2018 Detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in Taiwan
Study of MTCYB gene sequence in populations of Taiwan
12
Study of MTCYB gene sequence in populations of Taiwan Hsiao-Lin Hwa 1,2,3 , Tsang-Ming Ko 4 , Yao-Chang Chen 1 , Yih-Yuan Chang 4 , Li-Hui Tseng 3 , Yi-Ning Su 3 , James Chun-I Lee 1, * 1 Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University 2 Department of Obstetrics and Gynecology, National Taiwan University Hospital and College of Medicine, National Taiwan University 3 Department of Medical Genetics, National Taiwan University Hospital 4 Genephile Bioscience Laboratory, Taipei, Taiwan Correspondence to: Professor James Chun-I Lee Telephone No: +886-2-2312-3456 ext. 5504 Fax No: +886-2-8369-3450 E-mail address: [email protected] Abstract The cytochrome B gene (MTCYB) within the mitochondrial genome has been widely used in species identification and taxonomic research. In this study, the population variation of the MTCYB gene in humans was demonstrated. The sequence polymorphism of the MTCYB gene was determined in 417 subjects in 8 populations in Taiwan (Taiwan Chinese, mainland Chinese, Filipino, Thai, Vietnamese, and Caucasian). Single nucleotide polymorphisms of the populations and the genetic distance between these populations were analyzed. There were 108 variable positions with a total of 99 haplotypes. The distribution of varied sequences from the revised Cambridge Reference Sequence (rCRS) was from 1 to 9 positions, with an average of 4.26. Discrimination powers of the MTCYB gene in the 8 populations, ranging from 0.7888 (Tao) to 0.9224 (Filipino), were observed. A population-specific position of the MTCYB gene was noted in Tao and Caucasian populations in this study. There were statistically significant differences of genetic distance between Taiwan Chinese and Caucasian, between Taiwan Chinese and Tao, and between Taiwan Chinese and Filipino. A phylogenic tree using the neighbor-joining method based on the MTCYB gene sequence of these populations was constructed, which grouped the Taiwan Chinese, indigenous Taiwanese, mainland Chinese, Thais, and Vietnamese in the same cluster. In conclusion, there are sufficient sequence polymorphisms of the MTCYB gene in individuals of different populations, which can be used in the identification of human ethnic groups, and the analyses of forensic casework. Key Words: mitochondrial DNA, MTCYB gene, sequence polymorphism A-1
Transcript of Study of MTCYB gene sequence in populations of Taiwan
Materials & Methods1Department and Graduate Institute of
Forensic Medicine, College of Medicine, National
Taiwan University 2Department of Obstetrics and Gynecology, National Taiwan University Hospital and
College of Medicine, National Taiwan University 3Department of Medical Genetics, National Taiwan University Hospital
4Genephile Bioscience Laboratory, Taipei, Taiwan
Correspondence to: Professor James Chun-I Lee Telephone No: +886-2-2312-3456 ext. 5504
Fax No: +886-2-8369-3450 E-mail address: [email protected]
Abstract
The cytochrome B gene (MTCYB) within the mitochondrial genome has been widely used in species identification and taxonomic research. In this study, the population variation of the MTCYB gene in humans was demonstrated. The sequence polymorphism of the MTCYB gene was determined in 417 subjects in 8 populations in Taiwan (Taiwan Chinese, mainland Chinese, Filipino, Thai, Vietnamese, and Caucasian). Single nucleotide polymorphisms of the populations and the genetic distance between these populations were analyzed. There were 108 variable positions with a total of 99 haplotypes. The distribution of varied sequences from the revised Cambridge Reference Sequence (rCRS) was from 1 to 9 positions, with an average of 4.26. Discrimination powers of the MTCYB gene in the 8 populations, ranging from 0.7888 (Tao) to 0.9224 (Filipino), were observed. A population-specific position of the MTCYB gene was noted in Tao and Caucasian populations in this study. There were statistically significant differences of genetic distance between Taiwan Chinese and Caucasian, between Taiwan Chinese and Tao, and between Taiwan Chinese and Filipino. A phylogenic tree using the neighbor-joining method based on the MTCYB gene sequence of these populations was constructed, which grouped the Taiwan Chinese, indigenous Taiwanese, mainland Chinese, Thais, and Vietnamese in the same cluster. In conclusion, there are sufficient sequence polymorphisms of the MTCYB gene in individuals of different populations, which can be used in the identification of human ethnic groups, and the analyses of forensic casework.
Key Words: mitochondrial DNA, MTCYB gene, sequence polymorphism
1
87 96
14,733 10,636 4,081 16
87 7.4% 96 10.8%
40%
166
2.4-3.0
25% 30%
50%(17.3%)
10% 35-44
45-54 93
A-2
mailto:[email protected]
2.70 9.15 /
36.3551.72 20.58
2.553.10 6.44 /
1
DNA DNA
(National Institute of Health,
USA) NCBI (National Center for Biotechnology Information) DNA
B (Cytochrome B) DNA
8 DNA PCR
DNA
DNA PCR 111bp-
158bp-228bp-273bp-334bp-397bp-438bp- 468bp-
DNA PCR DNA NCBI DNA
DNA 8
DNA-PCR
A-4
E-mail*: [email protected] Tel: +61 432067779
Abstract
Palynology, the study of pollen, spores and other acid-resistant microscopic plant bodies
collectively known as palynomorphs, has been used as a geological, botanical, geographical and
archaeological tool since the early 20th century, but has only recently emerged as a forensic tool.
Pollen and spores are produced in vast numbers and are abundant in soil and dust, they are
microscopic in size, resistant to decay, and can be morphologically identified to the plant species that
produced them. Palynomorph assemblages that occur in soil from any one locality can be
distinguished from assemblages found in soil only metres away, and from those found in soil from
other places and even different countries.
Palynomorph assemblages from soil and water at a crime scene or area of interest can be compared
with those found in dust, dirt or soil from people or items of interest to prove or disprove a relationship
between them. In addition, they can also help determine the geographic origin of items of interest
including illicit drugs and illegal imports. Although palynology can be used to help bring about a
conviction, it can be especially useful in suggesting what direction an investigation should take, and as
corroborative evidence.
Forensic palynology is commonly used in New Zealand and the United Kingdom and now
becoming used more often in Australia and the United States of America, but elsewhere in the world
its application is more novel than routine. Why? Because those who could use it know little or nothing
about it. It is time to widely educate those who could use it. We will briefly outline how palynology
can be used as a forensic tool, illustrated with case histories including how palynology has helped to
catch a murderer, disprove a rapist’s alibi and identify a robber, and how cannabis can leave evidence
on clothing.
28 11 20
16 7 8
35 42
13 21
Boettcherisca peregrina
1
DNA DNA
DNA C ICytochrome c oxidase subunit I
COI
62 100 COI PCR
263 750 bp BioEdit 7.0 MEGA 4
Kimura’s
2-parameter method Neighbor-joining method
COI
A-7
1
DNA D-loop
DNA D-loopD-loopD-loop 5 (SNP)D-loop 3(VNTR)
(STR) 10 D-loop 5SNP 3 D-loop 3VNTR 3 6
STR
STR
A-8
DNADNA extractor FM kitDNAAmpFlSTR Cofiler PCR Amplification KitSTR
DNADNADNA
0.125ng 32 DNA 0.250.5ng 30
STR 9 10
89% 1
5
DNADNA
A-9
The variation in spatially adjacent pollen assemblages from a potential assault location
Han Lin1* and Lynne Milne2
1 Centre for Forensic Science, University of Western Australia, Australia 2 School of Earth and Geographical Sciences, University of Western Australia, Australia
E-mail: *[email protected]; Tel: +61 432067779
Abstract Dispersed pollen assemblages recovered from soil and dust samples are characterised by the
pollen types present and their relative occurrence in a 200 or more grain count. From this, a
palynologist can qualitatively determine if samples are from the same locality. Unlike some types of
forensic evidence, no two pollen assemblages will be theoretically identical because of numerous
taphonomic processes. The disadvantage of this qualitative type of analysis in a forensic case is the
difficulties in convincing lay persons that minor differences in pollen assemblages from the same
locality is normal. Although statistical analysis can not replace qualitative assessment in this
discipline, it may support and validate it in courts.
This project focused on determining the degree of dissimilarity that can occur between pollen
assemblages from the same site and other localities. Three replicate soil samples were collected
from each of ten quadrants within a small isolated garden considered a potential assault location.
Pollen analysis of these samples and soil samples from three different environments was conducted
and the results statistically analysed. Results indicate that the natural range of dissimilarity between
replicate, comparator and evidentiary pollen assemblages from the same locality can be delimited.
These findings will potentially assist in the future presentation and validation of palynological
evidence in courts.
A-10
Sample
DNA COI
C. megacephalaC.rufifaciesC. pinguisL. porphyrinaO. spinigeraS. ruficornisS. javanica
(2006/7)
(2005/3-4)
2007/9-10
2007/9-10
21
A-11
)
60-90
(RAPD, Random Amplified Polymorphic DNA)(ITS)5.8S18S26S RNADNARAPDDNA
(26S ribosome RNA)
PA-12
Taiwan University 2Department of Obstetrics and Gynecology, National Taiwan University Hospital and
College of Medicine, National Taiwan University 3Department of Medical Genetics, National Taiwan University Hospital
4Genephile Bioscience Laboratory, Taipei, Taiwan
Correspondence to: Professor James Chun-I Lee Telephone No: +886-2-2312-3456 ext. 5504
Fax No: +886-2-8369-3450 E-mail address: [email protected]
Abstract
The cytochrome B gene (MTCYB) within the mitochondrial genome has been widely used in species identification and taxonomic research. In this study, the population variation of the MTCYB gene in humans was demonstrated. The sequence polymorphism of the MTCYB gene was determined in 417 subjects in 8 populations in Taiwan (Taiwan Chinese, mainland Chinese, Filipino, Thai, Vietnamese, and Caucasian). Single nucleotide polymorphisms of the populations and the genetic distance between these populations were analyzed. There were 108 variable positions with a total of 99 haplotypes. The distribution of varied sequences from the revised Cambridge Reference Sequence (rCRS) was from 1 to 9 positions, with an average of 4.26. Discrimination powers of the MTCYB gene in the 8 populations, ranging from 0.7888 (Tao) to 0.9224 (Filipino), were observed. A population-specific position of the MTCYB gene was noted in Tao and Caucasian populations in this study. There were statistically significant differences of genetic distance between Taiwan Chinese and Caucasian, between Taiwan Chinese and Tao, and between Taiwan Chinese and Filipino. A phylogenic tree using the neighbor-joining method based on the MTCYB gene sequence of these populations was constructed, which grouped the Taiwan Chinese, indigenous Taiwanese, mainland Chinese, Thais, and Vietnamese in the same cluster. In conclusion, there are sufficient sequence polymorphisms of the MTCYB gene in individuals of different populations, which can be used in the identification of human ethnic groups, and the analyses of forensic casework.
Key Words: mitochondrial DNA, MTCYB gene, sequence polymorphism
1
87 96
14,733 10,636 4,081 16
87 7.4% 96 10.8%
40%
166
2.4-3.0
25% 30%
50%(17.3%)
10% 35-44
45-54 93
A-2
mailto:[email protected]
2.70 9.15 /
36.3551.72 20.58
2.553.10 6.44 /
1
DNA DNA
(National Institute of Health,
USA) NCBI (National Center for Biotechnology Information) DNA
B (Cytochrome B) DNA
8 DNA PCR
DNA
DNA PCR 111bp-
158bp-228bp-273bp-334bp-397bp-438bp- 468bp-
DNA PCR DNA NCBI DNA
DNA 8
DNA-PCR
A-4
E-mail*: [email protected] Tel: +61 432067779
Abstract
Palynology, the study of pollen, spores and other acid-resistant microscopic plant bodies
collectively known as palynomorphs, has been used as a geological, botanical, geographical and
archaeological tool since the early 20th century, but has only recently emerged as a forensic tool.
Pollen and spores are produced in vast numbers and are abundant in soil and dust, they are
microscopic in size, resistant to decay, and can be morphologically identified to the plant species that
produced them. Palynomorph assemblages that occur in soil from any one locality can be
distinguished from assemblages found in soil only metres away, and from those found in soil from
other places and even different countries.
Palynomorph assemblages from soil and water at a crime scene or area of interest can be compared
with those found in dust, dirt or soil from people or items of interest to prove or disprove a relationship
between them. In addition, they can also help determine the geographic origin of items of interest
including illicit drugs and illegal imports. Although palynology can be used to help bring about a
conviction, it can be especially useful in suggesting what direction an investigation should take, and as
corroborative evidence.
Forensic palynology is commonly used in New Zealand and the United Kingdom and now
becoming used more often in Australia and the United States of America, but elsewhere in the world
its application is more novel than routine. Why? Because those who could use it know little or nothing
about it. It is time to widely educate those who could use it. We will briefly outline how palynology
can be used as a forensic tool, illustrated with case histories including how palynology has helped to
catch a murderer, disprove a rapist’s alibi and identify a robber, and how cannabis can leave evidence
on clothing.
28 11 20
16 7 8
35 42
13 21
Boettcherisca peregrina
1
DNA DNA
DNA C ICytochrome c oxidase subunit I
COI
62 100 COI PCR
263 750 bp BioEdit 7.0 MEGA 4
Kimura’s
2-parameter method Neighbor-joining method
COI
A-7
1
DNA D-loop
DNA D-loopD-loopD-loop 5 (SNP)D-loop 3(VNTR)
(STR) 10 D-loop 5SNP 3 D-loop 3VNTR 3 6
STR
STR
A-8
DNADNA extractor FM kitDNAAmpFlSTR Cofiler PCR Amplification KitSTR
DNADNADNA
0.125ng 32 DNA 0.250.5ng 30
STR 9 10
89% 1
5
DNADNA
A-9
The variation in spatially adjacent pollen assemblages from a potential assault location
Han Lin1* and Lynne Milne2
1 Centre for Forensic Science, University of Western Australia, Australia 2 School of Earth and Geographical Sciences, University of Western Australia, Australia
E-mail: *[email protected]; Tel: +61 432067779
Abstract Dispersed pollen assemblages recovered from soil and dust samples are characterised by the
pollen types present and their relative occurrence in a 200 or more grain count. From this, a
palynologist can qualitatively determine if samples are from the same locality. Unlike some types of
forensic evidence, no two pollen assemblages will be theoretically identical because of numerous
taphonomic processes. The disadvantage of this qualitative type of analysis in a forensic case is the
difficulties in convincing lay persons that minor differences in pollen assemblages from the same
locality is normal. Although statistical analysis can not replace qualitative assessment in this
discipline, it may support and validate it in courts.
This project focused on determining the degree of dissimilarity that can occur between pollen
assemblages from the same site and other localities. Three replicate soil samples were collected
from each of ten quadrants within a small isolated garden considered a potential assault location.
Pollen analysis of these samples and soil samples from three different environments was conducted
and the results statistically analysed. Results indicate that the natural range of dissimilarity between
replicate, comparator and evidentiary pollen assemblages from the same locality can be delimited.
These findings will potentially assist in the future presentation and validation of palynological
evidence in courts.
A-10
Sample
DNA COI
C. megacephalaC.rufifaciesC. pinguisL. porphyrinaO. spinigeraS. ruficornisS. javanica
(2006/7)
(2005/3-4)
2007/9-10
2007/9-10
21
A-11
)
60-90
(RAPD, Random Amplified Polymorphic DNA)(ITS)5.8S18S26S RNADNARAPDDNA
(26S ribosome RNA)
PA-12
