A noninvasive molecular approach: exploiting species-locus-specific PCR primers in defeating numts and DNA cross-contamination of cercopithecidae

The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts)

Agonistic behavior of captive saltwater crocodile, crocodylus porosus in Kota Tinggi, Johor

Agonistic behavior in Crocodylus porosus is well known in the wild, but the available data regarding this behavior among the captive individuals especially in a farm setting is rather limited. Studying the aggressive behavior of C. porosus in captivity is important because the data obtained may contribute for conservation and the safety for handlers and visitors. Thus, this study focuses on C. porosus in captivity to describe systematically the agonistic behaviour of C. porosus in relation to feeding time, daytime or night and density per pool. This study was carried out for 35 days in two different ponds. The data was analysed using Pearson’s chi-square analysis to see the relationship between categorical factors. The study shows that C. porosus was more aggressive during daylight, feeding time and non-feeding time in breeding enclosure (Pond C, stock density =0.0369 crocodiles/m2) as compared to non-breeding pond (Pond B, stock density =0.3317 crocodiles/m2) where it is only aggressive during the nighttime. Pond C shows the higher domination in the value of aggression in feeding and non-feeding time where it is related to its function as breeding ground. Chi-square analysis shows that there is no significant difference between ponds (p=0.47, χ2= 2.541, df= 3), thus, there is no relationship between categorical factors. The aggressive behaviour of C. porosus is important for the farm management to evaluate the risk in future for the translocation process and conservation of C. porosus generally

Isolation of a pigment-producing bacterium chryseobacterium sp. from the tentacle of holothuria (lessonothuria) pardalis (Selenka 1867) from Pulau Tinggi, Johor

Chryseobacterium sp, a bacteria producing pigment was isolated from the tentacles of Holothuria (Lessonothuria) pardalis (Selenka 1867) from Pulau Tinggi, Johor. This study aimed to observe and genetically identified the presence of bacteria focusing on pigmentproducing bacteria. Thus, the partial 16S ribosomal RNA gene sequence of bacteria obtained and the shape, number of bacteria and gram staining observed using a digital compound microscope. Six gene sequence successfully obtained and the Basic Local Alignment Search Tool (BLAST) analysis suggested three species of bacteria identified from genus Pseudomonas, Chryseobacterium and Klebsiella. Besides, the neighbourhood-joining and Maximum Likelihood method had been used in the phylogenetic analysis to support the identification of bacteria species. The visible spectra of Chryseobacterium sp. were recorded between 400nm to 600nm which is a visible spectrum for carotenoid; orange pigment. However, further analysis is needed to confirm the characterisation and the potential of this pigment in industria

Molecular systematic position of the Sarawak Malay badger, Mydaus javanensis

The presence of the Malay badger, Mydaus javanensis, has been recorded for nearly 100 years in Sarawak, Malaysia, but it has rarely been seen. In addition, this animal is among the least studied carnivores in Borneo. The Malay badger is not protected under the Sarawak Wildlife Protection Ordinance. To initiate conservation efforts, we conducted a phylogenetic analysis to characterize the Malay badger’s genetic attributes. In August 2013, a Malay badger was trapped at Mentung Berawan, Serian, and sent to the Matang Wildlife Centre. We managed to collect its genetic materials and sequenced 356 bp of 12S rRNA and 405 bp of cytochrome b (Cyt b) genes. We portrayed its phylogenetic relationships with other Mephitidae family members and calculated its molecular divergence. Our results indicated that the Malay badger could be distinguished from its sister taxon, M. marchei. The teledu clade diverged 2.71 million years ago, after the divergences of Mephitis mephitis and Spilogale putorius

Agonistic Behavior of Captive Saltwater Crocodile, Crocodylus Porosus in Kota Tinggi, Johor

Agonistic behavior in Crocodylus porosus is well known in the wild, but the available data regarding this behavior among the captive individuals especially in a farm setting is rather limited. Studying the aggressive behavior of C. porosus in captivity is important because the data obtained may contribute for conservation and the safety for handlers and visitors. Thus, this study focuses on C. porosus in captivity to describe systematically the agonistic behaviour of C. porosus in relation to feeding time, daytime or night and density per pool. This study was carried out for 35 days in two different ponds. The data was analysed using Pearson’s chi-square analysis to see the relationship between categorical factors. The study shows that C. porosus was more aggressive during daylight, feeding time and non-feeding time in breeding enclosure (Pond C, stock density =0.0369 crocodiles/m2) as compared to non-breeding pond (Pond B, stock density =0.3317 crocodiles/m2) where it is only aggressive during the nighttime. Pond C shows the higher domination in the value of aggression in feeding and non-feeding time where it is related to its function as breeding ground. Chi-square analysis shows that there is no significant difference between ponds (p=0.47, χ2= 2.541, df= 3), thus, there is no relationship between categorical factors. The aggressive behaviour of C. porosus is important for the farm management to evaluate the risk in future for the translocation process and conservation of C. porosus generally.&nbsp

Review of SQL injection : problems and prevention

SQL injection happened in electronic records in database and it is still exist even after two decades since it first happened. Most of the web-based applications are still vulnerable to the SQL injection attacks. Although technology had improved a lot during these past years, but, hackers still can find holes to perform the SQL injection. There are many methods for this SQL injection to be performed by the hackers and there is also plenty of prevention for the SQL injection to be happened. The vulnerability to SQL injection is very big and this is definitely a huge threat to the web based application as the hackers can easily hacked their system and obtains any data and information that they wanted anytime and anywhere. This paper can conclude that several proposed techniques from existing journal papers used for preventing SQL injection. Then, it comes out with Blockchain concept to prevent SQL injection attacks on database management system (DBMS) via IP

Feeding Regime and Management of Captive Saltwater Crocodile, Crocodylus Porosus in Kota Tinggi, Johor

Crocodylus porosus is the largest species of crocodile and can be found in estuarine and riverine area in Malaysia. Crocodile in captivity can be found in Malaysia for various purposes such as tourism, conservation and leather industry. However, the management practice in established crocodile farm varies across park for example in terms of feeding regime. Thus, this study focusses on the feeding regime of C. porosus in captivity and evaluation of management of crocodile of Teluk Sengat Crocodile Farm. This study was carried out for 35 days in two different ponds of Teluk Sengat Crocodile Farm, Kota Tinggi, Johor. The results show majority of the food given to crocodile were chicken (64%), followed by fish (28%) and prawn (8%). Prawn was only given to juvenile crocodile every day, while fish and whole chicken were given to adult crocodile once a week. The feeding frequency are adequate for the juvenile crocodile however, the feeding quantity for adult pond are worrying. Future research should be conducted on other captive population of C. porosus in other areas in Malaysia as well to better understand the overall management practices in Malaysia

Molecular phylogenetic inference of White-Spotted Guitarfish (Rhynchobatus australiae) collected from local Malaysian fish markets

The white-spotted guitarfish (Rhynchobatus australiae) is in high demand at local Malaysian fish markets because its fins are a valuable food source. To date, few molecular studies have characterized their genetic identity. We have conducted a molecular study to infer the phylogenetic relationships of white-spotted guitarfish, which portray a similar morphology to sharks and rays. The main objective of this study was to determine the phylogenetic position of R. australiae using cytochrome oxidase I (COI) sequences of mitochondrial DNA based on fish samples collected from local Malaysian fish markets. This study included nine genetic samples of R. australiae and fourteen samples from other members of the shark and ray families, including Sphyrna lewini (Sphyrnidae), Rhizoprionodon oligolinx and Carcharhinus sorrah (Carcharhinidae), Dasyatis zugei, Himantura walga, Himantura gerradi, Himantura jenkinsii and Neotrygon kuhlii (Dasyatidae). Chimaera fulva, a member of the Chimaera family, was used as the outgroup. Sequences in size of ~701 base pairs were successfully obtained from all fish samples. The phylogenetic tree topology was reconstructed using distance-based (neighbor-joining) and character-based (maximum parsimony) methods using MEGA and PAUP software. Results indicated that R. australiae formed monophyletic clade and is closely related to sharks (Sphyrnidae and Carcharhinidae). This conclusion was also supported by genetic distance analysis which indicated that Rhynchobatidae and sharks (Carcharhinidae and Sphyrnidae) were closer to each other than to rays (Dasyatidae). This study has proven the efficiency of the COI mitochondrial locus in revealing the phylogenetic position of R. australiae. Research findings from this study have increased our understanding of the phylogenetic relationships among guitarfish, sharks, and rays, and their respective taxonomic positions are given their shared morphological characters. This will benefit us in identifying these fish species before consumption from local fish markets

Isolation of bacteria associated with the tentacles of holothuria (lessonothuria) pardalis (selenka 1867) from Pulau Tinggi, Johor including pigment-producing chryseobacterium sp.

Pigment-producing microorganisms have become a main focus due to the search of food-grade microbial pigments for natural food colourant industry. Therefore, this study aimed to isolate and genetically identify bacteria including pigmentproducing bacterial strains associated with the tentacles of Holothuria (Lessonothuria) pardalis (Selenka 1867) from Pulau Tinggi, Johor. Morphological characteristics of bacteria based on Gram staining were observed using a digital compound microscope. Partial 16S ribosomal RNA (rRNA) gene sequencing was also incorporated to support the morphological approach. A number of six partial gene sequences of non-protein coding 16S rRNA were obtained and the Basic Local Alignment Search Tool (BLAST) analysis suggested the presence of three known bacteria species from the genera of Pseudomonas, Chryseobacterium and Klebsiella. The neighbourhood-joining method and Maximum Likelihood method used in the phylogenetic analysis supported the identification and classification of the bacteria species. Among the bacterial isolates, only strain B14 identified as Chryseobacterium sp. produced pigment i.e. orange pigment. The highest point of cell density of Chryseobacterium sp. was recorded at 16 hours. However, further analysis is needed to confirm the pigment characterisation and the potential of this pigment to be exploited as natural colourant in the food industry

Molecular phylogenetics and phylogeography of Malaysian mousedeer (Tragulus kanchil) based on mitochondrial DNA sequences of the D-loop region

Two sympatric mousedeer species, Tragulus kanchil and Tragulus napu, inhabit the Malaysian tropical rainforests. Previous studies have established their phylogenetic relationships based on morphological variations; however, comprehensive genetic data have yet to be extensively used to relate the relationships especially from different populations. The main objectives of this study were to determine the phylogenetic relationships, population genetics, and phylogeography of mousedeer species based on DNA sequences of the mitochondrial D-loop region. DNA from 32 mousedeer samples, representing various populations in Malaysia, was sequenced and analyzed using NeighborJoining, Maximum Parsimony, and Bayesian Inference approaches. The phylogenetic analyses showed two main clades representing the populations of T. kanchil and T. napu. The results also showed that the T. kanchil populations in Borneo was separated from Peninsular Malaysia taxa in MP and BI phylogenetic tree. However, Borneo population was nested in east population of Peninsular Malaysia in NJ tree. In addition, the T. kanchil population in Peninsular Malaysia further separated into east and west coast populations of Titiwangsa Range. It was supported with finding in population genetic relation that showed relatively low levels among population. This is expected because some of the populations are isolated geographically. The divergence of these populations is likely due to the Titiwangsa Range which acts as a barrier separating the east and west Peninsular Malaysia populations, and the South China Sea separates the populations of Peninsular Malaysia and Borneo. Molecular clock tree reconstruction showed that the separation of T. kanchil and T. napu occurred around 17.11 million years ago (MYAs). Furthermore, the T. kanchil populations from the east and west Peninsular Malaysia showed a branching pattern from those of Borneo of about 11.04 and 9.14 MYAs, respectively. The results of this study increase our understanding of Malaysian mousedeer phylogeny and phylogeograph