Lethal Mutagenesis in Viruses and Bacteria

Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins. Mutations occur upon replications so that stabilities of some proteins in daughter cells differ from those in parent cell by random amounts drawn from experimental distribution of mutational effects on protein stability. The genotype-phenotype relationship posits that unstable proteins confer lethal phenotype to a cell and in addition the cells fitness (duplication rate) is proportional to the concentration of its folded proteins. Simulations reveal that lethal mutagenesis occurs at mutation rates close to 7 mutations per genome per replications for RNA viruses and about half of that for DNA based organisms, in accord with earlier predictions from analytical theory and experiment. This number appears somewhat dependent on the number of genes in the organisms and natural death rate. Further, our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. Our model predicts that species with high mutation rates, tend to have less stable proteins compared to species with low mutation rate

A first-principles model of early evolution: Emergence of gene families, species and preferred protein folds

In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the Big Bang scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at time scales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary time scales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species, subpopulations which carry similar genomes. Further we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first principles picture of how first gene families developed in the course of early evolutionComment: In press, PLoS Computational Biolog

Anti-Obese Effect of Glucosamine and Chitosan Oligosaccharide in High-Fat Diet-Induced Obese Rats

Objective: This study is to evaluate the anti-obese effects of glucosamine (GLC) and chitosan oligosaccharide (COS) on high-fat diet-induced obese rats. Methods: The rats were randomly divided into twelve groups: a normal diet group (NF), a high-fat diet group (HF), Orlistat group, GLC high-, middle-, and low-dose groups (GLC-H, GLC-M, GLC-L), COS1 (COS, number-average molecular weight ≤1000) high-, middle-, and low-dose groups (COS1-H, COS1-M, COS1-L), and COS2 (COS, number-average molecular weight ≤3000) high-, middle-, and low-dose groups (COS2-H, COS2-M, COS2-L). All groups received oral treatment by gavage once daily for a period of six weeks. Results: Rats fed with COS1 gained the least weight among all the groups (P < 0.01), and these rats lost more weight than those treated with Orlistat. In addition to the COS2-H and Orlistat groups, the serum total cholesterol (CHO) and low-density lipoprotein cholesterol (LDL-C) levels were significantly reduced in all treatment groups compared to the HF group (P < 0.01). The various doses of GLC, COS1 and COS2 reduced the expression levels of PPARγ and LXRα mRNA in the white adipose tissue. Conclusions: The results above demonstrated that GLC, COS1, and COS2 improved dyslipidemia and prevented body weight gains by inhibiting the adipocyte differentiation in obese rats induced by a high-fat diet. Thus, these agents may potentially be used to treat obesity

Hypolipidemic effects of chitosan and its derivatives in hyperlipidemic rats induced by a high-fat diet

Background: Hyperlipidemia (HLP) is the primary risk factor of cardiovascular disease (CVD). Various factors, including genetics, physical inactivity, and daily nutritional habits, affect the prevalence of HLP. Recently, it was revealed that dietary fibers, such as pectin, psyllium, and especially chitosan (CTS), may play important roles in hypolipidemic management. Thus, this study aims to determine the hypolipidemic effect and mechanism of CTS and its water-soluble derivatives, chitosan oligosaccharides (MN≤1,000 Da (COSI) and MN≤3,000 Da (COSIII)), in male hyperlipidemic rats induced by a high-fat diet (HFD). Design: After the model creation, 120 Sprague-Dawley (SD) rats were equally assigned to 12 groups fed various diets as follows: the normal group with basic diet, an HFD group, an HFD group supplemented with three doses of CTS, COSI and COSIII groups, and an HFD group treated with simvastatin (7 mg/kg·d). After 6 weeks, body weight, fat/body ratio, and the relevant biomarkers of serum, liver, and feces were measured. Additionally, the histological analysis of liver and adipose tissue was performed, and the mRNA expressions of liver peroxisome proliferator-activated receptor-α (PPARα) and hepatic lipase (HL) were examined. Results: Compared with HFD group, rats fed CTS, COSI, and COSIII showed a better ability to regulate their body weight, liver and cardiac indices, fat/body ratio, as well as serum, liver, and fecal lipids, and simultaneously to maintain the appropriate activity of liver and serum superoxide dismutase (SOD), alanine aminotransferase (ALT), aspartate aminotransferase (AST), as well as liver and fecal total bile acids (TBA). Simultaneously, there had been a higher mRNA expression of PPARα and HL in the treatment groups. Conclusion: The obtained results suggested that these three function foods can effectively improve liver lipid metabolism by normalizing the expressions of PPARα and HL, and protect liver from the oxidized trauma by enhancing hepatic function, which could be potentially used to remedy hyperlipidemia