Simple sequence repeat (SSR)-based gene diversity in <Emphasis Type="Italic">Burkholderia pseudomallei</Emphasis> and <Emphasis Type="Italic">Burkholderia mallei</Emphasis>

Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.     

Usefulness of Multiple-Locus VNTR Fingerprinting in detection of clonality of community- and hospital-acquired <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> isolates

Staphylococcus aureus has become a major source of hospital infections and the risk of colonisation and infection by community-acquired methicillin-resistant S. aureus (CA-MRSA) is increasingly higher. Because of the importance of S. aureus to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. In this study we evaluated the usefulness of multiplex PCR based Multi-Locus VNTR Fingerprinting (MLVF) as the first step method for rapid differentiation of Croatian and Polish S. aureus isolates in hospital and community settings. This is a first report of the usefulness of MLVF in typing of hospital-acquired methicillin-sensitive S. aureus (HA-MSSA) and four CA-MRSA isolates. A total of 47 isolates of S. aureus recovered in Croatia in 2004 and in Poland in 2006 and 2007 were tested. The MLVF results were compared to those produced by other typing methods, such as Pulsed-Field Gel Electrophoresis (PFGE), Multi-Locus Sequence Typing (MLST) and spa typing. The MLVF analysis showed almost the same clonality results as the remaining typing methods although some differences were found. Epidemiological data about the relation among S. aureus isolates and the results produced by typing methods applied in the present study indicate that because of the advantages in ease and speed of Variable Number of Tandem Repeats (VNTR) procedure over PFGE, spa typing and MLST, MLVF can be used as a first screening method followed by additional typing.     

Cold storage and cryopreservation of hairy root cultures of medicinal plant <Emphasis Type="Italic">Eruca sativa</Emphasis> Mill., <Emphasis Type="Italic">Astragalus membranaceus</Emphasis> and <Emphasis Type="Italic">Gentiana macrophylla</Emphasis> Pall.

To explore the possibility of an effectively long-term preservation of the germplasm of the HR lines of medicinal plant Astragalus membranaceus, Gentiana macrophylla Pall., and Eruca sativa Mill., both cold storage and cryopreservation approaches were attempted and compared. After 5-month cold storage on half strength Murashige and Skoog (1962) (1/2 MS) agar medium (AM), up to 82.9, 75.7, and 100% of the A. membranaceus, G. macrophylla and E. sativa hairy roots (HRs) recovered growth, respectively. The survival rates of A. membranaceus and G. macrophylla HRs significantly decreased, whereas that of E. sativa HR was unchanged with the addition of increased levels of exogenous abscisic acid (ABA) during cold storage. Using the encapsulation–vitrification (EV) method for cryopreservation, the G. macrophylla HRs died, whereas up to 6 and 73% of the A. membranaceus and E. sativa HRs survived, respectively. The HR lines evaluated with both methods showed no significant differences in morphology and growth rate compared with controls that were not subjected to preservation methods. These results suggest that cold storage is a more suitable alternative for the HR lines of the three studied plant species and that specificity of plant species have profound effects on the effectiveness of preservation.     

Development of SSR markers from an ectomycorrhizal fungus, <Emphasis Type="Italic">Suillus bovinus</Emphasis>

Nine simple sequence repeat (SSR) loci were isolated from an ectomycorrhizal fungus Suillus bovinus by dual-suppression PCR. Three of the SSR loci isolated were polymorphic. The number of alleles per locus was between two and seven, and expected heterozygosities ranged from 0.087 to 0.740. One of these was confirmed to be species specific and codominant, suggesting applicability for the analysis of belowground population structure and gene flow of S. bovinus.     

Influence of the<Emphasis Type="Italic">SMT2</Emphasis> knock-out on hypocotyl elongation in<Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Inhibitors are very important in the study of hormone function. Brasinazole (Brz) is a specific inhibitor of brassinosteroids (BRs) biosynthesis. To expand our knowledge of the molecular mechanisms of plant steroid signaling, we performed genetic screening using medium containing Brz under dark conditions. Mutants insensitive to Brz developlonger hypocotyls than their wild type counterparts. We isolatedabz453 as a Brz insensitive mutant. TAIL-PCR and the segregation ratio of T2 plants indicated a single T-DNA insertion at the 24-Sterol C-methyltransferase (SMT2) gene in theabz453 mutant. Recapitulation for putative FCP serine phosphatase (FSP), the gene neighboringSMT2, indicated no significant phenotypes, but theSMT2 anti-sense (SMT2-AS) line developed longer hypocotyls than the wild type in medium containing Brz. Additionally, theSMT2-AS line displayed similar phenotypes to theabz453 line in soil including enhanced growth and smaller silique. Theabz453 andSMT2-AS mutants showed phenotypes similar to those of wild type in medium containing benzylaminopurine, pacrobutrazol and ACC (precursor for ethylene) under dark conditions. However, when brassinolide (BL) dose response was observed, theabz453 andSMT2-AS lines showed higher sensitivity than wild type. Theabz453/det2 andabz453/bri1-119 double mutants showed enhanced growth compared to thedet2 andbri1-119 line under both dark and light conditions. Specially, in dark conditions double mutants displayed nearly 2- and 1.5-fold longer hypocotyls thandet2 andbri1-119 plants. Brz insensitivity to theSMT2 knock-out mutant and phenotypes of double mutants indicate that not only do BRI1 and DET2 influence the BRs response, as evidenced by hypocotyl elongation, but another sterol derived signals may also be affected in mutants, suggesting that another pathway is involved in hypocotyl elongation due to SMT2.     

`Cloning of <Emphasis Type="Italic">vip1/vip2</Emphasis> genes and expression of Vip1Ca/Vip2Ac proteins in <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis>

Forty-one Bacillus thuringiensis (Bt) standard reference strains and 118 Bt local isolates were screened for vip1/vip2 genes by PCR amplification, with only three strains (HD201, HD109 and HD12) producing the desired bands. Southern blot showed that vip1/vip2 genes were located on a 10 Kb EcoRV fragment of their total DNAs. Furthermore, the vip1Ca/vip2Ac genes were cloned from a partial genomic library of HD201. Sequence homologous analysis revealed that vip2Ac gene was highly conserved and encoded a protein possibly having ADP-ribosyltransferase activity, and that vip1Ca gene was of low homology, especially at its 3-terminus. Western blot showed that Vip1Ca and Vip2Ac proteins could be detected from middle logarithmic phase to the stationary phase in Bt HD201. However, bioassays of HD201 supernatants exhibited no activity against Culex quinquefasciatus, Spodoptera exigua, S. litura, Helicoverpa amigera and Tenebrio molitor larvae. Whether Vip1Ca and Vip2Ac proteins have any toxicity to other susceptible targets still needs to be investigated.     

Microsatellite diversity in tetraploid <Emphasis Type="Italic">Gossypium</Emphasis> germplasm: assembling a highly informative genotyping set of cotton SSRs

A series of 320 mapped simple sequence repeats (SSRs) have been used to screen the allelic diversity of tetraploid Gossypium species. Fourty-seven genotypes were analyzed representing (i) the wide spectrum of diversity of the cultivated pool and of the primitive landraces of species G. hirsutum (‘marie-galante’, ‘punctatum’, ‘richmondi’, ‘morrilli’, ‘palmeri’, and ‘latifolium’, and ‘yucatanense’), and (ii) species G. barbadense, G. darwinii and G. tomentosum. The polymorphism of 201 SSR loci revealed 1128 allelic variants ranging from 3 to 17 per locus. Neighbor-joining (NJ) method based on genetic dissimilarities produced groupings consistent with the assignments of accessions both at species and at race level. Our data confirmed the proximity of the Galapagos endemic species G. darwinii to species G. barbadense. Within species G. hirsutum, and as compared to the other 6 races, race yucatanense appeared as the most distant from cultivated genotypes. Race yucatanense also exhibited the highest number of unique alleles. The important informative heterogeneity of the 201 SSR loci was exploited to select the most polymorphic ones that were assembled into three series of genome-wide (i.e. each homoeologous AD chromosome pair being equally represented) and mutliplexable (× 3) SSRs. Using one of these ‘genotyping set’, consisting of 39 SSRs (one 3-plex for each of the 13 AD chromosomes pairs) or 45 loci, we were able to assess the relationships between accessions and the topology in the genetic diversity sampled. Such genotyping set of highly informative SSR markers assembled in PCR-multiplex, while increasing genotyping throughput, will be applicable for molecular genetic diversity studies of large germplasm collections. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (<Emphasis Type="Italic">Phleum pratense</Emphasis> L.)

To develop simple sequence repeat (SSR) markers for the hexaploid forage grass timothy (Phleum pratense L.), we used four SSR-enriched genomic libraries to isolate 1,331 SSR-containing clones. All four libraries contained a high percentage of perfect clones, ranging from 78.1% to 91.6%. From these clones, we developed 355 SSR markers when tested from 502 SSR primer pairs. Using all 355 SSR markers we tested one screening panel consisting of eight timothy clones to detect the level of polymorphism and identify a set of loci suitable for framework mapping. The SSR markers detected 90.4% polymorphism between the parents of a pseudo-testcross F₁ population. These SSR markers will provide an ideal marker system to assist with gene targeting, QTL (quantitative trait locus) mapping, and marker-assisted selection in timothy.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Development of ten microsatellite markers for <Emphasis Type="Italic">Quercus mongolica</Emphasis> var. <Emphasis Type="Italic">crispula</Emphasis> by database mining

Simple sequence repeats (SSRs) in the NCBI dbEST database were surveyed to identify potential SSR markers for Quercus mongolica. In total, 2,691 gene sequences, mainly from expressed sequence tags (ESTs) for Q. robur and Q. petraea had been registered. Twenty-two PCR primers were designed for SSRs in these sequences and screened for polymorphisms in 16 Q. mongolica trees. Ten loci were easily genotyped and showed polymorphism, with numbers of alleles and expected heterozygosity ranging from 3 to 15 and 0.28 to 0.94, respectively. These EST-SSR markers should be useful for studying the genetic diversity of Quercus species.     

Molecular genetic mapping of the <Emphasis Type="Italic">sy1</Emphasis> and <Emphasis Type="Italic">sy9</Emphasis> asynaptic genes in rye (<Emphasis Type="Italic">Secale cereale</Emphasis> L.) using microsatellite and isozyme markers

Studies of phenotypical expression of synaptic mutations in combination with the localization of corresponding genes on a genetic map permit individual stages of the meiotic process to be differentiated. Two rye asynaptic genes, sy1 and sy9, were mapped with the use of microsatellite markers (SSR) in the pericentromeric regions of the long chromosome arms 7R and 2R, respectively. The sy9 gene cosegregated with two SSR markers Xscm43 and Xgwm132. The asynaptic gene sy1 was mapped within the interval between the isozyme locus Aat2 and two cosegregating loci Xrems1188 and Xrems1135 that are located at a distance of 0.4 cM proximally and 0.1 cM distally with respect to the gene lous. Possible evolutionary relationships of the mapped genes with homeological loci of the Triticeae species and more distant cereal species, such as maize and rice, are discussed.     

Genetic diversity analysis of a world-wide collection of <Emphasis Type="Italic">Ascochyta rabiei</Emphasis> isolates using sequence tagged microsatellite markers

A previously characterized compound microsatellite locus ARMS1, containing penta- and decameric repeat units, has been reported to reveal genetic diversity in Ascochyta rabiei (Pass.) Labr. isolates. Therefore, 37 isolates of Ascochyta rabiei collected from different states of India and 38 isolates from fifteen other countries in the world were examined for their diversity at this locus. Twenty-six alleles on the basis of size (228--451 base pairs) were detected in the world isolates examined, while 15 alleles (287--418 base pairs) were observed in isolates from the Indian subcontinent. To the best of our knowledge, this study is the first to demonstrate diversity in representative Ascochyta rabiei isolates from different parts of the world at the ARMS1 locus.     

A new name in <Emphasis Type="Italic">Pavetta</Emphasis> L. (<Emphasis Type="Italic">Rubiaceae</Emphasis>)

Summary  The name Pavetta modesta (Hiern) S. E. Dawson is a later homonym of P. modesta Bremek. Pavetta crystalensis is proposed as a new name.     

Molecular subtyping of clinical isolates of <Emphasis Type="Italic">Candida albicans</Emphasis> and identification of <Emphasis Type="Italic">Candida dubliniensis</Emphasis>in Malaysia

The genotypes of 221 recent isolates of Candida albicans from various clinical specimens of 213 patients admitted to the University Malaya Medical Centre, Malaysia was determined based on the amplification of a transposable intron region in the 25 S rRNA gene. The analyses of 178 C. albicansisolated from nonsterile clinical specimens showed that they could be classified into three genotypes: genotype A (138 isolates), genotype B (38 isolates) and genotype C (2 isolates). The genotyping of 43 clinical isolates from sterile specimens showed that they belonged to genotype A (29 isolates), genotype B (10 isolates), genotype C (2 isolates) and genotype D (2 isolates). The overall distribution of C. albicans genotypes in sterile and nonsterile specimens appeared similar, with genotype A being the most predominant type. This study reported the identification of C. dubliniensis (genotype D) in 2 HIV-negative patients with systemic candidiasis, which were missed by the routine mycological procedure. The study demonstrated the genetic diversity of clinical isolates of C. albicans in Malaysia.     

Decolourisation and dephenolisation potential of selected <Emphasis Type="Italic">Aspergillus</Emphasis> section <Emphasis Type="Italic">Nigri</Emphasis> strains – <Emphasis Type="Italic">Aspergillus tubingensis</Emphasis> in olive mill wastewater

Aspergillus section Nigri strains Aspergillus aculeatus Ege-K 258, A. foeditus var. pallidus Ege-K156, A. niger Ege-K 4 and A. tubingensis Ege-K 265 were used to treat olive mill wastewater (OMW) in an investigation aimed at exploring their dephenolisation and decolourisation ability and, consequently, the economic feasibility of using any or all of these strains in a pre-treatment step in the processing of OMW. Of these strains A. tubingensis Ege-K 265 resulted in an 80% decolourisation of twofold-diluted OMW and a 30% decolourisation of undiluted OMW; in addition, it was able to remove approximately 30% of all phenolic compounds in both twofold-diluted and undiluted OMW. We conclude that A. tubingensis Ege-K 265 could be effectively used in the pre-treatment step of a combined aerobic-anaerobic process to solve the environmental problems caused by OMW in Mediterranean countries.     

Muscular architecture of <Emphasis Type="Italic">Milnesium tardigradum </Emphasis>and <Emphasis Type="Italic">Hypsibius </Emphasis>sp. (Eutardigrada,Tardigrada) with some data on <Emphasis Type="Italic">Ramazottius oberhaeuseri</Emphasis>

The architecture of the musculature of the eutardigrade species Milnesium tardigradum Doyère, 1840, Hypsibius sp. and Ramazzottius oberhaeuseri (Doyère in Ann Sci Nat Zool Sér 2(14):269–369, 1840) is investigated by phalloidin staining and confocal laser scanning microscopy. There are methodological problems in staining eutardigrades due to physiological alterations under stress (anhydrobiosis) and due to penetration problems of the cuticle. It is helpful to fix specimens in the state of asphyxy, where animals are stretched following an oxygen shortage in their environment. The musculatures of all three species correspond in their general architecture, but differ in detail, such as in the number of muscles. All muscles are isolated muscle strands. There are on each body side two dorsal and one ventral muscle strands, in addition to a system of dorsoventral, lateral and lateroventral muscles. Seven median ventral attachment points give rise to dorsoventral, ventrolateral and appendage muscles. The appendages receive several muscles originating dorsally and ventrally. The number of muscles and the arrangement differ in each appendage. The fourth appendage shows the greatest differences with a far smaller number of muscles compared to other species. The musculature shows comparably few strict segmental patterns, for example, the musculature of each appendage differs from the other ones. By comparison with literature data on the same species and data of Macrobiotus hufelandi it can be shown that eutardigrades have a roughly comparable muscular architecture, but that there are several differences in detail. Dedicated to Professor Westheide on the occasion of his 70th birthday.     

Screening of <Emphasis Type="Italic">cry2</Emphasis> genes in <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> isolates from Argentina

A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for identification of cry2 genes from Bacillus thuringiensis (Bt) was established. Strains from different sources of Argentina were analyzed to study the distribution of cry2 genes. The results showed that cry2Aa/cry2Ab profile was the most abundant irrespective of source and represented 56 of 59 Bt isolates (94.9%). Three different cry2 profiles were found in this collection, one of which was novel.     

In vitro propagation of <Emphasis Type="Italic">Helleborus</Emphasis> species

A general in vitro cloning system was established for four Helleborus species: H. argutifolius, H. foetidus, H. niger and H. orientalis. The plant material was introduced in vitro from axillary buds. A Murashige and Skoog (MS)—based medium (Murashige and Skoog 1962) was used supplemented with 2% (w/v) sucrose, 2-isopentenyladenine (2-iP) and 6-benzylaminopurine (BA). Multiplication rates depended on the genotype and varied from 1.3 for H. foetidus till 3.8 for H. niger. The first results showed that the rooting phase could be done ex vitro. Rooting was induced by a drench for one week in a solution of indole-3-butyric acid (IBA -3 mg l⁻¹) and 1-naphthaleneacetic acid (NAA-1 mg l⁻¹) at 5°C.     

Synergistic effect between dieckol from <Emphasis Type="Italic">Ecklonia stolonifera</Emphasis> and β-lactams against methicillin-resistant <Emphasis Type="Italic">Staphylococcus aureus</Emphasis>

We have been attempting for some time to discover a compound evidencing antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). The dieckol isolated from Ecklonia stolonifera has been shown to exhibit antibacterial activity against methicillin-susceptible S. aureus (MSSA) and MRSA. The minimum inhibitory concentrations (MICs) of dieckol were determined in a range of 32 to 64 μg/mL against standard MSSA and MRSA strains. Furthermore, dieckol clearly reversed the high-level ampicillin and penicillin resistance of MRSA. The MICs of ampicillin against two standard strains of MRSA were dramatically reduced from 512 to 0.5 μg/mL in combination with 1/4 MIC of dieckol (16 μg/mL). The fractional inhibitory concentration (FIC) indices of ampicillin and penicillin were measured from 0.066 to 0.266 in combination with 8 or 16 μg/mL of dieckol against all tested MRSA strains, thereby suggesting that dieckol-ampicillin or dieckol-penicillin combinations exert a synergistic effect against MRSA. The results of this study indicate that dieckol, administered in combination with β-lactams, may prove effective in the treatment of MRSA infections. Our finding may also contribute to the development of an alternative phytotherapeutic anti-MRSA agent.     

Conserved Region Amplification Polymorphism (CoRAP), a Novel Marker Technique for Plant Genotyping in <Emphasis Type="Italic">Salvia miltiorrhiza</Emphasis>

Salvia miltiorrhiza (SM), a widely popular Chinese herb, is grown in various regions in China. Identifying SMs grown in different provinces of China is difficult, and therefore genotyping these collections would be highly valuable. Based on the techniques of sequence-related amplified polymorphism and target region amplified polymorphism, a novel PCR-based molecular marker technique called conserved region amplification polymorphism (CoRAP) is reported in this study to genotype SMs. The CoRAP technique is based on the use of two primers: fixed and arbitrary primers. The former is derived from target EST sequences deposited in Genbank; while, the core sequence (CACGC) of the latter is a conserved region found in most introns. In the present study, we utilized CoRAP to genotype SMs from different geographical origins. PCR amplification is performed for 30 cycles at an annealing temperature of 52°C. Each PCR reaction has generated as many as 30–50 fragments of 50 to 1,000 bp in size. The successful DNA genotyping of SMs by CoRAP was achieved. This new genotyping method is rapid, efficient, and reproducible.