Search

A morphological and genetic characterization of autochthonous ‘Saragolla’ wheats, currently cultivated in Abruzzo Region (Italy), was carried out. Using 15 simple sequence repeat (SSR) markers and 24 UPOV morphological traits we compared: (a) 13 ‘Saragolla’ genotypes with traits of the italicum/apulicum botanical varieties (Saragolla (Sar.) italicum), (b) 26 ‘Saragolla’ genotypes with traits of leucurum/affine botanical varieties (Sar. leucurum), (c) 8 breeding varieties (pure lines), and (d) 5 Italian autochthonous wheats and 1 turanicum line (old wheats). One hundred twenty-six (126) alleles were identified. The number of alleles per locus spanned from 4 to 15 and the number of alleles per genotype varied between 12 and 21. Values of gene diversity (Nei) across the 53 genotypes was 0.17. The groups of Sar. leucurum and Sar. italicum genotypes were morphologically distinguishable from the groups of old wheats and pure lines. Likewise, the analysis of molecular data using the discriminant analysis revealed that genotypes with the Sar. italicum phenotype displayed distinct genetic differences from Sar. leucurum, pure lines and old wheats. These results make Sar. italicum genotypes distinguishable and eligible as a conservation variety. Ward's clustering analysis of the 53-genotype pool showed that the ‘Saragolla’ landrace is a valuable repository of genetic diversity.

Background: Wilson’s disease (WD) is an autosomal recessive disease that is caused by mutations in the ATP7B (a copper-transporting P-type ATPase) gene. The disease has a low prevalence and is characterized by a copper metabolism disorder. However, various characteristics of the disease are determined by race and geographic region. We aimed to discover novel ATP7B mutations in pediatric patients with WD from Yunnan province, where there is a high proportion of ethnic minorities. We also performed a comprehensive analysis of ATP7B mutations in the different ethnic groups found in Southwest China.Methods: We recruited 45 patients who had been clinically diagnosed with WD, from 44 unrelated families. Routine clinical examinations and laboratory evaluations were performed and details of age, gender, ethnic group and symptoms at onset were collected. Direct sequencing of the ATP7B gene was performed in 39 of the 45 patients and their families.Results: In this study, participants came from seven different ethnic groups in China: Han, Bai, Dai, Zhuang, Yi, Hui and Jingpo. Three out of ten patients from ethnic minorities presented with elevated transaminases, when compared to the majority of the Han patients. Forty distinct mutations (28 missense, six splicing, three non-sense, two frameshift and one mutation of uncertain significance) were identified in the 39 patients with WD. Four of the mutations were novel and the most frequent mutation was c.2333G > T (p.R778L, allelic frequency: 15.38%). Using the phenotype-genotype correlation analysis, patients from ethnic minorities were shown to be more likely to have homozygous mutations (p = 0.035) than Han patients. The patients who carried the c.2310C > G mutation had lower serum ceruloplasmin levels (p = 0.012). In patients with heterozygous mutations, c.3809A > G was significantly associated with ethnic minorities (p = 0.042). The frequency of a protein-truncating variant (PTV) in Han patients was 34.38% (11/32), while we did not find PTV in patients from ethnic minorities.Conclusion: This study revealed genetic defects in 39 pediatric patients with WD from Yunnan province. Four novel mutations were identified and have enriched the WD database. We characterized the genotypes and phenotypes in different minorities, which will enhance the current knowledge on the population genetics of WD in China.

Tongde County is located in the southeast of Qinghai Province, China, harboring rich yak genetic resources. In the present study, the complete mitochondrial genome (mitogenome) of the Tongde yak (Bos grunniens) was firstly sequenced using Illumina sequencing technique and the corresponding sequence characterization was identified. Our results showed that the mitogenome of Tongde yak is a circular molecule with 16,323 bp length consisting of 37 genes (13 protein-coding genes, 2 rRNA genes, 22 tRNA genes) and a non-coding control region (D-loop), which is consistent with most bovine species. The overall nucleotide composition was found as: A (33.72%), T (27.27%), C (25.80%), and G (13.21%), respectively, yielding a higher AT content (60.99%). The complete mitogenome sequence of Tongde yak would provide useful information for further studies on its genetic resource conservation and molecular breeding programmes in the future.

Fifteen Brassica oleracea L. var. acephala DC accessions were collected and evaluated for their genetic diversity and molecular characteristics using 10 previously developed and used codominant SSR markers. The SSR loci used revealed a total of 51 alleles. The domestic kale varieties were collected locally and the hybrids kales were found in markets. The averages of total heterozygosity (H) and polymorphic information content (PIC) was 0.6774 and 0.6201, respectively. The average number of alleles was 4.2 per locus, where 8 of 10 markers showed high polymorphic information content (PIC), being more than 0.5. The genetic relationships among the populations revealed by Unweighted Pair Group Method with Arithmetic mean (UPGMA), showed a clear clustering into three distinct groups. As expected, all local varieties were separated within two separated clusters, whereas only two domestic varieties shared one cluster with the group of hybrids, indicating similar genetic background shared by domestic and hybrid varieties. These results indicate and confirm the regional and physiological differences between the kale varieties and confirm the SSR marker efficiency for genetic characterization assays

Abstract Background The Suwan population is a well-known maize germplasm that has greatly contributed to the development of maize breeding in tropical and subtropical regions, especially in southern China. Inbred lines derived from the Suwan population always contain stronger resistance and extensive adaptability in different environments. To evaluate the genetic character of inbred lines derived from the Suwan population, a panel including 226 inbred line derived from the Suwan population and temperate resources was assembled and genotyped by using MaizeSNP50 BeadChip, which contained 56,110 genome-wide single nucleotide polymorphism (SNP) markers. This panel contained 98 temperate inbred line and 128 lines derived from the Suwan population. Results The results showed that high genetic diversity was found, with PIC and GD to be 0.67 and 0.60, respectively. In addition, two novel subgroups were identified, with representative inbred lines as HCL645 and Ki32, respectively. One acknowledged heterotic group of Iowa Stiff Stalk Synthetic (SS) was also identified in this study. This study can provide some additional scientific evidence for heterotic group division and use in maize. Additionally, lower linkage disequilibrium (LD) levels and weaker genetic relationships were found, with an average LD level of 41.15 kb that varied from 3.5 to 96 kb. A total of 82.8% of paired relative kinships ranged from 0.05 to 0.28. Conclusions These results would not only facilitate maize breeding practices in tropical and subtropical regions, but also revealed that this panel can be used in dissecting the genetic basis of complex quantitative traits’ variations by using genome-wide association studies (GWAS).

Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%–98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise FST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise FST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.

n this paper, we present the results of the examination of the genetic characteristics of 7 autochthonous varieties of "Lubeničarka" pear (watermelon pear) that are typical for the Banjaluka region, using AFLP molecular markers. In order to reliably confirm that there are differences among selected varieties we have analyzed their genetic profiles using AFLP genetic markers and established, based on the Jaccard similarity coefficient, that there is a genetic variability among the studied varieties. Furthermore, based on these analyzes we have classified these varieties into 3 groups of which variety G_19 has a very large coefficient (0.4369) when compared to other varieties. These results might be immensely important for present and future pear breeding and genetic improvement program.

Abstract The first horses were brought to Brazil by the colonizers after 1534. Over the centuries, these animals evolved and adapted to local environmental conditions usually unsuitable for exotic breeds, thereby originating locally adapted Brazilian breeds. The present work represents the first description of maternal genetic diversity in these horse breeds based on D-loop sequences. A D-Loop HSV-I fragment of 252 bp, from 141 horses belonging to ten Brazilian breeds / genetic groups (locally adapted and specialized breeds) were analysed. Thirty-five different haplotypes belonging to 18 haplogroups were identified with 33 polymorphic sites. Haplotype diversity (varying from 0.20 to 0.96) and nucleotide diversity (varying from 0.0039 to 0.0239) was lower for locally adapted than for specialized breeds, with the same pattern observed for FST values. Haplogroups identified in Brazilian breeds are in agreement with previous findings in South American samples. The low variability observed mainly in locally adapted breeds, indicates that, to ensure conservation of these breeds, careful reproductive management is needed. Additional genetic characterization studies are required to support accurate decision-making.

Abstract Background Interferon inducible transmembrane (IFITM) proteins are effectors of the immune system widely characterized for their role in restricting infection by diverse enveloped and non-enveloped viruses. The chicken IFITM (chIFITM) genes are clustered on chromosome 5 and to date four genes have been annotated, namely chIFITM1, chIFITM3, chIFITM5 and chIFITM10. However, due to poor assembly of this locus in the Gallus Gallus v4 genome, accurate characterization has so far proven problematic. Recently, a new chicken reference genome assembly Gallus Gallus v5 was generated using Sanger, 454, Illumina and PacBio sequencing technologies identifying considerable differences in the chIFITM locus over the previous genome releases. Methods We re-sequenced the locus using both Illumina MiSeq and PacBio RS II sequencing technologies and we mapped RNA-seq data from the European Nucleotide Archive (ENA) to this finalized chIFITM locus. Using SureSelect probes capture probes designed to the finalized chIFITM locus, we sequenced the locus of a different chicken breed, namely a White Leghorn, and a turkey. Results We confirmed the Gallus Gallus v5 consensus except for two insertions of 5 and 1 base pair within the chIFITM3 and B4GALNT4 genes, respectively, and a single base pair deletion within the B4GALNT4 gene. The pull down revealed a single amino acid substitution of A63V in the CIL domain of IFITM2 compared to Red Jungle fowl and 13, 13 and 11 differences between IFITM1, 2 and 3 of chickens and turkeys, respectively. RNA-seq shows chIFITM2 and chIFITM3 expression in numerous tissue types of different chicken breeds and avian cell lines, while the expression of the putative chIFITM1 is limited to the testis, caecum and ileum tissues. Conclusions Locus resequencing using these capture probes and RNA-seq based expression analysis will allow the further characterization of genetic diversity within Galliformes.

Genetic characterization refers to variation detection using genetic markers. In this study, 28 simple sequence repeat (SSR) markers were used to characterize five selected Sarawak rice cultivars, namely Bali1, Bali2, Bali3, Bubok, and Mamut. An analysis based on these 28 polymorphic SSR markers revealed that the number of alleles ranged from 2 (RM312, RM510, and RM536) to 9 (RM307) with an average of 3.86. The polymorphism information content (PIC) values ranged from 0.0175 (RM489) to 0.8174 (RM19) with an average of 0.5179. A dendogram constructed on the basis of the genetic similarity to Nei's 1983 genetic distance showed a high similarity between Bali2 and Bali3, which was further supported by a principal coordinate analysis (PCoA). The population structure analysis illustrated the log likelihood peaking at K = 2, indicating that the entire population could be divided into two distinct groups. To develop an SSR fingerprinting panel, 10 SSR markers were selected on the basis of a high PIC value. As this panel provides a better discrimination power in cultivar identification, it could be an efficient and effective tool in cultivar identification, particularly for these selected Sarawak varieties, thus helping breeders to protect their intellectual property rights (IPR). Moreover, the markers could be used to evaluate the seed purity of the selected rice cultivars. [ABSTRACT FROM AUTHOR]

Current research aimed to characterize Sinai chickens genetically by using nine microsatellite genetic marckers. Twenty-eight birds used in the study were randomly collected (12 males + 16 females). Sinai chickens are a mongrel fowl raised by dwellers and farmers in Sinai Peninsula desert areas and chiefly habituated and adapted to fluctuating circumstances in this region. This strain has a small body size, golden neck feather, brown or golden saddle and brown or black feathered tail for males, while females had golden feathered body with some black feathers in tail and neck, red single comb and they have variable plumage color. Nine microsatellites used produced 53 alleles with mean value of 5.88 allel/locus. Averages of observed and expected heterozygosity were 0.174 and 0.773, respectively. Informative content revealed was high overall loci ranging between 0.608 and 0.811 with average value of 0.718. Six out of 9 loci (66.66%) were not in genetic equaliprium. Bottleneck analysis revealed that, under graphical and SMM model analysis, Sinai chickens nonbottlenecked in recent past history. Results insured that, the utilized panel of markers showed their efficiency capturing genetic characteristics of Sinai chickens reflecting the valuable genetic variation in the studied population, enabling future genetic improvement for this strain avoiding inbreeding. [ABSTRACT FROM AUTHOR]

Background: There is very limited genetic knowledge in Prosopis africana, an important sub-Saharan multi-purpose tree species. Availability of highly polymorphic genetic markers would be helpful for future genetic work. Findings: Leaf samples from 15 trees were used to develop simple sequence repeat (SSR) markers. Size-selected fragments from genomic DNA were enriched for repeats and the library was analyzed on an Illumina MiSeq platform. Fourteen SSRs were selected and applied in two Burkinabe populations (40 adult trees each). The number of alleles varied from 4 to 20, evenness (effective number of alleles/observed number of alleles) averaged to 0.54 and unbiased heterozygosity ranged from 0.305 to 0.925 over all loci and populations. Null alleles were not detected. Conclusions: Due to the high level of polymorphism and lack of null alleles the developed SSRs can be effectively employed in population genetic studies. [ABSTRACT FROM AUTHOR]

Newcastle disease (ND) is one of the most serious diseases amongst many species of birds and causes huge economic losses in the poultry sector. Backyard poultry are the main source of food in rural areas of many developing countries and play a crucial role in the epidemiology of ND. The sequence of the F protein cleavage site is the major virulence determinant of Newcastle disease virus (NDV). The aim of this study was to understand the molecular characterization of F proteins of Iranian backyard poultry in NDVs. The complete open reading frame sequences of the F gene of six isolates were amplified and sequenced. All characterized NDVs had high similarities to Chinese isolates. The phylogenetic analysis revealed that the studied strains fell into genotype VII and grouped in a specific subgenotype. All tested NDVs have a cleavage site of 112RRQKR↓F117, representing that all of them belonged to velogenic strains. Rearing methods of backyard poultry increase the chance of contact between a variety of poultry and wild birds; subsequently, new strains evolve and are transmitted between them. Therefore, continuous monitoring of NDVs in backyard poultry would help us to obtain more information about the evolution of NDVs and improve new control strategies in backyard poultry. [ABSTRACT FROM AUTHOR]

Various genetic markers, including microsatellites, have been used to analyze the genetic polymorphism and heterozygosity in canine breeds. In this work, we used nine microsatellite markers to investigate the genetic variability in Cimarron Uruguayo dogs, the only officially recognized native canine breed in Uruguay. DNA from 30 Cimarron Uruguayo dogs from northeastern and southern Uruguay was analyzed. The allelic frequencies for each micro-satellite, the genetic variability and the consanguinity were calculated, as were the polymorphic information content (PIC) and the probability of exclusion (PE). All of the microsatellites studied were polymorphic. FH 2361, FH 2305 and PEZ 03 were the most informative, with PIC values > 0.7, in agreement with results for other canine breeds. The PE values for the markers were within the ranges previously described and were generally greater for microsatellites with higher PIC values. The heterozygosity value (0.649) was considered high since only nine microsatellites were analyzed. Compared with data for other breeds, the results obtained here indicate that Cimarron Uruguayo dogs have high genetic diversity.

Mithun is a strongly built hill animal of Southeast Asia and plays an important role in the socio-economic and cultural life of the tribal population. Setaria digitata isolated from peritoneal cavity of mithun both from Arunachal Pradesh and Nagaland were characterized based on conserved region of 12SrDNA, 28SrDNA and ITS-2 and mitochondrial gene CoxI. Based on sequence analysis, it was found to be 99% similarity with Srilankan isolate of S. digitata. [ABSTRACT FROM AUTHOR]

Background and Objectives: Bacillus anthracis is one of the most homogenous bacteria ever described. Some level of diversity. Bacillus anthracis 17JB is a laboratory strain It is broadly used as a challenge strain in guinea pigs for potency test of anthrax vaccine. Material and Methods: This work describes genetic characterization of B. anthracis 17 JB strain using the SNPs and MLVA genotyping. Results and Conclusion: In SNPs typing, the originally French 17JB strain represented the A.Br. 008/009 subgroup. In Levy's genotyping method, 843, 451 and 864 bp long fragments were identified at AA03, AJ03 and AA07 loci, respectively. In the vaccine manufacturer perspective these findings are much valuable on their own account, but similar research is required to extend molecular knowledge of B. anthracis epidemiology in Persia. [ABSTRACT FROM AUTHOR]

Toxoplasma gondii is widely distributed in humans and other animals including birds throughout the world. However, little is known of the molecular epidemiology and genotypes of T. gondii infecting quails in China. Therefore, the present study was conducted to characterize T. gondii genotypes in common quails in China. During December 2014 to October 2015, a total of 390 muscle tissue samples of common quails were collected and the T. gondii B1 gene was amplified using a nested PCR, and the positive samples were genotyped at 11 genetic markers (SAG1, 5′-and 3′-SAG2, alternative SAG2, SAG3, BTUB, GRA6, L358, PK1, c22-8, c29-2, and Apico) using multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. Twenty-five of the 390 common quails (6.41%) were tested positive by nested PCR. Three DNA samples from the 25 positive samples were typed completely and were identified as ToxoDB Genotype #9 ( http://toxodb.org/toxo/ ). The results of the present study indicated that T. gondii infection in common quails was common in China, which provided the information of T. gondii genetic diversity in this host species. This is the first genetic characterization of T. gondii isolates from quails in China, which is useful for monitoring and controlling the T. gondii infection in quails, other animals and humans. [ABSTRACT FROM AUTHOR]

Cryptosporidiun, the protozoan parasite, has several transmission routes, including anthroponotic and zoonotic transmission, as well as the foodborne way, but mainly by water. The oocysts, the resistant stage produced by Cryptosporidium, are remarkably stable, and can survive for weeks or even months in the environment. Furthermore, the tnfective dose is low, probably even a single oocyst can cause infection. The Cryptosporidiurn genus includes at least 16 species; nevertheless, only a few can cause cryptosporidiosis, an intestinal disease in human and domestic mammals. Thus, the genetic characteristics of different Crvptosporidium species became fundamental in the diagnosis, monitoring, prevention and control of infections caused by this pathogen. Unfortunately, the traditional phenotypic techniques meet with difficulties in the specific diagnosis of cryptosporidiosis, therefore the new molecular tools must be applied. The RT-qPCR method can be used to differentiate viable and dead Crypiosporidium oocysts, and the LAMP assays have advantages for detection of organisms at relatively low concentration in environmental samples; however, the NASBA assay specifically detects as few as one oocyst of a viable human pathogenic Cryptosporidium species. Reverse line blot hybridization (RLB) has been successfully used for specific identification and for differentiation of Cryptosporidium species. Described techniques are the most promising methods for the sensitive and accurate detection, but require a considerable selection of appropriate tools, genetic markers and analytical techniques for interpretations of database. However, the applicability of most of these methods to detect Cryptosporidium species or genotypes from environmental samples needs to be evaluated and standardized. [ABSTRACT FROM AUTHOR]

Abstract: Newcastle disease (ND) is an OIE listed disease caused by virulent avian paramyxovirus type 1 (APMV-1) strains, which affect many species of birds and may cause severe economic losses in the poultry sector. The disease has been officially and unofficially reported in many African countries and still remains the main poultry disease in commercial and rural chickens of Africa. Unfortunately, virological and epidemiological information concerning ND strains circulating in the Western and Central regions of Africa is extremely scarce. In the present study, sequence analysis, pathotyping and detailed genetic characterization of virulent ND strains detected in rural poultry in West and Central Africa revealed the circulation of a new genetic lineage, distinguishable from the lineages described in the Eastern and Southern parts of the continent. Several mismatches were observed in the segment of the matrix gene targeted by the primers and probe designed for the molecular detection of APMV-1, which were responsible for the false negative results in the diagnostic test conducted. Furthermore, deduced amino acid sequences of the two major antigens eliciting a protective immune response (F and HN glycoprotein) revealed protein similarities <90% if compared to some common vaccine strains. Distinct mutations located in the neutralizing epitopes were revealed, indicating the need for detailed assessment of the efficacy of the current vaccines and vaccination practices in Africa. The present investigation provides important information on the epidemiology, diagnosis and control of NDV in Africa and highlights the importance of supporting surveillance in developing countries for transboundary animal diseases. [Copyright &y& Elsevier]

Abstract: To date, three subtypes of swine influenza viruses, H1N1, H1N2, and H3N2 have been isolated in Italy. In 2006, a novel swine influenza virus subtype (H3N1) was isolated from coughing pigs. RT-PCR performed on lung tissues, experimental infection in pigs with the novel isolate, and cloning the virus by plaque assay confirmed this unique H and N combination. The novel isolate was also antigenically and genetically characterized. Genetic and phylogenetic analysis showed that the complete HA gene of the H3N1 strain has the highest nucleotide identity to three Italian H3N2 strains, one isolated in 2001 and two in 2004, whereas the full length NA sequence is closely related to three H1N1 subtype viruses isolated in Italy in 2004. The remaining genes are also closely related to respective genes found in H1N1 and H3N2 SIVs currently circulating in Italy. This suggests that the novel SIV could be a reassortant between the H3N2 and H1N1 SIVs circulating in Italy. [Copyright &y& Elsevier]

Most human gliomas are characterized by diffuse infiltrative growth in the brain parenchyma. Partly because of this characteristic growth pattern, gliomas are notorious for their poor response to current therapies. Many animal models for human gliomas, however, do not display this diffuse infiltrative growth pattern. Furthermore, there is a need for glioma models that represent adequate genocopies of different subsets of human gliomas (e.g., oligodendrogliomas). Here, we assessed the intracerebral growth patterns and copy number changes [using multiplex ligation-dependent probe amplification (MLPA)/comparative genomic hybridization (CGH)] of 15 human glioma lines in nude mice. Most xenografts present with compact growing lesions intracerebrally. Only the E98 and, to a lesser degree, E106 xenograft lines (propagated through subcutaneous growth) consistently produced intracerebral tumors, displaying diffuse infiltrative growth in the brain parenchyma. In contrast, four xenograft lines (E434, E468, E473 and E478), established by direct intracerebral inoculation of human glioma cells and serially propagated intracerebrally, consistently showed extensive diffuse infiltration throughout the brain. After several passages, the neoplastic cells still carry typical chromosomal aberrations [(−1p/−19q in oligodendroglioma, +7/−10 in glioblastoma multiforme (GBM)]. Especially these latter four models and the E98 line thus represent adequate geno- and phenocopies of human gliomas and form an attractive platform to investigate different therapeutic approaches in a preclinical setting. [ABSTRACT FROM AUTHOR]

Variation of 15 nuclear allozyme genes and a 708 bp fragment of DNA sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene were surveyed in a population of a hoverfly species, Merodon desuturinus Vujić, &Sscaron;imić & Radenković, 1995 (Diptera, Syrphidae), endemic to the Balkan Peninsula. Based on phylogeography and taxonomy, Merodon desuturinus is of special interest from a biogeographical and conservation perspective. Characterization and determination of genetic relationships between M. desuturinus and taxa of the M. aureus, M. avidus, and M. ruficornis groups on the Balkan Peninsula were estimated based on molecular markers (allozymes and COI sequences). We observed that the mean number of alleles per allozyme locus was 1.1, frequency of polymorphic loci 0.067, and heterozygotes were absent. Our results showed an extremely low genetic variability in the M. desuturinus population sampled. We suggest that this taxon calls for a conservation management plan, as it is likely a vulnerable and threatened taxon, an endemic, spatially divided species and represents a unique genetic unit on the Balkan Peninsula. [ABSTRACT FROM AUTHOR]

Infectious pancreatic necrosis (IPN) is a highly contagious disease of young salmonid fish, and is one of the most serious economic diseases in aquaculture. In Scotland, an increase in IPN virus (IPNV) outbreaks in seawater Atlantic salmon, Salmo salar, has been reported in recent years. The aim of this study was to analyse the VP2 gene from recent IPNV isolates from Scotland, to determine whether there are epidemiological links between IPNV isolates from farms (13), wild fish (17) and the environment (6) in order to investigate potential wild and farmed fish interactions. Comparison of the nucleotide sequence of the VP2 gene revealed that 34 of 36 isolates were 97.1–100% similar and the deduced amino acid sequences showed 97–100% identity. Two isolates from wild fish exhibited the most divergence at 85–87.3% similarity to the other isolates at the nucleotide level and 88.2–90.8% identity at the deduced amino acid level. Phylogenetic analyses revealed that 34 of 36 of the isolates from Scotland were genetically closely related to the A2 (Sp) serotype of IPNV. The two wild isolates from seatrout, Salmo trutta, and flounder, Platichthys flesus, were most closely related to the European A5 (Te) serotype. This study represents a comprehensive IPNV phylogenetic study that indicates that there are closely related or identical isolates in circulation in the marine environment, which adds evidence that disease interactions between wild and farmed fish may occur. This type of analysis is a useful tool in the management and control of fish diseases because it can assist in the identification of epidemiological links and highlight potential risks to aquaculture. [ABSTRACT FROM AUTHOR]

Examines the seroprevalence, and the genetic heterogeneity of circulating subtypes of HIV-1 in the general population of Djibouti. Collection of serum samples from Djiboutians representing the general population of urban and rural districts during a national survey in 2002; Rate of HIV-1 seroprevalence in the general population of Djibouti; Detection of a large majority of subtype C as well as other subtypes in the HIV-isolates following phylogenetic analysis.

Characterization of genetic diversity among maize inbred lines can facilitate organization of germplasm and improve efficiency of breeding programs. A set of 218 phenotypically diverse inbred maize lines developed at CIMMYT for hybrid production was characterized using 32 RFLP markers to: (1) analyze the genetic diversity present; (2) define potential heterotic groups based on clusters formed with marker data; and (3) identify the most representative testers for each potential heterotic group. Lines were clustered using five different genetic distance measurements to find consensus non-hierarchical clusters. Dendrograms were produced to study hierarchical classification within smaller groups of lines. A very high average allelic diversity was seen in this germplasm. Lines did not cluster based on phenotype, environmental adaptation, grain color or type, maturity, or heterotic response (as determined based on hybrid performance with testers), but lines related by pedigree usually did cluster together. Previously defined testers from opposite heterotic groups were not genetically differentiated, and did not represent well their heterotic group. Discrete clusters were difficult to find; thus, potential heterotic groups will be difficult to suggest using RFLP markers alone. However, suggestions on how to use molecular markers and cross performance information to refine heterotic groups and select representative testers are presented. [ABSTRACT FROM AUTHOR]

Porcine circovirus type 2 (PCV2) has been associated with a newly identified and described disease in swine called the postweaning multisystemic wasting syndrome (PMWS). An association of PCV2 with various other clinical conditions in pigs are also increasingly being reported. To date molecular studies to determine the extent of genetic variations of this virus have been limited. To more fully understand the extent of genetic diversity we report the sequencing of 34 PCV2 strains from Eastern Canada originating from a variety of clinical conditions spanning years 1990–2001 along with the phylogenetic analysis of these strains and that of 36 PCV2 sequences published in GenBank. Sequence analysis of the complete genome indicated that the Canadian PCV2 strains analyzed in the present study are closely related to each other but also to other PCV2 strains originating from Western Canada, US, Europe and Asia. Sequence analysis of ORF1 and ORF2 genes of the 34 strains revealed that the extent of nucleotide variation was greater for the ORF2 than for the ORF1. The amino acid sequences alignment of the PCV2 capsid protein identified three major regions of amino acid heterogeneity, two of which correspond with dominant immunoreactive areas. No repeatable amino acid motifs for these two regions could be associated with PCV2 strains identified from cases of PMWS or other clinical conditions. Phylogenetic analysis of all 70 strains revealed one large cluster composed of strains from Europe, Taiwan, China and Canada. This large cluster could be divided in several sub clusters, in two of which Canadian strains were found closely related to strains from Germany. The remaining strains from Canada and the US were spread in small groupings along the phylogenetic tree and an association with geographic origin could not be established. The genomic characterizations performed in this study indicate that PCV2 strains associated with PMWS are scattered throughout the phylogenetic tree often in groupings including PCV2 strains identified from cases other that PMWS such as, porcine reproductive and respiratory syndrome (PRRS), generalized tremors, porcine dermatitis and nephropathy syndrome (PDNS), arthritis, nervous signs, erysipelas and even healthy pigs. [Copyright &y& Elsevier]

We examined the genetic characteristics of a human oral treponeme isolated from subgingival plaque of a patient with periodontal disease that could not be assigned to any of the previously described oral Treponema species. The guanine-plus-cytosine content of its DNA was 51 mole%. The levels of DNA-DNA relatedness of the organism to other Treponema species, including Treponema denticola, Treponema vincentii, Treponema socranskii, Treponema pallidum and Treponema phagedenis, were less than 30%. This study clearly demonstrated that the isolated treponeme could be completely distinct from the established oral Treponema species genetically. Also, the study indicated remarkable genetic heterogeneity among human oral Treponema species. [ABSTRACT FROM AUTHOR]