Freeprotmap: waiting-free prediction method for protein distance map.

BACKGROUND: Protein residue-residue distance maps are used for remote homology detection, protein information estimation, and protein structure research. However, existing prediction approaches are time-consuming, and hundreds of millions of proteins are discovered each year, necessitating the development of a rapid and reliable prediction method for protein residue-residue distances. Moreover, because many proteins lack known homologous sequences, a waiting-free and alignment-free deep learning method is needed. RESULT: In this study, we propose a learning framework named FreeProtMap. In terms of protein representation processing, the proposed group pooling in FreeProtMap effectively mitigates issues arising from high-dimensional sparseness in protein representation. In terms of model structure, we have made several careful designs. Firstly, it is designed based on the locality of protein structures and triangular inequality distance constraints to improve prediction accuracy. Secondly, inference speed is improved by using additive attention and lightweight design. Besides, the generalization ability is improved by using bottlenecks and a neural network block named local microformer. As a result, FreeProtMap can predict protein residue-residue distances in tens of milliseconds and has higher precision than the best structure prediction method. CONCLUSION: Several groups of comparative experiments and ablation experiments verify the effectiveness of the designs. The results demonstrate that FreeProtMap significantly outperforms other state-of-the-art methods in accurate protein residue-residue distance prediction, which is beneficial for lots of protein research works. It is worth mentioning that we could scan all proteins discovered each year based on FreeProtMap to find structurally similar proteins in a short time because the fact that the structure similarity calculation method based on distance maps is much less time-consuming than algorithms based on 3D structures.

Chitosan-based nanopesticides enhanced anti-fungal activity against strawberry anthracnose as "sugar-coated bombs".

A chitosan-based nanoparticle was prepared using chitosan (CS) and O-carboxymethyl chitosan (O-CMCS). Our study revealed that chitosan/O-carboxymethyl chitosan/tebuconazole nanoparticles (CS/O-CMCS/TBA NPs) exhibited superior antifungal activity, foliar adhesion, and microbial target adhesion performance compared to commercial suspension concentrate (SC). The antifungal activity of CS/O-CMCS/TBA NPs against C. gloeosporioides, with a 3.13-fold increase in efficacy over TBA (SC). We also found that low concentrations of CS/O-CMCS NPs promoted the growth of C. gloeosporioides and enhanced the fungal catabolism of chitosan. Overall, the CS/O-CMCS/TBA NPs were found to possess the remarkable capability to selectively aggregate around pathogenic microorganisms and CS/O-CMCS NPs can enhance the fungal catabolism of chitosan. CS/O-CMCS/TBA NPs, as a "sugar-coated bomb", was a promising asset for effective plant disease management and pesticide utilization through the affinity of chitosan-based nanoparticles and C. gloeosporioides, enabling targeted delivery and targeted release of their encapsulated active ingredient, which was important for the development and application of biocompatible chitosan-based nanopesticides.

Effect of bifenthrin application at different maturity stages on its dissipation and residues in kumquat (Citrus japonica) and dietary intake risk assessment.

Bifenthrin is a pyrethroid pesticide widely used on kumquats, but the residues in the peel and pulp after bifenthrin application at different maturity stages of kumquats have not been evaluated. This study developed a simple and rapid high-performance liquid chromatography (HPLC) method for the quantitative analysis of bifenthrin residues in whole fruit, kumquat peel, kumquat pulp, and soil. The results showed that regardless of whether bifenthrin was applied one or three times during the near-mature period, the half-lives of the fruit peel and fruit pulp were longer than those in the immature period. Kumquat fruit residues decreased with time at both maturity levels. The residues of bifenthrin in near-mature fruit exceeded the MRL in Guangxi and Fujian 14 days after the three applications of bifenthrin, suggesting that this issue should be focused on in kumquat production and supervision. However, for bifenthrin application in either the near-mature or the immature fruit period, the calculated risks for chronic dietary intake of kumquat were well below 100%. The data demonstrate that the chronic dietary intake risk of bifenthrin through kumquat consumption is low and within acceptable limits. These results provide a reference and risk assessment data for the safe and rational use of bifenthrin insecticides.

Dissipation and Distribution of Prochloraz in Bananas and a Risk Assessment of Its Dietary Intake.

BACKGROUND: As a systematic fungicide, prochloraz is often used to control banana freckle disease, and it is significant to assess the safety and risk of prochloraz. METHODS: The dissipation kinetics and distribution of prochloraz in bananas were measured by high-performance liquid chromatography (HPLC). RESULTS: The results showed that the fortified recoveries in bananas were 83.01-99.12%, and the relative standard deviations (RSDs) were 2.45-7.84%. The half-life of prochloraz in banana peel (3.93-5.60 d) was significantly lower than it was in whole banana (8.25-10.80 d) and banana pulp (10.35-12.84 d). The terminal residue of prochloraz in banana fruits was below the maximum residue level (MRL, China) at pre-harvest intervals (PHI) of 21 d. Moreover, the residue of prochloraz in banana peel was always 1.06-7.71 times greater than it was in banana pulp. The dietary risk assessment results indicated that the prochloraz residue in bananas at PHI of 21 d was safe for representative populations. (4) Conclusions: We found that a 26.7% prochloraz emulsion oil in water (EW) diluted 1000-fold and sprayed three times under field conditions was safe and reliable, providing a reference for the safe application of prochloraz in bananas.

The validity, reliability and feasibility of four instruments for assessing the consciousness of stroke patients in a neurological intensive care unit compared.

BACKGROUND: Early rehabilitation is the foundation for recovery for those admitted to an intensive care unit. Appropriate assessment of consciousness is needed before any rehabilitative intervention begins. METHODS: This prospective study compared the validity, reliability and applicability of the sedation-agitation scale, the Richmond Agitation-Sedation Scale, the motor activity assessment scale and the Glasgow Coma Scale in a working neurological intensive care unit. Eighty-three stroke patients were assessed with the four scales by the same 3 raters acting independently: a senior physician, a senior therapist and a trainee. That generated 996 assessment records for comparison. RESULTS: Good agreement (r=0.98-0.99) was found among the sedation-agitation scale, the Richmond Agitation-Sedation Scale, the motor activity assessment scale scores, but the Glasgow Coma Scale ratings correlated less well (r=0.72-0.76) with the others. Consistent results were also found among the three raters. After stratification of the ratings by age, gender, level of consciousness and Acute Physiology and Chronic Health Evaluation score, the scales reported significant differences among the levels of consciousness and among those with different Acute Physiology and Chronic Health Evaluation results, but not with different age or gender strata. CONCLUSIONS: The four instruments tested are all reliable enough and feasible for use as a tool for consciousness screening in a neurological intensive care unit.

Identification of RoCYP01 (CYP716A155) enables construction of engineered yeast for high-yield production of betulinic acid.

Betulinic acid (BA) and its derivatives possess potent pharmacological activity against cancer and HIV. As with many phytochemicals, access to BA is limited by the requirement for laborious extraction from plant biomass where it is found in low amounts. This might be alleviated by metabolically engineering production of BA into an industrially relevant microbe such as Saccharomyces cerevisiae (yeast), which requires complete elucidation of the corresponding biosynthetic pathway. However, while cytochrome P450 enzymes (CYPs) that can oxidize lupeol into BA have been previously identified from the CYP716A subfamily, these generally do not seem to be specific to such biosynthesis and, in any case, have not been shown to enable high-yielding metabolic engineering. Here RoCYP01 (CYP716A155) was identified from the BA-producing plant Rosmarinus officinalis (rosemary) and demonstrated to effectively convert lupeol into BA, with strong correlation of its expression and BA accumulation. This was further utilized to construct a yeast strain that yields > 1 g/L of BA, providing a viable route for biotechnological production of this valuable triterpenoid.

High-Level Butanol Production from Cassava Starch by a Newly Isolated Clostridium acetobutylicum.

A new Clostridium acetobutylicum strain, exhibiting the ability to resist butanol stress and produce butanol, was identified and named GX01. Strain GX01 can use a wide variety of carbohydrates, especially cassava starch, to produce butanol. After the optimization of culture conditions, C. acetobutylicum GX01 could produce 27.3 g/L solvent, including 17.1 g/L butanol, 7.9 g/L acetone, and 2.3 g/L ethanol, from 100 g/L cassava flour and 3 g/L soybean meal. Furthermore, when its acetone-butanol-ethanol (ABE) fermentation was performed in 10- and 30-L bioreactors, the production of total solvent and butanol reached 29.2 and 18.3 g/L, respectively, and 28.8 and 18.8 g/L, respectively. Thus, the high level and stability of butanol production make strain GX01 a promising candidate for ABE fermentation using the low-cost cassava starch.