Scale invariance of immune system response rates and times: perspectives on immune system architecture and implications for artificial immune systems

Most biological rates and times decrease systematically with increasing organism body size. We use an ordinary differential equation (ODE) model of West Nile Virus in birds to show that pathogen replication rates decline with host body size, but natural immune system (NIS) response rates do not change systematically with body size. The scale-invariant detection and response of the NIS is surprising since the NIS has to search for small quantities of pathogens through larger physical spaces in larger organisms, and also respond by producing larger absolute quantities of antibody in larger organisms. We hypothesize that the NIS has evolved an architecture to efficiently neutralize pathogens. We investigate three different hypothesized NIS architectures using an Agent Based Model (ABM). We find that a sub-modular NIS architecture, in which lymph node number and size both increase sublinearly with body size, efficiently balances the tradeoff between local pathogen detection and global response. This leads to nearly scale-invariant detection and response consistent with experimental data. Similar to the NIS, physical space and resources are also important constraints on distributed systems, for example low-powered robots connected by short-range wireless communication. We show that the sub-modular design principles of the NIS can be applied to problems such as distributed robot control to efficiently balance the tradeoff between local search for a solution and global response or proliferation of the solution. We demonstrate that the lymphatic network of the NIS efficiently balances local and global communication, and we suggest a new approach for Artificial Immune Systems (AIS) that uses a sub-modular architecture to facilitate distributed search.     

Cost-Effectiveness of HIV Testing Referral Strategies among Tuberculosis Patients in India

Background

Indian guidelines recommend routine referral for HIV testing of all tuberculosis (TB) patients in the nine states with the highest HIV prevalence, and selective referral for testing elsewhere. We assessed the clinical impact and cost-effectiveness of alternative HIV testing referral strategies among TB patients in India.

Methods and Findings

We utilized a computer model of HIV and TB disease to project outcomes for patients with active TB in India. We compared life expectancy, cost, and cost-effectiveness for three HIV testing referral strategies: 1) selective referral for HIV testing of those with increased HIV risk, 2) routine referral of patients in the nine highest HIV prevalence states with selective referral elsewhere (current standard), and 3) routine referral of all patients for HIV testing. TB-related data were from the World Health Organization. HIV prevalence among TB patients was 9.0% in the highest prevalence states, 2.9% in the other states, and 4.9% overall. The selective referral strategy, beginning from age 33.50 years, had a projected discounted life expectancy of 16.88 years and a mean lifetime HIV/TB treatment cost of US$100. The current standard increased mean life expectancy to 16.90 years with additional per-person cost of US$10; the incremental cost-effectiveness ratio was US$650/year of life saved (YLS) compared to selective referral. Routine referral of all patients for HIV testing increased life expectancy to 16.91 years, with an incremental cost-effectiveness ratio of US$730/YLS compared to the current standard. For HIV-infected patients cured of TB, receiving antiretroviral therapy increased survival from 4.71 to 13.87 years. Results were most sensitive to the HIV prevalence and the cost of second-line antiretroviral therapy.

Conclusions

Referral of all patients with active TB in India for HIV testing will be both effective and cost-effective. While effective implementation of this strategy would require investment, routine, voluntary HIV testing of TB patients in India should be recommended.     

NMR Structure of the C-terminal domain of a tyrosyl-tRNA synthetase that functions in group I intron splicing

The mitochondrial tyrosyl-tRNA synthetases (mt TyrRSs) of Pezizomycotina fungi are bifunctional proteins that aminoacylate mitochondrial tRNA(Tyr) and are structure-stabilizing splicing cofactors for group I introns. Studies with the Neurospora crassa synthetase (CYT-18 protein) showed that splicing activity is dependent upon Pezizomycotina-specific structural adaptations that form a distinct group I intron-binding site in the N-terminal catalytic domain. Although CYT-18's C-terminal domain also binds group I introns, it has been intractable to X-ray crystallography in the full-length protein. Here, we determined an NMR structure of the isolated C-terminal domain of the Aspergillus nidulans mt TyrRS, which is closely related to but smaller than CYT-18's. The structure shows an S4 fold like that of bacterial TyrRSs, but with novel features, including three Pezizomycontia-specific insertions. (15)N-(1)H two-dimensional NMR showed that C-terminal domains of the full-length A. nidulans and Geobacillus stearothermophilus synthetases do not tumble independently in solution, suggesting restricted orientations. Modeling onto a CYT-18/group I intron cocrystal structure indicates that the C-terminal domains of both subunits of the homodimeric protein bind different ends of the intron RNA, with one C-terminal domain having to undergo a large shift on its flexible linker to bind tRNA(Tyr) or the intron RNA on either side of the catalytic domain. The modeling suggests that the C-terminal domain acts together with the N-terminal domain to clamp parts of the intron's catalytic core, that at least one C-terminal domain insertion functions in group I intron binding, and that some C-terminal domain regions bind both tRNA(Tyr) and group I intron RNAs.     

Measuring the magnitude of internal motion in a complex hexasaccharide

For the development of a scheme for quantitative experimental estimation of internal motion in the complex human milk hexasaccharide lacto‐N‐di‐fuco hexose I (LNDFH I), we measured a large number of experimental residual dipolar couplings in liquid crystal orienting media. We present a total of 40 ¹³C? ¹H and ¹H? ¹H dipolar coupling values, each representing distinct directions of internuclear vectors. The NMR data were interpreted with established methods for analysis of rigid subdomains of the oligosaccharide as well as a novel method in which dipolar couplings were calculated over an ensemble of conformers from a solvent Molecular Dynamics trajectory using multiple linear regression analysis. The Lewis^b epitope region of LNDFH I assumed a single unique conformation with internal motion described by fluctuations of 5–10° in glycosidic dihedral angles consistent with previous studies. Greater flexibility was observed for the remaining GlcNAc1→3‐β‐D ‐Gal and β‐D ‐Gal1→4Glc linkages, with the former glycosidic linkage existing in a conformational exchange among three states. The results were also supported by similar results of calculations carried out with conformers obtained from a simple Monte Carlo simulation without explicit solvent. © 2010 Wiley Periodicals, Inc. Biopolymers 95: 39–50, 2011.     

High-Sensitivity Monoclonal Antibodies Specific for Homoserine Lactones Protect Mice from Lethal Pseudomonas aeruginosa Infections

A number of bacteria, including pathogens like Pseudomonas aeruginosa, utilize homoserine lactones (HSLs) as quorum sensing (QS) signaling compounds and engage in cell-to-cell communication to coordinate their behavior. Blocking this bacterial communication may be an attractive strategy for infection control as QS takes a central role in P. aeruginosa biology. In this study, immunomodulation of HSL molecules by monoclonal antibodies (MAbs) was used as a novel approach to prevent P. aeruginosa infections and as tools to detect HSLs in bodily fluids as a possible first clue to an undiagnosed Gram-negative infection. Using sheep immunization and recombinant antibody technology, a panel of sheep-mouse chimeric MAbs were generated which recognized HSL compounds with high sensitivity (nanomolar range) and cross-reactivity. These MAbs retained their nanomolar sensitivity in complex matrices and were able to recognize HSLs in P. aeruginosa cultures grown in the presence of urine. In a nematode slow-killing assay, HSL MAbs significantly increased the survival of worms fed on the antibiotic-resistant strain PA058. The therapeutic benefit of these MAbs was further studied using a mouse model of Pseudomonas infection in which groups of mice treated with HSL-2 and HSL-4 MAbs survived, 7 days after pathogen challenge, in significantly greater numbers (83 and 67%, respectively) compared with the control groups. This body of work has provided early proof-of-concept data to demonstrate the potential of HSL-specific, monoclonal antibodies as theranostic clinical leads suitable for the diagnosis, prevention, and treatment of life-threatening bacterial infections.     

Mutational and Structural Analysis of Conserved Residues in Ribose-5-Phosphate Isomerase B from Leishmania donovani: Role in Substrate Recognition and Conformational Stability

Ribose-5-phosphate isomerase B from Leishmania donovani (LdRpiB) is one of the potential drug targets against visceral leishmaniasis. In the present study, we have targeted several conserved amino acids for mutational analysis (i.e. Cys69, His11, His102, His138, Asp45, Tyr46, Pro47 and Glu149) to gain crucial insights into their role in substrate binding, catalysis and conformational stability of the enzyme. All the eight LdRpiB variants were cloned, sequenced, expressed and purified. C69S, H102N, D45N and E149A mutants exhibited complete loss of enzyme activity indicating that they are indispensable for the enzyme activity. Kinetic parameters were altered in case of H138N, H11N and P47A variants; however Y46F exhibited similar kinetic behaviour as wild type. All the mutants except H138N exhibited altered protein structure as determined by CD and fluorescence spectral analysis. This data was supported by the atomic level details of the conformational changes and substrate binding using molecular dynamic simulations. LdRpiB also exhibited activity with D-form of various aldose substrates in the order of D-ribose > D-talose > D-allose > D-arabinose. Our study provides insights for better understanding of substrate enzyme interactions which can rationalize the process of drug design against parasite RpiB.