Technical note: compatibility of microtomographic imaging systems for dental measurements

Modern micro-computed tomography techniques allow the accurate visualization of internal dental structures, and are becoming widely used within (paleo-) anthropological dental studies. There exist several types and name brands of microtomographic systems, however, which have been demonstrated to produce images that vary in resolution and signal-to-noise ratio. As a growing body of dental research using disparate microtomographic techniques is likely to continue accumulating, it is imperative that different systems are compared to ensure that results are comparable and not machine-dependent. In the present study, we compare volume, surface area, and linear measurements recorded on a sample of modern and fossil teeth using four microtomographic systems (three laboratory scanners, and the ID19 beamline of the European Synchrotron Radiation Facility). Results indicate that measurements are comparable between systems (within 3%), but that synchrotron radiation is superior to the other systems because its monochromatic X-rays prevent beam hardening and its parallel beam prevents geometric artifacts in the resultant images, making it easier to record measurements and see fine details at the enamel cervix or dentine horn tips. Although the synchrotron produces higher resolution images with less artifacts, results indicate that for gross morphological measurements (e.g., enamel cap volume, intercuspal distances), each of the scanners produces approximately the same measurements. Combining measurements of teeth from multiple microCT systems presupposes that measurements from each system are comparable; the research presented here indicates that this is the case when teeth are not severely diagenetically remineralized.     

Thermodynamic benchmark study using Biacore technology

A total of 22 individuals participated in this benchmark study to characterize the thermodynamics of small-molecule inhibitor-enzyme interactions using Biacore instruments. Participants were provided with reagents (the enzyme carbonic anhydrase II, which was immobilized onto the sensor surface, and four sulfonamide-based inhibitors) and were instructed to collect response data from 6 to 36 degrees C. van't Hoff enthalpies and entropies were calculated from the temperature dependence of the binding constants. The equilibrium dissociation and thermodynamic constants determined from the Biacore analysis matched the values determined using isothermal titration calorimetry. These results demonstrate that immobilization of the enzyme onto the sensor surface did not alter the thermodynamics of these interactions. This benchmark study also provides insights into the opportunities and challenges in carrying out thermodynamic studies using optical biosensors.     

Characterization of the Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase: potential for drug development

Mycobacterium tuberculosis utilizes the methylerythritol phosphate (MEP) pathway for biosynthesis of isopentenyl diphosphate and its isomer, dimethylallyl diphosphate, precursors of all isoprenoid compounds. This pathway is of interest as a source of new drug targets, as it is absent from humans and disruption of the responsible genes has shown a lethal phenotype for Escherichia coli. In the MEP pathway, 4-diphosphocytidyl-2-C-methyl-D-erythritol is formed from 2-C-methyl-D-erythritol 4-phosphate (MEP) and CTP in a reaction catalyzed by a 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase (IspD). In the present work, we demonstrate that Rv3582c is essential for M. tuberculosis: Rv3582c has been cloned and expressed, and the encoded protein has been purified. The purified M. tuberculosis IspD protein was capable of catalyzing the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the presence of MEP and CTP. The enzyme was active over a broad pH range (pH 6.0 to 9.0), with peak activity at pH 8.0. The activity was absolutely dependent upon divalent cations, with 20 mM Mg2+ being optimal, and replacement of CTP with other nucleotide 5'-triphosphates did not support activity. Under the conditions tested, M. tuberculosis IspD had Km values of 58.5 microM for MEP and 53.2 microM for CTP. Calculated kcat and kcat/Km values were 0.72 min(-1) and 12.3 mM(-1) min(-1) for MEP and 1.0 min(-1) and 18.8 mM(-1) min(-1) for CTP, respectively.     

Comparative genomic analysis of the Hsp70s from five diverse photosynthetic eukaryotes

We have identified 24 members of the DnaK subfamily of heat shock 70 proteins (Hsp70s) in the complete genomes of 5 diverse photosynthetic eukaryotes. The Hsp70s are a ubiquitous protein family that is highly conserved across all domains of life. Eukaryotic Hsp70s are found in a number of subcellular compartments in the cell: cytoplasm, mitochondrion (MT), chloroplast (CP), and endoplasmic reticulum (ER). Although the Hsp70s have been the subject of intense study in model organisms, very little is known of the Hsp70s from early diverging photosynthetic lineages. The sequencing of the complete genomes of Thalassiosira pseudonana (a diatom), Cyanidioschyzon merolae (a red alga), and 3 green algae (Chlamydomonas reinhardtii, Ostreococcus lucimarinus, Ostreococcus tauri) allow us to conduct comparative genomics of the Hsp70s present in these diverse photosynthetic eukaryotes. We have found that the distinct lineages of Hsp70s (MT, CP, ER, and cytoplasmic) each have different evolutionary histories. In general, evolutionary patterns of the mitochondrial and endoplasmic reticulum Hsp70s are relatively stable even among very distantly related organisms. This is not true of the chloroplast Hsp70s and we discuss the distinct evolutionary patterns between "green" and "red" plastids. Finally, we find that, in contrast to the angiosperms Arabidopsis thaliana and Oryza sativa that have numerous cytoplasmic Hsp70, the 5 algal species have only 1 cytoplasmic Hsp70 each. The evolutionary and functional implications of these differences are discussed.     

Expression of Mycobacterium tuberculosis Rv1991c using an arabinose-inducible promoter demonstrates its role as a toxin

Conditional gene expression systems are useful tools for studying the role of essential or toxic gene products in bacterial systems. There is a paucity of such systems available for use in the mycobacteria. The utility of the Escherichia coli arabinose-inducible system was looked into, since it is tightly controlled in response to the presence of arabinose and glucose. It was demonstrated that the P(BAD) promoter can be used to express heterologous genes in Mycobacterium smegmatis. Expression of a lacZ reporter gene demonstrated that promoter activity was inducible in response to the presence of glucose, but only on solid medium. This system was utilized to study the functional consequences of expressing one member of a putative toxin-antitoxin pair (Rv1991c). Rv1991c has homology with a number of bacterial toxins, including ChpK, MazF and PemK. A potential antitoxin gene has been identified, adjacent to Rv1991c in the genome, which was coexpressed with the toxin. Expression of the toxin alone inhibited the growth of E. coli, whereas coexpression with the antitoxin did not. Expression of Rv1991c also led to a marked reduction of cell viability in M. smegmatis, confirming its role as a potent toxin.     

Structure, function and regulation of the Toll/IL-1 receptor adaptor proteins

The Toll/IL-1 receptor (TIR) domain plays a central role in Toll-like receptor (TLR) signalling. All TLRs contain a cytoplasmic TIR domain, which, upon activation, acts as a scaffold to recruit adaptor proteins. The adaptor proteins MyD88, Mal, TRIF, TRAM and SARM are also characterized by the presence of a TIR domain. MyD88, Mal, TRIF and TRAM associate with the TLRs via homophilic TIR domain interactions whereas SARM utilizes its TIR domain to negatively regulate TRIF. It is well established that the differential recruitment of adaptors to TLRs provides a significant amount of specificity to the TLR-signalling pathways. Despite this, the TIR-TIR interface has not been well defined. However, structural studies have indicated the importance of TIR domain surfaces in mediating specific TIR-TIR interactions. Furthermore, recent findings regarding the regulation of adaptors provide further insight into the crucial role of the TIR domain in TLR signalling.     

The GacA global regulator of Vibrio fischeri is required for normal host tissue responses that limit subsequent bacterial colonization

Harmful and beneficial bacterium-host interactions induce similar host-tissue changes that lead to contrasting outcomes of association. A life-long association between Vibrio fischeri and the light organ of its host Euprymna scolopes begins when the squid collects bacteria from the surrounding seawater using mucus secreted from ciliated epithelial appendages. Following colonization, the bacterium causes changes in host tissue including cessation of mucus shedding, and apoptosis and regression of the appendages that may limit additional bacterial interactions. We evaluated whether delivery of morphogenic signals is influenced by GacA, a virulence regulator in pathogens, which also influences squid-colonization by V. fischeri. Low-level colonization by a GacA mutant led to regression of the ciliated appendages. However, the GacA mutant did not induce cessation of mucus shedding, nor did it trigger apoptosis in the appendages, a phenotype that normally correlates with their regression. Because apoptosis is triggered by lipopolysaccharide, we examined the GacA mutant and determined that it had an altered lipopolysaccharide profile as well as an increased sensitivity to detergents. GacA-mutant-colonized animals were highly susceptible to invasion by secondary colonizers, suggesting that the GacA mutant's inability to signal the full programme of light-organ responses permitted the prolonged recruitment of additional symbionts.     

Rab27b regulates mast cell granule dynamics and secretion

The Rab GTPase family regulates membrane domain organization and vesicular transport pathways. Recent studies indicate that one member of the family, Rab27a, regulates transport of lysosome-related organelles in specialized cells, such as melanosomes and lytic granules. Very little is known about the related isoform, Rab27b. Here we used genetically modified mice to study the involvement of the Rab27 proteins in mast cells, which play key roles in allergic responses. Both Rab27a and Rab27b isoforms are expressed in bone marrow-derived mast cells (BMMC) and localize to secretory granules. Nevertheless, secretory defects as measured by beta-hexosaminidase release in vitro and passive cutaneous anaphylaxis in vivo were found only in Rab27b and double Rab27 knockout (KO) mice. Immunofluorescence studies suggest that a subset of Rab27b and double Rab27-deficient BMMCs exhibit mild clustering of granules. Quantitative analysis of live-cell time-lapse imaging revealed that BMMCs derived from double Rab27 KO mice showed almost 10-fold increase in granules exhibiting fast movement (>1.5 microm/s), which could be disrupted by nocodazole. These results suggest that Rab27 proteins, particularly Rab27b, play a crucial role in mast cell degranulation and that their action regulates the transition from microtubule to actin-based motility.     

An integrative approach combining ion mobility mass spectrometry,X-ray crystallography,and nuclear magnetic resonance spectroscopy to study the conformational dynamics of α1-antitrypsin upon ligand binding

Native mass spectrometry (MS) methods permit the study of multiple protein species within solution equilibria, whereas ion mobility (IM)-MS can report on conformational behavior of specific states. We used IM-MS to study a conformationally labile protein (α₁-antitrypsin) that undergoes pathological polymerization in the context of point mutations. The folded, native state of the Z-variant remains highly polymerogenic in physiological conditions despite only minor thermodynamic destabilization relative to the wild-type variant. Various data implicate kinetic instability (conformational lability within a native state ensemble) as the basis of Z α₁-antitrypsin polymerogenicity. We show the ability of IM-MS to track such disease-relevant conformational behavior in detail by studying the effects of peptide binding on α₁-antitrypsin conformation and dynamics. IM-MS is, therefore, an ideal platform for the screening of compounds that result in therapeutically beneficial kinetic stabilization of native α₁-antitrypsin. Our findings are confirmed with high-resolution X-ray crystallographic and nuclear magnetic resonance spectroscopic studies of the same event, which together dissect structural changes from dynamic effects caused by peptide binding at a residue-specific level. IM-MS methods, therefore, have great potential for further study of biologically relevant thermodynamic and kinetic instability of proteins and provide rapid and multidimensional characterization of ligand interactions of therapeutic interest.PDB Code(s): 4PYW