Solubilization of trichloroacetic acid (TCA) precipitated microbial proteins via naOH for two-dimensional electrophoresis

Potential protein biomarkers in saliva for detection of frailty syndrome by targeted proteomics

Frailty is a physiological geriatric syndrome, caused by immunosenescence, inflammation and alterations at the protein level leading to metabolic and microbiota changes. Currently, this syndrome is evaluated clinically with the Frailty-VIG index. The aim of the study was therefore to investigate the potential suitability of saliva as a non-invasive proximal biological fluid for the characterisation and identification of possible protein-level biomarkers in frailty syndrome. This cross-sectional study was conducted in a rural population of older Spanish adults using the SMR proteomics technique. A differential protein profile of eight potential and surrogate proteins (CYTC, CYTD, CYTS, CYTB, MIF, ALBU, CD44 and B2MG) was detected in saliva, all of which correlated with factors characterising frailty syndrome, such as vascular ageing (arterial stiffness and cardiovascular disease), obesity, mood problems, global cognitive impairment, changes in gait and hand pressure strength. The proteins CYTD (r = 0.415, p = 0.013) and CYTC (r = 0.280, p = 0.026), which were detected differentially in the protein profile, were associated with the Frailty-VIG index. All analysed proteins are associated not only with the clinical symptoms of frailty syndrome, but also with an acute inflammatory response, endothelial cell proliferation and the complement system, among others.

Optimum Fermentation Conditions for Bovine Lactoferricin-Lactoferrampin-Encoding LimosiLactobacillus reuteri and Regulation of Intestinal Inflammation

The multifunctional antibacterial peptide lactoferricin-lactoferrampin (LFCA) is derived from bovine lactoferrin. Optimization of the fermentation process should be studied since different microorganisms have their own favorable conditions and processes for growth and the production of metabolites. In this study, the culture conditions of a recombinant strain, pPG-LFCA-E/LR-CO21 (LR-LFCA), expressing LFCA was optimized, utilizing the high-density fermentation process to augment the biomass of LimosiLactobacillus reuteri and the expression of LFCA. Furthermore, an assessment of the protective effect of LR-LFCA on intestinal inflammation induced by lipopolysaccharide (LPS) was conducted to evaluate the impact of LR-LFCA on the disease resistance of piglets. The findings of this study indicate that LR-LFCA fermentation conditions optimally include 2% inoculation volume, 36.5 °C fermentation temperature, 9% dissolved oxygen concentration, 200 revolutions/minute stirring speed, pH 6, 10 mL/h glucose flow, and 50% glucose concentration. The inclusion of fermented LR-LFCA in the diet resulted in an elevation of immunoglobulin levels, significant upregulation of tight junction proteins ZO-1 and occludin, reinforcement of the intestinal barrier function, and significant amelioration of the aberrant alterations in blood physiological parameters induced by LPS. These results offer a theoretical framework for the implementation of this micro-ecological preparation in the field of piglet production to enhance intestinal well-being.

Production of L-Malic Acid by Metabolically Engineered Aspergillus nidulans Based on Efficient CRISPR-Cas9 and Cre-loxP Systems

Aspergillus nidulans has been more extensively characterized than other Aspergillus species considering its morphology, physiology, metabolic pathways, and genetic regulation. As it has a rapid growth rate accompanied by simple nutritional requirements and a high tolerance to extreme cultural conditions, A. nidulans is a promising microbial cell factory to biosynthesize various products in industry. However, it remains unclear for whether it is also a suitable host for synthesizing abundant L-malic acid. In this study, we developed a convenient and efficient double-gene-editing system in A. nidulans strain TN02A7 based on the CRISPR-Cas9 and Cre-loxP systems. Using this gene-editing system, we made a L-malic acid-producing strain, ZQ07, derived from TN02A7, by deleting or overexpressing five genes (encoding Pyc, pyruvate carboxylase; OahA, oxaloacetate acetylhydrolase; MdhC, malate dehydrogenase; DctA, C4-dicarboxylic acid transporter; and CexA, citric acid transporter). The L-malic acid yield in ZQ07 increased to approximately 9.6 times higher (up to 30.7 g/L titer) than that of the original unedited strain TN02A7, in which the production of L-malic acid was originally very low. The findings in this study not only demonstrate that A. nidulans could be used as a potential host for biosynthesizing organic acids, but also provide a highly efficient gene-editing strategy in filamentous fungi.

Combination of untargeted and targeted proteomics for secretome analysis of L-WRN cells

Organoid culture is a promising biomedical technology that requires specialized growth factors. Recently, a recombinant L-WRN cell line has been extensively used to generate conditioned medium (L-CM) for organoid culture. Nevertheless, methods for evaluating the stability of the L-WRN cells have been limited. In this study, a novel proteomics-based approach was developed to analyze the secretome of the cells. Serum-free L-CM was lyophilized, precipitated by trichloroacetic acid, and desalted prior to analysis by liquid chromatography-tandem mass spectrometry. Data-dependent acquisition (DDA) was conducted for the untargeted secretome profiling of the cells, and parallel reaction monitoring (PRM) was applied for the targeted quantification of the Wnt3A, R-spondin3, and noggin proteins (WRNs). This study also compared the performance of two types of PRM methods, namely MS1-independent PRM and MS1-dependent PRM, that can be executed on an Orbitrap instrument. The results showed that the growth of mouse intestinal organoids was closely related to the use of L-CM. The composition of L-CM could be markedly affected by the medium collection scheme. A total of 1725, 2302, and 2681 proteins were identified from the L-CM collected on day 5, day 9, and day 13, respectively. The MS1-independent PRM outperformed the MS1-dependent PRM and effectively quantified the WRNs with high repeatability and specificity. In conclusion, by integrating untargeted and targeted proteomics, this study develops a mass spectrometry-based method for the secretome analysis and quality control of the L-WRN cells. The methodology and findings of the present work will benefit future studies on organoids and secretomes.

In Vitro Modulation of Rumen Fermentation by Microbiota from the Recombination of Rumen Fluid and Solid Phases

Rumen microbiota transplantation (RMT) can improve rumen fermentation and ruminant performance. However, due to the microbial distinction in the fluid and solid phases, the current understanding of their specific roles in RMT is insufficient. Thus, this study was conducted to determine the effects of the microbiota from the recombination of the rumen fluid and solid phases on in vitro fermentation. The rumen fresh fluid (FF) and fresh solid (FS) phases were collected, and FS was washed for the fresh solid washing solution (FW). The fractions of FF, FS, and FW were autoclaved to obtain autoclaved fluid (AF), solid (AS), and washing solution (AW). Then, these phases were recombined to form eight treatments: FFFS, FFAS, FFFW, FFAW, AFFS, AFAS, AFFW, and AFAW. After 24 h of fermentation, the gas production in AFFS, FFFS, and FFAS was significantly higher than that of other groups. AFAS and AFAW had significantly lower alpha diversity than did other groups. The solid phase was enriched with fiber-degrading bacteria, including Treponema, Succinivibrio, and Ruminococcus. The fluid phase was dominated by Prevotella, Christensenellaceae R-7 group, and Rikenellaceae RC9 gut group. The washing solution had more Ruminobacter, Lachnospiraceae, and Fibrobacter. Moreover, the double-autoclaved phases displayed increased abundances of harmful bacteria, as AFAS and AFAW had higher Streptococcus and Prevotellaceae YAB2003 group abundances. A network analysis showed that the signature microbiota in AFAS and AFAW were negatively associated with the keystone microbiota in the other groups. In summary, the recombination of the solid phase and the autoclaved fluid phase had the best in vitro fermentation result, which provided certain references for RMT. IMPORTANCE This is the first study to systematically evaluate the in vitro fermentation efficiency of diets by bacteria harvested and recombined from the fluid and solid phases of rumen contents, and it took into account the effect of washing the rumen solid phase. Using "reconstituted rumen content", this study confirmed that bacteria from different fractions of the rumen digesta resulted in different fermentation production of diets and found the characteristic bacteria in each phase of rumen contents. Our data reveal that the bacteria in the solid phase have more positive effects on the in vitro fermentation parameters, that the combination of the autoclaved fluid phase and the fresh solid phase have the most ideal fermentation effect, and that the autoclave process significantly influenced the microbial composition and increased the abundance of harmful bacteria. This study provides a landmark reference for the future use of rumen microbiota transplantation to improve animal feed utilization and growth performance.

De-oiled palm kernel cake for stall-fed buffaloes: effect on milk constituents, nutrient digestibility, biochemical parameters, and rumen fermentation

Palm kernel cake, the main by-product of the palm kernel oil extraction process, is a highly available and low-priced agro-industrial by-product. However, several concerns exist to arriving at a safe inclusion level, especially for buffaloes. Two experiments were conducted to evaluate the effects of feeding de-oiled palm kernel cake (DPKC) to tropical buffaloes. In trial I, four fistulated Murrah buffaloes arranged in a 4 × 4 Latin square design were fed diets containing DPKC inclusions at 0, 15, 30, and 45% levels of compound feed to study their effects on rumen fermentation parameters. Trial II involves feeding twelve lactating buffaloes with DPKC inclusion levels at 0 or 15% of the compound feed to evaluate the effect of DPKC on the nutrient digestibility, serum biochemical constituents, rumen fermentation patterns, and lactation profile. The DPKC diets did not affect rumen pH, TCA-ppt nitrogen, and TVFA proportion; nevertheless, the NH₃-N data revealed a decreased trend (P = 0.076). The acetate fraction decreased linearly (P < 0.05) with increased DPKC diets. Replacing the conventional protein sources with DPKC at a 15% level did not influence the nutrient intake and digestibility coefficients. No significant effects were observed for serum biochemical and mineral profiles of the lactating buffaloes fed the DPKC diet. Neither milk yield nor milk constituents (SNF, total solids, density, lactose, protein) were altered with the diets fed, except for milk fat%, which tended to increase (P = 0.092) on feeding DPKC diets. All the lactation parameters varied with time of collection, and diet × time interactions were noticed for fat, density, protein, 6% FCM yield, and butterfat yield. The feed efficiency tended to increase (P = 0.070) in the buffaloes fed DPKC diets. The profit margins were ₹6.07 and ₹1.63 for the DPKC included diets and feed cost per Kg 6% FCMY, respectively. In  conclusion, the inclusion of DPKC in the diet decreases feed cost without affecting the nutrient intakes, digestibility coefficients, serum biochemical and mineral profile, and lactation parameters.

A bovine lactoferricin-lactoferrampin-encoding Lactobacillus reuteri CO21 regulates the intestinal mucosal immunity and enhances the protection of piglets against enterotoxigenic Escherichia coli K88 challenge

Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in human and animal. To determine the mechanism of a bovine lactoferricin-lactoferrampin (LFCA)-encoding Lactobacillus reuteri CO21 (LR-LFCA) to enhance the intestinal mucosal immunity, we used a newborn piglet intestine model to study the intestinal response to ETEC. Pigs were chosen due to the anatomical similarity between the porcine and the human intestine.4-day-old piglets were orally administered with LR-LFCA, LR-con (L. reuteri CO21 transformed with pPG612 plasmid) or phosphate buffered saline (PBS) for three consecutive days, within 21 days after these treatments, we found that LR-LFCA can colonize the intestines of piglets, improve the growth performance, enhance immune response and is beneficial for intestinal health of piglets by improving intestinal barrier function and modulating the composition of gut microbiota. Twenty-one days after, piglets were infected with ETEC K88 for 5 days, we found that oral administration of LR-LFCA to neonatal piglets attenuated ETEC-induced the weight loss of piglets and diarrhea incidence. LR-LFCA decreased the production of inflammatory factors and oxidative stress in intestinal mucosa of ETEC-infected piglets. Additionally, LR-LFCA increased the expression of tight junction proteins in the ileum of ETEC-infected piglets. Using LPS-induced porcine intestinal epithelial cells (IPEC-J2) in vitro, we demonstrated that LR-LFCA-mediated increases in the tight junction proteins might depend on the MLCK pathway; LR-LFCA might increase the anti-inflammatory ability by inhibiting the NF-κB pathway. We also found that LR-LFCA may enhance the antioxidant capacity of piglets by activating the Nrf2/HO-1 pathway. This study demonstrates that LR-LFCA is effective at maintaining intestinal epithelial integrity and host homeostasis as well as at repairing intestinal damage after ETEC infection and is thus a promising alternative therapeutic method for intestinal inflammation.

The CCAAT-binding complex mediates azole susceptibility of Aspergillus fumigatus by suppressing SrbA expression and cleavage

In fungal pathogens, the transcription factor SrbA (a sterol regulatory element-binding protein, SREBP) and CBC (CCAAT binding complex) have been reported to regulate azole resistance by competitively binding the TR34 region (34 mer) in the promoter of the drug target gene, erg11A. However, current knowledge about how the SrbA and CBC coordinately mediate erg11A expression remains limited. In this study, we uncovered a novel relationship between HapB (a subunit of CBC) and SrbA in which deletion of hapB significantly prolongs the nuclear retention of SrbA by increasing its expression and cleavage under azole treatment conditions, thereby enhancing Erg11A expression for drug resistance. Furthermore, we verified that loss of HapB significantly induces the expression of the rhomboid protease RbdB, Dsc ubiquitin E3 ligase complex, and signal peptide peptidase SppA, which are required for the cleavage of SrbA, suggesting that HapB acts as a repressor for these genes which contribute to the activation of SrbA by proteolytic cleavage. Together, our study reveals that CBC functions not only to compete with SrbA for binding to erg11A promoter region but also to affect SrbA expression, cleavage, and translocation to nuclei for the function, which ultimately regulate Erg11A expression and azole resistance.

Effect of Sample Preparation on the Detection and Quantification of Selected Nuts Allergenic Proteins by LC-MS/MS

The detection and quantification of nut allergens remains a major challenge. The liquid chroma-tography tandem mass spectrometry (LC-MS/MS) is emerging as one of the most widely used methods, but sample preparation prior to the analysis is still a key issue. The objective of this work was to establish optimized protocols for extraction, tryptic digestion and LC-MS analysis of almond, cashew, hazelnut, peanut, pistachio and walnut samples. Ammonium bicar-bonate/urea extraction (Ambi/urea), SDS buffer extraction (SDS), polyvinylpolypyrroli-done (PVPP) extraction, trichloroacetic acid/acetone extraction (TCA/acetone) and chloro-form/methanol/sodium chloride precipitation (CM/NaCl) as well as the performances of con-ventional tryptic digestion and microwave-assisted breakdown were investigated. Overall, the protein extraction yields ranged from 14.9 ± 0.5 (almond extract from CM/NaCl) to 76.5 ± 1.3% (hazelnut extract from Ambi/urea). Electrophoretic profiling showed that the SDS extraction method clearly presented a high amount of extracted proteins in the range of 0-15 kDa, 15-35 kDa, 35-70 kDa and 70-250 kDa compared to the other methods. The linearity of the LC-MS methods in the range of 0 to 0.4 µg equivalent defatted nut flour was assessed and recovery of internal standards GWGG and DPLNV(d8)LKPR ranged from 80 to 120%. The identified bi-omarkers peptides were used to relatively quantifier selected allergenic protein form the inves-tigated nut samples. Considering the overall results, it can be concluded that SDS buffer allows a better protein extraction from almond, peanut and walnut samples while PVPP buffer is more appropriate for cashew, pistachio and hazelnut samples. It was also found that conventional overnight digestion is indicated for cashew, pistachio and hazelnut samples, while microwave assisted tryptic digestion is recommended for almond, hazelnut and peanut extracts.

The study of stress conditions on growth and proteome of Raoultella planticola: a new emerging pathogen

All bacteria can survive and adapt to different stresses, such as fluctuations in temperature, pH oxidative, and osmotic pressure occurring in their surrounding environments. This study aims to evaluate the effects of a variety of stress conditions on the growth, and proteome of Raoultella planticola PTCC 1598. R. planticola cells were exposed to different values of temperatures, sodium chloride, pH, and hydrogen peroxide stresses. Among the stress conditions, oxidative stress, upon exposure to hydrogen peroxide (H₂O₂) at 4000 ppm concentration was selected for proteomics analysis in detail. Approximately, 1400 spots were identified in two-dimensional gel electrophoresis (2-DE). Among the identified spots, 85 spots were repeatable using 2D-Platinum software and eye confirmation and, nine protein spots were differentially expressed. Among nine proteins, six proteins identified successfully with an MASCOT score greater than 40 (p < 0.05) were 2,3-dihydroxybenzoate-2,3-dehydrogenase (oxidoreductase family), hypothetical protein G787-04832, periplasmic D-galactose-binding protein, uridine phosphorylase (glycosyltransferases), a single peptide match to cysteine-binding periplasmic protein, and NADP(H) nitroreductase. All identified proteins showed decreased level expression. Based on the obtained results, we concluded that hydrogen peroxide as an antiseptic compound could affect cell growth and proteomics of R. planticola. Therefore, we recommend using an antiseptic solution containing H₂O₂ to prevent the spread of R. planticola as a new emerging pathogen.

Ccm1p is a 15S rRNA primary transcript processing factor as elucidated by a novel in vivo system in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the mitoribosomal RNA of the minor subunit, 15S rRNA, is transcribed as a bicistronic transcript along with tRNA^W. 5' and 3' sequences flanking the mature transcript must be removed by cleavage at the respective junctions before incorporating it into the mitoribosome. An in vivo dose-response triphasic system was created to elucidate the role of Ccm1p in the processing of 15S rRNA: Ccm1p supply ("On"), deprivation ("Off"), and resupply ("Back on"). After 72 h under "Off" status, the cells started to exhibit a complete mutant phenotype as assessed by their lack of growth in glycerol medium, while keeping their mitochondrial DNA integrity (ρ⁺). Full functionality of mitochondria was reacquired upon "Back on." 15S rRNA levels and phenotype followed the Ccm1p intramitochondrial concentrations throughout the "On-Off-Back on" course. Under "Off" status, cells gradually accumulated unprocessed 5' and 3' junctions, which reached significant levels at 72-96 h, probably due to a saturation of the mitochondrial degradosome (mtEXO). The Ccm1p/mtEXO mutant (Δccm1/Δdss1) showed a copious accumulation of 15S rRNA primary transcript forms, which were cleaved upon Ccm1p resupply. The gene that codes for the RNA component of RNase P was conserved in wild-type and mutant strains. Our results indicate that Ccm1p is crucial in processing the 15S rRNA primary transcript and does not stabilize the already mature 15S rRNA. Consequently, failure of this function in Δccm1 cells results, as it happens to any other unprocessed primary transcripts, in total degradation of 15S rRNA by mtEXO, whose mechanism of action is discussed.

Towards the Properties of Different Biomass-Derived Proteins via Various Extraction Methods

This study selected three representative protein-rich biomass-brewer's spent grain (BSG), pasture grass (PG), and cyanobacteria (Arthrospira platensis; AP) for protein extraction with different extraction methods (alkaline treatment, aqueous extraction, and subcritical water extraction). The yield, purity, molecular weight, oil-water interfacial tension, and thermal stability of the obtained proteins derived from different biomass and extraction methods were comprehensively characterized and compared. In the view of protein yield and purity, alkaline treatment was found optimal for BSG (21.4 and 60.2 wt.%, respectively) and AP (55.5 and 68.8 wt.%, respectively). With the decreased oil-water interfacial tension, the proteins from all biomass showed the potential to be emulsifier. BSG and AP protein obtained with chemical treatment presented excellent thermal stability. As a novel method, subcritical water extraction is promising in recovering protein from all three biomass with the comparable yield and purity as alkaline treatment. Furthermore, the hydrolyzed protein with lower molecular weight by subcritical water could promote its functions of foaming and emulsifying.

Environmental sustainability assessment of tropical dairy buffalo farming vis-a-vis sustainable feed replacement strategy

Feeding management in dairy animals is crucial for ensuring optimal production apart from making the farming as a whole, a more sustainable activity. In our study we evaluated the production and environmental effects of two different feeding regimens i.e., one dominated by traditional cottonseed meal (CSM) and other with coated urea (slow release urea - SRU) as a replacement for CSM on dairy buffalo production. The SRU at 2% level was evaluated by conducting two different trials using twelve lactating Murrah buffaloes and four adult Murrah buffalo bulls. Neither diet nor dry period management showed any substantial effect on milk components, intakes, nutrients’ digestibility coefficients, and nutritive values. The SRU diet revealed increased (P < 0.01) rumen pH, ammonia nitrogen, volatile fatty acids, and microbial nitrogen yield, which were interacted with time of post-prandial sampling. The dynamics of nitrogen metabolism revealed unaltered N-based parameters, except for degradable-N intake and serum urea-N at 3 hr post-feeding. The CSM replacements did not influence (P > 0.05) the residual feed intake, but led to an enhanced milk retention efficiency of nitrogen, calcium, and phosphorus contents, thus reducing their impact on soil pollution and eutrophication of water bodies. Despite an unaltered (P > 0.05) enteric methane emission, SRU diets achieved in decreasing manure methane and nitrous oxide emission. Furthermore, the virtual water flow and lifecycle assessment revealed a water sparing effect and low carbon foot print per unit milk production. In summary, the CSM replacements with SRU could achieve an economical and eco-friendly production system from animal nutrition perspective.

Expression of metallothionein encoding gene bmtA in biofilm-forming marine bacterium Pseudomonas aeruginosa N6P6 and understanding its involvement in Pb(II) resistance and bioremediation

The genetic basis and biochemical aspects of heavy metal endurance abilities have been precisely studied in planktonic bacteria; however, in nature, bacteria mostly grows as surface-attached communities called biofilms. A hallmark trait of biofilm is increased resistance to heavy metals compared with the resistance of planktonic bacteria. A proposed mechanism that contributes to this increased resistance is the enhanced expression of metal-resistant genes. bmtA gene coding for metallothionein protein is one such metal-resistant gene found in many bacterial spp. In the present study, lead (Pb) remediation potential of a biofilm-forming marine bacterium Pseudomonas aeruginosa N6P6 was explored. Biofilm-forming marine bacterium P. aeruginosa N6P6 possess bmtA gene and shows resistance towards many heavy metals, i.e., Pb, Cd, Hg, Cr, and Zn. The expression of metallothionein encoding gene bmtA is significantly high in 48-h-old biofilm culture (11. 4 fold) followed by 24-h-old biofilm culture of P. aeruginosa N6P6 (4.7 fold) (P < 0.05). However, in the case of planktonically grown culture of P. aeruginosa N6P6, the highest expression of bmtA gene was observed in 24-h-old culture. The expression of bmtA also increased significantly with increase in Pb concentration up to 800 ppm. CSLM analysis indicated significant reduction in the raw integrated density of biofilm-associated lipids and polysaccharides (PS) of P. aeruginosa N6P6 biofilm grown in Pb (sub-lethal concentration)-amended medium (P < 0.05), whereas no significant reduction was observed in the raw integrated density of EPS-associated protein. The role of bmtA gene as Pb(II)-resistant determinant was characterized by overexpressing the bmtA gene derived from P. aeruginosa N6P6 in Escherichia coli BL21(DE3). ESI-MS and SDS-PAGE analyses validated the presence of 11.5-kDa MT protein isolated from Pb(II)-induced recombinant E. coli BL21(DE3) harboring bmtA gene.

Effects of Lactococcus lactis MG1363 producing fusion proteins of bovine lactoferricin-lactoferrampin on growth, intestinal morphology and immune function in weaned piglet

AIMS

We developed a strategy for localized delivery of the LFCA (lactoferricinlactoferrampin), which is actively synthesized in situ by Lactococcus lactis (pAMJ399-LFCA/LLMG1363), and explored the possibility of using pAMJ399-LFCA/LLMG1363 as an alternative additive diet to antibiotics.

METHODS AND RESULTS

The antimicrobial activities of the LFCA derived from pAMJ399-LFCA/LLMG1363 were tested in vitro. The results showed that LFCA had an inhibitory effect on Staphylococcus aureus, Escherichia coli and Salmonella enteritidis. Then, the pAMJ399-LFCA/LLMG1363 was used as an additive diet for piglets. Our data demonstrated that oral administration of pAMJ399-LFCA/LLMG1363 significantly improved the average daily gain, feed-to-gain ratio, intestinal mucosal integrity and decreased the serum endotoxin and d-lactic acid levels. The mRNA expression levels of intestinal tight junction proteins (including occludin, Claudin-1 and ZO-1) were significantly upregulated by pAMJ399-LFCA/LLMG1363 administration. The serum immunoglobulin G (IgG) levels, intestinal secretory immunoglobulin A (sIgA) levels, IL-2, IL-10 and TGF-β levels were significantly increased by pAMJ399-LFCA/LLMG1363. Furthermore, our data revealed that oral administration of pAMJ399-LFCA/LLMG1363 significantly increased the number of general Lactobacillus, and decreased the total viable E. coli counts in the ileum and cecum contents.

CONCLUSIONS

We developed a novel pAMJ399-LFCA/LLMG1363 secreting LFCA, which had probiotic effects on the growth performance, intestinal morphology, intestinal barrier function and immunological indices of weaned piglets.

SIGNIFICANCE AND IMPACT OF THE STUDY

pAMJ399-LFCA/LLMG1363, with probiotic effects on the health of weaned piglets, may be a promising feed additive for weaned piglets.

Oral delivery of a Lactococcus lactis strain secreting bovine lactoferricin-lactoferrampin alleviates the development of acute colitis in mice

Ulcerative colitis (UC) is a chronic relapsing disease. Treatment of UC would benefit from specific targeting of therapeutics to the intestine. Previous studies have demonstrated that bovine lactoferricin and lactoferrampin have bactericidal, anti-inflammatory, and immunomodulatory effects. Here, we investigated whether oral administration of a bovine lactoferricin-lactoferrampin (LFCA)-encoding Lactococcus lactis (LL-LFCA) strain could alleviate experimental colitis. LFCA derived from LL-LFCA inhibited the growth of Escherichia coli and Staphylococcus aureus in vitro. In mice, administration of LL-LFCA decreased the disease activity index and attenuated dextran sulfate sodium (DSS)-induced body weight loss and colon shortening. LL-LFCA treatment also ameliorated DSS-induced colon damage, inhibited inflammatory cell infiltration, significantly decreased myeloperoxidase activity, and ameliorated DSS-induced disruption of intestinal permeability and tight junctions. In addition, 16S rDNA sequencing showed that LL-LFCA reversed DSS-induced gut dysbiosis. The production of proinflammatory mediators in serum and the colon was also reduced by administration of LL-LFCA. In vitro, LFCA derived from LL-LFCA decreased the messenger RNA expression of proinflammatory factors. The underlying mechanisms may involve inhibition of the nuclear factor kappa B (NF-κB) pathway. The results demonstrate that LL-LFCA ameliorates DSS-induced intestinal injury in mice, suggesting that LL-LFCA might be an effective drug for the treatment of inflammatory bowel diseases.

Modified TCA/acetone precipitation of plant proteins for proteomic analysis

Protein extracts obtained from cells or tissues often require removal of interfering substances for the preparation of high-quality protein samples in proteomic analysis. A number of protein extraction methods have been applied to various biological samples. TCA/acetone precipitation and phenol extraction, a common method of protein extraction, is thought to minimize protein degradation and activity of proteases as well as reduce contaminants like salts and polyphenols. However, the TCA/acetone precipitation method relies on the complete pulverization and repeated rinsing of tissue powder to remove the interfering substances, which is laborious and time-consuming. In addition, by prolonged incubation in TCA/acetone, the precipitated proteins are more difficult to re-dissolve. We have described a modified method of TCA/acetone precipitation of plant proteins for proteomic analysis. Proteins of cells or tissues were extracted using SDS-containing buffer, precipitated with equal volume of 20% TCA/acetone, and washed with acetone. Compared to classical TCA/acetone precipitation and simple acetone precipitation, this protocol generates comparable yields, spot numbers, and proteome profiling, but takes less time (ca. 45 min), thus avoiding excess protein modification and degradation after extended-period incubation in TCA/acetone or acetone. The modified TCA/acetone precipitation method is simple, fast, and suitable for proteomic analysis of various plant tissues in proteomic analysis.

Influence of dietary supplementation with Bacillus licheniformis and Saccharomyces cerevisiae as alternatives to monensin on growth performance, antioxidant, immunity, ruminal fermentation and microbial diversity of fattening lambs

Alternatives to antibiotics for improving productivity and maintaining the health of livestock health are urgently needed. The scope of this research was conducted to investigate the effects of two alternatives (Bacillus licheniformis and Saccharomyces cerevisiae) to monensin on growth performance, antioxidant capacity, immunity, ruminal fermentation and microbial diversity of fattening lambs. One hundred and sixty Dorper × Thin-tailed Han sheep (32 ± 3.45 kg BW) were randomly assigned into 5 treatments of n = 32 lambs/group. Lambs in the control group were fed a basal diet (NC) while the other four treatments were fed basal diets supplemented with monensin (PC), Bacillus licheniformis (BL), Saccharomyces cerevisiae (SC), and the combination of Bacillus licheniformis and Saccharomyces cerevisiae with protease (BS), respectively. The experiment lasted for 66 d. Feed intake was recorded every 2 d and lambs were weighed every 20 d. Ten lambs from each group were slaughtered at the end of the trial, and samples of serum and rumen fluid were collected. The results indicated that the dietary regimen did not affect the dry matter intake (DMI). The average daily gain (ADG) of BS treatment was significantly higher than NC group (P < 0.05). Compared with the NC treatment, the other four supplementation treatments increased the concentration of growth hormone (GH), insulin-like growth factor I (IGF-I) and insulin (INS) (P < 0.05). The malondialdehyde (MDA) and total antioxidant capacity (TAOC) showed no significant difference among the 5 treatments while the activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) of BS group was significantly increased (P < 0.05). The supplementation regimen decreased the concentration of ammonia Nitrogen (NH3-N) and increased the content of microbial crude proteins (MCP) (P < 0.05). The supplementation of antibiotics and probiotics reduced the concentrations of acetate and increased the concentrations of propionate (P < 0.05). The supplementation treatments increased the relative abundance of Lentisphaerae, Fibrobacteres and Tenericutes at the phylum level, whereas at the genus level, they increased the relative abundance of Fibrobacter (P < 0.05). Overall, this study confirmed the facilitating effect of B. licheniformis, S. cerevisiae and their compounds on growth performance, improve the antioxidant capacity and immune function, and beneficially manipulate ruminal fermentation and microbial diversity of fatting lambs.

Predicted Glycerol 3-Phosphate Dehydrogenase Homologs and the Glycerol Kinase GlcA Coordinately Adapt to Various Carbon Sources and Osmotic Stress in Aspergillus fumigatus

Glycerol plays an important role in the adaptation of fungi to various microenvironments and stressors, including heat shock, anoxic conditions and osmotic stress. Glycerol 3-phosphate dehydrogenase (G3PDH) is able to catalyze dihydroxyacetone phosphate to glycerol 3-phosphate (G3P), which is subsequently dephosphorylated into glycerol. However, current knowledge about the functions of G3PDH homologs in glycerol biosynthesis in Aspergillus fumigatus is limited. Here, we show that the A. fumigatus G3PDH gene, gfdA, is crucial for normal colony growth in glucose media under both normoxic and hypoxic conditions. In addition, failure of the overexpression of the gfdA homolog, gfdB, to rescue the phenotype of a gfdA null mutant suggests that gfdA plays a predominant role in the synthesis of G3P and glycerol. However, in a wild-type background, overexpressing either gfdA or gfdB is able to significantly enhance biomass production of mycelia, suggesting that gfdA and gfdB have similar functions in promoting the use of glucose. Interestingly, overexpression of the gene encoding the predicted glycerol kinase, GlcA, which is capable of phosphorylating glycerol to form G3P, significantly rescues the growth defects of gfdA null mutants in glucose media, indicating that the growth defects of gfdA null mutants might be due to the absence of G3P rather than glycerol. Moreover, Western blotting analysis revealed that gfdA is inducibly expressed by osmotic mediators. However, in the absence of gfdA, osmotic stress can rescue colony growth defects and allow colonies to partially bypass the gfdA requirement in a high osmolarity glycerol pathway-dependent manner. Therefore, the findings of this study elucidate how saprophytic filamentous fungi have developed pathways distinct from those of budding yeasts to adapt to varied carbon sources and survive environmental stresses.

Genetic Variability and Proteome Profiling of a Radiation Induced Cellulase Mutant Mushroom Pleurotus florida

We report the genetic similarity changes between a mutant mushroom (Pleurotus florida, designated as PfCM4) having increased cellulolytic activity developed through radiation mutagenesis and its wild type by amplified fragment length polymorphism (AFLP). On average, 23 AFLP fragments were amplified per primer combination, and a total of 286 polymorphic fragments (78.57% polymorphism) with maximal fragment length of 1365 base pairs (bp) were obtained. The genetic similarity between wild type and PfCM4 was found to be 22.30%. In addition, mycelial and secreted protein profiling by 2D-PAGE showed at least three and five different protein spots in the range of 25 kD to 100 kD, respectively, in PfCM4. It seems that the variation in genetic similarity and different expression of both mycelial and secreted proteins in PfCM4 in comparison to the wild type could likely be correlated with its increased cellulolytic activity effected by the irradiation.

Addition of urea and thiourea to electrophoresis sample buffer improves efficiency of protein extraction from TCA/acetone-treated smooth muscle tissues for phos-tag SDS-PAGE

Phosphorylation analysis by using phos-tag technique has been reported to be suitable for highly sensitive quantification of smooth muscle myosin regulatory light chain (LC₂₀ ) phosphorylation. However, there is another factor that will affect the sensitivity of phosphorylation analysis, that is, protein extraction. Here, we optimized the conditions for total protein extraction out of trichloroacetic acid (TCA)-fixed tissues. Standard SDS sample buffer extracted less LC₂₀ , actin and myosin phosphatase targeting subunit 1 (MYPT1) from TCA/acetone treated ciliary muscle strips. On the other hand, sample buffer containing urea and thiourea in addition to lithium dodecyl sulfate (LDS) or SDS extracted those proteins more efficiently, and thus increased the detection sensitivity up to 4-5 fold. Phos-tag SDS-PAGE separated dephosphorylated and phosphorylated LC₂₀ s extracted in LDS/urea/thiourea sample buffer to the same extent as those in standard SDS buffer. We have concluded that LDS (or SDS) /urea/thiourea sample buffer is suitable for highly sensitive phosphorylation analysis in smooth muscle, especially when it is treated with TCA/acetone.

An Improved 2-Dimensional Gel Electrophoresis Method for Resolving Human Erythrocyte Membrane Proteins

The 2-dimensional gel electrophoresis (2-DE) technique is widely used for the analysis of complex protein mixtures extracted from biological samples. It is one of the most commonly used analytical techniques in proteomics to study qualitative and quantitative protein changes between different states of a cell or an organism (eg, healthy and diseased), conditionally expressed proteins, posttranslational modifications, and so on. The 2-DE technique is used for its unparalleled ability to separate thousands of proteins simultaneously. The resolution of the proteins by 2-DE largely depends on the quality of sample prepared during protein extraction which increases results in terms of reproducibility and minimizes protein modifications that may result in artifactual spots on 2-DE gels. The buffer used for the extraction and solubilization of proteins influences the quality and reproducibility of the resolution of proteins on 2-DE gel. The purification by cleanup kit is another powerful process to prevent horizontal streaking which occurs during isoelectric focusing due to the presence of contaminants such as salts, lipids, nucleic acids, and detergents. Erythrocyte membrane proteins serve as prototypes for multifunctional proteins in various erythroid and nonerythroid cells. In this study, we therefore optimized the selected major conditions of 2-DE for resolving various proteins of human erythrocyte membrane. The modification included the optimization of conditions for sample preparation, cleanup of protein sample, isoelectric focusing, equilibration, and storage of immobilized pH gradient strips, which were further carefully examined to achieve optimum conditions for improving the quality of protein spots on 2-DE gels. The present improved 2-DE analysis method enabled better detection of protein spots with higher quality and reproducibility. Therefore, the conditions established in this study may be used for the 2-DE analysis of erythrocyte membrane proteins for different diseases, which may help to identify the proteins that may serve as markers for diagnostics as well as targets for development of new therapeutic potential.

Enzyme-Linked Immunosorbent Assay (ELISA)

Food allergy is a public health concern especially after recognizing its constantly increased prevalence and severity. Despite careful reading of food ingredient statements, food allergic individuals may experience reactions caused by "hidden", "masked", or "contaminated" proteins that are known major allergens. Many techniques have been developed to detect even small traces of food allergens, for clinical or laboratory purposes. Enzyme-linked immunosorbent assay (ELISA) is one of the best validated and most routinely used immunoassay in allergy research, in allergy diagnosis in allergy-related quality control in various industries. Although as a technique it has been implemented for the last 45 years, the evolution in biochemistry allowed the development of ultrasensitive ELISA variations that are capable of measuring quantities in the scale of picograms, rendering ELISA attractive, robust, and very famous.

An effective placental cotyledons proteins extraction method for 2D gel electrophoresis

Effective protein extraction is essential especially in producing a well-resolved proteome on 2D gels. A well-resolved placental cotyledon proteome, with good reproducibility, have allowed researchers to study the proteins underlying the physiology and pathophysiology of pregnancy. The aim of this study is to determine the best protein extraction protocol for the extraction of protein from placental cotyledons tissues for a two-dimensional gel electrophoresis (2D-GE). Based on widely used protein extraction strategies, 12 different extraction methodologies were carefully selected, which included one chemical extraction, two mechanical extraction coupled protein precipitations, and nine chemical extraction coupled protein precipitations. Extracted proteins were resolved in a one-dimensional gel electrophoresis and 2D-GE; then, it was compared with set criteria: extraction efficacy, protein resolution, reproducibility, and recovery efficiency. Our results revealed that a better profile was obtained by chemical extraction in comparison to mechanical extraction. We further compared chemical extraction coupled protein precipitation methodologies, where the DNase/lithium chloride-dense sucrose homogenization coupled dichloromethane-methanol precipitation (DNase/LiCl-DSH-D/MPE) method showed good protein extraction efficiency. This, however, was carried out with the best protein resolution and proteome reproducibility on 2D-gels. DNase/LiCl-DSH-D/MPE was efficient in the extraction of proteins from placental cotyledons tissues. In addition, this methodology could hypothetically allow the protein extraction of any tissue that contains highly abundant lipid and glycogen.

A protein extraction method for low protein concentration solutions compatible with the proteomic analysis of rubber particles

The extraction of high-purity proteins from the washing solution (WS) of rubber particles (also termed latex-producing organelles) from laticifer cells in rubber tree for proteomic analysis is challenging due to the low concentration of proteins in the WS. Recent studies have revealed that proteins in the WS might play crucial roles in natural rubber biosynthesis. To further examine the involvement of these proteins in natural rubber biosynthesis, we designed an efficiency method to extract high-purity WS proteins. We improved our current borax and phenol-based method by adding reextraction steps with phenol (REP) to improve the yield from low protein concentration samples. With this new method, we extracted WS proteins that were suitable for proteomics. Indeed, compared to the original borax and phenol-based method, the REP method improved both the quality and quantity of isolated proteins. By repeatedly extracting from low protein concentration solutions using the same small amount of phenol, the REP method yielded enough protein of sufficiently high-quality from starting samples containing less than 0.02 mg of proteins per milliliter. This method was successfully applied to extract the rubber particle proteins from the WS of natural rubber latex samples. The REP-extracted WS proteins were resolved by 2DE, and 28 proteins were positively identified by MS. This method has the potential to become widely used for the extraction of proteins from low protein concentration solutions for proteomic analysis.

Unraveling Mesenchymal Stem Cells' Dynamic Secretome Through Nontargeted Proteomics Profiling

The modulatory and regenerative potential shown by the use of MSC secretomes has emphasized the importance of their proteomics profiling. Proteomic analysis, initially focused on the targeted analysis of some candidate proteins or the identification of the secreted proteins, has been changing to an untargeted profiling also based on the quantitative evaluation of the secreted proteins.The study of the secretome can be accomplished through several different proteomics-based approaches; however this analysis must overcome one key challenge of secretome analysis: the low amount of secreted proteins and usually their high dilution.In this chapter, a general workflow for the untargeted proteomic profile of MSC's secretome is presented, in combination with a comprehensive description of the major techniques/procedures that can be used. Special focus is given to the main procedures to obtain the secreted proteins, from secretome concentration by ultrafiltration to protein precipitation. Lastly, different proteomics-based approaches are presented, emphasizing alternative digestion techniques and available mass spectrometry-based quantitative methods.

Mucosal delivery of allergen peptides expressed by Lactococcus lactis inhibit allergic responses in a BALB/c mouse model

Allergen-specific immunotherapy (SIT) is considered to be the only curative treatment of allergy, but its safety is always affected by immunologic properties and quality of allergen. Recombinant allergen derivative could be a potential therapeutic strategy, but clinical studies showed that macromolecular derivatives could not avoid T cell-mediated side effects. In this study, five Der p2-derived peptides (DPs) containing major T cell epitopes of Der p2 were first artificially synthesized. Compared with Der p2 macromolecular derivative DM, these DPs not only fully eliminated IgE-binding capacity but also reduced T cells reactivity, suggesting these DPs could be better therapeutic molecules. For their application in vivo, Lactococcus lactis was engineered to express these DPs, and their protective effects were evaluated in BALB/c mice models. Western blot showed that all DPs could be produced in the recombinant strains. Mucosal delivery of these strains could inhibit Der p2-induced allergic responses in Der p2-sensitized mice, characterized by a reduction in specific IgE antibody and lung inflammatory responses. These protective effects were associated with an increase of specific IgG2a in serum and regulatory T cells in the mesenteric lymph nodes. On the whole, the suppressive effect induced by the DP mixture could be better than single DP, but a bit weaker than DM. These DPs could be promising candidate molecules for active vaccination and induction of tolerance, and thus promote the development of non-allergenic peptide in the treatment and prevention of allergy.

Variable Efficacy of the Proteinaceous Antifungal YvgO in Select Fruit Juices and Teas as a Complement with UV Methods of Food Protection

Heat-resistant fungal spores present a processing challenge for beverages and fruit juices, as thermal and UV strategies are often inadequate in reducing heat-resistant fungal burdens to acceptable levels. While effective against pathogenic or invasive bacteria, germicidal UV light treatments also fail to achieve an appreciable reduction of heat-resistant fungal spores. As an alternative, the efficacy of the antifungal protein YvgO was examined across a selection of fruit juices and teas, as well as solid model matrices. Compared with its efficacy in analogous liquid matrices, the apparent efficacy of YvgO was diminished on acidified solid matrices due to a reduction in YvgO diffusion. Using an XTT [2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] tetrazolium dye cytotoxicity assay, the effective concentrations to reduce growth by 50% were elucidated in samples challenged with Byssochlamys fulva H25. The MICs were determined and ranged from 2 ppm in apple juice and acidified teas to approximately 3 to 12 ppm for lemonade and orange, white cranberry, blueberry, prune, cherry, and grape juices. Apple cider and nonacidified teas showed reduced efficacy, with MICs exceeding 100 ppm. Tannin-rich products readily removed YvgO from the product, impairing its efficacy. Adding bovine serum albumin as a competitive inhibitor effectively reversed the YvgO-tannin association and restored efficacy in black but not green tea matrices. When challenged with a 5-log CFU inoculum of B. fulva, the shelf lives of the products were extended for various times up to 28 days in a concentrationdependent manner. However, initial efficacy was not predictive of shelf life extension, as some products exhibited improved protection at just two- and fourfold concentrations above the MIC, while others only exhibited long-term stability when concentrations exceeded 20 times the MIC. As such, YvgO may be an attractive alternative to currently available protection strategies and will provide needed diversity for natural food protectants.

Improved proteomic analysis following trichloroacetic acid extraction of Bacillus anthracis spore proteins

Proteomic analysis of bacterial samples provides valuable information about cellular responses and functions under different environmental pressures. Analysis of cellular proteins is dependent upon efficient extraction from bacterial samples, which can be challenging with increasing complexity and refractory characteristics. While no single method can recover 100% of the bacterial proteins, selected protocols can improve overall protein isolation, peptide recovery, or enrichment for certain classes of proteins. The method presented here is technically simple, does not require specialized equipment such as a mechanical disrupter, and is effective for protein extraction of the particularly challenging sample type of Bacillus anthracis Sterne spores. The ability of Trichloroacetic acid (TCA) extraction to isolate proteins from spores and enrich for spore-specific proteins was compared to the traditional mechanical disruption method of bead beating. TCA extraction improved the total average number of proteins identified within a sample as compared to bead beating (547 vs 495, respectively). Further, TCA extraction enriched for 270 spore proteins, including those typically identified by first isolating the spore coat and exosporium layers. Bead beating enriched for 156 spore proteins more typically identified from whole spore proteome analyses. The total average number of proteins identified was equal using TCA or bead beating for easily lysed samples, such as B. anthracis vegetative cells. As with all assays, supplemental methods such as implementation of an alternative preparation method may simplify sample preparation and provide additional insight to the protein biology of the organism being studied.

Effect of dietary supplementation of rutin on lactation performance, ruminal fermentation and metabolism in dairy cows

The effect of long-term dietary supplementation with rutin on the lactation performance, ruminal fermentation and metabolism of dairy cows were investigated in this study. Twenty multiparous Chinese Holstein cows were randomly divided into four groups, and each was offered a basal diet supplemented with 0, 1.5, 3.0 or 4.5 mg rutin/kg of diet. The milk yield of the cows receiving 3.0 and 4.5 mg rutin/kg was higher than that of the control group, and the milk yield was increased by 10.06% and 3.37% (p < 0.05). On the basis of that finding, the cows supplemented with 0 or 3.0 mg rutin/kg of diet were used to investigate the effect of rutin supplementation on blood metabolites and hormone levels. Compared with the control group, the serum blood urea nitrogen (BUN) concentration of the 3.0 mg rutin/kg group is significantly decreased (p < 0.05). In another trial, four adult cows with permanent rumen fistula and duodenal cannulae were attributed in a self-control design to investigate the peak occurrence of rutin and quercetin in different parts of the gastrointestinal tract, ruminal fermentation and microbial population in dairy cows. The cows supplemented with 3.0 mg rutin/kg in the diet differed from the control period. Samples of rumen fluid, duodenal fluid and blood were collected at 1, 2, 3, 4, 5, 6, 7 and 8 h after morning feeding. Compared to the control group, the pH, ammonia nitrogen concentration, number and protein content of rumen protozoa and blood urea nitrogen were lower, but the concentration of total volatile fatty acid (TVFA), microbial crude protein (MCP) and serum lysozyme content were higher for the cows fed the rutin diets. The addition of 3.0 mg rutin/kg to diets for a long term tended to increase the milk yield and improve the metabolism and digestibility of the dairy cows.

An Optimized Trichloroacetic Acid/Acetone Precipitation Method for Two-Dimensional Gel Electrophoresis Analysis of Qinchuan Cattle Longissimus Dorsi Muscle Containing High Proportion of Marbling

Longissimus dorsi muscle (LD) proteomics provides a novel opportunity to reveal the molecular mechanism behind intramuscular fat deposition. Unfortunately, the vast amounts of lipids and nucleic acids in this tissue hampered LD proteomics analysis. Trichloroacetic acid (TCA)/acetone precipitation is a widely used method to remove contaminants from protein samples. However, the high speed centrifugation employed in this method produces hard precipitates, which restrict contaminant elimination and protein re-dissolution. To address the problem, the centrifugation precipitates were first grinded with a glass tissue grinder and then washed with 90% acetone (TCA/acetone-G-W) in the present study. According to our result, the treatment for solid precipitate facilitated non-protein contaminant removal and protein re-dissolution, ultimately improving two-dimensional gel electrophoresis (2-DE) analysis. Additionally, we also evaluated the effect of sample drying on 2-DE profile as well as protein yield. It was found that 30 min air-drying did not result in significant protein loss, but reduced horizontal streaking and smearing on 2-DE gel compared to 10 min. In summary, we developed an optimized TCA/acetone precipitation method for protein extraction of LD, in which the modifications improved the effectiveness of TCA/acetone method.

Nucleotide second messenger-mediated regulation of a muralytic enzyme in Streptomyces

Peptidoglycan degradative enzymes have important roles at many stages during the bacterial life cycle, and it is critical that these enzymes be stringently regulated to avoid compromising the integrity of the cell wall. How this regulation is exerted is of considerable interest: promoter-based control and protein-protein interactions are known to be employed; however, other regulatory mechanisms are almost certainly involved. In the actinobacteria, a class of muralytic enzymes - the 'resuscitation-promoting factors' (Rpfs) - orchestrates the resuscitation of dormant cells. In this study, we have taken a holistic approach to exploring the mechanisms governing RpfA function using the model bacterium Streptomyces coelicolor and have uncovered unprecedented multilevel regulation that is coordinated by three second messengers. Our studies show that RpfA is subject to transcriptional control by the cyclic AMP receptor protein, riboswitch-mediated transcription attenuation in response to cyclic di-AMP, and growth stage-dependent proteolysis in response to ppGpp accumulation. Furthermore, our results suggest that these control mechanisms are likely applicable to cell wall lytic enzymes in other bacteria.

Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis

Filamentous fungi possess the extraordinary ability to digest complex biomasses and mineralize numerous xenobiotics, as consequence of their aptitude to sensing the environment and regulating their intra and extra cellular proteins, producing drastic changes in proteome and secretome composition. Recent advancement in proteomic technologies offers an exciting opportunity to reveal the fluctuations of fungal proteins and enzymes, responsible for their metabolic adaptation to a large variety of environmental conditions. Here, an overview of the most commonly used proteomic strategies will be provided; this paper will range from sample preparation to gel-free and gel-based proteomics, discussing pros and cons of each mentioned state-of-the-art technique. The main focus will be kept on filamentous fungi. Due to the biotechnological relevance of lignocellulose degrading fungi, special attention will be finally given to their extracellular proteome, or secretome. Secreted proteins and enzymes will be discussed in relation to their involvement in bio-based processes, such as biomass deconstruction and mycoremediation.

Suppression of dust mite allergy by mucosal delivery of a hypoallergenic derivative in a mouse model

Allergic asthma caused by house dust mite (HDM) is becoming a public health problem. Specific immunotherapy is considered to be the only curative treatment, but it is always associated with IgE-mediated side effects in the therapy process. A few studies showed that the disruption of allergen IgE epitopes could reduce IgE reactivity and thus reduce allergenic activity. In this study, a hypoallergenic derivative of the major HDM allergen Der p2 was constructed by genetic engineering. This derivative was confirmed to have a considerably reduced IgE reactivity compared with Der p2. For its application in vivo, recombinant Lactococcus lactis (LL-DM) was engineered to deliver the Der p2 derivative to the intestinal mucosal surface. Oral administration of LL-DM significantly alleviated Der p2-induced airway inflammation, as shown by reduced inflammatory infiltration and a reduction in Th2 cytokines in bronchoalveolar lavage. This protective effect was associated with an up-regulation of specific IgG2a and a decrease in IL-4 level in the spleen which may affect specific IgE response. Moreover, the levels of regulatory T cells in the mesenteric lymph nodes and spleen were markedly increased in mice fed with LL-DM, suggesting that LL-DM can inhibit allergic responses via the induction of regulatory T cell. Our results indicate that the Der p2 derivative is a promising therapeutic molecule for specific immunotherapy and recombinant lactic acid bacteria could be developed as a promising treatment or prevention strategy for allergic diseases.

Metabolomic differentiation of nutritional stress in an aquatic invertebrate

Poor diet quality frequently constrains the growth and reproduction of primary consumers, altering their population dynamics, interactions in food webs, and contributions to ecosystem services such as nutrient cycling. The identification and measurement of an animal's nutritional state are thus central to studying the connections between diet and animal ecology. Here we show how the nutritional state of a freshwater invertebrate, Daphnia magna, can be determined by analyzing its endogenous metabolites using hydrogen nuclear magnetic resonance-based metabolomics. With a multivariate analysis, we observed the differentiation of the metabolite composition of animals grown under control conditions (good food and no environmental stress), raised on different diets (low quantity, nitrogen limited, and phosphorus limited), and exposed to two common environmental stressors (bacterial infection and salt stress). We identified 18 metabolites that were significantly different between control animals and at least one limiting food type or environmental stressor. The unique metabolite responses of animals caused by inadequate nutrition and environmental stress are reflective of dramatic and distinctive effects that each stressor has on animal metabolism. Our results suggest that dietary-specific induced changes in metabolite composition of animal consumers hold considerable promise as indicators of nutritional stress and will be invaluable to future studies of animal nutrition.

Genetically engineered Lactococcus lactis protect against house dust mite allergy in a BALB/c mouse model

Background

Mucosal vaccine based on lactic acid bacteria is an attractive concept for the prevention and treatment of allergic diseases, but their mechanisms of action in vivo are poorly understood. Therefore, we sought to investigate how recombinant major dust mite allergen Der p2-expressing Lactococcus lactis as a mucosal vaccine induced the immune tolerance against house dust mite allergy in a mouse model.

Methods

Three strains of recombinant L. lactis producing Der p2 in different cell components (extracellular, intracellular and cell wall) were firstly constructed. Their prophylactic potential was evaluated in a Der p2-sensitised mouse model, and immunomodulation properties at the cellular level were determined by measuring cytokine production in vitro.

Results

Der p2 expressed in the different recombinant L. lactis strains was recognized by a polyclonal anti-Der p2 antibody. Oral treatment with the recombinant L. lactis prior sensitization significantly prevented the development of airway inflammation in the Der p2-sensitized mice, as determined by the attenuation of inflammatory cells infiltration in the lung tissues and decrease of Th2 cytokines IL-4 and IL-5 levels in bronchoalveolar lavage. In addition, the serum allergen-specific IgE levels were significantly reduced, and the levels of IL-4 in the spleen and mesenteric lymph nodes cell cultures were also markedly decreased upon allergen stimulation in the mice fed with the recombinant L. lactis strains. These protective effects correlated with a significant up-regulation of regulatory T cells in the mesenteric lymph nodes.

Conclusion

Oral pretreatment with live recombinant L. lactis prevented the development of allergen-induced airway inflammation primarily by the induction of specific mucosal immune tolerance.

Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism

Sea ice is a highly dynamic and productive environment that includes a diverse array of psychrophilic prokaryotic and eukaryotic taxa distinct from the underlying water column. Because sea ice has only been extensive on Earth since the mid-Eocene, it has been hypothesized that bacteria highly adapted to inhabit sea ice have traits that have been acquired through horizontal gene transfer (HGT). Here we compared the genomes of the psychrophilic bacterium Psychroflexus torquis ATCC 700755^T, associated with both Antarctic and Arctic sea ice, and its closely related nonpsychrophilic sister species, P. gondwanensis ACAM 44^T. Results show that HGT has occurred much more extensively in P. torquis in comparison to P. gondwanensis. Genetic features that can be linked to the psychrophilic and sea ice-specific lifestyle of P. torquis include genes for exopolysaccharide (EPS) and polyunsaturated fatty acid (PUFA) biosynthesis, numerous specific modes of nutrient acquisition, and proteins putatively associated with ice-binding, light-sensing (bacteriophytochromes), and programmed cell death (metacaspases). Proteomic analysis showed that several genes associated with these traits are highly translated, especially those involved with EPS and PUFA production. Because most of the genes relating to the ability of P. torquis to dwell in sea-ice ecosystems occur on genomic islands that are absent in closely related P. gondwanensis, its adaptation to the sea-ice environment appears driven mainly by HGT. The genomic islands are rich in pseudogenes, insertional elements, and addiction modules, suggesting that gene acquisition is being followed by a process of genome reduction potentially indicative of evolving ecosystem specialism.

(Post-)genomics approaches in fungal research

To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functional studies beyond genomes are required. Thanks to the developments of current -omics techniques, it is possible to produce large amounts of fungal functional data in a high-throughput fashion (e.g. transcriptome, proteome, etc.). The increasing ease of creating -omics data has also created a major challenge for downstream data handling and analysis. Numerous databases, tools and software have been created to meet this challenge. Facing such a richness of techniques and information, hereby we provide a brief roadmap on current wet-lab and bioinformatics approaches to study functional genomics in fungi.

Silicon enhances the growth of Phaeodactylum tricornutum Bohlin under green light and low temperature

Phaeodactylum tricornutum Bohlin is an ideal model diatom; its complete genome is known, and it is an important economic microalgae. Although silicon is not required in laboratory and factory culture of this species, previous studies have shown that silicon starvation can lead to differential expression of miRNAs. The role that silicon plays in P. tricornutum growth in nature is poorly understood. In this study, we compared the growth rate of silicon starved P. tricornutum with that of normal cultured cells under different culture conditions. Pigment analysis, photosynthesis measurement, lipid analysis, and proteomic analysis showed that silicon plays an important role in P. tricornutum growth and that its presence allows the organism to grow well under green light and low temperature.