A novel α-amylase was isolated successfully from Glaciozyma antarctica PI12 using DNA walking and reverse transcription-polymerase chain reaction (RT-PCR) methods. The structure of this psychrophilic α-amylase (AmyPI12) from G. antarctica PI12 has yet to be studied in detail. A 3D model of AmyPI12 was built using a homology modelling approach to search for a suitable template and to generate an optimum target-template alignment, followed by model building using MODELLER9.9. Analysis of the AmyPI12 model revealed the presence of binding sites for a conserved calcium ion (CaI), non-conserved calcium ions (CaII and CaIII) and a sodium ion (Na). Compared with its template-the thermostable α-amylase from Bacillus stearothermophilus (BSTA)-the binding of CaII, CaIII and Na ions in AmyPI12 was observed to be looser, which suggests that the low stability of AmyPI12 allows the protein to work at different temperature scales. The AmyPI12 amino acid sequence and model were compared with thermophilic α-amylases from Bacillus species that provided the highest structural similarities with AmyPI12. These comparative studies will enable identification of possible determinants of cold adaptation.
Goniothalamus macrophyllus (Blume) Hook. f. & Thoms. is a plant widely distributed in Malaysia. The aim of this study is to identify compounds from the roots of G. macrophyllus. The ground roots were extracted with aqueous methanol and partitioned sequentially with n-hexane, chloroform and butanol. Purification from this extracts afforded six compounds with two new compounds, namely goniolandrene-A (1), -B (2). The absolute configuration of goniolandrene B (2) was established by circular dichrosim. The compounds were cytotoxic against the P388 cells with IC50 values ranging from 0.42 to 160 μM. Goniothalamin (3) exhibited the highest inhibition of 0.42 μM.
The fermentation selectivity of a commercial source of a-gluco-oligosaccharides (BioEcolians; Solabia) was investigated in vitro. Fermentation by faecal bacteria from four lean and four obese healthy adults was determined in anaerobic, pH-controlled faecal batch cultures. Inulin was used as a positive prebiotic control. Samples were obtained at 0, 10, 24 and 36 h for bacterial enumeration by fluorescent in situ hybridisation and SCFA analyses. Gas production during fermentation was investigated in non-pH-controlled batch cultures. a-Gluco-oligosaccharides significantly increased the Bifidobacterium sp. population compared with the control. Other bacterial groups enumerated were unaffected with the exception of an increase in the Bacteroides–Prevotella group and a decrease in Faecalibacterium prausnitzii on both a-gluco-oligosaccharides and inulin compared with baseline. An increase in acetate and propionate was seen on both substrates. The fermentation of a-gluco-oligosaccharides produced less total gas at a more gradual rate of production than inulin. Generally, substrates fermented with the obese microbiota produced similar results to the lean fermentation regarding bacteriology and metabolic activity. No significant difference at baseline (0 h) was detected between the lean and obese individuals in any of the faecal bacterial groups studied.
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.
Influences of river hydrodynamic behaviours on hydrochemistry (salinity, pH, dissolved oxygen saturations and dissolved phosphorus) were evaluated through high spatial and temporal resolution study of a sandbar-regulated coastal river. River hydrodynamic during sandbar-closed event was characterized by minor dependency on tidal fluctuations, very gradual increase of water level and continual low flow velocity. These hydrodynamic behaviours established a hydrochemistry equilibrium, in which water properties generally were characterized by virtual absence of horizontal gradients while vertical stratifications were significant. In addition, the river was in high trophic status as algae blooms were visible. Conversely, river hydrodynamic in sandbar-opened event was tidal-controlled and showed higher flow velocity. Horizontal gradients of water properties became significant while vertically more homogenised and with lower trophic status. In essence, this study reveals that estuarine sandbar directly regulates river hydrodynamic behaviours which in turn influences river hydrochemistry.
Visible and near infrared spectroscopy is a non-destructive, green, and rapid technology that can be utilized to estimate the components of interest without conditioning it, as compared with classical analytical methods. The objective of this paper is to compare the performance of artificial neural network (ANN) (a nonlinear model) and principal component regression (PCR) (a linear model) based on visible and shortwave near infrared (VIS-SWNIR) (400-1000 nm) spectra in the non-destructive soluble solids content measurement of an apple. First, we used multiplicative scattering correction to pre-process the spectral data. Second, PCR was applied to estimate the optimal number of input variables. Third, the input variables with an optimal amount were used as the inputs of both multiple linear regression and ANN models. The initial weights and the number of hidden neurons were adjusted to optimize the performance of ANN. Findings suggest that the predictive performance of ANN with two hidden neurons outperforms that of PCR.
Burgers were prepared using duck surimi-like material (DSLM) with polydextrose added (SL) and DSLM with sucrose-sorbitol added (SS), and the properties of these burgers were compared with those of burgers made of chicken meat (CB) and duck meat (DB). Quality characteristics such as chemical composition, cooking loss, diameter shrinkage, color, and texture were measured. The DB had a lower moisture content (55.58%) and higher fat content (21.44%) and cooking loss (11.01%) compared with other samples, whereas CB, SS, and SL did not differ significantly in moisture (65.21-66.10%) and fat (10.42-11.16%) content or cooking loss (5.32-6.15%). The SS and SL were positioned below CB and above DB in terms of hardness, chewiness, and springiness. Ten trained panelists assessed the burgers using quantitative descriptive analysis. Among the burgers, CB had the greatest brightness of color, hardness, springiness, and chewiness. The SS had greater sweetness than the other burgers. Both SL and SS had significantly less animalic odor, meaty flavor, oiliness, juiciness, and saltiness compared with DB. The physicochemical and sensory characteristics of burgers prepared from DSLM approached those of burgers made of chicken.
Orthosiphon stamineus Benth. (Lambiaceae) is an important plant in traditional folk medicine. This review is a comprehensive summary of the currently available chemical, pharmacological, and toxicological investigations as well as the traditional and therapeutic uses of this plant. Different in vitro and in vivo models have been addressed along with a survey of all phytochemicals identified in this plant, including flavonoids, terpenoids, and essential oils. Previous studies revealed that O. stamineus possesses several pharmacological activities, which are attributed to its phytochemical content. It was found that O. stamineus exhibits diuretic, hypouricemic, renal protective, antioxidant, anti-inflammatory, hepatoprotective, gastroprotective, antihypertensive, antidiabetic, antihyperlipidemic, antimicrobial, and anorexic activities. In conclusion, O. stamineus has wide traditional and pharmacological uses in various pathophysiological conditions. Therefore, it is an attractive subject for further experimental and clinical investigations.
Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/.
The characteristic flavor of exotic tropical fruits is one of their most attractive attributes to consumers. In this article, the enormous diversity of exotic fruit flavors is reviewed. Classifying some of the exotic fruits into two classes on the basis of whether esters or terpenes predominate in the aroma was also attempted. Indeed, as far as exotic tropical fruits are concerned, the majority of fruits have terpenes predominating in their aroma profile. Some of the fruits in this group are the Amazonian fruits such as pitanga, umbu-caja, camu-camu, garcinia, and bacuri. The ester group is made up of rambutan, durians, star fruit, snake fruit, acerola, tamarind, sapodilla, genipap, soursop, cashew, melon, jackfruit, and cupuacu respectively. Also, the role of sulphur-volatiles in some of the exotic fruits is detailed.
The quality of a nucleotide-based library such as a synthetic antibody library is highly dependent on the diversity available. Diversity can be generated using degenerate oligonucleotides introduced during gene assembly. Conventional approaches to gene assembly are not efficient for oligonucleotides with long stretches of degeneracy. We propose an efficient alternative for simultaneous introduction of three randomized regions in a synthetic antibody gene via temperature cascading. The strategy takes advantage of DNA reannealing kinetics. The strategy can be adopted for generating diversity of gene inserts during the construction of nucleotide-based libraries.
Orthosiphon stamineus is considered an important traditional folk medicine. In this study ethanol and aqueous extracts of O. stamineus were evaluated in vitro for their antioxidant, antimicrobial as well as for their immunomodulatory properties on human peripheral blood mononuclear cells (PBMCs). The DPPH radical scavenging method was used for the determination of antioxidant activity, while the antibacterial efficacy was investigated by both disc diffusion method and Minimum Inhibitory Concentration (MIC) against four bacterial strains (Gram-positive and Gram-negative). Furthermore, the immunomodulatory potential of the extracts was investigated through the MTT assay. Aqueous extract of O. stamineus exhibited significant free radical scavenging activity with IC₅₀ 50 9.6 µg/mL, whereas the IC₅₀ for the ethanol extract was 21.4 µg/mL. The best antimicrobial activity was shown by the aqueous extract of O. stamineus against Staphylococcus aureus, with inhibition zone of 10.5 mm and MIC value 1.56 mg/mL. Moreover, the results observed from the MTT assay showed that both plant extracts stimulated the PBMCs proliferation in vitro in a concentration-dependent manner, but the aqueous extract has remarkable activity against PBMCs. These findings indicate that O. stamineus showed high antioxidant activity and may be considered as an immunomodulatory agent.
Transplantation of cultivated limbal epithelium on substrates such as amniotic membrane is an established treatment for severe ocular surface disease with limbal stem cell deficiency. In this study, we adapted an established method to generate sheets of limbal epithelium on amniotic membrane and characterized the cells contained in these sheets and tested them for safety with regard to microbial contamination. Human limbal biopsies were cultivated on denuded amniotic membranes. After three weeks of culture, the phenotypes of cultivated cells were analyzed by immunohistochemistry and real-time RT-PCR for the expression of a panel of specific markers. Cultivated limbal epithelial cell sheets were also analyzed by scanning (SEM) and transmission (TEM) electron microscopy. Sterility tests and mycoplasma assays were conducted for the safety of product. A confluent layer of polygonal cells was formed in 2 weeks and 1-3 stratified layer of cells were observed after three weeks of culture. Cultivated cells were positive for p63, K3, K19, and involucrin but negative for K14, integrin alpha9 and ABCG2 when analyzed by immunohistochemistry. Expression of molecular markers was detectable with real-time RT-PCR. SEM showed multilayer of flat squamous polygonal epithelial cells. Desmosomal and hemidesmosomal attachments were evident. Our study showed that cultivated limbal epithelium consists of limbal progenitors as well as differentiated corneal epithelial cells. SEM and TEM analysis showed cultivated cells demonstrated typical features of corneal epithelium. The risk of contamination is low and can be prevented by culturing the cells in a clean room facility complying to Good Manufacturing Practice standard.
We evaluated 38 dura x pisifera (DP) oil palm progenies in four locations in Malaysia for genotype by environment interaction and genotypic stability studies. The DP progenies derived from crosses between pisifera palms of AVROS, Serdang S27B, Serdang 29/36, and Lever Cameroon were chosen to be the males' parent and Deli dura palms designated as females' parent. All the locations differed in terms of soil physical and chemical properties, and the soil types ranged from coastal clay to inland soils. The genotype by environment interaction and stability of the individual genotypes were analyzed for oil yield trait using several stability techniques. A genotype by environment interaction was detected for oil yield and it had a larger variance component than genotypic variance (σ(2)(gl)/σ(2)(g) = 139.7%). Genotype by environment interaction of oil yield was largely explained by a non-linear relationship between genotypic and environmental values. Overall assessment of individual genotypic stability showed that seven genotypes were highly stable and had consistent performance over the environments for the oil yield trait [total individual genotype stability scored more than 10 and mean oil yielded above the average of the environment (genotype means are more than 34.37 kg·palm(-1)·year(-1))]. These genotypes will be useful for oil palm breeding and tissue culture programs for developing high oil yielding planting materials with stable performance.
In this study, the effect of the addition of different cryoprotectants on the freeze-thaw stability of duck surimi-like material (DSLM) was tested. A 6% (wt/wt) low-sweetness cryoprotectant (i.e., polydextrose, trehalose, lactitol, or palatinit) was added to a 3-kg portion of DSLM, and the mixture was subjected to freeze-thaw cycles during 4 mo of frozen storage. The DSLM with no cryoprotectant added (control) and with a 6% sucrose-sorbitol blend (high-sweetness cryoprotectant) added also were tested. The polydextrose-added sample had the highest water-holding capacity among the sample types tested (P < 0.05), and it retained its higher value during frozen storage. The protein solubility of the cryoprotectant-added samples decreased significantly (P < 0.05) from 58.99 to 59.60% at initial frozen storage (0 mo) to 48.60 to 54.61% at the end of the experiment (4 mo). The gel breaking force of all samples significantly decreased (P < 0.05) at 1 mo; this breaking force then stabilized after further frozen storage for the cryoprotectant-added samples, whereas it continued to decrease in the control samples. Gel deformation fluctuated during frozen storage and was significantly lower (P < 0.05) at the end of experiment than at the beginning. The presence of cryoprotectants reduced the whiteness of DSLM. Samples containing polydextrose, trehalose, lactitol, and palatinit were able to retain the protein solubility, gel breaking force, and deformation of DSLM better than control samples after 4 mo of frozen storage and exposure to freeze-thaw cycles. The effects of these low-sweetness cryoprotectants are comparable to those of sucrose-sorbitol, thus, these sugars could be used as alternatives in protecting surimi-like materials during frozen storage.
Spaceflight represents a complex environmental condition. Space mutagenesis breeding has achieved marked results over the years. The objective of this study is to determine the chemical changes in medicinal mushroom Ganoderma lucidum cultivated after spaceflight in 1999. Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) correlation spectroscopy were used in analysis. The sample Sx and its control Cx showed the least dissimilarities in one-dimensional FTIR spectra, but absorbance of Sx is twice as high as Cx. Sx presented a clear peak at 1648 cm in 2nd derivative spectra, which could not be detected in the Cx. The 2DIR spectra showed the intensity of Sx in the range 1800-1400 cm-1 for protein is higher than the control. The sample Sx produced some carbohydrate peaks in the area of 889 cm-1 compared with the Cx. The spaceflight set up an extreme condition and caused changes of chemical properties in G. lucidum strain.
The intercalation of a drug active, perindopril, into Mg/Al-layered double hydroxide for the formation of a new nanocomposite, PMAE, was accomplished using a simple ion exchange technique. A relatively high loading percentage of perindopril of about 36.5% (w/w) indicates that intercalation of the active took place in the Mg/Al inorganic interlayer. Intercalation was further supported by Fourier transform infrared spectroscopy, and thermal analysis shows markedly enhanced thermal stability of the active. The release of perindopril from the nanocomposite occurred in a controlled manner governed by pseudo-second order kinetics. MTT assay showed no cytotoxicity effects from either Mg/Al-layered double hydroxide or its nanocomposite, PMAE. Mg/Al-layered double hydroxide showed angiotensin-converting enzyme inhibitory activity, with 5.6% inhibition after 90 minutes of incubation. On incubation of angiotensin-converting enzyme with 0.5 μg/mL of the PMAE nanocomposite, inhibition of the enzyme increased from 56.6% to 70.6% at 30 and 90 minutes, respectively. These results are comparable with data reported in the literature for Zn/Al-perindopril.
This paper determines the controlling factors that influence the metals' behavior water-sediment interaction facies and distribution of elemental content ((75)As, (111)Cd, (59)Co, (52)Cr, (60)Ni, and (208)Pb) in water and sediment samples in order to assess the metal pollution status in the Langat River. A total of 90 water and sediment samples were collected simultaneously in triplicate at 30 sampling stations. Selected metals were analyzed using ICP-MS, and the metals' concentration varied among stations. Metal concentrations of water ranged between 0.08-24.71 μg/L for As, <0.01-0.53 μg/L for Cd, 0.06-6.22 μg/L for Co, 0.32-4.67 μg/L for Cr, 0.80-24.72 μg/L for Ni, and <0.005-6.99 μg/L for Pb. Meanwhile, for sediment, it ranged between 4.47-30.04 mg/kg for As, 0.02-0.18 mg/kg for Cd, 0.87-4.66 mg/kg for Co, 4.31-29.04 mg/kg for Cr, 2.33-8.25 mg/kg for Ni and 5.57-55.71 mg/kg for Pb. The average concentration of studied metals in the water was lower than the Malaysian National Standard for Drinking Water Quality proposed by the Ministry of Health. The average concentration for As in sediment was exceeding ISQG standards as proposed by the Canadian Sediment Quality Guidelines. Statistical analyses revealed that certain metals (As, Co, Ni, and Pb) were generally influenced by pH and conductivity. These results are important when making crucial decisions in determining potential hazardous levels of these metals toward humans.
Purification of RNA fragments from a complex mixture is a very common technique, and requires consideration of the time, cost, purity and yield of the purified RNA fragments. This study describes the fastest method of purifying small RNA with the lowest cost possible, without compromizing the yield and purity. The technique describes the purification of small RNA from polyacrylamide gel, resulting in a good yield of small RNA with minimum experimental steps in avoiding degradation of the RNA, obviating the use of ethidium bromide and phenol-chloroform extraction, as well as siliconized glass wools to remove the polyacrylamide gel particles. The purified small RNA is suitable for a wide variety of applications such as ligation, end labelling with radio isotope, RT-PCR (Reverse Transcriptase-PCR), Northern blotting, experimental RNomics study and also Systematic Evolution of Ligands by Exponential Enrichment (SELEX).
Calamansi juices from three countries (Malaysia, the Philippines and Vietnam) were characterised through measuring volatiles, physicochemical properties and non-volatiles (sugars, organic acids and phenolic acids). The volatile components of manually squeezed calamansi juices were extracted using dichloromethane and headspace solid-phase microextraction, and then analysed using gas chromatography-mass spectrometry/flame ionisation detector, respectively. A total of 60 volatile compounds were identified. The results indicated that the Vietnam calamansi juice contained the highest amount of volatiles. Two principal components obtained from principal component analysis (PCA) represented 89.65% of the cumulative total variations of the volatiles. Among the non-volatile components, these three calamansi juices could be, to some extent, differentiated according to fructose and glucose concentrations. Hence, this study of calamansi juices could lead to a better understanding of calamansi fruits.