Probing binding mechanism of interleukin-6 and olokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases

Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated in silico to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag???Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag???Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.     

The determination of spatial pattern inDictyostelium discoideum

Free-living amoebae of the cellular slime mouldDictyostelium discoideum aggregate when starved and give rise to a long and thin multicellular structure, the slug. The slug resembles a metazoan embryo, and as with other embryos it is possible to specify a fate map. In the case ofDictyostelium discoideum the map is especially simple: cells in the anterior fifth of the slug die and form a stalk while the majority of those in the posterior differentiate into spores. The genesis of this anterior-posterior distinction is the subject of our review. In particular, we ask: what are the relative roles of individual pre-aggregative predispositions and post-aggregative position in determining cell fate? We review the literature on the subject and conclude that both factors are important. Variations in nutritional status, or in cell cycle phase at starvation, can bias the probability that an amoeba differentiates into a stalk cell or a spore. On the other hand, isolates, or slug fragments, consisting of only prestalk cells or only prespore cells can regulate so as to result in a normal range of both cell types. We identify three levels of control, each being responsible for guiding patterning in normal development: (i) ‘coin tossing’, whereby a cell autonomously exhibits a preference for developing along either the stalk or the spore pathway with relative probabilities that can be influenced by the environment; (ii) ‘chemical kinetics’, whereby prestalk and prespore cells originate from undifferentiated amoebae on a probabilistic basis but, having originated, interact (e.g. via positive and negative feedbacks), and the interaction influences the possibility of conversion of one cell type into the other; and (iii) ‘positional information’, in which the spatial distribution of morphogens in the slug influences the pathway of differentiation. In the case of possibilities (i) and (ii), sorting out of like cell types leads to the final spatial pattern. In the case of possibility (iii), the pattern arisesin situ     

Plant contents and quality of makhana (Euryale ferox)

Summary As a part of integrated study of makhana, the mineral contents of the plant parts and the fruits of makhana (Euryale ferox) have been presented here. It has been observed that the fruits were not only rich in minerals but also in protein. The plant parts also contained high amounts of micronutrients. Its fruits are, therefore, a good supplement for minerals which are produced from otherwise agriculturally waste (water-logged) areas.     

In vitro regeneration of Ruscus hypophyllum L. plants

Callus cultures were established from stem explants of Ruscus hypophyllum on a modified basal medium of Murashige and Skoog (1962) supplemented with 1 mg l^-1 2,4-D+0.1 mg l^-1 BAP. The optimal 2,4-D concentration for promoting shoot bud formation and growth was 0.05 mg l^-1 along with 0.5 mg l^-1 BAP. Sixty percent of rootless shoots produced flowers on the regenerating medium. Rooting was induced when shoots were transferred to half strength MS inorganic salts supplemented with 2 mg l^-1 IBA. Eighty percent of plants transferred to soil have survived.     

The effect of 2-deoxy-D-glucose on insulin release by neonatal rat B cells in culture

The culture for 7 days in medium with 5.5 mM glucose and 1 mM 2-deoxy-D-glucose enhanced the glucose sensitivity of neonatal rat B cells, and even stimulated their growth in vitro. Also, 2-deoxy-D-glucose supplementation maintained insulin release evoked by leucine and 2-ketoisocaproate from B cells at day 7 at levels several times higher than at day 1. The effect of leucine was greatly augmented by glutamine, whereas that of the 2-keto acid remained almost unchanged irrespective of the presence of glutamine. These results suggest an increase in oxidative catabolism of medium nutrients in B cells grown in medium with 2-deoxy-D-glucose for 7 days, and such metabolic changes may promote the growth of B cells in vitro.     

Rhizogenesis fromNigella sativa protoplasts

Summary Protoplasts were isolated for the first time from cell suspensions ofNigella sativa. These were then cultured in media and observed at regular intervals. Different concentrations of auxin and kinetin were tried with success to obtain root from the callus tissues of the protoplasts.     

Spoil characteristics and vegetation development of an age series of mine spoils in a dry tropical environment

A series of coal mine spoils (5, 10, 12, 16 and 20-yr old) in a dry tropical environment was sampled to assess the changes with time in spoil characteristics, species composition and plant biomass. Coarse fragments (>2 mm) decreased with age of mine spoil while the proportion of 0.2–0.1 mm particles increased. Total soil N, mineral N, NaHCO₃-extractable Pi, and exchangeable K increased with age of mine spoil and these parameters were lower in mine spoils than native forest soil even after 20 years of succession. Exchangeable Na decreased with age of mine spoil and in 20-yr old spoil it was higher than native forest soil. Plant community composition changed with age. Only a few species participated in community formation. Species richness increased with age, while evenness and species diversity declined from 5-yr old to 16-yr old community with an increase in the 20-yr old community. A reverse trend occurred for concentration of dominance. Area-weighted shoot and root biomass of other species increased with the age of the mine spoil while that of Xanthium strumarium patches declined with age. Data collected on spoil features, microbial C, N and P, and shoot and root biomass when subjected to Discriminant Analysis indicated a continued profound effect of age. 10 and 12-yr old mine spoils were closer to each other, and 5 and 20-yr old spoils were farthest apart.     

Subtractive Proteome Analysis of Candida albicans Divulges Promising Antifungal Targets

International Journal of Peptide Research and Therapeutics - Candida albicans is the most common nosocomial systemic fungal infections causing high mortality/morbidity. Existing antifungal...     

Unraveling the camel rumen microbiome through metaculturomics approach for agriculture waste hydrolytic potential

Archives of Microbiology - Cellulose is the most abundant natural polymer present on Earth in the form of agriculture waste. Hydrolysis of agriculture waste for simple fermentable reducing sugars...