Download Orientation for new graduate students Department of genetics

Orientation for new graduate students
Department of genetics @SciKU
July 7, 2014
www.genetics.sci.ku.ac.th
Department of Genetics, the 1st Genetic
Department in Thailand, was established in 1981.
We offer three degree programs:
• Bachelor of Science (Genetics)
• Master of Science (Genetics)
• Doctor of Philosophy in Genetics.
• The
• 23 academic staff, 120 undergraduate students, 50
masters students and 15 doctoral students.
• Diverse courses in both classical and molecular genetics
are offered for all programs.
Research Activities in the Department
Plant Genetics
• Molecular cloning,
genetic transformation and
molecular marker development
Animal Genetics
• Insect and aquatic animal population, genetic
diversity and molecular systematics and phylogenetic
analysis
Microbial Genetics
• Antibiotic biosynthesis, endophytic actinomycetes and
algal genetic and transformation
Assoc. Prof. Dr. Arinthip Thamchaipenet
Endophytic actinomycetes
Endophytic actinomycetes isolated from Thai tropical plants including endemic, medicinal and agricultural important species are high
potential sources for discovery of new genus/species, bioactive compounds and plant growth promoting (PGP) agents.
This aim is to identify new genus/species and bioactive compounds of endophytic actinomycetes and to screen for PGP properties
Endophytic actinomycetes interaction with plants
The aim of this project is to make mutants of endophytic actinomycetes at targeting genes involved in PGP traits and evaluate the PGP of
those traits in pot experiment as well as studying transcription profile and proteomics of plant and endophyte interaction
New drug discovery from genome scanning of actinomycetes
Department of Genetics
New taxa, bioactive compounds and PGPB
After genome analysis of various actinomycete strains, there are several antibiotic gene clusters so-called ‘cryptic cluster’ that located in the
genomes but have never been expressed in general culture condition. With development of new technology of gene manipulation, these gene
clusters are tempting targets to be expressed in heterologous friendly host to force to production of new secondary metabolites.
Host manipulation and gene cluster cloning and expression
This aim of this project is to manipulate host strain to be able produce high level of secondary metabolites with low background of
biosynthetic gene clusters. Whole genome sequencing of endophytic and marine actinomycetes will be analysed to search for interesting
biosynthetic gene clusters involved in production of polyketides, non-ribosomal peptides and lantibiotics.
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Population genetic of blue swimming crab (Portunus pelagicus)
in Sikao bay, Trang province
Blue swimming crab is economically important species sustaining
local communities living along the gulf of Thailand and Andaman
coastlines. Wild populations of the crab have been under
commercial fishery. Population status and an enhancing program,
namely ‘crab bank’, need to be evaluated.
Mixed-stock fishery analysis and major spawning grounds of
short-bodied mackerel (Rastrelliger brachysoma) in the Gulf of
Thailand
Short-bodied mackerel is the most commercially valuable
pelagic fish in the gulf of Thailand. It has been highly exploited
for >50 years, while major spawning grounds are not largely
studied.
Department of Genetics
Population and conservation genetics
Dr. Chatuporn Kuleung
1. Genetic difference of male and female cycads
Compare DNA fingerprint of male and female plants using DNA markers to develop
specific marker for identifying male and female plants.
2. Isolation of sex determining genes from cycads
Clone sex determining genes and investigate their expression to understand
what and how the related genes work in determining sex of the plant.
Contact: [email protected]
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Evolutionary Genetics of Infectious-disease mosquitoes
Current research projects:
1. Evolutionary genetic studies of immune system genes in malaria vectors
2. Population structure and linkage disequilibrium of dengue virus vector
3. Phenotypic plasticity of malaria mosquitoes in Thailand
Department of Genetics
My main interest is to understand evolutionary aspects of malaria and dengue vectors,
using SNP data and statistical analyses of population genetic models, in order to achieve
an effective malaria and dengue vectors control program.
Photo
Molecular markers such as multiplex PCR and
nucleotide sequences of mitochondrial DNA
(mtDNA) have been widely accepted for
identification of animal species. The markers were
applied to several different purposes e.g. food
safety, conservation and law enforcement.
Therefore, a number of animal species both
vertebrate and invertebrate are targets to identify
their effective species-specific markers.
Molecular systematic and Evolution
Population structure, historical demography,
phylogenetic relationship and lineage tracing are
important information for genetic resource
management. Nucleotide sequences of mtDNA were
applied to study population genetic, taxonomy and
phylogeny of animal species native to Thailand.
Department of Genetics
Development of Species-Specific Markers
Plant genetic engineering, cell manipulation
and DNA marker application in cucumber
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Main problem: Low yield, too few female flowers
per plant. Use genetic engineering to increase
number of fruits.
Cucurmis sativus
Optical tweezers in biological application
a) Genetics diversity study
b) Genome mapping
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Use microsatellite marker to assess the genetic
variation of cucumber in Thailand and to create a
genetic map.
Optical tweezers is a
highly focused laser
beam that can move
an object. Research
focuses on trapping
plant cells.
Department of Genetics
Jatropha curcas
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Plant and Microbe Interactions
Rice blast disease is one of the most important
constraints to rice production worldwide.
Understanding the interaction between rice and rice
blast fungus will facilitate the breeding program for
resistance to rice blast disease.
Mapping rice blast resistant genes in rice genome using DNA markers and studying the genetic
variation of R gene in rice and Avr gene in rice blast fungus.
Oil Palm Genetics & Genomics
Identification and Characterization of genes involved in
somatic embryogenesis in oil palm
We are interested in identifying genes involved in
somatic embryogenesis in oil palm in order to
understand the mechanism and regulation of this
developmental process as well as to shortening
the tissue culture process in oil palm for mass
propagation.
Department of Genetics
Dissecting rice and rice blast fungus interaction
Photo
http://www.learners.in.th/blogs/posts/345770
Ants are among the most successful insects in the world, which occupy
about 30% of the biomass. A colony of ants contains hundreds or
thousands individual workers which are daughter of one or a few
mothers, namely "queens". Their social structure is highly organized and
this makes ants and other social insects like wasps, bees, and termites
most successful compared to other insects. To understand the biology
and ecology of ants, at least for two focal species, weaver ants and fire
ants, we need to know whether a colony is headed by a single fertile
queens or multiple queens.
http://wingedpuff.wordpress.com/2012/01/13/colony-of-weaver-ants/
Why would one queen or multiple queens matter?
Because there are several ecological factor associated with
different types of social forms which will be applied to:
1. Weaver ants: to increase colony production in agriculture.
3. Fire ants: to find basic ecological information for pest
control and get some insights into the basic research on sex
determination in ants.
How to find the answer?
Molecular techniques will be used and some analysis on
http://www.visualphotos.com/image/1x9092241/fire_ant_solenopsis_geminata_colony_with
_queen_ant
population genetics and colony relatedness will be applied.
Department of Genetics
Genetics of social behavior
Molecular genetic analysis of ancient DNA
The aim of this project is to estimate the prevalence of dengue serotypes and evaluate dengue genotypic variations in mosquito vectors
living in the endemic areas in Thailand and to examine the relationship between the prevalence of dengue viruses in mosquito vectors and
the dengue diseases incidence. We expected that the results of this project would be useful for developing an effective public plan for
preventing dengue virus infection in Thailand.
Diversity of microorganisms
Isolation and identification of microbes in gut of earthworms.
Trash overloading is one of the environmental problem in many countries. To solve this problem, earthworms have
been used for waste management. The degradation of organic waste occurs in the gut of earthworms and it was
found that gut microorganisms have a major role in the process. Isolation and identification of the gut microbiota
using culture and unculture methods would provide us the bacterial and fungal diversity living in earthworms’ gut.
The information might be useful for the improvement of waste management in the future.
Here, we will screen and isolate of bacteria and fungi residing in the gut of earthworms which some of
them might be used to improve the efficiency of organic waste management.
Department of Genetics
Origin and distribution of domestic
and wild animals using ancient DNA.
The analysis of ancient DNA is playing an important role in conservation genetic, phylogenetic and
population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and
adds time depth to population genetics studies. Ancient DNA studies have been used to test the
historical theories resulting from archaeological studies. The historical studies regarding dispersal and
domestication of domestic animals could imply human demographic history. In the case of wild
animals , ancient DNA studies could give us a clue when wild animals have been domesticated and
the origin of those animals.
Serotype & genotype identification
Genotypic variation of dengue virus of dengue virus in mosquitoes
Dengue diseases are mosquito-borne infectious diseases and considered as a significant public health
burden of more than 100 countries, including Thailand. Several factors have been proposed to be associated
with dengue disease pathogenesis, including viral virulence. The virulence of dengue virus could be possibly
determined by the virus genetic background since different genotypes may cause different symptoms.
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Mutant screening and genetic engineering of
microalgae for biodiesel production
One of the reason that biodiesel production from
microalgae is still not commercially realized is because of its
high cost. One way to reduce cost is to improve algal
growth in outdoor conditions, which impose stresses on
algal cells.
The main goal of this project is to improve microalgal strains for higher efficiency of biodiesel
production by improving their tolerance to environmental stresses such as high light, high
temperature, and high concentration of reactive oxygen species.
Antioxidants in microalgae
The importance of each antioxidant and its interaction
with others in stress responses
The main goal of this project is to study the
role of each antioxidant in fighting against
stresses especially oxidative stress and to
understand its interaction with other
antioxidants.
Department of Genetics
Microalgal strain improvement
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Studying autophagic process and its functions in microalgae
Department of Genetics
Genetic engineering of microalgae for biofuel production
Dr. Anchanee Kubera
Study of inhibitors against key enzymes/virulence factors
The aim of this project is to identify Thai
medicinal plants as inhibitors against HIV-1
protease
HIV-1 protease
Subunit vaccine of porcine virus
The aim of this project is to develop subunit vaccines for porcine virus (PRRSV, PEDV)
Department of Genetics
The aim of this project is to Identify the
transmission blocking compounds against
malaria
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I Plant cell wall research


Genetic transformations enhancing growth and
biomass in Eucalyptus, Grasses and Arabidopsis
Understanding plant cell wall functions via
biosynthesis process and cell wall engineering
II Biofuel from microalgae

Genetic transformation in microalgae for
biodiesel production
III Genome editing

CRISPR genome editing tools for plants and
microalgae
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Mitochondrial DNA heteroplasmy inheritance
Revealing mtDNA heteroplasmy in Portunus pelagicus
Portunus pealgicus is chosen as a
model organism to study the
transmission pattern of neutral
mtDNA heteroplasmy. Nextgeneration sequencing technology
will be applied to reveal positions
of mtDNA heteroplasmy in mtCR
and mtCOI.
Mitochondrial DNA mutations have been observed
to cause various diseases. Typically, an affected
individuals receives mutant mtDNA from the
mother who transmits a random proportion of
mutant mtDNA to her offspring. The random shift
in mtDNA heteroplasmy level complicates
recurrence risk estimation.
http://lslab.lscore.ucla.edu/MTDNA/mtDNAMap.htm
A web-based tool for bacterial strain identification
Multi-locus sequence typing (MLST) is a
popular approach used for bacterial
strain identification. Due to the
complication of using many programs to
analyze this multiple steps method, all
necessary programs will be integrated
and set up as a web-based tool for
bacterial strain identification.
Department of Genetics
Pedigree model of human mtDNA heteroplasmy
inheritance
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Metagenomics of Mycorrhizal Fungi Community in Paphiopedilum (Orchidacae)
crucial for the orchid survival in natural environment. However,
the number of mycorrhiza isolated from its host is limited as
some of the fungi in the plant roots are unculturable. This
study we aim to identify fungal communities in the root of
Lady’s slipper orchids using NGS Metagenomics which should
guide us toward the future of orchid conservation.
Species Identification of Firefly (Lampyridae) using Molecular Technique
Over 2,000 species of fireflies have been identified around the
world. Firefly taxonomy and evolutionary relationship analyses
have been performed using mainly morphological features. This
method alone is unable to identify some ambiguous individual
and closely related species. Therefore we aim to generate
nucleotide data for firefly species identification for more reliable
result.
Department of Genetics
Orchid mycorrhiza, an important orchid root symbiont, is
Department of Genetics
Laboratory of Animal Cytogenetics and Comparative Genomics
 Karyotypic & genomic evolution
 Origin, differentiation of sex chromosomes and
diversity of sex determining systems
 Organization of repetitive element in vertebrate
genome
 Cancer chromosome analysis
 Mitochondrial genome analysis and DNA barcoding
Department of Genetics
The aim of my study is to clarify genome and chromosome structure
as well as their evolutionary process in vertebrates following topics:-
Dr. Teerasak E-kobon
Identification of Vaccine Candidates for Improvement of Animal Welfare
Pasteurella multocida is one of many pathogenic bacteria that causes
infectious diseases in various farm animals. Genetic diversity of this
bacterium in Thailand has not been fully understood. Investigating of
genetic diversity and the presence of virulence genes of P. multocida
strains associated with diseases in Thailand will provide specific
solutions for selecting of vaccine candidates.
The aim of this project is to study genetic diversity and distribution of
virulence genes of Pasteurella multocida strains associated with
diseased pigs, cattle and water buffaloes in Thailand.
Medical and Pharmaceutical
Applications of Gastropod Mucus
Proteomics and Glycomics of Snail Mucus
Snail mucus contains a variety of bio-reactive compounds. Some of
them have been used in medical and cosmetic industries. However,
there remain other proteins and carbohydrate compounds which have
not been ellucidated.
The aim of this project is to characterize proteins and carbohydrate
composition of the snail mucus in Thailand using proteomics and
glycomic methods.
Department of Genetics
Genetic diversity and distribution patterns of virulence genes in animal pathogenic bacteria