Curation and analysis of tRNA and aminoacyl-tRNA synthetase genes in the nuclear genome of Myceliophthora thermophila

Transfer ribonucleic acids (tRNAs) and aminoacyl-tRNA synthetases (AARSs) have long been known for their indispensable roles in the translational process to synthesize proteins in living cells. Therefore, detecting and analyzing the comprehensive sets of tRNA and AARS genes would enhance understanding of the translation system and the results could potentially be used to optimize the translation efficiency for the protein production in the organisms of interest. This research aims to detect the complete sets of cytoplasmic tRNA genes and AARS genes from the nuclear genome of Myceliophthora thermophila, a filamentous fungus used in the enzyme production industry and the first thermophilic eukaryote with a finished genome sequence. In this study, 194 cytoplasmic tRNA genes and 35 aminoacyl-tRNA synthetase genes in M. thermophila were determined by comparing the gene models predicted from the genome with the sequenced RNAs and the experimentally characterized tRNA and AARS genes. The experimentally verified tRNA genes in M. thermophila can encode all of the 20 universal amino acids. The 35 AARS genes code for cytoplasmic and mitochondrial AARS enzymes of all of the 20 amino acid specificities except for the mitochondrial glutaminyl-tRNA synthetase. Four commonly used tools – tRNAscan-SE, SPLITSX, ARAGORN and tRNAfinder – were deployed for the tRNA gene prediction, and we showed that tRNAscan-SE and SPLITSX give more accurate results than ARAGORN and tRNAfinder. Analysis of the tRNA genes showed that there are significant correlations between tRNA gene number in the genome and tRNA abundance in the cell, as well as between tRNA gene number and codon usage bias of protein-encoding genes in M. thermophila. Based on the complete tRNA gene set and the codon frequencies in the protein-encoding gene set, a set of preferred codons in M. thermophila was determined. The manually curated tRNA and AARS genes of M. thermophila, as well as the experimentally characterized ones collected from tRNA and protein databases along with the supporting literature provided in this study, can be used as reliable datasets for tRNA and AARS gene annotation processes

Characterization of a novel AA3_1 xylooligosaccharide dehydrogenase from Thermothelomyces myriococcoides CBS 398.93

Background: The Carbohydrate-Active enZymes (CAZy) auxiliary activity family 3 (AA3) comprises flavin adenine dinucleotide-dependent (FAD) oxidoreductases from the glucose-methanol-choline (GMC) family, which play auxiliary roles in lignocellulose conversion. The AA3 subfamily 1 predominantly consists of cellobiose dehydrogenases (CDHs) that typically comprise a dehydrogenase domain, a cytochrome domain, and a carbohydrate-binding module from family 1 (CBM1).Results: In this work, an AA3_1 gene from T. myriococcoides CBS 398.93 encoding only a GMC dehydrogenase domain was expressed in Aspergillus niger. Like previously characterized CDHs, this enzyme (TmXdhA) predominantly accepts linear saccharides with beta-(1 -> 4) linkage and targets the hydroxyl on the reducing anomeric carbon. TmXdhA was distinguished, however, by its preferential activity towards xylooligosaccharides over cellooligosaccharides. Amino acid sequence analysis showed that TmXdhA possesses a glutamine at the substrate-binding site rather than a threonine or serine that occupies this position in previously characterized CDHs, and structural models suggest the glutamine in TmXdhA could facilitate binding to pentose sugars.Conclusions: The biochemical analysis of TmXdhA revealed a catalytic preference for xylooligosaccharide substrates. The modeled structure of TmXdhA provides a reference for the screening of oxidoreductases targeting xylooligosac-charides. We anticipate TmXdhA to be a good candidate for the conversion of xylooligosaccharides to added-value chemicals by its exceptional catalytic ability.Peer reviewe

Village Baseline Study: Site Analysis Report for Tra Hat Village, Vinh Loi, Bac Lieu, Viet Nam (VNM 03)

This report presents data collected from the Village Baseline Study conducted on 2-4 October 2014 at the Tra Hat village, Vinh Loi district, Bac Lieu, Vietnam. Data were collected through focus group discussions and participatory resource mapping with community members in the village. The Village Baseline Study is part of the baseline activities conducted under the CGIAR Research Program on Climate Change, Agriculture, and Food Security (CCAFS) in South East Asia. The purpose is to collect data for indicators that will allow site comparability and monitoring to assess changes in terms of food security and natural resource management across time. Results show that the men and women in Tra Hat village consider farmland, rivers and canals as important natural resources. The quality, however, of land, water and wildlife habitats has declined in the last decade along with the improvement of farming techniques and intensive use of chemical fertilizers and pesticides. Infrastructures such as roads, internal canals, hospitals, schools, water supply station and electricity transformer station have improved. The future is envisioned to have improved internal canals in farmlands and a developed irrigation system, dykes and sluices to support high agriculture production. Home garden diversification was also believed to enhance food security and improve livelihood resilience. To turn the vision into reality, the community expects support from the different organizations working in the area considering current impacts of salinity intrusion and sea level rise, the need interventions of CCAFS and its partners. Strengthening the irrigation system, improving local rice variety, and introducing modern farming techniques taking into account negative impacts of climate change are major recommendation for future intervention

QUÁ TRÌNH CHUYỂN PHA PHI CÂN BẰNG CỦA VẬT LIỆU HAI CHIỀU PENTA-GRAPHENE

Graphene has received enormous attention in the semiconductor industry during the last two decades. However, since graphene is a gapless semiconductor, it has critical challenges to be engineered into semiconductor devices. Recent reports have shown that penta-graphene stands out as a promising semiconductor candidate with an electronic bandgap between 2.2 and 4.3 eV; thus, it can surmount graphene’s obstacles. However, when being heated, penta-graphene can transform its configurations from pentagonal lattices to hexagonal graphene-like heterostructures, resulting in a significant electronic modification. In this paper, we investigate the effect of heating rates on the non-equilibrium phase transition of a two-dimensional penta-graphene by using molecular dynamic simulations. We have shown that, with a fast-heating process, penta-graphene naturally transforms to graphene without a clear phase separation point. Nevertheless, with a sufficiently slow heating protocol, this transition is a first-order phase transition from a pentagonal to a more stable hexagonal configuration. These results provide the possibility to implement penta-graphene in future optoelectronic devices.Graphene đã được chứng minh là vật liệu mang tính đột phá cho ngành vật liệu bán dẫn. Tuy nhiên, với độ rộng vùng cấm gần như bằng không, graphene có những hạn chế nhất định khi được ứng dụng để chế tạo linh kiện điện tử. Các nghiên cứu gần đây cho thấy penta-graphene với độ rộng vùng cấm 2,2–4,3 eV và độ bền cơ – nhiệt cao có thể dung hòa nhược điểm của graphene. Tuy nhiên, khi bị nung nóng, penta-graphene có thể chuyển từ cấu trúc vòng 5 điển hình sang cấu trúc vòng 6 của graphene, nhưng điều kiện cụ thể để quá trình chuyển pha này hình thành vẫn chưa được nghiên cứu chi tiết. Trong bài báo này, chúng tôi nghiên cứu sự ảnh hưởng của tốc độ nung đến tính chất nhiệt động phi cân bằng của penta-graphene bằng phương pháp mô phỏng động học phân tử. Ở tốc độ nung lớn, penta-graphene sẽ dần chuyển sang graphene mà không có điểm chuyển pha rõ nét. Tuy nhiên, nếu penta-graphene được nung rất chậm, quá trình chuyển pha từ penta-graphene sang graphene là quá trình chuyển pha loại I với sự gián đoạn của thông số nhiệt động tại điểm chuyển pha. Kết quả này sẽ góp phần bổ sung các thông số kỹ thuật quan trọng trong việc ứng dụng vật liệu penta-graphene để chế tạo các linh kiện quang – điện tử trong tương lai

Prospects of Blended Learning Implementation at FPT University Can Tho, Vietnam

Drawing on the evaluations of students’ attitudes toward learning aspects the mixed-method research aims to examine the prospects of Blended Learning at FPT University in Can Tho. Four hundred sixty-seven students partook in the study by providing answers for a 30-item questionnaire with open-ended questions. The results showed that most students have positive attitudes towards factors constructing their Blended Learning adaptability, including (1) Study Management and Online Learning, (2) Classroom Learning, and (3) Learning Flexibility. The results of Binary Logistic Regression also clarified the good promise of Blended Learning implementation and the discovery of other concerns that hindered informants’ willingness, namely Worriment about Learning Effectiveness, Online Learning Barriers, and Learners’ Ego. The research findings served as a reference for FPT University and other higher institutions to better grasp how students perceive Blended Learning to develop strategies for successful practices

A preliminary study to establish the transfected CHO cell lines which highly express Trastuzumab - A biosimilar product of Herceptin

Human epidermal growth factor receptor 2 (HER2) has been identified as a molecular target for breast cancer therapy, such as Trastuzumab (Herceptin®). This has been shown to improve patient survival substantially. The current study is aiming to locally produce an anti-HER2 monoclonal antibody (named Trastuzumab) which has an equivalent biological properties in comparison with the original version, Herceptin®). In silico design and construction of recombinant vectors, as well as the establishment of transfected cell lines with high expression of Trastuzumab were performed. Based on the protein sequences obtained from the Drugbank, the DNA sequences encoding for the light chain (Tras-Lc) and heavy chain (Tras-Hc) of Trastuzumab were optimized and integrated into pNanogen-Hygro and pNanogen-Puro vectors, respectively. The Neon Transfection System was used to co-transfect the pNanogen-Tras-Lc-Hygro and pNanogen-Tras-Hc-Puro constructs into CHO cells. Different co-transfected single-cell-colonies selected on media supplemented with hygromycin and puromycin were used for ELISA and SDS-PAGE assays to identify the CHO cell lines which highly express Trastuzumab. Based on the present results, 30μg of both constructs were suitable for DNA co-transfection. After 07 days of culture, the highest amount of Trastuzumab (561 µg/ml) was obtained from the H06LD68 cell line

Kinetics of neutralizing antibodies against Omicron variant in Vietnamese healthcare workers after primary immunization with ChAdOx1-S and booster immunization with BNT162b2

We studied the development and persistence of neutralizing antibodies against SARS-CoV-2 ancestral strain, and Delta and Omicron (BA.1 and BA.2) variants in Vietnamese healthcare workers (HCWs) up to 15 weeks after booster vaccination. We included 47 HCWs, including group 1 (G1, N = 21) and group 2 (G2; N = 26) without and with breakthrough Delta variant infection before booster immunization, respectively). The study participants had completed primary immunization with ChAdOx1-S and booster vaccination with BNT162b2. Neutralizing antibodies were measured using a surrogate virus neutralization assay. Of the 21 study participants in G1, neutralizing antibodies against ancestral strain, Delta variant, BA.1, and BA.2 were (almost) abolished at month 8 after the second dose, but all had detectable neutralizing antibodies to the study viruses at week 2 post booster dose. Of the 26 study participants in G2, neutralizing antibody levels to BA.1 and BA.2 were significantly higher than those to the corresponding viruses measured at week 2 post breakthrough infection and before the booster dose. At week 15 post booster vaccination, neutralizing antibodies to BA.1 and BA.2 dropped significantly, with more profound changes observed in those without breakthrough Delta variant infection. Booster vaccination enhanced neutralizing activities against ancestral strain and Delta variant compared with those induced by primary vaccination. These responses were maintained at high levels for at least 15 weeks. Our findings emphasize the importance of the first booster dose in producing cross-neutralizing antibodies against Omicron variant. A second booster to maintain long-term vaccine effectiveness against the currently circulating variants merits further research

THÀNH PHẦN HÓA HỌC VÀ HOẠT TÍNH KHÁNG VI SINH VẬT GÂY BỆNH CỦA TINH DẦU TỪ VỎ BƯỞI DA XANH (Citrus maxima (Burm.) Merr.)

Pomelo is a Vietnam’s plant species with high nutritional and economic value. Besides, pomelo essential oil contains numerous compounds with high biological activity. The essential oil is extracted by using steam distillation, and its chemical composition is determined by means of GC-MS. The major components are limonene (91.19%), b-myrcene (2.92%), a-phellandrene (1.98%), and a-pinene (1.19%). The antimicrobial activity of essential oils is tested against pathogenic Gram-positive bacteria (Bacillus cereus, Staphylococcus aureus), Gram-negative bacteria (Escherichia coli), and Aspergillus flavus at different concentrations with the agar well diffusion method. This essential oil is active against B. cereus, S. aureus, and E. coli with inhibition diameter zones at 8.3–11.3, 10.3–18.7, and 9.0–11.7 mm, respectively, and inhibits A. flavus mold with 18.9–65.0% efficiency.Bưởi là loài cây không chỉ có giá trị cao về mặt dinh dưỡng mà còn có giá trị cao về mặt kinh tế và được trồng phổ biến ở Việt Nam. Ngoài ra, tinh dầu bưởi chứa nhiều hợp chất có hoạt tính sinh học cao. Tinh dầu bưởi được chiết xuất bằng phương pháp chưng cất lôi cuốn hơi nước và thành phần hóa học được phân tích bằng phương pháp GC-MS. Thành phần chính của tinh dầu gồm limonene (91,19%), b-myrcene (2,92%), a-phellandrene (1,98%) và a-pinene (1,19%). Hoạt tính kháng vi sinh vật của tinh dầu được khảo sát với vi khuẩn Gram dương (Bacillus cereus, Staphylococcus aureus), Gram âm (Escherichia coli) và nấm mốc Aspergillus flavus ở nồng độ 5, 10, 25 và 50% bằng phương pháp khuếch tán giếng thạch. Tinh dầu có khả năng kháng B. cereus, S. aureus và E. coli với đường kính vòng kháng khuẩn lần lượt là 8,3–11,3, 10,3–18,7 và 9,0–11,7 mm và ức chế sự phát triển của A. flavus (18,9–65,0%)