Evaluation of models for the evolution of protein sequences and functions under structural constraint

In the field of evolutionary structural genomics, methods are needed to evaluate why genomes evolved to contain the fold distributions that are observed. In order to study the effects of population dynamics in the evolved genomes we need fast and accurate evolutionary models which can analyze the effects of selection, drift and fixation of a protein sequence in a population that are grounded by physical parameters governing the folding and binding properties of the sequence. In this study, various knowledge-based, force field, and statistical methods for protein folding have been evaluated with four different folds: SH2 domains, SH3 domains, Globin-like, and Flavodoxin-like, to evaluate the speed and accuracy of the energy functions. Similarly, knowledge-based and force field methods have been used to predict ligand binding specificity in SH2 domain. To demonstrate the applicability of these methods, the dynamics of evolution of new binding capabilities by an SH2 domain is demonstrated.     

Moderate severity heart failure does not involve a downregulation of myocardial fatty acid oxidation

Recent human and animal studies have demonstrated that in severe end-stage heart failure (HF), the cardiac muscle switches to a more fetal metabolic phenotype, characterized by downregulation of free fatty acid (FFA) oxidation and an enhancement of glucose oxidation. The goal of this study was to examine myocardial substrate metabolism in a model of moderate coronary microembolization-induced HF. We hypothesized that during well-compensated HF, FFA oxidation would predominate as opposed to a more fetal metabolic phenotype of greater glucose oxidation. Cardiac substrate uptake and oxidation were measured in normal dogs (n = 8) and in dogs with microembolization-induced HF (n = 18, ejection fraction = 28%) by infusing three isotopic tracers ([9,10-(3)H]oleate, [U-(14)C]glucose, and [1-(13)C]lactate) in anesthetized open-chest animals. There were no differences in myocardial substrate metabolism between the two groups. The total activity of pyruvate dehydrogenase, the key enzyme regulating myocardial pyruvate oxidation (and hence glucose and lactate oxidation) was not affected by HF. We did not observe any difference in the activity of carnitine palmitoyl transferase I (CPT-I) and its sensitivity to inhibition by malonyl-CoA between groups; however, malonyl-CoA content was decreased by 22% with HF, suggesting less in vivo inhibition of CPT-I activity. The differences in malonyl-CoA content cannot be explained by changes in the Michaelis-Menten constant and maximal velocity for malonyl-CoA decarboxylase because neither were affected by HF. These results support the concept that there is no decrease in fatty acid oxidation during compensated HF and that the downregulation of fatty acid oxidation enzymes and the switch to carbohydrate oxidation observed in end-stage HF is only a late-stage phenomenon.     

Evidence that the capsule around mycobacteria grown in axenic media contains mycobacterial antigens: implications at the level of cell envelope architecture

The intracellular growth of pathogenic mycobacteria has been linked to the presence of an electron transparent zone (ETZ or capsule), which surrounds the phagocytized bacteria and prevents the diffusion of lysosomal enzymes in infected macrophages. Recently, it was suggested that this capsule may be a bacterial structures, even being present in test tube-grown pathogenic mycobacteria (FEMS Microbiol. Lett. 1988, 56, 225-230). In the present paper, we show that under special fixation and embedding conditions, this capsule was clearly observed among 7 strains of mycobacteria grown in axenic media and also in M. leprae extracted and purified from experimentally infected armadillo or nude mice. In the case of bacteria treated likewise but subject to a prior dehydration step, this capsular structure disappeared suggesting its lipidic nature. Ultrathin sections of M. intracellular after immunolabelling showed for the first time that this capsule obtained mycobacterial antigens confirming its mycobacterial origin. It is suggested that the mycobacterial capsule may be formed of inert lipids, in which surface antigens are embedded.     

A single lycaenid caterpillar gets an ant‐constructed shelter and uninterrupted ant attendance

Ant‐lycaenid associations range from mutualism to parasitism and the caterpillars of some species of lycaenids are reported to enter ant nests for shelter, diapause, or pupation. The present study aimed to examine the nature of the association between Euchrysops cnejus (Fabricius) (Lepidoptera: Lycaenidae) and Camponotus compressus (Fabricius) (Hymenoptera: Formicidae) worker ants on the extrafloral nectary‐bearing cowpea plant, Vigna unguiculata (L.) Walp. (Fabaceae). The abundance patterns of the ants and the lycaenid caterpillars together with the spatial patrolling patterns of the ants on the plants revealed that ant abundance increased with the occurrence of the lycaenid caterpillars and the ants preferred the lycaenids over the extrafloral nectar. Camponotus compressus worker ants constructed a shelter at the cowpea plant base after interaction with one or more lycaenid caterpillar(s) and tended the caterpillars and pupae till the emergence of the butterfly. The ant‐constructed shelters (ACSs) inhabited by the minor caste workers (13 ± 1.3 ants per ACS), were utilized by the caterpillars to undergo pupation. The ants confined their activities predominantly to tending the pod‐feeding caterpillars and the solitary pupa within each ACS. It appears that the behavior of the tending worker ants is modulated by the lycaenid vulnerable stages.     

Reverse micelles‐mediated transport of lipase in liquid emulsion membrane for downstream processing

This work deals with the downstream processing of lipase (EC 3.1.1.3, from Aspergillus niger) using liquid emulsion membrane (LEM) containing reverse micelles for the first time. The membrane phase consisted of surfactants [cetyltrimethylammonium bromide (CTAB) and Span 80] and cosolvents (isooctane and paraffin light oil). The various process parameters for the extraction of lipase from aqueous feed were optimized to maximize activity recovery and purification fold. The mechanism of lipase transport through LEM consisted of three steps namely solubilization of lipase in reverse micelles, transportation of reverse micelles loaded with lipase through the liquid membrane, and release of the lipase into internal aqueous phase. The results showed that the optimum conditions for activity recovery (78.6%) and purification (3.14‐fold) were feed phase ionic strength 0.10 M NaCl and pH 9.0, surfactants concentration (Span 80 0.18 M and CTAB 0.1 M), volume ratio of organic phase to internal aqueous phase 0.9, ratio of membrane emulsion to feed volume 1.0, internal aqueous phase concentration 1.0 M KCl and pH 7.0, stirring speed 450 rpm, and contact time 15 min. This work indicated the feasibility of LEM for the downstream processing of lipase. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Estimation of levels of IgG to multiple sclerosis specific brain antigens in the cerebrospinal fluid of MS patients

The binding of partially purified multiple sclerosis (MS) specific brain antigens (MSG2) and of the corresponding antigens of non-MS brains (KG2) to cerebrospinal fluid IgG of patients with MS and other neurological diseases was assayed employing sandwich enzyme linked immunosorbent assay (ELISA). Assay of the antigen-antibody binding revealed that the concentration of MSG2 required for the optimum binding to IgG in the undiluted MS CSFs was lower than that of KG2 in all cases. The index for IgG binding capacity of an antigen (IgBC) was expressed as a ratio of the optical density of the enzymic products in ELISA at the optimal antigen-antibody binding to the lowest concentration of the antigen required for the optimal binding. The IgBC of MSG2 was found to be linearly correlated with the IgG concentration in the CSF of MS patients. These results indicate that IgG with specificity to MSG2 may be present in the CSF of MS patients.     

Functional relevance and health benefits of soymilk fermented by lactic acid bacteria

The growing interest of consumers towards nutritionally enriched, and health promoting foods, provoke interest in the eventual development of fermented functional foods. Soymilk is a growing trend that can serve as a low-cost non-dairy alternative with improved functional and nutritional properties. Soymilk acts as a good nutrition media for the growth and proliferation of the micro-organism as well as for their bioactivities. The bioactive compounds produced by fermentation of soymilk with lactic acid bacteria (LAB) exhibit enhanced nutritional values, and several improved health benefits including antihypertensive, antioxidant, antidiabetic, anticancer and hypocholesterolaemic effects. The fermented soymilk is acquiring a significant position in the functional food industry due to its increased techno-functional qualities as well as ensuring the survivability of probiotic bacteria producing diverse metabolites. This review covers the important benefits conferred by the consumption of soymilk fermented by LAB producing bioactive compounds. It provides a holistic approach to obtain existing knowledge on the biofunctional attributes of fermented soymilk, with a focus on the functionality of soymilk fermented by LAB.     

Isolation and characterization of a new osmotolerant, non-virulent Klebsiella pneumoniae strain SAP for biosynthesis of succinic acid

In the present study, isolation of anaerobic bacteria from 24 different eco-niches was carried out. A total number of 300 bacterial isolates, including 230 obligate and 70 facultative anaerobes were obtained using anaerobic techniques. All the isolates were initially screened for succinic acid production by Fluorescein test and TLC method. During screening, 10 isolates found to produce succinic acid were further examined by HPLC and then finally confirmed for succinic acid by LC-MS analysis. Amongst 10 isolates, isolate SAP, a facultative anaerobe isolated from buffalo rumen fluid, showed maximum yield of 2.1 g/l of succinic acid from 10 g of glucose in 24 hr under anaerobic condition. This isolate was identified as Klebsiella pneumoniae strain SAP by 16S rDNA sequence and signature sequence analysis. Mouse lethality test for the strain SAP showed LD50 value of 3.3 x 10(8) CFU/ml, which shows non-virulent nature of the strain. This strain may become a candidate strain for succinic acid production because of its osmotolerant nature and higher succinate:acetate ratio.