Dickeya sp. strain 2B12 was isolated from a freshwater lake in Malaysia. Here, we report the draft genome sequence of Dickeya sp. 2B12 sequenced by the Illumina MiSeq platform. With the genome sequence available, this genome sequence will be useful for the study of quorum-sensing activity in this isolate.
Members of the Mycobacterium terrae complex are slow-growing, non-chromogenic acid-fast bacilli found in the natural environment and occasionally in clinical material. These genetically closely-related members are difficult to differentiate by conventional phenotypic and molecular tests. In this paper we describe the use of whole genome data for the identification of four strains genetically similar to Mycobacterium sp. JDM601, a newly identified member of the M. terrae complex. Phylogenetic information from the alignment of genome-wide orthologous genes and single nucleotide polymorphisms show consistent clustering of the four strains together with M. sp. JDM601 into a distinct clade separate from other rapid and slow growing mycobacterial species. More detailed inter-strain comparisons using average nucleotide identity, tetra-nucleotide frequencies and analysis of synteny indicate that our strains are closely related to but not of the same species as M. sp. JDM601. Besides the 16S rRNA signature described previously for the M. terrae complex, five more hypothetical proteins were found that are potentially useful for the rapid identification of mycobacterial species belonging to the M. terrae complex. This paper illustrates the versatile utilization of whole genome data for the delineation of new bacterial species and introduces four new genomospecies to add to current members in the M. terrae complex.
Poor biopharmaceutical properties and toxicities associated with the intravenous formulation of docetaxel (DTX) necessitate the exploration of an alternate oral route of delivery.
This analytical cross-sectional study examined the nutrient intakes, dietary compliance, dietary supplementation and traditional remedy usage in type 2 diabetes mellitus (T2DM) patients from selected tertiary hospitals in multi-racial Malaysia. We compared the different characteristics of T2DM patients with and without cardiovascular disease (CVD). Socio-demographic status, dietary intakes, dietary supplementation, traditional remedy use, medical history, anthropometric measurements and clinical characteristics were obtained from face-to-face interviews. A total of 313 patients who were treated for T2DM participated in this study, in which 36.1% of them had CVD. The mean age of study subjects was 55.7 ± 9.2 years; mean diabetes duration was 10.1 ± 8.1 years; 52.1% were females; and 47.0% were Malays. The mean total energy intake of the subjects was 1674 ± 694 kcal/day, and patients with CVD consumed higher total calories (p = 0.001). Likewise, the mean carbohydrate, protein and total fat intake of CVD patients were significantly higher than non-CVD patients (p < 0.05), while mean intakes of cholesterol, fibre, minerals and all vitamins were comparable between CVD and non-CVD patients. Regardless of CVD status, a notably high proportion of the subjects did not meet the recommendations of the Medical Nutrition Therapy Guidelines for Type 2 Diabetes for total energy, carbohydrate, protein, total fat, and fibre intakes. Meanwhile, 52.4% used at least one dietary supplement and 12.1% took single traditional remedy or in various combinations. Traditional remedies and supplement intake did not differ between CVD and non-CVD subjects. It is suggested that T2DM patients should be educated based on their personalized dietary intake, dietary supplementation and traditional remedy usage. The recommendations for T2DM patients shall be met to achieve the optimal metabolic goals and minimize the potential diabetic complications.
This paper reports an unusual case of a transsphenoidal encephalocele and discusses our experience with a minimally invasive management. To the best of our knowledge, we present the first case of a combined endoscopic transnasal and transoral approach to a transsphenoidal encephalocele in an infant.
An Agrobacterium-mediated transformation method was applied to introduce the luciferase reporter gene under the control of the CaMV35S promoter in the pGreen0049 binary vector into strawberry cv. Camarosa. The in vitro regeneration system of strawberry leaves to be used in the transformation was optimized using different TDZ concentrations in MS medium. TDZ at 16 µM showed the highest percentage (100%) of shoot formation and the highest mean number of shoots (24) produced per explant. Studies on the effects of different antibiotics, namely timentin, cefotaxime, carbenicillin and ampicillin, on shoot regeneration of strawberry leaf explants showed the best shoot regeneration in the presence of 300 mg/L timentin and 150 mg/L cefotaxime. Assessment of the different factors affecting Agrobacterium mediated-transformation of strawberry with the luciferase gene showed the highest efficiency of putative transformant production (86%) in the treatment with no preculture, bacterial OD600 of 0.6 and the addition of 150 mg/L cefotaxime in the pre-selection and selection media. The presence of the luciferase gene in the plant genome was verified by the luciferase reporter gene assay, nested PCR amplification and dot blot of genomic DNA isolated from the young leaves of each putatively transformed plantlet.
Nanodispersion systems allow incorporation of lipophilic bioactives, such as astaxanthin (a fat soluble carotenoid) into aqueous systems, which can improve their solubility, bioavailability, and stability, and widen their uses in water-based pharmaceutical and food products. In this study, response surface methodology was used to investigate the influences of homogenization time (0.5-20 minutes) and speed (1,000-9,000 rpm) in the formation of astaxanthin nanodispersions via the solvent-diffusion process. The product was characterized for particle size and astaxanthin concentration using laser diffraction particle size analysis and high performance liquid chromatography, respectively. Relatively high determination coefficients (ranging from 0.896 to 0.969) were obtained for all suggested polynomial regression models. The overall optimal homogenization conditions were determined by multiple response optimization analysis to be 6,000 rpm for 7 minutes. In vitro cellular uptake of astaxanthin from the suggested individual and multiple optimized astaxanthin nanodispersions was also evaluated. The cellular uptake of astaxanthin was found to be considerably increased (by more than five times) as it became incorporated into optimum nanodispersion systems. The lack of a significant difference between predicted and experimental values confirms the suitability of the regression equations connecting the response variables studied to the independent parameters.
The mitogenome of Paranephrops planifrons, was obtained by next generation sequencing. This crayfish has a mitochondrial genome of 16,174 base pairs with 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs (tRNA), and a non-coding AT-rich region of 771 bp. The P. planifrons nucleotide composition is: 33.63% for T, 21.92% for C, 34.46% for A, and 9.98% for G and has a 68.09% AT bias. While the mitogenome gene order for this species is consistent with aspects of the highly distinctive parastacid crayfish mitogenome gene arrangement, it has a novel gene order involving the rearrangements of a protein coding and several tRNA genes.
The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the second for a ray from Australian waters, the first for the genus Taeniura and the ninth for the family Dasyatidae.
The present study was based on the reverse transcription polymerase chain reaction (RT-PCR) of the 16S ribosomal nucleic acid (rRNA) of Mycoplasma for detection of viable Mycoplasma gallisepticum. To determine the stability of M. gallisepticum 16S rRNA in vitro, three inactivation methods were used and the suspensions were stored at different temperatures. The 16S rRNA of M. gallisepticum was detected up to approximately 20-25 h at 37 °C, 22-25 h at 16 °C, and 23-27 h at 4 °C. The test, therefore, could detect viable or recently dead M. gallisepticum (< 20 h). The RT-PCR method was applied during an in vivo study of drug efficacy under experimental conditions, where commercial broiler-breeder eggs were inoculated with M. gallisepticum into the yolk. Hatched chicks that had been inoculated in ovo were treated with Macrolide 1. The method was then applied in a flock of day 0 chicks with naturally acquired vertical transmission of M. gallisepticum, treated with Macrolide 2. Swabs of the respiratory tract were obtained for PCR and RT-PCR evaluations to determine the viability of M. gallisepticum. This study proved that the combination of both PCR and RT-PCR enables detection and differentiation of viable from non-viable M. gallisepticum.
Microalgae have caught the world's attention for its potential to solve one of the world's most pressing issues-sustainable green energy. Compared to biofuels supplied by oil palm, rapeseed, soybean and sugar cane, microalgae alone can be manipulated to generate larger amounts of biodiesel, bioethanol, biohydrogen and biomass in a shorter time. Apart from higher productivity, microalgae can also grow using brackish water on non-arable land, greatly reducing the competition with food and cash crops. Hence, numerous efforts have been put into the commercialisation of microalgae-derived biofuel by both the government and private bodies. This paper serves to review conventional and novel methods for microalgae culture and biomass harvest, as well as recent developments in techniques for microalgal biofuel production.
Pantoea stewartii strain M073a is a Gram-negative bacterium isolated from a tropical waterfall. This strain exhibits quorum-sensing activity. Here, the assembly and annotation of its genome are presented.
Virus-like particles composed of the core antigen of hepatitis B virus (HBcAg) have been shown to be an effective platform for the display of foreign epitopes in vaccine development. Heterologous sequences have been successfully inserted at both amino and carboxy termini as well as internally at the major immunodominant epitope. We used cryogenic electron microscopy (CryoEM) and three-dimensional image reconstruction to investigate the structure of VLPs assembled from an N-terminal extended HBcAg that contained a polyhistidine tag. The insert was seen to form a trimeric spike on the capsid surface that was poorly resolved, most likely owing to it being flexible. We hypothesise that the capacity of N-terminal inserts to form trimers may have application in the development of multivalent vaccines to trimeric antigens. Our analysis also highlights the value of tools for local resolution assessment in studies of partially disordered macromolecular assemblies by cryoEM.
The juice of the entire fresh herb and infusion of dried sample of Murdannia bracteata are consumed to treat liver cancer and diabetes in Malaysia. However, no scientific evidence of these bioactivities has been reported.
Water-in-diesel emulsion (WiDE) is an alternative fuel for CI engines that can be employed with the existing engine setup with no additional engine retrofitting. It has benefits of simultaneous reduction of both NO x and particulate matters in addition to its impact in the combustion efficiency improvement, although this needs further investigation. This review paper addresses the type of emulsion, the microexplosion phenomenon, emulsion stability and physiochemical improvement, and effect of water content on the combustion and emissions of WiDE fuel. The review also covers the recent experimental methodologies used in the investigation of WiDE for both transport and stationary engine applications. In this review, the fuel injection pump and spray nozzle arrangement has been found to be the most critical components as far as the secondary atomization is concerned and further investigation of the effect of these components in the microexplosion of the emulsion is suggested to be center of focus.
Andrographolides, the diterpene lactones, are major bioactive phytochemicals which could be found in different parts of the medicinal herb Andrographis paniculata. A number of such compounds namely andrographolide (AG), neoandrographolide (NAG), and 14-deoxy-11,12-didehydroandrographolide (DDAG) have already attracted a great deal of attention due to their potential therapeutic effects in hard-to-treat diseases such as cancers and HIV. Recently, they have also been considered as substrates for the discovery of novel pharmaceutical compounds. Nevertheless, there is still a huge gap in knowledge on the genetic pattern of the biosynthesis of these bioactive compounds. Hence, the present study aimed to investigate the genetic mechanisms controlling the biosynthesis of these phytochemicals using a diallel analysis. The high performance liquid chromatography analysis of the three andrographolides in 210 F1 progenies confirmed that the biosynthesis of these andrographolides was considerably increased via intraspecific hybridization. The results revealed high, moderate and low heterosis for DDAG, AG and NAG, respectively. Furthermore, the preponderance of non-additive gene actions was affirmed in the enhancement of the three andrographolides contents. The consequence of this type of gene action was the occurrence of high broad-sense and low narrow-sense heritabilities for the above mentioned andrographolides. The prevalence of non-additive gene action suggests the suitability of heterosis breeding and hybrid seed production as a preferred option to produce new plant varieties with higher andrographolide contents using the wild accessions of A. paniculata. Moreover, from an evolutionary point of view, the occurrence of population bottlenecks in the Malaysian accessions of A. paniculata was unveiled by observing a low level of additive genetic variance (VA ) for all the andrographolides.
In this study, Centella asiatica and surface soils were collected from 12 sampling sites in Peninsular Malaysia, and the barium (Ba) concentrations were determined. The Ba concentration [μg/g dry weight (dw)] was 63.72 to 382.01 μg/g in soils while in C. asiatica, Ba concentrations ranged from 5.05 to 21.88 μg/g for roots, 3.31 to 11.22 μg/g for leaves and 2.37 to 6.14 μg/g for stems. In C. asiatica, Ba accumulation was found to be the highest in roots followed by leaves and stems. The correlation coefficients (r) of Ba between plants and soils were found to be significantly positively correlated, with the highest correlation being between roots-soils (r=0.922, p<005), followed by leaves-soils (r=0.890, p<005) and stems-soils (r=0.848, p<005). This indicates that these three parts of C. asiatica are good biomonitors of Ba pollution. For the transplantation study, four sites were selected as unpolluted [(Universiti Putra Malaysia (UPM)], semi-polluted (Seri Kembangan and Balakong) and polluted sites (Juru). Based on the transplantation study under experimental field and laboratory conditions, Ba concentrations in C. asiatica were significantly (p<0.05) higher after three weeks of exposure at Seri Kembangan, Balakong and Juru. Thus, these experimental findings confirm that the leaves, stems and roots of C. asiatica can reflect the Ba levels in the soils where this plant is found. Three weeks after back transplantation to clean soils, the Ba levels in C. asiatica were still higher than the initial Ba level even though Ba elimination occurred. In conclusion, the leaves, stems and roots of C. asiatica are good biomonitors of Ba pollution.
A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.
In recent years, carbon nanotubes have received widespread attention as promising carbon-based nanoelectronic devices. Due to their exceptional physical, chemical, and electrical properties, namely a high surface-to-volume ratio, their enhanced electron transfer properties, and their high thermal conductivity, carbon nanotubes can be used effectively as electrochemical sensors. The integration of carbon nanotubes with a functional group provides a good and solid support for the immobilization of enzymes. The determination of glucose levels using biosensors, particularly in the medical diagnostics and food industries, is gaining mass appeal. Glucose biosensors detect the glucose molecule by catalyzing glucose to gluconic acid and hydrogen peroxide in the presence of oxygen. This action provides high accuracy and a quick detection rate. In this paper, a single-wall carbon nanotube field-effect transistor biosensor for glucose detection is analytically modeled. In the proposed model, the glucose concentration is presented as a function of gate voltage. Subsequently, the proposed model is compared with existing experimental data. A good consensus between the model and the experimental data is reported. The simulated data demonstrate that the analytical model can be employed with an electrochemical glucose sensor to predict the behavior of the sensing mechanism in biosensors.
Titanium dioxide (TiO2) is one of the most widely investigated metal oxides due to its extraordinary surface, electronic and catalytic properties. However, the large band gap of TiO2 and massive recombination of photogenerated electron-hole pairs limit its photocatalytic and photovoltaic efficiency. Therefore, increasing research attention is now being directed towards engineering the surface structure of TiO2 at the most fundamental and atomic level namely morphological control of {001} facets in the range of microscale and nanoscale to fine-tune its physicochemical properties, which could ultimately lead to the optimization of its selectivity and reactivity. The synthesis of {001}-faceted TiO2 is currently one of the most active interdisciplinary research areas and demonstrations of catalytic enhancement are abundant. Modifications such as metal and non-metal doping have also been extensively studied to extend its band gap to the visible light region. This steady progress has demonstrated that TiO2-based composites with {001} facets are playing and will continue to play an indispensable role in the environmental remediation and in the search for clean and renewable energy technologies. This review encompasses the state-of-the-art research activities and latest advancements in the design of highly reactive {001} facet-dominated TiO2via various strategies, including hydrothermal/solvothermal, high temperature gas phase reactions and non-hydrolytic alcoholysis methods. The stabilization of {001} facets using fluorine-containing species and fluorine-free capping agents is also critically discussed in this review. To overcome the large band gap of TiO2 and rapid recombination of photogenerated charge carriers, modifications are carried out to manipulate its electronic band structure, including transition metal doping, noble metal doping, non-metal doping and incorporating graphene as a two-dimensional (2D) catalyst support. The advancements made in these aspects are thoroughly examined, with additional insights related to the charge transfer events for each strategy of the modified-TiO2 composites. Finally, we offer a summary and some invigorating perspectives on the major challenges and new research directions for future exploitation in this emerging frontier, which we hope will advance us to rationally harness the outstanding structural and electronic properties of {001} facets for various environmental and energy-related applications.