Total Number Of Bands Research Articles

Population variation of codling moth Cydia pomonella (Lep.; Tortricidae) based on molecular data from northwestern Iran

In order to study population structure in the codling moth (Cydia pomonella L.) using RAPD markers, 13 geographical populations from northwestern Iran were collected during 2003 and 2004. Genomic DNA was extracted from 10 overwintering larvae of each population. Out of 60 tested primers, 18 amplified 236 polymorphic bands. The total number of bands in the population varied from 169 to 206 in the Mughan and Zunuz populations, respectively. Within-population genetic diversity, based on Nei's genetic index, ranged from 0.228 to 0.281 for the Shabestar and Zunuz populations, respectively. An analysis of the molecular variance revealed significant differences within and between population variance. Between-population variation accounted for 14.44% and within-population variation accounted for 85.56% of the total molecular variance. Cluster analysis based on molecular data assigned the studied codling moth populations to 2 groups. In this grouping, Group 1 consisted of the Mughan population only. The maximum and minimum genetic distances were observed between the Mughan-Ahar and Shabestar-Mahabad populations, respectively. Canonical correlation analysis showed significant association between RAPD markers and the latitude of the studied regions. A principal coordinate analysis showed high discrimination between geographic populations and confirmed the results of the cluster analysis. A significant correlation was found between genetic and geographic distance matrices as revealed by the Mantel test.

Probiotic Psychrobacter sp. improved the autochthonous microbial diversity along the gastrointestinal tract of grouper Epinephelus coioides

The effect of dietary administration of probiotic Psychrobacter sp. SE6 for 60 days on the autochthonous microbiota in the foregut, midgut and hindgut of juvenile grouper Epinephelus coioides was assessed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). A complex and generally similar bacterial composition was present along the gastrointestinal (GI) tract of fish fed the probiotic or control diet. However, samples collected from the probiotic group and control group showed different DGGE patterns. The similarity dendrogram demonstrated that all nine samples from the control group were closely related and distinctly different to the probiotic samples. The total number of bands and Shannon index of the foregut, midgut and hindgut samples in the probiotic group were significantly higher than those in the control group, suggesting probiotic Psychrobacter sp. improved the autochthonous microbial diversity along the GI tract of E. coioides. Some potentially beneficial and uncultured bacteria were stimulated, while some potentially harmful species, such as Staphylococcus saprophyticus, were suppressed. Sequence analysis showed that the majority of bacterial sequences (48.0%) in this study were highly similar to unidentified clones, suggesting a considerable proportion of unknown bacteria in the gut of E. coioides.

Genetic diversity analysis in date palm (Phoenix dactylifera L.): a comparative assessment using ISSR and RAPD marker assays

SUMMARYA comparative study was conducted to evaluate genetic diversity in 45 genotypes of date palm (Phoenix dactylifera L.), including both male and female plants, employing RAPD and ISSR marker systems. The data were analysed to calculate the total number of bands, the number of polymorphic bands, the percentage polymorphism, the average number of bands per primer, the effective multiplex ratio (EMR), the polymorphic information content (PIC), the marker index (MI), and genetic similarity coefficients. The 37 RAPD and 53 ISSR primers used generated 363 and 608 scorable amplified products, respectively, of which 95.0% and 90.9% were polymorphic. The ISSR markers produced more information than the RAPD markers due to their higher EMR and MI values. Jaccard similarity values among male plants, female plants, and between all male and all female plants varied between 0.72 – 0.80. The results indicate the effectiveness of these two marker systems for demonstrating genetic relationships among date palm genotypes.

A set of microsatellite markers for Arrabidaea chica (Bignoniaceae), a medicinal liana from the Neotropics

Microsatellite markers were developed, optimized, and characterized for Arrabidaea chica (Humb. & Bonpl.) Verl. (Bignoniaceae), a Neotropical liana extensively used in folk medicine. The aim of this study was to develop molecular tools to investigate the genetic structure and diversity of natural populations and germplasm collections of this species. • Eight highly polymorphic microsatellite markers revealed a multibanded pattern, suggesting that the species is polyploid. The total number of bands per locus ranged from 9 to 17, revealing high levels of polymorphism. • The high level of polymorphism detected with these markers indicates their utility in devising conservation strategies and rational exploitation of A. chica.

Development and characterisation of microsatellite markers for Cordia verbenacea (Boraginaceae), an important medicinal species from the Brazilian coast

Cordia verbenacea DC (Boraginaceae) is a Brazilian coastal shrub species extensively utilized in the folk medicine and also by the pharmaceutical industry. Despite its enormous economic and pharmacological potential, little is known about its reproductive biology, genetic structure and genetic diversity of natural populations. Due to the rapid degradation of its natural habitat, this knowledge became imperative. We developed a set of eight highly polymorphic microsatellite markers for the study of genetic structure and diversity of C. verbenacea natural populations and germplasm collections. Six of them revealed a multibanded pattern typical of polyploid species. The total number of bands per locus ranged from 2 to 12 and the number of bands per locus per individual ranged from 1 to 8. The primer pairs presented here will be used to generate information to guide conservation programs and rational exploitation of C. verbenacea.

Genetic fingerprinting of chickpea (Cicer arietinum L.) germplasm using ISSR markers and their relationships

Genetic diversity analysis of chickpea germplasm can provide practical Information for selection of parental material and thus, assist in forecasting breeding strategies. Released cultivars and breeding lines of total twelve chickpea genotypes were subjected to ISSR analysis for assessment of genetic diversity. A total of 10 ISSR primers were used in the present investigation. Amplification of genomic DNA of the 12 genotypes using ISSR analysis yielded 492 fragments that could be scored. The total number of bands amplified by 3’ anchored primers varied from 36 to 96. The primers based on poly (ATG) and (GAA) motifs produced least number of fragments (36) whereas, primers (AC) T and (AC) TT, produced maximum number of fragments (96). The unique band as produced by the GGAGA primer in the BCP-15 genotype may be attributed to temperature tolerance phenotype. Key words: Chickpea, Genetic diversity, ISSR.

Gradient expansion approach to multiple-band Fermi liquids

Promoted by the recent progress of Berry phase physics in spin galvanomagnetic communities, we develop a systematic derivation of the reduced Keldysh equation (RKE) which captures the low-energy dynamics of quasiparticles constrained within doubly degenerate bands forming a single Fermi surface. The derivation begins with the Keldysh equation for a quite general multiple-band interacting Fermi system, which is originally an ${N}_{b}\ifmmode\times\else\texttimes\fi{}{N}_{b}$ matrix-formed integral (or infinite-order differential) equation, with ${N}_{b}$ being the total number of bands. To derive the RKE for quasiparticle on a Fermi surface in question, we project out both the fully occupied and empty band degrees of freedom perturbatively in the gradient expansion, whose coupling constant measures how a system is disequilibrated. As for the electron-electron interactions, however, we only employ the so-called adiabatic assumption of the Fermi liquid theory, so that the electron correlation effects onto the adiabatic transport of quasiparticles, i.e., the Hermitian (real) part of the self-energy, are taken into account in an unbiased manner. The RKE thus derived becomes an SU(2) covariant differential equation and treats the spin and charge degrees of freedom on an equal footing. Namely, the quasiparticle spin precessions due to the non-Abelian gauge fields are automatically encoded into its covariant derivatives. When further solved in favor of spectral functions, this covariant differential equation suggests that quasiparticles on a doubly degenerate Fermi surface acquire spin-selective Berry curvature corrections under the applied electromagnetic fields. This theoretical observation gives us some hints of possible experimental methodology for measuring the SU(2) Berry's curvatures by spin-resolved photoemission experiments. Due to the nontrivial frequency dependence of (the Hermitian part of) self-energy, our RKE is composed of Berry's curvatures in the $d+1$ dual space, i.e., $k\text{\ensuremath{-}}\ensuremath{\omega}$ space, so that the dual electric field is already introduced. To provide a simple way to understand this ``temporal'' component of the U(1) Berry's curvature, we also provide the dual analog of the Ampere's law, where the ``spatial'' rotation of the electric field in combination with the temporal derivative of the well-known magnetic component is determined by the U(1) magnetic monopole ``current.''

Changes in cellular macromolecules (DNA, RNA and protein) during seed germination in tomato, following the use of a butenolide, isolated from plant-derived smoke

A butenolide, 3-methyl-2H-furo[2,3-c]pyran-2-one, isolated from plant-derived smoke is responsible for the stimulatory role of smoke or aqueous smoke extracts on seed germination. The present study aimed at determining the changes induced by the butenolide at the level of macromolecules (DNA, RNA and proteins) during seed germination. To ascertain changes at the level of DNA, 25 random decamer primers were used. DNA was isolated from 2-week-old seedlings raised in water or butenolide. Amplification products generated ranged in size from 250 bp to 2,500 bp, while in number they ranged from 1 to 9. Ninety-one bands were scored with 17.6% of polymorphism. Total number of bands recorded for 25 primers in control and butenolide-treated seedlings were not significantly different from each other according to the non-parametrical Kruskal–Wallis test. Differential display was used to isolate differentially expressed genes. A total of 48 differentially expressed cDNAs were observed, out of which 20 were cloned into pGEM-T vectors. Alignment of sequences of these cloned products revealed that several bands isolated from differential display gels contained multiple sequences. Four sequences were tentatively identified, while the remaining sequences did not show any significant homology. Electronic homology revealed identity with expansin, photosystem I P700 apoprotein and polyproteins. Similarity index (SI) values for the banding patterns of SDS-PAGE gels was 65.2% for embryos isolated from seeds imbibed either with water or butenolide for 36 h. SI values indicate that the butenolide did not alter the protein profiles drastically. Results of the present study revealed that butenolide does not affect the integrity of DNA. However, it does play some role during transcription and translation.

New Insights into a Controversial Topic: The Methylation–Cancer Connection

New Insights into a Controversial Topic: The Methylation–Cancer Connection

Assessment of genetic diversity among Chinese upland cottons with Fusarium and/or Verticillium wilts resistance by AFLP and SSR markers

Genetic diversity among 95 Chinese upland cottons with Fusarium and/or Verticillium wilts resistance was estimated using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR) markers. Twenty EcoRI-MseI AFLP and 19 SSR primers with polymorphism were selected to perform the fingerprinting. The results showed that 20 AFLP primer pairs produced a total of 1 480 major bands among 95 genotypes, and 214 were polymorphic bands. The number of total bands per primer pair ranged from 47 to 109, with an average of 74.0. The polymorphism information content (PIC) values for the 20 primer pairs varied from 0.01 (E-ACT/M-CAT) to 0.24 (E-ACA/M-CTA), and the average value was 0.09. Nineteen SSR primers generated 89 DNA bands, of which 61 were polymorphic. The total number of alleles per locus varied from 3 to 8, with an average of 4.7. The average PIC value for the SSR amplification products was 0.69. Genetic similarity estimates for the entire data set ranged from 0.978 to 0.998 based on AFLP and SSR bands. It was proved that the close genetic relationship and narrow genetic diversity existed in the tested cultivars. The clustering patterns could not be correlated to the geographic origin, the pedigree and common parentage of the cultivars.

The Effects of the Number of Rubber Bands Placed at Each Endoscopic Session Upon Variceal Outcomes: A Prospective, Randomized Study

To determine the role of the number of bands placed per session upon patient-related and procedural-related outcomes. Patients were assigned to receive as many bands as could be possibly placed (group 1) or up to a maximum of six bands (group 2) per session. The primary outcome measured was the number of sessions to achieve obliteration. Other outcomes measured included: rebleeding, variceal recurrence, mortality (within 6 wk and within 1 yr), complications, banding and total procedure times, and number of bands misfired. A total of 86 patients were enrolled: 45 in group 1 and 41 in group 2. The two groups had similar age, Child-Pugh scores, grade of varices at entry. The overall proportion of patients achieving obliteration was 56% (53% and 59% for groups 1 and 2, respectively). Despite receiving significantly more mean bands per session, patients in group 1 required similar (mean +/- SEM) number of sessions to obliteration (2.9 +/- 0.3 vs 3.3 +/- 0.3) and total number of bands (20.0 +/- 2.4 vs 16.6 +/- 1.8) to achieve this goal compared with group 2. The overall proportion of patients with variceal rebleeding was 25%, the 1-yr variceal recurrence 31.3%, and the overall early- and 1-yr mortality were 18.6% and 33.7%, respectively. These proportions were similar in the two groups. Banding and total procedure times were significantly longer and associated with significantly more misfired bands per session in group 1. Compared with a maximum of six bands per session, the placement of >6 bands per session was not associated with better patient outcomes but with significantly more prolonged banding and total procedure times and significantly more misfired bands.

Biodegradation kinetics and microbial communities associated with methyl tert-butyl ether removal in a biotrickling filter

A microbial culture capable of degrading methyl tertiary butyl ether (MTBE) was enriched in a laboratory-scale biotrickling filter. The reactor was continuously operated in a temperature-controlled condition for more than 100 days. Removal of MTBE vapors from air streams in a biotrickling filter was studied under various operating conditions, including the MTBE loading rate and the type of media in the circulating liquid. The changes in an MTBE-degrading bacterial community were investigated by using polymerase chain reaction (PCR) amplification of bacterial 16S rDNA. A subsequent analysis of the PCR products was performed by a single-strand-conformation polymorphism (SSCP) based on genetic profiles. Our results show that the MTBE removal efficiencies of 98.6–57.3% were observed at the MTBE loading rates of 2.67–50.76 g m −3 h −1 in the biotrickling filter. The removal efficiency appeared to increase by 27% (from 68 to 95%) in a later phase operation when the nitrogen source of (NH 4 ) 2 SO 4 was replaced by NaNO 3 . Due to the high MTBE loads in the inlet section, MTBE was removed mostly from the inlet section. The parameters estimated by using the Michaelis–Menten equation were 1.607 ± 0.208 ppmv s −1 for the maximum removal rate ( V m ), and 24.91 ± 0.794 ppmv for the half-saturation constant ( K s ). The total number of bands in an electrophoresis gel for various sections in the biotrickling filter using the same nitrogen source was similar, thus indicating similar compositions of species in the biotrickling filter. Nevertheless, communities grown in the presence of (NH 4 ) 2 SO 4 and NaNO 3 media exhibited a very different pattern, thus revealing a small change in community structure due to the type of media.

The promiscuity of immunoglobulin E binding to peanut allergens, as determined by Western blotting, correlates with the severity of clinical symptoms

IgE binding to a specific protein has been shown to be associated with severe anaphylaxis to hazelnuts; however, the relationship between IgE binding to specific peanut allergens and symptom severity is currently unclear. To determine if the pattern of IgE binding to specific peanut allergens is associated with the severity of clinical symptoms. Forty peanut allergic patients underwent a double-blind placebo-controlled low-dose peanut challenge, during which the severity of the patients' peanut allergy was scored. Serum peanut-specific IgE (psIgE) was measured and IgE binding patterns to peanut proteins analysed. Seventeen IgE binding bands were identified between 5 and 100 kDa with eight bound by >50% of patients. The total number of bands per patient correlated significantly with challenge score (P=0.001, r=0.505) and psIgE (P<0.001, r=0.820). Cluster analysis failed to reveal any association between a particular protein or pattern of proteins (based on presence/absence) and challenge score. However, two protein bands ( approximately 43 and 41 kDa) had peak intensities that correlated positively with challenge score and a third band ( approximately 48 kDa) that correlated negatively. The bands were identified as subunits of Ara h 3/4 and 1, respectively. Promiscuity of IgE binding appears more important than the recognition of individual proteins. This may mean that clinically useful specific immunotherapy for peanut allergy will be difficult to achieve if only selected allergenic proteins are used. Further investigation of Ara h 1 and 3/4 subunits and a possible association with symptom severity are also highlighted by this study.

The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints.

Nuclear DNA content (C-value) varies approximately 1000-fold across the angiosperms, and this variation has been reported to have an effect on the quality of AFLP fingerprints. Various methods have been proposed for circumventing the problems associated with small and large genomes. Here we investigate the range of nuclear DNA contents across which the standard AFLP protocol can be used. AFLP fingerprinting was conducted on an automated platform using the standard protocol (with 3 + 3 selective bases) in which DNA fragments are visualized as bands. Species with nuclear DNA contents ranging from 1C = 0.2 to 32.35 pg were included, and the total number of bands and the number of polymorphic bands were counted. For the species with the smallest C-value (Bixa orellana) and for one of the species with a large C-value (Damasonium alisma), alternative protocols using 2 + 3 and 3 + 4 selective bases, respectively, were also used. Acceptable AFLP traces were obtained using the standard protocol with 1C-values of 0.30-8.43 pg. Below this range, the quality was improved by using 2 + 3 selective bases. Above this range, the traces were generally characterized by a few strongly amplifying bands and noisy baselines. Damasonium alisma, however, gave more even traces, probably due to it being a tetraploid. We propose that for known polyploids, genome size is a more useful indicator than the 1C-value in deciding which AFLP protocol to use. Thus, knowledge of ploidy (allowing estimation of genome size) and C-value are both important. For small genomes, the number of interpretable bands can be increased by decreasing the number of selective bases. For larger genomes, increasing the number of bases does not necessarily decrease the number of bands as predicted. The presence of a small number of strongly amplifying bands is likely to be linked to the presence of repetitive DNA sequences in high copy number in taxa with large genomes.

Restriction enzyme digestion chromosome banding in Crassostrea and Ostrea species: comparative karyological analysis within Ostreidae

Reliable banding techniques are a major necessity for genetic research in oysters. In this study, we carried out the cytogenetic characterization of four oyster species (family Ostreidae) using restriction endonuclease treatments. Chromosomes were treated with three different restriction enzymes, stained with Giemsa, and examined for banding patterns. The following species were studied: Crassostrea gigas (2n = 20; total number of bands with ApaI, 74; HaeIII, 61; PstI, 76), Crassostrea angulata (2n = 20; ApaI, 62; HaeIII, 61; PstI, 55) (subfamily Crassostreinae), Ostrea edulis (2n = 20; ApaI, 82; HaeIII, 59; PstI, 66), and Ostrea conchaphila (2n = 20; ApaI, 68; HaeIII, 62; PstI, 69) (subfamily Ostreinae). Treatment of samples with ApaI, HaeIII, and PstI produced specific banding patterns, which demonstrates the potential of these enzymes for chromosome banding in oysters. This is of special interest, since it has been recently shown in mammalian chromosomes that restriction enzyme banding is compatible with fluorescence in situ hybridization. This study therefore provides a fundamental step in genome mapping of oysters, since chromosome banding with restriction enzymes facilitates physical gene mapping in these important aquaculture species. The analysis of the banded karyotypes revealed a greater similarity within the genera of Crassostrea and Ostrea than between them.

Oligoclonal accumulations of T-cell clones in gingivitis and periodontitis lesions.

Gingivitis and periodontitis have distinct clinical and immunopathological characteristics. We have previously demonstrated that T cells infiltrating periodontitis lesions recognize a restricted repertoire of antigens or antigenic epitopes. However, the clonality of T cells in the gingivitis lesion is not known. Therefore, we carried out a clonal analysis of T cells infiltrating gingivitis lesions using combined reverse transcription-polymerase chain reaction and single-strand conformation polymorphism (SSCP) analysis. As with periodontitis lesions, SSCP analysis demonstrated the emergence of a number of distinct bands suggesting clonal accumulation in the gingivitis lesion. Although the mean number of distinct bands in gingival tissue was significantly higher than that in peripheral blood mononuclear cells, numerical analysis clearly demonstrated that there was no difference in the total number of bands in gingival tissue specimens between the different disease types. Although there were slight variations in the number of distinct bands in each Vbeta family, there was no significant difference between gingivitis lesions and periodontitis lesions. These results demonstrate that antigen-specific T-cell responses also take place in gingivitis lesions. It remains to be determined, however, what role these antigen-specific T cells play and what antigens the T cells recognize in the pathogenesis of periodontal disease.

Application of inter-simple sequence repeat PCR to mouse models: assessment of genetic alterations in carcinogenesis.

Genomic instability is believed to play a significant role in cancer development by facilitating tumor progression and tumor heterogeneity. Inter-simple sequence repeat (inter-SSR) PCR has been proved to be a fast and reproducible technique for quantitation of genomic instability (amplifications, deletions, translocations, and insertions) in human sporadic tumors. However, the use of inter-SSR PCR in animal models of cancer has never been described. This new technique has been adapted in our laboratory for the analysis of spontaneous and induced mouse tumors. We established the best PCR conditions for each microsatellite-anchored primer and critically evaluated the reproducibility of the band patterns. We also studied the variation of the fingerprints between and within various inbred mouse strains, including wild-derived lines. Tumor-specific alterations were detected as gains, losses, or intensity changes in bands when compared with matched normal DNA. We quantitated the extent of alterations by dividing the number of altered bands in the tumor by the total number of bands in normal DNA (instability index). By means of inter-SSR PCR, we successfully analyzed genomic alterations in various mouse tumors, including spontaneous thymic lymphomas developed in Msh2 knockout mice as well as chemically induced squamous cell carcinomas and thymic lymphomas. Instability index values ranged between 0 and 9%, the highest levels observed in N-methyl-N-nitrosourea-induced thymic lymphomas generated in Trp53 (p53) nullizygote (-/-) mice. We report here, for the first time, the use of inter-SSR PCR to detect somatic mutations in mouse tumoral DNA, including laser-capture microdissected, methanol-fixed tissues. These PCR-based fingerprints provide a novel approach to assessing the number and onset of mutational events in mouse tumors and will help to understand better the mechanisms of carcinogenesis in mouse models.

The polytene dot chromosome of Drosophila: D. melanogaster and D. subobscura.

The chromosome arms are assumed to be homologous within the genus Drosophila. Homology at the level of the polytene chromosome banding pattern between non-sibling species is, however, almost impossible to establish as different processes such as inversion, transposition and unequal crossing over, have disturbed it. Even though the band sequences cannot be followed, we may ask whether there is a correlation in the total number of bands between species. The polytene dot chromosome is an excellent starting point for such an approach. Here we present the detailed cytology of polytene chromosome 4 of D. melanogasterand the polytene dot chromosome of D. subobscura using electron microscopy. The results show that the number of bands is about the same, around 30, in both species. We predict that by using thin sections and electron microscopy for the longer polytene chromosome arms, both species will turn out to have approximately equal band numbers.

Anti-Pseudomonas aeruginosa antibody detection in patients with bronchiectasis without cystic fibrosis

BACKGROUNDPseudomonas aeruginosa is a frequent cause of infection in patients with bronchiectasis. Differentiation between non-infected patients and those with different degrees of P aeruginosainfection could influence the management and prognosis...

Anti-Pseudomonas aeruginosa antibody detection in patients with bronchiectasis without cystic fibrosis

BACKGROUNDPseudomonas aeruginosa is a frequent cause of infection in patients with bronchiectasis. Differentiation between non-infected patients and those with different degrees of P aeruginosainfection could influence the management and prognosis of these patients. The diagnostic usefulness of serum IgG antibodies againstP aeruginosa outer membrane proteins was determined in patients with bronchiectasis without cystic fibrosis.METHODSFifty six patients were classified according to sputum culture into three groups: group A (n=18) with no P aeruginosain any sample; group B (n=18) with P aeruginosa alternating with other microorganisms; and group C (n=20) with P aeruginosa in all sputum samples. Each patient had at least three sputum cultures in the 6 months prior to serum collection. Detection of antibodies was performed by Western blot and their presence against 20 protein bands (10–121 kd) was assessed.RESULTSAntibodies to more than four bands in total or to five individual bands (36, 26, 22, 20 or 18 kd) differentiated group B from group A, while antibodies to a total of more than eight bands or to 10 individual bands (104, 69, 63, 56, 50, 44, 30, 25, 22, 13 kd) differentiated group C from group B. When discordant results between the total number of bands and the frequency of P aeruginosa isolation were obtained, the follow up of patients suggested that the former, in most cases, predicted chronic P aeruginosacolonisation.CONCLUSIONIn patients with bronchiectasis the degree of P aeruginosa infection can be determined by the number and type of outer membrane protein bands indicating which serum antibodies are present.