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Type 2 diabetes (T2DM) is a group of chronic and systemic metabolic diseases. Nephropathy (NP) and neuropathy (NR) are two common complications that severely affect the quality of life of patients with T2DM. In this study, our aim was to investigate the association between TNF-alpha (-308) gene polymorphism and the risk of developing NP and NR in patients with T2DM We also aimed to determine the association between TNF-alpha (-308) gene polymorphism and several demographic characteristics and biochemical parameters of patients with T2DM developed NP and/or NR. First, blood samples of patients were collected, and DNA isolation was performed. Then, real-time PCR analysis was used for genotyping the TNF-α (-308) gene utilising fluorescently labelled probes. Patients' demographical data and biochemical parameters were also obtained. Our study did not detect any significant difference in the frequency of possessing the gene polymorphism (A allele) between the groups. Additionally, no significant difference was detected when the data on various biochemical parameters were evaluated in GG, GA, and AA genotypes. [ABSTRACT FROM AUTHOR]

Aedes aegypti and Aedes albopictus mosquitoes spread major vector-borne viral diseases in tropical and sub-tropical regions of the globe. In this study, we sequenced the genome of Indian Ae. aegypti and Ae. albopictus and mapped to their reference genomes. Comparative genomics were performed between our strain and the reference strains. A total of 14,416,484 single nucleotide polymorphisms (SNPs) and 156,487 insertions and deletions (InDels) were found in Ae. aegypti, and 28,940,433 SNPs and 188,987 InDels in Ae. albopictus. Particular emphasis was given to gene families involved in mosquito digestion, development, and innate immunity, which could be putative candidates for vector control. Serine protease cascades and their inhibitors called serpins, play a central role in these processes. We extracted high-impact variants in genes associated with serine proteases and serpins. This study reports for the first time a high coverage genome sequence data of an Indian Ae. albopictus mosquito. The results from this study will provide insights into Indian Aedes specific polymorphisms and the evolution of immune related genes in mosquitoes, which can serve as a resource for future comparative genomics and those pursuing the development of targeted biopesticides for effective mosquito control strategies. [ABSTRACT FROM AUTHOR]

Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations. [ABSTRACT FROM AUTHOR]

The genetic diversity of Pacific rainbow smelt Osmerus dentex from the seas of Okhotsk and Japan has been studied based on nine microsatellite loci and the control region of mitochondrial DNA (940 base pairs). The lowest values of all parameters of genetic diversity of mitochondrial DNA were observed in the group of samples from the northern coast of the Sea of Okhotsk. The highest value of the haplotype diversity was found in the sample from the Sakhalin Island and in rainbow smelt from the Sea of Japan. The star-shaped topology of the genealogical structures indicates a rapid expansion of the abundance and the origin of all populations of the species from a single common ancestor from the main refugium. Based on the results of analysis of nuclear markers, we have revealed a statistically significant genetic structuring of rainbow smelt within its Pacific range (the coefficient of genetic differentiation (FST) is 0.033), which is adequately described by the model of isolation by distance. The greatest genetic differences in two types of markers from the other samples have been found in rainbow smelt from the Shkotovka and Botchi rivers of the basin of the Sea of Japan and from the Naiba River (Sakhalin). The observed patterns of genetic differentiation of Pacific rainbow smelt by the nuclear and mitochondrial markers complement each other well and are most likely associated with differences in the distribution of smelt larvae from the spawning grounds, which are determined by the differentiation of oceanographic conditions. [ABSTRACT FROM AUTHOR]

Background: Ryegrass is a promising crop for the development of meadow farming in the world. More than 1000 cultivated varieties widely used in feed production have been developed, based on the main species — perennial ryegrass (Lolium perenne L.) and annual one (Lolium multiflorum Lam.). Development and implementation of the modern methods of plant varietal and species identification are of great importance. In recent years, molecular markers have been successfully used for these purposes, which increase the accuracy of the breeding material evaluation at a significant reduction of time and labor costs. The aim of this study was to assess the discriminatory potential of the new SCoT marking technique for the identification of Russian perennial (Lolium perenne L.) and annual (Lolium multiflorum Lam.) ryegrass varieties. Results: Out of the total number of the tested SCoT-primers, 8 polymorphic ones were selected, which demonstrates the high stability and reproducibly amplified DNA fragments. These primers generated 107 PCR products, where 37 were found to be polymorphic. The average number of amplicons per primer was 13. The size of the PCR products varied from 349 to 2718 bp (see Table 3). The polymorphic ratio of the tested markers was 30.8%. The marker SCoT-06 was characterized by the maximum number of PCR products and the highest level of polymorphism (50%). The effective number of alleles (ne) ranged from 1.35 to 1.58 with a mean of 1.48 per locus. The average value of the PIC and Shannon index (I) were 0.35 and 0.46, respectively. The unique PCR fragments were revealed for the identification of tested varieties. Analysis of molecular variance (AMOVA) showed that the level of genetic diversity between ryegrass species (59%) was more than between varieties within a species (41%). Based on binary matrix data, clustering and PCoA analysis (see Figs. 1 and 2) of the samples were carried out that divided them into two groups according to species. Conclusions: We found a set of markers that can be useful tools for ryegrass varieties identification. The level of intravarietal polymorphism turned out to be higher than the differences between varieties because of the possible significant heterogeneity of the varietal material. The information obtained can be used in breeding programs to create improved ryegrass varieties adapted to Russian climatic conditions. [ABSTRACT FROM AUTHOR]

Rice is one of staple food crops in the world. Improving the drought tolerance of rice has become an important issue for maintaining or increasing its grain production under water stress caused by the greenhouse effect. For achieving this goal, quantitative trait loci (QTL) mapping is considered to be useful in plant breeding. In this study, a doubled-haploid (DH) population was used as elite materials. Based on results of polymorphism detection, 108 polymorphic markers were identified. The mapping analysis results indicated that 40 QTLs putatively associated with seven traits were found in nine linkage groups. [ABSTRACT FROM AUTHOR]

An efficacious and reproducible in vitro regeneration technique for safflower was established using varying concentrations and composition of plant growth regulators (PGRs) supplemented Murashige and Skoog (MS) medium. Successful in vitro seed germination in half strength MS (H-MS) with 1.4 µM GA3 resulted in procurement of sterile explants (cotyledons, apical meristems) for in vitro study. Callogenesis (2.2 µM BAP + 2.7 µM NAA), indirect organogenesis of shoot buds (0.54 µM NAA + 9.08 µM TDZ), somatic embryogenesis (2.2 µM BAP + 5.4 µM NAA) and somatic embryo germinated plantlets (H-MS + 1.4 µM GA3 + 2.2 µM BAP + 5.4 µM NAA) were successfully obtained. Histological study and scanning electron micrographs of embryogenic callus revealed pre-globular, heart-shaped and torpedo stages of dicot embryogeny. H-MS + 8 µM NAA showed maximum rhizogenic response with a mean root and shoot length of 17.5 mm and 48.50 mm respectively in 2.2 µM BAP + 0.54 µM NAA bearing an average of 9 capitula per plantlet with 70% post transplantation survival rate. True to type nature of the regenerates was confirmed using Start Codon Targeted (SCoT) marker, exhibiting 100% and 97.3% monomorphic bands for direct and somatic embryo regenerated plants respectively. Flow cytometry method (FCM) was employed for 2C DNA content analysis. The histogram peaks of 2C nuclear DNA content of in vitro regenerated safflower (direct and embryo derived) were similar to the peak of field grown donor plant. 2C nuclear DNA content of field grown, direct and somatic embryo regenerated C. tinctorius was 2.65 ± 0.04 pg, 2.62 ± 0.06 pg and 2.68 ± 0.04 pg respectively, further verifying genetic homogeneity. All things considered, the above protocol is insusceptible to genetic alteration and can be used for large scale production and sustainable utilization of desired genotype. Key message: An efficient, reproducible in vitro regeneration protocol was achieved for safflower via direct, callus mediated organogenesis and somatic embryogenesis. Histology and SEM study revealed typical dicot embryogenic stages. SCoT molecular marker and flow cytometric 2C genome size analysis were further applied for evaluating genetic fidelity of in vitro regenerated safflower. [ABSTRACT FROM AUTHOR]

We attempted to conduct an intraspecific analysis of 30 peony cultivars in Japan and to authenticate five herbal medicine samples derived from Paeoniae Radix by polymorphism analysis of the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) gene region. We focused on cultivar-dependent differences in leaf margin undulation and analyzed the sequence of the related TCP gene region. As a result, we found that the nucleotide sequences of 29 cultivars of Paeonia lactiflora except 'America' exhibit interspecific variations compared with the nucleotide sequences of Paeonia suffruticosa and Paeonia tenuifolia. Therefore, in the dendrogram constructed on the basis of the sequence similarity in the TCP gene region, the 29 cultivars of P. lactiflora were separated from P. suffruticosa, P. tenuifolia, and 'America', and clustered into three subgroups. There were 16 variations containing heterogenous DNA sequences within P. lactiflora species, and two characteristic variations in subgroup I. Some P. lactiflora cultivars showed the same nucleotide sequence in the TCP gene region, whereas the five herbal medicine samples showed different sequences, although all of them could be authenticated. The results suggest that Paeoniae Radix in the Japanese crude drug market can be authenticated by analysis of the TCP gene region. [ABSTRACT FROM AUTHOR]

Citrus unshiu Marc. cv. Miyagawa-wase is the most widely cultivated citrus variety in Korea. To determine whether the C. unshiu genome used in this study shows genetic variation compared to the published reference genome (C. unshiu Marc. Miyagawa-wase), we conducted genome re-sequencing of two C. unshiu cultivars (Miyagawa-1 and Miyagawa-2) cultivated on Jeju in Korea. Compared with the reference genome, 1,198,650 and 1,207,084 single-nucleotide polymorphisms (SNPs) and 172,259 and 172,391 insertion/deletion polymorphisms (InDels) were detected in the Miyagawa-1 and -2 genomes, respectively. In SNP and InDel classifications by genome annotation, 367,591 and 369,068 SNPs and 45,362 and 45,464 InDels were located in the genic regions of Miyagawa-1 and -2, respectively. Among the SNPs of Miyagawa-1 and -2, transitions were more frequent than transversions. The majority of InDels was distributed in 1-bp InDels in both cultivars. The comparative number of total SNPs between Miyagawa-1 and -2 was smaller than the number of SNPs between the reference genome and Miyagawa-1 or -2. Gene ontology (GO) analysis showed that 23,164 and 23,049 genes with SNPs and 16,830 and 16,774 genes with InDels were annotated in the GO database. Taken together, Miyagawa-1 and -2 show genome-wide variation, including SNPs and InDels, compared to the published C. unshiu Marc. cv. Miyagawa-wase genome. This study suggests it would be more accurate to use the Miyagawa-1 and -2 genome sequences as a reference when conducting research using C. unshiu cultivated in Korea. [ABSTRACT FROM AUTHOR]

Cajanus cajan (L.) Millsp. is an important legume crop that grows in semiarid tropic continents such as Asia, South America and Africa. Sub-Saharan African countries, particularly Nigeria, have to achieve food, crop and nutrition security, because the population faces hunger and malnutrition. Thus, to mitigate these challenges, developing and improving landraces of crop plants is essential. Improving the cultivation and breeding of grain legumes, especially Cajanus cajan (pigeon pea), is an option, given the drought-tolerant nature of the crop. An ecological imbalance has led to a decreasing natural population of C. cajan, thereby creating a potential decrease in genetic diversity. In this study, genetic markers (matK, ITS and PetB) were used to identify a series of single nucleotide polymorphisms (SNPs), selection types, haplotypes and traced evolutionary lineage within C. cajan accessions. We noted the detection of these SNPs among the molecular markers reflecting the origin of the crop plant, thus detecting shared haplotype for ITS and unshared haplotypes for matK and PetB. This study provides insight on the genetic diversity of C. cajan and useful in identifying genetic fingerprints that correlate with other properties of C. cajan, and thus, which could assist in preventing loss of diversity. [ABSTRACT FROM AUTHOR]

This study was carried out to estimate the genetic diversity between cultivars of alfalfa using SRAP marker system (sequence-related amplified polymorphism). We tested 25 combinations of SRAP markers and revealed that seven of them were informative for DNA polymorphism identification. These combinations generated 129 PCR products with the percentage of polymorphic bands per pair ranging from 21 to 50%. Specific amplification products were identified for 14 cultivars for genetic certification. [ABSTRACT FROM AUTHOR]

The aim of the study was an identification of PGLYRP1 gene polymorphism in Polish Holstein-Friesian (PHF) cattle with relation to both productivity and health traits. PCR-RFLP method was used to identify T254C substitution in PGLYRP1 gene (Tyr76His; dbSNP ID: ss104796364). The frequencies of geno-types analyzed were: PGLYRP1TT = 0.41, PGLYRP1CT = 0.50 and PGLYRP1CC = 0.09. In our study cows with rare PGLYRP1CC genotype produced more milk and protein (kg) than PGLYRP1CT ones, but only in the first lactation. Concerning culling reasons and morbidity with respect to the PGLYRP1 genotypes showed that cows with PGLYRP1CC genotype are the most resistant to infectious diseases (no infectious disease reported). In case of PGLYRP1CT and PGLYRP1TT cows, the percentage of sick individuals were ~50% in the period studied. To confirm this observation, further researches in different breeds of dairy cattle are required. [ABSTRACT FROM AUTHOR]

Basal cell carcinoma (BCC) is the most prevalent human neoplasm, with constantly increasing annual incidence. Despite its slow growth, BCC is locally invasive and, if left untreated, can cause severe complications, including metastasis and death. The renin-angiotensin system (RAS) plays a key role in electrolyte balance, atrial pressure, tissue development, homeostasis, and inflammation, but also in cancer development. After binding to its type 1 receptor (AT1R), angiotensin II (ANGII), the system's principal hormonal effector, regulates cancer pathways spanning from the formation of the initial cancer cell to the construction and nutrition of the tumor microenvironment, angiogenesis, proliferation, and metastasis. Although the role of RAS in the development of skin pathologies has not been widely researched, RAS-targeting antihypertensive medications have been shown to have a chemoprotective effect against BCC. Based on those findings, our group conducted a series of genetic association studies to investigate the association between common functional variations in key genes related to ANGII production (AGT, ACE, ACE2, AT1R, AT2R, and CMA1) and the risk of BCC occurrence. This review provides a summary of the current understanding of the ANGII involvement in BCC development. The reliable and easily assessed pool of genetic biomarkers may be used for predictive testing and prevention purposes in high-risk individuals. [ABSTRACT FROM AUTHOR]

Sea buckthorn (Hippophae rhamnoides L.) is a perennial dioecious shrub or tree whose juvenile period lasts from 3 to 5 years. Sea buckthorn grows in many European and Asian countries and is widely used in cosmetology, biotechnology, pharmacology, and agriculture. This crop is a source of valuable vitamins, minerals, carotenoids, and flavonoids. Its phenotypic description does not provide accurate characteristics of a taxon at the species, subspecies, variety, and population levels; therefore, one should use molecular analysis. For this study, a collection of sea buckthorn samples of different ecological and geographical origin, which consisted from herbarium samples and samples harvested in natural populations, was prepared. ISSR markers efficiently revealing genotypic difference between the samples were selected, and binary matrices were created for the further dendrogram construction. The performed analysis revealed a high level of intraspecific polymorphism and showed that samples of a similar ecological and geographical origin tended to group into clusters and were located at different genetic distance. The results of the study can be used to evaluate the diversity of forms of this crop, relations between them, their ecological and geographical origin, and the evolution of certain taxa. These results may also be used for a genetic passportization and identification of varieties prior to them reaching the generative period and for the pair selection for crossing. [ABSTRACT FROM AUTHOR]

The published data indicate that the bacterium Clavibacter michiganensis subsp. sepedonicus (Cms) shows a notably low degree of intraspecific variation, and most of the molecular diagnostic methods could differentiate among subspecies groups but lacked the resolution to detect genetic diversity within subspecies. The present study describes effective differentiation of 50 isolates of C. michiganensis subsp. sepedonicus by the PCR MP method using five restriction enzymes (ApaI, PstI, BamHI, XmaI, HindIII). By analysing the electrophoretic patterns obtained by the PCR MP method performed with the applied restriction enzymes, each of the 50 tested isolates could be identified and distinguished from the remaining isolates. The PCR MP method of bacterial strain identification can be used in epidemiological studies, particularly for excluding the isolates of C. michiganensis subsp. sepedonicus as a source of primary infection. [ABSTRACT FROM AUTHOR]

Thidiazuron (TDZ) is a proven effective and potent synthetic plant growth regulator for organogenic, regeneration, and developmental pathways, including axillary and adventitious shoot proliferation, somatic embryogenesis, and in vitro flowering. TDZ has facilitated the establishment of in vitro cultures for several plant species, especially woody and recalcitrant plants, which has enabled their genetic transformation and improvement. Despite the effectiveness and advantages of using TDZ, several drawbacks are associated with its application in plant tissue culture. This review addresses the morphological, physiological, and cytogenetic abnormalities associated with the use of TDZ in vitro, and provides a summary of these abnormalities in several plant species. [ABSTRACT FROM AUTHOR]

It was found that food preferences and conditions of breeding of Habrobracon hebetor laboratory populations vary considerably. In this regard, it is necessary to identify populations within the studied species using DNA markers: an effective and reliable means for assessing the genetic differences between samplings of this insect species. A molecular genetic analysis of two different geographic populations of the Habrobracon hebetor entomophage (from Krasnodar, Russia, and Chimkent, Kazakhstan) was carried out using RAPD markers; 21 RAPD primers were tested for specificity to H. hebetor DNA. Five RAPD primers (OPA05, OPA10, OPB01, OPB04, and UBC519) were identified that have high specificity and the ability to differentiate H. hebetor populations. DNA markers that are specific for the Krasnodar and Chimkent entomophage populations and that can clearly identify them were revealed: for the Krasnodar population, RAPD markers with a molecular weight of 550 bp (UBC 519); 500 and 700 bp (OPA05); 1100, 1200, and 1300 bp (OPA10); 220 and 800 bp (OPB04); and 880 bp (OPB01); for the Chimkent population, 400, 600 and 1200 bp (UBC519); 600 and 950 bp (OPA10); and 800 bp (OPB01). It is concluded that these RAPD primers can be used for identification and differentiation of other H. hebetor populations. [ABSTRACT FROM AUTHOR]

A historical review of the advent and improvement of the methods for detecting multilocus DNA polymorphism that do not require preliminary knowledge of the individual gene and complete genome sequences of eukaryotes is presented. The first group of these methods includes approaches based on the use of primers with arbitrary sequence (random priming). Another group of methods to detect DNA polymorphism is based on the use of primers that consist of short repetitive sequences having anchor nucleotides at the 5'- or 3'-ends that position the annealing sites of these primers (microsatellite priming). Another approach for revealing polymorphism that does not require knowledge of the DNA sequence is based on cleavage of total DNA by a combination of restriction endonucleases (random cleavage) accompanied by PCR amplification. Considerable attention is paid to the opportunities of using these approaches to detect DNA polymorphism in the form of converting the obtained data to digital format and creation of integrative databases for all organisms, regardless of the methods used. [ABSTRACT FROM AUTHOR]

The genetic variation of seven genes in the carotenoid biosynthetic pathway was investigated in thirteen papaya cultivars. DNA analysis revealed a total of 46 polymorphisms; 42 SNPs (29 positions in introns and 13 positions in exons) and four insertions/deletions. Six SNPs were transversions resulting in amino acid changes. Most variations were found in cpLCYE (21), followed by cpVDE (10). In cpLCYB and cpNCED3, only one polymorphism was found in each gene. Expression studies indicated the differential expression of caroteogenic genes in red, orange and yellow-fleshed papaya during ripening. At ripe stage, the expression level of cpZEP, cpLYCE, cpVDE, cpLCYB and cpNCED3 was higher in red-fleshed than in orange- and yellow-fleshed papaya. The expression level of cpBCH in ripe red-fleshed papaya was significantly lower than that of both orange and yellow-fleshed papaya. Yellow-fleshed papaya cv. Krung Yellow had highest level of beta-carotene at 1428 ± 32 µg/g FW. Lycopene content of red-fleshed papaya cv. Mexico was 1830 ± 208 µg/g FW was highest among the three cultivars. This study revealed DNA polymorphisms in cartenogenic genes among papaya cultivars and their differential expressions in red, orange and yellow-fleshed papaya correlated with carotenoid content and flesh colour. [ABSTRACT FROM AUTHOR]

Till this day, there is not much known about the phylogeny of the Secale genus; therefore, in our research, we tried to shed some lights on the issue of rye ( Secale genus) taxonomy. The genetic diversity and phylogenetic relationships were evaluated using 13,842 DArTseq™ polymorphic markers. The model-based clustering (STRUCTURE software) separated our 84 samples into three main clusters: perennial cluster, annual cluster, and S. sylvestre cluster. The same result was obtained using Neighbour Joining tree and self-organizing maps. Secale sylvestre, S. strictum, and S. cereale are the three main species of the Secale genus. Three samples of rye are in basal positions in phylogenetic trees. These accessions share ancient morphological characters and are probably the ancestors of different lineages within Secale. Annual Secale taxa, with the exception of S. sylvestre, create one mutual taxon. We have found out that the semi-perennial taxa of S. cereale var. multicaule and S. strictum subsp. ciliatoglume are genetically closest to the annual species of S. cereale. Phylogenetic signals for semi-perennial and annual taxa are also present in S. strictum subsp. africanum. SNP-based analysis revealed that evolution of annual S. cereale has already begun in S. strictum subsp. africanum. The results showed that S. vavilovii cannot be considered as a separate species but a subspecies of S. cereale Secale cereale subsp. dighoricum is a hybrid. It is still not clear whether we can consider S. strictum subsp. strictum and S. strictum subsp. kuprijanovii as two separate species. [ABSTRACT FROM AUTHOR]

Universal RAPD primers (OPA02 and OPA07) have been revealed for ladybird beetles of the Coccinellidae family. Using these primers, comparative PCR analysis of ten different ladybird beetle species was conducted. It was shown that Harmonia axyridis beetle species had the highest level of DNA polymorphism and genetic diversity. The RAPD-PCR method for analysis of interspecies differences along with other molecular genetics methods can be used. [ABSTRACT FROM AUTHOR]

Primula veris L. (Primulaceae) is a long lived perennial and well known pharmaceutical plant, widely collected for these reasons in almost all SE Europe and particularly in Kosovo. The aim of the study is to determine molecular polymorphism of cowslip ( P. veris L.) populations from Kosovo. DNA extracted from leaves were investigated in details for presence of polymorphism. RAPD analyses were conducted using 20 different short primers. Genomic DNA amplification profiles were analyzed and processed using data labelling. Comparison between cowslip populations in genetic composition revealed that samples from Bogaj were too distinct on their own. Molecular variation was observed to be more within populations (73 %) as compared to among populations (27 %). On the other hand, genetic distance of populations revealed that the highest genetic distance is between Leqinat and Maja e Madhe. Mean values of expected heterozygosity were highest in Bogaj population, while lowest in Maja e Madhe population. The obtained results indicated that Bogaj population are more polymorphic. From the obtained data it can be concluded that RAPD markers provided a useful technique to study genetic diversity in P. veris L. populations. This technology allows identification and assessment of the genetic similarities and differences among plant populations. [ABSTRACT FROM AUTHOR]

Ethyl methanesulphonate (EMS) has been employed in a number of genotoxic studies in plants as a model alkylated agent that readily reacts with DNA-producing alkylated nucleotides. Therefore, the present study was aimed at assessing DNA polymorphism induced by different concentrations (control, 1, 2, 3, and 4%) of EMS through a Randomly Amplified Polymorphic DNA (RAPD) marker analysis. The improved agronomic traits such as germination, flowering, maturity, seed traits, and oil content were recorded in 1% EMS-treated plants, while the corresponding parameters reduced significantly ( P > 0.05) in 4% EMS-treated plants as compared to the control. Among 25 random primers used, 19 primers produced polymorphic bands. The number of amplicons varied from 1 to 8 with an average of 3.68 bands, of which 2.12 were polymorphic. The highest polymorphic bands (6) and percentage of polymorphism (85.71) were produced by the primer OPAK-20. In a dendrogram constructed based on Jaccard's coefficient similarity, the treated plants and control were grouped into three clusters: (a) control and 2 and 3% concentrations of EMS-treated plants merged together; (b) 1% concentration of EMS-treated plants clustered alone; (c) 4%concentration of EMS-treated plants also clustered alone. We conclude that the effect of EMS could change the pattern of germination, flowering, seed yield, and oil content of J. curcas. DNA polymorphism detected by RAPD marker analysis offered a useful biomarker assay for the evaluation of effects of chemical mutagens. [ABSTRACT FROM AUTHOR]

The identification of DNA polymorphisms associated to increased cell wall (CW) degradability could accelerate the development of alfalfa ( Medicago sativa L.) cultivars with superior ethanol conversion yields. Genotypes with high (D+) or low (D−) CW degradability were recently identified within a biomass-type and three winter-hardy-type populations using near-infrared reflectance spectroscopy (NIRS) prediction of CW glucose released by enzyme saccharification. In this report, we used sequence-related amplified polymorphism to search for DNA variations associated to differences in enzyme-released glucose. A bulk segregant analysis (BSA) of pooled DNA samples (20 plants/bulk) from D+, D−, and randomly chosen genotypes uncovered polymorphisms associated to CW degradability. Polymorphisms that increase or decrease in intensity between D+ and D− bulks indicated the presence of genomic regions with either positive or negative effects on CW degradability. A primer pair (Me4-R14) generated a fragment, which increased in intensity in the D+ bulk of the biomass-type population. Conversely, the amplification of that fragment declined in the D+ bulks of the winter-hardy-type populations. Interestingly, these populations differ in their degradability. Assessment of the genotypic occurrence of this fragment confirmed that polymorphism detected with BSA reflects changes in the frequency of occurrence within populations. Sequence analysis of the Me4-R14 fragment revealed homologies with sequences from Medicago truncatula, a model species for legumes with documented synteny with M. sativa. Our results show that genomic regions associated to CW degradability can be identified using the combination of BSA of genotypes with contrasted degradability and a PCR-based amplification technique. [ABSTRACT FROM AUTHOR]

Wild emmer wheat, Triticum turgidum subsp. dicoccoides, (2n = 4x = 28; genome BBAA), the progenitor of domesticated wheat, is genetically very close to durum and common wheat. This wild taxon has many characteristics that would be valuable if transferred to domesticated wheat. An appropriate exploitation of the 'wild' genome requires its dissection into segments and evaluation of the contribution of each segment separately to the performance of domesticated wheat. This work describes the production of a series of chromosome-arm substitution lines (CASLs) of wild emmer in the background of the Israeli common wheat cultivar Bethlehem (2n = 6x = 42; genome BBAADD). The identity of the 'wild' arm in each CASL was confirmed through the use of RFLP and SSR markers that were polymorphic between the two taxa. The product of this work is a series of true-breeding agronomic lines the breeding value of which can be evaluated under field conditions in different geographic regions. The usefulness of CASLs in studying the improvement of qualitative and quantitative traits in wheat is discussed. [ABSTRACT FROM AUTHOR]

Fusarium equiseti (Corda) Saccardo is a soil saprophyte and a weak pathogen, associated with several diseases of fruit and other crops in subtropical and tropical areas, but also in countries with temperate climate. A wide range of secondary metabolites has been identified among natural F. equiseti populations, with zearalenone (ZEA), fusarochromanone and fusarenon-X being the most common. In present study, the genetic diversity of strains from two populations (from Italy and Poland) was evaluated by analysing the translation elongation factor 1α ( tef-1α) sequences, two polyketide synthases from the ZEA biosynthetic pathway ( PKS13 and PKS4) and the TRI5 gene from the trichothecene biosynthetic pathway. ZEA was produced in rice cultures by 20 of the 27 tested isolates in concentrations ranging from 1.34 ng/g to 34,000 ng/g). The ability to produce enniatins and trichothecenes was evaluated in all strains by identifying esyn1, TRI13 and TRI4 genes. The presence of PKS4 and PKS13 genes was confirmed by polymerase chain reaction (PCR) in only some ZEA-producing isolates. Similarly, the TRI5 gene was found in 14 of the 27 isolates tested. This is likely to have been caused by the divergence of those genes between F. equiseti and F. graminearum (the latter species was used for the primers design) and can be exploited in phylogenetic studies. The analysis of the mycotoxin biosynthetic gene sequences can be used to differentiate the studied genotypes even more precisely than the analysis of the non-coding regions (like tef-1α). [ABSTRACT FROM AUTHOR]

Allele frequencies at six RFLP sites ( Ins/Del, ApaLI, AluI, XbaI, MspI, and EcoRI) of the apolipoprotein B gene ( APOB) and the relationship of genotypes with plasma lipid and lipoprotein levels in the Mongolian Buryat were investigated. Common alleles at these sites in 110 Buryat subjects were I, G, A−, X−, M+, and E+; the frequencies of 0.809-0.991 differed strikingly from those of a few Asians and most Europeans. Five unambiguous haplotypes of all sites were revealed at 74%; haplotype IGA− X− M+ E+ (000000) was the most frequent (67%), followed by IGA+ X− M+ E+ (001000) (19%). The frequency constitution differed significantly from the Chinese, Malaysians, and Caucasians but resembled the Indians. No APOB polymorphisms were associated with cholesterol levels (total, HDL and LDL). Significant associations of genotypes were shown with the triglyceride level only at the AluI and XbaI sites. The lipid level of A− A+ females or X− X+ males was higher than that of A− A− females or X− X− males, respectively. [ABSTRACT FROM AUTHOR]

Web blight, an important foliar disease of dry beans in the Americas, is a challenge to manage. We studied genetic variation of 92 isolates of Rhizoctonia solani subgroups AG-1-IE and AG-1-IF using DNA fingerprinting methods and mycelial compatibility grouping. The isolates were collected over 13 years from bean fields in the Dominican Republic, Honduras and Puerto Rico. Cluster and AMOVA analysis of combined data from two universal rice primers and two internal sequence repeats revealed significant genetic variation among and within populations of both subgroups. Variation was influenced by geographic origin and sampling year for AG-1-IE isolates and geographic origin for AG-1-IF isolates. Mycelial compatibility of paired isolates was mostly scored as incompatible in both subgroups and supported many unique phenotypes. Only two isolates of AG-1-IE displayed mycelial compatibility and DNA fingerprints, suggesting clonal origin. Genetic variation in these AG-1-IE and AG-1-IF isolate populations may explain the lack of durable resistance to web blight reported in dry beans. [ABSTRACT FROM AUTHOR]

The population-genetic processes leading to the genetic degeneration of non-recombining regions have mainly been studied in animal and plant sex chromosomes. Here, we report population genetic analysis of the processes in the non-recombining mating-type-specific regions of the smut fungus Microbotryum violaceum. M. violaceum has A1 and A2 mating types, determined by mating-type-specific 'sex chromosomes' that contain 1-2 Mb long non-recombining regions. If genetic degeneration were occurring, then one would expect reduced DNA polymorphism in the non-recombining regions of this fungus. The analysis of DNA diversity among 19 M. violaceum strains, collected across Europe from Silene latifolia flowers, revealed that (i) DNA polymorphism is relatively low in all 20 studied loci (π∼0.15%), (ii) it is not significantly different between the two mating-type-specific chromosomes nor between the non-recombining and recombining regions, (iii) there is substantial population structure in M. violaceum populations, which resembles that of its host species, S. latifolia, and (iv) there is significant linkage disequilibrium, suggesting that widespread selfing in this species results in a reduction of the effective recombination rate across the genome. We hypothesise that selfing-related reduction of recombination across the M. violaceum genome negates the difference in the level of DNA polymorphism between the recombining and non-recombining regions, and may possibly lead to similar levels of genetic degeneration in the mating-type-specific regions of the non-recombining 'sex chromosomes' and elsewhere in the genome. [ABSTRACT FROM AUTHOR]

α- and β-Galactosidases find application in food processing, health and nutrition. Aspergillus niger is one of the potent producer of these enzymes and was genotypically improved using gamma-ray induced mutagenesis. The mutant-derivative produced two-fold higher α- and β-galactosidases. For testing genetic variability and its relationship with phenotypic properties of the two organisms, DNA samples of the mutant and parental strains of A. niger were amplified with 28 deca-nucleotide synthetic primers. RAPD analysis showed significantly different pattern between parental and mutant cultures. The mutant derivative yielded homogeneous while parental strain formed heterogeneous amplification patterns. Seven primers identified 42.9% polymorphism in the amplification products, indicating that these primers determined some genetic variability between the two strains. Thus RAPD was found to be an efficient technique to determine genetic variability in the mutant and wild organisms. Both wild and mutant strains were analyzed for their potential to produce galactosidases. Comparison of different carbon sources on enzyme yield revealed that wheat bran is significant ( P < 0.01) effective producer and economical source followed by rice bran, rice polishing and lactose. The mutant was significantly better enzyme producer and could be considered for its prospective application in food, nutrition and health and that RAPD can be effectively used to differentiate mutant strain from the parental strain based on the RAPD patterns. [ABSTRACT FROM AUTHOR]

Smoking during pregnancy has been identified as one of the major modifiable risk factors of sudden infant death syndrome (SIDS). It has been demonstrated that the risk of SIDS increases with increasing cigarette consumption. A variety of hypotheses have been proposed for explanation, including a genetic predisposition. The flavin-monooxygenase 3 ( FMO3) is one of the enzymes metabolising nicotine, and several polymorphisms have already been described in this gene. Here, we studied variations in the exons and introns of the FMO3 gene by direct sequencing analysis and minisequencing in 159 SIDS cases and 170 controls. The three common variants G472A (E158K), G769A (V257M) and A923G (E308G) in the exons of the FMO3 gene were identified. The homozygote 472AA genotype occurred more frequently in SIDS cases than in controls ( p = 0.0054) and was more frequent in those SIDS cases for which the mothers reported heavy smoking ( p = 0.0084). This study is the first to demonstrate a gene–environment interaction in SIDS. The findings suggest that the common polymorphism G472A of FMO3 could act as an additional genetic SIDS risk factor in children whose mothers smoke. Parents who could pass on the 472A allele should be informed of the increased risk associated with smoking. Smoking mothers should be strongly advised to give up smoking during pregnancy and for at least the first year of the child’s life. [ABSTRACT FROM AUTHOR]

Knowledge about the genes implicated in lipid biosynthesis acquired from the model plant Arabidopsis is useful in understanding the formation of seed oil in Brassica oilseeds. In this paper, we report the screening of polymorphic markers at the loci putative for the seed oil formation between two geographically different genotypes: the Chinese cultivar Ningyou-7 and the European cultivar Tapidor. These primer pairs (150) were designed based on 75 Brassica genes that were Arabidopsis orthologues implicated in the oil formation. A total of 52 out of the 150 primer pairs associated with 47 of the 75 genes showed polymorphisms between the two genotypes. The type of polymorphisms that could be detected on capillary electrophoresis images and their respective visual futures are described. Further, we selected 34 polymorphic markers to scan allelic variations and found rich DNA polymorphisms among the 54 Brassica oilseed cultivars. On the average, each primer pair resulted in 5.6 alleles at the region that was covered. The correlation between the alleles and seed quality traits revealed that the alleles of BnFAD7 were related to the variation of linolenic acid (C18:3) contents among the cultivars. The allele FAD7-ics11170 (3/4)-b that was significantly correlated with high linolenic acid content can be used as an efficient marker for the selection of breeding materials with high linolenic acid content. [ABSTRACT FROM AUTHOR]

The potential of microsatellite markers for use in genetic studies has been evaluated in Allium cultivated species ( Allium cepa, A. fistulosum) and its allied species ( A. altaicum, A. galanthum, A. roylei, A. vavilovii). A total of 77 polymerase chain reaction (PCR) primer pairs were employed, 76 of which amplified a single product or several products in either of the species. The 29 AMS primer pairs derived from A. cepa and 46 microsatellites primer pairs from A. fistulosum revealed a lot of polymorphic amplicons between seven Allium species. Some of the microsatellite markers were effective not only for identifying an intraspecific F1 hybrid between shallot and bulb onion but also for applying to segregation analyses in its F2 population. All of the microsatellite markers can be used for interspecific taxonomic analyses among two cultivated and four wild species of sections Cepa and Phyllodolon in Allium. Generally, our data support the results obtained from recently performed analyses using molecular and morphological markers. However, the phylogeny of A. roylei, a threatened species with several favorable genes, was still ambiguous due to its different positions in each dendrogram generated from the two primer sets originated from A. cepa and A. fistulosum. [ABSTRACT FROM AUTHOR]

DNA variants in a 31-kb region of the human major histocompatibility complex, encompassing the tumor necrosis factor (TNF) gene cluster, were surveyed by direct sequencing of 283 unrelated individuals from six Chinese populations. A total of 273 polymorphic sites were identified, with nearly half of them novel. We observed an excess of rare variants and negative values of selection tests of the region, implying either that these populations experienced a historical expansion or that the surveyed region was subjected to natural selection. Different characteristics of the sequence variation in the six populations outline the genetic differentiation between Northern and Southern Chinese populations. The distributions of recombination rates are similar among all the populations, with variation in the magnitude and/or in the fine location of hot spots. Tag single-nucleotide polymorphisms (SNPs) selected from HapMap (Phase II) CHB data accounted for an average of 64% of common SNPs from the six Chinese populations. We also observed a limited transferability of tag SNPs between Chinese populations on the 31-kb region with an excess of untaggable SNPs and ragged linkage disequilibrium blocks. It suggested that the design and interpretation of future association studies should be more cautious, and that a resequencing approach may refine tag SNP selection on Chinese-specific disease mapping. [ABSTRACT FROM AUTHOR]

Despite almost a hundred years of studies on the Pacific cod’s biological and ecological peculiarities, many of them and especially population structure remain poorly understood. The variability of DNA microsatellite loci Gmo3, Gmo34, Gmo35, Pgmo32, and Gmo 19 was analyzed for the cod sampled in different areas of the North Pacific. The cod sampled nearby the Southern Kurils, differed significantly by Gmo3 and Pgmo32 compared to the populations inhabiting the Bering Sea, the Sea of Okhotsk and the coastal waters off Canada. Further, Pacific cod of the three latter populations demonstrated high similarity (I = 0.996) in spite of considerable geographic remoteness of these areas from one another. [ABSTRACT FROM AUTHOR]

In this study, microsatellite markers were utilized to reveal the genetic diversity of 56 strains of Lentinula edodes grown in China. A total of 224 DNA bands were detected through 25 primer pairs, of which, 223 bands (99.6%) were polymorphic between two or more strains. The variation in SSR (Simple Sequence Repeat) DNA band patterns and average genetic similarity among the wild strains of L. edodes obtained from the same region uncovered a vast genetic diversity in the natural germplasm found in China. Compared with L. edodes strains from other areas, the genetic diversity of those from the Yunnan Plateau, Hengduanshan mountains, Taiwan, and south China was significantly greater. Based on cluster analysis and principal coordinate analysis, the results indicated that all L. edodes strains could be divided into three major groups. These results effectively displayed the differences between the strains from North and South China, and those from the same or adjoining regions could cluster preferentially into small groups in most cases, suggesting the positive correlation between the cluster results and the geographical origin for the natural germplasm of Chinese L. edodes. To our knowledge, this is a pioneering report on the utilization of the SSR marker technique in analyzing L. edodes' genetic diversity. [ABSTRACT FROM AUTHOR]

Genetic and environmental factors have long been suspected to influence on athletic performance and bone metabolism. We have therefore investigated a population-based association study of Korean elite athletes relative to the general population with PvuII polymorphism of the ER-α gene. In addition, interactions between the ER-a genotype distribution and variation of biochemical parameters for bone metabolism during short-duration aerobic performance development were analyzed in a Korean middle-aged women population. The ER-a gene locus was found to be deviation from Hardy-Weinberg equilibrium ( p<0.05), but not in the female athlete group. The most common ER-α genotype was Pp in elite athletes (44/72) and controls (74/109), with higher than expected number of heterozygotes ( p<0.05). No statistically significant difference in the distribution of ER-a genotype frequency was observed between the elite athletes and control groups. In contrast, almost all biochemical markers studied here appeared to be significantly higher levels after 12-week exercise training compared with baseline in both groups of Korean women, although there was no genotype effect on the change of levels of the bone metabolic parameters. Thus, our data imply that regularly exercise training may affect bone metabolism, but the genetic marker of ER-a gene polymorphism may not be valuable indicator for the development of elite athletes and physical therapy educational program. [ABSTRACT FROM AUTHOR]

Rice is the first cereal genome with a finished sequence and a model crop that has important syntenic relationships with other cereal species. The objectives of our study were to identify resistance gene analogue (RGA) sequences from chromosome 11 of rice, understand their expression in other cereals and dicots by in silico analysis, determine their presence on other rice chromosomes, and evaluate the extent of polymorphism and actual expression in a set of rice genotypes. A total of 195 RGAs were predicted and physically localised. Of these, 91.79% expressed in rice, and 51.28% expressed in wheat, which was the highest among other cereals. Among monocots, sugarcane showed the highest (78.92%) expression, while among dicots, RGAs were maximally expressed in Arabidopsis (11.79%). Interestingly, two of the chromosome 11-specific RGAs were found to be expressing in all the organisms studied. Eighty RGAs of chromosome 11 had significant homology with chromosome 12, which was the maximum among all the rice chromosomes. Thirty-one per cent of the RGAs used in polymerase chain reaction (PCR) amplifi cation showed polymorphism in a set of rice genotypes. Actual gene expression analysis revealed post-inoculation induction of one RGA in the rice line IRBB-4 carrying the bacterial blight resistance gene Xa-4. Our results have implications for the development of sequence-based markers and functional validation of specific RGAs in rice. [ABSTRACT FROM AUTHOR]

Random amplified polymorphic DNA (RAPD) is an efficient tool to detect DNA polymorphisms and to distinguish different clones and cultivars. We have applied the RAPD technique to distinguish, starting from a single rice seed, among some Italian rice cultivars from market and from National Institute for research on food and nutrition, Italy. We also estimated the genomic similarity among the rice cultivars object of this study taking advantage of the amplification patterns. Despite the low genomic variability among Italian rice cultivars, RAPD technique allowed us to distinguish among them. This indicates that RAPD can be used routinely to verify the identity of Italian rice cultivars in order to prevent fraudulent commercial activity. [ABSTRACT FROM AUTHOR]

The article presents a study on allele frequencies of ten 10 short tandem repeats (STR) loci in the population in central Tunisia. It cites statistical parameters that were estimated for the loci, including the polymorphism information content (PIC). An ABI PRISM 310 Genetic Analyser from Applied Biosystems was used to examine polymerase chain reaction (PCR)-amplified fragments. The researchers also made use of the genetic data analysis GENEPOP to carry out statistical analysis.

Gastrodia tuber and its component gastrodin have many pharmacological effects. The chemical fingerprints and gastrodin contents of eight Gastrodia populations were determined, and the genomic DNA polymorphism of the populations was investigated. Genetic distance coefficients among the populations were calculated using the DNA polymorphism data. A dendrogram of the genetic similarities between the populations was constructed using the genetic distance coefficients. The results indicated that the genomic DNA of Gastrodia tubers was highly polymorphic; the eight populations clustered into three major groups, and the gastrodin content varied greatly among these groups. There were obvious correlations among genetic makeup, gastrodin content, and place of origin. The ecological environments in Guizhou and Shanxi may be conducive to evolution and to gastrodin biosynthesis, and more suitable for cultivation of Gastrodia tubers. These findings may provide a scientific basis for overall genetic resource management and for the selection of locations for cultivating Gastrodia tubers. [ABSTRACT FROM AUTHOR]

Purpose To evaluate the association between phenotype and follicle stimulating hormone receptor (FSHR) genotype in women with ovarian dysfunction and patients with "poor response" to gonadotropin stimulation of ovulation. Methods FSHR gene SNPs were analyzed by PCR and RFLP. "Poor responders" (ovarian dysfunction) group and "good responders" group constituted the study group. Normoovulatory women who gave birth to naturally conceived children formed control groups: under 35 years of age (control I) and over 35 years of age (control II). Results The frequency of Ala307-Ser680/Ala307-Ser680 genotype was significantly more prevalent in the ovarian dysfunction group (26%) compared to the control I (7.7%) (P<0.001) and a "good responders" group (12.5%) (P< 0.05); and in a "poor responders" group (33.3%) compared to a "good responders" group (P<0.05), control I (P<0.001) and control II (17.5%) (P<0.05). Conclusions Our data shows the prevalence of the Ala307- Ser680/ Ala307-Ser680 genotype in the both groups of patients. The finding should have impact on the delineation of stimulation protocols. [ABSTRACT FROM AUTHOR]

DNA variations have contributed enormously to the fields of medical and forensic science, especially through their use in studies on genes responsible or susceptible to various diseases and those on screening of chromosomal abnormalities in tumors. The types of genetic variations used in these studies have changed in the past 25 years and can be classified into five major classes: RFLP (restriction fragment length polymorphism), VNTR (variable number of tandem repeat), STR (short tandem repeat or microsatellite), SNP (single-nucleotide polymorphism) and CNV (copy-number variation). Genetic linkage analysis using these tools helped to map and discover genes responsible for hundreds of hereditary diseases. Furthermore, construction of the international SNP database and recent development of high-throughput SNP typing platforms enabled us to perform genome-wide association studies, which have identified genes (or genetic variations) susceptible to common diseases or those associated with drug responses. Genome-wide sequencing of individual DNAs is gaining immense scope. Here, I summarize the history of polymorphic DNA markers and their contribution to the genetic analysis of both rare hereditary diseases and common diseases, as well as recent advances in pharmacogenetics, including our contribution to these areas.Journal of Human Genetics (2009) 54, 1–8; doi:10.1038/jhg.2008.6; published online 9 January 2009 [ABSTRACT FROM AUTHOR]

In order to evaluate effects of the population structure and natural selection on organisms having long generation times, we surveyed DNA polymorphisms at five loci encoding 9-cis-epoxycarotenoid dioxygenase ( NCED) , ammonium transporter , calmodulin , aquaporin, and the second major allergen with polymethylgalacturonase enzyme activity in the pollen ( Cryj2) in a conifer, Cryptomeria japonica. The average nucleotide diversity at silent sites across 12 loci including the previously analyzed seven loci was 0.0044. The population recombination rate (4 Nr, where N and r are the effective population size and recombination rate per base per generation, respectively) was estimated as 0.00046 and a slow reduction in the population size was indicated, according to the maximum likelihood method implemented in LAMARC. At NCED, the McDonald-Kreitman (MK) test revealed an excess of replacement polymorphisms, suggesting contributions of slightly deleterious mutations . In contrast, the MK test revealed an excess of replacement divergence at Cryj2 and a maximum likelihood approach using the PAML package revealed that certain amino acid sites had a nonsynonymous/synonymous substitution rate ratio ( ω) > 4.0, indicating adaptive evolution at this locus. The overall analysis of the 12 loci suggested that adaptive, neutral, and slightly deleterious evolution played important roles in the evolution of C. japonica. [ABSTRACT FROM AUTHOR]

Gene and genome duplications play a major role in the evolution of plant species. The Brassica nigra genome is highly replicated as a result of ancient polyploidization events. Two copies of the flowering time gene CONSTANS (COa and COb) have been identified in B. nigra, and previous studies showed that COa is functional. In the present study, the polymorphism of 92 COb alleles sampled in seven populations was analyzed. Both polymorphism and recombination levels were elevated and varied strongly among populations and 8% of COb alleles exhibit apparently disabling mutations. Sequence data, however, do not provide unambiguous support for the presence of relaxed selective constraint on COb as compared to known functional CO genes. On the one hand, some of the disabling mutations reached high-frequency arguing for a loss of function but, on the other hand, the ratio of nonsynonymous to synonymous nucleotide polymorphism and diversity is low and similar to that observed in other B. nigra CO and CO-like genes, supporting the conservation of some function. We also showed that COb is still transcribed. Finally, the flowering time of Arabidopsis thaliana co mutant plants transformed with COb alleles with and without apparent disabling mutations was similar. We propose that COb was retained for a long period after duplication, but a recent fixation of a detrimental mutation, possibly as an effect of a bottleneck, resulted in its nonfunctionalization. We also speculate as to the presence of subsequent selection for rapid degeneration of the gene.Heredity (2007) 98, 375–384. doi:10.1038/sj.hdy.6800951; published online 7 March 2007 [ABSTRACT FROM AUTHOR]

The area between the Dniester and the eastern Carpathian mountain range is at a geographical crossroads between eastern Europe and the Balkans. Little is known about the genetics of the population of this region. We performed an analysis of 12 binary autosomal markers in samples from six Dniester–Carpathian populations: two Moldavian, one Romanian, one Ukrainian and two Gagauz populations. The results were compared with gene frequency data from culturally and linguistically related populations from Southeast Europe and Central Asia. Small genetic differences were found among southeastern European populations (in particular those of the Dniester–Carpathian region). The observed homogeneity suggests either a very recent common ancestry of all southeastern European populations or strong gene flow between them. Despite this low level of differentiation, tree reconstruction and principle component analyses allowed a distinction between Balkan–Carpathian (Macedonians, Romanians, Moldavians, Ukrainians and Gagauzes) and eastern Mediterranean (Turks, Greeks and Albanians) population groups. The genetic affinities among Dniester–Carpathian and southeastern European populations do not reflect their linguistic relationships. The results indicate that the ethnic and genetic differentiations occurred in these regions to a considerable extent independently of each other. In particular, Gagauzes, a Turkic-speaking population, show closer affinities to their geographical neighbors than to other Turkic populations. [ABSTRACT FROM AUTHOR]

In this study, inter-simple sequence repeats (ISSR) ans simple sequence repeat (SSR) markers were used to investigate genetic diversity of 27 mulberry accessions including 19 cultivated accessions (six M. multicaulis, three M. alba, two M. atropurpurea, two M. bombycis, one M. australis, two M. rotundiloba, one M. alba var. pendula, one M. alba var. macrophylla, and one M. alba var. venose) and 8 wild accessions (two M. cathayana, two M. laevigata, two M. wittiorum, one M. nigra and one M. mongolica). ISSRs and SSRs were compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among 27 mulberry genotypes. SSRs presented a higher level of polymorphism and greater information content. All index values of genetic diversity both markers analyzed using Popgene 32 software indicated that within wild species had higher genetic diversity than within cultivated species. Cultivation may caused the lose of genetic diversity of mulberry compared with wild species revealed by ISSR and SSR markers. The mean genetic similarity coefficients among all mulberry genotypes ascribed by ISSR and SSR matrices were 0.7677 and 0.6131, respectively. For all markers a high similarity in dendrogram topologies was obtained although some differences were observed. Cluster analysis of ISSR and SSR using UPGMA method revealed that the wild species are genetically distant from the domesticated species studied here. The correlation coefficients of similarity were statistically significant for both marker systems used. Principal coordinates analysis (PCA) for ISSR and SSR data also supports their UPGMA clustering. These results have an important implication for mulberry germplasm characterization, improvement, molecular systematics and conservation. [ABSTRACT FROM AUTHOR]

Decreased sensing of the innate immune system may lead to chronic activation of the inflammatory cascade. We hypothesised that mannan-binding lectin (MBL) deficiency may confer risk of obesity and insulin resistance. We performed a cross-sectional study of MBL protein concentration ( n=434) and MBL2 gene mutations (exon 1) ( n=759) in association with obesity, markers of inflammation and insulin action (euglycaemic clamp, n=113), and a longitudinal study of MBL protein before and after weight loss in obese patients ( n=10). We also studied the effects of MBL in vitro in muscle cells and circulating MBL-A (mouse equivalent of human MBL) in a mouse model. Among 434 consecutive non-diabetic men, the age-adjusted serum MBL concentration was lower in obese subjects than in lean subjects (median: 959 μg/ml [interquartile range: 116.8–2,044 μg/ml] vs 1,365 [467–2,513] μg/ml; p=0.01) and was accompanied by increased serum inflammatory markers. Insulin action correlated significantly with serum MBL ( r=0.49, p<0.0001). Serum MBL concentration increased by a median of 110.2% after weight loss. The change in serum concentration of MBL was positively associated with the increase in insulin sensitivity ( r=0.713, p=0.021). At least one MBL2 gene mutation was present in 48.2% of obese vs 39.3% of non-obese subjects ( p=0.037). The plasma concentration of MBL-A was lower in insulin-resistant obese ob/ ob mice, as was the glucose/insulin ratio. Incubation of rat soleus muscle with human MBL markedly increased fatty acid oxidation. These findings suggest that MBL, previously thought only to be involved in inflammation and immune system function, affects metabolic pathways. [ABSTRACT FROM AUTHOR]

The thirty-three 5′ flanking conserved sequences of the known low-molecular-weight subunit (LMW-GS) genes have been divided into eight clusters, which was in agreement with the classification based on the deduced N-terminal protein sequences. The DNA polymorphism between the eight clusters was obtained by sequence alignment, and a total of 34 polymorphic positions were observed in the approximately 200 bp regions, among which 18 polymorphic positions were candidate SNPs. Seven cluster-specific primer sets were designed for seven out of eight clusters containing cluster-specific bases, with which the genomic DNA of the ditelosomic lines of group 1 chromosomes of a wheat variety ‘Chinese Spring’ was employed to carry out chromosome assignment. The subsequent cloning and DNA sequencing of PCR fragments validated the sequences specificity of the 5′ flanking conserved sequences between LMW-GS gene groups in different genomes. These results suggested that the coding and 5′ flanking regions of LMW-GS genes are likely to have evolved in a concerted fashion. The seven primer sets developed in this study could be used to isolate the complete ORFs of seven groups of LMW-GS genes, respectively, and therefore possess great value for further research in the contributions of a single LMW-GS gene to wheat quality in the complex genetic background and the efficient selections of quality-related components in breeding programs. [ABSTRACT FROM AUTHOR]

Polymorphisms of leptin receptor (LEPR) may contribute to a common form of obesity and, as a consequence, obesity-related diseases. We evaluated the potential role of genetic variation at the LEPR gene in heart sympathetic activity and other traits related to obesity in Mexican adolescents. Adolescents aged between 12 and 17 years, with steady body weight for the last 3 months were included. We evaluated anthropometric measurements, blood pressure, seric glucose, insulin, leptin levels, heart sympathetic activity (by electrocardiograph monitoring at rest), and the Gln223Arg and Pro1019Pro LEPR polymorphisms in each subject. In total, 103 adolescents (55 obese and 48 nonobese) were included. The group of obese adolescents showed higher sympathetic activity, blood pressure, glucose, insulin, and leptin levels. The genotype frequencies for the two polymorphisms were found to be in Hardy-Weinberg equilibrium. There was no difference in the genotype frequencies for Gln223Arg or Pro1019Pro polymorphisms between obese and nonobese adolescents. However, there was a higher prevalence of Gln223 allele among subjects with higher insulin levels (0.72 vs 0.57; P=0.04 for adolescents with insulin levels higher and lower than 100?pmol/l, respectively). According to Gln223Arg polymorphism, those with Gln allele (Gln/Gln and Gln/Arg) had higher heart sympathetic activity, body fat percentage, and leptin levels. To conclude, our results support the hypothesis that Gln223Arg polymorphism of LEPR in Mexican adolescents is associated with haemodynamic and metabolic disturbances related to obesity.Journal of Human Hypertension (2005) 19, 341-346. doi:10.1038/sj.jhh.1001824 Published online 20 January 2005 [ABSTRACT FROM AUTHOR]