Isolation and characterization of a c-repeat binding factor gene from Tevang-1 maize cultivar

C-repeat binding factor (CBF) proteins are transcription factors involved in plant response to abiotic stresses, especially low-temperature condition. In this research, a CBF3-coding gene was isolated from a cold-acclimation maize variety, Zea mays var. Tevang-1 and denoted as ZmCBF3tv. The isolated gene shared 96.49% homology with the B73-reference gene and had no intron in the coding sequence. By using bioinformatic tools, a number of variations in the nucleotide and amino acid sequences were identified. An alignment between ZmCBF3tv and other CBF/DREB1 proteins from various species revealed functional regions and typical features, such as nuclear localization signal (NLS), the AP2 DNA-binding domain, and acidic-amino-acid-rich segments. Additionally, a phylogenetic analysis based on the AP2 domain showed that the maize CBF3 transcription factor had the highest similarity with that from rice and closely related to other DREB1/CBF protein of monocots. The function of the ZmCBF3tv product is suggested to be a CBF/DREB1 transcription factor.    

Prediction of potential drug targets based on simple sequence properties

<p>Abstract</p> <p>Background</p> <p>During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification and validation of new and effective drug targets are of great value for drug discovery in both academia and pharmaceutical industry. If a protein can be predicted in advance for its potential application as a drug target, the drug discovery process targeting this protein will be greatly speeded up. In the current study, based on the properties of known drug targets, we have developed a sequence-based drug target prediction method for fast identification of novel drug targets.</p> <p>Results</p> <p>Based on simple physicochemical properties extracted from protein sequences of known drug targets, several support vector machine models have been constructed in this study. The best model can distinguish currently known drug targets from non drug targets at an accuracy of 84%. Using this model, potential protein drug targets of human origin from Swiss-Prot were predicted, some of which have already attracted much attention as potential drug targets in pharmaceutical research.</p> <p>Conclusion</p> <p>We have developed a drug target prediction method based solely on protein sequence information without the knowledge of family/domain annotation, or the protein 3D structure. This method can be applied in novel drug target identification and validation, as well as genome scale drug target predictions.</p

sj-pptx-2-sci-10.1177_00368504221148843 - Supplemental material for Evolutionary analysis and expression profiling of the <i>HSP70</i> gene family in response to abiotic stresses in tomato (<i>Solanum lycopersicum</i>)

Supplemental material, sj-pptx-2-sci-10.1177_00368504221148843 for Evolutionary analysis and expression profiling of the HSP70 gene family in response to abiotic stresses in tomato (Solanum lycopersicum) by Nam Tuan Vu, Ngoc Bich Thi Nguyen, Hanh Hong Ha, Linh Nhat Nguyen, Ly Han Luu, Ha Quang Dao, Trinh Thi Vu, Hue Thu Thi Huynh and Hien Thu Thi Le in Science Progress</p

sj-xlsx-1-sci-10.1177_00368504221148843 - Supplemental material for Evolutionary analysis and expression profiling of the <i>HSP70</i> gene family in response to abiotic stresses in tomato (<i>Solanum lycopersicum</i>)

Supplemental material, sj-xlsx-1-sci-10.1177_00368504221148843 for Evolutionary analysis and expression profiling of the HSP70 gene family in response to abiotic stresses in tomato (Solanum lycopersicum) by Nam Tuan Vu, Ngoc Bich Thi Nguyen, Hanh Hong Ha, Linh Nhat Nguyen, Ly Han Luu, Ha Quang Dao, Trinh Thi Vu, Hue Thu Thi Huynh and Hien Thu Thi Le in Science Progress</p

sj-docx-3-sci-10.1177_00368504221148843 - Supplemental material for Evolutionary analysis and expression profiling of the <i>HSP70</i> gene family in response to abiotic stresses in tomato (<i>Solanum lycopersicum</i>)

Supplemental material, sj-docx-3-sci-10.1177_00368504221148843 for Evolutionary analysis and expression profiling of the HSP70 gene family in response to abiotic stresses in tomato (Solanum lycopersicum) by Nam Tuan Vu, Ngoc Bich Thi Nguyen, Hanh Hong Ha, Linh Nhat Nguyen, Ly Han Luu, Ha Quang Dao, Trinh Thi Vu, Hue Thu Thi Huynh and Hien Thu Thi Le in Science Progress</p

Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen

The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats’ rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes’ modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter