Forensic DNA profiling of tropical timber species in Peninsular Malaysia

Illegal logging poses a significant threat to the sustainability of tropical forest ecosystems. By using Neobalanocarpus heimii (Dipterocarpaceae) as an example, the study assessed the feasibility of using short tandem repeats (STRs) as a tool to identify the source of illegally logged timber. Thirty natural populations of N. heimii were profiled using 12 STRs to develop the DNA profiling databases. As the cluster analysis divided the 30 populations into three genetic clusters, corresponding to three subregions within Peninsular Malaysia. The DNA databases were characterised at the levels of population, subregion and Peninsular Malaysia. Independence tests within and among loci were violated in all the databases due to significant levels of population differentiation and inbreeding. Thus, the effects of population substructure and inbreeding should be incorporated into the calculation of random match probability. The random match probabilities estimated using subpopulation and subpopulation-cum-inbreeding models were biased in favour of the defendant, whereas the random match probabilities estimated using product rule were biased in favour of the prosecutor. The conservativeness tests showed that the subregion and Peninsular Malaysia databases were conservative, and these databases should be able to provide legal evidence for court proceedings against illegal loggers in Peninsular Malaysia.     

Microbiology. Arresting features of bacterial toxins

Bacteria produce an arsenal of sophisticated toxins that disrupt the normal processes of the host cell, usually by modifying or inactivating host cell proteins. Now, as Coburn and Leong discuss in their Perspective, members of the cytolethal distending toxin (CDT) family have been identified as enzymes that attack DNA (and not protein) within the host cell (Lara-Tejero and Galán). By attacking DNA, perhaps during chromosomal replication, CDTs cause the host cell to halt in G2 phase of the cell cycle.     

Geographical traceability of an important tropical timber (Neobalanocarpus heimii) inferred from chloroplast DNA

The inbuilt unique properties of DNA within the timber could serve as tracking and monitoring tools to verify the legality of a suspected timber in the context of illegal logging, forest certification and chain of custody certification. By using Neobalanocarpus heimii (Dipterocarpaceae) as an example, a population identification database and haplotype distribution map in Peninsular Malaysia were generated for authenticity testing based on four chloroplast DNA markers (trnL intron, trnG intron, trnK intron and psbK-trnS spacer). Twenty one haplotypes were identified from 10 significant intraspecific variable sites. The results clearly revealed that only northern and southern regions of Peninsular Malaysia were distinguishable. Thus, this database could only be used to determine the wood lot of unknown origin at the regional level. Statistical procedure based on the composition of wood lot was used to test whether a suspected timber conforms to a given regional origin. Overall, the observed type I and II errors of the database showed good concordance with the predicted 5% threshold, which might indicate that the database is useful to reveal provenance and establish conformity of wood lot from northern and southern regions of Peninsular Malaysia. Applications of this database for timber tracking are discussed.     

Visual thresholds for feeding and optimum light intensity for larval rearing of Asian seabass,Lates calcarifer (Bloch)

This study examined the retinomotor responses and prey ingestion rates of 10‐, 15‐, 20‐ and 30‐day‐old Asian seabass Lates calcarifer under different light intensities from 0 to 1000 lx to determine the visual thresholds. Subsequently, two age groups of seabass larvae were reared under light intensities of 10, 100 and 1000 lx to determine the optimum illumination in hatchery tanks. Retinomotor response was absent in 10‐day‐old larvae, but quite marked in 15‐ and 20‐day‐old seabass at 1 lx and higher. Ingestion of Artemia nauplii by 10‐day‐old larvae was almost zero at <1 lx, increased significantly at 1 lx, and was maximal at 10–100 lx. Artemia ingestion under dim light <1 lx improved with age, and older larvae took more prey in complete darkness due to the presence of rod cells (and also free neuromasts). Larvae from 13 to 26 days group had similar survival and growth at 10–1000 lx, however, from 5 to 10 days group showed similar survival rate with highest weight gain at 100 lx. Therefore, we recommend that hatchery rearing tanks be illuminated such that the larvae in the water are exposed to approximately100 lx.     

Inhibition of infectious haematopoietic necrosis virus in cell cultures with peptide-conjugated morpholino oligomers

Delivery of phosphorodiamidate morpholino oligomers (PMO) into fish cells in vitro and tissues in vivo was examined. Uptake was evaluated by fluorescence microscopy and flow cytometry after treating cultured cells or live rainbow trout with 3' fluorescein-tagged PMO. Arginine-rich peptide conjugated to the 5' end of the PMO markedly enhanced cellular uptake in culture by 8- to 20-fold compared with non-peptide-conjugated PMO as determined by flow cytometry. Enhanced uptake of PMO conjugated to peptide was also observed in tissues of fish treated by immersion. The efficacy of PMO as inhibitors of infectious haematopoietic necrosis virus (IHNV) replication was determined in vitro. Peptide-conjugated PMOs targeting sequences within the IHNV genomic RNA (negative polarity) or antigenomic RNA (positive polarity) significantly inhibited replication in a dose-dependent and sequence-specific manner. A PMO complementary to sequence near the 5' end of IHNV genomic RNA was the most effective, diminishing titre by 97%, as measured by plaque assay and Western blot. These data demonstrate that replication of a negative-stranded non-segmented RNA virus can be inhibited by antisense compounds that target positive polarity viral RNA, or by a compound that targets negative polarity viral RNA.     

Understanding the stability of Samanea saman trees through tree pulling,analytical calculations and numerical models

There have been several cases of tree failure in Singapore. Many studies have shown that soil properties and root architecture of trees are important factors that govern tree stability. Twenty Samanea saman trees were planted in different soil media, which were original in situ soil, top soil, mixture of 50% granite chips and 50% top soil, and mixture of 80% granite chips and 20% top soil. The objectives of this study were to investigate tree overturning processes and also to compare the results of tree pulling tests with results from an analytical calculation and numerical modeling for different soil types. The results showed that stability of the trees were not governed by the shear strength of the soil. Factors that affected tree stability included cross-sectional area of the roots and root plate area. Tree pulling test and numerical modeling results showed that there were two modes of failure which occurred when a tree was overturned. The first mode was the shear failure of soil and the second was a combination of shear failure of soil and root breakage. The maximum overturning force obtained from the tree pulling test was in the same order of magnitude as the maximum overturning forces obtained from the analytical calculation and numerical modeling.     

Characterization of antioxidants and change of antioxidant levels during storage of Manilkara zapota L

Antioxidants found in fruits and vegetables play an important role via their protective effects against the onset of aging-related chronic diseases. Our previous research has indicated that unripe ciku fruits (Manilkara zapota L.) are an excellent source of antioxidants, with over 3000 mg of L-ascorbic acid equivalent antioxidant capacity (AEAC) per 100 g of fresh sample. In this study, 24 antioxidants in an extract of ciku king were characterized through a free radical spiking test. Their chemical structures were proposed using high-performance liquid chromatography-mass spectrometry (HPLC-MS) and tandem MS (HPLC/MSn). The antioxidant capacity of ciku king fruits was mainly attributed to polyphenolics with basic blocks of gallocatechin or catechin or both. The changes of total antioxidant capacity (TAC) and total phenolics content (TPC) of ciku king fruits with storage time were also investigated. It was found that the TAC and TPC decreased significantly as the fruits gradually changed from the unripe to the overripe stage. The best time for one to consume ciku king fruits at a flavorful stage with high amounts of antioxidants with AEAC values ranging from 600 to 1200 mg per 100 g fresh sample is suggested. The change of the content of major antioxidant peaks was also consistent with changes of antioxidant levels during storage.