Quantifying Inter-Laboratory Variability in Stable Isotope Analysis of Ancient Skeletal Remains

Over the past forty years, stable isotope analysis of bone (and tooth) collagen and hydroxyapatite has become a mainstay of archaeological and paleoanthropological reconstructions of paleodiet and paleoenvironment. Despite this method''s frequent use across anthropological subdisciplines (and beyond), the present work represents the first attempt at gauging the effects of inter-laboratory variability engendered by differences in a) sample preparation, and b) analysis (instrumentation, working standards, and data calibration). Replicate analyses of a ¹⁴C-dated ancient human bone by twenty-one archaeological and paleoecological stable isotope laboratories revealed significant inter-laboratory isotopic variation for both collagen and carbonate. For bone collagen, we found a sizeable range of 1.8‰ for δ¹³C_col and 1.9‰ for δ¹⁵N_col among laboratories, but an interpretatively insignificant average pairwise difference of 0.2‰ and 0.4‰ for δ¹³C_col and δ¹⁵N_col respectively. For bone hydroxyapatite the observed range increased to a troublingly large 3.5‰ for δ¹³C_ap and 6.7‰ for δ¹⁸O_ap, with average pairwise differences of 0.6‰ for δ¹³C_ap and a disquieting 2.0‰ for δ¹⁸O_ap. In order to assess the effects of preparation versus analysis on isotopic variability among laboratories, a subset of the samples prepared by the participating laboratories were analyzed a second time on the same instrument. Based on this duplicate analysis, it was determined that roughly half of the isotopic variability among laboratories could be attributed to differences in sample preparation, with the other half resulting from differences in analysis (instrumentation, working standards, and data calibration). These findings have serious implications for choices made in the preparation and extraction of target biomolecules, the comparison of results obtained from different laboratories, and the interpretation of small differences in bone collagen and hydroxyapatite isotope values. To address the issues arising from inter-laboratory comparisons, we devise a novel measure we term the Minimum Meaningful Difference (MMD), and demonstrate its application.     

Molecular Paleoparasitological Hybridization Approach as Effective Tool for Diagnosing Human Intestinal Parasites from Scarce Archaeological Remains

Paleoparasitology is the science that uses parasitological techniques for diagnosing parasitic diseases in the past. Advances in molecular biology brought new insights into this field allowing the study of archaeological material. However, due to technical limitations a proper diagnosis and confirmation of the presence of parasites is not always possible, especially in scarce and degraded archaeological remains. In this study, we developed a Molecular Paleoparasitological Hybridization (MPH) approach using ancient DNA (aDNA) hybridization to confirm and complement paleoparasitological diagnosis. Eight molecular targets from four helminth parasites were included: Ascaris sp., Trichuris trichiura, Enterobius vermicularis, and Strongyloides stercoralis. The MPH analysis using 18^th century human remains from Praça XV cemetery (CPXV), Rio de Janeiro, Brazil, revealed for the first time the presence E. vermicularis aDNA (50%) in archaeological sites of Brazil. Besides, the results confirmed T. trichiura and Ascaris sp. infections. The prevalence of infection by Ascaris sp. and E. vermicularis increased considerably when MPH was applied. However, a lower aDNA detection of T. trichiura (40%) was observed when compared to the diagnosis by paleoparasitological analysis (70%). Therefore, based on these data, we suggest a combination of Paleoparasitological and MPH approaches to verify the real panorama of intestinal parasite infection in human archeological samples.     

Reading the Body: Representations and Remains in the Archaeological Record

Reading the Body: Representations and Remains in the Archaeological Record. Alison E. Rautman. ed. Philadelphia: University of Pennsylvania Press, 2000. 283 pp.     

Assessing Raman Spectroscopy as a Prescreening Tool for the Selection of Archaeological Bone for Stable Isotopic Analysis

Stable isotope analyses for paleodiet investigations require good preservation of bone protein, the collagen, to obtain reliable stable isotope values. Burial environments cause diagenetic alterations to collagen, especially in the leaching of the organic bone content. The survival of bone protein may be assessed by the weight % collagen, % carbon and % nitrogen yields, but these values are achieved only after destructive chemical processing. A non-destructive method of determining whether bone is suitably preserved would be desirable, as it would be less costly than chemical processing, and would also preserve skeletal collections. Raman analysis is one such potential non-destructive screening method. In previous applications, Raman spectroscopy has been used to test both the alteration of the mineral portion of bone, as well as to indicate the relative amount of organic material within the bone structure. However, there has been no research to test the relationship between the Raman spectroscopic results and the survival of bone protein. We use a set of 41 bone samples from the prehistoric archaeological site of Ban Non Wat, Northeast Thailand, to assess if Raman spectroscopy analysis of the organic-phosphate ratio has a significant correlation with the weight % collagen, and carbon and nitrogen yields obtained by isotopic analysis. The correlation coefficients are highly statistically significant in all cases (r = 0.716 for collagen, r = 0.630 for carbon and r = 0.706 for nitrogen, p≤0.001 for all) with approximately or close to half of the variation in each explained by variation in the organic-phosphate ratio (51.2% for collagen, 39.6% for carbon, and 49.8% for nitrogen). Although the Raman screening method cannot directly quantify the extent of collagen survival, it could be of use in the selection of bone most likely to have viable protein required for reliable results from stable isotope analysis.     

Variability of the MIR196A2 Gene as a Risk Factor in Primary-Progressive Multiple Sclerosis Development

Molecular Biology - Multiple sclerosis is a chronic disease of the central nervous system, combining in its pathogenesis both autoimmune and neurodegenerative components, and is characterized by a...     

An Objective Uncertainty Factor Adjustment for Methyl mercury Pharmacokinetic Variability

While default uncertainty factor (UF) adjustments have been proposed for pharmacokinetic variability in the derivation of Reference Doses (RfDs), few attempts have been made to derive chemical-specific UFs for such variability. In recent epidemiologic data on the neuro-developmental effects of MeHg, Hg concentration in either hair or blood is the point-of-departure for RfD derivation. The application of a pharmacokinetic model to derive an intake dose from the measured biomarker concentration allows examination of the inter-individual variability in the relationship between intake dose and biomarker concentration through specification of the variability in model parameters. Three independent studies of this variability, using different models and/or different parameter values, are compared. While differences in central tendency estimates give different predictions of the intake dose corresponding to a given biomarker concentration, normalization of the central tendency estimate resulted in strong agreement among the studies. Starting with Hg concentration in hair or blood, and dividing a central tendency estimate of the corresponding intake dose by a UF of 2 to 3, accounts for 95 to 99% of the variability in the relationship between intake dose and biomarker concentration. This variability, however, encompasses only a portion of the maternal ingestion-to-fetal brain pathway. It is therefore likely that this UF underestimates the overall pharmacokinetic variability in this pathway.     

Carnitine as a Growth Factor for Pediococcus soyae

Pediococcus soyae, the soy sauce lactic acid bacteria, requires two kinds of factors for growth as well as for salt-tolerance. These two factors are: glycine-betaine and an unknown substance tentatively named P-factor. The present paper reports that carnitine (vitamin Bt) is substitutable for glycine-betaine for its growth promoting effect on the organism. This is the first microorganism requiring carnitine as a specific growth factor.     

Betaine as a Growth Factor for Pediococcus soyae

Besides P-factor, Pediococcus soyae requires betaine (glycine-betaine) as a specific growth promotant. The maximal growth is obtained with the supplementation of both betaine and P-factor to the synthetic medium, while betaine only gives the half-maximal growth. When the organism is cultured in 18% salted media, the addition of both betaine and P-factor is essential for the occurrence of growth. Thus, betaine is requisite for Ped. soyae as a growth promoting factor and also as a factor bestowing the osmotelerant ability.     

Detection of Mycobacterium leprae DNA from Archaeological Skeletal Remains in Japan Using Whole Genome Amplification and Polymerase Chain Reaction

Background

Identification of pathogen DNA from archaeological human remains is a powerful tool in demonstrating that the infectious disease existed in the past. However, it is very difficult to detect trace amounts of DNA remnants attached to the human skeleton, especially from those buried in a humid atmosphere with a relatively high environmental temperature such as in Asia.

Methodology/Principal Findings

Here we demonstrate Mycobacterium leprae DNA from archaeological skeletal remains in Japan by polymerase chain reaction, DNA sequencing and single nucleotide polymorphism (SNP) analysis. In addition, we have established a highly sensitive method of detecting DNA using a combination of whole genome amplification and polymerase chain reaction, or WGA-PCR, which provides superior sensitivity and specificity in detecting DNA from trace amounts of skeletal materials.

Conclusion/Significance

We have detected M. leprae DNA in archaeological skeletal remains for the first time in the Far East. Its SNP genotype corresponded to type 1; the first detected case worldwide of ancient M. leprae DNA. We also developed a highly sensitive method to detect ancient DNA by utilizing whole genome amplification.     

Telomerase as a Growth-Promoting Factor

Beyond its role in telomere maintenance, telomerase provides additional functions in tumorogenesis, DNA repair, and cell survival. Telomerase protects cells from apoptosis and necrosis, and stimulates growth in adverse conditions. Furthermore, gross overexpression of the catalytic subunit of telomerase (hTERT) may act as a hyperproliferative signal to induce a senescence-like phenotype in normal fibroblasts, which is similar to the senescence induced by overexpression of oncogenes. As some of these functions can be dissociated from telomere lengthening, the question arises as to how the mere presence of telomerase can serve as a survival and growth-promoting factor.     

Inadequate Exercise as a Risk Factor for Sepsis Mortality

Objective

Test whether inadequate exercise is related to sepsis mortality.

Research Design and Methods

Mortality surveillance of an epidemiological cohort of 155,484 National Walkers'' and Runners'' Health Study participants residing in the United States. Deaths were monitored for an average of 11.6-years using the National Death index through December 31, 2008. Cox proportional hazard analyses were used to compare sepsis mortality (ICD-10 A40-41) to inadequate exercise (<1.07 METh/d run or walked) as measured on their baseline questionnaires. Deaths occurring within one year of the baseline survey were excluded.

Results

Sepsis was the underlying cause in 54 deaths (sepsis_underlying) and a contributing cause in 184 deaths (sepsis_contributing), or 238 total sepsis-related deaths (sepsis_total). Inadequate exercise was associated with 2.24-fold increased risk for sepsis_underlying (95%CI: 1.21 to 4.07-fold, P = 0.01), 2.11-fold increased risk for sepsis_contributing (95%CI: 1.51- to 2.92-fold, P<10⁻⁴), and 2.13-fold increased risk for sepsis_total (95%CI: 1.59- to 2.84-fold, P<10⁻⁶) when adjusted for age, sex, race, and cohort. The risk increase did not differ significantly between runners and walkers, by sex, or by age. Sepsis_total risk was greater in diabetics (P = 10⁻⁵), cancer survivors (P = 0.0001), and heart attack survivors (P = 0.003) and increased with waist circumference (P = 0.0004). The sepsis_total risk associated with inadequate exercise persisted when further adjusted for diabetes, prior cancer, prior heart attack and waist circumference, and when excluding deaths with cancer, or cardiovascular, respiratory, or genitourinary disease as the underlying cause. Inadequate exercise also increased sepsis_total risk in 2163 baseline diabetics (4.78-fold, 95%CI: 2.1- to 13.8-fold, P = 0.0001) when adjusted, which was significantly greater (P = 0.03) than the adjusted risk increase in non-diabetics (1.80-fold, 95%CI: 1.30- to 2.46-fold, P = 0.0006).

Conclusion

Inadequate exercise is a risk factor for sepsis mortality, particular in diabetics.     

Axonal Noise as a Source of Synaptic Variability

Post-synaptic potential (PSP) variability is typically attributed to mechanisms inside synapses, yet recent advances in experimental methods and biophysical understanding have led us to reconsider the role of axons as highly reliable transmission channels. We show that in many thin axons of our brain, the action potential (AP) waveform and thus the Ca⁺⁺ signal controlling vesicle release at synapses will be significantly affected by the inherent variability of ion channel gating. We investigate how and to what extent fluctuations in the AP waveform explain observed PSP variability. Using both biophysical theory and stochastic simulations of central and peripheral nervous system axons from vertebrates and invertebrates, we show that channel noise in thin axons (<1 µm diameter) causes random fluctuations in AP waveforms. AP height and width, both experimentally characterised parameters of post-synaptic response amplitude, vary e.g. by up to 20 mV and 0.5 ms while a single AP propagates in C-fibre axons. We show how AP height and width variabilities increase with a ¾ power-law as diameter decreases and translate these fluctuations into post-synaptic response variability using biophysical data and models of synaptic transmission. We find for example that for mammalian unmyelinated axons with 0.2 µm diameter (matching cerebellar parallel fibres) axonal noise alone can explain half of the PSP variability in cerebellar synapses. We conclude that axonal variability may have considerable impact on synaptic response variability. Thus, in many experimental frameworks investigating synaptic transmission through paired-cell recordings or extracellular stimulation of presynaptic neurons, causes of variability may have been confounded. We thereby show how bottom-up aggregation of molecular noise sources contributes to our understanding of variability observed at higher levels of biological organisation.     

Heart Rate Variability as a Marker of Self-Regulation

Self-regulation is central to many of the most important individual and societal problems today. We sought to determine whether the relationship between self-regulation and heart rate variability (HRV) could be replicated and extended. We hypothesized that baseline HRV would predict persistence on an anagram task, and that under conditions requiring greater self-control, HRV would increase. Two groups were given the same set of difficult and unsolvable anagrams. To induce self-regulatory fatigue, the suppression group was asked to try to not think of a white bear while the expression group was asked to try to think of a white bear. Baseline HRV predicted persistence on the unsolvable anagram. Both groups demonstrated changes in HRV relative to baseline, although we were unable to replicate findings that HRV was elevated during high self-regulatory effort. We were, however, able to replicate findings that the expression group persisted longer on the anagram task compared to the suppression group but only when accounting for physical activity scores. The present study advances our knowledge of the relationship between HRV and self-regulation, so that we can more successfully treat those with seriously impaired self-control.     

Analysis of Subfossil Molecular Remains of Purple Sulfur Bacteria in a Lake Sediment

Molecular remains of purple sulfur bacteria (Chromatiaceae) were detected in Holocene sediment layers of a meromictic salt lake (Mahoney Lake, British Columbia, Canada). The carotenoid okenone and bacteriophaeophytin a were present in sediments up to 11,000 years old. Okenone is specific for only a few species of Chromatiaceae, including Amoebobacter purpureus, which presently predominates in the chemocline bacterial community of the lake. With a primer set specific for Chromatiaceae in combination with denaturing gradient gel electrophoresis, 16S rRNA gene sequences of four different Chromatiaceae species were retrieved from different depths of the sediment. One of the sequences, which originated from a 9,100-year-old sample, was 99.2% identical to the 16S rRNA gene sequence of A. purpureus ML1 isolated from the chemocline. Employing primers specific for A. purpureus ML1 and dot blot hybridization of the PCR products, the detection limit for A. purpureus ML1 DNA could be lowered to 0.004% of the total community DNA. With this approach the DNA of the isolate was detected in 7 of 10 sediment layers, indicating that A. purpureus ML1 constituted at least a part of the ancient purple sulfur bacterial community. The concentrations of A. purpureus DNA and okenone in the sediment were not correlated, and the ratio of DNA to okenone was much lower in the subfossil sediment layers (2.7 · 10⁻⁶) than in intact cells (1.4). This indicates that degradation rates are significantly higher for genomic DNA than for hydrocarbon cell constituents, even under anoxic conditions and at the very high sulfide concentrations present in Mahoney Lake.     

Exploring vaccinia virus as a tool for large-scale recombinant protein expression

A recombinant vaccinia virus was engineered to express enhanced green fluorescent protein (EGFP) under control of the T7 promoter using the VOTE expression system in HeLa cells. Infection of HeLa cells with this virus and induction with IPTG demonstrated the utility of this construct for easily measuring protein expression. This construct was used to evaluate several production parameters, specifically, multiplicity of infection (MOI), volume during infection, and serum concentration during the infection phase. In static culture, increasing multiplicity of infection was found to increase expression of EGFP up to a plateau around MOI of 1.0. Expression was also shown to increase with decreasing volume during the infection phase. Serum concentration during the infection phase was only marginally significant from 0 to 7.5%. Cytodex 3 microcarriers were found to have the best characteristics for HeLa cell growth. These cells were grown and infected in microcarrier spinner flask culture, and the maximum expression was 2.2 microg EGFP/(million cells at the time of infection), demonstrating the ability of this system to successfully express recombinant proteins at larger scale.