Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules

Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence analysis and linear modeling) on 2,909 common and rare HLA-A, HLA-B, and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defense. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intraprotein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.     

Maffucci syndrome and soft tissue sarcoma: a case report

Background

Maffucci syndrome, a congenital mesodermal dysplasia characterized by multiple enchondromas and hemangiomas, was first described in 1881, and 200 cases have been reported in the literature since then. Its etiology is unknown, there is no predilection for race or sex, and the development of lesions usually occurs in puberty. The risk of sarcomatous transformation is about 25%.

Case presentation

The initial investigation of the case reported here focused on the diagnosis and treatment of malignancy, and the first diagnostic hypothesis was thrombosed hemangioma. After histopathologic confirmation of soft tissue sarcoma, examinations were performed to stage the tumor and enchondromas were found in ribs. The final diagnosis was Maffucci syndrome with malignant transformation.

Conclusion

Treatment should aim at symptom relief and early detection of malignancies; no therapy is indicated for asymptomatic patients. As in the case reported here, bone or soft tissue lesions that grow or become painful should be biopsied.

     

Next-Generation Phage Display: Integrating and Comparing Available Molecular Tools to Enable Cost-Effective High-Throughput Analysis

Background

Combinatorial phage display has been used in the last 20 years in the identification of protein-ligands and protein-protein interactions, uncovering relevant molecular recognition events. Rate-limiting steps of combinatorial phage display library selection are (i) the counting of transducing units and (ii) the sequencing of the encoded displayed ligands. Here, we adapted emerging genomic technologies to minimize such challenges.

Methodology/Principal Findings

We gained efficiency by applying in tandem real-time PCR for rapid quantification to enable bacteria-free phage display library screening, and added phage DNA next-generation sequencing for large-scale ligand analysis, reporting a fully integrated set of high-throughput quantitative and analytical tools. The approach is far less labor-intensive and allows rigorous quantification; for medical applications, including selections in patients, it also represents an advance for quantitative distribution analysis and ligand identification of hundreds of thousands of targeted particles from patient-derived biopsy or autopsy in a longer timeframe post library administration. Additional advantages over current methods include increased sensitivity, less variability, enhanced linearity, scalability, and accuracy at much lower cost. Sequences obtained by qPhage plus pyrosequencing were similar to a dataset produced from conventional Sanger-sequenced transducing-units (TU), with no biases due to GC content, codon usage, and amino acid or peptide frequency. These tools allow phage display selection and ligand analysis at >1,000-fold faster rate, and reduce costs ∼250-fold for generating 10⁶ ligand sequences.

Conclusions/Significance

Our analyses demonstrates that whereas this approach correlates with the traditional colony-counting, it is also capable of a much larger sampling, allowing a faster, less expensive, more accurate and consistent analysis of phage enrichment. Overall, qPhage plus pyrosequencing is superior to TU-counting plus Sanger sequencing and is proposed as the method of choice over a broad range of phage display applications in vitro, in cells, and in vivo.     

Xylan-hydrolyzing enzyme system from Bacillus pumilus CBMAI 0008 and its effects on Eucalyptus grandis kraft pulp for pulp bleaching improvement

The extracellular productions of beta-xylanase, beta-xylosidase, beta-glucosidase, beta-mannanase, arabinosidase, alpha-glucuronidase, alpha-galactosidase and Fpase from Bacillus pumilus CBMAI 0008 were investigated with three different xylan sources as substrate. The enzymatic profiles on birchwood, Eucalyptus grandis and oat were studied at alkaline and acidic pH conditions. B. pumilus CBMAI 0008 grown on the three carbon sources produced mainly beta-xylanase. At pH 10, the levels of xylanase were 328, 160 and 136 U/ml, for birch, oat and E. grandis, respectively. beta-Mannanase production was induced on E. grandis (5 U/ml) and arabinofuranosidase on oat (5 U/ml). Although small quantities of alpha-glucuronidase had been produced at pH 10, activity at pH 4.8 was 1.5 U/ml, higher than observed for Aspergillus sp. in literature reports. Preliminary assays carried out on E. grandis kraft pulp from an industrial paper mill (RIPASA S.A. Celulose e Papel, Limeira, SP, Brazil) showed a reduction of 0.3% of chlorine use in the pulp treated with the enzymes, resulting in increased brightness, compared to conventional bleaching. The enzymes were more efficient if applied before the initial bleaching sequence, in a non-pre-oxygenated pulp.     

Host-Defense Mechanism of the Ocular Surfaces

The defense of the ocular surfaces presents an unique challenge in that not only must integrity be maintained against microbial, inflammatory and physical assault, but it must be done while minimizing the risk of loss of corneal transparency. This puts severe limitations on the degree to which scarring or neovascularization can occur in the cornea secondary to any infectious, inflammatory, immunological or wound healing process. Moreover, this defense system must be equally effective under two extremes of conditions: those found in the open eye and the closed eye environments. It is our contention that these constraints have resulted in the evolution of a highly complex fail-safe defense system that utilizes distinctly different strategies in open and closed eye conditions. The extraordinary effectiveness of this system is evidenced by the fact that despite continued exposure to a microbe rich environment, the external ocular surfaces maintain a very low microbial titer and are highly resistant to breaching by all but a few pathogens. It is the intent of this review to provide a working model of this defense system as it operates under both open and closed eye conditions, to provide evidence in support of this model as well as highlight some of the many areas of uncertainty.     

Effects of litter size on maternal care, body weight and infant development in golden hamsters (Mesocricetus auratus)

The effects of litter size on maternal care, body weight and infant development of golden hamsters were investigated from a longitudinal perspective. Litters were culled to 1,3,6 and 9 pups, and the behavior and body weight of mothers and pups were recorded from the 5th to the 25th postpartum day. We noted that the time spent by mothers in bodily interactions with pups decreased as a function of litter size; maternal pup retrievals reached their maximum around the 13-15th day, which coincided with the increased locomotor activity of pups at this time; the total number of pup retrievals by the mother increased as a function of the litter size, but mothers of larger litters were more 'efficient' (i.e. they failed less frequently in exhibiting a full sequence of retrievals) and exhibited a low litter-size proportional mean number of retrievals. All mothers gradually lost body mass throughout lactation, and decrease in body weight was significantly related to litter size. The mean body weight gain (%) by pups decreased as a function of litter size, but we also noted that single and larger litter pups exhibited a decreased body mass (grams) by the 15th day, suggesting that infant development may be impaired at both extremes of experimental conditions. We concluded that the behavior of mothers and pups was affected by the litter size, and it appeared that the litter had an optimal size-not so large as to overlap the mother's physical capacity, and not so small as to fail to compensate for the parental investment.     

Protocol to refine intestinal motility test in mice

We propose a new protocol intended to conform to the 3Rs (replacement, reduction, and refinement) principle, using animals fasted for 3 h to control intestinal motility, which reduced stress in the animals. In this new protocol, mice are deprived of food for a short time (3 h) and are not killed. The mice are observed until evacuation containing charcoal is observed, and the experimental results are based on the charcoal evacuation time. The present study may aid the formulation of recommendations that can be included in revised guidelines relating to the fasting time of mice. This new concept of an intestinal motility test conforms with respectful science.     

Thiol modification of cysteine 327 in the eighth transmembrane domain of the light subunit xCT of the heteromeric cystine/glutamate antiporter suggests close proximity to the substrate binding site/permeation pathway

We measured sensitivity to thiol modification of the heteromeric glutamate/cystine transporter 4F2hc-xCT expressed in Xenopus oocytes. p-Chloromercuribenzoate (pCMB) and p-chloromercuribenzenesulfonate (pCMBS) rapidly blocked transport activity. Cys(327), located in the middle of the eighth transmembrane domain of the light subunit (xCT), was found to be the main target of inactivation. Cysteine, an impermeant reducing reagent, reversed pCMB and pCMBS effects only when applied from the extracellular medium. l-Glutamate and l-cystine, but not l-arginine, protected from the inactivation with an IC(50) similar to the K(m). Protection was not temperature-dependent, suggesting that it did not depend on large substrate-induced conformational changes. Mutation of Cys(327) to Ala and Ser slightly modified the K(m) and a C327L mutant abolished transport function without compromising transporter expression at the plasma membrane. The results indicate that Cys(327) is a functionally important residue accessible to the aqueous extracellular environment and is structurally linked to the permeation pathway and/or the substrate binding site.