SUPERMAGO: Protein Function Prediction Based on Transformer Embeddings.

Recent technological advancements have enabled the experimental determination of amino acid sequences for numerous proteins. However, analyzing protein functions, which is essential for understanding their roles within cells, remains a challenging task due to the associated costs and time constraints. To address this challenge, various computational approaches have been proposed to aid in the categorization of protein functions, mainly utilizing amino acid sequences.

TEMPROT: protein function annotation using transformers embeddings and homology search.

Background: Although the development of sequencing technologies has provided a large number of protein sequences, the analysis of functions that each one plays is still difficult due to the efforts of laboratorial methods, making necessary the usage of computational methods to decrease this gap. As the main source of information available about proteins is their sequences, approaches that can use this information, such as classification based on the patterns of the amino acids and the inference based on sequence similarity using alignment tools, are able to predict a large collection of proteins. The methods available in the literature that use this type of feature can achieve good results, however, they present restrictions of protein length as input to their models.

Ensemble of Template-Free and Template-Based Classifiers for Protein Secondary Structure Prediction.

Protein secondary structures are important in many biological processes and applications. Due to advances in sequencing methods, there are many proteins sequenced, but fewer proteins with secondary structures defined by laboratory methods. With the development of computer technology, computational methods have (started to) become the most important methodologies for predicting secondary structures.

Phaseolin ingestion affects vesicular traffic causing oxidative stress in the midgut of Callosobruchus maculatus larvae.

It has been reported that phaseolin, the major storage globulin of the common bean (Phaseolus vulgaris), is toxic to Callosobruchus maculatus larvae, an Old World bruchid beetle that is not capable of infesting this New World edible bean. It has also been demonstrated that vicilin, the major storage globulin found in cowpea (Vigna unguiculata) seeds, is absorbed through receptor-mediated endocytosis in the insect midgut. A putative vicilin receptor has been purified and showed high homology to α-tocopherol transfer protein.

Receptor mediated endocytosis of vicilin in Callosobruchus maculatus (Coleoptera: Chrysomelidae) larval midgut epithelial cells.

The transport of proteins across the intestinal epithelium of insects is still not well understood. There is evidence that vicilin, a major storage protein of cowpea seeds (Vigna unguiculata), is internalized in larvae of the seed-beetle Callosobruchus maculatus. It has been reported that this vicilin interacts with proteins present in the microvillar membranes of columnar cells along the digestive tract of the larvae.

Simultaneous determination of fumonisins B1 and B2 in different types of maize by matrix solid phase dispersion and HPLC-MS/MS.

This work involved the optimization and validation of a method, according to Directive 2002/657/EC and the Analytical Quality Assurance Manual of Ministério da Agricultura, Pecuária e Abastecimento, Brazil, for simultaneous extraction and determination of fumonisins B1 and B2 in maize. The extraction procedure was based on a matrix solid phase dispersion approach, the optimization of which employed a sequence of different factorial designs. A liquid chromatography-tandem mass spectrometry method was developed for determining these analytes using the selected reaction monitoring mode.

Spatial distribution of digestive proteinases in the midgut of the Pacific white shrimp (Litopenaeus vannamei) indicates the existence of endo-ectoperitrophic circulation in Crustacea.

The effect of dietary protein concentration on the spatial distribution of digestive proteinases in the shrimp Litopenaeus vannamei indicates the existence of endo-ectoperitrophic enzyme circulation in this species. Samples recovered from the midgut gland tissues, stomach contents, three different portions of the midgut and feces were used for quantitative and qualitative analyses of the composition and distribution of the digestive proteinases. Animals were divided into three different groups: (1) animals (controls) fed with a commercial 35% protein diet, (2) animals fed with a commercial diet supplemented with ovalbumin to a final protein concentration of 60%; (3) animals fed with an 80% protein diet.

Variant vicilins from a resistant Vigna unguiculata lineage (IT81D-1053) accumulate inside Callosobruchus maculatus larval midgut epithelium.

It has been demonstrated that variant vicilins are the main resistance factor of cowpea seeds (Vigna unguiculata) against attack by the cowpea beetle Callosobruchus maculatus. There is evidence that the toxic properties of these storage proteins may be related to their interaction with glycoproteins and other microvillar membrane constituents along the digestive tract of the larvae. New findings have shown that following interaction with the microvilli, the vicilins are absorbed across the intestinal epithelium and thus reach the internal environment of the larvae.

Synergistic bactericidal activity of Eremanthus erythropappus oil or beta-bisabolene with ampicillin against Staphylococcus aureus.

The activity of Eremanthus erythropappus oil (EO) and some of its compounds and their potential synergistic interaction with ampicillin against different strains of Staphylococcus aureus were investigated. Determination of chemical composition of EO by gas chromatography-mass spectrometry (GC/MS) and bioguided chemical fractionation led to the identification of beta-bisabolene as the main active compound. A synergistic bactericidal activity of EO or beta-bisabolene with ampicillin against Staphylococcus aureus was observed in a time-kill assay.