Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate

The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts.     

Inhibition of matrix metalloproteinase-3 and -13 synthesis induced by IL-1beta in chondrocytes from mice lacking microsomal prostaglandin E synthase-1

Joint destruction in arthritis is in part due to the induction of matrix metalloproteinase (MMP) expression and their inhibitors, especially MMP-13 and -3, which directly degrade the cartilage matrix. Although IL-1β is considered as the main catabolic factor involved in MMP-13 and -3 expression, the role of PGE(2) remains controversial. The goal of this study was to determine the role of PGE(2) on MMP synthesis in articular chondrocytes using mice lacking microsomal PGE synthase-1 (mPGES-1), which catalyses the rate-limiting step of PGE(2) synthesis. MMP-3 and MMP-13 mRNA and protein expressions were assessed by real-time RT-PCR, immunoblotting, and ELISA in primary cultures of articular chondrocytes from mice with genetic deletion of mPGES-1. IL-1β-induced PGE(2) synthesis was dramatically reduced in mPGES-1(-/-) and mPGES-1(+/-) compared with mPGES-1(+/+) chondrocytes. A total of 10 ng/ml IL-1β increased MMP-3 and MMP-13 mRNA, protein expression, and release in mPGES-1(+/+) chondrocytes in a time-dependent manner. IL-1β-induced MMP-3 and MMP-13 mRNA expression, protein expression, and release decreased in mPGES-1(-/-) and mPGES-1(+/-) chondrocytes compared with mPGES-1(+/+) chondrocytes from 8 up to 24 h. Otherwise, MMP inhibition was partially reversed by addition of 10 ng/ml PGE(2) in mPGES-1(-/-) chondrocytes. Finally, in mPGES-1(-/-) chondrocytes treated by forskolin, MMP-3 protein expression was significantly decreased compared with wild-type, suggesting that PGE(2) regulates MMP-3 expression via a signaling pathway dependent on cAMP. These results demonstrate that PGE(2) plays a key role in the induction of MMP-3 and MMP-13 in an inflammatory context. Therefore, mPGES-1 could be considered as a critical target to counteract cartilage degradation in arthritis.     

Genomic Diversity of Campylobacter coli and Campylobacter jejuni Isolates Recovered from Free-Range Broiler Farms and Comparison with Isolates of Various Origins

In many industrialized countries, the incidence of campylobacteriosis exceeds that of salmonellosis. Campylobacter bacteria are transmitted to humans mainly in food, especially poultry meat products. Total prevention of Campylobacter colonization in broiler flocks is the best way to reduce (or eliminate) the contamination of poultry products. The aim of this study was to establish the sources and routes of contamination of broilers at the farm level. Molecular typing methods (DNA macrorestriction pulsed-field gel electrophoresis and analysis of gene polymorphism by PCR-restriction fragment length polymorphism) were used to characterize isolates collected from seven broiler farms. The relative genomic diversity of Campylobacter coli and Campylobacter jejuni was determined. Analysis of the similarity among 116 defined genotypes was used to determine clusters within the two species. Furthermore, evidence of recombination suggested that there were genomic rearrangements within the Campylobacter populations. Recovery of related clusters from different broiler farms showed that some Campylobacter strains might be specifically adapted to poultry. Analysis of the Campylobacter cluster distribution on three broiler farms showed that soil in the area around the poultry house was a potential source of Campylobacter contamination. The broilers were infected by Campylobacter spp. between days 15 and 36 during rearing, and the type of contamination changed during the rearing period. A study of the effect of sanitary barriers showed that the chickens stayed Campylobacter spp. free until they had access to the open area. They were then rapidly colonized by the Campylobacter strains isolated from the soil.     

Recurrent disturbances, recovery trajectories, and resilience of coral assemblages on a South Central Pacific reef

Coral reefs are increasingly threatened by various disturbances, and a critical challenge is to determine their ability for resistance and resilience. Coral assemblages in Moorea, French Polynesia, have been impacted by multiple disturbances (one cyclone and four bleaching events between 1991 and 2006). The 1991 disturbances caused large declines in coral cover (~51% to ~22%), and subsequent colonization by turf algae (~16% to ~49%), but this phase-shift from coral to algal dominance has not persisted. Instead, the composition of the coral community changed following the disturbances, notably favoring an increased cover of Porites, reduced cover of Montipora and Pocillopora, and a full return of Acropora; in this form, the reef returned to pre-disturbance coral cover within a decade. Thus, this coral assemblage is characterized by resilience in terms of coral cover, but plasticity in terms of community composition.     

Some safety aspects of Salmonella vaccines for poultry: in vivo study of the genetic stability of three Salmonella typhimurium live vaccines

Live vaccine strains of Salmonella should be avirulent, immunogenic and genetically stable. Some isolates of three commercially available live vaccine strains of Salmonella typhimurium, sampled during a study on their persistence in a vaccinated flock of chickens, were analyzed for genetic stability using macrorestriction analysis of their genome. Two out of the three vaccine strains showed genetic instabilities. Two of the 51 isolates of Zoosaloral vaccine strain and nine of the 32 analyzed isolates of chi(3985), a genetically modified organism, were variants and showed different macrorestriction profiles.     

Disseminated inflammatory tinea: An unusual presentation.

Tinea incognito represents a new entity caused basically by the careless application of corticosteroidal creams. We present a 71-year-old man with disseminated erythematous and squamous lesions treated with corticosteroid creams for seven months; the clinical aspect worsened and new pustular lesions appeared. The diagnosis of disseminated inflammatory tinea was confirmed by culture, with the growth of Trichophyton mentagrophytes. We comment on the clinical findings and the factors that contribute to spread the process.     

Factors influencing spatial distribution of fish communities on a fringing reef at Mauritius, S.W. Indian Ocean

This paper analyses the spatial patterns of fish communities on a narrow fringing reef of Mauritius and identifies some controlling factors. Canonical Correspondence Analysis revealed that the location in the reef ecosystem, the living coral coverage, and the proximity to a dredged area were the major factors controlling the distribution and abundance of fish species. Two distinct communities were observed across the fringing reef, representing a land-ocean gradient. The low diversity of fish species, and also of invertebrates such as corals, molluscs, and echinoderms is probably a consequence of the narrowness of the fringing reef and of anthropogenic impacts, notably the high pollution by nutrients.     

Evaluation of a multiplex PCR assay for simultaneous identification of Salmonella sp., Salmonella enteritidis and Salmonella typhimurium from environmental swabs of poultry houses

A Multiplex PCR-based assay (m-PCR) with three sets of primers was developed for the detection of all serotypes of Salmonella enterica and the identification of Salmonella Enteritidis and Salmonella Typhimurium. This method was evaluated against a bacteriological method for the analysis of environmental swabs of poultry houses. Samples were preenriched in phosphate-buffered peptone water for 24 h and subjected to three different protocols prior to PCR: (i) an immunomagnetic separation using Dynabeads anti-Salmonella (Dynal); (ii) a DNA extraction procedure using the Instagene matrix; (iii) an additional step of culture on an MSRV medium. With protocols 1 and 2, eight positive results were found by PCR and 20 with the bacteriological method. Protocol 3 combining MSRV and PCR gave similar results to those obtained from bacteriological methods and allowed Salmonella detection within 2 days.     

Glucuronidation of bile acids in human liver, intestine and kidney. An in vitro study on hyodeoxycholic acid

The activities of UDP-glucuronyl transferase(s) in homogenates and microsomal preparations of human liver, kidney and intestine were tested with hyodeoxycholic acid (HDC). The various kinetic parameters of the UDC-glucuronidation were determined from time course experiments. In both liver and kidney preparations, HDC underwent a very active metabolic transformation: liver Km = 78 microM, Vmax = 3.3 nmol . min-1 . mg-1 protein; kidney Km = 186 microM, Vmax = 9.9 nmol . min-1 . mg-1 protein. To our knowledge this is the first observation of both an extensive and comparable bile acid glucuronidation occurring in renal and hepatic tissues.