Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain

APOBEC3G (A3G) belongs to the AID/APOBEC cytidine deaminase family and is essential for antiviral immunity. It contains two zinc-coordinated cytidine-deaminase (CD) domains. The N-terminal CD1 domain is non-catalytic but has a strong affinity for nucleic acids, whereas the C-terminal CD2 domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains in DNA binding and editing is not fully understood. Here, our studies on rhesus macaque A3G (rA3G) show that the DNA editing function in linear and hairpin loop DNA is greatly enhanced by AA or GA dinucleotide motifs present downstream (in the 3'-direction) but not upstream (in the 5'-direction) of the target-C editing sites. The effective distance between AA/GA and the target-C sites depends on the local DNA secondary structure. We present two co-crystal structures of rA3G bound to ssDNA containing AA and GA, revealing the contribution of the non-catalytic CD1 domain in capturing AA/GA DNA and explaining our biochemical observations. Our structural and biochemical findings elucidate the molecular mechanism underlying the cooperative function between the non-catalytic and the catalytic domains of A3G, which is critical for its antiviral role and its contribution to genome mutations in cancer.

Abstract 3733: Disconnect between APOBEC3 expressions and mutations across cancers

DNA of many tumors is barraged by C-to-T/G mutations within TCW (W:T,A). These mutations are attributed to the aberrant expression and activity of APOBEC3 enzymes. They have been shown to account for many driver mutations in genes such as PIK3CA, ERBB2, and PPP2R1A, however their precise source and also their roles in tumor development, evolution, and patient survival are debated. Currently, quantification of APOBEC3 expression changes in tumor cells is confounded by the ubiquitous expression of these enzymes in infiltrating immune cells. In this study, we used quantitative biology approaches to separate the expression profiles of APOBEC3 enzymes in tumor and tumor microenvironment cells and determine their associations with tumor mutational signatures. For this purpose, we analyzed diverse datasets including TCGA tumor/matched normal RNAseqs, tumor somatic mutations, cell line RNAseqs and mutations, estimates of tumor purities and immune cell compositions, and expression of purified cell populations to precisely determine how APOBEC3 enzymes are dysregulated across tumors and whether their dysregulations are proportional to tumor mutational signatures. Unexpectedly, we found that dysregulation of APOBEC3 enzymes is independent of tumor C-to-T/G mutational burden. Importantly, our data suggest that this disconnect is likely not due to the episodic bursts of APOBEC3-induced mutations in cancer.

Citation Format: Azad Khosh, Hamid Hamidi, Hamzeh Rahimi, Diako Ebrahimi. Disconnect between APOBEC3 expressions and mutations across cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3733.

Abstract P5-13-05: Profiling of APOBEC3 dysregulation in breast cancer

DNA of many breast tumors is barraged by C-to-T/G mutations within TCW (W:T,A). These mutations are attributed to the aberrant expression and activity of APOBEC3 enzymes. They have been shown to account for many driver mutations in genes such as PIK3CA, ERBB2, and PPP2R1A, however their precise source and also their roles in tumor development, evolution, and patient survival are debated. Currently, quantification of APOBEC3 expression changes in tumor cells is confounded by the ubiquitous expression of these enzymes in immune infiltrating cells. In this study, we used a novel quantitative biology approach to determine the expression profiles of APOBEC3 enzymes in breast tumor and tumor microenvironment cells from >1,000 patients. We combined diverse datasets including tumor/matched normal RNAseqs, tumor somatic mutations, cell line RNAseqs and mutations, estimates of tumor purities and immune cell compositions, and expression of purified cell populations to show that in breast cancer there is only a single APOBEC3 dysregulation process. This process is subtype-independent and is represented by APOBEC3B upregulation and and extreme APOBEC3C downregulation. Compared to all other tumor types, breast tumors are affected the most by this process.

Citation Format: Hamid Hamidi, Azad Khosh, Hamzeh Rahimi, Diako Ebrahimi. Profiling of APOBEC3 dysregulation in breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-13-05.

Human APOBEC3 Variations and Viral Infection

Human APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) enzymes are capable of inhibiting a wide range of endogenous and exogenous viruses using deaminase and deaminase-independent mechanisms. These enzymes are essential components of our innate immune system, as evidenced by (a) their strong positive selection and expansion in primates, (b) the evolution of viral counter-defense mechanisms, such as proteasomal degradation mediated by HIV Vif, and (c) hypermutation and inactivation of a large number of integrated HIV-1 proviruses. Numerous APOBEC3 single nucleotide polymorphisms, haplotypes, and splice variants have been identified in humans. Several of these variants have been reported to be associated with differential antiviral immunity. This review focuses on the current knowledge in the field about these natural variations and their roles in infectious diseases.

A systematic review of long non-coding RNAs with a potential role in breast cancer

The human transcriptome contains many non-coding RNAs (ncRNAs), which play important roles in gene regulation. Long noncoding RNAs (lncRNAs) are an important class of ncRNAs with lengths between 200 and 200,000 bases. Unlike mRNA, lncRNA lacks protein-coding features, specifically, open-reading frames, and start and stop codons. LncRNAs have been reported to play a role in the pathogenesis and progression of many cancers, including breast cancer (BC), acting as tumor suppressors or oncogenes. In this review, we systematically mined the literature to identify 65 BC-related lncRNAs. We then perform an integrative bioinformatics analysis to identify 14 lncRNAs with a potential regulatory role in BC. The biological function of these 14 lncRNAs, their regulatory mechanisms, and roles in the initiation and progression of BC are discussed in this review. Additionally, we elaborate on the current and future applications of lncRNAs as diagnostic and/or therapeutic biomarkers in BC.

Epstein-Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity

The APOBEC family of single-stranded (ss)DNA cytosine deaminases provides innate immunity against virus and transposon replication^1–4. A well-studied mechanism is APOBEC3G restriction of HIV-1, which is counteracted by a virus-encoded degradation mechanism^1–4. Accordingly, most work has focused on retroviruses with obligate ssDNA replication intermediates and it is unclear whether large double-stranded (ds)DNA viruses may be similarly susceptible to restriction. Here, we show that the large dsDNA herpesvirus Epstein-Barr virus (EBV), which is the causative agent of infectious mononucleosis and multiple cancers⁵, utilizes a two-pronged approach to counteract restriction by APOBEC3B. The large subunit of the EBV ribonucleotide reductase, BORF2^6,7, bound to APOBEC3B in proteomics studies and immunoprecipitation experiments. Mutagenesis mapped the interaction to the APOBEC3B catalytic domain, and biochemical studies demonstrated that BORF2 stoichiometrically inhibits APOBEC3B DNA cytosine deaminase activity. BORF2 also caused a dramatic relocalization of nuclear APOBEC3B to perinuclear bodies. Upon lytic reactivation, BORF2-null viruses were susceptible to APOBEC3B-mediated deamination as evidenced by lower viral titers, lower infectivity, and hypermutation. The Kaposi’s sarcoma herpesvirus (KSHV) homolog, ORF61, also bound APOBEC3B and mediated relocalization. These data support a model in which the genomic integrity of human γ-herpesviruses is maintained by active neutralization of the antiviral enzyme APOBEC3B.

Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease

Human APOBEC3H (A3H) is a single-stranded DNA cytosine deaminase that inhibits HIV-1. Seven haplotypes (I–VII) and four splice variants (SV154/182/183/200) with differing antiviral activities and geographic distributions have been described, but the genetic and mechanistic basis for variant expression and function remains unclear. Using a combined bioinformatic/experimental analysis, we find that SV200 expression is specific to haplotype II, which is primarily found in sub-Saharan Africa. The underlying genetic mechanism for differential mRNA splicing is an ancient intronic deletion [del(ctc)] within A3H haplotype II sequence. We show that SV200 is at least fourfold more HIV-1 restrictive than other A3H splice variants. To counteract this elevated antiviral activity, HIV-1 protease cleaves SV200 into a shorter, less restrictive isoform. Our analyses indicate that, in addition to Vif-mediated degradation, HIV-1 may use protease as a  counter-defense mechanism against A3H in >80% of sub-Saharan African populations.

Human APOBEC3H has several haplotypes and splice variants with distinct anti-HIV-1 activities, but the genetics underlying the expression of these variants are unclear. Here, the authors identify an intronic deletion in A3H haplotype II resulting in production of the most active splice variant, which is counteracted by HIV-1 protease.

Mutation Signatures Including APOBEC in Cancer Cell Lines

Background:

Multiple endogenous and exogenous sources of DNA damage contribute to the overall mutation burden in cancer, with distinct and overlapping combinations contributing to each cancer type. Many mutation sources result in characteristic mutation signatures, which can be deduced from tumor genomic DNA sequences. Examples include spontaneous hydrolytic deamination of methyl-cytosine bases in CG motifs (AGEING signature) and C-to-T and C-to-G mutations in 5'-TC(A/T) motifs (APOBEC signature).

Methods:

The deconstructSigs R package was used to analyze single-base substitution mutation signatures in more than 1000 cancer cell lines. Two additional approaches were used to analyze the APOBEC mutation signature.

Results:

Most cell lines show evidence for multiple mutation signatures. For instance, the AGEING signature, which is the largest source of mutation in most primary tumors, predominates in the majority of cancer cell lines. The APOBEC mutation signature is enriched in cancer cell lines from breast, lung, head/neck, bladder, and cervical cancers, where this signature also comprises a large fraction of all mutations.

Conclusions:

The single-base substitution mutation signatures of cancer cell lines often reflect those of the original tumors from which they are derived. Cancer cell lines with enrichments for distinct mutation signatures such as APOBEC have the potential to become model systems for fundamental research on the underlying mechanisms and for advancing clinical strategies to exploit these processes.

HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation

APOBEC3 (A3) family proteins are DNA cytosine deaminases recognized for contributing to HIV-1 restriction and mutation. Prior studies have demonstrated that A3D, A3F, and A3G enzymes elicit a robust anti-HIV-1 effect in cell cultures and in humanized mouse models. Human A3H is polymorphic and can be categorized into three phenotypes: stable, intermediate, and unstable. However, the anti-viral effect of endogenous A3H in vivo has yet to be examined. Here we utilize a hematopoietic stem cell-transplanted humanized mouse model and demonstrate that stable A3H robustly affects HIV-1 fitness in vivo. In contrast, the selection pressure mediated by intermediate A3H is relaxed. Intriguingly, viral genomic RNA sequencing reveled that HIV-1 frequently adapts to better counteract stable A3H during replication in humanized mice. Molecular phylogenetic analyses and mathematical modeling suggest that stable A3H may be a critical factor in human-to-human viral transmission. Taken together, this study provides evidence that stable variants of A3H impose selective pressure on HIV-1.

Source of CpG Depletion in the HIV-1 Genome

The dinucleotide CpG is highly underrepresented in the genome of human immunodeficiency virus type 1 (HIV-1). To identify the source of CpG depletion in the HIV-1 genome, we investigated two biological mechanisms: (1) CpG methylation-induced transcriptional silencing and (2) CpG recognition by Toll-like receptors (TLRs). We hypothesized that HIV-1 has been under selective evolutionary pressure by these mechanisms leading to the reduction of CpG in its genome. A CpG depleted genome would enable HIV-1 to avoid methylation-induced transcriptional silencing and/or to avoid recognition by TLRs that identify foreign CpG sequences. We investigated these two hypotheses by determining the sequence context dependency of CpG depletion and comparing it with that of CpG methylation and TLR recognition. We found that in both human and HIV-1 genomes the CpG motifs flanked by T/A were depleted most and those flanked by C/G were depleted least. Similarly, our analyses of human methylome data revealed that the CpG motifs flanked by T/A were methylated most and those flanked by C/G were methylated least. Given that a similar CpG depletion pattern was observed for the human genome within which CpGs are not likely to be recognized by TLRs, we argue that the main source of CpG depletion in HIV-1 is likely host-induced methylation. Analyses of CpG motifs in over 100 viruses revealed that this unique CpG representation pattern is specific to the human and simian immunodeficiency viruses.

The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis

Cytosine mutations within TCA/T motifs are common in cancer. A likely cause is the DNA cytosine deaminase APOBEC3B (A3B). However, A3B-null breast tumours still have this mutational bias. Here we show that APOBEC3H haplotype I (A3H-I) provides a likely solution to this paradox. A3B-null tumours with this mutational bias have at least one copy of A3H-I despite little genetic linkage between these genes. Although deemed inactive previously, A3H-I has robust activity in biochemical and cellular assays, similar to A3H-II after compensation for lower protein expression levels. Gly105 in A3H-I (versus Arg105 in A3H-II) results in lower protein expression levels and increased nuclear localization, providing a mechanism for accessing genomic DNA. A3H-I also associates with clonal TCA/T-biased mutations in lung adenocarcinoma suggesting this enzyme makes broader contributions to cancer mutagenesis. These studies combine to suggest that A3B and A3H-I, together, explain the bulk of ‘APOBEC signature' mutations in cancer.

The APOBEC family of enzymes are cytidine deaminases with APOBEC3A and APOBEC3B thought to contribute to DNA damage signatures detected in cancer genomes. Here, the authors demonstrate an unappreciated role for APOBEC3H haplotype I in the generation of DNA damage in breast cancer.

A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods

The human genome encodes for a family of editing enzymes known as APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like3). They induce context dependent G-to-A changes, referred to as "hypermutation", in the genome of viruses such as HIV, SIV, HBV and endogenous retroviruses. Hypermutation is characterized by aligning affected sequences to a reference sequence. We show that indels (insertions/deletions) in the sequences lead to an incorrect assignment of APOBEC3 targeted and non-target sites. This can result in an incorrect identification of hypermutated sequences and erroneous biological inferences made based on hypermutation analysis.

Gas chromatography with parallel hard and soft ionization mass spectrometry

RATIONALE

Mass spectrometric identification of compounds in chromatography can be obtained from molecular masses from soft ionization mass spectrometry techniques such as field ionization (FI) and fragmentation patterns from hard ionization techniques such as electron ionization (EI). Simultaneous detection by EI and FI mass spectrometry allows alignment of the different information from each method.

METHODS

We report the construction and characteristics of a combined instrument consisting of a gas chromatograph and two parallel mass spectrometry ionization sources, EI and FI. When considering both ion yield and signal-to-noise it was postulated that good-quality EI and FI mass spectra could be obtained simultaneously using a post-column splitter with a split fraction of 1:10 for EI/FI. This has been realised and we report its application for the analysis of several complex mixtures.

RESULTS

The differences between the full width at half maximum (FWHM) of the EI and FI chromatograms were statistically insignificant, and the retention times of the chromatograms were highly correlated (r(2) =0.9999) with no detectable bias. The applicability and significance of this combined instrument and the attendant methodology are illustrated by the analysis of standard samples of 13 compounds with diverse structures, and the analysis of mixtures of fatty acids, fish oil, hydrocarbons and yeast metabolites.

CONCLUSIONS

This combined dual-source instrument saves time and resources, and more importantly generates equivalent chromatograms aligned in time, in EI and FI (i.e. peaks with similar shapes and identical positions). The identical FWHMs and retention times of the EI and FI chromatograms in this combined instrument enable the accurate assignment of fragment ions from EI to their corresponding molecular ions in FI.

Footprint of APOBEC3 on the genome of human retroelements

Almost half of the human genome is composed of transposable elements. The genomic structures and life cycles of some of these elements suggest they are a result of waves of retroviral infection and transposition over millions of years. The reduction of retrotransposition activity in primates compared to that in nonprimates, such as mice, has been attributed to the positive selection of several antiretroviral factors, such as apolipoprotein B mRNA editing enzymes. Among these, APOBEC3G is known to mutate G to A within the context of GG in the genome of endogenous as well as several exogenous retroelements (the underlining marks the G that is mutated). On the other hand, APOBEC3F and to a lesser extent other APOBEC3 members induce G-to-A changes within the nucleotide GA. It is known that these enzymes can induce deleterious mutations in the genome of retroviral sequences, but the evolution and/or inactivation of retroelements as a result of mutation by these proteins is not clear. Here, we analyze the mutation signatures of these proteins on large populations of long interspersed nuclear element (LINE), short interspersed nuclear element (SINE), and endogenous retrovirus (ERV) families in the human genome to infer possible evolutionary pressure and/or hypermutation events. Sequence context dependency of mutation by APOBEC3 allows investigation of the changes in the genome of retroelements by inspecting the depletion of G and enrichment of A within the APOBEC3 target and product motifs, respectively. Analysis of approximately 22,000 LINE-1 (L1), 24,000 SINE Alu, and 3,000 ERV sequences showed a footprint of GG→AG mutation by APOBEC3G and GA→AA mutation by other members of the APOBEC3 family (e.g., APOBEC3F) on the genome of ERV-K and ERV-1 elements but not on those of ERV-L, LINE, or SINE.

Measurement and modeling of acid dissociation constants of tri-peptides containing Glu, Gly, and His using potentiometry and generalized multiplicative analysis of variance

We report pK(a) values with measurement uncertainties for all labile protons of the 27 tri-peptides prepared from the amino acids glutamic acid (E), glycine (G) and histidine (H). Each tri-peptide (GGG, GGE, GGH, …, HHH) was subjected to alkali titration and pK(a) values were calculated from triplicate potentiometric titrations data using HyperQuad 2008 software. A generalized multiplicative analysis of variance (GEMANOVA) of pK(a) values for the most acidic proton gave the optimum model having two terms, an interaction between the end amino acids plus an isolated main effect of the central amino acid.

APOBEC3G and APOBEC3F rarely co-mutate the same HIV genome

Background

The human immune proteins APOBEC3G and APOBEC3F (hA3G and hA3F) induce destructive G-to-A changes in the HIV genome, referred to as ‘hypermutation’. These two proteins co-express in human cells, co-localize to mRNA processing bodies and might co-package into HIV virions. Therefore they are expected to also co-mutate the HIV genome. Here we investigate the mutational footprints of hA3G and hA3F in a large population of full genome HIV-1 sequences from naturally infected patients to uniquely identify sequences hypermutated by either or both of these proteins. We develop a method of identification based on the representation of hA3G and hA3F target and product motifs that does not require an alignment to a parental/consensus sequence.

Results

Out of nearly 100 hypermutated HIV-1 sequences only one sequence from the HIV-1 outlier group showed clear signatures of co-mutation by both proteins. The remaining sequences were affected by either hA3G or hA3F.

Conclusion

Using a novel method of identification of HIV sequences hypermutated by the hA3G and hA3F enzymes, we report a very low rate of co-mutation of full-length HIV sequences, and discuss the potential mechanisms underlying this.

Bio-activity of natural polymers from the genus Pistacia: a validated model for their antimicrobial action

The polymers from mastic gum of Pistacia lentiscose and subspecies of Pistacia atlantica, (sp. kurdica, mutica and cabolica) have been isolated and characterised by gel permeation chromatography (GPC) and 13C NMR spectroscopy as cis-1,4-poly-?-myrcenes. They were screened against Helicobacter pylori and other Gram-negative and Gram-positive bacteria to evaluate their antimicrobial action. In order to further test their hypothesised mode of action, two polymer types were synthesized: one from myrcene, and four from polyvinyl alcohols of different molecular weights, derivatised with p-hydroxybenzoate. The anti-microbial activity of these polymers, evaluated through their 'kill' kinetics, was found to be related to their functional groups, their molecular weight and their solubility.

APOBEC3 has not left an evolutionary footprint on the HIV-1 genome

It is known that the human immune proteins APOBEC3G and -F (hA3G/F) can inhibit Vif-deficient HIV by G-to-A mutation; however, the roles of these enzymes in the evolution of HIV are debated. We argue that if evolutionary pressure from hA3G/F exists there should be evidence of their imprint on the HIV genome in the form of (i) underrepresentation of hA3G/F target motifs (e.g., TGGG [targeted position is underlined]) and overrepresentation of product motifs (e.g., TAGG) and/or (ii) an increase in the ratio of nonsynonymous to synonymous (NS/S) G-to-A changes among hA3G/F target motifs and a decrease of NS/S A-to-G changes among hA3G/F product motifs. To test the first hypothesis, we studied the representation of hA3G/F target and product motifs in 1,932 complete HIV-1 genomes using Markov models. We found that the highly targeted motifs are not underrepresented and their product motifs are not overrepresented. To test the second hypothesis, we determined the NS/S G↔A changes among the hA3G/F target and product motifs in 1,540 complete sets of nine HIV-1 genes. The NS/S changes did not show an increasing/decreasing trend within the target/product motifs, but the NS/S changes within the motif AG was exceptionally low. We observed the same pattern by analyzing 740 human genes. Given that hA3G/F do not act on the human genome, this suggests a small NS/S change within AG has arisen by other mechanisms. We therefore find no evidence of an evolutionary footprint of hA3G/F. We postulate several mechanisms to explain why the HIV-1 genome does not contain the hA3G/F footprint.

Mass and relative elution time profiling: two-dimensional analysis of sphingolipids in Alzheimer's disease brains

Current lipidomic profiling methods rely mainly on MS to identify unknown lipids within a complex sample. We describe a new approach, involving LC×MS/MS (liquid chromatography×tandem MS) analysis of sphingolipids based on both mass and hydrophobicity, and use this method to characterize the SM (sphingomyelin), ceramide and GalCer (galactosylceramide) content of hippocampus from AD (Alzheimer's disease) and control subjects. Using a mathematical relationship we exclude the influence of sphingolipid mass on retention time, and generate two-dimensional plots that facilitate accurate visualization and characterization of the different ceramide moieties within a given sphingolipid class, because related molecules align horizontally or vertically on the plots. Major brain GalCer species that differ in mass by only 0.04 Da were easily differentiated on the basis of their hydrophobicity. The importance of our method's capacity to define all of the major GalCer species in the brain samples is illustrated by the novel observation that the proportion of GalCer with hydroxylated fatty acids increased approximately 2-fold in the hippocampus of AD patients, compared with age- and gender-matched controls. This suggests activation of fatty acid hydroxylase in AD. Our method greatly improves the clarity of data obtained in a lipid profiling experiment and can be expanded to other lipid classes.

A probabilistic approach to heroin signatures

The probability density functions of amount ratios of compounds (total codeine/total morphine, 6-monoacetylemorphine/total morphine, papaverine/total morphine, and noscapine/total morphine) from the analysis of seized heroin, originating from known world regions (South East Asia, South West Asia, South America, Mexico) allows calculation of likelihood ratios for 'unknown' samples. Application of Bayes Theorem with a suitable prior probability, for example the frequency of a particular region in the database, leads to the probability that a particular profile comes from a given target region. Data from 2549 seizures of heroin at Australia's border illustrates the method, and results are compared with simple HS1 ratio approaches for assigning geographical origin. The method can be implemented in a spreadsheet and gives more refined intelligence of the origins of seized drugs than simple ranges.

Discrimination among geometrical isomers of alpha-linolenic acid methyl ester using low energy electron ionization mass spectrometry

There is a consensus that electron impact ionization mass spectrometry is not capable of discriminating among geometrical isomers of unsaturated fatty acid methyl esters (and in general olefinic compounds). In this paper, we report the identification of all eight geometrical isomers of alpha-linolenic acid, one of the few essential omega-3 fatty acids that has attracted great attention, using low-energy electron ionization mass spectrometry. Three electron energies 70, 50, and 30 eV were studied and the mass spectrum of each isomer was obtained from the analysis of different concentrations of a standard mixture of alpha-linolenic acid methyl ester geometrical isomers to ensure the robustness of the method. Principal component analysis was employed to model the complex variation of m/z intensities across the isomers. Only using the data of 30 eV energy was complete differentiation among geometrical isomers observed. The unique cleavage pattern of the alpha-linolenic acid methyl ester isomers leading to a benzenium ion structure is discussed and general fragmentation rules are derived using the mass spectra of over 300 compounds with different kinds and levels of unsaturation. Application of the proposed method is not limited to alpha-linolenic acid. It can potentially be used to identify the geometrical isomers of any compounds with an olefinic chain.

Compatibility of electron ionization and soft ionization methods in gas chromatography/orthogonal time-of-flight mass spectrometry

Orthogonal acceleration time-of-flight (oa-TOF) mass spectrometry (MS) was coupled to gas chromatography (GC) to measure ion yields (ratio of ion counts to number of neutrals entering the ion source) and signal-to-noise (S/N) in the electron ionization (EI) mode (hard ionization) as well as in the soft ionization modes of chemical ionization (CI), electron capture negative ion chemical ionization (NICI) and field ionization (FI). Mass accuracies of the EI and FI modes were also investigated. Sixteen structurally diverse volatile organic compounds were chosen for this study. The oa-TOF mass analyzer is highly suited for FI MS and provided an opportunity to compare the sensitivity of this ionization method to the more conventional ionization methods. Compared to the widely used quadrupole mass filter, the oa-TOF platform offers significantly greater mass accuracy and therefore the possibility of determining the empirical formula of analytes. The findings of this study showed that, for the instrument used, EI generated the most ions with the exception of compounds able to form negative ions readily. Lower ion yields in the FI mode were generally observed but the chromatograms displayed greater S/N and in many cases gave spectra dominated by a molecular ion. Ion counts in CI are limited by the very small apertures required to maintain sufficiently high pressures in the ionization chamber. Mass accuracy for molecular and fragment ions was attainable at close to manufacturer's specifications, thus providing useful information on molecular ions and neutral losses. The data presented also suggests a potentially useful instrumental combination would result if EI and FI spectra could be collected simultaneously or in alternate scans during GC/MS.

Classification of weathered petroleum oils by multi-way analysis of gas chromatography–mass spectrometry data using PARAFAC2 parallel factor analysis

The application of multi-way parallel factor analysis (PARAFAC2) is described for the classification of different kinds of petroleum oils using GC-MS. Oils were subjected to controlled weathering for 2, 7 and 15 days and PARAFAC2 was applied to the three-way GC-MS data set (MSxGCxsample). The classification patterns visualized in scores plots and it was shown that fitting multi-way PARAFAC2 model to the natural three-way structure of GC-MS data can lead to the successful classification of weathered oils. The shift of chromatographic peaks was tackled using the specific structure of the PARAFAC2 model. A new preprocessing of spectra followed by a novel use of analysis of variance (ANOVA)-least significant difference (LSD) variable selection method were proposed as a supervised pattern recognition tool to improve classification among the highly similar diesel oils. This lead to the identification of diagnostic compounds in the studied diesel oil samples.

Application of N-PLS calibration to the simultaneous determination of Cu2+, Cd2+ and Pb2+ using peptide modified electrochemical sensors

The simultaneous determination of Cu(2+), Cd(2+) and Pb(2+) is demonstrated at four modified gold electrodes using N-PLS calibration. Three of the electrodes were modified with the peptides Gly-Gly-His, gamma-Glu-Cys Gly and human angiotensin I which were covalently attached to thioctic acid self-assembled monolayers and the fourth electrode was modified with thioctic acid only. Voltammetry at the modified electrodes in the presence of the three metal ions revealed one peak due to the reduction of copper and another due to the overlapping peaks of cadmium and lead which made quantification using conventional methods difficult. N-PLS was used to calibrate and predict trace concentrations (100 nM to 10 microM) of mixtures of Cu(2+), Cd(2+) and Pb(2+).

Peripheral vision lipreading aid

Lipreading provides a limited amount of information about speech signals to profoundly deaf people. Visual displays using peripheral vision as an alternative sensory modality can provide supplementary speech information. The utility of a cosmetically acceptable peripheral vision display was explored. A pair of eyeglasses with a commercially available two-dimensional red LED array (5 x 7), and its associated electronics was developed. The display is visible only to the wearer, and is located in the temporal field and the horizontal meridian of the right eye. Selected speech features were encoded as visual patterns for presentation to the lipreader. These features of the speech signal (the fundamental frequency of the speech, high-frequency energy, and low-passed speech signal or total energy envelope) were presented with the objective of providing information about voicing and plosion/frication. Experiments demonstrate the capability of the peripheral display in conveying speech information. Presenting vowel-consonant-vowel syllables, the performance was in excess of 76% with aided lipreading as compared to 41% by lipreading only.

Measurement of performance of a peripheral vision lipreading aid

Lipreading, as the most important tool of speech understanding for profoundly deaf people, carries only a limited amount of information about speech. We explored the usefulness of a peripheral vision display in providing profoundly deaf people with supplementary information to lipreading. A pair of eye-glasses with a commercially available two-dimensional red LED array, and associated electronics was developed. The display is located on the rim of the eyeglasses in the temporal field and the horizontal meridian of the right eye. Selected speech features were encoded as visual patterns for presentation to the lipreader. These features (the fundamental frequency of the speech, high-frequency energy, and low-passed speech signal or total energy envelope) provide information about voicing and plosion/friction in order to supplement lipreading. Experiments with 3 normal and 5 deaf subjects demonstrated the capability of the aid to convey speech information for video taped vowel-consonant-vowel (VCV) nonsense syllables. Average identification of 12 VCV syllables using the aid was about 76%, as compared with 40% without the aid.