Horizontal Gel Research Articles

Polymorphism Data of Two STR Loci DYS632 and DYS634 in a Chinese Han Population

Blood samples were collected from 100 unrelated healthy males of the Chinese Han ethnic group in Chengdu of China. DNA was extracted using the Chelex method (1). The allelic variation at the two Y-STR loci named as DYS632 and DYS634 were analyzed by PCR amplification system. PCR amplification conditions can be accessed at: http://www.legalmed.org/dna/DYS632.htm. The volume of PCR reaction for each locus was 37.5 μL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Alleles were designated according to the recommendation of the International Society of Forensic Genetics (3). The gene diversity, the haplotype diversity, and the standard errors of diversity were calculated in accordance with Hou’s method (4). The complete data can be accessed at: http://www.legalmed. org/dna/DYS632.htm.

Characterization and haplotype analysis of 10 novel Y-STR loci in Chinese Han population

In this study, we analyzed allelic sequences of 10 novel Y-specific STR loci, DYS454, DYS510, DYS513, DYS520, DYS542, DYS544, DYS552, DYS561, DYS587 and DYS593, surveyed the distribution of haplotypes in a Chinese Han population. Extracted DNA was amplified with PCR, followed by a horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system. Purified alleles were sequenced on DNA sequencer (ABI Model 377) to verify the number of motif repeats. The number of alleles observed at each locus ranged from 3 to 8, yielding 102 haplotypes in 103 unrelated males samples. The allele diversity values for each locus ranged from 0.2099 (DYS544) to 0.7523 (DYS552). The haplotype diversity using all these loci was 0.9998. Our study revealed that they were valuable Y-specific markers for forensic applications.

Genetic diversity in wild Tunisian populations of Mentha pulegium L. (Lamiaceae)

The allozyme variation of 15 Tunisian wild populations of Mentha pulegium L. threatened by human activities (clearing, hard-grazing, ploughing, traditional uses) was surveyed by the analysis of 14 isozyme loci using horizontal gel starch electrophoresis. The species exhibited a high level of genetic variation within populations (the mean Ap = 2.20, P = 72%, Ho = 0.349 and He = 0.229), which indicates a predominately outcrossing mating system and the recruitment of new genotypes via dispersal seeds. The genetic structure analysis of the populations using F statistics indicates no inbreeding, and showed an excess of heterozygosity for few loci. The moderate differentiation of populations (FST = 0.110) and the low rate of gene flow between them (Nm = 2.02) might been caused by recent isolation of the populations through biotope disturbances. The value of Nei's genetic identity varied from 0.839 to 0.999 reflecting a relatively low genetic divergence between populations. Cluster analysis using UPGMA method and Nei's genetic identity values, showed that populations geographically close didn't always cluster together. However, populations within the same bioclimatic stage generally subclustered together indicating that differentiation between bioclimatic regions occurred.

Mobilisation of bacteria in soils by electro-osmosis

A prerequisite for effective bioremediation of contaminated soil is the presence of microorganisms able to degrade the contaminants. If such microorganisms are absent initially, dissemination of bacteria and nutrients becomes necessary; this is a challenge, especially in dense soils. We studied the feasibility of disseminating bacteria by electro-osmosis in three different soil types; garden soil, fine sand, and clay. We tested migration velocities in a horizontal gel electrophoresis setup and used microcosms specially designed with electrodes in order to simulate field conditions. When an electric current is applied, the bacteria co-migrate with water to the cathode. Results were compared to those of controls without electricity, showing that electro-osmosis stimulates bacterial spreading even in low-permeability soil such as clay, although the migration velocity was lower than in the other soils tested. In fine sand, the bacteria migrated ca. 1 cm h −1, in garden soil ca. 0.6 cm h −1, and in clay ca. 0.1 cm h −1. Phenol served as a growth substrate in the microcosm tests; it appeared to improve the migration of bacteria and the number of recoverable bacteria in most tests. In clay, a moisture gradient formed, which is a factor to consider in designing field applications.

Y-Chromosome STR Haplotypes in a Han Ethnic Group of Chinese Population

Abstract Blood samples were obtained from 120 healthy unrelated males from the Han ethnic group in Chengdu of China. The DNA was extracted by using Chelex 100 protocol as described by Walsh et al. (1). The allelic variation at the three Y-STR loci, named as DYS447, DYS449 and DYS450, were analyzed by PCR amplification system. Each PCR reaction was performed in a 37.5 µL containing 2-10 ng DNA, 1 X Taq buffer, 1.5 mM MgCl2, 200 RM each dNTP (Pharmacia Biotech, Sweden), 1.5 U Taq polymerase (NEB, UK), 0.3 RM each primer in a Perkin-Elmer 9600 thermocycler (ABI, Foster City, CA). The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Alleles were designated according to recommendation of the International Society of Forensic Genetics (3). The gene diversities, the haplotypes diversity and the standard errors of diversity were calculated in accordance with Hou's method (4).

Allele Frequencies of Two Y-STRs in a Chinese Population

Abstract A total of 74 blood samples were collected from unrelated males of Han ethnic group in Chongqing of China. DNA was extracted by utilizing Chelex method (1). Each PCR reaction contained 2-10 ng DNA, 1 X Taq buffer, 1.5 mM MgCl2, 200 RM each dNTP (Pharmacia Biotech, Sweden), 1.5 U Taq polymerase (NEB, UK), 0.3 RM each primer. PCR amplifications were performed in a GeneAmp PCR System 9600 (Perkin-Elmer, Foster City, CA),with denaturing for 2 min at 94°C, followed by 30 cycles of 94°C for 50 s, 58°C for 50 s and 72°C for 30 s. PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system, gels were silver stained (2). Alleles were designated according to recommendation of the International Society of Forensic Genetics (3). The gene diversities, the haplotypes diversity, and the standard errors of diversity were calculated in accordance with Hou's method (4).

Gene Frequencies for Two Y-Chromosomal STR Loci in Chinese Population

Abstract Blood samples were collected from unrelated males of Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/DYS442 and DYS446.htm. The PCR reaction volume for each locus was 37.5 µL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data of population genetics and forensic science were analyzed according to Hou's method (3). The complete dataset can be accessed at http://www.legalmed.org/dna/ DYS442 and DYS446.htm.

Chinese Population Data on DXS6797 and GATA144D04 Loci

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/DXS6797.htm. The volume of PCR reaction for each locus was 37.5 µL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data of female population genetics and forensic science were analyzed using POWERSTATS program (3). The complete dataset can be accessed at http://www. legalmed.org/dna/DXS6797.htm.

Polymorphism of Two STR Loci on Chromosome 21 in a Chinese Population

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/d21s1809.htm. The volume of PCR reaction for each locus was 37.5 µL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2,3). Data were analyzed using POWERSTATS program (4). The genotype distribution was analyzed for Hardy-Weinberg equilibrium according to Hou's method (5) and no deviation from Hardy-Weinberg equilibrium was observed.

Two X-Chromosome STR Loci DXS6804 and DXS9896 Frequency Data in Chinese Population

Abstract Blood samples were collected from unrelated individuals of the Chinese Han ethnic group in Chengdu, China. DNA was extracted using the Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/DXS6804.htm. The volume of PCR reaction for each locus was 37.5 µL. The PCR products were analyzed by horizontal nondenaturing polyacrylamide gel electrophoresis with a discontinuous buffer system and visualized by silver staining (2). Data of female population genetics and forensic science were analyzed using the POWERSTATS program (3). The complete dataset can be accessed at http://www.legalmed. org/dna/DXS6804.htm

Distributions of Allelic Frequencies and Haplotypes of Two New Y-STR Loci in a Chinese Han Population

Abstract Blood samples were collected from 109 unrelated males of Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). The volume of PCR reaction for each locus was 37.5 µL, which contained 2-10 ng human genome, 1 X Taq buffer, 1.5 mM MgCl2, 1.6 . g/mL BSA, 200 RM each dNTP (Pharmacia Biotech, Sweden), 1.5 U Taq polymerase (Promega Corporation, Madison, WI), 0.3 RM each primer. PCR amplifications were carried out in a GeneAmp PCR System 9600 (Perkin-Elmer, Foster City, CA) with pre-denaturing for 3 min at 94°C, 36 cycles of denaturing for 30 s at 94°C, annealing for 60 s at 61°C and extension for 30 s at 72°C. The amplicons were analyzed by horizontal nondenaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Alleles were designated according to recommendation of the DNA commission of the International Society of Forensic Genetics (3). Data of population genetics and forensic science were analyzed according to Hou's method (4).

Allele Frequencies for Two STR Loci D9S1118 and D20S161 in Chinese Han Ethnic Group in Chengdu

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/D9S1118.htm. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). The allele classification for each STR locus was based on the number of repeat motifs according to the recommendations of the International Society of Forensic Haemogenetics (3), which now is known as the Interna tional Society of Forensic Genetics, ISFG. The alleles at D20S161 locus was named according to Susukida et al. (4). Data were analyzed using POWERSTATS program (5). The genotype distribution was analyzed for Hardy-Weinberg equilibrium according to Hou's method (6) and no deviation from Hardy-Weinberg equilibrium was observed.

Two X-Chromosome STR Loci DXS6807 and DXS7133 Frequency Data in Chinese Population

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/DXS6807.htm. The volume of PCR reaction for each locus was 37.5 L. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data of female population genetics and forensic science were analyzed using POWERSTATS program (3).

Distributions of Allelic Frequencies and Haplotypes of Two Novel Y-Chromosome STR in a Chinese Population

Abstract Whole blood obtained by venipuncture from 107 unrelated males of the Han ethnic group in Chengdu, China. DNA was extracted using the Chelex method (1). The reaction volume of PCR was 37.5 μL, containing 2–4 ng human genome DNA, 200 μM each dNTP (Pharmacia, Sweden), 1.5μ Taq polymerase (Promega, Madison, WI), 3.75 μL 10 × buffer, Mg2+ 1.5 mM, 1.6 μg/mL BSA, 0.3 μM each primer. Amplification reactions were carried out in a Perkin Elmer 9600 (Foster City, CA) with pre-denaturing for 2 min at 94°C, followed by 35 cycles of denaturing for 40 s at 94°C, annealing for 40 s at 58°C and extension for 25 s at 72°C. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data of population genetics and forensic science were analyzed according to Hou's method (3).

Allele Frequencies for Two STR Loci D21S1436, D21S2052 in Chinese Population

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/d21s1436.htm. The volume of PCR reaction for each locus was 37.5 µL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2,3). Data were analyzed using POWERSTATS program (4). The genotype distribution was analyzed for Hardy-Weinberg equilibrium according to Hou's method (5) and no deviation from Hardy-Weinberg equilibrium was observed.

Allozyme variation in Sophora moorcroftiana , an endemic species of Tibet, China

The genetic diversity of ten populations of Sophora moorcroftiana in the middle reaches of the Yarlung Zangbo River, Tibet, China was assessed using allozyme analysis by horizontal sliceable starch gel electrophoresis. Twenty four loci (46 alleles) of 13 enzyme systems demonstrate low levels of genetic variation within populations, with the value of P p=25.0%～37.5%, A p=1.3～1.7 and H ep=0.112～0.169. At the species level, the genetic diversity of S. moocroftiana (P s=37.5%, A s=1.9, H es=0.171) was lower than the mean value of angiosperms of long-lived woody species (P s=59.5%, A s=2.10, H es= 0.183). Wright′s F statistics analysis indicated that F IS, a measure of the deviation from random mating within the 10 populations, was -0.0071, suggesting deviation from Hardy-Weinberg equilibrium and a slight heteroygote excess in some populations. The higher level of differentiation (F ST=0.1748) among populations than those of other long-lived woody plants may result from habitat fragmentation and low levels of gene flow (Nm=1.1802) caused by environmental deterioration and human disturbance, including over-felling and over-grazing. It was worth noting that populations H2 (Xietongmen), H31 (Jiangdang1), H32 (Jiangdang2), and H5 (Langsailing) harbored the majority of alleles and had high levels of genetic diversity, suggesting that these populations in particular should be conserved in situ.

Allele Frequencies for Two STR Loci D11S1977 and D22S444 in Chinese Population

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). Reaction condition of PCR amplification can be accessed at http://www.legalmed.org/ dna/D11S1977.htm. The volume of PCR reaction for each locus was 37.5 µL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system, and visualized by silver staining (2,3). Data of population genetics and forensic science were analyzed using POWERSTATS program (4). The genotype distribution was analyzed for Hardy-Weinberg equilibrium according to Hou's method (5) and no deviation from Hardy-Weinberg equilibrium was observed. The complete data can be accessed at http://www.legalmed.org/dna/D11S1977.htm.

SE33 (HumACTBP2): native gel electrophoresis versus denaturing capillary electrophoresis, and population data

The aim of the study was to compare results obtained by electrophoresis under denaturing conditions with results of native horizontal gel electrophoresis and to investigate additional population data on the STR locus SE33 (HumACTBP2) in an Austrian Caucasoid population sample. The results of the comparative study showed that a conversion of results between both typing strategies is not feasible for the entire size range of this locus.

Lithium dodecyl sulfate, sodium dodecyl sulfate-agarose gel electrophoresis for separating proteins according to molecular weight

We have improved the agarose gel electrophoresis method reported previously for size-dependent separation of proteins. Good resolution in protein separation was achieved using a novel agarose gel, containing both sodium dodecyl sulfate (SDS) and lithium dodecyl sulfate (LDS). The gel was divided into stacking and separating gels. We determined the optimal conditions for horizontal gel electrophoresis to be a voltage of 100V for the separating gel and 50V for the stacking gel, in an electrophoretic buffer solution of 25mM Tris-190mM glycine containing 0.03% LDS and 0.02% SDS (pH 8.3), which was also used to make the agarose gel. Separation of proteins in the molecular weight range 14.2-205K and of the proteins in human serum showed good resolution under these conditions. This method should be useful for clinical laboratories because it is simple and requires little bench space.

Allele Frequencies for Two STR Loci D1S1676, D2S2735 in Chinese Population

Abstract Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/d1s1676.htm. The volume of PCR reaction for each locus was 37.5 μL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data were analyzed using POWERSTATS program (3). The genotype distribution was analyzed for HardyWeinberg equilibrium according to Hou's method (4) and no deviation from Hardy-Weinberg equilibrium was observed.