Unweighted Pair-group Method Using Arithmetic Averages Research Articles

Phytochemical attributes of endemic endangered primrose (Primula heterochroma Stapf.) accessions grown in Iran.

Primula heterochroma is indigenous to Caspian coast forests in the north of Iran. Total phenols, total flavnoids, total carotenoids and antioxidant capacity of 50 P. heterochroma accessions were investigated. The highest total phenol (1272.31mg GA equivalent/100g fresh weight) and total flavonoids (615mg catechin/100g fresh weight) were observed in G5 accession from Saravan. The highest antioxidant activity was observed in G14 accession (73.03%) from Kacha, followed by G2 accession (69.75%) and G5 accession (66.84%) from Saravan. The results of HPLC analysis showed that quercetin-3-glucoside was the major phenolic compound widely found in these accessions followed by chlorogenic acid. There was a linear relationship between the antioxidant capacities and the total phenols and total flavonoid. Inversely, there was no statistically significant correlation between total carotenoid and antioxidant activity. Based on the path coefficient analysis, the maximum direct effect on antioxidant was observed in total phenols (0.908). In addition, the cluster analysis based on Euclidean distance with Unweighted pair-group method using arithmetic average (UPGMA) method separated the accessions into four main groups. Our results supported that Iranian wild primrose accessions possess valuable antioxidant properties for therapeutic and potential medicinal use.

Molecular epidemiology of invasive Candida albicans at a tertiary hospital in northern Taiwan from 2003 to 2011.

Candida albicans is a common cause of bloodstream fungal infections in hospitalized patients. To investigate its epidemiology, multilocus sequence typing (MLST) was performed on 285 C. albicans bloodstream isolates from patients in Chang Gung Memorial Hospital at Linkou (CGMHL), Taiwan from 2003 to 2011. Among these isolates, the three major diploid sequence types (DSTs) were 693, 659, and 443 with 19, 16, and 13 isolates, respectively. The 179 DSTs were classified into 16 clades by unweighted pair-group method using arithmetic averages (UPGMA). The major ones were clades 1, 4, 3, and 17 (54, 49, 31, and 31 isolates, respectively). Further analyses with eBURST clustered the 285 isolates into 28 clonal complexes (CC). The most common complexes were CC8, CC20, and CC9. DST 693 that had the highest number of isolates was determined to be the cluster founder of CC20, which belonged to clade 3. So far, 33 isolates worldwide including 29 from Taiwan and 4 from Korea, are CC20, suggesting that CC20 is an Asian cluster. Two fluconazole-resistant isolates belonging to CC12 and CC19 were detected. All other CGMHL isolates were susceptible to 5-flucytosine, amphotericin B, anidulfungin, caspofungin, fluconazole, itraconazole, micafungin, posaconazole, and voriconazole. However, CC20 isolates exhibited significantly lower susceptibility to fluconazole. In conclusion, the 285 CGMHL C. albicans isolates displayed geographically clustering with Asian isolates, and most of them are susceptible to common antifungal drugs. Isolates of DST 693, a Taiwanese major genotype belonging to MLST clade 3, were more resistant to fluconazole than other isolates.

Mediterranean basin Ficus carica L.: from genetic diversity and structure to authentication of a Protected Designation of Origin cultivar using microsatellite markers

The selected germplasm of Ficus carica established in a gene bank collection will be useful for conservation and management and important for fig tree breeding programs. Advancement in plant breeding is assisted by accurate information on genetic diversity and structure. A collection of ninety fig tree (Ficus carica L.) cultivars originating from the Mediterranean basin and conserved in an ex situ gene bank collection was genotyped using seven microsatellite markers. A total of 91 alleles were detected presenting an average of 13 alleles per locus. The gene bank fig tree collection preserved a high level of genetic diversity. The mean expected and observed heterozygosities over the seven single locus microsatellites averaged 0.747 and 0.784, respectively. The total value of the probability of identity was 2 × 10−6. The 90 fig tree accessions formed four clusters in the unweighted pair group method using arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the fig tree accessions based on their geographical origin. Moreover, the 90 fig tree accessions could be divided into two clusters based on STRUCTURE analysis. Additionally, microsatellites coupled with high-resolution melting analysis enabled both the distinction, identification and authentication of the ‘Kymis’ fig tree Protected Designation of Origin cultivar and its products. In conclusion, results presented here are significant for the management of gene bank collections, breeding programs and authentication of fig tree cultivars.

Rep-PCR typing of Staphylococcus spp. strains in meat paste production line and identification of their origin

A meat paste production line and its microbial parameters have been evaluated in single Czech company. The raw meat paste samples before heat treatment were tested positively for the presence of three staphylococci species: Staphylococcus aureus, Staphylococcus haemolyticus and Staphylococcus epidermidis. Subsequent microbial analysis of meat paste components and ingredients (fresh meat, water, spices, equipment) identified only the spices used as positive for S. aureus (coriander, cinnamon, badian, mustard – (10 - 40 cfu/g)) and S. haemolyticus strains (juniper, ginger). The collection of sixteen collected strains (S. aureus (n = 4), S. haemolyticus (n = 4), S. epidermidis (n = 8)) has been typed with the rep-PCR method utilising (GTG)5 primer. Analysis of the fingerprints using the unweighted pair-group method using arithmetic averages (UPGMA) clustering method revealed presence of eleven strain clusters with similarity lower than 90%: two fingerprint clusters of S. aureus, three individual clusters characteristic for S. haemolyticus and six different S. epidermidis specific clusters. The S. aureus strains from different types of spice were identical, resp. very similar. Molecular tracking composed from the rep-PCR analysis of acquired isolates and comparison among all collected fingerprints confirmed the spices to be the source of both S. aureus and S. haemolyticus strains identified in raw meat paste. The additional rep-PCR analysis of the S. epidermidis collection confirmed usability and performance of this method. The antibiotic susceptibility to fourteen individual antibiotics has been examined among the collected staphylococci strains. The predominant erythromycin resistance (68.8%) was followed with the resistance to amoxicillin/clavulanic acid (56.2%). Other resistances observed were less frequent (clindamycin – 12.5%, oxacillin – 6.3%, tetracycline – 6.3%, sulphamethoxazole-trimethoprim – 6.3%, chloramphenicol – 6.3%, novobiocin – 6.3%). As shown by our experimental results, rep-PCR with the (GTG)5 primer is an applicable tool for typing of bacterial strains and may be used for identifying the source of contamination.

Genetic characterization of microsporidians infecting Indian non-mulberry silkworms (Antheraea assamensis and Samia cynthia ricini) by using PCR based ISSR and RAPD markers assay

This study established the genetic characterisation of 10 microsporidian isolates infecting non-mulberry silkworms (Antheraea assamensis and Samia cynthia ricini) collected from biogeographical forest locations in the State of Assam, India, using PCR-based markers assays: inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD). A Nosema type species (NIK-1s_mys) was used as control for comparison. The shape of mature microsporidian spores were observed oval to elongated, measuring 3.80 to <TEX>$4.90{\mu}m$</TEX> in length and 2.60 to <TEX>$3.05{\mu}m$</TEX> in width. Fourteen ISSR primers generated reproducible profiles and yielded 178 fragments, of which 175 were polymorphic (98%), while 16 RAPD primers generated reproducible profiles with 198 amplified fragments displaying 95% of polymorphism. Estimation of genetic distance coefficients based on dice coefficients method and clustering with un-weighted pair group method using arithmetic average (UPGMA) analysis was done to unravel the genetic diversity of microsporidians infecting Indian muga and eri silkworm. The similarity coefficients varied from 0.385 to 0.941 in ISSR and 0.083 to 0.938 in RAPD data. UPGMA analysis generated dendrograms with two microsporidian groups, which appear to be different from each other. Based on Euclidean distance matrix method, 2-dimensional distribution also revealed considerable variability among different identified microsporidians. Clustering of these microsporidian isolates was in accordance with their host and biogeographic origin. Both techniques represent a useful and efficient tool for taxonomical grouping as well as for phylogenetic classification of different microsporidians in general and genotyping of these pathogens in particular.

Purification, characterization and molecular cloning of alpha-2-macroglobulin in cobia, Rachycentron canadum

Alpha-2-macroglobulin (α-2-M) is a broad spectrum protease inhibitor which is abundant in the plasma of vertebrates and several invertebrates. The α-2-M was purified from cobia (Rachycentron canadum) plasma by a four-step procedure: poly ethylene glycol fractionation, affinity chromatography, hydrophobic interaction chromatography and ion exchange chromatography on Fast Protein liquid chromatography system in the present study. It migrated as one protein band with a molecular mass of about 360 kDa in the native state, whereas in SDS-PAGE it was about 180 kDa under non-reducing condition. This result revealed that the native protein was a dimer. In addition, it was cleaved into two different fragments of molecular mass about 93 and 87 kDa when reduced by dithiothreitol (DTT). The anti-protease activity of the purified α-2-M was apparently decreased as temperature elevated above 50 °C. The α-2-M exhibited highest protease inhibitory activity at pH 9. The results indicate that the α-2-M is a heat-labile and alkaline protease inhibitor. The purified α-2-M exhibited more than 50％ protease inhibitory activity against extracellular products (ECP) of Vibrio alginolytius isolated from diseased cobia. It seems that the protease activities in ECP may be affected by the plasma α-2-M. The protease inhibitory activities of cobia plasma or purified α-2-M were decreased when incubated with 10 mM methylamine for 30 min.The α-2-M cDNA consisted of 4611 bp with an open reading frame of 4374 bp had been cloned from cobia liver. This sequence contained thioester domain (GCGEQ) and thirteen predicted N-linked glycosylation sites. In addition, the amino acid sequence of thioester domain and genes of adjacent regions of cobia α-2-M were further compared with sequences of known fish species in GenBank. The unweighted pair group method using arithmetic average (UPGMA) was employed to construct the phylogenetic trees of α-2-M among different fish species (freshwater fish, sea water fish and primitive fish), and all these fish species were then clustered into three groups. The cobia α-2-M was closer to that of sea water fish than that of freshwater fish compared basing on its similarity of amino acid sequence and phylogenetic analysis of the partial gene.

Phylogenetic Tree Generation using Different Scoring Methods

Data Mining is a branch of knowledge discovery in the field of research and development. The biological data is available in different formats and is comparatively more complex. Knowledge discovery from these large and complex databases is the key problem of this era. Data mining and machine learning techniques are needed which can scale to the size of the problems and can be customized to the application of biology. Hierarchical Clustering is the one of the main techniques for data mining. Phylogeny is the evolutionary history for a set of evolutionary related species. One approach on determining the evolutionary histories of a dataset are scoring based methods. There are number of different distance based methods of which two are details with here: the UPGMA (Unweighted Pair Group Method using Arithmetic average) and Neighbor Joining. A method for construction of distance based phylogenetic tree using hierarchical clustering is proposed and implemented on different rice varieties. The sequences are downloaded from NCBI databank. Evolutionary distances are calculated using jukes cantor distance method. Multiple sequence alignment is applied on different datasets. Trees are constructed for different datasets from available data using both the distance based methods and pruning technique. SNAP calculates synonymous and nonsynonymous substitution rates based on a set of codon aligned nucleotide sequences. The DNA Multiple sequences to calculate the GC content of eukaryotes, molecular weight, melting temperature and tree information. Extractions of closely related varieties are performed by applying threshold condition. Then, final tree is constructed using these closely related rice varieties.

Characterization of Eastern Filbert Blight-resistant Hazelnut Germplasm Using Microsatellite Markers

The development of new cultivars resistant to the disease eastern filbert blight (EFB), caused by Anisogramma anomala, is of primary importance to hazelnut (Corylus sp.) breeders in North America. Recently, a large number of EFB-resistant cultivars, grower selections, and seedlings from foreign germplasm collections were identified. However, for a significant number of these, little is known of their origin, relationships, or genetic background. In this study, 17 microsatellite markers were used to investigate the genetic diversity and population structure of 323 unique accessions, including EFB-resistant and tolerant germplasm of uncertain origins, in comparison with a panel of known reference accessions representing a wide diversity of Corylus cultivars, breeding selections, and interspecific hybrids. The resulting allelic data were used to construct an unweighted pair group method using arithmetic averages (UPGMA) dendrogram and STRUCTURE diagram to elucidate relationships among the accessions. Results showed 11 consensus groups with EFB-resistant or tolerant accessions in all, providing strong evidence that EFB resistance is relatively widespread across the genus Corylus. Furthermore, open-pollinated seedlings tended to group together with reference accessions of similar geographic origins, providing insight into their genetic backgrounds. The results of this study add to the growing body of knowledge of hazelnut genetic resources and highlight recently introduced EFB-resistant seedling germplasm as new, unrelated genetic pools of resistance.

Biogeography of western Mediterranean butterflies: combining turnover and nestedness components of faunal dissimilarity

AbstractAimUnpartitioned dissimilarity indices such as the Sørensen index (βsor) tend to categorize areas according to species number. The use of turnover indices, such as the Simpson index (βsimp), may lead to the loss of important information represented by the nestedness component (βnest). Recent studies have suggested the importance of integrating nestedness and turnover information. We evaluated this proposition by comparing biogeographical patterns obtained by unpartitioned (βsor) and partitioned indices (βsimp and βnest) on presence data of western Mediterranean butterflies.LocationWestern Mediterranean.MethodsWe assessed the regionalization of 81 mainland and island faunas according to partitioned and unpartitioned dissimilarity by using cluster analyses with the unweighted pair‐group method using arithmetic averages (UPGMA) combined with non‐metric multidimensional scaling (NMDS). We also carried out dissimilarity interpolation for βsor, βsimp, βnest and the βnest/βsor ratio, to identify geographical patterns of variation in faunal dissimilarity.ResultsWhen the unpartitioned βsor index was used, the clustering of sites allowed a clear distinction between insular and mainland species assemblages. Most islands were grouped together, irrespective of their mainland source, because of the dominant effect of their shared low richness. βsimp was the most effective index for clustering islands with their respective mainland source. βsimp clustered mainland sites into broader regions than clusters obtained using βsor. A comparison of regionalization and interpolation provided complementary information and revealed that, in different regions, the patterns highlighted by βsor could largely be determined either by nestedness or turnover.Main conclusionsPartitioned and unpartitioned indices convey complementary information, and are able to reveal the influence of historical and ecological processes in structuring species assemblages. When the effect of nestedness is strong, the exclusive use of turnover indices can generate geographically coherent groupings, but can also result in the loss of important information. Indeed, various factors, such as colonization–extinction events, climatic parameters and the peninsular effect, may determine dissimilarity patterns expressed by the nestedness component.

Phenotypic variations in cones and seeds of natural Pinus kesiya var. langbianensis populations in Yunnan Province, China

Aims Our objectives were to determine phenotypic variations in 11 natural Pinus kesiya var. langbianensis populations and their relationship with distributions. Methods We investigated 16 phenotypic traits for 330 individuals in 11 natural populations of P. kesiya var. langbianensis in Yunnan Province, and used nested analysis, variation coefficient, correlation analysis, and un-weighted pair-group method using arithmetic averages(UPGMA) cluster analysis to analyze results. Important findings There are significant differences in phenotypic variation among and within populations. Variation is greater within populations(54.76%) than among populations(10.44%). Mean phenotypic differentiation coefficient is 11.95% among populations. Differentiations among populations are relatively small. The average variation coefficient of seed weight is highest(35.51%), followed by cone weight(35.1%); the average variation coefficient of seed size is smallest(8.86%). The seed size is the most stable phenotypic traits. Phenotypic diversity is greatest in Jinggu County and smallest in Jinghong City. There are significant or highly significant correlations among most phenotypic traits in cones and seed, indicating that greater the cone length and cone weight, larger the seed scales, seed size, seed wing, 1 000 seeds weight, and the number of seed scales and seeds per cone. The mean annual temperature appears to be the most prominent ecological factor influencing phenotypic traits, followed by the January mean temperature and growing degree days at 5 °C. According to UPGMA cluster analysis, the 11 populations can be divided into two groups and four subgroups due to difference in geographic distance, which is significantly related to annual precipitation and growing degree days at 5 °C.

Zbiorowiska namułkowe z klasy Isoëto-Nanojuncetea Br.-Bl. et Tx. 1943 w Polsce [Occurrence of the Isoëto-Nanojuncetea-class communities in Poland

The &lt;em&gt;Isoëto-Nanojuncetea&lt;/em&gt;-class includes short-lived and ephemerical communities occurring on temporarily flooded places in Western, Southern and Central Europe and Northern Africa. Results of the numerical classification of 739 phytosociological releves of the communities occurring in Poland are presented and discussed. Ali the releves were made in accordance with the principles of the BRAUN-BLANQUET school of syntaxonomy. The calculations were performed using NCLAS program of the SYN-TAX IV package. The JACCARD formuła and the unweighted pair-group method, using arithmetic averages (UPGMA) were applied. There is a strong habitat and floristic differentation of the communities of the &lt;em&gt;Isoëto-Nanojuncetea&lt;/em&gt;-class occurring in Poland. The results of the numerical classification indicate that, the distuinguished communities belong to two alliances: the &lt;em&gt;Radiolion linoidis&lt;/em&gt; (Rivas Goday 1961) Pietsch 1965 (for associations occurring on synanthropic localities like stubble fields) and the &lt;em&gt;Elatini-Eleocharition ovatae&lt;/em&gt; Pietsch 1965 (for communities growing on bottoms of dried ponds and exposed river or lakę banks). The distinguished communities arę phytosociologically characterized on basis of 223 selected releves. These arę: &lt;em&gt;Spergulario-Illecebretum verticillati, Ranunculo-Myosuretum minimi, Centaurium pulchellum-Pottia truncata-commumiy, Heleocharetum ovatae, Cyperetum flavescentis&lt;/em&gt; and &lt;em&gt;Cyperus fuscus-Limosella aquatica&lt;/em&gt;-commumiy. The study focused on: (1) attempting to solve the problem of phytosociological classification for the communities occurring in Poland, (2) preparing a complete catalogue of them and (3) giving the full list of character species (also among bryophytes) of distinguished syntaxa. It has led to finding out the relation between the communities occurring in Poland and the associations of Western Europe. The problem of the naturality of certain distinguished associations was discussed. The paper gives also some open questions demanding further studies and some suggestions of methods to be applied.

Estimation of genetic relationships among 39 cultivars of avocado (Persea americana Mill.) by analysing the volatile constituents of leaves

SummaryThe volatile constituents of leaf samples were analysed to determine genetic relationships among 39 avocado (Persea americana Mill.) cultivars (25 from Taiwan and 14 from El Salvador) representing all three horticultural races (Mexican, Gutemalan, and West-Indian). A stable isotope, internal standard-based, solid-phase micro-extraction (SPME) GC-MS method was used to provide calibrated, quantitative measures of the concentrations and compositions of volatile organic compounds (VOCs) in avocado leaves in heated headspace vials. The calibrated intensity of VOCs in the leaves of Mexican race avocados was higher than in the Guatemalan and West-Indian races. Twelve race-specific VOCs, and ten VOCs of variable abundance were selected as indicators for further analysis. A similarity matrix of VOCs was calculated using Euclidean distances of the log10 values of the calibrated abundances of the indicator compounds. A dendrogram was produced based on the unweighted pair group method using arithmetic averages (UPGMA). The 39 avocado cultivars clustered into three major groups based on their VOCs. Thirteen Taiwanese cultivars and three West-Indian cultivars were clustered in the same group in the dendrogram. The results showed that most Taiwanese cultivars were closely related to cultivars of the West-Indian race.

Evaluation of vertical and horizontal changes in community structure of zooplankton in a deep dam lake

The purpose of this study was to describe the horizontal and vertical distributions of the zooplankton community structure in Karakaya Dam Lake. Rotifers were numerically dominant (81.89%) in the community during the study period; they were followed by Copepoda (10.32%) and Cladocera (7.79%). In the metalimnetic maximum oxygen zone between 5 and 10 m, cladocerans made up 70.1% of the total number of zooplankton in June and 27.3% of the total number of zooplankton in November. Oxygen values decreased at 10 and 15 m in September and November. While the abundance of rotifers and cladocerans decreased as well, cyclopoids increased (60% of total zooplankton at 10 m). Nitrogen and soluble reactive phosphate were at low concentrations. Relationships among zooplankton, abundance, and environmental factors were analyzed using the unweighted pair-group method using arithmetic averages (UPGMA) and canonical correspondence analysis (CCA). UPGMA cluster analysis was used to illustrate unimodal species distribution by classification into 2 groups. Eigenvalues of axes clarified 42.7% of the cumulative variance in species data and 62.9% of the relationship between species and environmental data in the CCA. Many zooplankton species, rather tolerant to different environmental conditions, are good indicators for water quality and can be used for the biomonitoring of water ecosystems.

Genetic structure of a population of Rhizoctonia solani AG 2-2 IIIB from Agrostis stolonifera revealed by inter-simple sequence repeat (ISSR) markers

Rhizoctonia solani anastomosis group (AG) 2-2 IIIB is an important pathogen of creeping bentgrass (Agrostis stolonifera) worldwide. Limited information is currently available concerning levels of genetic diversity and population structure within this pathogen on creeping bentgrass. Twenty-three isolates were obtained from 17 symptomatic patches of a creeping bentgrass field at the Guelph Turfgrass Institute, Ontario. Anastomosis grouping was identified on the basis of morphological and cultural characteristics, and by PCR amplification using specific primers. The population structure was analyzed using five inter-simple sequence repeat (ISSR) primers, which generated 34 polymorphic loci out of 50 band positions. Distance analysis with the unweighted pair group method using arithmetic averages (UPGMA) resulted in a dendrogram which clustered the 23 isolates into four main groups, with genetic distances (1 – Dice coefficient of genetic similarity) ranging from 0 to 12%. This level of variation among isolates of R. solani AG 2-2 IIIB present in a small field of creeping bentgrass and even within single patches implied some level of recombination, but the distribution of ISSR haplotypes and gametic disequilibrium analyses revealed that asexual propagule movement was the dominant force in the population structure in this small area.

Genetic variation of some goat populations in Ethiopia by means of blood protein polymorphism

Genetic variability of 298 individuals from four indigenous goat types (Afar, Hararghe Highland, Western Highland and Western Lowland of Ethiopia), two exotic breeds (Toggenburg and Anglo-Nubian) and three crossbreed populations (crosses between the exotic breeds and Hararghe Highland and Somali goat types) were investigated. The red blood cell lysates and plasma proteins were analyzed by starch gel electrophoresis. From a total of five loci studied, two were found to be polymorphic. Two alleles were detected at each of Haemoglobin (Hb) and Transferrin (Tf) loci. Only one allele was detected at each of the loci Carbonic anhydrase (CA), Albumin (Al) and Post Transferrin (PTF) in all the populations of goats studied. In most cases, the observed genotypic frequencies were not significantly different from that expected under the Hardy-Weinburg equilibrium. The proportion of polymorphic loci (P%) varied between 20.0% and 40.0%, with mean number of alleles per locus between 1.2 and 1.4, and expected heterozygosities (HE) between 0.030 and 0.177 while mean observed heterozygosities (HO) were between 0.032 to 0.217. Among the three groups of goat populations, higher variability was found in crossbred populations. Afar goat type was more variable (HO=6.7%) among the indigenous goat types. Cluster analysis based on Nei’s standard genetic distance and the unweighted pair-group method using arithmetic averages (UPGMA) revealed low level of genetic distance among populations. The results indicated a higher proportion of genetic variation between populations. Keywords: Afar goat, Ethiopia, Hararghe goat, Western Highland goat, Western Lowland goat.

English

Genetic diversity of eighteen glory lily (Gloriosa superba&nbsp;L.) accessions of diverse geographical origin was studied using Random Amplified Polymorphic DNA (RAPD) markers. Fifty eight out of seventy primers screened showed polymorphism across the present set of accessions. A total of 413 amplicons were scored using these 58 primers. Eighty eight per cent of the amplified product showed polymorphism, indicating a fair amount of variation at the DNA level among these accessions. Cluster analysis delineated the accessions into two groups. &nbsp; Key words:&nbsp;Genetic diversity,&nbsp;Gloriosa&nbsp;superba, random amplification of polymorphic DNA (RAPD), unweighted pair group method using arithmetic averages (UPGMA).

Rep-PCR-based typing as a tool for tracking of MRSA infection origin

A performance of rep-PCR fingerprinting method with the (GTG)5 primer was explored in order to evaluate its practical application for confirmation the source of human staphylococci infection. A laboratory worker daily working with the MRSA and Staphylococcus aureus strains has been tested positively for MRSA nosocomial infection. The collection of nine MRSA strains held in the laboratory has been typed with the rep-PCR method. Analysis of the fingerprints with the unweighted pair-group method using arithmetic averages (UPGMA) clustering method revealed presence of six strain clusters with similarity lower than 85%. The fingerprint of MRSA strain infecting the human differed significantly from remaining fingerprints. This provided clear evidence that MRSA strain infecting the personal did not come from the laboratory strains collection. Our experimental results showed rep-PCR with the (GTG)5 primer as an effective tool applicable for differentiation of individual S. aureus strains. However, the reproducibility and discrimination power of the method depended on strict observance of the optimal PCR time and temperature profile and PCR composition as well.

Divergência genética entre cafeeiros do germoplasma Maragogipe

Este trabalho objetivou identificar a divergência genética entre acessos de cafeeiro do grupo Maragogipe, situados no Banco Ativo de Germoplasma de Café do Estado de Minas Gerais, no município de Patrocínio (MG), por meio de análises multivariadas. Foram avaliados 27 descritores morfo-agronômicos, e a distância generalizada de Mahalanobis foi usada para quantificar a divergência genética entre os acessos. Como estratégias de agrupamento, foram empregados o agrupamento de Tocher, o método hierárquico Unweighted Pair-Group Method Using Arithmetic Averages (UPGMA) e a análise de variáveis canônicas. A análise de agrupamento pelos métodos de Tocher e UPGMA separaram os acessos em três e seis grupos, respectivamente. A análise da contribuição relativa de cada característica para a dissimilaridade genética destacou as características intensidade da ondulação da folha, quantidade de inflorescência por axila foliar e produtividade média como as que mais contribuíram para a obtenção da divergência genética. Observou-se que as três primeiras variáveis canônicas explicaram mais de 90% da variância total contida no conjunto das características analisadas. A combinação entre os acessos MG0167 e MG0170 é a mais promissora em um possível cruzamento para uso imediato em programas de melhoramento.

Genetic variation in oriental tobacco (Nicotiana tabacum L.) by agro-morphological traits and simple sequence repeat markers

The objectives of this study were to assess genetic diversity and determine differences between several oriental tobacco genotypes by examining both agro-morphological traits and molecular markers. Simple lattice design with two replications was used to evaluate 100 oriental tobacco genotypes. Analysis of variance manifested that there is high level of genetic diversity in oriental-type tobaccos based on morphological traits including number of leaf, days to 50% flowering, leaf length, leaf width, leaf fresh weight, leaf dry weight, stem height and stem girth. Classification of genotypes using agro-morphological data by means of un-weighted pair-group method using arithmetic average (UPGMA) algorithm based on squared standardized Euclidean distances resulted four distinguishable groups that pursuit own geographical distribution. In the molecular marker investigations, a total of 13 simple sequence repeats (SSR) primer pairs were used to determine polymorphism of the test germplasm. Thirty five alleles were scored at 13 SSR loci. The average number of alleles per locus (na) and the effective allele number (Ae) were 2.69 and 2.34, respectively. By using SSR data, pair wise Jaccard's similarity coefficients were produced. Grouping of genotypes via Jaccard's similarity coefficients and using UPGMA clustering method lead to three groups that had not any accommodated with own origins. Results reveled that there is not completely agreement for classification based on agro-morphological and SSR loci in oriental-type tobaccos. Because of non influence of environmental effects on molecular marker, heterotic groups based on SSR markers could be closer to reality.

Description of Trichodorus japonicus n. sp. (Triplonchida: Trichodoridae) from Japan

Trichodorus japonicus n. sp. was intercepted from soil around roots of Acer palmatum and Camellia japonica imported from Japan. It is characterised in the male by having three ventromedian cervical papillae between the onchiostyle base and the secretory-excretory pore, nearly straight or slightly ventrally curved spicules with a finely striated blade except at extremities, three (rarely four) ventromedian precloacal supplements, the posterior supplement (SP1) opposite the middle of the retracted spicules, the presence of a bursa-like thickening, and terminal tail cuticle not or only slightly thickened. The female has a pore-like vulva in ventral view, pear-shaped to cylindrical-shaped vagina, vagina length 36% (31-41%) of the corresponding body diam., vaginal sclerotised pieces 1.9-2.5 μm in size, triangular to rounded triangular in lateral view and slightly separated (1-2 μm), and a pair of ventrosubmedian to ventrosublateral advulvar body pores (located within one-third body diam. posterior to vulva). The results of phylogenetic analysis based on the rDNA-ITS2 and 28S-D2/D3 sequences data using UPGMA (Unweighted pair group method using arithmetic average) and ME (Minimum Evolution) confirmed the close relationships of T. japonicus n. sp. with T. cedarus, T. paracedarus and T. nanjingensis.