RESUMEN

This study evaluated the feasibility of contextually producing hydrogen, microbial proteins, and polyhydroxybutyrate (PHB) using a mixed culture of purple phototrophic bacteria biomass under photo fermentative conditions. To this end, three consecutive batch tests were conducted to analyze the biomass growth curve and to explore the potential for optimizing the production process. Experimental findings indicated that inoculating reactors with microorganisms from the exponential growth phase reduced the duration of the process. Furthermore, the most effective approach for simultaneous hydrogen production and the valorization of microbial biomass was found when conducting the process during the exponential growth phase of the biomass. At this stage, achieved after 3 days of fermentation, the productivities of hydrogen, PHB, and microbial proteins were measured at 63.63 L/m3 d, 0.049 kg/m3 d, and 0.045 kg/m3 d, respectively. The biomass composition comprised a total intracellular compound percentage of 56%, with 27% representing PHB and 29% representing proteins. Under these conditions, the estimated daily revenue was maximized, amounting to 0.6 $/m3 d.

Asunto(s)

RESUMEN

Parkinson's disease (PD) is a neurodegenerative disease characterized by the degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and the formation of Lewy bodies (LBs). The main proteinaceous component of LBs is aggregated α-synuclein (α-syn). However, the mechanisms underlying α-syn aggregation are not yet fully understood. Converging lines of evidence indicate that, under certain pathological conditions, various proteins can interact with α-syn and regulate its aggregation. Understanding these protein-protein interactions is crucial for unraveling the molecular mechanisms contributing to PD pathogenesis. In this review we provide an overview of the current knowledge on protein-protein interactions that regulate α-syn aggregation. Additionally, we briefly summarize the methods used to investigate the influence of protein-protein interactions on α-syn aggregation and propagation.

Asunto(s)

RESUMEN

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Asunto(s)

RESUMEN

After spinal cord injury (SCI), use chronic urinary catheters for bladder management is common, making these patients especially vulnerable to catheter-associated complications. Chronic catheterization is associated with bacterial colonization and frequent catheter-associated urinary tract infections (CAUTI). One determinant of infection success and treatment resistance is production of catheter-associated biofilms, composed of microorganisms and host- and microbial-derived components. To better understand the biofilm microenvironment, we performed proteomics analysis of catheter-associated biofilms and paired urine samples from four people with SCI with chronic indwelling urinary catheters. We developed a novel method for the removal of adhered cellular components on catheters that contained both human and microbial homologous proteins. Proteins from seven microbial species were identified including: Escherichia coli, Klebsiella species (spp), Enterococcus spp, Proteus mirabilis, Pseudomonas spp, Staphylococcus spp, and Candida spp. Peptides identified from catheter biofilms were assigned to 4,820 unique proteins, with 61% of proteins assigned to the biofilm-associated microorganisms, while the remainder were human-derived. Contrastingly, in urine, only 51% were assigned to biofilm-associated microorganisms and 4,554 proteins were identified as a human-derived. Of the proteins assigned to microorganisms in the biofilm and paired urine, Enterococcus, Candida spp, and P. mirabilis had greater associations with the biofilm phase, whereas E. coli and Klebsiella had greater associations with the urine phase, thus demonstrating a significant difference between the urine and adhered microbial communities. The microbial proteins that differed significantly between the biofilm and paired urine samples mapped to pathways associated with amino acid synthesis, likely related to adaptation to high urea concentrations in the urine, and growth and protein synthesis in bacteria in the biofilm. Human proteins demonstrated enrichment for immune response in the catheter-associated biofilm. Proteomic analysis of catheter-associated biofilms and paired urine samples has the potential to provide detailed information on host and bacterial responses to chronic indwelling urinary catheters and could be useful for understanding complications of chronic indwelling catheters including CAUTIs, urinary stones, and catheter blockages.

RESUMEN

Dietary levels of undegraded neutral detergent fiber (uNDF240) and rumen-fermentable starch (RFS) can affect the rumen microbiome and milk composition. The objective of the study is to investigate the use of milk proteins as biomarkers of rumen microbial activity through a comparative evaluation of the rumen microbial and milk protein profiles produced by Holstein cows fed diets with varying contents of physically effective uNDF240 (peuNDF240) and RFS. Eight ruminally cannulated lactating Holstein cows were included in a larger study as part of a 4 × 4 Latin square design with 4 28-d periods to assess 4 diets varying in peuNDF240 and RFS content. For this experiment, cows received one of 2 dietary treatments: (1) low-peuNDF240, high-RFS (LNHR) diet or (2) high-peuNDF240, low-RFS (HNLR) diet. Within each period, rumen fluid samples were collected from each cow on d 26 (1400 h) and d 27 (0600 h and 1000 h), and milk samples were collected from each cow on d 25 (2030 h), d 26 (0430 h, 1230 h, and 2030 h), and d 27 (0430 h and 1230 h). Microbial proteins were isolated from each rumen fluid sample. For milk samples, milk proteins were fractionated, and the whey fraction was subsequently isolated. Isolated proteins within each rumen fluid or milk sample were isobarically labeled and analyzed by liquid chromatography-tandem mass spectrometry. Product ion spectra acquired from rumen fluid samples were searched using SEQUEST against 71 composite databases. In contrast, product ion spectra acquired from milk samples were searched against the Bos taurus database. Data were analyzed using the PROC MIXED procedure in SAS 9.4 to assess the effect of diet and time of sampling. To increase stringency, the false discovery rate-adjusted P-value (PFDR) was also calculated to account for multiple comparisons. Using the mixed procedure, a total of 129 rumen microbial proteins were quantified across 24 searched microbial species. Of these, the abundance of 14 proteins across 9 microbial species was affected due to diet and diet × time interaction, including 7 proteins associated with energetics pathways. Among the 159 quantified milk proteins, the abundance of 21 proteins was affected due to the diet and diet × time interaction. The abundance of 19 of these milk proteins was affected due to diet × time interactions. Of these, 16 proteins had the disparity across diets at the 0430 h sampling time, including proteins involved in host defense, nutrient synthesis, and transportation, suggesting that biological shifts resulting from diet-induced rumen changes are not diurnally uniform across milkings. The concentration of lipoprotein lipase (LPL) was statistically higher in the milk from the cows fed with the LNHR diet, which was numerically confirmed with an ELISA. Further, as determined by ELISA, the LPL concentration was significantly higher in the milk from the cows fed with the LNHR diet at 0430 h sampling point, suggesting that LPL concentration may indicate dietary carbohydrate-induced ruminal changes. The results of this study suggest that diet-induced rumen changes can be reflected in milk in a diurnal pattern, further highlighting the need to consider sampling time points for using milk proteins as a representative biomarker of rumen microbial activity.

Asunto(s)

RESUMEN

Arthrospira platensis is an edible cyanobacterium with high nutritional value. Even though A. platensis is not a marine species, it can be adapted to higher salinities, a strategy that could allow mass cultivation using brackish or saline water. In this work A. platensis was long-term adapted at different salinities (5-60 g/L NaCl added as natural sea salt) to evaluate the growth and biochemical composition of the biomass produced. Biomass production was enhanced in salinity up to 40 g/L NaCl, while at 60 g/L NaCl biomass production slightly decreased. However, it displayed higher values compared to the conventional Zarrouk growth medium. By increasing the salinity, carbohydrate content increases, while proteins, phycocyanin, carotenoids, and total phenolics decreased. Biomass content in lipids, and chlorophyll along with the antioxidant capacity of extracts, was not significantly affected. A. platensis tended to increase the unsaturated fatty acids, while amino acid composition was not significantly affected by the increased salinity. However, in vitro protein digestibility was negatively affected when salinity was above 20 g/L NaCl. It was macroscopically observed that trichomes were longer at higher salinities, and especially at 40 g/L NaCl. The results suggest that A. platensis when acclimated in long-term can be grown successfully at various salinities.

RESUMEN

We aimed to determine the optimal inclusion level of sunflower cake (0, 90, 180, and 270 g/kg total DM) as a partial replacement of soybean meal and corn ground in young bulls' diets by examining nutrient intake and digestibility, ingestive behavior, nitrogen balance, metabolic serum profile, growth performance, and carcass traits. Thirty-two intact Nellore bulls (BW 374 ± 42.5) were distributed in a completely randomized design. The experiment lasted 90 days. The final BW of the animals was 515.25 ± 24.7. There was a linear decrease effect in the intake of DM, crude protein and nonfibrous carbohydrates, eating and rumination efficiency, N-urinary, N-total excretion, and blood urea nitrogen. Sunflower cake did not affect the NDF digestibility, nitrogen (N)-fecal excretion, blood metabolites, Longissimus lumborum muscle area, or subcutaneous fat deposition. There were linear and quadratic effects on the eating and rumination time, microbial protein production and efficiency, gamma-glutamyl transferase and cholesterol serum concentrations, and muscle carcass tissue. There was a quadratic effect on ether extract intake, final BW, and total gain with the inclusion of sunflower cake in the young bull's diet. The replacement of soybean meal and corn ground with sunflower cake at the level of 90 g/kg of DM in the diet of young bulls is recommended because it reduces the DM intake and digestibility, increases microbial protein synthesis and muscle tissue deposition, and consequently improves the performance, feed efficiency, and carcass traits.

RESUMEN

Opposing roles have been proposed for IL-22 in intestinal pathophysiology. We have optimized human small intestinal organoid (hSIO) culturing, constitutively generating all differentiated cell types while maintaining an active stem cell compartment. IL-22 does not promote the expansion of stem cells but rather slows the growth of hSIOs. In hSIOs, IL-22 is required for formation of Paneth cells, the prime producers of intestinal antimicrobial peptides (AMPs). Introduction of inflammatory bowel disease (IBD)-associated loss-of-function mutations in the IL-22 co-receptor gene IL10RB resulted in abolishment of Paneth cells in hSIOs. Moreover, IL-22 induced expression of host defense genes (such as REG1A, REG1B, and DMBT1) in enterocytes, goblet cells, Paneth cells, Tuft cells, and even stem cells. Thus, IL-22 does not directly control the regenerative capacity of crypt stem cells but rather boosts Paneth cell numbers, as well as the expression of AMPs in all cell types.

Asunto(s)

RESUMEN

Autoimmune diseases develop when the immune system targets healthy cells and tissues of an individual. In developing countries, S. typhi (a gram-negative pathogenic bacteria) remains a major public health issue. This study aimed to employ bioinformatics analyses to determine the 3D structural-based molecular mimicry and sequence of S. typhi and human host proteins. In addition, to classify possible antigenic microbial peptides homologous to human peptides and comprehend the molecular basis of S. typhi-related autoimmune disorders. Protein sequences were obtained from the NCBI database, and redundancy was removed using the CD-HIT tool. The BLASTp comparative sequence analysis was followed for molecular mimicry identification of human and S. typhi protein sequences. The PathDIP database was utilized to simulate essential physical relationships between proteins and curated pathways for metabolic processes. Subsequently, the IEDB database was used to find cross-reactive MHC class-II binding epitopes that could trigger an autoimmune reaction. SPARKS-X computational biology resource was also used to determine the structural homology between human and S. typhi peptides. The BLASTp study showed that S. typhi and the human host have several proteins holding considerable sequence similarities based on a set threshold of e ≤ 10-6 and bit score ≥100. The PathDIP putatively identified that these proteins enriched in a total of 68 metabolic pathways by a significant P-value (P < 0.005). The PSORTb analysis predicted that 26 out of these proteins are cytosolic, 1 predicted to be periplasmic protein, and 1 predicted to be localized in the cytoplasmic membrane. IEDB data analysis predicted many S.typhi and human homologs epitopes as a good binder of human HLA, i.e. DRB1*01:01, DPA1*03:01/DPB1*04:02, and DQA1*01:02/DQB1*06:02 with IC50 < 50 nM. Finally, the docking data demonstrated that homolog lead epitopes promisingly interact with HLA and immune TLR4 receptors by exhibiting the best docking scores and molecular interactions. The analyses ultimately identified several potential candidate proteins and peptides that could cause S.typhi infection-mediated autoimmune diseases in humans.

Asunto(s)

RESUMEN

Consumer interest in protein rich diets is increasing, with more attention being paid to the protein source. Despite the occurrence of animal proteins in the human diet, non-animal proteins are gaining popularity around the world due to their health benefits, environmental sustainability, and ethical merit. These sources of protein qualify for vegan, vegetarian, and flexitarian diets. Non-animal proteins are versatile, derived mainly from cereals, vegetables, pulses, algae (seaweed and microalgae), fungi, and bacteria. This review's intent is to analyze the current and future direction of research and innovation in non-animal proteins, and to elucidate the extent (limitations and opportunities) of their applications in food and beverage industries. Prior knowledge provided relevant information on protein features (processing, structure, and techno-functionality) with particular focus on those derived from soy and wheat. In the current food landscape, beyond conventionally used plant sources, other plant proteins are gaining traction as alternative ingredients to formulate animal-free foodstuffs (e.g., meat alternatives, beverages, baked products, snack foods, and others). Microbial proteins derived from fungi and algae are also food ingredients of interest due to their high protein quantity and quality, however there is no commercial food application for bacterial protein yet. In the future, key points to consider are the importance of strain/variety selection, advances in extraction technologies, toxicity assessment, and how this source can be used to create food products for personalized nutrition.

Asunto(s)

RESUMEN

The present study aimed to explore the antimicrobial potentials of soil bacteria and identify the bioactive compounds and their likely targets through in silico studies. A total 53 bacterial isolates were screened for their antimicrobial potential of which the strain JRBHU6 showing highest antimicrobial activity was identified as Burkholderia seminalis (GenBank accession no. MK500868) based on 16S ribosomal RNA (rRNA) gene sequencing and phylogenetic analysis. B. seminalis JRBHU6 also produced hydrolytic enzymes chitinases and cellulase of significance in accrediting its antimicrobial nature. The bioactive metabolites produced by the isolate were extracted in different organic solvents among which methanolic extract showed best growth-suppressing activities toward multidrug resistant Staphylococcus aureus and fungal strains, viz Fusarium oxysporum, Aspergillus niger, Microsporum gypseum, Trichophyton mentagrophytes, and Trichoderma harzianum. The antimicrobial compounds were purified using silica gel thin layer chromatography and high-performance liquid chromatography (HPLC). On the basis of spectroscopic analysis, the bioactive metabolites were identified as pyrrolo(1,2-a)pyrazine-1,4-dione,hexahydro (PPDH) and pyrrolo(1,2-a)pyrazine-1,4-dione, hexahydro-3(2-methylpropyl) (PPDHMP). In silico molecular docking studies showed the bioactive compounds targeting fungal and bacterial proteins, among which PPDHMP was multitargeting in nature as reported for the first time through this study.

RESUMEN

Metaproteomics is a powerful tool for obtaining data on all proteins recovered directly from environmental samples at a given time. It provides a direct evidence of functional diversity and structure among microbiota present in niches and significant insights into microbial activity together with metabolomics, which is the study of the intermediate and end-products of cellular processes. Metaproteomics is a comparatively new approach which is facing a number of empirical, technical, computational and experimental design challenges that needs to be addressed. Presently only little efforts have been made to have information on microbial proteins in rhizospheric soil of maize through metagemonics approach but there is no direct evidence on functions of microbial community in this very important niche. Since rhizosphere microbiome plays important role in plant growth and development the present study is conducted to optimize the metaproteomic extraction protocol from maize rhizosphere and analyse functionality of microbial communities. We present metaproteome data from maize rhizospheric soil. Isolation of metaproteome from maize rhizosphere collected from ICAR-IISS, Mau experimental Farm was done with the standardized protocol at our laboratory and metaproteome analysis was done with the standardized pipeline. In total 696 proteins with different functions representing 244 genus and 393 species were identified. The proteome data provides direct evidence on the biological processes in soil ecosystem and is the first reported reference data from maize rhizosphere. The LC MS/MS proteomic data are available via ProteomeXchange with identifier PXD014519.

RESUMEN

The objective of this study was to characterise the variation of utilisable crude protein at the duodenum (uCP) of dried distillers' grains with solubles (DDGS) for ruminants using a modified gas test and to predict the uCP in DDGS based on chemical composition. Thirteen samples originating from wheat, maize, barley or blends of different substrates were studied. The in vitro uCP was estimated using the modified Hohenheim gas test (moHGT). Samples were incubated in rumen fluid for 8 h, 24 h and 48 h followed by ammonia distillation. The obtained values were compared to reference values of uCP (based on the contents of crude protein (CP), in situ undegraded CP and metabolisable energy). The reference and in vitro values of uCP were calculated according to passage rates of 2, 5 and 8%/h (i.e., uCP2, uCP5 and uCP8, respectively). The in vitro uCP8 ranged from 214 to 320 g/kg DM and reference values from 158 to 302 g/kg DM. The in vitro uCP2 was on average lower (by 7 g/kg DM) and in vitro uCP8 was higher (by 56 g/kg DM) than their respective reference values. The in vitro uCP5 and uCP8 were correlated with reference values and the correlations were improved with increasing passage rates. When the differences of uCP content between in vitro and reference values were related to CP fractions, they increased with increasing content of CP fraction A and decreasing content of CP fraction B3 for uCP8. The prediction of uCP values from chemical composition was not reliable. It was concluded that uCP can be predicted on the basis of the moHGT method and CP fractions. The accuracy of prediction improved upon the inclusion of CP fractions and neutral-detergent insoluble nitrogen. The present study revealed a significant variation in the uCP content of DDGS, which should be considered when formulating rations for dairy cows.

Asunto(s)