Identification of troponin I and actin, alpha cardiac muscle 1 as potential biomarkers for hearts of electrically stimulated chickens

Biomarker discovery and authentication of cold-slaughtered chicken through classical analytical procedures and mass spectrometry based proteomic approaches

1. This study evaluated the suitability of routine analytical procedures and used mass spectrometry-based proteomic approaches to distinguish meat from dead chicken/ cold-slaughtered birds (CS), electrically stunned and slaughtered birds, as per standard protocols (ES), and birds slaughtered according to halal guidelines (HS).2. Meat from CS birds had lower (P < 0.05) pH, water-holding capacity and higher (P < 0.05) lipid oxidation, haem iron content, residual blood and total viable counts relative to ES and HS meat indicating poor quality.3. The results demonstrated the presence of unique protein bands on SDS-PAGE only in CS meat that can be used for routine screening.4. Protein analysis using MALDI-TOF mass spectrometry identified haemoglobin subunit alpha-A and alpha-D; Adenylate kinase isoenzyme 1 as reliable and stable marker proteins for authentication of dead chicken meat under raw and cooked conditions and halal slaughtered chicken, respectively.5. The methods used may be employed by the food safety and regulatory agencies for regular screening of meat quality and to authenticate CS or HS chicken.

Collagen for neural tissue engineering: Materials, strategies, and challenges

Neural tissue engineering (NTE) has made remarkable strides in recent years and holds great promise for treating several devastating neurological disorders. Selecting optimal scaffolding material is crucial for NET design strategies that enable neural and non-neural cell differentiation and axonal growth. Collagen is extensively employed in NTE applications due to the inherent resistance of the nervous system against regeneration, functionalized with neurotrophic factors, antagonists of neural growth inhibitors, and other neural growth-promoting agents. Recent advancements in integrating collagen with manufacturing strategies, such as scaffolding, electrospinning, and 3D bioprinting, provide localized trophic support, guide cell alignment, and protect neural cells from immune activity. This review categorises and analyses collagen-based processing techniques investigated for neural-specific applications, highlighting their strengths and weaknesses in repair, regeneration, and recovery. We also evaluate the potential prospects and challenges of using collagen-based biomaterials in NTE. Overall, this review offers a comprehensive and systematic framework for the rational evaluation and applications of collagen in NTE.

Proteomics for abiotic stresses in legumes: present status and future directions

Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics provides an important molecular approach to investigate proteins involved in stress response. Both the gel-based and gel-free-based techniques have significantly contributed to understanding the proteome regulatory network in leguminous plants. In the present review, we have discussed the role of different proteomic approaches (2-DE, 2 D-DIGE, ICAT, iTRAQ, etc.) in the identification of various stress-responsive proteins in important leguminous crops, including soybean, chickpea, cowpea, pigeon pea, groundnut, and common bean under variable abiotic stresses including heat, drought, salinity, waterlogging, frost, chilling and metal toxicity. The proteomic analysis has revealed that most of the identified differentially expressed proteins in legumes are involved in photosynthesis, carbohydrate metabolism, signal transduction, protein metabolism, defense, and stress adaptation. The proteomic approaches provide insights in understanding the molecular mechanism of stress tolerance in legumes and have resulted in the identification of candidate genes used for the genetic improvement of plants against various environmental stresses. Identifying novel proteins and determining their expression under different stress conditions provide the basis for effective engineering strategies to improve stress tolerance in crop plants through marker-assisted breeding.

A waste-to-wealth initiative exploiting the potential of Anabaena variabilis for designing an integrated biorefinery

The current research work was an innovative approach providing dual advantages of waste bioremediation and an effective biorefinery. The study attempted to exploit wastewater like aqua discharge and solid wastes like poultry litter/cow dung for cyanobacterial cultivation. Aqua discharge appended with 7.5 g L⁻¹ poultry litter turned out as the best combination generating 46% higher carbohydrate yield than BG-11 control. A. variabilis cultivation in this waste-utilized medium also revealed its excellent bioremediation ability. While 100% removal was observed for nitrite, nitrate, and orthophosphate, a respective 74% and 81% reduction was noted for ammonium and total organic carbon. Chemical and biological oxygen demands were also reduced by 90%. This work was also novel in developing a sequential design for the production of bioethanol and co-products like exopolysaccharides, sodium copper chlorophyllin, C-phycocyanin, and poly-β-hydroxybutyrate from the same cyanobacterial biomass. The developed biorefinery implementing the waste-utilized medium was one of its kind, enabling biomass valorization of 61%. Therefore, the present study would provide a leading-edge for tackling the high production costs that limit the practical viability of biorefinery projects. The recyclability of the bioremediated wastewater would not only curtail freshwater usage, the waste disposal concerns would also be mitigated to a great extent.

Impact of stunning before slaughter on expression of skeletal muscles proteome in sheep

The commercial production of halal and kosher meat and controversy surrounding the slaughter without stunning is rapidly growing across the globe. Huge global market for halal and kosher meat warrants conciliation of religious practices and animal welfare for the betterment of meat industry. In the present study, we investigated changes in muscle proteome of sheep (Ovis aries) subjected to either electrical stunning and slaughtering or slaughter without any stunning (halal). The 2DE gel analysis detected approximately 377 protein spots in which 243 (119 up regulated and 124 down regulated) protein spots were significantly (p ≤ 0.05) differentially expressed with a fold change ratio ≥1.5/≤1.5. The in-gel digestion and MALDI-TOF/TOF MS analysis of statistically significant protein spots revealed 35 differentially abundant proteins out of which 26 were up-regulated and 9 were down-regulated. The study demonstrated that slaughtering of sheep without stunning resulted in changes in the abundance of proteins involved in catalytic, structural, and stress related processes. This understanding of protein alterations in sheep slaughtered with and without stunning have the potential to act as possible signature for animal welfare index.

Binge Alcohol Is More Injurious to Liver in Female than in Male Rats: Histopathological, Pharmacologic, and Epigenetic Profiles

Binge alcohol consumption is a health problem, but differences between the sexes remain poorly defined. We have examined the in vivo effects of three acute, repeat binge alcohol administration on the liver in male and female rats. Sprague-Dawley rats were gavaged with alcohol (5 g/kg body weight) three times at 12-hour intervals. Blood and liver tissues were collected 4 hours after the last binge ethanol. Subsequently, several variables were analyzed. Compared with male rats, females had higher levels of blood alcohol, alanine aminotransferase, and triglycerides. Liver histology showed increased lipid vesicles that were larger in females. Protein levels of liver cytochrome P4502E1 were higher in the liver of females than in the liver of males after binge. Hepatic phospho-extracellular signal-regulated kinase 1/2 and phosph-p38 mitogen-activated protein kinase levels were lower in females compared with males after binge alcohol, but no differences were found in the phospho-C-jun N-terminal kinase levels. Peroxisome proliferator-activated receptor γ-coactivator 1α and cyclic AMP response element binding (CREB) protein levels increased more in female than in male livers; however, increases in phospho-CREB levels were lower in females. Remarkably, c-fos was reduced substantially in the livers of females, but no differences in c-myc protein were found. Binge ethanol caused elevation in acetylated (H3AcK9) and phosphoacetylated (H3AcK9PS10) histone H3 in both sexes but without any difference. Binge alcohol caused differential alterations in the levels of various species of phosphatidylethanol and a larger increase in the diacylglycerol kinase-α protein levels in the liver of female rats compared with male rats. These data demonstrate, for the first time, similarities and differences in the sex-specific responses to repeat binge alcohol leading to an increased susceptibility of female rats to have liver injury in vivo. SIGNIFICANCE STATEMENT: This study examines the molecular responses of male and female rat livers to acute binge alcohol in vivo and demonstrates significant differences in the susceptibility between sexes.

iTRAQ-based proteomic analysis to identify molecular mechanisms of the selenium deficiency response in the Przewalski's gazelle

The Przewalski's gazelle shows long-term survival in a selenium (Se)-deficient environment, but fails to exhibit obvious pathological manifestations. To reveal proteomic changes in the Przewalski's gazelle in response to Se-deficiency, twenty Przewalski's gazelle were randomly divided into control group and Se-deficient group. After induction of Se-deficiency animal model, blood samples were collected from eight animals. An isobaric tag for relative and absolute quantitation (iTRAQ)-liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was employed to explore blood protein alterations and potential mechanisms of the response to Se-deficiency challenge. Se deficiency contributed to a remarkable change in blood Se levels and routine blood indexes. In proteomic analyses, 130 proteins were differentially accumulated in the Se-deficient and control groups. The differentially expressed proteins were annotated mainly as single-organism process, extracellular region, or binding, respectively, and they were highly enriched in the coagulation and complement cascades. Protein-protein interaction analysis showed several important nodal proteins involved in the regulation of binding, cellular biochemical processes, and signal transduction pathways. To our knowledge, this study is the first to comprehensively analyze blood protein changes in the Przewalski's gazelle under Se-deficient conditions, which reveal that this species has developed physiological mechanisms of adaptation in response to Se-deficiency stress. SIGNIFICANCE: The present study is the first to comprehensively analyze alterations in the protein profiles induced by Se deficiency in the blood of the Przewalski's gazelle, showing that Se-deficiency contributed to a significant reduction in blood Se levels and marked changes in blood parameters, which will likely contribute to a better understanding of the molecular mechanisms of the changes in protein abundance in the Przewalski's gazelle in response to Se-deficiency stress.

Traditional halal slaughter without stunning versus slaughter with electrical stunning of sheep (Ovis aries)

Thirty Nellore crossbred male sheep (Ovis aries) were divided into two groups of 15 animals each and subjected to either pre-slaughter electrical stunning followed by slaughter (ST) or traditional halal slaughter without stunning (NST) to investigate the changes in blood biochemical parameters, meat quality and proteomic profile. Higher (P < .05) pH, water holding capacity and Warner-Bratzler shear force were observed in meat from stunned sheep. Quantitative proteomic approach using DIGE was employed to find a panel of protein markers that could differentiate ST and NST muscle proteome. Comparison of muscle proteome of ST and NST samples by 2D-DIGE and MALDI-TOF/TOF MS analysis revealed 46 significant (P < .05) differentially expressed proteins. Our analysis revealed changes in the abundance of proteins involved in catalytic, structural, and stress related process. Current study has demonstrated variation meat quality and identified important proteins that correlate with meat texture and pre-slaughter stress in sheep that are slaughtered without and with electrical stunning.

Differential expression analysis of the broiler tracheal proteins responsible for the immune response and muscle contraction induced by high concentration of ammonia using iTRAQ-coupled 2D LC-MS/MS

Ammonia has been considered the contaminant primarily responsible for respiratory disease in poultry. Even though it can cause tracheal lesions, its adverse effects on the trachea have not been sufficiently studied. The present study investigated tracheal changes in Arbor Acres broilers (Gallus gallus) induced by high concentration of ammonia using isobaric tag for relative and absolute quantification (iTRAQ)-based proteome analysis. In total, 3,706 proteins within false discovery rate of 1% were identified, including 119 significantly differentially expressed proteins. Functional analysis revealed that proteins related to immune response and muscle contraction were significantly enriched. With respect to the immune response, up-regulated proteins (like FGA) were pro-inflammatory, while down-regulated proteins participated in antigen processing and antigen presenting (like MYO1G), immunoglobulin and cathelicidin production (like fowlicidin-2), and immunodeficiency (like PTPRC). Regarding muscle contraction, all differentially expressed proteins (like TPM1) were up-regulated. An over-expression of mucin, which is a common feature of airway disease, was also observed. Additionally, the transcriptional alterations of 6 selected proteins were analyzed by quantitative RT-PCR. Overall, proteomic changes suggested the onset of airway obstruction and diminished host defense in trachea after ammonia exposure. These results may serve as a valuable reference for future interventions against ammonia toxicity.

Changes in serum proteins after endotoxin administration in healthy and choline-treated calves

BACKGROUND

This study aimed to investigate the possible serum protein changes after endotoxin administration in healthy and choline-treated calves using proteomics. These results are expected to contribute to the understanding of the pathophysiological mechanisms of endotoxemia and the beneficial effect of choline administration in this clinical situation.

METHODS

Healthy-calves (n = 20) were divided into 4 groups: Control, Choline treated (C), Lipopolysaccharide administered (LPS), and LPS + C. Control calves received 0.9 % NaCl injection. Calves in C and LPS + C groups received choline chloride (1 mg/kg/iv). Endotoxin (LPS) was injected (2 μg/kg/iv) to the calves in LPS and LPS + C groups. Serum samples were collected before and after the treatments. Differentially expressed proteins (> 1.5 fold-change relative to controls) were identified by LC-MS/MS.

RESULTS

After LPS administration, 14 proteins increased, and 13 proteins decreased within 48 h as compared to controls. In the LPS group, there were significant increases in serum levels of ragulator complex protein (189-fold) and galectin-3-binding protein (10-fold), but transcription factor MafF and corticosteroid binding globulin were down regulated (≥ 5 fold). As compared with the LPS group, in LPS + C group, fibrinogen gamma-B-chain and antithrombin were up-regulated, while hemopexin and histone H4 were down-regulated. Choline treatment attenuated actin alpha cardiac muscle-1 overexpression after LPS.

CONCLUSIONS

LPS administration produces changes in serum proteins associated with lipid metabolism, immune and inflammatory response, protein binding/transport, cell adhesion, venous thrombosis, cardiac contractility and blood coagulation. The administration of choline is associated with changes in proteins which can be related with its beneficial effect in this clinical situation.

Nano-LC-Q-TOF Analysis of Proteome Revealed Germination of Aspergillus flavus Conidia is Accompanied by MAPK Signalling and Cell Wall Modulation

Aspergillus flavus is the second most leading cause of aspergillosis. The ability of A. flavus to adapt within the host environment is crtical for its colonization. Onset of germination of conidia is one of the crucial events; thus, in order to gain insight into A. flavus molecular adaptation while germination, protein profile of A. flavus was obtained. Approximately 82 % of conidia showed germination at 7 h; thus, samples were collected followed by protein extraction and subjected to nLC-Q-TOF mass spectrometer. Q-TOF data were analysed using Protein Lynx Global Services (PLGS 2.2.5) software. A total of 416 proteins were identified from UniProt Aspergillus species database. Orthologues of A. flavus was observed in A. fumigatus, A. niger, A. terreus, A. oryzae, etc. Proteins were further analysed in NCBI database, which showed that 27 proteins of A. flavus are not reported in UniProt and NCBI database. Functional characterization of proteins resulted majorly to cell wall synthesis and degradation, metabolisms (carbohydrate and amino acid metabolism), protein synthesis and degradation. Proteins/enzymes associated with aflatoxin biosynthesis were observed. We also observed Dicer-like proteins 1, 2 and autophagy-related proteins 2, 9, 18, 13, 11, 22. Expression of protein/enzymes associated with MAPK signalling pathway suggests their role during the germination process. Overall, the data present a catalogue of proteins/enzymes involved in the germination of A. flavus conidia and could also be applied to other Aspergillus species.

Comparative proteomic analysis of cauliflower under high temperature and flooding stresses

High-temperature and waterlogging are major abiotic stresses that affect the yield and quality of cauliflower. Cauliflower cultivars 'H41' and 'H69' are tolerant to high temperature and flooding, respectively; however, 'H71' is sensitive to both stresses. The objectives of this study were to identify the proteins that were differentially regulated and the physiological changes that occurred during different time periods in 'H41', 'H69', and 'H71' when responding to treatments of flooding, 40 °C, and both stresses combined. Changes in the leaf proteome were analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) and identified by Mascot peptide mass fingerprint (PMF) and database searching. Stress treatments caused significant reductions in electrolyte leakage, chlorophyll fluorescence Fv/Fm, chlorophyll content, and water potential as stress times were prolonged. By the comparative proteomic analysis, 85 protein peaks that were differentially expressed in response to combination treatments at 0, 6, and 24 h, 69 (33 in 'H41', 29 in 'H69', and 9 in 'H71') were identified, of which were cultivar specific. Differentially regulated proteins predominantly functioned in photosynthesis and to a lesser extent in energy metabolism, cellular homeostasis, transcription and translation, signal transduction, and protein biosynthesis. This is the first report that utilizes proteomics to discover changes in the protein expression profile of cauliflower in response to heat and flooding.

Protein sequence classification with improved extreme learning machine algorithms

Precisely classifying a protein sequence from a large biological protein sequences database plays an important role for developing competitive pharmacological products. Comparing the unseen sequence with all the identified protein sequences and returning the category index with the highest similarity scored protein, conventional methods are usually time-consuming. Therefore, it is urgent and necessary to build an efficient protein sequence classification system. In this paper, we study the performance of protein sequence classification using SLFNs. The recent efficient extreme learning machine (ELM) and its invariants are utilized as the training algorithms. The optimal pruned ELM is first employed for protein sequence classification in this paper. To further enhance the performance, the ensemble based SLFNs structure is constructed where multiple SLFNs with the same number of hidden nodes and the same activation function are used as ensembles. For each ensemble, the same training algorithm is adopted. The final category index is derived using the majority voting method. Two approaches, namely, the basic ELM and the OP-ELM, are adopted for the ensemble based SLFNs. The performance is analyzed and compared with several existing methods using datasets obtained from the Protein Information Resource center. The experimental results show the priority of the proposed algorithms.

Proteomic study of a tolerant genotype of durum wheat under salt-stress conditions

Salinity is one of the major abiotic stress conditions limiting crop growth and productivity. Duilio is a wheat genotype that shows tolerant behavior in both salt-stress and drought-stress conditions. Toward better understanding of the biochemical response to salinity in this genotype of durum wheat, a comparative label-free shotgun proteomic analysis based on normalized spectral abundance factors was conducted on wheat leaf samples subjected to increasing salt-stress levels (100 and 200 mmol L(-1) NaCl) with respect to untreated samples. We found significant changes in 71 proteins for the first stress level, in 83 proteins at the higher salinity level, and in 88 proteins when comparing salt-stress levels with each other. The major changes concerned the proteins involved in primary metabolism and production of energy, followed by those involved in protein metabolism and cellular defense mechanisms. Some indications of different specific physiological and defense mechanisms implicated in increasing tolerance were obtained. The enhanced salinity tolerance in Duilio appeared to be governed by a higher capacity for osmotic homeostasis, a more efficient defense, and an improvement of protection from mechanical stress by increased cell wall lignifications, allowing a better potential for growth recovery.

Expression of PiABP19, Picdc2 and PiSERK3 during induction of somatic embryogenesis in leaflets of Prunus incisa (Thunb.)

Somatic embryogenesis is a useful tool of plant breeding. In this context, a procedure for inducing somatic embryogenesis in Prunus incisa leaf explants had been previously developed. The original in vitro protocol relies on picloram treatments and exposure to darkness as inductive conditions, the best frequency of embryogenesis being obtained on the second leaf (F(2)) exposed to 4 μM picloram during 30 days. The morphological and biochemical changes observed during somatic embryogenesis occur in response to alterations in gene expression regulation patterns. A molecular study was conducted in order to provide deeper insight into the fundamental biological factors involved in the induction of this process using a gene candidate strategy and semi-quantitative reverse transcription polymerase chain reaction analysis. So far, no sequence data related to somatic embryogenesis has been available in cherry. In the present study, we cloned and sequenced cDNA fragments of putative genes encoding auxin-binding protein, cell cycle regulator and somatic embryogenesis receptor kinase. Time-course differential transcript accumulations were observed for all investigated genes in leaves or derived callus tissues during the observation period (first month of culture). Their possible involvement in the sequential steps of the embryogenic pathway (dedifferentiation, cell proliferation, differentiation through somatic embryogenesis) is presented and discussed.