A simulation of selected statistical process control methods :a thesis presented in partial fulfilment of the requirements for the degree of Master of Technology at Massey University

A simulation program, SQC, was developed at the Production Technology Department, Massey University. The program was written in Vax Basic 3.0 which is structured programming language and is run on the Vax computer under the VAX/VMS operating system 4.5. SQC is a menu-driven program which was designed to simulate data from a variety of production processes subject to inherent random variation and predetermined changes; sample selection for statistical quality purposes. Such decisions were made via the available feature to allow for user interactive control of the process parameters and sample selection methods while the chart of selected method was plotted on the terminal screen as well as optionally on the printer. The exercise has been done to test and to observe how the program performed and produced the output on the screen and terminal-format files. Moreover, the program evaluation was carried out by comparing with a published article, which is satisfactorily acceptable. The SQC can be utilized as a teaching tool for students in practising how each statistical process control method performs and how to make a right decision at a right time and as a research tool to observe and use the simulated results to predict and to improve the production process in the future

WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

BACKGROUND: Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. RESULTS: This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. CONCLUSION: WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at http://bioinfo.biotec.or.th/WASP

Flavonoid component determination and apoptotic induction evaluation of houttuynia cordata thunb extract on human acute leukemic cells

Development of resistance to currently used drugs and side effects of several allopathic drugs have led to increased emphasis on plant materials uses as a source of medicines for a wide variety of human illnesses including leukemia. Houttuynia cordata Thunb (H.cordata), a Northern Thailand local plant and commonly known as Plucao, has various biological activities such as anti-inflammatory, anti-cancer and anti-leukemic activities. We aimed to determine active flavonoid components of H.cordata and to investigate the effect of H.cordata ethanolic extract on apoptotic induction on human acute lymphoblastic leukemia cells. In this study, we found that H.cordata ethanolic extract had total flavonoid of 231.21 ± 4.19 mg QE/g dried H.cordata. The extract analyzed by quantitative LC-MS consists of several flavonoid components including hyperin 6.35 ± 0.41, quercetin 0.34 ± 0.02, isoquercetin 1.10 ± 0.03, and rutin 0.88 ± 0.04 (%w/w). The cytotoxicity results showed dose dependent decrease in growth of Jurkat leukemic cells. Blebbing pattern of cell apoptosis was found in cells treated with H.cordata ethanolic extract for 24 and 48 hrs. Moreover, we found that the extract could substantially induce Jurkat cell death through apoptosis at both 12 and 24 hrs. In conclusion, these results indicated that H.cordata ethanolic extract which is composed of several flavonoids, possesses anti-leukemic activity through apoptotic induction in Jurkat leukemia cells

Effect of Trimeresurus albolabris (green pit viper) venom on mean corpuscular volume, osmotic fragility and red blood cell morphology: A preliminary report

An in vitro study was conducted by mixing small amounts of green pit viper venom with blood and observing changes. At a concentration of 10 mg crude venom, red blood cells (RBC) osmotic fragility slightly increased. RBC morphology changed to spherical shape which was compatible with what was observed in scanning electron microscope (SEM). However, there was no change in mean corpuscular volume (p > 0.05)

Novel Adiponectin Variants Identified in Type 2 Diabetic Patients Reveal Multimerization and Secretion Defects

ADIPOQ, encoding adiponectin, is a candidate gene for type 2 diabetes (T2D) identified by genome-wide linkage analyses with supporting evidence showing the protein function in sensitizing insulin actions. In an endeavor to characterize candidate genes causing T2D in Thai patients, we identified 10 novel ADIPOQ variations, several of which were non-synonymous variations observed only in the patients. To examine the impact of these non-synonymous variations on adiponectin structure and biochemical characteristics, we conducted a structural analysis of the wild-type and variant proteins by in silico modeling and further characterized biochemical properties of the variants with predicted structural abnormalities from the modeling by molecular and biochemical studies. The recombinant plasmids containing wild-type and variant ADIPOQ cDNAs derived from the variations identified by our study (R55H, R112H, and R131H) and previous work (G90S and R112C) were constructed and transiently expressed and co-expressed in cultured HEK293T cells to investigate their oligomerization, interaction, and secretion. We found that the novel R55H variant impaired protein multimerization but it did not exert the effect over the co-expressed wild-type protein while novel R131H variant impaired protein secretion and also affected the co-expressed wild-type protein in a dominant negative fashion. The R131H variant could traffic from the endoplasmic reticulum to the Golgi, trans-Golgi network, and early endosome but could not be secreted. The R131H variant was likely to be degraded through the lysosomal system and inhibition of its degradation rescued the variant protein from secretion defect. We have shown the possibility of using in silico modeling for predicting the effect of amino acid substitution on adiponectin oligomerization. This is also the first report that demonstrates a dominant negative effect of the R131H variant on protein secretion and the possibility of using protein degradation inhibitors as therapeutic agents in the patients carrying adiponectin variants with secretion defect

Induced pluripotent stem cell–derived human platelets: one step closer to the clinic

One step closer to on-demand platelet production

Impact of neonicotinoid seed treatment of cotton on the cotton leafhopper, Amrasca devastans(Hemiptera: Cicadellidae), and its natural enemies

BACKGROUND Neonicotinoid seed treatments suppress populations of pest insects efficiently and can enhance crop growth, but they may have negative effects on beneficial arthropods. We evaluated the effects of either imidacloprid or thiamethoxam on the abundances of a sucking pest, the cotton leafhopper (Amrasca devastans), and its arthropod predators under field conditions. We also evaluated the impact of seed treatment on transgenic cotton plant growth, with pests and natural enemies present or absent. RESULTS Imidacloprid and thiamethoxam reduced pest abundance, with greater effects when dosages were higher. Treatment at recommended doses delayed the pest in reaching the economic damage threshold by around 10–15 days (thiamethoxam) and 20 days (imidacloprid). Recommended doses also enhanced plant growth under all tested conditions; growth is affected directly as well as via pest suppression. Neonicotinoid applications reduced abundance of beneficial arthropods, with lower populations after higher doses, but negative effects of imidacloprid were not apparent unless the manufacturer-recommended dose was exceeded. CONCLUSION Imidacloprid applied at the recommended dose of 5 g kg−1 seed is effective against A. devastans and appears to be safer than thiamethoxam for natural enemies, and also enhances plant growth directly. We caution, however, that possible sublethal negative effects on individual beneficial arthropods were not evaluated

Transcriptome Sequencing of Hevea brasiliensis for Development of Microsatellite Markers and Construction of a Genetic Linkage Map

To obtain more information on the Hevea brasiliensis genome, we sequenced the transcriptome from the vegetative shoot apex yielding 2 311 497 reads. Clustering and assembly of the reads produced a total of 113 313 unique sequences, comprising 28 387 isotigs and 84 926 singletons. Also, 17 819 expressed sequence tag (EST)-simple sequence repeats (SSRs) were identified from the data set. To demonstrate the use of this EST resource for marker development, primers were designed for 430 of the EST-SSRs. Three hundred and twenty-three primer pairs were amplifiable in H. brasiliensis clones. Polymorphic information content values of selected 47 SSRs among 20 H. brasiliensis clones ranged from 0.13 to 0.71, with an average of 0.51. A dendrogram of genetic similarities between the 20 H. brasiliensis clones using these 47 EST-SSRs suggested two distinct groups that correlated well with clone pedigree. These novel EST-SSRs together with the published SSRs were used for the construction of an integrated parental linkage map of H. brasiliensis based on 81 lines of an F1 mapping population. The map consisted of 97 loci, consisting of 37 novel EST-SSRs and 60 published SSRs, distributed on 23 linkage groups and covered 842.9 cM with a mean interval of 11.9 cM and ∼4 loci per linkage group. Although the numbers of linkage groups exceed the haploid number (18), but with several common markers between homologous linkage groups with the previous map indicated that the F1 map in this study is appropriate for further study in marker-assisted selection