Modeling the Impact of Alternative Immunization Strategies: Using Matrices as Memory Lanes

Existing modeling approaches are divided between a focus on the constitutive (micro) elements of systems or on higher (macro) organization levels. Micro-level models enable consideration of individual histories and interactions, but can be unstable and subject to cumulative errors. Macro-level models focus on average population properties, but may hide relevant heterogeneity at the micro-scale. We present a framework that integrates both approaches through the use of temporally structured matrices that can take large numbers of variables into account. Matrices are composed of several bidimensional (time×age) grids, each representing a state (e.g. physiological, immunological, socio-demographic). Time and age are primary indices linking grids. These matrices preserve the entire history of all population strata and enable the use of historical events, parameters and states dynamically in the modeling process. This framework is applicable across fields, but particularly suitable to simulate the impact of alternative immunization policies. We demonstrate the framework by examining alternative strategies to accelerate measles elimination in 15 developing countries. The model recaptured long-endorsed policies in measles control, showing that where a single routine measles-containing vaccine is employed with low coverage, any improvement in coverage is more effective than a second dose. It also identified an opportunity to save thousands of lives in India at attractively low costs through the implementation of supplementary immunization campaigns. The flexibility of the approach presented enables estimating the effectiveness of different immunization policies in highly complex contexts involving multiple and historical influences from different hierarchical levels.     

Purification and Amino Acid Sequence of MP-III 4R D49 Phospholipase A2 from Bothrops pirajai Snake Venom, a Toxin with Moderate PLA2 and Anticoagulant Activities and High Myotoxic Activity

MP-III 4R PLA₂ was purified from the venom of Bothrops pirajai venom (Bahia's jararacussu) after three chromatographic steps which started with RP-HPLC. The complete amino acid sequence of MP-III 4R PLA₂ from Bothrops pirajai was determined by amino acid sequencing of reduced and carboxymethylated MP-III 4R and the isolated peptides from clostripain and protease V8 digestion. MP-III 4R is a D49 PLA₂ with 121 amino acid residues and has a molecular weight estimated at 13,800 Da, with 14 half-cysteines. This protein showed moderate PLA₂ and anticoagulant activity. This PLA₂ does not have a high degree of homology with other bothropic PLA₂-like myotoxins (~75%) and nonbothropic myotoxins (~60%). MP-III 4R is a new PLA₂, which was isolated using exclusively analytical and preparative HPLC methods. Based on the N-terminal sequence and biological activities, MP-III 4R was identified as similar to piratoxin-III (PrTX-III), which was isolated by conventional chromatography based on molecular exclusion ion exchange chromatography. Clinical manifestations indicate that at the site of toxin injection, there may be pain of variable intensity, because animals continue to lick the limb. No clinical sign indicating general toxicity was noticed. Myotoxicity was observed in gastrocnemius muscle cells after exposure to MP-III 4R, with a high frequency (70%) of affected muscle fibers.     

Distribution of living planktonic foraminifera in the Ross Sea and the Pacific sector of the Southern Ocean (Antarctica)

In order to determine the factors controlling the distribution of planktonic foraminifera as a proxy for reconstruction of paleoenvironments, we present data on live assemblages collected in the Southern Ocean. Plankton tows and hydrographic measurements were taken in the upper 400 m of the water column at different sites in the Ross Sea (site B) and at the Polar Front of the Pacific Ocean (site O) during austral summers from 1998 to 2003.Based on qualitative micropaleontological observations we discriminated between Neogloboquadrina pachyderma dextral (dex) and N. pachyderma sinistral (sin). In addition for N. pachyderma (sin) we distinguished four morphs: the first one (1) has a thickened test and depressed sutures; the second morph (2) is represented by specimens characterized by a subspheric and heavily encrusted test; the third morph (3) has a thin and lobate walled test; the fourth one (4) represent the juvenile stage of N. pachyderma (sin) and is characterized by a smaller average size.The microfauna collected in the Ross Sea (site B) is characterized by the dominance of N. pachyderma (sin) (morphs 1 and 2), whereas low occurrences of Turborotalia quinqueloba, N. pachyderma (dex) and Neogloboquadrina dutertrei were noted in the first 50 m of the water column. The water column at this station is characterized by a marked and shallow stratification and a marked thermocline during the sampling season.At the ocean station (site O), the assemblage shows increasing diversification: T. quinqueloba, G. bulloides, N. pachyderma (dex) and few specimens of Globigerinita uvula characterize the planktonic microfauna. There is a predominance of non-encrusted morphs and juvenile specimens (3 and 4). At this station the mixed surface layer is deeper than in the Ross Sea (60–70 m), the pycnocline and the thermocline less marked.The depth and the intensity of the Deep Chlorophyll Maximum (DCM) influence foraminiferal distribution: N. pachyderma (sin) shows abundance peaks at or just below the DCM while G. bulloides peaks above the DCM. Coiling direction of N. pachyderma seems to be not controlled exclusively by Sea Surface Temperature (SST): probably the two coiling types are genetically different.Results document that diversity of planktonic foraminifera, number of specimens and variations in test morphology are related to regional differences in water properties (temperature, salinity, and DCM depth).     

Organization and evolution of the cotG and cotH genes of Bacillus subtilis

The cotG and cotH genes of Bacillus subtilis encode two previously characterized spore coat proteins. The two genes are adjacent on the chromosome and divergently transcribed by σ(K), a sporulation-specific σ factor of the RNA polymerase. We report evidence that the cotH promoter maps 812 bp upstream of the beginning of its coding region and that the divergent cotG gene is entirely contained between the promoter and the coding part of cotH. A bioinformatic analysis of all entirely sequenced prokaryotic genomes showed that such chromosomal organization is not common in spore-forming bacilli. Indeed, CotG is present only in B. subtilis, B. amyloliquefaciens, and B. atrophaeus and in two Geobacillus strains. When present, cotG always encodes a modular protein composed of tandem repeats and is always close to but divergently transcribed with respect to cotH. Bioinformatic and phylogenic data suggest that such genomic organizations have a common evolutionary origin and that the modular structure of the extant cotG genes is the outcome of multiple rounds of gene elongation events of an ancestral minigene.     

Ribitol dehydrogenase of Klebsiella aerogenes. Sequence and properties of wild-type and mutant strains.

Evidence is presented for the sequence of 249 amino acids in ribitol dehydrogenase-A from Klebsiella aerogenes. Continuous culture on xylitol yields strains that superproduce 'wild-type' enzyme but mutations appear to have arisen in this process. Other strains selected by such continuous culture produce enzymes with increased specific activity for xylitol but without loss of ribitol activity. One such enzyme, ribitol dehydrogenase-D, has Pro-196 for Gly-196. Another, ribitol dehydrogenase-B, has a different mutation.     

Primary structure and biological activity of bradykinin potentiating peptides fromBothrops insularis snake venom

Several bradykinin potentiating peptides (BPPs) were isolated from the venom of the Brazilian arboricole snake Bothrops insularis by gel filtration on Sephadex G-150-120, followed by sequencial high-voltage paper electrophoreses atpH 3.5, 6.5, and 2.1. The BPPs were assayed by their ability to potentiate the contractile activity, on the isolated guinea pig ileum, and the hypotensive activity, on anesthetized rats, of bradykinin. Eight BPPs, containing 3–13 amino acid residues, were sequenced and their primary structures were shown to have a marked degree of homology with those of several BPPs from other venoms.