Twelve single locus trinucleotide microsatellite markers were developed to characterize the Asian river catfish, Mystus nemurus, an important food fish in South East Asia. They were obtained by using a rapid method namely the 5' anchored PCR enrichment protocol. The specific primers were designed to flank the repeat sequences and these were subsequently used to characterize 90 unrelated fish from Malaysia. The number of alleles per locus ranged from 2 (MnVj2-281) to 12 (MnBp8-4-43b) while the levels of heterozygosity ranged from 0.0444 (MnVj2-1-19) to 0.7458 (MnVj2-291).
The river catfish Mystus nemurus is an important fresh water species for aquaculture in Malaysia. We report the first genetic linkage map of M. nemurus based on segregation analysis and a linkage map using newly developed microsatellite markers of M. nemurus. A total of 70 of the newly developed polymorphic DNA microsatellite markers were analyzed on pedigrees generated using a pseudo-testcross strategy from 2 mapping families. In the first mapping family, 100 offspring were produced from randomly selected dams of the same populations; dams of the second family were selected from 2 different populations, and this family had 50 offspring. Thirty-one of the 70 markers segregated according to the Mendelian segregation ratio. Linkage analysis revealed that 17 microsatellite markers belonging to 7 linkage groups were obtained at a logarithm of the odds score of 1.2 spanning 584 cM by the Kosambi mapping function, whereas the other 14 remained unlinked. The results from this study will act as primer to a more extensive genetic mapping study aimed towards identifying genetic loci involved in determining economically important traits.
A total of 143 microsatellites were isolated from Mystus nemurus using a 5' anchored polymerase chain reaction technique or the random amplified hybridization microsatellite method, the first set of microsatellite markers developed for the Southeast Asian river catfish. Twenty polymorphic microsatellite loci were used as markers for population characterization of M. nemurus from six different geographical locations in Malaysia (Perak, Kedah, Johor, UPM, Sarawak and Terengganu). The number of alleles per locus ranged from 2 to 11 with 6.3 as the average number of alleles per locus. Characterization of the populations showed relatively high levels of genetic variation compared with previous studies using allozyme markers. The highest genetic similarity was found between Perak and Kedah, while the highest genetic distance was found between Terengganu and Kedah. The majority of clustering was in accordance with geographical locations and the histories of the populations. Microsatellite analysis indicated that the Sarawak population might be genetically closer to the Peninsular Malaysian populations than has been previously shown by other molecular marker studies.
Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.
During the intermonsoon period from mid-September to mid-October 1986, wild-caught Anopheles balabacensis Baisas females were marked and released in a host-choice experiment. Association between capture and recapture of marked mosquitoes from human and bovid hosts and blood meal host identification of recaptured females were determined on a daily basis. Although the mark-recapture and blood meal data indicated behavioral heterogeneity between buffalo and human biters, restriction endonuclease fragment length polymorphism analysis revealed no differences in repeat sequence profiles. Doubly-marked recaptures strongly indicated a "learning" component involved in a separate host preference experiment. In a "habitat loyalty" experiment conducted in January 1987, females of An. balabacensis preferentially returned to the resting sites (indoor surfaces and exit traps) where they were first caught. Of nine isozyme loci found to be polymorphic, the genotypic frequencies of Esterase-3 and Isocitrate dehydrogenase-3 were different in "faithfully" endophilic and exophilic subpopulations. Genetic heterozygosity, as determined by polyacrylamide gel electrophoresis, was greater in exophilic than endophilic population components. These results confirm that genetic and learning components can significantly influence house resting and host seeking behavior and may contribute to local epidemiological patterns of malaria transmission observed in Sabah, Malaysia.
We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic markers for this species.
Laboratories intending to adopt cycle sequencing of PCR products in their routine analysis often face a confusing range of methods and kits. Through the study of mitochondrial cytochrome b, we have shown that clean and highly reproducible sequences could be obtained by using a combination of existing simple and economical methods in the preparation of DNA templates, PCR, purification of PCR products and sequencing. Our protocol is useful in itself or as a standard in typing other PCR-amplified DNA at the population level.
Canine babesiosis caused by Babesia spp. is a noteworthy tick-borne zoonotic disease of domestic dogs and wild canids. In present study, a total of 556 blood samples were randomly collected from pet dogs in eight cities of Hunan province, subtropical China. Genomic DNA was extracted and Babesia DNA was detected by amplification of partial 18S rRNA gene sequences. A total of 56 (10.1%) blood samples were tested positive for Babesia species. Sequence analysis showed that 29 dogs (5.2%) were positive for B. gibsoni, and other 27 dogs for B. vogeli (4.9%). The age and health status were considered as important risk factors for B. gibsoni and B. vogeli infections in pet dogs in this study (P<0.05). Phylogenetic analysis showed that the examined positive samples were highly clustered in the same branch with B. gibsoni and B. vogeli, respectively. This is the first molecular report of B. gibsoni infection in pet dogs in Hunan province, subtropical China. Our finding has provided a guide for the control of dog babesiosis in China and elsewhere.
We have developed the methodologies for typing and family studies to establish the modes of inheritance of water buffalo red cell acid phosphatase (Acp), protease inhibitor (Pi), and group-specific component (Gc) on isoelectric focusing and albumin (Alb), red cell alpha-esterase-3 (Est-3), and catalase (Cat) on polyacrylamide gel electrophoresis. Family studies showed that Pi, Gc, Alb, and Cat are coded by autosomal genes with two codominant alleles, while Est-3 is autosomal with two codominant alleles and a recessive null allele and Acp exhibits three codominant alleles.
A total of 640 Malaysians, 355 of Malay, 155 of Chinese, and 130 of Indian ancestries have been examined for saliva acid phosphatases. The three ethnic groups were polymorphic for saliva acid phosphatase A (Sap-A) and saliva acid phosphatase (B (Sap-B). The gene frequencies were: Sap-A, Malays: A = 0.469, A' = 0.001, A degrees = 0.530; Chinese: A = 0.436, A' = 0.010, A degrees = 0.555; Indians: A = 0.533, A' = 0.012, A degrees = 0.456. For Sap-B, Malays: B = 0.925, B degrees = 0.075; Chinese: B = 0.797, B1 = 0.016, B degrees = 0.187; Indians: B 0.752, B degrees = 0.248. Phenotype ABB1 is described.
Three human saliva genetic markers, namely, salivary peroxidase (SAPX), Pm, and Ph proteins, were investigated in the three major ethnic groups of Malaysia: Malays, Chinese, and Indians. For Pm, the allelic frequencies of Pm+ for Malays, Chinese, and Indians are 0.385 +/- 0.030, 0.282 +/- 0.026, and 0.289 +/- 0.026 respectively. For Ph, the allelic frequencies of Ph+ are 0.082 +/- 0.016 for Malays, 0.109 +/- 0.017 for Chinese, and 0.062 +/- 0.013 for Indians. For SAPX, the allelic frequencies of SAPX1 in Malays, Chinese, and Indians are 0.762 +/- 0.027, 0.755 +/- 0.027, and 0.723 +/- 0.026 respectively.
The first objective of this study was to provide data of arsenic (As) levels in Peninsular Malaysia based on soil samples and accumulation of As in Centella asiatica collected from 12 sampling sites in Peninsular Malaysia. The second objective was to assess the accumulation of As in transplanted C. asiatica between control and semi-polluted or polluted sites. Four sites were selected which were UPM (clean site), Balakong (semi-polluted site), Seri Kembangan (semi-polluted site) and Juru (polluted site). The As concentrations of plant and soil samples were determined by Instrumental Neutron Activation Analysis. The As levels ranged from 9.38 to 57.05 μg/g dw in soils, 0.21 to 4.33 μg/g dw in leaves, 0.18 to 1.83 μg/g dw in stems and 1.32-20.76 μg/g dw in roots. All sampling sites had As levels exceeding the CCME guideline (12 μg/g dw) except for Kelantan, P. Pauh, and Senawang with P. Klang having the highest As in soil (57.05 μg/g dw). In C. asiatica, As accumulation was highest in roots followed by leaves and stems. When the As level in soils were higher, the uptake of As in plants would also be increased. After the transplantation of plants to semi-polluted and polluted sites for 3 weeks, all concentration factors were greater than 50 % of the initial As level. The elimination factor was around 39 % when the plants were transplanted back to the clean sites for 3 weeks. The findings of the present study indicated that the leaves, stems and roots of C. asiatica are ideal biomonitors of As contamination. The present data results the most comprehensive data obtained on As levels in Malaysia.
Direct amplified length polymorphism (DALP) combines the advantages of a high-resolution fingerprint method and also characterizing the genetic polymorphisms. This molecular method was also found to be useful in brown planthopper, Nilaparvata lugens species complex for the analysis of genetic polymorphisms. A total of 11 populations of Nilaparvata spp. were collected from 6 locations from Malaysia. Two sympatric populations of brown planthopper, N. lugens, one from rice and the other from a weed grass (Leersia hexandra), were collected from each of five locations. N. bakeri was used as an out group. Three oligonucleotide primer pairs, DALP231/DALPR'5, DALP234/DALPR'5, and DALP235/DALPR'5 were applied in this study. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on genetic distances for the 11 populations of Nilaparvata spp. revealed that populations belonging to the same species and the same host type clustered together irrespective of their geographical localities of capture. The populations of N. lugens formed into two distinct clusters, one was insects with high esterase activities usually captured from rice and the other was with low esterase activities usually captured from L. hexandra. N. bakeri, an out group, was the most isolated group. Analyses of principal components, molecular variance, and robustness also supported greatly to the findings of cluster analysis.
It has been widely reported that allozyme frequency variation is a potential indicator of heavy metal-induced impacts in aquatic populations. In the present study, wild populations of horseshoe crab (Carcinoscorpius rotundicauda) were collected from contaminated and uncontaminated sites of Peninsular Malaysia. By adopting horizontal starch gel electrophoresis, seven enzyme systems were used to study allozyme polymorphisms. Nine polymorphic loci were observed in C. rotundicauda. The relationships of allozyme variations with the concentrations of Cd, Cu, Ni, and Zn in sediments and in muscle tissues of horseshoe crabs were determined. Based on genetic distance, the lower mean value of Nei's D (0.017) indicated that both of the contaminated populations of Kg. Pasir Puteh and Kuala Juru were very closely related when compared to the relatively uncontaminated Pantai Lido population. Higher heterozygosities were shown by the contaminated populations when compared to the uncontaminated population. Different allelic frequencies could be observed for the aldolase (ALD; E.C. 2.7.5.1) locus between the contaminated and uncontaminated populations of C. rotundicauda. The dendrogram of genetic relationships of the three populations of C. rotundicauda showed the same clustering pattern as the dendrograms are based on heavy metals in the sediments and in the horseshoe crabs' abdominal muscles. From the F statistics, the present study showed that the three populations of horseshoe crabs were considered to have undergone moderate genetic differentiation with a mean F (ST) value of 0.092 .The current results suggest that allozyme polymorphism in horseshoe crabs is a potential biomonitoring tool for metal contamination, although further validation is required.
Eight single locus microsatellite markers were developed to characterize the Malaysian giant freshwater prawn, Macrobrachium rosenbergii. These microsatellites were isolated from an enriched genomic library contained by using a 5'-anchored polymerase chain reaction technique. Primers were designed to flank the repeat sequences and subsequently used to characterize 30 unrelated individuals of the giant freshwater prawn. The polymerase chain reaction amplification products of these eight microsatellite loci were polymorphic with the number of alleles ranging from two to 10 alleles per locus while the levels of heterozygosity ranged from 0.6333 to 0.8667.
The distributions of Cu, Zn, and Pb concentrations in the selected soft tissues (foot, cephalic tentacle, mantle, muscle, gill, digestive caecum, and remaining soft tissues) and shells of the mud-flat snail Telescopium telescopium were determined in snails from eight geographical sites in the south-western intertidal area of Peninsular Malaysia. Generally, the digestive caecum compared with other selected soft tissues, accumulated higher concentration of Zn (214.35+/-14.56 microg/g dry weight), indicating that the digestive caecum has higher affinity for the essential Zn to bind to metallothionein. The shell demonstrated higher concentrations of Pb (41.23+/-1.20 microg/g dry weight) when compared to the selected soft tissues except gill from Kuala Sg. Ayam (95.76+/-5.32 microg/g dry weight). The use of different soft tissues also can solve the problem of defecation to reduce error in interpreting the bioavailability of heavy metals in the intertidal area.
The concentrations of Cu, Pb, and Zn in the crystalline style (CS) and in the remaining soft tissues (ST) of the green-lipped mussel Perna viridis from 10 geographical sites along the coastal waters off peninsular Malaysia were determined. The CS, compared with the remaining ST, accumulated higher levels of Cu in both contaminated and uncontaminated samples, indicating that the style has a higher affinity for the essential Cu to bind with metallothioneins. The similar pattern of Cu accumulation in the different ST of mussels collected from clean and Cu-contaminated sites indicated that the detoxification capacity of the metallothioneins had not been overloaded. For Pb, higher levels of the metal in the CS than in the remaining ST were found only in mussels collected from a contaminated site at Kg. Pasir Puteh. This indicated a tissue redistribution of Pb due to its binding to metallothioneins for Pb detoxification and the potential of the CS as an indicator organ of Pb bioavailability and contamination. For Zn, the above two phenomena were not found since no obvious patterns were observed (lower levels of Zn in the CS than in the remaining ST) in contaminated and uncontaminated samples due to the mechanism of partial regulation. Generally, all the different STs studied (foot, mantle, gonad, CS, gill, muscle, and byssus) are good biomonitoring tissues for Cu and Pb bioavailabilities and contamination. Among these organs, the CS was found to be the best organ for biomonitoring Cu. The present data also suggest the use of the tissue redistribution of Pb in P. viridis as an indicator of Pb bioavailability and contamination in coastal waters.
Termites from the genus Odontotermes are known to contain numerous species complexes that are difficult to tell apart morphologically or with mitochondrial DNA sequences. We developed markers for one such cryptic species complex, that is, Odontotermes srinakarinensis sp. nov. from Maxwell Hill Forest Reserve (Perak, Malaysia), and characterised them using a sample of 41 termite workers from three voucher samples from the same area. We then genotyped 150 termite individuals from 23 voucher samples/colonies of this species complex from several sites in Peninsular Malaysia. We analysed their population by constructing dendograms from the proportion of shared-alleles between individuals and genetic distances between colonies; additionally, we examined the Bayesian clustering pattern of their genotype data. All methods of analysis indicated that there were two distinct clusters within our data set. After the morphologies of specimens from each cluster were reexamined, we were able to separate the two species morphologically and found that a single diagnostic character found on the mandibles of its soldiers could be used to separate the two species quite accurately. The additional species in the clade was identified as Odontotermes denticulatus after it was matched to type specimens at the NHM London and Cambridge Museum of Zoology.
A study of the impacts of anthropogenic activities on the distribution and biodiversity of benthic macroinvertebrates and water quality of the Langat River (Peninsular Malaysia) was conducted. Four pristine stations from the upstream and 4 stations at the downstream receiving anthropogenic impacts were selected along the river. For 4 consecutive months (March-June 1999), based on the Malaysian DOE (Malaysia Environmental Quality Report 2000, Department of Environment, Ministry of Science, Technology and Environment Malaysia. Maskha Sdn. Bhd. Kuala Lumpur, 86pp; Malaysia Environmental Quality Report 2001, Department of Environment, Ministry of Science, Technology and the Environment Malaysia) water quality index classes, the upstream stations recorded significantly (P<0.05) higher Biological Monitoring Working Party scores and better water quality indices than those of the downstream. The total number of macrobenthic taxa and their overall richness indices and diversity indices were significantly (P<0.05) higher at the upstream stations (54 taxa) than at the downstream stations (5 taxa). The upstream of the Langat River was dominated by Ephemeroptera and chironomid dipterans while other orders found in small quantities included Trichoptera, Diptera, Plecoptera, Odonata, Ephemeraptera, Coleoptera, and Gastropoda. On the other hand, the downstream of the river was mainly inhabited by the resistant Oligochaeta worms Limnodrilus spp. and Branchiodrilus sp. and Hirudinea in small numbers. The relationships between the physicochemical and the macrobenthic data were investigated by Pearson correlation analysis and multiple stepwise regression analysis. These statistical analyses showed that the richness and diversity indices were generally influenced by the total suspended solids and the conductivity of the river water. This study also highlighted the impacts of anthropogenic land-based activities such as urban runoff on the distribution and species diversity of macrobenthic invertebrates in the downstream of the Langat River. The data obtained in this study supported the use of the bioindicator concept for Malaysian rivers. Some sensitive (Trichopteran caddisflies and Ephemeraptera) and resistant species (Oligochaeta such as Limnodrilus spp.) are identified as potential bioindicators of clean and polluted river ecosystems, respectively, for Malaysian rivers.