Computational Modeling,Formal Analysis,and Tools for Systems Biology

As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.     

Recurring Plankton Bloom Dynamics Modeled via Toxin-Producing Phytoplankton

A simple nutrient–phytoplankton model is proposed and analyzed in the presence of toxic chemicals released by toxin-producing phytoplankton (TPP) to understand the dynamics of seasonally recurring bloom phenomena. We observe that the presence of toxic chemicals helps to explain the bloom phenomenon. We have further studied our proposed system by varying the toxin liberation rate. Our model displays a wide range of dynamical behaviours, from simple cyclical blooms to irregular chaotic blooms. We also observe skipping phenomenon. The effect of toxic chemicals released by TPP cannot, thus, be ignored in ‘bottom-up’ models. J. Chattopadhyay is supported by the Ministry of Foreign Affairs Indo-Italian program of cooperation in Science and Technology, “Biomedical Sciences”. S. Chatterjee is supported by Ministero dell’Istruzione, dell’Università e della Ricerca, Bando per borse a favore di giovani ricercatori indiani. S. Chakraborty is supported by the Council of Scientific and Industrial Research, Human Resource Development Group, New Delhi.     

Identification of novel NK1/NK3 dual antagonists for the potential treatment of schizophrenia

During the lead optimization of NK(1)/NK(3) receptor antagonists program, a focused exploration of molecules bearing a lactam moiety was performed. The aim of the investigation was to identify the optimal position of the carbonyl and hydroxy methyl group in the lactam moiety, in order to maximize the in vitro affinity and the level of insurmountable antagonism at both NK(1) and NK(3) receptors. The synthesis and biological evaluation of these novel lactam derivatives, with potent and balanced NK(1)/NK(3) activity, were reported in this paper.     

Functional Independence and Interdependence of the Src Homology Domains of Phospholipase C-γ1 in B-Cell Receptor Signal Transduction

B-cell receptor (BCR)-induced activation of phospholipase C-gamma1 (PLCgamma1) and PLCgamma2 is crucial for B-cell function. While several signaling molecules have been implicated in PLCgamma activation, the mechanism coupling PLCgamma to the BCR remains undefined. The role of PLCgamma1 SH2 and SH3 domains at different steps of BCR-induced PLCgamma1 activation was examined by reconstitution in a PLCgamma-negative B-cell line. PLCgamma1 membrane translocation required a functional SH2 N-terminal [SH2(N)] domain, was decreased by mutation of the SH3 domain, but was unaffected by mutation of the SH2(C) domain. Tyrosine phosphorylation did not require the SH2(C) or SH3 domains but depended exclusively on a functional SH2(N) domain, which mediated the association of PLCgamma1 with the adapter protein, BLNK. Forcing PLCgamma1 to the membrane via a myristoylation signal did not bypass the SH2(N) domain requirement for phosphorylation, indicating that the phosphorylation mediated by this domain is not due to membrane anchoring alone. Mutation of the SH2(N) or the SH2(C) domain abrogated BCR-stimulated phosphoinositide hydrolysis and signaling events, while mutation of the SH3 domain partially decreased signaling. PLCgamma1 SH domains, therefore, have interrelated but distinct roles in BCR-induced PLCgamma1 activation.     

Diseased Social Predators

Social predators benefit from cooperation in the form of increased hunting success, but may be at higher risk of disease infection due to living in groups. Here, we use mathematical modeling to investigate the impact of disease transmission on the population dynamics benefits provided by group hunting. We consider a predator–prey model with foraging facilitation that can induce strong Allee effects in the predators. We extend this model by an infectious disease spreading horizontally and vertically in the predator population. The model is a system of three nonlinear differential equations. We analyze the equilibrium points and their stability as well as one- and two-parameter bifurcations. Our results show that weakly cooperating predators go unconditionally extinct for highly transmissible diseases. By contrast, if cooperation is strong enough, the social behavior mediates conditional predator persistence. The system is bistable, such that small predator populations are driven extinct by the disease or a lack of prey, and large predator populations survive because of their cooperation even though they would be doomed to extinction in the absence of group hunting. We identify a critical cooperation level that is needed to avoid the possibility of unconditional predator extinction. We also investigate how transmissibility and cooperation affect the stability of predator–prey dynamics. The introduction of parasites may be fatal for small populations of social predators that decline for other reasons. For invasive predators that cooperate strongly, biocontrol by releasing parasites alone may not be sufficient.     

TGF-beta1 genotypes in cirrhosis: relationship with the occurrence of liver cancer

This study aimed to verify whether specific single nucleotide polymorphisms (SNPs) of the transforming growth factor-beta1 (TGF-beta1) may predispose to end-stage liver disease and/or hepatocellular carcinoma (HCC). One hundred eighty-eight consecutive patients transplanted for liver cirrhosis (HBV N=21, HCV N=68, alcoholic N=55 and others N=23) and a control group of 140 healthy blood donors were investigated. Four SNPs were studied by restriction fragment length assays: -800G>A, -509C>T, Leu10Pro and Arg25Pro. Patients were found to possess the -509T/ * (TT 53/188, CT 85/188, CC 50/188 vs TT 22/140, CT 61/140, CC 57/140; p<0.002) and Arg25Pro C/ * genotypes (CC 1/188, CG 31/188, GG 156/188 vs CC 0/140, CG 13/140, GG 127/140; p<0.05) more frequently than controls. Patients with cirrhosis complicated by HCC possessed more frequently the Leu10Pro T/ * genotype than patients without HCC (TT 20/54, CT 26/54, CC 8/54 vs TT 31/134, CT 69/134, CC 34/134; p<0.05). The analysis of molecular variance detected significant genotypic differentiations between controls and cirrhotics but not between cirrhotics with or without HCC. In conclusion, TGF-beta1 SNPs probably facilitate the development of liver cirrhosis, while they seem to have a limited role in predicting the occurrence of HCC.