOR) syndrome is an autosomal dominantly inherited developmental disorder, which is characterized by anomalies of the ears, the branchial arches and the kidneys. It is caused by mutations in the genes EYA1,SIX1 and SIX5. Genomic rearrangements of chromosome 8 affecting the EYA1 gene have also been described. Owing to this fact, methods for the identification of abnormal copy numbers such as multiplex ligation-dependent probe amplification (MLPA) have been introduced as routine laboratory techniques for molecular diagnostics of BOR syndrome. The advantages of these techniques are clear compared to standard cytogenetic and array approaches as well as Southern blot. MLPA detects deletions or duplications of a part or the entire gene of interest, but not balanced structural aberrations such as inversions and translocations. Consequently, disruption of a gene by a genomic rearrangement may escape detection by a molecular genetic analysis, although this gene interruption results in haploinsufficiency and, therefore, causes the disease. In a patient with clinical features of BOR syndrome, such as hearing loss, preauricular fistulas and facial dysmorphisms, but no renal anomalies, neither sequencing of the 3 genes linked to BOR syndrome nor array comparative genomic hybridization and MLPA were able to uncover a causative mutation. By routine cytogenetic analysis, we finally identified a pericentric inversion of chromosome 8 in the affected female. High-resolution multicolor banding confirmed the chromosome 8 inversion and narrowed down the karyotype to 46,XX,inv(8)(p22q13). By applying fluorescence in situ hybridization, we narrowed down both breakpoints on chromosome 8 and found the EYA1 gene in q13.3 to be directly disrupted. We conclude that standard karyotyping should not be neglected in the genetic diagnostics of BOR syndrome or other Mendelian disorders, particularly when molecular testing failed to detect any causative alteration in patients with

  9. Unique mosaicism of tetraploidy and trisomy 8: Clinical, cytogenetic, and molecular findings in a live-born infant

    SciTech Connect

    Roberts, H.E.; Saxe, D.F.; Muralidharan, K.

    1996-03-29

    We report on a live-born infant with mosaicism of tetraploidy and trisomy 8 who had craniofacial abnormalities, cardiac and genitourinary defects, agenesis of the corpus callosum, and anomalies of limbs. The infant died at age 14 weeks. Molecular studies were done on peripheral blood lymphocytes and cultured amniocytes to determine the origin of the cytogenetic abnormalities. On the basis of the results, we describe a possible mechanism to explain these abnormalities. To our knowledge, this infant represents the first reported case of mosaic trisomy 8 with a tetraploid cell line. 14 refs., 4 figs., 2 tabs.

  10. Angelman syndrome: Validation of molecular cytogenetic analysis of chromosome 15q11-q13 for deletion detection

    SciTech Connect

    White, L.; Knoll, J.H.M.

    1995-03-13

    In a series of 18 individuals comprising parents of Angelman syndrome (AS) patients and AS patients with large deletions, microdeletions, and no deletions, we utilized fluorescence in situ hybridization (FISH) with genomic phage clones for loci D15S63 and GABRB3 for deletion detection of chromosome 15q11-q13. Utilization of probes at these loci allows detection of common large deletions and permits discrimination of less common small deletions. In all individuals the molecular cytogenetic data were concordant with the DNA deletion analyses. FISH provides an accurate method of deletion detection for chromosome 15q11-q13. 23 refs., 2 figs., 1 tab.

  11. Cytogenetic and molecular characterization of a hepatosplenic T-cell lymphoma: report of a novel chromosomal aberration.

    PubMed

    Mandava, Swarna; Sonar, Reshma; Ahmad, Firoz; Yadav, Anil K; Chheda, Pratiksha; Ramani, Manisha; Gupta, Amar D; Das, Bibhu R

    2011-02-01

    Hepatosplenic T-cell lymphomas (HSTCL) are rare cancers and comprise 5% of peripheral T-cell lymphomas. These well-characterized extranodal lymphomas have a disguised onset, secondary to intrasinusoidal infiltration of the spleen, liver, and bone marrow, with a rapidly progressive course that is poorly responsive to chemotherapy and often ensues in the setting of immune system suppression. We describe the clinical, immunophenotypic, cytogenetic, fluorescence in situ hybridization, and molecular analyses for T cell receptor gene rearrangement in a 21-year-old man diagnosed with HSTCL. Immunophenotypic analysis revealed negativity for CD5 as well as double negativity for CD4/CD8 mature T-cell immunophenotype, which suggested the diagnosis of hepatosplenic T-cell lymphoma. Molecular analysis confirmed a TCR gene rearrangement, thereby verifying the common T-cell origin of the present HSTCL case. Furthermore, cytogenetic analysis revealed a novel chromosomal rearrangement, t(7;15)(p22;q21). Metaphase fluorescence in situ hybridization analysis confirmed the translocation of a chromosomal segment from 15q21 to 7p22.

  12. Methods in human cytogenetics

    SciTech Connect

    1993-12-31

    Chapter 4, discusses the various techniques used in the study human cytogenetics. The methods are discussed in historical order, from direct methods to tissue culture techniques, prenatal studies, meiotic studies, sex chromatin techniques, banding techniques, prophase banding and replication studies. Nomenclature of human chromosomes and quantitative methods are also mentioned. 60 refs., 3 figs.

  13. Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat.

    PubMed

    Koo, Dal-Hoe; Tiwari, Vijay K; Hřibová, Eva; Doležel, Jaroslav; Friebe, Bernd; Gill, Bikram S

    2016-01-01

    Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and Aegilops geniculata (2n = 4x = 28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected Aegilops species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of Ae. geniculata. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in Ae. geniculata and in the M genome of the putative diploid donor species Ae. comosa subsp. subventricosa but not in Ae. comosa subsp. comosa, suggesting that the Mg genome of Ae. geniculata was probably derived from subsp. subventricosa.

  14. Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat.

    PubMed

    Koo, Dal-Hoe; Tiwari, Vijay K; Hřibová, Eva; Doležel, Jaroslav; Friebe, Bernd; Gill, Bikram S

    2016-01-01

    Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and Aegilops geniculata (2n = 4x = 28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected Aegilops species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of Ae. geniculata. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in Ae. geniculata and in the M genome of the putative diploid donor species Ae. comosa subsp. subventricosa but not in Ae. comosa subsp. comosa, suggesting that the Mg genome of Ae. geniculata was probably derived from subsp. subventricosa. PMID:27403741

  15. Particular aspects in the cytogenetics and molecular biology of salivary gland tumours – current review of reports

    PubMed Central

    Osuch-Wójcikiewicz, Ewa

    2016-01-01

    Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours. The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours. PMID:27688723

  16. Particular aspects in the cytogenetics and molecular biology of salivary gland tumours – current review of reports

    PubMed Central

    Osuch-Wójcikiewicz, Ewa

    2016-01-01

    Salivary gland tumours are a group of lesions whose heterogeneity of biological and pathological features is widely reflected in the molecular aspect. This is demonstrated by an increasing number of studies in the field of genetics of these tumours. The aim of this study was to collect the most significant scientific reports on the cytogenetic and molecular data concerning these tumours, which might facilitate the identification of potential biomarkers and therapeutic targets. The analysis covered 71 papers included in the PubMed database. We focused on the most common tumours, such as pleomorphic adenoma, Warthin tumour, mucoepidermoid carcinoma, and others. The aim of this study is to present current knowledge about widely explored genotypic alterations (such as PLAG1 gene in pleomorphic adenoma or MECT1 gene in mucoepidermoid carcinoma), and also about rare markers, like Mena or SOX10 protein, which might also be associated with tumourigenesis and carcinogenesis of these tumours.

  17. Trisomy and tetrasomy 15q11-q13 diagnosed by molecular cytogenetic analysis in two patients with mental retardation

    PubMed Central

    Bouhjar, Inesse Ben Abdallah; Gmidène, Abir; Soyah, Najla; Hanene, Hannachi; Mougou, Soumaya; Elghezal, Hatem; Saad, Ali

    2012-01-01

    In this study, we report two patients with the supernumerary marker chromosome (15)s. The first case is an 8.5-year-old girl with an inv dup (15) syndrome, mental retardation and dysmorphic features. The second case is a 13-year-old boy with a ring chromosome 15, who was referred to the Laboratory of Cytogenetic and Biology of Reproduction in Sousse, Tunisia for mental retardation, epilepsy, speech delay, hypotonia and other mild dysmorphic features. R banding showed the presence of a marker chromosome in both cases. Molecular cytogenetic investigation using fluorescence in situ hybridization method allowed us to characterize the markers including the Prader-Willi syndrome locus that contains the small nuclear ribonucleoprotein polypeptide N (SNRPN) gene. Tetrasomy and trisomy for the 15q11-q13 chromosomal region were found in the first and the second patient, respectively. This observation reinforces the hypothesis that additional copies of proximal chromosome 15q11 segment may be causally related to mental retardation and dysmorphic features.

  18. Trisomy and tetrasomy 15q11-q13 diagnosed by molecular cytogenetic analysis in two patients with mental retardation.

    PubMed

    Bouhjar, Inesse Ben Abdallah; Gmidène, Abir; Soyah, Najla; Hanene, Hannachi; Mougou, Soumaya; Elghezal, Hatem; Saad, Ali

    2012-03-01

    In this study, we report two patients with the supernumerary marker chromosome (15)s. The first case is an 8.5-year-old girl with an inv dup (15) syndrome, mental retardation and dysmorphic features. The second case is a 13-year-old boy with a ring chromosome 15, who was referred to the Laboratory of Cytogenetic and Biology of Reproduction in Sousse, Tunisia for mental retardation, epilepsy, speech delay, hypotonia and other mild dysmorphic features. R banding showed the presence of a marker chromosome in both cases. Molecular cytogenetic investigation using fluorescence in situ hybridization method allowed us to characterize the markers including the Prader-Willi syndrome locus that contains the small nuclear ribonucleoprotein polypeptide N (SNRPN) gene. Tetrasomy and trisomy for the 15q11-q13 chromosomal region were found in the first and the second patient, respectively. This observation reinforces the hypothesis that additional copies of proximal chromosome 15q11 segment may be causally related to mental retardation and dysmorphic features. PMID:27625804

  19. A Comprehensive Update on Molecular and Cytogenetic Abnormalities in T-cell Prolymphocytic Leukemia (T-pll).

    PubMed

    Delgado, Paul; Starshak, Phillip; Rao, Nagesh; Tirado, Carlos A

    2012-01-01

    T-cell prolymphocytic leukemia (T-PLL) is a rare form of leukemia composed of mature T-cells that usually presents in older people (median age of 65) with initial high white cell counts, massive splenomegaly, lymphadenopathy, and skin lesions. One of the cornerstones for diagnosing T-PLL includes cytogenetic studies. Most cases of T-PLL will harbor characteristic chromosomal abnormalities involving 14q11. 2 (TCR alpha/delta), 14q32 (TCL1 gene) or Xq28 (MTCP-1 gene), abnormalities of chromosome 8, 12p, and deletions of the long arm of chromosomes 5, 6, 11, and 13. In searching for new T-PLL target genes, recent studies have used techniques such as comparative genomic hybridization (CGH), 50k single nucleotide polymorphism (SNP) arrays with gene expression analysis. More recently, SNP arrays with higher resolution analysis have frequently provided more precise information about submicroscopic gene and genomic lesions as well as breakpoints involved in the pathogenesis of this disease. Herein, we summarize a review of the current literature of cytogenetic findings in T-PLL emphasizing those that may relate to the underlying mechanisms of leukemogenesis in T-PLL. Additionally, we stress the importance of karyotype characterization to accurately diagnose this disease because it usually carries a dismal prognosis that requires aggressive treatment strategies as it is poorly responsive to conventional chemotherapy used for other mature T-cell malignancies.

  20. De novo tandem duplication of chromosome segement 22q11-q12: Clinical, cytogenetic, and molecular characterization

    SciTech Connect

    Lindsay, E.A.; Shaffer, L.G.; Carrozzo, R.

    1995-04-10

    We report on a case of duplication of the segment 22q11-q12 due to a de novo duplication. Molecular cytogenetics studies demonstrated this to be a tandem duplication, flanked proximally by the marker D22Z4, a centromeric alpha satellite DNA repeat, and distally by D22S260, an anonymous DNA marker proximal to the Ewing sarcoma breakpoint. The segment includes the regions responsible for the {open_quotes}cat-eye{close_quotes}, Di George, and velo-cardio-facial syndromes and extends distal to the breakpoint cluster region (BCR). The clinical picture is dominated by the cardiac defects and includes findings reminiscent of {open_quotes}cat-eye{close_quotes} syndrome. These findings reinforce the hypothesis that the proximal 22q region contains dosage-sensitive genes involved in development. 20 refs., 3 figs.

  1. Identification of ins(8;21) with AML1/ETO fusion in acute myelogenous leukemia M2 by molecular cytogenetics.

    PubMed

    Urioste, M; Martínez-Ramírez, A; Cigudosa, J C; Mateo, M S; Martínez, P; Contra, T; Benítez, J

    2002-02-01

    A high percentage of cases of acute myelogenous leukemia (AML) of the M2 subtype show a rearrangement between the AML1 and ETO genes. The detection of the AML1/ETO fusion has clinical relevance because patients with this subtype have a good prognosis. We present the results of conventional and molecular cytogenetic studies in a patient with acute myelogenous leukemia French-American-British M2 classification, who had a complex karyotype involving chromosomes 8 and 21. Dual-color fluorescence in situ hybridization (FISH) using the AML1/ETO probe demonstrated a recombination of both genes on an add(8) chromosome. The use of other FISH probes (CEP8, c-myc and TEL21) and spectral karyotyping indicated that AML1/ETO fusion occurred as a consequence of a previously undescribed ins(8;21)(q22;q22.1q22.3).

  2. Cytogenetic, FISH and molecular characterization of 3q27/BCL-6 rearrangements in NHL

    SciTech Connect

    Wiodarska, I.; Styl, M.; Mecucci, C.

    1994-09-01

    Reciprocal translocations involving the chromosomal region 3q27 and one of the immunoglobulin loci at 14q32, 2p12 or 22q11 have been identified as the third most common type of chromosomal abnormality in Non Hodgkin`s lymphomas (NHLs), in addition to t(14;18) and t(8;14). These abnormalities appeared to be strongly associated with a diffuse, large cell subtype of B-cell NHL. Recently, a t(3;14) and t(3;22) have been cloned and a new transcriptional unit at 3q27, designated BCL-5, BCL-6 or LAZ3, has been identified. The gene appears to encode a new zinc finger protein with the putative function of a transcription factor. Rearrangements of the BCL-6 gene have been detected not only in cases with a typical t(3;14), t(2;3) and t(3;22), but also in a few NHL cases carrying 3q27 translocations not involving Ig genes. We report on nine B-NHL cases with a 3q27/BCL-6 rearrangement demonstrated by cytogenetic, FISH, and Southern analysis. Cytogenetic analysis complemented by FISH studies showed the presence of a classical t(3;14) or a t(3;22) in three cases and a variety of chromosomal aberrations involving the 3q27 locus in the remaining cases. Some of these translocations were not previously identified by conventional banding analysis. In three patients chromosome painting demonstrated involvement of both chromosome at the 3q24 band. We conclude: 3q27/BCL-6 rearrangements seem not to be restricted to diffuse large cell lymphoma. We here documented 3q27/BCL-6 abnormalities in Richter syndrome and follicular lymphomas. The variety of 3q27 aberrations at cytogenetic level suggests that, in addition to immunoglobulin genes, a number of other genes spreading over the human genome may deregulate BCL-6 in lymphomas. Chromosome painting is a powerful tool to demonstrate 3q27 abnormalities, not identified by conventional banding analysis.

  3. Identification and molecular cytogenetic characterization of a novel complex Y chromosome rearrangement in a boy with disorder of sexual development.

    PubMed

    Dutta, Usha R; Pidugu, Vijaya Kumar; Goud, Ch Venkateshwar; Hoefers, Christiane; Hagemann, Monika; Dalal, Ashwin

    2013-05-01

    Ambiguous genitalia or disorder of the sexual development is a birth defect where the external genitals do not have the typical appearance of either a male or female. Here we report a boy with ambiguous genitalia and short stature. The cytogenetic analysis by G-banding revealed a small Y chromosome and an additional material on the 15p arm. Further, molecular cytogenetic analysis by Fluorescence in situ hybridization (FISH) using whole chromosome paint probes showed the presence of Y sequences on the 15p arm, confirming that it is a Y;15 translocation. Subsequent, FISH with centromere probe Y showed two signals depicting the presence of two centromeres and differing with a balanced translocation. The dicentric nature of the derivative 15 chromosome was confirmed by FISH with both 15 and Y centromeric probes. Further, the delineation of the Y chromosomal DNA was also done by quantitative real time PCR. Additional Y-short tandem repeat typing was performed to find out the extent of deletion on small Y chromosome. Fine mapping was carried out with 8 Y specific BAC clones which helped in defining the breakpoint regions. MLPA was performed to check the presence or absence of subtelomeric regions and SHOX regions on Y. Finally array CGH helped us in confirming the breakpoint regions. In our study we identified and characterized a novel complex Y chromosomal rearrangement with a complete deletion of the Yq region and duplication of the Yp region with one copy being translocated onto the15p arm. This is the first report of novel and unique Y complex rearrangement showing a deletion, duplication and a translocation in the same patient. The possible mechanism of the rearrangement and the phenotype-genotype correlation are discussed.

  4. Molecular cytogenetic characterisation of a mosaic add(12)(p13.3) with an inv dup(3)(q26.31 → qter) detected in an autistic boy

    PubMed Central

    Carreira, Isabel M; Melo, Joana B; Rodrigues, Carlos; Backx, Liesbeth; Vermeesch, Joris; Weise, Anja; Kosyakova, Nadezda; Oliveira, Guiomar; Matoso, Eunice

    2009-01-01

    Background Inverted duplications (inv dup) of a terminal chromosome region are a particular subset of rearrangements that often results in partial tetrasomy or partial trisomy when accompanied by a deleted chromosome. Associated mosaicism could be the consequence of a post-zygotic event or could result from the correction of a trisomic conception. Tetrasomies of distal segments of the chromosome 3q are rare genetic events and their phenotypic manifestations are diverse. To our knowledge, there are only 12 cases reported with partial 3q tetrasomy. Generally, individuals with this genomic imbalance present mild to severe developmental delay, facial dysmorphisms and skin pigmentary disorders. Results We present the results of the molecular cytogenetic characterization of an unbalanced mosaic karyotype consisting of mos 46,XY,add(12)(p13.3) [56]/46,XY [44] in a previously described 11 years old autistic boy, re-evaluated at adult age. The employment of fluorescence in situ hybridization (FISH) and multicolor banding (MCB) techniques identified the extra material on 12p to be derived from chromosome 3, defining the additional material on 12p as an inv dup(3)(qter → q26.3::q26.3 → qter). Subsequently, array-based comparative genomic hybridization (aCGH) confirmed the breakpoint at 3q26.31, defining the extra material with a length of 24.92 Mb to be between 174.37 and 199.29 Mb. Conclusion This is the thirteenth reported case of inversion-duplication 3q, being the first one described as an inv dup translocated onto a non-homologous chromosome. The mosaic terminal inv dup(3q) observed could be the result of two proposed alternative mechanisms. The most striking feature of this case is the autistic behavior of the proband, a characteristic not shared by any other patient with tetrasomy for 3q26.31 → 3qter. The present work further illustrates the advantages of the use of an integrative cytogenetic strategy, composed both by conventional and molecular techniques, on

  5. Cancer Cytogenetics: Methodology Revisited

    PubMed Central

    2014-01-01

    The Philadelphia chromosome was the first genetic abnormality discovered in cancer (in 1960), and it was found to be consistently associated with CML. The description of the Philadelphia chromosome ushered in a new era in the field of cancer cytogenetics. Accumulating genetic data have been shown to be intimately associated with the diagnosis and prognosis of neoplasms; thus, karyotyping is now considered a mandatory investigation for all newly diagnosed leukemias. The development of FISH in the 1980s overcame many of the drawbacks of assessing the genetic alterations in cancer cells by karyotyping. Karyotyping of cancer cells remains the gold standard since it provides a global analysis of the abnormalities in the entire genome of a single cell. However, subsequent methodological advances in molecular cytogenetics based on the principle of FISH that were initiated in the early 1990s have greatly enhanced the efficiency and accuracy of karyotype analysis by marrying conventional cytogenetics with molecular technologies. In this review, the development, current utilization, and technical pitfalls of both the conventional and molecular cytogenetics approaches used for cancer diagnosis over the past five decades will be discussed. PMID:25368816

  6. Cytogenetic and molecular characteristics of 25 Chilean patients with a variant Ph translocation.

    PubMed

    Legues, Maria E; Encina, Andrea; Valenzuela, Mercedes; Palma, Tamara; Undurraga, Maria S

    2011-07-01

    Chronic myeloid leukemia (CML) is characterized by the presence of the Philadelphia chromosome (Ph), which results from a balanced translocation between chromosomes 9 and 22, the t(9;22)(q34;q11.2). In 5-10% of the cases, variants of the Ph (vPh) are detected, involving various breakpoints in addition to 9q34 and 22q11.2. Deletions on the der(9) and der(22) can be detected in approximately 10-15% of CML patients. The frequency of a deletion of the der(9) in vPh CML is variable. Most studies have shown high frequencies (30-45%) in this subgroup. We report the cytogenetic evaluation of 25 vPh cases, which represents 6.8% of the CML cases diagnosed at one institution in 20 years. The breakpoints of the partners of the vPh in our patients agree with those reported previously, except for a novel 18q23. We found a low incidence of deletions of the der(9) (10%) and der(22) (5%) in these patients, contrasting with several reports in the literature. This finding may reflect the extensive spectrum of aberrations in vPh, and the possibility that a considerable group of these aberrations may not affect the genetic stability of 5'ABL1 and 3'BCR. Epidemiologic differences may also exist and could explain our results. These differences would require further investigation. PMID:21872829

  7. Molecular cytogenetic insights to the phylogenetic affinities of the giraffe (Giraffa camelopardalis) and pronghorn (Antilocapra americana).

    PubMed

    Cernohorska, Halina; Kubickova, Svatava; Kopecna, Olga; Kulemzina, Anastasia I; Perelman, Polina L; Elder, Frederick F B; Robinson, Terence J; Graphodatsky, Alexander S; Rubes, Jiri

    2013-08-01

    Five families are traditionally recognized within higher ruminants (Pecora): Bovidae, Moschidae, Cervidae, Giraffidae and Antilocapridae. The phylogenetic relationships of Antilocapridae and Giraffidae within Pecora are, however, uncertain. While numerous fusions (mostly Robertsonian) have accumulated in the giraffe's karyotype (Giraffa camelopardalis, Giraffidae, 2n = 30), that of the pronghorn (Antilocapra americana, Antilocapridae, 2n = 58) is very similar to the hypothesised pecoran ancestral state (2n = 58). We examined the chromosomal rearrangements of two species, the giraffe and pronghorn, using a combination of fluorescence in situ hybridization painting probes and BAC clones derived from cattle (Bos taurus, Bovidae). Our data place Moschus (Moschidae) closer to Bovidae than Cervidae. Although the alternative (i.e., Moschidae + Cervidae as sister groups) could not be discounted in recent sequence-based analyses, cytogenetics bolsters conclusions that the former is more likely. Additionally, DNA sequences were isolated from the centromeric regions of both species and compared. Analysis of cenDNA show that unlike the pronghorn, the centromeres of the giraffe are probably organized in a more complex fashion comprising different repetitive sequences specific to single chromosomal pairs or groups of chromosomes. The distribution of nucleolar organiser region (NOR) sites, often an effective phylogenetic marker, were also examined in the two species. In the giraffe, the position of NORs seems to be autapomorphic since similar localizations have not been found in other species within Pecora. PMID:23896647

  8. Development of new techniques of using irradiation in the genetic improvement of warm season grasses, the assessment of their genetic and cytogenetic effects and biomass production from grass. Annual progress report, November 1, 1979 to October 31, 1980

    SciTech Connect

    Burton, G W; Hanna, W W

    1980-01-01

    New techniques are described for using irradiation and chemical mutagens in the genetic improvement of several warm season grasses. Genetic and cytogenetic effects of these treatments are also being studied. (ACR)

  9. Delayed cytogenetic and major molecular responses associated to increased BMI at baseline in chronic myeloid leukemia patients treated with imatinib.

    PubMed

    Breccia, Massimo; Loglisci, Giuseppina; Salaroli, Adriano; Serrao, Alessandra; Mancini, Marco; Diverio, Daniela; Latagliata, Roberto; Alimena, Giuliana

    2013-06-01

    Obesity, measured as body mass index (BMI), has been identified as a possible risk factor for several solid tumors as well as for chronic myeloid leukemia (CML). To date, no correlations have been reported in this latter disease between BMI at baseline and response to targeted therapies. We refer here on the impact of BMI on clinical response in 339 chronic phase (CP) CML patients treated with imatinib and 35 CP-CML patients treated frontline with nilotinib. If compared to patients with low BMI (<18.5-25), patients with increased BMI (>25-40) at diagnosis who received imatinib showed a significantly longer median time to achieve complete cytogenetic response (6.8 months vs 3.3 months, p=0.001), a reduced rate of major molecular response (77% vs 58%, p=0.01) which was also achieved in a longer median time (29 months compared to 14 months, p=0.01). Conversely, no differences were revealed with respect to BMI in patients treated frontline with nilotinib and also patients with increased BMI obtained rapidly CCyR and MMR with an incidence similar to that of underweight/normal weight patients. These results suggest that CML patients with increased weight at baseline should be followed and carefully monitored if treated with standard dose imatinib frontline for a possible early switch.

  10. Molecular Cytogenetics in Digenean Parasites: Linked and Unlinked Major and 5S rDNAs, B Chromosomes and Karyotype Diversification.

    PubMed

    García-Souto, Daniel; Pasantes, Juan J

    2015-01-01

    Digenetic trematodes are the largest group of internal metazoan parasites, but their chromosomes are poorly studied. Although chromosome numbers and/or karyotypes are known for about 300 of the 18,000 described species, molecular cytogenetic knowledge is mostly limited to the mapping of telomeric sequences and/or of major rDNA clusters in 9 species. In this work we mapped major and 5S rDNA clusters and telomeric sequences in chromosomes of Bucephalus minimus, B. australis, Prosorhynchoides carvajali (Bucephaloidea), Monascus filiformis (Gymnophalloidea), Parorchis acanthus (Echinostomatoidea), Cryptocotyle lingua (Opisthorchioidea), Cercaria longicaudata, Monorchis parvus (Monorchioidea), Diphterostomum brusinae, and Bacciger bacciger (Microphalloidea). Whilst single major and minor rDNA clusters were mapped to different chromosome pairs in B. minimus and P. acanthus, overlapping signals were detected on a single chromosome pair in the remaining taxa. FISH experiments using major rDNA and telomeric probes clearly demonstrated the presence of highly stretched NORs in most of the digenean taxa analyzed. B chromosomes were detected in the B. bacciger samples hosted by Ruditapes decussatus. Although the cercariae specimens obtained from Donax trunculus, Tellina tenuis, and R. decussatus were in agreement with B. bacciger, their karyotypes showed striking morphological differences in agreement with the proposed assignation of these cercariae to different species of the genus Bacciger. Results are discussed in comparison with previous data on digenean chromosomes. PMID:26680763

  11. Rapid molecular cytogenetic analysis of X-chromosomal microdeletions: Fluorescence in situ hybridization (FISH) for complex glycerol kinase deficiency

    SciTech Connect

    Worley, K.C.; Lindsay, E.A.; McCabe, E.R.B.

    1995-07-17

    Diagnosis of X-chromosomal microdeletions has relied upon the traditional methods of Southern blotting and DNA amplification, with carrier identification requiring time-consuming and unreliable dosage calculations. In this report, we describe rapid molecular cytogenetic identification of deleted DNA in affected males with the Xp21 contiguous gene syndrome (complex glycerol kinase deficiency, CGKD) and female carriers for this disorder. CGKD deletions involve the genes for glycerol kinase, Duchenne muscular dystrophy, and/or adrenal hypoplasia congenita. We report an improved method for diagnosis of deletions in individuals with CGKD and for identification of female carriers within their families using fluorescence in situ hybridization (FISH) with a cosmid marker (cosmid 35) within the glycerol kinase gene. When used in combination with an Xq control probe, affected males demonstrate a single signal from the control probe, while female carriers demonstrate a normal chromosome with two signals, as well as a deleted chromosome with a single signal from the control probe. FISH analysis for CGKD provides the advantages of speed and accuracy for evaluation of submicroscopic X-chromosome deletions, particularly in identification of female carriers. In addition to improving carrier evaluation, FISH will make prenatal diagnosis of CGKD more readily available. 17 refs., 2 figs.

  12. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques

    PubMed Central

    2013-01-01

    Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries. PMID:24191931

  13. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques.

    PubMed

    Yangquanwei, Zhong; Neethirajan, Suresh; Karunakaran, Chithra

    2013-01-01

    Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.

  14. Cytogenetic analysis of quinoa chromosomes using nanoscale imaging and spectroscopy techniques

    NASA Astrophysics Data System (ADS)

    Yangquanwei, Zhong; Neethirajan, Suresh; Karunakaran, Chithra

    2013-11-01

    Here we present a high-resolution chromosomal spectral map derived from synchrotron-based soft X-ray spectromicroscopy applied to quinoa species. The label-free characterization of quinoa metaphase chromosomes shows that it consists of organized substructures of DNA-protein complex. The analysis of spectra of chromosomes using the scanning transmission X-ray microscope (STXM) and its superposition of the pattern with the atomic force microscopy (AFM) and scanning electron microscopy (SEM) images proves that it is possible to precisely locate the gene loci and the DNA packaging inside the chromosomes. STXM has been successfully used to distinguish and quantify the DNA and protein components inside the quinoa chromosomes by visualizing the interphase at up to 30-nm spatial resolution. Our study represents the successful attempt of non-intrusive interrogation and integrating imaging techniques of chromosomes using synchrotron STXM and AFM techniques. The methodology developed for 3-D imaging of chromosomes with chemical specificity and temporal resolution will allow the nanoscale imaging tools to emerge from scientific research and development into broad practical applications such as gene loci tools and biomarker libraries.

  15. Relevance of Stereotyped B-Cell Receptors in the Context of the Molecular, Cytogenetic and Clinical Features of Chronic Lymphocytic Leukemia

    PubMed Central

    Fabris, Sonia; Colombo, Monica; Tuana, Giacomo; Agnelli, Luca; Matis, Serena; Lionetti, Marta; Gentile, Massimo; Recchia, Anna Grazia; Di Raimondo, Francesco; Musolino, Caterina; Ilariucci, Fiorella; Di Renzo, Nicola; Pesce, Emanuela; Molica, Stefano; Federico, Massimo; Cortelezzi, Agostino; Morabito, Fortunato; Ferrarini, Manlio; Neri, Antonino

    2011-01-01

    Highly homologous B-cell receptors, characterized by non-random combinations of immunoglobulin heavy-chain variable (IGHV) genes and heavy-chain complementarity determining region-3 (HCDR3), are expressed in a recurrent fraction of patients affected by chronic lymphocytic leukemia (CLL). We investigated the IGHV status of 1131 productive IG rearrangements from a panel of 1126 CLL patients from a multicenter Italian study group, and correlated the presence and class of HCDR3 stereotyped subsets with the major cytogenetic alterations evaluated by FISH, molecular prognostic factors, and the time to first treatment (TTFT) of patients with early stage disease (Binet A). Stereotyped HCDR3 sequences were found in 357 cases (31.7%), 231 of which (64.7%) were unmutated. In addition to the previously described subsets, 31 new putative stereotypes subsets were identified. Significant associations between different stereotyped HCDR3 sequences and molecular prognostic factors, such as CD38 and ZAP-70 expression, IGHV mutational status and genomic abnormalities were found. In particular, deletion of 17p13 was significantly represented in stereotype subset #1. Notably, subset #1 was significantly correlated with a substantially reduced TTFT compared to other CLL groups showing unmutated IGHV, ZAP-70 or CD38 positivity and unfavorable cytogenetic lesions including del(17)(p13). Moreover, subset #2 was strongly associated with deletion of 13q14, subsets #8 and #10 with trisomy 12, whereas subset #4 was characterized by the prevalent absence of the common cytogenetic abnormalities. Our data from a large and representative panel of CLL patients indicate that particular stereotyped HCDR3 sequences are associated with specific cytogenetic lesions and a distinct clinical outcome. PMID:21897877

  16. Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

    PubMed

    Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

    2004-01-01

    To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented.

  17. Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

    PubMed

    Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

    2004-01-01

    To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented. PMID:15218250

  18. Distal monosomy 16p13.3/distal trisomy 2p24.2-pter: molecular-cytogenetic characterisation and phenotype.

    PubMed

    Mach, M; Windpassinger, C; Wagner, K; Kroisel, P M; Petek, E

    2007-01-01

    We describe a 4-year-old boy with various facial dysmorphic features such as downslanting palpebral fissures, ptosis, hypertelorism, broad nasal bridge, small and low-set ears, broad philtrum, and micrognathia. In addition, profound mental retardation, myopia, muscular hypotonia as well as genital and cardiovascular abnormalities are also present. Refinement of the breakpoints by cytogenetic techniques, in particular the increase of banding resolution in conventional cytogenetic analysis, has enabled the correct diagnosis, as proven by fluorescence in situ hybridisation (FISH) using whole chromosome painting and single copy probes. We were able to demonstrate an unbalanced translocation that the patient inherited from his father resulting in a submicroscopic monosomy 16p13.3 and a trisomy 2p24.2-pter.

  19. Cytogenetic and molecular delineation of the smallest commonly deleted region of chromosome 5 in malignant myeloid diseases.

    PubMed Central

    Le Beau, M M; Espinosa, R; Neuman, W L; Stock, W; Roulston, D; Larson, R A; Keinanen, M; Westbrook, C A

    1993-01-01

    Loss of a whole chromosome 5 or a deletion of its long arm (5q) is a recurring abnormality in malignant myeloid neoplasms. To determine the location of genes on 5q that may be involved in leukemogenesis, we examined the deleted chromosome 5 homologs in a series of 135 patients with malignant myeloid diseases. By comparing the breakpoints, we identified a small segment of 5q, consisting of band 5q31, that was deleted in each patient. This segment has been termed the critical region. Distal 5q contains a number of genes encoding growth factors, hormone receptors, and proteins involved in signal transduction or transcriptional regulation. These include several genes that are good candidates for a tumor-suppressor gene, as well as the genes encoding five hematopoietic growth factors (CSF2, IL3, IL4, IL5, and IL9). By using fluorescence in situ hybridization, we have refined the localization of these genes to 5q31.1 and have determined the order of these genes and of other markers within 5q31. By hybridizing probes to metaphase cells with overlapping deletions involving 5q31, we have narrowed the critical region to a small segment of 5q31 containing the EGR1 gene. The five hematopoietic growth factor genes and seven other genes are excluded from this region. The EGR1 gene was not deleted in nine other patients with acute myeloid leukemia who did not have abnormalities of chromosome 5. By physical mapping, the minimum size of the critical region was estimated to be 2.8 megabases. This cytogenetic map of 5q31, together with the molecular characterization of the critical region, will facilitate the identification of a putative tumor-suppressor gene in this band. PMID:8516290

  20. Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

    PubMed Central

    Nie, Wenhui; Fu, Beiyuan; O'Brien, Patricia CM; Wang, Jinhuan; Su, Weiting; Tanomtong, Alongkoad; Volobouev, Vitaly; Ferguson-Smith, Malcolm A; Yang, Fengtang

    2008-01-01

    Background Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates. PMID:18452598

  1. High susceptibility of neonatal mice to molecular, biochemical and cytogenetic alterations induced by environmental cigarette smoke and light.

    PubMed

    De Flora, Silvio; D'Agostini, Francesco; Balansky, Roumen; Camoirano, Anna; Cartiglia, Cristina; Longobardi, Mariagrazia; Travaini, Giorgia; Steele, Vernon E; Pesce, Carlo; Izzotti, Alberto

    2008-01-01

    Our recent studies have shown that both cigarette smoke and UV-containing light, which are the most widespread and ubiquitous mutagens and carcinogens in the world, cause systemic genotoxic damage in hairless mice. Further studies were designed with the aim of evaluating the induction of genotoxic and carcinogenic effects in Swiss albino mice exposed to smoke and/or light since birth. We observed that a 4-month whole-body exposure of mice to mainstream cigarette smoke, starting at birth, caused an early and potent carcinogenic response in the lung and other organs. Our further experiments showed that exposure of mice to environmental cigarette smoke, during the first 5 weeks of life, resulted in a variety of significant alterations of intermediate biomarkers, including cytogenetic damage in bone marrow and peripheral blood, formation of lipid peroxidation products, increase of bulky DNA adduct levels, induction of oxidative DNA damage, and overexpression of OGG1 gene in lung, stimulation of apoptosis, hyperproliferation and loss of Fhit protein in pulmonary alveolar macrophages and/or bronchial epithelial cells, and early histopathological alterations in the respiratory tract. Moreover, exposure of mice to UV-containing light, mimicking solar irradiation, significantly enhanced oxidative DNA damage and bulky DNA adduct levels in lung, and synergized with smoke in inducing molecular alterations in the respiratory tract. The baseline OGG1 expression in lung was particularly high at birth and decreased in post-weanling mice. Oxidative DNA damage and other investigated end-points exhibited differential patterns in post-weanling mice and adult mice. The findings of these studies provide a mechanistic clue to the general concept that the neonatal period and early stages of life are critical in affecting susceptibility to carcinogens.

  2. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal

    PubMed Central

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-01-01

    Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies—IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)—were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs. PMID:26861283

  3. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal.

    PubMed

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-01-01

    Genomic diversity of Portuguese accessions of Avena species--diploid A. strigosa and hexaploids A. sativa and A. sterilis--was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species--rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies--IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)--were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs. PMID:26861283

  4. Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal.

    PubMed

    Tomás, Diana; Rodrigues, Joana; Varela, Ana; Veloso, Maria Manuela; Viegas, Wanda; Silva, Manuela

    2016-02-04

    Genomic diversity of Portuguese accessions of Avena species--diploid A. strigosa and hexaploids A. sativa and A. sterilis--was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species--rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies--IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)--were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs.

  5. Molecular cytogenetics in the monitoring of bone marrow engraftment: Pathophysiological and clinical implications

    SciTech Connect

    Gyger, M.; Lapointe, C.; Forest, L.

    1994-09-01

    1. Background: Bone marrow engraftment is mediated by stem cells with complex self-renewal, proliferative and differentiation potentials. This process is empirically documented by the progressive rise in the absolute neutrophil count occurring 2 to 3 weeks post-marrow infusion. 2. Purpose: To investigate the kinetics of early engraftment using in situ hybridization with an X and Y chromosome probe mixture in a sex-mismatch allogeneic setting. 3. Methods: Interphase cells from peripheral blood smears consisting of 98% pure granulocytic and lymphocytic populations were studied according to the following time frame: (a) 2 HR before marrow infusion, 12, 24, 48, 72 and 96 HR post-infusion in 3 pts (b) 5, 10, 15, 20, 25 and 50 days posttransplantation in 4 pts. The X and Y chromosome probes were indirectly labeled with different colour fluorochromes and could be observed simultaneously. The X-chromosome component was a single probe that hybridizes to the centromeric region while the Y chromosome component was a collection of probes that hybridizes to most of the Y chromosome q-arm. 4. Results: Donor neutrophils were documented as early as 12 HR post-infusion with a steady rise beginning 24 HR post. By day 5, all circulating neutrophils were of donor origin. A steady rise of donor lymphoid cells could be documented only between day 10 and 15 post-marrow infusion. By day 25 most of the lymphoid cells were of donor origin. 5. Conclusion: This molecular study reveals that donor hematopoietic cells appear very early post-marrow infusion and are presumed to be the progeny of stem cells in a late stage of differentiation, responsible for a transitory phase of engraftment. The timing of permanent engraftment remains to be determined by other molecular approaches. In situ hybridization in sexmismatch transplants can be of great clinical benefit in predicting very early graft rejection especially in the setting of unrelated donors.

  6. Comparative cytogenetics and molecular phylogeography in the group astyanax altiparanae--Astyanax aff. bimaculatus (Teleostei, Characidae).

    PubMed

    Kavalco, K F; Pazza, R; Brandão, K D O; Garcia, C; Almeida-Toledo, L F

    2011-01-01

    The genus Astyanax comprises small characin fish of the neotropical region. The so-called 'yellow-tailed characins' compose one of the most widely distributed Astyanax groups. A. altiparanae and A. aff. bimaculatus, are evolutionarily closely related and commonly found in several Brazilian hydrographic basins. In the present work, chromosomal data of specimens of A. altiparanae and A. aff. bimaculatus from 4 hydrographic basins in the states of São Paulo (Upper Tietê, Paranapanema, Ribeira de Iguape) and Rio de Janeiro (Guapimirim) are shown. All the populations showed 50 chromosomes, with different karyotypic formula. Although only a single Ag-NOR bearing chromosome pair was observed, all populations possess multiple cistrons of 18S rDNA. FISH with the 5S rDNA probe showed single signals at the interstitial position of one metacentric chromosome pair. C-bands are distributed in the terminal and interstitial regions of several chromosomes. However, the As-51 satDNA are frugally located in a few chromosomes of fishes from Upper Tietê, Paranapanema and Guapimirim Rivers, being absent in individuals of A. aff. bimaculatus from Ribeira de Iguape River basin. Beside these 4 populations, molecular phylogeography studies were also performed in individuals from Middle and Lower Tietê River basin and from 2 additional collection sites in the Paranapanema and Ribeira de Iguape River basins. The phylogeographic analysis using 2 mtDNA regions (totalizing 1.314 bp of ND2 and ATPase6/8 genes) of 8 populations of the group of 'yellow-tailed characins' from 3 major hydrographic basins showed structuring of populations, suggesting a correlation between chromosomal (nuclear) and molecular (mitochondrial) data. PMID:21447941

  7. MicroRNA expression at diagnosis adds relevant prognostic information to molecular categorization in patients with intermediate-risk cytogenetic acute myeloid leukemia.

    PubMed

    Díaz-Beyá, M; Brunet, S; Nomdedéu, J; Tejero, R; Díaz, T; Pratcorona, M; Tormo, M; Ribera, J M; Escoda, L; Duarte, R; Gallardo, D; Heras, I; Queipo de Llano, M P; Bargay, J; Monzo, M; Sierra, J; Navarro, A; Esteve, J

    2014-04-01

    Acute myeloid leukemia (AML) is a heterogeneous disease, and optimal treatment varies according to cytogenetic risk factors and molecular markers. Several studies have demonstrated the prognostic importance of microRNAs (miRNAs) in AML. Here we report a potential association between miRNA expression and clinical outcome in 238 intermediate-risk cytogenetic AML (IR-AML) patients from 16 institutions in the CETLAM cooperative group. We first profiled 670 miRNAs in a subset of 85 IR-AML patients from a single institution and identified 10 outcome-related miRNAs. We then validated these 10 miRNAs by individual assays in the total cohort and confirmed the prognostic impact of 4 miRNAs. High levels of miR-196b and miR-644 were independently associated with shorter overall survival, and low levels of miR-135a and miR-409-3p with a higher risk of relapse. Interestingly, miR-135a and miR-409-3p maintained their independent prognostic value within the unfavorable molecular subcategory (wild-type NPM1 and CEBPA and/or FLT3-ITD), and miR-644 retained its value within the favorable molecular subcategory. miR-409-3p, miR-135a, miR-196b and mir-644 arose as prognostic markers for IR-AML, both overall and within specific molecular subgroups. PMID:24072101

  8. Cytogenetic and Molecular Data Demonstrate that the Bryconinae (Ostariophysi, Bryconidae) Species from Southeastern Brazil Form a Phylogenetic and Phylogeographic Unit

    PubMed Central

    Travenzoli, Natália Martins; Silva, Priscilla Caroline; Santos, Udson; Zanuncio, José Cola; Oliveira, Claudio; Dergam, Jorge Abdala

    2015-01-01

    Brycon spp. occur in Neotropical watersheds to the west and east of the Andes, and as they are sensitive to anthropogenic changes, many these species are endangered in southeastern Brazil. Coastal rivers in southeastern Brazil are characterized by the presence of relatively few freshwater fish species and high endemism of this fauna. The objective of this study was to examine whether Brycon spp. occurring in the coastal basins of southeastern Brazil are monophyletic, using cytogenetic data, mitochondrial, and nuclear molecular markers. All the species showed a diploid number of 50 chromosomes, a conserved number within the subfamily Bryconinae. However, the karyotypic formulas were unique to most species, including Brycon devillei (26m+22sm+2st), Brycon ferox (26m+12sm+12st), Brycon insignis (22m+20sm+8st), Brycon opalinus, and Brycon vermelha (24m+20sm+6st), indicating the prevalence of pericentric and paracentric inversions in the chromosomal evolution of these species. All of them had nucleolar organizer regions in the first pair of subtelocentric chromosomes and no equilocal distribution of heterochromatin in the first pair of chromosomes of the karyotype. These two features, not seen in any other Brycon spp. examined to date, indicate that Bryconinae species from the Brazilian southeastern coastal basins, including the monotypic genus Henochilus, are monophyletic. Also, this is the first study that reports NOR location and C-banding patterns as synapomorphies for a Neotropical fish species group. The monophyly was also supported by a phylogenetic analysis of 16S rDNA (16S), cytochrome oxidase subunit I (COI), alpha-myosin (MYH6) genes and S72 intron molecular data. Our results partially corroborate the “Brycon acuminatus” group proposed by Howes in 1982: our proposed clade keeps B. devillei, B. ferox, and B. insignis; but it also includes B. opalinus, B. vermelha, and H. weatlandii whereas it excludes B. nattereri. The phylogeographic unit formed by

  9. Cytogenetic and molecular characterization of inverted duplicated chromosomes 15 from 11 patients

    SciTech Connect

    Cheng, Sou-De; Knoll, J.H.M.; Spinner, N.B.; Zackai, E.H.

    1994-10-01

    We have studied the inverted duplicated chromosomes 15 (inv dup(15)) from 11 individuals - 7 with severe mental retardation and seizures, 3 with a normal phenotype, and 1 with Prader-Willi syndrome (PWS). Through a combination of FISH and quantitative DNA analyses, three different molecular sizes of inv dup(15) were identified. The smallest inv dup(15) was positive only for the centromeric locus D15Z1 (type 1); the next size was positive for D15Z1 and D15S18 (type 2); and the largest inv dup(15) was positive for two additional copies of loci extending from D15Z1 and D15S18 through D15S12 (type 3). Type 1 or type 2 was observed in the three normal individuals and the PWS patient. Type 3 was observed in all seven individuals with mental retardation and seizures but without PWS or Angelman Syndrome (AS). The PWS patient, in addition to being mosaic for a small inv dup(15), demonstrated at D15S63 a methylation pattern consistent with material uniparental inheritance of the normal chromosomes 15. The results from this study show (a) two additional copies of proximal 15q loci, D15S9 through D15S12, in mentally retarded patients with an inv dup(15) but without AS or PWS and (b) no additional copies of these loci in patients with a normal phenotype or with PWS. 36 refs., 3 figs., 2 tabs.

  10. Cytogenetic and molecular characterization of heterochromatin gene models in Drosophila melanogaster.

    PubMed

    Rossi, Fabrizio; Moschetti, Roberta; Caizzi, Ruggiero; Corradini, Nicoletta; Dimitri, Patrizio

    2007-02-01

    In the past decade, genome-sequencing projects have yielded a great amount of information on DNA sequences in several organisms. The release of the Drosophila melanogaster heterochromatin sequence by the Drosophila Heterochromatin Genome Project (DHGP) has greatly facilitated studies of mapping, molecular organization, and function of genes located in pericentromeric heterochromatin. Surprisingly, genome annotation has predicted at least 450 heterochromatic gene models, a figure 10-fold above that defined by genetic analysis. To gain further insight into the locations and functions of D. melanogaster heterochromatic genes and genome organization, we have FISH mapped 41 gene models relative to the stained bands of mitotic chromosomes and the proximal divisions of polytene chromosomes. These genes are contained in eight large scaffolds, which together account for approximately 1.4 Mb of heterochromatic DNA sequence. Moreover, developmental Northern analysis showed that the expression of 15 heterochromatic gene models tested is similar to that of the vital heterochromatic gene Nipped-A, in that it is not limited to specific stages, but is present throughout all development, despite its location in a supposedly "silent" region of the genome. This result is consistent with the idea that genes resident in heterochromatin can encode essential functions.

  11. [Significance of molecular-cytogenetic findings in mucoepidermoid carcinoma as an example of salivary gland tumors].

    PubMed

    Röser, K; Jäkel, K T; Bullerdiek, J; Löning, T

    2005-09-01

    Chromosome translocations in tumors frequently give rise to fusion genes encoding proteins with oncogenic activities. Mucoepidermoid carcinomas (MEC) are characterized by a t(11;19)(q21-22;p13) translocation found in approximately 60% of the tumors. This t(11;19) translocation results in a fusion gene consisting of exon 1 of the MECT 1 gene and exons 2-5 of the MAML 2 gene. As a result of the t(11;19) a fusion protein is generated which, independent of NOTCH-ligands, activates the transcription of the NOTCH target gene HES 1. The altered function of MAML 2 causes a disruption of NOTCH signalling which suggests a novel mechanism of tumorigenesis. Pending the elucidation of the t(11;19) at the molecular level of an apparently identical chromosomal translocation in Warthin's tumor, the identification of the translocation in MEC by FISH- and/or RT-PCR-analyses may become important in diagnosis and might have prognostic relevance. Warthin's tumors are benign salivary gland neoplasms with a distinctive histomorphology and histogenesis completely different from MEC.

  12. Molecular cytogenetic characterisation and phylogenetic analysis of the seven cultivated Vigna species (Fabaceae).

    PubMed

    She, C-W; Jiang, X-H; Ou, L-J; Liu, J; Long, K-L; Zhang, L-H; Duan, W-T; Zhao, W; Hu, J-C

    2015-01-01

    The genomic organisation of the seven cultivated Vigna species, V. unguiculata, V. subterranea, V. angularis, V. umbellata, V. radiata, V. mungo and V. aconitifolia, was determined using sequential combined PI and DAPI (CPD) staining and dual-colour fluorescence in situ hybridisation (FISH) with 5S and 45S rDNA probes. For phylogenetic analyses, comparative genomic in situ hybridisation (cGISH) onto somatic chromosomes and sequence analysis of the internal transcribed spacer (ITS) of 45S rDNA were used. Quantitative karyotypes were established using chromosome measurements, fluorochrome bands and rDNA FISH signals. All species had symmetrical karyotypes composed of only metacentric or metacentric and submetacentric chromosomes. Distinct heterochromatin differentiation was revealed by CPD staining and DAPI counterstaining after FISH. The rDNA sites among all species differed in their number, location and size. cGISH of V. umbellata genomic DNA to the chromosomes of all species produced strong signals in all centromeric regions of V. umbellata and V. angularis, weak signals in all pericentromeric regions of V. aconitifolia, and CPD-banded proximal regions of V. mungo var. mungo. Molecular phylogenetic trees showed that V. angularis and V. umbellata were the closest relatives, and V. mungo and V. aconitifolia were relatively closely related; these species formed a group that was separated from another group comprising V. radiata, V. unguiculata ssp. sesquipedalis and V. subterranea. This result was consistent with the phylogenetic relationships inferred from the heterochromatin and cGISH patterns; thus, fluorochrome banding and cGISH are efficient tools for the phylogenetic analysis of Vigna species.

  13. Detection of circulating tumour cells in patients with breast or ovarian cancer by molecular cytogenetics

    PubMed Central

    Engel, H; Kleespies, C; Friedrich, J; Breidenbach, M; Kallenborn, A; Schöndorf, T; Kolhagen, H; Mallmann, P

    1999-01-01

    Detection of micrometastases in patients with solid tumours may aid the establishment of prognosis and development of new therapeutic approaches. This study was designed to investigate the presence and frequency of tumour cells in the peripheral blood (PB) of patients with breast or ovarian cancer by using a combination of magnetic activated cell sorting (MACS) and fluorescence in situ hybridization (FISH). Separated tumour cell and PB-samples from 48 patients (35 breast cancers, 12 ovarian tumours, one uterine sarcoma) were analysed for the presence of numerical aberrations of chromosomes 7, 12, 17 and 17 q11.2–q12. Twenty-five patients had primary disease and 23 had relapsed. The technique allows the detection of one tumour cell in 106 normal cells. Circulating tumour cells were detected in 35/48 cases (17 patients had relapsed and 13 primary carcinoma with lymph node or solid metastases) by the expression of anti-cytokeratin and the presence of numerical chromosomal abnormalities. PB-tumour cells of patients with a primary carcinoma and without solid metastases had a significantly lower percentage of chromosomal aberrations, especially for chromosome 12 (P = 0.035; P = 0.038) compared to those with relapsed disease and solid metastases. Detection and quantification of minimal residual disease may monitor the response to cytotoxic or hormonal therapy and may identify women at risk of relapse. © 1999 Cancer Research Campaign PMID:10584878

  14. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect

    Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

    2008-12-16

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  15. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect

    Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-12-04

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  16. Molecular cytogenetic search for cryptic sex chromosomes in painted turtles Chrysemys picta.

    PubMed

    Valenzuela, Nicole; Badenhorst, Daleen; Montiel, Eugenia E; Literman, Robert

    2014-01-01

    Sex determination is triggered by factors ranging from genotypic (GSD) to environmental (ESD), or both GSD + EE (GSD susceptible to environmental effects), and its evolution remains enigmatic. The presence/absence of sex chromosomes purportedly separates species at the ESD end of the continuum from the rest (GSD and GSD + EE) because the evolutionary dynamics of sex chromosomes and autosomes differ. However, studies suggest that turtles with temperature-dependent sex determination (TSD) are cryptically GSD and possess sex chromosomes. Here, we test this hypothesis in painted turtles Chrysemys picta (TSD), using comparative-genome-hybridization (CGH), a technique known to detect morphologically indistinguishable sex chromosomes in other turtles and reptiles. Our results show no evidence for the existence of sex chromosomes in painted turtles. While it remains plausible that cryptic sex chromosomes may exist in TSD turtles that are characterized by minor genetic differences that cannot be detected at the resolution of CGH, previous attempts have failed to identify sex-specific markers. Genomic sequencing should prove useful in providing conclusive evidence in this regard. If such efforts uncover sex chromosomes in TSD turtles, it may reveal the existence of a fundamental constraint for the evolution of a full spectrum of sex determination (from pure GSD to pure TSD) that is predicted theoretically. Finding sex chromosomes in ESD organisms would question whether pure ESD mechanisms exist at all in nature, or whether those systems currently considered pure ESD simply await the characterization of an underlying GSD architecture.

  17. Cytogenetic and Molecular Findings in Children with Acute Lymphoblastic Leukemia: Experience of a Single Institution in Argentina

    PubMed Central

    Coccé, Mariela C.; Alonso, Cristina N.; Rossi, Jorge G.; Bernasconi, Andrea R.; Rampazzi, Maria A.; Felice, Maria S.; Rubio, Patricia L.; Eandi Eberle, Silvia; Medina, Adriana; Gallego, Marta S.

    2015-01-01

    The purpose of the current study was to evaluate the cytogenetic findings in 1,057 children with acute lymphoblastic leukemia (ALL) referred to the cytogenetics laboratory at the Hospital de Pediatría Dr. Juan P. Garrahan, between 1991 and 2014. Chromosomal abnormalities were evaluated by G-banding and FISH. Since December 2002, RT-PCR determinations were systematically carried out for BCR-ABL1, KMT2A-AFF1, ETV6-RUNX1, and TCF3-PBX1 rearrangements in children, adding KMT2A-MLLT3 and KMT2A-MLLT1 in infants. The percentage of abnormalities detected by cytogenetics was 70.1%. Four novel abnormalities, t(2;8)(p11.2;p22), inv(4)(p16q25), t(1;7)(q25;q32), and t(5;6)(q21;q21), were found in this cohort. We compared cytogenetic and RT-PCR results for BCR-ABL1, KMT2A-AFF1 and TCF3-PBX1 rearrangements in 497 children evaluated by both methods. The results were highly concordant (p < 0.7), and interestingly, FISH was relevant to confirm G-banding findings that were discordant with RT-PCR studies. This study showed the importance of performing G-banding, FISH and RT-PCR simultaneously to improve the detection of chromosomal abnormalities considering their important value in the diagnosis and prognosis of childhood ALL patients. Finally, to the best of our knowledge, this is the first series of cytogenetic findings in children with ALL reported in Argentina. PMID:26648836

  18. Cytogenetics and cladistics.

    PubMed

    Dobigny, Gauthier; Ducroz, Jean-François; Robinson, Terence J; Volobouev, Vitaly

    2004-06-01

    Chromosomal data have been underutilized in phylogenetic investigations despite the obvious potential that cytogenetic studies have to reveal both structural and functional homologies among taxa. In large part this is associated with difficulties in scoring conventional and molecular cytogenetic information for phylogenetic analysis. The manner in which chromosomal data have been used by most authors in the past was often conceptionally flawed in terms of the methods and principles underpinning modern cladistics. We present herein a review of the different methods employed, examine their relative strengths, and then outline a simple approach that considers the chromosomal change as the character, and its presence or absence the character state. We test this using one simulated and several empirical data sets. Features that are unique to cytogenetic investigations, including B-chromosomes, heterochromatic additions/deletions, and the location and number of nucleolar organizer regions (NORs), as well as the weighting of chromosomal characters, are critically discussed with regard to their suitability for phylogenetic reconstruction. We conclude that each of these classes of data have inherent problems that limit their usefulness in phylogenetic analyses and in most of these instances, inclusion should be subject to rigorous appraisal that addresses the criterion of unequivocal homology. PMID:15503674

  19. Techniques for Molecular Imaging Probe Design

    PubMed Central

    Reynolds, Fred; Kelly, Kimberly A.

    2011-01-01

    Molecular imaging allows clinicians to visualize disease specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology; all essential to progress in molecular imaging probe development. In this review, we will discuss target selection, screening techniques and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents. PMID:22201532

  20. The use of a novel combination of diagnostic molecular and cytogenetic approaches in horses with sexual karyotype abnormalities: a rare case with an abnormal cellular chimerism.

    PubMed

    Demyda-Peyrás, S; Anaya, G; Bugno-Poniewierska, M; Pawlina, K; Membrillo, A; Valera, M; Moreno-Millán, M

    2014-05-01

    Sex chromosome aberrations are known to cause congenital abnormalities and unexplained infertility in horses. Most of these anomalies remain undiagnosed because of the complexity of the horse karyotype and the lack of specialized laboratories that can perform such diagnoses. On the other hand, the utilization of microsatellite markers is a technique widely spread in horse breeding, mostly because of their usage in parentage tests. We studied the usage of a novel combination of diagnostic approaches in the evaluation of a very uncommon case of chromosomal abnormalities in a Spanish purebred colt, primarily detected using a commercial panel of short tandem repeat (STR) makers. Based on these results, we performed a full cytogenetic analysis using conventional and fluorescent in situ hybridization techniques with individual Equus caballus chromosome X and Equus caballus chromosome Y painting probes. We also tested the presence of two genes associated with the sexual development in horses and an extra novel panel of eight microsatellite markers specifically located in the sex chromosome pair. This is the first case report of a leukocyte chimerism between chromosomally normal (64,XY) and abnormal (63,X0) cell lines in horses. Our results indicate that the use of the short tandem repeat markers as a screening technique and as a confirmation utilizing cytogenetic techniques can be used as a very interesting, easy, and nonexpensive diagnostic approach to detect chromosomal abnormalities in the domestic horse.

  1. A new case of interstitial 1q 25.3-32.1 deletion: cytogenetic analysis molecular characterization and ultrasound findings

    PubMed Central

    Libotte, Francesco; Bizzoco, Domenico; Gabrielli, Ivan; Tamburrino, Caterina; Ernandez, Cristina; Carpineto, Lorena; D’Aleo, Maria Pia; Cima, Antonella; Mesoraca, Alvaro; Cignini, Pietro; Aloisi, Alessia; Angioli, Roberto; Vitale, Salvatore Giovanni; Giorlandino, Claudio

    2015-01-01

    Introduction deletion of long arm of chromosome 1(1q-) is a rare condition. Clinical features include Dwarfism, severe mental retardation, microcephaly and short neck delineating the “intermediate 1q deletion syndrome”. Case Report we report a new case of interstitial deletion of the long arm of chromosome 1, diagnosed in a 22+3 weeks gestation fetus in which cytogenetic analysis localized a loss of genetic materials of 18Mb in the 1q25.3-32.1. Fetal ultrasound showed neurodegenerative defects resembling Dandy-Walker’s syndrome and bilateral clubfoot. Conclusions clinical characteristics of our case are markedly mild. This suggests that the type and the extension of the mutation obtained through cytogenetic studies, CGH array and ultrasound evaluation should be taken into account for prognostic evaluation and management of these patients. PMID:26918092

  2. Loss of the Y chromosome PAR2 region and additional rearrangements in two familial cases of satellited Y chromosomes: cytogenetic and molecular analysis.

    PubMed

    Velissariou, V; Sismani, C; Christopoulou, S; Kaminopetros, P; Hatzaki, A; Evangelidou, P; Koumbaris, G; Bartsocas, C S; Stylianidou, G; Skordis, N; Diakoumakos, A; Patsalis, P C

    2007-01-01

    Two cases of rare structural aberrations of the Y chromosome were detected: a del(Y) (q12) chromosome in a child with mild dysmorphic features, obesity and psychomotor delay, and two identical satellited Y chromosomes (Yqs) in a normal twin, which were originally observed during routine prenatal diagnosis. In both cases a Yqs chromosome was detected in the father which had arisen from a reciprocal translocation involving the short arm of chromosome 15 and the heterochromatin of the long arm of the Y chromosome (Yqh). Cytogenetic and molecular studies demonstrated that in the reciprocal product of chromosomes 15 and Y PAR2 could not be detected, showing that PAR2 had been deleted. It is discussed whether the translocation of the short arm of an acrocentric chromosome to the heterochromatin of the long arm of the Y chromosome causes instability of this region which results either in loss of genetic material or interference with the normal mechanism of disjunction.

  3. Molecular cytogenetic analysis of Inv Dup(15) chromosomes, using probes specific for the Pradar-Willi/Angelman syndrome region: Clinical implications

    SciTech Connect

    Leana-Cox, J. ); Jenkins, L. ); Palmer, C.G.; Plattner, R. ); Sheppard, L. ); Flejter, W.L. ); Zackowski, J. ); Tsien, F. ); Schwartz, S. )

    1994-05-01

    Twenty-seven cases of inverted duplications of chromosome 15 (inv dup[15]) were investigated by FISH with two DNA probes specific for the Prader-Willi syndrome/Angelman syndrome (PWS/AS) region on proximal 15q. Sixteen of the marker chromosomes displayed two copies of each probe, while in the remaining 11 markers no hybridization was observed. A significant association was found between the presence of this region and an abnormal phenotype (P<.01). This is the largest study to date of inv dup(15) chromosomes, that uses molecular cytogenetic methods and is the first to report a significant association between the presence of a specific chromosomal region in such markers and an abnormal phenotype. 30 refs., 1 fig., 4 tabs.

  4. Clinical, cytogenetic, and molecular findings in a patient with a 46,XX,del(18)(q22)/46,XX,idic(18)(q22) karyotype.

    PubMed

    Rittinger, Olaf; Krabichler, Birgit; Kronberger, Gabriela; Kotzot, Dieter

    2015-11-01

    Pseudoisodicentric or asymmetrical dicentric chromosomes 18 are rare findings in clinical cytogenetics. So far, only 8 patients with breakpoints in 18q have been reported and in none of them breakpoints were narrowed down to the molecular level. Here, we describe a 17 months old girl with a perimembranous ventricular septal defect, cleft palate, and minor dysmorphism including hypertelorism, flat nose, frontal bossing and low set ears as well as mosaicism for a cell line with a pseudoisodicentric chromosome 18q and a second cell line with a terminal deletion of 11 Mb in 18q22.2→qter. SNP-array investigation revealed a symmetric breakpoint in 18q22.2 and most likely postzygotic formation from the maternal chromosome 18. Clinical findings in all patients reported so far as well as in the patient presented here were in part overlapping with the clinical phenotypes of trisomy 18 and partial monosomy 18q.

  5. Molecular cytogenetic analysis of the crucian carp, Carassius carassius (Linnaeus, 1758) (Teleostei, Cyprinidae), using chromosome staining and fluorescence in situ hybridisation with rDNA probes

    PubMed Central

    Spoz, Aneta; Boron, Alicja; Porycka, Katarzyna; Karolewska, Monika; Ito, Daisuke; Abe, Syuiti; Kirtiklis, Lech; Juchno, Dorota

    2014-01-01

    Abstract The crucian carp Carassius carassius (Linnaeus, 1758) is a species with restricted and decreasing distribution in Europe. Six males and six females of the species from the Baltic Sea basin in Poland were examined to show sequentially CMA3/AgNO3 staining pattern, DAPI staining, and, for the first time in literature, molecular cytogenetic analysis using double-colour fluorescence in situ hybridisation (FISH) with 28S and 5S rDNA probes. The karyotype consisted of 20 m, 36 sm and 44 sta chromosomes, NF=156. The AgNO3 stained NORs were most frequently located terminally in the short arms of two sm and two sta elements, and CMA3-positive sites were also observed suggesting abundant GC-rich repetitive DNA in the regions. Other CMA3-positive sites in the short arms of six to ten sm and sta chromosomes were detected. The results based on 28S rDNA FISH confirmed the location of rDNA sites. DAPI-negative staining of NORs suggested the scarcity of AT-rich DNA in the regions. FISH with 5S rDNA probe revealed 8–14 loci (ten and 12 in respectively 49 and 29% of metaphases). They were located in two sm and eight to ten sta chromosomes and six of them were larger than others. Simultaneously, mapping of the two rDNA families on the chromosomes of C. carassius revealed that both 28S and 5S rDNA probes were located in different chromosomes. Molecular cytogenetic data of C. carassius presented here for the first time give an important insight into the structure of chromosomes of this polyploid and declining species and may be useful in its systematics. PMID:25349674

  6. Molecular and cytogenetic studies of an X; autosome translocation in a patient with premature ovarian failure and review of the literature

    SciTech Connect

    Powell, C.M.; Wangsa, D.; Nelson, L.M.; White, B.J.

    1994-08-01

    We have identified a patient with premature ovarian failure (POF) and a balanced X;autosome translocation: 46,X,t(X;6)(q13.3 or q21;p12) using high-resolution cytogenetic analysis and FISH. BrdU analysis showed that her normal X was late-replicating and translocated X earlier-replicating which is typical of balanced X;autosome rearrangements. Molecular studies were done to characterize the breakpoint on Xq and to determine the parental origin. PCR probes of tetranucleotide and dinucleotide repeat polymorphisms, and genomic probes were used to study DNA from the patient, her chromosomally normal parents and brother, and somatic cell hybrids containing each translocation chromosome. The translocation is paternally derived and is localized to Xq13.3-proximal Xq21.1, between PGK1 and DXS447 loci, a distance of 0.1 centimorgans. A {open_quotes}critical region{open_quotes} for normal ovarian function has been proposed for Xq13-q26 based on cytogenetic and clinical studies of patients with X;autosome translocations. Few cases have had molecular characterization of the breakpoints to further define the region. While translocations in the region may lead to ovarian dysfunction by disrupting normal meiosis or by a position effect, two recent reports of patients with premature ovarian failure and Xq deletions suggest that there is a gene (POF1) localized to Xq21.3-q27 or within Xq26.1-q27 responsible for POF. We now propose that there may be a second gene for POF (POF2) located at Xq13.3-q21.1. 52 refs., 5 figs., 2 tabs.

  7. An idic(15) associated with POF (premature ovarian failure): molecular cytogenetic definition of a case and review of the literature.

    PubMed

    Bertini, Veronica; Viola, David; Vitti, Paolo; Simi, Paolo; Valetto, Angelo

    2012-07-15

    We report on a 36-year-old infertile woman, presenting a premature ovarian failure with an otherwise normal female phenotype. Cytogenetic analyses showed the presence of a supernumerary marker chromosome, that was characterized by FISH (fluorescent in situ hybridization) and array CGH (comparative genomic hybridization). This marker chromosome was derived from chromosome 15, and contained only heterochromatic material. The Prader Willi/Angelman region was not present. No duplications of the 15q regions were detected by array CGH. Supernumerary markers of chromosome 15 have been reported in cases of infertility and amenorrhea, that is also described in cases with marker derived by other acrocentric chromosomes. The case here presented constitutes a further example that etiology of POF is not always associated with a defective gene, but in some cases oocytes atresia can be the consequence of the abnormal meiotic pairing of chromosomes.

  8. Early molecular and cytogenetic response is predictive for long-term progression-free and overall survival in chronic myeloid leukemia (CML).

    PubMed

    Hanfstein, B; Müller, M C; Hehlmann, R; Erben, P; Lauseker, M; Fabarius, A; Schnittger, S; Haferlach, C; Göhring, G; Proetel, U; Kolb, H-J; Krause, S W; Hofmann, W-K; Schubert, J; Einsele, H; Dengler, J; Hänel, M; Falge, C; Kanz, L; Neubauer, A; Kneba, M; Stegelmann, F; Pfreundschuh, M; Waller, C F; Branford, S; Hughes, T P; Spiekermann, K; Baerlocher, G M; Pfirrmann, M; Hasford, J; Saußele, S; Hochhaus, A

    2012-09-01

    In the face of competing first-line treatment options for CML, early prediction of prognosis on imatinib is desirable to assure favorable survival or otherwise consider the use of a second-generation tyrosine kinase inhibitor (TKI). A total of 1303 newly diagnosed imatinib-treated patients (pts) were investigated to correlate molecular and cytogenetic response at 3 and 6 months with progression-free and overall survival (PFS, OS). The persistence of BCR-ABL transcript levels >10% according to the international scale (BCR-ABL(IS)) at 3 months separated a high-risk group (28% of pts; 5-year OS: 87%) from a group with >1-10% BCR-ABL(IS) (41% of pts; 5-year OS: 94%; P=0.012) and from a group with ≤1% BCR-ABL(IS) (31% of pts; 5-year OS: 97%; P=0.004). Cytogenetics identified high-risk pts by >35% Philadelphia chromosome-positive metaphases (Ph+, 27% of pts; 5-year OS: 87%) compared with ≤35% Ph+ (73% of pts; 5-year OS: 95%; P=0.036). At 6 months, >1% BCR-ABL(IS) (37% of pts; 5-year OS: 89%) was associated with inferior survival compared with ≤1% (63% of pts; 5-year OS: 97%; P<0.001) and correspondingly >0% Ph+ (34% of pts; 5-year OS: 91%) compared with 0% Ph+ (66% of pts; 5-year OS: 97%; P=0.015). Treatment optimization is recommended for pts missing these landmarks. PMID:22446502

  9. CYTOGENETIC AND MOLECULAR RESPONSES OF AMMONIUM SULPHATE APPLICATION FOR TOLERANCE TO EXTREME TEMPERATURES IN VICIA FABA L.

    PubMed

    Öney, S; Tabur, S; Tuna, M

    2015-01-01

    Effects of ammonium sulphate [(NH4)2SO4] on mitosis, cell cycle and chromosomes in Vicia faba L. seeds exposed to extreme temperatures were investigated using flowcytometric and cytogenetic analysis. Seeds germinated at high and low temperatures showed a signiicant decrease in mitotic index as compared to those of optimum temperature conditions. Application of 50 and 1000 µM (NH4)2SO4 were successful in alleviating the negative effects of low and high temperature on mitotic activity, respectively. 50 µM (NH4)2SO4 showed the most positive effect on cell cycle at the extreme temperatures. This concentration increased the cell division removing or decreasing the negative effects of temperature stress. Namely, the highest G2/M and S phase percentages under stress conditions were obtained with application of 50 µM (NH4)2SO4. Chromosomal aberrations were not observed in cells of seeds germinated in distilled water and also at any temperatures. However, the frequency of chromosomal aberrations increased significantly by increasing (NH4)2SO4 concentration. The highest aberration frequency in all temperature degree tested was found at 1000 µM (NH4)2SO4 concentration.

  10. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution.

    PubMed

    Razumova, Olga V; Alexandrov, Oleg S; Divashuk, Mikhail G; Sukhorada, Tatiana I; Karlov, Gennady I

    2016-05-01

    Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants. PMID:26149370

  11. Cytogenetic and molecular evaluation of centromere-associated DNA sequences from a marsupial (Macropodidae: Macropus rufogriseus) X chromosome.

    PubMed

    Bulazel, Kira; Metcalfe, Cushla; Ferreri, Gianni C; Yu, Jingwei; Eldridge, Mark D B; O'Neill, Rachel J

    2006-02-01

    The constitution of the centromeric portions of the sex chromosomes of the red-necked wallaby, Macropus rufogriseus (family Macropodidae, subfamily Macropodinae), was investigated to develop an overview of the sequence composition of centromeres in a marsupial genome that harbors large amounts of centric and pericentric heterochromatin. The large, C-band-positive centromeric region of the X chromosome was microdissected and the isolated DNA was microcloned. Further sequence and cytogenetic analyses of three representative clones show that all chromosomes in this species carry a 178-bp satellite sequence containing a CENP-B DNA binding domain (CENP-B box) shown herein to selectively bind marsupial CENP-B protein. Two other repeats isolated in this study localize specifically to the sex chromosomes yet differ in copy number and intrachromosomal distribution. Immunocytohistochemistry assays with anti-CENP-E, anti-CREST, anti-CENP-B, and anti-trimethyl-H3K9 antibodies defined a restricted point localization of the outer kinetochore at the functional centromere within an enlarged pericentric and heterochromatic region. The distribution of these repeated sequences within the karyotype of this species, coupled with the apparent high copy number of these sequences, indicates a capacity for retention of large amounts of centromere-associated DNA in the genome of M. rufogriseus.

  12. Cytologically balanced t(2; 20) in a two-generation family with Alagille syndrome: Cytogenetic and molecular studies

    SciTech Connect

    Spinner, N.B.; Genin, A.; Rand, E.B.; Fortina, P.; Semeraro, A.; Piccoli, D.A. ); Taub, R. )

    1994-08-01

    Alagille syndrome is a clinically defined, dominantly inherited disorder affecting the liver, heart, face, eye, and vertebrae. Alagille syndrome has previously been localized to the short arm of chromosome 20, on the basis of reports of a small number of patients with chromosomal deletions of 20p. The authors undertook a cytogenetic study of patients with Alagille syndrome and identified a family in which a cytologically balanced translocation between chromosomes 2 and 20, 46, XX/XY, t(2;20)(q21.3;p12), is segregating concordantly with the disease. The break-point on chromosome 20p in this t(2;20) is consistent with the shortest region of overlap demonstrated in the reported deletion patients. This is the first report of a translocation associated with 20p and Alagille syndrome, and this rearrangement confirms the location of the Alagille disease gene at 20p12. They have established a somatic cell hybrid from a lymphoblastoid cell line from one of the affected individuals that contains the derivative chromosome 20 (20qter[yields]p12::2q21.3[yields]qter) but not the derivative chromosome 2, the normal chromosome 2, or the normal chromosome 20. Southern blot and PCR analysis of probes and sequences from 20p have been studied to define the location of the translocation breakpoint. The results show that the breakpoint lies distal to D20S61 and D20S56 within band 20p12. 33 refs., 5 figs.

  13. Cytologically balanced t(2;20) in a two-generation family with alagille syndrome: cytogenetic and molecular studies.

    PubMed Central

    Spinner, N. B.; Rand, E. B.; Fortina, P.; Genin, A.; Taub, R.; Semeraro, A.; Piccoli, D. A.

    1994-01-01

    Alagille syndrome is a clinically defined, dominantly inherited disorder affecting the liver, heart, face, eye, and vertebrae. Alagille syndrome has previously been localized to the short arm of chromosome 20, on the basis of reports of a small number of patients with chromosomal deletions of 20p. We undertook a cytogenetic study of patients with Alagille syndrome and identified a family in which a cytologically balanced translocation between chromosomes 2 and 20, 46,XX/XY, t(2;20)(q21.3;p12), is segregating concordantly with the disease. The breakpoint on chromosome 20p in this t(2;20) is consistent with the shortest region of overlap demonstrated in the reported deletion patients. This is the first report of a translocation associated with 20p and Alagille syndrome, and this rearrangement confirms the location of the Alagille disease gene at 20p12. We have established a somatic cell hybrid from a lymphoblastoid cell line from one of the affected individuals that contains the derivative chromosome 20 (20qter-->p12::2q21.3-->qter) but not the derivative chromosome 2, the normal chromosome 2, or the normal chromosome 20. Southern blot and PCR analysis of probes and sequences from 20p have been studied to define the location of the translocation breakpoint. Our results show that the breakpoint lies distal to D20S61 and D20S56 within band 20p12. Images Figure 1 Figure 3 Figure 4 PMID:8037203

  14. CYTOGENETIC AND MOLECULAR RESPONSES OF AMMONIUM SULPHATE APPLICATION FOR TOLERANCE TO EXTREME TEMPERATURES IN VICIA FABA L.

    PubMed

    Öney, S; Tabur, S; Tuna, M

    2015-01-01

    Effects of ammonium sulphate [(NH4)2SO4] on mitosis, cell cycle and chromosomes in Vicia faba L. seeds exposed to extreme temperatures were investigated using flowcytometric and cytogenetic analysis. Seeds germinated at high and low temperatures showed a signiicant decrease in mitotic index as compared to those of optimum temperature conditions. Application of 50 and 1000 µM (NH4)2SO4 were successful in alleviating the negative effects of low and high temperature on mitotic activity, respectively. 50 µM (NH4)2SO4 showed the most positive effect on cell cycle at the extreme temperatures. This concentration increased the cell division removing or decreasing the negative effects of temperature stress. Namely, the highest G2/M and S phase percentages under stress conditions were obtained with application of 50 µM (NH4)2SO4. Chromosomal aberrations were not observed in cells of seeds germinated in distilled water and also at any temperatures. However, the frequency of chromosomal aberrations increased significantly by increasing (NH4)2SO4 concentration. The highest aberration frequency in all temperature degree tested was found at 1000 µM (NH4)2SO4 concentration. PMID:26638498

  15. Molecular cytogenetic analysis of monoecious hemp (Cannabis sativa L.) cultivars reveals its karyotype variations and sex chromosomes constitution.

    PubMed

    Razumova, Olga V; Alexandrov, Oleg S; Divashuk, Mikhail G; Sukhorada, Tatiana I; Karlov, Gennady I

    2016-05-01

    Hemp (Cannabis sativa L., 2n = 20) is a dioecious plant. Sex expression is controlled by an X-to-autosome balance system consisting of the heteromorphic sex chromosomes XY for males and XX for females. Genetically monoecious hemp offers several agronomic advantages compared to the dioecious cultivars that are widely used in hemp cultivation. The male or female origin of monoecious maternal plants is unknown. Additionally, the sex chromosome composition of monoecious hemp forms remains unknown. In this study, we examine the sex chromosome makeup in monoecious hemp using a cytogenetic approach. Eight monoecious and two dioecious cultivars were used. The DNA of 210 monoecious plants was used for PCR analysis with the male-associated markers MADC2 and SCAR323. All monoecious plants showed female amplification patterns. Fluorescence in situ hybridization (FISH) with the subtelomeric CS-1 probe to chromosomes plates and karyotyping revealed a lack of Y chromosome and presence of XX sex chromosomes in monoecious cultivars with the chromosome number 2n = 20. There was a high level of intra- and intercultivar karyotype variation detected. The results of this study can be used for further analysis of the genetic basis of sex expression in plants.

  16. Prenatal diagnosis of a partial trisomy 13q (q14-->qter): phenotype, cytogenetics and molecular characterization by spectral karyotyping and array comparative genomic hybridization.

    PubMed

    Machado, I N; Heinrich, J K; Campanhol, C; Rodrigues-Peres, R M; Oliveira, F M; Barini, R

    2010-03-16

    Partial trisomy 13q is an uncommon chromosomal abnormality with variable phenotypic expression. We report prenatal diagnosis of partial trisomy 13q in a fetus with partial agenesis of the cerebellar vermis, partial agenesis of the corpus callosum, hydrops and polyhydramnios. G-banding karyotyping, spectral karyotyping and array comparative genomic hybridization (aCGH) analysis of fetal blood were performed. Cytogenetic analysis of fetal blood displayed 46,XX,add(4)(q28). The parental karyotypes were normal. A girl was delivered at 34 weeks gestation; she died within 2 h. Autopsy confirmed all the prenatal findings and also showed agenesis of the diaphragm. Spectral karyotyping identified the additional material's origin as chromosome 13. aCGH was carried out and showed amplification of distal regions of the long arm of chromosome 13 from region 13q14 to qter. This is the first report of a fetus with molecular characterization of a partial trisomy 13q (q14-->qter), present as a de novo unbalanced translocation at chromosome 4q. This case demonstrates the usefulness of molecular characterization of malformed fetuses for prenatal diagnosis and counseling.

  17. Prenatal diagnosis of a partial trisomy 13q (q14-->qter): phenotype, cytogenetics and molecular characterization by spectral karyotyping and array comparative genomic hybridization.

    PubMed

    Machado, I N; Heinrich, J K; Campanhol, C; Rodrigues-Peres, R M; Oliveira, F M; Barini, R

    2010-01-01

    Partial trisomy 13q is an uncommon chromosomal abnormality with variable phenotypic expression. We report prenatal diagnosis of partial trisomy 13q in a fetus with partial agenesis of the cerebellar vermis, partial agenesis of the corpus callosum, hydrops and polyhydramnios. G-banding karyotyping, spectral karyotyping and array comparative genomic hybridization (aCGH) analysis of fetal blood were performed. Cytogenetic analysis of fetal blood displayed 46,XX,add(4)(q28). The parental karyotypes were normal. A girl was delivered at 34 weeks gestation; she died within 2 h. Autopsy confirmed all the prenatal findings and also showed agenesis of the diaphragm. Spectral karyotyping identified the additional material's origin as chromosome 13. aCGH was carried out and showed amplification of distal regions of the long arm of chromosome 13 from region 13q14 to qter. This is the first report of a fetus with molecular characterization of a partial trisomy 13q (q14-->qter), present as a de novo unbalanced translocation at chromosome 4q. This case demonstrates the usefulness of molecular characterization of malformed fetuses for prenatal diagnosis and counseling. PMID:20391329

  18. Triparental origin of triploid onion, Allium × cornutum (Clementi ex Visiani, 1842), as evidenced by molecular, phylogenetic and cytogenetic analyses

    PubMed Central

    2014-01-01

    Background Reconstruction of the parental origins of cultivated plants from wild relatives, especially after long periods of domestication, is not a trivial task. However, recent advances in molecular phylogenetics, among other approaches, have proved to be very informative in analyses of the origin and evolution of polyploid genomes. An established minor garden crop, triploid onion Allium × cornutum (Clementi ex Visiani, 1842) (2n = 3x = 24), is widespread in southeastern Asia and Europe. Our previous cytogenetic analyses confirmed its highly heterozygous karyotype and indicated its possible complex triparental genome origin. Allium cepa L. and Allium roylei Stearn were suggested as two putative parental species of A. × cornutum, whereas the third parental species remained hitherto unknown. Results Here we report the phylogenetic analyses of the internal transcribed spacers ITS1-5.8S-ITS2 of 35S rDNA and the non-transcribed spacer (NTS) region of 5S rDNA of A. × cornutum and its relatives of the section Cepa. Both ITS and NTS sequence data revealed intra-individual variation in triploid onion, and these data clustered into the three main clades, each with high sequence homology to one of three other species of section Cepa: A. cepa, A. roylei, and unexpectedly, the wild Asian species Allium pskemense B. Fedtsh. Allium pskemense is therefore inferred to be the third, so far unknown, putative parental species of triploid onion Allium × cornutum. The 35S and 5S rRNA genes were found to be localised on somatic chromosomes of A. × cornutum and its putative parental species by double fluorescent in situ hybridisation (FISH). The localisation of 35S and 5S rDNA in A. × cornutum chromosomes corresponded to their respective positions in the three putative parental species, A. cepa, A. pskemense, and A. roylei. GISH (genomic in situ hybridisation) using DNA of the three putative parental diploids corroborated the results of the phylogenetic study

  19. Molecular techniques for diagnosing prosthetic joint infections.

    PubMed

    Hartley, John C; Harris, Kathryn A

    2014-09-01

    Prosthetic joint infections (PJI) can be broadly classed into two groups: those where there is a strong clinical suspicion of infection and those with clinical uncertainty, including 'aseptic loosening'. Confirmation of infection and identification of the causative organism along with provision of antibiotic susceptibility data are important stages in the management of PJI. Conventional microbiological culture and susceptibility testing is usually sufficient to provide this. However, it may fail due to prior antimicrobial treatment or the presence of unusual and fastidious organisms. Molecular techniques, in particular specific real-time and broad-range PCR, are available for diagnostic use in suspected PJI. In this review, we describe the techniques available, their current strengths, limitations and future development. Real-time pathogen-specific and broad-range PCR (with single sequence determination) are suitable for use as part of the routine diagnostic algorithm for clinically suspected PJI. Further development of broad-range PCR with high-throughput (next-generation) sequencing is necessary to understand the microbiome of the prosthetic joint further before this technique can be used for routine diagnostics in clinically unsuspected PJI, including aseptic loosening. PMID:25135084

  20. Molecular cytogenetic characterization of Rumex papillaris, a dioecious plant with an XX/XY(1)Y (2) sex chromosome system.

    PubMed

    Navajas-Pérez, Rafael; Schwarzacher, Trude; Rejón, Manuel Ruiz; Garrido-Ramos, Manuel A

    2009-01-01

    Rumex papillaris Boiss, & Reut., an Iberian endemic, belongs to the section Acetosa of the genus Rumex whose main representative is R. acetosa L., a species intensively studied in relation to sex-chromosome evolution. Here, we characterize cytogenetically the chromosomal complement of R. papillaris in an effort to enhance future comparative genomic approaches and to better our understanding of sex chromosome structure in plants. Rumex papillaris, as is common in this group, is a dioecious species characterized by the presence of a multiple sex chromosome system (with females 2n = 12 + XX and males 2n = 12 + XY(1)Y(2)). Except for the X chromosome both Y chromosomes are the longest in the karyotype and appear heterochromatic due to the accumulation of at least two satellite DNA families, RAE180 and RAYSI. Each chromosome of pair VI has an additional major heterochromatin block at the distal region of the short arm. These supernumerary heterochromatic blocks are occupied by RAE730 satellite DNA family. The Y-related RAE180 family is also present in an additional minor autosomal locus. Our comparative study of the chromosomal organization of the different satellite-DNA sequences in XX/XY and XX/XY(1)Y(2) Rumex species demonstrates that of active mechanisms of heterochromatin amplification occurred and were accompanied by chromosomal rearrangements giving rise to the multiple XX/XY(1)Y(2) chromosome systems observed in Rumex. Additionally, Y(1) and Y(2) chromosomes have undergone further rearrangements leading to differential patterns of Y-heterochromatin distribution between Rumex species with multiple sex chromosome systems.

  1. Molecular diagnostics complementing morphology in superficial mesenchymal tumors.

    PubMed

    Cheah, Alison L; Goldblum, John R; Billings, Steven D

    2013-02-01

    Molecular techniques are increasingly important in the practice of surgical pathology. In soft tissue tumors, there are a number of tumors with recurring cytogenetic abnormalities. Knowledge of these abnormalities has furthered our understanding of these tumors and has also allowed development of molecular techniques to aid in the diagnosis. This review will focus on mesenchymal tumors with specific cytogenetic abnormalities that may present as a superficial tumor of the dermis or subcutis.

  2. Automatic Molecular Design using Evolutionary Techniques

    NASA Technical Reports Server (NTRS)

    Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

    1998-01-01

    Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.

  3. The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1.

    PubMed

    Sola-Campoy, Pedro J; Robles, Francisca; Schwarzacher, Trude; Ruiz Rejón, Carmelo; de la Herrán, Roberto; Navajas-Pérez, Rafael

    2015-01-01

    This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176-178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree.

  4. New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes for radiation molecular cytogenetics

    PubMed Central

    Repin, Mikhail V; Golubev, Pavel I; Repina, Ludmila A

    2009-01-01

    Background The objective of this work is to obtain the correct relative DNA contents of chromosomes in the normal male and female human diploid genomes for the use at FISH analysis of radiation-induced chromosome aberrations. Results The relative DNA contents of chromosomes in the male and female human diploid genomes have been calculated from the publicly available international Human Genome Project data. New sequence-based data on the relative DNA contents of human chromosomes were compared with the data recommended by the International Atomic Energy Agency in 2001. The differences in the values of the relative DNA contents of chromosomes obtained by using different approaches for 15 human chromosomes, mainly for large chromosomes, were below 2%. For the chromosomes 13, 17, 20 and 22 the differences were above 5%. Conclusion New sequence-based data on the relative DNA contents of chromosomes in the normal male and female human diploid genomes were obtained. This approach, based on the genome sequence, can be recommended for the use in radiation molecular cytogenetics. PMID:19500331

  5. Molecular cytogenetic characterization of an ins(4;X) occurring as the sole abnormality in an aggressive, poorly differentiated soft tissue sarcoma.

    PubMed

    Surace, Cecilia; Storlazzi, Clelia Tiziana; Engellau, Jacob; Domanski, Henryk A; Gustafson, Pelle; Panagopoulos, Ioannis; D'Addabbo, Pietro; Rocchi, Mariano; Mandahl, Nils; Mertens, Fredrik

    2005-11-01

    Cytogenetic and fluorescence in situ hybridization (FISH) analysis of an aggressive undifferentiated soft tissue sarcoma diagnosed as primitive neuroectodermal tumor (PNET) revealed an insertion ins(4;X)(q31-32;p11p22) as the sole aberration. To identify the molecular genetic consequences, contigs of bacterial artificial chromosomes (BACs) covering Xp11-p22 and 4q31-32 were constructed. The breakpoint in Xp22 was considered unlikely to be of pathogenetic significance, as it was very close to the Xp telomere, a region devoid of known or predicted genes. The breakpoint in Xp11 was mapped within a BAC clone containing BCOR, encoding a BCL6 (B-cell lymphoma 6)-interacting protein that may influence apoptosis, as the only known gene. FISH analysis with three overlapping clones on normal chromosomes 4 disclosed that the insertion of Xp11 material in der(4) was accompanied by a deletion of chromosome 4 material. Only a predicted gene (XM_094074) was shown to be partially included in the deletion. This gene displays a high similarity with the gene encoding the embryonic blastocoelar extracellular matrix (ECM) protein in sea urchin, which is involved in the migration of the primary mesenchyme cells during embryogenesis. Our results suggest that BCOR and/or an ECM-like protein could be involved in the pathogenesis of a subgroup of PNET or PNET-like sarcomas. PMID:16133367

  6. Molecular Cytogenetic Characterization of New Wheat-Rye 1R(1B) Substitution and Translocation Lines from a Chinese Secale cereal L. Aigan with Resistance to Stripe Rust

    PubMed Central

    Li, Zhi; Ren, Zhenglong; Tan, Feiquan; Tang, Zongxiang; Fu, Shulan; Yan, Benju; Ren, Tianheng

    2016-01-01

    Secale cereale L. has been used worldwide as a source of genes for agronomic and resistance improvement. In this study, a stable wheat-rye substitution line and 3 primary 1RS.1BL translocation lines were selected from the progeny of the crossing of the Chinese local rye Aigan variety and wheat cultivar Mianyang11. The substitution and translocation lines were identified by molecular cytogenetic analysis. PCR results, fluorescence in situ hybridization and acid polyacrylamide gel electrophoresis indicated that there were a pair of 1R chromosomes in the substitution line which have been named RS1200-3, and a pair of 1RS.1BL translocation chromosomes in the other 3 translocation lines, which have been named RT1163-4, RT1217-1, and RT1249. When inoculated with stripe rust isolates, these 4 lines expressed high resistance to several Puccinia striiformis f. sp Tritici pathotypes that are virulent on Yr9. Moreover, the different response pattern of resistance among them suggested that the diversity of resistance genes for wheat stripe rust exists in the rye. These 4 lines also showed better agronomic performances than their wheat parent. The GS indices also showed the genetic diversity of the 1RS which derived from same rye variety. The present study indicates that rye cultivars may carry untapped variations that could potentially be used for wheat improvement. PMID:27668423

  7. The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1.

    PubMed

    Sola-Campoy, Pedro J; Robles, Francisca; Schwarzacher, Trude; Ruiz Rejón, Carmelo; de la Herrán, Roberto; Navajas-Pérez, Rafael

    2015-01-01

    This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176-178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree. PMID:26633808

  8. The Molecular Cytogenetic Characterization of Pistachio (Pistacia vera L.) Suggests the Arrest of Recombination in the Largest Heteropycnotic Pair HC1

    PubMed Central

    Sola-Campoy, Pedro J.; Robles, Francisca; Schwarzacher, Trude; Ruiz Rejón, Carmelo; de la Herrán, Roberto; Navajas-Pérez, Rafael

    2015-01-01

    This paper represents the first molecular cytogenetic characterization of the strictly dioecious pistachio tree (Pistacia vera L.). The karyotype was characterized by fluorescent in situ hybridization (FISH) with probes for 5S and 45S rDNAs, and the pistachio specific satellite DNAs PIVE-40, and PIVE-180, together with DAPI-staining. PIVE-180 has a monomeric unit of 176–178 bp and high sequence homology between family members; PIVE-40 has a 43 bp consensus monomeric unit, and is most likely arranged in higher order repeats (HORs) of two units. The P. vera genome is highly heterochromatic, and prominent DAPI positive blocks are detected in most chromosomes. Despite the difficulty in classifying chromosomes according to morphology, 10 out of 15 pairs (2n = 30) could be distinguished by their unique banding patterns using a combination of FISH probes. Significantly, the largest pair, designated HC1, is strongly heteropycnotic, shows differential condensation, and has massive enrichment in PIVE-40 repeats. There are two types of HC1 chromosomes (type-I and type-II) with differing PIVE-40 hybridization signal. Only type-I/II heterozygotes and type-I homozygotes individuals were found. We speculate that the differentiation between the two HC1 chromosomes is due to suppression of homologous recombination at meiosis, reinforced by the presence of PIVE-40 HORs and differences in PIVE-40 abundance. This would be compatible with a ZW sex-determination system in the pistachio tree. PMID:26633808

  9. The use of molecular and cytogenetic methods as a valuable tool in the detection of chromosomal abnormalities in horses: a case of sex chromosome chimerism in a Spanish purebred colt.

    PubMed

    Demyda-Peyrás, S; Membrillo, A; Bugno-Poniewierska, M; Pawlina, K; Anaya, G; Moreno-Millán, M

    2013-01-01

    Chromosomal abnormalities associated to sex chromosomes are reported as a problem more common than believed to be in horses. Most of them remain undiagnosed due to the complexity of the horse karyotype and the lack of interest of breeders and veterinarians in this type of diagnosis. Approximately 10 years ago, the Spanish Purebred Breeders Association implemented a DNA paternity test to evaluate the pedigree of every newborn foal. All candidates who showed abnormal or uncertain results are routinely submitted to cytogenetical analysis to evaluate the presence of chromosomal abnormalities. We studied the case of a foal showing 3 and even 4 different alleles in several loci in the short tandem repeat (STR) -based DNA parentage test. To confirm these results, a filiation test was repeated using follicular hair DNA showing normal results. A complete set of conventional and molecular cytogenetic analysis was performed to determine their chromosomal complements. C-banding and FISH had shown that the foal presents a sex chimerism 64,XX/64,XY with a cellular percentage of approximately 70/30, diagnosed in blood samples. The use of a diagnostic approach combining routine parentage QF-PCR-based STR screening tested with classical or molecular cytogenetic analysis could be a powerful tool that allows early detection of foals that will have a poor or even no reproductive performance due to chromosomal abnormalities, saving time, efforts and breeders' resources.

  10. Molecular Technique to Understand Deep Microbial Diversity

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  11. Interphase Molecular Cytogenetic Detection Rates of Chronic Lymphocytic Leukemia-Specific Aberrations Are Higher in Cultivated Cells Than in Blood or Bone Marrow Smears.

    PubMed

    Alhourani, Eyad; Aroutiounian, Rouben; Harutyunyan, Tigran; Glaser, Anita; Schlie, Cordula; Pohle, Beate; Liehr, Thomas

    2016-08-01

    Banding cytogenetics is still the gold standard in many fields of leukemia diagnostics. However, in chronic lymphocytic leukemia (CLL), GTG-banding results are hampered by a low mitotic rate of the corresponding malignant lymphatic cells. Thus, interphase fluorescence in situ hybridization (iFISH) for the detection of specific cytogenetic aberrations is done nowadays as a supplement to or even instead of banding cytogenetics in many diagnostic laboratories. These iFISH studies can be performed on native blood or bone marrow smears or in nuclei after cultivation and stimulation by a suitable mitogen. As there are only few comparative studies with partially conflicting results for the detection rates of aberrations in cultivated and native cells, this question was studied in 38 CLL cases with known aberrations in 11q22.2, 11q22.3, 12, 13q14.3, 14q32.33, 17p13.1, or 18q21.32. The obtained results implicate that iFISH directly applied on smears is in general less efficient for the detection of CLL-specific genetic abnormalities than for cultivated cells. This also shows that applied cell culture conditions are well suited for malignant CLL cells. Thus, to detect malignant aberrant cells in CLL, cell cultivation and cytogenetic workup should be performed and the obtained material should be subjected to banding cytogenetics and iFISH. PMID:27315825

  12. Development and Molecular Cytogenetic Identification of a Novel Wheat-Leymus mollis Lm#7Ns (7D) Disomic Substitution Line with Stripe Rust Resistance.

    PubMed

    Yang, Xiaofei; Wang, Changyou; Li, Xin; Chen, Chunhuan; Tian, Zengrong; Wang, Yajuan; Ji, Wanquan

    2015-01-01

    Leymus mollis (2n = 4x = 28, NsNsXmXm) possesses novel and important genes for resistance against multi-fungal diseases. The development of new wheat-L. mollis introgression lines is of great significance for wheat disease resistance breeding. M11003-3-1-15-8, a novel disomic substitution line of common wheat cv. 7182 -L. mollis, developed and selected from the BC1F5 progeny between wheat cv. 7182 and octoploid Tritileymus M47 (2n = 8x = 56, AABBDDNsNs), was characterized by morphological and cytogenetic identification, analysis of functional molecular markers, genomic in situ hybridization (GISH), sequential fluorescence in situ hybridization (FISH)-genomic in situ hybridization (GISH) and disease resistance evaluation. Cytological observations suggested that M11003-3-1-15-8 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. The GISH investigations showed that line contained 40 wheat chromosomes and a pair of L. mollis chromosomes. EST-STS multiple loci markers and PLUG (PCR-based Landmark Unique Gene) markers confirmed that the introduced L. mollis chromosomes belonged to homoeologous group 7, it was designated as Lm#7Ns. While nulli-tetrasomic and sequential FISH-GISH analysis using the oligonucleotide Oligo-pSc119.2 and Oligo-pTa535 as probes revealed that the wheat 7D chromosomes were absent in M11003-3-1-15-8. Therefore, it was deduced that M11003-3-1-15-8 was a wheat-L. mollis Lm#7Ns (7D) disomic substitution line. Field disease resistance demonstrated that the introduced L. mollis chromosomes Lm#7Ns were responsible for the stripe rust resistance at the adult stage. Moreover, M11003-3-1-15-8 had a superior numbers of florets. The novel disomic substitution line M11003-3-1-15-8, could be exploited as an important genetic material in wheat resistance breeding programs and genetic resources. PMID:26465140

  13. Clinical, immunophenotypic, cytogenetic, and molecular genetic features in 117 adult patients with mixed-phenotype acute leukemia defined by WHO-2008 classification.

    PubMed

    Yan, Lingzhi; Ping, Nana; Zhu, Mingqing; Sun, Aining; Xue, Yongquan; Ruan, Changgeng; Drexler, Hans G; Macleod, Roderick A F; Wu, Depei; Chen, Suning

    2012-11-01

    Among 4,780 consecutive adult acute lymphoblastic/myeloblastic leukemia patients, we identified 117 (2.4%) patients with mixed-phenotype acute leukemia fulfilling WHO 2008 criteria; these were classified as: Blymphoid+ myeloid (n=64), T-lymphoid+myeloid (n=38), B+T-lymphoid (n=14) and trilineage (n=1). Of 92 patients karyotyped, 59 were abnormal and were classified as: complex (22 of 92), t(9;22)(q34;q11) (14 of 92), monosomy 7 (7 of 92), polysomy 21 (7 of 92), t(v;11q23) (4 of 92), t(10;11)(p15;q21) (3 of 92), while STIL-TAL1 fusion was detected in one (T+My) patient. After investigating common acute leukemia-related mutations in 17 genes, 12 of 31 (39%) patients were found to have at least one mutation, classified with: IKZF1 deletion (4 of 31), and EZH2 (3 of 31), ASXL1 (3 of 31), ETV6 (2 of 31), NOTCH1 (1 of 31), and TET2 (1 of 31) mutations. Array-CGH revealed genomic deletions of CDKN2A (4 of 12), IKZF1 (3 of 12), MEF2C (2 of 12), BTG1 (2 of 12), together with BCOR, EBF1, K-RAS, LEF1, MBNL1, PBX3, and RUNX1 (one of 12 each). Our results indicate that mixed-phenotype acute leukemia is a complex entity with heterogeneous clinical, immunophenotypic, cytogenetic, and molecular genetic features. PMID:22581002

  14. Molecular cytogenetic identification of a wheat-rye 1R addition line with multiple spikelets and resistance to powdery mildew.

    PubMed

    Yang, Wujuan; Wang, Changyou; Chen, Chunhuan; Wang, Yajuan; Zhang, Hong; Liu, Xinlun; Ji, Wanquan

    2016-04-01

    Alien addition lines are important for transferring useful genes from alien species into common wheat. Rye is an important and valuable gene resource for improving wheat disease resistance, yield, and environment adaptation. A new wheat-rye addition line, N9436B, was developed from the progeny of the cross of common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) cultivar Shaanmai 611 and rye (Secale cereal L., 2n = 2x = 14, RR) accession Austrian rye. We characterized this new line by cytology, genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), molecular markers, and disease resistance screening. N9436B was stable in morphology and cytology, with a chromosome composition of 2n = 42 + 2t = 22II. GISH investigations showed that this line contained two rye chromosomes. GISH, FISH, and molecular maker identification suggested that the introduced R chromosome and the missing wheat chromosome arms were 1R chromosome and 2DL chromosome arm, respectively. N9436B exhibited 30-37 spikelets per spike and a high level of resistance to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) isolate E09 at the seedling stage. N9436B was cytologically stable, had the trait of multiple spikelets, and was resistant to powdery mildew; this line should thus be useful in wheat improvement.

  15. A novel microdeletion syndrome involving 5q14.3-q15: clinical and molecular cytogenetic characterization of three patients

    PubMed Central

    Engels, Hartmut; Wohlleber, Eva; Zink, Alexander; Hoyer, Juliane; Ludwig, Kerstin U; Brockschmidt, Felix F; Wieczorek, Dagmar; Moog, Ute; Hellmann-Mersch, Birgit; Weber, Ruthild G; Willatt, Lionel; Kreiß-Nachtsheim, Martina; Firth, Helen V; Rauch, Anita

    2009-01-01

    Molecular karyotyping is being increasingly applied to delineate novel disease causing microaberrations and related syndromes in patients with mental retardation of unknown aetiology. We report on three unrelated patients with overlapping de novo interstitial microdeletions involving 5q14.3-q15. All three patients presented with severe psychomotor retardation, epilepsy or febrile seizures, muscular hypotonia and variable brain and minor anomalies. Molecular karyotyping revealed three overlapping microdeletions measuring 5.7, 3.9 and 3.6 Mb, respectively. The microdeletions were identified using single nucleotide polymorphism (SNP) arrays (Affymetrix 100K and Illumina 550K) and array comparative genomic hybridization (1 Mb Sanger array-CGH). Confirmation and segregation studies were performed using fluorescence in situ hybridization (FISH) and quantitative PCR. All three aberrations were confirmed and proven to have occurred de novo. The boundaries and sizes of the deletions in the three patients were different, but an overlapping region of around 1.6 Mb in 5q14.3 was defined. It included five genes: CETN3, AC093510.2, POLR3G, LYSMD3 and the proximal part of GPR98/MASS1, a known epilepsy gene. Haploinsufficiency of GPR98/MASS1 is probably responsible for the seizure phenotype in our patients. At least one other gene contained in the commonly deleted region, LYSMD3, shows a high level of central nervous expression during embryogenesis and is also, therefore, a good candidate gene for other central nervous system (CNS) symptoms, such as psychomotor retardation, brain anomalies and muscular hypotonia of the 5q14.3 microdeletion syndrome. PMID:19471318

  16. IDH1 and IDH2 Gene Mutations Identify Novel Molecular Subsets Within De Novo Cytogenetically Normal Acute Myeloid Leukemia: A Cancer and Leukemia Group B Study

    PubMed Central

    Marcucci, Guido; Maharry, Kati; Wu, Yue-Zhong; Radmacher, Michael D.; Mrózek, Krzysztof; Margeson, Dean; Holland, Kelsi B.; Whitman, Susan P.; Becker, Heiko; Schwind, Sebastian; Metzeler, Klaus H.; Powell, Bayard L.; Carter, Thomas H.; Kolitz, Jonathan E.; Wetzler, Meir; Carroll, Andrew J.; Baer, Maria R.; Caligiuri, Michael A.; Larson, Richard A.; Bloomfield, Clara D.

    2010-01-01

    Purpose To analyze the frequency and associations with prognostic markers and outcome of mutations in IDH genes encoding isocitrate dehydrogenases in adult de novo cytogenetically normal acute myeloid leukemia (CN-AML). Patients and Methods Diagnostic bone marrow or blood samples from 358 patients were analyzed for IDH1 and IDH2 mutations by DNA polymerase chain reaction amplification/sequencing. FLT3, NPM1, CEBPA, WT1, and MLL mutational analyses and gene- and microRNA-expression profiling were performed centrally. Results IDH mutations were found in 33% of the patients. IDH1 mutations were detected in 49 patients (14%; 47 with R132). IDH2 mutations, previously unreported in AML, were detected in 69 patients (19%; 13 with R172 and 56 with R140). R172 IDH2 mutations were mutually exclusive with all other prognostic mutations analyzed. Younger age (< 60 years), molecular low-risk (NPM1-mutated/FLT3-internal tandem duplication–negative) IDH1-mutated patients had shorter disease-free survival than molecular low-risk IDH1/IDH2-wild-type (wt) patients (P = .046). R172 IDH2-mutated patients had lower complete remission rates than IDH1/IDH2wt patients (P = .007). Distinctive microarray gene- and microRNA-expression profiles accurately predicted R172 IDH2 mutations. The highest expressed gene and microRNAs in R172 IDH2-mutated patients compared with the IDH1/IDH2wt patients were APP (previously associated with complex karyotype AML) and miR-1 and miR-133 (involved in embryonal stem-cell differentiation), respectively. Conclusion IDH1 and IDH2 mutations are recurrent in CN-AML and have an unfavorable impact on outcome. The R172 IDH2 mutations, previously unreported in AML, characterize a novel subset of CN-AML patients lacking other prognostic mutations and associate with unique gene- and microRNA-expression profiles that may lead to the discovery of novel, therapeutically targetable leukemogenic mechanisms. PMID:20368543

  17. Cytogenetic, molecular and testicular tissue studies in an infertile 45,X male carrying an unbalanced (Y;22) translocation: case report.

    PubMed

    Brisset, S; Izard, V; Misrahi, M; Aboura, A; Madoux, S; Ferlicot, S; Schoevaert, D; Soufir, J C; Frydman, R; Tachdjian, G

    2005-08-01

    (Y;autosome) translocations have been reported in association with male infertility. Different mechanisms have been suggested to explain the male infertility, such as deletion of the azoospermic factor (AZF) on the long arm of the Y chromosome, or meiosis impairment. We describe a new case with a de novo unbalanced translocation t(Y;22) and discuss the genotype-phenotype correlation. A 36 year old male with azoospermia was found to have a mosaic 45,X/46,X, + mar karyotype. Fluorescence in situ hybridization (FISH) showed the presence of a derivative Y chromosome containing the short arm, the centromere and a small proximal part of the long-arm euchromatin of the Y chromosome and the long arm of chromosome 22. The unstable small marker chromosome included the short arm and the centromere of chromosome 22. This unbalanced translocation t(Y;22)(q11.2;q11.1) generated the loss of the long arm of the Y chromosome involving a large part of AZFb, AZFc and Yq heterochromatin regions. Testicular tissue analyses showed sperm in the wet preparation. Our case shows the importance of documenting (Y;autosome) translocations with molecular and testicular tissue analyses.

  18. Cytogenetic and molecular studies of a familial paracentric inversion of Y chromosome present in a patient with ambiguous genitalia.

    PubMed

    Liou, J D; Ma, Y Y; Gibson, L H; Su, H; Charest, N; Lau, Y F; Yang-Feng, T L

    1997-05-16

    Here we describe the first reported case of a patient with a familial paracentric inversion in the long arm of the Y chromosome and ambiguous genitalia. FISH analyses with Y chromosome YACs demonstrated that the inversion breakpoints of the patients and the father's Ys appear to be the same and lie within interval 5B of the Y chromosome. PCR and sequence analysis indicated that our patient carries a normal SRY gene. For an additional comparison of the patient's inv(Y) with the father, two other Y chromosome sequences were examined. Molecular studies of this familial inverted Y chromosome showed no differences in the ZFY and TSPY genes between the father and the patient suggesting that the short arm of our patient's inv(Y) is identical to that of the patient's father. Southern analysis using a probe of the DAX-1 gene indicated that a single copy of DSS (dosage sensitive sex reversal) locus was present in the patient. Our results suggest that the abnormal sexual development in our patient is likely attributable to (an)other mechanism(s) than mutation in the SRY gene and dosage alteration of the DAX-1 gene.

  19. Clinical, molecular and cytogenetic analysis of 46, XX testicular disorder of sex development with SRY-positive

    PubMed Central

    2014-01-01

    Background To review the possible mechanisms proposed to explain the etiology of 46, XX sex reversal by investigating the clinical characteristics and their relationships with chromosomal karyotype and the SRY(sex-determining region Y)gene. Methods Five untreated 46, XX patients with SRY-positive were referred for infertility. Clinical data were collected, and Karyotype analysis of G-banding in lymphocytes and Fluorescence in situ hybridization (FISH) were performed. Genomic DNA from peripheral blood of the patients using QIAamp DNA Blood Kits was extracted. The three discrete regions, AZFa, AZFb and AZFc, located on the long arm of the Y chromosome, were performed by multiplex PCRs(Polymerase Chain Reaction) amplification. The set of PCR primers for the diagnosis of microdeletion of the AZFa, AZFb and AZFc region included: sY84, sY86, sY127, sY134, sY254, sY255, SRY and ZFX/ZFY. Results Our five patients had a lower body height. Physical examination revealed that their testes were small in volume, soft in texture and normal penis. Semen analyses showed azoospermia. All patients had a higher follicle-stimulating hormone(FSH), Luteinizing Hormone(LH) level, lower free testosterone, testosterone level and normal Estradiol, Prolactin level. Karyotype analysis of all patients confirmed 46, XX karyotype, and FISH analysis showed that SRY gene were positive and translocated to Xp. Molecular analysis revealed that the SRY gene were present, and the AZFa, AZFb and AZFc region were absent. Conclusions This study adds cases on the five new 46, XX male individuals with SRY-positive and further verifies the view that the presence of SRY gene and the absence of major regions in Y chromosome should lead to the expectance of a completely masculinised phenotype, abnormal hormone levels and infertility. PMID:25169080

  20. Prenatal diagnosis of chromosome 15 abnormalities in the Prader-Willi/Angelman syndrome region by traditional and molecular cytogenetics

    SciTech Connect

    Toth-Fejel, S.; Magenis, R.E.; Leff, S.

    1995-02-13

    With improvements in culturing and banding techniques, amniotic fluid studies now achieve a level of resolution at which the Prader-Willi syndrome (PWS) and Angelman syndrome (AS) region may be questioned. Chromosome 15 heteromorphisms, detected with Q- and R-banding and used in conjunction with PWS/AS region-specific probes, can confirm a chromosome deletion and establish origin to predict the clinical outcome. We report four de novo cases of an abnormal-appearing chromosome 15 in amniotic fluid samples referred for advanced maternal age or a history of a previous chromosomally abnormal child. The chromosomes were characterized using G-, Q-, and R-banding, as well as isotopic and fluorescent in situ hybridization of DNA probes specific for the proximal chromosome 15 long arm. In two cases, one chromosome 15 homolog showed a consistent deletion of the ONCOR PWS/AS region A and B. In the other two cases, one of which involved an inversion with one breakpoint in the PWS/AS region, all of the proximal chromosome 15 long arm DNA probes used in the in situ hybridization were present on both homologs. Clinical follow-up was not available on these samples, as in all cases the parents chose to terminate the pregnancies. These cases demonstrate the ability to prenatally diagnose chromosome 15 abnormalities associated with PWS/AS. In addition, they highlight the need for a better understanding of this region for accurate prenatal diagnosis. 41 refs., 5 figs.

  1. A simple method for fixation and microdissection of frozen fresh tissue sections for molecular cytogenetic analysis of cancers.

    PubMed

    Huang, Q; Sacks, P G; Mo, J; McCormick, S A; Iacob, C E; Guo, L; Schaefer, S; Schantz, S P

    2005-01-01

    Microdissection has been widely used for procuring DNA from specific microscopic regions of formalin fixed, paraffin embedded tissue sections. We have developed a method for fixation and microdissection of frozen fresh biopsy tissue sections. Five micrometer frozen fresh tissue sections were fixed with ethanol and stored at room temperature. Well defined regions from hematoxylin and eosin (H & E) stained or unstained sections were briefly steamed and microdissected using a needle. The dissected tissue was digested with proteinase K and DNA was isolated. Whole genome amplifications were obtained by degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) from these samples. The reliability of this technique was demonstrated by comparing conventional comparative genomic hybridization (CGH) with DOP-PCR-CGH. The advantages of this method are that frozen fresh sections can be fixed easily and stored for more than 4 years, it is easy to microdissect and pick-up very minute regions (0.1 mm(2)), and it is rapid; microdissection and purification can be accomplished within 3 h. Using DNA from microdissected sections, DOP-PCR-CGH revealed genetic abnormalities more accurately than conventional CGH. Although this novel method was demonstrated using DOP-PCR-CGH, we believe that it will be useful for other genetic analyses of specific small regions and cell populations. We also observed whether storage time, H & E staining and crude DNA extracts affected the quality of amplified DNA. DNA integrity was maintained for at least 49 months in ethanol fixed sections that were stored at room temperature, but DNA was gradually degraded after one month if the ethanol fixed sections had been H & E stained and stored. When crude DNA extracts from H & E stained sections were used, the size of the DOP-PCR product was reduced. Our study suggests that ethanol fixed tissue sections may be stored at room temperature for at least 4 years without DNA degradation, the H & E stains may

  2. Airborne myxomycete spores: detection using molecular techniques

    NASA Astrophysics Data System (ADS)

    Kamono, Akiko; Kojima, Hisaya; Matsumoto, Jun; Kawamura, Kimitaka; Fukui, Manabu

    2009-01-01

    Myxomycetes are organisms characterized by a life cycle that includes a fruiting body stage. Myxomycete fruiting bodies contain spores, and wind dispersal of the spores is considered important for this organism to colonize new areas. In this study, the presence of airborne myxomycetes and the temporal changes in the myxomycete composition of atmospheric particles (aerosols) were investigated with a polymerase chain reaction (PCR)-based method for Didymiaceae and Physaraceae. Twenty-one aerosol samples were collected on the roof of a three-story building located in Sapporo, Hokkaido Island, northern Japan. PCR analysis of DNA extracts from the aerosol samples indicated the presence of airborne myxomycetes in all the samples, except for the one collected during the snowfall season. Denaturing gradient gel electrophoresis (DGGE) analysis of the PCR products showed seasonally varying banding patterns. The detected DGGE bands were subjected to sequence analyses, and four out of nine obtained sequences were identical to those of fruiting body samples collected in Hokkaido Island. It appears that the difference in the fruiting period of each species was correlated with the seasonal changes in the myxomycete composition of the aerosols. Molecular evidence shows that newly formed spores are released and dispersed in the air, suggesting that wind-driven dispersal of spores is an important process in the life history of myxomycetes. This study is the first to detect airborne myxomycetes with the use of molecular ecological analyses and to characterize their seasonal distribution.

  3. Hybrid opto-electric techniques for molecular diagnostics

    SciTech Connect

    Haque, Aeraj Ul

    2012-01-01

    Hybrid optoelectric techniques reflect a new paradigm in microfluidics. In essence, these are microfluidic techniques that employ a synergistic combination of optical and electrical forces to enable noninvasive manipulation of fluids and/or particle-type entities at the micro/nano-scale [1]. Synergy between optical and electrical forces bestows these techniques with several unique features that are promising to bring new opportunities in molecular diagnostics. Within the scope of molecular diagnostics, several aspects of optoelectric techniques promise to play a relevant role. These include, but are not limited to, sample preparation, sorting, purification, amplification and detection.

  4. Application of molecular techniques on heterotrophic hydrogen production research.

    PubMed

    Li, R Y; Zhang, T; Fang, H H P

    2011-09-01

    This paper reviews the application of molecular techniques in heterotrophic hydrogen production studies. Commonly used molecular techniques are introduced briefly first, including cloning-sequencing after polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP), fluorescence in situ hybridization (FISH) and quantitative real-time PCR. Application of the molecular techniques in heterotrophic hydrogen production studies are discussed in details, focusing on identification of new isolates for hydrogen production, characterization of microbial compositions in bioreactors, monitoring microbial diversity variation, visualization of microbial distribution in hydrogen-producing granular sludge, and quantification of various microbial populations. Some significant findings in recent hydrogen production studies with the application of molecular techniques are discussed, followed by a research outlook of the heterotrophic biohydrogen field.

  5. Molecular cytogenetic monitoring from CD34+ peripheral blood cells in myelodysplastic syndromes: first results from a prospective multicenter German diagnostic study.

    PubMed

    Braulke, Friederike; Jung, Klaus; Schanz, Julie; Götze, Katharina; Müller-Thomas, Catharina; Platzbecker, Uwe; Germing, Ulrich; Brümmendorf, Tim H; Bug, Gesine; Ottmann, Oliver; Giagounidis, Aristoteles A N; Stadler, Michael; Hofmann, Wolf-Karsten; Schafhausen, Philippe; Lübbert, Michael; Schlenk, Richard F; Blau, Igor W; Ganster, Christina; Pfeiffer, Sebastian; Shirneshan, Katayoon; Metz, Michael; Detken, Sven; Seraphin, Jörg; Jentsch-Ullrich, Kathleen; Böhme, Angelika; Schmidt, Burkhard; Trümper, Lorenz; Haase, Detlef

    2013-08-01

    The gold standard of cytogenetic analysis in myelodysplastic syndromes (MDS) is conventional chromosome banding (CCB) analysis of bone marrow (BM) metaphases. Most aberrations can also be detected by fluorescence-in situ-hybridization (FISH). For this prospective multicenter German diagnostic study (www.clinicaltrials.gov: #NCT01355913) 360 patients, as yet, were followed up to 3 years by sequential FISH analyses of immunomagnetically enriched CD34+ peripheral blood (PB) cells using comprehensive FISH probe panels, resulting in a total number of 19,516 FISH analyses. We demonstrate that CD34+ PB FISH correlates significantly with CCB analysis and represents a feasible method for a reliable non-invasive cytogenetic monitoring from PB.

  6. Teaching Molecular Biological Techniques in a Research Content

    ERIC Educational Resources Information Center

    Stiller, John W.; Coggins, T. Chad

    2006-01-01

    Molecular biological methods, such as the polymerase chain reaction (PCR) and gel electrophoresis, are now commonly taught to students in introductory biology courses at the college and even high school levels. This often includes hands-on experience with one or more molecular techniques as part of a general biology laboratory. To assure that most…

  7. Molecular diagnosis of Prader-Willi syndrome: Comparison of cytogenetic and molecular genetic data including parent of origin dependent methylation DNA patterns

    SciTech Connect

    Butler, M.G.

    1996-01-11

    This letter to the editor discusses a recent study concerning the parent-of-origin methylation site at D15S63 and its application in molecular diagnostics confirming Prader-Willi syndrome (PWS). It concludes that more research is needed to clear up questions which remain regarding the causation of PWS. 20 refs., 1 tab.

  8. Analytical cytology applied to detection of induced cytogenetic abnormalities

    SciTech Connect

    Gray, J.W.; Lucas, J.; Straume, T.; Pinkel, D.

    1987-08-06

    Radiation-induced biological damage results in formation of a broad spectrum of cytogenetic changes such as translocations, dicentrics, ring chromosomes, and acentric fragments. A battery of analytical cytologic techniques are now emerging that promise to significantly improve the precision and ease with which these radiation induced cytogenetic changes can be quantified. This report summarizes techniques to facilitate analysis of the frequency of occurrence of structural and numerical aberrations in control and irradiated human cells. 14 refs., 2 figs.

  9. Molecular cytogenetic findings in a three-way novel variant of t(1;8;21)(p35;q22;q22): a unique relocation of the AML1/ETO fusion gene 1p35 in AML-M2.

    PubMed

    Ahmad, Firoz; Kokate, Prajakta; Chheda, Pratiksha; Dalvi, Rupa; Das, Bibhu Ranjan; Mandava, Swarna

    2008-01-15

    Acute myeloid leukemia (AML) is a malignant neoplasm of hematopoietic stem cells characterized by an abnormal proliferation of myeloid precursors, a reduced rate of apoptosis, and an arrest in cellular differentiation. The present report deals with the results of hematologic, immunophenotypic, cytogenetic, fluorescence in situ hybridization (FISH), and molecular analyses of a 53-year-old female patient diagnosed with AML-M2. Cytogenetic and FISH analysis revealed a complex translocation involving three chromosomes showing t(1;8;21)(p35;q22;q22). The observation of breakpoints at 8q22 and 21q22 suggests a rearrangement of the ETO and AML1 genes, respectively. Using a dual-color FISH test with ETO and AML1 probes, an AML1/ETO fusion signal on the derivative 1p35 instead of der(8) was demonstrated. To the best of our knowledge, this is the first report about the relocation of the AML1/ETO fusion gene to the 1p35 rather than der(8), suggesting the presence of a novel variant of t(8;21)(q22;q22) in the observed patient. PMID:18206543

  10. Uterine leiomyoma cytogenetics.

    PubMed

    Nibert, M; Heim, S

    1990-05-01

    Uterine leiomyoma--a benign smooth muscle tumor--has recently been found to contain tumor-specific chromosome aberrations. Although only normal karyotypes were detected in 50 to 80% of cytogenetically investigated tumors, 104 leiomyomas with karyotypic aberrations have already been reported. At least four cytogenetically abnormal subgroups have been identified thus far, characterized by rearrangements of 6p, del(7)(q21.2q31.2), +12, and t(12;14)(q14-15;q23-24). The remaining abnormal tumors have had various nonrecurrent anomalies. Secondary karyotypic rearrangements, sometimes including ring chromosomes, have been found in one-third and reflect clonal evolution. Occasional leiomyomas have contained multiple numerical and structural rearrangements. Though benign, these cytogenetically grossly aberrant tumors often displayed more atypical histological features than are usually seen in leiomyoma. Multiple leiomyomas have been investigated from 69 patients, with detection of chromosome anomalies in at least two separate tumors from the same uterus in ten cases. In half of these patients unrelated aberrations were found in different leiomyomas from the same uterus. On other occasions the aberrations were identical, indicating that although some uterine leiomyomas originate independently, others may develop by intra-myometrial spreading from a common neoplastic clone. Some common features are discernible between the karyotypic pictures of uterine leiomyoma and angioleiomyoma; rearrangements of 6p, 13q, and 21q have been described in both tumor types. The cytogenetic similarities so far detected between leiomyoma and the malignant muscle tumors--leiomyosarcoma and rhabdomyosarcoma--are few and may be fortuitous. The cytogenetic profiles of leiomyoma and lipoma are strikingly similar; both tumor types have nonrandom rearrangements of 12q13-15, t(12;14) in leiomyoma and t(3;12) in lipoma, as well as variant rearrangements of the same 12q segment. Both also have cytogenetic

  11. Cytogenetic analysis of three species of Pseudacteon (Diptera, Phoridae) parasitoids of the fire ants using standard and molecular techniques

    PubMed Central

    2009-01-01

    Pseudacteon flies, parasitoids of worker ants, are being intensively studied as potentially effective agents in the biological control of the invasive pest fire ant genus Solenopsis (Hymenoptera: Formicidae). This is the first attempt to describe the karyotype of P. curvatus Borgmeier, P. nocens Borgmeier and P. tricuspis Borgmeier. The three species possess 2n = 6; chromosomes I and II were metacentric in the three species, but chromosome pair III was subtelocentric in P. curvatus and P. tricuspis, and telocentric in P. nocens. All three species possess a C positive band in chromosome II, lack C positive heterochromatin on chromosome I, and are mostly differentiated with respect to chromosome III. P. curvatus and P. tricuspis possess a C positive band, but at different locations, whereas this band is absent in P. nocens. Heterochromatic bands are neither AT nor GC rich as revealed by fluorescent banding. In situ hybridization with an 18S rDNA probe revealed a signal on chromosome II in a similar location to the C positive band in the three species. The apparent lack of morphologically distinct sex chromosomes is consistent with proposals of environmental sex determination in the genus. Small differences detected in chromosome length and morphology suggests that chromosomes have been highly conserved during the evolutionary radiation of Pseudacteon. Possible mechanisms of karyotype evolution in the three species are suggested. PMID:21637448

  12. LS-CAP: an algorithm for identifying cytogenetic aberrations in hepatocellular carcinoma using microarray data.

    PubMed

    He, Xianmin; Wei, Qing; Sun, Meiqian; Fu, Xuping; Fan, Sichang; Li, Yao

    2006-05-01

    Biological techniques such as Array-Comparative genomic hybridization (CGH), fluorescent in situ hybridization (FISH) and affymetrix single nucleotide pleomorphism (SNP) array have been used to detect cytogenetic aberrations. However, on genomic scale, these techniques are labor intensive and time consuming. Comparative genomic microarray analysis (CGMA) has been used to identify cytogenetic changes in hepatocellular carcinoma (HCC) using gene expression microarray data. However, CGMA algorithm can not give precise localization of aberrations, fails to identify small cytogenetic changes, and exhibits false negatives and positives. Locally un-weighted smoothing cytogenetic aberrations prediction (LS-CAP) based on local smoothing and binomial distribution can be expected to address these problems. LS-CAP algorithm was built and used on HCC microarray profiles. Eighteen cytogenetic abnormalities were identified, among them 5 were reported previously, and 12 were proven by CGH studies. LS-CAP effectively reduced the false negatives and positives, and precisely located small fragments with cytogenetic aberrations.

  13. Prognostic Significance of the European LeukemiaNet Standardized System for Reporting Cytogenetic and Molecular Alterations in Adults With Acute Myeloid Leukemia

    PubMed Central

    Mrózek, Krzysztof; Marcucci, Guido; Nicolet, Deedra; Maharry, Kati S.; Becker, Heiko; Whitman, Susan P.; Metzeler, Klaus H.; Schwind, Sebastian; Wu, Yue-Zhong; Kohlschmidt, Jessica; Pettenati, Mark J.; Heerema, Nyla A.; Block, AnneMarie W.; Patil, Shivanand R.; Baer, Maria R.; Kolitz, Jonathan E.; Moore, Joseph O.; Carroll, Andrew J.; Stone, Richard M.; Larson, Richard A.; Bloomfield, Clara D.

    2012-01-01

    Purpose To evaluate the prognostic significance of the international European LeukemiaNet (ELN) guidelines for reporting genetic alterations in acute myeloid leukemia (AML). Patients and Methods We analyzed 1,550 adults with primary AML, treated on Cancer and Leukemia Group B first-line trials, who had pretreatment cytogenetics and, for cytogenetically normal patients, mutational status of NPM1, CEBPA, and FLT3 available. We compared complete remission (CR) rates, disease-free survival (DFS), and overall survival (OS) among patients classified into the four ELN genetic groups (favorable, intermediate-I, intermediate-II, adverse) separately for 818 younger (age < 60 years) and 732 older (age ≥ 60 years) patients. Results The percentages of younger versus older patients in the favorable (41% v 20%; P < .001), intermediate-II (19% v 30%; P < .001), and adverse (22% v 31%; P < .001) genetic groups differed. The favorable group had the best and the adverse group the worst CR rates, DFS, and OS in both age groups. Both intermediate groups had significantly worse outcomes than the favorable but better than the adverse group. Intermediate-I and intermediate-II groups in older patients had similar outcomes, whereas the intermediate-II group in younger patients had better OS but not better CR rates or DFS than the intermediate-I group. The prognostic significance of ELN classification was confirmed by multivariable analyses. For each ELN group, older patients had worse outcomes than younger patients. Conclusion The ELN classification clearly separates the genetic groups by outcome, supporting its use for risk stratification in clinical trials. Because they have different proportions of genetic alterations and outcomes, younger and older patients should be reported separately when using the ELN classification. PMID:22987078

  14. Morphology, cytogenetics and classification of MDS.

    PubMed

    Giagounidis, Aristoteles; Haase, Detlef

    2013-12-01

    Myelodysplastic syndromes are heterogeneous bone marrow diseases with a variable pathogenetic background. Cytomorphological alterations in peripheral blood films as well as bone marrow aspirates and histological findings in trephine biopsies result from cytogenetic and molecular abnormalities, epigenetic dysregulation and immune dysfunction and are key elements for setting the diagnosis of MDS. Whereas diagnosis can be made quite easily in advanced MDS this is much more difficult in early MDS, especially in cases with cytopenias or dysplasias of uncertain significance (ICUS and IDUS). Recommendations, illustrated by case reports for a stepwise annealing to the final diagnosis and exclusion of differential diagnoses are given. Furthermore, the problem of correct counting and identification of blasts is covered and features defining dysplasia in all three cell lineages are recapitulated thoroughly. Histopathology is not mandatory but has a distinct diagnostic and prognostic value especially in cases with hypoplasia or fibrosis and when the TP53 mutational status is of relevance. In up to 70% of patients with MDS clonal chromosome abnormalities can be identified which have a high impact on setting the correct diagnosis and estimation of prognosis. Incidence, type, molecular background and clinical relevance of distinct anomalies as well as cytogenetic subgroups are presented in detail and the development of the new cytogenetic prognostic scoring system as part of the IPSS-R is explained. The value of FISH-Analysis as a complementary tool for chromosome analysis in MDS is demonstrated with special emphasis on the possibility to perform frequent cytogenetic monitoring by CD34-FISH examination of peripheral blood. Finally the evolution of MDS-classification systems from FAB to WHO with a critical discussion of their shortcomings like degree of dysplasia, blast thresholds, inclusion/exclusion of CMML, and the lack of dynamic information is presented.

  15. Engineering molecular mechanics: an efficient static high temperature molecular simulation technique.

    PubMed

    Subramaniyan, Arun K; Sun, C T

    2008-07-16

    Inspired by the need for an efficient molecular simulation technique, we have developed engineering molecular mechanics (EMM) as an alternative molecular simulation technique to model high temperature (T>0 K) phenomena. EMM simulations are significantly more computationally efficient than conventional techniques such as molecular dynamics simulations. The advantage of EMM is achieved by converting the dynamic atomistic system at high temperature (T>0 K) into an equivalent static system. Fundamentals of the EMM methodology are derived using thermal expansion to modify the interatomic potential. Temperature dependent interatomic potentials are developed to account for the temperature effect. The efficiency of EMM simulations is demonstrated by simulating the temperature dependence of elastic constants of copper and nickel and the thermal stress developed in a confined copper system.

  16. Cytogenetic highlights and transitions.

    PubMed

    Spinner, Nancy B

    2016-06-01

    Medical cytogenetics, genetic diagnostics, and medical genetics had their origins in the late 1950's, as evaluation of human chromosomes became possible, and it was recognized that chromosomal abnormalities could cause a variety of clinical phenotypes. Dr. Laird Jackson began his medical and scientific career just as this field was emerging and he was an early adopter and driver of several key trends in the development of these fields, notably in the area of prenatal diagnostics. Laird's greatest impact was in his work to demonstrate the clinical utility of amniocentesis, chorionic villous sampling, and chromosomal microarray analysis for prenatal diagnosis. © 2016 Wiley Periodicals, Inc. PMID:27097074

  17. Phase behaviors of polymer solutions using molecular simulation technique.

    PubMed

    Yang, Jung Ho; Bae, Young Chan

    2008-08-14

    Phase behaviors of polymer solutions are estimated using a combination of thermodynamic models and molecular simulation technique. In general, many parameters of binary systems are determined by fitting a thermodynamic model with experimental data. In this study, we obtained all parameters using molecular simulation. To take the specific interaction into account, we assume that it only occurs between a solvent molecule and a specific group. Our results show that the theoretical treatment accounting for the specific interaction gives more accurate predictions than those without consideration of specific interaction. Also, our approach describes the phase equilibria of various polymer solutions over the entire concentration remarkably well.

  18. Comparative genomic hybridization in clinical cytogenetics

    SciTech Connect

    Bryndorf, T.; Kirchhoff, M.; Rose, H.

    1995-11-01

    We report the results of applying comparative genomic hybridization (CGH) in a cytogenetic service laboratory for (1) determination of the origin of extra and missing chromosomal material in intricate cases of unbalanced aberrations and (2) detection of common prenatal numerical chromosome aberrations. A total of 11 fetal samples were analyzed. Seven cases of complex unbalanced aberrations that could not be identified reliably by conventional cytogenetics were successfully resolved by CGH analysis. CGH results were validated by using FISH with chromosome-specific probes. Four cases representing common prenatal numerical aberrations (trisomy 21, 18, and 13 and monosomy X) were also successfully diagnosed by CGH. We conclude that CGH is a powerful adjunct to traditional cytogenetic techniques that makes it possible to solve clinical cases of intricate unbalanced aberrations in a single hybridization. CGH may also be a useful adjunct to screen for euchromatic involvement in marker chromosomes. Further technical development may render CGH applicable for routine aberration screening. 16 refs., 4 figs., 2 tabs.

  19. Molecular genetics, recombinant DNA techniques, and genetic neurological disease.

    PubMed

    Rosenberg, R N

    1984-06-01

    The molecular defects responsible for Huntington's disease, the spinocerebellar degenerations, myotonic muscular dystrophy, neurofibromatosis, and tuberous sclerosis, among other major dominant inherited diseases of the nervous system, will be identified using the new techniques of molecular genetics. With synthesized nucleic acid segments complementary to portions of the patient's DNA, known as complementary DNA probes, it will be possible to identify and isolate the mutant gene responsible for a particular disease. These events are referred to as gene cloning. In addition, complex genetic regulatory mechanisms involved in cell differentiation during neuroembryogenesis will be elucidated with the application of these strategies. It is important for the clinician to become familiar with the precision and potential of these new methodologies, because they will soon influence significantly the practice of neurology.

  20. Cytogenetic analysis of a primary salivary gland myoepithelioma.

    PubMed

    el-Naggar, A K; Lovell, M; Callender, D L; Ordonez, N G; Killary, A M

    1999-08-01

    Myoepithelioma, a rare benign salivary gland neoplasm, is a tumor composed entirely of myoepithelial cells. Unlike pleomorphic adenoma, these tumors lack any ductal epithelial differentiation, and manifest a minor stromal element. Previous cytogenetic and molecular genetic studies have mainly investigated pleomorphic adenomas and reported recurring specific chromosomal alterations at 8q12 and 12q13-q15 regions. The cell origin of these alterations, however, remains speculative. We report the cytogenetic analysis of a parotid myoepithelioma and discuss the putative origin for the cells with cytogenetic alterations. Our analysis shows 12q12 involved in a translocation with a previously unreported partner (1q), and nonrandom del(9)(q22.1q22.3) and del(13)(q12q22). Our results indicate that the myoepithelial cell is the source of those cells with chromosomal alterations, and that myoepithelioma shares 12q alterations reported in a subset of pleomorphic adenomas.

  1. Hybrid molecular-continuum techniques for micro and nano flows

    NASA Astrophysics Data System (ADS)

    Reese, Jason; Ritos, Konstantinos; Borg, Matthew; Lockerby, Duncan

    2015-11-01

    Nano- and micro-confined fluid flows are often characterised by non-continuum effects that require special treatment beyond the scope of conventional continuum-fluid modelling. However, if the flow system has high-aspect-ratio components (e.g. long narrow channels) the computational cost of a fully molecular-based simulation can be prohibitive. In this talk we present some important elements of a heterogeneous molecular-continuum method that exploits the various degrees of scale separation in both time and space that are very often present in these types of flows. We demonstrate the ability of these techniques to predict the flow of water in aligned carbon nanotube (CNT) membranes: the tube diameters are 1-2 nm and the tube lengths (i.e. the membrane thicknesses) are 2-6 orders of magnitude larger. We compare our results with experimental data. We also find very good agreement with experimental results for a 1 mm thick membrane that has CNTs of diameter 1.59 nm. In this case, our hybrid multiscale simulation is orders of magnitude faster than a full molecular dynamics simulation.

  2. Double-Edge Molecular Technique for Doppler Lidar Wind Measurement

    NASA Technical Reports Server (NTRS)

    Flesia, Cristina; Korb, C. Laurence

    1998-01-01

    The double-edge lidar technique for measuring the wind using molecular backscatter is described. Two high spectral resolution edge filters are located in the wings of the Rayleigh-Brillouin profile. This doubles the signal change per unit Doppler shift, the sensitivity, and gives nearly a factor of two improvement in measurement accuracy. The use of a crossover region is described where the sensitivity of a molecular and aerosol-based measurement are equal. This desensitizes the molecular measurement to the effects of aerosol scattering over a frequency range of +/- 100 m/s. We give methods for correcting for short-term frequency jitter and drift using a laser reference frequency measurement and methods for long-term frequency correction using a servo control system. The effects of Rayleigh-Brillouin scattering on the measurement are shown to be significant and are included in the analysis. Simulations for a conical scanning satellite-based lidar at 355 nm show an accuracy of 2-3 m/s for altitudes of 2 to 15 km for a 1 km vertical resolution, a satellite altitude of 400 km and a 200 km x 200 km spatial resolution. Results of ground based wind measurements are presented.

  3. Highly species-specific centromeric repetitive DNA sequences in lizards: molecular cytogenetic characterization of a novel family of satellite DNA sequences isolated from the water monitor lizard (Varanus salvator macromaculatus, Platynota).

    PubMed

    Chaiprasertsri, Nampech; Uno, Yoshinobu; Peyachoknagul, Surin; Prakhongcheep, Ornjira; Baicharoen, Sudarath; Charernsuk, Saranon; Nishida, Chizuko; Matsuda, Yoichi; Koga, Akihiko; Srikulnath, Kornsorn

    2013-01-01

    Two novel repetitive DNA sequences, VSAREP1 and VSAREP2, were isolated from the water monitor lizard (Varanus salvator macromaculatus, Platynota) and characterized using molecular cytogenetics. The respective lengths and guanine-cytosine (GC) contents of the sequences were 190 bp and 57.5% for VSAREP1 and 185 bp and 59.7% for VSAREP2, and both elements were tandemly arrayed as satellite DNA in the genome. VSAREP1 and VSAREP2 were each located at the C-positive heterochromatin in the pericentromeric region of chromosome 2q, the centromeric region of chromosome 5, and 3 pairs of microchromosomes. This suggests that genomic compartmentalization between macro- and microchromosomes might not have occurred in the centromeric repetitive sequences of V. salvator macromaculatus. These 2 sequences did only hybridize to genomic DNA of V. salvator macromaculatus, but no signal was observed even for other squamate reptiles, including Varanus exanthematicus, which is a closely related species of V. salvator macromaculatus. These results suggest that these sequences were differentiated rapidly or were specifically amplified in the V. salvator macromaculatus genome.

  4. The Chromosome Microdissection and Microcloning Technique.

    PubMed

    Zhang, Ying-Xin; Deng, Chuan-Liang; Hu, Zan-Min

    2016-01-01

    Chromosome microdissection followed by microcloning is an efficient tool combining cytogenetics and molecular genetics that can be used for the construction of the high density molecular marker linkage map and fine physical map, the generation of probes for chromosome painting, and the localization and cloning of important genes. Here, we describe a modified technique to microdissect a single chromosome, paint individual chromosomes, and construct single-chromosome DNA libraries. PMID:27511173

  5. Molecular cytogenetic analyses of HIG, a novel human cell line carrying t(1;3)(p36.3;q25.3) established from a patient with chronic myelogenous leukemia in blastic crisis.

    PubMed

    Hosoya, Noriko; Ogawa, Seishi; Motokura, Tohru; Hangaishi, Akira; Wang, Lili; Qiao, Ying; Nannya, Yasuhito; Kogi, Mieko; Hirai, Hisamaru

    2003-12-01

    Chromosomal abnormalities involving 1p36, 3q21, and/or 3q26 have been reported in a subset of myeloid neoplasms having characteristic dysmegakaryopoiesis, and the overexpression of EVI1 on 3q26 or of MEL1 on 1p36 has been implicated in their pathogenesis. We describe molecular cytogenetic analyses of a novel human cell line, HIG, established from a unique case in which a novel translocation t(1;3)(p36;q26) appeared as the sole additional chromosomal abnormality at the time of blastic transformation of chronic myelogenous leukemia. The patient displayed clinical features resembling those of the 3q21q26 syndrome. The HIG cell line retained der(1)t(1;3)(p36;q26) but lost t(9;22)(q34;q11). To identify the relevant gene that would be deregulated by this translocation, we molecularly cloned the translocation's breakpoints. They were distant from the breakpoint cluster regions of the 3q21q26 syndrome or t(1;3)(p36;q21), and neither the EVI1 nor the MEL1 transcript was detected in the HIG cell line. None of the genes located within 150 kilobase pairs of the breakpoints were aberrantly expressed, suggesting that in this case other gene(s) more distant from the breakpoints are deregulated by possible remote effects. Further analyses of the deregulated genes in the HIG cell line should provide important insight into the mechanisms involved in these types of leukemias.

  6. Isolation, proliferation, cytogenetic, and molecular characterization and in vitro differentiation potency of canine stem cells from foetal adnexa: a comparative study of amniotic fluid, amnion, and umbilical cord matrix.

    PubMed

    Filioli Uranio, M; Valentini, L; Lange-Consiglio, A; Caira, M; Guaricci, A C; L'Abbate, A; Catacchio, C R; Ventura, M; Cremonesi, F; Dell'Aquila, M E

    2011-05-01

    The possibility to isolate canine mesenchymal stem cells (MSCs) from foetal adnexa is interesting since several canine genetic disorders are reported to resemble similar dysfunctions in humans. In this study, we successfully isolated, cytogenetically and molecularly characterized, and followed the differentiation potency of canine MSCs from foetal adnexa, such as amniotic fluid (AF), amniotic membrane (AM), and umbilical cord matrix (UCM). In the three types of cell lines, the morphology of proliferating cells typically appeared fibroblast-like, and the population doubling time (DT) significantly increased with passage number. For AF- and AM-MSCs, cell viability did not change with passages. In UCM-MSCs, cell viability remained at approximately constant levels up to P6 and significantly decreased from P7 (P < 0.05). Amnion and UCM-MSCs expressed embryonic and MSC markers, such as Oct-4 CD44, CD184, and CD29, whereas AF-MSCs expressed Oct-4, CD44. Expression of the hematopoietic markers CD34 and CD45 was not found. Dog leucocyte antigens (DLA-DRA1 and DLA-79) were expressed only in AF-MSCs at P1. Isolated cells of the three cell lines at P3 showed multipotent capacity, and differentiated in vitro into neurocyte, adipocyte, osteocyte, and chondrocyte, as demonstrated by specific stains and expression of molecular markers. Cells at P4 showed normal chromosomal number, structure, and telomerase activity. These results demonstrate that, in dog, MSCs can be successfully isolated from foetal adnexa and grown in vitro. Their proven stemness and chromosomal stability indicated that MSCs could be used as a model to study stem cell biology and have an application in therapeutic programs. PMID:21491540

  7. Isolation, proliferation, cytogenetic, and molecular characterization and in vitro differentiation potency of canine stem cells from foetal adnexa: a comparative study of amniotic fluid, amnion, and umbilical cord matrix.

    PubMed

    Filioli Uranio, M; Valentini, L; Lange-Consiglio, A; Caira, M; Guaricci, A C; L'Abbate, A; Catacchio, C R; Ventura, M; Cremonesi, F; Dell'Aquila, M E

    2011-05-01

    The possibility to isolate canine mesenchymal stem cells (MSCs) from foetal adnexa is interesting since several canine genetic disorders are reported to resemble similar dysfunctions in humans. In this study, we successfully isolated, cytogenetically and molecularly characterized, and followed the differentiation potency of canine MSCs from foetal adnexa, such as amniotic fluid (AF), amniotic membrane (AM), and umbilical cord matrix (UCM). In the three types of cell lines, the morphology of proliferating cells typically appeared fibroblast-like, and the population doubling time (DT) significantly increased with passage number. For AF- and AM-MSCs, cell viability did not change with passages. In UCM-MSCs, cell viability remained at approximately constant levels up to P6 and significantly decreased from P7 (P < 0.05). Amnion and UCM-MSCs expressed embryonic and MSC markers, such as Oct-4 CD44, CD184, and CD29, whereas AF-MSCs expressed Oct-4, CD44. Expression of the hematopoietic markers CD34 and CD45 was not found. Dog leucocyte antigens (DLA-DRA1 and DLA-79) were expressed only in AF-MSCs at P1. Isolated cells of the three cell lines at P3 showed multipotent capacity, and differentiated in vitro into neurocyte, adipocyte, osteocyte, and chondrocyte, as demonstrated by specific stains and expression of molecular markers. Cells at P4 showed normal chromosomal number, structure, and telomerase activity. These results demonstrate that, in dog, MSCs can be successfully isolated from foetal adnexa and grown in vitro. Their proven stemness and chromosomal stability indicated that MSCs could be used as a model to study stem cell biology and have an application in therapeutic programs.

  8. Is Having Clonal Cytogenetic Abnormalities the Same as Having Leukaemia.

    PubMed

    Farina, Mirko; Rossi, Giuseppe; Bellotti, Daniella; Marchina, Eleonora; Gale, Robert Peter

    2016-01-01

    A finding of cytogenetic abnormalities, even when these are clonal and even when the abnormalities are typically associated with leukaemia, is not the same as a person having leukaemia. We describe a person who had acute myeloid leukaemia (AML) and achieved a complete haematological remission and who then had persistent and transient clonal cytogenetic abnormalities for 22 years but no recurrence of leukaemia. These data suggest that clones of myeloid cells with mutations and capable of expanding to levels detectable by routine cytogenetic analyses do not all eventuate in leukaemia, even after a prolonged observation interval. The possibility of incorrectly diagnosing a person as having leukaemia becomes even greater when employing more sensitive techniques to detect mutations such as by polymerase chain reaction and whole-exome or whole-genome sequencing. Caution is needed when interpreting clonal abnormalities in AML patients with normal blood and bone marrow parameters.

  9. Diagnosis of Whipple's disease using molecular biology techniques.

    PubMed

    Cosme, Ángel; Ojeda, Evelia; Muñagorri, Ana I; Gaminde, Eduardo; Bujanda, Luis; Larzabal, Mikel; Gil, Inés

    2011-04-01

    The diagnosis of Whipple's disease (WD) is based on the existence of clinical signs and symptoms compatible with the disease and in the presence of PAS-positive diastase-resistant granules in the macrophages of the small intestine. If there is suspicion of the disease but no histological findings or only isolated extraintestinal manifestations, species-specific PCR using different sequences of the T. whippleii genome from different tissue types and biological fluids is recommended.This study reports two cases: the first patient had diarrhea and the disease was suspected after an endoscopic examination of the ileum, while the second patient had multi-systemic manifestations,particularly abdominal, thoracic, and peripheral lymphadenopathies. In both cases, the diagnosis was confirmed using molecular biology techniques to samples from the small intestine or from a retroperineal lymph node, respectively. PMID:21526877

  10. Practical Instruction in Tissue Culture and Cytogenetics for Sandwich Students.

    ERIC Educational Resources Information Center

    Williams, D. C.; Bishun, N. P.

    1973-01-01

    Describes the training and practical techniques taught to students involved in a sandwich course at the Tissue Culture and Cytogenetics Unit of the Marie Curie Memorial Foundation, Surrey, England. Students spend a minimum of six months involved in the sandwich course before returning to university for a final academic year. (JR)

  11. Molecular Genetic Tools and Techniques for Marchantia polymorpha Research.

    PubMed

    Ishizaki, Kimitsune; Nishihama, Ryuichi; Yamato, Katsuyuki T; Kohchi, Takayuki

    2016-02-01

    Liverworts occupy a basal position in the evolution of land plants, and are a key group to address a wide variety of questions in plant biology. Marchantia polymorpha is a common, easily cultivated, dioecious liverwort species, and is emerging as an experimental model organism. The haploid gametophytic generation dominates the diploid sporophytic generation in its life cycle. Genetically homogeneous lines in the gametophyte generation can be established easily and propagated through asexual reproduction, which aids genetic and biochemical experiments. Owing to its dioecy, male and female sexual organs are formed in separate individuals, which enables crossing in a fully controlled manner. Reproductive growth can be induced at the desired times under laboratory conditions, which helps genetic analysis. The developmental process from a single-celled spore to a multicellular body can be observed directly in detail. As a model organism, molecular techniques for M. polymorpha are well developed; for example, simple and efficient protocols of Agrobacterium-mediated transformation have been established. Based on them, various strategies for molecular genetics, such as introduction of reporter constructs, overexpression, gene silencing and targeted gene modification, are available. Herein, we describe the technologies and resources for reverse and forward genetics in M. polymorpha, which offer an excellent experimental platform to study the evolution and diversity of regulatory systems in land plants. PMID:26116421

  12. A retrospective review of cytogenetic studies on methyl isocyanate with special reference to the Bhopal gas tragedy: is the next generation also at risk?

    PubMed

    Samarth, Ravindra M; Gandhi, Puneet; Maudar, Kewal K

    2013-06-01

    The world's worst industrial disaster, at Union Carbide, Bhopal, India, took place on 2-3 December 1984, leading to the leakage of poisonous methyl-isocyanate into the environment, causing thousands of deaths, pregnancy loss and for some, incapacitation for life. More than a quarter of a century later, the Indian Council of Medical Research undertook to redefine the abysmal consequences of the toxic gas exposure on the exposed population. This invigorated the interest of scientific community in the evaluation of the long-term effects, with reference to cytogenetic parameters. The thrust area was identified in terms of genetic disorders, low birth weight, developmental/growth disorders and congenital malformations. Also the impact on epigenetic factors, which may have contributed to variations in the functional expression of genes, was not negated, stimulating intense scientific research on in utero exposure and the progeny of the exposed population. To accomplish this mammoth task, molecular cytogenetic investigations must be undertaken in conjunction with conventional cytogenetics, using techniques such as FISH, Immuno-FISH, SKY and SNP analysis, to build up a cytogenetic database of the surviving population.

  13. Molecular techniques to interrogate and edit the Chlamydomonas nuclear genome.

    PubMed

    Jinkerson, Robert E; Jonikas, Martin C

    2015-05-01

    The success of the green alga Chlamydomonas reinhardtii as a model organism is to a large extent due to the wide range of molecular techniques that are available for its characterization. Here, we review some of the techniques currently used to modify and interrogate the C. reinhardtii nuclear genome and explore several technologies under development. Nuclear mutants can be generated with ultraviolet (UV) light and chemical mutagens, or by insertional mutagenesis. Nuclear transformation methods include biolistic delivery, agitation with glass beads, and electroporation. Transforming DNA integrates into the genome at random sites, and multiple strategies exist for mapping insertion sites. A limited number of studies have demonstrated targeted modification of the nuclear genome by approaches such as zinc-finger nucleases and homologous recombination. RNA interference is widely used to knock down expression levels of nuclear genes. A wide assortment of transgenes has been successfully expressed in the Chlamydomonas nuclear genome, including transformation markers, fluorescent proteins, reporter genes, epitope tagged proteins, and even therapeutic proteins. Optimized expression constructs and strains help transgene expression. Emerging technologies such as the CRISPR/Cas9 system, high-throughput mutant identification, and a whole-genome knockout library are being developed for this organism. We discuss how these advances will propel future investigations.

  14. Basic Cytogenetics for Office Practice

    PubMed Central

    Roland, Birgitte; Cox, David M.

    1988-01-01

    There is a wide range of clinical problems, from the relatively common to the extremely rare, that result from alterations in the chromosome complement. These numerical and structural abnormalities of the chromosomes can be detected readily by cell culture and analysis in the cytogenetics laboratory, and the chromosome complement is defined by means of a simple nomenclature. The family physician can expect to see patients with potential chromosome abnormalities from infancy to adulthood and may request that the appropriate cytogenetic investigation be undertaken. The diagnosis of chromosome disorders allows more accurate patient counselling and improved patient care. ImagesFigure 1 PMID:21253093

  15. Cytogenetic studies in patients with gastric cancer.

    PubMed

    Abarbanel, J; Shabtai, F; Kyzer, S; Chaimof, C

    1991-01-01

    Banded cytogenetic studies of gastric carcinoma are still relatively scarce, comprised of only a small number of patients. This study was performed on peripheral blood lymphocytes and malignant cells of 16 patients with gastric carcinoma. The lymphocytes were analyzed by standard techniques. All patients had a normal constitutional karyotype; 90% of the patients presented an increased breakage rate and nonrandom chromosomal instability mainly in the heterochromatic regions of chromosomes 1, 9, and 16. Decreased response to phytohemagglutinin was observed in 6 (38%) patients. The tissue specimens were analyzed using direct techniques. Normal ploidy was observed in only one patient, 3 tumors were near-diploid, 4 hyperdiploid, 4 near-triploid, and 4 near-tetraploid. Those with the near-triploid or near-tetraploid constitution were in a more advanced pathological stage, most of them with a more complex cytogenetic profile. Particular involvement was found for chromosomes 1 to 4, 7 to 9, 17, and 20, but the more specific nonrandom changes seemed to involve chromosomes 7, 8, 9, and 17. PMID:1767545

  16. Cytogenetic analysis of Epicauta atomaria (Meloidae) and Palembus dermestoides (Tenebrionidae) with Xyp sex determination system using standard staining, C-bands, NOR and synaptonemal complex microspreading techniques.

    PubMed

    De Almeida, M C; Zacaro, A A; Cella, D M

    2000-01-01

    The mitotic and meiotic chromosomes of the beetles Epicauta atomaria (Meloidae) and Palembus dermestoides (Tenebrionidae) were analysed using standard staining, C-banding and silver impregnation techniques. We determine the diploid and haploid chromosome numbers, the sex determination system and describe the chromosomal morphology, the C-banding pattern and the chromosome(s) bearing NORs (nucleolar organizer regions). Both species shown 2n = 20 chromosomes, the chromosomal meioformula 9 + Xyp, and regular chromosome segregation during anaphases I and II. The chromosomes of E. atomaria are basically metacentric or submetacentric and P. dermestoides chromosomes are submetacentric or subtelocentric. In both beetles the constitutive heterochromatin is located in the pericentromeric region in all autosomes and in the Xp chromosome; additional C-bands were observed in telomeric region of the short arm in some autosomes in P. dermestoides. The yp chromosome did not show typical C-bands in these species. As for the synaptonemal complex, the nucleolar material is associated to the 7th bivalent in E. atomaria and 3rd and 7th bivalents in P. dermestoides. Strong silver impregnated material was observed in association with Xyp in light and electron microscopy preparations in these species and this material was interpreted to be related to nucleolar material.

  17. Cytogenetic analysis of Epicauta atomaria (Meloidae) and Palembus dermestoides (Tenebrionidae) with Xyp sex determination system using standard staining, C-bands, NOR and synaptonemal complex microspreading techniques.

    PubMed

    De Almeida, M C; Zacaro, A A; Cella, D M

    2000-01-01

    The mitotic and meiotic chromosomes of the beetles Epicauta atomaria (Meloidae) and Palembus dermestoides (Tenebrionidae) were analysed using standard staining, C-banding and silver impregnation techniques. We determine the diploid and haploid chromosome numbers, the sex determination system and describe the chromosomal morphology, the C-banding pattern and the chromosome(s) bearing NORs (nucleolar organizer regions). Both species shown 2n = 20 chromosomes, the chromosomal meioformula 9 + Xyp, and regular chromosome segregation during anaphases I and II. The chromosomes of E. atomaria are basically metacentric or submetacentric and P. dermestoides chromosomes are submetacentric or subtelocentric. In both beetles the constitutive heterochromatin is located in the pericentromeric region in all autosomes and in the Xp chromosome; additional C-bands were observed in telomeric region of the short arm in some autosomes in P. dermestoides. The yp chromosome did not show typical C-bands in these species. As for the synaptonemal complex, the nucleolar material is associated to the 7th bivalent in E. atomaria and 3rd and 7th bivalents in P. dermestoides. Strong silver impregnated material was observed in association with Xyp in light and electron microscopy preparations in these species and this material was interpreted to be related to nucleolar material. PMID:11338427

  18. [Benefit of human gamete cytogenetics: results and perspectives].

    PubMed

    Vialard, F; Pellestor, F

    2008-09-01

    In man, the incidence of reproductive failures is high and chromosomal abnormalities remains the major cause of pregnancy wastage. The advent of molecular cytogenetic techniques and assisted reproduction technology have brought forth new approaches for the chromosomal analysis of human oocytes and spermatozoa. The oocyte analyses have evidenced the high rate of chromosomal abnormalities in women and identified premature separation of sister chromatid as a major mechanism in aneuploidy occurrence. High frequencies of aneuploidy have been found in various groups of women, such as patients over 35 or 38 years old, patients with recurrent implantation failures or recurrent miscarriages. The polar body analysis has confirmed the major contribution of premature separation of sister chromatids in aneuploidies and the effect of maternal ageing on its occurrence. In spermatozoa, the efficient adaptation of in situ chromosomal detection techniques has facilitated the segregation analysis of chromosomal abnormalities. Despite the consensus observed in sperm studies of robertsonnian translocations and inversions, new data are required for accurate estimates of imbalances in various types of structural rearrangements. For infertile patients with normal karyotypes, there is significant increase in aneuploidy frequencies, which can be extremely elevated in some groups of subjects, such as patients with large headed spermatozoa syndrome.

  19. Spreading and fluorescence in situ hybridization of male and female meiocyte chromosomes from Arabidopsis thaliana for cytogenetical analysis.

    PubMed

    Armstrong, Susan

    2013-01-01

    Advances in molecular biology and in the genetics of Arabidopsis thaliana have led to it becoming an important model for the analysis of meiosis in plants. Cytogenetic investigations are pivotal to meiotic studies and a number of technological improvements for Arabidopsis cytology have provided a range of tools to investigate chromosome behavior during meiosis. This chapter contains a detailed description of cytological techniques currently used in our laboratory for the basic preparation of meiotic chromosomes for investigation of the female and male meiotic pathway and fluorescence in situ hybridization (FISH) analysis for the frequency and distribution of crossovers (chiasmata) at metaphase I.

  20. Cytogenetic analysis of salivary gland type tumors.

    PubMed

    Mark, H F; Hanna, I; Gnepp, D R

    1996-08-01

    Fourteen salivary gland type tumors were analyzed with a combination of conventional cytogenetics via GTG-banding, molecular cytogenetics via fluorescent in situ hybridization, and chromosome morphometry. Nine tumors were benign (eight pleomorphic adenomas and one Warthin tumor) five tumors were malignant (one carcinoma ex pleomorphic adenoma, two adenoid cystic carcinomas including one from the breast, a basal cell adenocarcinoma, and an acinic cell carcinoma). Thirteen specimens grew in tissue culture; the basal cell adenocarcinoma did not grow. The Warthin tumor had a normal karyotype, one pleomorphic adenoma was normal, one had a clone with a missing Y chromosome, and the other pleomorphic adenomas had structural chromosomal abnormalities including the following: translocations between chromosomes 3 and 8, chromosomes 6 and 16, chromosomes 8 and 9, chromosomes 8 and 12, chromosomes 8 and 14, and chromosomes 8 and 21. Of the four malignant tumors with karyotypes, the acinic cell carcinoma and one adenoid cystic carcinoma were normal, the second adenoid cystic carcinoma showed a normal polymorphic variant, whereas the carcinoma ex pleomorphic adenoma demonstrated the following karyotype: 46,XX,dir ins(8;5)(q12;q12q35), add(12)(p13)/46,XX. In conclusion, 66% of the benign tumors and 25% of the malignant tumors demonstrated abnormal karyotypes.

  1. Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

    NASA Technical Reports Server (NTRS)

    Clancy, Thomas C.; Gates, Thomas S.

    2005-01-01

    The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

  2. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization.

    PubMed

    Singchat, Worapong; Hitakomate, Ekarat; Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology.

  3. Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location.

    PubMed

    García-Souto, Daniel; Troncoso, Tomás; Pérez, Montse; Pasantes, Juan José

    2015-01-01

    The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species. PMID:26716701

  4. Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location

    PubMed Central

    García-Souto, Daniel; Troncoso, Tomás; Pérez, Montse; Pasantes, Juan José

    2015-01-01

    The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species. PMID:26716701

  5. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization.

    PubMed

    Singchat, Worapong; Hitakomate, Ekarat; Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology. PMID:27501229

  6. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization

    PubMed Central

    Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology. PMID:27501229

  7. Molecular Genetics Techniques to Develop New Treatments for Brain Cancers

    SciTech Connect

    Fox, Jacob; Fathallan-Shaykh, Hassan

    2006-09-22

    The objectives of this report are: (1) to devise novel molecular gene therapies for malignant brain tumors, (2) advance our understanding of the immune system in the central nervous system; and (3) apply genomics to find molecular probes to diagnose brain tumors, predict prognosis, biological behavior and their response to treatment.

  8. [Cytogenetic studies in primary amenorrhea].

    PubMed

    Baron, J; Warenik-Szymankiewicz, A

    1975-01-01

    Cytogenetic analysis in 125 women with primary amenorrhea consisting of determinations of sex chromatin and karyotype, and in some cases of autoradiography were performed. On the basis of clinical, endocrinologic and cytogenetic criteria, the women were divided into ten clinical groups. In Turner's syndrome 45,X monosomie was observed only in 9 patients and in the remaining 12 cases varies types of mosaicism or of structural aberrations of the X chromosome. In pure gonadal dysgenesis, the patients exhibited 46,XY karyotype have the tendency to malign tumors of the gonads. In all cases with male pseudohermaphroditism the karyotypes 46,XY were observed. The remaining patients with primary amenorrhea exhibited 46,XX karyotype and belonged to the cases with Mayer-Rokitansky-Kustner syndrome, with adrenogenital syndrome, with hypoplasia of the ovaries, with primary amenorrhea of uterine or pituitary origin or at last with pubertas tarda. PMID:1189755

  9. CELLULAR, BIOCHEMICAL, AND MOLECULAR TECHNIQUES IN DEVELOPMENTAL TOXICOLOGY

    EPA Science Inventory

    Cellular, molecular and biochemical approaches vastly expand the possibilities for revealing the underlying mechanisms of developmental toxicity. The increasing interest in embryonic development as a model system for the study of gene expression has resulted in a cornucopia of i...

  10. Molecular Cytogenetic Analysis of Telomere Rearrangements

    PubMed Central

    Martin, Christa Lese; Ledbetter, David H.

    2015-01-01

    Genomic imbalances involving the telomeric regions of human chromosomes, which contain the highest gene concentration in the genome, are proposed to have severe phenotypic consequences. For this reason, it is important to identify telomere rearrangements and assess their contribution to human pathology. This unit describes the structure and function of human telomeres and outlines several FISH-based methodologies that can be employed to study these unique regions of human chromosomes. It is a revision of the original version of the unit published in 2000, now including an introductory section describing advances in the discipline that have taken place since the original publication. PMID:25599669

  11. Molecular Cytogenetics of Human Single Pronucleated Zygotes

    PubMed Central

    Azevedo, Ana Raquel; Pinho, Maria João; Silva, Joaquina; Sá, Rosália; Thorsteinsdóttir, Sólveig; Barros, Alberto

    2014-01-01

    The aim of the present study was to use fluorescence in situ hybridization to analyze the chromosome status of zygotes with a single pronucleus from in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) treatment cycles. In addition, we performed immunocytochemical detection of nuclear lamins and histone H3 trimethylated at lysine-9, Me(3)H3K9. Zygotes were processed 24 hours after insemination or injection to assure the absence of asynchrony. In opposition to previous results, we observed 2 pronuclei in 16 of 18 IVF zygotes and 40 of 64 ICSI zygotes, suggesting premature pronuclear breakdown. In IVF and ICSI zygotes, the rate of normal diploidy was only 6 of 16 and 27 of 56, respectively, suggesting that monopronucleated zygotes should not be used in assisted reproductive treatments. The possible mechanisms are discussed and compared to previous studies of monopronucleated zygotes. PMID:24717739

  12. Whole genome scanning as a cytogenetic tool in hematologic malignancies

    PubMed Central

    Mufti, Ghulam J.

    2008-01-01

    Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture. Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects. In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications. Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies. Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases. PMID:18505780

  13. Molecular alignment and orientation with a hybrid Raman scattering technique

    NASA Astrophysics Data System (ADS)

    Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

    2012-11-01

    We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

  14. Cytogenetic telomere and telomerase studies in lumbo-sacral chordoma

    SciTech Connect

    Schwartz, H.S.; Dahir, G.A.; Miller, L.K.

    1994-09-01

    Lumbo-sacral chordomas are rare skeletal sarcomas that originate from the remnant notochord. There are approximately 35 lumbo-sacral chordomas reported annually in the U.S.A. The understanding of this rare human cancer is limited to observations of its clinical behavior and embryonic link. We performed chromosome and molecular analyses from five surgically harvested chordomas in an effort to document genetic abnormalities and to further understand its tumor biology. Cytogenetically, four of five patients had entirely normal chromosomes. One patient had several abnormalities seen in one of 100 cells including a translocation with breakpoints at bands 5q13 and 7q22, loss of one X chromosome and an extra chromosome 14. There was no evidence of monosomy X or trisomy 14 seen with interphase in situ hybridization using biotin-labeled alpha satellite chromosome specific probes for chromosome 14/22 and X. Telomere integrity is required to protect termini from illegitimate recombination. Typically telomeric reduction occurs in senescent fibroblasts in vivo aging and several human solid tumors. A telomeric probe (TTAGGG){sub 50} was hybridized to genomic DNA isolated from chordoma cells and digested with Hinf I which allows the telomeric DNA to remain intact. The tumor DNA was paired with leukocyte DNA from age-matched controls and revealed telomere elongation in all four patients studied with molecular genetic techniques. Telomerase activity is required to maintain telomere integrity and is not present in normal somatic cells. It is determined by visualizing the sizes of the electrophoresis gel-separated radioactive telomeric fragments assembled during incubation of cytoplasmic extracts containing telomerase. Telomerase activity was detected when compared with HeLa cells, a positive control. In addition, no telomerase activity was detected from the chordoma patient`s fibroblasts.

  15. The Use of Molecular Techniques at Hazardous Waste Sites

    EPA Science Inventory

    It is clear that typical protocols used for soil analysis would certainly fail to adequately interrogate ground-water treatment systems unless they were substantially modified. The modifications found necessary to compensate for the low biomass include molecular tools and techniq...

  16. Protocols, practices, and the reproduction of technique in molecular biology.

    PubMed

    Lynch, Michael

    2002-06-01

    Protocols are one of the main organizational resources in molecular biology. They are written instructions that specify ingredients, equipment, and sequences of steps for making technical preparations. Some protocols are published in widely used manuals, while others are hand-written variants used by particular laboratories and individual technicians. It is widely understood, both in molecular biology and in social studies of science, that protocols do not describe exactly what practitioners do in the laboratory workplace. In social studies of science, the difference between protocols and the actual practices of doing them often is used to set up ironic contrasts between 'messy' laboratory practices and the appearance of technical order. Alternatively, in ethnomethodological studies of work, the difference is examined as a constitutive feature, both of the lived-work of doing technical projects, and of the administrative work of regulating and evaluating such projects. The present article takes its point of departure from ethnomethodology, and begins with a discussion of local problems with performing molecular biology protocols on specific occasions. The discussion then moves to particular cases in criminal law in which defense attorneys cross-examine forensic technicians and lab administrators. In these interrogations, the distinction between protocols and actual practices animates the dialogue and becomes consequential for judgments in the case at hand. The article concludes with a discussion of administrative science: the work of treating protocols and paper trails as proxies for actual 'scientific' practices.

  17. Cytogenetic analysis from DNA by comparative genomic hybridization.

    PubMed

    Tachdjian, G; Aboura, A; Lapierre, J M; Viguié, F

    2000-01-01

    Comparative genomic hybridization (CGH) is a modified in situ hybridization technique which allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment. In CGH analysis, two differentially labelled genomic DNA (study and reference) are co-hybridized to normal metaphase spreads. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome. Since its development, CGH has been applied mostly as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. CGH may also have a role in clinical cytogenetics for detection and identification of unbalanced chromosomal abnormalities.

  18. Biochemistry and Molecular Biology Techniques for Person Characterization

    ERIC Educational Resources Information Center

    Herrero, Salvador; Ivorra, Jose Luis; Garcia-Sogo, Magdalena; Martinez-Cortina, Carmen

    2008-01-01

    Using the traditional serological tests and the most novel techniques for DNA fingerprinting, forensic scientists scan different traits that vary from person to person and use the data to include or exclude suspects based on matching with the evidence obtained in a criminal case. Although the forensic application of these methods is well known,…

  19. Optimization techniques in molecular structure and function elucidation.

    PubMed

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866

  20. A new translocation t(1p;18) in an Italian Mediterranean river buffalo (Bubalus bubalis, 2n = 50) bull: cytogenetic, fertility and inheritance studies.

    PubMed

    Albarella, S; Ciotola, F; Coletta, A; Genualdo, V; Iannuzzi, L; Peretti, V

    2013-01-01

    In recent years increasing attention has been paid to the cytogenetic control of Italian Mediterranean river buffalo (BBU) bulls authorized as sires which are registered in the stud book. Chromosome abnormalities described in this species are mainly numerical and affecting sex chromosomes. During routine cytogenetic analyses performed on young Italian Mediterranean river buffalo bulls in the progeny test, 1 animal was found to be carrier of a never before reported translocation t(1p;18) originated by fission of BBU1 and subsequent centric fusion of BBU1p with BBU18 as demonstrated by both R-banding and FISH-mapping techniques using specific molecular markers of BBU1p (DEFB1) and BBU18 (GPI). According to sperm analyses the semen characteristics were in physiological ranges, but the calf crop percentage was only 48.77% instead of 70-80%. Cytogenetic analyses performed on 50 offspring (36 females and 14 males) showed that 15 of them (30%) were carriers of the same translocation. PMID:22986410

  1. Toward a cytogenetically based physical map of the wheat genome.

    PubMed Central

    Werner, J E; Endo, T R; Gill, B S

    1992-01-01

    Bread wheat (Triticum aestivum L. em Thell) is well suited for cytogenetic analysis because the genome, buffered by polyploidy, can tolerate structurally and numerically engineered chromosomes for analysis over infinite generations. This feature of polyploidy can be used in developing a high-resolution, cytogenetically based physical map of the wheat genome. We show that numerous deletions, observed in the progeny of a monosomic addition of a chromosome from Triticum cylindricum in wheat, result from single breakpoints and a concomitant loss of distal fragments. Breakages occurred in euchromatic and heterochromatic regions. Forty-one deletions for chromosomes 7A, 7B, and 7D, and a set of genetically mapped DNA probes, were used to construct physical maps. Recombination was low in proximal chromosomal regions and very high toward the distal ends. Deletion mapping was more efficient than genetic mapping in resolving the order of proximal loci. Despite variation in size and arm ratio, relative gene position was largely conserved among chromosomes 7A, 7B, and 7D and a consensus group 7 physical map was constructed. Several molecularly tagged chromosome regions (MTCRs) of approximately one to a few million base pairs were identified that may be resolved by long-range mapping of DNA fragments. Thus, a cytogenetically based physical map may be used to integrate chromosome and DNA-based maps. The MTCRs may simplify strategies for cloning of agronomically useful genes despite the genetic complexity and the large genome size of wheat. Images PMID:1360666

  2. Detection of Molecular signatures of life using immunoassay techniques

    NASA Astrophysics Data System (ADS)

    McKay, D.; Steele, A.; Warmflash, D.; Maule, J.; Lynch, K.

    The Miniaturized Array for Solar System Exploration (MASSE) will use a microarray of antibody assays to search for biomarkers in extraterrestrial environments. We have now used enzyme linked immunosorbent assay (ELISA) to demonstrate the feasibility of immuno-detection of biomarkers in terrestrial soil, JSC-1 Mars regolith simulant, and terrestrial polar permafrost as analogues f ro extraterrestrial materials. We have also demonstrated that the technique works at microgravity and Martian gravity. Studies are now underway to test immunoassay techniques and antibody arrays at varying pressures and temperatures. It is expected that these studies will lead to a flight ready biomarker detection instrument that will be landed and operated on the Martian surface in 2009.

  3. Monitoring disease in lymphoma and CLL patients using molecular techniques.

    PubMed

    Gribben, John G

    2002-03-01

    Over the past decade considerable advances have been made in the sensitivity of detection of residual lymphoma and leukaemia cells. Assays based on the polymerase chain reaction (PCR) can detect one tumour cell in up to 10(5) to 10(6) normal cells. The identification and cloning of breakpoints associated with specific chromosomal translocations has made possible the application of these techniques to a variety of lymphoid malignancies. In parallel, B cell malignancies exhibit rearrangements of their immunoglobulin genes that are also suitable targets for PCR amplification to identify residual cells. Although these techniques provide a useful adjunct to standard methods of detection and diagnosis, their role in determining disease outcome remains investigational. There is confusion as to whether it is necessary to eradicate PCR-detectable lymphoma cells for cure, so it is not yet possible to determine whether the detection of residual lymphoma cells by PCR is an indication to continue therapy. PMID:11987923

  4. Complex cytogenetic abnormalities including telomeric associations and MEN1 mutation in a pediatric ependymoma.

    PubMed

    Urioste, M; Martínez-Ramírez, A; Cigudosa, J C; Colmenero, I; Madero, L; Robledo, M; Martínez-Delgado, B; Benítez, J

    2002-10-15

    Ependymomas are neuroectodermal tumors of the brain and spinal cord. Some recurrent cytogenetic aberrations have been reported in these tumors, including alterations involving chromosomes 22, 6, and 11. However, consistent molecular alterations have not been identified in ependymal tumors. We studied a recurrent ependymoma in a 3-year-old patient by standard cytogenetic and molecular analysis of TP53 and MEN1 genes. In the present case, we found many of the cytogenetic features previously described as being recurrent in ependymomas, including unstable telomeric alterations. Furthermore, we detected a novel acquired heterozygous mutation in the MEN1 gene. The chromosomal instability produced by the telomeric alterations and the mutation in the MEN1 gene could be important events in the tumorigenesis of ependymomas.

  5. Improved Molecular Technique for the Differentiation of Neotropical Anopheline Species

    PubMed Central

    Matson, Ryan; Rios, Carlos Tong; Chavez, Cesar Banda; Gilman, Robert H.; Florin, David; Sifuentes, Victor Lopez; Greffa, Roldan Cardenas; Yori, Pablo Peñataro; Fernandez, Roberto; Portocarrero, Daniel Velasquez; Vinetz, Joseph M.; Kosek, Margaret

    2008-01-01

    We evaluated a PCR-RFLP of the ribosomal internal transcribed spacer 2 region (ITS2) to distinguish species of Anopheles commonly reported in the Amazon and validated this method using reared F1 offspring. The following species of Anopheles were used for molecular analysis: An. (Nys.) benarrochi, An. (Nys.) darlingi, An. (Nys.) nuneztovari, An. (Nys.) konderi, An. (Nys.) rangeli, and An. (Nys.) triannulatus sensu lato (s.l.). In addition, three species of the subgenus Anopheles, An. (Ano.) forattini, An. (Ano.) mattogrossensis, and An. (Ano.) peryassui were included for testing. Each of the nine species tested yielded diagnostic banding patterns. The PCR-RFLP method was successful in identifying all life stages including exuviae with small fractions of the sample. The assay is rapid and can be applied as an unbiased confirmatory method for identification of morphologic variants, disputed samples, imperfectly preserved specimens, and life stages from which taxonomic keys do not allow for definitive species determination. PMID:18337348

  6. Advanced techniques for constrained internal coordinate molecular dynamics.

    PubMed

    Wagner, Jeffrey R; Balaraman, Gouthaman S; Niesen, Michiel J M; Larsen, Adrien B; Jain, Abhinandan; Vaidehi, Nagarajan

    2013-04-30

    Internal coordinate molecular dynamics (ICMD) methods provide a more natural description of a protein by using bond, angle, and torsional coordinates instead of a Cartesian coordinate representation. Freezing high-frequency bonds and angles in the ICMD model gives rise to constrained ICMD (CICMD) models. There are several theoretical aspects that need to be developed to make the CICMD method robust and widely usable. In this article, we have designed a new framework for (1) initializing velocities for nonindependent CICMD coordinates, (2) efficient computation of center of mass velocity during CICMD simulations, (3) using advanced integrators such as Runge-Kutta, Lobatto, and adaptive CVODE for CICMD simulations, and (4) cancelling out the "flying ice cube effect" that sometimes arises in Nosé-Hoover dynamics. The Generalized Newton-Euler Inverse Mass Operator (GNEIMO) method is an implementation of a CICMD method that we have developed to study protein dynamics. GNEIMO allows for a hierarchy of coarse-grained simulation models based on the ability to rigidly constrain any group of atoms. In this article, we perform tests on the Lobatto and Runge-Kutta integrators to determine optimal simulation parameters. We also implement an adaptive coarse-graining tool using the GNEIMO Python interface. This tool enables the secondary structure-guided "freezing and thawing" of degrees of freedom in the molecule on the fly during molecular dynamics simulations and is shown to fold four proteins to their native topologies. With these advancements, we envision the use of the GNEIMO method in protein structure prediction, structure refinement, and in studying domain motion.

  7. Using "Pseudomonas Putida xylE" Gene to Teach Molecular Cloning Techniques for Undergraduates

    ERIC Educational Resources Information Center

    Dong, Xu; Xin, Yi; Ye, Li; Ma, Yufang

    2009-01-01

    We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. "Pseudomonas putida xylE" gene, encoding catechol 2, 3-dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students a chance…

  8. Techniques for studying protein trafficking and molecular motors in neurons

    PubMed Central

    Feng, Shanxi; Arnold, Don B.

    2016-01-01

    This review focuses on techniques that facilitate the visualization of protein trafficking. In the mid-1990’s the cloning of GFP allowed fluorescently tagged proteins to be expressed in cells and then visualized in real time. This advance allowed a glimpse, for the first time, of the complex system within cells for distributing proteins. It quickly became apparent, however, that time-lapse sequences of exogenously expressed GFP-labeled proteins can be difficult to interpret. Reasons for this include the relatively low signal that comes from moving proteins and high background rates from stationary proteins and other sources, as well as the difficulty of identifying the origins and destinations of specific vesicular carriers. In this review we will examine a range of techniques that have overcome these issues to varying degrees and discuss the insights into protein trafficking that they have enabled. We will concentrate on neurons, as they are highly polarized and, thus, their trafficking systems tend to be accessible for study. PMID:26800506

  9. Detecting Molecular Properties by Various Laser-Based Techniques

    SciTech Connect

    Hsin, Tse-Ming

    2007-01-01

    Four different laser-based techniques were applied to study physical and chemical characteristics of biomolecules and dye molecules. These techniques are liole burning spectroscopy, single molecule spectroscopy, time-resolved coherent anti-Stokes Raman spectroscopy and laser-induced fluorescence microscopy. Results from hole burning and single molecule spectroscopy suggested that two antenna states (C708 & C714) of photosystem I from cyanobacterium Synechocystis PCC 6803 are connected by effective energy transfer and the corresponding energy transfer time is ~6 ps. In addition, results from hole burning spectroscopy indicated that the chlorophyll dimer of the C714 state has a large distribution of the dimer geometry. Direct observation of vibrational peaks and evolution of coumarin 153 in the electronic excited state was demonstrated by using the fs/ps CARS, a variation of time-resolved coherent anti-Stokes Raman spectroscopy. In three different solvents, methanol, acetonitrile, and butanol, a vibration peak related to the stretch of the carbonyl group exhibits different relaxation dynamics. Laser-induced fluorescence microscopy, along with the biomimetic containers-liposomes, allows the measurement of the enzymatic activity of individual alkaline phosphatase from bovine intestinal mucosa without potential interferences from glass surfaces. The result showed a wide distribution of the enzyme reactivity. Protein structural variation is one of the major reasons that are responsible for this highly heterogeneous behavior.

  10. Bioluminescence: a versatile technique for imaging cellular and molecular features

    PubMed Central

    Paley, Miranda A.

    2016-01-01

    Bioluminescence is a ubiquitous imaging modality for visualizing biological processes in vivo. This technique employs visible light and interfaces readily with most cell and tissue types, making it a versatile technology for preclinical studies. Here we review basic bioluminescence imaging principles, along with applications of the technology that are relevant to the medicinal chemistry community. These include noninvasive cell tracking experiments, analyses of protein function, and methods to visualize small molecule metabolites. In each section, we also discuss how bioluminescent tools have revealed insights into experimental therapies and aided drug discovery. Last, we highlight the development of new bioluminescent tools that will enable more sensitive and multi-component imaging experiments and, thus, expand our broader understanding of living systems. PMID:27594981

  11. Exploitation of molecular profiling techniques for GM food safety assessment.

    PubMed

    Kuiper, Harry A; Kok, Esther J; Engel, Karl-Heinz

    2003-04-01

    Several strategies have been developed to identify unintended alterations in the composition of genetically modified (GM) food crops that may occur as a result of the genetic modification process. These include comparative chemical analysis of single compounds in GM food crops and their conventional non-GM counterparts, and profiling methods such as DNA/RNA microarray technologies, proteomics and metabolite profiling. The potential of profiling methods is obvious, but further exploration of specificity, sensitivity and validation is needed. Moreover, the successful application of profiling techniques to the safety evaluation of GM foods will require linked databases to be built that contain information on variations in profiles associated with differences in developmental stages and environmental conditions.

  12. Pleuropulmonary blastoma: cytogenetic and spectral karyotype analysis.

    PubMed

    Taube, Janis M; Griffin, Constance A; Yonescu, Raluca; Morsberger, Laura; Argani, Pedram; Askin, Frederic B; Batista, Denise A S

    2006-01-01

    Pleuropulmonary blastoma (PPB) is a rare neoplasm of the pleuropulmonary mesenchyme. The molecular mechanisms underlying the genesis of this tumor are of particular interest as a large number of affected patients as well as their relatives have concurrent disease including additional dysplasia or neoplasia. To date, detailed karyotypes have been published on a limited number of cases. We report clinical, pathologic, and cytogenetic data in 2 cases of PPB including spectral karyotyping in 1 of them. Additionally, we conducted a review of the literature and compiled 15 published karyotypes of this tumor. Gain of chromosome 8 material was a highly prevalent finding in PPB, most times occurring as trisomy, but tetrasomy of the long arm was also frequent. Other occurring abnormalities, in order of observed frequency, included loss of 17p, loss of chromosome 10 or 10q, rearrangement of 11p, loss of chromosome X or Xp, gain of chromosomes/arms 1q, 2, and 7q, and loss of 6q and 18p. Loss of 10q has not been previously emphasized in PPB. The significance of these chromosome findings is discussed in relation to tumorigenesis. PMID:17163790

  13. Achieving molecular selectivity in imaging using multiphoton Raman spectroscopy techniques

    SciTech Connect

    Holtom, Gary R. ); Thrall, Brian D. ); Chin, Beek Yoke ); Wiley, H Steven ); Colson, Steven D. )

    2000-12-01

    In the case of most imaging methods, contrast is generated either by physical properties of the sample (Differential Image Contrast, Phase Contrast), or by fluorescent labels that are localized to a particular protein or organelle. Standard Raman and infrared methods for obtaining images are based upon the intrinsic vibrational properties of molecules, and thus obviate the need for attached flurophores. Unfortunately, they have significant limitations for live-cell imaging. However, an active Raman method, called Coherent Anti-Stokes Raman Scattering (CARS), is well suited for microscopy, and provides a new means for imaging specific molecules. Vibrational imaging techniques, such as CARS, avoid problems associated with photobleaching and photo-induced toxicity often associated with the use of fluorescent labels with live cells. Because the laser configuration needed to implement CARS technology is similar to that used in other multiphoton microscopy methods, such as two -photon fluorescence and harmonic generation, it is possible to combine imaging modalities, thus generating simultaneous CARS and fluorescence images. A particularly powerful aspect of CARS microscopy is its ability to selectively image deuterated compounds, thus allowing the visualization of molecules, such as lipids, that are chemically indistinguishable from the native species.

  14. Cytogenetic risk stratification in chronic myelomonocytic leukemia

    PubMed Central

    Such, Esperanza; Cervera, José; Costa, Dolors; Solé, Francesc; Vallespí, Teresa; Luño, Elisa; Collado, Rosa; Calasanz, María J.; Hernández-Rivas, Jesús M.; Cigudosa, Juan C.; Nomdedeu, Benet; Mallo, Mar; Carbonell, Felix; Bueno, Javier; Ardanaz, María T.; Ramos, Fernando; Tormo, Mar; Sancho-Tello, Reyes; del Cañizo, Consuelo; Gómez, Valle; Marco, Victor; Xicoy, Blanca; Bonanad, Santiago; Pedro, Carmen; Bernal, Teresa; Sanz, Guillermo F.

    2011-01-01

    Background The prognostic value of cytogenetic findings in chronic myelomonocytic leukemia is unclear. Our purpose was to evaluate the independent prognostic impact of cytogenetic abnormalities in a large series of patients with chronic myelomonocytic leukemia included in the database of the Spanish Registry of Myelodysplastic Syndromes. Design and Methods We studied 414 patients with chronic myelomonocytic leukemia according to WHO criteria and with a successful conventional cytogenetic analysis at diagnosis. Different patient and disease characteristics were examined by univariate and multivariate methods to establish their relationship with overall survival and evolution to acute myeloid leukemia. Results Patients with abnormal karyotype (110 patients, 27%) had poorer overall survival (P=0.001) and higher risk of acute myeloid leukemia evolution (P=0.010). Based on outcome analysis, three cytogenetic risk categories were identified: low risk (normal karyotype or loss of Y chromosome as a single anomaly), high risk (presence of trisomy 8 or abnormalities of chromosome 7, or complex karyotype), and intermediate risk (all other abnormalities). Overall survival at five years for patients in the low, intermediate, and high risk cytogenetic categories was 35%, 26%, and 4%, respectively (P<0.001). Multivariate analysis confirmed that this new CMML-specific cytogenetic risk stratification was an independent prognostic variable for overall survival (P=0.001). Additionally, patients belonging to the high-risk cytogenetic category also had a higher risk of acute myeloid leukemia evolution on univariate (P=0.001) but not multivariate analysis. Conclusions Cytogenetic findings have a strong prognostic impact in patients with chronic myelomonocytic leukemia. PMID:21109693

  15. Cytogenetic Investigation in a Group of Ten Infertile Men with Non-Obstructive Azoospermia: First Algerian 46, XX Syndrome

    PubMed Central

    BAZIZ, Meriem; HAMOULI-SAID, Zohra; RATBI, Ilham; HABEL, Mohamed; GUAOUA, Soukaina; SBITI, Aziza; SEFIANI, Abdelaziz

    2016-01-01

    Background: In Algeria, the data on infertility and its various causes are rare. Recently, the introduction of assisted reproduction has allowed expecting that 300000 couples, which represent 7% of couples of reproductive age, face difficulty conceiving a child. Knowing that most idiopathic cases are likely to be due to chromosomal abnormalities, we aimed to investigate genetic defects by karyotype analysis in Algerian infertile men, using peripheral blood lymphocytes. Methods: A cytogenetic study was conducted on 10 men from infertile couples by Karyotype analysis of R-banding performed by lymphocyte culture technique. Fluorescence in situ hybridization was performed and molecular abnormalities were investigated by polymerase chain reaction. Follicle stimulating hormone (FSH) and luteinizing hormone (LH) levels were evaluated by immunoradiometric method. Results: Chromosomal abnormalities were observed in 30% of the patients. We identified a homogenous Klinefelter syndrome patient with 47, XXY karyotype, a mosaic Klinefelter syndrome patient with 47, XXY/46, XY karyotype and a 46, XX male. Fluorescence in situ hybridization showed that the sex-determining region Y was translocated to the short arm of the X chromosome in patient with 46, XX chromosomal constitution and the presence of the SRY gene was confirmed by polymerase chain reaction and electrophoresis. Conclusion: The occurrence of chromosomal abnormalities in 30% of the infertile men strongly supports the inclusion of routine cytogenetic testing for diagnostic establishment and suitable counseling for couples seeking for assisted reproduction technologies. PMID:27648416

  16. Clinical, cytogenetic, and molecular outcomes in a series of 66 patients with Pierre Robin sequence and literature review: 22q11.2 deletion is less common than other chromosomal anomalies.

    PubMed

    Gomez-Ospina, Natalia; Bernstein, Jonathan A

    2016-04-01

    Pierre Robin sequence (PRS) is an important craniofacial anomaly that can be seen as an isolated finding or manifestation of multiple syndromes. 22q11.2 deletion and Stickler syndrome are cited as the two most common conditions associated with PRS, but their frequencies are debated. We performed a retrospective study of 66 patients with PRS and reviewed their genetic testing, diagnoses, and clinical findings. The case series is complemented by a comprehensive literature review of the nature and frequency of genetic diagnosis in PRS. In our cohort 65% of patients had associated anomalies; of these, a genetic diagnosis was established in 56%. Stickler syndrome was the most common diagnosis, comprising approximately 11% of all cases, followed by Treacher Collins syndrome (9%). The frequency of 22q11.2 deletion was 1.5%. Chromosome arrays, performed for 72% of idiopathic PRS with associated anomalies, revealed two cases of 18q22→qter deletion, a region not previously reported in association with PRS. A review of the cytogenetic anomalies identified in this population supports an association between the 4q33-qter, 17q24.3, 2q33.1, and 11q23 chromosomal loci and PRS. We found a low frequency of 22q11.2 deletion in PRS, suggesting it is less commonly implicated in this malformation. Our data also indicate a higher frequency of cytogenetic anomalies in PRS patients with associated anomalies, and a potential new link with the 18q22→qter locus. The present findings underscore the utility of chromosomal microarrays in cases of PRS with associated anomalies and suggest that delaying testing for apparently isolated cases should be considered.

  17. New insight into biodegradation of polylactide (PLA)/clay nanocomposites using molecular ecological techniques.

    PubMed

    Sangwan, Parveen; Way, Cameron; Wu, Dong-Yang

    2009-07-01

    Novel molecular ecological techniques were used to study changes in microbial community structure and population during degradation of polylactide (PLA)/organically modified layered silicates (OMLS) nanocomposites. Cloned gene sequences belonging to members of the phyla Actinobacteria and Ascomycota comprized the most dominant groups of microorganisms during biodegradation of PLA/OMLS nanocomposites. Due to their numerical abundance, members of these microbial groups are likely to play an important role during biodegradation process. This paper presents new insights into the biodegradability of PLA/OMLS nanocomposites and highlights the importance of using novel molecular ecological techniques for in situ identification of new microorganisms involved in biodegradation of polymeric materials.

  18. Insights into the molecular interactions between aminopeptidase and amyloid beta peptide using molecular modeling techniques.

    PubMed

    Dhanavade, Maruti J; Sonawane, Kailas D

    2014-08-01

    Amyloid beta (Aβ) peptides play a central role in the pathogenesis of Alzheimer's disease. The accumulation of Aβ peptides in AD brain was caused due to overproduction or insufficient clearance and defects in the proteolytic degradation of Aβ peptides. Hence, Aβ peptide degradation could be a promising therapeutic approach in AD treatment. Recent experimental report suggests that aminopeptidase from Streptomyces griseus KK565 (SGAK) can degrade Aβ peptides but the interactive residues are yet to be known in detail at the atomic level. Hence, we developed the three-dimensional model of aminopeptidase (SGAK) using SWISS-MODEL, Geno3D and MODELLER. Model built by MODELLER was used for further studies. Molecular docking was performed between aminopeptidase (SGAK) with wild-type and mutated Aβ peptides. The docked complex of aminopeptidase (SGAK) and wild-type Aβ peptide (1IYT.pdb) shows more stability than the other complexes. Molecular docking and MD simulation results revealed that the residues His93, Asp105, Glu139, Glu140, Asp168 and His255 are involved in the hydrogen bonding with Aβ peptide and zinc ions. The interactions between carboxyl oxygen atoms of Glu139 of aminopeptidase (SGAK) with water molecule suggest that the Glu139 may be involved in the nucleophilic attack on Ala2-Glu3 peptide bond of Aβ peptide. Hence, amino acid Glu139 of aminopeptidase (SGAK) might play an important role to degrade Aβ peptides, a causative agent of Alzheimer's disease.

  19. [Molecular techniques for cyanobacteria detection at Riogrande II and La Fe water reservoirs, Colombia].

    PubMed

    Hurtado-Alarcón, Julio César; Polanía-Vorenberg, Jaime

    2014-03-01

    In lentic water bodies as reservoirs occur eutrophication processes, originated mainly from human activities (i.e. agriculture, animal exploitation). This influx of nutrients in aquatic ecosystems could promote blooms of potentially toxic cyanobacteria. The purpose of this work is to detect the presence of cyanobacteria strains in water samples, using molecular techniques to help in preventive management of reservoirs dedicated to water purification. We used two molecular techniques to detect genes implied with the synthesis of hepatotoxic microcystins from potentially toxic cyanobacteria strains, and to evaluate the molecular diversity of cyanobacteria in water samples from two high-mountain reservoirs used for purification of drinking water for the metropolitan area of Medellin, Colombia. Between 2010-2011 collections of 12 water samples were taken and DNA extraction together with PCR and DGGE analyses where carried out. We amplified 22 sequences between 250-300bp of the genes mcyA and mcyE, and these sequences were related with several strains and cyanobacteria genera accessions from NCBI-GenBank databases. Moreover, sequence amplifications of the 16S small ribosomal RNA subunit - 16S rRNA- between 400-800bp were also performed in order to use them for the DGGE technique. The amplification products of DGGE were set in polyacrilamide gel with posterior denaturing electrophoresis, and the scanned images of the gel bands were analysed with the software GelCompar II. For Riogrande II and La Fe reservoirs we found 35 and 30 different DGGE bands, respectively, as a measurement of molecular diversity in these artificial ecosystems. Here, we demonstrated the utility of two molecular techniques for the detection of genes associated with toxicity and molecular diversity of cyanobacteria in reservoirs destined for drinking water in urban centers. We recommend strongly following with periodically molecular biology studies in these ecosystems combined with limnological and

  20. Banding cytogenetic analysis in pediatric patients with acute lymphoblastic leukemia (ALL) in a Brazilian population

    PubMed Central

    2013-01-01

    Background Cytogenetic studies in Brazilian population about childhood acute lymphoblastic leukemia (ALL), the most common childhood malignancy, are scarce. Moreover, Brazilian race is very heterogeneous and is made by the confluence of people of several different origins, from the original Native Brazilians, with the influx of Portuguese colonizers, Black African slaves, and recent European, Arab and Japanese immigration. The purpose of this prospective, multicentric study was to assess the sociodemographic, clinic and cytogenetic characteristics of the children treated for ALL in the Northeast region of Brazil. Results This study includes thirty patients between 4 months and 17 years old treated for ALL from January 1st, 2009 to November 30th, 2010. Cytogenetic analysis showed that in nineteen out of thirty patients (64%) presented some chromosome abnormalities, in which 53% corresponds to numerical abnormalities, 21% structural and numerical abnormalities, and 26% only structural changes. Moreover, seven patients presented complexes karyotype not yet described in the literature. Taken together these results show the importance of the cytogenetic analysis in ALL pediatric patients and illustrates that the studied population presented unexpected complexes karyotypes which were correlated to poor outcome. Conclusion The results demonstrate the importance of banding cytogenetics for ALL diagnosis despite the use of most modern techniques such as FISH and aCGH, and provide reliable insight into the ALL in Brazil. PMID:24025689

  1. Molecular and clinical study of 61 Angelman syndrome patients

    SciTech Connect

    Saitoh, Shinji; Harada, Naoki; Jinno, Yoshihiro; Niikawa, Norio; Imaizumi, Kiyoshi; Kuroki, Yoshikazu; Fukushima; Yoshimitsu; Sugimoto, Tateo; Renedo, Monica

    1994-08-15

    We analyzed 61 Angelman syndrome (AS) patients by cytogenetic and molecular techniques. On the basis of molecular findings, the patients were classified into the following 4 groups: familial cases without deletion, familial cases with submicroscopic deletion, sporadic cases with deletion, and sporadic cases without deletion. Among 53 sporadic cases, 37 (70%) had molecular deletion, which commonly extended from D15S9 to D15S12, although not all deletions were identical. Of 8 familial cases, 3 sibs from one family had a molecular deletion involving only 2 loci, D15S10 and GABRB3, which define the critical region for AS phenotypes. The parental origin of deletion, both in sporadic and familial cases, was exclusively maternal and consistent with a genomic imprinting hypothesis. Among sporadic and familial cases without deletion, no uniparental disomy was found and most of them were shown to inherit chromosomes 15 from both parents (biparental inheritance). A discrepancy between cytogenetic and molecular deletion was observed in 14 (26%) of 53 patients in whom cytogenetic analysis could be performed. Ten (43%) of 23 patients with a normal karyotype showed a molecular deletion, and 4 (13%) of 30 patients with cytogenetic deletion, del(15) (q11q13), showed no molecular deletion. Most clinical manifestations, including neurological signs and facial characteristics, were not distinct in each group except for hypopigmentation of skin or hair. Familial cases with submicroscopic deletion were not associated with hypopigmentation. These findings suggested that a gene for hypopigmentation is located outside the critical region of AS and is not imprinted. 37 refs., 2 figs., 4 tabs.

  2. Cytogenetic analysis in a large series of children with non-syndromic mental retardation.

    PubMed

    Bouhjar, Inesse Ben Abdallah; Gmidène, Abir; Mougou-Zrelli, Soumaya; Hannachi, Hanene; Soyah, Najla; Gadour, Naoufel; Harrabi, Imed; Elghezal, Hatem; Saad, Ali

    2012-09-01

    Mental retardation affects 1-3% of the population. To evaluate the implication of chromosomal abnormalities in the etiology of mental retardation, 1420 patients with non-syndromic mental retardation recruited at the department of cytogenetics of Farhat Hached hospital (Sousse, Tunisia) between January 2005 and December 2009, were analyzed using standard cytogenetic techniques. Age ranged between 3 and 18 years with a median of 8 years. Chromosomal abnormalities were detected in 7.8% of patients and an increased prevalence of chromosome anomalies was observed in patients when the mental retardation is associated with a severe degree of intellectual disability, facial dysmorphic features and/or congenital malformations or epilepsy. PMID:27625819

  3. Cytogenetic analysis in a large series of children with non-syndromic mental retardation

    PubMed Central

    Bouhjar, Inesse Ben Abdallah; Gmidène, Abir; Mougou-Zrelli, Soumaya; Hannachi, Hanene; Soyah, Najla; Gadour, Naoufel; Harrabi, Imed; Elghezal, Hatem; Saad, Ali

    2012-01-01

    Mental retardation affects 1–3% of the population. To evaluate the implication of chromosomal abnormalities in the etiology of mental retardation, 1420 patients with non-syndromic mental retardation recruited at the department of cytogenetics of Farhat Hached hospital (Sousse, Tunisia) between January 2005 and December 2009, were analyzed using standard cytogenetic techniques. Age ranged between 3 and 18 years with a median of 8 years. Chromosomal abnormalities were detected in 7.8% of patients and an increased prevalence of chromosome anomalies was observed in patients when the mental retardation is associated with a severe degree of intellectual disability, facial dysmorphic features and/or congenital malformations or epilepsy.

  4. [Non-radioactive in situ hybridization of alpha-satellite sequences in cytogenetic diagnosis].

    PubMed

    Perfumo, C; Arslanian, A; Zara, F; Piombo, G; Pierluigi, M

    1992-01-01

    Non isotopic in situ hybridization with alpha-satellite DNA probes in the cytogenetic diagnosis. Standard banding cytogenetic techniques do not always allow to define the structure and the origin of chromosome rearrangements involving the centromere region. Non-isotopic in situ hybridization of alphoid sequences has allowed to determine the origin of the centromeres in the metaphases of 5 patients referred to us for: 2 structural rearrangements involving chromosome 21, 2 structural rearrangements involving chromosome Y and 1 reciprocal translocation involving on chromosome 20 and one chromosome 15.

  5. [Non-radioactive in situ hybridization of alpha-satellite sequences in cytogenetic diagnosis].

    PubMed

    Perfumo, C; Arslanian, A; Zara, F; Piombo, G; Pierluigi, M

    1992-01-01

    Non isotopic in situ hybridization with alpha-satellite DNA probes in the cytogenetic diagnosis. Standard banding cytogenetic techniques do not always allow to define the structure and the origin of chromosome rearrangements involving the centromere region. Non-isotopic in situ hybridization of alphoid sequences has allowed to determine the origin of the centromeres in the metaphases of 5 patients referred to us for: 2 structural rearrangements involving chromosome 21, 2 structural rearrangements involving chromosome Y and 1 reciprocal translocation involving on chromosome 20 and one chromosome 15. PMID:1465321

  6. Significance of FISH in clinical cytogenetics

    SciTech Connect

    Gopal Rao, V.V.N.; Harris, S.; Roop, H.

    1994-09-01

    Ever since its discovery, FISH technology has become an invaluable adjunct to conventional cytogenetics. FISH has been instrumental in resolving previously unresolved cytogenetic dilemmas. FISH has been used to elucidate complex as well as subtle chromosomal translocations, in detection of microdeletions, to confirm duplications and inversions and to identify marker chromosomes. We report a few selected cases where FISH proved to be invaluable in not only confirming the anomaly, but also in arriving at an accurate diagnosis and appropriate counseling of the patients. These include 3 cases of prenatal and 3 cases of postnatal diagnosis. The results clearly demonstrate the significance of FISH in identifying and interpreting the difficult karyotype in clinical cytogenetics. In addition, FISH has been used to rule out microdeletions in Prader-Willi (16), Angelman (3), Miller-Dieker (7), DiGeorge (4) and Smith-Magenis (1) syndrome patients. Without FISH in the majority of these cases, it would not have been possible to accurately identify the karyotype and interpret the results. Hence, we recommend that FISH be used as a powerful adjunct to conventional cytogenetics in order to arrive at an accurate interpretation of the results but not to replace routine cytogenetic studies.

  7. Canine Cytogenetics - From band to basepair

    PubMed Central

    Breen, Matthew

    2008-01-01

    Humans and dogs have coexisted for thousands of years, during which time we have developed a unique bond, centered on companionship. Along the way, we have developed purebred dog breeds in a manner that has resulted unfortunately in many of them being affected by serious genetic disorders, including cancers. With serendipity and irony the unique genetic architecture of the 21st Century genome of Man's best friend may ultimately provide many of the keys to unlock some of nature's most intriguing biological puzzles. Canine cytogenetics has advanced significantly over the past 10 years, spurred on largely by the surge of interest in the dog as a biomedical model for genetic disease and the availability of advanced genomics resources. As such the role of canine cytogenetics has moved rapidly from one that served initially to define the gross genomic organization of the canine genome and provide a reliable means to determine the chromosomal location of individual genes, to one that enabled the assembled sequence of the canine genome to be anchored to the karyotype. Canine cytogenetics now presents the biomedical research community with a means to assist in our search for a greater understanding of how genome architectures altered during speciation and in our search for genes associated with cancers that affect both dogs and humans. The cytogenetics ‘toolbox’ for the dog is now loaded. This review aims to provide a summary of some of the recent advancements in canine cytogenetics. PMID:18467825

  8. [Neuropathology and molecular pathology of gliomas].

    PubMed

    Janzer, Robert-Charles

    2009-07-15

    Gliomas are the most frequent primary brain tumours. The WHO classification is essentially based on histological and immunohistochemical criteria. More recently multiple cytogenetic and molecular alterations associated with initiation and progression have been shown and the genetic profiles of tumour entities have been incorporated in the WHO classifiacation. Molecular testing of the MGMT promotor methylation in glioblastoma, predictive for the response to combined radio-/chimiothérapie, and the LOH 1p/19q in oligodendroglial tumours, as prognostic factor supplements the histopathological diagnosis. In the near futur array-based profiling techniques will contribute to a refinement of glioma classification and identify targets for more individualized glioma therapies.

  9. Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

    PubMed Central

    Ding, Chang; He, Jianzhong

    2012-01-01

    Summary Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction‐based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next‐generation sequencing, provide unsurpassed detection ability, which has enabled large‐scale comparative genomic and whole‐genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic‐acid‐based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions. PMID:22070763

  10. Molecular tagging techniques and their applications to the study of complex thermal flow phenomena

    NASA Astrophysics Data System (ADS)

    Chen, Fang; Li, Haixing; Hu, Hui

    2015-08-01

    This review article reports the recent progress in the development of a new group of molecule-based flow diagnostic techniques, which include molecular tagging velocimetry (MTV) and molecular tagging thermometry (MTT), for both qualitative flow visualization of thermally induced flow structures and quantitative whole-field measurements of flow velocity and temperature distributions. The MTV and MTT techniques can also be easily combined to result in a so-called molecular tagging velocimetry and thermometry (MTV&T) technique, which is capble of achieving simultaneous measurements of flow velocity and temperature distribution in fluid flows. Instead of using tiny particles, the molecular tagging techniques (MTV, MTT, and MTV&T) use phosphorescent molecules, which can be turned into long-lasting glowing marks upon excitation by photons of appropriate wavelength, as the tracers for the flow velocity and temperature measurements. The unique attraction and implementation of the molecular tagging techniques are demonstrated by three application examples, which include: (1) to quantify the unsteady heat transfer process from a heated cylinder to the surrounding fluid flow in order to examine the thermal effects on the wake instabilities behind the heated cylinder operating in mixed and forced heat convection regimes, (2) to reveal the time evolution of unsteady heat transfer and phase changing process inside micro-sized, icing water droplets in order to elucidate the underlying physics pertinent to aircraft icing phenomena, and (3) to achieve simultaneous droplet size, velocity and temperature measurements of "in-flight" droplets to characterize the dynamic and thermodynamic behaviors of flying droplets in spray flows.

  11. 42 CFR 493.1225 - Condition: Clinical cytogenetics.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Testing § 493.1225 Condition: Clinical cytogenetics. If the laboratory provides services in the specialty of Clinical cytogenetics, the laboratory must meet the requirements specified in §§ 493.1230 through... 42 Public Health 5 2010-10-01 2010-10-01 false Condition: Clinical cytogenetics. 493.1225...

  12. HMGI-C rearrangements as the molecular basis for the majority of pulmonary chondroid hamartomas: a survey of 30 tumors.

    PubMed

    Kazmierczak, B; Rosigkeit, J; Wanschura, S; Meyer-Bolte, K; Van de Ven, W J; Kayser, K; Krieghoff, B; Kastendiek, H; Bartnitzke, S; Bullerdiek, J

    1996-02-01

    Pulmonary chondroid hamartomas (PCH) are benign tumors of the lung characterized by a more or less high degree of mesenchymal metaplasia. In our series we investigated 30 PCH by a combination of cytogenetic and molecular methods. 18 tumors (60%) had cytogenetically detectable aberrations involving either 12q14-15 or 6p21 with a clear predominance of chromosomal abnormalities involving 12q14-15 (15 tumors). As in subgroups of pleomorphic adenomas of the salivary glands, leiomyomas of the uterus, and lipomas with 12q14-15 abnormalities the HMGI-C gene is frequently rearranged we tested PCH with either 12q14-15 abnormalities or normal karyotype by FISH and 3' RACE experiments for rearrangements of HMGI-C. Rearrangements were found in all cases with chromosomal 12q14-15 abnormalities and further six cases with an apparently normal karyotype. By the combination of cytogenetics with molecular techniques the percentage of cases with intragenic rearrangements of HMGI-C or rearrangements of its immediate surrounding was thus increased to 70% (21/30 cases). Considering all types of aberrations within this series 80% (24/30) of all PCH were aberrant. This is the first report on a combined molecular and cytogenetic analysis of a large series of pulmonary chondroid hamartomas indicating that rearrangements of HMGI-C, a member of the high mobility group protein gene family, are the leading molecular events in the genesis of PCH.

  13. Molecular Techniques for Detection, Species Differentiation, and Phylogenetic Analysis of Microsporidia

    PubMed Central

    Franzen, Caspar; Müller, Andreas

    1999-01-01

    Microsporidia are obligate intracellular protozoan parasites that infect a broad range of vertebrates and invertebrates. These parasites are now recognized as one of the most common pathogens in human immunodeficiency virus-infected patients. For most patients with infectious diseases, microbiological isolation and identification techniques offer the most rapid and specific determination of the etiologic agent. This is not a suitable procedure for microsporidia, which are obligate intracellular parasites requiring cell culture systems for growth. Therefore, the diagnosis of microsporidiosis currently depends on morphological demonstration of the organisms themselves. Although the diagnosis of microsporidiosis and identification of microsporidia by light microscopy have greatly improved during the last few years, species differentiation by these techniques is usually impossible and transmission electron microscopy may be necessary. Immunfluorescent-staining techniques have been developed for species differentiation of microsporidia, but the antibodies used in these procedures are available only at research laboratories at present. During the last 10 years, the detection of infectious disease agents has begun to include the use of nucleic acid-based technologies. Diagnosis of infection caused by parasitic organisms is the last field of clinical microbiology to incorporate these techniques and molecular techniques (e.g., PCR and hybridization assays) have recently been developed for the detection, species differentiation, and phylogenetic analysis of microsporidia. In this paper we review human microsporidial infections and describe and discuss these newly developed molecular techniques. PMID:10194459

  14. Oncocytic lipoadenoma of the parotid gland: Immunohistochemical and cytogenetic analysis.

    PubMed

    Ilie, Marius; Hofman, Véronique; Pedeutour, Florence; Attias, Rita; Santini, Joseph; Hofman, Paul

    2010-01-15

    Salivary gland oncocytic lipoadenoma is an exceptional benign tumor composed of mature adipose tissue associated with a mixture of oncocytes. We report a case of oncocytic lipoadenoma showing sebaceous differentiation, and provide a cytogenetic analysis, which has not yet been described. A 64-year-old male developed a left parotid gland, well-encapsulated tumor measuring 3.5 x 3 cm(2), showing mature fat cells associated with oncocytic changes of epithelial components. Immunohistochemistry showed a dual epithelial population with ductal (positivity for AE1/AE3, CK19, CK7 antibodies) and basal-cell (positivity for p63, CK14, CK5,6 antibodies) differentiation in oncocytic areas. Moreover, oncocytic cells were stained with anti-alpha-1 antichymotrypsin antibody and phosphotungstic acid-hematoxylin staining. Molecular cytogenetic analysis showed a translocation t(12;14), resulting in structural rearrangement of the region framing the HMGA2 gene at 12q14.3. Such alterations in HMGA2 have been described in both lipomas and pleomorphic adenomas of the salivary glands.

  15. Wing Membrane Biopsies for Bat Cytogenetics: Finding of 2n = 54 in Irish Rhinolophushipposideros (Rhinolophidae, Chiroptera, Mammalia) Supports Two Geographically Separated Chromosomal Variants in Europe.

    PubMed

    Kacprzyk, Joanna; Teeling, Emma C; Kelleher, Conor; Volleth, Marianne

    2016-01-01

    In Europe, 2 different diploid chromosome numbers, 2n = 54 and 2n = 56, have been described in the lesser horseshoe bat (Rhinolophushipposideros). The eastern form with 2n = 56 extends from the Czech Republic to Greece. To date, specimens with 54 chromosomes have been reported only from Spain and Germany. This study expands the distributional area of the western variant to Ireland. Strikingly, this distribution of European chromosomal variants is in contrast to the available molecular data that indicate little genetic differentiation of R. hipposideros populations spanning Northwestern to Central Europe. Further, we have developed an optimized protocol for establishing fibroblast cell cultures, suitable for karyotype analyses, from 3-mm wing membrane biopsies. This is a useful technique for cytogenetic studies of endangered bat species, as this non-lethal sampling method imposes only minimum stress to the animal without lasting adverse effects and is routinely used to sample tissue probes for molecular genetic studies in bats. PMID:27333200

  16. Treatment of multiple myeloma with high-risk cytogenetics: a consensus of the International Myeloma Working Group

    PubMed Central

    Avet-Loiseau, Hervé; Lonial, Sagar; Usmani, Saad; Siegel, David; Anderson, Kenneth C.; Chng, Wee-Joo; Moreau, Philippe; Attal, Michel; Kyle, Robert A.; Caers, Jo; Hillengass, Jens; San Miguel, Jesús; van de Donk, Niels W. C. J.; Einsele, Hermann; Bladé, Joan; Durie, Brian G. M.; Goldschmidt, Hartmut; Mateos, María-Victoria; Palumbo, Antonio; Orlowski, Robert

    2016-01-01

    The International Myeloma Working Group consensus updates the definition for high-risk (HR) multiple myeloma based on cytogenetics Several cytogenetic abnormalities such as t(4;14), del(17/17p), t(14;16), t(14;20), nonhyperdiploidy, and gain(1q) were identified that confer poor prognosis. The prognosis of patients showing these abnormalities may vary with the choice of therapy. Treatment strategies have shown promise for HR cytogenetic diseases, such as proteasome inhibition in combination with lenalidomide/pomalidomide, double autologous stem cell transplant plus bortezomib, or combination of immunotherapy with lenalidomide or pomalidomide. Careful analysis of cytogenetic subgroups in trials comparing different treatments remains an important goal. Cross-trial comparisons may provide insight into the effect of new drugs in patients with cytogenetic abnormalities. However, to achieve this, consensus on definitions of analytical techniques, proportion of abnormal cells, and treatment regimens is needed. Based on data available today, bortezomib and carfilzomib treatment appear to improve complete response, progression-free survival, and overall survival in t(4;14) and del(17/17p), whereas lenalidomide may be associated with improved progression-free survival in t(4;14) and del(17/17p). Patients with multiple adverse cytogenetic abnormalities do not benefit from these agents. FISH data are implemented in the revised International Staging System for risk stratification. PMID:27002115

  17. Cytogenetic activity of the coumarin glucoside seseloside

    SciTech Connect

    Arshava, E.A.

    1986-05-01

    The cytogenetic effect of the coumarin glucoside seseloside on plant objects was studied. It was established that low concentrations of the preparation (from 1 x 10/sup -5/ to 1 x 10/sup -3/ ..mu..g/ml) inhibit both spontaneous and radiation-induced mutagenesis. The effect of high concentrations (10 and 100 ..mu..g/ml) causes a mutagenic effect.

  18. Nonlinear Raman Techniques in Femtosecond Time Resolved Spectroscopy for the Analysis and Control of Molecular Dynamics

    SciTech Connect

    Materny, Arnulf; Konradi, Jakow; Namboodiri, Vinu; Namboodiri, Mahesh; Scaria, Abraham

    2008-11-14

    The use of four-wave mixing techniques in femtosecond time-resolved spectroscopy has considerable advantages. Due to the many degrees of freedom offered e.g. by coherent anti-Stokes Raman scattering (CARS), the dynamics even of complex systems can be analyzed in detail. Using pulse shaping techniques in combination with a self-learning loop approach, molecular mode excitation can be controlled very efficiently in a multi-photon excitation process. Results obtained from the optimal control of CARS on {beta}-carotene are discussed.

  19. SPECT and PET serve as molecular imaging techniques and in vivo biomarkers for brain metastases.

    PubMed

    Palumbo, Barbara; Buresta, Tommaso; Nuvoli, Susanna; Spanu, Angela; Schillaci, Orazio; Fravolini, Mario Luca; Palumbo, Isabella

    2014-06-03

    Nuclear medicine techniques (single photon emission computerized tomography, SPECT, and positron emission tomography, PET) represent molecular imaging tools, able to provide in vivo biomarkers of different diseases. To investigate brain tumours and metastases many different radiopharmaceuticals imaged by SPECT and PET can be used. In this review the main and most promising radiopharmaceuticals available to detect brain metastases are reported. Furthermore the diagnostic contribution of the combination of SPECT and PET data with radiological findings (magnetic resonance imaging, MRI) is discussed.

  20. SPECT and PET Serve as Molecular Imaging Techniques and in Vivo Biomarkers for Brain Metastases

    PubMed Central

    Palumbo, Barbara; Buresta, Tommaso; Nuvoli, Susanna; Spanu, Angela; Schillaci, Orazio; Fravolini, Mario Luca; Palumbo, Isabella

    2014-01-01

    Nuclear medicine techniques (single photon emission computerized tomography, SPECT, and positron emission tomography, PET) represent molecular imaging tools, able to provide in vivo biomarkers of different diseases. To investigate brain tumours and metastases many different radiopharmaceuticals imaged by SPECT and PET can be used. In this review the main and most promising radiopharmaceuticals available to detect brain metastases are reported. Furthermore the diagnostic contribution of the combination of SPECT and PET data with radiological findings (magnetic resonance imaging, MRI) is discussed. PMID:24897023

  1. Trisomy 12 in chronic lymphocytic leukemia and hairy cell leukemia: a cytogenetic and interphase cytogenetic study.

    PubMed

    Cuneo, A; Bigoni, R; Balboni, M; Carli, M G; Piva, N; Fagioli, F; Latorraca, A; Wlodarska, I; van den Berghe, H; Castoldi, G

    1994-09-01

    Fluorescent in situ hybridization (FISH) with a chromosome 12-specific pericentromeric probe was performed in 42 patients with B-cell chronic lymphocytic leukemia (CLL) and in 10 patients with hairy cell leukemia (HCL). In all cases, a normal karyotype in more than 10 metaphase cells was obtained by conventional chromosome study. FISH documented that 6/42 patients with CLL in fact had trisomy 12 in 15-49% interphase cells. Sequential FISH studies were performed in 2 cases, showing an increase of percentage of trisomic cells over a 2-month to 4-year period. Two out of 10 patients with HCL, one of whom had morphologic features consistent with a diagnosis of HCL variant, showed 5.5 and 10% interphase nuclei with three fluorescent signals, a finding suggestive of the presence of trisomy 12. Combined immunophenotyping and FISH staining in these patients with HCL documented that trisomic cells were CD11c-positive, CD13-negative, and CD2-negative. We conclude that FISH is a sensitive technique allowing for the detection of trisomy 12 in a fraction of cytogenetically normal patients affected with CLL and HCL. PMID:7858495

  2. Fiber optic profenofos sensor based on surface plasmon resonance technique and molecular imprinting.

    PubMed

    Shrivastav, Anand M; Usha, Sruthi P; Gupta, Banshi D

    2016-05-15

    A successful approach for the fabrication and characterization of an optical fiber sensor for the detection of profenofos based on surface plasmon resonance (SPR) and molecular imprinting is introduced. Molecular imprinting technology is used for the creation of three dimensional binding sites having complementary shape and size of the specific template molecule over a polymer for the recognition of the same. Binding of template molecule with molecularly imprinted polymer (MIP) layer results in the change in the dielectric nature of the sensing surface (polymer) and is identified by SPR technique. Spectral interrogation method is used for the characterization of the sensing probe. The operating profenofos concentration range of the sensor is from 10(-4) to 10(-1)µg/L. A red shift of 18.7 nm in resonance wavelength is recorded for this profenofos concentration range. The maximum sensitivity of the sensor is 12.7 nm/log (µg/L) at 10(-4)µg/L profenofos concentration. Limit of detection (LOD) of the sensor is found to be 2.5×10(-6)µg/L. Selectivity measurements predict the probe highly selective for the profenofos molecule. Besides high sensitivity due to SPR technique and selectivity due to molecular imprinting, proposed sensor has numerous other advantages like immunity to electromagnetic interference, fast response, low cost and capability of online monitoring and remote sensing of analyte due to the fabrication of the probe on optical fiber.

  3. Fiber optic profenofos sensor based on surface plasmon resonance technique and molecular imprinting.

    PubMed

    Shrivastav, Anand M; Usha, Sruthi P; Gupta, Banshi D

    2016-05-15

    A successful approach for the fabrication and characterization of an optical fiber sensor for the detection of profenofos based on surface plasmon resonance (SPR) and molecular imprinting is introduced. Molecular imprinting technology is used for the creation of three dimensional binding sites having complementary shape and size of the specific template molecule over a polymer for the recognition of the same. Binding of template molecule with molecularly imprinted polymer (MIP) layer results in the change in the dielectric nature of the sensing surface (polymer) and is identified by SPR technique. Spectral interrogation method is used for the characterization of the sensing probe. The operating profenofos concentration range of the sensor is from 10(-4) to 10(-1)µg/L. A red shift of 18.7 nm in resonance wavelength is recorded for this profenofos concentration range. The maximum sensitivity of the sensor is 12.7 nm/log (µg/L) at 10(-4)µg/L profenofos concentration. Limit of detection (LOD) of the sensor is found to be 2.5×10(-6)µg/L. Selectivity measurements predict the probe highly selective for the profenofos molecule. Besides high sensitivity due to SPR technique and selectivity due to molecular imprinting, proposed sensor has numerous other advantages like immunity to electromagnetic interference, fast response, low cost and capability of online monitoring and remote sensing of analyte due to the fabrication of the probe on optical fiber. PMID:26706813

  4. Charge transport in molecular junctions: From tunneling to hopping with the probe technique

    SciTech Connect

    Kilgour, Michael; Segal, Dvira

    2015-07-14

    We demonstrate that a simple phenomenological approach can be used to simulate electronic conduction in molecular wires under thermal effects induced by the surrounding environment. This “Landauer-Büttiker’s probe technique” can properly replicate different transport mechanisms, phase coherent nonresonant tunneling, ballistic behavior, and hopping conduction. Specifically, our simulations with the probe method recover the following central characteristics of charge transfer in molecular wires: (i) the electrical conductance of short wires falls off exponentially with molecular length, a manifestation of the tunneling (superexchange) mechanism. Hopping dynamics overtakes superexchange in long wires demonstrating an ohmic-like behavior. (ii) In off-resonance situations, weak dephasing effects facilitate charge transfer, but under large dephasing, the electrical conductance is suppressed. (iii) At high enough temperatures, k{sub B}T/ϵ{sub B} > 1/25, with ϵ{sub B} as the molecular-barrier height, the current is enhanced by a thermal activation (Arrhenius) factor. However, this enhancement takes place for both coherent and incoherent electrons and it does not readily indicate on the underlying mechanism. (iv) At finite-bias, dephasing effects may impede conduction in resonant situations. We further show that memory (non-Markovian) effects can be implemented within the Landauer-Büttiker’s probe technique to model the interaction of electrons with a structured environment. Finally, we examine experimental results of electron transfer in conjugated molecular wires and show that our computational approach can reasonably reproduce reported values to provide mechanistic information.

  5. The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses.

    PubMed

    Davey, Peter A; Pernice, Mathieu; Sablok, Gaurav; Larkum, Anthony; Lee, Huey Tyng; Golicz, Agnieszka; Edwards, David; Dolferus, Rudy; Ralph, Peter

    2016-09-01

    Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events. PMID:27443314

  6. The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses.

    PubMed

    Davey, Peter A; Pernice, Mathieu; Sablok, Gaurav; Larkum, Anthony; Lee, Huey Tyng; Golicz, Agnieszka; Edwards, David; Dolferus, Rudy; Ralph, Peter

    2016-09-01

    Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.

  7. Cytogenetic Profile of de novo Acute Myeloid Leukemia Patients in Malaysia.

    PubMed

    Meng, Chin Yuet; Noor, Puteri J; Ismail, Azli; Ahid, Mohd Fadly Md; Zakaria, Zubaidah

    2013-03-01

    Acute myeloid leukemia (AML) is a heterogeneous disease in terms of cytogenetics and molecular genetics. AML is the most common acute leukemia in adults and its incidence increases with age. Diagnostic cytogenetics is an important prognostic indicator for predicting outcome of AML. We examined the karyotypic patterns of 480 patients with de novo AML seen at government hospitals throughout the country and evaluated the association of chromosome aberrations with the age of patient. Chromosome abnormalities were detected in 146 (30.4%) patients. The most common cytogenetic abnormality was balanced translocation t (8; 21), followed by trisomy 8 (as sole abnormality) and t (15; 17). The age of our Malaysian patients at diagnosis ranged from four months to 81 years, with a median age of 39 years. The normal karyotype was found mainly in patients aged 15-30 years. About 75% of patients with t (8; 21) were below 40 years of age, and the complex karyotype was found with the highest frequently (34.3%) in elderly patients (age above 60 years). More than half of the patients with complex karyotype were above 50 years of age. The deletion 5q was detected only in patients aged above 50 years. Different cytogenetic abnormalities in AML show different frequencies with increasing age. Probably different genetic mechanisms are involved in the pathogenesis of AML and these mechanisms might occur at different frequencies over lifetime. PMID:23675286

  8. Cytogenetic profiles of 2806 patients with acute myeloid leukemia-a retrospective multicenter nationwide study.

    PubMed

    Byun, Ja Min; Kim, Young Jin; Yoon, Hwi-Joong; Kim, Si-Young; Kim, Hee-Je; Yoon, Jaeho; Min, Yoo Hong; Cheong, Jun-Won; Park, Jinny; Lee, Jae Hoon; Hong, Dae Sik; Park, Seong Kyu; Kim, Hyeoung-Joon; Ahn, Jae-Sook; Shin, Ho-Jin; Chung, Joo Seop; Lee, Won Sik; Lee, Sang Min; Park, Yong; Kim, Byung Soo; Lee, Je-Hwan; Lee, Kyoo-Hyung; Jung, Chul Won; Jang, Jun Ho; Min, Woo-Sung; Park, Tae Sung

    2016-08-01

    The cytogenetic and molecular data is recognized as the most valuable prognostic factor in acute myeloid leukemia (AML). Our aim was to systemically analyze the cytogenetics of Korean AML patients and to compare the cytogenetic profiles of various races to identify possible geographic heterogeneity. We retrospectively reviewed medical records of 2806 AML patients diagnosed at 11 tertiary teaching hospitals in Korea between January 2007 and December 2011. The most common recurrent chromosomal abnormality was t(8;21) (8.8 %, 238/2717), but t(15;17) showed an almost same number (8.6 %,235/2717). Among de novo AML, the most frequent aberrations were t(15;17), observed in 229 (10.7 %). The most common French-American-British (FAB) classification type was M2 (32.2 %), and recurrent cytogenetic abnormalities correlated with the FAB subtypes. Among 283 secondary AML cases, myelodysplastic syndrome was the most common predisposing factor. About 67.1 % of the secondary AML cases were associated with chromosomal aberrations, and chromosome 7 abnormalities (n = 45, 15.9 %) were most common. The incidence of FLT3 internal tandem duplication mutation was relatively low at 15 %. Our study reports certain similarities and differences in comparison to previous reports. Such discrepancies call for extensive epidemiological studies to clarify the role of genetic as well as geographic heterogeneity in the pathogenesis of AML.

  9. Cytogenetic profiles of 2806 patients with acute myeloid leukemia-a retrospective multicenter nationwide study.

    PubMed

    Byun, Ja Min; Kim, Young Jin; Yoon, Hwi-Joong; Kim, Si-Young; Kim, Hee-Je; Yoon, Jaeho; Min, Yoo Hong; Cheong, Jun-Won; Park, Jinny; Lee, Jae Hoon; Hong, Dae Sik; Park, Seong Kyu; Kim, Hyeoung-Joon; Ahn, Jae-Sook; Shin, Ho-Jin; Chung, Joo Seop; Lee, Won Sik; Lee, Sang Min; Park, Yong; Kim, Byung Soo; Lee, Je-Hwan; Lee, Kyoo-Hyung; Jung, Chul Won; Jang, Jun Ho; Min, Woo-Sung; Park, Tae Sung

    2016-08-01

    The cytogenetic and molecular data is recognized as the most valuable prognostic factor in acute myeloid leukemia (AML). Our aim was to systemically analyze the cytogenetics of Korean AML patients and to compare the cytogenetic profiles of various races to identify possible geographic heterogeneity. We retrospectively reviewed medical records of 2806 AML patients diagnosed at 11 tertiary teaching hospitals in Korea between January 2007 and December 2011. The most common recurrent chromosomal abnormality was t(8;21) (8.8 %, 238/2717), but t(15;17) showed an almost same number (8.6 %,235/2717). Among de novo AML, the most frequent aberrations were t(15;17), observed in 229 (10.7 %). The most common French-American-British (FAB) classification type was M2 (32.2 %), and recurrent cytogenetic abnormalities correlated with the FAB subtypes. Among 283 secondary AML cases, myelodysplastic syndrome was the most common predisposing factor. About 67.1 % of the secondary AML cases were associated with chromosomal aberrations, and chromosome 7 abnormalities (n = 45, 15.9 %) were most common. The incidence of FLT3 internal tandem duplication mutation was relatively low at 15 %. Our study reports certain similarities and differences in comparison to previous reports. Such discrepancies call for extensive epidemiological studies to clarify the role of genetic as well as geographic heterogeneity in the pathogenesis of AML. PMID:27230620

  10. Molecular Dynamics and Monte Carlo simulations in the microcanonical ensemble: Quantitative comparison and reweighting techniques.

    PubMed

    Schierz, Philipp; Zierenberg, Johannes; Janke, Wolfhard

    2015-10-01

    Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For three test examples, we study first- and second-order phase transitions with a focus on liquid-gas like transitions. We present MD analysis techniques to compensate for conservation law effects due to linear and angular momentum conservation. Additionally, we apply the weighted histogram analysis method to microcanonical histograms reweighted from MD simulations. By this means, we are able to estimate the density of states from many microcanonical simulations at various total energies. This further allows us to compute estimates of canonical expectation values.

  11. Molecular Rayleigh Scattering Techniques Developed for Measuring Gas Flow Velocity, Density, Temperature, and Turbulence

    NASA Technical Reports Server (NTRS)

    Mielke, Amy F.; Seasholtz, Richard G.; Elam, Kristie A.; Panda, Jayanta

    2005-01-01

    Nonintrusive optical point-wise measurement techniques utilizing the principles of molecular Rayleigh scattering have been developed at the NASA Glenn Research Center to obtain time-averaged information about gas velocity, density, temperature, and turbulence, or dynamic information about gas velocity and density in unseeded flows. These techniques enable measurements that are necessary for validating computational fluid dynamics (CFD) and computational aeroacoustic (CAA) codes. Dynamic measurements allow the calculation of power spectra for the various flow properties. This type of information is currently being used in jet noise studies, correlating sound pressure fluctuations with velocity and density fluctuations to determine noise sources in jets. These nonintrusive techniques are particularly useful in supersonic flows, where seeding the flow with particles is not an option, and where the environment is too harsh for hot-wire measurements.

  12. Diagnostic procedures in tularaemia with special focus on molecular and immunological techniques.

    PubMed

    Splettstoesser, W D; Tomaso, H; Al Dahouk, S; Neubauer, H; Schuff-Werner, P

    2005-08-01

    Tularaemia is a severe bacterial zoonosis caused by the highly infectious agent Francisella tularensis. It is endemic in countries of the northern hemisphere ranging from North America to Europe, Asia and Japan. Very recently, Francisella-like strains causing disease in humans were described from tropical northern Australia. In the last decade, efforts have been made to develop sensitive and specific immunological and molecular techniques for the laboratory diagnosis of tularaemia and also for the definite identification of members of the species F. tularensis and its four subspecies. Screening for the keyword 'Francisella' a Medline search over the last decade was performed and articles describing diagnostic methods for tularaemia and its causative agent were selected. Besides classical microbiological techniques (cultivation, biochemical profiling, susceptibility testing) several new immunological and molecular approaches to identify F. tularensis have been introduced employing highly specific antibodies and various polymerase chain reaction (PCR)-based methods. Whereas direct antigen detection by enzyme-linked immunosorbent assay (ELISA) or immunofluorescence might allow early presumptive diagnosis of tularaemia, these methods--like all PCR techniques--still await further evaluation. Therefore, diagnosis of tularaemia still relies mainly on the demonstration of specific antibodies in the host. ELISA and immunoblot methods started to replace the standard tube or micro-agglutination assays. However, the diagnostic value of antibody detection in the very early clinical phase of tularaemia is limited. Francisella tularensis is regarded as a 'highest priority' biological agent (category 'A' according to the CDC, Atlanta, GA, USA), thus rapid and reliable diagnosis of tularaemia is required not only for a timely onset of therapy, the handling of outbreak investigations but also for the surveillance of endemic foci. Only very recently, evaluated test kits for

  13. Integrating Nanostructured Artificial Receptors with Whispering Gallery Mode Optical Microresonators via Inorganic Molecular Imprinting Techniques

    PubMed Central

    Hammond, G. Denise; Vojta, Adam L.; Grant, Sheila A.; Hunt, Heather K.

    2016-01-01

    The creation of label-free biosensors capable of accurately detecting trace contaminants, particularly small organic molecules, is of significant interest for applications in environmental monitoring. This is achieved by pairing a high-sensitivity signal transducer with a biorecognition element that imparts selectivity towards the compound of interest. However, many environmental pollutants do not have corresponding biorecognition elements. Fortunately, biomimetic chemistries, such as molecular imprinting, allow for the design of artificial receptors with very high selectivity for the target. Here, we perform a proof-of-concept study to show how artificial receptors may be created from inorganic silanes using the molecular imprinting technique and paired with high-sensitivity transducers without loss of device performance. Silica microsphere Whispering Gallery Mode optical microresonators are coated with a silica thin film templated by a small fluorescent dye, fluorescein isothiocyanate, which serves as our model target. Oxygen plasma degradation and solvent extraction of the template are compared. Extracted optical devices are interacted with the template molecule to confirm successful sorption of the template. Surface characterization is accomplished via fluorescence and optical microscopy, ellipsometry, optical profilometry, and contact angle measurements. The quality factors of the devices are measured to evaluate the impact of the coating on device sensitivity. The resulting devices show uniform surface coating with no microstructural damage with Q factors above 106. This is the first report demonstrating the integration of these devices with molecular imprinting techniques, and could lead to new routes to biosensor creation for environmental monitoring. PMID:27314397

  14. Integrating Nanostructured Artificial Receptors with Whispering Gallery Mode Optical Microresonators via Inorganic Molecular Imprinting Techniques.

    PubMed

    Hammond, G Denise; Vojta, Adam L; Grant, Sheila A; Hunt, Heather K

    2016-01-01

    The creation of label-free biosensors capable of accurately detecting trace contaminants, particularly small organic molecules, is of significant interest for applications in environmental monitoring. This is achieved by pairing a high-sensitivity signal transducer with a biorecognition element that imparts selectivity towards the compound of interest. However, many environmental pollutants do not have corresponding biorecognition elements. Fortunately, biomimetic chemistries, such as molecular imprinting, allow for the design of artificial receptors with very high selectivity for the target. Here, we perform a proof-of-concept study to show how artificial receptors may be created from inorganic silanes using the molecular imprinting technique and paired with high-sensitivity transducers without loss of device performance. Silica microsphere Whispering Gallery Mode optical microresonators are coated with a silica thin film templated by a small fluorescent dye, fluorescein isothiocyanate, which serves as our model target. Oxygen plasma degradation and solvent extraction of the template are compared. Extracted optical devices are interacted with the template molecule to confirm successful sorption of the template. Surface characterization is accomplished via fluorescence and optical microscopy, ellipsometry, optical profilometry, and contact angle measurements. The quality factors of the devices are measured to evaluate the impact of the coating on device sensitivity. The resulting devices show uniform surface coating with no microstructural damage with Q factors above 10⁶. This is the first report demonstrating the integration of these devices with molecular imprinting techniques, and could lead to new routes to biosensor creation for environmental monitoring. PMID:27314397

  15. A multiscale modeling technique for bridging molecular dynamics with finite element method

    SciTech Connect

    Lee, Yongchang Basaran, Cemal

    2013-11-15

    In computational mechanics, molecular dynamics (MD) and finite element (FE) analysis are well developed and most popular on nanoscale and macroscale analysis, respectively. MD can very well simulate the atomistic behavior, but cannot simulate macroscale length and time due to computational limits. FE can very well simulate continuum mechanics (CM) problems, but has the limitation of the lack of atomistic level degrees of freedom. Multiscale modeling is an expedient methodology with a potential to connect different levels of modeling such as quantum mechanics, molecular dynamics, and continuum mechanics. This study proposes a new multiscale modeling technique to couple MD with FE. The proposed method relies on weighted average momentum principle. A wave propagation example has been used to illustrate the challenges in coupling MD with FE and to verify the proposed technique. Furthermore, 2-Dimensional problem has also been used to demonstrate how this method would translate into real world applications. -- Highlights: •A weighted averaging momentum method is introduced for bridging molecular dynamics (MD) with finite element (FE) method. •The proposed method shows excellent coupling results in 1-D and 2-D examples. •The proposed method successfully reduces the spurious wave reflection at the border of MD and FE regions. •Big advantages of the proposed method are simplicity and inexpensive computational cost of multiscale analysis.

  16. Theory of the double-edge molecular technique for Doppler lidar wind measurement.

    PubMed

    Flesia, C; Korb, C L

    1999-01-20

    The theory of the double-edge lidar technique for measuring the wind with molecular backscatter is described. Two high-spectral-resolution edge filters are located in the wings of the Rayleigh-Brillouin profile. This doubles the signal change per unit Doppler shift, the sensitivity, and improves measurement accuracy relative to the single-edge technique by nearly a factor of 2. The use of a crossover region where the sensitivity of a molecular- and an aerosol-based measurement is equal is described. Use of this region desensitizes the molecular measurement to the effects of aerosol scattering over a velocity range of +/-100 m/s. We give methods for correcting short-term, shot-to-shot, frequency jitter and drift with a laser reference frequency measurement and methods for long-term frequency correction with a servo control system. The effects of Rayleigh-Brillouin scattering on the measurement are shown to be significant and are included in the analysis. Simulations for a conical scanning satellite-based lidar at 355 nm show an accuracy of 2-3 m/s for altitudes of 2-15 km for a 1-km vertical resolution, a satellite altitude of 400 km, and a 200 km x 200 km spatial resolution. PMID:18305631

  17. Control of molecular weight of polystyrene using the reverse iodine transfer polymerization (RITP)-emulsion technique.

    PubMed

    Oh, Hyeong Geun; Shin, Hongcheol; Jung, Hyejun; Lee, Byung Hyung; Choe, Soonja

    2011-01-15

    The RITP-emulsion polymerization of styrene in the presence of molecular iodine has been successfully performed using potassium persulfate (KPS) as an initiator and 1-hexadecanesulfonate as an emulsifier under argon atmosphere at 80°C for 7 hrs in the absence of light. The effects of the iodine concentration, molar ratio between KPS and iodine, and solid contents on the molecular weight of polystyrene (PS) were studied. As the iodine concentration increased from 0.05 to 0.504 mmol under the fixed [KPS]/[I(2)] ratio at 4.5, the weight-average molecular weight of PS substantially decreased from 126,120 to 35,690 g/mol, the conversion increased from 85.0% to 95.2%, and the weight-average particle diameter decreased from 159 to 103 nm. In addition, as the ratio of [KPS]/[I(2)] increased from 0.5 to 6.0 at the fixed [I(2)] of 0.504 mmol, the weight-average molecular weight of PS decreased from 72,170 to 30,640 g/mol with high conversion between 81.7% and 96.5%. Moreover, when the styrene solid content increased from 10 to 40 wt.% at the fixed [KPS]/[I(2)] ratio of 4.5, the weight-average molecular weight of PS varied between 33,500 and 37,200 g/mol, the conversion varied between 94.9% and 89.7% and the weight-average diameter varied from 122 to 205 nm. Thus, the control of molecular weight of PS less than 100,000g/mol with high conversion (95%) and particle stability of up to 40 wt.% solid content were easily achieved through the usage of iodine with suitable ratio of [KPS]/[I(2)] in the RITP-emulsion polymerization technique, which is of great industrial importance.

  18. Molecular-Based Optical Measurement Techniques for Transition and Turbulence in High-Speed Flow

    NASA Technical Reports Server (NTRS)

    Bathel, Brett F.; Danehy, Paul M.; Cutler, Andrew D.

    2013-01-01

    High-speed laminar-to-turbulent transition and turbulence affect the control of flight vehicles, the heat transfer rate to a flight vehicle's surface, the material selected to protect such vehicles from high heating loads, the ultimate weight of a flight vehicle due to the presence of thermal protection systems, the efficiency of fuel-air mixing processes in high-speed combustion applications, etc. Gaining a fundamental understanding of the physical mechanisms involved in the transition process will lead to the development of predictive capabilities that can identify transition location and its impact on parameters like surface heating. Currently, there is no general theory that can completely describe the transition-to-turbulence process. However, transition research has led to the identification of the predominant pathways by which this process occurs. For a truly physics-based model of transition to be developed, the individual stages in the paths leading to the onset of fully turbulent flow must be well understood. This requires that each pathway be computationally modeled and experimentally characterized and validated. This may also lead to the discovery of new physical pathways. This document is intended to describe molecular based measurement techniques that have been developed, addressing the needs of the high-speed transition-to-turbulence and high-speed turbulence research fields. In particular, we focus on techniques that have either been used to study high speed transition and turbulence or techniques that show promise for studying these flows. This review is not exhaustive. In addition to the probe-based techniques described in the previous paragraph, several other classes of measurement techniques that are, or could be, used to study high speed transition and turbulence are excluded from this manuscript. For example, surface measurement techniques such as pressure and temperature paint, phosphor thermography, skin friction measurements and

  19. Mass spectrometric techniques for characterizing low-molecular-weight resins used as paint varnishes.

    PubMed

    Bonaduce, I; Colombini, M P; Degano, I; Di Girolamo, F; La Nasa, J; Modugno, F; Orsini, S

    2013-01-01

    The molecular structure of three low-molecular-weight resins used as paint varnishes has been characterized by use of an approach based on three different mass spectrometric techniques. We investigated the ketone resin MS2A, the aldehyde resin Laropal A81, and the hydrocarbon resin Regalrez 1094, now commonly used in restoration. To date, the molecular structures of these resins have not been completely elucidated. To improve current knowledge of the chemical composition of these materials, information obtained by gas chromatography-mass spectrometry (GC/MS), pyrolysis-gas chromatography-mass spectrometry (Py/GC/MS), and electrospray ionization mass spectrometry (ESI-Q-ToF) was combined. Analysis, in solution, of the whole polymeric fraction of the resins by flow-injection ESI-Q-ToF, and of the non-polymeric fraction by GC-MS, enabled us to identify previously unreported features of the polymer structures. In addition, the Py-GC/MS profiles that we obtained will help to enhance the databases currently available in the literature. The proposed approach can be extended to other low-molecular-weight resins used as varnishes in conservation.

  20. Photo-metalorganic molecular-beam epitaxy: A new epitaxial growth technique

    SciTech Connect

    Tokumitsu, E.; Yamada, T.; Konagai, M.; Takahashi, K.

    1989-05-01

    Metalorganic molecular-beam epitaxy (MOMBE) combines many important advantages of molecular-beam epitaxy and metalorganic chemical vapor deposition. One of the most important features of MOMBE is that photochemical reaction can be used and we can call this new technique ''photo-MOMBE.'' Triisobutylaluminum (TIBA) has been used in photo-MOMBE instead of triethylaluminum (TEA) as a new aluminum source in order to enhance the photodecomposition. The optical absorption coefficient of TIBA for 193 nm was found to be three times greater than that of TEA. Selective deposition of Al, AlAs, and GaAlAs was carried out by using an ArF excimer laser. The Al mole fraction of GaAlAs ternary alloy grown with the excimer laser irradiation was greater than that of the film grown without the laser irradiation.

  1. Future Directions in Pain Management: Integrating Anatomically Selective Delivery Techniques With Novel Molecularly Selective Agents.

    PubMed

    Pleticha, Josef; Maus, Timothy P; Beutler, Andreas S

    2016-04-01

    Treatment for chronic, locoregional pain ranks among the most prevalent unmet medical needs. The failure of systemic analgesic drugs, such as opioids, is often due to their off-target toxicity, development of tolerance, and abuse potential. Interventional pain procedures provide target specificity but lack pharmacologically selective agents with long-term efficacy. Gene therapy vectors are a new tool for the development of molecularly selective pain therapies, which have already been proved to provide durable analgesia in preclinical models. Taken together, advances in image-guided delivery and gene therapy may lead to a new class of dual selective analgesic treatments integrating the molecular selectivity of analgesic genes with the anatomic selectivity of interventional delivery techniques.

  2. Cytogenetic Findings in Mentally Retarded Iranian Patients

    PubMed Central

    Nasiri, F; Mahjoubi, F; Manouchehry, F; Razazian, F; Mortezapour, F; Rahnama, M

    2012-01-01

    We conducted a cytogenetic study on 865 individuals with idiopathic mental retardation (MR) who were admitted to the Cytogenetics Department of the Iran Blood Transfusion Organisation (IBTO) Research Centre, Tehran, Iran; these were performed on blood samples using conventional staining methods. Chromosome anomalies were identified in 205 of the patients (23.6%). The majority were Down’s syndrome cases (n = 138). In 33 males, a positive fragile X anomaly was found. The remainder (n = 34) had other chromosomal abnormalities including structural chromosome aberrations (n = 23), marker chromosomes with an unknown origin (n = 3), sex chromosome aneuploidy (n = 6) and trisomy 18 (n = 2). The contribution of chromosome aberrations to the cause of MR in this group of patients is discussed. PMID:24052729

  3. Interpretation of cytogenetic results in multiple myeloma for clinical practice

    PubMed Central

    Rajan, A M; Rajkumar, S V

    2015-01-01

    The interpretation of cytogenetic abnormalities in multiple myeloma (MM) is often a challenging task. MM is characterized by several cytogenetic abnormalities that occur at various time points in the disease course. The interpretation of cytogenetic results in MM is complicated by the number and complexity of the abnormalities, the methods used to detect them and the disease stage at which they are detected. Specific cytogenetic abnormalities affect clinical presentation, progression of smoldering multiple myeloma (SMM) to MM, prognosis of MM and management strategies. The goal of this paper is to provide a review of how MM is classified into specific subtypes based on primary cytogenetic abnormalities and to provide a concise overview of how to interpret cytogenetic abnormalities based on the disease stage to aid clinical practice and patient management. PMID:26517360

  4. Applied Protein and Molecular Techniques for Characterization of B Cell Neoplasms in Horses

    PubMed Central

    Badial, Peres R.; Tallmadge, Rebecca L.; Miller, Steven; Stokol, Tracy; Richards, Kristy; Borges, Alexandre S.

    2015-01-01

    Mature B cell neoplasms cover a spectrum of diseases involving lymphoid tissues (lymphoma) or blood (leukemia), with an overlap between these two presentations. Previous studies describing equine lymphoid neoplasias have not included analyses of clonality using molecular techniques. The objective of this study was to use molecular techniques to advance the classification of B cell lymphoproliferative diseases in five adult equine patients with a rare condition of monoclonal gammopathy, B cell leukemia, and concurrent lymphadenopathy (lymphoma/leukemia). The B cell neoplasms were phenotypically characterized by gene and cell surface molecule expression, secreted immunoglobulin (Ig) isotype concentrations, Ig heavy-chain variable (IGHV) region domain sequencing, and spectratyping. All five patients had hyperglobulinemia due to IgG1 or IgG4/7 monoclonal gammopathy. Peripheral blood leukocyte immunophenotyping revealed high proportions of IgG1- or IgG4/7-positive cells and relative T cell lymphopenia. Most leukemic cells lacked the surface B cell markers CD19 and CD21. IGHG1 or IGHG4/7 gene expression was consistent with surface protein expression, and secreted isotype and Ig spectratyping revealed one dominant monoclonal peak. The mRNA expression of the B cell-associated developmental genes EBF1, PAX5, and CD19 was high compared to that of the plasma cell-associated marker CD38. Sequence analysis of the IGHV domain of leukemic cells revealed mutated Igs. In conclusion, the protein and molecular techniques used in this study identified neoplastic cells compatible with a developmental transition between B cell and plasma cell stages, and they can be used for the classification of equine B cell lymphoproliferative disease. PMID:26311245

  5. Challenges in determining causation in structure-function studies using molecular biological techniques.

    PubMed

    de los Reyes, Francis L

    2010-09-01

    The use of molecular biological techniques for determining the levels and types of different microbial populations in bioreactors has led to the emergence of the microbial community 'structure-function' paradigm that is often used in research. Typically, lab- or full-scale systems are monitored for the relevant parameters, and these parameters are related to the changes in microbial populations. Research in activated sludge phenomena, such as filamentous bulking, filamentous foaming, nitrogen removal, and phosphorus removal, are replete with many examples of this 'structure-function' paradigm, most commonly those that involve 16S rRNA gene-based analysis of the microbial populations. In many cases, such studies assume a causal microbial population (e.g., a species that causes bulking or foaming), or conclude in identifying a causal population. However, assigning cause to specific organisms and populations is problematic in a complex environment such as wastewater bioreactors. The Koch-Henle postulates, the gold standard in evaluating causation of disease, have limitations when applied to systems with mixed microbial communities with complex interactions, particularly if pure cultures are not available. Molecular techniques that allow specific identification and quantification of organisms have been used by researchers to overcome the limitations of culture-based techniques, and at the same time, raised new questions on the applicability of causation postulates in environmental systems. In this paper, various causation criteria improving on the Koch-Henle postulates are presented. Complicating issues in assigning cause in wastewater bioreactors are identified. Approaches for determining cause-effect relationships are illustrated using 16S rDNA-based investigations of filaments that cause bulking and foaming in activated sludge. The hope is that a causation framework that accounts for the assumptions in molecular studies, as applied to wastewater treatment research

  6. [Cytogenetic analysis of cosmonaut's blood lymphocytes exposed to low space radiation doses and its place in clinical-physiological health monitoring].

    PubMed

    Fedorenko, B S; Snigireva, G P; Ivanov, A A

    2010-01-01

    The article discusses the informative significance and pertinence of cytogenetic analysis of peripheral blood lymphocytes to the clinical-physiological investigations of cosmonauts conducted before and after space missions (SM) of varying duration. The authors point out high sensitivity of the technique, relative simplicity and affordability of the analysis of instable chromosomal aberrations including such radiation effect markers as dicentrics and centric rings. Cytogenetic investigation of cosmonauts could be used to estimate ionizing radiation dose, and to predict delayed effects. PMID:21033391

  7. A modified staining technique for arbuscular mycorrhiza compatible with molecular probes.

    PubMed

    Pitet, M; Camprubí, A; Calvet, C; Estaún, V

    2009-02-01

    The effects of the different steps of the root staining on the arbuscular mycorrhizal (AM) fungal rDNA extraction and amplification have been assessed. The results obtained using molecular techniques are compared with those obtained from fresh, non-stained leek roots. A modified staining procedure that eliminates heating, the use of hydrochloric acid and trypan blue, has been proved to be the most adequate to observe the AM colonisation in different plant species with/without lignified roots allowing at the same time the subsequent rDNA extraction and amplification from the stained roots. The staining technique decreased the sensitivity of the process and a higher number of roots had to be used to obtain enough material for a positive amplification. The extraction and amplification process was reliable up to 3 days after staining. A week after staining, the amplification was not dependable and after 2 weeks there was no amplification from stained material.

  8. Gender identification of Grasshopper Sparrows comparing behavioral, morphological, and molecular techniques

    USGS Publications Warehouse

    Ammer, F.K.; Wood, P.B.; McPherson, R.J.

    2008-01-01

    Correct gender identification in monomorphic species is often difficult especially if males and females do not display obvious behavioral and breeding differences. We compared gender specific morphology and behavior with recently developed DNA techniques for gender identification in the monomorphic Grasshopper Sparrow (Ammodramus savannarum). Gender was ascertained with DNA in 213 individuals using the 2550F/2718R primer set and 3% agarose gel electrophoresis. Field observations using behavior and breeding characteristics to identify gender matched DNA analyses with 100% accuracy for adult males and females. Gender was identified with DNA for all captured juveniles that did not display gender specific traits or behaviors in the field. The molecular techniques used offered a high level of accuracy and may be useful in studies of dispersal mechanisms and winter assemblage composition in monomorphic species.

  9. Rapid identification of chromosomal rearrangements by PRINS technique

    SciTech Connect

    Pellestor, F.; Giradet, A.; Andreo, B.

    1994-09-01

    Chromosomal rearrangements contribute significantly to human reproductive failure, malformation/mental retardation syndromes and carcinogenesis. The variety of structural rearrangements is almost infinite and an identification by conventional cytogenetics is often labor intensive and may remain doubtful. Recent advances in molecular cytogenetics have provided new tools for detecting chromosomal abnormalities. The fluorescence in situ hybridization (FISH) procedure is actually the most employed technique and has led to numerous clinical applications. However, techniques required to produce suitable probes are time consuming and not accessible to all cytogenetics laboratories. The PRimed In Situ labeling (PRINS) method provides an alternate way for in situ chromosome screening. In this procedure, the chromosomal detection is performed by in situ annealing of a specific primer and subsequent primer extension by a Taq DNA polymerase in the presence of labeled nucleotides. Application of PRINS in clinical diagnosis is still limited. We have developed a semi-automatic PRINS protocol and used it to identify the origin of several chromosomal abnormalities. We report here the results of studies of three structural rearrangements: a translocation t(21;21), a supernumerary ring marker chromosome 18 and a complex chromosome 13 mosaicism involving a 13;13 Robertsonian translocation and a ring chromosome 13.

  10. Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes.

    PubMed

    Justé, A; Thomma, B P H J; Lievens, B

    2008-09-01

    In the last two decades major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids. These methods are now increasingly applied in food microbiology as well. This review presents an overview of current community profiling techniques with their (potential) applications in food and food-related ecosystems. We critically assessed both the power and limitations of these techniques and present recent advances in the field of food microbiology attained by their application. It is unlikely that a single approach will be universally applicable for analyzing microbial communities in unknown matrices. However, when screening samples for well-defined species or functions, techniques such as DNA arrays and real-time PCR have the potential to overtake current culture-based methods. Most importantly, molecular methods will allow us to surpass our current culturing limitations, thus revealing the extent and importance of the 'non-culturable' microbial flora that occurs in food matrices and production.

  11. An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

    An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

  12. Recent applications of boxed molecular dynamics: a simple multiscale technique for atomistic simulations

    PubMed Central

    Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R.; Shalashilin, Dmitrii V.

    2014-01-01

    In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely. PMID:24982247

  13. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    PubMed

    Genoni, Alessandro

    2013-07-01

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  14. Application of different molecular techniques for characterization of catalase-positive cocci isolated from sucuk.

    PubMed

    Kesmen, Zülal; Yarimcam, Burcu; Aslan, Hakiye; Ozbekar, Esra; Yetim, Hasan

    2014-02-01

    This study was carried out for the characterization and discrimination of the indigenous Gram positive, catalase-positive cocci (GCC) population in sucuk, a traditional Turkish dry-fermented sausage. Sucuk samples, produced by the traditional method without starter culture were collected from 8 local producers in Kayseri/Turkey and a total of 116 GCC isolates were identified by using different molecular techniques. Two different molecular fingerprinting methods; namely, randomly amplified polymorphic DNA-PCR (RAPD-PCR) and repetitive extragenic palindrome-PCR (rep-PCR), were used for the clustering of isolates and identification at species level was carried out by full length sequencing of 16S rDNA. Combining the results obtained from molecular fingerprinting and 16S rDNA sequencing showed that the dominant GCC species isolated from the sucuk samples was Staphylococcus saprophyticus followed by Staphylococcus succinus and Staphylococcus equorum belonging to the Staphylococcus genus. Real-time PCR DNA melting curve analysis and high-resolution melting (HRM) analysis targeting the V1 + V3 regions of 16S rDNA were also applied for the discrimination of isolates belonging to different species. It was observed statistically different Tm values and species-specific HRM profiles for all except 2 species (S. saprophyticus and Staphylococcus xylosus) that have high 16S rDNA sequence similarity. The combination of rep-PCR and/or PCR-RAPD with 16S rRNA gene sequencing was an efficient approach for the characterization and identification of the GCC population in spontaneously fermented sucuk. On the other hand, intercalating dye assays were found to be a simple and very promising technique for the differentiation of the GCC population at species level.

  15. Application of different molecular techniques for characterization of catalase-positive cocci isolated from sucuk.

    PubMed

    Kesmen, Zülal; Yarimcam, Burcu; Aslan, Hakiye; Ozbekar, Esra; Yetim, Hasan

    2014-02-01

    This study was carried out for the characterization and discrimination of the indigenous Gram positive, catalase-positive cocci (GCC) population in sucuk, a traditional Turkish dry-fermented sausage. Sucuk samples, produced by the traditional method without starter culture were collected from 8 local producers in Kayseri/Turkey and a total of 116 GCC isolates were identified by using different molecular techniques. Two different molecular fingerprinting methods; namely, randomly amplified polymorphic DNA-PCR (RAPD-PCR) and repetitive extragenic palindrome-PCR (rep-PCR), were used for the clustering of isolates and identification at species level was carried out by full length sequencing of 16S rDNA. Combining the results obtained from molecular fingerprinting and 16S rDNA sequencing showed that the dominant GCC species isolated from the sucuk samples was Staphylococcus saprophyticus followed by Staphylococcus succinus and Staphylococcus equorum belonging to the Staphylococcus genus. Real-time PCR DNA melting curve analysis and high-resolution melting (HRM) analysis targeting the V1 + V3 regions of 16S rDNA were also applied for the discrimination of isolates belonging to different species. It was observed statistically different Tm values and species-specific HRM profiles for all except 2 species (S. saprophyticus and Staphylococcus xylosus) that have high 16S rDNA sequence similarity. The combination of rep-PCR and/or PCR-RAPD with 16S rRNA gene sequencing was an efficient approach for the characterization and identification of the GCC population in spontaneously fermented sucuk. On the other hand, intercalating dye assays were found to be a simple and very promising technique for the differentiation of the GCC population at species level. PMID:24410408

  16. New Molecular Techniques to Study the Skin Microbiota of Diabetic Foot Ulcers

    PubMed Central

    Lavigne, Jean-Philippe; Sotto, Albert; Dunyach-Remy, Catherine; Lipsky, Benjamin A.

    2015-01-01

    Significance: Diabetic foot ulcers (DFU) are a major and growing public health problem. They pose difficulties in clinical practice in both diagnosis and management. Bacterial interactions on the skin surface are important in the pathophysiology of DFU and may contribute to a delay in healing. Fully identifying bacteria present in these wounds is difficult with traditional culture methods. New molecular tools, however, have greatly contributed to our understanding of the role of the cutaneous microbiota in DFU. Recent Advances: Molecular technologies revealed new information concerning how bacteria are organized in DFU. This has led to the concept of “functionally equivalent pathogroups,” meaning that certain bacterial species which are usually nonpathogenic (or at least incapable of maintaining a chronic infection on their own) may coaggregate symbiotically in a pathogenic biofilm and act synergistically to cause a chronic infection. The distribution of pathogens in multispecies biofilms is nonrandom. The high bacterial diversity is probably related to the development of a microbial biofilm that is irreversibly attached to the wound matrix. Critical Issues: Using molecular techniques requires a financial outlay for high-cost equipment. They are still too time-consuming to perform and reporting is too delayed for them to be used in routine practice. Finally, they do not differentiate live from dead or pathogenic from nonpathogenic microorganisms. Future Directions: Molecular tools have better documented the composition and organization of the skin flora. Further advances are required to elucidate which among the many bacteria in the DFU flora are likely to be pathogens, rather than colonizers. PMID:25566413

  17. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

    PubMed Central

    Katchalski-Katzir, E; Shariv, I; Eisenstein, M; Friesem, A A; Aflalo, C; Vakser, I A

    1992-01-01

    A geometric recognition algorithm was developed to identify molecular surface complementarity. It is based on a purely geometric approach and takes advantage of techniques applied in the field of pattern recognition. The algorithm involves an automated procedure including (i) a digital representation of the molecules (derived from atomic coordinates) by three-dimensional discrete functions that distinguishes between the surface and the interior; (ii) the calculation, using Fourier transformation, of a correlation function that assesses the degree of molecular surface overlap and penetration upon relative shifts of the molecules in three dimensions; and (iii) a scan of the relative orientations of the molecules in three dimensions. The algorithm provides a list of correlation values indicating the extent of geometric match between the surfaces of the molecules; each of these values is associated with six numbers describing the relative position (translation and rotation) of the molecules. The procedure is thus equivalent to a six-dimensional search but much faster by design, and the computation time is only moderately dependent on molecular size. The procedure was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted. The molecular pairs were deoxyhemoglobin and methemoglobin, tRNA synthetase-tyrosinyl adenylate, aspartic proteinase-peptide inhibitor, and trypsin-trypsin inhibitor. A more realistic test was performed with the last two pairs by using the structures of uncomplexed aspartic proteinase and trypsin inhibitor, respectively. The results are indicative of the extent of conformational changes in the molecules tolerated by the algorithm. Images PMID:1549581

  18. A retrospective analysis of cytogenetic alterations in patients with newly diagnosed multiple myeloma: a single center study in Korea

    PubMed Central

    Li, Shuhua; Lim, Hyeon-Ho; Woo, Kwang-Sook; Kim, Sung-Hyun

    2016-01-01

    Background The accurate identification of cytogenetic abnormalities in multiple myeloma (MM) has become more important over recent years for the development of new diagnostic and prognostic markers. In this study, we retrospectively analyzed the cytogenetic aberrations in MM cases as an initial assessment in a single institute. Methods We reviewed the cytogenetic results from 222 patients who were newly diagnosed with MM between January 2000 and December 2015. Chromosomal analysis was performed on cultured bone marrow samples by standard G-banding technique. At least 20 metaphase cells were analyzed for karyotyping. Results Clonal chromosome abnormalities were detected in 45.0% (100/222) of the patients. Among these results, 80 cases (80.0%) had both numerical and structural chromosome abnormalities. Overall hyperdiploidy with structural cytogenetic aberrations was the most common finding (44.0%), followed by hypodiploidy with structural aberrations (28.0%). Amplification of the long arm of chromosome 1 and -13/del(13q) were the most frequent recurrent abnormalities, and were detected in 50 patients (50.0%) and 40 patients (40.0%) with clonal abnormalities, respectively. The most common abnormality involving 14q32 was t(11;14)(q13;q32), which was observed in 19 cases. Conclusion These findings demonstrate that myeloma cells exhibit complex aberrations regardless of ploidy, even from a single center in Korea. Conventional cytogenetic analysis should be included in the initial diagnostic work-up for patients suspected of having MM. PMID:27382557

  19. Case report: Concomitant Chronic Lymphocytic Leukaemia and Cytogenetically Normal de novo Acute Leukaemia in a Patient.

    PubMed

    Kajtár, Béla; Rajnics, Péter; Egyed, Miklós; Alizadeh, Hussain

    2015-01-01

    The simultaneous occurrence of acute myeloid leukaemia with untreated chronic lymphocytic leukemia is extremely rare. We report a case of a 74-year-old man who was evaluated for macrocytic anaemia. Based on the morphology and immunophenotyping analysis of peripheral blood, a diagnosis of chronic lymphocytic leukemia was established. Subsequently, the bone marrow examination revealed the presence of two distinct, coexisting CLL and AML clones. Cytogenetic and molecular genetic analysis detected deletion 13q14.3 and unmutated immunoglobulin variable heavy-chain in the CLL clone, only. The AML and CLL clones did not share clonality, and the AML did not involve the peripheral blood. A diagnosis of cytogenetically normal de novo AML occurring concurrently with untreated CLL has not been reported previously in English literature.

  20. Comparison of JAK2V617F mutation assessment employing different molecular diagnostic techniques

    PubMed Central

    Veneri, Dino; Capuzzo, Enrico; de Matteis, Giovanna; Franchini, Massimo; Baritono, Elisabetta; Benati, Marco; Solero, G. Pietro; Ambrosetti, Achille; Quaresmini, Giulia; Pizzolo, Giovanni

    2009-01-01

    Background The JAK2V617F mutation is present in the majority of patients with polycythaemia vera and in approximately half of patients with essential thrombocythaemia and primary myelofibrosis. In this study we compare the results of JAK2V617F mutation detection using three different molecular techniques in the same group of patients affected by essential thrombocythaemia. Patients and methods The JAK2 mutation was investigated with a qualitative method in 115 consecutive outpatients with a diagnosis of essential thrombocythaemia made according to WHO 2001 criteria. In 48/115 (41.7%) the allele burden was also evaluated with two different qualitative methods, of which one was a method developed in-house and the other was a commercially available method. Results The JAK2V617F mutation was detected by the qualitative method in 81/115 (69.6%) of the patients. Among the 48/115 patients in whom all three methods were applied, the qualitative method detected the mutation in 38 (79%). According to the quantitative method developed in-house, the mutation was present in 35/48 (73%) of the patients: of these, 2/35 (5.7%) patients were homozygous for the JAK2V617F mutation. The commercial quantitative method showed the mutation in 37/48 (77%) patients: of these, 9/37 (18%) patients were homozygous. Three of the 13 patients in whom no mutation was detected by the in-house method were positive for the JAK2V617F according to the commercial method. In one patient the search for the JAK2V617F mutation was positive with the in-house method but negative with the commercial kit. Conclusion Detection of the JAK2V617F mutation may depend on the molecular technique used. Considering that detection of this mutation will not only have a diagnostic value, but also a role in treatment given the development of JAK2V617F pathway inhibiting drugs, indications on a reference molecular diagnostic technique for JAK2V617F assessment and quantification of its allele burden from a panel of experts

  1. A Research Project-Based and Self-Determined Teaching System of Molecular Biology Techniques for Undergraduates

    ERIC Educational Resources Information Center

    Zhang, Shuping

    2008-01-01

    Molecular biology techniques play a very important role in understanding the biological activity. Students who major in biology should know not only how to perform experiments, but also the reasons for performing them. Having the concept of conducting research by integrating various techniques is especially important. This paper introduces a…

  2. [Cytogenetic and FISH findings are complementary in childhood ALL].

    PubMed

    Haltrich, Irén; Csóka, Monika; Kovács, Gábor; Fekete, György

    2008-09-01

    Primary genetic abnormalities of leukemia cells have important prognostic significance in childhood acute leukemia. In the last two years 30 newly diagnosed or recurrent childhood ALL bone marrow samples were analyzed for chromosomal abnormalities with conventional G-banding and interphase-fluorescence in situ hybridization (I-FISH) using probes to detect BCR/ABL fusions, cryptic TEL/AML1 and MLL rearrangements and p16(9p21) tumor suppressor gene deletions. G-banded karyotype analysis found clonal chromosomal aberrations in 50% of cases. With the use of complementary I-FISH techniques, ALL-specific structural and numerical changes could be identified in 70% of the patients. Nine cases (30%) had subtle chromosomal aberrations with prognostic importance that had not been detected in G-banded analysis. Conventional G-banding yielded additional information (rare and complex structural aberrations) in 19% of patients. The most common aberration (30%) was AML1 copy number increase present in G-banded hyperdiploid karyotype as a chromosome 21 tetrasomy in the majority of cases; one case displayed 5-6 copies and in another case amplification of AML1 gene on der(21) was combined with TEL/AML1 fusion of the homologue AML1 gene and deletion of the remaining TEL allele. High hiperdiploidy was detected in 6 cases, in one patient with normal G-banding karyotype. TEL/AML1 fusion signals were identified in four patients. Deletion of p16 locus was found in eight cases (23%), of which only two had cytogenetically visible rearrangements. G-banding in combination with I-FISH has produced major improvements in the sensitivity and accuracy of cytogenetic analysis of ALL patients and this method helps to achieve a more precise identification of different risk categories in order to choose the optimal treatment. PMID:18845499

  3. Cytogenetic investigations in four canine lymphomas.

    PubMed

    Winkler, Susanne; Murua Escobar, Hugo; Reimann-Berg, Nicola; Bullerdiek, Jörn; Nolte, Ingo

    2005-01-01

    Four cases of canine lymphoma are presented, including histological examination and cytogenetic investigation. The first case showed a derivative chromosome 13, the second case showed a clonal trisomy 8 and the third case showed a complex karyotype with a clonal trisomy 13 and additional clonal trisomies of the chromosomes 20, 30 and 37, as well as a non-clonal tetrasomy 9. Case four showed a single trisomy 2. Comparing these results with human hematopoietic malignancies, there are notable similarities between both species. PMID:16309190

  4. Vibrio parahaemolyticus: a review on the pathogenesis, prevalence, and advance molecular identification techniques

    PubMed Central

    Letchumanan, Vengadesh; Chan, Kok-Gan; Lee, Learn-Han

    2014-01-01

    Vibrio parahaemolyticus is a Gram-negative halophilic bacterium that is found in estuarine, marine and coastal environments. V. parahaemolyticus is the leading causal agent of human acute gastroenteritis following the consumption of raw, undercooked, or mishandled marine products. In rare cases, V. parahaemolyticus causes wound infection, ear infection or septicaemia in individuals with pre-existing medical conditions. V. parahaemolyticus has two hemolysins virulence factors that are thermostable direct hemolysin (tdh)-a pore-forming protein that contributes to the invasiveness of the bacterium in humans, and TDH-related hemolysin (trh), which plays a similar role as tdh in the disease pathogenesis. In addition, the bacterium is also encodes for adhesions and type III secretion systems (T3SS1 and T3SS2) to ensure its survival in the environment. This review aims at discussing the V. parahaemolyticus growth and characteristics, pathogenesis, prevalence and advances in molecular identification techniques. PMID:25566219

  5. Synthesis and Bioconjugation of Gold Nanoparticles as Potential Molecular Probes for Light-Based Imaging Techniques

    PubMed Central

    Rayavarapu, Raja Gopal; Petersen, Wilma; Ungureanu, Constantin; Post, Janine N.; van Leeuwen, Ton G.; Manohar, Srirang

    2007-01-01

    We have synthesized and characterized gold nanoparticles (spheres and rods) with optical extinction bands within the “optical imaging window.” The intense plasmon resonant driven absorption and scattering peaks of these nanoparticles make them suitable as contrast agents for optical imaging techniques. Further, we have conjugated these gold nanoparticles to a mouse monoclonal antibody specific to HER2 overexpressing SKBR3 breast carcinoma cells. The bioconjugation protocol uses noncovalent modes of binding based on a combination of electrostatic and hydrophobic interactions of the antibody and the gold surface. We discuss various aspects of the synthesis and bioconjugation protocols and the characterization results of the functionalized nanoparticles. Some proposed applications of these potential molecular probes in the field of biomedical imaging are also discussed. PMID:18354723

  6. A Coupled Meshless Technique/Molecular Dynamics Approach for Deformation Characterization of Mono-crystalline Metal

    SciTech Connect

    Gu, Y. T.; Yarlagadda, Prasad K. D. V.

    2010-05-21

    This paper presents a multiscale study using the coupled Meshless technique/Molecular Dynamics (M{sup 2}) for exploring the deformation mechanism of mono-crystalline metal (focus on copper) under uniaxial tension. In M{sup 2}, an advanced transition algorithm using transition particles is employed to ensure the compatibility of both displacements and their gradients, and an effective local quasi-continuum approach is also applied to obtain the equivalent continuum strain energy density based on the atomistic potentials and Cauchy-Born rule. The key parameters used in M{sup 2} are firstly investigated using a benchmark problem. Then, M{sup 2} is applied to the multiscale simulation for a mono-crystalline copper bar. It has found that the mono-crystalline copper has very good elongation property, and the ultimate strength and Young's modulus are much higher than those obtained in macro-scale.

  7. Operation mechanism of rotary molecular motor F1 probed by single-molecule techniques

    NASA Astrophysics Data System (ADS)

    Iino, Ryota

    2013-03-01

    F1 is a rotary motor protein. Three catalytic β - subunitsinthestator 33ring are torque generators, and rotate the rotor γ-subunit by sequential and cooperative conformational changes coupled with adenosine triphosphate (ATP) hydrolysis reaction. F1 shows remarkable performances such as rotation rate faster than 10,000 rpm, high reversibility and efficiency in chemo-mechanical energy conversion. I will introduce basic characteristics of F1 revealed by single-molecule imaging and manipulation techniques based on optical microscopy and high-speed atomic force microscopy. I will also discuss the possible operation mechanism behind the F1, along with structurally-related hexameric ATPases, also mentioning the possibility of generating hybrid molecular motors.

  8. Molecular and cytogenetic characterization of a recurrent unbalanced translocation (4;21) (p16.3;q22.1): Relevance to the Wolf-Hirschhorn and Down syndrome critical regions

    SciTech Connect

    Sebastio, G.; Perone, L.; Guzzetta, V.

    1996-05-17

    We report on an aneuploidy syndrome due to the unbalanced segregation of a familial translocation (4;21)(p16.3;q22.1) causing a partial 4p monosomy and a partial 21q trisomy. The three affected children presented with severe failure to thrive, short stature, microcephaly, profound hypotonia, and mental retardation. The face, very similar in the three children, is characterized by frontal bossing, upslanting of the palpebral fissures, short nose, and deep set ears, giving the overall appearance of the Down syndrome. The molecular study has defined the aneuploid segment on both 4p and 21q. Most of the Down syndrome critical region was found to be trisomic, while only part of the candidate Wolf-Hirschhorn syndrome critical region was deleted, suggesting that this region is not critical for the major malformations characteristic for WHS. 15 refs., 5 figs., 1 tab.

  9. Application of molecular techniques for the assessment of microorganism diversity on cultural heritage objects.

    PubMed

    Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

    2014-01-01

    As a result of their unpredictable ability to adapt to varying environmental conditions, microorganisms inhabit different types of biological niches on Earth. Owing to the key role of microorganisms in many biogeochemical processes, trends in modern microbiology emphasize the need to know and understand the structure and function of complex microbial communities. This is particularly important if the strategy relates to microbial communities that cause biodeterioration of materials that constitute our cultural heritage. Until recently, the detection and identification of microorganisms inhabiting objects of cultural value was based only on cultivation-dependent methods. In spite of many advantages, these methods provide limited information because they identify only viable organisms capable of growth under standard laboratory conditions. However, in order to carry out proper conservation and renovation, it is necessary to know the complete composition of microbial communities and their activity. This paper presents and characterizes modern techniques such as genetic fingerprinting and clone library construction for the assessment of microbial diversity based on molecular biology. Molecular methods represent a favourable alternative to culture-dependent methods and make it possible to assess the biodiversity of microorganisms inhabiting technical materials and cultural heritage objects.

  10. Recent advances in molecular medicine techniques for the diagnosis, prevention, and control of infectious diseases.

    PubMed

    França, R F O; da Silva, C C; De Paula, S O

    2013-06-01

    In recent years we have observed great advances in our ability to combat infectious diseases. Through the development of novel genetic methodologies, including a better understanding of pathogen biology, pathogenic mechanisms, advances in vaccine development, designing new therapeutic drugs, and optimization of diagnostic tools, significant infectious diseases are now better controlled. Here, we briefly describe recent reports in the literature concentrating on infectious disease control. The focus of this review is to describe the molecular methods widely used in the diagnosis, prevention, and control of infectious diseases with regard to the innovation of molecular techniques. Since the list of pathogenic microorganisms is extensive, we emphasize some of the major human infectious diseases (AIDS, tuberculosis, malaria, rotavirus, herpes virus, viral hepatitis, and dengue fever). As a consequence of these developments, infectious diseases will be more accurately and effectively treated; safe and effective vaccines are being developed and rapid detection of infectious agents now permits countermeasures to avoid potential outbreaks and epidemics. But, despite considerable progress, infectious diseases remain a strong challenge to human survival. PMID:23339016

  11. Recent advances in molecular medicine techniques for the diagnosis, prevention, and control of infectious diseases.

    PubMed

    França, R F O; da Silva, C C; De Paula, S O

    2013-06-01

    In recent years we have observed great advances in our ability to combat infectious diseases. Through the development of novel genetic methodologies, including a better understanding of pathogen biology, pathogenic mechanisms, advances in vaccine development, designing new therapeutic drugs, and optimization of diagnostic tools, significant infectious diseases are now better controlled. Here, we briefly describe recent reports in the literature concentrating on infectious disease control. The focus of this review is to describe the molecular methods widely used in the diagnosis, prevention, and control of infectious diseases with regard to the innovation of molecular techniques. Since the list of pathogenic microorganisms is extensive, we emphasize some of the major human infectious diseases (AIDS, tuberculosis, malaria, rotavirus, herpes virus, viral hepatitis, and dengue fever). As a consequence of these developments, infectious diseases will be more accurately and effectively treated; safe and effective vaccines are being developed and rapid detection of infectious agents now permits countermeasures to avoid potential outbreaks and epidemics. But, despite considerable progress, infectious diseases remain a strong challenge to human survival.

  12. A comparative study of phytohaemagglutinin and extract of Phaseolus vulgaris seeds by characterization and cytogenetics

    NASA Astrophysics Data System (ADS)

    Badari Nath, A. R. S.; Sivaramakrishna, A.; Marimuthu, K. M.; Saraswathy, Radha

    2015-01-01

    Phytohaemagglutinin (PHA) is a lectin obtained from Phaseolus vulgaris (red kidney beans), that acts as a mitogen in human leucocyte culture and is commercially available from Gibco®. This PHA (Gibco®) was found to be very expensive, hence other inexpensive sources that can be used in all kinds of cytogenetics labs (rich and poor), were attempted. One such successful attempt was PHA extract from seeds of P.vulgaris. This paper details the methodology of extraction and application of PHA from seeds of P.vulgaris. Attempts has been made to identify the chemical and physical properties of the products in the extract, analyzed by various spectroscopic and analytical techniques. The analysis clearly indicates that the product from Phaseolus seeds extract was found to be similar to the commercially available PHA (Gibco®) in the cytogenetic study of human leucocyte cultures. The present study enforces the possible utility of the plant extract directly for human leucocyte cultures.

  13. A comparative study of phytohaemagglutinin and extract of Phaseolus vulgaris seeds by characterization and cytogenetics.

    PubMed

    Badari Nath, A R S; Sivaramakrishna, A; Marimuthu, K M; Saraswathy, Radha

    2015-01-01

    Phytohaemagglutinin (PHA) is a lectin obtained from Phaseolus vulgaris (red kidney beans), that acts as a mitogen in human leucocyte culture and is commercially available from Gibco. This PHA (Gibco) was found to be very expensive, hence other inexpensive sources that can be used in all kinds of cytogenetics labs (rich and poor), were attempted. One such successful attempt was PHA extract from seeds of P.vulgaris. This paper details the methodology of extraction and application of PHA from seeds of P.vulgaris. Attempts has been made to identify the chemical and physical properties of the products in the extract, analyzed by various spectroscopic and analytical techniques. The analysis clearly indicates that the product from Phaseolus seeds extract was found to be similar to the commercially available PHA (Gibco) in the cytogenetic study of human leucocyte cultures. The present study enforces the possible utility of the plant extract directly for human leucocyte cultures. PMID:25004904

  14. Comparative Cytogenetic Study on the Toxicity of Magnetite and Zinc Ferrite Nanoparticles in Sunflower Root Cells

    NASA Astrophysics Data System (ADS)

    Foca-nici, Ecaterina; Capraru, Gabriela; Creanga, Dorina

    2010-12-01

    In this experimental study the authors present their results regarding the cellular division rate and the percentage of chromosomal aberrations in the root meristematic cells of Helianthus annuus cultivated in the presence of different volume fractions of magnetic nanoparticle suspensions, ranging between 20 and 100 microl/l. The aqueous magnetic colloids were prepared from chemically co-precipitated ferrites coated in sodium oleate. Tissue samples from the root meristeme of 2-3 day old germinated seeds were taken to prepare microscope slides following Squash method combined with Fuelgen techniques. Microscope investigation (cytogenetic tests) has resulted in the evaluation of mitotic index and chromosomal aberration index that appeared diminished and respectively increased following the addition of magnetic nanoparticles in the culture medium of the young seedlings. Zinc ferrite toxic influence appeared to be higher than that of magnetite, according to both cytogenetic parameters.

  15. Development of Ultra-High Molecular Weight Polyethylene (UHMWPE) Coating by Cold Spray Technique

    NASA Astrophysics Data System (ADS)

    Ravi, Kesavan; Ichikawa, Yuji; Deplancke, Tiana; Ogawa, Kazuhiro; Lame, Olivier; Cavaille, Jean-Yves

    2015-08-01

    Ultra-high molecular weight polyethylene or UHMWPE is an extremely difficult material to coat with, as it is rubbery and chemically very inert. The Cold Spray process appears to be a promising alternative processing technique but polymers are in general difficult to deposit using this method. So, attempts to develop UHMWPE coatings were made using a downstream injection cold spray technique incorporating a few modifications. A conventional cold spray machine yielded only a few deposited particles of UHMWPE on the substrate surface, but with some modifications in the nozzle geometry (especially the length and inner geometry) a thin coating of 45 μm on Al substrate was obtained. Moreover, experiments with the addition of fumed nano-alumina to the feedstock yielded a coating of 1-4 mm thickness on Al and polypropylene substrates. UHMWPE was seen to be melt crystallized during the coating formation, as can be seen from the differential calorimetry curves. Influence of nano-ceramic particles was explained by observing the creation of a bridge bond between UHMWPE particles.

  16. Chloride molecular doping technique on 2D materials: WS2 and MoS2.

    PubMed

    Yang, Lingming; Majumdar, Kausik; Liu, Han; Du, Yuchen; Wu, Heng; Hatzistergos, Michael; Hung, P Y; Tieckelmann, Robert; Tsai, Wilman; Hobbs, Chris; Ye, Peide D

    2014-11-12

    Low-resistivity metal-semiconductor (M-S) contact is one of the urgent challenges in the research of 2D transition metal dichalcogenides (TMDs). Here, we report a chloride molecular doping technique which greatly reduces the contact resistance (Rc) in the few-layer WS2 and MoS2. After doping, the Rc of WS2 and MoS2 have been decreased to 0.7 kΩ·μm and 0.5 kΩ·μm, respectively. The significant reduction of the Rc is attributed to the achieved high electron-doping density, thus a significant reduction of Schottky barrier width. As a proof-of-concept, high-performance few-layer WS2 field-effect transistors (FETs) are demonstrated, exhibiting a high drain current of 380 μA/μm, an on/off ratio of 4 × 10(6), and a peak field-effect mobility of 60 cm(2)/(V·s). This doping technique provides a highly viable route to diminish the Rc in TMDs, paving the way for high-performance 2D nanoelectronic devices.

  17. Grand-Canonical-like Molecular-Dynamics Simulations by Using an Adaptive-Resolution Technique

    NASA Astrophysics Data System (ADS)

    Wang, Han; Hartmann, Carsten; Schütte, Christof; Delle Site, Luigi

    2013-01-01

    In this work, we provide a detailed theoretical analysis, supported by numerical tests, of the reliability of the adaptive-resolution-simulation (AdResS) technique in sampling the grand-canonical ensemble. We demonstrate that the correct density and radial distribution functions in the hybrid region, where molecules change resolution, are two necessary conditions for considering the atomistic and coarse-grained regions in AdResS to be equivalent to subsystems of a full atomistic system with an accuracy up to the second order with respect to the probability distribution of the system. Moreover, we show that the work done by the thermostat and a thermodynamic force in the transition region is formally equivalent to balancing the chemical potential difference between the different resolutions. From these results follows the main conclusion that the atomistic region exchanges molecules with the coarse-grained region in a grand-canonical fashion with an accuracy up to (at least) second order. Numerical tests, for the relevant case of liquid water at ambient conditions, are carried out to strengthen the conclusions of the theoretical analysis. Finally, in order to show the computational convenience of AdResS as a grand-canonical setup, we compare our method to the insertion particle method in its most efficient computational implementation. This fruitful combination of theoretical principles and numerical evidence makes the adaptive-resolution technique a candidate for a natural, general, and efficient protocol for grand-canonical molecular dynamics for the case of large systems.

  18. New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces

  19. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    SciTech Connect

    Pang, Yuan-Ping

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  20. State-of-the-art applications of cyclodextrins as functional monomers in molecular imprinting techniques: a review.

    PubMed

    Lay, Sovichea; Ni, Xiaofeng; Yu, Haining; Shen, Shengrong

    2016-06-01

    As a versatile tool in separation science, cyclodextrins and their derivatives, known as emerging functional monomers, have been used extensively in molecular imprinting techniques. The attributes of cyclodextrins and their derivatives are widely known to form host-guest inclusion complex processes between the polymer and template. The exploitation of the imprinting technique could produce a product of molecularly imprinted polymers, which are very robust with long-term stability, reliability, cost-efficiency, and selectivity. Hence, molecularly imprinted polymers have gained popularity in chemical separation and analysis. Molecularly imprinted polymers containing either cyclodextrin or its derivatives demonstrate superior binding effects for a target molecule. As noted in the previous studies, the functional monomers of cyclodextrins and their derivatives have been used in molecular imprinting for selective separation with a wide range of chemical compounds, including steroidals, amino acids, polysaccharides, drugs, plant hormones, proteins, pesticides, and plastic additives. Therefore, the main goal of this review is to illustrate the exotic applications of imprinting techniques employing cyclodextrins and their derivatives as single or binary functional monomers in synthesizing molecularly imprinted polymers in areas of separation science by reviewing some of the latest studies reported in the literature. PMID:27324352

  1. Development of radiation dose reduction techniques for cadmium zinc telluride detectors in molecular breast imaging

    NASA Astrophysics Data System (ADS)

    O'Connor, Michael K.; Hruska, Carrie B.; Weinmann, Amanda; Manduca, Armando; Rhodes, Deborah J.

    2010-08-01

    Background: Molecular breast imaging (MBI) is a novel breast imaging technique that uses Cadmium Zinc Telluride (CZT) gamma cameras to detect the uptake of Tc-99m sestamibi in breast tumors. Current techniques employ an administered dose of 20-30 mCi Tc-99m, delivering an effective dose of 6.5-10 mSv to the body. This is ~ 5-10 times that of mammography. The goal of this study was to reduce the radiation dose by a factor of 5-10, while maintaining image quality. Methods: A total of 4 dose reduction schemes were evaluated - a) optimized collimation, b) improved utilization of the energy spectrum below the photopeak, c) adaptive geometric mean algorithm developed for combination of images from opposing detectors, and d) non local means filtering (NLMF) for noise reduction and image enhancement. Validation of the various schemes was performed using a breast phantom containing a variety of tumors and containing activity matched to that observed in clinical studies. Results: Development of tungsten collimators with holes matched to the CZT pixels yielded a 2.1-2.9 gain in system sensitivity. Improved utilization of the energy spectra yielded a 1.5-2.0 gain in sensitivity. Development of a modified geometric mean algorithm yielded a 1.4 reduction in image noise, while retaining contrast. Images of the breast phantom demonstrated that a factor of 5 reduction in dose was achieved. Additional refinements to the NLMF should enable an additional factor of 2 reduction in dose. Conclusion: Significant dose reduction in MBI to levels comparable to mammography can be achieved while maintaining image quality.

  2. Clinical and cytogenetic features of 508 Chinese patients with myelodysplastic syndrome and comparison with those in Western countries.

    PubMed

    Chen, B; Zhao, W-L; Jin, J; Xue, Y-Q; Cheng, X; Chen, X-T; Cui, J; Chen, Z-M; Cao, Q; Yang, G; Yao, Y; Xia, H-L; Tong, J-H; Li, J-M; Chen, J; Xiong, S-M; Shen, Z-X; Waxman, S; Chen, Z; Chen, S-J

    2005-05-01

    Myelodysplastic syndrome (MDS) is a clonal hematopoietic stem cell disorder characterized by ineffective hematopoiesis and leukemia progression. Racial differences may exist on clinical pictures and the molecular events leading to MDS, which are heterogeneous. To better define the clinical and cytogenetic features in Chinese patients, a retrospective multicentric study was performed in 508 MDS cases. Compared with Western countries, Chinese patients showed younger age (median: 49 vs 65-73 years), lower percentages of RARS (2.8 vs 6.6-15.3%), and CMML (5.2 vs 11.7-30.6%). Cytogenetically, among 367 cases with evaluable data, abnormal karyotypes were found in 136 cases, including 56 numerical and 80 structural changes. Incidences of single chromosome 5 and 7 abnormalities were lower than those in Western countries (2.2 vs 17.8-42.5%). However, complex cytogenetic aberrations and chromosome translocations were frequently observed and related to poor prognosis. Both multiple chromosome deletions and translocations were detected in advanced subtypes (RAEB and RAEB-T). Analysis of 200 cases revealed a higher incidence of hepatitis-B-virus infection than that in non-MDS population (21.00 vs 9.75%). This study further confirmed: (1) different genetic/environmental backgrounds between Asian and Western MDS populations; (2) a strong predictive value of cytogenetic abnormalities on disease outcome and involvement of genomic instability in leukemia clone development. PMID:15759035

  3. Atlas of genetics and cytogenetics in oncology and haematology in 2013.

    PubMed

    Huret, Jean-Loup; Ahmad, Mohammad; Arsaban, Mélanie; Bernheim, Alain; Cigna, Jérémy; Desangles, François; Guignard, Jean-Christophe; Jacquemot-Perbal, Marie-Christine; Labarussias, Maureen; Leberre, Vanessa; Malo, Anne; Morel-Pair, Catherine; Mossafa, Hossein; Potier, Jean-Claude; Texier, Guillaume; Viguié, Franck; Yau Chun Wan-Senon, Sylvie; Zasadzinski, Alain; Dessen, Philippe

    2013-01-01

    The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology.org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlas are researchers and/or clinicians. PMID:23161685

  4. Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013

    PubMed Central

    Huret, Jean-Loup; Ahmad, Mohammad; Arsaban, Mélanie; Bernheim, Alain; Cigna, Jérémy; Desangles, François; Guignard, Jean-Christophe; Jacquemot-Perbal, Marie-Christine; Labarussias, Maureen; Leberre, Vanessa; Malo, Anne; Morel-Pair, Catherine; Mossafa, Hossein; Potier, Jean-Claude; Texier, Guillaume; Viguié, Franck; Yau Chun Wan-Senon, Sylvie; Zasadzinski, Alain; Dessen, Philippe

    2013-01-01

    The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology.org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlas are researchers and/or clinicians. PMID:23161685

  5. Cytogenetics findings in a histiocytic sarcoma case.

    PubMed

    Alonso-Dominguez, J M; Calbacho, M; Talavera, M; Villalon, C; Abalo, L; Garcia-Gutierrez, J V; Lozano, S; Tenorio, M; Villarrubia, J; Lopez-Jimenez, J; Ferro, M T

    2012-01-01

    Histiocytic sarcoma (HS) is a neoplasm derived from histiocytes. Its diagnosis was not clear until its immunohistochemistry profile was correctly established. Not much is known about its genetic properties. We report a case of a 48-year-old male patient whose bone marrow was almost completely occupied by monomorphic medium size neoplastic cellularity. Its immunohistochemical profile was CD68(+), CD4(+), CD45(+) with negativity of other dendritic cells, and other lineage markers. Cytogenetic study showed 4 related clones: one with trisomy 8 and extra material on the short arms of chromosome 4; a second line with tetrasomy of chromosome 8, add(4)(p16); the third clone had the same alterations as the previous and deletion of chromosome 3 at q11; the fourth line had tetrasomy 8 and translocation t(3;5)(q25;q35). To our knowledge this is the first HS case showing chromosome 8 trisomy and tetrasomy and the other described alterations. PMID:22937328

  6. [Review of two Japanese cases with tinea faciei identified by molecular biological techniques as Arthroderma vanbreuseghemii].

    PubMed

    Noguchi, Hiromitsu; Sakae, Hitoko; Hattori, Mariko; Hiruma, Masataro

    2010-01-01

    A 26-year-old female (Case 1) presented with scaly erythema on the left cheek. Positive direct microscopic examination results indicated a diagnosis of tinea faciei. Colonies were isolated after incubation on Mycosel agar medium. Trichophyton mentagrophytes was morphologically identified based on giant colony formation and slide culture. Furthermore, nucleotide sequence analysis of the internal transcribed spacer 1 (ITS1) region of the rDNA gene identified Arthroderma vanbreuseghemii. The patient had 9 cats in her home, and similar colonies were isolated from 2 of these 9 cats by the hairbrush culture method. The isolated organism was identified as A. vanbreuseghemii , suggesting the cats to be the source of infection. An 11-year-old boy (Case 2) had palm-sized erythematous plaques from the nasal base to the area around the left eye and on the left cheek. Positive direct microscopic examination results indicated a diagnosis of tinea faciei. The patient had been treated with topical steroids for 6 weeks before the onset of these manifestations. The isolated organism was identified as A. vanbreuseghemii . His dog and two cats were tested but did not appear to be the source of infection. Since 2000, there have been 25 cases of tinea in Japan, identified as A. vanbreuseghemii by molecular biological techniques. Twelve cases had tinea on the face, and 11 had used topical steroids. A. vanbreuseghemii was found to be one of the important pathogens in tinea faciei.

  7. Resolution improvement of the molecular imaging technique based on magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Ishihara, Yasutoshi; Kusayama, Yusuke

    2009-02-01

    Magnetic particle imaging (MPI) based on the nonlinear interaction between internally administered magnetic nanoparticles and electromagnetic waves that externally irradiate the body has attracted attention for the early diagnosis of diseases such as cancer. In MPI, the local magnetic field distribution is scanned, and the magnetization signals are detected from the magnetic nanoparticles inside a target region. However, interference of the magnetization signals generated from the magnetic nanoparticles outside a target region due to nonlinear responses results in the degradation of image resolution. In this study, we clearly show that the degradation of image resolution is a result of the presence of even harmonics in the magnetization response of magnetic nanoparticles. We propose a new image reconstruction method for reducing these even harmonics and a correction method for suppressing the interference of the signals. This is achieved by taking into account the difference between the saturated waveform of the magnetization signal detected from the magnetic nanoparticles outside a target region and that detected from the magnetic nanoparticles inside a target region. In this study, we perform numerical analyses to prove that the image resolution in the molecular imaging technique can be improved by using our proposed image reconstruction method, which is based on the abovementioned ideas. Furthermore, a fundamental system is constructed and the numerical analyses are experimentally validated by using magnetic nanoparticles with a diameter of ~20 nm.

  8. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions

    PubMed Central

    Jorgensen, Wiliiam L.

    2014-01-01

    A recent review (Acc. Chem. Res. 2010, 43:142–151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., “on water” and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost. PMID:25431625

  9. Probing the interaction of anthraquinone with DNA by spectroscopy, molecular modeling and cancer cell imaging technique.

    PubMed

    Yang, Lei; Fu, Zheng; Niu, Xiaoqing; Zhang, Guisheng; Cui, Fengling; Zhou, Chunwu

    2015-05-25

    A new anthraquinone derivative, (E)-2-(1-(4,5-dihydroxy-6-(hydroxymethyl)-tetrahydro-2H-pyran-2-yloxyimino)ethyl)-1,4-dihydroxyanthracene-9,10-dione (AODGlc), was synthesized and its binding properties towards DNA were explored under physiological conditions by fluorescence spectroscopy, DNA melting as well as docking techniques. The experimental results revealed that AODGlc could bind to calf thymus DNA (ctDNA) through intercalation between DNA base pairs. The values of thermodynamic parameters at different temperatures including ΔG, ΔH, and ΔS and the molecular modeling study implied that hydrophobic interactions and hydrogen bonds were the main interactions in the AODGlc-ctDNA system. Cervical cancer cells (HepG2 cells) were used in cell viability assay and cell imaging experiment. AODGlc could interact with HepG2 cells and kill HepG2 cells under high concentration with nice curative effect, indicating its potential bioapplication in the future.

  10. Sensing picornaviruses using molecular imprinting techniques on a quartz crystal microbalance.

    PubMed

    Jenik, Michael; Schirhagl, Romana; Schirk, Christian; Hayden, Oliver; Lieberzeit, Peter; Blaas, Dieter; Paul, Guntram; Dickert, Franz L

    2009-07-01

    Molecular imprinting techniques were adapted to design a sensor for the human rhinovirus (HRV) and the foot-and-mouth disease virus (FMDV), which are two representatives of picornaviruses. Stamp imprinting procedures lead to patterned polyurethane layers that depict the geometrical features of the template virus, as confirmed by AFM for HRV. Quartz crystal microbalance (QCM) measurements show that the resulting layers incorporate the template viruses reversibly and lead to mass effects that are almost an order of magnitude higher than those of nonspecific adsorption. Thus, for example, the sensor yields a net frequency effect of -300 Hz when applying a virus suspension with a concentration of approximately 100 microg/mL with an excellent signal-to-noise ratio. The cavities are not only selective to shape but also to surface chemistry: different HRV serotypes (HRV1A, HRV2, HRV14, and HRV16, respectively) can be distinguished with the sensor materials by a selectivity factor of 3, regardless of the group (major/minor) to which they belong. The same selectivity factor can be observed between HRV and FMDV. Hence, imprinting leads to an "artificial antibody" toward viruses, which does not only recognize their receptor binding sites, but rather detects the whole virus as an entity. Brunauer-Emmett-Teller (BET) studies allow simulation of the sensor characteristics and reveal the number of favorable binding sites in the coatings. PMID:19469532

  11. Investigation of Nalidixic Acid Resistance Mechanism in Salmonella enterica Using Molecular Simulation Techniques.

    PubMed

    Preethi, B; Shanthi, V; Ramanathan, K

    2015-09-01

    The emergence of nalidixic acid-resistant strains of Salmonella typhimurium remains to be a major public health problem. In particular, the substitution of Asn in place of Asp at the 87 loci in the GyrA of S. typhimurium was experimentally stated for nalidixic acid resistance. However, the data on the possible mechanism of nalidixic acid resistance are limited. In this study, I-Mutant2.0 and DUET program were employed to explore the impact of mutation on the stability of GyrA protein. Subsequently, molecular simulation techniques were employed to provide detailed information on the nalidixic acid-resistant associates with the D87N mutation in the GyrA of S. typhimurium. The binding free energy data depicts that nalidixic acid forms stable complex only with native-type GyrA than mutant (D87N) type GyrA protein. Moreover, our results theoretically suggest that hydrogen bonding formed by the Arg91 is certainly responsible for the GyrA of S. typhimurium drug selectivity. It is hoped that these evidences are immensely important for the development of new antibiotic and to overcome the nalidixic acid resistance in the near future. PMID:26208690

  12. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions.

    PubMed

    Acevedo, Orlando; Jorgensen, Wiliiam L

    2014-09-01

    A recent review (Acc. Chem. Res. 2010, 43:142-151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., "on water" and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost. PMID:25431625

  13. Real-time single cell analysis of molecular mechanism of apoptosis and proliferation using FRET technique

    NASA Astrophysics Data System (ADS)

    Chen, Tongsheng; Xing, Da; Gao, Xuejuan; Wang, Fang

    2006-09-01

    Bcl-2 family proteins (such as Bid and Bak/Bax) and 14-3-3 proteins play a key role in the mitochondria-mediated cell apoptosis induced by cell death factors such as TNF-α and lower power laser irradiation (LPLI). In this report, fluorescence resonance energy transfer (FRET) has been used to study the molecular mechanism of apoptosis in living cells on a fluorescence scanning confocal microscope. Based on the genetic code technique and the green fluorescent proteins (GFPs), single-cell dynamic analysis of caspase3 activation, caspase8 activation, and PKCs activation are performed during apoptosis induced by laser irradiation in real-time. To investigate the cellular effect and mechanism of laser irradiation, human lung adenocarcinoma cells (ASTC-a-1) transfected with plasmid SCAT3 (pSCAT3)/ CKAR FRET reporter, were irradiated and monitored noninvasively with both FRET imaging. Our results show that high fluence lower power laser irradiation (HFLPLI) can induce an increase of caspase3 activation and a decrease of PKCs activation, and that LPLI induces the ASTC-a-1 cell proliferation by specifically activating PKCs.

  14. Increasing role of cytogenetics in pediatric practice.

    PubMed

    Dayakar, Seetha; Rani, Didala Swaroopa; Babu, Sidam Jangu; Srilatha, Komanduri; Jayanthi, Undamatla; Goud, Kalal Iravathy; Jain, Dharmendra; Raina, Vimarsh

    2010-04-01

    Karyotyping was done in 100 children suspected of having chromosomal abnormalities of genetically uncertain syndromes, multiple congenital anomalies, short stature, dysmorphic features, unclassified mental retardation, and Down syndrome. A total of 56 patients had an abnormal karyotype: ring chromosome of 13 was seen in 1 patient (1.78%), and trisomy 21 was seen in 29 patients (51.78%) who were diagnosed as Down syndrome patients. Among them, 9 were male patients (31.03%) (47,XY+21) and 18 were female patients (47,XX+21) (62.06%); 2 patients showed 47,XY+21/46,XY (mosaicism) (6.89%). Chromosomal rearrangements involving chromosome numbers 13, 14, and 21 were seen in three patients. Among them, one patient had t(13;21) [45,XX,t(13;21)] and two patients had 45,XY,t(14;21). Trisomy 22 was seen in three patients (5.3%), marker chromosome was seen in two patients (3.57%), 46,XY,16qh variant was seen in one patient (1.78%), 46,XX,der(2) was seen in one patient (1.78%), 46,XX,14ps+ was seen in two patients (3.57%), and 46,XY,r(18) was seen in three patients (5.37%). Apart from this, 11 patients (19.64%) had sex chromosome aberrations: 45,XO was seen in 3 patients (27.7%), 4 patients were mosaic for Turner syndrome (45,XO/46,XX) (36.36%), and 4 patients had 46,Xi(Xp) (36.36%), and the remaining 44 patients had normal karyotypes. All of them showed phenotypic-cytogenetic heterogeneity. These findings suggest that cytogenetic analysis is useful in the investigation of children with genetic disorders of unknown origin to confirm clinical diagnosis and to allow for proper genetic counseling. PMID:20384456

  15. Increasing role of cytogenetics in pediatric practice.

    PubMed

    Dayakar, Seetha; Rani, Didala Swaroopa; Babu, Sidam Jangu; Srilatha, Komanduri; Jayanthi, Undamatla; Goud, Kalal Iravathy; Jain, Dharmendra; Raina, Vimarsh

    2010-04-01

    Karyotyping was done in 100 children suspected of having chromosomal abnormalities of genetically uncertain syndromes, multiple congenital anomalies, short stature, dysmorphic features, unclassified mental retardation, and Down syndrome. A total of 56 patients had an abnormal karyotype: ring chromosome of 13 was seen in 1 patient (1.78%), and trisomy 21 was seen in 29 patients (51.78%) who were diagnosed as Down syndrome patients. Among them, 9 were male patients (31.03%) (47,XY+21) and 18 were female patients (47,XX+21) (62.06%); 2 patients showed 47,XY+21/46,XY (mosaicism) (6.89%). Chromosomal rearrangements involving chromosome numbers 13, 14, and 21 were seen in three patients. Among them, one patient had t(13;21) [45,XX,t(13;21)] and two patients had 45,XY,t(14;21). Trisomy 22 was seen in three patients (5.3%), marker chromosome was seen in two patients (3.57%), 46,XY,16qh variant was seen in one patient (1.78%), 46,XX,der(2) was seen in one patient (1.78%), 46,XX,14ps+ was seen in two patients (3.57%), and 46,XY,r(18) was seen in three patients (5.37%). Apart from this, 11 patients (19.64%) had sex chromosome aberrations: 45,XO was seen in 3 patients (27.7%), 4 patients were mosaic for Turner syndrome (45,XO/46,XX) (36.36%), and 4 patients had 46,Xi(Xp) (36.36%), and the remaining 44 patients had normal karyotypes. All of them showed phenotypic-cytogenetic heterogeneity. These findings suggest that cytogenetic analysis is useful in the investigation of children with genetic disorders of unknown origin to confirm clinical diagnosis and to allow for proper genetic counseling.

  16. Comparative Cytogenetics of the Congo African Grey Parrot (Psittacus erithacus).

    PubMed

    Seibold-Torres, Cassandra; Owens, Elaine; Chowdhary, Renuka; Ferguson-Smith, Malcolm A; Tizard, Ian; Raudsepp, Terje

    2015-01-01

    The Congo African grey parrot (Psittacus erithacus, PER) is an endemic species of Central Africa, valued for its intelligence and listed as vulnerable due to poaching and habitat destruction. Improved knowledge about the P. erithacus genome is needed to address key biological questions and conservation of this species. The P. erithacus genome was studied using conventional and molecular cytogenetic approaches including Zoo-FISH. P. erithacus has a 'typical' parrot karyotype with 2n = 62-64 and 8 pairs of macrochromosomes. A distinct feature was a sharp macro-microchromosome boundary. Telomeric sequences were present at all chromosome ends and interstitially in PER2q, the latter coinciding with a C-band. NORs mapped to 4 pairs of microchromosomes which is in contrast to a single NOR in ancestral type avian karyotypes. Zoo-FISH with chicken macrochromosomes GGA1-9 and Z revealed patterns of conserved synteny similar to many other avian groups, though neighboring synteny combinations of GGA6/7, 8/9, and 1/4 were distinctive only to parrots. Overall, P. erithacus shared more Zoo-FISH patterns with neotropical macaws than Australian species such as cockatiel and budgerigar. The observations suggest that Psittaciformes karyotypes have undergone more extensive evolutionary rearrangements compared to the majority of other avian genomes.

  17. Comparative Cytogenetics of the Congo African Grey Parrot (Psittacus erithacus).

    PubMed

    Seibold-Torres, Cassandra; Owens, Elaine; Chowdhary, Renuka; Ferguson-Smith, Malcolm A; Tizard, Ian; Raudsepp, Terje

    2015-01-01

    The Congo African grey parrot (Psittacus erithacus, PER) is an endemic species of Central Africa, valued for its intelligence and listed as vulnerable due to poaching and habitat destruction. Improved knowledge about the P. erithacus genome is needed to address key biological questions and conservation of this species. The P. erithacus genome was studied using conventional and molecular cytogenetic approaches including Zoo-FISH. P. erithacus has a 'typical' parrot karyotype with 2n = 62-64 and 8 pairs of macrochromosomes. A distinct feature was a sharp macro-microchromosome boundary. Telomeric sequences were present at all chromosome ends and interstitially in PER2q, the latter coinciding with a C-band. NORs mapped to 4 pairs of microchromosomes which is in contrast to a single NOR in ancestral type avian karyotypes. Zoo-FISH with chicken macrochromosomes GGA1-9 and Z revealed patterns of conserved synteny similar to many other avian groups, though neighboring synteny combinations of GGA6/7, 8/9, and 1/4 were distinctive only to parrots. Overall, P. erithacus shared more Zoo-FISH patterns with neotropical macaws than Australian species such as cockatiel and budgerigar. The observations suggest that Psittaciformes karyotypes have undergone more extensive evolutionary rearrangements compared to the majority of other avian genomes. PMID:26894300

  18. Lipomatous Change in Uveal Melanoma: Histopathological, Immunohistochemical and Cytogenetic Analysis

    PubMed Central

    Yavuzyigitoglu, Serdar; Kilic, Emine; Vaarwater, Jolanda; de Klein, Annelies; Paridaens, Dion; Verdijk, Robert M.

    2016-01-01

    Purpose The aim of this study was to describe a case of lipomatous change in uveal melanoma. Procedures The patient presented with a 2-year history of blurry vision. A full examination of the right eye revealed a dome-shaped pigmented subretinal mass in the choroid with a thickness of 9 mm and a diameter of 15 mm. The eye was enucleated and prepared for histopathologic, genetic and molecular investigation. Results Histopathology revealed a small circumscribed area consisting of mature adipocytic appearing cells with abundant clear cytoplasm and small peripheral flattened nuclei within a spindle-cell melanoma of the uvea. The cytoplasm of the adipocytic cells stained negative for periodic acid-Schiff and Alcian blue and positive for Melan-A, HMB-45 and tyrosinase, confirming melanocytic lineage. Fluorescence in situ hybridization analysis confirmed trisomy of chromosome 6p22 and disomy of chromosome 3p13 in the nuclei of both the tumor spindle type B cells and in the nuclei of lipomatous tumor cells. Conclusions Lipomatous change can be added to the many histopathologic faces of uveal melanoma. To our knowledge, this is the first report of lipomatous change in uveal melanoma performed with cytogenetic investigations. PMID:27239451

  19. Clinical and molecular analyses of Beckwith-Wiedemann syndrome: Comparison between spontaneous conception and assisted reproduction techniques.

    PubMed

    Tenorio, Jair; Romanelli, Valeria; Martin-Trujillo, Alex; Fernández, García-Moya; Segovia, Mabel; Perandones, Claudia; Pérez Jurado, Luis A; Esteller, Manel; Fraga, Mario; Arias, Pedro; Gordo, Gema; Dapía, Irene; Mena, Rocío; Palomares, María; Pérez de Nanclares, Guiomar; Nevado, Julián; García-Miñaur, Sixto; Santos-Simarro, Fernando; Martinez-Glez, Víctor; Vallespín, Elena; Monk, David; Lapunzina, Pablo

    2016-10-01

    Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome characterized by an excessive prenatal and postnatal growth, macrosomia, macroglossia, and hemihyperplasia. The molecular basis of this syndrome is complex and heterogeneous, involving genes located at 11p15.5. BWS is correlated with assisted reproductive techniques. BWS in individuals born following assisted reproductive techniques has been found to occur four to nine times higher compared to children with to BWS born after spontaneous conception. Here, we report a series of 187 patients with to BWS born either after assisted reproductive techniques or conceived naturally. Eighty-eight percent of BWS patients born via assisted reproductive techniques had hypomethylation of KCNQ1OT1:TSS-DMR in comparison with 49% for patients with BWS conceived naturally. None of the patients with BWS born via assisted reproductive techniques had hypermethylation of H19/IGF2:IG-DMR, neither CDKN1 C mutations nor patUPD11. We did not find differences in the frequency of multi-locus imprinting disturbances between groups. Patients with BWS born via assisted reproductive techniques had an increased frequency of advanced bone age, congenital heart disease, and decreased frequency of earlobe anomalies but these differences may be explained by the different molecular background compared to those with BWS and spontaneous fertilization. We conclude there is a correlation of the molecular etiology of BWS with the type of conception. © 2016 Wiley Periodicals, Inc.

  20. A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

    PubMed

    Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

    2013-12-20

    A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

  1. Molecular analysis of genes on Xp controlling Turner syndrome and premature ovarian failure (POF).

    PubMed

    Zinn, A R; Ross, J L

    2001-06-01

    Monosomy X has been known to be the chromosomal basis of Turner syndrome (TS) for more than four decades. A large body of cytogenetic data indicates that most TS features are due to reduced dosage of genes on the short arm of the X chromosome (Xp). Phenotype mapping studies using molecular cytogenetic and genetic techniques are beginning to localize the Xp genes that are important for various TS features, and a comprehensive catalog of candidate genes is becoming available through the Human Genome Project and related research. It is now possible to assess the contributions of individual genes to the TS phenotype by mutational analysis of karyotypically normal persons with specific TS features. This strategy has succeeded in identifying a gene involved in short stature and is being applied to premature ovarian failure and other TS phenotypes.

  2. An opportune life: 50 years in human cytogenetics.

    PubMed

    Jacobs, Patricia A

    2014-01-01

    This article is one person's view of human cytogenetics over the past 50 years. The flowering of human cytogenetics led the way to the establishment of clinical genetics as one of the most important developments in medicine in the twentieth century. The article is written from the viewpoint of a scientist who never tired of analyzing the images of dividing cells on the light microscope and interpreting the wealth of information contained in them. PMID:25184528

  3. Molecular cytogenetic studies in structural abnormalities of chromosome 13

    SciTech Connect

    Lozzio, C.B.; Bamberger, E.; Anderson, I.

    1994-09-01

    A partial trisomy 13 was detected prenatally in an amniocentesis performed due to the following ultrasound abnormalities: open sacral neural tube defect (NTD), a flattened cerebellum, and lumbar/thoracic hemivertebrae. Elevated AFP and positive acetylcholinesterase in amniotic fluid confirmed the open NTD. Chromosome analysis showed an extra acrocentric chromosome marker. FISH analysis with the painting probe 13 showed that most of the marker was derived from this chromosome. Chromosomes on the parents revealed that the mother had a balanced reciprocal translocation t(2;13)(q23;q21). Dual labeling with painting chromosomes 2 and 13 on cells from the mother and from the amniotic fluid identified the marker as a der(13)t(2;13)(p23;q21). Thus, the fetus had a partial trisomy 13 and a small partial trisomy 2p. The maternal grandfather was found to be a carrier for this translocation. Fetal demise occurred a 29 weeks of gestation. The fetus had open lumbar NTD and showed dysmorphic features, overlapping fingers and imperforate anus. This woman had a subsequent pregnancy and chorionic villi sample showed that this fetus was normal. Another case with an abnormal chromosome 13 was a newborn with partial monosomy 13 due to the presence of a ring chromosome 13. This infant had severe intrauterine growth retardation, oligohydramnios, dysmorphic features and multiple congenital microphthalmia, congenital heart disease, absent thumbs and toes and cervical vertebral anomalies. Chromosome studies in blood and skin fibroblast cultures showed that one chromosome 3 was replaced by a ring chromosome of various sizes. This ring was confirmed to be derived from chromosome 13 using the centromeric 21/13 probe.

  4. Cytogenetic and molecular analysis of sex-chromosome monosomy.

    PubMed Central

    Hassold, T; Benham, F; Leppert, M

    1988-01-01

    X chromosome- and Y chromosome-specific DNA probes were used to study different aspects of the genesis of sex-chromosome monosomy. Using X-linked RFLPs, we studied the parental origin of the single X chromosome in 35 spontaneously aborted and five live-born 45,X conceptions. We determined the origin in 35 cases; 28 had a maternal X (Xm) and seven had a paternal X (Xp). There was a correlation between parental origin and parental age, with the Xp category having a significantly reduced mean maternal age by comparison with the Xm group. Studies aimed at detecting mosaicism demonstrated the presence of a Y chromosome or a second X chromosome in three of 33 spontaneous abortions, a level of mosaicism much lower than that reported for live-born Turner syndrome individuals. Images p[539]-a Figure 1 Figure 2 PMID:2894760

  5. Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

    NASA Technical Reports Server (NTRS)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of

  6. Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique

    PubMed Central

    2014-01-01

    Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies. PMID:25470996

  7. Advances in molecular techniques for the detection and quantification of genetically modified organisms.

    PubMed

    Elenis, Dimitrios S; Kalogianni, Despina P; Glynou, Kyriaki; Ioannou, Penelope C; Christopoulos, Theodore K

    2008-10-01

    Progress in genetic engineering has led to the introduction of genetically modified organisms (GMOs) whose genomes have been altered by the integration of a novel sequence conferring a new trait. To allow consumers an informed choice, many countries require food products to be labeled if the GMO content exceeds a certain threshold. Consequently, the development of analytical methods for GMO screening and quantification is of great interest. Exponential amplification by the polymerase chain reaction (PCR) remains a central step in molecular methods of GMO detection and quantification. In order to meet the challenge posed by the continuously increasing number of GMOs, various multiplex assays have been developed for the simultaneous amplification and/or detection of several GMOs. Classical agarose gel electrophoresis is being replaced by capillary electrophoresis (CE) systems, including CE chips, for the rapid and automatable separation of amplified fragments. Microtiter well-based hybridization assays allow high-throughput analysis of many samples in a single plate. Microarrays have been introduced in GMO screening as a technique for the simultaneous multianalyte detection of amplified sequences. Various types of biosensors, including surface plasmon resonance sensors, quartz crystal microbalance piezoelectric sensors, thin-film optical sensors, dry-reagent dipstick-type sensors and electrochemical sensors were introduced in GMO screening because they offer simplicity and lower cost. GMO quantification is performed by real-time PCR (rt-QPCR) and competitive PCR. New endogenous reference genes have been validated. rt-QPCR is the most widely used approach. Multiplexing is another trend in this field. Strategies for high-throughput multiplex competitive quantitative PCR have been reported.

  8. Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique.

    PubMed

    Raphael, Kathryn A; Shearman, Deborah C A; Gilchrist, A Stuart; Sved, John A; Morrow, Jennifer L; Sherwin, William B; Riegler, Markus; Frommer, Marianne

    2014-01-01

    Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies. PMID:25470996

  9. [Evaluation of discriminatory power of molecular epidemiology techniques in Mycobacterium tuberculosis Venezuelan isolates].

    PubMed

    Méndez, Marìa Victoria; León, Cristy; Escalona, Arnelly; Abadia, Edgar; Da Mata, Omaira; de Waard, Jacobus; Takiff, Howard Eugene

    2016-03-01

    The techniques of spoligotyping and mycobacterial interspersed repetitive unit and variable-number tandem repeat typing with 24 loci (MIRU-VNTR-24), have been used to study the molecular epidemiology of tuberculosis. The aim of this study was: to evaluate the discriminative power of MIRU-VNTR 24 loci alone and in association with spoligotyping in clinical isolates of M tuberculosis in Venezuela; the allelic diversity of the 24 loci; and the discriminative power for the combination of 24 and 15 loci, 12 traditional loci (12t), those with higher allelic diversity and a new combination named 12inv. We analyzed one set of 104 strains of different lineages and a second set of 431 strains belonging to the Latin-America and Mediterranean lineage (LAM) that is predominant in Venezuela. The determination of allelic diversity showed that 4052, 2163b, 424 y 2996 are highly discriminative. Clustering rates of MIRU-VNTR 24 loci, spoligotyping and MIRU-VNTR combined with spoligotyping for 104 isolates were 18.27%, 71.15% and 14.4%, respectively, whereas with the 431 LAM strains the values were 43.2 %, 95.8% and 37.4%. MIRU-VNTR combinations of 15, 12inv and 4 loci were more discriminatory than 12t. Clustering rates for MIRU-VNTR 15 and 12inv loci coupled with spoligotyping in the 104 isolated was 21% and 23%, while for LAM strains was 52% and 46% respectively. The number of different genetics patterns for 15 and 12inv loci were similar. In conclusion, we propose the use of a small number of informative loci MIRU-VNTR coupled to spoligotyping to investigate the transmission of tuberculosis in Venezuela.

  10. The impact of additional cytogenetic abnormalities at diagnosis and during therapy with tyrosine kinase inhibitors in Chronic Myeloid Leukaemia

    PubMed Central

    Crisan, AM; Coriu, D; Arion, C; Colita, A; Jardan, C

    2015-01-01

    kinase inhibitor treatment, ACAs = additional cytogenetic abnormalities, CCyR = complete cytogenetic response, PCyR = partial cytogenetic response, mCyR = minor cytogenetic response, MMR = major molecular response, HSCT = hematopoietic stem cell transplant, HLA = human leukocyte antigens, CP = chronic phase, AP = accelerated phase, BP = blast phase, OS = overall survival, CBA = chromosome banding analysis, +8 = trisomy 8, i(17q) = isochromosome (17q), +Ph = second Philadelphia chromosome, -7 = monosomy 7, -17 = monosomy 17, +17 = trisomy 17, -21 = monosomy 21, +21 = trisomy 21, -Y = loss of Y chromosome, ELN = European LeukemiaNet, IMA600 = Imatinib 600 mg daily, IMA400 = Imatinib 400 mg daily, NILO600 = Nilotinib 600 mg daily, DASA100 = Dasatinib 100mg daily, DASA140 = Dasatinib 140 mg daily PMID:26664479

  11. Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology

    PubMed Central

    Donner, Erica; Punshon, Tracy; Guerinot, Mary Lou; Lombi, Enzo

    2013-01-01

    Functional characterisation of the genes regulating metal(loid) homeostasis in plants is a major focus of crop biofortification, phytoremediation, and food security research. This paper focuses on the potential for advancing plant metal(loid) research by combining molecular biology and synchrotron-based techniques. Recent advances in x-ray focussing optics and fluorescence detection have greatly improved the potential of synchrotron techniques for plant science research, allowing metal(loids) to be imaged in vivo in hydrated plant tissues at sub-micron resolution. Laterally resolved metal(loid) speciation can also be determined. By using molecular techniques to probe the location of gene expression and protein localisation and combining it with this synchrotron-derived data, functional information can be effectively and efficiently assigned to specific genes. This paper provides a review of the state of the art in this field, and provides examples as to how synchrotron-based methods can be combined with molecular techniques to facilitate functional characterisation of genes in planta. PMID:22200921

  12. Increased cytogenetic damage in outdoor painters.

    PubMed

    Pinto, D; Ceballos, J M; García, G; Guzmán, P; Del Razo, L M; Vera, E; Gómez, H; García, A; Gonsebatt, M E

    2000-05-01

    Painters are exposed to an extensive variety of hazardous substances such as organic solvents, lead-containing pigments and residual plastic monomers. In this particular case, workers used commercially available exterior paints and occasionally gasoline or thinner as solvents. The application or removal of paints was performed without protection (masks or gloves). To determine occupational exposure risk, a monitoring study was designed. Group selection was made after a questionnaire administration, which included questions about lifestyle and medical history to exclude exposure to other potential sources of genotoxics. Smoking and drinking habits were also considered. Blood and buccal cell samples were obtained from 25 public building male painters and from a similar number of age- and gender-matched controls. Lead levels were measured in paint samples and in individuals' blood. Organic solvents and/or its metabolites were also determined in blood. Chromosomal aberrations (CA) and sister chromatid exchanges (SCE) were determined in peripheral blood lymphocyte cultures. Also, the frequency of micronuclei (MN) in buccal cells was investigated. Painters had higher lead levels in blood (p<0.05); CA and SCE in lymphocytes and MN in epithelial cells were also elevated (p<0.05). Cytogenetic damage was significantly associated with occupational exposure time but not with the levels of lead found in blood. PMID:10838197

  13. Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

    DOEpatents

    Brennan, Thomas M.; Hammons, B. Eugene; Tsao, Jeffrey Y.

    1992-01-01

    A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth.

  14. Reflection mass spectrometry technique for monitoring and controlling composition during molecular beam epitaxy

    DOEpatents

    Brennan, T.M.; Hammons, B.E.; Tsao, J.Y.

    1992-12-15

    A method for on-line accurate monitoring and precise control of molecular beam epitaxial growth of Groups III-III-V or Groups III-V-V layers in an advanced semiconductor device incorporates reflection mass spectrometry. The reflection mass spectrometry is responsive to intentional perturbations in molecular fluxes incident on a substrate by accurately measuring the molecular fluxes reflected from the substrate. The reflected flux is extremely sensitive to the state of the growing surface and the measurements obtained enable control of newly forming surfaces that are dynamically changing as a result of growth. 3 figs.

  15. Molecular dynamics in azobenzene liquid crystal polymer films measured by time-resolved techniques.

    PubMed

    Fujii, T; Kuwahara, S; Katayama, K; Takado, K; Ube, T; Ikeda, T

    2014-06-14

    Photo-induced molecular motion in a liquid crystal polymer film including azobenzene was studied by the heterodyne transient grating method. The film was confined in a liquid crystal cell, where it is a photomobile film under free-standing conditions. By observation of the refractive index change induced by a laser pulse, contraction of the film was observed on the order of several hundreds of nanoseconds, and the subsequent reorientation and molecular rotation dynamics were observed from a few microseconds to a hundred milliseconds. Finally, the cis isomer of azobenzene was thermally returned back to the trans isomer in about ten seconds because the film could not be bent in the liquid crystal cell. Since the contraction, reorientation and molecular rotation took place before the cis to trans back-transformation, these processes correspond to the preliminary molecular motion preceding the macroscopic bending of the film. PMID:24736859

  16. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    SciTech Connect

    Agarwal, Animesh Delle Site, Luigi

    2015-09-07

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  17. Three dimensional imaging technique suitable for the measurements of the internal energies of asymmetrical diatomic molecular ions

    NASA Astrophysics Data System (ADS)

    Sauza, J. B.; Panchenko, D. I.; Duot, A. C.; Strom, R. A.; Andrianarijaona, V. M.

    2015-05-01

    We propose a three dimensional imaging technique that could be used to measure the internal energy of asymmetrical diatomic molecular ions such as HeH+ and CO+. The detection scheme is similar to the one used for symmetrical diatomic molecular ions, which accesses the internal energy of the ion through the kinetic energy release in a resonant dissociative charge transfer (see for instance). In that technique, the fragments hit two detectors which send the positions of the impacts along with the difference between the times of impacts to a computer. The computed kinetic energy release is related to the vibrational excitation level of the initial molecular ion. In the case of an asymmetrical ion, the lighter fragment has a higher recoil velocity and goes further away transversally from the center of mass direction. The heavier fragment would not hit the first detector if the beam is judiciously misaligned. Therefore, we make distinction between the two particles. Details of the technique will be presented. Authors wish to give special thanks to Pacific Union College Student Senate for their financial support.

  18. Diagnostic Implication and Clinical Relevance of Ancillary Techniques in Clinical Pathology Practice

    PubMed Central

    Makki, Jaafar S.

    2016-01-01

    Hematoxylin–eosin-stained slide preparation is one of the most durable techniques in medicine history, which has remained unchanged since implemented. It allows an accurate microscopic diagnosis of the vast majority of tissue samples. In many circumstances, this technique cannot answer all the questions posed at the initial diagnostic level. The pathologist has always been looking for additional ancillary techniques to answer pending questions. In our daily histopathology practice, we referred to those techniques as special stains, but nowadays, they are more than stains and are collectively called ancillary tests. They include a wide range of techniques starting from histochemical stains and ending in one or more advanced techniques, such as immunohistochemistry, immunofluorescence, molecular studies, cytogenetic studies, electron microscopy, flow cytometry, and polymerase chain reaction. PMID:27042154

  19. Diagnostic Implication and Clinical Relevance of Ancillary Techniques in Clinical Pathology Practice.

    PubMed

    Makki, Jaafar S

    2016-01-01

    Hematoxylin-eosin-stained slide preparation is one of the most durable techniques in medicine history, which has remained unchanged since implemented. It allows an accurate microscopic diagnosis of the vast majority of tissue samples. In many circumstances, this technique cannot answer all the questions posed at the initial diagnostic level. The pathologist has always been looking for additional ancillary techniques to answer pending questions. In our daily histopathology practice, we referred to those techniques as special stains, but nowadays, they are more than stains and are collectively called ancillary tests. They include a wide range of techniques starting from histochemical stains and ending in one or more advanced techniques, such as immunohistochemistry, immunofluorescence, molecular studies, cytogenetic studies, electron microscopy, flow cytometry, and polymerase chain reaction. PMID:27042154

  20. Prognostic Impact of Cytogenetic Abnormalities in Multiple Myeloma

    PubMed Central

    Jian, Yuan; Chen, Xiaolei; Zhou, Huixing; Zhu, Wanqiu; Liu, Nian; Geng, Chuanying; Chen, Wenming

    2016-01-01

    Abstract The identification of specific cytogenetic abnormalities by interphase fluorescence in situ hybridization (i-FISH) has become a routine procedure for prognostic stratification of multiple myeloma (MM) patients. In this study, the prognostic significance of cytogenetic abnormalities detected by interphase fluorescence in situ hybridization (iFISH) in 229 newly diagnosed multiple myeloma patients was retrospectively analyzed. Results showed that del (17p), t(4;14), and 1q21 gain were adverse predictors of progression-free survival (PFS). Patients who carried these cytogenetic abnormalities were more likely to have more adverse biological parameters and lower response rate. Multivariate analysis showed that del (17p), t(4;14), and 1q21 gain were statistically independent predictors of PFS, whereas del (17p) was also adverse predictor of overall survival. Multiple coexisting cytogenetic abnormalities also had a negative correlation with PFS. Bortezomib-based therapy could improve the rate and depth of response in patients with t(4;14) translocation and 1q21 gain. Autologous stem cell transplantation could improve, but not overcome the adverse prognostic effect of high-risk cytogenetic abnormalities. These results demonstrate that MM patients with iFISH abnormalities, especially del (17p), are more likely to have a poor prognosis. PMID:27175647

  1. Cytogenetic surveillance of workers exposed to genotoxic chemicals: Preliminary experiences from a prospective cancer study in a cytogenetic cohort

    SciTech Connect

    Sorsa, M.; Ojajaervi, A.S.; Salomaa, S. )

    1990-01-01

    Cytogenetic endpoints, conventionally chromosomal aberrations, and later sister chromatid exchanges and micronuclei have long been used to assess exposure of human populations to genotoxic agents. Although the adverse nature of somatic chromosome damage is recognized at the group level, no ill-health manifestations have been causally related to cytogenetic damage at the individual level. In work-related exposures, e.g., ethylene oxide, styrene, benzene, vinyl chloride, and alkylating anticancer agents have been shown to induce somatic chromosomal damage in several studies. For all of these, a carcinogenic risk to humans has also been documented. The possible association of somatic chromosome damage and cancer will be elucidated in a Nordic prospective study. The objective is to find out the significance of a high or low score in any of the cytogenetic parametres to risk of cancer. In the Finnish part of the cohort of 806 individuals, 10 cases of cancer were observed during the first follow-up period. Although the cohort is young and the numbers small, a slightly significant (P = 0.04) trend was observed for individuals with cancer and a score of chromosomal aberrations. No trend was observed for sister chromatid exchanges. The application of cytogenetic surveillance is still not routine methodology, but it is useful and informative in carefully controlled study designs. Special efforts should be directed toward combining different disciplines, i.e., cytogenetics, adduct monitoring, and end-effect epidemiology, in order to reach quantitativeness in risk assessment.13 references.

  2. Cytogenetic abnormalities in Tunisian women with premature ovarian failure.

    PubMed

    Ayed, Wiem; Amouri, Ahlem; Hammami, Wajih; Kilani, Olfa; Turki, Zinet; Harzallah, Fatma; Bouayed-Abdelmoula, Nouha; Chemkhi, Imen; Zhioua, Fethi; Slama, Claude Ben

    2014-12-01

    To identify the distribution of chromosome abnormalities among Tunisian women with premature ovarian failure (POF) referred to the department of Cytogenetic at the Pasteur Institute of Tunis (Tunisia), standard cytogenetic analysis was carried out in a total of 100 women younger than 40 affected with premature ovarian failure. We identified 18 chromosomal abnormalities, including seven X-numerical anomalies in mosaic and non-mosaic state (45,X; 47,XXX), four sex reversal, three X-structural abnormalities (terminal deletion and isochromosomes), one autosomal translocation and one supernumerary marker. The overall prevalence of chromosomal abnormalities was 18% in our cohort. X chromosome aneuploidy was the most frequent aberration. This finding confirms the essential role of X chromosome in ovarian function and underlies the importance of cytogenetic investigations in the routine management of POF. PMID:25433561

  3. Cytogenetic characterization and B chromosome diversity in direct-developing frogs of the genus Oreobates (Brachycephaloidea, Craugastoridae)

    PubMed Central

    Ferro, Juan Martín; Taffarel, Alberto; Cardozo, Darío; Grosso, Jimena; Puig, María Pía; Suárez, Pablo; Akmentins, Mauricio Sebastián; Baldo, Diego

    2016-01-01

    Abstract Oreobates Jiménez de la Espada, 1872 is a large group of South American frogs with terrestrial reproduction and direct development, located in the superfamily Brachycephaloidea. About 260 brachycephaloidean species have been cytogenetically studied so far, at least with standard techniques. However, this information represents fewer than 17% species of the family Craugastoridae Hedges, Duellman & Heinicke, 2008, where the genus Oreobates is included. In the present work, using a diversity of standard and molecular techniques, we describe the karyotype of Oreobates barituensis Vaira & Ferrari, 2008, Oreobates berdemenos Pereyra, Cardozo, Baldo & Baldo, 2014 and Oreobates discoidalis (Peracca, 1895), from northwestern Argentina. The three species analyzed showed a diploid karyotype with 2n = 22 biarmed chromosomes, fundamental number (FN) = 44, nucleolus organizer regions (NORs) located pericentromerically on pair 7, and a centromeric and pericentromeric C-banding pattern. We observed variations in the chromosome number in Oreobates barituensis due the presence of two morphs of B chromosomes, one medium-sized telocentric (BT) and another subtelocentric and smaller (Bst). Both B chromosomes are mitotically stable and were recorded in all somatic and germinal cells analyzed. The BT chromosome occurred at a maximum of one per individual (2n = 22+BT), and the other one was observed single (2n = 22 + Bst) or as a pair in two doses (2n = 22 + 2BT). We additionally observed other supernumerary chromosomes in the three species analyzed, all of them euchromatic, small, dot-shaped and with instability during mitoses, showing a frequency of occurrence below 50% in studied specimens. The occurrence of polymorphic and spontaneous chromosomal rearrangements and supernumerary chromosomes is a recurrent feature reported in frogs with terrestrial habits (Brachycephaloidea and Hemiphractidae Peters, 1862), which suggests that Brachycephaloidea may be a promising group for

  4. Molecular pathology in lung cancer: a guide to the techniques used in clinical practice.

    PubMed

    Walsh, Kathy; Wallace, William A

    2014-12-01

    Five year survival rates for lung cancer patients are poor; however the development of new therapeutic options, which benefit subsets of the population, offer hope of improvement. These novel therapies frequently rely upon the analysis of biomarkers in pathology samples; in lung cancer patients, testing is now routinely carried out to identify small mutations and chromosomal rearrangements in order to predict response to treatment. The recent increase in biomarker analyses in pathology samples has lead to the development of a new specialty, molecular pathology. The use of molecular pathology assays in clinical samples is largely under the control of the histopathologist; who is likely to be asked, as a minimum, to select tissue sections for molecular analysis and mark areas of H&E stained slides for macro or microdissection. Many histopathologists will also be involved in the sourcing and implementation of new assays. This review aims to provide a guide to some of the most commonly used molecular pathology methods - their advantages and their limitations.

  5. SCIENCE RESULTS INTEGRATION. BRINGING MOLECULAR BIOLOGY TECHNIQUES TO REGIONAL WATER MONITORING PROGRAMS

    EPA Science Inventory

    EPA's Office of Research and Development (ORD) develops innovative methods for use in environmental monitoring and assessment by scientists in Regions, states, and Tribes. Molecular-biology-based methods are not yet established in the environmental monitoring "tool box". SRI (Sci...

  6. Cytogenetic findings in persons living near the Love Canal

    SciTech Connect

    Heath, C.W. Jr.; Nadel, M.R.; Zack, M.M. Jr.; Chen, A.T.L.; Bender, M.A.; Preston, R.J.

    1984-03-16

    Cytogenetic analyses were performed on peripheral blood from 46 present or past residents of the areas surrounding Love Canal, a former dump site for chemical wastes in Niagara Falls, NY. Participants included 17 persons in whom cytogenetic analyses had been performed in 1980 and 29 persons who had been living in 1978 in seven homes that directly adjoined the canal and in which environmental tests showed elevated levels of chemicals spreading from the canal. Frequencies of chromosomal aberrations and of sister chromatid exchange (SCE) did not differ significantly from control levels. For all participants, cigarette smoking was associated with an increase in sister chromatid exchange frequency.

  7. Cytogenetic findings in persons living near the Love Canal.

    PubMed

    Heath, C W; Nadel, M R; Zack, M M; Chen, A T; Bender, M A; Preston, R J

    1984-03-16

    Cytogenetic analyses were performed on peripheral blood from 46 present or past residents of the area surrounding Love Canal, a former dump site for chemical wastes in Niagara Falls, NY. Participants included 17 persons in whom cytogenetic analyses had been performed in 1980 and 29 persons who had been living in 1978 in seven homes that directly adjoined the canal and in which environmental tests showed elevated levels of chemicals spreading from the canal. Frequencies of chromosomal aberrations and of sister chromatid exchange (SCE) did not differ significantly from control levels. For all participants, cigarette smoking was associated with an increase in sister chromatid exchange frequency. PMID:6700040

  8. Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy: An analytical technique to understand therapeutic responses at the molecular level

    PubMed Central

    Kalmodia, Sushma; Parameswaran, Sowmya; Yang, Wenrong; Barrow, Colin J.; Krishnakumar, Subramanian

    2015-01-01

    Rapid monitoring of the response to treatment in cancer patients is essential to predict the outcome of the therapeutic regimen early in the course of the treatment. The conventional methods are laborious, time-consuming, subjective and lack the ability to study different biomolecules and their interactions, simultaneously. Since; mechanisms of cancer and its response to therapy is dependent on molecular interactions and not on single biomolecules, an assay capable of studying molecular interactions as a whole, is preferred. Fourier Transform Infrared (FTIR) spectroscopy has become a popular technique in the field of cancer therapy with an ability to elucidate molecular interactions. The aim of this study, was to explore the utility of the FTIR technique along with multivariate analysis to understand whether the method has the resolution to identify the differences in the mechanism of therapeutic response. Towards achieving the aim, we utilized the mouse xenograft model of retinoblastoma and nanoparticle mediated targeted therapy. The results indicate that the mechanism underlying the response differed between the treated and untreated group which can be elucidated by unique spectral signatures generated by each group. The study establishes the efficiency of non-invasive, label-free and rapid FTIR method in assessing the interactions of nanoparticles with cellular macromolecules towards monitoring the response to cancer therapeutics. PMID:26568521

  9. Eigensolution techniques, their applications and Fisherʼs information entropy of the Tietz-Wei diatomic molecular model

    NASA Astrophysics Data System (ADS)

    Falaye, B. J.; Oyewumi, K. J.; Ikhdair, S. M.; Hamzavi, M.

    2014-11-01

    In this study, the approximate analytical solutions of Schrödinger, Klein-Gordon and Dirac equations under the Tietz-Wei (TW) diatomic molecular potential are represented by using an approximation for the centrifugal term. We have applied three types of eigensolution techniques: the functional analysis approach, supersymmetry quantum mechanics and the asymptotic iteration method to solve the Klein-Gordon, Dirac and Schrödinger equations, respectively. The energy eigenvalues and the corresponding eigenfunctions for these three wave equations are obtained, and some numerical results and figures are reported. It has been shown that these techniques yielded exactly the same results. some expectation values of the TW diatomic molecular potential within the framework of the Hellmann-Feynman theorem have been presented. The probability distributions that characterize the quantum mechanical states of TW diatomic molecular potential are analyzed by means of complementary information measures of a probability distribution called Fisher's information entropy. This distribution has been described in terms of Jacobi polynomials, whose characteristics are controlled by quantum numbers.

  10. Cytogenetic analysis of trophoblasts by comparative genomic hybridization in embryo-fetal development anomalies.

    PubMed

    Tabet, A C; Aboura, A; Dauge, M C; Audibert, F; Coulomb, A; Batallan, A; Couturier-Turpin, M H; Feldmann, G; Tachdjian, G

    2001-08-01

    Cytogenetic studies of spontaneous abortions or intrauterine fetal death depend on conventional tissue culturing and karyotyping. This technique has limitations such as culture failure and selective growth of maternal cells. Fluorescent in situ hybridization (FISH) using specific probes permits diagnosis of aneuploidies but is limited to one or a few chromosomal regions. Comparative genomic hybridization (CGH) provides an overview of chromosomal gains and losses in a single hybridization directly from DNA samples. In a prospective study, we analyzed by CGH trophoblast cells from 21 fetuses in cases of spontaneous abortions, intrauterine fetal death or polymalformed syndrome. Six numerical chromosomal abnormalities including one trisomy 7, one trisomy 10, three trisomies 18, one trisomy 21 and one monosomy X have been correctly identified by CGH. One structural abnormality of the long arm of chromosome 1 has been characterized by CGH. One triploidy and two balanced pericentromeric inversions of chromosome 9 have not been identified by CGH. Sexual chromosomal constitutions were concordant by both classical cytogenetic technique and CGH. Contribution of trophoblast analysis by CGH in embryo-fetal development anomalies is discussed. PMID:11536256

  11. Drug-induced premature chromosome condensation (PCC) protocols: cytogenetic approaches in mitotic chromosome and interphase chromatin.

    PubMed

    Gotoh, Eisuke

    2015-01-01

    Chromosome analysis is a fundamental technique which is used in wide areas of cytogenetic study including karyotyping species, hereditary diseases diagnosis, or chromosome biology study. Chromosomes are usually prepared from mitotic cells arrested by colcemid block protocol. However, obtaining mitotic chromosomes is often hampered under several circumstances. As a result, cytogenetic analysis will be sometimes difficult or even impossible in such cases. Premature chromosome condensation (PCC) (see Note 1) is an alternative method that has proved to be a unique and useful way in chromosome analysis. Former, PCC has been achieved following cell fusion method (cell-fusion PCC) mediated either by fusogenic viruses (e.g., Sendai virus) or cell fusion chemicals (e.g., polyethylene glycol), but the cell fusion PCC has several drawbacks. The novel drug-induced PCC using protein phosphatase inhibitors was introduced about 20 years ago. This method is much simpler and easier even than the conventional mitotic chromosome preparation protocol use with colcemid block and furthermore obtained PCC index (equivalent to mitotic index for metaphase chromosome) is usually much higher than colcemid block method. Moreover, this method allows the interphase chromatin to be condensed to visualize like mitotic chromosomes. Therefore drug-induced PCC has opened the way for chromosome analysis not only in metaphase chromosomes but also in interphase chromatin. The drug-induced PCC has thus proven the usefulness in cytogenetics and other cell biology fields. For this second edition version, updated modifications/changes are supplemented in Subheadings 2, 3, and 4, and a new section describing the application of PCC in chromosome science fields is added with citation of updated references.

  12. Comparison of the detection of periodontal pathogens in bacteraemia after tooth brushing by culture and molecular techniques

    PubMed Central

    Figuero, Elena; González, Itziar; O´Connor, Ana; Diz, Pedro; Álvarez, Maximiliano; Herrera, David; Sanz, Mariano

    2016-01-01

    Background The prevalence and amounts of periodontal pathogens detected in bacteraemia samples after tooth brushing-induced by means of four diagnostic technique, three based on culture and one in a molecular-based technique, have been compared in this study. Material and Methods Blood samples were collected from thirty-six subjects with different periodontal status (17 were healthy, 10 with gingivitis and 9 with periodontitis) at baseline and 2 minutes after tooth brushing. Each sample was analyzed by three culture-based methods [direct anaerobic culturing (DAC), hemo-culture (BACTEC), and lysis-centrifugation (LC)] and one molecular-based technique [quantitative polymerase chain reaction (qPCR)]. With culture any bacterial isolate was detected and quantified, while with qPCR only Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans were detected and quantified. Descriptive analyses, ANOVA and Chi-squared tests, were performed. Results Neither BACTEC nor qPCR detected any type of bacteria in the blood samples. Only LC (2.7%) and DAC (8.3%) detected bacteraemia, although not in the same patients. Fusobacterium nucleatum was the most frequently detected bacterial species. Conclusions The disparity in the results when the same samples were analyzed with four different microbiological detection methods highlights the need for a proper validation of the methodology to detect periodontal pathogens in bacteraemia samples, mainly when the presence of periodontal pathogens in blood samples after tooth brushing was very seldom. Key words:Bacteraemia, periodontitis, culture, PCR, tooth brushing. PMID:26946197

  13. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

    SciTech Connect

    Fry-Petit, A. M. E-mail: afry@fullerton.edu; Sheckelton, J. P.; McQueen, T. M. E-mail: afry@fullerton.edu; Rebola, A. F.; Fennie, C. J.; Mourigal, M.; Valentine, M.; Drichko, N.

    2015-09-28

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn{sub 2}Mo{sub 3}O{sub 8}, this approach allows direct assignment of the constrained rotational mode of Mo{sub 3}O{sub 13} clusters and internal modes of MoO{sub 6} polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems.

  14. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique.

    PubMed

    Fry-Petit, A M; Rebola, A F; Mourigal, M; Valentine, M; Drichko, N; Sheckelton, J P; Fennie, C J; McQueen, T M

    2015-09-28

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn2Mo3O8, this approach allows direct assignment of the constrained rotational mode of Mo3O13 clusters and internal modes of MoO6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems.

  15. Molecular Techniques for the Detection and Differentiation of Host and Parasitoid Species and the Implications for Fruit Fly Management

    PubMed Central

    Jenkins, Cheryl; Chapman, Toni A.; Micallef, Jessica L.; Reynolds, Olivia L.

    2012-01-01

    Parasitoid detection and identification is a necessary step in the development and implementation of fruit fly biological control strategies employing parasitoid augmentive release. In recent years, DNA-based methods have been used to identify natural enemies of pest species where morphological differentiation is problematic. Molecular techniques also offer a considerable advantage over traditional morphological methods of fruit fly and parasitoid discrimination as well as within-host parasitoid identification, which currently relies on dissection of immature parasitoids from the host, or lengthy and labour-intensive rearing methods. Here we review recent research focusing on the use of molecular strategies for fruit fly and parasitoid detection and differentiation and discuss the implications of these studies on fruit fly management. PMID:26466628

  16. Direct assignment of molecular vibrations via normal mode analysis of the neutron dynamic pair distribution function technique

    NASA Astrophysics Data System (ADS)

    Fry-Petit, A. M.; Rebola, A. F.; Mourigal, M.; Valentine, M.; Drichko, N.; Sheckelton, J. P.; Fennie, C. J.; McQueen, T. M.

    2015-09-01

    For over a century, vibrational spectroscopy has enhanced the study of materials. Yet, assignment of particular molecular motions to vibrational excitations has relied on indirect methods. Here, we demonstrate that applying group theoretical methods to the dynamic pair distribution function analysis of neutron scattering data provides direct access to the individual atomic displacements responsible for these excitations. Applied to the molecule-based frustrated magnet with a potential magnetic valence-bond state, LiZn2Mo3O8, this approach allows direct assignment of the constrained rotational mode of Mo3O13 clusters and internal modes of MoO6 polyhedra. We anticipate that coupling this well known data analysis technique with dynamic pair distribution function analysis will have broad application in connecting structural dynamics to physical properties in a wide range of molecular and solid state systems.

  17. Study on the cytogenetic changes induced by benzene and hydroquinone in human lymphocytes.

    PubMed

    Peng, D; Jiaxing, W; Chunhui, H; Weiyi, P; Xiaomin, W

    2012-04-01

    Benzene (BN) is a prototypical hematotoxicant, genotoxic carcinogen, and ubiquitous environmental pollutant. Although the molecular mechanisms of BN-induced cytotoxicity and genotoxic damage are poorly understood in humans, previous studies suggested that bioactivated BN metabolites are capable of oxidative stress, cell cycle arrest, apoptosis, and DNA damage. The objective of the current study was to investigate the BN-induced cytogenetic changes and underlying mechanisms based on these hypotheses. Peripheral blood lymphocytes (PBLs) might be the targets for BN-induced cytotoxicity and genotoxicity, and therefore DNA damage responses of PBLs after exposure to different concentrations of BN (0.25, 3.5, 50 μmol/L) or BN metabolite, hydroquinone (HQ; 50, 150, 450 μmol/L) were studied in vitro. Microculture tetrazolium assay, flow cytometry, 2',7'-dichlorodihydrofluorescein-diacetate assay, comet assay, micronuclei assay, and attenuated total reflectance microspectroscope were chosen for this study. Based on the results, we reached the conclusion that different concentrations of BN or HQ significantly inhibited cell growth, induced the arrest of S phase and G2/M phase, and increased late apoptosis in a concentration-dependent manner. Furthermore, evidence was also provided to support the conclusion that BN and HQ induced DNA strand breaks and chromosomal mutations in PBL, which indicated the genotoxicity of BN and HQ. Current evidence has indicated that multiple mechanisms including dysfunction of cell cycle, programmed cell death, oxidative stress, and DNA lesions are likely to contribute to BN-induced cytogenetic changes. PMID:22297702

  18. Cytogenetics and characterization of microsatellite loci for a South American pioneer tree species, Croton floribundus.

    PubMed

    Silvestrini, Milene; Pinto-Maglio, Cecília A F; Zucchi, Maria I; dos Santos, Flavio A M

    2013-12-01

    Despite the recent advances in plant population genetic studies, the lack of information regarding pedigree, ploidy level, or mode of inheritance for many polyploids can compromise the analysis of the molecular data produced. The aim of this study was to examine both microsatellite and cytogenetic characteristics of the pioneer tree Croton floribundus Spreng. (Euphorbiaceae) to test for the occurrence of polyploidy in the species and to evaluate its implications for the appropriate use of SSR markers. Seven microsatellite markers were developed and screened for 62 individuals from a semi-deciduous tropical forest in Brazil. Chromosome number, meiotic behavior, and pollen viability were evaluated from male flower buds. All SSR loci were highly polymorphic. The number of bivalents observed in meiosis n = 56 (2n = 8× = 112) and the maximum number of alleles per individual (Ni = 8) demonstrated the occurrence of polyploidy in C. floribundus. The normal meiotic pairing and the high pollen viability suggested that C. floribundus is a regular and stable polyploid, most likely an allopolyploid. The combined SSR and cytogenetic data provided new evidence on the origin and evolution of the species as well as assured the accurate use of SSR loci for population genetic studies of the polyploid pioneer species.

  19. Comparison of molecular and microscopic technique for detection of Theileria annulata from the field cases of cattle

    PubMed Central

    Chauhan, H. C.; Patel, B. K.; Bhagat, A. G.; Patel, M. V.; Patel, S. I.; Raval, S. H.; Panchasara, H. H.; Shrimali, M. D.; Patel, A. C.; Chandel, B. S.

    2015-01-01

    Aim: Tropical theileriosis is fatal hemoprotozoal disease of dairy animals caused by Theileria annulata. The aim of the present study was to detect the T. annulata and comparison of results of molecular and microscopic techniques. Materials and Methods: A total of 52 blood samples were collected from the cattle suspected for theileriosis across the Banaskantha district. All the samples were screened for theileriosis using Giemsa’s staining technique and polymerase chain reaction (PCR). Results: Total of 17 (32.69%) and 24 (46.15%) samples were found positive for theileriosis by microscopic examination and PCR test, respectively. It revealed that the study area is endemic for theileriosis, and the microscopic technique has 70.83% sensitivity and 100% specificity with respect to PCR technique. Conclusion: It may be concluded from the present study that the PCR is comparatively sensitive technique than microscopic examination and may be recommended to use in the field for screening of theileriosis in the study area, where a high prevalence of diseases have been reported due to intensive dairy farming. PMID:27047045

  20. Sjögren's syndrome and MALT lymphomas of salivary glands: a DNA-cytometric and interphase-cytogenetic study.

    PubMed

    Ihrler, S; Baretton, G B; Menauer, F; Blasenbreu-Vogt, S; Löhrs, U

    2000-01-01

    Few and conflicting cytogenetic data are available concerning the chromosomal constitution of (mainly gastric) extranodal marginal zone B-cell non-Hodgkin's lymphoma arising from mucosa-associated lymphoid tissue (MALT)-type lymphoma. The majority of salivary gland MALT lymphomas are thought to develop from longstanding Sjögren's syndrome/benign lymphoepithelial lesion (BLEL). We tried to achieve a better comprehension of related cytogenetic alterations by comparing DNA-ploidy and numerical chromosomal (#) aberrations, assessed by different techniques of DNA cytometry (image cytometry) and interphase cytogenetics using nonradiographic in situ hybridization (centromere specific probes for #3, 7, 12, 18) on 12 cases of BLEL, 13 low-grade MALT lymphomas (LG-MALT-L) and 4 high-grade MALT lymphomas (HG-MALT-L) of salivary gland. Both techniques were applied on tissue sections preferentially, enabling a reliable measurement of histomorphologically identified areas. No case of BLEL showed cytogenetic abnormalities. Three of 4 HG- and 2 of 13 LG-MALT-L exhibited complex chromosomal gains in nonisotopic in situ hybridization, which were reflected by DNA nondiploidy in image cytometry. In 6 of 13 LG- and lof 4 HG-MALT-L, one or two numerical chromosomal aberrations were demonstrated by nonisotopic in situ hybridization, which could not be resolved by image cytometry. In the 11 DNA-diploid LG-MALT-L, trisomies 18, 3, and 12 were found in 36, 12, and 9%, respectively. In conclusion, comparing BLEL, which showed no chromosomal aberrations, with LG- and HG-MALT-L, an increase in frequency and number of numerical aberrations and DNA nondiploidy was seen. Peritetraploid DNA nondiploidy might be characteristic for HG-MALT-L of salivary gland as it is a rare finding in MALT lymphomas of other sites. It is unclear whether the documented chromosomal aberrations in LG-MALT-L, especially increased rate of trisomy 18, indicate a pathogenic impact or merely reflect genetic instability.

  1. Some interesting aspects of physisorption stay-time measurements obtained using molecular-beam techniques. [on Ni surface

    NASA Technical Reports Server (NTRS)

    Wilmoth, R. G.; Fisher, S. S.

    1974-01-01

    Stay-time distributions have been obtained for Xe physisorbing on polycrystalline nickel as a function of the target temperature using a pulsed molecular-beam technique. Some interesting effects due to ion bombardment of the surface using He, Ar, and Xe ions are presented. Measured detector signal shapes are found to deviate from those predicted for first-order desorption with velocities corresponding to Maxwellian effusion at the surface temperature. Evidence is found for interaction between beam pulse adsorption and steady-state adsorption of beam species background atoms.

  2. Fabrication of IrSi(3)/p-Si Schottky diodes by a molecular beam epitaxy technique

    NASA Technical Reports Server (NTRS)

    Lin, T. L.; Iannelli, J. M.

    1990-01-01

    IrSi(3)/p-Si Schottky diodes have been fabricated by a molecular beam epitaxy technique at 630 C. Good surface morphology was observed for IrSi(3) layers grown at temperatures below 680 C, and an increasing tendency to form islands is observed in samples grown at higher temperatures. Good diode current-voltage characteristics were observed and Schottky barrier heights of 0.14-0.18 eV were determined by activation energy analysis and spectral response measurement.

  3. Preparation of an ochre suppressor tRNA recognizing exclusively UAA codon by using the molecular surgery technique.

    PubMed

    Yokogawa, Takashi; Hassan, Hanim Munirah Binti Che; Yokota, Yukiko; Ohno, Satoshi; Nishikawa, Kazuya

    2009-01-01

    In order to create an ochre suppressor tRNA which exclusively recognizes UAA codon, we replaced the G34 at the first position of yeast tRNA(Tyr)[GPsiA] anticodon with pseudouridine34 (Psi34) by using the molecular surgery technique. This tRNA(Tyr)[PsiPsiA] recognized only the UAA codon as expectedly, but tRNA(Tyr)[UPsiA] made as a control also behaved similarly. This result may suggest that U34 must be somehow modified to facilitate the wobble-pairing to G at the third position of codon. PMID:19749377

  4. Cytogenetic analysis in Polypterus ornatipinnis (Actinopterygii, Cladistia, Polypteridae) and 5S rDNA.

    PubMed

    Morescalchi, Maria Alessandra; Stingo, Vincenzo; Capriglione, Teresa

    2011-03-01

    Polypteridae is a family of archaic freshwater African fish that constitute an interesting subject for the study of the karyological evolution in vertebrates, on account of their primitive morphological characters and peculiar relationships with lower Osteichthyans. In this paper, a cytogenetic analysis on twenty specimens of both sexes of Polypterus ornatipinnis the ornate "bichir", coming from the Congo River basin, was performed by using both classical and molecular techniques. The karyotypic formula (2n=36; FN=72) was composed of 26 M+10 SM. The Alu I banding, performed to characterize heterochromatin in this species, was mainly centromeric. Both the chromosome location of the ribosomal 5S and 18S rRNA genes were examined by using Ag-NOR, classical C-banding, CMA(3) staining and FISH. CMA(3) marked all centromerical regions and showed the presence of two GC rich regions on the p arm of the chromosome pair n°1 and on the q arm of the pair n°14. Staining with Ag-NOR marked the only telomeric region of the chromosome n°1 p arm. After PCR, the 5S rDNA in this species was cloned, sequenced and analyzed. In the 665bp 5S rDNA sequence of P.ornatipinnis, a conserved 120bp gene region for the 5S rDNA was identified, followed by a non-transcribed variable spacer (NTS) which included simple repeats, microsatellites and a fragment of a non-LTR retrotransposon R-TEX. FISH with 5S rDNA marked the subtelomeric region of the q arm of the chromosome pair n°14, previously marked by CMA(3). FISH with 18S rDNA marked the telomeric region of the p arm of the pair n°1, previously marked both by Ag-NOR and CMA(3). The (GATA)(7) repeats marked the telomeric regions of all chromosome pairs, with the exclusion of the n°1, n°3 and n°14; hybridization with telomeric probes (TTAGGG)(n) showed signals at the end of all chromosomes. Karyotype evolution in Polypterus genus was finally discussed, including the new data obtained.

  5. Cytogenetic analysis in Polypterus ornatipinnis (Actinopterygii, Cladistia, Polypteridae) and 5S rDNA.

    PubMed

    Morescalchi, Maria Alessandra; Stingo, Vincenzo; Capriglione, Teresa

    2011-03-01

    Polypteridae is a family of archaic freshwater African fish that constitute an interesting subject for the study of the karyological evolution in vertebrates, on account of their primitive morphological characters and peculiar relationships with lower Osteichthyans. In this paper, a cytogenetic analysis on twenty specimens of both sexes of Polypterus ornatipinnis the ornate "bichir", coming from the Congo River basin, was performed by using both classical and molecular techniques. The karyotypic formula (2n=36; FN=72) was composed of 26 M+10 SM. The Alu I banding, performed to characterize heterochromatin in this species, was mainly centromeric. Both the chromosome location of the ribosomal 5S and 18S rRNA genes were examined by using Ag-NOR, classical C-banding, CMA(3) staining and FISH. CMA(3) marked all centromerical regions and showed the presence of two GC rich regions on the p arm of the chromosome pair n°1 and on the q arm of the pair n°14. Staining with Ag-NOR marked the only telomeric region of the chromosome n°1 p arm. After PCR, the 5S rDNA in this species was cloned, sequenced and analyzed. In the 665bp 5S rDNA sequence of P.ornatipinnis, a conserved 120bp gene region for the 5S rDNA was identified, followed by a non-transcribed variable spacer (NTS) which included simple repeats, microsatellites and a fragment of a non-LTR retrotransposon R-TEX. FISH with 5S rDNA marked the subtelomeric region of the q arm of the chromosome pair n°14, previously marked by CMA(3). FISH with 18S rDNA marked the telomeric region of the p arm of the pair n°1, previously marked both by Ag-NOR and CMA(3). The (GATA)(7) repeats marked the telomeric regions of all chromosome pairs, with the exclusion of the n°1, n°3 and n°14; hybridization with telomeric probes (TTAGGG)(n) showed signals at the end of all chromosomes. Karyotype evolution in Polypterus genus was finally discussed, including the new data obtained. PMID:21429462

  6. Development of a molecular beam technique to study early solar system silicon reactions

    NASA Technical Reports Server (NTRS)

    Dong, Q. W.; Thiemens, M. H.

    1993-01-01

    Silicon monoxide is one of the major gas phase silicon bearing components observed in astronomical environments. Silicon oxide serves as the major rock forming material for terrestrial and meteoritic bodies. It is known that several gas phase reactions produce mass independent isotopic fractionations which possess the same delta(O-17)/delta(O-18) ratio observed in Allende inclusions. The general symmetry dependence of the chemically produced mass independent isotopic fractionation process suggests that there are several plausible reactions which could occur in the early solar system which may lead to production of the observed meteoritic oxygen isotopic anomalies. An important component in exploring the role of such processes is the need to experimentally determine the isotopic fractionations for specific reactions of relevance to the early solar system. It has already been demonstrated that atomic oxygen reaction with CO, a major nebular oxygen bearing species, produces a large (approximately 90 percent), mass independent isotopic fractionation. The next hurdle regarding assessing the involvement of symmetry dependent isotopic fractionation processes in the pre-solar nebula is to determine isotopic fractionation factors associated with gas phase reactions of metallic oxides. In particular, a reaction such as O + SiO yields SiO2 is a plausible nebular reaction which could produce a delta(O-17) is approximately delta(O-18) fractionation based upon molecular symmetry considerations. While the isotopic fractionations during silicate evaporation and condensation have been determined, there are no isotopic studies of controlled, gas phase nucleation processes. In order to carefully control the reaction kinetics, a molecular beam apparatus has been constructed. This system produces a supersonic, collimated beam of SiO molecules which is reacted with a second beam of oxygen atoms. An important feature of molecular beams is that they operate at sufficiently low pressures

  7. Cytogenetic studies of five gastric carcinomas metastatic to the pleura.

    PubMed

    Trigo, M I; San Martín, M V; Novales, M A; Maraví, J

    1994-07-15

    A cytogenetic analysis was made of five pleural effusions from gastric carcinoma metastasis. Two had hyperdiploid karyotypes, another two were near-triploid, and one was between triploid and tetraploid. Our results show chromosome 16 gain in a high percentage of cells.

  8. [Cytogenetic activity of the butylcaptax defoliant transformation product].

    PubMed

    Vesmanova, O Ia; Semykina, E E; Koblov, R K; Ergashev

    1989-01-01

    Cytogenetical activity of the product of metabolitic butylcaptax transformations in cells of cotton plants G. barbadense has been studied. It is shown that butylcaptax, with a significant mutagenicity, looses its mutagenic activity, metabolizing in low mutagenic 2-oxyamylthiobenzthiazole. Low water solubility prevents its concentration to exceed 0.005% in tissue liquids and to exert a mutagenic action on cotton plants. PMID:2773061

  9. 40 CFR 798.5375 - In vitro mammalian cytogenetics.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... structural or numerical. However, because cytogenetic assays are usually designed to analyse cells at their... metaphases containing ±2 centromeres of the modal number shall be analyzed. Uniform criteria for scoring... specified under 40 CFR part 792, subpart J the following specific information shall be reported: (i)...

  10. [Cytogenetic activity of the butylcaptax defoliant transformation product].

    PubMed

    Vesmanova, O Ia; Semykina, E E; Koblov, R K; Ergashev

    1989-01-01

    Cytogenetical activity of the product of metabolitic butylcaptax transformations in cells of cotton plants G. barbadense has been studied. It is shown that butylcaptax, with a significant mutagenicity, looses its mutagenic activity, metabolizing in low mutagenic 2-oxyamylthiobenzthiazole. Low water solubility prevents its concentration to exceed 0.005% in tissue liquids and to exert a mutagenic action on cotton plants.

  11. Cytogenetic studies of three triazine herbicides. I. In vitro studies

    EPA Science Inventory

    Atrazine, simazine, and cyanazine are widely used pre-emergence and post-emergence triazine herbicides that have made their way into the potable water supply of many agricultural communities. Because of this and the prevalence of contradictory cytogenetic studies in the literatur...

  12. Growth of CdTe on Si(100) surface by ionized cluster beam technique: Experimental and molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Araghi, Houshang; Zabihi, Zabiholah; Nayebi, Payman; Ehsani, Mohammad Mahdi

    2016-10-01

    II-VI semiconductor CdTe was grown on the Si(100) substrate surface by the ionized cluster beam (ICB) technique. In the ICB method, when vapors of solid materials such as CdTe were ejected through a nozzle of a heated crucible into a vacuum region, nanoclusters were created by an adiabatic expansion phenomenon. The clusters thus obtained were partially ionized by electron bombardment and then accelerated onto the silicon substrate at 473 K by high potentials. The cluster size was determined using a retarding field energy analyzer. The results of X-ray diffraction measurements indicate the cubic zinc blende (ZB) crystalline structure of the CdTe thin film on the silicon substrate. The CdTe thin film prepared by the ICB method had high crystalline quality. The microscopic processes involved in the ICB deposition technique, such as impact and coalescence processes, have been studied in detail by molecular dynamics (MD) simulation.

  13. Absolute molecular transition frequencies measured by three cavity-enhanced spectroscopy techniques

    NASA Astrophysics Data System (ADS)

    Cygan, A.; Wójtewicz, S.; Kowzan, G.; Zaborowski, M.; Wcisło, P.; Nawrocki, J.; Krehlik, P.; Śliwczyński, Ł.; Lipiński, M.; Masłowski, P.; Ciuryło, R.; Lisak, D.

    2016-06-01

    Absolute frequencies of unperturbed 12C16O transitions from the near-infrared (3-0) band were measured with uncertainties five-fold lower than previously available data. The frequency axis of spectra was linked to the primary frequency standard. Three different cavity enhanced absorption and dispersion spectroscopic methods and various approaches to data analysis were used to estimate potential systematic instrumental errors. Except for a well established frequency-stabilized cavity ring-down spectroscopy, we applied the cavity mode-width spectroscopy and the one-dimensional cavity mode-dispersion spectroscopy for measurement of absorption and dispersion spectra, respectively. We demonstrated the highest quality of the dispersion line shape measured in optical spectroscopy so far. We obtained line positions of the Doppler-broadened R24 and R28 transitions with relative uncertainties at the level of 10-10. The pressure shifting coefficients were measured and the influence of the line asymmetry on unperturbed line positions was analyzed. Our dispersion spectra are the first demonstration of molecular spectroscopy with both axes of the spectra directly linked to the primary frequency standard, which is particularly desirable for the future reference-grade measurements of molecular spectra.

  14. Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques

    NASA Astrophysics Data System (ADS)

    Shekhar, Prabhanshu; Nanda, Hirsh; Lösche, Mathias; Heinrich, Frank

    2011-11-01

    Biological membranes are composed of a thermally disordered lipid matrix and therefore require non-crystallographic scattering approaches for structural characterization with x-rays or neutrons. Here we develop a continuous distribution (CD) model to refine neutron or x-ray reflectivity data from complex architectures of organic molecules. The new model is a flexible implementation of the composition-space refinement of interfacial structures to constrain the resulting scattering length density profiles. We show this model increases the precision with which molecular components may be localized within a sample, with a minimal use of free model parameters. We validate the new model by parameterizing all-atom molecular dynamics (MD) simulations of bilayers and by evaluating the neutron reflectivity of a phospholipid bilayer physisorbed to a solid support. The determination of the structural arrangement of a sparsely-tethered bilayer lipid membrane (stBLM) comprised of a multi-component phospholipid bilayer anchored to a gold substrate by a thiolated oligo(ethylene oxide) linker is also demonstrated. From the model we extract the bilayer composition and density of tether points, information which was previously inaccessible for stBLM systems. The new modeling strategy has been implemented into the ga_refl reflectivity data evaluation suite, available through the National Institute of Standards and Technology (NIST) Center for Neutron Research (NCNR).

  15. Phospholipid Membrane Protection by Sugar Molecules during Dehydration-Insights into Molecular Mechanisms Using Scattering Techniques

    SciTech Connect

    Garvey, Christopher J.; Lenné, Thomas; Koster, Karen L.; Kent, Ben; Bryant, Gary

    2014-09-24

    Scattering techniques have played a key role in our understanding of the structure and function of phospholipid membranes. These techniques have been applied widely to study how different molecules (e.g., cholesterol) can affect phospholipid membrane structure. However, there has been much less attention paid to the effects of molecules that remain in the aqueous phase. One important example is the role played by small solutes, particularly sugars, in protecting phospholipid membranes during drying or slow freezing. In this paper, we present new results and a general methodology, which illustrate how contrast variation small angle neutron scattering (SANS) and synchrotron-based X-ray scattering (small angle (SAXS) and wide angle (WAXS)) can be used to quantitatively understand the interactions between solutes and phospholipids. Specifically, we show the assignment of lipid phases with synchrotron SAXS and explain how SANS reveals the exclusion of sugars from the aqueous region in the particular example of hexagonal II phases formed by phospholipids.

  16. Molecular dynamics in azobenzene liquid crystal polymer films studied by transient grating technique

    NASA Astrophysics Data System (ADS)

    Katayama, Kenji; Fujii, Tomomi; Kuwahara, Shota; Takado, Kiyohide; Ikeda, Tomiki

    2014-10-01

    We studied the effect of the ratio between the monomer and cross-linker molecules in the azobenene included liquid crystal polymer films by using the heterodyne transient grating (HD-TG) technique, which is one of the time-resolved measurement techniques. Depending on the ratio, the magnitude of the refractive index change, its anisotropy, and the lifetime of the cis isomer of azobenzene, generated by a UV pulse irradiation. By increasing the cross-linker ratio, the refractive index change and its anisotropy was reduced, indicating less ability for the motion, while slower lifetime was observed by increasing the monomer ratio, indicating that the film is difficult to return the original shape by a visiblelight irradiation. The obtained dynamics was consistent with the functionality of the films.

  17. Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.

    PubMed

    Nakamura, Eiichi

    2013-01-01

    "The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education. PMID:23280645

  18. Molecular Imaging in Preclinical Models of IBD with Nuclear Imaging Techniques: State-of-the-Art and Perspectives.

    PubMed

    Kaaru, Eric; Bianchi, Andrea; Wunder, Andreas; Rasche, Volker; Stiller, Detlef

    2016-10-01

    Inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn's disease, is characterized by chronic unregulated inflammation of the intestinal mucosa of the gastrointestinal tract. To date, this pathology has no cure. Colonoscopy and biopsies are the current gold standard diagnostic tools. However, being a chronic disease, IBD requires continuous follow-up to check for disease progress, treatment response, and remission. Unfortunately, these 2 diagnostic procedures are invasive and generally unable to show the cellular and molecular changes that take place in vivo. In this context, it is clear that there is a strong need for optimized noninvasive imaging techniques able to overcome the aforementioned limitations. This review aims to bring to light the scientific advancements that have been achieved so far in nuclear medicine in relation to tracking of immune cells involved in the preclinical models of IBD. In particular, this review will explore the advantages and limitations of the radiopharmaceuticals that aim to track whole cells like neutrophils, those that involve the radiolabeling of immune cell substrates or available human IBD medical therapies, and those that aim to track cell signaling molecules (e.g., cytokines and cell adhesion molecules). After a detailed critical summary of the state-of-the art, the challenges and perspectives of molecular imaging applied to IBD studies will be analyzed. Special attention will be paid to the translational potential of the described techniques and on the potential impact of these innovative approaches on the drug discovery pipelines and their contribution to the evolution of personalized medicine.

  19. Movies of molecular motions and reactions: the single-molecule, real-time transmission electron microscope imaging technique.

    PubMed

    Nakamura, Eiichi

    2013-01-01

    "The truth is, the Science of Nature has been already too long made only a work of the Brain and the Fancy: It is now high time that it should return to the plainness and soundness of Observations on material and obvious things," proudly declared Robert Hooke in his highly successful picture book of microscopic and telescopic images, "Micrographia" in 1665. Hooke's statement has remained true in chemistry, where a considerable work of the brain and the fancy is still necessary. Single-molecule, real-time transmission electron microscope (SMRT-TEM) imaging at an atomic resolution now allows us to learn about molecules simply by watching movies of them. Like any dream come true, the new analytical technique challenged the old common sense of the communities, and offers new research opportunities that are unavailable by conventional methods. With its capacity to visualize the motions and the reactions of individual molecules and molecular clusters, the SMRT-TEM technique will become an indispensable tool in molecular science and the engineering of natural and synthetic substances, as well as in science education.

  20. [Which molecular biology techniques must conform to the armamentarium for basic research in uro-oncology?].

    PubMed

    Oriola, Josep

    2013-06-01

    Molecular biology has been one of the scientific disciplines in which there has been more advances in the last years. The first impulse in the study of genetic alterations came from the discovery of DNA structure, followed by elucidation of the genetic code, the discovery of restriction enzymes and subsequently the invention of PCR, not forgetting the exponential development of computer science. All of them have allowed us to know much more about our genome and its regulation than we could imagine. The impulse in proteomics has been especially in tune up of soft methods of ionization coupled with mass spectrometry. Nevertheless, this seems to be only the beginning since today there are continuous methodological advances that will increase more, without doubt, the knowledge and applications in this discipline. PMID:23793758

  1. Synthesizing a Cellulase like Chimeric Protein by Recombinant Molecular Biology Techniques

    PubMed Central

    Banerjee, Hirendra Nath; Krauss, Christopher; Smith, Valerie; Mahaffey, Kelly; Boston, Ava

    2016-01-01

    In order to meet the Renewable Fuels Standard demands for 30 billion gallons of biofuels by the end of 2020, new technologies for generation of cellulosic ethanol must be exploited. Breaking down cellulose by cellulase enzyme is very important for this purpose but this is not thermostable and degrades at higher temperatures in bioreactors. Towards creation of a more ecologically friendly method of rendering bioethanol from cellulosic waste, we attempted to produce recombinant higher temperature resistant cellulases for use in bioreactors. The project involved molecular cloning of genes for cellulose-degrading enzymes based on bacterial source, expressing the recombinant proteins in E. coli and optimizing enzymatic activity. We were able to generate in vitro bacterial expression systems to produce recombinant His-tag purified protein which showed cellulase like activity. PMID:27468362

  2. Formation mechanism of monodisperse, low molecular weight chitosan nanoparticles by ionic gelation technique.

    PubMed

    Fan, Wen; Yan, Wei; Xu, Zushun; Ni, Hong

    2012-02-01

    Chitosan nanoparticles have been extensively studied for drug and gene delivery. In this paper, monodisperse, low molecular weight (LMW) chitosan nanoparticles were prepared by a novel method based on ionic gelation using sodium tripolyphosphate (TPP) as cross-linking agent. The objective of this study was to solve the problem of preparation of chitosan/TPP nanoparticles with high degree of monodispersity and stability, and investigate the effect of various parameters on the formation of LMW chitosan/TPP nanoparticles. It was found that the particle size distribution of the nanoparticles could be significantly narrowed by a combination of decreasing the concentration of acetic acid and reducing the ambient temperature during cross-linking process. The optimized nanoparticles exhibited a mean hydrodynamic diameter of 138 nm with a polydispersity index (PDI) of 0.026 and a zeta potential of +35 mV, the nanoparticles had good storage stability at room temperature up to at least 20 days.

  3. Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques.

    PubMed

    Fournier, René; Mohareb, Amir

    2016-01-14

    We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of CumSnn (+) (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each CumSnn (+) species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV. PMID:26772561

  4. Molecularly Imprinted Polymer Integrated with a Surface Acoustic Wave Technique for Detection of Sulfamethizole.

    PubMed

    Ayankojo, Akinrinade George; Tretjakov, Aleksei; Reut, Jekaterina; Boroznjak, Roman; Öpik, Andres; Rappich, Jörg; Furchner, Andreas; Hinrichs, Karsten; Syritski, Vitali

    2016-01-19

    The synergistic effect of combining molecular imprinting and surface acoustic wave (SAW) technologies for the selective and label-free detection of sulfamethizole as a model antibiotic in aqueous environment was demonstrated. A molecularly imprinted polymer (MIP) for sulfamethizole (SMZ) selective recognition was prepared in the form of a homogeneous thin film on the sensing surfaces of SAW chip by oxidative electropolymerization of m-phenylenediamine (mPD) in the presence of SMZ, acting as a template. Special attention was paid to the rational selection of the functional monomer using computational and spectroscopic approaches. SMZ template incorporation and its subsequent release from the polymer was supported by IR microscopic measurements. Precise control of the thicknesses of the SMZ-MIP and respective nonimprinted reference films (NIP) was achieved by correlating the electrical charge dosage during electrodeposition with spectroscopic ellipsometry measurements in order to ensure accurate interpretation of label-free responses originating from the MIP modified sensor. The fabricated SMZ-MIP films were characterized in terms of their binding affinity and selectivity toward the target by analyzing the binding kinetics recorded using the SAW system. The SMZ-MIPs had SMZ binding capacity approximately more than eight times higher than the respective NIP and were able to discriminate among structurally similar molecules, i.e., sulfanilamide and sulfadimethoxine. The presented approach for the facile integration of a sulfonamide antibiotic-sensing layer with SAW technology allowed observing the real-time binding events of the target molecule at nanomolar concentration levels and could be potentially suitable for cost-effective fabrication of a multianalyte chemosensor for analysis of hazardous pollutants in an aqueous environment. PMID:26704414

  5. Molecularly Imprinted Polymer Integrated with a Surface Acoustic Wave Technique for Detection of Sulfamethizole.

    PubMed

    Ayankojo, Akinrinade George; Tretjakov, Aleksei; Reut, Jekaterina; Boroznjak, Roman; Öpik, Andres; Rappich, Jörg; Furchner, Andreas; Hinrichs, Karsten; Syritski, Vitali

    2016-01-19

    The synergistic effect of combining molecular imprinting and surface acoustic wave (SAW) technologies for the selective and label-free detection of sulfamethizole as a model antibiotic in aqueous environment was demonstrated. A molecularly imprinted polymer (MIP) for sulfamethizole (SMZ) selective recognition was prepared in the form of a homogeneous thin film on the sensing surfaces of SAW chip by oxidative electropolymerization of m-phenylenediamine (mPD) in the presence of SMZ, acting as a template. Special attention was paid to the rational selection of the functional monomer using computational and spectroscopic approaches. SMZ template incorporation and its subsequent release from the polymer was supported by IR microscopic measurements. Precise control of the thicknesses of the SMZ-MIP and respective nonimprinted reference films (NIP) was achieved by correlating the electrical charge dosage during electrodeposition with spectroscopic ellipsometry measurements in order to ensure accurate interpretation of label-free responses originating from the MIP modified sensor. The fabricated SMZ-MIP films were characterized in terms of their binding affinity and selectivity toward the target by analyzing the binding kinetics recorded using the SAW system. The SMZ-MIPs had SMZ binding capacity approximately more than eight times higher than the respective NIP and were able to discriminate among structurally similar molecules, i.e., sulfanilamide and sulfadimethoxine. The presented approach for the facile integration of a sulfonamide antibiotic-sensing layer with SAW technology allowed observing the real-time binding events of the target molecule at nanomolar concentration levels and could be potentially suitable for cost-effective fabrication of a multianalyte chemosensor for analysis of hazardous pollutants in an aqueous environment.

  6. Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques

    NASA Astrophysics Data System (ADS)

    Fournier, René; Mohareb, Amir

    2016-01-01

    We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of Cu m Snn + (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each Cu m S nn + species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV.

  7. Cytogenetic monitoring of industrial populations potentially exposed to genotoxic chemicals and of control populations.

    PubMed

    de Jong, G; van Sittert, N J; Natarajan, A T

    1988-03-01

    Currently the most applied technique for monitoring biological effects of exposure to genotoxic chemicals in industrial workers is the measurement of chromosome aberrations in peripheral blood lymphocytes. In the Shell petrochemical complex in The Netherlands cytogenetic monitoring studies have been carried out from 1976 till 1981 inclusive, in workers potentially exposed to a variety of genotoxic chemicals, i.e. vinyl chloride, ethylene oxide, benzene, epichlorohydrin, epoxy resins. Average exposure levels to these chemicals were well below the occupational exposure limits. Results of these studies indicate that no biologically significant increase in the frequencies of chromosome aberrations in the exposed populations occurred compared with control populations. Our experience with this methodology has shown that the results of chromosome analyses are difficult to interpret, due to the variable and high background levels of chromosome aberrations in control populations and in individuals. It is concluded that the method is not sufficiently sensitive for routine monitoring of cytogenetic effects in workers exposed to the low levels of genotoxic compounds.

  8. Contributions to cytogenetics of Plectranthus barbatus Andr. (Lamiaceae): a medicinal plant

    PubMed Central

    Reis, Aryane Campos; Viccini, Lyderson Facio; de Sousa, Saulo Marçal

    2015-01-01

    Abstract Accessions of Plectranthus barbatus (Lamiaceae), a medicinal plant, were investigated using a cytogenetic approach and flow cytometry (FCM). Here, we describe for the first time details of the karyotype including chromosome morphology, physical mapping of GC rich bands (CMA3 banding), as well as the mapping of 45S and 5S rDNA sites. All accessions studied showed karyotypes with 2n = 30 small metacentric and submetacentric chromosomes. The CMA3 banding and fluorescent in situ hybridization techniques revealed coincidence between CMA3 bands and 45S rDNA sites (6 terminal marks) while for the 5S rDNA were observed 4 subterminal marks no coincident with CMA3 marks. For nuclear genome size measurement, the FCM procedure provided histograms with G0/G1 peaks exhibiting CV between 2.0–4.9 and the mean values obtained for the species was 2C = 2.78 pg, with AT% = 61.08 and GC% = 38.92. The cytogenetic data obtained here present new and important information which enables the characterization of Plectranthus barbatus. PMID:26312133

  9. Absolute vacuum ultraviolet photoabsorption cross section studies of atomic and molecular species: Techniques and observational data

    NASA Technical Reports Server (NTRS)

    Judge, D. L.; Wu, C. Y. R.

    1990-01-01

    Absorption of a high energy photon (greater than 6 eV) by an isolated molecule results in the formation of highly excited quasi-discrete or continuum states which evolve through a wide range of direct and indirect photochemical processes. These are: photoionization and autoionization, photodissociation and predissociation, and fluorescence. The ultimate goal is to understand the dynamics of the excitation and decay processes and to quantitatively measure the absolute partial cross sections for all processes which occur in photoabsorption. Typical experimental techniques and the status of observational results of particular interest to solar system observations are presented.

  10. Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique

    NASA Astrophysics Data System (ADS)

    Peters, J. H.; Klein, R.; Delle Site, L.

    2016-08-01

    We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.

  11. Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique.

    PubMed

    Peters, J H; Klein, R; Delle Site, L

    2016-08-01

    We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics. PMID:27627414

  12. A genetic algorithm based molecular modeling technique for RNA stem-loop structures.

    PubMed Central

    Ogata, H; Akiyama, Y; Kanehisa, M

    1995-01-01

    A new modeling technique for arriving at the three dimensional (3-D) structure of an RNA stem-loop has been developed based on a conformational search by a genetic algorithm and the following refinement by energy minimization. The genetic algorithm simultaneously optimizes a population of conformations in the predefined conformational space and generates 3-D models of RNA. The fitness function to be optimized by the algorithm has been defined to reflect the satisfaction of known conformational constraints. In addition to a term for distance constraints, the fitness function contains a term to constrain each local conformation near to a prepared template conformation. The technique has been applied to the two loops of tRNA, the anticodon loop and the T-loop, and has found good models with small root mean square deviations from the crystal structure. Slightly different models have also been found for the anticodon loop. The analysis of a collection of alternative models obtained has revealed statistical features of local variations at each base position. Images PMID:7533901

  13. Utility of magnetic cell separation as a molecular sperm preparation technique.

    PubMed

    Said, Tamer M; Agarwal, Ashok; Zborowski, Maciej; Grunewald, Sonja; Glander, Hans-Juergen; Paasch, Uwe

    2008-01-01

    Assisted reproductive techniques (ARTs) have become the treatment of choice in many cases of infertility; however, the current success rates of these procedures remain suboptimal. Programmed cell death (apoptosis) most likely contributes to failed ART and to the decrease in sperm quality after cryopreservation. There is a likelihood that some sperm selected for ART will display features of apoptosis despite their normal appearance, which may be partially responsible for the low fertilization and implantation rates seen with ART. One of the features of apoptosis is the externalization of phosphatidylserine (PS) residues, which are normally present on the inner leaflet of the sperm plasma membrane. Colloidal superparamagnetic microbeads ( approximately 50 nm in diameter) conjugated with annexin V bind to PS and are used to separate dead and apoptotic spermatozoa by magnetic-activated cell sorting (MACS). Cells with externalized PS will bind to these microbeads, whereas nonapoptotic cells with intact membranes do not bind and could be used during ARTs. We have conducted a series of experiments to investigate whether the MACS technology could be used to improve ART outcomes. Our results clearly indicate that integrating MACS as a part of sperm preparation techniques will improve semen quality and cryosurvival rates by eliminating apoptotic sperm. Nonapoptotic spermatozoa prepared by MACS display higher quality in terms of routine sperm parameters and apoptosis markers. The higher sperm quality is represented by an increased oocyte penetration potential and cryosurvival rates. Thus, the selection of nonapoptotic spermatozoa by MACS should be considered to enhance ART success rates. PMID:18077822

  14. Evaluation of molecular techniques for identification and enumeration of Raoultella terrigena ATCC 33257 in water purifier efficacy testing.

    PubMed

    Saha, Ratul; Bechanko, Robin; Bestervelt, Lorelle L; Donofrio, Robert S

    2011-09-01

    Raoultella terrigena ATCC 33257, a representative of the coliform group, is commonly used as a challenge organism in water purifier efficacy testing. In addition to being time consuming, traditional culturing techniques and metabolic identification systems (including automated systems) also fail to accurately differentiate this organism from its closely related neighbors belonging to the Enterobacteriaceae group. Molecular-based techniques, such as real-time quantitative polymerase chain reaction (qPCR) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting, are preferred methods of detection because of their accuracy, reproducibility, specificity, and sensitivity, along with shorter turnaround time. ERIC-PCR performed with the 1R primer set demonstrated stable unique banding patterns (~800, ~300 bp) for R. terrigena ATCC 33257 different from patterns observed for R. planticola and R. ornithinolytica. The primer pair developed from gyraseA (gyrA) sequence of R. terrigena for the SYBR Green qPCR assay using the AlleleID(®) 7.0 primer probe design software was highly specific and sensitive for the target organism. The sensitivity of the assay was 10(1) colony forming units (CFU)/ml for whole cells and 4.7 fg with genomic DNA. The primer pair was successful in determining the concentration (5.5 ± 0.3 × 10(6) CFU/ml) of R. terrigena from water samples spiked with equal concentration of Escherichia coli and R. terrigena. Based on these results from the ERIC-PCR and the SYBR Green qPCR assay, these molecular techniques can be efficiently used for rapid identification and quantification of R. terrigena during water purifier testing. PMID:21132347

  15. Evaluation of molecular techniques for identification and enumeration of Raoultella terrigena ATCC 33257 in water purifier efficacy testing.

    PubMed

    Saha, Ratul; Bechanko, Robin; Bestervelt, Lorelle L; Donofrio, Robert S

    2011-09-01

    Raoultella terrigena ATCC 33257, a representative of the coliform group, is commonly used as a challenge organism in water purifier efficacy testing. In addition to being time consuming, traditional culturing techniques and metabolic identification systems (including automated systems) also fail to accurately differentiate this organism from its closely related neighbors belonging to the Enterobacteriaceae group. Molecular-based techniques, such as real-time quantitative polymerase chain reaction (qPCR) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting, are preferred methods of detection because of their accuracy, reproducibility, specificity, and sensitivity, along with shorter turnaround time. ERIC-PCR performed with the 1R primer set demonstrated stable unique banding patterns (~800, ~300 bp) for R. terrigena ATCC 33257 different from patterns observed for R. planticola and R. ornithinolytica. The primer pair developed from gyraseA (gyrA) sequence of R. terrigena for the SYBR Green qPCR assay using the AlleleID(®) 7.0 primer probe design software was highly specific and sensitive for the target organism. The sensitivity of the assay was 10(1) colony forming units (CFU)/ml for whole cells and 4.7 fg with genomic DNA. The primer pair was successful in determining the concentration (5.5 ± 0.3 × 10(6) CFU/ml) of R. terrigena from water samples spiked with equal concentration of Escherichia coli and R. terrigena. Based on these results from the ERIC-PCR and the SYBR Green qPCR assay, these molecular techniques can be efficiently used for rapid identification and quantification of R. terrigena during water purifier testing.

  16. The FADE mass-stat: a technique for inserting or deleting particles in molecular dynamics simulations.

    PubMed

    Borg, Matthew K; Lockerby, Duncan A; Reese, Jason M

    2014-02-21

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually "fades-in" (inserts) or "fades-out" (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C60 Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors.

  17. The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations

    SciTech Connect

    Borg, Matthew K.; Lockerby, Duncan A.; Reese, Jason M.

    2014-02-21

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C{sub 60} Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors.

  18. The application of rarefaction techniques to molecular inventories of microbial diversity.

    PubMed

    Hughes, Jennifer B; Hellmann, Jessica J

    2005-01-01

    With the growing capacity to inventory microbial community diversity, the need for statistical methods to compare community inventories is also growing. Several approaches have been proposed for comparing the diversity of microbial communities: some adapted from traditional ecology and others designed specifically for molecular inventories of microbes. Rarefaction is one statistical method that is commonly applied in microbial studies, and this chapter discusses the procedure and its advantages and disadvantages. Rarefaction compares observed taxon richness at a standardized sampling effort using confidence intervals. Special emphasis is placed here on the need for precise, rather than unbiased, estimation methods in microbial ecology, but precision can be judged only with a very large sample or with multiple samples drawn from a single community. With low sample sizes, rarefaction curves also have the potential to lead to incorrect rankings of relative species richness, but this chapter discusses a new method with the potential to address this problem. Finally, this chapter shows how rarefaction can be applied to the comparison of the taxonomic similarity of microbial communities.

  19. Cytogenetic evidences of genome rearrangement and differential epigenetic chromatin modification in the sea lamprey (Petromyzon marinus).

    PubMed

    Covelo-Soto, Lara; Morán, Paloma; Pasantes, Juan J; Pérez-García, Concepción

    2014-12-01

    This work explores both the chromatin loss and the differential genome methylation in the sea lamprey (Petromyzon marinus) from a molecular cytogenetic point of view. Fluorescent in situ hybridization experiments on meiotic bivalents and mitotic chromosomes corroborate the chromatin loss previously observed during the development of the sea lamprey and demonstrate that the elimination affects not only to Germ1 sequences but also to the rpt200 satellite DNA and most part of the major ribosomal DNA present on the germinal line. 5-Methylcytosine immunolocation revealed that the GC-rich heterochromatin is highly methylated in the germ line but significantly less in somatic chromosomes. These findings not only support previous observations about genome rearrangements but also give new information about epigenetic changes in P. marinus. The key position of lampreys in the vertebrate phylogenetic tree makes them an interesting taxon to provide relevant information about genome evolution in vertebrates.

  20. Cytogenetic evidences of genome rearrangement and differential epigenetic chromatin modification in the sea lamprey (Petromyzon marinus).

    PubMed

    Covelo-Soto, Lara; Morán, Paloma; Pasantes, Juan J; Pérez-García, Concepción

    2014-12-01

    This work explores both the chromatin loss and the differential genome methylation in the sea lamprey (Petromyzon marinus) from a molecular cytogenetic point of view. Fluorescent in situ hybridization experiments on meiotic bivalents and mitotic chromosomes corroborate the chromatin loss previously observed during the development of the sea lamprey and demonstrate that the elimination affects not only to Germ1 sequences but also to the rpt200 satellite DNA and most part of the major ribosomal DNA present on the germinal line. 5-Methylcytosine immunolocation revealed that the GC-rich heterochromatin is highly methylated in the germ line but significantly less in somatic chromosomes. These findings not only support previous observations about genome rearrangements but also give new information about epigenetic changes in P. marinus. The key position of lampreys in the vertebrate phylogenetic tree makes them an interesting taxon to provide relevant information about genome evolution in vertebrates. PMID:25432678

  1. Evaluation and comparison of molecular techniques for epidemiological typing of Salmonella enterica subsp. enterica serovar dublin.

    PubMed Central

    Liebisch, B; Schwarz, S

    1996-01-01

    A total of 28 unrelated isolates of the Salmonella enterica subsp. enterica serovar dublin (S. dublin) collected during a 6-year period, as well as four samples of the S. dublin live vaccine strain Bovisaloral and its prototype strain S. dublin 442/039, were investigated by different molecular typing methods for the following reasons: (i) to find the most discriminatory method for the epidemiological typing of isolates belonging to this Salmonella serovar and (ii) to evaluate these methods for their capacity to discriminate among the live vaccine strain Bovisaloral, its prototype strain S. dublin 442/039, and field isolates of the serovar dublin. Five different plasmid profiles were observed; a virulence plasmid of 76 kbp as identified by hybridization with an spvB-spvC gene probe was present in all isolates. The detection of 16S rRNA genes and that of IS200 elements proved to be unsuitable for the epidemiological typing of S. dublin; only one hybridization pattern could be observed with each of these methods. The results obtained from macrorestriction analysis strongly depended on the choice of restriction enzyme. While the enzyme NotI yielded the lowest discriminatory index among all enzymes tested, it was the only enzyme that allowed discrimination between the Bovisaloral vaccine strain and its prototype strain. In contrast to the enzymes XbaI and SpeI, which only differentiated among the S. dublin field isolates, XhoI as well as AvrII also produced restriction fragment patterns of the Bovisaloral strain and of its prototype strain that were not shared by any of the S. dublin field isolates. Macrorestriction analysis proved to be the most discriminatory method not only for the epidemiological typing of S. dublin field isolates but also for the identification of the S. dublin live vaccine strain Bovisaloral. PMID:8904430

  2. Measurement of surface stay times for physical adsorption of gases. Ph.D. Thesis - Va. Univ.; [using molecular beam time of flight technique

    NASA Technical Reports Server (NTRS)

    Wilmoth, R. G.

    1973-01-01

    A molecular beam time-of-flight technique is studied as a means of determining surface stay times for physical adsorption. The experimental approach consists of pulsing a molecular beam, allowing the pulse to strike an adsorbing surface and detecting the molecular pulse after it has subsequently desorbed. The technique is also found to be useful for general studies of adsorption under nonequilibrium conditions including the study of adsorbate-adsorbate interactions. The shape of the detected pulse is analyzed in detail for a first-order desorption process. For mean stay times, tau, less than the mean molecular transit times involved, the peak of the detected pulse is delayed by an amount approximately equal to tau. For tau much greater than these transit times, the detected pulse should decay as exp(-t/tau). However, for stay times of the order of the transit times, both the molecular speed distributions and the incident pulse duration time must be taken into account.

  3. Columnar and subsurface silicide growth with novel molecular beam epitaxy techniques

    NASA Technical Reports Server (NTRS)

    Fathauer, R. W.; George, T.; Pike, W. T.

    1992-01-01

    We have found novel growth modes for epitaxial CoSi2 at high temperatures coupled with Si-rich flux ratios or low deposition rates. In the first of these modes, codeposition of metal and Si at 600-800 C with excess Si leads to the formation of epitaxial silicide columns surrounded by single-crystal Si. During the initial stages of the deposition, the excess Si grows homoepitaxially in between the silicide, which forms islands, so that the lateral growth of the islands is confined. Once a template layer is established by this process, columns of silicide form as a result of selective epitaxy of silicide on silicide and Si on Si. This growth process allows nanometer control over silicide particles in three dimensions. In the second of these modes, a columnar silicide seed layer is used as a template to nucleate subsurface growth of CoSi2. With a 100 nm Si layer covering CoSi2 seeds, Co deposited at 800C and 0.01 nm/s diffuses down to grow on the buried seeds rather than nucleating surface silicide islands. For thicker Si caps or higher deposition rates, the surface concentration of Co exceeds the critical concentration for nucleation of islands, preventing this subsurface growth mode from occurring. Using this technique, single-crystal layers of CoSi2 buried under single-crystal Si caps have been grown.

  4. Airborne Fungi in Sahara Dust Aerosols Reaching the Eastern Caribbean: II. Species Identification Using Molecular Techniques

    NASA Astrophysics Data System (ADS)

    de La Mota, A.; Betancourt, C.; Detres, Y.; Armstrong, R.

    2003-12-01

    Fungi samples from filters collected in Castle Bruce, Dominica from March through July 2002, were previously purified and identified to genus level using classic macroscopic and microscopic techniques. A total of 105 isolated colonies were cultured in liquid media and the mycelial mats used for DNA extraction. PCR was used to amplify the ITS region of the rDNA using the ITS1 and ITS4 primers. Both strands of the amplified products were sequenced and the final identification to species level was completed by a GenBank search. Fourteen different species and one fungal endophyte were identified from genders Aspergillus,Penicillium, Fusarium, Cladosporium, Curvularia and Phanerochaete. Some of these species such as A. fumigatus, A. japonicus, P. citrinum and C. cladosporoides are known to cause respiratory disorders in humans. A. fumigatus causes an aggressive pulmonary allergic response that might result in allergic bronchopulmonary aspergillosis. Other species such as F. equiseti and C. brachyspora are plant pathogens affecting economically important crops. Sahara dust is an important source of fungal spores of species that are not common in the Caribbean region.

  5. Molecular genetics of ependymoma

    PubMed Central

    Yao, Yuan; Mack, Stephen C.; Taylor, Michael D.

    2011-01-01

    Brain tumors are the leading cause of cancer death in children, with ependymoma being the third most common and posing a significant clinical burden. Its mechanism of pathogenesis, reliable prognostic indicators, and effective treatments other than surgical resection have all remained elusive. Until recently, ependymoma research was hindered by the small number of tumors available for study, low resolution of cytogenetic techniques, and lack of cell lines and animal models. Ependymoma heterogeneity, which manifests as variations in tumor location, patient age, histological grade, and clinical behavior, together with the observation of a balanced genomic profile in up to 50% of cases, presents additional challenges in understanding the development and progression of this disease. Despite these difficulties, we have made significant headway in the past decade in identifying the genetic alterations and pathways involved in ependymoma tumorigenesis through collaborative efforts and the application of microarray-based genetic (copy number) and transcriptome profiling platforms. Genetic characterization of ependymoma unraveled distinct mRNA-defined subclasses and led to the identification of radial glial cells as its cell type of origin. This review summarizes our current knowledge in the molecular genetics of ependymoma and proposes future research directions necessary to further advance this field. PMID:21959044

  6. Pulmonary embolization of immature Fascioloides magna causing fatal hemothorax confirmed by molecular technique in a heifer in the United States.

    PubMed

    Lee, Jung Keun; Rosser, Thomas Graham; Cooley, Jim

    2016-09-01

    The current report describes the use of a molecular technique to identify immature Fascioloides magna An 18-month-old Brangus heifer was found dead in the field without any prior clinical signs. The cause of death was exsanguination into the thoracic cavity associated with pulmonary embolization and infection by immature Fascioloides magna resulting in 2 large foci of pulmonary necrosis and focal arteriolar and lung rupture. The liver had a few random migratory tracts with typical iron and porphyrin fluke exhaust, but no identified fluke larvae. A single immature fluke was found in the lungs, and species level identification as F. magna was confirmed by DNA sequence analysis of the ribosomal internal transcribed spacer regions (ITS1 region, 5.8S rRNA gene, and ITS2) and of partial 28S rRNA gene sequence. This is one of only a few pulmonary fascioloidiasis cases associated with hemothorax in the veterinary literature. PMID:27423736

  7. Determination of acetamiprid partial-intercalative binding to DNA by use of spectroscopic, chemometrics, and molecular docking techniques.

    PubMed

    Zhang, Yue; Zhang, Guowen; Zhou, Xiaoyue; Li, Yu

    2013-11-01

    Acetamiprid (ACT) is an insecticide widely used for controlling a variety of insect pests. The binding mode associated with calf thymus DNA (ctDNA) upon interaction with ACT was determined using spectroscopic, chemometrics, and molecular docking techniques to clarify the interaction mechanism at the molecular level. Fluorescence titration suggested that the fluorescence quenching of ACT by ctDNA is a static procedure. The binding constants between ACT and ctDNA at different temperatures were calculated to be of the order 10(3)-10(4) L mol(-1). The positive values of enthalpy and entropy change suggested that the binding process is primarily driven by hydrophobic interactions. Multivariate curve resolution-alternating least squares (MCR-ALS), a chemometrics approach, was used to resolve the expanded UV-visible spectral data matrix. The concentration profiles and the spectra for the three reaction components (ACT, ctDNA, and ACT-ctDNA complex) of the system, which formed a highly overlapping composite response, were then successfully obtained and used to evaluate the progress of ACT interacting with ctDNA. The results of the single-stranded ctDNA and iodide quenching experiments, ctDNA-melting investigations, and viscosity measurements indicated that ACT binds to ctDNA by means of a partial intercalation. Molecular docking studies showed that the specific binding site is mainly located between the ACT and G-C base pairs of ctDNA. This docking prediction was confirmed by use of Fourier-transform infrared (FT-IR) spectral analysis. Results from circular dichroism (CD) spectroscopy revealed that ACT induced a conformational change from the B-ctDNA form to the A-ctDNA form. PMID:23975088

  8. Molecular Imaging in Preclinical Models of IBD with Nuclear Imaging Techniques: State-of-the-Art and Perspectives.

    PubMed

    Kaaru, Eric; Bianchi, Andrea; Wunder, Andreas; Rasche, Volker; Stiller, Detlef

    2016-10-01

    Inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn's disease, is characterized by chronic unregulated inflammation of the intestinal mucosa of the gastrointestinal tract. To date, this pathology has no cure. Colonoscopy and biopsies are the current gold standard diagnostic tools. However, being a chronic disease, IBD requires continuous follow-up to check for disease progress, treatment response, and remission. Unfortunately, these 2 diagnostic procedures are invasive and generally unable to show the cellular and molecular changes that take place in vivo. In this context, it is clear that there is a strong need for optimized noninvasive imaging techniques able to overcome the aforementioned limitations. This review aims to bring to light the scientific advancements that have been achieved so far in nuclear medicine in relation to tracking of immune cells involved in the preclinical models of IBD. In particular, this review will explore the advantages and limitations of the radiopharmaceuticals that aim to track whole cells like neutrophils, those that involve the radiolabeling of immune cell substrates or available human IBD medical therapies, and those that aim to track cell signaling molecules (e.g., cytokines and cell adhesion molecules). After a detailed critical summary of the state-of-the art, the challenges and perspectives of molecular imaging applied to IBD studies will be analyzed. Special attention will be paid to the translational potential of the described techniques and on the potential impact of these innovative approaches on the drug discovery pipelines and their contribution to the evolution of personalized medicine. PMID:27580387

  9. Development of Laser Spectroscopic Techniques and Their Application to the Study of Self-Organizing Molecular Assemblies.

    NASA Astrophysics Data System (ADS)

    Reed, Wayne Frederick

    Laser spectroscopic techniques have been developed and adapted to computer based data gathering, reduction and analysis. The systems implemented are a laser flash photolysis and transient dichroism spectrometer, a single photon counting spectrometer for determination of fluorescence lifetimes and time-resolved fluorescence polarization anisotropy, and a light scattering system for both static and dynamic measurements. These techniques have been concerted to study self-organizing molecular assemblies, particularly surfactant vesicles. Quaternary ammonium surfactant monomers with polymerizable styrene moieties on the headgroup have been sonicated into unilamellar vesicles and these in turn have been photopolymerized by both steady state and pulsed laser irradiation. The detailed kinetics of photopolymerization have been determined and a model developed which permits, in conjunction with the laser spectroscopic data, the characterization of the process in terms of average polymer chain length, quantum efficiency of free radical formation, free radical lifetime, and a characteristic rate parameter. Subsequent to characterizing and modelling the photopolymerization process the consequences of it on vesicle surface properties have been investigated with molecular probes. Strong evidence has been obtained that indicates that photopolymerization leads to the formation of clefts or pockets on the vesicle surface and to extensive surface inhomogeneity. Based on the experimental data, a computer simulation has been developed to help graphically visualize the photopolymerization process and to semi-quantitatively characterize the resulting surface inhomogeneity. As a first step in exploring the possibilities opened up by the discovery of clefts in the vesicle surface, the interaction between a photoexcitable proton transfer agent, 8-hydroxy-1,3,6 - pyrenetrisulfonate (POH), and vesicles has been studied. In unpolymerized vesicles POH loses its proton ejection capacity after

  10. Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review

    PubMed Central

    Kuznetsova, Valentina; Aguin-Pombo, Dora

    2015-01-01

    Abstract A comprehensive review of cytogenetic features is provided for the large hemipteran suborder Auchenorrhyncha, which currently contains approximately 42,000 valid species. This review is based on the analysis of 819 species, 483 genera, and 31 families representing all presently recognized Auchenorrhyncha superfamilies, e.i. Cicadoidea (cicadas), Cercopoidea (spittle bugs), Membracoidea (leafhoppers and treehoppers), Myerslopioidea (ground-dwelling leafhoppers), and Fulgoroidea (planthoppers). History and present status of chromosome studies are described, as well as the structure of chromosomes, chromosome counts, trends and mechanisms of evolution of karyotypes and sex determining systems, their variation at different taxonomic levels and most characteristic (modal) states, occurrence of parthenogenesis, polyploidy, B-chromosomes and chromosome rearrangements, and methods used for cytogenetic analysis of Auchenorrhyncha. PMID:26807037

  11. Study on the interaction of the epilepsy drug, zonisamide with human serum albumin (HSA) by spectroscopic and molecular docking techniques

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Khorshidi, Aref; Moghadam, Neda Hossinpour

    2013-10-01

    In the present investigation, an attempt has been made to study the interaction of zonisamide (ZNS) with the transport protein, human serum albumin (HSA) employing UV-Vis, fluorometric, circular dichroism (CD) and molecular docking techniques. The results indicated that binding of ZNS to HSA caused strong fluorescence quenching of HSA through static quenching mechanism, hydrogen bonds and van der Waals contacts are the major forces in the stability of protein ZNS complex and the process of the binding of ZNS with HSA was driven by enthalpy (ΔH = -193.442 kJ mol-1). The results of CD and UV-Vis spectroscopy showed that the binding of this drug to HSA induced conformational changes in HSA. Furthermore, the study of molecular docking also indicated that zonisamide could strongly bind to the site I (subdomain IIA) of HSA mainly by hydrophobic interaction and there were hydrogen bond interactions between this drug and HSA, also known as the warfarin binding site.

  12. Bacterial community structure and activity of sulfate reducing bacteria in a membrane aerated biofilm analyzed by microsensor and molecular techniques.

    PubMed

    Liu, Hong; Tan, Shuying; Sheng, Zhiya; Liu, Yang; Yu, Tong

    2014-11-01

    The activities and vertical spatial distribution of sulfate reducing bacteria (SRB) in an oxygen (O2 )-based membrane aerated biofilm (MAB) were investigated using microsensor (O2 and H2 S) measurements and molecular techniques (polymerase chain reaction-denaturing gradient gel electrophoresis [PCR-DGGE] and fluorescence in situ hybridization [FISH]). The O2 concentration profile revealed that O2 penetrated from the bottom (substratum) of the gas permeable membrane, and was gradually consumed within the biofilm until it was completely depleted near the biofilm/bulk liquid interface, indicating oxic and anoxic zone in the MAB. The H2 S concentration profile showed that H2 S production was found in the upper 285 µm of the biofilm, indicating a high activity of SRB in this region. The results from DGGE of the PCR-amplified dissimilatory sulfite reductase subunit B (dsrB) gene and FISH showed an uneven spatial distribution of SRB. The maximum SRB biomass was located in the upper biofilm. The information from the molecular analysis can be supplemented with that from microsensor measurements to better understand the microbial community and activity of SRB in the MAB.

  13. First prokaryotic biodiversity assessment using molecular techniques of an acidic river in Neuquén, Argentina.

    PubMed

    Urbieta, M Sofía; González Toril, E; Aguilera, A; Giaveno, M Alejandra; Donati, E

    2012-07-01

    Two acidic hot springs close to the crater of Copahue Volcano (Neuquén, Argentina) are the source of the Río Agrio. The river runs several kilometres before flowing into Caviahue Lake. Along the river, temperature, iron, other metal and proton concentrations decrease gradually with distance downstream. From the source to the lake and depending on the season, pH can rise from 1.0 (or even less) to about 4.0, while temperature values decrease from 70°C to 15°C. Water samples were taken from different stations on the river selected according to their physicochemical parameters. In order to assess prokaryotic biodiversity throughout the water column, different and complementary molecular biology techniques were used, mainly in situ hybridisation and 16S rRNA gene cloning and sequencing. All microorganisms found are typical of acidic environments. Sulphur-oxidizing bacteria like Acidithiobacillus thiooxidans and Acidithiobacillus albertensis were detected in every station. Moderately thermophile iron- and sulphur-oxidizing bacteria like members of Alicyclobacillus and Sulfobacillus genera were also ubiquitous. Strict iron-oxidizing bacteria like Leptospirillum and Ferrimicrobium were present at the source of the river, but disappeared downstream where iron concentrations were much lower. Iron-oxidizing, mesophilic Ferroplasma spp. were the main archaea found. The data presented in this work represent the first molecular assessment of this rare natural acidic environment.

  14. Risk Assessment of Radiation Exposure using Molecular Biodosimetry

    NASA Technical Reports Server (NTRS)

    Elliott, Todd F.; George, K.; Hammond, D. K.; Cucinotta, F. A.

    2007-01-01

    Current cytogenetic biodosimetry methods would be difficult to adapt to spaceflight operations, because they require toxic chemicals and a substantial amount of time to perform. In addition, current biodosimetry techniques are limited to whole body doses over about 10cGy. Development of new techniques that assess radiation exposure response at the molecular level could overcome these limitations and have important implications in the advancement of biodosimetry. Recent technical advances include expression profiling at the transcript and protein level to assess multiple biomarkers of exposure, which may lead to the development of a radiation biomarker panel revealing possible fingerprints of individual radiation sensitivity. So far, many biomarkers of interest have been examined in their response to ionizing radiation, such as cytokines and members of the DNA repair pathway. New technology, such as the Luminex system can analyze many biomarkers simultaneously in one sample.

  15. Cocculus hirsutus: Molecular Docking to Identify Suitable Targets for Hepatocellular Carcinoma by In silico Technique

    PubMed Central

    Thavamani, B. Samuel; Mathew, Molly; Dhanabal, S. P.

    2016-01-01

    Background: Protein–ligand interaction plays a major role in identification of the possible mechanism by which a ligand can bind with the target and exerts the pharmacological action. Objective: The aim is to identify the best candidate of Cocculus hirsutus which binds with the hepatocellular carcinoma (HCC) targets by docking studies. Materials and Methods: The reported phytoconstituents such as coclaurine, hirsutine, cohirsine, cohirsinine, lirioresinol, cohirsitinine, haiderine, jamtinine, isotrilobine, shaheenine, jamtine, and cocsoline present in the plant, C. hirsutus were docked with the HCC targets such as Aurora kinase, c-Kit, fibroblast growth factor, nuclear factor kappa B (NF-kB), B-cell lymphoma-extra large, and vascular endothelial growth factor (VEGF) using in silico technique with the software Grid-Based Ligand Docking with Energies. Results: Haiderine, shaheenine, and coclaurine had good interaction with Aurora kinase with the glide score and glide energy of − 7.632, −7.620, −7.464; and − 56.536, −55.203, −52,822, respectively. Coclaurine, lirioresinol, and haiderine possess good binding with c-Kit with the glide score and glide energy of − 8.572, −6.640, −6.478; and − 56.527, −57.138, −20,522, respectively. Lirioresinol, hirsutine, and coclaurine exhibit good binding with c-Kit with the glide score and glide energy of − 5.702, −5.694, −5.678; and − 48.666, −35.778, −41,673, respectively. Similarly, coclaurine, haiderine, and hisutine had good interaction with NF-kB. Haiderine, jamtinine, and coclaurine had good binding with VEGF receptors (VEGFR) and coclaurine, lirioresinol, and haiderine exhibit good bonding with VEGFR. Conclusion: Coclaurine, haiderine, and lirioresinol exibited good hydrogen bonding interactions and binding energy with the select targets. Hence, these compounds have to be taken up for experimental work against hepatocellular carcinoma. SUMMARY Compounds of interest showed good interaction

  16. [Chorionic Villus Sampling in cytogenetic analysis--disadvantages and advantages].

    PubMed

    Gnyś-Wiercioch, Agnieszka; Bloch, Renata; Grolik, Barbara; Hadaś, Jolanta; Kania, Agnieszka; Szołtysik-Szot, Mariola; Sodowska, Henryka

    2012-05-01

    Chorionic villus sampling is used in prenatal diagnosis, enabling to detect fetal genetic abnormalities. Its advantages include the possibility of performing the procedure during the first trimester of pregnancy relatively fast result, risk of miscarriage comparable to that in case of amniocentesis. The disadvantages of this method are: difficult cytogenetic analysis, the possibility of contamination with maternal cells and the risk of mosaicism. There should always be a valid indication to perform the CVS procedure.

  17. Cytogenetics of monosomes in Zea mays. Final report

    SciTech Connect

    Weber, D.F.

    1984-11-01

    The cytogenetics of monosomics in maize generated using the r-X1 system was studied. The goal was to isolate as many as possible of the ten possible primary monosomic types and to characterize them by studying: (1) the cytology of meiosis; (2) the cytological behavior of monosomic chromosomes in meiosis; (3) the effect of monosomic on recombination in heterozygous bivalents; and (4) the frequency and types of spontaneous chromosomal aberrations arising in monosomics. 113 references, 1 figure, 5 tables. (ACR)

  18. JAK2 V617F in myeloid disorders: molecular diagnostic techniques and their clinical utility: a paper from the 2005 William Beaumont Hospital Symposium on Molecular Pathology.

    PubMed

    Steensma, David P

    2006-09-01

    In early 2005, several groups of investigators studying myeloid malignancies described a novel somatic point mutation (V617F) in the conserved autoinhibitory pseudokinase domain of the Janus kinase 2 (JAK2) protein, which plays an important role in normal hematopoietic growth factor signaling. The V617F mutation is present in blood and marrow from a large proportion of patients with classic BCR/ABL-negative chronic myeloproliferative disorders and of a few patients with other clonal hematological diseases such as myelodysplastic syndrome, atypical myeloproliferative disorders, and acute myeloid leukemia. The JAK2 V617F mutation causes constitutive activation of the kinase, with deregulated intracellular signaling that mimics continuous hematopoietic growth factor stimulation. Within 7 months of the first electronic publication describing this new mutation, clinical molecular diagnostic laboratories in the United States and Europe began offering JAK2 mutation testing on a fee-for-service basis. Here, I review the various techniques used by research groups and clinical laboratories to detect the genetic mutation underlying JAK2 V617F, including fluorescent dye chemistry sequencing, allele-specific polymerase chain reaction (PCR), real-time PCR, DNA-melting curve analysis, pyrosequencing, and others. I also discuss diagnostic sensitivity, performance, and other practical concerns relevant to the clinical laboratorian in addition to the potential diagnostic utility of JAK2 mutation tests.

  19. Cytogenetic analysis of Scinax auratus and Scinax eurydice (Anura, Hylidae) with emphasis on cytotaxonomy

    PubMed Central

    Nogueira, Lídia; Paim, Fabilene; Diniz, Débora; Solé, Mirco; Affonso, Paulo; Siqueira, Sérgio; Sampaio, Iracilda

    2015-01-01

    Abstract Scinax Wagler, 1830 is a species-rich genus of amphibians with relatively few detailed chromosomal reports. In this work, cytogenetic analyses of Scinax auratus (Wied-Neuwied, 1821) and Scinax eurydice (Bokermann, 1968) were carried out based on conventional (Giemsa staining, Ag-NOR and C-banding) and cytomolecular (base-specific fluorochrome staining and fluorescence in situ hybridization – FISH of ribosomal probes) techniques. Both species shared the same karyotype, location of active nucleolar organizer regions on pair 11 and GC-rich heterochromatin, as reported for most species in Scinax ruber clade. Interpopulation chromosomal variation was observed in Scinax eurydice, indicating the occurrence of cryptic species. The mapping of 18S ribosomal genes by FISH is reported for the first time in both species. PMID:26140164

  20. CML patients in the molecular era – report of five years experience of diagnosis and treatment in a single center

    PubMed Central

    Voican, I; Vladareanu, AM; Bumbea, H; Barsan, L; Vasile, D

    2013-01-01

    Chronic myeloid leukemia (CML) represents about 15% of all leukemia cases. Although the incidence of the disease is rather low, the therapeutic progress of the last decade has dramatically changed the evolution of this disease, whose survival considerably increased and in whom we now speak even about cure. The success of the therapy is strongly connected to the precocity of the diagnosis and molecular targeted therapy that implies a close monitoring of the patient. The specific molecular assay, that developed a lot in the last years, became an important tool in the management of these patients, providing the possibility of efficient changing in therapy. The purpose of our study was to identify the characteristics of our CML patients in terms of clinical and biological behavior. We analyzed 21 patients diagnosed between October 2007 and December 2010 and compared the data with a historical group of patients, also diagnosed in our department between March 2005 and September 2007. We found a better outcome and overall survival in the study group, due to improved diagnosis and monitoring techniques as well as to better access to therapy. Abbreviations accelerated phase (AP), blast phase (BP), Chronic myeloid leukemia (CML), chronic phase (CP), complete cytogenetic response (CCyR), complete hematologic response (CHR), complete molecular response (CMolR), European LeukemiaNet (ELN), Imatinib mesylate (IM) , major molecular response (MMolR), minimal cytogenetic response (minCyR), partial cytogenetic response (PCyR), polymerase-chain-reaction (PCR), Qualitative Polymerase-Chain-Reaction (Q-PCR), Quantitative Real-Time Polymerase-Chain-Reaction (RT-PCR), tyrosine kinase inhibitors (TKI) PMID:24146695

  1. Rare cytogenetic abnormalities in acute myeloid leukemia transformed from Fanconi anemia – a case report

    PubMed Central

    2013-01-01

    Background Fanconi’s anemia (FA) is an inherited bone marrow failure syndrome that carries a higher risk of transformation to acute myeloid leukemia (AML) when compared with general population. AML is the initial presentation in approximately one third of patients. Case presentation A 17 year old male presented to the emergency room with history of high grade fever since two weeks. Examination revealed pallor, short stature and thumb polydactyly. There was no visceromegaly or lymphadenopathy. Complete blood count showed haemoglobin 3.4 gm/dl, MCV 100 fl and MCH 36 pg, white blood cell count 55.9 × 10 E9/L and platelet count 8 × 10E9/L. Peripheral blood smear revealed 26% blast cells. Bone marrow was hypercellular exhibiting infiltration with 21% blast cells. Auer rods were seen in few blast cells. These findings were consistent with acute myelomonocytic leukemia. These blasts cells expressed CD33, CD13, HLA-DR, CD117, CD34 antigens and cytoplasmic myeloperoxidase on immunophenotyping. Bone marrow cytogenetics revealed 46, XY, t (8:21) (q22; q22) [11] / 46, XY, add (2) (q37), t (8; 21) [4] / 46, XY [5]. Molecular studies showed positivity of FLT 3 D835 variant and negativity of NPM 1 and FLT3 ITD (internal tandem domain) mutation. Peripheral blood analysis for chromosomal breakage exhibited tri-radial and complex figures. He received induction chemotherapy with cytarabine and daunorubicin (3 + 7). Day 14 marrow revealed clearance of blast cells. Conclusion The recognition of specific cytogenetic abnormalities present in FA known to predispose to AML is crucial for early haematopoietic stem cell transplant (HSCT) before transformation to leukemia. PMID:23937881

  2. Response to lenalidomide in myelodysplastic syndromes with del(5q): influence of cytogenetics and mutations.

    PubMed

    Mallo, Mar; Del Rey, Mónica; Ibáñez, Mariam; Calasanz, M José; Arenillas, Leonor; Larráyoz, M José; Pedro, Carmen; Jerez, Andrés; Maciejewski, Jaroslaw; Costa, Dolors; Nomdedeu, Meritxell; Diez-Campelo, María; Lumbreras, Eva; González-Martínez, Teresa; Marugán, Isabel; Such, Esperanza; Cervera, José; Cigudosa, Juan C; Alvarez, Sara; Florensa, Lourdes; Hernández, Jesús M; Solé, Francesc

    2013-07-01

    Lenalidomide is an effective drug in low-risk myelodysplastic syndromes (MDS) with isolated del(5q), although not all patients respond. Studies have suggested a role for TP53 mutations and karyotype complexity in disease progression and outcome. In order to assess the impact of complex karyotypes on treatment response and disease progression in 52 lenalidomide-treated patients with del(5q) MDS, conventional G-banding cytogenetics (CC), single nucleotide polymorphism array (SNP-A), and genomic sequencing methods were used. SNP-A analysis (with control sample, lymphocytes CD3+, in 30 cases) revealed 5q losses in all cases. Other recurrent abnormalities were infrequent and were not associated with lenalidomide responsiveness. Low karyotype complexity (by CC) and a high baseline platelet count (>280 × 10(9) /l) were associated with the achievement of haematological response (P = 0·020, P = 0·013 respectively). Unmutated TP53 status showed a tendency for haematological response (P = 0·061). Complete cytogenetic response was not observed in any of the mutated TP53 cases. By multivariate analysis, the most important predictor for lenalidomide treatment failure was a platelet count <280 × 10(9) /l (Odds Ratio = 6·17, P = 0·040). This study reveals the importance of a low baseline platelet count, karyotypic complexity and TP53 mutational status for response to lenalidomide treatment. It supports the molecular study of TP53 in MDS patients treated with lenalidomide.

  3. Thermodynamic study of β-cyclodextrin-dye inclusion complexes using gradient flow injection technique and molecular modeling.

    PubMed

    Izadmanesh, Y; Ghasemi, Jahan B

    2016-08-01

    Gradient flow injection technique-diode array spectrophotometry was applied for β-cyclodextrin (β-CD)-dye inclusion complex studies. A single injection of a small amount of mixed β-CD-dye solution (100μl) into the carrier solution of the dye and recording the spectra gave the titration data. The mole ratio data were calculated by calibrating the dispersion pattern using a calibrator dye (rose bengal). Model-based multivariate methods were used to analyze the spectral-mole ratio data and, as a result, estimate stability constants and concentration-spectral profiles. Reliability was tested by applying this method to study the β-CD host-guest complexes with several dyes as guest molecules. Singular value decomposition (SVD) was used to select the chemical model and reduce noise. Molecular modeling provided the ability to predict the guest conformation-orientation (posing) within the cavity of β-CD and the nature of the involved interactions. Among those dyes showing observable spectral variation, the stoichiometric ratio of β-CD: dye (and log Kf) of methyl orange, fluorescein, phenol red, 4-(2-pyridylazo) resorcinol (PAR), and crystal violet were calculated to be 1:1 (4.26±0.01), 1:1 (1.53±0.08), 1:1 (3.11±0.04), 1:1 (1.06±0.12), and 2:1 (5.27±0.03), respectively. Compared with the classical method of titration, this method is simple and fast and has the advantage of needing reduced human interference. Molecular modeling facilitates a better understanding of the type of interactions and conformation of guest molecules in the β-CD cavity. The details of the proposed method are discussed in this paper.

  4. Thermodynamic study of β-cyclodextrin-dye inclusion complexes using gradient flow injection technique and molecular modeling

    NASA Astrophysics Data System (ADS)

    Izadmanesh, Y.; Ghasemi, Jahan B.

    2016-08-01

    Gradient flow injection technique-diode array spectrophotometry was applied for β-cyclodextrin (β-CD)-dye inclusion complex studies. A single injection of a small amount of mixed β-CD-dye solution (100 μl) into the carrier solution of the dye and recording the spectra gave the titration data. The mole ratio data were calculated by calibrating the dispersion pattern using a calibrator dye (rose bengal). Model-based multivariate methods were used to analyze the spectral-mole ratio data and, as a result, estimate stability constants and concentration-spectral profiles. Reliability was tested by applying this method to study the β-CD host-guest complexes with several dyes as guest molecules. Singular value decomposition (SVD) was used to select the chemical model and reduce noise. Molecular modeling provided the ability to predict the guest conformation-orientation (posing) within the cavity of β-CD and the nature of the involved interactions. Among those dyes showing observable spectral variation, the stoichiometric ratio of β-CD: dye (and log Kf) of methyl orange, fluorescein, phenol red, 4-(2-pyridylazo) resorcinol (PAR), and crystal violet were calculated to be 1:1 (4.26 ± 0.01), 1:1 (1.53 ± 0.08), 1:1 (3.11 ± 0.04), 1:1 (1.06 ± 0.12), and 2:1 (5.27 ± 0.03), respectively. Compared with the classical method of titration, this method is simple and fast and has the advantage of needing reduced human interference. Molecular modeling facilitates a better understanding of the type of interactions and conformation of guest molecules in the β-CD cavity. The details of the proposed method are discussed in this paper.

  5. Thermodynamic study of β-cyclodextrin-dye inclusion complexes using gradient flow injection technique and molecular modeling.

    PubMed

    Izadmanesh, Y; Ghasemi, Jahan B

    2016-08-01

    Gradient flow injection technique-diode array spectrophotometry was applied for β-cyclodextrin (β-CD)-dye inclusion complex studies. A single injection of a small amount of mixed β-CD-dye solution (100μl) into the carrier solution of the dye and recording the spectra gave the titration data. The mole ratio data were calculated by calibrating the dispersion pattern using a calibrator dye (rose bengal). Model-based multivariate methods were used to analyze the spectral-mole ratio data and, as a result, estimate stability constants and concentration-spectral profiles. Reliability was tested by applying this method to study the β-CD host-guest complexes with several dyes as guest molecules. Singular value decomposition (SVD) was used to select the chemical model and reduce noise. Molecular modeling provided the ability to predict the guest conformation-orientation (posing) within the cavity of β-CD and the nature of the involved interactions. Among those dyes showing observable spectral variation, the stoichiometric ratio of β-CD: dye (and log Kf) of methyl orange, fluorescein, phenol red, 4-(2-pyridylazo) resorcinol (PAR), and crystal violet were calculated to be 1:1 (4.26±0.01), 1:1 (1.53±0.08), 1:1 (3.11±0.04), 1:1 (1.06±0.12), and 2:1 (5.27±0.03), respectively. Compared with the classical method of titration, this method is simple and fast and has the advantage of needing reduced human interference. Molecular modeling facilitates a better understanding of the type of interactions and conformation of guest molecules in the β-CD cavity. The details of the proposed method are discussed in this paper. PMID:27111153

  6. Influence of heavy ions on cell survival, cytogenetic damage and mitochondrial function of human endothelial cells

    NASA Astrophysics Data System (ADS)

    Ritter, Sylvia; Helm, Alexander; Lee, Ryonfa; Pollet, Dieter; Durante, Marco

    There is increasing evidence that there is an elevated risk of cardiovascular disease among atomic bomb survivors and radiotherapy patients, typically developing with a long latency. However, essentially no information is available on the potential cardiovascular risks associated with space radiation, in particular heavy ions. To address this issue, we have chosen human umbilical vein endothelial cells (HUVEC) as a model system. Cells at an early passage number were irradiated with 0.1 to 4 Gy of either 9.8 MeV/u C-ions (LET=170 keV/µm), 91 MeV/u C-ions (LET=29 keV/µm) or 250 kV X-rays. Cells were regularly subcultured up to 40 days (20 population doublings) post-irradiation. Immediately after exposure cell inactivation was deter-mined by the colony forming assay. Furthermore, at selected time-points cytogenetic damage (formation of micronuclei in binucleated cells) and the mitochondrial membrane potential ΨM (flow cytometric analysis following JC-1 staining) were assessed. Measurement of the directly induced radiation damage showed that 9.8 MeV/u and 91 MeV/u C-ions were more effective than X-rays (i.e. about 3 and 2 times, respectively) with respect to cell inactivation or the in-duction of cytogenetic damage. At the subsequent days in the irradiated cultures the number of cells with micronuclei declined to the control level (3-5Altogether our data indicate that under the applied radiation conditions the integrity of mitochondria which play a significant role in the regulation of cardiovascular cell function is not impaired. With respect to directly induced genetic damage C-ions are more effective than X-rays as observed in other cell systems. If the effectiveness of charged particles for the occurrence of late chromosomal damage in endothelial cells is higher than that of sparsely ionizing radiation needs further clarification. The data obtained up to now indicate that sophisticated cytogenetic techniques have to be applied in order to draw any firm

  7. Nanoparticle removal using laser induced plasma (LIP) technique and study of detachment modes based on molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Peri, M. D. Murthy

    Nanoparticle contamination is a major problem in many industries. In the semiconductor industry, as the device (integrated circuit) size shrinks with each technological node (DRAM half-pitch), the feature size that has to be fabricated shrinks. Consequently, the minimum tolerable particle defect size also reduces to sub-100 nm level. In order to attain the stringent small size features, Extreme Ultraviolet Lithography (EUVL) technique is being explored in the semiconductor industry. As the EUVL masks are reflective and pellicle free, the cleaning techniques employed to remove the native particle defects must be more effective for the removal of the sub-100 nm particles without any substrate damage. The effectiveness of Laser Induced Plasma (LIP) technique, considered as a next generation cleaning method, for removal of 30 nm PSL particles from silicon substrate was previously demonstrated by our group. In the current study, the removal of 100 nm PSL particles from photomask and 300 nm PSL particles from 500 nm patterns was investigated. It was observed that the patterns were damaged which could be attributed to the radiation heating of the plasma, and this necessitated pressure amplification techniques to amplify the transient pressure and minimize the risk of damage. As a potential solution, shocktubes were designed and transient pressure measurements were carried out in air medium. Also, plasma was generated in water, in order to take advantage of the density of the medium, to generate stronger shocks and consequently higher pressure. The performance of the shocktubes was characterized based on their pressure amplification factor. The shocktubes resulted in a pressure amplification factor of 11 in air. The particle removal experiments with shocktubes on 150 nm patterns were performed and no damage to the patterns was observed. However, there were particle adders due to the ablation of the shocktube material. Molecular Dynamics (MD) simulations were initiated and

  8. SF3B1 mutations correlated to cytogenetics and mutations in NOTCH1, FBXW7, MYD88, XPO1 and TP53 in 1160 untreated CLL patients.

    PubMed

    Jeromin, S; Weissmann, S; Haferlach, C; Dicker, F; Bayer, K; Grossmann, V; Alpermann, T; Roller, A; Kohlmann, A; Haferlach, T; Kern, W; Schnittger, S

    2014-01-01

    We analyzed a large cohort of 1160 untreated CLL patients for novel genetic markers (SF3B1, NOTCH1, FBXW7, MYD88, XPO1) in the context of molecular, immunophenotypic and cytogenetic data. NOTCH1 mutations (mut) (12.3%), SF3B1mut (9.0%) and TP53mut (7.1%) were more frequent than XPO1mut (3.4%), FBXW7mut (2.5%) and MYD88mut (1.5%). SF3B1mut, NOTCH1mut, TP53mut and XPO1mut were highly correlated to unmutated, whereas MYD88mut were associated with mutated IGHV status. Associations of diverse cytogenetic aberrations and mutations emerged: (1) SF3B1mut with del(11q), (2) NOTCH1mut and FBXW7mut with trisomy 12 and nearly exclusiveness of SF3B1mut, (3) MYD88mut with del(13q) sole and low frequencies of SF3B1mut, NOTCH1mut and FBXW7mut. In patients with normal karyotype only SF3B1mut were frequent, whereas NOTCH1mut rarely occurred. An adverse prognostic impact on time to treatment (TTT) and overall survival (OS) was observed for SF3B1mut, NOTCH1mut and TP53 disruption. In multivariate analyses SF3B1mut, IGHV mutational status and del(11q) were the only independent genetic markers for TTT, whereas for OS SF3B1mut, IGHV mutational status and TP53 disruption presented with significant impact. Finally, our data suggest that analysis of gene mutations refines the risk stratification of cytogenetic prognostic subgroups and confirms data of a recently proposed model integrating molecular and cytogenetic data. PMID:24113472

  9. Endolithic growth of two Lecidea lichens in granite from continental Antarctica detected by molecular and microscopy techniques.

    PubMed

    De Los Ríos, A; Sancho, L G; Grube, M; Wierzchos, J; Ascaso, C

    2005-01-01

    Through the combined use of molecular and microscopy techniques, the endolithic lichens Lecidea cancriformis and Lecidea sp. were identified, even in the absence of fruiting bodies, and positioned under epilithic lichens. Cells of both algal and fungal symbionts were observed in fissures and cracks of the lithic substrate with no clear heteromerous structure. At the ultrastructural level, the two lichens differed in terms of their algal-fungal relationships. Only one genotype of Trebouxia ITS sequence was identified from specimens of Lecidea sp., Umbilicaria aprina and Buellia frigida from the same zone, which could be mainly determined by low availability of alga in these extreme environments. These lichens showed features typical of both chasmoendolithic and euendolithic microorganisms. Signs of biogeophysical and biogeochemical action on the substrate were detected close to fungal cells. This action seemed to be mainly conditioned by the local physico-chemical features of the substrate. Evidence for the biomobilization of elements by these endolithic lichens was found. L. cancriformis was observed to accumulate substantial amounts of calcium-rich biominerals. The combined approach proposed is useful for mapping the distribution of endolithic lichens and analysing the processes that occur in their microscopic environment.

  10. Identification of acetic acid bacteria in traditionally produced vinegar and mother of vinegar by using different molecular techniques.

    PubMed

    Yetiman, Ahmet E; Kesmen, Zülal

    2015-07-01

    Culture-dependent and culture-independent methods were combined for the investigation of acetic acid bacteria (AAB) populations in traditionally produced vinegars and mother of vinegar samples obtained from apple and grape. The culture-independent denaturing gradient gel electrophoresis (DGGE) analysis, which targeted the V7-V8 regions of the 16S rRNA gene, showed that Komagataeibacter hansenii and Komagataeibacter europaeus/Komagataeibacter xylinus were the most dominant species in almost all of the samples analyzed directly. The culture-independent GTG5-rep PCR fingerprinting was used in the preliminary characterization of AAB isolates and species-level identification was carried out by sequencing of the 16S rRNA gene, 16S-23S rDNA internally transcribed to the spacer (ITS) region and tuf gene. Acetobacter okinawensis was frequently isolated from samples obtained from apple while K. europaeus was identified as the dominant species, followed by Acetobacter indonesiensis in the samples originating from grape. In addition to common molecular techniques, real-time PCR intercalating dye assays, including DNA melting temperature (Tm) and high resolution melting analysis (HRM), were applied to acetic acid bacterial isolates for the first time. The target sequence of ITS region generated species-specific HRM profiles and Tm values allowed discrimination at species level.

  11. Semi-Empirical Validation of the Cross-Band Relative Absorption Technique for the Measurement of Molecular Mixing Ratios

    NASA Technical Reports Server (NTRS)

    Pliutau, Denis; Prasad, Narasimha S

    2013-01-01

    Studies were performed to carry out semi-empirical validation of a new measurement approach we propose for molecular mixing ratios determination. The approach is based on relative measurements in bands of O2 and other molecules and as such may be best described as cross band relative absorption (CoBRA). . The current validation studies rely upon well verified and established theoretical and experimental databases, satellite data assimilations and modeling codes such as HITRAN, line-by-line radiative transfer model (LBLRTM), and the modern-era retrospective analysis for research and applications (MERRA). The approach holds promise for atmospheric mixing ratio measurements of CO2 and a variety of other molecules currently under investigation for several future satellite lidar missions. One of the advantages of the method is a significant reduction of the temperature sensitivity uncertainties which is illustrated with application to the ASCENDS mission for the measurement of CO2 mixing ratios (XCO2). Additional advantages of the method include the possibility to closely match cross-band weighting function combinations which is harder to achieve using conventional differential absorption techniques and the potential for additional corrections for water vapor and other interferences without using the data from numerical weather prediction (NWP) models.

  12. Identification of acetic acid bacteria in traditionally produced vinegar and mother of vinegar by using different molecular techniques.

    PubMed

    Yetiman, Ahmet E; Kesmen, Zülal

    2015-07-01

    Culture-dependent and culture-independent methods were combined for the investigation of acetic acid bacteria (AAB) populations in traditionally produced vinegars and mother of vinegar samples obtained from apple and grape. The culture-independent denaturing gradient gel electrophoresis (DGGE) analysis, which targeted the V7-V8 regions of the 16S rRNA gene, showed that Komagataeibacter hansenii and Komagataeibacter europaeus/Komagataeibacter xylinus were the most dominant species in almost all of the samples analyzed directly. The culture-independent GTG5-rep PCR fingerprinting was used in the preliminary characterization of AAB isolates and species-level identification was carried out by sequencing of the 16S rRNA gene, 16S-23S rDNA internally transcribed to the spacer (ITS) region and tuf gene. Acetobacter okinawensis was frequently isolated from samples obtained from apple while K. europaeus was identified as the dominant species, followed by Acetobacter indonesiensis in the samples originating from grape. In addition to common molecular techniques, real-time PCR intercalating dye assays, including DNA melting temperature (Tm) and high resolution melting analysis (HRM), were applied to acetic acid bacterial isolates for the first time. The target sequence of ITS region generated species-specific HRM profiles and Tm values allowed discrimination at species level. PMID:25828705

  13. Direct, immunological and molecular techniques for a fasciolosis survey in a rural area of San Luis, Argentina.

    PubMed

    Carnevale, Silvana; Cabrera, Marta Graciela; Cucher, Marcela Alejandra; di Risio, Cecilia Alicia; Malandrini, Jorge Bruno; Kamenetzky, Laura; Alazraqui, Marcio; Etchart, Cristina Beatriz; Pantano, María Laura; Velásquez, Jorge Néstor

    2013-10-01

    Fasciolosis is a zoonosis caused by the trematode Fasciola hepatica, prevalent in cattle, that is actually emerging as a cause of disease in humans. The goal of this work was to describe the characteristics of fasciolosis in arroyo El Juncal region, La Toma, San Luis province, Argentina. In order to get this objective, a transversal, quantitative study was carried out by a fieldwork that allowed the collection of data, human, animal, and environmental samples. The materials were processed by direct, immunological and/or molecular diagnostic techniques. According to the geographical characteristics and in presence of all the definitive and intermediate hosts, reservoirs, and sources of infection, it was possible to describe the persistence of fasciolosis in the area. The prevalence was 11.90 % in humans (by serology), 5.26 % in cattle (by coprological analysis) and 61.76 % in snails (by PCR). The situation that was found for this area indicates that any measure of intervention for the control of this zoonosis should be adopted by multidisciplinary teams. PMID:24431579

  14. Lack of Bystander Effects From High LET Radiation For Early Cytogenetic Endpoints.

    SciTech Connect

    Groesser, Torsten; Cooper, Brian; Rydberg, Bjorn

    2008-05-07

    The aim of this work was to study radiation-induced bystander effects for early cytogenetic end points in various cell lines using the medium transfer technique after exposure to high- and low-LET radiation. Cells were exposed to 20 MeV/ nucleon nitrogen ions, 968 MeV/nucleon iron ions, or 575 MeV/nucleon iron ions followed by transfer of the conditioned medium from the irradiated cells to unirradiated test cells. The effects studied included DNA double-strand break induction, {gamma}-H2AX focus formation, induction of chromatid breaks in prematurely condensed chromosomes, and micronucleus formation using DNA repair-proficient and -deficient hamster and human cell lines (xrs6, V79, SW48, MO59K and MO59J). Cell survival was also measured in SW48 bystander cells using X rays. Although it was occasionally possible to detect an increase in chromatid break levels using nitrogen ions and to see a higher number of {gamma}-H2AX foci using nitrogen and iron ions in xrs6 bystander cells in single experiments, the results were not reproducible. After we pooled all the data, we could not verify a significant bystander effect for any of these end points. Also, we did not detect a significant bystander effect for DSB induction or micronucleus formation in these cell lines or for clonogenic survival in SW48 cells. The data suggest that DNA damage and cytogenetic changes are not induced in bystander cells. In contrast, data in the literature show pronounced bystander effects in a variety of cell lines, including clonogenic survival in SW48 cells and induction of chromatid breaks and micronuclei in hamster cells. To reconcile these conflicting data, it is possible that the epigenetic status of the specific cell line or the precise culture conditions and medium supplements, such as serum, may be critical for inducing bystander effects.

  15. Methylphenidate and Amphetamine Do Not Induce Cytogenetic Damage in Lymphocytes of Children with ADHD

    ERIC Educational Resources Information Center

    Witt, Kristine L.; Shelby, Michael D.; Itchon-Ramos, Nilda; Faircloth, Melissa; Kissling, Grace E.; Chrisman, Allan K.; Ravi, Hima; Murli, Hemalatha; Mattison, Donald R.; Kollins, Scott H.

    2008-01-01

    The inducement of chromosomal damage in lymphocytes among children with attention deficit hyperactivity disorder receiving treatment with methylphenidate- or amphetamine-based drugs is investigated. Findings did not reveal significant increases in cytogenetic damage related to the treatment. The risk for cytogenetic damage posed by such products…

  16. Cytogenetic Profile of Down Syndrome Cases Seen by a General Genetics Outpatient Service in Brazil

    ERIC Educational Resources Information Center

    Biselli, Joice; Goloni-Bertollo, Eny; Ruiz, Mariangela; Pavarino-Bertelli, Erika

    2009-01-01

    Down syndrome or trisomy 21 can be caused by three types of chromosomal abnormalities: free trisomy 21, translocation or mosaicism. The cytogenetic diagnosis, made through karyotypic examination, is important mainly to determine recurrence risks to assist genetic counselling. The object of this work was to carry out a cytogenetic profile of…

  17. Dysregulation of apoptotic death in the pathogenesis of virus-induced cytogenetic instability of blood lymphocytes.

    PubMed

    Ryazantseva, N V; Novitskii, V V; Zhukova, O B; Radzivil, T T; Mikheev, S L; Chechina, O E; Zima, A P; Shilov, B V

    2006-05-01

    The cytogenetic status and activity of regulatory systems for stability of the cell genome were evaluated in patients with chronic viral persistence. Hepatitis B and C viruses damage the chromosome apparatus of peripheral blood lymphocytes. Cytogenetic instability of immunocompetent cells during chronic viral infection was associated with inhibition of DNA excision repair system and dysregulation of apoptosis in target cells. PMID:17181065

  18. Cytogenetic changes induced by aqueous ferrofluids in agricultural plants

    NASA Astrophysics Data System (ADS)

    Răcuciu, Mihaela; Creangă, Dorina

    2007-04-01

    In this paper, the authors present their results regarding the cellular division rate and the percentage of chromosomal aberrations in the root meristematic cells of agricultural plants when cultivated in the presence of different concentrations of aqueous ferrofluid, ranging between 10 and 250 μL/L. The agricultural species ( Zea mays) with a major role in the life of people was chosen for the experimental project. The water-based ferrofluid was prepared following the chemical co-precipitation method, using tetramethylammonium hydroxide as magnetite core stabilizer. Microscopic investigations (cytogenetic tests) resulted in the evaluation of the mitotic and chromosomal aberration index. They appeared to increase following ferrofluid addition.

  19. ENVIROSUITE: USING STATE-OF-THE-ART SYNCHROTRON TECHNIQUES TO UNDERSTAND ENVIRONMENTAL REMEDIATION SCIENCE ISSUES AT THE MOLECULAR LEVEL.

    SciTech Connect

    FITTS,J.P.; KALB,P.D.; FRANCIS,A.J.; FUHRMANN,M.; DODGE,C.J.; GILLOW,J.B.

    2004-03-01

    Although DOE's Environmental Management program has made steady progress in cleaning up environmental legacies throughout the DOE complex, there are still significant remediation issues that remain to be solved. For example, DOE faces difficult challenges related to potential mobilization of radionuclides (e.g., actinides) and other hazardous contaminants in soils, removal and final treatment of high-level waste and residuals from leaking tanks, and the long-term stewardship of remediated sites and engineered disposal facilities, to name just a few. In some cases, new technologies and technology applications will be required based on current engineering expertise. In others, however, basic scientific research is needed to understand the mechanisms of how contaminants behave under specific conditions and how they interact with the environment, from which new engineering solutions can emerge. At Brookhaven National Laboratory (BNL) and Stony Brook University, scientists have teamed to use state-of-the-art synchrotron techniques to help understand the basic interactions of contaminants in the environment. Much of this work is conducted at the BNL National Synchrotron Light Source (NSLS), which is a user facility that provides high energy X-ray and ultraviolet photon beams to facilitate the examination of contaminants and materials at the molecular level. These studies allow us to determine how chemical speciation and structure control important parameters such as solubility, which in turn drive critical performance characteristics such as leaching. In one study for example, we are examining the effects of microbial activity on actinide contaminants under conditions anticipated at the Waste Isolation Pilot Plant. One possible outcome of this research is the identification of specific microbes that can trap uranium or other contaminants within the intracellular structure and help mitigate mobility. In another study, we are exploring the interaction of contaminants with

  20. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins

    NASA Astrophysics Data System (ADS)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-01

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm- 1 and 1545 cm- 1, respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties.

  1. A new technique to improve the mechanical and biological performance of ultra high molecular weight polyethylene using a nylon coating.

    PubMed

    Firouzi, Dariush; Youssef, Aya; Amer, Momen; Srouji, Rami; Amleh, Asma; Foucher, Daniel A; Bougherara, Habiba

    2014-04-01

    A new patent pending technique is proposed in this study to improve the mechanical and biological performance of ultra high molecular weight polyethylene (UHMWPE), i.e., to uniformly coat nylon onto the UHMWPE fiber (Firouzi et al., 2012). Mechanical tests were performed on neat and new nylon coated UHMWPE fibers to examine the tensile strength and creep resistance of the samples at different temperatures. Cytotoxicity and osteolysis induced by wear debris of the materials were investigated using (MTT) assay, and RT-PCR for tumor necrosis factor alpha (TNFα) and interleukin 6 (IL-6) osteolysis markers. Mechanical test results showed substantial improvement in maximum creep time, maximum breaking force, and toughness values of Nylon 6,6 and Nylon 6,12 coated UHMWPE fibers between average 15% and 60% at 25, 50, and 70°C. Furthermore, cytotoxicity studies have demonstrated significant improvement in cell viability using the nylon coated UHMWPE over the neat one (72.4% vs 54.8%) for 48h and (80.7 vs 5%) for 72h (P<0.01). Osteolysis test results have shown that the expression levels of TNFα and IL-6 markers induced by the neat UHMWPE fiber were significantly higher than those induced by the Nylon 6,6 coated UHMWPE (2.5 fold increase for TNFα at 48h, and three fold increase for IL-6 at 72h (P<0.01)). This study suggests that UHMWPE coated with nylon could be used as a novel material in clinical applications with lower cytotoxicity, less wear debris-induced osteolysis, and superior mechanical properties compared to neat UHMWPE.

  2. Cytogenetic Biodosimetry Using the Blood Lymphocytes of Astronauts

    NASA Technical Reports Server (NTRS)

    George, Kerry; Rhone, J.; Chappell, L. J.; Cucinotta, F. A.

    2010-01-01

    Cytogenetic analysis of blood lymphocytes remains the most sensitive and reliable method available for in vivo assessment of the biological effects of exposure to radiation and provides the most informative measurement of radiation induced health risks. To date chromosome damage has been assessed in lymphocytes from more than 30 astronauts before and after they participated in long-duration space missions of three months or more on board the International Space Station. For all individuals, the frequency of chromosome damage measured within a month of return from space was higher than their prefight yield and biodosimetry estimates lie within the range expected from physical dosimetry. Biodosimetry data provides a direct measurement of space radiation damage, which takes into account individual radiosensitivity in the presence of confounding factors such as microgravity and other stress conditions. In contrast to physical measurements, which are external to body and require multiple devices to detect all radiation types all of which have poor sensitivity to neutrons, biodosimetry is internal and includes the effects of shielding provided by the body itself plus chromosome damage shows excellent sensitivity to protons, heavy ions, and neutrons. In addition, chromosome damage is reflective of cancer risk and biodosimetry values can therefore be used to validate and develop risk assessment models that can be used to characterize excess health risk incurred by crewmembers. A review of astronaut biodosimetry data will be presented along with recent findings on the persistence of space radiation induced chromosome damage and the cytogenetic effects of repeat long duration missions

  3. Comparative cytogenetic analysis of marine needlefishes (Beloniformes) from southern Brazil.

    PubMed

    Cipriano, Roger Raupp; Noleto, Rafael Bueno; Kantek, Daniel Luis Zanella; da Silva Cortinhas, Maria Cristina; Cestari, Marta Margarete

    2016-08-01

    Cytogenetic studies have assisted in the taxonomic classification of organisms, especially those involving species with highly similar morphologic characteristics, or so-called cryptic species. Strongylura marina and Strongylura timucu collected from Paranaguá Bay, Paraná Coast in Southern Brazil are considered cryptic species, and the identification of interspecific variations based on the number and/or morphology of its chromosomes may serve as differentiating cytotaxonomic markers. Chromosomes of the two species were subjected to different banding and staining methods (C-, Ag-, and DAPI-CMA3), as well as chromosomal mapping of major rDNA (45S), revealed with an 18S probe by fluorescence in situ hybridization (FISH). The pattern of distribution of constitutive heterochromatin showed distinct features involving the pericentromeric and telomeric bands in both species. In S. marina, chromosome 1 represents the main species-specific marker, appearing almost entirely heterochromatic. In both species, the 45S rDNA is located at terminal region of the short arm of the chromosome 6, as detected by silver nitrate staining and FISH. Despite the apparent conserved diploid number of 48 chromosomes, data on the karyotype microstructure characterize the cytogenetic profile of the genus and may allow the establishment of cytotaxonomic and evolutionary inferences for these fishes. PMID:25388873

  4. First cytogenetic study of Cavernicola pilosa Barber, 1937 (Hemiptera, Triatominae).

    PubMed

    Souza, E S; Alevi, K C C; Ribeiro, A R; Furtado, M B; Atzingen, N C B V; Azeredo-Oliveira, M T V; Rosa, J A

    2015-01-01

    Cavernicola pilosa is a triatomine species that lives in caves and feeds on bat blood. This vector has a wide geographical distribution, and is found in Brazil, Colombia, Panama, Peru, and Venezuela. Little is known about the reproductive biology of this species, because most previous studies have only characterized its morphology, morphometry, ecology, and epidemiology. Therefore, this study aimed to obtain preliminary data related to spermatogenesis in C. pilosa by conducting cytogenetic analysis. Analysis of the heterochromatic pattern of C. pilosa during the initial prophases revealed that heterochromatic blocks are only present in the sex chromosomes. Based on the analyses of the meiotic metaphase and prophases, we found that the sex determination system of C. pilosa is XY and the chromosomes are holocentric. C. pilosa spermatids are filamentous and have long flagella. It was not possible to detect corpuscle or filament heteropycnosis in spermatids of this species. The initial cytogenetic data presented in this study are important in characterizing the spermatogenesis and heterochromatic patterns of C. pilosa. Our results suggest that adaptation to troglodytism did not result in differences in spermatogenesis in this vector. PMID:26535704

  5. First cytogenetic study of Cavernicola pilosa Barber, 1937 (Hemiptera, Triatominae).

    PubMed

    Souza, E S; Alevi, K C C; Ribeiro, A R; Furtado, M B; Atzingen, N C B V; Azeredo-Oliveira, M T V; Rosa, J A

    2015-10-30

    Cavernicola pilosa is a triatomine species that lives in caves and feeds on bat blood. This vector has a wide geographical distribution, and is found in Brazil, Colombia, Panama, Peru, and Venezuela. Little is known about the reproductive biology of this species, because most previous studies have only characterized its morphology, morphometry, ecology, and epidemiology. Therefore, this study aimed to obtain preliminary data related to spermatogenesis in C. pilosa by conducting cytogenetic analysis. Analysis of the heterochromatic pattern of C. pilosa during the initial prophases revealed that heterochromatic blocks are only present in the sex chromosomes. Based on the analyses of the meiotic metaphase and prophases, we found that the sex determination system of C. pilosa is XY and the chromosomes are holocentric. C. pilosa spermatids are filamentous and have long flagella. It was not possible to detect corpuscle or filament heteropycnosis in spermatids of this species. The initial cytogenetic data presented in this study are important in characterizing the spermatogenesis and heterochromatic patterns of C. pilosa. Our results suggest that adaptation to troglodytism did not result in differences in spermatogenesis in this vector.

  6. Cytogenetic analysis of myoepithelial cell carcinoma of salivary gland.

    PubMed

    Magrini, Elisabetta; Pragliola, Antonella; Farnedi, Anna; Betts, Christine M; Cocchi, Roberto; Foschini, Maria P

    2004-01-01

    Myoepithelial cell carcinoma (MCC) of the salivary gland is a rare entity. Here, we describe the karyotype of MCC. The patient was a 53-year-old man, with a rapidly growing lesion of the palate. Despite complete surgical excision, radio- and chemotherapy, the lesion rapidly harboured local and distant metastases leading to the death of the patient, 4 months after the diagnosis. On histological and ultrastructural examination, the primary tumour and the related metastases were composed of oval and spindle cells, with features of myoepithelial cell differentiation reported in the literature. Cytogenetic analysis showed a composite karyotype in the primary tumour: 45-46,XY, +3[cp3]/ 44-45,XY, -17[cp4]/ 46,XY[5]. The lymph-node metastasis was near-triploid and showed a complex karyotype. Our cytogenetic data differ from those described in benign or slowly growing salivary gland tumours showing myoepithelial cell differentiation. It is suggested that highly aggressive tumours might follow a different pathway of malignant transformation.

  7. Chromosome Painting in Three Species of Buteoninae: A Cytogenetic Signature Reinforces the Monophyly of South American Species

    PubMed Central

    de Oliveira, Edivaldo Herculano C.; Tagliarini, Marcella Mergulhão; dos Santos, Michelly S.; O'Brien, Patricia C. M.; Ferguson-Smith, Malcolm A.

    2013-01-01

    Buteoninae (Falconiformes, Accipitridae) consist of the widely distributed genus Buteo, and several closely related species in a group called “sub-buteonine hawks”, such as Buteogallus, Parabuteo, Asturina, Leucopternis and Busarellus, with unsolved phylogenetic relationships. Diploid number ranges between 2n = 66 and 2n = 68. Only one species, L. albicollis had its karyotype analyzed by molecular cytogenetics. The aim of this study was to present chromosomal analysis of three species of Buteoninae: Rupornis magnirostris, Asturina nitida and Buteogallus meridionallis using fluorescence in situ hybridization (FISH) experiments with telomeric and rDNA probes, as well as whole chromosome probes derived from Gallus gallus and Leucopternis albicollis. The three species analyzed herein showed similar karyotypes, with 2n = 68. Telomeric probes showed some interstitial telomeric sequences, which could be resulted by fusion processes occurred in the chromosomal evolution of the group, including the one found in the tassociation GGA1p/GGA6. In fact, this association was observed in all the three species analyzed in this paper, and also in L. albicollis, suggesting that it represents a cytogenetic signature which reinforces the monophyly of Neotropical buteoninae species. PMID:23922908

  8. Cytogenetic analyses of five amazon lizard species of the subfamilies Teiinae and Tupinambinae and review of karyotyped diversity the family Teiidae

    PubMed Central

    Carvalho, Natália Dayane Moura; Arias, Federico José; da Silva, Francijara Araújo; Schneider, Carlos Henrique; Gross, Maria Claudia

    2015-01-01

    Abstract Lizards of the family Teiidae (infraorder Scincomorpha) were formerly known as Macroteiidae. There are 13 species of such lizards in the Amazon, in the genera Ameiva (Meyer, 1795), Cnemidophorus (Wagler, 1830), Crocodilurus (Spix, 1825), Dracaena (Daudin, 1801), Kentropyx (Spix, 1825) and Tupinambis (Daudin, 1802). Cytogenetic studies of this group are restricted to karyotype macrostructure. Here we give a compilation of cytogenetic data of the family Teiidae, including classic and molecular cytogenetic analysis of Ameiva ameiva (Linnaeus, 1758), Cnemidophorus sp.1, Kentropyx calcarata (Spix, 1825), Kentropyx pelviceps (Cope, 1868) and Tupinambis teguixin (Linnaeus, 1758) collected in the state of Amazonas, Brazil. Ameiva ameiva, Kentropyx calcarata and Kentropyx pelviceps have 2n=50 chromosomes classified by a gradual series of acrocentric chromosomes. Cnemidophorus sp.1 has 2n=48 chromosomes with 2 biarmed chromosomes, 24 uniarmed chromosomes and 22 microchromosomes. Tupinambis teguixin has 2n=36 chromosomes, including 12 macrochromosomes and 24 microchromosomes. Constitutive heterochromatin was distributed in the centromeric and terminal regions in most chromosomes. The nucleolus organizer region was simple, varying in its position among the species, as evidenced both by AgNO3 impregnation and by hybridization with 18S rDNA probes. The data reveal a karyotype variation with respect to the diploid number, fundamental number and karyotype formula, which reinforces the importance of increasing chromosomal analyses in the Teiidae. PMID:26753079

  9. Cytogenetic analyses of five amazon lizard species of the subfamilies Teiinae and Tupinambinae and review of karyotyped diversity the family Teiidae.

    PubMed

    Carvalho, Natália Dayane Moura; Arias, Federico José; da Silva, Francijara Araújo; Schneider, Carlos Henrique; Gross, Maria Claudia

    2015-01-01

    Lizards of the family Teiidae (infraorder Scincomorpha) were formerly known as Macroteiidae. There are 13 species of such lizards in the Amazon, in the genera Ameiva (Meyer, 1795), Cnemidophorus (Wagler, 1830), Crocodilurus (Spix, 1825), Dracaena (Daudin, 1801), Kentropyx (Spix, 1825) and Tupinambis (Daudin, 1802). Cytogenetic studies of this group are restricted to karyotype macrostructure. Here we give a compilation of cytogenetic data of the family Teiidae, including classic and molecular cytogenetic analysis of Ameiva ameiva (Linnaeus, 1758), Cnemidophorus sp.1, Kentropyx calcarata (Spix, 1825), Kentropyx pelviceps (Cope, 1868) and Tupinambis teguixin (Linnaeus, 1758) collected in the state of Amazonas, Brazil. Ameiva ameiva, Kentropyx calcarata and Kentropyx pelviceps have 2n=50 chromosomes classified by a gradual series of acrocentric chromosomes. Cnemidophorus sp.1 has 2n=48 chromosomes with 2 biarmed chromosomes, 24 uniarmed chromosomes and 22 microchromosomes. Tupinambis teguixin has 2n=36 chromosomes, including 12 macrochromosomes and 24 microchromosomes. Constitutive heterochromatin was distributed in the centromeric and terminal regions in most chromosomes. The nucleolus organizer region was simple, varying in its position among the species, as evidenced both by AgNO3 impregnation and by hybridization with 18S rDNA probes. The data reveal a karyotype variation with respect to the diploid number, fundamental number and karyotype formula, which reinforces the importance of increasing chromosomal analyses in the Teiidae. PMID:26753079

  10. Efficiency of rep-PCR fingerprinting as a useful technique for molecular typing of plant pathogenic fungal species: Botryosphaeriaceae species as a case study.

    PubMed

    Abdollahzadeh, Jafar; Zolfaghari, Sajedeh

    2014-12-01

    Progress in molecular biology and the advent of rapid and accurate molecular techniques have contributed to precise and rapid detection and differentiation of microbial pathogens. Identification of the Botryosphaeriaceae species based on morphology has been problematic over time. In this study, we used rep-PCR technique as a molecular tool for typing and differentiation of the Botryosphaeriaceae species, well-known and cosmopolitan fungal pathogens on woody plants. Three primer sets BOX, ERIC and REP were used to differentiate 27 species belong to eight genera. The majority of them were examined in terms of typing and differentiation using molecular methods for the first time. All the primer sets were able to generate species-specific DNA fingerprints from all the tested strains, with two exceptions in the genera Diplodia and Spencermartinsia. Despite the deficiency of each primer sets to separate a few species, cluster analysis of combined data sets indicated the ability of rep-PCR technique to separate 26 out of 27 examined species in highly supported clusters corresponded to the species recognized based on DNA sequence data. Our findings revealed the efficiency of rep-PCR for detection and differentiation of the Botryosphaeriaceae species, especially cryptic species with the same ITS sequences and similar morphology.

  11. Occurrence and prognostic significance of cytogenetic evolution in patients with multiple myeloma

    PubMed Central

    Binder, M; Rajkumar, S V; Ketterling, R P; Dispenzieri, A; Lacy, M Q; Gertz, M A; Buadi, F K; Hayman, S R; Hwa, Y L; Zeldenrust, S R; Lust, J A; Russell, S J; Leung, N; Kapoor, P; Go, R S; Gonsalves, W I; Kyle, R A; Kumar, S K

    2016-01-01

    Cytogenetic evaluation at the time of diagnosis is essential for risk stratification in multiple myeloma, however little is known about the occurrence and prognostic significance of cytogenetic evolution during follow-up. We studied 989 patients with multiple myeloma, including 304 patients with at least two cytogenetic evaluations. Multivariable-adjusted regression models were used to assess the associations between the parameters of interest and cytogenetic evolution as well as overall survival. The prognostic significance of baseline cytogenetic abnormalities was most pronounced at the time of diagnosis and attenuated over time. In the patients with serial cytogenetic evaluations, the presence of t(11;14) at the time of diagnosis was associated with decreased odds of cytogenetic evolution during follow-up (odds ratio (OR)=0.22, 95% confidence interval (CI)=0.09–0.56, P=0.001), while the presence of at least one trisomy or tetrasomy was associated with increased odds (OR=2.96, 95% CI=1.37–6.42, P=0.006). The development of additional abnormalities during the 3 years following diagnosis was associated with increased subsequent mortality (hazard ratio=3.31, 95% CI=1.73–6.30, P<0.001). These findings emphasize the importance of the underlying clonal disease process for risk assessment and suggest that selected patients may benefit from repeated risk stratification. PMID:26967818

  12. Bond dissociation mechanism of ethanol during carbon nanotube synthesis via alcohol catalytic CVD technique: Ab initio molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Oguri, Tomoya; Shimamura, Kohei; Shibuta, Yasushi; Shimojo, Fuyuki; Yamaguchi, Shu

    2014-03-01

    Dissociation of ethanol on a nickel cluster is investigated by ab initio molecular dynamics simulation to reveal the bond dissociation mechanism of carbon source molecules during carbon nanotube synthesis. C-C bonds in only CHxCO fragments are dissociated on the nickel cluster, whereas there is no preferential structure among the fragments for C-O bond dissociation. The dissociation preference is uncorrelated with the bond dissociation energy of corresponding bonds in freestanding molecules but is correlated with the energy difference between fragment molecules before and after dissociation on the nickel surface. Moreover, carbon-chain formation occurs after C-C bond dissociation in a continuous simulation. What determines the chirality of CNTs? What happens at the dissociation stage of carbon source molecules? Regarding the former question, many researchers have pointed out the good epitaxial relationship between a graphite network and a close-packed facet (i.e., fcc(1 1 1) or hcp(0 0 0 1)) of transition metals [17-19]. Therefore, the correlation between the chirality of CNTs and the angle of the step edge on metal (or metal carbide) surfaces has been closely investigated [20-22]. In association with this geometric matching, the epitaxial growth of graphene on Cu(1 1 1) and Ni(1 1 1) surfaces has recently been achieved via CCVD technique [23-25], which is a promising technique for the synthesis of large-area and monolayer graphene.Regarding the latter question, it is empirically known that the yield and quality of CNT products strongly depend on the choice of carbon source molecules and additives. For example, it is well known that the use of ethanol as carbon source molecules yields a large amount of SWNTs without amorphous carbons (called the alcohol CCVD (ACCVD) technique) compared with the CCVD process using hydrocarbons [4]. Moreover, the addition of a small amount of water dramatically enhances the activity and lifetime of the catalytic metal (called the

  13. Molecular Genetic Markers in Acute Myeloid Leukemia

    PubMed Central

    Yohe, Sophia

    2015-01-01

    Genetics play an increasingly important role in the risk stratification and management of acute myeloid leukemia (AML) patients. Traditionally, AML classification and risk stratification relied on cytogenetic studies; however, molecular detection of gene mutations is playing an increasingly important role in classification, risk stratification, and management of AML. Molecular testing does not take the place of cytogenetic testing results, but plays a complementary role to help refine prognosis, especially within specific AML subgroups. With the exception of acute promyelocytic leukemia, AML therapy is not targeted but the intensity of therapy is driven by the prognostic subgroup. Many prognostic scoring systems classify patients into favorable, poor, or intermediate prognostic subgroups based on clinical and genetic features. Current standard of care combines cytogenetic results with targeted testing for mutations in FLT3, NPM1, CEBPA, and KIT to determine the prognostic subgroup. Other gene mutations have also been demonstrated to predict prognosis and may play a role in future risk stratification, although some of these have not been confirmed in multiple studies or established as standard of care. This paper will review the contribution of cytogenetic results to prognosis in AML and then will focus on molecular mutations that have a prognostic or possible therapeutic impact. PMID:26239249

  14. Cytogenetics of the true bug infraorder Cimicomorpha (Hemiptera, Heteroptera): a review

    PubMed Central

    Kuznetsova, Valentina G.; Grozeva, Snejana M.; Nokkala, Seppo; Nokkala, Christina

    2011-01-01

    Abstract The Cimicomorpha is one of the largest and highly diversified infraorders of the Heteroptera. This group is also highly diversified cytogenetically and demonstrates a number of unusual cytogenetic characters such as holokinetic chromosomes; m-chromosomes; multiple sex chromosome systems; post-reduction of sex chromosomes in meiosis; variation in the presence/absence of chiasmata in spermatogenesis; different types of achiasmate meiosis. We present here a review of essential cytogenetic characters of the Cimicomorpha and outline the chief objectives and goals of future investigations in the field. PMID:22287915

  15. Cytogenetic characterization of acute myeloid leukemia in Shwachman's syndrome. A case report.

    PubMed

    Spirito, F R; Crescenzi, B; Matteucci, C; Martelli, M F; Mecucci, C

    2000-11-01

    We report on a case of acute myeloid leukemia in a 17-year old boy affected by Shwachman Diamond syndrome (SDS). Conventional cytogenetics at diagnosis revealed an abnormal clone with complex karyotypic changes including typical myeloid aberrations, such as monosomy 5, tetrasomy of chromosome 8, trisomy 9, and deletion of the short arm of chromosome 12. The boy was treated with conventional chemotherapy and reached complete remission of leukemia, confirmed by cytogenetics and fluorescence in situ hybridization. Nevertheless he failed to regenerate normal marrow cellularity and blood cell count. Cytogenetic information on hematologic malignancies in SDS patients are discussed. PMID:11064470

  16. Chromosomal DNA content of sweet pepper determined by association of cytogenetic and cytometric tools.