Differences In Amount Of DNA Research Articles

Composition and Predominance of Fusarium Species Causing Fusarium Head Blight in Winter Wheat Grain Depending on Cultivar Susceptibility and Meteorological Factors.

Fusarium head blight (FHB) is one of the most important diseases of wheat, causing yield losses and mycotoxin contamination of harvested grain. A complex of different toxigenic Fusarium species is responsible for FHB and the composition and predominance of species within the FHB complex are determined by meteorological and agronomic factors. In this study, grain of three different susceptible winter wheat cultivars from seven locations in northern Germany were analysed within a five-year survey from 2013 to 2017 by quantifying DNA amounts of different species within the Fusarium community as well as deoxynivalenol (DON) and zearalenone (ZEA) concentrations. Several Fusarium species co-occur in wheat grain samples in all years and cultivars. F. graminearum was the most prevalent species, followed by F. culmorum, F. avenaceum and F. poae, while F. tricinctum and F. langsethiae played only a subordinate role in the FHB complex in terms of DNA amounts. In all cultivars, a comparable year-specific quantitative occurrence of the six detected species and mycotoxin concentrations were found, but with decreased DNA amounts and mycotoxin concentrations in the more tolerant cultivars, especially in years with higher disease pressure. In all years, similar percentages of DNA amounts of the six species to the total Fusarium DNA amount of all detected species were found between the three cultivars for each species, with F. graminearum being the most dominant species. Differences in DNA amounts and DON and ZEA concentrations between growing seasons depended mainly on moisture factors during flowering of wheat, while high precipitation and relative humidity were the crucial meteorological factors for infection of wheat grain by Fusarium. Highly positive correlations were found between the meteorological variables precipitation and relative humidity and DNA amounts of F. graminearum, DON and ZEA concentrations during flowering, whereas the corresponding correlations were much weaker several days before (heading) and after flowering (early and late milk stage).

The effects of various household cleaning methods on DNA persistence on mugs and knives

With the prevalence of forensic science in popular media, offenders are becoming more forensically aware and can employ precautionary methods, such as cleaning used items or rubbing away fingermarks, to reduce their traces left at a crime scene. This study examined the effects of various cleaning methods on DNA persistence on commonly encountered casework exhibits, specifically knives and mugs. Aliquots of acellular DNA were added to the knife handles or mug rims, allowed to dry, and then the substrates were either sampled directly or were cleaned and then sampled. The plastic- and wood-handled knives were cleaned with a cloth in a sink of water, diluted dish washing liquid or diluted household bleach, whereas the ceramic, glass and steel mugs were cleaned with a dry or wet cloth, or by wiping with a cloth after applying a cleaning product (dish washing liquid or household bleach spray) directly into the mug and then rinsing it with water. DNA samples were collected with wet and dry swabs, in triplicate, and extracted and quantified. In both experiments, DNA was not detected on items after cleaning with dish washing liquid or household bleach, irrespective of the differences in amounts of DNA initially deposited, substrates, and cleaning methods. Even without a cleaning product, rubbing with a dry cloth decreased DNA recovery from the mugs, regardless of the mug substrate. These results contribute to our understanding of the impact of various cleaning methods on DNA recovery at the crime scene and will help inform DNA recovery strategies.

Evaluación de la utilidad de un dispositivo para toma y preservación del ADN del virus del papiloma humano de muestras cérvico-vaginales autorrecolectadas y almacenadas en seco en mujeres con displasia cervical, Bogotá, Colombia

Objetivo: evaluar la utilidad de un dispositivo para toma y preservación del DNA del virus del papiloma humano (VPH) de muestras vaginales recolectadas por autotoma y almacenadas en seco durante 14 días.Materiales y métodos: estudio piloto de concordancia diagnóstica. Se incluyeron mujeres mayores de 24 años no gestantes con un resultado de neoplasia intraepitelial cervical (NIC) grado 1 o más, confirmado por biopsia en dos instituciones de referencia en Bogotá, Colombia. Se excluyeron mujeres con antecedente de histerectomía total. Se realizó un muestreo por conveniencia. El dispositivo utiliza PCR (reacción en cadena de la polimerasa) en tiempo real para detección del ADN. Se midieron variables sociodemográficas y clínicas, así como el resultado de la prueba por autotoma y tomada por el médico, y la cantidad de ADN de las muestras tomadas el día 1 procesadas ese día, y el día 14, por medio del Ct umbral. Se realizó estadística descriptiva. Se calculó la concordancia global por medio del índice de kappa ponderado y la diferencia de medias de la cantidad de ADN.Resultados: la concordancia en la detección de VPH de alto riesgo mostró un kappa = 0,84 (IC 95 %: 0,71-0,96) entre la muestra cervicovaginal recolectada por autotoma frente a la muestra cervical recolectada por el médico. No hubo diferencias en la cantidad de ADN viral entre el día 1 y el 14 (DM -0,34 ciclos; IC 95 %: -2,29 a 1,61).Conclusión: las muestras vaginales recolectadas por autotoma usando el dispositivo de almacenamiento son confiables para la detección de VPH de alto riesgo en pacientes con displasia cervical, y preservan el ADN viral por 14 días si se almacenan en seco a temperatura ambiente. Se requieren estudios en población general para poder confirmar.

Variation of karyotype and nuclear DNA content among four species of Plectranthus L' Héritier, 1788 (Lamiaceae) from Brazil.

Plectranthus is a genus which includes species of ornamental and medicinal potential. It faces taxonomic problems due to aggregating species previously belonging to the genus Coleus, a fact that has contributed to the existence of various synonymies. The species Plectranthus amboinicus, Plectranthus barbatus, Plectranthus grandis and Plectranthus neochilus are included in this context. Some authors consider Plectranthus barbatus and Plectranthus grandis as synonyms. The present work was carried out with the aim of comparing plants of the above-mentioned species, originating from different localities in Brazil, with regards to chromosome number and karyotypic morphology, correlated to the nuclear DNA content. There was no variation in chromosome number among plants of the same species. Plectranthus amboinicus was the only species to exhibit 2n=34, whereas the others had 2n=30. No karyotypic differences were found among the plants of each species, except for Plectranthus barbatus. The plants of the Plectranthus species revealed little coincidence between chromosome pairs. The nuclear DNA content allowed grouping Plectranthus amboinicus and Plectranthus neochilus, with the highest mean values, and Plectranthus grandis and Plectranthus barbatus with the lowest ones. Differences in DNA amount among the plants were identified only for Plectranthus barbatus. These results allow the inference that the populations of Plectranthus amboinicus and Plectranthus neochilus present coincident karyotypes among their plants, and Plectranthus grandis is probably a synonym of Plectranthus barbatus.

Morphometric and molecular evidence of intraspecific biogeographical differentiation of Rhodnius pallescens (HEMIPTERA: REDUVIIDAE: RHODNIINI) from Colombia and Panama

Rhodnius pallescens is considered the main vector of Chagas disease in Panama and a relevant secondary vector in northern Colombia. Previous data reported that this species presents cytogenetically heterogeneous populations, which are probably biogeographically segregated. To provide new information on the diversity of R. pallescens, we compared several populations from Colombia and Panama based on the morphometric analyses of wings, mitochondrial cytochrome b (cyt b) gene sequencing, and genomic DNA measurements. Although no differences in DNA amount were detected, significant differences in cyt b sequences as well as wing size and shape were identified among populations. The results obtained in this work indicate R. pallescens comprises two evolutionary lineages with genetic and morphological differences that could be explained by their geographic isolation in distinct ecological zones. These results provide new insight into R. pallescens population diversity and the underlying biological processes that shape its evolution.

HNF1α and SREBP2 are important regulators of NPC1L1 in human liver

HNF1α and SREBP2 are important regulators of NPC1L1 in human liver

Blended construct consisting of thermo-reversible hydrogels and heparinized nanoparticles for increasing the proliferation activity of the rabbit chondrocyte in vivo test

To use nano-structured materials as a novel cell therapeutic agent, we have devised a novel method for the fabrication of nano-scaled 3D scaffolds consisting of heparin/poly(ethylenimine) (PEI) nanoparticles in a thermo-reversible hydrogel, attached via a layer-by-layer system. Bioassay results showed significant difference in DNA amount between groups. Specifically, groups with heparin/PEI nanoparticles had almost twice the glycosaminoglycan content per construct starting at day 7 as compared to controls. Gene expression of total collagen was evident in groups containing heparin/PEI nanoparticles.

Injectable biodegradable hydrogel composites for rabbit marrow mesenchymal stem cell and growth factor delivery for cartilage tissue engineering

We investigated the development of an injectable, biodegradable hydrogel composite of oligo(poly(ethylene glycol) fumarate) (OPF) with encapsulated rabbit marrow mesenchymal stem cells (MSCs) and gelatin microparticles (MPs) loaded with transforming growth factor- β1 (TGF- β1) for cartilage tissue engineering applications. Rabbit MSCs and TGF- β1-loaded MPs were mixed with OPF, a poly(ethylene glycol)-diacrylate crosslinker and the radical initiators ammonium persulfate and N, N, N′, N′-tetramethylethylenediamine, and then crosslinked at 37 °C for 8 min to form hydrogel composites. Three studies were conducted over 14 days in order to examine the effects of: (1) the composite formulation, (2) the MSC seeding density, and (3) the TGF- β1 concentration on the chondrogenic differentiation of encapsulated rabbit MSCs. Bioassay results showed no significant difference in DNA amount between groups, however, groups with MPs had a significant increase in glycosaminoglycan content per DNA starting at day 7 as compared to controls at day 0. Chondrocyte-specific gene expression of type II collagen and aggrecan were only evident in groups containing TGF- β1-loaded MPs and varied with TGF- β1 concentration in a dose-dependent manner. Specifically, type II collagen gene expression exhibited a 161±49-fold increase and aggrecan gene expression a 221±151-fold increase after 14 days with the highest dose of TGF- β1 (16 ng/ml). These results indicate that encapsulated rabbit MSCs remained viable over the culture period and differentiated into chondrocyte-like cells, thus suggesting the potential of OPF composite hydrogels as part of a novel strategy for localized delivery of stem cells and bioactive molecules.

Easy and rapid method of zygosity determination in transgenic mice by SYBR® Green real-time quantitative PCR with a simple data analysis

Establishment and maintenance of transgenic mouse strains require being able to distinguish homozygous from heterozygous animals. To date, the developed real-time quantitative PCR techniques are often complicated, time-consuming and expensive. Here, we propose a very easy and rapid method with a simple data analysis to determine zygosity in transgenic mice. We show that the real-time quantitative PCR using SYBR Green fluorescent dye can be applied to discriminate two-fold differences in copy numbers of the transgene. Our procedure has to fit only three simple requirements: (1) to design primers capable of detecting one Ct difference for two-fold differences in DNA amounts (2) to measure genomic DNA concentrations accurately and (3) to have a reference animal of known zygosity in each run. Then, if the Ct values for the control gene are similar in all samples, we are able to compare directly the Ct values for the transgene in every sample, and so, to deduce the zygosity status of each mouse relative to the reference animal. This method is really simple and reliable, and it may be valuable as a rapid screening tool for zygosity status in transgenic animals.

Climate and Growth Form: The Consequences for Genome Size in Plants

The adaptive significance of nuclear DNA variation in angiosperms is still widely debated. The discussion mainly revolves round the causative factors influencing genome size and the adaptive consequences to an organism according to its growth form and environmental conditions. Nuclear DNA values are now known for 3874 angiosperm species (including 773 woody species) from over 219 families (out of a total of 500) and 181 species of woody gymnosperms, representing all the families. Therefore, comparisons have been made on not only angiosperms, taken as a whole, but also on the subsets of data based on taxonomic groups, growth forms, and environment. Nuclear DNA amounts in woody angiosperms are restricted to less than 23.54 % of the total range of herbaceous angiosperms; this range is further reduced to 6.8 % when woody and herbaceous species of temperate angiosperms are compared. Similarly, the tropical woody dicots are restricted to less than 50.5 % of the total range of tropical herbaceous dicots, while temperate woody dicots are restricted to less than 10.96 % of the total range of temperate herbaceous dicots. In the family Fabaceae woody species account for less than 14.1 % of herbaceous species. Therefore, in the total angiosperm sample and in subsets of data, woody growth form is characterized by a smaller genome size compared with the herbaceous growth form. Comparisons between angiosperm species growing in tropical and temperate regions show highly significant differences in DNA amount and genome size in the total angiosperm sample. However, when only herbaceous angiosperms were considered, significant differences were obtained in DNA amount, while genome size showed a non-significant difference. An atypical result was obtained in the case of woody angiosperms where mean DNA amount of tropical species was almost 25.04 % higher than that of temperate species, which is because of the inclusion of 85 species of woody monocots in the tropical sample. The difference becomes insignificant when genome size is compared. Comparison of tropical and temperate species among dicots and monocots and herbaceous monocots taken separately showed significant differences both in DNA amount and genome size. In herbaceous dicots, while DNA amount showed significant differences the genome size varies insignificantly. There was a non-significant difference among tropical and temperate woody dicots. In three families, i.e., Poaceae, Asteraceae, and Fabaceae the temperate species have significantly higher DNA amount and genome size than the tropical ones. Woody gymnosperms had significantly more DNA amount and genome size than woody angiosperms, woody eudicots, and woody monocots. Woody monocots also had significantly more DNA amount and genome size than woody eudicots. Lastly, there was no significant difference between deciduous and evergreen hardwoods. The significance of these results in relation to present knowledge on the evolution of genome size is discussed.

Nuclear DNA Content and Chromosome Number in Some Diploid and Tetraploid Centaurea (Asteraceae: Cardueae) from the Dalmatia Region

Given the paucity of information about genome size in the genus Centaurea, nuclear DNA content of 15 Centaurea taxa, belonging to four subgenera and six different sections, has been investigated for the first time. The sample concerns 21 populations from the Dalmatia region of Croatia. The 2C DNA content and GC percentage were assessed by flow cytometry and chromosome number was determined using standard methods. Genome size of studied Centaurea ranged from 2C=1.67 to 3.72 pg. These results were in accordance with chromosome number and especially with ploidy level that varies throughout this group; 2C DNA values ranged from 1.67 to 3.43 pg for diploid, and from 3.19 to 3.72 for polyploid taxa. No significant intraspecific variations of DNA amount were found between two subspecies of C. visiani and C. ragusina, nor between two varieties of C. gloriosa. However, some populations of C. glaberrima and C. cuspidata showed a significant difference in DNA amount. Three different basic chromosome numbers were observed in studied species (x=9, 10, and 11). The most frequent basic number was x=9. C. rupestris, C. ragusina ssp. ragusina, and C. r. ssp. lungensis possessed x=10 and C. tuberosa x=11. The species with a basic chromosome number of x=9 had a small genome size and the smallest chromosomes (on average 0.09 to 0.12 pg/chromosome) but frequently present polyploidy. Centaurea ragusina ssp. ragusina and C. r. ssp. lungensis had a mean base composition 41.3% GC.

Flow cytometric analysis for ploidy level differentiation of 45 hairy vetch accessions

SummaryDetermining the ploidy of plant germplasm is a necessary step in breeding or genetic studies in species. The purpose of this research was to determine the presence of ploidy level differentiation of hairy vetch (Vicia villosd) germplasm. Flow cytometry and root tip chromosome squashing methods were employed to assess 45 accessions labeled V. villosa available through the USDA germplasm collection. Flow cytometry determined that 43 of the accessions were 2C, one accession was 4C, and one accession was 6C. Analysis of accessions by root tip chromosome counts indicated that all accessions were diploid. The 2C accession contains 14 chromosomes and their chromosomes were approximately one‐half and one‐third in size as compared to the chromosomes of the 4C and 6C accessions, respectively. The 4C accession was observed to have 16 chromosomes and the 6C accession was observed to have 14 chromosomes. The large‐scale differences in DNA amounts were due to chromosomal size variability as opposed to ploidy differences. This revealed the incidence of species misidentification of these two V. villosa accessions to be Vicia pannonica. All the V. villosa accessions were observed to be diploid and have similar DNA amounts. Flow cytometry proved to be useful in the efficient assessment of these accessions.

Variation in Nuclear DNA Content at the Species Level in Armeria Maritima

Intraspecific variation in nuclear DNA content in 19 populations of Armeria maritima was investigated. Significant differences in DNA amount among ecogeographic groups and among populations were observed. These differences are related to geographic origin, with Californian populations having 7 % more DNA than their European counterparts. Within Europe, the four ecogeographic groups tested are not distinct, whatever their geographic origin (maritime versus continental) and their ecological characteristics (heavy-metal polluted versus non-toxic soils). However, significant differences in DNA amount appeared among population clusters identified from biochemical classification of European populations based on flavonoid compounds and isozyme markers. Variation in genome size among populations was found to be significantly correlated to variation in pollen size. Weak interpopulational variation has been detected for the nucleotidic base ratio, but was not correlated to variation in DNA amount.

Allium cepa L. Cultivars from Four Continents Compared by Flow Cytometry show Nuclear DNA Constancy

In 1965 Van't Hof estimated the nuclear DNA amount of an unidentified Allium cepa L. cultivar as 2C=33.55pg (Experimental Cell Research39: 8–58). This value has been adopted by common usage as the main calibration standard for angiosperm DNA C-value estimations. However, different cultivars have been used while assuming species DNA C-value constancy. Surprisingly this assumption has never been tested. A. cepa is an outbreeder with telomeric heterochromatic segments, so intraspecific variation in C-value, possibly correlated with environmental factors as seen in Zea mays L., might be expected. We used laser flow cytometry to compare nuclear DNA amounts in roots of six A. cepa cultivars used as calibration standards or from different environments. Tissues from one cultivar, or similar volumes of tissue from two cultivars, were run and the variance between nuclei in 2C peaks compared. Only one shoulderless 2C peak was seen for all pairs of co-chopped cultivars. Thus, no large differences in C-value between cultivars from different environments were found. Moreover, comparing cultivars run singly or as pairs showed no evidence for increased variation in 2C peaks in the latter, and hence of critical differences in DNA amounts between ‘Ailsa Craig’ and another cultivar. Such variation was insufficient to make their use as alternative calibration standards, or the practice of imputing Van't Hof's original C-value estimate to them, unacceptable for most practical purposes. Given the mechanisms known which can generate genome size variation, the degree of constancy in DNA C-value found seems remarkable.

Genome Size Variation and Plant Systematics

The importance of genome size, as a useful taxonomic marker, has been stressed in many studies based on different groups. A critical appraisal of intraspecific variability reported in various species so far shows that the plant genome is fairly stable (taking a narrow species concept) and is one of the salient features defining a biological species. Large differences in DNA amounts may exist at the infrageneric level which may be correlated with various adaptive traits at nuclear, cellular, tissue and organismic levels. Therefore, being an adaptive character, a comparison of nuclear C-values in conjunction with other characters may provide a natural way to elucidate evolutionary relationships. In a number of cases it is possible to study whether gain or loss of DNA has occurred during speciation which may coincide with the existing taxonomic treatment and presumed evolutionary relationships within a narrow taxonomic group. The present account deals with many recent examples which highlight the importance of genome size in microsystematics.

A Colorimetric Inhibition Study of Single-Stranded DNA Decamer Sequence Interactions with Dinitrotoluene

A novel colored reaction between 2,4-dinitrotoluene (DNT) and dimethylsulfoxide (DMSO) on carbonate-activated plastic surfaces is described. In a preliminary study of the potential of oligonucleotides to bind nitroaromatic explosives, a random library of 1,040 single stranded (ss) DNA decamers (10 bases) in polystyrene microtitre plates were screened for inhibition of color development. The vast majority (89%) of sequences in the library completely inhibited color formation, suggesting that hydrogen bonding between DNA and the nitro groups of DNT was the predominate attractive force. Of the 114 sequences which allowed some visible color development, absorbance (405nm) values were negatively correlated with GC content (r = −0.764), suggesting that some specific binding “pocket” structures for DNT may exist in the small library examined. Among the color evolving combinations, differences in amount of DNA were not correlated with absorbance.

Meiosis of triploid Lolium. II. Discrepancies between the analyses of chromosome configurations at metaphase I in inverse autoallotriploid combinations

Chromosome configurations were analysed at metaphase I in six plants of each of the two inverse autoallotriploid types of Lolium temulentum × L. multiflorum with the genome combinations TTM and TMM. In the combination with two large genomes and one small (TTM), there was no preferential pairing but with two small genomes and one large (TMM) there was preferential pairing. The findings are discussed in relation to the differences in DNA amounts of the two species and the associated differences in meiotic times of larger and smaller genomes. The results question the value of pairing data in triploids for the assessment of the relatedness of diploid species.

Chromosomal DNA variation, genomic constraints and recombination in Lathyrus

There is approximately a doubling of the total nuclear DNA between the 8 Lathyrus species and there are significant differences in the amounts of DNA in euchromatin and heterochromatin. Between the 8 species chiasma frequency and total nuclear DNA are not correlated but within complements it is positively correlated with the amount of DNA in the chromosomes. There is no significant correlation between chiasma frequency and euchromatin DNA nor between chiasma frequency and heterochromatin DNA among species, but among chromosomes, as with total DNA, it is positively correlated with euchromatin DNA and heterochromatin DNA. Results show that despite the large differences in DNA amounts between species there are genomic constraints underlying the frequency and distribution of chiasmata in the chromosome complements.

The distribution and divergence during evolution of families of repetitive DNA sequences inLathyrus species

Evolution and divergence among, species within the genusLathyrus have involved an approximately fivefold increase in the amounts of nuclear DNA. Most species inLathyrus are diploids with the same chromosome number, 2n=14. Significant changes in the amounts of repetitive sequences have accounted for much of the evolutionary DNA variation between species. Seven diploidLathyrus species with a twofold variation in nuclear DNA amounts between them were investigated. Using higher derivative analysis of the thermal denaturation profiles of the reassociated repetitive DNA, the reiteration frequency and divergence of repetitive families were compared. Much variation in the reiteration frequency was observed within and between species. In species with larger 2C DNA amounts repetitive families had on average greater amounts of DNA. Despite the massive differences in DNA amounts, six species were consistently similar in the number of repetitive families in their genomes, and they showed a similar pattern in base sequence divergence. In terms of base sequence relationships the repetitive families appeared to be heterogeneous. The evolutionary significance is discussed.

Somatic Mutagenesis inPinus Laricio. A Cytophotometric Analysis of DNA and Histone Content in 2C Meristematic Nuclei

SUMMARYGenomic changes in Pinus laricio were observed affecting a terminal bud which stops its growth thereby stimulating supernumerary lateral bud production. The changes which occur in the bud meristem results in a compact branch able to produce small ovulate cones, but it never produces pollen cones. Nevertheless sexual reproduction occurs and this genomic change can be transmitted by seeds. In the present study root meristematic nuclei in P. laricio plants grown from seeds with genomic variation and root meristematic nuclei from normal control plants were considered. Significant differences in DNA amount (pg), histones/DNA ratio and nuclear volume against a constant chromosome number (2n = 24) were found. Since in Pinus similar intraspecific differences are reported in litterature, the question arises about the evolution of Gymnosperm chromosomes. In this context the reported results seem to indicate that rapid genetic changes might have a role in the genus evolution.