Amplification Profiles Research Articles

Agro-morphological and molecular characterization of traditional scented Radhatilak rice of lower Gangetic plains of West Bengal

Radhatilak, an indigenous tall-indica type scented rice, is presently cultivated in small pockets in 3-4 districts within lower gangetic plains of West Bengal, India. With a view to register as a farmers' variety, its agro-morphological characterization was done at 'C' Block Farm, B.C.K.V., Kalyani, West Bengal during kharif (wet) season of 2012, 2013 and 2014 following DUS test guidelines of Protection of Plant Varieties and Farmers' Rights Authority (PPV&FRA). The variety has late heading (115-120 days) and late maturity (140-150 days), which produces long-statured plants (130-140 cm height) with no anthocyanin colouration on leaf blade and sheath, nodes and internodes. The colour of lemma and palea is golden-yellow with red or reddish-purple spot at tip at maturity, while sterile lemma is red in colour. The awnless grains are short in length (6.3 mm) with very low test weight (10.95 g). The white- coloured kernels are short-bold in shape with low amylose (18.6%), medium gelatinization temperature (alkali value 3.3) and medium-strong aroma. Twenty three SSR markers were used for DNA amplification profiling of Radhatilak rice against non-aromatic international check variety IR 36. The study could identify two markers (RM 339 and RM 341) which can clearly distinguish Radhatilak and IR 36 (182.39 vs. 143.09 bp and 135.39 vs. 174.97 bp, respectively).

Kerr instability amplification of Bessel–Gauss beams

Recently it was shown that Kerr instability via degenerate four-wave mixing can amplify single-cycle Gaussian seed pulses from the visible to the deep infrared [Optica5, 271 (2018OPTIC82334-253610.1364/OPTICA.5.000271)]. Pump-to-seed energy conversion efficiency was found to be around 0.15–0.2%, which is lower than that of conventional second-order nonlinear optical parametric amplifiers (OPAs). Here we show that replacing the Gaussian seed with a Bessel–Gaussian seed can yield efficiencies around 1%, which is comparable with OPAs. This increase in efficiency is a result of improved overlap between the seed beam and the Kerr instability amplification profile. Further, the transverse symmetry of the Bessel–Gaussian profile results in no spatial walk-off between pump and seed beams, and hence amplification at longer wavelengths than in the Gaussian case is possible.

Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity

Being an economical and nutritional crop, Capsicum appeases people's peppery taste and is found to bewidely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of C. frutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.

Framework for DNA Quantification and Outlier Detection Using Multidimensional Standard Curves.

Real-time PCR is a highly sensitive and powerful technology for the quantification of DNA and has become the method of choice in microbiology, bioengineering, and molecular biology. Currently, the analysis of real-time PCR data is hampered by only considering a single feature of the amplification profile to generate a standard curve. The current “gold standard” is the cycle-threshold (Ct) method which is known to provide poor quantification under inconsistent reaction efficiencies. Multiple single-feature methods have been developed to overcome the limitations of the Ct method; however, there is an unexplored area of combining multiple features in order to benefit from their joint information. Here, we propose a novel framework that combines existing standard curve methods into a multidimensional standard curve. This is achieved by considering multiple features together such that each amplification curve is viewed as a point in a multidimensional space. Contrary to only considering a single-feature, in the multidimensional space, data points do not fall exactly on the standard curve, which enables a similarity measure between amplification curves based on distances between data points. We show that this framework expands the capabilities of standard curves in order to optimize quantification performance, provide a measure of how suitable an amplification curve is for a standard, and thus automatically detect outliers and increase the reliability of quantification. Our aim is to provide an affordable solution to enhance existing diagnostic settings through maximizing the amount of information extracted from conventional instruments.

Diurnal changes in central blood pressure and pulse pressure amplification in patients with obstructive sleep apnoea

Study objectivesRecent evidence suggests that compared to peripheral blood pressure (BP), central BP may be more strongly associated with target organ damage and cardiovascular morbidity and mortality. Technological advances now allow the ambulatory measurement of peripheral and central BP over 24 ​h. For the first time, we set out to characterise the diurnal profile of central BP and pulse pressure amplification (PPA) in patients with obstructive sleep apnoea (OSA). MethodsIn this observational study, patients with moderate to severe OSA underwent 24 ​h central and peripheral BP testing before and after at least 4 weeks of CPAP therapy. Concurrent actigraphy was performed to confirm sleep and wake times. Results36 patients were screened, 31 had successful testing (mean (SD) age 45 ​± ​10 years, AHI 58 ​± ​27 events/hr, Office BP 136/89 ​± ​10.7/9.5 ​mmHg, 32% on anti-hypertensives, 77% dippers), 21 completed testing post CPAP. Central systolic and diastolic BP followed the same nocturnal dipping profile as peripheral BP, however the peripheral pulse pressure (PP) narrowed in sleep (−3.2 ​mmHg, p ​< ​0.001), whereas the central PP remained unchanged (0.124 ​mmHg, NS), causing a significant reduction in PPA overnight (−10.7%, p ​< ​0.001). The magnitude of dip in central systolic pressure was less than peripheral systolic pressure (by 2.3 ​mmHg, p ​< ​0.001). After treatment with CPAP, the PPA reduction overnight was attenuated (by −3.3%, p ​= ​0.004). ConclusionsIn moderate to severe OSA, central BP and PPA reduce overnight during sleep. Further randomised controlled studies are needed to quantify the differential effects of CPAP and anti-hypertensives on central versus peripheral BP.

Dedifferentiated liposarcoma with inflammatory myofibroblastic tumor-like features: a clinicopathological analysis of five cases

Objective: To investigate the clinicopathological features, diagnosis and differential diagnosis of dedifferentiated liposarcoma (DDLPS) with inflammatory myofibroblastic tumor (IMT)-like features. Methods: Five cases of DDLPS with IMT-like features were collected from the First Affiliated Hospital of Nanjing Medical University, the Affiliated Hospital of Nanjing University of Traditional Chinese Medicine and the First People's Hospital of Qinzhou between 2013 and 2018. EnVision method and fluorescence in situ hybridization (FISH) were used to detect the immunophenotype of the tumor cells and the profile of MDM2 gene amplification respectively. Results: All five cases were male and the median age was 61 (range 53 to 65) years. The clinical symptoms were mainly related to the space-occupying lesions. The tumors were located in duodenal mesentery (two cases), intestinal wall (one case), retroperitoneum (one case), and spermatic cord (one case). Grossly, the tumors were not well encapsulated, ranging from 3 to 13 cm (median 6.7 cm) in diameter, with tan to gray and firm cut surface. Histologically, the dedifferentiated component closely resembled inflammatory myofibroblastic tumor (IMT), with spindle/polygonal/stellate-shaped cells arranged in storiform, sheet-like, or random pattern, with varying degrees of chronic inflammation and fibrosis. All three major patterns seen in IMT (myxoid, cellular and hypocellular fibrous) were observed, the hypocellular fibrous pattern was the most common. Well-differentiated liposarcomatous component was found in the peripheral areas of all the tumors. One case had high grade dedifferentiated component. Four cases were strongly positive for MDM2 and p16. Two cases were positive for SMA, and one case was focally positive for desmin and one for CD34. None of the cases stained for ALK-1. FISH demonstrated MDM2 gene amplification in all five cases. Clinical follow-ups were available in all five cases and the interval ranged from 3 to 66 months (median 23 months). Two patients developed recurrences and one patient had metastasis. The remaining two patients were alive with no evidence of tumor recurrence at 3 and 14 months after surgery respectively. Conclusions: DDLPS with IMT-like features is a more aggressive neoplasm than its histological mimic (IMT), and should not be misdiagnosed as other intermediate or low-grade malignant tumors, such as IMT, sclerosing liposarcoma, inflammatory liposarcoma, aggressive fibromatosis, solitary fibrous tumors, low-grade myofibroblastic sarcoma, and low-grade fibrosarcoma.

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

BackgroundSubunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a ‘theoretical’ to ‘actual’ delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.ResultsInterfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers’ preferences for certain sequences were detected, depending on the MBCs’ composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.ConclusionsDue to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.

Can listeners reliably identify their preferred amplification profiles for speech listening?

Can listeners reliably identify their preferred amplification profiles for speech listening?

Seedling stage salt stress response specific characterization of genetic polymorphism and validation of SSR markers in rice.

Salt tolerance status at early seedling stage in 30 rice varieties including two tolerant (Pokkali and CSR-36) and two susceptible (IR-29 and IR-64) checks was assessed under different levels of salinity (0, 4, 8 and 16dSm-1) created by salt mixture of NaCl, CaCl2, Na2SO4 in 7:2:1 ratio. Overall salinity tolerance indices clearly reflected that 17 varieties including the two tolerant checks were highly tolerant, seven varieties exhibited moderately tolerant, whereas six varieties including the two susceptible checks had highly susceptible response to salt stress. Molecular profiling of 13 tolerant and 5 susceptible rice varieties by using 24 SSR markers revealed 8.5 alleles per primer with altogether 114 shared and 91 unique allelic variants. Considering the allele number, polymorphism information content and polymorphism percent, SSR primers RM 302, RM 8094, RM 10665, RM 10694, RM 10748 and RM 10825 appeared to be highly polymorphic and comparatively more informative. Hierarchical classification and spatial distribution patterns based on amplification profiles dependent similarity indices unambiguously discriminated these 18 varieties in accordance with their salt tolerance response. Sequential exclusion of primers in further analysis led to validation of RM 140, RM 1287, RM 3412, RM 10745, RM 10764 and RM 10772 for their efficiency to distinguish salt tolerant varieties from susceptible ones. A specific combination of either four (RM 1287, RM 3412, RM 10764 and RM 10772) or even two markers (RM 1287 and RM 3412) also seemed to be equally effective in discrimination of entries according to their salt stress responsiveness. Principal coordinate analysis completely corroborated hierarchical classification of the varieties. Salt tolerance donors identified and SSR primers validated in the present study may be further utilized in the development of salt stress tolerant varieties of rice.

Assessment of genetic stability in somatic embryo derived plantlets of Pterocarpus marsupium Roxb. using inter-simple sequence repeat analysis.

An efficient plantlet regeneration protocol using immature zygotic embryos (IZEs) via somatic embryogenesis has been developed in Pterocarpus marsupium Roxb. The regenerated plantlets were evaluated for their genetic stability. IZEs were incubated on Murashige and Skoog (MS) media augmented with 1.07-16.11μM naphthalene acetic acid (NAA) or 0.90-13.97μM 2,4-dichlorophenoxyacetic acid. The optimum callus induction (96.6%) was observed on MS medium augmented with 5.37μM NAA. Induction of somatic embryos (SEs) was observed after sub-culture of callion medium with decreased concentrations of NAA (0.54-5.37μM), either alone or 2.69μM NAA in combination with 2.22-8.90μM benzyladenine (BA) or 2.32-9.30μM Kinetin. Maximum number (33.4 ± 0.85) of SEs occurred on MS medium augmented with 2.69μM NAA + 4.40μM BA + 3% sucrose. Highest percentage (67.3 ± 0.37) of SEs matured and developed into cotyledonary stage by subsequent subculture on the same medium. SE formation and maturation decreased when sucrose concentrations were higher than 3%. Seventy percent of mature somatic embryos developed into plantlets on half strength MS medium augmented with 5.80µM gibberellic acid. The various stages of development during somatic embryogenesis includeglobular, heart, torpedo and mature stages as revealed by thestereomicroscopic and histological studies of explants. Plantlets derived from SEs were successfully acclimatized in the greenhouse with a survival rate of 78%. Among the survived plantlets, 9 plantlets were randomly selected for inter-simple sequence repeat (ISSR) analysis. Of the 13 primers used, 8 produced reproducible and monomorphic bands. ISSR analysis revealed a homogenous amplification profile for all regenerated plantlets analyzed validating the genetic stability of somatic embryo derived plantlets.

Evaluation of the BRCAness phenotype and its correlations with clinicopathological features in triple-negative breast cancers

Some sporadic triple-negative breast cancers (TNBCs) share similar clinicopathological and molecular characteristics to BRCA1/2-mutant breast cancers, a phenotype described as "BRCAness." Identifying BRCAness in TNBCs could expand the target group for platinum salts and poly(adenosine diphosphate-ribose) polymerase inhibitors. The aims of our study were to assess the clinical validity of BRCA1/2 promoter methylation and BRCA1-like genomic profile to identify BRCAness and to evaluate its correlations with clinicopathological features in TNBCs. Formalin-fixed, paraffin-embedded tissues and fresh tissues of 151 primary invasive TNBCs were collected. BRCA1/2 promoter methylation and BRCA1-like genomic profile were detected using methylation-specific multiplex ligation-dependent probe amplification and multiplex ligation-dependent probe amplification assay, respectively. BRCA1/2 messenger RNA expression was evaluated by quantitative reverse-transcription polymerase chain reaction. Of the 151 patients, 38 (25.2%) showed BRCA1 promoter methylation. Of the 124, 52 (41.9%) had a BRCA1-like multiplex ligation-dependent probe amplification profile. The frequency of BRCAness phenotype was 54.8% (68/124). BRCA1 germline mutation and BRCA1 promoter methylation were mutually exclusive (P = .002). The BRCAness phenotype was significantly associated with large tumor size (>2 cm, P = .009), positive lymph nodes (P = .008), grade 3 tumor (P = .0001), high Ki-67 levels (P = .001), and basal-like breast cancers (P = .0001). Combined detections of BRCA1 promoter methylation and BRCA1-like genomic profile could identify more BRCAness cases in TNBCs. BRCA1 promoter methylation might rule out BRCA1 germline mutation in TNBCs. BRCAness was associated with aggressive clinicopathological features. These findings might have clinical values in hereditary breast cancer screening and target treatment of TNBCs.

Large-scale propagation of Myrobolan (Prunus cerasifera) in RITA® bioreactors and ISSR-based assessment of genetic conformity

An efficient protocol for the micropropagation of Prunus cerasifera using temporary immersion bioreactors was described. One-node cuttings excised from field-grown plants were successfully disinfected using 12% sodium hypochlorite for 10 min. Immersion duration, frequency and medium composition in Bioreactors type RITA® were evaluated. A high multiplication rate was obtained using RITA® bioreactors containing Murashige and Skoog’s medium (MS) supplemented with 1 mg L−1 N6-benzyladenine (BAP) and 1 mg L−1 indole-3-butyric acid (IBA) with 20 min/12 h as immersion time. RITA®-derived shoots were found to be more vigorous than those regenerated using the standard procedure. Higher levels of photosynthetic pigments were observed in shoots cultured in bioreactors, during the proliferation and rooting stages, which proved a certain degree of photoautotrophy of RITA®-derived vitroplants. A high proportion of shoots was successfully rooted in an MS liquid medium supplemented with 1 g L−1 activated charcoal in RITA® bioreactors. During plant acclimatization, survival rates exceeding 80% were recorded. The genetic fidelity of micropropagated plants was investigated using inter simple sequence repeat (ISSR) markers. Results proved the generation of homogenous amplification profiles and thus supported the clonal fidelity of regenerated vitroplants.

A pilot study for an innovative approach highlighting Actin and COI mRNAs as potential biomarkers of quality of the edible crustacean Nephrops norvegicus (Linnaeus, 1758)

Widely appreciated in gastronomy, many harvested and farmed Crustacean species are a great economic resource in the fishery business, throughout the world. Factors like pollutants and/or improper management in on-board/on-shore practices may adversely affect their edible quality and shelf-life. Recent studies from applied scientific research have been supporting the fishing industry and trading companies, in order to improve post-harvest practices and offer a safe and competitive product of high quality. Here, we developed an innovative molecular approach to get basic information on crustacean quality by using the European lobster Nephrops norvegicus (Linnaeus, 1758). For the first time, we investigated muscle-exudates of thawed lobsters for the presence of nucleic acids and analysed mRNA targets selected at NCBI to test their potential use as biomarkers of quality in frozen-thawed seafood. By RT-PCRs and sequencing we validated small amplicons of Actin, Cytochrome oxidase subunit 1 (COI), Calpain M, Prophenoloxidase (ppo) and Crustin-like antimicrobial peptide. In comparative One Step RT-PCR and/or One Step RT-qPCR assays, we analysed their amplification profiles at 1, 4 and 7 days after thawing (a.t.), in lobsters maintained to checked temperatures from capture. Based on amplification efficiency (AE), inversely correlated to the time after thawing and loss of RNA targets integrity, we identified new highly sensitive, species specific early indicators of quality. Our results highlight the advantage of using amplicons from exudates in different food science applications including authenticity/traceability, and provide new insights for the development of scientific tools applicable to crustacean quality monitoring on industrial-scale.

Mutator-Based Transposon Display: A Genetic Tool for Evolutionary and Crop-Improvement Studies in Maize.

Transposable elements account for up to 85% of the maize genome and have significant implications in crop-improvement and evolutionary analyses. The Mutator (Mu) transposon superfamily, a class of DNA transposons, comprises the most complex and active elements in the maize genome, suggesting a special role in plant evolution. Here, we designed a set of Mu-specific primers based on terminal invert repeats and used a transposon display (TD) method for genotyping. We analyzed the distribution pattern of Mu insertions in teosinte (wild relative), sorghum (distant relative), and domesticated maize accessions (dent, sweet, and waxy). The MU-TD analysis suggested the presence of high polymorphic insertions among the species and subspecies, indicating the utility of the method in studying genetic variation and species relationships. Furthermore, we analyzed 80 maize recombinant inbred line populations. Mu-TD generated an average of 60% Mu-anchored polymorphic fragments in which insertions appeared to be segregating in significantly high numbers. The amplification profile was highly reproducible, confirming the utility of Mu elements as a new set of TD markers for developing high-density genetic maps.

Analysis of genetic diversity of passion fruit (Passiflora edulis Sims) genotypes grown in Kenya by sequence-related amplified polymorphism (SRAP) markers

Abstract Passion fruit (Passiflora edulis [Sims]) is currently ranked third among fruit exports from Kenya and has great potential since demand for both fresh fruit and processed juice is on a continuous increase. Although assessment of genetic variability of germplasm is indispensable for improvement and development of superior cultivars, little information is available on the genetic diversity of passion fruit cultivated in Kenya. The objective of this study was to determine the genetic diversity of passion fruit genotypes from major growing regions in Kenya using sequence-related amplified polymorphism (SRAP) markers. Twenty four SRAP primer combinations were screened using three passion fruit genotypes and only seven that displayed polymorphic and stable amplification profiles were used to analyze 22 genotypes. The seven primer combinations amplified a total of 931 clear bands with an average of 133 bands per primer pair, of which 610 (65.5%) bands were polymorphic. The similarity coefficients among the 22 passion fruit germplasms ranged from 0.51 to 1.0 with an average of 0.755. The 22 passion fruit genotypes were classified into two groups by cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) with 12% similarity. Shannon's diversity index was 0.0934 and Nei's gene diversity index was 0.1370 in the present study. The study findings demonstrate the existence of a considerable amount of genetic variability among passion fruit genotypes grown in different regions of Kenya. This indicates the potential application of these genotypes in breeding programs by exploiting the use of molecular markers for selection of specific agronomic traits.

Prognostic stratification of adult primary glioblastoma multiforme patients based on their tumor gene amplification profiles.

Several classification systems have been proposed to address genomic heterogeneity of glioblastoma multiforme, but they either showed limited prognostic value and/or are difficult to implement in routine diagnostics. Here we propose a prognostic stratification model for these primary tumors based on tumor gene amplification profiles, that might be easily implemented in routine diagnostics, and potentially improve the patients management. Gene amplification profiles were prospectively evaluated in 80 primary glioblastoma multiforme tumors using single-nucleotide polymorphism arrays and the results obtained validated in publicly available data from 267/347 cases. Gene amplification was detected in 45% of patients, and chromosome 7p11.2 including the EGFR gene, was the most frequently amplified chromosomal region – either alone (18%) or in combination with amplification of DNA sequences in other chromosomal regions (10% of cases). Other frequently amplified DNA sequences included regions in chromosomes 12q(10%), 4q12(7%) and 1q32.1(4%). Based on their gene amplification profiles, glioblastomas were subdivided into: i) tumors with no gene amplification (55%); ii) tumors with chromosome 7p/EGFR gene amplification (with or without amplification of other chromosomal regions) (38%); and iii) glioblastoma multiforme with a single (11%) or multiple (6%) amplified DNA sequences in chromosomal regions other than chromosome 7p. From the prognostic point of view, these amplification profiles showed a significant impact on overall survival of glioblastoma multiforme patients (p>0.001). Based on these gene amplification profiles, a risk-stratification scoring system was built for prognostic stratification of glioblastoma which might be easily implemented in routine diagnostics, and potentially contribute to improved patient management.

Morpho-genetic Characterization of Traditional Aromatic Tulaipanji Rice of North Bengal, India

Tulaipanji is a non-Basmati type aromatic rice landrace of old alluvial region of North Bengal in eastern part of India, which is presently cultivated in about 7,000 ha. land with production of 14,000–15,000 tonnes paddy every year. With a view to develop the phenotypic and genetic database of the unique variety, its agro-morphological characterization was done at ‘C’ Block Farm, B.C.K.V., Kalyani, West Bengal during kharif (wet) season of 2011, 2012 and 2013 following the DUS test guidelines of Protection of Plant Varieties and Farmers’ Rights Authority (PPV&FRA). The variety had late heading (110–115 days) and late maturity (140–150 days), which produced long statured plants (125–135 cm height) with no anthocyanin colouration on leaf blade, sheath, nodes and internodes. The flower was bi-sexual including six yellow coloured anthers, and an ovary with white or yellowish-white feathery stigma. The lemma and palea were straw in colour with long awns (mean length 17.3 mm), and the grains were short in length (7.5 mm) with low test weight (15.6 g). The kernels were medium-slender (length 5.27 mm and width 1.91 mm) in shape and white in colour, which had low amylose content (17.2%), medium gelatinization temperature (alkali value 4.3) and medium aroma. 23 simple sequence repeat (SSR) markers were used for DNA amplification profile to develop molecular base-pair length database of Tulaipanji rice against non-aromatic international check variety IR 36 in the study. Among them, one marker (RM 182) recorded similar molecular weights for both the varieties, while two markers (RM 207 and RM 339) made greater genetic distances between Tulaipanji and IR 36 (75.82 vs. 128.48 bp and 182.76 vs. 143.09 bp, respectively).

Potential of random amplified microsatellites (RAMS) to typify and discriminate varieties of Physalis ixocarpa Brot. ex Hornem.

Physalis ixocarpa is an edible species of Solanaceae. This is one of the few cultivated and economically important species of the genus in Mesoamerica. In Mexico, several varieties and landraces have been developed, which have not been molecularly characterized. In the current study, five RAMS primers were used to characterize and assess the genetic variability of two varieties and three landraces of this species. The capacity of these markers to discriminate between them was also evaluated. With comparative aims, Physalis peruviana, the most economically important species of the genus in South America, was analyzed in the same manner. The results revealed that the varieties and landraces of P. ixocarpa conserve important levels of genetic variability (21.75% &gt; Polymorphism &lt; 42.75%), which were higher than that found for P. peruviana (10.75% Polymorphism). RAMS were useful specific markers, as P. peruviana and P. ixocarpa were clearly distinguished one from each other by both cluster analysis and principal components analysis. Close genetic relationships were found between the landraces San Isidro Chihuiro and Verde Puebla, and between the varieties Diamante and Rendidora. In spite of the genetic closeness, the RAMS amplification profiles had a clear varietal-specific tendency, in such a way that they may represent varietal fingerprints, which can be used as authentication tool for varieties and landraces of P. ixocarpa.

Mutagenic effects of spent potliner and derivatives on Allium cepa L. and Lactuca sativa L.: A molecular approach

Spent potliner (SPL) is a solid residue generated by the aluminum industry. Its composition is variable and complex, containing fluoride and cyanide salts as well as aluminum, which contributes to its toxicity. SPL is sometimes released directly into the soil, where it is prone to leaching and has the potential to cause alterations and damage to DNA. Considering that polymorphism analysis of simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) DNA markers is an interesting tool to determine the mutagenicity of an environmental pollutant, the present study adopted this approach to verify the mutagenic potential of SPL and its main toxic components (aluminum, fluoride, and cyanide) on root tip cells of Lactuca sativa and Allium cepa. Alterations in ISSR and SSR regions were identified by DNA fingerprinting (gain and loss of bands and changes in band intensity). The estimated dissimilarities indicated differences between treatments and the negative control. Furthermore, the relationship between the amplification profile of the markers and alterations in cell mitosis was discussed.

Comparison of the phenolic contents and epigenetic and genetic variability of wild and cultivated watercress ( Rorippa nasturtium var. aquaticum L.)

Background: Epigenetic modifications are key factors modulating the expression of genes involved in the synthesis of phytochemicals. The knowledge of plant epigenetic and genetic variations can contribute to enhance the production of bioactive compounds. These issues have been little explored thus far in Rorippa nasturtium var. aquaticum L. (watercress), an edible and medicinal plant. The aim of the current study was to determine and compare the phenolic composition and epigenetic and genetic variations between wild and cultivated watercress. Results: Significant differences were found in the quantitative phenolic composition between wild and cultivated watercress. The eight primer combinations used in the methylation-sensitive amplification polymorphism (MSAP) method revealed different epigenetic status for each watercress type, the cultivated one being the most epigenetically variable. The genetic variability revealed by the EcoRI/MspI amplification profile and also by eight inter-simple sequence repeat (ISSR) primers was different between the two types of watercress. The results of the Mantel test showed that the correlation between genetic and epigenetic variations has diminished in the cultivated type. Cluster analyses showed that the epigenetic and genetic characterizations clearly discriminated between wild and cultivated watercress. Conclusions: Relevant chemical, epigenetic, and genetic differences have emerged between wild and cultivated watercress. These differences can contribute to fingerprint and develop quality control tools for the integral and safety use and the commercialization of watercress. The richness of epialleles could support the development of tools to manipulate the watercress epigenome to develop high bioproduct-producing cultivars.