Dietary Phytase: an ideal approach for a cost effective and low-polluting aquafeed

Global fishmeal production from wild-catch sources cannot continue to increase indefinitely; suitable alternatives have to be found for sustainable aquaculture. Plant-based aquafeed seems to be the ideal alternative to this, but has its own limitations. Plant ingredients are rich in phytic acid, which reduces the bioavailability of nutrients like minerals and protein to the fish, thereby causing aquaculture pollution. Dietary phytase treatment reduces the aquaculture pollution by improving the bioavailability of nutrients, and reduces the feed cost as evident from poultry and piggery. Phytase activity is highly dependent upon the pH of the gut. Unlike mammals, fish are either gastric or agastric, and hence, the action of dietary phytase varies from species to species. In this article, the authors attempt to summarise various effects of phytase on nutrient utilization, growth of fish and aquatic pollution

Estimates of the loss of main-chain conformational entropy of different residues on protein folding

The average contribution of conformational entropy for individual amino acid residues towards the free energy of protein folding is not well understood. We have developed empirical scales for the loss of the main-chain (torsion angles, φ and ψ) conformational entropy by taking its side-chain into account. The analysis shows that the main-chain component of the total conformational entropy loss for a residue is significant and reflects intrinsic characteristics associated with individual residues. The values have direct correlation with the hydrophobicity values and this has important bearing on the folding process

Disulfide bonds, their stereospecific environment and conservation in protein structures

We studied the specificity of the non-bonded interaction in the environment of 572 disulfide bonds in 247 polypeptide chains selected from the Protein Data Bank. The preferred geometry of interaction of peptide oxygen atoms is along the back of the two covalent bonds at the sulfur atom of half cystine. With aromatic residues the geometries that direct one of the sulfur lone pair of electrons into the aromatic Π-system are avoided; an orientation in which the sulfide plane is normal or inclined to the aromatic plane and on top of its edge is normally preferred. The importance of the S···aromatic interaction is manifested in the high degree of its conservation across members in homologous protein families. These interactions, while providing extra overall stability to the native fold and reducing the accessibility of the disulfide bond and thereby preventing exchange reactions, also set the orientation of the conserved aromatic rings for further interactions and binding to another molecule. The conformational features and the mode of interactions of disulfide bridges should be useful for molecular design and protein engineering experiments

Packing of aromatic rings against tryptophan residues in proteins

The geometry of the interaction of the aromatic side chains of phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His) with the indole ring of Trp has been analyzed using the structures in the Protein Data Bank in order to understand the dependence of the packing behaviour on the size and chemical nature of the aromatic rings. The Phe ring prefers to interact either perpendicularly, with its edge pointing towards the Trp face, or in an offset-stacked arrangement. The edge-to-face motif is typical of a Trp-Trp pair. While parallel stacking is the dominant feature of Trp-His interaction, Tyr packs in a more uniform manner around Trp with a higher than expected occurrence at the edge and a few cases of possible OH-Π interaction

Secondary structures at polypeptide-chain termini and their features

An analysis of secondary structures (α-helices and β-strands) in the two terminal regions of polypeptide chains reveals features different from those observed over the whole protein structure. Compared with the overall distribution, the helices in the N-terminal region tend to be smaller and have higher propensities to contain Gln and Leu, while the C-terminal helices are longer and have a greater proportion of Lys and Glu. As a strand, the C-terminal region is never found in the interior of parallel β-sheets and has a higher propensity to be at the edge of antiparallel β-sheets. In contrast, compared with the whole structure the N-terminal region has a higher propensity to be in the interior of parallel β-sheets. Compared with the overall distributions, terminal helices and strands show distinct periodicities in length. The Schellman motif, which is a prevalent C-capping motif in helices, is not common in C-terminal helices. There are other observations that can be used in the design of helical peptides: more residues beyond the C-terminus of helices are used for capping interactions than residues before the N-terminus. Consideration of the distribution of terminal strands in the interior and at the edge of β-sheets suggests a sequential folding mechanism beginning at the N-terminus of the polypeptide chain

Implication of Urban Agriculture and Vertical Farming for Future Sustainability

Urban agriculture (UA) is defined as the production of agricultural goods (crop) and livestock goods within urban areas like cities and towns. In the modern days, the urbanization process has raised a question on the sustainable development and growing of urban population. UA has been claimed to contribute to urban waste recycling, efficient water use and energy conservation, reduction in air pollution and soil erosion, urban beautification, climate change adaptation and resilience, disaster prevention, and ecological and social urban sustainability. Therefore, UA contributes to the sustainability of cities in various ways—socially, economically, and environmentally. An urban farming technology that involves the large-scale agricultural production in the urban surroundings is the vertical farming (VF) or high-rise farming technology. It enables fast growth and production of the crops by maintaining the environmental conditions and nutrient solutions to crop based on hydroponics technology. Vertical farms are able to grow food year-round because they maintain consistent growing conditions regardless of the weather outside and are much less vulnerable to climate changes. This promises a steady flow of products for the consumers and a consistent income for growers. Various advantages of VF over traditional farming, such as reduced farm inputs and crop failures and restored farmland, have enabled scientists to implement VF on a large scale

Role of Vertex Index in Substructure Identification and Activity Prediction: A Study on Antitubercular Activity of a Series of Acid Alkyl Ester Derivatives

Tuberculosis (TB) is a life threatening disease caused due to infection from Mycobacterium tu¬berculosis (Mtb). That most of the TB strains have become resistant to various existing drugs, develop¬ment of effective novel drug candidates to combat this disease is a need of the day. In spite of intensive research world-wide, the success rate of discovering a new anti-TB drug is very poor. Therefore, novel drug discovery methods have to be tried. We have used a rule based computational method that utilizes a vertex index, named ‘distance exponent index (Dx)’ (taken x = –4 here) for predicting anti-TB activity of a series of acid alkyl ester derivatives. The method is meant to identify activity related substructures from a series a compounds and predict activity of a compound on that basis. The high degree of successful pre¬diction in the present study suggests that the said method may be useful in discovering effective anti-TB compound. It is also apparent that substructural approaches may be leveraged for wide purposes in com¬puter-aided drug design. (doi: 10.5562/cca2306

Acclimation to warm temperatures modulates lactate and malate dehydrogenase isozymes in juvenile Horabagrus brachysoma (Günther)

Differential expression of isozymes enables fish to tolerate temperature fluctuations in their environment. The present study explores the modulation of lactate dehydrogenase (LDH) and cytoplasmic malate dehydrogenase (sMDH) isozyme expression in the heart, muscle, brain, liver, gill, and kidney of juvenile Horabagrus brachysoma after 30 days of acclimation at 26, 31, 33, and 36°C. LDH and sMDH zymography were performed using native polyacrylamide gel electrophoresis. The zymography revealed five distinct bands of LDH isoenzymes (labelled from cathode to anode as LDH-A4, LDH-A3B1, LDH-A2B2, LDH-A1B3, and LDH-B4) and three distinct bands of sMDH isoenzymes (labelled from cathode to anode as sMDH-A2, sMDH-AB, and sMDH-B2), with considerable variation in their expression in the tissues. Acclimation to the test temperatures did not influence the expression patterns of LDH or sMDH isozymes. Densitometric analysis of individual isozyme bands revealed a reduction in the densities of bands containing the LDH-B and sMDH-B molecules, while the densities of bands containing the LDH-A and sMDH-A molecules increased in the gills and muscle, indicating the role of these organs in adaptive responses to thermal acclimation. However, the total densities of the LDH and sMDH isozymes increased with higher acclimation temperatures, indicating that adaptation to increased temperatures in H. brachysoma is primarily characterised by quantitative changes in isozyme expression