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Introduction Proteomic analysis of human plasma by LC–ESI–MS/MS has discovered a limited number of new cellular protein biomarkers that may be confirmed by independent biochemical methods. Analysis of COVID-19 plasma has indicated the re-purposing of known biomarkers that might be used as prognostic markers of COVID-19 infection. However, multiple molecular approaches have previously indicated that the SARS-COV2 infection cycle is linked to the biology of mitochondria and that the response to infections may involve the action of heme containing oxidative enzymes. Methods Human plasma from COVID-19 and ICU-ARDS was analyzed by classical analytical biochemistry techniques and classical frequency-based statistical approaches to look for prognostic markers of severe COVID-19 lung damage. Plasma proteins from COVID-19 and ICU-ARDS were identified and enumerated versus the controls of normal human plasma (NHP) by LC–ESI–MS/MS. The observation frequency of proteins detected in COVID-19 and ICU-ARDS patients were compared to normal human plasma, alongside random and noise MS/MS spectra controls, using the Chi Square (χ2) distribution. Results PCR showed the presence of MT-ND1 DNA in the plasma of COVID-19, ICU-ARDS, as well as normal human plasma. Mitochondrial proteins such as MRPL, L2HGDH, ATP, CYB, CYTB, CYP, NDUF and others, were increased in COVID-19 and ICU-ARDS plasma. The apparent activity of the cytochrome components were tested alongside NHP by dot blotting on PVDF against a purified cytochrome c standard preparation for H2O2 dependent reaction with luminol as measured by enhanced chemiluminescence (ECL) that showed increased activity in COVID-19 and ICU-ARDS patients. Discussion The results from PCR, LC–ESI–MS/MS of tryptic peptides, and cytochrome ECL assays confirmed that mitochondrial components were present in the plasma, in agreement with the established central role of the mitochondria in SARS-COV-2 biology. The cytochrome activity assay showed that there was the equivalent of at least nanogram amounts of cytochrome(s) in the plasma sample that should be clearly detectable by LC–ESI–MS/MS. The release of the luminol oxidase activity from cells into plasma forms the basis of a simple and rapid test for the severity of cell damage and lung injury in COVID-19 infection and ICU-ARDS. Graphical Abstract

Background Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at – 80 °C prior to experiments. Plasma test samples from the – 80 °C freezer were thawed on ice or intentionally warmed to room temperature. Methods Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) and correlated with X!TANDEM. Results Fully tryptic peptides by X!TANDEM returned a similar set of proteins, but was more computationally efficient, than “no enzyme” correlations. Plasma samples maintained on ice, or ice with a cocktail of protease inhibitors, showed lower background amounts of plasma peptides compared to samples incubated at room temperature. Regression analysis indicated that warming plasma to room temperature, versus ice cold, resulted in a ~ twofold increase in the frequency of peptide identification over hours–days of incubation at room temperature. The type I error rate of the protein identification from the X!TANDEM algorithm combined was estimated to be low compared to a null model of computer generated random MS/MS spectra. Conclusion The peptides of human plasma were identified and quantified with low error rates by random and independent sampling that revealed 1000s of peptides from hundreds of human plasma proteins from endogenous tryptic peptides. Electronic supplementary material The online version of this article (10.1186/s12014-017-9176-7) contains supplementary material, which is available to authorized users.

Fetal serum supports the immortal growth of mammalian cell lines in culture while adult serum leads to the terminal differentiation and death of cells in culture. Many of the proteins in fetal serum that support the indefinite division and growth of cancerous cell lines remain obscure. The peptides and proteins of fetal versus adult serum were analyzed by liquid chromatography, nano electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS). Three batches of fetal serum contained the Alpha Fetoprotein marker while adult serum batches did not. Insulin (INS), and insulin-like growth factor (ILGF), fibroblast growth factor (FGF), epidermal growth factor (EGF) and platelet derived growth factor (PDGF) were increased in fetal serum. New fetal growth factors including MEGF, HDGFRP and PSIP1 and soluble growth receptors such as TNFR, EGFR, NTRK2 and THRA were discovered. Addition of insulin or the homeotic transcription factor PSIP1, also referred to as Lens Epithelium Derived Growth Factor (LEDGF), partially restored the rounded phenotype of rapidly dividing cells but was not as effective as fetal serum. Thus, a new growth factor in fetal serum, LEDGF/PSIP1, was directly observed by tandem mass spectrometry and confirmed by add back experiments to cell culture media alongside insulin.

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There is a great desire to relate the patterns of endogenous peptides in blood to human disease and drug response. The best practices for the preparation of blood fluids for analysis are not clear and also relatively few of the peptides in blood have been identified by tandem mass spectrometry. We compared a number of sample preparation methods to extract endogenous peptides including C18 reversed phase, precipitation, and ultrafiltration. We examined the results of these sample preparation methods by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and liquid chromatography-tandem mass spectrometry (MS/MS) using MALDI-TOF/TOF and electrospray ionization-ion trap. Peptides from solid-phase extraction with C18 in the range of hundreds of femtomoles per spot were detected from the equivalent of 1 μL of serum by MALDI-TOF. We observed endogenous serum peptides from fibrinogen α- and β-chain, complement C3, α-2-HS-glycoprotein, albumin, serine (or cysteine) proteinase inhibitor, factor VIII, plasminogen, immunoglobulin, and other abundant blood proteins. However, we also recorded significant MS/MS spectra from tumor necrosis factor-α-, major histocompatibility complex-, and angiotensin-related peptides, as well as peptides from collagens and other low-abundance proteins. Amino acid substitutions were detected and a phosphorylated peptide was also observed. This is the first time the endogenous peptides of fetal serum have been examined by MS and where peptides from low-abundance proteins, phosphopeptides, and amino acid substitutions were detected.

The tryptic peptides from ice cold versus room temperature plasma were identified by C18 liquid chromatography and micro electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS). Samples collected on ice showed low levels of endogenous tryptic peptides compared to the same samples incubated at room temperature. Plasma on ice contained peptides from albumin, complement, and apolipoproteins and others that were observed by the X!TANDEM and SEQUEST algorithms. In contrast to ice cold samples, after incubation at room temperature, greater numbers of tryptic peptides from well characterized plasma proteins, and from cellular proteins were observed. A total of 583,927 precursor ions and MS/MS spectra were correlated to 94,669 best fit peptides that reduced to 22,287 correlations to the best accession within a gene symbol and to 7174 correlations to at least 510 gene symbols with ≥ 5 independent MS/MS correlations (peptide counts) that showed FDR q-values ranging from E−9 (i.e. FDR = 0.000000001) to E−227. A set of 528 gene symbols identified by X!TANDEM and SEQUEST including C4B showed ≥ fivefold variation between ice cold versus room temperature incubation. STRING analysis of the protein gene symbols observed from endogenous peptides in normal plasma revealed an extensive protein-interaction network of cellular factors associated with cell signalling and regulation, the formation of membrane bound organelles, cellular exosomes and exocytosis network proteins. Taken together the results indicated that a pool of cellular proteins, or protein complexes, in plasma are apparently not stable and degrade soon after incubation at room temperature. Electronic supplementary material The online version of this article (10.1186/s12014-017-9174-9) contains supplementary material, which is available to authorized users.

The classical S–I–A-type granites from the Lachlan Orogen, SE Australia, formed as a tectonic end-member of the accretionary orogenic spectrum, the Paleozoic Tasmanides. The sequence of S-to I-to A-type granite is repeated at least three times. All the granites are syn-extensional, formed in a dominantly back-arc setting behind a single, stepwise-retreating arc system between 530 and 230 Ma. Peralkaline granites are rare. Systematic S–I–A progressions indicate the progressive dilution of an old crustal component as magmatism evolved from arc (S-type) to proximal back-arc (I-type) to distal back-arc (A-type) magmatism. The alkaline and peralkaline A-type Younger granites of Nigeria were generally hotter and drier than the Lachlan A-type granites and were emplaced into an anhydrous Precambrian basement during intermittent intracontinental rifting. This geodynamic environment contrasts with the distal back-arc setting of the Lachlan A-type granites, where magmatism migrated rapidly across the orogen. Tectonic discrimination diagrams are inappropriate for the Lachlan granites, placing them in the wrong settings. Only the peralkaline Narraburra suite of the Lachlan Orogen fits the genuine ‘within-plate’ setting of the Nigerian A-type granites. Such discrimination diagrams require re-evaluation in the light of an improved modern understanding of tectonic processes, particularly the role of extensional tectonism and its geodynamic drivers.

Background A practical strategy to discover proteins specific to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological conditions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution-matched controls, and normal samples collected directly onto ice. Methods Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma samples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were fit to fully tryptic peptides within proteins identified using the X!TANDEM algorithm. Observation frequency of the identified proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specific to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm. The average protein or peptide log10 precursor intensity was compared across disease and control treatments by ANOVA in the R statistical system. Results Peptides and/or phosphopeptides of common plasma proteins such as complement C2, C7, and C1QBP among others showed increased observation frequency by Chi Square and/or precursor intensity in AD. Cellular gene symbols with large Chi Square values (χ2 ≥ 25, p ≤ 0.001) from tryptic peptides included KIF12, DISC1, OR8B12, ZC3H12A, TNF, TBC1D8B, GALNT3, EME2, CD1B, BAG1, CPSF2, MMP15, DNAJC2, PHACTR4, OR8B3, GCK, EXOSC7, HMGA1 and NT5C3A among others. Similarly, increased frequency of tryptic phosphopeptides were observed from MOK, SMIM19, NXNL1, SLC24A2, Nbla10317, AHRR, C10orf90, MAEA, SRSF8, TBATA, TNIK, UBE2G1, PDE4C, PCGF2, KIR3DP1, TJP2, CPNE8, and NGF amongst others. STRING analysis showed an increase in cytoplasmic proteins and proteins associated with alternate splicing, exocytosis of luminal proteins, and proteins involved in the regulation of the cell cycle, mitochondrial functions or metabolism and apoptosis. Increases in mean precursor intensity of peptides from common plasma proteins such as DISC1, EXOSC5, UBE2G1, SMIM19, NXNL1, PANO, EIF4G1, KIR3DP1, MED25, MGRN1, OR8B3, MGC24039, POLR1A, SYTL4, RNF111, IREB2, ANKMY2, SGKL, SLC25A5, CHMP3 among others were associated with AD. Tryptic peptides from the highly conserved C-terminus of DISC1 within the sequence MPGGGPQGAPAAAGGGGVSHRAGSRDCLPPAACFR and ARQCGLDSR showed a higher frequency and highest intensity in AD compared to all other disease and controls. Conclusion Proteins apparently expressed in the brain that were directly related to Alzheimer’s including Nerve Growth Factor (NFG), Sphingomyelin Phosphodiesterase, Disrupted in Schizophrenia 1 (DISC1), the cell death regulator retinitis pigmentosa (NXNl1) that governs the loss of nerve cells in the retina and the cell death regulator ZC3H12A showed much higher observation frequency in AD plasma vs the matched control. There was a striking agreement between the proteins known to be mutated or dis-regulated in the brains of AD patients with the proteins observed in the plasma of AD patients from endogenous peptides including NBN, BAG1, NOX1, PDCD5, SGK3, UBE2G1, SMPD3 neuronal proteins associated with synapse function such as KSYTL4, VTI1B and brain specific proteins such as TBATA.

The Empirical Statistical Model (ESM) for decoy library searching fused the expected amino acid sequence of 18 non-human protein standards to a human decoy library. The ESM assumed a priori the standards were pure such that only the 18 nominal proteins were true positive, all other proteins were false positive, there was no overlap in the peptides of non-human proteins versus human proteins, and that the score distribution of individual peptides would resolve true positive from false positive results or noise. The results of random and independent sampling by LC-ESI-MS/MS indicated that the fundamental assumptions of the ESM were not in good agreement with the actual purity of the commercial test standards and so the method showed a 99.7% false negative rate. The ESM for decoy library searching apparently showed poor agreement with SDS-PAGE using silver staining, goodness of fit of MS/MS spectra by X!TANDEM, FDR correction by Benjamini and Hochberg, or comparison to the observation frequency of null random MS/MS spectra, that all confirmed the standards contain hundreds of proteins with a low FDR of primary structural identification. The protein observation frequency increased with abundance and the log

International audience; The Tuareg shield in North-West Africa is composed of an assembly of Neoproterozoic continental and oceanic terranes, as well as Archean and Paleoproterozoic terranes separated by major continental shear zones. In the Silet terrane, the igneous suite of Silet-Taourirts is composed of post-collisional ring-complexes of ferroan alkaline and alkali-calcic granites. Six ring-complexes have been dated using the U–Pb SHRIMP technique on zircon. The alkaline Tin Erit (584.8 ± 2.0 Ma), Tihoiiarene (569.8 ± 4.8 Ma) and Tioueine (561 ± 6 Ma) complexes are older than the alkali-calcic Issedienne (538.7 ± 2.9 Ma), Tesnou (536.5 ± 6.7 Ma) and Ait Oklan (529.3 ± 3.1 Ma) complexes. Sharing an enriched mantle source, the complexes display a secular variation of crustal contamination marked by decreasing εHf(t). The oldest alkaline complexes are related to the tectonic escape of the Tuareg terranes to the north after the climax of Pan-African orogeny, while the youngest alkali-calcic complexes were emplaced after the 575-555 Ma intra-continental Murzukian event.

A Rabbit myosin standard, like that used to create the empirical statistical model, was randomly and independently sampled by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) with a linear quadrupole ion trap. The rabbit myosin protein standard appeared pure by SDS-PAGE and CBBR staining but showed many other proteins by silver staining. The LC-MS intensity from myosin and IgG samples were above the 99% safe limit of detection and quantification computed from 36 blank LC-ESI-MS/MS runs. The myosin contained ≤406 Gene Symbols, open reading frames or loci where 79 protein types showed ≥3 peptides from X!TANDEM. Myosins, actin, troponin, other proteins showed 95%–100% homology between the rabbit versus the human decoy library. The myosin protein complex from STRING was true positive compared to random or noise spectra MS/MS with a low type I error (p-value) and low FDR (q-value) computed in R. SDS-PAGE, Western blot, comparison to random and noise MS/MS spectra, X!TANDEM p-values, FDR corrected q-values, and STRING all agreed that the error rate of LC-ESI-MS/MS with a quadrupole ion trap is far below that assumed a priori by the design of the empirical statistical model for decoy library searching.

Thirty human EDTA plasma samples from male and female subjects ranging in age from 24 to 74 years were collected on ice, processed ice cold and stored frozen at −80 °C, in liquid nitrogen (LN2), or freeze dried and stored at room temperature in a desiccator (FDRT) or freeze dried and stored at −20 °C for 1 year (FD-20). In a separate experiment, EDTA plasma samples were collected onto ice, processed ice cold and maintained on ice ± protease inhibitors versus incubated at room temperature for up to 96 h. Random and independent sampling by liquid chromatography and tandem mass spectrometry (LC–ESI–MS/MS), as correlated by the MASCOT, OMSSA, X!TANDEM and SEQUEST algorithms, showed that tryptic peptides from complement component 4B (C4B) were rapidly released in plasma at room temperature. Random sampling by LC–ESI–MS/MS showed that peptides from C4B were undetectable on ice, but peptides were cleaved from the mature C4B protein including NGFKSHALQLNNR within as little as 1 h at room temperature. The frequency and intensity of precursors within ± 3 m/z of the C4B peptide NGFKSHALQLNNR was confirmed by automated targeted analysis where the precursors from MS/MS spectra that correlated to the target sequence were analyzed in SQL/R. The C4B preproprotein was processed at the N terminus to release the mature chain that was cleaved on the carboxyl side of the isoprene C2 domain within a polar C terminal sequence of the mature C4B protein, to reveal the thioester reaction site, consistent with LC–ESI–MS/MS and Western blot. Random sampling showed that proteolytic peptides from complement component C4B were rarely observed with long term storage at − 80 °C in a freezer or in liquid nitrogen (LN2), freeze drying with storage at − 20 °C (FD-20 °C) or freeze drying and storage at room temperature (FDRT). Plasma samples maintained at room temperature (RT) showed at least 10-fold to 100-fold greater frequency of peptide correlation to C4B and measured peptide intensity compared to samples on ice for up to 72 h or stored at − 80 °C, LN2, FDRT or FD-20 °C for up to a year. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9170-0) contains supplementary material, which is available to authorized users.

© 2017 The Author(s). Background: The Root model of normal and abnormal foot function remains the basis for clinical foot orthotic practice globally. Our aim was to investigate the relationship between foot deformities and kinematic compensations that are the foundations of the model. Methods: A convenience sample of 140 were screened and 100 symptom free participants aged 18-45 years were invited to participate. The static biomechanical assessment described by the Root model was used to identify five foot deformities. A 6 segment foot model was used to measure foot kinematics during gait. Statistical tests compared foot kinematics between feet with and without foot deformities and correlated the degree of deformity with any compensatory motions. Results: None of the deformities proposed by the Root model were associated with distinct differences in foot kinematics during gait when compared to those without deformities or each other. Static and dynamic parameters were not correlated. Conclusions: Taken as part of a wider body of evidence, the results of this study have profound implications for clinical foot health practice. We believe that the assessment protocol advocated by the Root model is no longer a suitable basis for professional practice. We recommend that clinicians stop using sub-talar neutral position during clinical assessments and stop assessing the non-weight bearing range of ankle dorsiflexion, first ray position and forefoot alignments and movement as a means of defining the associated foot deformities. The results question the relevance of the Root assessments in the prescription of foot orthoses.

It will be important to determine if the parent and fragment ion intensity results of liquid chromatography, electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) experiments have been randomly and independently sampled from a normal population for the purpose of statistical analysis by general linear models and ANOVA. The tryptic parent peptide and fragment ion m/z and intensity data in the mascot generic files from LC-ESI-MS/MS of purified standard proteins, and human blood protein fractionated by partition chromatography, were parsed into a Structured Query Language (SQL) database and were matched with protein and peptide sequences provided by the X!TANDEM algorithm. The many parent and/or fragment ion intensity values were log transformed, tested for normality, and analyzed using the generic Statistical Analysis System (SAS). Transformation of both parent and fragment intensity values by logarithmic functions yielded intensity distributions that closely approximate the log-normal distribution. ANOVA models of the transformed parent and fragment intensity values showed significant effects of treatments, proteins, and peptides, as well as parent versus fragment ion types, with a low probability of false positive results. Transformed parent and fragment intensity values were compared over all sample treatments, proteins or peptides by the Tukey-Kramer Honestly Significant Difference (HSD) test. The approach provided a complete and quantitative statistical analysis of LC-ESI-MS/MS data from human blood.

The binding and activation of macrophages by microscopic aggregates of oxLDL in the intima of the arteries may be an important step towards atherosclerosis leading to heart attack and stroke. Microbeads coated with oxLDL were used to activate, capture and isolate the oxLDL receptor complex from the surface of live cells. Analysis of the resulting tryptic peptides by liquid chromatography and tandem mass spectrometry revealed the Spleen Tyrosine Kinase (SYK), and many of SYK's known interaction network including Fc receptors (FCGR2A, FCER1G and FCGR1A) Toll receptor 4 (TLR4), receptor kinases like EGFRs, as well as RNA binding and metabolism proteins. High-intensity precursor ions (∼9*E3 to 2*E5 counts) were correlated to peptides and specific phosphopeptides from long isoform of SYK (SYK-L) by the SEQUEST, OMSSA and X!TANDEM algorithms. Peptides or phosphopeptides from SYK were observed with the oxLDL-microbeads. Pharmacological inhibitors of SYK activity significantly reduced the engulfment of oxLDL microbeads in the presence of serum factors, but had little effect on IgG phagocytosis. Anti SYK siRNA regulated oxLD engulfment in the context of serum factors and or SYK-L siRNA significantly inhibited engulfment of oxLDL microbeads, but not IgG microbeads.

This paper explores the question of whether the identification of many wrongdoings in an organisation requires knowledge of the technical and operating mechanisms of that organisation. If such is the case, many ethical problems cannot be resolved by a generalist. They must be left to people with knowledge of that industry. In attempting to answer the question, the paper examines 11 different types of organisations. It then asks how the ethical issues in those organisations might be resolved. The organisations are veterinarians, pharmacies, media companies, engineering firms, doctors, general businesses, including two sub disciplines, marketing and accounting organisations, nursing institutions, political parties, scientific research organisations, legal firms and information technology companies. Each can be a small professional company, locally based, or a large organisation, possibly international. Each exhibits one or more ethical problems that are not easily resolved by accepted ethical theory. Accepted theory, as further defined in the text, is the mainline ethical theories that would be core components of most ethics texts or courses. The question arises then on how would ethics be taught if the ethical issues require specialised knowledge of that industry sector. After examining the 11 industries, the paper puts forth two views. One is that a number of wrongs can be identified in industries and organisations where the ethical problems are complex and difficult to resolve, and where the standard ethical theories are of little or no help. Resolving these issues requires action from the organisation, or from the industry association encompassing all companies within that sector. A further complication has developed in the near explosive growth in whistleblower protection systems. These systems, now introduced in close to 30 countries around the world, have their own lists of wrongdoings for which the whistleblower will receive administrative and legal support. These lists of wrongs are distinct from any moral theory One conclusion to be drawn is that new methods possibly need to be found for teaching the identification and resolution of ethical issues. A second is a consequence of the first – that the teacher of ethics in these courses has to be drawn from within the industry. Further questions then arise: One is whether this demand then requires that this industry specialist learn moral theory? A second is then how would generalist applied ethics causes be taught (in humanities departments for instance)? Alternate viewpoints on joint teaching by a moral specialist and an industry specialist have been put forward. The paper puts forward one possible approach for the industry courses – that the industry specialist has to present the course, with new methods and content, but that a theoretical content is taught by someone knowledgeable in ethical theory. For generalist courses, the moral theorist has to include a sufficiently wide sample of industry and organisational ethical issues to ensure that students are aware of the wide range of ethical concerns that can arise, as well as approaches to resolving them.

The Fc receptor complex and its associated phagocytic cytoskeleton machinery were captured from the surface of live cells by IgG coated microbeads and identified by mass spectrometry. The random and independently sampled intensity values of peptides were similar in the control and IgG samples. After log transformation, the parent and fragment intensity values showed a normal distribution where ≥ 99.9% of the data was well above the background noise. Some proteins showed significant differences in intensity between the IgG and control samples by ANOVA followed by the Tukey–Kramer honestly significant difference test. However many proteins were specific to the IgG beads or the control beads. The set of detected cytoskeleton proteins, binding proteins and enzymes detected on the IgG beads were used to predict the network of actin-associated regulatory factors. Signaling factors/proteins such as PIK3, PLC, GTPases (such CDC42, Rho GAPs/GEFs), annexins and inositol triphosphate receptors were all identified as being specific to the activated receptor complex by mass spectrometry. In addition, the tyrosine kinase Fak was detected with the IgG coated beads. Hence, an activated receptor cytoskeleton complex and its associated regulatory proteins were captured from the surface of live human primary leukocytes.

The simplest model-that authentic tandem mass spectrometry (MS/MS) spectra are no different from noise, random spectra, or false-positive results-may be directly examined by chi-square comparison of the peptide-to-protein distribution. The peptide-to-protein distribution of a set of 4151 redundant blood proteins identified by X!TANDEM indicated that there is a low probability that the authentic data were the same as noise, random spectra, or false-positive correlations (P0.0001). In contrast, a competition for significance failed to distinguish approximately 90% of authentic blood proteins from those of noise, random spectra, or false-positive results (P0.01) and apparently incurred a large type II error (false negative). The chi-square test of peptide-to-protein frequency distributions was found to be an efficient means to distinguish authentic data from false-positive results. Frequency-based statistics unambiguously demonstrated that proteins can be identified by liquid chromatography-electrospray ionization-MS/MS from human blood with acceptable confidence. Thus, the chi-square fit of the peptide-to-protein distribution could distinguish authentic data from random or false-positive data, but the score distribution method could not separate real results from false results.

Proteomics uses tandem mass spectrometers and correlation algorithms to match peptides and their fragment spectra to amino acid sequences. The replication of multiple liquid chromatography experiments with electrospray ionization of peptides and tandem mass spectrometry (LC-ESI-MS/MS) produces large sets of MS/MS spectra. There is a need to assess the quality of large sets of experimental results by statistical comparison with that of random expectation. Classical frequency-based statistics such as goodness-of-fit tests for peptide-to-protein distributions could be used to calculate the probability that an entire set of experimental results has arisen by random chance. The frequency distributions of authentic MS/MS spectra from human blood were compared with those of false positive MS/MS spectra generated by a computer, or instrument noise, using the chi-square test. Here the mechanics of the chi-square test to compare the results in toto from a set of LC-ESI-MS/MS experiments with those of random expectation is detailed. The chi-square analysis of authentic spectra demonstrates unambiguously that the analysis of blood proteins separated by partition chromatography prior to tryptic digestions has a low probability that the cumulative peptide-to-protein distribution is the same as that of random or noise false positive spectra.

It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.

This paper describes research underpinning a course, developed in Australia, on ethics for engineers. The methodology used, that of identifying the principal ethical issues facing the discipline and designing the course around these issues, would be applicable to other disciplines and in other countries. The course was based on the assumption that identifying the major ethical issues in the discipline, and subsequently presenting and analysing them in the classroom, would provide the future professional with knowledge of the ethical problems that they were likely to face on graduation. The student has then to be given the skills and knowledge to combat these concerns, should he/she wish to. These findings feed into several components of the course, such as the development of a code of ethics, the role of a professional society or industry association and the role of ethical theory The sources employed to identify the issues were surveys of the literature and about 30 case studies, in Australia and oversea...

Hydrothermally altered basaltic lava-units in the northern Kerguelen Archipelago contain a wide variety of secondary silicate and carbonate minerals, including zeolites, hydrothermal calcite, dolomite and magnesite, as well as celadonite, orthoclase (adularia) and quartz. Petrography, fluid-inclusion microthermometry, trace-elements geochemistry, Sr isotopes and stable-isotope compositions indicate hydrothermal fluid cells derived from meteoric water interacting with basalts and Rb-rich subvolcanic peralkaline rocks at temperatures ranging from 50 to 200 °C associated with the cooling of the lava pile. The calculated δ 18 O values of meteoric-hydrothermal waters in fossil hydrothermal systems are identical to those in present-day hot springs, suggesting that meteoric recharge was continuous throughout the igneous cooling cycles of the 28–23 Ma older host basalts and the younger 15–5 Ma old peralkaline intrusions. The Kerguelen northern coastline hydrothermal system in the basaltic pile demonstrates that much of the silicate mineralogy and almost all carbonate secondary minerals in altered basalts were derived from meteoric-hydrothermal fluids, rather than products of seawater interaction, or even magmatic-hydrothermal fluids associated with peralkaline intrusions.

Many proteomics studies are limited to the identification of only the most abundant proteins in a sample due to the high sample complexity in most proteomes. We have here addressed this problem by prefractionation of human blood samples using microchromatography. We show that our approach resulted in high-stringency tryptic peptides identified by LC-ESI-MS/MS. Serum proteins were fractionated by batch and stepwise preparative chromatography using various types of chromatography resins (propyl sulfate, quaternary amine, diethylaminoethanol, cibachron blue, phenol Sepharose, carboxy methyl sepharose, hydroxyl apatite, heparin, concanavalin A and protein G) that were compared. The efficacy of sample fractionation was determined by protein assays, electrophoresis, and mass spectrometry. Tryptic peptides were separated by C18 liquid chromatography with electrospray ionization via metal needle at 2 microL/min with ion trap tandem mass spectrometry. The MS/MS spectra were correlated to some 4396 distinct sequences of the human forward RefSeq by X!TANDEM. Of these, 61% have been detected by other algorithms, but 3219 (73%) were never previously reported from blood by X!TANDEM. The use of a simple apparatus for making gravity microchromatography columns that permits the rapid side-by-side fractionation of many serum samples is described. Disposable microcolumns rapidly prepared blood samples for LC ESI-MS/MS that detected both tissue and cell leakage proteins known to exist in the approximately 1 ng/mL range and some circulating receptor sequences. Our results demonstrate that the depletion of albumin or IgG was not necessary prior to LC-MS/MS and that multiple forms of protein chromatography will be useful for complete identification of blood proteins.

PurposeThe aim of this paper is to explore the rationale for teaching sustainability and engineering ethics within a decision‐making paradigm, and critically appraise ways of achieving related learning outcomes.Design/methodology/approachThe paper presents the experience of the School of Civil Engineering at the University of Sydney in teaching environmental sustainability and engineering ethics to third‐year undergraduate students. It discusses the objectives of the course and the merits and drawbacks of incorporating ethics and sustainability in the same teaching framework. In addition, it evaluates ways of incorporating theoretical and applied perspectives on sustainability.FindingsEthics and sustainability overlap but do not coincide; incorporating them in the same engineering course can be effective, provided that points of linkage are clearly recognized in the syllabus, a suitable combination of theory and practical applications is drawn upon and adequate teaching methods, including decision‐making case problems, are used.Research limitations/implicationsWhile environmental sustainability, economic rationality and ethical reasoning can be easily fitted into the syllabus, social sustainability is more difficult to teach because it requires a significant conceptual departure from deep‐seated preconceptions on the part of students and teachers, and does not lend itself easily to conventional classroom activity, such as lectures and weekly workshops. Further research on effective ways of incorporating social sustainability in engineering curricula is therefore needed.Originality/valueThe paper evaluates sustainability issues within the context of civil engineering education.

The cell surface proteome controls numerous cellular functions including cell migration and adhesion, intercellular communication and nutrient uptake. Cell surface proteins are controlled by acute changes in protein abundance at the plasma membrane through regulation of endocytosis and recycling (endomembrane traffic). Many cellular signals regulate endomembrane traffic, including metabolic signaling; however, the extent to which the cell surface proteome is controlled by acute regulation of endomembrane traffic under various conditions remains incompletely understood. AMP-activated protein kinase (AMPK) is a key metabolic sensor that is activated upon reduced cellular energy availability. AMPK activation alters the endomembrane traffic of a few specific proteins, as part of an adaptive response to increase energy intake and reduce energy expenditure. How increased AMPK activity during energy stress may globally regulate the cell surface proteome is not well understood. To study how AMPK may regulate the cell surface proteome, we used cell-impermeable biotinylation to selectively purify cell surface proteins under various conditions. Using ESI-MS/MS, we found that acute (90 min) treatment with the AMPK activator A-769662 elicits broad control of the cell surface abundance of diverse proteins. In particular, A-769662 treatment depleted from the cell surface proteins with functions in cell migration and adhesion. To complement our mass spectrometry results, we used other methods to show that A-769662 treatment results in impaired cell migration. Further, A-769662 treatment reduced the cell surface abundance of β1-integrin, a key cell migration protein, and AMPK gene silencing prevented this effect. While the control of the cell surface abundance of various proteins by A-769662 treatment was broad, it was also selective, as this treatment did not change the cell surface abundance of the transferrin receptor. Hence, the cell surface proteome is subject to acute regulation by treatment with A-769662, at least some of which is mediated by the metabolic sensor AMPK.

Building on previous work that was cadaver based or involved invasive techniques, this study quantifies the kinematics of an approximation of the midtarsal joint with a noninvasive method. Three-dimensional kinematic data describing the motion of the forefoot and heel during transverse plane rotation of the leg were collected from 25 subjects by means of reflective markers and four infrared cameras. The motion between these segments was assumed to be the best possible clinical approximation of the midtarsal joint. The kinematic characteristics of the midtarsal joint were described in terms of the range and direction of motion in each cardinal body plane, the ratio of the range of motion in each plane, and the orientation of the axis of rotation. The characteristics of the midtarsal joint changed during the range of motion; thus, multiple axes of rotation could be calculated and joint characteristics were varied among subjects. The results of this in vivo method were generally consistent with those of cadaver studies and invasive in vivo studies. (J Am Podiatr Med Assoc 92(2): 77-81, 2002)

Structure- and tectonic-related gas migration into Ordovician sandstone reservoirs and its impact on diagenesis history were reconstructed in two fields in the Sbaa Basin, in SW Algeria. This was accomplished by petrographical observations, fluid inclusion microthermometry and stable isotope geochemistry on quartz, dickite and carbonate cements and veins. Two successive phases of quartz cementation (CQ1 and CQ2) occurred in the reservoirs. Two- phase aqueous inclusions show an increase in temperatures and salinities from the first CQ1 diagenetic phase toward CQ2 in both fields. Microthermometric data on gas inclusions in quartz veins reveal the presence of an average of 92 ± 5 mole% of CH4 considering a CH4-CO2 system, which is similar to the present-day gas composition in the reservoirs. The presence of primary methane inclusions in early quartz overgrowths and in quartz and calcite veins suggests that hydrocarbon migration into the reservoir occurred synchronically with early quartz cementation in the sandstones located near the contact with the Silurian gas source rock at 100-140°C during the Late Carboniferous period and the late Hercynian episode fracturing at temperatures between 117 and 185°C, which increased in the NW-direction of the basin. During the fracture filling, three main types of fluids were identified with different salinities and formation temperatures. A supplementary phase of higher fluid temperature (up to 226°C) recorded in late quartz, and calcite veins is related to a Jurassic thermal event. The occurrence of dickite cements close to the Silurian base near the main fault areas in both fields is mainly correlated with the sandstones where the early gas was charged. It implies that dickite precipitation is related to acidic influx. Late carbonate cements and veins (calcite - siderite - ankerite and strontianite) occurred at the same depths resulting from the same groundwater precipitation. The absence o

A Carbonatite workshop reception and registration was arranged at the Brasserie le Glasgow, Place Hotel de Ville, St Etienne, France on Sunday afternoon and evening, 20* February, with video projections of the 1995 eruption of the active carbonatite volcano, Oldoinyo Lengai, East Africa and a display of posters, followed by an evening meal. It gave all participants attending the workshop the ideal opportunity to meet and discuss topics of mutual interest. The reception was organised by Chantal and Jean-Christophe Perrin and sponsored by the Journal of African Earth Sciences.

The Tertiary (22 Ma) carbonatite centre at Buru hill is located towards the eastern end of the Nyanza rift, western Kenya. As revealed by geochemistry and petrology of drill core samples, the Buru centre ranges in composition from surficial lateritized pyroclastic ferrocarbonatite to recrystallized ferruginous calciocarbonatite at depth.Mineralogically the lateritic cover of the Buru carbonatite centre is characterized by goethite, hematite, psilomelane, baryte, fluorite with minor calcite, bastnäsite and significant amounts of monazite. A transitional middle zone consists of ferrocarbonatite grading into ferruginous calciocarbonatite containing siderite, baryte and fluorite, a greater proportion of bastnäsite replacing calcite, but lesser proportions of monazite. The lowermost zone consists of ferruginous calciocarbonatite containing intimate mixtures of siderite and calcite, with parisite and synchysite existing as major replacive components of calcite down to depths of 200 m. Synchysite appears to be the more stable form of lanthanide fluorcarbonate at depths below 150 m.Oxygen isotope measurements on separated calcite concentrates from three of the Buru drill cores reveal significant deviations from primary igneous carbonatite values suggesting isotopic re-equilibration with meteoric water. Accepting that the African plate may have been stationery during the past 30 Ma, it is possible to use a modern sample of water from the Kenya rift to estimate the equilibration temperature at which Buru carbonatite in western Kenya has recrystallized. Temperatures of ∼60 to 90°C suggest that the hot-spring activity encouraged the formation of replacive lanthanide fluorcarbonate in ferruginous calciocarbonatite. Lanthanide enrichment also occurred closer to the surface within the pyroclastic ferrocarbonatite at temperatures of ∼40 to 60°C corresponding to waning stages of hot-spring activity. Further lanthanide enrichment redistribution and oxide formation occurred at surface supergene temperatures of ∼20 to 30°C forming the lateritized top of the carbonatite.The wider implications from these carbonatite studies are the recognition that lanthanide enrichment can be preserved in volcanic-subvolcanic centres, and that lanthanide fluorcarbonates can replace calcite in response to circulating hot-spring waters. From a classification point of view, ferrocarbonatites should be seen as products of meteoric hydrothermal systems unrelated to carbonatite magmatic processes

The central Damaran (Pan-African) Orogenic Belt in western Namibia is dominated by elongated granite-gneiss domes, surrounded by Neoproterozoic Damaran cover as periclinal synclinoria, mainly composed of amphibolite-facies metasedimentary rocks. The domes consist of remnants of pre-Damaran gneissic basement and/or Damaran granitoids. There is a high strain zone along the margin between the granite-gneiss domes and the Damaran cover, interpreted in terms of a late extensional mid-crustal detachment, following oblique north-south collision of the Kalahari and Congo Cratons (ca 550 Ma). The present paper focusses on two granite-gneiss domes (Khan and Ida) in western-central Namibia, where a previously unrecognised generation of early post-collisional Damaran granitoids (ca 530 Ma old), have invaded the pre-Damaran basement and cross-cut the detachment zone. These granitoids are classified as syeno-monzogranites with peraluminous high-K calc-alkaline compositions and I/S-type signatures. Geochemical data suggest that the syeno-monzogranites were derived from a lower crustal source, tentatively ascribed to the pre-Damaran gneissic basement. The granitoids also show evidence for magma contamination through partial assimilation with dark, amphibolitic cover rocks. As a result of this hybridisation of the syeno-monzogranites, granitoids with more dioritic compositions were developed. The syeno-monzogranites were then cross-cut by Damaran pegmatitic leucogranites (ca 510 Ma). Further evidence of episodic post-collisional magmatic activity is provided by late-stage mineralisation, and by a ca 465 Ma (40Ar-39Ar) thermal overprint in the cover rocks. It is proposed that the post-collisional magmatic activity emanated from the endogenic part of a mid-crustal Damaran granitic batholith, whose cupola-like emplacement in dome structures coincided with regional uplift, and subsequent cooling before ca 465 Ma.

Carbon and O isotopic compositions were determined for calcite and siderite from the Buru and Kuge carbonatite centres. Wide ranges in the isotopic compositions of these minerals were observed with values of δ13C and δ18O for the Buru calcites ranging from +1.3 to −3.2% (PDB) and + 11.3 to +26.2% (SMOW), respectively. The δ13C and δ18O ranges for the Kuge calcites are −3.1 to −8.4% (PDB) and +18.1 to + 25.7% (SMOW). The Buru siderites plot in a narrow and restricted range at −3.1 to −4.4% (PDB) and +12.6 to + 16.1% (SMOW). Calcite and siderite from the Buru and Kuge volcanic carbonatite centres do not retain their isotope signatures expected for primary magmatic carbonatites. Most of the variations in CO isotope composition can be attributed to secondary processes involving low-temperature hydrothermal alteration and isotope exchange between carbonatites and meteoric water. Higher δ18O values (+21.9 to +26.2%) with a significant increase in δ13C values (−1.5 to + 1.3%) shown by the most oxidised samples from the Buru carbonatite may indicate the involvement of supergene exchange with atmospheric CO2 at surface temperatures.

Background There is no consensus on which protocols should be used to assess foot and lower limb biomechanics in clinical practice. The reliability of many assessments has been questioned by previous research. The aim of this investigation was to (i) identify (through consensus) what biomechanical examinations are used in clinical practice and (ii) evaluate the inter-assessor reliability of some of these examinations. Methods Part1: Using a modified Delphi technique 12 podiatrists derived consensus on the biomechanical examinations used in clinical practice. Part 2: Eleven podiatrists assessed 6 participants using a subset of the assessment protocol derived in Part 1. Examinations were compared between assessors. Results Clinicians choose to estimate rather than quantitatively measure foot position and motion. Poor inter-assessor reliability was recorded for all examinations. Intra-class correlation coefficient values (ICC) for relaxed calcaneal stance position were less than 0.23 and were less than 0.14 for neutral calcaneal stance position. For the examination of ankle joint dorsiflexion, ICC values suggest moderate reliability (less than 0.61). The results of a random effects ANOVA highlight that participant (up to 5.7°), assessor (up to 5.8°) and random (up to 5.7°) error all contribute to the total error (up to 9.5° for relaxed calcaneal stance position, up to 10.7° for the examination of ankle joint dorsiflexion). Kappa Fleiss values for categorisation of first ray position and mobility were less than 0.05 and for limb length assessment less than 0.02, indicating slight agreement. Conclusion Static biomechanical assessment of the foot, leg and lower limb is an important protocol in clinical practice, but the key examinations used to make inferences about dynamic foot function and to determine orthotic prescription are unreliable.

This unit describes the isolation of activated Fc receptor complexes from RAW 264.7 macrophages using live-cell affinity receptor chromatography (LARC). The Fc receptor complex is activated and captured by IgG-coated microbeads on the surface of live macrophages. After the cells are disrupted, the receptor complexes are isolated by washing and sucrose gradient ultracentrifugation. Soluble proteins associated with the receptor complex are then eluted from the beads using a stepwise series of salt buffers and aqueous acetonitrile. The eluted proteins and the residual insoluble proteins on the beads can then be digested with trypsin and subjected to liquid chromatography, electrospray ionization, and tandem mass spectrometry (LC-ESI-MS/MS). Controls include IgG-coated beads incubated with crude cell lysates or growth medium and beads coated with oxidized LDL or bovine serum albumin. Using this method, proteins present in IgG-FcR complexes can be distinguished from those in control scavenger receptor complexes (oxLDL or BSA). Thus, LARC is capable of detecting specific members of IgG receptor supramolecular complexes. Keywords: receptor complex; live cells; cognate ligand; ligand coated microbeads; live-cell affinity receptor chromatography; LC-ESI-MS/MS; SQL

This chapter explores the question of harm to others, either inflicting it or alleviating it, and whether it is the overriding determinant of ethical conduct. The purpose behind this exploration lies in the benefits that a dominant measure, or perhaps even a single measure, could bring to ethical behaviour in our companies and government agencies. A single measure bypasses the multiplicity of competing and conflicting ethical theories on what constitutes ethical or unethical behaviour. The chapter points out the problems arising from the conflicting moral theories, and the benefits that would arise for ordinary people if we could simplify the process. It then documents those moral philosophers who assign a high ethical priority to avoiding the harming of others, or redressing harm already incurred. One problem is that harm can be defined widely. The possibilities of harm in the future, of offending others, or failing to respect others are examples. We also frequently face a choice between two harms. Numerous examples include business or government decisions which will be of advantage to one party, but of disadvantage to another. Analytical techniques to help make these choices are of limited applicability. Helping others is part of the harm scenario, for we almost invariably help them overcome some possible or actual harm they are facing. But such thinking is normally considered as an altruistic act, not avoiding harm. A more universal approach is a three-part guideline ‘do-no-harm/correct for or prevent harm/do good’.

The proteins secreted by prostate cancer cells (PC3(AR)6) were separated by strong anion exchange chromatography, digested with trypsin and analyzed by unbiased liquid chromatography tandem mass spectrometry with an ion trap. The spectra were matched to peptides within proteins using a goodness of fit algorithm that showed a low false positive rate. The parent ions for MS/MS were randomly and independently sampled from a log-normal population and therefore could be analyzed by ANOVA. Normal distribution analysis confirmed that the parent and fragment ion intensity distributions were sampled over 99.9% of their range that was above the background noise. Arranging the ion intensity data with the identified peptide and protein sequences in structured query language (SQL) permitted the quantification of ion intensity across treatments, proteins and peptides. The intensity of 101,905 fragment ions from 1421 peptide precursors of 583 peptides from 233 proteins separated over 11 sample treatments were computed together in one ANOVA model using the statistical analysis system (SAS) prior to Tukey–Kramer honestly significant difference (HSD) testing. Thus complex mixtures of proteins were identified and quantified with a high degree of confidence using an ion trap without isotopic labels, multivariate analysis or comparing chromatographic retention times.

Sequence analysis of the blood peptides and their qualities will be key to understanding the mechanisms that contribute to error in LC-ESI-MS/MS. Analysis of peptides and their proteins at the level of sequences is much more direct and informative than the comparison of disparate accession numbers. A portable database of all blood peptide and protein sequences with descriptor fields and gene ontology terms might be useful for designing immunological or MRM assays from human blood. The results of twelve studies of human blood peptides and/or proteins identified by LC-MS/MS and correlated against a disparate array of genetic libraries were parsed and matched to proteins from the human ENSEMBL, SwissProt and RefSeq databases by SQL. The reported peptide and protein sequences were organized into an SQL database with full protein sequences and up to five unique peptides in order of prevalence along with the peptide count for each protein. Structured query language or BLAST was used to acquire descriptive information in current databases. Sampling error at the level of peptides is the largest source of disparity between groups. Chi Square analysis of peptide to protein distributions confirmed the significant agreement between groups on identified proteins.

The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography-electrospray ionization-tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.

A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides.

We present a new analysis of the lithospheric architecture of Africa, and its evolution from ca. 3.6 Ga to the present. Upper-lithosphere domains , generated or reworked in different time periods, have been delineated by integrating regional tectonics and geochronology with geophysical data (magnetic, gravity, and seismic). The origins and evolution of lower-lithosphere domains are interpreted from a high-resolution global shear-wave tomographic model, using thermal/compositional modeling and xenolith/xenocryst data from volcanic rocks. These data are integrated to map the distribution of ancient highly depleted subcontinental lithospheric mantle (SCLM), zones of younger or strongly modified SCLM and zones of active mantle upwelling, and to relate these to the evolution of the upper lithosphere domains. The lithospheric architecture of Africa consists of several Archean cratons and smaller cratonic fragments, stitched together and flanked by younger fold belts; the continental assembly as we see it has only existed since lower Paleozoic time. The larger cratons are underlain by geochemically depleted, rigid, and mechanically robust SCLM; these cratonic roots have steep sides, extending in some cases to ≥300-km depth. Beneath smaller cratons (e.g., Kaapvaal) extensive refertilization has reduced the lateral and vertical extent of strongly depleted SCLM. Some cratonic roots extend ≥300 km into the Atlantic Ocean, suggesting that the upper lithosphere may detach during continental breakup, leaving fragments of SCLM scattered in the ocean basin. The cratonic margins, and some intracratonic domain boundaries, have played a major role in the tectonics of Africa. They have repeatedly focused ascending magmas, leading to refertilization and weakening of the SCLM. These boundaries have localized successive cycles of extension, rifting, and renewed accretion; the ongoing development of the East Africa Rift and its branches is only the latest stage in this process. The less depleted SCLM that underlies some accretionary belts may have been generated in Archean time, and repeatedly refertilized by the passage of magmas during younger tectonic events. Our analysis indicates that originally Archean SCLM is far more extensive beneath Africa than previously recognized, and implies that post-Archean SCLM rarely survives the collision/accretion process. Where continental crust and SCLM have remained connected, there is a strong linkage between the tectonic evolution of the crust and the composition and modification of its underlying SCLM.

This paper argues that people from all walks of life are required to make ethical decisions. Assessing the consequences of what we decide provides us with a workable method of reaching an answer – by deciding whether the consequences are good or bad. The decisions we make in the institutions that organise our lives – be it the workplace, our professional lives, in our industry associations or our social or public structures are often complex, difficult to choose between conflicting alternatives, between good or bad consequences. Most people have little or no training in moral decision making. This paper argues that utility is more likely to provide a defendable response. But utilitarianism has been attacked on many fronts, and by renowned philosophers. The paper refutes these attacks, further arguing that the version of utilitarianism set out by John Stuart Mill provides a simpler, preferable way to make an ethical choice than competing theories, particularly deontology and virtue. The principles that he sets out, readily identifiable in his text: Encourage happiness; Do good; Minimise pain; Do no harm; Ensure justice; Respect individuals and their freedoms, will not answer all issues. But they will, with some weighing of utilities, bring greater rationality into our ethical decisions.