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Biomedical subjects

William Martin

Publications and source records attributed to William Martin.

At least 55 records · Page 3Linked to original sources

Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.

For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs to lineage separations that might have occurred approximately 4 billion years ago. Because the appearance of accuracy has an irresistible allure, non-specialists frequently treat these estimates as factual. In this article, we show that all of these divergence-time estimates were generated through improper methodology on the basis of a single calibration point that has been unjustly denuded of error. The illusion of precision was achieved mainly through the conversion of statistical estimates (which by definition possess standard errors, ranges and confidence intervals) into errorless numbers. By employing such techniques successively, the time estimates of even the most ancient divergence events were made to look deceptively precise. For example, on the basis of just 15 genes, the arthropod-nematode divergence event was 'calculated' to have occurred 1167+/-83 million years ago (i.e. within a 95% confidence interval of approximately 350 million years). Were calibration and derivation uncertainties taken into proper consideration, the 95% confidence interval would have turned out to be at least 40 times larger ( approximately 14.2 billion years).

Animals↗

Engineering immunogenic consensus T helper epitopes for a cross-clade HIV vaccine.

Developing a vaccine that will stimulate broad HIV-specific T cell responses is difficult because of the variability in HIV T cell epitope sequences, which is in turn due to the high mutation rate and consequent strain diversity of HIV-1. We used a new Class II version of the EpiMatrix T cell epitope-mapping tool and Conservatrix to select highly conserved and promiscuous Class II HLA-restricted T cell epitopes from a database of 18,313 HIV-1 env sequences. Criteria for selection were: (1) number of HIV-1 strains represented as measured by Conservatrix; (2) EpiMatrix score; and (3) promiscuity (number of unique MHC motifs contained in the peptide). Using another vaccine design tool called the EpiAssembler, a new set of overlapping, conserved and immunogenic HIV-1 peptides were engineered creating extended "immunogenic consensus" sequences. Each overlapping 9-mer of the 20-23 amino acid long immunogenic consensus peptides was conserved in a large number (range 893-2254) of individual HIV-1 strains, although the novel peptides were not representative of any single strain of HIV. We synthesized nine representative peptides. T helper cell responses to the peptides were evaluated by ELISpot (gamma-interferon) assay, using peripheral blood monocytes (PBMC) obtained from 34 healthy long term non-progressor (LT) or moderate-progressor (MP) donors (median years infected = 8.88, median CD4 T cells = 595, median VL = 1044). Nine peptides were tested, of which eight were confirmed in ELISpot assays using PBMC from the LT/MP subjects. These epitopes were ranked by Conservation and EpiMatrix score 1, 2, 3, 5, 7, 11, and 14 out of the set of 9 original peptides. Five of these peptides were selected for inclusion in an epitope-driven cross-clade HIV-1 vaccine (the GAIA vaccine). These data confirm the utility of bioinformatics tools to select and construct novel "immunogenic consensus sequence" T cell epitopes for a globally relevant vaccine against HIV.

AIDS Vaccines↗

Chloroplast phosphoglycerate kinase from Euglena gracilis: endosymbiotic gene replacement going against the tide.

Two chloroplast phosphoglycerate kinase isoforms from the photosynthetic flagellate Euglena gracilis were purified to homogeneity, partially sequenced, and subsequently cDNAs encoding phosphoglycerate kinase isoenzymes from both the chloroplast and cytosol of E. gracilis were cloned and sequenced. Chloroplast phosphoglycerate kinase, a monomeric enzyme, was encoded as a polyprotein precursor of at least four mature subunits that were separated by conserved tetrapeptides. In a Neighbor-Net analysis of sequence similarity with homologues from numerous prokaryotes and eukaryotes, cytosolic phosphoglycerate kinase of E. gracilis showed the highest similarity to cytosolic and glycosomal homologues from the Kinetoplastida. The chloroplast isoenzyme of E. gracilis did not show a close relationship to sequences from other photosynthetic organisms but was most closely related to cytosolic homologues from animals and fungi.

Amino Acid Sequence↗

Legal and public policy responses of states to bioterrorism.

In late 2001, during the aftermath of the anthrax letter attacks, model legislation was proposed to relevant state agencies to update their states' public health laws to meet the threat of bioterrorism. This legislation was the Model State Emergency Health Powers Act. A concern underlying this and related efforts to address future bioterrorism threats was the perceived inadequacy of state laws to respond effectively when such threats occur. We evaluated how 4 states--Utah, Maine, South Dakota, and Indiana--addressed this concern in the context of the model legislation. The conclusion is that the model legislation generally served as an important catalyst for state action in the field of bioterrorism preparation.

Anthrax↗

Optimizing esthetics for implant restorations in the anterior maxilla: anatomic and surgical considerations.

The placement of dental implants in the anterior maxilla is a challenge for clinicians because of patients' exacting esthetic demands and difficult pre-existing anatomy. This article presents anatomic and surgical considerations for these demanding indications for implant therapy. First, potential causes of esthetic implant failures are reviewed, discussing anatomic factors such as horizontal or vertical bone deficiencies and iatrogenic factors such as improper implant selection or the malpositioning of dental implants for an esthetic implant restoration. Furthermore, aspects of preoperative analysis are described in various clinical situations, followed by recommendations for the surgical procedures in single-tooth gaps and in extended edentulous spaces with multiple missing teeth. An ideal implant position in all 3 dimensions is required. These mesiodistal, apicocoronal, and orofacial dimensions are well described, defining "comfort" and "danger" zones for proper implant position in the anterior maxilla. During surgery, the emphasis is on proper implant selection to avoid oversized implants, careful and low-trauma soft tissue handling, and implant placement in a proper position using either a periodontal probe or a prefabricated surgical guide. If missing, the facial bone wall is augmented using a proper surgical technique, such as guided bone regeneration with barrier membranes and appropriate bone grafts and/or bone substitutes. Finally, precise wound closure using a submerged or a semi-submerged healing modality is recommended. Following a healing period of between 6 and 12 weeks, a reopening procedure is recommended with a punch technique to initiate the restorative phase of therapy.

Alveolar Bone Loss↗

Preoperative lymphoscintigraphy and internal mammary sentinel lymph node biopsy do not enhance the accuracy of lymphatic mapping for breast cancer.

Lymphoscintigraphy (LS) may identify sentinel lymph nodes (SLNs) outside the axilla. Biopsy of these nodes could improve the accuracy of lymphatic mapping (LM) for breast cancer (BC) if a significant number of tumor-positive extra-axillary sentinel nodes are identified. To address this, we evaluated the impact of the use of preoperative LS and biopsy of axillary and internal mammary SLNs in women with BC. From October 1997 to July 2003, 175 women with breast cancer received technetium sulfur colloid, and images were obtained. Isosulfan blue dye was injected intraoperatively, and LM of the axillary and internal mammary lymph node basins was performed with a hand-held gamma probe. The anatomic location and histologic status of all SLNs identified with LS and LM was recorded, and the impact of the findings on LS and internal mammary LM were evaluated. LS showed SLN in 127/175 (73%) women and "hot spots" were found with the gamma probe in 142/175 (81%). At least one SLN was identified by LM in 168/175 (96%) patients, and 48/168 (29%) had metastases. One hundred sixty-two of 168 (96%) patients had SLN exclusively in the axilla. Only 10 of 175 (6%) women had internal mammary (IM) SLNs seen on LS. LM identified IM sentinel nodes in 6 of these 10 patients, but none were involved with tumor. Preoperative lymphoscintigraphy and biopsy of internal mammary sentinel nodes do not enhance the accuracy of lymphatic mapping for breast cancer. Omitting lymphoscintigraphy reduces the complexity and cost of lymphatic mapping without compromising the identification of tumor-positive sentinel nodes.

Adult↗

A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales.

Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a monophyletic order sister to the lineage carrying the Poales and possess economically important plants such as asparagus, garlic, and onion. To assess the genomic differences between the Asparagales and Poales, we generated 11,008 unique ESTs from a normalized cDNA library of onion. Sequence analyses of these ESTs revealed microsatellite markers, single nucleotide polymorphisms, and homologs of transposable elements. Mean nucleotide similarity between rice and the Asparagales was 78% across coding regions. Expressed sequence and genomic comparisons revealed strong differences between the Asparagales and Poales for codon usage and mean GC content, GC distribution, and relative GC content at each codon position, indicating that genomic characteristics are not uniform across the monocots. The Asparagales were more similar to eudicots than to the Poales for these genomic characteristics.

Cytosine↗

Carvedilol alone or in combination with digoxin for the management of atrial fibrillation in patients with heart failure?

OBJECTIVES: This study examined the relative merits of digoxin, carvedilol, and their combination for the management of patients with atrial fibrillation (AF) and heart failure (HF). BACKGROUND: In patients with AF and HF, both digoxin and beta-blockers reduce the ventricular rate, and both may improve symptoms, but only beta-blockers have been shown to improve prognosis. If combined therapy is not superior to beta-blockers alone, treatment of patients with HF and AF could be simplified by stopping digoxin. METHODS: We enrolled 47 patients (29 males; mean age 68 years) with persistent AF and HF (mean left ventricular ejection fraction [LVEF] 24%) in a randomized, double-blinded, placebo-controlled study. In the first phase of the study, digoxin was compared with the combination of digoxin and carvedilol (four months). In the second phase, digoxin was withdrawn in a double-blinded manner in the carvedilol-treated arm, thus allowing a comparison between digoxin and carvedilol (six months). Investigations were undertaken at baseline and at the end of each phase. RESULTS: Compared with digoxin alone, combination therapy lowered the ventricular rate on 24-h ambulatory electrocardiographic monitoring (p < 0.0001) and during submaximal exercise (p < 0.05), whereas LVEF (p < 0.05) and symptom score (p < 0.05) improved. In phase 2, there was no significant difference between digoxin alone and carvedilol alone in any variable. The mean ventricular rate rose and LVEF fell when patients switched from combination therapy to carvedilol alone. Six-minute walk distance was not significantly influenced by any therapy. CONCLUSIONS: The combination of carvedilol and digoxin appears generally superior to either carvedilol or digoxin alone in the management of AF in patients with HF.

Adrenergic beta-Antagonists↗

Mapping cross-clade HIV-1 vaccine epitopes using a bioinformatics approach.

UNLABELLED: The genomic variability of HIV viruses circulating in different regions of the world has impeded the development of a globally relevant HIV vaccine. Broadly conserved HIV-1 cytotoxic T cell (CTL) epitopes were identified by screening protein sequences in the Los Alamos National Laboratory (LANL) HIV sequence database with a sequence parsing and matching algorithm (Conservatrix). Putative HIV-1 CTL epitopes were selected from this list using the epitope prediction tool EpiMatrix. METHODS: One hundred peptides representing putative HLA A*0201, HLA A*1101, HLA A*0301, and HLA B*07 ligands conserved in many isolates of HIV-1 were synthesized. Seventy-five HLA A*0201, HLA A*1101 and HLA B*07 peptides were incubated with transport associated protein (TAP)-deficient T2 cells transfected with the gene for the corresponding human HLA molecule (HLA A*0201, HLA A*1101, and HLA B*07). Binding and stabilization of peptide-HLA complexes on the surface of the T2 cells was measured by FACS. T cell responses to the entire set of 100 peptides (HLA A*0201, HLA A*1101, HLA A*0301, and HLA B*07) were measured in ELIspot assays using PBMC from healthy HIV-1 infected subjects who possessed a matching HLA allele. RESULTS: Fifty-seven (76%) of the 75 peptides tested in binding studies, including all (three of three) of the control (published) ligands bound to the T2 cells expressing the corresponding MHC molecule. Forty-three of the 100 peptides (43%) including all (four of four) of the control (published) epitopes tested in ELIspot assays stimulated gamma-interferon release. Thirty-one of these 43 epitopes are novel, highly conserved HIV-1 epitopes. EpiMatrix predicted and assays confirmed MHC-restriction by more than one HLA allele for nine of the 43 novel epitopes; of these epitopes five were recognized in the context of MHC "supertypes" and four were promiscuous epitopes. CONCLUSION: Epitopes identified using this approach were conserved in a broad range of HIV-1 sequences derived from isolates obtained in Latin America, Africa, Asia, the Pacific Islands, Europe and the US. The successful identification of cross-clade epitopes by this bioinformatics approach may accelerate the development of a globally relevant HIV-1 vaccine.

AIDS Vaccines↗

Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times.

Mitochondria occur as aerobic, facultatively anaerobic, and, in the case of hydrogenosomes, strictly anaerobic forms. This physiological diversity of mitochondrial oxygen requirement is paralleled by that of free-living alpha-proteobacteria, the group of eubacteria from which mitochondria arose, many of which are facultative anaerobes. Although ATP synthesis in mitochondria usually involves the oxidation of reduced carbon compounds, many alpha-proteobacteria and some mitochondria are known to use sulfide (H2S) as an electron donor for the respiratory chain and its associated ATP synthesis. In many eubacteria, the oxidation of sulfide involves the enzyme sulfide:quinone oxidoreductase (SQR). Nuclear-encoded homologs of SQR are found in several eukaryotic genomes. Here we show that eukaryotic SQR genes characterized to date can be traced to a single acquisition from a eubacterial donor in the common ancestor of animals and fungi. Yet, SQR is not a well-conserved protein, and our analyses suggest that the SQR gene has furthermore undergone some lateral transfer among prokaryotes during evolution, leaving the precise eubacterial lineage from which eukaryotes obtained their SQR difficult to discern with phylogenetic methods. Newer geochemical data and microfossil evidence indicate that major phases of early eukaryotic diversification occurred during a period of the Earth's history from 1 to 2 billion years before present in which the subsurface ocean waters contained almost no oxygen but contained high concentrations of sulfide, suggesting that the ability to deal with sulfide was essential for prokaryotes and eukaryotes during that time. Notwithstanding poor resolution in deep SQR phylogeny and lack of a specifically alpha-protebacterial branch for the eukaryotic enzyme on the basis of current lineage sampling, a single eubacterial origin of eukaryotic SQR and the evident need of ancient eukaryotes to deal with sulfide, a process today germane to mitochondrial quinone reduction, are compatible with the view that eukaryotic SQR was an acquisition from the mitochondrial endosymbiont.

Amino Acid Sequence↗

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.

All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.

Biochemical Phenomena↗

T cell epitope identification for bovine vaccines: an epitope mapping method for BoLA A-11.

T cell responses play an important role in immunity to parasites and other microbial agents of infectious diseases, therefore a number of T cell-directed vaccines are in development. Computer-driven algorithms that facilitate the discovery of T cell epitopes from protein and genome sequences are now being used to accelerate preclinical studies of human vaccines. Similar tools are not yet available for predicting T cell epitopes for animal vaccines, but there may be sufficient data available to begin the process of compiling the algorithms. We describe the construction of a novel mathematical 'matrix' that describes the properties of bovine major histocompatibility complex (BoLA) system antigen (BoLA) A-11 peptide ligands, developed for use with EpiMatrix, an existing T cell epitope-mapping algorithm. An alternative means of developing BoLA matrices, using the pocket profile method, is also discussed. Matrices such as the one described here may be used to develop T cell epitope-mapping tools for cattle and other ruminants. Epitope-mapping algorithms offer a significant advantage over other methods of epitope selection, such as the screening of synthetic overlapping peptides, because high throughput screening can be performed in silico, followed by ex vivo confirmatory studies. Furthermore, using epitope-mapping algorithms, putative T cell epitopes can be derived directly from genomic sequences, allowing researchers to circumvent labor-intensive cloning steps in the genome-to-vaccine discovery pathway.

Algorithms↗

Bioinformatics tools for identifying class I-restricted epitopes.

The lack of simple methods to identify relevant T-cell epitopes, the high mutation rate of many pathogens, and restriction of T-cell response to epitopes due to human lymphocyte antigen (HLA) polymorphism have significantly hindered the development of cytotoxic T-lymphocyte (CTL) epitope-based or "epitope-driven" vaccines. Previously, CTL epitopes were mapped using large arrays of overlapping synthetic peptides. The large number of protein sequences available for mapping is now making this method prohibitively expensive and time-consuming. Bioinformatics tools such as EpiMatrix and Conservatrix, which search for unique or multi-HLA-restricted (promiscuous) T-cell epitopes and identify epitopes that are conserved across variant strains of the same pathogen, accelerate epitope mapping. These tools offer a significant advantage over other methods of epitope selection because high-throughput screening can be performed in silico, followed by confirmatory studies in vitro. CTL epitopes discovered using these tools might be used to develop novel vaccines and therapeutics for the prevention and treatment of infectious diseases such as human immunodeficiency virus, hepatitis C, tuberculosis, and some cancers.

Algorithms↗

Bifunctional aldehyde/alcohol dehydrogenase (ADHE) in chlorophyte algal mitochondria.

Protein profiles of mitochondria isolated from the heterotrophic chlorophyte Polytomella sp. grown on ethanol at pH 6.0 and pH 3.7 were analyzed by Blue Native and denaturing polyacrylamide gel electrophoresis. Steady-state levels of oxidative phosphorylation complexes were influenced by external pH. Levels of an abundant, soluble, mitochondrial protein of 85 kDa and its corresponding mRNA increased at pH 6.0 relative to pH 3.7. N-terminal and internal sequencing of the 85 kDa mitochondrial protein together with the corresponding cDNA identified it as a bifunctional aldehyde/alcohol dehydrogenase (ADHE) with strong similarity to homologues from eubacteria and amitochondriate protists. A mitochondrial targeting sequence of 27 amino acids precedes the N-terminus of the mature mitochondrial protein. A gene encoding an ADHE homologue was also identified in the genome of Chlamydomonas reinhardtii, a photosynthetic relative of Polytomella. ADHE reveals a complex picture of sequence similarity among homologues. The lack of ADHE from archaebacteria indicates a eubacterial origin for the eukaryotic enzyme. Among eukaryotes, ADHE has hitherto been characteristic of anaerobes since it is essential to cytosolic energy metabolism of amitochondriate protists such as Giardia intestinalis and Entamoeba histolytica. Its abundance and expression pattern suggest an important role for ADHE in mitochondrial metabolism of Polytomella under the conditions studied. The current data are compatible with the view that Polytomella ADHE could be involved either in ethanol production or assimilation, or both, depending upon environmental conditions. Presence of ADHE in an oxygen-respiring algal mitochondrion and co-expression at ambient oxygen levels with respiratory chain components is unexpected with respect to the view that eukaryotes acquired ADHE genes specifically as an adaptation to an anaerobic lifestyle.

Alcohol Dehydrogenase↗