Production and characterization of cellulase from <Emphasis Type="Italic">E. coli</Emphasis> EgRK2 recombinant based oil palm empty fruit bunch

Oil Palm Empty Fruit Bunch (OPEFB) is an abundant biomass resource in Indonesia, which contains 41.3 ~ 46.5% (w/w) of cellulose. This research examined the production of cellulase by the E. coli EgRK2 recombinant strain using an OPEFB substrate. The production of the enzyme was initially examined to identify optimum growth conditions, by observing the growth and activity of E. coli EgRK2 compared to its wild type. Our results showed that the optimum production time, pH and temperature of the recombinant growth and cellulase activity were achieved at 24 h, and at 7 and 40°C, respectively. Using these optimum conditions, the enzyme was produced, and experiments were carried out to examine the enzyme characteristics, produced from both strains, on hydrolysis of cellulose from OPEFB. Our results showed that the activity of the enzyme produced by the recombinant almost doubled compared to that of the wild type, although the optimum pH for both strains was pH 6. Higher activity was achieved by the recombinant compared to the wild type strain, and values were 1.905 and 1.366 U/mL, respectively. The optimum temperature for hydrolysis by cellulase occurred at 50°C for Bacillus sp. RK2, and 60°C for Bacillus sp. EgRK2. The Michaelis-Menten constant (Km) and maximum velocity (Vmax) for OPEFB degradation by E. coli EgRK2 were 0.26% and 1.750 μmol/mL/sec, which were significantly better values than those of the wild type. Control experiments for the degradation test using CMC also showed a better Vmax value for E. coli EgRK2 compared to the wild type, which is 2.543 and 1.605 μmol/mL/sec, respectively.     

Switching from monoculture to polyculture farming benefits birds in oil palm production landscapes: Evidence from mist netting data

Monoculture farming is pervasive in industrial oil palm agriculture, including those RSPO plantations certified as sustainably managed. This farming practice does not promote the maintenance of farmland biodiversity. However, little scientific attention has been given to polyculture farming in oil palm production landscapes. Polyculture farming is likely to increase the floristic diversity and stand structural complexity that underpins biodiversity. Mist nets were used to sample birds at 120 smallholdings in Peninsular Malaysia. At each site, 12 vegetation structure characteristics were measured. We compared bird species richness, abundance, and composition between monoculture and polyculture smallholdings and used predictive models to examine the effects of habitat quality on avian biodiversity. Bird species richness was significantly greater in polyculture than that of monoculture smallholdings. The number of fallen and standing, dead oil palms were also important positive predictors of species richness. Bird abundance was also strongly increased by standing and dead oil palms and decreased with oil palm stand height. Our results indicate that polyculture farming can improve bird species richness in oil palm production landscapes. In addition, key habitat variables that are closely associated with farming practices, such as the removal of dead trees, should and can be managed by oil palm growers in order to promote biodiversity. To increase the sustainability of oil palm agriculture, it is imperative that stakeholders modify the way oil palms are currently planted and managed. Our findings can guide policy makers and certification bodies to promote oil palm production landscapes that will function more sustainably and increase existing biodiversity of oil palm landscapes.     

Geraniin extracted from the rind of <Emphasis Type="Italic">Nephelium lappaceum</Emphasis> binds to dengue virus type-2 envelope protein and inhibits early stage of virus replication

Background

The rapid rise and spread in dengue cases, together with the unavailability of safe vaccines and effective antiviral drugs, warrant the need to discover and develop novel anti-dengue treatments. In this study the antiviral activity of geraniin, extracted from the rind of Nephelium lappaceum, against dengue virus type-2 (DENV-2) was investigated.

Methods

Geraniin was prepared from Nephelium lappaceum rind by reverse phase C-18 column chromatography. Cytotoxicity of geraniin towards Vero cells was evaluated using MTT assay while IC₅₀ value was determined by plaque reduction assay. The mode-of-action of geraniin was characterized using the virucidal, attachment, penetration and the time-of-addition assays’. Docking experiments with geraniin molecule and the DENV envelope (E) protein was also performed. Finally, recombinant E Domain III (rE-DIII) protein was produced to physiologically test the binding of geraniin to DENV-2 E-DIII protein, through ELISA competitive binding assay.

Results

Cytotoxicity assay confirmed that geraniin was not toxic to Vero cells, even at the highest concentration tested. The compound exhibited DENV-2 plaque formation inhibition, with an IC₅₀ of 1.75 μM. We further revealed that geraniin reduced viral infectivity and inhibited DENV-2 from attaching to the cells but had little effect on its penetration. Geraniin was observed to be most effective when added at the early stage of DENV-2 infection. Docking experiments showed that geraniin binds to DENV E protein, specifically at the DIII region, while the ELISA competitive binding assay confirmed geraniin’s interaction with rE-DIII with high affinity.

Conclusions

Geraniin from the rind of Nephelium lappaceum has antiviral activity against DENV-2. It is postulated that the compound inhibits viral attachment by binding to the E-DIII protein and interferes with the initial cell-virus interaction. Our results demonstrate that geraniin has the potential to be developed into an effective antiviral treatment, particularly for early phase dengue viral infection.

     

Severity-Based Adaptation with Limited Data for ASR to Aid Dysarthric Speakers

Automatic speech recognition (ASR) is currently used in many assistive technologies, such as helping individuals with speech impairment in their communication ability. One challenge in ASR for speech-impaired individuals is the difficulty in obtaining a good speech database of impaired speakers for building an effective speech acoustic model. Because there are very few existing databases of impaired speech, which are also limited in size, the obvious solution to build a speech acoustic model of impaired speech is by employing adaptation techniques. However, issues that have not been addressed in existing studies in the area of adaptation for speech impairment are as follows: (1) identifying the most effective adaptation technique for impaired speech; and (2) the use of suitable source models to build an effective impaired-speech acoustic model. This research investigates the above-mentioned two issues on dysarthria, a type of speech impairment affecting millions of people. We applied both unimpaired and impaired speech as the source model with well-known adaptation techniques like the maximum likelihood linear regression (MLLR) and the constrained-MLLR(C-MLLR). The recognition accuracy of each impaired speech acoustic model is measured in terms of word error rate (WER), with further assessments, including phoneme insertion, substitution and deletion rates. Unimpaired speech when combined with limited high-quality speech-impaired data improves performance of ASR systems in recognising severely impaired dysarthric speech. The C-MLLR adaptation technique was also found to be better than MLLR in recognising mildly and moderately impaired speech based on the statistical analysis of the WER. It was found that phoneme substitution was the biggest contributing factor in WER in dysarthric speech for all levels of severity. The results show that the speech acoustic models derived from suitable adaptation techniques improve the performance of ASR systems in recognising impaired speech with limited adaptation data.     

The relationship between job satisfaction and job factors in industrial work design: a case study of the automotive industries in Malaysia

A survey was conducted to investigate the relationship between job satisfaction and job factors that affect work design in two automotives manufacturing companies in Malaysia. A set of multiple choices questionnaires was developed and data were collected by interviewing the employees at the production plant. Hundred and seventy male subjects between the ages of 18 to 40 years with the mean age of 26.8 and SD of 5.3 years and mean work experience of 6.5 and SD of 4.9 years took part in the survey. The survey focused on job factors, i.e. skill variety, task identity, task significance, autonomy and feedback. The results support the previous findings that job factors are significantly correlated to job satisfaction. Furthermore, it also highlights the significant influence of age, work experience and marital status.     

Molecular docking studies of bioactive compounds from <Emphasis Type="Italic">Annona muricata</Emphasis> Linn as potential inhibitors for Bcl-2, Bcl-w and Mcl-1 antiapoptotic proteins

Annona muricata Linn or usually identified as soursop is a potential anticancer plant that has been widely reported to contain valuable chemopreventive agents known as annonaceous acetogenins. The antiproliferative and anticancer activities of this tropical and subtropical plant have been demonstrated in cell culture and animal studies. A. muricata L. exerts inhibition against numerous types of cancer cells, involving multiple mechanism of actions such as apoptosis, a programmed cell death that are mainly regulated by Bcl-2 family of proteins. Nonetheless, the binding mode and the molecular interactions of the plant’s bioactive constituents have not yet been unveiled for most of these mechanisms. In the current study, we aim to elucidate the binding interaction of ten bioactive phytochemicals of A. muricata L. to three Bcl-2 family of antiapoptotic proteins viz. Bcl-2, Bcl-w and Mcl-1 using an in silico molecular docking analysis software, Autodock 4.2. The stability of the complex with highest affinity was evaluated using MD simulation. We compared the docking analysis of these substances with pre-clinical Bcl-2 inhibitor namely obatoclax. The study identified the potential chemopreventive agent among the bioactive compounds. We also characterized the important interacting residues of protein targets which involve in the binding interaction. Results displayed that anonaine, a benzylisoquinoline alkaloid, showed a high affinity towards the Bcl-2, thus indicating that this compound is a potent inhibitor of the Bcl-2 antiapoptotic family of proteins.     

A Contribution to the Life History of the Rare Indonesian Holoparasite Rafflesia patma (Rafflesiaceae)1

Fates and growth of Rafflesia patma buds and insect visitation to the flowers were monitored in an evergreen tropical rain forest in the Pangandaran Nature Reserve, Java, Indonesia, Of 59 buds marked in December 1985, 44 percent died before flowering, 7 percent flowered, and 49 percent were still in bud in May 1986. Mammals and birds caused the deaths of buds before they reached maturity. Only four buds flowered between December 1985 and May 1986; all were male. Rate of increase in diameter (cm/d) was much faster in large than in small buds. Once opening began, the flower opened fully in 24 to 48 hours; the flower remained open for three to five days before rotting. Only two genera of insects visited a male flower of R. patma: Lucilia and Sarcophaga (Diptera). Insect visitation was highest in the afternoon (1300–1700 h) and on the second or third day after flower opening. The increased number of flies visiting the flower coincided with the increasing odor emitted from it. Results of the present study were combined with information from the literature to construct a life cycle diagram of R. patma.     

Genotyping of microsatellite markers to study genetic structure of the wild striped snakehead Channa striata in Malaysia

Genetic variability and differences in wild striped snakehead Channa striata from Malaysia were analysed by genotyping nine novel nuclear microsatellite loci. Analysis revealed moderate‐to‐high genetic diversity in most of the populations, indicative of large effective population sizes. The highly diversified populations are admixed populations and, therefore, can be recommended as potential candidates for selective breeding and conservation since they each contain most of the alleles found in their particular region. Three homogenous groups of the wild populations were identified, apparently separated by effective barriers, in accordance with contemporary drainage patterns. The highest population pairwise F_ST found between members of the same group reflects the ancient population connectivity; yet prolonged geographical isolation resulted in adaptation of alleles to local contemporary environmental change. A significant relationship between genetic distance and geographical isolation was observed (r = 0·644, P < 0·01). Anthropogenic perturbations indicated apparent genetic proximity between distant populations.     

Selective determination of dopamine with an amperometric biosensor using electrochemically pretreated and activated carbon/tyrosinase/Nafion®-modified glassy carbon electrode

Dopamine, the most important neurotransmitter in the human brain, controls various functions. Dopamine deficiency causes fatal neurological disorders such as Parkinson’s disease. Even though various types of electrochemical sensors have been studied to measure dopamine levels, they often have poor selectivity for dopamine due to co-existence of interfering substances (e.g. ascorbic acid). Herein, we aimed to develop a highly sensitive dopamine detection method in the co-existence of ascorbic acid, a major interfering substance in real sample by designing an electrochemically pretreated and activated carbon/tyrosinase/Nafion®-modified GCE as an amperometric dopamine biosensor. To maximize the biosensor performance, pH, volume of Nafion®, and scan rate were optimized. This electrochemically pretreated and activated carbon/tyrosinase/ Nafion®-modified GCE could detect as low as 50 μM of dopamine with a wide linear range (50 ~ 1,000 μM) within a few seconds. In addition, it had a sensitivity of 103mAM/cm², which was higher than all previously reported tyrosinasebased dopamine biosensors. In addition, interference effect caused by 4 mM of ascorbic acid was negligible in the co-existence of 1 mM of dopamine. Consequently, this electrochemically pretreated and activated carbon/tyrosinase/ Nafion®-modified GCE might be applicable as amperometric biosensor for selective detection of dopamine in real samples with interfering substances.     

Nutrient Amendments of Inorganic Fertiliser and Oil Palm Empty Fruit Bunch and Their Influence on Bacterial Species Dominance and Degradation of the Associated Crude Oil Constituents

The effects of inorganic commercial fertiliser (N:P:K = 8:8:1) and oil palm empty fruit bunch (EFB) as nutrient amendments for crude oil degradation and microbial population shift by a microbial consortium [Pseudomonas sp. (UKMP-14T), Acinetobacter sp. (UKMP-12T), Trichoderma sp. (TriUKMP-1M and TriUKMP-2M)] were assessed. The bacterial populations present during crude oil degradation were analysed by spread plate method and 16S rRNA sequences, whereas the presence of fungi was assessed by growth on potato dextrose agar. Crude oil degradation analysed using gas chromatography-flame ionisation detection showed total petroleum hydrocarbon reduced between 70 and 100%, depending on the type of amendments compared to control (≈55%) after 30 days of incubation. Nutrient amendments using NPK fertiliser or EFB were found to influence the domination of different bacterial species, which in turn preferentially utilised different hydrocarbons. This study suggested different nutrient amendments could be used to preferentially select bacteria to degrade different components of crude oil, particularly pertaining to the recalcitrant phytane. This information is very useful for application of in situ bioremediation of soil hydrocarbon contamination.