Bayesian Analyses of Genetic Variation and Population Differentiation in Pacific Swordfish (Xiphias gladius L.) and the Development of High Resolution Melting Assays for Species Identification and Potential Sex-Linked Marker Survey in Istiophorid Billfish

Swordfish (Xiphias gladius L.) and istiophorid billfish fisheries in all ocean basins are important commercially and recreationally. Proper assessments of these fisheries are hampered by species misidentification, unknown sex ratios, and unclarified population structure. This dissertation focuses on: 1) genetic assays to identify Pacific billfishes, 2) the characterization of molecular markers potentially linked to gender determination in swordfish and billfishes, and 3) the characterization of the genetic population structure of Pacific swordfish. Unambigous identification of black marlin (Istiompax indica), blue marlin (Makaira nigricans), striped marlin (Kajikia audax) and sailfish (Istiophorus platypterus) was accomplished with two variants of high resolution melting (HRM), including HRM of a 491 bp segment, and melting profiles of a 48 bp unlabeled probe. Both HRM assays target variation in the mitochondrial DNA NADH dehydrogenase subunit 2 (ND2) gene and represent fast and robust alternatives to identify Pacific billfish. Surveys to identify gender-linked molecular markers were conducted using gender-validated samples. The characterization of Randomly Amplified Polymorphic DNA (RAPD) primers suggests a XY chromosomal system in blue marlin, and a ZW chromosomal system in sailfish, and possibly swordfish. Nucleotide sequence analyses of 12 loci known linked to gender determination in other teleosts showed no linkage in blue marlin, sailfish and swordfish. The genetic population structure of Pacific swordfish was surveyed using 16 samples (n=891) with an ample geographic coverage and that included early stages (n=150) and adults (n=741). Bayesian analyses of 20 single nucleotide polymorphisms (SNPs) contained in 10 nuclear loci indicate statistically significant genetic heterogeneity of tropical samples relative to temperate samples, but also with respect to other tropical samples, but no differences among temperate samples. The observed patterns are discussed in light of differences among regions in oceanographic conditions, adult and larval distributions, and tagging experiments

The effect of prestressing force on natural frequencies of concrete beams - A numerical validation of existing experiments by modelling shrinkage crack closure

This paper investigates the effect of prestressing force on the natural frequencies of reinforced concrete beams. From a pure theoretical point of view, such effects in different prestressing conditions appear to involve no ambiguity; however, in practice contradictory observations have been reported in existing research publications. Theoretical studies showed that natural frequencies would be decreasing or unchanged in different scenarios. On the other hand, some experiments that were conducted on prestressed concrete beams indicated an increasing trend of the natural frequencies with the prestressing force. This paper is aimed to provide a systematic explanation of the reasons causing the discrepancies and propose a coherent framework for the prediction of the natural frequencies under a prestressed condition. Numerical simulations using finite element model are carried out to simulate the influence of prestressing force on natural frequencies with the existence of the shrinkage cracks. The results demonstrate that such shrinkage-type cracks inside the concrete indeed tend to close when the prestressing force is applied, and this in turn increases the bending stiffness and consequently results in an increase of the natural frequencies of the beams.MOE (Min. of Education, S’pore)Accepted versio

A novel and non-invasive approach utilising nasal washings for the detection of nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is an epithelial cancer of the nasopharynx which is highly associated with Epstein–Barr virus (EBV). Worldwide, most of the top 20 countries with the highest incidence and mortality rates of NPC are low- and middle-income countries. Many studies had demonstrated that EBV could be detected in the tissue, serum and plasma of NPC patients. In this study, we explored the potential of assays based on non-invasive nasal washings (NW) as a diagnostic and prognostic tool for NPC. A total of 128 patients were evaluated for NW EBV DNA loads and a subset of these samples were also tested for 27 EBV and human miRNAs shortlisted from literature. EBV DNA and seven miRNAs showed area under the receiver operating characteristic curve (AUC) values of more than 0.7, suggestive of their potential utility to detect NPC. Logistic regression analyses suggested that combination of two NW assays that test for EBNA-1 and hsa-miR-21 had the best performance in detecting NPC. The trend of NW EBV DNA load matched with clinical outcome of 71.4% (10 out of 14) NPC patients being followed-up. In summary, the non-invasive NW testing panel may be particularly useful for NPC screening in remote areas where healthcare facilities and otolaryngologists are lacking, and may encourage frequent testing of individuals in the high risk groups who are reluctant to have their blood tested. However, further validation in an independent cohort is required to strengthen the utility of this testing panel as a non-invasive detection tool for NPC. © 2019 The Authors. International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UIC

A 9 bp cis-element in the promoters of class I small heat shock protein genes on chromosome 3 in rice mediates L-azetidine-2-carboxylic acid and heat shock responses

In rice, the class I small heat shock protein (sHSP-CI) genes were found to be selectively induced by L-azetidine-2-carboxylic acid (AZC) on chromosome 3 but not chromosome 1. Here it is shown that a novel cis-responsive element contributed to the differential regulation. By serial deletion and computational analysis, a 9 bp putative AZC-responsive element (AZRE), GTCCTGGAC, located between nucleotides –186 and –178 relative to the transcription initiation site of Oshsp17.3 was revealed. Deletion of this putative AZRE from the promoter abolished its ability to be induced by AZC. Moreover, electrophoretic mobility shift assay (EMSA) revealed that the AZRE interacted specifically with nuclear proteins from AZC-treated rice seedlings. Two AZRE–protein complexes were detected by EMSA, one of which could be competed out by a canonical heat shock element (HSE). Deletion of the AZRE also affected the HS response. Furthermore, transient co-expression of the heat shock factor OsHsfA4b with the AZRE in the promoter of Oshsp17.3 was effective. The requirement for the putative AZRE for AZC and HS responses in transgenic Arabidopsis was also shown. Thus, AZRE represents an alternative form of heat HSE, and its interaction with canonical HSEs through heat shock factors may be required to respond to HS and AZC

Energy-effective Predictive Temperature Control for Soy Mash Fermentation Based on Compartmental Pharmacokinetic Modelling

Compartment modelling has been successfully used in pharmacokinetics to describe the kinetics of drug distribution in body tissues. In this study, the technique is adopted to describe the dynamics of temperature response and energy exchange in a soy mash fermentation system. The objective is to provide a precise temperature-controlled atmosphere for effective fermentation with the premise of energy saving. In analogy to pharmacokinetics, water and mash tanks are treated as compartments, energy flow as drug delivery, and the temperature as the drug concentration in a specific compartment. The model allows us to estimate the time of injecting a certain amount of energy to a specific tank (compartment) in a cost-effective way. Thus, model-based temperature control and energy management can be possible

Morphological and Molecular Defects in Human Three-Dimensional Retinal Organoid Model of X-Linked Juvenile Retinoschisis

X-linked juvenile retinoschisis (XLRS), linked to mutations in the RS1 gene, is a degenerative retinopathy with a retinal splitting phenotype. We generated human induced pluripotent stem cells (hiPSCs) from patients to study XLRS in a 3D retinal organoid in vitro differentiation system. This model recapitulates key features of XLRS including retinal splitting, defective retinoschisin production, outer-segment defects, abnormal paxillin turnover, and impaired ER-Golgi transportation. RS1 mutation also affects the development of photoreceptor sensory cilia and results in altered expression of other retinopathy-associated genes. CRISPR/Cas9 correction of the disease-associated C625T mutation normalizes the splitting phenotype, outer-segment defects, paxillin dynamics, ciliary marker expression, and transcriptome profiles. Likewise, mutating RS1 in control hiPSCs produces the disease-associated phenotypes. Finally, we show that the C625T mutation can be repaired precisely and efficiently using a base-editing approach. Taken together, our data establish 3D organoids as a valid disease model

Biomechanical investigation of flexor digitorum tendons in trigger finger patients using sonography

Trigger finger (TF) has generally been ascribed to primary changes in the first annular (A1) pulley. Repeated friction between the A1 pulley and flexor digitorum tendons could result in swelling of soft tissues, and thus it has been speculated that TF affects tendons’ biomechanical behaviors. However, the pathology mechanism related to these behaviors remains unclear. The purposes of this study are to understand (1) the variations in the morphologies of the flexor digitorum profundus (FDP) and flexor digitorum superficialis (FDS) between normal fingers and TFs, (2) the differences in the biomechanical behaviors of the FDP and FDS between normal fingers and TFs in various finger flexion positions, and (3) the effect of various finger positions on the biomechanical behaviors of the FDP and FDS

A Controlled Fermentation Environment for Producing Quality Soya Sauce

Soy sauce fermentation under controlled temperature is a way to shorten the fermentation time. An energy-saving fermentation system was developed to power a heat pump for maintaining the temperature of sauce moromi at 37±1°C during fermentation. The chemical properties of the sauce moromi and the sensory properties of the soy sauce produced using the controlled fermentation system were evaluated and compared to those of the sauce moromi fermented outdoors without temperature control. The sauce moromi processed using the controlled fermentation system had significantly higher total nitrogen, formal nitrogen, amino nitrogen, reducing sugar and organic acid contents than the moromi fermented outdoor. However, no significant difference was found in overall liking score between two soy sauces. The soy sauce fermented under the control temperature showed higher Brix and salt concentration, but lower pH value than the sauce fermented outdoor. It was possible that the beneficial effects of reducing sugar and organic acid contents were rebuffed by the disadvantage of salt concentration. It was concluded that a controlled fermentation environment deserves the potential to produce a high quality soy sauce

A Controlled Fermentation Environment for Producing Quality Soya Sauce

Soy sauce fermentation under controlled temperature is a way to shorten the fermentation time. An energy-saving fermentation system was developed to power a heat pump for maintaining the temperature of sauce moromi at 37±1°C during fermentation. The chemical properties of the sauce moromi and the sensory properties of the soy sauce produced using the controlled fermentation system were evaluated and compared to those of the sauce moromi fermented outdoors without temperature control. The sauce moromi processed using the controlled fermentation system had significantly higher total nitrogen, formal nitrogen, amino nitrogen, reducing sugar and organic acid contents than the moromi fermented outdoor. However, no significant difference was found in overall liking score between two soy sauces. The soy sauce fermented under the control temperature showed higher Brix and salt concentration, but lower pH value than the sauce fermented outdoor. It was possible that the beneficial effects of reducing sugar and organic acid contents were rebuffed by the disadvantage of salt concentration. It was concluded that a controlled fermentation environment deserves the potential to produce a high quality soy sauce