Plant DNA Extraction Kit – fasTiP-XTM

Plant DNA extraction is prerequisite to any downstream DNA molecular application. However, the conventional DNA extraction from plant tissues are time consuming, tedious and labour intensive which involve liquid nitrogen and hazardous chemicals, such as CIA and phenol-chloroform. In addition, more than half of the DNA would be lost along this process as well. Hence, the development of rapid DNA extraction method, such as fasTiP-X kit, was greatly needed. fasTiP-X kit is a rapid and efficient plant DNA extraction kit which only involves 3 simple steps before PCR amplification. The basic concept of this kit is touch which is transferring plant samples into the extraction buffer; incubate to lyses the plant cells; and finally the solution can be directly use for further analysis. The detailed technical procedure for operating this kit is first by punching the fresh leaf using Harris micro punch®. Then, 6 punched leaf discs are incubated together with 50 μl of Extraction Buffer for 10 minutes in 95°C. After incubation, the incubated solution is mixed by inverting and tapping. Next, 120 μl of Dilution Buffer is added to the incubated solution. Eventually, the mixture can be directly used for PCR amplification. The overall process for the preparation of DNA for PCR amplification using fasTiP-X Kit can be completed in 20 minutes. Besides, it uses small amount (about 5mm2) of samples which reduces the lost of sample to minimal. This kit is applicable in forestry forensic analysis, genetic diversity study and species and clone identification

Applications Of Genomics To Plantation Forestry With Kelampayan In Sarawak

Wood-based industries in Sarawak are increasingly encouraged to adapt to “new wood” from planted forests composed of fast-growing species such as Kelampayan with short rotation cycle (6-8 years). The rationale is that natural forests at the most produce about 3m3 /ha/yr of commercial timber, whereas plantations can produce annually from 10m3 /ha to 30m3 /ha of commercial timber. It is estimated at least 30 million seedlings are required for annual planting or reforestation programmes to meet the increasing global demand for raw materials. To date, several molecular genetics studies have been completed for Kelampayan. These include genetic diversity of Kelampayan, genetic marker (SSRs) development, ‘Touch-incubate-PCR’ approach for preparing plant tissues for high throughput genotyping, and transcriptomics and bioinformatics on wood formation of Kelampayan. This information provides a useful resource for genomic selection of Kelampayan aiming at the production of high value forests for maximum returns

Effects of Organic Amendments Produced from Agro-Wastes on Sandy Soil Properties and Black Pepper Morpho-Physiology and Yield

Sandy textured soil infertility poses a problem for sustainable crop cultivation. This problem is usually dealt with by the addition of chemical fertilizers, which are expensive and can cause serious environmental issues if not managed well. A better alternative to improve and manage sandy soil infertility is the use of organic amendments produced from agro-wastes. This two (2)- year field study was conducted in a sandy-textured soil grown with black pepper to evaluate mainly the effects of chemical fertilizer, fermented plant and fruit juices, compost, and biochar on soil properties and morpho-physiological characteristics and yield of black pepper. Generally, the results indicated that the combination of fermented fruit juice, compost, and biochar was comparable to and in some cases better than chemical fertilizer in terms of soil physical, chemical, and biological properties as well as crop performance. These findings were even more pronounced in the second year of measurements. There were strong positive relationships between soil N and pepper leaf chlorophyll content and between soil microbes and soil respiration. The findings showed that these soil amendments produced from agro-wastes are a good alternative to the use of chemical fertilizers on sandy soils to improve soil fertility and productivity and the yield of black pepper sustainably

Genomics studies on plantation tree species in Sarawak

Rapid socio-economic changes in the world are having profound impacts on all sectors, including forestry. The increase in global demand for wood requires increase in forest productivity. The alternative is to farm trees in plantations composed of fast-growing species with short rotation cycles (6–8 y). The rationale is that natural forests at the most produce about 3 m3 ha y-1 of commercial timber, whereas plantations can produce annually from 10 m3 ha y-1 of hardwoods to 30 m3 ha-1 of softwoods and thus, decrease the effects of human pressure on our ecosystems while increasing the competitiveness of Sarawak’s forest industry. This is in line with the state government’s aspiration to establish one million hectares of planted forests by year 2020 to meet the increasing demand from both domestic and international markets for raw materials. It is estimated at least 30 million seedlings are required for annual planting or reforestation programmes. In this regard, forest genomics research will help respond to the need to develop adequate tools that enable us to produce quality planting materials that are of faster growth, high yield and high wood quality, and also adapted to local conditions, so that we may achieve economic benefits of great significance. Realizing the need, we have centred our research on the development of tools via biotechnological innovations for tree breeders. Over the years, we have successfully developed: 1) simple sequence repeat (SSR) 173 DNA markers specific for identifying the genetic make-up of two fastgrowing indigenous tree species, i.e. kelampayan and sawih; 2) the ‘Touch-incubate-PCR’ approach for preparing plant tissues for high throughput genotyping, and 3) a kelampayan tree transcriptome database (NcdbEST aka CADAMOMICS) for wood formation. These tools will greatly facilitate the selection of quality planting materials for planted forest development in Sarawak as well as long-term tree improvement activities by integrating genomics into our breeding programme via association mapping. The overall benefit of genomics application to tree improvement programme will be in terms of greater certainty in the outcome of results, specifically the performance of the forest plantations, as well as the savings in time and cost in the production and supply of quality planting materials

From Conservation To Innovation Building Research Capacity For Planted Forest Development In Sarawak

The increase in global demand for wood requires increase in forest productivity. The alternative is to farm trees in plantations composed of fast-growing species with short rotation cycle (6-8 years). The rationale is that natural forests at the most produce about 3m3/ha/yr of commercial timber, whereas plantations can produce annually from 10m3/ha of hardwoods to 30m3/ha of softwoods and thus, decrease the effects of human pressure on our ecosystems while increasing the competitiveness of Sarawak‘s forest industry. This is in line with State Government‘s aspiration to establish one million hectares of planted forests by year 2020 to meet the increasing demand from both domestic and international markets for raw materials. It is estimated at least 30 million seedlings are required for annual planting or reforestation programmes. In this regard, the forest genomics research will help respond to the need to develop adequate tools that enable us to produce quality planting materials that are of faster growth, high-yield and high wood quality, and also adapted to local conditions, so that we may achieve economic benefits of great significance. Realizing the needs, we have centered our research on the development of tools via biotechnological innovations for tree breeders. We have successfully developed: 1) an array of highly informative and polymorphic DNA markers specific for identifying the genetic makeup of two fast growing indigenous tree species, i.e. Kelampayan and Sawih; 2) the one step ‗Touchincubate- PCR‘ approach for preparing plant tissues for high throughput genotyping, and 3) a genomic resource database, aka CADAMOMICS (10,368 ESTs) for wood formation in Kelampayan via high-throughput DNA sequencing. These tools will greatly facilitate the selection of quality planting materials for planted forest development in Sarawak as well as longterm tree improvement activities by integrating genomics into our breeding programme via association mapping. The overall benefit of genomics application to tree improvement programme will be in terms of greater certainty in the outcome of results, specifically the performance of the forest plantations, as well as the savings in time and cost in the production and supply of quality planting materials

Meta-analysis Followed by Replication Identifies Loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as Associated with Systemic Lupus Erythematosus in Asians

Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with a strong genetic involvement and ethnic differences. Susceptibility genes identified so far only explain a small portion of the genetic heritability of SLE, suggesting that many more loci are yet to be uncovered for this disease. In this study, we performed a meta-analysis of genome-wide association studies on SLE in Chinese Han populations and followed up the findings by replication in four additional Asian cohorts with a total of 5,365 cases and 10,054 corresponding controls. We identified genetic variants in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with the disease. These findings point to potential roles of cell-cycle regulation, autophagy, and DNA demethylation in SLE pathogenesis. For the region involving TET3 and that involving CDKN1B, multiple independent SNPs were identified, highlighting a phenomenon that might partially explain the missing heritability of complex diseases

The prevalence of obesity and the knowledge, attitude and practice of healthy lifestyle among the adult population in Kampung Banyuk, Kampung Kerto and Kampung Langup

Background Obesity has become a great public health concern and prevent!ive measures need to be done. Objective The objective of this research is to determine the prevalence ofobesity and their knowledge, attitude and practices (KAP) towards a healthy lifestyle among the residents in Kampung Banyok, Kampung Kerto and Kampung Langup. Methods A cross-sectional study was done among 126 randomly selected villagers aged 18 years and above from the three selected villages. They were interviewed based on a questionnaire and their body mass index (BMI) was calculated. Results It was found that more than half of the respondents are obese. Among the respondents, for the healthy lifestyle component, the level of good KAP is 69.2%, 46.8% and 60.3% respectively. As for obesity component, the level of good KAP is 60.3%, 54% and 54.8% respectively. Among the obese respondents, the level of knowledge and attitude on healthy lifestyle and obesity is better. Obese respondents have better obesity preventive practice while the non-obese respondents have better practice on healthy lifestyle. The only significant correlation noted was between knowledge and practice on obesity albeit a negative one. Conclusion The level of knowledge and attitude and practice on healthy lifestyle among the obese respondents are encouraged but more effort in the preventive practice ofobesity shou1d be done to reduce the prevalence.

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Hypertriton Production in p-Pb Collisions at √sNN = 5.02 TeV

The study of nuclei and antinuclei production has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high-energy hadronic collisions. The first measurement of the production of ${\rm ^{3}_{\Lambda}\rm H}$ in p-Pb collisions at $\sqrt{s_{\rm{NN}}}$ = 5.02 TeV is presented in this Letter. Its production yield measured in the rapidity interval -1 < y < 0 for the 40% highest multiplicity p-Pb collisions is ${\rm d} N /{\rm d} y =[\mathrm{6.3 \pm 1.8 (stat.) \pm 1.2 (syst.) ] \times 10^{-7}}$. The measurement is compared with the expectations of statistical hadronisation and coalescence models, which describe the nucleosynthesis in hadronic collisions. These two models predict very different yields of the hypertriton in small collision systems such as p-Pb and therefore the measurement of ${\rm d} N /{\rm d} y$ is crucial to distinguish between them. The precision of this measurement leads to the exclusion with a significance larger than 6$\sigma$ of some configurations of the statistical hadronisation, thus constraining the production mechanism of loosely bound states

General balance functions of identified charged hadron pairs of (pi,K,p) in Pb-Pb collisions at 2.76 TeV

First measurements of balance functions (BFs) of all combinations of identified charged hadron ( π , K, p) pairs in Pb–Pb collisions at √sNN = 2.76 TeV recorded by the ALICE detector are presented. The BF measurements are carried out as two-dimensional differential correlators versus the relative rapidity (delta-y) and azimuthal angle (delta-φ) of hadron pairs, and studied as a function of collision centrality. The delta-φ dependence of BFs is expected to be sensitive to the light quark diffusivity in the quark–gluon plasma. While the BF azimuthal widths of all pairs substantially decrease from peripheral to central collisions, the longitudinal widths exhibit mixed behaviors: BFs of π π and cross-species pairs narrow significantly in more central collisions, whereas those of KK and pp are found to be independent of collision centrality. This dichotomy is qualitatively consistent with the presence of strong radial flow effects and the existence of two stages of quark production in relativistic heavy-ion collisions. Finally, the first measurements of the collision centrality evolution of BF integrals are presented, with the observation that charge balancing fractions are nearly independent of collision centrality in Pb–Pb collisions. Overall, the results presented provide new and challenging constraints for theoretical models of hadron production and transport in relativistic heavy-ion collisions