Protein evolution: The deciphering of latent facets — correlation of synthesis profiles of ribosomally directed proteins and enzyme directed peptides

Key facets pertaining to the evolution of proteins have been probed, using as springboard, the relevant data bases constructed from (i) 60 ribosomally directed proteins, whose 3D structures are known and having 10,000 residues and (ii) from 73 enzyme directed peptides, comprising of 524 residues. The preference profiles, both in terms of the choice of neighbours and the placement of the peptide bonds, have been delineated with respect to each of the 20 coded amino acids. By and large, the preference profile from both the sets are similar, thus giving importance to the nature of the side chains of the coded amino acids. The predictive power of the preference profile has been tested with good results, thus demonstrating the evidence of common preference pathways for peptide formation during evolution. The ribosomally directed protein synthesis, controlled by the genome, proceeds by the addition of single residues at a time. On the other hand, the enzyme directed peptide synthesis largely operates in a more energy conscious block mode, where each constituent of a large enzyme ensemble is engaged in precisely assembling the modules and transfering them to the adjacent one, thus realizing a sequence specific peptide synthesis. Of significance is the fact that, in spite of such divergence in assembly, predictions for neighbour preferences in ribosomally directed protein synthesis work well when applied to enzyme directed peptide synthesis. The findings here are significant since they provide (i) a clear picture of directed peptide synthesis in the absence of direct genomic control, (ii) evidence for the preferred formation of peptide bonds using protein templates, (iii) they also provide evidence for the presence of protein like structures, with catalytic activity, prior to the freezing of the genetic code arising from dominance of the information system and (iv) a logical approach to the evolution of a hierarchical pattern. Presented at the National Symposium on Evolution of Lite.     

Dosimetric comparison of normal breathing and deep inspiration breath hold technique for synchronous bilateral breast cancer using 6MV flattened beam and flattening filter free beam

BackgroundThe present study was to investigate the usefulness of deep inspiration breath hold (DIBH) in bilateral breast patients using 6MV flattened beam (FB) and flattening filter free beam (FFFB).Materials and methodsTwenty bilateral breast cancer patients were simulated, using left breast patients treated with DIBH technique. CT scans were performed in the normal breathing (NB) and DIBH method. Three-dimensional conformal radiotherapy (3DCRT) and volumetric arc therapy (VMAT) plans were generated.ResultsIn our study the best organ at risk (OAR) sparing is achieved in the 3DCRT DIBH plan with adequate PTV coverage (V₉₅ ≥ 47.5 Gy) as compared to 6MV FB and FFFB VMAT DIBH plans. The DIBH scan plan reduces the heart mean dose significantly at the rate of 49% in 3DCRT (p = 0.00) and 22% in VMAT (p = 0.010). Similarly, the DIBH scan plan produces lesser common lung mean dose of 18% in 3DCRT (p = 0.011) and 8% in VMAT (0.007) as compared to the NB scan. The conformity index is much better in VMAT FB (1.04 ± 0.04 vs. 1.04 ± 0.05), p =1.00 and VMAT FFFB (1.04 ± 0.05 vs. 1 ± 0.24, p = 0.345) plans as compared to 3DCRT (1.63 ± 0.2 vs. 1.47 ± 0.28, p = 0.002). The homogeneity index of all the plans is less than 0.15. The global dmax is more in VMAT FFFB DIBH plan (113.7%). The maximum MU noted in the NB scan plan (478 vs. 477MU, 1366 vs. 1299 MU and 1853 vs. 1788 MU for 3DCRT, VMAT FB and VMAT FFFB technique as compared to DIBH scan.ConclusionWe recommend that the use of DIBH techniques for bilateral breast cancer patients significantly reduces the radiation doses to OARs in both 3DCRT and VMAT plans.     

Stress transfer in cellulose nanowhisker composites--influence of whisker aspect ratio and surface charge

The mechanically induced molecular deformation of cellulose nanowhiskers embedded in subpercolation concentration in an epoxy resin matrix was monitored through Raman spectroscopy. Cellulose nanowhiskers isolated by sulfuric acid hydrolysis from tunicates and by sulfuric acid hydrolysis and hydrochloric acid hydrolysis from cotton were used to study how the aspect ratio (ca. 76 for tunicate and 19 for cotton) and surface charges (38 and 85 mmol SO(4)(-)/kg for sulfuric acid hydrolysis of cotton and tunicate, respectively; no detectable surface charges for hydrochloric acid hydrolysis) originating from the isolation process influence stress transfer in such systems. Atomic force microscopy confirmed that uncharged cellulose nanowhiskers produced by hydrochloric acid hydrolysis have a much higher tendency to aggregate than the charged cotton or tunicate nanowhiskers. Each of these nanowhisker types was incorporated in a concentration of 0.7 vol % in a thermosetting epoxy resin matrix. Mechanically induced shifts of the Raman peak initially located at 1095 cm(-1) were used to express the level of deformation imparted to the nanowhiskers embedded in the resin. Much larger shifts of the diagnostic Raman band were observed for nanocomposites with tunicate nanowhiskers than for the corresponding samples comprising cotton nanowhiskers. In the case of nanocomposites comprising nanowhiskers produced by hydrochloric acid hydrolysis, no significant Raman band shift was observed. These results are indicative of different modes of stress transfer, which in turn appear to originate from the different sample morphologies.     

Case-Mix,Care Processes,and Outcomes in Medically-Ill Patients Receiving Mechanical Ventilation in a Low-Resource Setting from Southern India: A Prospective Clinical Case Series

Background

Mechanical ventilation is a resource intensive organ support treatment, and historical studies from low-resource settings had reported a high mortality. We aimed to study the outcomes in patients receiving mechanical ventilation in a contemporary low-resource setting.

Methods

We prospectively studied the characteristics and outcomes (disease-related, mechanical ventilation-related, and process of care-related) in 237 adults mechanically ventilated for a medical illness at a teaching hospital in southern India during February 2011 to August 2012. Vital status of patients discharged from hospital was ascertained on Day 90 or later.

Results

Mean age of the patients was 40 ± 17 years; 140 (51%) were men. Poisoning and envenomation accounted for 98 (41%) of 237 admissions. In total, 87 (37%) patients died in-hospital; 16 (7%) died after discharge; 115 (49%) were alive at 90-day assessment; and 19 (8%) were lost to follow-up. Weaning was attempted in 171 (72%) patients; most patients (78 of 99 [79%]) failing the first attempt could be weaned off. Prolonged mechanical ventilation was required in 20 (8%) patients. Adherence to head-end elevation and deep vein thrombosis prophylaxis were 164 (69%) and 147 (62%) respectively. Risk of nosocomial infections particularly ventilator-associated pneumonia was high (57.2 per 1,000 ventilator-days). Higher APACHE II score quartiles (adjusted HR [95% CI] quartile 2, 2.65 [1.19–5.89]; quartile 3, 2.98 [1.24–7.15]; quartile 4, 5.78 [2.45–13.60]), and new-onset organ failure (2.98 [1.94–4.56]) were independently associated with the risk of death. Patients with poisoning had higher risk of reintubation (43% vs. 20%; P = 0.001) and ventilator-associated pneumonia (75% vs. 53%; P = 0.001). But, their mortality was significantly lower compared to the rest (24% vs. 44%; P = 0.002).

Conclusions

The case-mix considerably differs from other settings. Mortality in this low-resource setting is similar to high-resource settings. But, further improvements in care processes and prevention of nosocomial infections are required.     

Comparative molecular docking analysis of essential oil constituents as elastase inhibitors

Elastase is a protease or proteolytic enzyme, responsible for the breakdown of protein. There are eight human genes encoding for elastase, of which Elastase-1 (CELA-1) and Elastase-2 (ELANE) has significant implications on human diseases. Elastase-1 is primarily expressed in skin keratinocytes and is regarded as the major cause for the blistering in bullous pemphigoid, which affects the skin. On the other hand, Elastase-2 (ELANE), is expressed in the azurophil granules of neutrophils, is responsible for pulmonary emphysema and cyclic hematopoiesis a rare genetic disorder. Elastase is also produced by bacteria such as Pseudomonas aeruginosa, and forms the virulent factor in human. The ingredients from essential natural oils were found to have wound healing effects on non-healing wounds that is interfered by elastase due to microbial infection. Essential oils such as citral, citronellal, geranial, geraniol, and thymol were screened for their inhibitory activity on elastase produced by neutrophil, skin, and Pseudomonas aeruginosa by docking and were analyzed for their subcutaneous ADMET properties by ADME - TOX - Web server.     

A new class of RNA-binding oligomers: peptoid amide and ester analogues

Replication of human immunodeficiency virus type 1 (HIV-1) requires specific interactions of Tat protein with the trans-activation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5'-end of all HIV mRNAs. Here we report the design, synthesis and in vitro activities of oligopeptoid amide and ester analogues which bind TAR RNA with high affinities. These results show that we have identified a new class of unnatural oligomers for RNA targeting.