Soon -Guan Tan

ABSTRACT Miyun Reservoir is the main raw water source for Beijing’s domestic water supply. Flow discharge to Miyun Reservoir decreased drastically over a 50-year period, from 1956 to 2005, and had seriously affected Beijing’s water supply. Climate variability and human activity had been identified as the two main reasons for the decrease in flow. Here, climate variability refers to changes in precipitation and temperature. Impact of human activity includes direct withdrawal of water (referred to as “direct abstraction” in this paper) from the river (primary) or groundwater and indirect impact due to man-made changes in land use and vegetation in the upstream of the reservoir. According to the historical record, “direct abstraction” from the upstream of the reservoir has increased significantly since 1984. The study period was split into two sub-periods, from 1956 to 1983 and from 1984 to 2005. Based on the historical record, annual runoff in the upstream catchment of Miyun Reservoir (i.e., inflow into the reservoir) had decreased from 90.3 mm to 41.8 mm for the two sub-periods, a decrease of 48.5 mm. Over the same period, average annual “direct abstraction” increased from 2.2 mm to 13.4 mm, an increase of 11.2 mm. The latter accounted for 23% (11.2 mm/48.5 mm) of the decrease in inflow into the reservoir.This study utilised: (1) a distributed hydrological model (geomorphology-based hydrological model, or GBHM) and (2) a climate elasticity model to conduct a quantitative assessment of the impact of climate variability and the indirect impact of human activity on the inflow into the reservoir. Simulation results of GBHM and the climate elasticity model showed that climate impact was accountable for about 55% and 51% of the decrease in reservoir inflow, respectively. The indirect impact of human activity (mainly man-made land use and vegetation changes) accounted for 18% of the decrease in reservoir inflow.

Inter-simple sequence repeats (ISSRs) are regions in the genome flanked by microsatellite sequences.
PCR amplification of these regions using a single primer yields multiple amplification products that can
be used as a dominant multilocus marker system for the study of genetic variation in various organisms.
ISSR markers are easy to use, low-cost, and methodologically less demanding compared to other
dominant markers, making it an ideal genetic marker for beginners and for organisms whose genetic
information is lacking. Here, we comment upon some of the intricacies often overlooked in designing an
ISSR experiment, clarify some misconceptions, and provide recommendations on using ISSR markers
in genetic variation studies.

Horseshoe crabs are one of the oldest living organisms that still exist today. Given the overexploitation of horseshoe crabs
around the world, and the lack of information on their populations, it is crucial that genetic variation studies are done to
assess their levels and patterns of genetic variation for continuous monitoring and management of their populations. Here,
five populations of the Asian horseshoe crab Tachypleus gigas sampled from along the coasts of the Malay Peninsula were
studied using simple-sequence repeat (SSR) and inter-simple-sequence repeat (ISSR) markers. Different results were
obtained using the two different types of markers in terms of the levels of genetic variation estimated, but both concurred
that most of the genetic variations were distributed at the individual level rather than among populations of the species.
Inbreeding was also observed using the SSR data, although the presence of null alleles could have influenced the estimation.
Finally, both marker types revealed that T. gigas could have been subjected to the land barrier effect of the Malay Peninsula
that causes populations from the Indian Ocean to be genetically differentiated from the populations from the South
China Sea.
Key words: Dispersal, genetic monitoring, land barrier, peninsular Malaysia, population structure

Oryctes rhinoceros, a serious pest in young oil palm replanting areas, often causes reduced plant
productivity and plant death. Common control measures are species specific pheromone traps; however
discrepancy in attraction toward the pheromone traps has raised doubts on the possibility of cryptic
species complex in O. rhinoceros. To ascertain the possibilities of a cryptic species complex; species
specific single locus DNA microsatellite markers were used to study the genetic variation within and
between O. rhinoceros populations. Using 30 species specific single locus DNA microsatellite markers,
O. rhinoceros beetles from six populations originating from Malaysia and Indonesia revealed no isolated
gene pool. Pairwise population differentiation and gene flow values further revealed low to moderate
differentiation and a high gene flow between populations. Beetles of different population interacted
freely, permitting gene flow between closely and distantly located populations; thus ruling out the
possibility for cryptic species complex in O. rhinoce

Abstract
Background: The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human
Variome Project (HVP) country-specific nodes. Since its inception in 9th October 2010, MyHVP has attracted the
significant number of Malaysian clinicians and researchers to participate and contribute their data to this project.
MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian
population. A specialized database was developed to store and manage the data based on genetic variations
which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called
the Malaysian Node of the Human Variome Project database (MyHVPDb).
Findings: Currently, MyHVPDb provides only information about the genetic variations and mutations found in the
Malays. In the near future, it will expand for the other Malaysian ethnics as well. The data sets are specified based
on diseases or genetic mutation types which have three main subcategories: Single Nucleotide Polymorphism
(SNP), Copy Number Variation (CNV) followed by the mutations which code for the common diseases among
Malaysians. MyHVPDb has been open to the local researchers, academicians and students through the registration
at the portal of MyHVP (http://hvpmalaysia.kk.usm.my/mhgvc/index.php?id=register).
Conclusions: This database would be useful for clinicians and researchers who are interested in doing a study on
genomics population and genetic diseases in order to obtain up-to-date and accurate information regarding the
population-specific variations and also useful for those in countries with similar ethnic background.
Keywords: Malaysian Node of the Human Variome Project, Ethnic-specific molecular variation database, SNPs,
CNVs, Disease genes and their products

Horseshoe crabs are marine arthropods that are amongst the oldest living creatures that
still exist today. Among the four extant species of horseshoe crabs, Carcinoscorpius
rotundicauda differs from the other species by having poisonous eggs and lays its eggs in
sandy-mud areas near river mouths. With the rapid development of coastal areas
worldwide, C. rotundicauda habitats are decreasing. Until now, however, there has not
been any study on the species' genetic variation. Simple sequence repeat (SSR) and intersimple
sequence repeat (ISSR) markers were employed to study the genetic variation in
five C. rotundicauda populations from the east and west coasts of the Malay Peninsula. Both
markers showed differing levels of genetic variation, but concurred on the pattern of genetic
structuring among populations of the species. This includes showing that little,
although significant, genetic differentiation is present among populations, suggesting a
low rate of gene flow among populations. The results also suggested that C. rotundicauda
may be subjected to the land barrier effect of the Malay Peninsula, whereby gene flow is
limited between populations occurring on both sides of the peninsula, increasing their
genetic differentiation through time

Sampling for the mangrove snails, Nerita lineata, and surface sediments was carried out
from nine geographical sites of Peninsular Malaysia in April 2011. The concentrations of
Lithium (Li) were determined in the shells, opercula and soft tissues of N. lineata and in
the surface sediments by using ICP-MS. The ranges of Li concentrations (μg/g dry weight)
were found to be 0.107-0.283 for shells, 0.021-0.177 for opercula and 0.011-0.634 for
total soft tissues of N. lineata. For sediments, Li ranges were found to be between 21.84-
146.22 μg/g dry weight). The distribution of Li was found to be: sediment> ST> shell>
opercula. The Li sediment data in the present study were comparable with the results of Li
contaminated sediments which had been previously reported in the literature and higher
than those of continental crust materials and igneous rocks. There was no significant
correlation (P>0.05) for the Li levels between the sediments. The snails (shells, opercula
and soft tissues) and this indicated that Li is an essential metal for metabolism and thus is
being regulated in the body of the snail.

Oil palm breeding has been progressing very
well in Southeast Asia, especially in Malaysia and Indonesia.
Despite this progress, there are still problems due to
the difficulty of controlled crossing in oil palm. Contaminated/
illegitimate progeny has appeared in some
breeding programs; late and failure of detection by the
traditional method causes a waste of time and labor. The
use of molecular markers improves the integrity of breeding
programs in perennial crops such as oil palm. Four halfsib
families with a total of 200 progeny were used in this
study. Thirty polymorphic single locus DNA microsatellites
markers were typed to identify the illegitimate individuals
and to obtain the correct parental and progeny
assignments by using the CERVUS and COLONY programs.
Three illegitimate palms (1.5 %) were found, and
16 loci proved to be sufficient for sibship assignments
without parental genotypes by using the COLONY program.
The pairwise-likelihood score (PLS) method was
better for half-sib family assignments than the full likelihood
(FL) method.

Background: The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins
based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit;
the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and
Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which
were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions
of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu
Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from
Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian
SNP Initiative (PASNPI) Consortium and International HapMap project database.
Results: We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan
which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98%
of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly
admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced
back to have shared a common ancestor with the Proto-Malays and Chinese.
Conclusions: These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided
valuable information on the enigmatic demographical history as well as shed some insights into the origins of the
Malays in the Malay Peninsula.
Keywords: Malays; Single nucleotide polymorphisms; Genetic structure; Admixture; Haplotypes

The genetic diversity of the long-tailed macaques (Macaca fascicularis) from Penang, Malaysia, including Jerejak Island and
the mainland area of the state of Penang, Seberang Perai were examined using 1,042 bp control region (CR) segment of the
mitochondrial DNA (mtDNA). Twenty haplotypes were described with a single haplotype sharing between the mainland and the
island which suggests that it is a remnant of the genetic makeup from the mainland. Compared to previous studies based on
the CR, all the Penang haplotypes are newly described with none shared with the other regional populations of M. fascicularis.
A single deletion mutation unique to the Penang samples (Groups I and II) could be a good indicator for the conservation of the
genetic uniqueness and possibly should be managed as a management unit (MU). A summarised phylogenetic tree (NJ, MP, ML and
Bayesian) supports the monophyletic clustering of the M. fascicularis as described in previous studies. The topology separates the
Penang haplotypes into three major groups, which generally corresponds to their geographical distribution. We also noted that the
Penang haplotypes are of the continental lineage which separated from the insular lineage at around 1.04 mya. Finally, we showed
that the CR of the mtDNA is powerful and suitable for the quantification of intraspecific diversity in M. fascicularis.

Molecular markers in oil palm characterization and breeding began two decades ago. Microsatellite markers are a system that is commonly used in oil palm research since its development. Monomorphic SSR markers have been eliminated from all evolutionary and population genetics studies by researchers because of their lack of genetic variability. The goals of this study were to review polymorphic DNA microsatellite marker system also known as simple sequence repeats (SSR) in oil palm research since its development and to employ a monomorphic SSR marker for detection of illegitimacy in oil palm breeding programs. Ten monomorphic SSR markers and two half-sib families were used in this study. Illegitimate offspring IDs 97 and 180 were found by four monomorphic loci mEgCIR0425, mEgCIR3477, mEgCIR3769, and mEgCIR3902 in Family-1and Family-2. In addition, five loci (mEgCIR3574, mEgCIR3607, mEgCIR3672, mEgCIR3785 and mEgCIR3807)  detect one illegitimate offspring ID 180. This study showed that monomorphic SSR markers are suitable for the detection of illegitimate offsprings in oil palm breeding programs.

The oil palm is badly affected by basal stem rot (BSR) disease in Southeast Asia. BSR disease is caused by the fungus Ganoderma boninense, which is a major threat to oil palm compared with other Ganoderma spp. Molecular markers associated with BSR disease will accelerate the identification process of resistant breeding materials in screening of plants for tolerance to the disease at the nursery stage. In this study, 58 simple sequence repeat markers were utilized with three progeny types, namely, KA4G1, KA4G8, and KA14G8, to perform a comparative molecular mapping for association with BSR. A total of 319 alleles were identified with an average of 5.51 alleles per locus. Five markers, mEgCIR0793:180, mEgCIR0894:200, mEgCIR03295:210, mEgCIR3737:146 and mEgCIR3785:299 were found to be associated with Ganoderma disease with P-values of 0.018, 0.033, 0.037, 0.034 and 0.037, respectively, in single progeny analysis. However, in pooled data (KA4G1, KA4G8 and KA14G8), two alleles mEgCIR0804:213 (P-value =0.001) and mEgCIR3292:183 (P-value =0.001) were found to be associated with Ganoderma disease. These analyses confirmed that progeny type KA4G1 was tolerant, whereas the other two were susceptible progeny types. These markers and KA4 progeny will be useful in future work on BSR disease resistance in oil palm.

Genetic variation due to heavy metal contamination has always been an interesting topic of study.
Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion
and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors.
This study used a Single Primer Amplification Reaction (SPAR) technique, namely Random Amplified Polymorphic
DNA (RAPD), to determine the genetic diversity of the populations of the green-lipped mussel
Perna
viridis
collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively uncontaminated
sites (reference sites). Heavy metal levels (Cd, Cu, Pb, and Zn) were also measured in the soft tissues and
byssus of the mussels from all the sites. Cluster analyses employing UPGMA based on the RAPD markers
grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian, and Kg. Pasir Puteh
populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the
genetic diversity based on bands resulting from the use of all four RAPD primers on
P. viridis
did not indicate
its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis
between a particular metal and a band resulting from a specific RAPD primer revealed some significant
(
P
< 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues.
Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer
on
P. viridis
could be used as biomonitoring tool of heavy metal pollution.

lsozymes of 23 cultures of the anaerobic rumen fungi and seven cultures of
aerobic chytridiomycete fungi were analysed by PAGE. A total of 14 isozyme
loci were successfully typed by PAGE. They were peptidase A & C-I, peptidase
A & C-2, peptidase D-I, peptidase D-2, malate dehydrogenase-I, malate
dehydrogenase-2, esterase-I, esterase-2, malic enzyme-I, malic enzyme-2,
isocitrate dehydrogenase, shikimate dehydrogenase, phosphoglucomutase and
6-phosphogluconate dehydrogenase. lsozyme analysis can be used for
studying the genetic relationships among the different anaerobic rumen fungi
and the aerobic chytridiomycete fungi and the isozyme characteristics can
serve as additional taxonomic criteria in the classification of the anaerobic
rumen fungi. A dendrogram based on the isozyme data demonstrated that the
anaerobic rumen fungi formed a cluster, indicating a monophyletic group,
distinctly separated from the aerobic chytridiomycete fungi. Piromyces
communis and P. minutus showed a close relationship but P. spiralis showed a
more distant relationship to both P. communis and P. minutus. Piromyces as a
whole was more related to Caecomyces than to Neocallimastix. Orpinomyces
was also found to be more related to Piromyces and Caecomyces than to
Neocallimastix. Orpinomyces intercalaris C 70 from cattle showed large genetic
variation from 0. joyonii, indicating that it is a different species.

White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn
(Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium
rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in
positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and
internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20–29,
where 80% of amino acids are positively charged. Substitution of all these positively charged
residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still
assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly
domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding
region of MrNV capsid protein