Detection of Mycobacterium tuberculosis Peptides in the Exosomes of Patients with Active and Latent M. tuberculosis Infection Using MRM-MS

The identification of easily measured, accurate diagnostic biomarkers for active tuberculosis (TB) will have a significant impact on global TB control efforts. Because of the host and pathogen complexities involved in TB pathogenesis, identifying a single biomarker that is adequately sensitive and specific continues to be a major hurdle. Our previous studies in models of TB demonstrated that exosomes, such as those released from infected macrophages, contain mycobacterial products, including many Mtb proteins. In this report, we describe the development of targeted proteomics assays employing multiplexed multiple reaction monitoring mass spectrometry (MRM-MS) in order to allow us to follow those proteins previously identified by western blot or shotgun mass spectrometry, and enhance biomarker discovery to include detection of Mtb proteins in human serum exosomes. Targeted MRM-MS assays were applied to exosomes isolated from human serum samples obtained from culture-confirmed active TB patients to detect 76 peptides representing 33 unique Mtb proteins. Our studies revealed the first identification of bacteria-derived biomarker candidates of active TB in exosomes from human serum. Twenty of the 33 proteins targeted for detection were found in the exosomes of TB patients, and included multiple peptides from 8 proteins (Antigen 85B, Antigen 85C, Apa, BfrB, GlcB, HspX, KatG, and Mpt64). Interestingly, all of these proteins are known mycobacterial adhesins and/or proteins that contribute to the intracellular survival of Mtb. These proteins will be included as target analytes in future validation studies as they may serve as markers for persistent active and latent Mtb infection. In summary, this work is the first step in identifying a unique and specific panel of Mtb peptide biomarkers encapsulated in exosomes and reveals complex biomarker patterns across a spectrum of TB disease states.     

Interspecific pairwise relationships among body size, clutch size and latitude: deconstructing a macroecological triangle in birds

Aim Ecogeographical ‘rules’, large‐scale patterns in ecological variables across geographical space, can provide important insights into the mechanisms of evolution and ecological assembly. However, interactions between rules could obscure both the observation of large‐scale patterns and their interpretation. Here, we examine a system of three variables interrelated by ecogeographical rules – the latitudinal increase in body size within closely related homeotherms (Bergmann’s rule), the negative allometry of clutch size (Calder’s rule) and the latitudinal increase in clutch size (Lack’s rule) – in a global dataset of birds. Location Global. Methods We used linear regressions and meta‐analysis techniques to quantify the three rules across clades and through the taxonomic hierarchy. Path analysis was used to quantify interactions between rules at multiple taxonomic levels, as a function of both phylogenetic inheritance of traits and indirect feedbacks between the three rules. Independent contrasts analyses were performed on four clades with available phylogenies, and the taxonomic partitioning of variation in each trait was quantified. Results Standardizing across all clades, Lack’s and Bergmann’s rules were supported at all taxonomic levels, with Calder’s rule being supported at the order level. Lack’s rule was consistently stronger and more often detected than the other two rules. Path analysis showed that the indirect effects often outweighed the direct effects of Calder’s rule at the genus level and Bergmann’s rule at the order level. Strong interactions between Calder’s and Bergmann’s rules led to a trade‐off between the rules depending on taxonomic resolution. Main conclusions We found strong interactions between Bergmann’s, Lack’s and Calder’s rules in birds, and these interactions varied in strength and direction over the taxonomic hierarchy and among avian clades. Ecogeographical rules may be masked by feedbacks from other, correlated variables, even when the underlying selective mechanism is operating. The apparently conflicting pairwise relationships among clutch size, body size and latitude illustrate the difficulty of interpreting individual pairwise correlations without recognition of interdependence with other variables.     

Laboratory investigations of mars: Chemical and spectroscopic characteristics of a suite of clays as Mars Soil Analogs

Two major questions have been raised by prior explorations of Mars. Has there ever been abundant water on Mars? Why is the iron found in the Martian soil not readily seen in the reflectance spectra of the surface? The work reported here describes a model soil system of Mars Soil Analog Materials, MarSAM, with attributes which could help resolve both of these dilemmas. The first set of MarSAM consisted of a suite of variably iron/calcium-exchanged montmorillonite clays. Several properties, including chemical composition, surface-ion composition, water adsorption isotherms, and reflectance spectra, of these clays have been examined. Also, simulations of the Viking Labeled Release Experiment using the MarSAM were performed. The results of these studies show that surface iron and adsorbed water are important determinants of clay behavior as evidenced by changes in reflectance, water absorption, and clay surface reactions. Thus, these materials provide a model soil system which reasonably satisfies the constraints imposed by the Viking analyses and remote spectral observations of the Martian surface, and which offers a sink for significant amounts of water. Finally, our initial results may provide insights into the mechanisms of reactions that occur on clay surfaces as well as a more specific approach to determining the mineralogy of Martian soils.     

Isolation of cDNA clones and complete amino acid sequence of human erythrocyte glycophorin C

Two cDNA clones for glycophorin C, a transmembrane glycoprotein of the human erythrocyte which carries the blood group Gerbich antigens, have been isolated from a human reticulocyte cDNA library. The clones were identified with a mixture of 32 oligonucleotide probes (14-mer) which have been synthetized according to the amino acid sequence Asp-Pro-Gly-Met-Ala present in the N-terminal tryptic peptide of the molecule. The primary structure of glycophorin C deduced from the nucleotide sequence of the 460 base-pair insert of the pGCW5 clone indicates that the complete protein is a single polypeptide chain of 128 amino acids clearly organized in three distinct domains. The N-terminal part (residues 1-57, approximately) which is N- and O-glycosylated is connected to a hydrophilic C-terminal domain (residues 82-128, approximately) containing 4 tyrosine residues by a hydrophobic stretch of nonpolar amino acids (residues 58-81, approximately) probably interacting with the membrane lipids and permitting the whole molecule to span the lipid bilayer. Northern blot analysis using a 265-base-pair restriction fragment obtained by DdeI digestion of the inserted DNA shows that the glycophorin C mRNA from human erythroblasts is approximately 1.4 kilobases long and is present in the human fetal liver and the human K562 and HEL cell lines which exhibit erythroid features. The glycophorin C mRNA, however, is absent from adult liver and lymphocytes, indicating that this protein represents a new erythrocyte-specific probe which might be useful to study erythroid differentiation.     

Nonredundant role of Bax and Bak in Bid-mediated apoptosis

Animal models suggest that Bax and Bak play an essential role in the implementation of apoptosis and as a result can hinder tumorigenesis. We analyzed the expression of these proteins in 50 human glioblastoma multiforme (GBM) tumors. We found that all the tumors expressed Bak, while three did not express Bax. In vitro, Bax-deficient GBM (BdGBM) exhibited an important resistance to various apoptogenic stimuli (e.g., UV, staurosporine, and doxorubicin) compared to the Bax-expressing GBM (BeGBM). Using an antisense strategy, we generated Bak(-) BeGBM and Bak(-) BdGBM, which enabled us to show that the remaining sensitivity of the BdGBM to apoptosis was due to the overexpression of Bak. Bax/Bak single or double deficiency had no influence on either the clonogenicity or the growth of tumors in Swiss nude mice. Of note, Bak(-) BeGBM cells were resistant to apoptosis induced by caspase 8 (C8) but not to that induced by granzyme B (GrB). Cells lacking both Bax and Bak (i.e., Bak(-) BdGBM) were completely resistant to all stimuli including the microinjection of C8 and GrB. We show that GrB-cleaved Bid and C8-cleaved Bid differ in size and utilize preferentially Bax and Bak, respectively, to promote cytochrome c release from mitochondria. Our results suggest that Bax deficiency is compensated by an increase of the expression of Bak in GBM and show, for the first time in human cancer, that the double Bax and Bak deficiency severely impairs the apoptotic program.     

A possible energetic role of mineral surfaces in chemical evolution

The postulated roles of clays and other minerals in chemical evolution and the origin of life are reconsidered in terms of the interaction of these minerals with penetrating sources of energy such as ionizing radiation and mechanical stress. This interaction, including such facets as excitation, degradation, storage, and transfer, is considered here with regard to its profound potential for altering the capabilities of minerals to serve both as substrates for prebiological chemistry and as inorganic prototypic life forms. The interaction of minerals and energy in relationship to surface chemistry is discussed in terms of the spectroscopic properties of minerals, the interaction of energy with condensed phases, some commonly accepted concepts of heterogeneous catalysis in the absence of electronic energy inputs, and some commonly accepted and novel means by which surface activity might be enhanced in the presence of energy inputs.An estimation is made of the potential contribution of two poorly characterized prebiotic energy sources, natural radioactive decay and triboelectric energy. These estimates place a conservative lower limit on their prebiotic abundance. Also some special properties of these energy sources, relative to solar energy, are pointed out which might give them particular suitability for driving reactions occurring under geological conditions.Skeletal support for this broadly defined framework of demonstrated and potential relationships between minerals, electronic excitation, and surface reactivity, as applied to chemical evolution, is provided from the results of our studies on 1/1 clays. We have discovered and partially characterized a number of novel luminescent properties of these clays, that indicate energy storage and transfer processes in clays. These luminescent properties are interpreted in relationship to the electron spin resonance phenomena, to provide a basis for estimating the potential significance of energy storage and transduction in monitoring or driving clay surface chemistry.Consideration of the electronic structure of abundant minerals in terms of band theory and localized defect centers provides a predictive theoretical framework from which to rationalize the capacity of these materials to store and transduce energy. The bulk crystal is seen as a collecting antenna for electronic energy, with the defect centers serving as storage sites.The clay properties produced by isomorphic substitution appear to be intimately associated with all of the life-mimetic chemical processes that have been attributed to clays. It appears sensible to postulate that the energetic properties of these substitutional defect centers may also be influential in these biomimetic processes: the promotion of surface reactions, storage of information, replication with transfer of information, and asymmetric separation of electrical charges, as well as their more recently hypothesized roles in energy storage and transduction. The identity of the sites implicated in all of the biomimetic functions of clays as well as their capacity for energy storage is seen to offer significant potential for coupling these functions to an environmental energy source. A yet more specific and experimentally testable hypothesis is offered for a new biomimetic process performed by clays. This hypothesis is that energy stored near isomorphically substituted sites provides the energetic basis for the coupled transport of electrical charge and/or electronic energy through the clay layer, which operates via environmental activation of electron/hole mobility. This is to say that mobility of charge/electronic excitation between defect centers serves as the basis for a primordial inorganic electron transport chain.     

The ethical issues regarding consent to clinical trials with pre-term or sick neonates: a systematic review (framework synthesis) of the analytical (theoretical/philosophical) research

BackgroundConducting clinical trials with pre-term or sick infants is important if care for this population is to be underpinned by sound evidence. Yet, approaching the parents of these infants at such a difficult time raises challenges to obtaining valid informed consent for such research. In this study, we asked, What light does the analytical literature cast on an ethically defensible approach to obtaining informed consent in perinatal clinical trials?MethodsIn a systematic search, we identified 30 studies. We began our analysis by applying philosophical frameworks, which were then refined as concepts emerged from the analytical studies, to present a coherent picture of a broad literature.ResultsBetween them, the studies addressed four themes. The first three were the ethical basis for parental informed consent for neonatal and/or perinatal research, the validity of parental consent in this context, and the range of possible options in methods for gaining consent. The last was the issue of risk and the possibility of a double-standard or asymmetry in the current approaches to the requirement for consent for research and consent for clinical treatment.ConclusionsIn addressing these issues, the analysed studies showed that, whilst there are a variety of possible defences for seeking parental ‘consent’ to neonatal and/or perinatal clinical trials, these are all consistent with the strongly and widely held view that it is important that parents do give (or decline) consent for such research. So far as the method of obtaining consent is concerned, none of the existing consent processes reviewed by the research is satisfactory, and there are philosophical reasons for supposing that at least some parents will fail to give valid consent in a neonatal context. Furthermore, in giving parental ‘consent’ in a perinatal context, parents are authorising infant participation, not giving ‘proxy consent’. Finally, there are reasons for giving weight to both parental ‘consent’ and the infant’s best interests in both research and clinical treatment. However, there are also reasons to treat these factors differently in the two contexts, and this may be partly due to the differing relevance of risk in each case. A significant gap is the lack of any detailed discussion of a process of emergency and/or urgent ‘assent’, in which parents assent or refuse their baby’s participation as best they can during the emergency and later give full consent to continuing participation and follow-up.

Electronic supplementary material

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