The Blueprint of Logical Decisions in a NF-κB Signaling System.

Nearly identical cells can exhibit substantially different responses to the same stimulus that causes phenotype diversity. Such interplay between phenotype diversity and the architecture of regulatory circuits is crucial since it determines the state of a biological cell. Here, we theoretically analyze how the circuit blueprints of NF-κB in cellular environments are formed and their role in determining the cells' metabolic state. The NF-κB is a collective name for a developmental conserved family of five different transcription factors that can form homodimers or heterodimers and often promote DNA looping to reprogram the inflammatory gene response. The NF-κB controls many biological functions, including cellular differentiation, proliferation, migration, and survival. Our model shows that nuclear localization of NF-κB differentially promotes logic operations such as AND, NAND, NOR, and OR in its regulatory network. Through the quantitative thermodynamic model of transcriptional regulation and systematic variation of promoter-enhancer interaction modes, we can account for the origin of various logic gates as formed in the NF-κB system. We further show that the interconversion or switching of logic gates yielded under systematic variations of the stimuli activity and DNA looping parameters. Such computation occurs in regulatory and signaling pathways in individual cells at a molecular scale, which one can exploit to design a biomolecular computer.

Process Standardization of Functionally Enriched Millet-Based Nutri-Cereal Mix Using D-Optimal Design Approach for Enhancing Food and Nutritional Security.

Millets are currently employed in a variety of ways, including direct consumption and usage in the manufacture of certain cuisines or snacks. The present investigation was aimed at optimizing functionally enriched millet-based nutri-cereal mix comprising chicken and vegetable for a nutrition-deficient population. A total of 16 experiments were carried out by using optimal (custom) design model of mixture design with 60% major ingredients, including malted sorghum flour (20-30%), malted green gram flour (15-25%), and boiled chicken powder (5-15%). To make 100% of the total nutri-cereal mixture, other ingredients such as malted pearl millet (10%), finger millet flour (10%), beetroot powder (2.5%), pumpkin powder (7.5%), skimmed milk powder (9.5%), and stevia powder (0.5%) were added. Numerical optimization was done using Design Expert software, version 13. The optimized ratio was 30% malted sorghum flour, 15% malted green gram flour, and 15% chicken powder. The predicted values of responses 5.101%, 3.616%, 1.963%, 11.165%, 28.005%, 50.149%, 330.282 kcal, and 0.373 were in accordance with experimental values 6.426%, 3.455%, 1.714%, 11.432%, 29.12%, 47.853%, 323.318 kcal, and 0.385 for moisture, ash, fat, fiber, protein, carbohydrates, energy, and water activity, respectively, with a small error percentage. The results of mineral content, phenolic content, and amino acid profiling revealed that the optimized Nutri-cereal mix have higher amounts of these components. The results also suggested that the optimized Nutri-cereal mix of these malted millet flours can potentially enhance the nutritional deficiency as well as improve food and nutritional security.

Algae: A promising and sustainable protein-rich food ingredient for bakery and dairy products.

The consumer demand for protein rich foods urges the exploration for novel products of natural origin. Algae can be considered as a gold mine of different bioactive compounds, among which protein is distributed in significant amounts i.e., around 30% and can even reach to 55-60% in some cyanobacteria. Bakery and dairy products are extensively consumed worldwide due to product diversification and innovation. However, incorporation of algae biomass can lead to the development of green colour and fishy flavour that usually is not accepted in such products. Therefore, isolation and application of algae-derived proteins opens a new door for food industry. The present review provides a comprehensive understanding of incorporation of algae as a protein-rich ingredient in bakery and dairy products. The paper provides a deep insight for all the possible recent trends related to production and extraction of algae proteins accompanied by their incorporation in bakery and dairy foods.

Enhancing the bio-prospective of microalgae by different light systems and photoperiods.

Microalgae are a source of highly valuable bioactive metabolites and a high-potential feedstock for environmentally friendly and sustainable biofuel production. Recent research has shown that microalgae benefit the environment using less water than conventional crops while increasing oxygen production and lowering CO2 emissions. Microalgae are an excellent source of value-added compounds, such as proteins, pigments, lipids, and polysaccharides, as well as a high-potential feedstock for environmentally friendly and sustainable biofuel production. Various factors, such as nutrient concentration, temperature, light, pH, and cultivation method, effect the biomass cultivation and accumulation of high-value-added compounds in microalgae. Among the aforementioned factors, light is a key and essential factor for microalgae growth. Since photoautotrophic microalgae rely on light to absorb energy and transform it into chemical energy, light has a significant impact on algal growth. During micro-algal culture, spectral quality may be tailored to improve biomass composition for use in downstream bio-refineries and boost production. The light regime, which includes changes in intensity and photoperiod, has an impact on the growth and metabolic composition of microalgae. In this review, we investigate the effects of red, blue, and UV light wavelengths, different photoperiod, and different lighting systems on micro-algal growth and their valuable compounds. It also focuses on different micro-algal growth, photosynthesis systems, cultivation methods, and current market shares.

Theoretical investigation of functional responses of bio-molecular assembly networks.

Cooperative protein-protein and protein-DNA interactions form programmable complex assemblies, often performing non-linear gene regulatory operations involved in signal transductions and cell fate determination. The apparent structure of those complex assemblies is very similar, but their functional response strongly depends on the topology of the protein-DNA interaction networks. Here, we demonstrate how the coordinated self-assembly creates gene regulatory network motifs that corroborate the existence of a precise functional response at the molecular level using thermodynamic and dynamic analyses. Our theoretical and Monte Carlo simulations show that a complex network of interactions can form a decision-making loop, such as feedback and feed-forward circuits, only by a few molecular mechanisms. We characterize each possible network of interactions by systematic variations of free energy parameters associated with the binding among biomolecules and DNA looping. We also find that the higher-order networks exhibit alternative steady states from the stochastic dynamics of each network. We capture this signature by calculating stochastic potentials and attributing their multi-stability features. We validate our findings against the Gal promoter system in yeast cells. Overall, we show that the network topology is vital in phenotype diversity in regulatory circuits.

Anticipating response function in gene regulatory networks.

The origin of an ordered genetic response of a complex and noisy biological cell is intimately related to the detailed mechanism of protein-DNA interactions present in a wide variety of gene regulatory (GR) systems. However, the quantitative prediction of genetic response and the correlation between the mechanism and the response curve is poorly understood. Here, we report in silico binding studies of GR systems to show that the transcription factor (TF) binds to multiple DNA sites with high cooperativity spreads from specific binding sites into adjacent non-specific DNA and bends the DNA. Our analysis is not limited only to the isolated model system but also can be applied to a system containing multiple interacting genes. The controlling role of TF oligomerization, TF-ligand interactions, and DNA looping for gene expression has been also characterized. The predictions are validated against detailed grand canonical Monte Carlo simulations and published data for the lac operon system. Overall, our study reveals that the expression of target genes can be quantitatively controlled by modulating TF-ligand interactions and the bending energy of DNA.

In vitro immunomodulatory potential of Artemisia indica Willd. in chicken lymphocytes.

AIM: Evaluation of the in vitro immunomodulatory potential of Artemisia indica Willd. methanolic extract in chicken lymphocyte culture system through lymphocyte (B and T cells) proliferation assay, after standardizing the maximum non-cytotoxic dose (MNCD) in chicken lymphocytes. MATERIALS AND METHODS: Fresh aerial parts of A. indica Willd. (family: Asteraceae) specimens were collected (altitude 1560 m), gotten authenticated, processed, dried, and Soxhlet extracted to yield methanolic extract (AME). Chicken splenocytes were isolated from spleens collected from healthy birds; lymphocytes were separated by density gradient centrifugation, percentage cell viability determined and final cell count adjusted to 107 cells/ml in RPMI-1640 medium. MNCD of AME in chicken lymphocytes was determined through 3-(4,5-dimethylthiazol-2-y1)-2,5-diphenyltetrazolium bromide dye reduction assay. Immunomodulatory potential of AME was evaluated through lymphocytes proliferation or B and T cells blastogenesis assay in the presence of appropriate mitogens, namely, lipopolysaccharide (LPS) and concanavalin A (Con A), respectively. RESULTS: Maximum concentration of AME exhibiting 100% cell viability (MNCD) was 200 µg/ml and was selected for further in vitro analysis. The in vitro exposure of chicken lymphocytes to 200 µg/ml dose of AME, resulted in significant (p<0.05) upregulation of 11.76% in B cell proliferation in the presence of B cell mitogen (LPS) and a significant (p<0.05) increase of 12.018% T cells proliferation in the presence of the mitogen (Con A), as compared to the control. CONCLUSION: The significant upregulation in the proliferation of two major cell types modulating the immune system is an indication of the immunostimulatory potential of the plant. It would be worthwhile to further evaluate A. indica on relevant immunomodulatory aspects, especially the in vivo studies in a poultry system.

Novel aqueous foams for suppressing VOC emission.

Reducing volatile organic compound (VOC) emissions from crude oil/gasoline distribution and storage facilities is important in controlling environmental pollution and enhancing workplace safety. Stable aqueous foam formulations are developed to provide a mass transfer barrier to the emission of VOCs during loading of gasoline. Experiments are carried out in a bench-scale foam cell using liquid hexane as oil. The foam columns of 32 cm in height were able to suppress the plateau concentration of hexane vapors in the effluent by 87% under experimental conditions tested. Vapor suppression increased with foam height but was almost insensitive to liquid viscosity. These experiments are then upscaled from bench-scale to a vessel having an exposed surface area of roughly 2 orders of magnitude higher. Gasoline is used as oil in the upscaled experiments, and the concentrations of volatile hydrocarbons in the effluent are measured during oil loading. A 40-cm-thick foam column is found to reduce the emissions by 96% for foams prepared with deionized water and by 93.8% for foams prepared with 3.5 wt % NaCl brine for 10 h of oil loading.

Mass transfer of volatile organic carbons through aqueous foams.

A model is developed to study diffusive mass transfer of hydrocarbon vapor through a flexible foam blanket. The model accounts for the diffusion of hydrocarbon vapor through gas-phase and liquid lamellae, the combined gravity and capillary drainage from the plateau border, the thinning of foam lamellae caused by the forces of capillary suction, London-van der Waals attraction, and electrostatic double-layer repulsion, and foam collapse. Uniform bubble size is assumed, and hence, interbubble gas diffusion arising out of variation in bubble sizes alone is not incorporated into the model. A high-stability aqueous foam formulation that remains stable in the presence of oil (hexane) at foam-oil contact was developed using surfactants, stabilizers, and viscosifiers. Emission of hexane vapor through the foam was measured. The model predicts that the initially taller foam columns collapse faster. Their mass-transfer resistance is higher before the onset of collapse but not very different from that of the shorter foam columns at long times. If the solubility and diffusivity of the hexane gas in the foam liquid are unaffected, the foams with higher viscosities persist longer and provide greater diffusive mass-transfer resistance. Foam bubble size does not significantly impact the mass-transfer resistance of the foam column before the onset of foam collapse. However, the foams with smaller bubbles collapse earlier, and their ability to act as a mass-transfer barrier to the diffusing hydrocarbon vapor diminishes rapidly. The experimental results compared reasonably with the model for varying initial foam heights and bubble sizes.