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[学术文献 ] DIProT: A deep learning based interactive toolkit for efficient and effective Protein design 进入全文
Synthetic and Systems Biotechnology
The protein inverse folding problem, designing amino acid sequences that fold into desired protein structures, is a critical challenge in biological sciences. Despite numerous data-driven and knowledge-driven methods, there remains a need for a user-friendly toolkit that effectively integrates these approaches for in-silico protein design. In this paper, we present DIProT, an interactive protein design toolkit. DIProT leverages a non-autoregressive deep generative model to solve the inverse folding problem, combined with a protein structure prediction model. This integration allows users to incorporate prior knowledge into the design process, evaluate designs in silico, and form a virtual design loop with human feedback. Our inverse folding model demonstrates competitive performance in terms of effectiveness and efficiency on TS50 and CATH4.2 datasets, with promising sequence recovery and inference time. Case studies further illustrate how DIProT can facilitate user-guided protein design.
[政策法规 ] Risks for animal health related to the presence of ergot alkaloids in feed 进入全文
European Food Safety Authority
The European Commission requested EFSA to provide an update of the 2012 Scientific Opinion of the Panel on Contaminants in the Food Chain (CONTAM) on the risks for animal health related to the presence of ergot alkaloids (EAs) in feed. EAs are produced by several fungi of the Claviceps and Epichloë genera. This Opinion focussed on the 14 EAs produced by C. purpurea (ergocristine, ergotamine, ergocornine, α‐ and β‐ergocryptine, ergometrine, ergosine and their corresponding ‘inine’ epimers). Effects observed with EAs from C. africana (mainly dihydroergosine) and Epichloë (ergovaline/−inine) were also evaluated. There is limited information on toxicokinetics in food and non‐food producing animals. However, transfer from feed to food of animal origin is negligible. The major effects of EAs are related to vasoconstriction and are exaggerated during extreme temperatures. In addition, EAs cause a decrease in prolactin, resulting in a reduced milk production. Based on the sum of the EAs, the Panel considered the following as Reference Points (RPs) in complete feed for adverse animal health effects: for pigs and piglets 0.6 mg/kg, for chickens for fattening and hens 2.1 and 3.7 mg/kg, respectively, for ducks 0.2 mg/kg, bovines 0.1 mg/kg and sheep 0.3 mg/kg. A total of 19,023 analytical results on EAs (only from C. purpurea) in feed materials and compound feeds were available for the exposure assessment (1580 samples). Dietary exposure was assessed using two feeding scenarios (model diets and compound feeds). Risk characterisation was done for the animals for which an RP could be identified. The CONTAM Panel considers that, based on exposure from model diets, the presence of EAs in feed raises a health concern in piglets, pigs for fattening, sows and bovines, while for chickens for fattening, laying hens, ducks, ovines and caprines, the health concern related to EAs in feed is low.
[政策法规 ] Persistence of microbiological hazards in food and feed production and processing environments 进入全文
European Food Safety Authority
Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well‐designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a ‘seek‐and‐destroy’ approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom‐up and top‐down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.
[政策法规 ] Guidance for the assessment of detoxification processes in feed 进入全文
European Food Safety Authority
Directive 2002/32/EC of the European Parliament and of the Council, in its article 3, provides that the use of products intended for animal feed which contain levels of undesirable substances exceeding the maximum levels laid down in Annex I of that Directive cannot be placed in the European market. It is possible to use acceptable detoxification processes on these products in order to conform with the provisions of Annex I of that Directive. Commission Regulation (EU) 2015/7862 establishes the acceptability criteria for detoxification processes to ensure that the detoxified feed does not endanger animal and public health and the environment and that the characteristics of the feed are not adversely altered by the detoxification process. The Panel on Contaminants in the food chain (CONTAM Panel) has assessed a series of requests for feed detoxification processes since the entry into force of the Regulation (EU) 2015/786 on 1 July 2017. Frequently the information provided is insufficient for the Panel to come to conclusions if the detoxification process fulfils the criteria set in the legislation and additional clarifications are necessary which prolong the risk assessment process. To help the feed business operators in the preparation and submission of the necessary information for the evaluation of feed detoxification processes according to the Regulation, the CONTAM Panel, in its Plenary meeting on 15 December 2022, identified the need for guidance. The guidance will be provided in a statement addressing the implementation of the criteria for the acceptance of detoxification processes applied to products intended for animal feed, based on the Panel's experience gained during the last years while working under the provisions of the abovementioned Regulation.
[学术文献 ] Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering 进入全文
National Science Review
Enzymes, as paramount protein catalysts, occupy a central role in fostering remarkable progress across numerous fields. However, the intricacy of sequence-function relationships continues to obscure our grasp of enzyme behaviors and curtails our capabilities in rational enzyme engineering. Generative artificial intelligence (AI), known for its proficiency in handling intricate data distributions, holds the potential to offer novel perspectives in enzyme research. Generative models could discern elusive patterns within the vast sequence space and uncover new functional enzyme sequences. This review highlights the recent advancements in employing generative AI for enzyme sequence analysis. We delve into the impact of generative AI in predicting mutation effects on enzyme fitness, catalytic activity and stability, rationalizing the laboratory evolution of de novo enzymes, and decoding protein sequence semantics and their application in enzyme engineering. Notably, the prediction of catalytic activity and stability of enzymes using natural protein sequences serves as a vital link, indicating how enzyme catalysis shapes enzyme evolution. Overall, we foresee that the integration of generative AI into enzyme studies will remarkably enhance our knowledge of enzymes and expedite the creation of superior biocatalysts.
[学术文献 ] An efficient CRISPRCas9 genome editing system based on a multiple sgRNA processing platform in Trichoderma reesei for strain improvement and enzyme production 进入全文
Biotechnology for Biofuels and Bioproducts
Background The CRISPR/Cas9 technology is being employed as a convenient tool for genetic engineering of the industrially important filamentous fungus Trichoderma reesei. However, multiplex gene editing is still constrained by the sgRNA processing capability, hindering strain improvement of T. reesei for the production of lignocellulose-degrading enzymes and recombinant proteins. Results Here, a CRISPR/Cas9 system based on a multiple sgRNA processing platform was established for genome editing in T. reesei. The platform contains the arrayed tRNA−sgRNA architecture directed by a 5S rRNA promoter to generate multiple sgRNAs from a single transcript by the endogenous tRNA processing system. With this system, two sgRNAs targeting cre1 (encoding the carbon catabolite repressor 1) were designed and the precise deletion of cre1 was obtained, demonstrating the efficiency of sgRNAs processing in the tRNA−sgRNA architecture. Moreover, overexpression of xyr1-A824V (encoding a key activator for cellulase/xylanase expression) at the ace1 (encoding a repressor for cellulase/xylanase expression) locus was achieved by designing two sgRNAs targeting ace1 in the system, resulting in the significantly enhanced production of cellulase (up to 1- and 18-fold on the Avicel and glucose, respectively) and xylanase (up to 11- and 41-fold on the Avicel and glucose, respectively). Furthermore, heterologous expression of the glucose oxidase gene from Aspergillus niger ATCC 9029 at the cbh1 locus with the simultaneous deletion of cbh1 and cbh2 (two cellobiohydrolase coding genes) by designing four sgRNAs targeting cbh1 and cbh2 in the system was acquired, and the glucose oxidase produced by T. reesei reached 43.77 U/mL. Besides, it was found the ER-associated protein degradation (ERAD) level was decreased in the glucose oxidase-producing strain, which was likely due to the reduction of secretion pressure by deletion of the major endogenous cellulase-encoding genes. Conclusions The tRNA−gRNA array-based CRISPR-Cas9 editing system was successfully developed in T. reesei. This system would accelerate engineering of T. reesei for high-level production of enzymes including lignocellulose-degrading enzymes and other recombinant enzymes. Furthermore, it would expand the CRISPR toolbox for fungal genome editing and synthetic biology.
