Four X-chromosomal STRs and their allele frequencies in a Chinese population

X-chromosomal markers are particularly useful for solving complex problems relating to kinship and deficiency paternity analysis. In the present study, population genetics data of four X-chromosomal short tandem repeats (STRs) DXS8378, HPRTB, DXS7423 and DXS7132 were obtained by analyzing 500 unrelated Chinese individuals (250 males and 250 females). Population genetics data obtained from the Chinese were compared with those of the Asian and European population. Mutations in X-chromosomal markers were analyzed based on a total of 61 proven father-child and 45 proven mother-child pairs.

Allele frequencies and haplotypes of 12 Y-STR loci for the local Chinese population in Hong Kong

Haplotype frequencies were established for 12 Y-chromosome STR loci, including all loci recommended by Scientific Working Group on DNA Analysis Methods Y-STR Subcommittee (DYS391, DYS389I/II, DYS439, DYS393, DYS390, DYS385a/b, DYS438, DYS19 and DYS392) plus DYS437, in the local Chinese population in Hong Kong. In a sample of 481 unrelated males, it was possible to define 424 different haplotypes of which 388 were unique, 26 was found in two individuals, 2 were shared in three individuals, 5 were shared in four individuals and 3 were shared in five individuals. The allele diversity values for each locus ranged from 0.4273 (DYS438) to 0.9555 (DYS385a/b). The observed haplotype diversity value and discrimination capacity were 0.9992 and 0.8815, respectively. In a genetic study of these unrelated males, triple alleles were found at the DYS358 locus in six individuals. The combined Y-chromosome STR polymorphisms provide a powerful discrimination tool for routine forensic applications.

STR data for the PowerPlex 16 loci for the Chinese population in Hong Kong

Allele frequencies for the 15 STR loci included in the PowerPlex 16 kit were obtained from a sample of 247 unrelated Chinese in Hong Kong.

Identification of differential gene expression by high throughput analysis

High throughput analysis of differential gene expression is a powerful tool that can be applied to many areas in molecular cell biology, including differentiation, development, physiology, and pharmacology. In recent years, a variety of techniques have been developed to analyze differential gene expression, including comparative expressed sequence tag sequencing, differential display, representational difference analysis, cDNA or oligonucleotide arrays, and serial analysis of gene expression. This review explains the technologies, their scopes, impact on science, as well as their costs and possible limitations. The application of differential display is presented as a tool to identify genes induced by darkness or yellowing process in rice leaves.

Molecular characterization of ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice leaves

A full-length cDNA (designated rcaII) encoding the Rubisco activase (RCA) of rice (Oryza sativa L.) has been cloned from a cDNA library constructed with mRNA from green leaves. Sequence analysis resulted in a reading frame of 432 amino acids with a calculated molecular mass of 47.9 kDa and an estimated isoelectric point of 5.97. The deduced amino acid sequence showed 74-89% identity with other Rubisco activases from higher plants. Two highly conserved motifs were identified. Southern blot analysis suggested the presence of a single rca gene in the rice genome. The accumulation of leaf rca mRNA was found to be regulated by an oscillating circadian rhythm, in rice plants grown in a light-dark photoperiod. To purify the rice RCA protein, total soluble protein from rice green leaves was fractionated by ammonium sulfate precipitation, followed by preparative gel electrophoresis. Two polypeptides, designated RCAI and RCAII, were isolated by two-dimensional gel electrophoresis and further confirmed by N-terminal sequencing. The polyclonal antibodies prepared against rice RCAI and RCAII were found to cross-react with two RCA polypeptides present in leaf extracts of spinach and tobacco. Furthermore, two different 3' ends of rca mRNA were detected by reverse transcription-polymerase chain reaction analysis. These cDNA fragments and the related genomic DNA fragment were cloned and sequenced. The sequence of rcaI is almost identical to the corresponding sequence of rcaII, except for its having 33 additional amino acids at the C-terminal portion. It can be concluded that a novel alternative splicing mechanism for a common rca mRNA precursor near the 3' end exists in rice plants.

Introduction and expression of foreign DNA in isolated spinach chloroplasts by electroporation

An electroporation-mediated method for the study of foreign gene expression within chloroplasts has been developed. The chloroplast expression vector pHD203-GUS, which consists of coding regions for beta-glucuronidase (GUS) and chloramphenicol acetyltransferase (CAT) separated by a double psbA promoter fragment from pea (in opposite orientation) was electroporated into spinach chloroplasts and the transient gene expression was examined. Conditions for the expression of the reporter genes have been optimized. Both CAT and GUS activities were detected in chloroplasts electroporated with pHD203-GUS, but not with nuclear expression vector pBI221 or negative control pUC18. No GUS activity was detected when pHD203-GUS was electroporated into spinach protoplasts. Dot immunoblot analysis using anti-GUS antibody confirmed the existence of GUS protein in chloroplasts electroporated with chloroplast-specific vector but not the negative controls, excluding the possibilities of endogenous GUS or bacterial contamination. The expression of GUS protein in treated chloroplasts was further confirmed by Western blot analysis.

Characterization of the light-responsive promoter of rice chloroplast psbD-C operon and the sequence-specific DNA binding factor

The transcription of rice plastid psbD-psbC genes encoding photosystem II reaction center protein D2 and chlorophyll alpha-binding protein CP43 is closely regulated by light. To elucidate the sequence requirement for the light-responsive promoter of psbD-psbC operon, transcriptional analysis of the rice promoter was performed with deleted mutants and site-directed mutants in vitro. Deletion of -546 approximately -100 upstream sequences resulted in 4- to 5-fold decrease in the transcription rate. Further deletion of -99 approximately -40 conserved region of repeated sequences resulted in 2-fold decrease in the transcription rate. The core light-responsive promoter requires "-10" element but not "-35" element for accurate initiation of basal transcription. No downstream promoter element was found in the +4 approximately +111 region. The competitive gel-retardation experiments revealed the presence of DNA-binding protein in the rice chloroplasts, which interacts specifically with the -60 approximately -37 repeated sequences. Southwestern blot analysis further demonstrated that the binding factor is composed of 36-kDa polypeptide(s).

Transcriptional activation of flanking sequences by Tn1000 insertion

The carotenoid biosynthesis operon of Erwinia herbicola Eho13 consists of five genes, which are organized in the order crtE-crtX-crtY-crtI-crtB. These genes, with the exception of crtX, encode functions of beta-carotene biosynthesis and give an orange-coloured phenotype in Escherichia coli. Since crtX is not involved in the biosynthesis of beta-carotene, deletion of this gene does not alter the phenotype of pigmented cells. On the other hand, insertion of Tn1000 into crtX or into the upstream untranslated region of the operon resulted in a light-yellow, rather than an unpigmented phenotype, indicating that Tn1000 does not exert a strong polar effect when inserted in this operon. RNA analysis revealed that the sequence downstream from the insertion site was transcribed at a low level. Primer extension showed that the "-35"-like sequence in the terminal inverted repeats was not responsible for the transcription of the downstream sequence. Furthermore, primer extension and polymerase chain reaction (PCR) studies revealed that RNA transcribed from the promoters inside of Tn1000 was extended through the terminal inverted repeats into the adjacent sequences. In addition Tn1000, in either orientation, was able to generate fusion transcripts when placed upstream of a promoter-less tetracycline-resistance gene and resulted in cells resistant to the drug. These results showed that Tn1000 insertion transcriptionally activates the DNA sequences adjacent to the transposon.

Point mutations in the chloroplast 16s rRNA gene confer streptomycin resistance in Nicotiana plumbaginifolia

In a previous paper we reported the isolation of streptomycin-resistant mutants from Nicotiana plumbaginifolia and presented evidence for chloroplast control of the resistance trait. To understand the molecular basis of the resistance in these mutants, we sequenced three regions in the chloroplast 16s rRNA gene, which correspond to the 5' terminus, the 530 loop, and the 900 stem/loop of Escherichia coli 16s rRNA, and compared them with the sequences of the wild-type. Our results show that: (1) nine mutants have a C to T change at position 912, (2) one mutant (SR1021) has a G to A change at position 885, (3) one mutant has a C to T change at position 526, based on E. coli numbering; and (4) three mutants do not have any change in the regions analyzed. The point mutation detected in SR1021 has not been reported previously. In E. coli 16s rRNA, position 885 is protected from chemical probing by ribosomal protein S12 and is closely juxtaposed with the streptomycin-binding region (positions 912-915) in the predicted secondary structure. It is likely that the G to A transition at this position is a novel mutation for streptomycin resistance.

Analysis of the gene cluster encoding carotenoid biosynthesis in Erwinia herbicola Eho13

Erwinia herbicola is known to synthesize carotenoids and gives an orange-coloured phenotype. These carotenoids play a role in the protection of the cells from the damage caused by near-UV irradiation in nature. The genes encoding these carotenoids in E. herbicola Eho13 are clustered in a 7 kb DNA fragment. The complete sequence of this fragment has been determined. DNA sequence analysis revealed that the entire sequence contains at least five genes, which are transcribed in the same direction. These five genes are organized in the order crtE-crtX-crtY-crtI-crtB. A gene fusion study showed that two different regions in this 7 kb gene cluster contain promoter activity. Primer-extension analysis identified two transcription start sites, located 147 bp upstream from the first gene of the cluster, crtE, and within the last gene of the cluster, crtB. An RNA-PCR study suggested that the five crt genes were organized in an operon and were transcribed from the promoter upstream from crtE.

Pulsed-field acceleration: the electrophoretic behavior of large spherical particles in agarose gels

In agarose gel electrophoresis, periodically inverting or interrupting the applied field may greatly accelerate the migration of polystyrene microspheres, in a manner varying with pulse times, and the observed zones are made sharper. The particles concerned are just large enough that under constant field they appear not to enter the gel at all or to migrate very slowly: and merely lowering the applied field may also enhance their electrophoretic migration, though to a lesser extent than with field pulsing. These effects may be accounted for by gel mesh flexibility which, varying with the nature of the migrating species, may either help or hinder migration.

Detection of point mutations in the chloroplast genome by single-stranded conformation polymorphism analysis

Single-stranded conformation polymorphism (SSCP) analysis was used to examine the mutations of the chloroplast 16S rRNA locus of streptomycin-resistant mutants in Nicotiana plumbaginifolia. DNA fragments of 121, 517, 968 and 1578 bp, each possessing a known point mutation, were generated by polymerase chain reaction (PCR). The resulting fragments were denatured and separated by nondenaturing polyacrylamide gel electrophoresis. Compared to the patterns of the wild-type DNA fragments, the bands of the single-stranded DNA fragments of 121 and 517 bp with base changes were shifted. However, no pattern variations were detected from the DNA fragments of 968 and 1578 bp generated from both wild-type and mutants.

Direct sequencing of tobacco chloroplast genome by the polymerase chain reaction

We have developed a polymerase chain reaction (PCR) method for sequencing of tobacco chloroplast genome. In a mixture containing chloroplast DNA, 5'-end-labeled oligonucleotide primer, Taq DNA polymerase and reaction buffer, we were able to sequence a segment of chloroplast 16S rRNA gene. The results showed that the 750 bp of DNA sequenced were identical to the sequence reported, indicating that direct sequencing method that we have developed is useful for the sequencing of chloroplast genome. To analyze the chloroplast genome more rapidly in those in vitro grown plantlets, we also developed a simple method which is applicable for the amplifications and sequencing of chloroplast 16S rRNA fragment from either 0.15 g of tobacco leaf or stem tissue. The readable sequences obtained from the presented methods were consistent with the published sequence.

Restriction endonuclease analysis of chloroplast DNA from streptomycin-resistant mutants of Nicotiana plumbaginifolia

Chloroplast DNA isolated from wild-type Nicotiana plumbaginifolia and 12 maternally inherited streptomycin-resistant mutants was digested with various restriction enzymes and the resultant patterns were compared. No gross structural alterations of the chloroplast genome were detected in any mutants; however, variant patterns owing to the gain or loss of a restriction site were found in three mutants, SR1007, SR1019, and SR1022. The variant patterns in SR1019 and SR1022 are identical and are the results of mutation in the psbG gene coding for a chloroplast membrane protein G, and that in SR1007 is due to mutation in the 16S rRNA gene. Inheritance of the variant patterns in mutants SR1007 and SR1019 was studied. The results showed that the variant patterns and streptomycin resistance were co-transmitted in reciprocal crosses.

Mendelian inheritance of streptomycin resistance in Nicotiana plumbaginifolia

In a previous study two haploid streptomycin-resistant clones of Nicotiana plumbaginifolia were isolated. The chromosome number of one of these clones has now been doubled through leaf-midvein culture and the resultant diploids were characterized genetically. Our results show that streptomycin resistance in this clone is conditioned by a recessive nuclear gene. Haploid protoplasts of this streptomycin-resistant mutant were selected for chlorate resistance. All clones obtained from the selection were deficient in nitrate reductase activity in addition to resistance to streptomycin. Genetic analysis of progeny of one of these clones revealed that the genes for streptomycin resistance and for the apoenzyme of nitrate reductase are unlinked.

Isolation and characterization of streptomycin-resistant mutants in Nicotiana plumbaginifolia

Streptomycin-resistant colonies were isolated from protoplast cultures of haploid Nicotiana plumbaginifolia based on their ability to green in medium containing 1 mg/ml streptomycin sulfate. The frequency of resistant colonies was 0.9×10(-5) in nonmutagenized culture, and increased ten-fold following treatment of culture with 10 μg/ml N-methyl-N'-nitro-N-nitrosoguanidine. Of a total of 52 resistant clones isolated, 2 gave rise to haploid, 15 to diploid, and 3 to tetraploid plants upon transfer of calli to differentiation medium. Leaf-segment and protoplast assays showed that all diploid regenerates were resistant to streptomycin but sensitive to chloramphenicol, kanamycin, lincomycin, neomycin, and spectinomycin. Plants in most diploid clones were fertile and able to set seeds when self-fertilized and crossed reciprocally to wild-type plants. Inheritance of streptomycin resistance was studied in the diploid clones and, without exception, the resistance was transmitted maternally. Comparative studies of the ultrastructure of organelles and protein synthesis in isolated chloroplasts between wild-type and resistant clones in the presence of streptomycin suggest that streptomycin resistance is controlled by chloroplasts.