Coccidiosis is a widespread, protozoan disease that continues to impose a high risk to the global poultry industry despite various control measures, including live, attenuated vaccines. To set the stage for next-generation vaccines that are broadly protective, our study aimed to identify sporozoite immunogens that are cross-reactive with hyper-immune sera against Eimeria maxima, E. tenella, E. necatrix and E.acervulina. In all, 2D electrophoresis, immunoblots and MALDI-TOF-MS/MS revealed 12 immunogenic proteins of interest, including 11 that have amino acid sequences matching those of non-redundant proteins in the NCBI database. Bioinformatics analyses revealed that these proteins are involved in protein translation, modification and degradation, signal transduction and regulation, cell structure and transport, metabolic regulation and RNA binding and processing. These findings now offer multiple feasible targets for the design of vaccine constructs.

There are limited options to quantify and characterize amyloid species from biological samples in a simple manner. Thioflavin T (ThT) has been used for decades to stain amyloid fibrils, but to our knowledge, we were the first to use it in-gel. Thioflavin T in-gel staining is convenient as it is fast, inexpensive, accessible to most laboratories, and compatible with other fluorescent stains and downstream analyses such as mass spectrometry (MS).

The proteomic and metabolomic differences in mice fed ε-polylysine were detected by high-throughput sequencing and screening. The effects of ε-polylysine on the proteome and metabolomics of C57 BL/6 J mice were studied. DIA proteome sequencing and liquid chromatography-mass spectrometry (LC-MS) were used to compare ε-polylysine-modified mouse proteome and metabolome. In this study, we analyzed the regulatory effects of ε-polysine on glycerophospholipid metabolism, glutathione metabolism, and ABC transporters pathways. The sequencing data and LC-MS/MS raw data of samples are stored in MetaboLights and ProteomeXchange databases for efficient reuse and to explore the differences in metabolism and protein expression among mice fed with different levels of ε-polylysine, aiming to screen for critical proteins and differential metabolites in valuable regulatory pathways.

Mytilus are sessile filter feeders that live in close contact with numerous marine microorganisms. Hemocytes, the immunocompetent cells of Mytilus, participate in the immune response in a very efficient manner. Lipopolysaccharide (LPS) and peptidoglycan (PGN) follow specific microbe/pathogen-associated molecular patterns (MAMPs or PAMPs) and are involved in immune stimulation in host cells. This study evaluated the molecular profiles and reactions at protein level of Mytilus hemocytes after stimulation with LPS and PGN. Mytilus coruscus was challenged in vivo with LPS and PGN. The hemocytes were collected after 48 h and analyzed for quantitative proteomics, cell subpopulations, and the free amino acid composition. 4D-DIA technology-based proteomic analysis revealed different protein profiles, as well as different responses at protein level, under either the LPS or PGN challenge. C-type lectins, collagens, and CD151 protein were highly upregulated in LPS-challenged mussels, while phospholipase A2 and dCMP deaminase were highly upregulated in PGN-challenged mussels. Moreover, LPS challenge disrupted dsRNA-mediated translation and stimulated energy-related metabolism, while PGN challenge stimulated proteins involved in the inflammatory response and suppressed amino acid metabolism. In addition, the LPS and PGN challenges differed in their effects on the free amino acid composition and granulocytes ratio of the hemocytes. These findings highlight the different strategies employed by mussel hemocytes in response to different MAMPs, providing insights into the effects of LPS and PGN on Mytilus.

Perturbation of gene expression using RNA interference (RNAi) or CRISPR interference (CRISPRi) is a useful strategy to explore the function of essential genes. In the archaeon Haloferax volcanii, the CRISPR-Cas system has been adapted as a CRISPRi tool to silence the expression of specific genes. We developed a laboratory class (LC) to conceptualize gene silencing through inactivation of the H. volcanii LonB protease gene, a negative regulator of carotenoid pigments biosynthesis, using CRISPRi. This LC has been successfully applied in the Biology and Biochemistry of Microorganisms course for undergraduate students of Biology in 2022 and 2023. The following objectives were proposed: (a) generate H. volcanii mutant strains with reduced expression of the lonB gene using CRISPRi; (b) examine the effect of lonB gene silencing on cell pigmentation and growth rate; (c) assess lonB gene repression by Western blotting (WB). This LC allows students to obtain and screen CRISPRi silenced-mutants by means of simple procedures using a non-pathogenic organism as well as handle basic microbiology, biochemistry and molecular biology protocols. Additionally, the LC fosters social actions through collaborative work (experimental work), the interpretation and discussion of data and the ability to communicate outcomes orally and in a written format (scientific report).

We report on the recent advancements in the sensing of proteins, both directly and with the use of a fluorescent probe, through the use of Fluorophore-Induced Plasmonic Current (FIPC). FIPC are a phenomenon where a fluorophore or excited state species is in close proximity to a plasmonically active metal nanoparticle film (MNF), and the excited state is able to couple to the particle, ultimately leading to enhanced spectroscopic properties. This phenomenon is similar to the well-reported metal-enhanced fluorescence (MEF) phenomenon, wherein the coupled complex produces an enhanced fluorescence emission and a shorter lifetime. However, if the particles themselves are sufficiently spaced and oriented, an induced current can transfer from each discreet particle to the next, creating a detectable current across the film. This detectable current has a magnitude that is proportional to the fluorescent properties of the species that produced it, and can be affected by the polarization of the excitation source; the spacing and size of the particles on the film; the overlap between the spectral properties of the film and the species; as well as externally applied voltages and currents. In this study, we examined whether it is possible to detect protein species, directly due to both their intrinsic fluorescent and absorptive properties, and how that compares to commercially available protein detection probes, in a similar manner to prior work by our group addressing analyte detection via turn-on fluorescent probes. This FIPC-based detection technique is a novel method that has not been used for the detection of proteins, and the use of this method could expand the dynamic sensing range of first-pass testing, while overcoming some of the physical limitations on the upper limit of detection of both absorption spectroscopy and fluorescence emission spectroscopy. Our experiments sought to highlight the selectivity of FIPC-based detection relative to both fluorescence and absorption spectroscopy, as well as its sensitivity when working with protein analytes. We examined the effects of protein concentration, intrinsic fluorescent properties, and turn-on probes, as well as how these techniques compare to traditional analytical techniques used today.

Brucellosis is a zoonosis that affects domestic and wild animals, causing reproductive disorders and significant economic losses in livestock. Brucella melitensis, B. abortus, and B. suis are the main agents of brucellosis in livestock and humans, thereby their control and eradication are crucial. Serological tests based on identification of antibodies against Brucella smooth lipopolysaccharides (sLPS) in the serum of infected animals are traditionally used. This approach shows two main limits: (i) tests can give false positives due to the similarity of Brucella sLPS with the LPS of other Gram-negative bacteria; (ii) antigen production represents a possible risk of zoonoses. In this work, a proteomic approach, starting from B. melitensis Brucellergene, was employed to identify possible Brucella antigenic proteins useful for a more specific and safe serological diagnosis. Four proteins binding to the infected swine serum were identified: (i) "probable sugar-binding periplasmic protein B. abortus str 2308A"; (ii) "peptide ABC transporter substrate-binding protein B. melitensis"; (iii) "GntR family transcriptional regulator B. melitensis"; (iv) "conserved hypothetical protein B. melitensis M28". These proteins could be promising specific antigens for serological investigations in swine. In the near future, these antigenic proteins could be synthesized in vitro and used to produce a safer and more specific diagnostic kit.

The unicellular soil alga Chlamydomonas reinhardtii forms diploid zygotes during its sexual cycle. The process of a zygote maturing into a highly resistant zygospore remains poorly understood despite its importance for survival under adverse environmental conditions. Here we describe the detailed timeline of morphological and physiological changes during zygote maturation in darkness on ammonium-free Tris-acetate-phosphate agar plates. The formation of a multilayered cell wall is primarily responsible for the increase in cell size in the first few days after zygote formation. Desiccation and freezing tolerance also develop in the period 3-7 days. Photosynthetic and respiratory activity decrease to reach minimal levels after 7-10 days, accompanied by a partial dedifferentiation of the chloroplast that includes chlorophyll degradation followed by the possible disappearance of the pyrenoid. In contrast to the decreasing concentrations of most carotenoids in the first few days after zygote formation, ketocarotenoids can first be detected after 3 days and their accumulation is completed after 10 days. Furthermore, the zygote degrades a large proportion of its starch and enriches oligosaccharides that may serve as osmoprotectants. The storage lipid triacylglycerol is accumulated at the expense of thylakoid membrane lipids, which mirrors the conversion of a metabolically active cell into a dormant spore on the metabolic level. Taken together, zygote maturation is a multifaceted process that yields mature zygospores after ~ 3 weeks. This work sheds light on the complete time course of the remodeling of a photosynthetically active eukaryotic cell into a dormant, highly resistant spore.

All organisms experience stress and must rapidly respond to changing conditions. Thus, cells have evolved sophisticated rapid-response mechanisms such as post-translational protein modification to rapidly and reversibly modulate protein activity. One such post-translational modification is reversible lysine acetylation, where proteomic studies have identified thousands of acetylated proteins across diverse organisms. While the sheer size of the 'acetylome' is striking, the function of acetylation for the vast majority of proteins remains largely obscure. Here, we show that global acetylation plays a previously unappreciated role in the heat shock response of Saccharomyces cerevisiae. We find that dysregulated acetylation renders cells heat sensitive, and moreover, that the acetylome is globally remodeled during heat shock over time. Using quantitative acetyl-proteomics, we identified ~400 high-confidence acetyl marks across ~200 proteins that significantly change in acetylation when cells are shifted to elevated temperature. Proteins with significant changes in lysine acetylation during heat shock strongly overlap with genes induced or repressed by stress. Thus, we hypothesize that protein acetylation augments the heat shock response by activating induced proteins and inactivating repressed proteins. Intriguingly, we find nearly 40 proteins with at least two acetyl marks that significantly change in the opposite directions. These proteins are strongly enriched for chaperones and ribosomal proteins, suggesting that these two key processes are coordinately regulated by protein acetylation during heat shock. Moreover, we hypothesize that the same type of activating and inactivating marks that exist on histones may be a general feature of proteins regulated by acetylation. Overall, this work has identified a new layer of post-translational regulation that likely augments the classic heat shock response.

The second-generation myosin activator danicamtiv (DN) has shown improved function compared with the first-generation myosin activator omecamtiv mecarbil (OM) in nonfailing myocardium by enhancing cardiac force generation but attenuating slowed relaxation. However, whether the functional improvement with DN compared with OM persists in remodeled failing myocardium remains unknown. Therefore, this study aimed to investigate the differential contractile responses to myosin activators in nonfailing and failing myocardium. Mechanical measurements were performed in detergent-skinned myocardium isolated from donor and failing human hearts. Steady-state force, stretch activation responses and loaded shortening velocity were analyzed at submaximal [Ca2+] in the absence or presence of 0.5 µmol/L OM or 2 µmol/L DN. The effects of DN and OM on Ca2+ sensitivity of force generation were determined by incubating myocardial preparations at various [Ca2+]. The inherent impairment in force generation and cross-bridge behavior sensitized the failing myocardium to the effects of myosin activators. Specifically, increased Ca2+ sensitivity of force generation, slowed rates of cross-bridge recruitment and detachment following acute stretch, slowed loaded shortening velocity, and diminished power output were more prominent following treatment with OM or DN in failing myocardium compared with donor myocardium. Although these effects were less pronounced with DN compared with OM in failing myocardium, DN impaired contractile properties in failing myocardium that were not affected in donor myocardium. Our results indicate that similar to first-generation myosin activators, the DN-induced slowing of cross-bridge kinetics may result in a prolongation of systolic ejection and delayed diastolic relaxation in the heart failure setting.NEW & NOTEWORTHY This is the first study to provide a detailed mechanistic comparison of omecamtiv mecarbil (OM) and danicamtiv (DN) in failing and nonfailing human myocardium. These findings have clinical implications and the potential to inform the clinical utility of myosin activators in the heart failure setting.

Venoms are biochemical arsenals that have emerged in numerous animal lineages, where they have co-evolved with morphological and behavioural traits for venom production and delivery. In centipedes, venom evolution is thought to be constrained by the morphological complexity of their venom glands due to physiological limitations on the number of toxins produced by their secretory cells. Here we show that the uneven toxin expression that results from these limitations have enabled Scolopendra morsitans to regulate the composition of their secreted venom despite the lack of gross morphologically complex venom glands. We show that this control is probably achieved by a combination of this heterogenous toxin distribution with a dual mechanism of venom secretion that involves neuromuscular innervation as well as stimulation via neurotransmitters. Our results suggest that behavioural control over venom composition may be an overlooked aspect of venom biology and provide an example of how exaptation can facilitate evolutionary innovation and novelty.

Behcet's disease (BD) is a rare and recurrent autoinflammatory disorder characterized by systemic vasculitis, frequently manifested as recurrent aphthous stomatitis (RAS). We aim to identify specific serum proteins to discriminate between BD and idiopathicRAS.

Peripheral blood was collected from 12 BD patients, 12 idiopathic RAS patients, and 21 healthy volunteers. The serum samples underwent Tandem Mass Tag-based mass spectrometry analysis. Differentially expressed proteins (DEPs) were identified for KEGG pathway enrichment, Gene Ontology (GO), and protein-protein interaction (PPI) analyses. ELISA was utilized to verify two BD-specific DEPs in another cohort consisting of 18 BD patients, 18 idiopathic RAS patients, and 18 controls.

Compared with RAS serum, BD serum showed 242 DEPs. 49 proteins were differentially expressed in BD but not RAS serum compared to healthy controls. KEGG pathway and GO analyses revealed that DEPs in BD and RAS have similar biological functions and cellular distributions, featuring a significant association with pathways regulating blood coagulation and immune response. When comparing DEPs between BD and RAS, several keratins emerged as markers that distinguish RAS from BD. We also identified multiple DEPs in BD but not RAS patients. PPI analysis uncovered that lipoprotein metabolism regulators serve as hub proteins, indicating their potentially essential roles in BD pathology. In addition, ELISA results confirmed the elevated LRG1 and SOD3 levels in BD, but not RAS patients, compared to healthy donors.

Our data uncovered novel serum proteins that distinguish BD from RAS, which may potentially be useful in BD diagnosis and treatment.

Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption. GroEL-SIP's main advantages are that (1) it can be performed with a sample-independent database and (2) sample complexity can be reduced by enriching GroEL proteins, increasing sensitivity and reducing instrument time. We applied GroEL-SIP to pure cultures, synthetic bicultures, and a human gut model using 2H-, 18O-, and 13C-labeled substrates. While 2H and 18O allowed assessing general activity, 13C enabled differentiation of substrate source and utilized metabolic pathways. GroEL-SIP offers fast and straightforward protein-SIP analyses of highly abundant families in mixed bacterial communities, but further work is needed to improve sensitivity, resolution, and database coverage.

Human milk proteins, a mixture of whey proteins including caseins, milk fat globule membrane (MFGM) proteins, various peptides, and their amino acids, play a crucial role in infant growth and development, as do non-nutritional bioactive components. The extracellular nicotinamide phosphoribosyltransferase (eNAMPT) or visfatin is a conserved cytokine/enzyme released by many mammalian cells, related to multiple metabolic and immune processes. Few investigations have been reported about detecting visfatin in skimmed milk and the hypothesis of its potential role in regulating infant adiposity through breast milk. Milk samples from a donated human milk bank were analyzed. After milk fractionation by centrifugation, skimmed milk and MFGM were analyzed by SDS-PAGE, MALDI-TOF mass spectrometry ELISA and/or Western blot. The ELISA assay showed a higher visfatin content in raw skimmed milk than in pasteurized samples. Meanwhile, MFGMs revealed higher visfatin levels in pasteurized samples. This is the first time visfatin has been identified associated with MFGM, and these results could suggest an affinity of this molecule for a lipidic environment.

Translation-targeting toxic small alarmone synthetases (toxSAS) are effectors of bacterial toxin-antitoxin systems that pyrophosphorylate the 3'-CCA end of transfer RNA (tRNA) to prevent aminoacylation. toxSAS are implicated in antiphage immunity: Phage detection triggers the toxSAS activity to shut down viral production. We show that the toxSAS FaRel2 inspects the tRNA acceptor stem to specifically select tRNAGly and tRNAThr. The first, second, fourth, and fifth base pairs of the stem act as the specificity determinants. We show that the toxSASs PhRel2 and CapRelSJ46 differ in tRNA specificity from FaRel2 and rationalize this through structural modeling: While the universal 3'-CCA end slots into a highly conserved CCA recognition groove, the acceptor stem recognition region is variable across toxSAS diversity. As phages use tRNA isoacceptors to overcome tRNA-targeting defenses, we hypothesize that highly evolvable modular tRNA recognition allows for the escape of viral countermeasures through tRNA substrate specificity switching.

Microplastics (MPs) and organophosphate flame retardants (OPFRs) have recently become ubiquitous and cumulative pollutants in the oceans. Since OPFRs are added to or adsorbed onto MPs as additives, it is necessary to study the composite contamination of OPFRs and MPs, with less focus on bio-based PLA. Therefore, this study focused on the ecotoxicity of the biodegradable MP polylactic acid (PLA) (5 μm, irregular fragments, 102 and 106 particles/L), and a representative OPFRs tris(1-chloro-2-propyl) phosphate (TCPP, 0.5 and 50 μg/L) at environmental and high concentrations. The mussel Mytilus coruscus was used as a standardised bioindicator for exposure experiments. The focus was on examining oxidative stress (catalase, CAT, superoxide dismutase, SOD, malondialdehyde, MDA), immune responses acid (phosphatase, ACP, alkaline phosphatase, AKP, lysozyme, LZM), neurotoxicity (acetylcholinesterase, AChE), energy metabolism (lactate dehydrogenase, LDH, succinate dehydrogenase, SDH, hexokinase, HK), and physiological indices (absorption efficiency, AE, excretion rate, ER, respiration rate, RR, condition index, CI) after 14 days exposure. The results of significantly increased oxidative stress and immune responses, and significantly disturbed energy metabolism and physiological activities, together with an integrated biomarker response (IBR) analysis, indicate that bio-based PLA MPs and TCPP could cause adverse effects on mussels. Meanwhile, TCPP interacted significantly with PLA, especially at environmental concentrations, resulting in more severe negative impacts on oxidative and immune stress, and neurotoxicity. The more severe adverse effects at environmental concentrations indicate higher ecological risks of PLA, TCPP and their combination in the real marine environment. Our study presents reliable data on the complex effects of bio-based MP PLA, TCPP and their combination on marine organisms and the environment.

Glucoamylases are exo-enzymes that cleave the ends of the starch chain, releasing glucose units. In the current work, we described a novel 1,4-α-glucoamylase from an A. brasiliensis strain isolated from an environmental sample. The purified glucoamylase, GlaAb, has a molecular mass of 69 kDa and showed a starch binding domain. GlaAb showed a similar sequence to other fungal glucoamylases, and the molecular 3D model analysis of GlaAb suggests an overall structure as described in the literature, except by elongation in the loop connecting the 4th and 5th α-helices. The enzyme showed activity over a wide range of pH and temperature, with maximum activity at pH 4.5 and 60 °C. GlaAb was stable at 50 °C for 7 h, maintaining 67% residual activity, and it was not inhibited by glucose up to 0.1 M. The glucoamylase was 65% more active in the presence of Mn2+ and showed a Km of 2.21 mg mL-1, Vmax of 155 U mg-1, Kcat 179 s-1, and Kcat/Km 81.06 mg mL-1 s-1 using potato starch as substrate. The results obtained are promising and provide the basis for the development of applications of GlaAb in the industrial process.

Temperature changes had a huge impact on the growth of aquaculture organisms, which mainly involved two parameters: the changing amplitude and the changing speed. Wide-adaptability and narrow-adaptability were divided by the amplitude, while fast-adaptability and slow-adaptability proposed in this article were divided based on the speed. Investigating the impact of the changing speed on artificial farming was vital. In this study, two fish species of wide-adaptability, Hippocampus kuda and Oryzias melatigma, were selected as research objects, explored the effects of temperature changing speeds on them under 2 changing amplitudes of 2°C and 4°C. The similarities and differences in their responses to temperature changes were analyzed and compared from the aspects of feeding, metabolism, physiology, immunity, and growth. The results showed that all 3 changing speeds (0.5°C/h, 1°C/h, and direct input) had no effect on the growth of O. melatigma under the 2°C amplitude, while there were significant differences in various aspects of H. kuda in the treatments with the speeds between 0.5°C/h and direct input, such as a significant difference in growth, in food intake, and in response speeds and response levels of several enzymes and related genes. Under 4°C amplitude, the impact of all 4 changing speeds (0.5°C/h, 1°C/h, 2°C/h and direct input) on both fish was more pronounced. H. kuda showed a significant difference of growth among 3 groups, and the critical safe speed was about 0.5°C/h in its heating treatments. And the growth decrease only occured the heating treatment of direct input in O. melatigma. Furthermore, some genes responded quickly and efficiently to the low-speed changes of temperature in H. kuda, but were inhibited in the treatments with high-speed changes. However, they can still express rapidly and efficiently in the high-speed treatments of O. melatigma, included several stress-related genes, lipid metabolic-related genes, and immune-related genes. Seen from these differences, the energy source used in H. kuda to resist stress was single and short-lived. So, under a long-term stress, H. kuda gradually transformed from normal physiological stress into pathological stress, leading to the outbreak of diseases. Therefore, for precise aquaculture of H. kuda, stricter and more precise control of environmental temperature is necessary to prevent rapid and big temperature changes from affecting the growth and survival of the seahorse.

Residual substances that are considered hazardous to the recipient must be removed from final cellular therapeutic products manufactured for clinical purposes. In doing so, quality rules determined by competent authorities (CAs) for the clinical use of tissue- and cell-based products can be met. In our study, we carried out residual substance analyses, and purity determination studies of trypsin and trypsin inhibitor in clinically manufactured bone marrow-derived mesenchymal stromal/stem cell products, using the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) method. Despite being a semiquantitative method, SDS-PAGE has several benefits over other methods for protein analysis, such as simplicity, convenience of use, and affordability. Due to its convenience and adaptability, SDS-PAGE is still a commonly used method in many laboratories, despite its limits in dynamic range and quantitative precision. Our goal in this work was to show that SDS-PAGE may be used effectively for protein measurement, especially where practicality and affordability are the major factors. The results of our study suggest a validated method to guide tissue and cell manufacturing sites for making use of an agreeable, accessible, and cost-effective method for residual substance analyses in clinically manufactured cellular therapies.

Shadow puppets are a popular art form in various regions, including China, Indonesia, and Turkey, and are rich in cultural significance. However, there is a considerable lack of research on the materials, diseases and conservation techniques related to shadow puppet relics. Material identification is the basis for understanding the production process of ancient shadow puppet relics and evaluating their deterioration degree. The microscopic morphology and infrared spectroscopy results in our experiments showed that the traditional methods of ancient skin identification were not effective in the shadow puppet samples. In order to achieve accurate identification, we used biological mass-spectrometry in proteomics to examine two puppet relics and commercially available modern shadow puppets. The results showed that the above samples could be detected by mass spectrometry with abundant peptides, including peptides specific for bovine skin. These peptides cannot be found in other commonly used materials for making shadow puppets, including the skins of pig, sheep, deer and horse. It is worth mentioning that we have found the peptides specific to yellow cowhide in two ancient shadow puppet relics samples. Therefore, the proteomic evidence shows that the raw materials of the two shadow puppet relics samples are yellow cowhide. Four modern samples also confirmed the reliability of material identification using proteomics. The proteomic evidence shows that the biological mass spectrometry will contribute to the scientific research of shadow puppet relics and other skin and leather cultural relics.

The binding of the HIV-1 Gag polyprotein to the plasma membrane is a critical step in viral replication. The association with membranes depends on the lipid composition, but its mechanisms remain unclear. Here, we report the binding of non-myristoylated Gag to lipid membranes of different lipid compositions to dissect the influence of each component. We tested the contribution of phosphatidylserine, PI(4,5)P2, and cholesterol to membrane charge density and Gag affinity to membranes. Taking into account the influence of the membrane surface potential, we quantitatively characterized the adsorption of the protein onto model lipid membranes. The obtained Gag binding constants appeared to be the same regardless of the membrane charge. Furthermore, Gag adsorbed on uncharged membranes, suggesting a contribution of hydrophobic forces to the protein-lipid interaction. Charge-charge interactions resulted in an increase in protein concentration near the membrane surface. Lipid-specific interactions were observed in the presence of cholesterol, resulting in a two-fold increase in binding constants. The combination of cholesterol with PI(4,5)P2 showed cooperative effects on protein adsorption. Thus, we suggest that the affinity of Gag to lipid membranes results from a combination of electrostatic attraction to acidic lipids, providing different protein concentrations near the membrane surface, and specific hydrophobic interactions.

Background: Apple (Malus domestica) is a fruit commonly associated with allergic oral symptoms in the Mexican pediatric population; however, knowledge of its allergenic proteins is limited. This information is crucial as sensitization frequencies to specific allergens can vary among different populations. The main allergic symptomatology before apple ingestion derives from primary sensitizations induced by pollen, promoting cross-reactivity with the main allergenic protein of apple. Therefore, this study aims to identify new potential sensitizing proteins to apple using immunoproteomic techniques. Methods: We collected serum samples from 14 pediatric patients with confirmed immunoglobulin E (IgE)-mediated apple allergy and used these samples to assess immunoreactivity to apple protein extracts through 2D-western blot assays. The spots corresponding to the 2D-SDS-PAGE were analyzed using nanoLC-MS/MS. Results: We identified 11 non-redundant proteins, including Mal d 2 and Mal d 1, the latter showing a high frequency of sensitization (79%) in our patients, and being considered the main apple allergenic protein. The remaining identified proteins have not been previously described as apple allergens in the International Union of Immunological Societies databases. However, three of these may be categorized as pan-allergens. Conclusions: This study shows evidence that the repertoire of apple allergens in the Mexican population could differ from those reported internationally, highlighting the importance of studies in different countries to improve the certainty of allergy diagnosis and allow the implementation of precision medicine.

Human immunodeficiency virus (HIV) assembly at an infected cell's plasma membrane requires membrane deformation to organize the near-spherical shape of an immature virus. While the cellular expression of HIV Gag is sufficient to initiate budding of virus-like particles, how Gag generates membrane curvature is not fully understood. Using highly curved lipid nanotubes, we have investigated the physicochemical basis of the membrane activity of recombinant nonmyristoylated Gag-Δp6. Gag protein, upon adsorption onto the membrane, resulted in the shape changes of both charged and uncharged nanotubes. This shape change was more pronounced in the presence of charged lipids, especially phosphatidylinositol bisphosphate (PI(4,5)P2). We found that Gag modified the interfacial tension of phospholipid bilayer membranes, as judged by comparison with the effects of amphipathic peptides and nonionic detergent. Bioinformatic analysis demonstrated that a region of the capsid and SP1 domains junction of Gag is structurally similar to the amphipathic peptide magainin-1. This region accounts for integral changes in the physical properties of the membrane upon Gag adsorption, as we showed with the synthetic CA-SP1 junction peptide. Phenomenologically, membrane-adsorbed Gag could diminish the energetic cost of increasing the membrane area in a way similar to foam formation. We propose that Gag acts as a surface-active substance at the HIV budding site that softens the membrane at the place of Gag adsorption, lowering the energy for membrane bending. Finally, our experimental data and theoretical considerations give a lipid-centric view and common mechanism by which proteins could bend membranes, despite not having intrinsic curvature in their molecular surfaces or assemblies.

Increasing the age of bulls results in a decrease in reproductive function, including a reduction in sperm quality, which plays a vital role in determining the fertility of bulls. Through a proteomic approach, this research aims to analyze the influence of age factors on various proteomes contained in bull sperm. Frozen semen samples from Simmental Bulls were categorized into three age groups: two, four, and ≥10 years old. Subsequently, the post-thaw sperm cells obtained were separated based on molecular weight using 1D-SDS-PAGE. Peptides extracted from the bands produced in each age group were subjected to LC-MS/MS analysis. A total of 72 protein types were identified, with 45 being detected in the 4-year-old group and 41 expressed in both the 2 and ≥10-year-old groups. The results provided insights into proteins' role in sperm metabolism across all age groups. Specifically, the 2-year-old group exhibited the expression of proteins associated with acrosome assembly and spermatid development (SPACA1). In contrast, those in the 4-year-old group were linked to motility (PEBP4) and sperm decapacitation factor (PEBP1). Proteins expressed in the 2 and -year-old groups were discovered to be involved in fertilization processes (TEX101). In contrast, the ≥10-year-old age group was associated with hyperactive movement related to capacitation (Tubulin). In conclusion, age influenced the differences observed in the proteomic profile of post-thaw Simmental bull sperm using the 1D-SDS-PAGE tandem LC-MS/MS approach.

We describe a microwave-assisted, methanol and acetic acid-free, inexpensive method for rapid staining of SDS-PAGE proteins. Only citric acid, benzoic acid, and Coomassie brilliant blue G-250 (CBG) were used. Microwave irradiation reduced the detection duration, and proteins in a clear background were visualized within 30 min of destaining, after 2 min of fixing and 12 min of staining. By using this protocol, comparable band intensities were obtained to the conventional methanol/acetic acid method.

Translation-targeting toxic Small Alarmone Synthetases (toxSAS) are effectors of bacterial Toxin-Antitoxin systems that pyrophosphorylate the 3'-CCA end of tRNA to prevent aminoacylation. toxSAS are implicated in antiphage immunity: phage detection triggers the toxSAS activity to shut down viral production. We show that the toxSAS FaRel2 inspects the tRNA acceptor stem to specifically select tRNAGly and tRNAThr. The 1st, 2nd, 4th and 5th base pairs the stem act as the specificity determinants. We show that the toxSASs PhRel2 and CapRelSJ46 differ in tRNA specificity from FaRel2, and rationalise this through structural modelling: while the universal 3'-CCA end slots into a highly conserved CCA recognition groove, the acceptor stem recognition region is variable across toxSAS diversity. As phages use tRNA isoacceptors to overcome tRNA-targeting defences, we hypothesise that highly evolvable modular tRNA recognition allows for the escape of viral countermeasures through tRNA substrate specificity switching.

Research laboratories generate a broad range of hazardous pharmacophoric chemical contaminants, from drugs to dyes used during various experimental procedures. In the recent past, biological methods have demonstrated great potential in the remediation of such contaminants. However, the presence of pharmacophoric chemicals containing antibiotics, xenobiotics, and heavy metals suppresses the growth and survivability of used microbial agents, thus decreasing the overall efficiency of biological remediation processes. Bacterial biofilm is a natural arrangement to counter some of these inhibitions but its use in a systemic manner, portable devices, and pollutant remediation plants post serious challenges. This could be countered by synthesizing a biodegradable carbon nanoparticle from bacterial biofilm. In this study, extracellular polymeric substance-based carbon nanoparticles (Bio-EPS-CNPs) were synthesized from bacterial biofilm derived from Bacillus subtilis NCIB 3610, as a model bacterial system. The produced Bio-EPS-CNPs were investigated for physiochemical properties by dynamic light scattering, optical, Fourier-transformed infrared, and Raman spectroscopy techniques, whereas X-ray diffraction study, scanning electron microscopy, and transmission electron microscopy were used to investigate structural and morphological features. The Bio-EPS-CNPs exhibited negative surface charge with spherical morphology having a uniform size of sub-100 nm. The maximum remediation of some laboratory-produced pharmacophoric chemicals was achieved through a five-round scavenging process and confirmed by UV/Vis spectroscopic analysis with respect to the used pharmacophore. This bioinspired remediation of used pharmacophoric chemicals was achieved through the mechanism of surface adsorption via hydrogen bonding and electrostatic interactions, as revealed by different characterizations. Further experiments were performed to investigate the effects of pH, temperature, stirring, and the protocol of scavenging to establish Bio-EPS-CNP as a possible alternative to be used in research laboratories for efficient removal of pharmacophoric chemicals by incorporating it in a portable, filter-based device.

Silyl ethers fulfil a fundamental role in synthetic organic chemistry as protecting groups and their selective cleavage is an important factor in their application. We present here for the first time two enzymes, SilE-R and SilE-S, which are able to hydrolyse silyl ethers. They belong to the stress-response dimeric A/B barrel domain (DABB) family and are able to cleave the Si-O bond with opposite enantiopreference. Silyl ethers containing aromatic, cyclic or aliphatic alcohols and, depending on the alcohol moiety, silyl functions as large as TBDMS are accepted. The X-ray crystal structure of SilE-R, determined to a resolution of 1.98 Å, in combination with mutational studies, revealed an active site featuring two histidine residues, H8 and H79, which likely act synergistically as nucleophile and Brønsted base in the hydrolytic mechanism, which has not previously been described for enzymes. Although the natural function of SilE-R and SilE-S is unknown, we propose that these 'silyl etherases' may have significant potential for synthetic applications.

Monopterus albus is one of China's renowned and superior aquaculture species, with its seedlings mainly sourced from wild capture. One of the bottlenecks in M. albus aquaculture is the high mortality rate and low feeding initiation rate from stocking wild fry to the initiation of feeding. In production, trash fish is commonly used to wean M. albus juveniles onto feeding. In this study, we introduced three other natural feeds, earthworms (EW), yellow mealworms (YMW), and fly maggots (FM), with frozen trash fish (TF) serving as the control group, to evaluate the effects of these four natural feeds on the survival rate, feeding initiation, antioxidant enzymes activity, and body composition of M. albus juveniles under recirculating water aquaculture conditions. The experiment comprised four treatments, each with three replicates. Each replicate consisted of stocking 150 M. albus juveniles weighing 10.02 ± 0.89 g in size, raised for 5 weeks. The survival rate of the YMW group was 73.33%-85.33%, which was significantly higher than that of the other three bait groups (p < 0.05). The four bait groups showed no significant differences in final body weight and specific growth rate (SGR) (p > 0.05). The EW group showed the highest final body weight, with an average SGR of 2.73, whereas the YMW group had an average SGR of 1.87. The average daily feeding amount was significantly higher in EW and YMW groups than in the other two groups (p < 0.05). The percentage of feeding amount to fish weight in the EW group reached 7.3% in the fifth week. After 5 weeks of cultivation, NO2 --N content was significantly higher in the waters of the TF and EW groups than in the waters of the FM and YMW groups (p < 0.05), there was no significant difference in TAN content among the treatment groups (p > 0.05). Liver malondialdehyde content was significantly higher in the TF group than in the other bait groups (p < 0.05). GSH-Px activity was significantly higher in the EW group than in the FM group and YMW group. No significant differences in SOD and CAT activity and T-AOC were observed among the bait groups (p > 0.05). The increase in crude protein content was significantly higher in the TF group than in the FM group, but the increase in crude ash content was significantly lower in the TFgroup. In conclusion, Tenebrio molitor could potentially serve as one of the alternative feeds during the initial stages of M. albus juveniles stocking.

Human mitoNEET (mNT) and CISD2 are two NEET proteins characterized by an atypical [2Fe-2S] cluster coordination involving three cysteines and one histidine. They act as redox switches with an active state linked to the oxidation of their cluster. In the present study, we show that reduced glutathione but also free thiol-containing molecules such as β-mercaptoethanol can induce a loss of the mNT cluster under aerobic conditions, while CISD2 cluster appears more resistant. This disassembly occurs through a radical-based mechanism as previously observed with the bacterial SoxR. Interestingly, adding cysteine prevents glutathione-induced cluster loss. At low pH, glutathione can bind mNT in the vicinity of the cluster. These results suggest a potential new regulation mechanism of mNT activity by glutathione, an essential actor of the intracellular redox state.

The bright red color of Parma ham is mainly derived from zinc protoporphyrin IX (ZnPP), which exists in both water-soluble and insoluble states. Water-soluble ZnPP mainly binds to hemoglobin, however, the presence of water-insoluble ZnPP remains unexplained. Therefore, we aimed to elucidate how ZnPP exists in a water-insoluble state by focusing on its binding substance. Depending on the skeletal muscle, water-insoluble ZnPP comprised 30-50% of total ZnPP. The ZnPP water extractability was positively correlated with muscle pH. Water-insoluble ZnPP was extractable with a high-pH solution and existed as a complex with myoglobin or hemoglobin; nevertheless, myoglobin-binding ZnPP was more abundant. Furthermore, the water solubility of the myoglobin globin moiety at pH 5.5-6.0 was reduced by ZnPP binding. These results suggest that water-insoluble ZnPP mainly exists as a ZnPP-Mb complex, with low solubility attributed to the low pH of the ham.

Low targeting efficacy and high toxicity continue to be challenges in Oncology. A promising strategy is the glycosylation of chemotherapeutic agents to improve their pharmacodynamics and anti-tumoral activity. Herein, we provide evidence of a novel approach using diglycosidases from fungi of the Hypocreales order to obtain novel rutinose-conjugates therapeutic agents with enhanced anti-tumoral capacity.

Screening for diglycosidase activity in twenty-eight strains of the genetically related genera Acremonium and Sarocladium identified 6-O-α-rhamnosyl-β-glucosidase (αRβG) of Sarocladium strictum DMic 093557 as candidate enzyme for our studies. Biochemically characterization shows that αRβG has the ability to transglycosylate bulky OH-acceptors, including bioactive compounds. Interestingly, rutinoside-derivatives of phloroglucinol (PR) resorcinol (RR) and 4-methylumbelliferone (4MUR) displayed higher growth inhibitory activity on pancreatic cancer cells than the respective aglycones without significant affecting normal pancreatic epithelial cells. PR exhibited the highest efficacy with an IC50 of 0.89 mM, followed by RR with an IC50 of 1.67 mM, and 4MUR with an IC50 of 2.4 mM, whereas the respective aglycones displayed higher IC50 values: 4.69 mM for phloroglucinol, 5.90 mM for resorcinol, and 4.8 mM for 4-methylumbelliferone. Further, glycoconjugates significantly sensitized pancreatic cancer cells to the standard of care chemotherapy agent gemcitabine.

αRβG from S. strictum transglycosylate-based approach to synthesize rutinosides represents a suitable option to enhance the anti-proliferative effect of bioactive compounds. This finding opens up new possibilities for developing more effective therapies for pancreatic cancer and other solid malignancies.

Alpha-gal syndrome (AGS) is a mammalian meat allergy associated with tick bites and specific IgE to the oligosaccharide galactose-α-1,3-galactose (α-gal). Recent studies have shown that 10-20% of AGS patients also react to the dairy proteins. Considering the already described role of the meat lipid fraction in AGS manifestations, the aim of this work has been to investigate whether the milk fat globule proteins (MFGPs) could be involved in AGS. The MFGPs are extracted and their recognition by the IgE of AGS patients is proved through immunoblotting experiments. The identification of the immunoreactive proteins by LC-HRMS analysis allows to demonstrate for the first time that butyrophillin, lactadherin, and xanthine oxidase (XO) are α-gal glycosylated. The role of xanthine oxidase seems to be prevalent since it is highly recognized by both the anti-α-gal antibody and AGS patient sera. The results obtained in this study provide novel insights in the characterization of α-Gal carrying glycoproteins in bovine milk, supporting the possibility that milk, especially in its whole form, may give reactions in AGS patients. Although additional factors are probably associated with the clinical manifestations, the avoidance of milk and milk products should be considered in individuals with AGS showing symptoms related to milk consumption.

The complex interplay between malignant cells and the cellular and molecular components of the tumor stroma is a key aspect of cancer growth and development. These tumor-host interactions are often affected by soluble bioactive molecules such as proteoglycans. Decorin, an archetypical small leucine-rich proteoglycan primarily expressed by stromal cells, affects cancer growth in its soluble form by interacting with several receptor tyrosine kinases (RTK). Overall, decorin leads to a context-dependent and protracted cessation of oncogenic RTK activity by attenuating their ability to drive a prosurvival program and to sustain a proangiogenic network. Through an unbiased transcriptomic analysis using deep RNAseq, we identified that decorin down-regulated a cluster of tumor-associated genes involved in lymphatic vessel (LV) development when systemically delivered to mice harboring breast carcinoma allografts. We found that Lyve1 and Podoplanin, two established markers of LVs, were markedly suppressed at both the mRNA and protein levels, and this suppression correlated with a significant reduction in tumor LVs. We further identified that soluble decorin, but not its homologous proteoglycan biglycan, inhibited LV sprouting in an ex vivo 3D model of lymphangiogenesis. Mechanistically, we found that decorin interacted with vascular endothelial growth factor receptor 3 (VEGFR3), the main lymphatic RTK, and its activity was required for the decorin-mediated block of lymphangiogenesis. Finally, we identified that Lyve1 was in part degraded via decorin-evoked autophagy in a nutrient- and energy-independent manner. These findings implicate decorin as a biological factor with antilymphangiogenic activity and provide a potential therapeutic agent for curtailing breast cancer growth and metastasis.

Macrophage-based drug delivery systems are promising, but their development is still in its infancy, with many limitations remaining to be addressed. Our aim was to design a system harnessing microbial effectors to facilitate controlled drug cargo expulsion from macrophages to enable the use of more toxic drugs without adding to the risk of off-target detrimental effects. The pore forming and actin polymerizing Listeria monocytogenes effectors listeriolysin-O (LLO) and actin assembly-inducing protein (ActA) were synthesized using a novel green fluorescent protein (GFP)-linked heterologous expression system. These effectors were coated onto polystyrene beads to generate "synthetic cargo" before loading into primary M1 macrophages. Bead uptake and release from macrophages were evaluated by using high-throughput quantitative imaging flow cytometry and confocal microscopy. In vitro results confirmed appropriate activity of synthesized effectors. Coating of these effector proteins onto polystyrene beads (simulated drug cargo) resulted in changes in cellular morphology, bead content, and intracellular bead localization, which may support an interpretation of the induced release of these beads from the cells. This forms the basis for further investigation to fully elucidate any potential release mechanisms. Bacterial effectors ActA and LLO successfully effectuated actin polarization and protrusions from cell membranes similar to those seen in cells infected with Listeria spp., illustrating the potential of using these effectors and production methods for the development of an endogenous drug delivery system capable of low-risk, targeted release of high potency drugs.

The 12th day of gestation is a critical period for embryo loss and the beginning of imminent implantation in sows. Data independent acquisition (DIA) technology is one of the high-throughput, high-resolution and reproducible proteomics technologies for large-scale digital qualitative and quantitative research. The aim of this study was to identify and characterize the protein abundance landscape of Yorkshire pig endometrium on the 12th day of pregnancy (P12) and estrous cycle (C12) using DIA proteomics. A total of 1251 differentially abundant proteins (DAPs) were identified, of which 882 were up-regulated and 369 were down-regulated at P12. Functional enrichment analysis showed that the identified proteins were related to metabolism, biosynthesis and signaling pathways. Three proteins were selected for Western blot (WB) validation and the results were consistent with the DIA data. Further combined with transcriptome data, fibrinogen like 2 (FGL2) and S100 calcium binding protein A8 (S100A8) were verified to be highly abundant in the P12 endometrial epithelium. In summary, there were significantly different abundance of proteome profiles in C12 and P12 endometrium, suggesting that DAPs are associated with changes in endometrial receptivity, which laid the foundation for further research on related regulatory mechanisms. SIGNIFICANCE: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation. SIGNIFICANCE OF THE STUDY: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation.

Avicennia marina is a salt-tolerance plant with high antioxidant and antibacterial potential. In the present work, a gene encoding MnSOD from Avicennia marina (AmSOD2) was cloned in the expression vectors pET28a. The resulting constructs were transformed into Escherichia coli strains Rosetta (DE3). Following the induction with Isopropyl β-D-1-thiogalactopyranoside, the protein His-AmSOD2 was expressed but dominantly found in the insoluble fraction of strain R-AmSOD2. Due to detection of mitochondrial transit peptide in the amino acid sequence of AmSOD2, the transit peptide was removed and AmSOD2 without transit peptide (tAmSOD2) was expressed in E. coli and dominantly found in the soluble fraction. The enzyme His-tAmSOD2 exhibited a molecular mass of 116 kDa in native condition. Nevertheless, in reducing conditions the molecular mass is 28 kDa indicating the enzyme His-tAmSOD2 is a tetramer protein. As shown by ICP analysis there is one mole Mn2+ in each monomer. The Pure His-tAmSOD2 was highly active in vitro, however the activity was almost three-fold lower than His-AmSOD1. Whereas the high stability of the recombinant His-AmSOD1was previously shown after incubation in a broad range pH and high temperature, His-tAmSOD2 was stable up to 50 °C and pH 6 for 1 h. The gene expression analysis showed that the gene encoding AmSOD2 is expressed in root, shoot and leaves of A. marina. In addition, the results show that the expression in the leaves was enhanced after treatment of plant with NaCl, H2O2, Cd2+ and Ni2+ indicating the important role of MnSOD in the resistant mechanism of mangroves.

Extracellular vesicles (EVs) are abundant in body fluid and are critical in cell interaction. Seminal plasma contains numerous EVs which affecting sperm function via transferring regulatory cargoes to the sperm. However, the mechanism of seminal plasma extracellular vesicles (SP-EVs) is still not clear. The present study aimed to isolate the boar SP-EVs and explore its potential function, then identify the key protein involved in SP-EVs and sperms interaction, and elucidate mechanism of SP-EVs protein on sperms. Here, we successfully isolated and concentrated boar SP-EVs, the SP-EVs showed a typical vesicle structure under transmission electron microscopy, most of their diameters range between 50 and 200 nm and express EVs biomarkers CD9 and CD63. We proved that SP-EVs could inhibit sperm acrosome reaction and in vitro fertility. Through a data-independent acquisition analysis of protein profiles of noncapacitated sperms, normal capacitated sperms and SP-EVs treated capacitated sperms, we identified that EZRIN was one of the active proteins that participated in SP-EVs and sperms interaction. Furthermore, we tested that the inhibition of EZRIN could promote boar sperm fertility, which is in consistence with the function of SP-EVs. The results may facilitate future research of SP-EVs on sperm function and male infertility.

The carnivorous plants in the order Caryophyllales co-opted jasmonate signalling from plant defence to botanical carnivory. However, carnivorous plants have at least 11 independent origins, and here we ask whether jasmonate signalling has been co-opted repeatedly in different evolutionary lineages. We experimentally wounded and fed the carnivorous plants Sarracenia purpurea (order Ericales), Cephalotus follicularis (order Oxalidales), Drosophyllum lusitanicum (order Caryophyllales), and measured electrical signals, phytohormone tissue level, and digestive enzymes activity. Coronatine was added exogenously to confirm the role of jasmonates in the induction of digestive process. Immunodetection of aspartic protease and proteomic analysis of digestive fluid was also performed. We found that prey capture induced accumulation of endogenous jasmonates only in D. lusitanicum, in accordance with increased enzyme activity after insect prey or coronatine application. In C. follicularis, the enzyme activity was constitutive while in S. purpurea was regulated by multiple factors. Several classes of digestive enzymes were identified in the digestive fluid of D. lusitanicum. Although carnivorous plants from different evolutionary lineages use the same digestive enzymes, the mechanism of their regulation differs. All investigated genera use jasmonates for their ancient role, defence, but jasmonate signalling has been co-opted for botanical carnivory only in some of them.