An amino acid map of inter-residue contact energies using metric multi-dimensional scaling

We present an amino map based on their inter-residue contact energies using the Miyazawa-Jernigan matrix. This work is based on the method of metric multi-dimensional scaling (MMDS). The MMDS map shows, among other things, that the MJ contact energies imply the hydrophobic-hydrophilic nature of the amino acid residues. With the help of the map we are able to compare and draw inferences from uncorrelated data sets such as BLOSUM and PAM with MJ methods. We also use a hierarchical clustering method on our MMDS distance matrix to group the amino acids and arrive at an optimum number of groups for simplifying the amino acid set.     

Ultrasound pretreatment of cassava chip slurry to enhance sugar release for subsequent ethanol production

The use of ultrasound pretreatment to enhance liquefaction and saccharification of cassava chips was investigated. Cassava chip slurry samples were subjected to sonication for 10-40 s at three power levels of low (2 W/mL), medium (5 W/mL), and high (8 W/mL). The samples were simultaneously exposed to enzymes to convert starch into glucose. The cassava particle size declined nearly 40-fold following ultrasonic pretreatment at high power input. Scanning electron micrographs of both unsonicated (control) and sonicated samples showed disruption of fibrous material in cassava chips but did not affect the granular structure of starch. Reducing sugar release improved in direct proportion to the power input and sonication time. The reducing sugar increase was as much as 180% with respect to the control groups. The slurry samples with enzyme addition during sonication resulted in better reducing sugar release than the samples with enzyme addition after sonication. The heat generated during sonication below starch gelatinization temperature apparently had no effect on the reducing sugar release. The reducing sugar yield and energy efficiency of ultrasound pretreated samples increased with total solids (TS) contents. The highest reducing sugar yield of 22 g/100 g of sample and efficiency of 323% were obtained for cassava slurry with 25% TS at high power. The reducing sugar yield at the completion of reaction (R(infinity)) were over twofold higher compared to the control groups. The integration of ultrasound into a cassava-based ethanol plant may significantly improve the overall ethanol yield.     

Statistical optimization of lipase catalyzed hydrolysis of methyloleate by response surface methodology

Hydrolysis of methyloleate was optimized using lipase from Chromobacterium viscosum immobilized on IRC-50. The optimization was studied by a statistical methodology using response surface methodology (RSM). The cumulative interactive effect of substrate, water concentration and time was studied in optimizing the hydrolysis of methyloleate. The interactive effect of substrate-time was found to be significant compared to substrate-water and time-water interactions. A well correlation was observed between the optimum values obtained from the response surface contour plots and from the quadratic regression model equation. The optimal values obtained for substrate, water and time were found to be in the experimental range chosen.     

Developments in industrially important thermostable enzymes: a review

Cellular components of thermophilic organisms (enzymes, proteins and nucleic acids) are also thermostable. Apart from high temperature they are also known to withstand denaturants of extremely acidic and alkaline conditions. Thermostable enzymes are highly specific and thus have considerable potential for many industrial applications. The use of such enzymes in maximising reactions accomplished in the food and paper industry, detergents, drugs, toxic wastes removal and drilling for oil is being studied extensively. The enzymes can be produced from the thermophiles through either optimised fermentation of the microorganisms or cloning of fast-growing mesophiles by recombinant DNA technology. In this review, the source microorganisms and properties of thermostable starch hydrolysing amylases, xylanases, cellulases, chitinases, proteases, lipases and DNA polymerases are discussed. The industrial needs for such specific thermostable enzyme and improvements required to maximize their application in the future are also suggested.     

Peptidic nanoparticles: for cancer diagnosis and therapy

A challenging topic in cancer research is to create drug delivery system that can bring in a specific and noncytotoxic manner a therapeutic compound. Usually, tumor targeting requires very specific compounds. Currently, peptide analogues like somatostatin, neurotensin, or bombesin are used to target G-coupled receptors, which are overexpressed on tumor cells. However, many of those analogues are rapidly degraded in the plasma and are cytotoxic [1–2]. Due to the limited efficiency and high toxicity of conventional chemotherapy different strategies have been developed for non-cytotoxic cancer treatment and cancer localization [3–5]. The recent development in bio-nanotechnology offers new avenues for cancer therapy. A lot of studies have been devoted to nanoparticulate delivery systems (10–100nm) like lipid or polymer particles [6–8]. Due to the nanometer sized of such cargos, the transportation of therapeutic compounds in the blood stream is increased in terms of time circulation. But their surface functionalization to improve drug-targeting properties is usually complicated and rather uneffective. We have recently designed a novel type of functional nanoparticles with regular icosahedral symmetry, mimicking small, rigid viral capsids (Fig. 1 (A)) and a diameter of about 17 nm (Fig. 1 (C)) which self-assemble from single polypeptide chains (Fig. 1 (B)).     

Identification, phylogenetic analysis and characterization of obligate halophilic fungi isolated from a man-made solar saltern in Phetchaburi province, Thailand

A total of 17 species from 43 isolates were obtained through serial dilutions of soil samples isolated from one of the man-made solar salterns located in Ban Laem district of Phetchaburi province, Thailand. Soil analysis of the sample revealed high salinity and moisture content, slight alkalinity and low amounts of nitrogen, total organic carbon and organic matter in the habitat. Morphological analysis was performed on all isolates, and molecular identification and phylogenetic analysis were carried out only on the halophilic fungi isolated. Six halophilic fungi, belonging to four species, were identified among the isolates, including five strains of Aspergillus genus [Aspergillus flavus, A. gracilis, A. penicillioides (2 strains) and A. restrictus]. One species was found to be a yeast, namely, Sterigmatomyces halophilus, which was the most frequent isolate found among the halophilic fungi. All other isolates were halotolerant fungi. Characterization of the halophilic fungal isolates showed that they were best adapted to conditions of 10–15 % NaCl (w/v), slight alkalinity (pH 7.0–7.5) and a temperature range of 30–35 °C.     

Protein–cofactor binding and ultrafast electron transfer in riboflavin binding protein under the spatial confinement of nanoscopic reverse micelles

In this contribution, we study the effect of confinement on the ultrafast electron transfer (ET) dynamics of riboflavin binding protein (RBP) to the bound cofactor riboflavin (Rf, vitamin B2), an important metabolic process, in anionic sodium bis(2‐ethylhexyl) sulfosuccinate reverse micelles (AOT‐RMs) of various hydration levels. Notably, in addition to excluded volume effect, various nonspecific interactions like ionic charge of the confining surface can influence the biochemical reactions in the confined environment of the cell. To this end, we have also studied the ET dynamics of RBP–Rf complex under the confinement of a cationic hexadecyltrimethylammonium bromide (CTAB) RMs with similar water pool size to the anionic AOT‐RMs towards simulating equal restricted volume effect. It has been found that the spatial confinement of RBP in the AOT‐RM of w₀ = 10 leads to the loss of its tertiary structure and hence vitamin binding capacity. Although, RBP regains its binding capacity and tertiary structure in AOT‐RMs of w₀ ≥20 due to its complete hydration, the ultrafast ET from RBP to Rf merely occurs in such systems. However, to our surprise, the ET process is found to occur in cationic CTAB‐RMs of similar volume restriction. It is found that under the spatial confinement of anionic AOT‐RM, the isoalloxazine ring of Rf is improperly placed in the protein nanospace so that ET between RBP and Rf is not permitted. This anomaly in the binding behaviour of Rf to RBP in AOT‐RMs is believed to be the influence of repulsive potential of the anionic AOT‐RM surface to the protein. Our finding thus suggests that under similar size restriction, both the hydration and surface charge of the confining volume could have major implication in the intraprotein ET dynamics in real cellular environments. Copyright © 2013 John Wiley & Sons, Ltd.     

Evaluation of SSR Markers for the Assessment of Genetic Diversity and Fingerprinting of Gossypium hirsutum Accessions

A total 177 simple sequence repeat (SSR) markers were screened using a set of 47 Upland cotton genotypes comprising 14 commercial varieties, 14 germplasm accessions and 19 advanced breeding lines to identify informative markers for genetic diversity assessment and fingerprinting in G. hirsutum. Only 21% (381177) of SSR markers tested showed polymorphism with a mean of 2.18 alleles per locus and with average polymorphism information content (PIC) of 0.32. The SSR markers revealed a Jaccard’ similarity coefficient ranging between 0.43 and 0.89, with an average of 0.67 among accessions. Cluster analysis using unweighted pair group method with arithmetic averages (UPGMA) and principal component analysis (PCA) indicated that majority of the genotypes were very closely related. All the 47 genotypes showed heterorygosity for at least one of the SSR loci. We discovered 19 rare and 6 unique alleles among the tested genotypes of cotton. Fingerprint based on all the 38 loci revealed a probability of identical match by chance of 3.98x10. A set of ten SSR markers was identified which could distinguish all the 47 genotypes with a moderate probability of identical match by chance (X?_D ⁿ = 0.01).     

Natural antioxidants attenuate mycolactone toxicity to RAW 264.7 macrophages

Mycobacterium ulcerans produces a macrolide exotoxin, mycolactone which suppresses immune cells activity, is toxic to most cells and the key virulence factor in the pathogenesis of Buruli ulcer disease. Mycolactone is reported to mediate the production of reactive oxygen species in keratinocytes; cells that play critical role in wound healing. Increased levels of reactive oxygen species have been shown to disrupt the well-ordered process of wound repair; hence, the function of wound-healing cells such as macrophages, keratinocytes, and fibroblast could be impaired in the presence of the reactive oxygen species mediator, mycolactone. To ensure regeneration of tissues in chronic ulcers, with proper and timely healing of the wounds, natural antioxidants that can combat the effects of induced reactive oxygen species in wound-healing cells ought to be investigated. Reactive oxygen species activity was determined in mycolactone-treated RAW 264.7 macrophages and the scavenging ability of the antioxidants (ascorbic acid, gallic acid, and green tea kombucha) against mycolactone-induced reactive oxygen species (superoxide anions) was assessed using fluorescein probe (DCF-DA) and nitroblue tetrazolium dye. Cytotoxicity of the antioxidants, mycolactone, and the protective effect of the antioxidants on the cells upon treatment with mycolactone were determined using the Alamar blue assay. The expression levels of endogenous antioxidant enzyme genes (superoxide dismutase, catalase, and glutathione peroxidase) in response to mycolactone-mediated reactive oxygen species were determined using RT-qPCR. Mycolactone induced the production of reactive oxygen species in RAW 264.7 macrophages, and the resulting superoxide anions were scavenged by some of the antioxidants. The selected endogenous antioxidant enzyme genes in the macrophages were upregulated in the presence of the antioxidants and mycolactone. The exogenously supplied ascorbic acid and green tea kombucha offered moderate protection to the macrophages against the toxicity of mycolactone. We conclude that the results provide insights into alternate and adjunct therapeutic approaches in Buruli ulcer treatment, which could significantly attenuate the toxicity of the pathogenic factor; mycolactone.     

Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes

During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.