Evaluating methods for B-cell clonal family assignment.

The adaptive immune response relies on a diverse repertoire of B-cell receptors, each of which is characterized by a distinct sequence resulting from VDJ-recombination. Upon binding to an antigen, B-cells undergo clonal expansion and in a process unique to B-cells the overall binding affinity of the repertoire is further enhanced by somatic hypermutations in the receptor sequence. For B-cell repertoires it is therefore particularly important to analyze the dynamics of clonal expansion and patterns of somatic hypermutations and thus it is necessary to group the sequences into distinct clones to determine the number and identity of expanding clonal families responding to an antigen. Multiple methods are currently used to identify clones from sequences, employing distinct approaches to the problem. Until now there has not been an extensive comparison of how well these methods perform under the same conditions. Furthermore, since this is fundamentally a phylogenetics problem, we speculated that the mPTP method, which delimits species based on an analysis of changes in the underlying process of diversification, might perform as well as or better than existing methods. Here we conducted extensive simulations of B-cell repertoires under a diverse set of conditions and studied errors in clonal assignment and in downstream ancestral state reconstruction. We demonstrated that SCOPer-H consistently yielded superior results across parameters. However, this approach relies on a good reference assembly for the germline immunoglobulin genes which is lacking for many species. Using mPTP had lower error rates than tailor-made immunogenetic methods and should therefore be considered by researchers studying antibody evolution in non-model organisms without a reference genome.

Traditional halal meat production without stunning versus commercial slaughter with electrical stunning of slow-growing broiler chicken: impact on meat quality and proteome changes.

Impact of traditional halal meat production without stunning (NST) and commercial slaughter with electrical stunning (ST) of 100 slow-growing broiler chicken on blood plasma and different biochemical, enzymatic, hormonal, meat quality, and proteomic changes was evaluated. The results revealed lower (P < 0.05) postmortem pH values and higher redness (a*) scores for ST samples relative to NST group. Myofibrillar fragmentation index and bleeding efficiency (%) were lower (P < 0.05) in ST compared to NST samples. The ST group had higher (P < 0.05) creatinine, total protein, alanine aminotransferase (ALT), and triiodothyronine (T3) than NST group, however, no difference (P > 0.05) in blood glucose, lactate dehydrogenase (LDH), creatine kinase (CK), thyroxine (T4), cortisol, and aspartate aminotransferase (AST) was observed relative to NST samples. The 2-dimensional gel electrophoresis (2-DE) coupled to MALDI-TOF MS of meat samples has identified 14 differentially abundant proteins between 2 groups. Proteins demonstrating positive correlation with stress namely adenylate kinase isoenzyme-1, Rho guanine nucleotide exchange factor (NST), and apolipoprotein A-I (ST) were overabundant. From the current study, it is concluded that electrical stunning of broilers prior to slaughter or traditional halal slaughter without stunning does not adversely affect the meat quality.

Lateral flow immunoassay-based absolute point-of-care technique for authentication of meat and commercial meat products.

Point-of-care (POC) assay is an emerging technique for rapid initial screening of meat fraud incidents in a resource-limited environment. To achieve this goal, a simple extraction protocol is proposed for efficient recovery of meat proteins from raw, heat-processed, and commercial samples as well as meat offals without utilizing sophisticated laboratory settings. A sandwich-format lateral flow immunoassay (LFIA) was developed based on gold nanoparticles as labels and immunoglobulins (IgG and IgY) as biomarkers for meat species identification in raw and cooked meat mixes. The test system showed a sensitivity of 10 ng/mL allowing the detection of as low as 0.063% pork and chicken meat and 0.125% sheep meat (lamb) in meat mixes within 15 min including sample preparation. Reproducibility of the assay was confirmed by the fully consistent intra- and inter-laboratory tests and RT-PCR method. The current study developed a field-deployable extraction technique and highly-specific, sensitive, reproducible, cost-effective, and user-friendly LFIA-based assay for rapid species authentication in raw, cooked, and commercial meat samples and meat offals. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-022-05663-2.

Antioxidant and angiotensin-I-converting enzyme (ACE-I) inhibitory activities of protein hydrolysates derived from water buffalo (Bubalus bubalis) liver.

In the current study, we attempted to use ginger as a novel and natural source of protease in comparison with other commercially available enzymes to extract and characterize antioxidant and antihypertensive hydrolysates from water buffalo liver, a protein rich offal. Hydrolysis of protein extracts from buffalo liver using proteinase-K, pronase-E and ginger protease significantly increased the %degree of hydrolysis (18.5-55%) and generated low-molecular weight peptides evident from SDS-PAGE. Enzyme treated hydrolysates exhibited higher (p < 0.05) DPPH radical scavenging activity (43.7-82.4%) and angiotensin-I-converting enzyme (ACE-I) inhibitory activity (46.9-50.1%) relative to control. Mass spectrometric analysis (MALDI-TOF MS) of selected gel-filtered fractions identified few important peptides derived from nuclear ribonucleoprotein, pyruvate kinase and phosphoglycerate kinase that possess strong antioxidant activity. Present findings indicate the efficacy of partially purified ginger as a novel source of protease in generating protein hydrolysates from water buffalo liver with significant antioxidant and antihypertensive activity in vitro. We successfully demonstrated the recovery of functional bioactive peptides from water buffalo liver which presents a potential opportunity for the meat industries to economically use this important byproduct.

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.

Exploring the dynamics of women consumer preference, attitude and behaviour towards meat and meat products consumption in India.

Urbanisation and changing food habits in India have resulted in a shift in consumption from cereals to protein-based foods. Women play a major role in India in all activities related to food at household and therefore, the current paper reports the findings of the qualitative work conducted to understand women consumers' preference and perception towards meat and its attributes as a function of their awareness. The study collected the responses from 510 women residents of Metropolitan city of Bengaluru, India using questionnaires directly by face-to-face interviews and generated data on preference for fresh meat, purchase habits, value added meat products consumption, awareness about meat quality, and future expectations about meat sector. Findings from the current study indicate that, chicken is the most preferred meat (41.76%) while beef was least preferred (5.88%). The 40.59% of respondents preferred meat tenderness as an important eating quality followed by juiciness (37.06%) and flavor (12.94%). Consumers rated ritual slaughter, animal welfare and food safety as relevant issues in meat production, whereas regulations pertaining to meat production, processing of meat and food labelling were of minor significance. The study provide an insight into the significance of various consumer behaviour with respect to choice of meat, awareness on ritual slaughter, animal welfare and processing which is helpful in prioritizing future consumer research and policy decisions in India.

Application of nanoemulsion-based approaches for improving the quality and safety of muscle foods: A comprehensive review.

Recently, there has been growing interest in implementing innovative nanoscience-based technologies to improve the health, safety, and quality of food products. A major thrust in this area has been to use nanoemulsions because they can easily be formulated with existing food ingredients and technologies. In particular, oil-in-water nanoemulsions, which consist of small oil droplets (<200 nm) dispersed in water, are being utilized as delivery systems for various hydrophobic substances in foods, including nutrients, nutraceuticals, antioxidants, antimicrobials, colors, and flavors. In this article, we focus on the application of nanoemulsion-based delivery systems for improving the quality, safety, nutritional profile, and sensory attributes of muscle foods, such as meat and fish. The article also critically reviews the formulation and fabrication of food-grade nanoemulsions, their potential benefits and limitations in muscle food systems.

Application of Enoki Mushroom (Flammulina Velutipes) Stem Wastes as Functional Ingredients in Goat Meat Nuggets.

The impact of different amounts (2%, 4% and 6%) of enoki (Flammulina velutipes) mushroom stem waste (MSW) powder on the physicochemical quality, color and textural, oxidative stability, sensory attributes and shelf-life of goat meat nuggets was evaluated. These mushroom by-products (MSW powder) contained a good source of protein (13.5%), ash (8.2%), total phenolics content (6.3 mg GAE/g), and dietary fiber (32.3%) and also exhibited the potential to be strong antioxidants, due to their good metal chelating ability (41.3%), reducing power (60.1%), and free radical scavenging activity (84.2%). Mushroom stem waste improved (p < 0.05) the emulsion stability, dietary fiber, ash and phenolics content of nuggets compared to control. Although no significant differences (p > 0.05) in expressible water and textural properties were observed among the formulations, but MSW powder improved the water holding capacity and slightly decreased the hardness. Further, the inclusion of MSW significantly (p < 0.05) improved the oxidative stability and shelf-life of treated nuggets by reducing lipid oxidation during the nine-day storage period. Again, the inclusion of MSW did not negatively affect the color and sensory attributes of treated meat nuggets. Overall, our results suggest that enoki mushroom stem waste (4%) can be used as a value-added functional ingredient to produce nutritionally improved and healthier meat products.

Superchilling of muscle foods: Potential alternative for chilling and freezing.

Superchilling is an attractive technique for preservation of muscle foods which freezes part of the water and insulate the food products from temperature fluctuations thereby enhancing the shelf-life during storage, transportation and retailing. Superchilling process synergistically improves the product shelf-life when used in combination with vacuum or modified atmospheric packaging. The shelf-life of muscle foods was reported to be increased by 1.5 to 4.0 times relative to traditional chilling technique. Advantages of superchilling and its ability to maintain the freshness of muscle foods over freezing has been discussed and its potential for Industrial application is highlighted. Present review also unravel the mechanistic bases for ice-crystal formation during superchilling and measures to ameliorate the drip loss. The future challenges especially automation in superchilling process for large scale Industrial application is presented.

Technological demands of meat processing-An Asian perspective.

A rapid increase in the economy, population, industrialization, and urbanization of Asian countries has driven the fast development of their meat industries over recent decades. This consistent increase in meat production and consumption in Asia has been the major cause for the development of the global meat industry. Meat production methods and consumption are very diverse across different regions and countries in Asia, and thus, it is impossible to cover the technological demands of all Asian countries in this review. Here, we have mainly highlighted the differences in meat production methods and consumption in Asia during recent decades and the meat technology demands of three east Asian countries, namely China, Korea, and Japan, and one south Asian country, India. A brief introduction of the meat industry, in particular the production and consumption trend in these countries, is provided in this article. The technology demands for fresh and processed meat products are then reviewed.

Quality characteristics of low fat chicken nuggets: effect of salt substitute blend and pea hull flour.

Effect of salt substitution (Treat I) and added pea hull flour (PHF) at 8 (Treat-II), 10 (Treat-III) and 12 % (Treat-IV) levels on the quality of low fat chicken nuggets (Control) was investigated. Replacement of NaCl significantly affected (P < 0.05) emulsion and product pH, emulsion stability, cooking yield, ash content while PHF had additional effect on moisture and protein. Dietary fibre content in the product significantly (P < 0.05) increased at each level of PHF. The colour parameters remained similar to control due to salt replacement while added PHF decreased their values. Textural properties were lower (P < 0.05) in the treated products. Addition of PHF significantly (P < 0.05) decreased cholesterol and glycolipids contents at 8 % and 12 % levels, respectively. Sensory evaluation exhibited that 40 % NaCl can efficiently be replaced and 8 % PHF can be incorporated as a source of fibre in low fat chicken nuggets without significant effect on various attributes.

Guava (Psidium guajava L.) Powder as an Antioxidant Dietary Fibre in Sheep Meat Nuggets.

This study was conducted to explore the antioxidant potential and functional value of guava (Psidium guajava L.) powder in muscle foods. Guava powder was used as a source of antioxidant dietary fibre in sheep meat nuggets at two different levels i.e., 0.5% (Treatment I) and 1.0% (Treatment II) and its effect was evaluated against control. Guava powder is rich in dietary fibre (43.21%), phenolics (44.04 mg GAE/g) and possesses good radical scavenging activity as well as reducing power. Incorporation of guava powder resulted in significant decrease (p<0.05) in pH of emulsion and nuggets, emulsion stability, cooking yield and moisture content of nuggets while ash and moisture content of emulsion were increased. Total phenolics, total dietary fibre (TDF) and ash content significantly increased (p<0.05) in nuggets with added guava powder. Product redness value was significantly improved (p<0.05) due to guava powder. Textural properties did not differ significantly except, springiness and shear force values. Guava powder was found to retard lipid peroxidation of cooked sheep meat nuggets as measured by TBARS number during refrigerated storage. Guava powder did not affect sensory characteristics of the products and can be used as source of antioxidant dietary fibre in meat foods.

Quality characteristics of low-fat chicken nuggets: effect of common salt replacement and added bottle gourd (Lagenaria siceraria L.).

BACKGROUND: There is growing demand for the meat products having healthier characteristics. In an endeavour to develop low-salt, low-fat and high-fibre chicken nuggets an investigation was carried out to observe the effects of partial replacement (40%) of sodium chloride in pre-standardised low-fat chicken nuggets (Control, 20 g kg⁻¹ NaCl) with a salt substitute blend as well as incorporation of bottle gourd (Lagenaria siceraria L.) in the resulting low-salt, low-fat products at three different levels, i.e. 50, 75 and 100 g kg⁻¹ (Treatments, 12 g kg⁻¹ NaCl) on the various quality attributes. RESULTS: Sodium chloride replacement decreased (P < 0.01) emulsion and product pH, cooking yield, moisture, ash, yellowness, hue value and textural properties. pH values, moisture and dietary fibre increased (P < 0.01) while cooking yield, % protein, textural properties and total cholesterol were decreased with the incorporation of bottle gourd in low-salt, low-fat nuggets. Sensory attributes of the product were not affected with salt replacement; however, inclusion of bottle gourd at higher levels decreased (P < 0.05) flavour and texture scores. CONCLUSION: The results suggest that low-salt, low-fat and high-fibre chicken nuggets can be developed with the use of a salt substitute blend and bottle gourd without affecting their acceptability.

Antioxidant effects of broccoli powder extract in goat meat nuggets.

The antioxidant potential of broccoli powder extract (BPE) was determined and evaluated in goat meat nuggets at three different levels 1, 1.5 and 2%, compared with control and butylated hydroxyl toluene (100ppm BHT). Total phenolics in 5mg broccoli powder was higher (P<0.05) than 100ppm BHT. Free radical scavenging activity of 2.25mg and 3mg broccoli powder was found similar to 50 and 100ppm BHT. Reducing power of 10mg broccoli powder was comparable to the 100ppm BHT. Incorporation of 1.5 and 2% BPE decreased (P<0.05) the pH value of the products. Total phenolics in product with 2% BPE was similar to BHT nuggets. Chroma value of products with 1.5 and 2% BPE was lower (P<0.05) than control and BHT nuggets. Thiobarbituric acid reactive substances number of BPE nuggets was lower (P<0.05) than control throughout the storage. Thus 2% BPE can be used as natural antioxidant in goat meat nuggets without affecting product acceptability.

Low-sodium meat products: retaining salty taste for sweet health.

There is a positive correlation between excessive intake of sodium and incidence of hypertension. As diet is the main source of sodium, awareness among people regarding its possible role upon health has driven demand for various low sodium foods including meat products. Meat products contribute a significant amount of dietary sodium, thus maligning their own image. However, this is not an easy task as common salt affects taste and flavor, functional attributes, stability, and food safety of meat products. The various properties such as taste and flavor, binding, as well as microbiological characteristics should be given due care while developing low salt meat products and accordingly different approaches have been proposed for processing of such products. Potassium chloride has been mostly used to replace sodium; however, a number of other salts, flavor enhancers, bitter blockers and water, as well as fat binders have also been attempted either alone or in different combinations. A number of low sodium meat products have been developed but their economy and consumer acceptability are the major concerns needing proper attention. In future it is anticipated that these challenges would be overcome to provide well acceptable and cost-effective healthier meat products to the consumers.

Quality of Low Fat Chicken Nuggets: Effect of Sodium Chloride Replacement and Added Chickpea (Cicer arietinum L.) Hull Flour.

While attempting to develop low salt, low fat and high fibre chicken nuggets, the effect of partial (40%) common salt substitution and incorporation of chickpea hull flour (CHF) at three different levels viz., 5, 7.5 and 10% (Treatments) in pre-standardized low fat chicken nuggets (Control) were observed. Common salt replacement with salt substitute blend led to a significant decrease in pH, emulsion stability, moisture, ash, hardness, cohesiveness, gumminess and chewiness values while incorporation of CHF in low salt, low fat products resulted in decreased emulsion stability, cooking yield, moisture, protein, ash, color values, however dietary fibre and textural properties were increased (p<0.01). Lipid profile revealed a decrease in total cholesterol and glycolipid contents with the incorporation of CHF (p<0.01). All the sensory attributes except appearance and flavor, remained unaffected with salt replacement, while addition of CHF resulted in lower sensory scores (p<0.01). Among low salt, low fat chicken nuggets with CHF, incorporation CHF at 5% level was found optimum having sensory ratings close to very good. Thus most acceptable low salt, low fat and high fibre chicken nuggets could be developed by a salt replacement blend and addition of 5% CHF.

Dietary fibre as functional ingredient in meat products: a novel approach for healthy living - a review.

There is a rapid change in our overall lifestyle due to impact of globalization. Every day hasty life has forced consumers to be dependent upon fast foods, which contain meagre amount of dietary fibre. Non-starch polysaccharides and resistant oligosaccharides, lignin, substances associated with NSP and lignin complex in plants, other analogous carbohydrates, such as resistant starch and dextrins, and synthesized carbohydrate compounds, like polydextrose are categorized as dietary fibre. They are mostly concentrated in cereals, pulses, fruits and vegetables. It has been proclaimed that daily dietary fibre intake helps in prevention of many nutritional disorders like gut related problems, cardiovascular diseases, type 2 diabetes, certain types of cancer and obesity. Meat is generally lacking this potential ingredient, which could be incorporated while products processing to make them more healthful. Various fibre rich sources have been attempted in different products attributed to their technological and health benefits and many are in the queue to be used in a variety of meat products. Selection of appropriate fibre rich ingredients and their proper incorporation can improve health image of meat products.

Transient expression in Nicotiana benthamiana fluorescent marker lines provides enhanced definition of protein localization, movement and interactions in planta.

Here, we report on the construction of a novel series of Gateway-compatible plant transformation vectors containing genes encoding autofluorescent proteins, including Cerulean, Dendra2, DRONPA, TagRFP and Venus, for the expression of protein fusions in plant cells. To assist users in the selection of vectors, we have determined the relative in planta photostability and brightness of nine autofluorescent proteins (AFPs), and have compared the use of DRONPA and Dendra2 in photoactivation and photoconversion experiments. Additionally, we have generated transgenic Nicotiana benthamiana lines that express fluorescent protein markers targeted to nuclei, endoplasmic reticulum or actin filaments. We show that conducting bimolecular fluorescence complementation assays in plants that constitutively express cyan fluorescent protein fused to histone 2B provides enhanced data quality and content over assays conducted without the benefit of a subcellular marker. In addition to testing protein interactions, we demonstrate that our transgenic lines that express red fluorescent protein markers offer exceptional support in experiments aimed at defining nuclear or endomembrane localization. Taken together, the new combination of pSITE-BiFC and pSITEII vectors for studying intracellular protein interaction, localization and movement, in conjunction with our transgenic marker lines, constitute powerful tools for the plant biology community.

PSITE vectors for stable integration or transient expression of autofluorescent protein fusions in plants: probing Nicotiana benthamiana-virus interactions.

Plant functional proteomics research is increasingly dependent upon vectors that facilitate high-throughput gene cloning and expression of fusions to autofluorescent proteins. Here, we describe the pSITE family of plasmids, a new set of Agrobacterium binary vectors, suitable for the stable integration or transient expression of various autofluorescent protein fusions in plant cells. The pSITE vectors permit single-step Gateway-mediated recombination cloning for construction of binary vectors that can be used directly in transient expression studies or for the selection of transgenic plants on media containing kanamycin. These vectors can be used to express native proteins or fusions to monmeric red fluorescent protein or the enhanced green fluorescent protein and its cyan and yellow-shifted spectral variants. We have validated the vectors for use in transient expression assays and for the generation of transgenic plants. Additionally, we have generated markers for fluorescent highlighting of actin filaments, chromatin, endoplasmic reticulum, and nucleoli. Finally, we show that pSITE vectors can be used for targeted gene expression in virus-infected cells, which should facilitate high-throughput characterization of protein dynamics in host-virus interactions.