Homoplasy corrected estimation of genetic similarity from AFLP bands,and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce.     

Thermoluminescence characteristics of sodium chloride salt‐stressed Indian mustard seedlings

The thermoluminescence (TL) parameters in the intact leaves and the thylakoids isolated from leaves of NaCl treated seedlings showed different patterns of change. NaCl treatment brings about a destabilization of Q_A and Q_B, leading to a decrease in Q and B bands in the leaves. However, the Q and B band intensity of isolated thylakoids increased in NaCl‐treated seedlings. The differences in the TL intensities are described as the action of NaCl on the density of quinones per unit leaf area and on chlorophyll units in isolated thylakoids. Copyright © 2002 John Wiley & Sons, Ltd.     

Protective Effect of Arachidonic Acid during Viral Infection: Synthesis of New Proteins by in vitroPotato Plants

The mechanisms of the protective, immunostimulating effects of arachidonic acid (AA) were studied, and its efficiency in the induction of defense reactions in the moderately virus-resistant potato cultivar Nevskii (Solanum tuberosumL.) was determined. Virus-free in vitropotato plants treated with AA and inoculated with phytopathogenic viruses were used as a model. The data on the X virus accumulation obtained by the enzyme-linked immunosorbent assay confirmed the immunizing effect of AA; the optimum concentration of the compound was 10^–8M. The antiviral effect of AA was maintained in infected in vitropotato plants for at least two or three weeks. The electrophoretic analysis of leaf proteins revealed a 33-kD polypeptide induced by the potato virus Y. Two weeks after inoculation with virus X, a 40-kD protein was identified in potato plants pretreated with AA. In addition, the relative content of the two groups of proteins consisting of two or three components with mol wts about 50 kD and above70 kD changed both upon viral infection and pretreatment with AA. Only small changes in the isozyme patterns of peroxidase in potato plants were observed during the development of systemic acquired resistance; they were manifested in some treatments in the band intensities. The existence of the alternative pathways of systemic acquired resistance in potato plants specifically activated by viral infection and AA was suggested.     

Biosynthesis of dextrans with different molecular weights by selecting the concentration of Leuconostoc mesenteroides B-512FMC dextransucrase, the sucrose concentration, and the temperature

Leuconostoc mesenteroides B-512FMC dextransucrase was found to synthesize dextrans of varying molecular weights by selecting the concentrations of dextransucrase and sucrose, as well as the temperature. Four enzyme concentrations (50, 10, 1.0, and 0.1 U/mL), five sucrose concentrations (20, 50, 100, 200 and 1000 mM), and two temperatures (20 °C and 30 °C) were studied. The highest amount of enzyme (50 U/mL), with the lowest concentration of sucrose (20 mM), and the lower temperature of 20 °C gave the lowest number-average molecular weight (MW_n) of 20,630 Da, respectively. As the sucrose concentration was increased, 50 mM, 100 mM, and 200 mM, the MW_n was 49,240 Da, 63,350 Da, and 126,720 Da, respectively. The next enzyme concentration (10 U/mL) gave a similar upward trend, starting at 73,130 Da and ending at 237,870 Da at 20 °C and 130,040 Da and ending at 415,770 Da at 30 °C. The upward trend continued for the 1.0 and 0.1 U/mL enzyme concentrations. An increase in the temperature had the overall effect of increasing the MW_n for each decreasing concentration of enzyme and increasing concentration of sucrose. For 0.1 U/mL and 1000 mM sucrose at 30 °C, the MW_n was 1,645,700 Da. The results of the study show that the molecular weights of the synthesized dextrans were inversely proportional to the concentration of the enzyme and directly proportional to the concentration of sucrose and the temperature.     

Heterogeneity of the internal transcribed spacer 1 (ITS1) inTulipa (Liliaceae)

Heterogeneity of the internal transcribed spacer ITS1 of the rDNA within individuals ofTulipa gesneriana L.,T. kaufmanniana Regel, and their interspecific hybrids was analyzed by PCRRFLP, using the polymorphic restriction enzymesRsaI andHinfI, and by nucleotide sequence analysis. In most cases, the sum of the sizes of the restriction fragments was higher than the entire length of the undigested ITS fragment, indicating heterogeneity at the restriction sites within an individual. Differences in band intensities within the restriction patterns indicate the occurrence of variation in copy number of these different ITS1 variants within individuals. Automated sequencing without a visual inspection often failed to detect existing heterogeneity within sequences, resulting in a discrepancy between the sequencing and restriction analysis results. By visual interpretation of the sequences, the restriction patterns could mostly be predicted well. Fluorescence in situ hybridization (FISH) experiments in fourTulipa species revealed the occurrence of several rDNA spots. The number of rDNA loci varied from seven inT. gesneriana Christmas Marvel to ten inT. australis Link. This might explain the occurrence of heterogeneity in ITS sequences inTulipa, as homogenization of variants has to take place over different loci.     

Restriction fragment length polymorphism (RFLP) of exon 2 of the MhcBibi-DRB3 gene in American bison (Bison bison)

Polymerase chain reaction (PCR) primers specific to exon 2 of the bovine lymphocyte antigen (BoLA)-DRB3 gene were successfully used to amplify the equivalent region in 469 American bison (Bison bison). In domestic cattle, alleles of DRB3 are assigned through a restriction fragment length polymorphism (RFLP) analysis of the patterns of fragment lengths observed after digestion with the restriction enzymes RsaI, BstYI and HaeIII. In bison, using the same procedure, the observed RFLP patterns provided evidence for the strong conservation of restriction sites previously reported in cattle.     

Simplified amplified-fragment length polymorphism method for genotyping Mycobacterium tuberculosis isolates

A simplified amplified-fragment length polymorphism (AFLP) method was developed and applied to genotype 52 Mycobacterium tuberculosis isolates. This method can be carried out using only one restriction enzyme (XhoI), one double strand adapter, and one PCR primer. The amounts of DNA and DNA polymerase, and the concentrations of primer and Mg²⁺ in the PCR step were optimized using the Basic Sequential Simplex method. AFLP analysis of the isolates generated a total of 24 differently sized bands ranging from 1537 to 121 bp, and 52 different band patterns, with a minimum of 2 and a maximum of 13 bands. The results were compared with the well-established IS6110 restriction fragment length polymorphism (IS6110-RFLP) typing method, which rendered a total of 32 differently sized bands from 1 to 12 kbp, and 52 different band patterns, with a minimum of 3 and a maximum of 15 bands. Therefore, both genotyping methods showed a discriminatory power of samples of 100%. Nevertheless, pairwise comparisons of the 1326 similarity indexes calculated for both typing methods showed a total absence of correlation between the similarity indexes of the two methods. The simplified AFLP method is expected to be more useful for genotyping M. tuberculosis isolates compared to the IS6110-RFLP method, since the former evaluates genetic variations throughout the M. tuberculosis genome. Furthermore, the relatively rapid and low-cost simplified AFLP method compares favorably to the IS6110-RFLP or conventional AFLP methods, and shows great promise for genotyping M. tuberculosis isolates, especially in developing countries or for preliminary screening.     

宁夏荒漠草原优势植物生长及生物量分配对放牧干扰的响应

于2011年植物生长旺季(8月)在围封禁牧(NG)、轻度放牧(LG)、中度放牧(MG)和重度放牧(HG)区分别随机选取荒漠草原优势植物甘草(Glycyrrhiza uralensis)和牛心朴子(Cynanchum komarovii)各15株为研究对象,对比分析其生长特征、各植物构件生物量及生物量资源分配差异对不同放牧强度的响应机制,为退化草原的恢复演替提供依据。结果表明:(1)甘草株高和地径、牛心朴子株高均随放牧强度的增加呈先升高后下降的趋势,而且均在轻度放牧条件下最高,重度放牧时则显著降低。(2)甘草和牛心朴子的总生物量、茎生物量和叶生物量随着放牧强度的增加呈先升高后降低的趋势,且不同放牧强度间差异显著;甘草和牛心朴子根系生物量随放牧强度的加强变化趋势不同。(3)甘草和牛心朴子生物量分配的总体格局为:根叶茎;随着放牧强度的增加,甘草根生物量比呈先升高后降低趋势,茎生物量比呈下降的趋势,叶生物量比呈上升趋势,而牛心朴子根生物量比呈先下降后升高的趋势,茎生物量和叶生物量呈先增加后下降的趋势。研究认为,不同放牧强度下两种植物形态可塑性和生物量分配格局的差异反映出植物生态适应策略的不同。     

Characterization of AFLP Markers Associated with Growth in the Kuruma Prawn, <Emphasis Type="Italic">Marsupenaeus japonicus</Emphasis>, and Identification of a Candidate Gene

Growth rate of the Kuruma prawn, Marsupenaeus japonicus is an important economic trait, with larger animals commanding higher market prices. To identify gene markers associated with growth, a genetic map of a full-sib F₂ intercross family of M. japonicus has previously been generated and quantitative trait loci (QTL) influencing weight, total length, and carapace length were identified. In this study, amplified fragment length polymorphism (AFLP) markers associated with the major QTL region, contributing 16% to phenotypic variation, were characterized. Flanking sequence has been obtained and allelic variants responsible for segregation patterns of these markers have been identified. The genomic sequence surrounding the AFLP band 7.21a, residing under the QTL peak, contains a gene sequence homologous to the elongation of very long chain fatty acids-like (ELOVL) protein family. A full-length mRNA (ELOVL-MJ) encoding this protein was isolated from M. japonicus, representing both the first ELOVL gene in crustacea and the first candidate gene identified via QTL studies in crustacea.     

Orosomucoid (ORM) typing by isoelectric focusing: evidence for gene duplication of ORM1 and genetic polymorphism of ORM2

Summary It has been demonstrated that the genetic polymorphism of human serum orosomucoid (ORM) is controlled by polymorphic ORM1 and monomorphic ORM2 loci. In this study a Japanese family was encountered in which several members had puzzling electrophoretic patterns consisting of four bands. The ORM patterns were due to the products of a duplicated ORM1 locus haplotype (ORM1 ^* 2·1) or the products of new variant alleles at the ORM2 locus. The ORM1 ^* 2·1 haplotype is very common in the Japanese population, occurring at an allele frequency of 0.16. The increased occurrence of ORM1 2-1 and the heterogeneity in band intensity among ORM1 2-1 phenotypes could be explained in terms of a duplicated gene ORM1 ^* 2·1. The ORM2 locus proved to be polymorphic, with six alleles in the Japanese population. Dedicated to Professor Dr. K. Nishigami on the occasion of his 60th birthday     

RFLP analysis in chrysanthemum. I. Probe and primer development

In order to study genetic variability at the DNA level in chrysanthemum (Dendranthema grandiflora Tzvelev) PstI and HindIII genomic libraries were constructed. Probes from both libraries were tested for the presence of restriction fragment length polymorphisms (RFLPs). Of the probes from the PstI library 91% appeared to hybridize to low-copy genes, while only 35% of those from the HindIII library appeared to do so. The PstI probes were used in further analyses as 79% of them showed RFLPs, whereas the HindIII low-copy number probes gave only 14% polymorphic patterns. Because of the hexaploid character of chrysanthemum, complex patterns generally consisting of 6–12 fragments were visible on a Southern blot after hybridization. To simplify the genetic analysis, locus-specific polymerase chain reaction (PCR) primers were developed that gave simple polymorphic patterns in a number of cases. The RFLP probes and primers developed will be used in future marker-assisted selection in this polyploid crop.     

Asymmetries in the Machband phenomena

The Mach bands are directly related to the size and the shape of on-center off-surround neural units in human vision. The effects of various stimulus parameters were studied on both bright and dark bands of equal plateau intensities. At low overall intensities, the dark band increases markedly in width, while the bright band does not. However, the bandwidth is more affected by the brightness slope, than by the plateau intensity per se. In this case, both bands vary approximately linearly and inversely with the log of the slope. The bright bands are slightly wider (4′) than the dark bands, for matched intensities. Both bands almost double in width with only a ±30′ para-foveal fixation. Optical blur enlarges the bands as predicted from the spread function. A comparable enlarging effect found with pupil size increase is not so readily understood. The apparent centers of the bright bands are positioned significantly more asymmetrically between the two edges than are the dark band centers. Eccentric neural units are considered as possible explanations for some of these non-linearities. Supported, in part, by Research Grant No. EY00319-05 from the National Eye Institute, National Institutes of Health, Bethesda, Maryland, and by a fight for Sight Grant-in-Aid G-428 from the National Council to Combat Blindness, Inc., New York, New York.     

Genetic aspects of wheat gliadin proteins

Inheritance of gliadin components unique to three different varieties of common wheat (Triticum aestivum L.) was studied in F₁ and F₂ seeds of intervarietal crosses using protein patterns obtained by polyacrylamide gel electrophoresis in aluminum lactate buffer (pH 3.2). The patterns of F₁ seeds of the crosses Cheyenne × Justin and INIA 66R × Justin evidenced all the bands present in the patterns of the parents; band intensities reflected gene dosage levels dependent on whether the contributing parent was maternal or paternal in accordance with the triploid nature of endosperm tissue. Most of the gliadin components examined segregated in accordance with control by a single dominant gene, but in two instances single bands in the one-dimensional electrophoretic patterns segregated in the F₂ as expected if controlled by two genes. A method of two-dimensional electrophoresis was developed that resolved these apparently single bands into two components each, which could segregate independently. Linkage analysis provided evidence of codominant alleles and closely linked genes coding for gliadin protein components in both coupling and repulsion situations. The gliadin protein components seem to be coded for by clusters of genes located on chromosomes of homoeologous groups 1 and 6 in hexaploid wheats.Reference to a company or product name does not imply approval by the U.S. Department of Agriculture to the exclusion of others which may also be suitable.     

Alteration of Bacteriolytic Enzyme Profile of Staphylococcus aureus during Growth

Profiles of cell-associated bacteriolytic activities and those in the culture supernatant of Staphylococcus aureus FDA209P at various stages of growth were analyzed using sodium dodecyl sulfate-polyacrylamide gels containing Micrococcus luteus or S. aureus. In the logarithmic growth phase, the cell-associated bacteriolytic activities extracted with Triton X-100 contained a number of bacteriolytic proteins, the profiles of which were similar to those we reported elsewhere (Sugai, M., Akiyama, T., Komatsuzawa, H., Miyake, Y., and Suginaka, H.(1990) J. Bacteriol., 172, 6494-6498). The proteins include P1, P2, P7, P9, PX, P13, P18 and other minor components. At the stationary growth phase, the bacteriolytic band-profile of the Triton X-100 extract changed dramatically. P1, P7 and P9 disappeared, and the other minor bands had markedly decreased band intensities. On the other hand, P2, PX, P13, and P18 retained their band intensities during the stationary growth phase. The band intensities of P7, P13, PX, and P18 increased in the supernatant during the logarithmic growth phase. These results indicated that the bacteriolytic band-profile changes during growth.     

Bamboo germplasm screening with nuclear restriction fragment length polymorphisms

Summary Bamboo species are difficult to identify because flowering material is seldom available and taxonomy is of necessity based on vegetative characters. To evaluate the utility of restriction fragment length polymorphism (RFLP) analysis in bamboo systematics and germplasm screening, a library of random genomic probes from a Phyllostachys nigra PstI library was constructed. Probes from the library were used to screen bamboo germplasm consisting mostly of temperate bamboos of the genus Phyllostachys. RFLP variation was abundant, and species-specific patterns were readily obtained. Chloroplast DNA showed little variation among the bamboo accessions analyzed.     

Raman spectroscopic investigation on the interaction of malignanthepatocytes with doxorubicin

Raman spectroscopy has proven to be a very powerful technique and is currently experiencing a renaissance. In this paper, it is used to explore the interaction between doxorubicin and malignant hepatocytes in vitro. For the addition of doxorubicin, the band intensity at 1609 cm^− 1, mainly assigned to CC in-plane bending mode of phenylalanine and/or tyrosine residues, increases significantly, and the intensities of the bands at 1585 and 1313 cm^− 1, mainly due to the guanine bases, decrease greatly. In addition, Raman spectra are investigated at different doxorubicin concentrations, and the mean areas ratios of the band at 1450 to that at 1003 cm^− 1, A₁₄₅₀/A₁₀₀₃, fluctuate according to the doxorubicin concentration increasing, which suggests that doxorubicin affects the relative content of lipid in cells.     

Variation in vertebral number and its morphological implication in Galaxias platei

Variation in the vertebral number of the puyen grande Galaxias platei was examined for specimens from 22 localities that span the entire distribution range of the species (from 40° to 55° S). The mean vertebral number (N_MW) increases towards high latitudes, i.e. Jordan's rule is applicable to this species. Owing to the wide geographic variation of the species, not only in latitude but also in altitude, the most explicative variable for N_MW was mean winter air temperature, showing negative dependence. Morphological data suggest that the increment in vertebral number lies in the pre‐pelvic region of the trunk and in the caudal region, but not in the segment between pelvic‐fin insertion and the origin of the anal fin. As these alterations in body shape have important consequences for hydrodynamics and swimming performance, vertebral number variation in G. platei also holds implications for both individual and population fitness.     

Design and Evaluation of a Specific Primer Pair for the Diagnosis and Identification of <Emphasis Type="Italic">Acanthamoeba polyphaga</Emphasis>

Random amplified polymorphism DNA (RAPD) is a useful tool for species identification. The obtained band patterns can be used for specific primer pair design that may be useful for species diagnosis. In this study, a distinctive a 962-bp band in A. polyphaga band patterns was found, by using the OPC20 primer (ACTTCGCCAC). The DNA fragment was used to design a specific primer pair that was useful for the identification of different isolates as A. polyphaga species. A case of A. polyphaga in disseminated acanthamoebiasis affecting mesenteric nodes is also reported.     

A polynucleotide CD probe: interactions with oligomers of a polycationic amine that exhibit positive extrinsic bands at greater than 300 nm

A set of large positive extrinsic CD bands ([θ]₃₃₃ = 2.6 X 10⁴ deg-cm²/decimole phosphate) in the > 300 nm region as well as diminution of the intrinsic signals (θ₂₇₅) have been observed in the CD spectra of various nucleic acids complexed with the achiral compound, N-poly{α-[N-(4-pyridylethylene-4-pyridyl-N′-)α′-p-xylyl]dibromide}-4-pyridylethylene-4-pyridinium bromide, (polymer X).^1,2,5 The signal changes are attributed to the binding of polymer X chromophores isogeometrically to the DNA helix in an ordered chiral arrangement. Fractionation of polymer X gives 10 well-separated oligomers. The oligomers were characterized by nmr. Their interactions with DNA have been investigated with respect to r(r = ratio of equivalents of polymer X charge/g-atoms DNA phosphorus) and n (oligomer chain length). In all cases where n ≥ 1, [θ]₃₃₃ increases linearly with increasing r between 0 and 0.32, and is accompanied by a corresponding decrease in [θ]₂₇₅, which becomes negative as r approaches .32. Extrinsic band intensities reveal a dependence on n up to n = 5, above which increases in nonspecific binding result in a reduction in normalized band intensities. Polymer X shows a strong preference for B-form nucleic acids and induces maximum extrinsic CD signal intensities with A-T homopolymers. Alterations in helix hydration are believed to accompany complex formation. Inversions in [θ]₂₇₅ of the octamer X-poly(dA-dT) complex have been attributed to the “alternating B” conformation of poly(dA-dT).³ Similar inversions are not observed in other nucleic acid-octamer X complexes. Visible and CD spectrometry data from competition studies in the presence of the antibiotics actinomycin D (AMD), daunomycin (DM), and distamycin A (DST) are consistent with “nonclassical” intercalation as the mode of binding, and these data place the potential binding site in or near the hydrophobic region of the minor groove. Reductions in [θ]₃₃₃ with increasing urea further implicate the involvement of hydrophobic interactions in the formation of an asymmetric complex. Stabilization of the helix results in all cases as evidenced by alterations in T_m; corresponding changes, however, in cooperativity are not clearly discernable. Viscosity and light-scattering data indicate no changes in molecular weight due to aggregation, and as such are not consistent with a transition to the ψ-DNA upon complex formation.