Cotton rat<Emphasis Type="Italic"> Sihi-</Emphasis>M3 is a minimally oligomorphic<Emphasis Type="Italic"> Mhc</Emphasis> I-b molecule that binds the chemotactic peptide fMLF under stringent conditions

The leading model for class I-b evolution suggests non-polymorphic I-b genes evolve by gene duplication from polymorphic I-a genes. We recently found N-formyl peptide-specific orthologs of the class I-b gene H2-M3 in the rodent subfamily Sigmodontinae. To test if sigmodont M3 is a I-b gene, we sequenced M3 from wild cotton rats (Sigmodon hispidus) diverse at the class II locus, Sihi-DQA. These haplotypes carry a single allele of M3 that closely resembles H2-M3. However, peptide-binding assays showed that cotton rat M3 bound the chemotactic N-formylpeptide fMLF better than did rat or mouse M3. The Ala116Lys substitution in cotton rat M3 might enhance binding of fMLF and is one of eight residues of M3 that interact with ligand residues P3 and P4 and that are positively selected, with a d_N/d_S ratio of 1.8. Thus, M3 is a class I-b gene in both sigmodontine and murine murids, but positive selection operates on a small subset of residues in the traditionally defined antigen recognition site.Electronic Supplementary Material Supplementary material is available in the online version of this article at     

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration

Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe in this paper the SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities.     

Towards a framework for the evolutionary genomics of Kinetoplastids: what kind of data and how much?

The current status of kinetoplastids phylogeny and evolution is discussed in view of the recent progresses on genomics. Some ideas on a potential framework for the evolutionary genomics of kinetoplastids are presented.     

Comparative enantiocontrol with allyl phenyldiazoacetates in asymmetric catalytic intramolecular cyclopropanation

Dirhodium(II) azetidinone-carboxylates are effective asymmetric catalysts for diazo decomposition of allyl diazoacetates and their subsequent intramolecular cyclopropanations. The effect of alkene substituents on enantiocontrol has been examined and modest selectivities have been achieved. Steric influences from substituents on the diazo carbon are seen to diminish enantioselectivities.     

Sensitivity of bacterial coaggregation to chelating agents

Coaggregation between pairs of microorganisms was found to be inhibited by chelating agents, such as acetylacetone, citrate, EDTA and carboxymethylcellulose. Assays were conducted on eight pairs of periodontopathogens and one pair consisting of Escherichia coli and Saccharomyces cerevisiae. The inhibitory effects of the chelating agents were reversible except for Actinomyces naeslundii 12104, the adhesin of which was irreversibly inactivated. Even though the bacteria possessed different kinds of adhesins, their sensitivity to chelating agents appears to be a common property. Non-toxic chelating agents, such as carboxymethylcellulose and citrate, may prove to be useful anti-adhesins.     

Elimination of Fc receptor-dependent effector functions of a modified IgG4 monoclonal antibody to human CD4

Several CD4 mAbs have entered the clinic for the treatment of autoimmune diseases or transplant rejection. Most of these mAbs caused CD4 cell depletion, and some were murine mAbs which were further hampered by human anti-mouse Ab responses. To obviate these concerns, a primatized CD4 mAb, clenoliximab, was generated by fusing the V domains of a cynomolgus macaque mAb to human constant regions. The heavy chain constant region is a modified IgG4 containing two single residue substitutions designed to ablate residual Fc receptor binding activity and to stabilize heavy chain dimer formation. This study compares and contrasts the in vitro properties of clenoliximab with its matched IgG1 derivative, keliximab, which shares the same variable regions. Both mAbs show potent inhibition of in vitro T cell responses, lack of binding to complement component C1q, and inability to mediate complement-dependent cytotoxicity. However, clenoliximab shows markedly reduced binding to Fc receptors and therefore does not mediate Ab-dependent cell-mediated cytotoxicity or modulation/loss of CD4 from the surface of T cells, except in the presence of rheumatoid factor or activated monocytes. Thus, clenoliximab retains the key immunomodulatory attributes of keliximab without the liability of strong Fcgamma receptor binding. In initial clinical trials, these properties have translated to a reduced incidence of CD4+ T cell depletion.     

Expression, purification, and crystallization of the Escherichia coli selenomethionyl beta-ketoacyl-acyl carrier protein synthase III

Bacterial beta-ketoacyl-acyl carrier protein (ACP) synthase III (KAS III, also called FabH) catalyzes the condensation and transacylation of acetyl-CoA with malonyl-ACP. In order to understand the mode of enzyme/substrate interaction and design small molecule inhibitors, we have expressed, purified, and crystallized a selenomethionyl-derivative of E. coli KAS III. Several lines of evidence confirmed that purified selenomethionyl KAS III was homogenous, stably folded, and enzymatically active. Dynamic light scattering, size exclusion chromatography, and mass spectrometry results indicated that selenomethionyl KAS III is a noncovalent homodimer. Diffraction quality crystals of selenomethionyl KAS III/acetyl-CoA complex, which grew overnight to a size of 0.2 mm(3), belonged to the tetragonal space group P4(1)2(1)2.     

Contribution of the hydrophobic effect to microbial infection

The hydrophobic effect has been known for decades. Numerous researchers have invoked the hydrophobic effect to explain how pathogens adhere to tissues. In some cases, inhibition of adhesion can be brought about by low concentrations of aromatic compounds, such as p-nitrophenol or tryptophan. Because the hydrophobic effect has been considered to be nonspecific, the molecular biology of adhesive hydrophobins has not been studied in as much detail as lectin adhesins. The literature provides compelling evidence that a large number of bacterial and fungal pathogens depend on hydrophobic interactions for successful colonization of a host. Several laboratories are now developing effective antiadhesins, based on inhibition of hydrophobic interactions between the host and the pathogen.     

The role of intravascular ultrasound imaging in vascular brachytherapy

Intracoronary brachytherapy has recently emerged as a new therapy to prevent restenosis. Initial experimental work was achieved in animal models and the results were assessed by histomorphometry. Initial clinical trials used angiography to guide dosimetry and to assess efficacy. Intravascular ultrasound (IVUS) permits tomographic examination of the vessel wall, elucidating the true morphology of the lumen and transmural components, which cannot be investigated on the lumenogram obtained by angiography. This paper reviews the use of IVUS in the clinical studies of brachytherapy conducted to date. IVUS allows clinicians to make a thorough assessment of the remodeling of the vessel and appears to have a major role to play in facilitating understanding of the underlying mechanisms of action in this emerging field. The authors propose that state-of-the-art IVUS techniques should be employed to further knowledge of the mechanisms of action of brachytherapy in atherosclerotic human coronary arteries.