Science & Technology Development Journal: Natural Sciences

Protein structure modeling using cloud-based servers

Trần Văn Hiếu — 2024-03-31

The structure of a protein plays an important role in determining its function. Deciphering how proteins fold has thus been a puzzle for nearly a half-century. Structure determination methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy or electron microscopy are tedious and time-consuming; meanwhile, new-generation sequencing methods are producing massive amounts of protein data in a matter of days. To bridge the protein sequence-structure gap, methods and algorithms for predicting protein 3D structure starting from only its amino acid sequence have been developed. In recent years, machine learning has been of interest to the research community thanks to its work in analyzing intrinsic features of proteins to predict their structure, novel computational methods capable of modeling protein structures to near experimental accuracy. Accurately predicted structures are used for drug and antibody design, understanding protein-protein interactions, and with other molecules. This review provides information about multiple prediction methods and tools for protein structure prediction.

Characteristics of Zircon gems related to Basalt in the Southeastern Vietnam

Lê Ngọc Năng — 2024-03-31

This paper presented the on gem–quality zircon found in the southeast, Vietnam which related Cenozoic alkaline basalt and deposited on hillsides or stream beds as placers. Zircon samples in this area is mainly brown, orange, gray and colorless; transparent and diamond luster. In addition, they mostly have the effect of changing color under different lights and often have the shape of 4-sided cylinders, typical of the tetragonal crystal type. The standard gemological characteristics such as refractive index, specific gravity, absorption spectrum, optic characteristic and ultraviolet fluorescence (long wave and short wave) confirmed the studied samples belonged to the zircon mineral group. Notably, the refractive index could not be measured by the refractometer and the high specific gravity (from 4.66 to 4.71) indicating that this belonged to a high zircon. The X-ray diffraction analysis determined a tetragonal crystallization and with the chemical formula ZrSiO4. The Raman spectrum with peaks at 226, 352, 438, 972 and 1004 cm-1 and the FTIR spectrum with peaks at 448, 607 and 898 cm-1 showed that the studied zircon was radioactive. The HfO2 content and Ti− thermometer showed that the studied zircon originated from the molten syenite with the crystallized temperature of 829.78−869.04°C. The result showed that the basalt in the southeastern Vietnam, an area of more than 1.000 km2 with the depths varying from 1 to more than 100 m, weathered crust from 1 m to more than 30 m, would be a potential source of gem–quality zircon for jewelry gemstone.

Study on the xanthine oxidase inhibitory activity of some medicinal plants in Vietnam

Truong Nhat Van Do — 2024-03-31

Xanthine oxidase is a crucial enzyme catalyzing the hydroxylation of hypoxanthine to xanthine and then xanthine into uric acid. Uric acid undergoes no further metabolism in humans and is excreted by the kidneys and intestinal tract. Hyperuricemia, associated with gout, results from the overproduction or underexcretion of uric acid. Xanthine oxidase inhibitors that block the terminal step in uric acid biosynthesis can lower the plasma uric acid concentration and are generally employed for the treatment of gout. Moreover, superoxide anion radicals generated by xanthine oxidase are involved in various pathological states such as hepatitis, inflammation, ischemia-reperfusion, carcinogenesis and aging. Thus, the search for novel xanthine oxidase inhibitors would be beneficial not only to treat gout but also to combat various other diseases. In this paper, results on investigating of xanthine oxidase inhibitory activity of 22 methanolic extracts from 18 medicinal plants in Vietnam, belonging to Moraceae, Anacardiaceae, Fabaceae, Euphorbiaceae, Boraginaceae, Rutaceae, Taxaceae, Gnetaceae, Plantaginaceae, Musaceae and Sapotaceae family were reported. The results indicated that 21 methanol extracts showed the inhibition at the concentration of 100 µg mL-1, 12 extracts showed greater than 50% inhibition at 100 µg mL-1, 6 showed greater than 50% inhibition at 100 µg mL-1 and 4 demonstrated over 50% inhibition at 25 µg mL-1. Among them, the methanol extracts from the stem of Buchanania lucida and Swintonia floribunda, belonging to Dipterocarpaceae family, displayed the highest xanthine oxidase inhibitors activity, with the IC50 values of 14.20 µg mL-1 and 15.76 µg mL-1, respectively. To the best of our knowledge, this is the first time that these extracts possessing the xanthine oxidase inhibitors activity were reported. The results of this study suggest that these herbs have potential for the treatment of rheumatism and inflammatory in Vietnam.

Effect of hydrochloric acid on the phase composition of cellulose/TiO2 composites fabricated by hydrothermal method

An Nang Vu — 2024-03-31

The cellulose nanocrystals (CNC), isolated from the agricultural by-products of Vietnamese rice husks by chemical method, were used as substrates for synthesizing CNC/TiO2 composites by the hydrothermal method in a hydrochloric acid (HCl) condition. The morphological structure, properties and crystal properties of the obtained products CNC/TiO2 were characterized by Fourier-transform infrared spectroscopy (FT-IR), energy dispersive X-ray spectroscopy (EDX), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and X-ray diffraction (XRD). The XRD results showed that HCl concentration affected the formation and phase transitions of TiO2. The increase of HCl concentration and Cl- ions content in the hydrothermal solution created favorable conditions for the formation of TiO2 brookite phase. The TiO2 brookite phase accelerated the transition from the TiO2 anatase phase to the TiO2 rutile phase. HCl, a catalyst changing the crystallization and reducing the activation energy, facilitated the formation of the TiO2 rutile phase. The phase transition between the allotropic forms of TiO2 greatly influenced the morphology of the CNC/TiO2 composite. The photocatalytic activity of CNC/TiO2 materials was investigated through methylene blue (MB) decomposition under UVA radiation. The results showed that the MB decomposition efficiency of CNC/TiO2 materials depended on the phase composition and crystalline size. The smaller crystalline size of CNC/TiO2 and the presence of TiO2 in both anatase and TiO2 rutile phases gave a better photocatalytic activity of the CNC/TiO2 compared to the pure TiO2 or to the commercial TiO2 (Degussa P25).

Exploring the species distribution and origin biodiversity of the freshwater fish at the Lang Biang plateau, Vietnam

Huy Đức Hoàng — 2024-03-31

Freshwater fish at the Lang Biang plateau, an important source of protein and sportfishing for the local people, remains poorly known. This lacking, due to the poor surveying and a situation of taxonomic chaos throughout Vietnam, makes difficulties in accurately identifying specimens and interpreting the published survey results. Our study from 2011 to 2022 on revising the indigenous fish fauna provided the phylogenetic relationship and the geographic distribution. The studied fish species were classified and phylogenetically deduced based on the molecular biology. The evolutionary and phylogenetic relationships, integrated the modified global fish phylogenetic data and delineated factors of fish distribution, were also discussed. A total of 55 indigenous species, belonging to 47 genera, 22 families, 07 orders from 444 specimens collected at seven sampling sites, were identified. Cypriniformes with 37 species (67%) was the most diverse order. Biogeographically, three distinct fish faunas occurred in the Lang Biang plateau: one associated with the Kratie–Stung Treng freshwater ecoregion, one with the Mekong delta, and the third with the Southern Annam. Fishes in the Lang Biang plateau’s middle are not particularly rich in species, but the percentage of endemic taxa is high (13% of 7 species). These species were suckers with flattened bodies in adaptation to the swift waterflow in the area.

Triterpene and phenolic compounds from the n-hexane extract of the lichen Usnea aciculifera (Parmeliaceae)

Quyên Hồng Ngọc Trần — 2024-03-31

The genus Usnea of the family Parmeliaceae, a genus of mainly light gray-green fruticose lichens that grow like mini shrubs without leaves or tendrils anchored on bark or branches, with about 350 known species growing in European boreal forests, but they are most commonly found in tropical and subtropical regions. In the traditional Chinese medicine, the lichen Usnea aciculifera is used to treat bladder infections, painful urination, urinary retention, and swollen kidneys. In Vietnam, there are still few studies on the chemical constituents and the biological activity of this lichen. The chemical studies of some species of the genus Usnea showed phenolic compounds, depsides, depsidones, dibenzofurans, xanthones, triterpenoids, steroids, macrolactones, quinones, phthalides and fatty, many of these compounds show biological activities such as anti-bacterial, anti-inflammatory, enzyme -glucosidase inhibition, and inhibition of cancer cell lines. From the fraction 5 of the n-hexane extract of the lichen Usnea aciculifera (Parmeliaceae), collected at Da Lat city, Lam Dong province, six phenolic and one triterpenic compounds were isolated. The chemical structures of these compounds were elucidated by one- and two-dimensional nuclear magnetic resonance spectroscopy, ESI-MS mass spectrometry, and HR-ESI-MS high-resolution mass spectrometry. They are ethyl 2,4-dimethoxy-3,6-dimethylbenzoate (1); ethyl 2,4-dihydroxy-3,6-dimethylbenzoate (2); -methyl orsellinate (3); methyl 2-hydroxy-4-methoxy-3,6-dimethylbenzoate (4); methyl haematomate (5); methyl 2,6-dihydroxy-4-methyl benzoate (6) and zeorin (7).

Tadpole identification and description of Marten’s Oriental Frog Occidozyga martensii based on marker 16S rRNA in Di Linh Plateau, Vietnam

Phuong Anh Tran Do — 2024-03-31

The tadpole identification can support providing important information on the larval stage of amphibian species, which helps for studying the conservation, ecology, and life history of them. Based on morphological and molecular data, this study accurately identified the tadpoles of Marten’s Oriental Frog Occidozyga martensii which had been recorded in the Di Linh Plateau, Lam Dong province. These tadpole specimens were collected in the wet season, July and August 2022. Analyzing the morphology and molecule of the tadpoles, amplifying the 16S rRNA marker by using a pair of primers AH-16S_S and AH-16S_R. Their 16S rRNA sequences matched to those collected at the type locality of O. martensii in Bangkok (Thailand) and closely related to those of O. laevis collected in Philippines. The results provided detailed morphological description of O. martensii tadpoles at stage 37 and the morphological changes from stage 37 to 41, with diagnostic characteristics: upper fin originates far posterior to trunk-tail junction, at approximately 17% of tail length, with black short-stripes in front of eyes and black short-stripe behind mouth, brown belly with many white spots. The tadpole morphology of O. martensii most resembles tadpole of O. laevis when compared with all congeners in genus Occidozyga. O. martensii differs from O. laevis in only having black short-stripes in front of eyes. It is easily confused when identifying these two species by their morphological characteristics. However, the molecular data from this study and previous studies suggested that O. martensii is a different taxon from O. laevis. These results from this study indicated the necessity of molecular methods in the identification of amphibians. The morphological and molecular data of O. martensii tadpole are helpful for the next taxonomic studies and management of Oriental Frog Occidozyga species in the future.

Phenolic compounds from the bark of Swietenia microphylla

Dương Hoàng Trịnh — 2024-03-31

Meliaceae, a large plant family with approximately 50 genera and 650 known species, mostly distributed in the pantropical regions of the world. Swietenia, a genus of the family Meliaceae, comprises 7−8 species which was widely used in the manufacture of furniture, food and traditional medicine. Previous studies revealed that Swietenia mainly contained limonoids, terpenoids, steroids and phenolic compounds. Antibacterial, antifungal, antimalarial, anticancer, antiviral activities of the isolated compounds and extracts of the genus were also reported. Swietenia microphylla is a species of genus Swietenia whose phytochemical composition and biological activities have not been studied. This paper showed the results of isolation and structural elucidation of five phenolic compounds from an ethyl acetate extract of Swietenia microphylla bark, collected at Trang Bom botanical garden, Dong Nai province. Dried and ground barks of the species were extracted with ethyl acetate by Soxhlet extraction. The ethyl acetate extract, obtained after removal of the solvent via rotary evaporation, was separated using column chromatography on silica gel and Sephadex LH-20. Chemical structures of isolated compounds were elucidated by analysis of 1D, 2D-NMR, HRESIMS spectra and comparison of the spectral data with relevant literature. They were identified as scopoletin (1), 3,4-dihydroxybenzoic acid (2), (+)-epiafzelechin (3) and a mixture at a 6:4 ratio of (+)-catechin (4) and (+)-epicatechin (5). All the compounds have been reported for the first time from this species.