Vietnam Journal of Science, Technology and Engineering

3-6

Authors: Thi Thuy Duy Nguyen, Hoang Phuong Tran*

The rapid and green procedure for the Knoevenagel reaction between aromatic aldehydes and diethyl malonate was developed by using 1-butyl-3-methylimidazolium hydroxide, [Bmim]OH, as an efficient catalyst. The condensations showed good yields with a wide range of aromatic aldehydes in solvent-free condition and short reaction times. [Bmim]OH was easy to recover and could be reused several times without significant loss of catalytic activity.

16-23

Authors: Van Quang Le*, Quang Minh Do, Minh Duc Hoang, Hoc Thang Nguyen

In this study, the alkaline solutions (NaOH) with concentrations from 1M to 18M, red mud (RM) and silica fume (SF) were used as reactors in geopolymer reactions. RM contains 7.40% SiO2 and 13.65% Al2o3and SF has 94.50% SiO2, but only the active oxides can participate in the geopolymer reactions. The activity of the oxides was investigated by determining the compressive strength of the samples under different curing conditions. The characteristics of the geopolymer samples were determined by using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), thermo-gravimetric analysis (TGA)/differential thermal analysis (DTA) and nuclear magnetic resonance analysis (NMR). The experimental results indicate that active silica mainly exists in SF. In the structure of geopolymers, the silicon can bond directly with each other (Si-Si) or be linked through ‘bridging’ oxygen (Si-O-Si) to form independent polymer chains, while aluminium atoms can only replace the silicon atoms in Si-O-Si polymer chains to form Si-O-Al instead

30-43

Authors: Hieu T. Nguyen*, Huong T.T. Le, Liem T. Nguyen, Hua Lou, Thomas La Framboise

Next-generation sequencing (NGS) is a high throughput sequencing technology, which has revolutionized both basic and clinical research of the human genetic disorders. This technology is also called massively parallel sequencing (MPS) due to its ability to generate a huge amount of output data in a cost- and time-effective manner. NGS is widely utilized for different sequencing applications such as targeted sequencing (a group of candidate genes), exome sequencing (all coding regions), and whole genome sequencing (the entire human genome). With NGS, a variety of genomic aberrations can be screened simultaneously such as common and rare variants, structural variations (amplifications and deletion), copy-number variation, and fusion transcripts. NGS technologies combined with advanced bioinformatic analysis have tremendously expanded our knowledge. On the one hand, the basic research area involves direct use of NGS to identify novel variations and determine human disease mechanisms. On the other hand, clinical research is being advanced by high-throughput genetic tests with high resolution and clinically relevant genetic information for molecular diagnoses of human disorders. In this communication, we introduce NGS technologies and review a few key areas where NGS has made a significant impact, with an emphasis on the application of NGS to the identification of the molecular bases of human genetic diseases.

51-55

Authors: Ngo Tat Trung*, Dao Thanh Quyen, Phan Quoc Hoan, Thirumalaisamy P.P. Velavan, Le Huu Song*

Background/aims: It has been shown that quinolone resistance arises due to mutations in the quinolone resistance-determining regions of the drug targets. This study aimed to optimise a multiplex PCR assay to track plasmid-mediated low-level quinolone resistance profiles.Subjects and methods: A multiplex PCR-based-method in which the primers were already established by our team. About 44 samples were collected from 44 patients who enrolled in this study by using surgical site infection (SSI).Results: By targeting the conserved domains of qnrA, qnrB, qnrS and the qnrVC gene families, the primer number was reduced significantly to only four pairs in one multiplex PCR. Using multiplex PCR, 3/44 SSI samples were found to be carrying fluoroquinolone-resistance genes (qnrA, qnrB, qnrS, qnrVC).Conclusion: A multiplex PCR for detecting pathogens as well as identifying quinolone resistance genes all in one reaction was successfully established

57-67

Authors: Van Canh Doan, Duc Nhan Dang*, Kien Chinh Nguyen

The origin and chemistry of the groundwater in the middle Pleistocene (qp23), lower Pleistocene (qp1), upper Pliocene (n22), lower Pliocene (n21), and the Miocene (n13) in the Mekong river delta (MKRD) were investigated by using isotopic and geochemical techniques. The origin of the groundwater was evaluated based on the composition of the water stable isotopes (d2H and d18O) in the local precipitation, in water from the rivers system, and in the groundwater samples. The hydraulic interaction between the surface water and the groundwater as well as between the aquifers was assessed by a statistical treatment for the mean and standard deviation of the d18O signature and based on the 14C-ages of the water samples taken from different aquifers. The salinization of groundwater in the deep aquifers was investigated using the d18O signature combined with the geochemical composition of the water samples. It was revealed that the groundwater in the deep aquifers in the MKRD could be divided into two groups. The first group is fresh and represents the regional precipitation with the long traveling time ranging from older than 100 years to older than 40 ka BP (kilo years Before Present). The second group is the regional precipitation that is recharged from the remote areas mixed with the seawater. Statistical treatment with the mean d18O using the Mann-Whitney test showed that the water from the Mekong river system did not or very weakly recharged the deep aquifers. The groundwater in the deep aquifers in that region was likely to be connate, so that fresh groundwater resource in the region seemed to be limited. The chemistry of the groundwater in the study region is controlled by the incongruent dissolution of the Mg-calcite as well as sulfate and iron oxy-hydroxide reductions by organic matters presented in the aquifer sediment. The groundwater in the deep aquifers in the MKRD from some locations was saline, but the salinity in most aquifers was thought to result from the migration of saline water entrapped in the marine sediment pores to the fresh water in the aquifers. Meanwhile, in other locations, the salinity was suggested to result from the salt intrusion due to the over-abstraction rate, as it was evident from the d18O vs. [Cl-] relationship, or due to the up conning of saline water from the deeper aquifers to the upper ones. Particular measures must be developed for the better management of groundwater in the MKRD to ensure a sustainable resource of freshwater being supplied to the local population in future

73-77

Authors: Lam Nguyen, Xuan Thi Trinh, Hien Trinh, Dang Hung Tran, Cuong Nguyen*

The development of next-generation sequencing tech-nologies has helped sequence large genomes easily, producing a huge number of short-reads - small frag-ments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to the reference genome, a crucial step of genome analysis, still remains a challenge. In this study, we develop a short-read alignment program, BWTaligner, based on the Burrows-Wheeler transform compression - exact and inexact matching. We tested it on the paired-end read data simulated from chromosome 9 of the rice genome to compare the alignment and single-nucleo-tide polymorphism (SNP) calling between our aligner and BWA - the preferred alignment program. The re-sults showed that the BWA delivers higher recall and F-score, while BWTaligner has better precision in high coveragedepth

84-91

Authors: Van Doanh Vu*, Ha Phong Doan, Thi Thu Trang Bui

Nam Dinh province is located in the Red river delta with a relatively flat terrain. The North East of Nam Dinh is bordered by the Red river and the southwest by the Day river and has a coastline of approximately 80 km. Given the geographical location, Nam Dinh has favourable conditions for agricultural and aquaculture production. Climate change creates a large number of potential risks for Nam Dinh. This includes sea level rise, typhoons, flood tide, etc. According to the climate change and sea level rise scenario in 2016, if the sea level rises by 100 cm, the flood risk area in coastal districts such as Hai Hau would be 67.34%, Giao Thuy 64.6%, Nghia Hung 81.61% and Xuan Truong 59.3% [1]. According to the monitoring data from Vietnam Institute of Meteorology, Hydrology and Climate Change (IMHEN), the salinity intrusion area due to sea level rise is likely to widen, which degrades and affects the area of the mangrove ecosystem [2]. In addition, the sea level rise may reduce the resilience of irrigation system due to the changes in estuarine and coastal dynamics such as water levels, flows, waves, etc. Through synthesising the local and international guidelines and in combination with expert consultation and field surveys, this paper develops an assessment procedure for sea level rise that causes economic damage to agricultural land use in order to quantify the impact of sea level rise in 4 coastal districts of Xuan Truong, Giao Thuy, Hai Hau and Nghia Hung in Nam Dinh province.