Isolation of polymorphic microsatellite loci in Hemerocallis fulva and Hemerocallis citrina (Hemerocallidaceae)

Twenty microsatellite loci were isolated from a hybrid of two daylilies, Hemerocallis fulva and Hemerocallis citrina. We characterized individuals from two H. fulva populations and two H. citrina populations in Japan and observed three to 20 alleles per locus in H. fulva and one to 19 alleles per locus in H. citrina. Mean observed heterozygosity within populations ranged from 0.35 to 0.85 in H. fulva and from 0 to 0.95 in H. citrina. In about a half of the loci, the observed heterozygosity did not deviate from Hardy–Weinberg equilibrium. These loci are proved useful in studying gene flow and qualitative trait loci mapping using the two species.     

Six polymorphic microsatellite markers for Plantago maritima

Plantago maritima displays an extraordinary variation in breeding system. In northern Europe, the species occurs as either self‐incompatible or self‐compatible, and as unisexual females or co‐sexual hermaphrodites. The isolation of polymorphic codominant markers will provide the necessary tools to investigate the proportion of self‐fertilized seeds and levels of inbreeding depression in natural populations of this species. Isolation of microsatellite loci was achieved using a membrane‐enrichment method for four loci, and a streptavidin‐coated‐beads method for two loci. Primers were designed in microsatellite flanking sequences and were analysed using fluorescent labels.     

Optimized conditions for rapd analysis inPinus radiata

Summary Pinus radiata is the most important softwood plantation species in Australia and New Zealand. The improtance of this species in forestry has led to an increasing demand to improve the efficiency of selection time of the production population, which currently takes 13 yr by traditional methods. With the application of molecular biology techniques such as random amplified polymorphic DNA (RAPD) the selection period can be reduced to 6 yr. In this study, the conditions for RAPD were optimized and the feasibility of this marker system was investigated with different families ofPinus radiata from Tasmania and South Australia. Best concentrations of Taq-polymerase (1 U), magnesium chloride (2 mM), and template DNA (20 ng) were selected to test different polymerase chain reaction (PCR) thermocycler profiles. Devey's et al. (1996) program was the most effective for production of clear RAPD bands. Best conditions were investigated to screen 10–12 bp arbitrary Breasatec and Operon primers. Both types were found useful at detecting genetic variation between families. Seventy percent and thirty percent of the selected Bresatec and Operon primers, respectively, produced polymorphic bands.     

Novel SCAR primers for specific and sensitive detection of Agrobacterium vitis strains

An Agrobacterium vitis-specific DNA fragment (pAVS3) was generated from PCR polymorphic bands amplified by primer URP 2R. A. vitis specificity of this fragment was confirmed by Southern hybridization with genomic DNA from different Agrobacterium species. Sequence-characterized amplified region (SCAR) markers were developed for A. vitis specific detection, using 24-mer oligonucleotide primers designed from the flanking ends of the 670 bp insert in pAVS3. The SCAR primers amplified target sequences only from A. vitis strains and not from other Agrobacterium species or other bacterial genera. First round PCR detected bacterial cells between 5×10² and 1×10³ cfu/ml and the detection sensitivity was increased to as few as 2 cfu/ml by nested PCR. This PCR protocol can be used to confirm the potential presence of infectious A. vitis strains in soil and furthermore, can identify A. vitis strains from naturally infected crown galls.     

Morphological,biochemical and molecular identification of petroleum hydrocarbons biodegradation bacteria isolated from oil polluted soil in Dhahran,Saud Arabia

Accumulation of petroleum hydrocarbon residual considered a major environmental problem in the kingdom of Saudi Arabia cause of intensive efforts for oil detecting. Until now, In situ biodegradation considered the most effective method for petroleum hydrocarbon residual biodegradation. The aim of this study is isolation and identification biodegradable capability bacteria from contaminated sites in Khurais oil field, Dhahran, Saud Arabia via Different morphological and biochemical and molecular methods. Furthermore, degradation level in contaminated liquid medium and soil were evaluated. Three bacterial strains were selected from petroleum-contaminated soils of Khurais oil field depending on their capacity to grow in the existence of hydrocarbon components and identified according to morphological, biochemical. Interestingly, 16S rDNA sequencing fingerprinting results confirmed our bacterial identification as Bacillus subtilis, Pseudomonas aeruginosa and Bacillus cereu. Phyllogenetic tree was constructed and genetic similarity was calculated according to alignments results. Biodegradation patterns for different three isolates were reflected varied degradation ability for three isolates regarding incubation time. Different features were studied for three biodegrading bacterial strains and identified as Bacillus subtilis, Pseudomonas aeruginosa and Bacillus cereus. Remarkable degradation rate % patterns for hydrocarbons residual were recorded for all three isolates with varied.     

Supramolecular arrangement of guanosine/5-guanosine monophosphate binary mixtures studied by methods of circular dichroism

Self-assembly of molecules is one of the fundamental processes in biology and in supramolecular chemistry. Guanosine (Guo) and its derivatives are among the widely studied molecules because of self-assembly abilities. Their tetrameric associates are the nature of telomeric DNA, and furthermore they are fundamental building blocks of supramolecular reversible gels, which may arise in certain physical and chemical conditions. Although poorly soluble in water, Guo forms interesting structures with guanosine 5'-monophosphate salt (GMP) in the TRIS buffer. We used electronic circular dichroism and vibrational circular dichroism to describe the thermal response of gels formed by the Guo/GMP binary mixture. Using these complementary techniques suitable to study conformational changes of chiral compounds, we obtained information about the involvement of functional groups and weak interactions in the guanosine quartet (G(4)) and stacked G(4) structures.     

Microsatellite DNA markers for population genetic studies and parentage assignment in cobia,Rachycentron canadum

Twenty nuclear‐encoded microsatellites from a genomic DNA library of cobia, Rachycentron canadum, were isolated and characterized. The microsatellites include two tetranucleotide, one trinucleotide, three combination tetranucleotide/dinucleotide, nine dinucleotide, and five imperfect (dinucleotide) repeat motifs. Gene diversity ranged between zero to 0.910; the number of alleles among a sample of 24 fish ranged from one to 15. Cobia support an important recreational fishery in the southeastern United States and recently have become of interest to aquaculture. The microsatellites developed will be useful tools for studying both population genetics (e.g. stock structure, effective population size) and inheritance of traits important to aquaculture.     

山地麻蜥7个Dmrt基因成员的克隆及序列分析

Dm rt基因家族是一个与性别决定相关的基因家族。该家族成员都含有一个具有DNA结合能力的保守基序———DM结构域,在性别决定和分化发育的调控中担负着重要的功能。本文采用简并PCR技术,扩增和克隆了山地麻蜥(Erem ias breuchleyi)基因组中的DM结构域,通过SSCP技术筛选和测序得到了7个具有不同DM序列的克隆。结果显示,在山地麻蜥基因组中存在着Dm rt基因家族的多个成员,与其他动物相关的Dm rt基因进行聚类分析,显示该基因家族在动物系统进化上具有高度的保守性。     

Inheritance of RAPD markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus), and their F1, F2 and backcross hybrids

The channel catfish ( Ictalurus punctatus ) has become the most important aquaculture species in the USA. A genetic linkage map in catfish is needed to improve efficiency of breeding by marker-assisted selection (MAS) and for identification of economically important genes such as disease resistance genes. To identify DNA-based genetic polymorphism, the present authors tested 42 randomly amplified polymorphic DNA (RAPD) primers for their utility in identifying genetic polymorphism in catfish. Out of these primers, 22 generated 171 highly reproducible RAPD markers, producing almost eight polymorphic bands per primer. The remaining 20 primers produced an additional 20 polymorphic bands. The RAPD markers were highly reproducible, transmitted to F1 hybrids, and segregated in F2 or backcross progeny in ratios that did not differ from Mendelian expectations. Because the interspecific hybrids of channel catfish and blue catfish are fertile, RAPD markers using the interspecific hybrid system will be useful for rapid construction of genetic linkage maps of catfish and for analysis of important quantitative trait loci.     

Gene digging

A method termed “gene digging” has been developed based on our observation of stretches of highly conserved nucleotide sequence in the coding region of many genes across related species. Rabbit-specific nucleotide sequences corresponding to desired coding segments of 14 different genes were obtained with primers that were designed based on conserved nucleotide stretches. Our success in gene digging could be attributable to the method’s inherent ability to reduce the degeneracy of primers by more than two orders of magnitude (sometimes by more than three orders of magnitude) compared to primers designed from conserved amino acids. Our results not only demonstrate the value of the method, but also hint at a thus far unknown functional significance of conserved nucleotide stretches in the coding region of various genes. In our hands the method worked 14 out of 14 times indicating generality of the concept.