Morphology and molecular phylogenetic placement of a coastal shipworm (Bactronophorus thoracites (Gould, 1862), Teredinidae) from Peninsular Malaysia

The wood-boring shipworm, Bactronophorus thoracites (Teredinidae), is the only species in the genus Bactronophorus, with wide distribution in the Indo-West Pacific biogeographic region. Besides rendering important ecosystem services such as in decaying wood and participating in C fluxes in mangroves, to several ethnic groups in Southeast Asia, this mollusk is a highly nutritious delicacy when eaten raw. There are near 20 shipworm species reported in Malaysian waters, however, in-depth studies have not been conducted on any of these species. Here, we characterized B. thoracites from a mangrove environment on the west coast of Peninsular Malaysia. This bivalve is distinguished by its non-segmented pallet, composed of a basal cup with a dagger-like extension. Molecular phylogenetic analyses using 16S gene sequences from six different species (family Teredinidae) including B. thoracites, revealed a monophyletic relationship. On the contrary, combined datasets of 18S and 28S rRNA gene sequences from 12 different species (family Teredinidae) suggested a paraphyletic relationship; B. thoracites appeared to be a sister to Neoteredo reynei. Using the DNA barcode COI, B. thoracites is clearly separated from other teredinids, albeit with moderate bootstrap support. Molecular dating analysis speculated the divergence time between B. thoracites and N. reynei was the Early Cretaceous period. We provide novel DNA sequences for B. thoracites, which could be useful for species identity validation and molecular taxonomical studies

Rapid detection of several endangered agarwood-producing Aquilaria species and their potential adulterants using plant DNA barcodes coupled with high-resolution melting (Bar-HRM) analysis

Aquilaria is an endangered agarwood-producing genus that is currently protected by international laws. The agarwood trade is strictly monitored to prevent illegal harvesting, which has caused high demand for this natural product. Other plant sources of similar appearance or fragrance as agarwood are used as adulterant species in counterfeit products. To promote species identification via the DNA barcoding technique, the existing DNA barcoding database in our laboratory was enriched with seven plant barcoding sequences from a commercially important Aquilaria species ( Aquilaria beccariana ) and seven adulterant species ( Cocos nucifera , Dalbergia latifolia , Pinus contorta var. latifolia , Santalum album , Strychnos ignatii , Thuja sp. and Terminalia catappa ). DNA barcoding with high-resolution melting analysis (Bar-HRM) showed that the mini-barcode internal transcribed spacer 1 (ITS1) was an effective gene locus that allows for a rapid and species-specific detection of Aquilaria and their adulterants, while four other mini-barcodes ( rbc L, trn L intron, ITS2 and 5.8s) functioned as a support and a crosscheck for the barcoding results. The accuracy of the Bar-HRM technique in species origin identification was further assessed with seven agarwood blind specimens. The Bar-HRM technique is a potential tool for validating agarwood-species origin and detecting products with adulterant species

Differentially expressed wound-response-related proteins from a major agarwood-producing tree, Aquilaria malaccensis Lam. identified via 2-D electrophoresis

The urban transit routing problem (UTRP) deals with public transport systems in determining a set of efficient transit routes on existing road networks to meet transit demands. The UTRP is a complex combinatorial optimization problem characterized with a large search space, multi-constraint, and multiobjective nature where the likelihood of generating infeasible route sets is high. In this paper, an improved sub-route reversal repair mechanism is proposed to deal with the infeasibility. A population-based metaheuristic, namely, Differential Evolution (DE) algorithm is then proposed to handle the multiobjective UTRP with the aim of devising an efficient transit route network that optimizes both passengers' and operators' costs. Computational experiments are performed on well-known benchmark instances to evaluate the effectiveness of the proposed repair mechanism and the DE algorithm. The computational results are reported to have better parameter values in most cases when compared to other approaches in the literature

Utilization of the internal transcribed spacer (ITS) DNA sequence to trace the geographical sources of Aquilaria malaccensis Lam. populations

Overexploitation in search of its valuable non-wood fragrance product has put pressure on the survival of the endangered Aquilaria trees in the wild. In this study, the pattern of genetic variation among wild populations was measured to aid in designing useful strategies for in situ conservation. We sequenced the internal transcribed spacer (ITS) of the nuclear region of 19 wild Aquilaria malaccensis populations from different states in Peninsular Malaysia, and compared the sequence with the same species residing outside of Malaysia, mainly from the Assam region in India and Sumatra in Indonesia. This widely distributed species is found in the Indomalesian region and is a major source of agarwood. In addition, we included five wild Aquilaria hirta populations for semblance purposes. Intraspecific variations were not found within A. malaccensis and A. hirta populations in Peninsular Malaysia. Interestingly, Single Nucleotide polymorphisms (SNPs) were identified when comparing A. malaccensis from three geographical regions, with a total of 25 SNPs detected. We imply that geographical segregation is a contributing factor toward genetic variation in A. malaccensis. This is the first report on utilizing the ITS region for analysing genetic variation in A. malaccensis of various geographical regions. The molecular information obtained in this study will serve as a useful reference in designing in situ programmes for this endangered species

Protein extraction protocol from Musa sp. shoots and roots tissue for non-reducing one dimensional SDS-PAGE analysis

Background: Protein extraction from plant tissues is a great challenge since they contain low amount of proteins and rich in proteases, secondary metabolites and oxidative enzymes. Besides, dealing with limited amount of starting material would pose another challenge in getting high protein yield. The aim of this study is to determine the best protein extraction protocol for recalcitrant tissues of banana (Musa sp.) specific for non-reducing one dimensional SDS-PAGE analysis. Methods: Three protein extraction protocols were compared which include TCA-acetone, phenol and phosphate buffer saline (PBS) using small amount of starting material. Modifications were done to each protocol to suit non-reducing SDS-PAGE analysis and subsequent downstream processes. Results: Of the three protocols compared, TCA-acetone protocol gave the highest yield and quality of protein extract from only a small amount of starting material based on protein quantification and non-reducing one dimensional SDS-PAGE analysis compared to phenol and phosphate buffer saline (PBS) protocol. Conclusion: Even though various protein extraction protocols have been developed to date, there is no one-size-fits-all when it comes to different types of plant tissues from varieties of plant species. TCA-acetone protocol was found to be most effective in extracting protein from banana shoot and root tissues even for small amount of starting material in absence of reducing agent

Comparing the effect of heat on tropomyosin isoforms patterns from water buffalo and wild boar meat by two-dimensional gel electrophoresis

Tropomyosin is one of the most abundant proteins in meat; however, very little is known about it due to the lack of scientific literature. In this study, the spot volume of tropomyosin (TPM) isoforms, TPM2 and TPM1, in meat from water buffalo and wild boar subjected to various cook treatments were compared. We hypothesized that primary structures of the tropomyosin isoforms from both species would remain stable despite the application of heat. Proteins extracted from the treated meats were analyzed using two-dimensional gel electrophoresis and mass spectrometry. A Kruskal-Wallis test showed that there were no significant differences in protein spot volumes for all treatments; however, a significant difference was observed between species. Changes in the amino acid sequence of TPM1 were observed between the two species, indicating that the isoforms could be used as thermostable proteins or peptide markers for species identification because of their resistance to high temperatures

Improved gel-enhanced liquid chromatography-mass spectrometry by chemometrics for halal proteomics

Numerous analytical methods for the authentication of halal meat are now well established, with gel-enhanced liquid chromatography-mass spectrometry (GeLCMS) being a popular approach. However, the selection of potential protein markers on 1-dimensional gel electrophoresis (1DE) prior to LCMS is considered problematic, because using the optical density for the selection process could introduce human error. In this study, an improved GeLCMS method assisted by multivariate principal component analysis (PCA) was developed to identify the potential protein markers for non-halal pork among halal beef and chicken. The improved GeLCMS technique allowed for the confident excising of identified protein bands prior to in-gel tryptic digestion. The inferential protein markers (myofibrillar proteins), which might be present in the samples, were determined based on the identified sequence of peptides. This chemometric-assisted GeLCMS could potentially be used as a guideline to assist chemists in analysis of any gel-based separation of biomolecules, regardless of the field of stud

Defatted coconut residue crude polysaccharides as potential prebiotics: study of their effects on proliferation and acidifying activity of probiotics in vitro

This paper reports on the extraction, partial characterization and the potential application of crude polysaccharides from defatted coconut residue as a prebiotic. The coconut residue was defatted and extracted to obtain the crude polysaccharides and its physicochemical properties were determined. The crude polysaccharides were assessed for monosaccharide composition, total carbohydrate content, reducing sugar concentration and protein content determination. The functional group and structural elucidation of crude polysaccharides was also done using Fourier transform infrared spectra analysis. The product was then subjected to artificial human gastric juice treatment to determine digestibility. Finally, an in vitro proliferation and acid production by two probiotic bacteria namely Lactobacillus casei Shirota and Lactobacillus bulgaricus were included in this study. It was found that the defatted coconut residue contained ash (0.54%), moisture (55.42%), protein (1.69%), crude fat (17.26%) and carbohydrate (25.73%). The percentage of crude polysaccharides extracted was 0.73 ± 0.04. The two fractions of monosaccharides obtained were glucose and fructose. Total carbohydrate content of DCR was 13.35% (w/v). The quantitative value of the reducing sugars obtained was 20.71%. Protein content in the crude polysaccharides was 0.009% and the peaks which indicated the presence of protein were observed at around 1640 cm−1 (amide I) and 1530 cm−1 (amide II). DCR crude polysaccharides were highly resistant (88%) to hydrolysis when subjected to artificial human gastric juice. The product was found to markedly stimulate two tested probiotics to proliferate and produce organic acids. All the above findings are supportive of the fact that polysaccharides extracted from DCR, an industrial waste, have a vast potential to be exploited as novel prebiotics

Protein expression patterns in HEK-blue-cells treated with Clinacanthus nutans extracts

Background: Clinacanthus nutans (CN) is a small shrub native to tropical Asia known for their anti-oxidant, anti-inflammation, anti-cancer, and anti-viral activities. Objectives: This study aimed to investigate the effect of CN extract on human embryonic kidney cell line (HEK-Blue™-4) in a proteomic perspective. Materials and Methods: Comparative proteomic profiling through two-dimensional sodium dodecyl sulfate gel electrophoresis was performed on HEK-Blue™-4 treated with CN leaf polar extract. Results: We successfully identified seven upregulated proteins, of which five promoted the growth of the HEK-Blue™-4 cells. Interestingly, a potent antioxidant enzyme which neutralizes reactive oxygen or nitrogen species, peroxiredoxin-1 was also upregulated in HEK-Blue™-4 cell lines after treatment with CN leaf polar extract. Conclusion: CN leaf polar extract promotes the growth of HEK-Blue™-4 cells and induced the expression of peroxiredoxin-1, which protects the cells from reactive oxygen species during the inflammation process

Polycyclic aromatic hydrocarbons: characteristics and its degradation by biocatalysis remediation

An excessive released of polycyclic aromatic hydrocarbons (PAHs) to surroundings is one of the major factors that cause environmental pollution to increase globally. This issue had gained scientist’s attention to study PAHs biodegradation pathways and their toxicity towards humans and the environment. They found that the major mechanism responsible for the ecological recovery of PAH-contaminated sites happened to be from the microbial degradation process. However, there are a few limitations faced by the PAHs degrading bacteria where the bacteria die due to extremely polluted areas. This leads the researchers to utilize genetic engineering to produce enzymes that can withstand and survive in extreme environments. Recent information and technology such as path sources, properties and biochemical pathways by means to produce the simplest and less harmful components in polluted ecosystems are discussed in this review. In-depth studies in regards to bacteria biocatalysis involving bacterialproduced-enzymes to degrade PAHs help develop new methods to enhance the bioremediation effectiveness in the future