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-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-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-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

Promoted Hydrogen Peroxide Production from Pure Water on g-C3N4 with Nitrogen Defects Constructed through Solvent-Precursor Interactions: Exploring A Complex Story in Piezo-Photocatalysis

Hydrogen peroxide (H2O2) production via oxygen (O2) reduction reaction (ORR) in pure water (H2O) through graphitic carbon nitrides (g-C3N4)-based piezo-photocatalysts is an exciting approach in many current studies. However, the low Lewis-acid properties of g-C3N4 limited the catalytic performance because of the low O2 adsorption efficacy. To overcome this challenge, we utilized the interaction of g-C3N4 precursors with various solvents to synthesize g-C3N4, possessing multiple nitrogen-vacant species via thermal shocking polymerization. Our results suggest that the lack of nitrogen in g-C3N4 and the incident introduction of oxygen-functional groups enhance the Lewis acid-base interactions and polarize the g-C3N4 lattices, leading to the enormous enhancement, roughly 7 times from the optimal samples compared to pristine g-C3N4 in pure water via piezo-photocatalysis. Meanwhile, we also observed the correlation between the charge separation kinetic and the crystalline degree of the synthesized materials, which can elucidate how the nitrogen defects impacted the catalytic outcomes. Furthermore, the catalytic mechanisms were thoroughly studied, with the formation of H2O2 proceeding via radical and water oxidation pathways, in which the roles of light and ultrasound were carefully investigated. Thus, our findings not only reinforce the potential view of metal-free photocatalysts, accelerating the understanding of g-C3N4 working principles to generate H2O2 based on the oxygen reduction and water oxidation reactions, but also propose a facile one-step way for fabricating highly efficient and scalable photocatalysts to produce H2O2 without using sacrificial agents, pushing the practical application of in-situ solar H2O2 toward real-world scenarios

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field