A systematic methodology to assess the identity of plants in historical texts: A case study based on the Byzantine pharmacy text John the Physician's Therapeutics

ETHNOPHARMACOLOGICAL RELEVANCE

In recent decades, the study of historical texts has attracted research interest, particularly in ethnopharmacology. All studies of the materia medica cited in ancient and medieval texts share a concern, however, as to the reliability of modern identifications of these substances. Previous studies of European or Mediterranean texts relied mostly on authoritative dictionaries or glossaries providing botanical identities for the historical plant names in question. Several identities they suggest, however, are questionable and real possibility of error exists.

AIM OF THE STUDY

This study aims to develop and document a novel and interdisciplinary methodology providing more objective assessment of the identity of the plants (and minerals) described in these resources.

MATERIALS AND METHODS

We developed an iterative experimental approach, using the 13th century Byzantine recipe text John the Physician's Therapeutics in its Commentary version (JC) as a case study. The methodology has six stages and relies on comparative analyses including statistical evaluation of botanical descriptions and information about medicinal uses drawn from both historical and modern sources. Stages 1-4 create the dataset, stage 5 derives the primary outcomes to be reviewed by experts in stage 6.

RESULTS

Using Disocorides' De Materia Medica (DMM) (1st century CE) as the culturally related reference text for the botanical descriptions of the plants cited in JC, allowed us to link the 194 plants used medicinally in JC with 252 plants cited in DMM. Our test sample for subsequent analyses consisted of the 50 JC plant names (corresponding to 61 DMM plants) for which DMM holds rich morphological information, and the 130 candidate species which have been suggested in the literature as potential botanical identities of those 50 JC plant names. Statistical evaluation of the comparative analyses revealed that in the majority of the cases, our method detected the candidate species having a higher likelihood of being the correct attribution from among the pool of suggested candidates. Final assessment and revision provided a list of the challenges associated with applying our methodology more widely and recommendations on how to address these issues.

CONCLUSIONS

We offer this multidisciplinary approach to more evidence-based assessment of the identity of plants in historical texts providing a measure of confidence for each suggested identity. Despite the experimental nature of our methodology and its limitations, its application allowed us to draw conclusions about the validity of suggested candidate plants as well as to distinguish between alternative candidates of the same historical plant name. Fully documenting the methodology facilitates its application to historical texts of any kind of cultural or linguistic background.

Pharmaceutical Terminology in Ancient and Medieval Time - andrachne, chrysocolla and Others

Ancient and medieval pharmacological and medical texts contain a substantial amount of plant and mineral names. In some cases, the identification is straightforward. But for the majority of the data, we are unable to identify these ingredients with high certainty. In this paper, we discuss a selection of plant and mineral names both from a humanities and sciences point of view. In one case, the scientists were even able to examine a plant in situ. The conclusion of our paper is that a close collaboration between sciences and humanities is essential to avoid mistakes in the identification of materia medica.

Ectopic activation of the miR-200c-EpCAM axis enhances antitumor T cell responses in models of adoptive cell therapy

Adoptive T cell therapy (ACT) is a promising strategy for treating cancer, but it often fails because of cell intrinsic regulatory programs that limit the degree or duration of T cell function. In this study, we found that ectopic expression of microRNA-200c (miR-200c) markedly enhanced the antitumor activity of CD8+ cytotoxic T lymphocytes (CTLs) during ACT in multiple mouse models. CTLs transduced with miR-200c exhibited reduced apoptosis during engraftment and enhanced in vivo persistence, accompanied by up-regulation of the transcriptional regulator T cell factor 1 (TCF1) and the inflammatory cytokine tumor necrosis factor (TNF). miR-200c elicited these changes by suppressing the transcription factor Zeb1 and thereby inducing genes characteristic of epithelial cells. Overexpression of one of these genes, Epcam, was sufficient to augment therapeutic T cell responses against both solid and liquid tumors. These results identify the miR-200c–EpCAM axis as an avenue for improving ACT and demonstrate that select genetic perturbations can produce phenotypically distinct T cells with advantageous therapeutic properties.

TOX is a critical regulator of tumour-specific T cell differentiation

Tumour-specific CD8 T cell dysfunction is a differentiation state that is distinct from the functional effector or memory T cell states^1–6. Here we identify the nuclear factor TOX as a crucial regulator of the differentiation of tumour-specific T (TST) cells. We show that TOX is highly expressed in dysfunctional TST cells from tumours and in exhausted T cells during chronic viral infection. Expression of TOX is driven by chronic T cell receptor stimulation and NFAT activation. Ectopic expression of TOX in effector T cells in vitro induced a transcriptional program associated with T cell exhaustion. Conversely, deletion of Tox in TST cells in tumours abrogated the exhaustion program: Tox-deleted TST cells did not upregulate genes for inhibitory receptors (such as Pdcd1, Entpd1, Havcr2, Cd244 and Tigit), the chromatin of which remained largely inaccessible, and retained high expression of transcription factors such as TCF-1. Despite their normal, ‘non-exhausted’ immunophenotype, Tox-deleted TST cells remained dysfunctional, which suggests that the regulation of expression of inhibitory receptors is uncoupled from the loss of effector function. Notably, although Tox-deleted CD8 T cells differentiated normally to effector and memory states in response to acute infection, Tox-deleted TST cells failed to persist in tumours. We hypothesize that the TOX-induced exhaustion program serves to prevent the overstimulation of T cells and activation-induced cell death in settings of chronic antigen stimulation such as cancer.

Depleting T regulatory cells by targeting intracellular Foxp3 with a TCR mimic antibody

Depletion of T regulatory cells (Tregs) in the tumor microenvironment is a promising cancer immunotherapy strategy. Current approaches for depleting Tregs are limited by lack of specificity and concurrent depletion of anti-tumor effector T cells. The transcription factor forkhead box p3 (Foxp3) plays a central role in the development and function of Tregs and is an ideal target in Tregs, but Foxp3 is an intracellular, undruggable protein to date. We have generated a T cell receptor mimic antibody, "Foxp3-#32," recognizing a Foxp3-derived epitope in the context of HLA-A*02:01. The mAb Foxp3-#32 selectively recognizes CD4 + CD25 + CD127low and Foxp3 + Tregs also expressing HLA-A*02:01 and depletes these cells via antibody-mediated cellular cytotoxicity. Foxp3-#32 mAb depleted Tregs in xenografts of PBMCs from a healthy donor and ascites fluid from a cancer patient. A TCRm mAb targeting intracellular Foxp3 epitope represents an approach to deplete Tregs.

Abstract A215: Thymocyte selection-associated HMG box protein TOX is a master regulator of tumor-specific T-cell dysfunction

Tumor-specific CD8 T-cells in cancers enter a state of dysfunction characterized by the expression of inhibitory receptors and failure to produce effector cytokines and cytotoxic molecules. Here we identify the nuclear factor, Thymocyte selection-associated HMG box protein, TOX, as a master regulator of tumor-specific T-cell dysfunction. TOX is uniquely expressed in dysfunctional CD8 T-cells from mouse and human tumors but absent in functional T-cells. TOX expression is driven by continuous TCR stimulation and NFAT activity. Forced expression of TOX in functional effector T-cells was sufficient to induce a transcriptional program of dysfunction through the concerted expression of genes encoding numerous inhibitory receptors and dysfunction-associated transcription factors. Notably, TOX-deficient tumor-infiltrating T-cells did not upregulate inhibitory receptors such as PD1, LAG3, CD38, or CD39 and maintained high TCF1 expression. Surprisingly, despite their normal, “non-exhausted” phenotype, TOX-deficient T-cells failed to make effector cytokines, suggesting that loss of effector function in tumor-specific T-cells is uncoupled from inhibitory receptor expression. Furthermore, TOX-deficient T-cells failed to persist in tumors, ultimately undergoing activation-induced cell death. We propose that the TOX-induced transcriptional program of hyporesponsiveness is a physiologic negative feedback mechanism that prevents overstimulation; thus TOX is absolutely required for T-cell survival in the setting of chronic antigen stimulation as in cancers.

Citation Format: Andrew C. Scott, Steven Camara, Peter Lauer, Alexandra Synder, Dmitriy Zamarin, Tyler Walther, Olivier Levy, Michael Glickman, Jonathan Kaye, Mary Philip, Andrea Schietinger. Thymocyte selection-associated HMG box protein TOX is a master regulator of tumor-specific T-cell dysfunction [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A215.

A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context

A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.

Global combustion: the connection between fossil fuel and biomass burning emissions (1997-2010)

Humans use combustion for heating and cooking, managing lands, and, more recently, for fuelling the industrial economy. As a shift to fossil-fuel-based energy occurs, we expect that anthropogenic biomass burning in open landscapes will decline as it becomes less fundamental to energy acquisition and livelihoods. Using global data on both fossil fuel and biomass burning emissions, we tested this relationship over a 14 year period (1997-2010). The global average annual carbon emissions from biomass burning during this time were 2.2 Pg C per year (±0.3 s.d.), approximately one-third of fossil fuel emissions over the same period (7.3 Pg C, ±0.8 s.d.). There was a significant inverse relationship between average annual fossil fuel and biomass burning emissions. Fossil fuel emissions explained 8% of the variation in biomass burning emissions at a global scale, but this varied substantially by land cover. For example, fossil fuel burning explained 31% of the variation in biomass burning in woody savannas, but was a non-significant predictor for evergreen needleleaf forests. In the land covers most dominated by human use, croplands and urban areas, fossil fuel emissions were more than 30- and 500-fold greater than biomass burning emissions. This relationship suggests that combustion practices may be shifting from open landscape burning to contained combustion for industrial purposes, and highlights the need to take into account how humans appropriate combustion in global modelling of contemporary fire. Industrialized combustion is not only an important driver of atmospheric change, but also an important driver of landscape change through companion declines in human-started fires.This article is part of the themed issue 'The interaction of fire and mankind'.

The interaction of fire and mankind: Introduction

Fire has been an important part of the Earth system for over 350 Myr. Humans evolved in this fiery world and are the only animals to have used and controlled fire. The interaction of mankind with fire is a complex one, with both positive and negative aspects. Humans have long used fire for heating, cooking, landscape management and agriculture, as well as for pyrotechnologies and in industrial processes over more recent centuries. Many landscapes need fire but population expansion into wildland areas creates a tension between different interest groups. Extinguishing wildfires may not always be the correct solution. A combination of factors, including the problem of invasive plants, landscape change, climate change, population growth, human health, economic, social and cultural attitudes that may be transnational make a re-evaluation of fire and mankind necessary. The Royal Society meeting on Fire and mankind was held to address these issues and the results of these deliberations are published in this volume.This article is part of the themed issue 'The interaction of fire and mankind'.

Fire history on the California Channel Islands spanning human arrival in the Americas

Recent studies have suggested that the first arrival of humans in the Americas during the end of the last Ice Age is associated with marked anthropogenic influences on landscape; in particular, with the use of fire which, would have given even small populations the ability to have broad impacts on the landscape. Understanding the impact of these early people is complicated by the dramatic changes in climate occurring with the shift from glacial to interglacial conditions. Despite these difficulties, we here attempt to test the extent of anthropogenic influence using the California Channel Islands as a smaller, landscape-scale test bed. These islands are famous for the discovery of the 'Arlington Springs Man', which are some of the earliest human remains in the Americas. A unifying sedimentary charcoal record is presented from Arlington Canyon, Santa Rosa Island, based on over 20 detailed sedimentary sections from eight key localities. Radiocarbon dating was based on thin, fragile, long fragments of charcoal in order to avoid the 'inbuilt' age problem. Radiocarbon dating of 49 such fragments has allowed inferences regarding the fire and landscape history of the Canyon ca 19-11 ka BP. A significant period of charcoal deposition is identified approximately 14-12.5 ka BP and bears remarkable closeness to an estimated age range of the first human arrival on the islands.This article is part of the themed issue 'The interaction of fire and mankind'.

Living on a flammable planet: interdisciplinary, cross-scalar and varied cultural lessons, prospects and challenges

Living with fire is a challenge for human communities because they are influenced by socio-economic, political, ecological and climatic processes at various spatial and temporal scales. Over the course of 2 days, the authors discussed how communities could live with fire challenges at local, national and transnational scales. Exploiting our diverse, international and interdisciplinary expertise, we outline generalizable properties of fire-adaptive communities in varied settings where cultural knowledge of fire is rich and diverse. At the national scale, we discussed policy and management challenges for countries that have diminishing fire knowledge, but for whom global climate change will bring new fire problems. Finally, we assessed major fire challenges that transcend national political boundaries, including the health burden of smoke plumes and the climate consequences of wildfires. It is clear that to best address the broad range of fire problems, a holistic wildfire scholarship must develop common agreement in working terms and build across disciplines. We must also communicate our understanding of fire and its importance to the media, politicians and the general public.This article is part of the themed issue 'The interaction of fire and mankind'.

Chromatin states define tumour-specific T cell dysfunction and reprogramming

Tumour-specific CD8 T cells in solid tumours are dysfunctional, allowing tumours to progress. The epigenetic regulation of T cell dysfunction and therapeutic reprogrammability (for example, to immune checkpoint blockade) is not well understood. Here we show that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming. We identified surface markers associated with each chromatin state that distinguished reprogrammable from non-reprogrammable PD1^hi dysfunctional T cells within heterogeneous T cell populations from tumours in mice; these surface markers were also expressed on human PD1^hi tumour-infiltrating CD8 T cells. Our study has important implications for cancer immunotherapy as we define key transcription factors and epigenetic programs underlying T cell dysfunction and surface markers that predict therapeutic reprogrammability.

Abstract A058: Selective targeting of T regulatory cells by a TCR-mimic monoclonal antibody specific for foxp3-derived epitopes

Immunosuppression by tumor-induced regulatory T (Treg) cells present major obstacles for successful immunotherapy. Treg expansion and its negative prognostic impact represent a general phenomenon seen in multiple types of cancer. Therefore, developing strategies for Treg depletion could enhance the reactivation of immune responses against the malignant tumor cells. However, the strategies of depleting Tregs have been hindered by the lack of specificity, which also leads to the depletion of anti-tumor effector cells. The transcription factor forkhead box p3 (FoxP3) is selectively expressed in and is essential to the suppressive function of Treg cells. FoxP3 thus would be an appealing target for eliminating Treg cells. However, Foxp3 is an undruggable intracellular protein. Here, we took a novel and unconventional approach to target Foxp3 by using a T cell receptor mimic (TCRm) mAb, which recognizes a human Foxp3-derived CD8 T cell epitope, presented by HLA-A*02:01 molecule. We show that the Foxp3 mAb specifically bound to CD4+CD25hiCD127lo Foxp3+ Treg cells from HLA-A0201 positive donors, and tumor cell lines co-expressing Foxp3 and HLA-A*02;01 molecule. Both afucosylated Fc enhanced human IgG1 and bispecific T cell engager formats of the Foxp3 mAb are able to kill in vitro-generated Treg clones from HLA-A0201+ donors and “Treg-like” cutaneous lymphoma cells (HLA-A*02:01+) that have a high level expression of CD4, CD25 and Fox3+. FoxP3-targeting antibodies could potentially be a novel approach in cancer immunotherapy by overcoming immunosuppression caused by Tregs and tumor cells expressing Foxp3.

Citation Format: Tao Dao, Casey Jarvis, Andrew C. Scott, Tatyana Korontsvit, Victoria Zakhaleva, Dmitry Pankov, Manuel Direito de Morais Guerrerio, Melissa Mathias, Neal Cheng, Cheng Liu, David A. Scheinberg. Selective targeting of T regulatory cells by a TCR-mimic monoclonal antibody specific for foxp3-derived epitopes [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A058.

The impact of fire on the Late Paleozoic Earth system

Analyses of bulk petrographic data indicate that during the Late Paleozoic wildfires were more prevalent than at present. We propose that the development of fire systems through this interval was controlled predominantly by the elevated atmospheric oxygen concentration (p(O2)) that mass balance models predict prevailed. At higher levels of p(O2), increased fire activity would have rendered vegetation with high-moisture contents more susceptible to ignition and would have facilitated continued combustion. We argue that coal petrographic data indicate that p(O2) rather than global temperatures or climate, resulted in the increased levels of wildfire activity observed during the Late Paleozoic and can, therefore, be used to predict it. These findings are based upon analyses of charcoal volumes in multiple coals distributed across the globe and deposited during this time period, and that were then compared with similarly diverse modern peats and Cenozoic lignites and coals. Herein, we examine the environmental and ecological factors that would have impacted fire activity and we conclude that of these factors p(O2) played the largest role in promoting fires in Late Paleozoic peat-forming environments and, by inference, ecosystems generally, when compared with their prevalence in the modern world.

Evolutionary stasis of sporopollenin biochemistry revealed by unaltered Pennsylvanian spores

The biopolymer sporopollenin present in the spore/pollen walls of all land plants is regarded as one of the most recalcitrant biomacromolecules (biopolymers), providing protection against a range of abiotic stresses. This long-term stability is demonstrated by the near-ubiquitous presence of pollen and spores in the fossil record with spores providing the first evidence for the colonization of the land. Here, we report for the first time chemical analyses of geologically unaltered sporopollenin from Pennsylvanian (c. 310 million yr before present (MyBP)) cave deposits. Our data show that Pennsylvanian Lycophyta megaspore sporopollenin has a strong chemical resemblance to extant relatives and indicates that a co-polymer model of sporopollenin formation is the most likely configuration. Broader comparison indicates that extant sporopollenin structure is similar across widely spaced phylogenetic groups and suggests land plant sporopollenin structure has remained stable since embryophytes invaded land.

The human dimension of fire regimes on Earth

Humans and their ancestors are unique in being a fire-making species, but 'natural' (i.e. independent of humans) fires have an ancient, geological history on Earth. Natural fires have influenced biological evolution and global biogeochemical cycles, making fire integral to the functioning of some biomes. Globally, debate rages about the impact on ecosystems of prehistoric human-set fires, with views ranging from catastrophic to negligible. Understanding of the diversity of human fire regimes on Earth in the past, present and future remains rudimentary. It remains uncertain how humans have caused a departure from 'natural' background levels that vary with climate change. Available evidence shows that modern humans can increase or decrease background levels of natural fire activity by clearing forests, promoting grazing, dispersing plants, altering ignition patterns and actively suppressing fires, thereby causing substantial ecosystem changes and loss of biodiversity. Some of these contemporary fire regimes cause substantial economic disruptions owing to the destruction of infrastructure, degradation of ecosystem services, loss of life, and smoke-related health effects. These episodic disasters help frame negative public attitudes towards landscape fires, despite the need for burning to sustain some ecosystems. Greenhouse gas-induced warming and changes in the hydrological cycle may increase the occurrence of large, severe fires, with potentially significant feedbacks to the Earth system. Improved understanding of human fire regimes demands: (1) better data on past and current human influences on fire regimes to enable global comparative analyses, (2) a greater understanding of different cultural traditions of landscape burning and their positive and negative social, economic and ecological effects, and (3) more realistic representations of anthropogenic fire in global vegetation and climate change models. We provide an historical framework to promote understanding of the development and diversification of fire regimes, covering the pre-human period, human domestication of fire, and the subsequent transition from subsistence agriculture to industrial economies. All of these phases still occur on Earth, providing opportunities for comparative research.

Fire and the spread of flowering plants in the Cretaceous

We suggest that the spread of angiosperms in the Cretaceous was facilitated by novel fire regimes. Angiosperms were capable of high productivity and therefore accumulated flammable biomass ('fuel') more rapidly than their predecessors. They were capable of rapid reproduction, allowing populations to spread despite frequent disturbance. We evaluate the evidence for physical conditions conducive to fires in the Cretaceous. These included high temperatures, seasonally dry climate and higher atmospheric oxygen than current levels. We evaluate novel properties of angiosperms that contributed to rapid biomass accumulation, and to their ability to thrive in frequently disturbed environments. We also review direct evidence for Cretaceous fires. Charcoal mesofossils are common in Cretaceous deposits of the Northern Hemisphere. Inertinite, the charcoal component of coal, is common throughout the Cretaceous and into the Palaeocene, but declined steeply from the Eocene when angiosperm-dominated forests became widespread. Direct and indirect evidence is consistent with angiosperms initiating novel fire regimes, promoting angiosperm spread in the Cretaceous. Several traits are consistent with frequent surface fires. We suggest that forest was slow to develop until the Eocene, when fire activity dropped to very low levels. The causes and consequences of fires in the deep past warrant greater attention.

Fire in the Earth system

Fire is a worldwide phenomenon that appears in the geological record soon after the appearance of terrestrial plants. Fire influences global ecosystem patterns and processes, including vegetation distribution and structure, the carbon cycle, and climate. Although humans and fire have always coexisted, our capacity to manage fire remains imperfect and may become more difficult in the future as climate change alters fire regimes. This risk is difficult to assess, however, because fires are still poorly represented in global models. Here, we discuss some of the most important issues involved in developing a better understanding of the role of fire in the Earth system.

Scanning electron microscopy and synchrotron radiation x-ray tomographic microscopy of 330 million year old charcoalified seed fern fertile organs

Abundant charcoalified seed fern (pteridosperm) pollen organs and ovules have been recovered from Late Viséan (Mississippian 330 Ma) limestones from Kingswood, Fife, Scotland. To overcome limitations of data collection from these tiny, sometimes unique, fossils, we have combined low vacuum scanning electron microscopy on uncoated specimens with backscatter detector and synchrotron radiation X-ray tomographic microscopy utilizing the Materials Science and TOMCAT beamlines at the Swiss Light Source of the Paul Scherrer Institut. In combination these techniques improve upon traditional cellulose acetate peel sectioning because they enable study of external morphology and internal anatomy in multiple planes of section on a single specimen that is retained intact. The pollen organ Melissiotheca shows a basal parenchymatous cushion bearing more than 100 sporangia on the distal face. Digital sections show the occurrence of pollen in some sporangia. The described ovule is new and has eight integumentary lobes that are covered in spirally arranged glandular hairs. Virtual longitudinal sections reveal the lobes are free above the pollen chamber. Results are applied in taxonomy and will subsequently contribute to our understanding of the former diversity and evolution of ovules, seeds, and pollen organs in the seed ferns, the first seed-bearing plants to conquer the land.

Geochemical evidence for combustion of hydrocarbons during the K-T impact event

It has been proposed that extensive wildfires occurred after the Cretaceous-Tertiary (K-T) impact event. An abundance of soot and pyrosynthetic polycyclic aromatic hydrocarbons (pPAHs) in marine K-T boundary impact rocks (BIRs) have been considered support for this hypothesis. However, nonmarine K-T BIRs, from across North America, contain only rare occurrences of charcoal yet abundant noncharred plant remains. pPAHs and soot can be formed from a variety of sources, including partial combustion of vegetation and hydrocarbons whereby modern pPAH signatures are traceable to their source. We present results from multiple nonmarine K-T boundary sites from North America and reveal that the K-T BIRs have a pPAH signature consistent with the combustion of hydrocarbons and not living plant biomass, providing further evidence against K-T wildfires and compelling evidence that a significant volume of hydrocarbons was combusted during the K-T impact event.

Increased terrestrial methane cycling at the Palaeocene–Eocene thermal maximum

The Palaeocene-Eocene thermal maximum (PETM), a period of intense, global warming about 55 million years ago, has been attributed to a rapid rise in greenhouse gas levels, with dissociation of methane hydrates being the most commonly invoked explanation. It has been suggested previously that high-latitude methane emissions from terrestrial environments could have enhanced the warming effect, but direct evidence for an increased methane flux from wetlands is lacking. The Cobham Lignite, a recently characterized expanded lacustrine/mire deposit in England, spans the onset of the PETM and therefore provides an opportunity to examine the biogeochemical response of wetland-type ecosystems at that time. Here we report the occurrence of hopanoids, biomarkers derived from bacteria, in the mire sediments from Cobham. We measure a decrease in the carbon isotope values of the hopanoids at the onset of the PETM interval, which suggests an increase in the methanotroph population. We propose that this reflects an increase in methane production potentially driven by changes to a warmer and wetter climate. Our data suggest that the release of methane from the terrestrial biosphere increased and possibly acted as a positive feedback mechanism to global warming.

Capillary HPLC/QTOF-MS for Characterizing Complex Naphthenic Acid Mixtures and Their Microbial Transformation

A rapidly expanding oil sands industry in Canada produces and indefinitely stores large volumes of toxic aqueous tailings containing high concentrations of naphthenic acids (NAs), a complex mixture of naturally occurring aliphatic or alicyclic carboxylic acids. Although there is an acknowledged need to reduce the environmental risks posed by NAs, little is understood about their environmental fate due to a lack of appropriate analytical methods. A dilute-and-shoot reversed-phase capillary HPLC/QTOF-MS method was developed that combines high specificity and sensitivity, quantitative capabilities, the ability to detect novel transformation products, and new structural information within each NA isomer class. HPLC separated NAs, based on carbon number, degree of cyclization, and the extent of alkyl branching, and in so doing increased analytical sensitivity up to 350-fold while providing additional specificity compared to infusion techniques. For tailings water, an interlaboratory study revealed many differences in isomer class profiles compared to an established GC/MS method, much of which was attributed to the misclassification of oxidized NAs (i.e., NA + O) by low-resolution GC/MS. HPLC/QTOF-MS enabled the detection of oxidized products in the same chromatographic run, and Van Krevelen diagrams were adapted to visualize the complex data. A marked decrease of retention times was evident in Syncrude tailings water compared to a commercial mixture, suggesting that tailings water is dominated by highly persistent alkyl-substituted isomers. A biodegradation study revealed that tailings water microorganisms preferentially deplete the least alkyl-substituted fraction and may be responsible for the NA profile in aged tailings water.

The diversification of Paleozoic fire systems and fluctuations in atmospheric oxygen concentration

By comparing Silurian through end Permian [approximately 250 million years (Myr)] charcoal abundance with contemporaneous macroecological changes in vegetation and climate we aim to demonstrate that long-term variations in fire occurrence and fire system diversification are related to fluctuations in Late Paleozoic atmospheric oxygen concentration. Charcoal, a proxy for fire, occurs in the fossil record from the Late Silurian (approximately 420 Myr) to the present. Its presence at any interval in the fossil record is already taken to constrain atmospheric oxygen within the range of 13% to 35% (the "fire window"). Herein, we observe that, as predicted, atmospheric oxygen levels rise from approximately 13% in the Late Devonian to approximately 30% in the Late Permian so, too, fires progressively occur in an increasing diversity of ecosystems. Sequentially, data of note include: the occurrence of charcoal in the Late Silurian/Early Devonian, indicating the burning of a diminutive, dominantly rhyniophytoid vegetation; an apparent paucity of charcoal in the Middle to Late Devonian that coincides with a predicted atmospheric oxygen low; and the subsequent diversification of fire systems throughout the remainder of the Late Paleozoic. First, fires become widespread during the Early Mississippian, they then become commonplace in mire systems in the Middle Mississippian; in the Pennsylvanian they are first recorded in upland settings and finally, based on coal petrology, become extremely important in many Permian mire settings. These trends conform well to changes in atmospheric oxygen concentration, as predicted by modeling, and indicate oxygen levels are a significant control on long-term fire occurrence.

Evaluating phenanthrene sorption on various wood chars

A certain amount of wood char or soot in a soil or sediment sample may cause the sorption of organic compounds to deviate significantly from the linear partitioning commonly observed with soil organic matter (SOM). Laboratory produced and field wood chars have been obtained and analyzed for their sorption isotherms of a model solute (phenanthrene) from water solution. The uptake capacities and nonlinear sorption effects with the laboratory wood chars are similar to those with the field wood chars. For phenanthrene aqueous concentrations of 1 microg l(-1), the organic carbon-normalized sorption coefficients (log K(oc)) ranging from 5.0 to 6.4 for field chars and 5.4-7.3 for laboratory wood chars, which is consistent with literature values (5.6-7.1). Data with artificial chars suggest that the variation in sorption potential can be attributed to heating temperature and starting material, and both the quantity and heterogeneity of surface-area impacts the sorption capacity. These results thus help to corroborate and explain the range of logK(oc) values reported in previous research for aquifer materials containing wood chars.

Quantum signatures of breather-breather interactions

The spectrum of the quantum discrete nonlinear Schrödinger equation, or boson Hubbard Hamiltonian, on a periodic 1D lattice shows some interesting detailed band structure, which may be interpreted as the quantum signature of a two-breather interaction in the classical case. This fine structure is studied using degenerate perturbation theory. We also present a modification to this model, which increases the mobility of bound states.

QSAR studies on P-glycoprotein-regulated multidrug resistance and on its reversal by phenothiazines

Multidrug resistance is brought about largely by membrane transport proteins such as P-glycoprotein (P-gp). We have developed a quantitative structure-activity relationship (QSAR) for P-gp-associated ATPase activity for a diverse set of 22 drugs, and found that such activity is related to substrate molecular size and polarity. We have also developed a QSAR for drug efflux from the blood-brain barrier of another diverse set of 22 drugs, and found that such efflux is a function of drug size and polarisability. Thirdly, we have carried out a QSAR analysis of the ability of 157 phenothiazines and related drugs to reverse multidrug resistance. We were unable to obtain a good QSAR for the whole data-set, but when we divided the data-set into sub-sets of closely related structures, a series of good correlations was obtained, most of which incorporated descriptors that model molecular size and polarity/polarisability. In no instance did we find any evidence that hydrogen bonding or hydrophobicity play a part in multidrug resistance or its reversal, despite that fact that several other workers have reported that these effects appear to be important here.

The serotonin transporter intronic VNTR enhancer correlated with a predisposition to affective disorders has distinct regulatory elements within the domain based on the primary DNA sequence of the repeat unit

We have demonstrated that a variable number tandem repeat domain (VNTR) within intron 2 of the serotonin transporter gene is a transcriptional regulatory domain which is potentially correlated with a predisposition to affective disorders and other behavioural conditions. This correlation based on copy number of the VNTR alone (nine, 10 or 12 copies of 16/17 base-pair element) has been controversial and not reproduced in all studies. We demonstrate that individual repeat elements within the VNTR domain differ in their enhancer activity in an embryonic stem cell model. This has implications for both the mechanism by which these VNTRs are correlated with the progression of the disease and suggests that clinical analysis should now be extended to correlate sequence variation within the VNTR with the disorder. The latter may resolve some of the conflicting data published to date.

Mode locking in reversed-field pinch experiments

The MHD mode trajectory in the Madison Symmetric Torus reversed-field pinch has been found to obey the sine-Gordon equation. Corresponding to experiment, a perturbation analysis predicts the locations of mode locking to be at the vacuum chamber poloidal and/or toroidal gaps. The mode's energy dissipates when it locks, as shown by a decaying spiral phase-plane trajectory. Unlocked modes travel around the torus without an abrupt energy loss. By varying key machine parameters obtained by statistical analysis, the probability of locking in accordance with the experimental results can be predicted.

Femtosecond study of self-trapped vibrational excitons in crystalline acetanilide

Femtosecond IR spectroscopy of delocalized NH excitations of crystalline acetanilide confirms that self-trapping in hydrogen-bonded peptide units exists and does stabilize the excitation. Two phonons with frequencies of 48 and 76 cm (-1) are identified as the major degrees of freedom that mediate self-trapping. After selective excitation of the free exciton, self-trapping occurs within a few 100 fs. Excitation of the self-trapped states disappears from the spectral window of this investigation on a 1 ps time scale, followed by a slow ground state recovery of the hot ground state within 18 ps.

Federico Cesi and his field studies on the origin of fossils between 1610 and 1630

In 1603 Federico Cesi, along with four of his friends, founded the first Scientific Academy in Europe, the Accademia dei Lincei, which included Galileo Galillei as a member. Between 1611 and 1630 Cesi undertook an ambitious project to collect and record fossils from his lands around Acquasparta in Umbria. He had drawings and descriptions made of all the excavated fossils, fossil woods and their sites of origin. He died before his work could be published and it was left to his friend Francesco Stelluti to publish a monograph in which he claimed that evidence demonstrated that the fossil woods were formed from stone and were 'not once living'. The corpus of drawings, now in the Royal Collection at Windsor, has allowed the project to be reconstructed and fieldwork in Italy has shown that the complex nature of the fossil preservation could have easily confused the researchers and have led to misinterpretation of the fossils. This research by Cesi is the first to combine field and specimen data to interpret the origin of fossils and has been widely neglected by historians of Science.

Effect of altering conditions of the sequence method on baroreflex sensitivity

BACKGROUND

The sequence method is widely used as a simple, non-invasive measure of baroreflex sensitivity (BRS). This technique, originally described in anaesthetized cats, has been transferred virtually unchanged to humans, without evidence that the optimal values in cats are the same as those in patients with cardiovascular disease.

OBJECTIVE

To study the effect of altering the components of the sequence method on the measured BRS in patients with chronic heart failure (CHF) and in normal individuals.

METHODS

Eighty patients with CHF [aged 62 +/- 12 years (mean +/- SD)] and 40 normal control individuals [aged 38 +/- 15 years (mean +/- SD)] underwent measurement of heart rate and non-invasive blood pressure. Altering only the shift between blood pressure and R-R interval and the required correlation coefficient of the regression line had no effect on the value of BRS, but had a significant effect on the number of valid sequences. Alteration of the blood pressure or R-R interval thresholds, however, affected not only the number of valid sequences, but also the value of BRS in both groups. In normal controls, agreement with the bolus phenylephrine method was improved by increasing the blood pressure threshold, although this led to a reduction in the number of valid sequences. In patients with CHF, agreement was optimized by decreasing both the blood pressure and R-R interval thresholds. This also had the effect of increasing the number of valid sequences.

CONCLUSION

Changes should be made to this technique, to optimize its validity in conscious humans, particularly when applied to patients with attenuated BRS.

Skeletal muscle training in chronic heart failure

Patients with heart failure are limited in their ability to tolerate exercise. Recent research has suggested that this limitation cannot be entirely attributed to cardiac or lung impairment but rather that changes in peripheral muscles may play an important role. There are objective similarities between heart failure and muscular deconditioning. Deficiencies in peripheral blood flow and skeletal muscle function, morphology, metabolism and function are present in both conditions. Moreover, an exaggerated activity of the receptors sensitive to exercise-derived metabolic signals (muscle ergoreceptors and peripheral and central chemoreceptors) leads to early and profound exercise-induced fatigue and dyspnoea. These muscle afferents contribute to the ventilatory, haemodynamic and autonomic responses to exercise both in physiological and pathological conditions, including chronic heart failure. Against this background, a skeletal muscle origin of symptoms in heart failure has been proposed. The protective effects of physical training have been described in many recent studies: training improves ventilatory control, skeletal muscle metabolism and autonomic nervous system activity. The exercise training appears to induce its beneficial effects on skeletal muscle both directly (on muscle function, histological and biochemical features) and indirectly (by reducing the activation of the muscle afferents). The metabolic mediators of these muscle afferents may become a potential target in the future therapy of heart failure symptoms.

Excitation wave propagation as a possible mechanism for signal transmission in pancreatic islets of Langerhans

In response to glucose application, beta-cells forming pancreatic islets of Langerhans start bursting oscillations of the membrane potential and intracellular calcium concentration, inducing insulin secretion by the cells. Until recently, it has been assumed that the bursting activity of beta-cells in a single islet of Langerhans is synchronized across the whole islet due to coupling between the cells. However, time delays of several seconds in the activity of distant cells are usually observed in the islets of Langerhans, indicating that electrical/calcium wave propagation through the islets can occur. This work presents both experimental and theoretical evidence for wave propagation in the islets of Langerhans. Experiments with Fura-2 fluorescence monitoring of spatiotemporal calcium dynamics in the islets have clearly shown such wave propagation. Furthermore, numerical simulations of the model describing a cluster of electrically coupled beta-cells have supported our view that the experimentally observed calcium waves are due to electric pulses propagating through the cluster. This point of view is also supported by independent experimental results. Based on the model equations, an approximate analytical expression for the wave velocity is introduced, indicating which parameters can alter the velocity. We point to the possible role of the observed waves as signals controlling the insulin secretion inside the islets of Langerhans, in particular, in the regions that cannot be reached by any external stimuli such as high glucose concentration outside the islets.

Contribution of skeletal muscle 'ergoreceptors' in the human leg to respiratory control in chronic heart failure

The role of skeletal muscle ergoreceptors (afferents sensitive to muscle contraction, differentiated into metaboreceptors, sensitive to metabolic changes, and mechanoreceptors, sensitive to mechanical changes) in the genesis of the increased ventilatory drive in chronic heart failure is controversial. We have aimed to clarify the contribution of muscle metaboreceptors in the leg to ventilation and to compare this with the contribution of mechanoreceptors. Eighteen heart failure patients and 12 controls were studied. Metaboreceptor and mechanoreceptor responses were measured in the leg by bicycle exercise with and without regional circulatory occlusion during recovery, and by active and equivalent passive limb movement, respectively.Patients, in comparison with controls, had a lower peak VO2 (Oxygen uptake) (18.1+/-1.6 vs. 24.5+/-2.5 ml min(-1) kg(-1), P< 0.05), and an evident metaboreceptor contribution to the ventilatory response (3.5+/-1.6 vs. -4.0+/-1.3 l min(-1), P<0.001). Passive limb movement increased ventilation in both patients and controls (+3.7+/-0.4 and +2.9+/-0.5 l min(-1) from baseline, P<0.003), but this was associated with an increase in VO2 (+0.1+/-0.01 and +0.1+/-0.02 l min(-1) from baseline, P<0.001). The ratio of the increase in ventilation to the increase in VO2 during passive movement was not significantly higher than that during active exercise for either patients or controls, suggesting a limited contribution from the mechanoreceptors. In chronic heart failure the presence of a muscle metaboreceptor reflex is also demonstrated in the leg, while mechanoreceptors exhibited a non-significant contribution in both patients and controls. The hypothesis of a peripheral origin of symptoms of exertional intolerance in this syndrome is confirmed as being mainly due to metabolic stimulation of the muscle metaboreceptors.

Plant nuclei can contain extensive grooves and invaginations

Plant cells can exhibit highly complex nuclear organization. Through dye-labeling experiments in untransformed onion epidermal and tobacco culture cells and through the expression of green fluorescent protein targeted to either the nucleus or the lumen of the endoplasmic reticulum/nuclear envelope in these cells, we have visualized deep grooves and invaginations into the large nuclei of these cells. In onion, these structures, which are similar to invaginations seen in some animal cells, form tubular or planelike infoldings of the nuclear envelope. Both grooves and invaginations are stable structures, and both have cytoplasmic cores containing actin bundles that can support cytoplasmic streaming. In dividing tobacco cells, invaginations seem to form during cell division, possibly from strands of the endoplasmic reticulum trapped in the reforming nucleus. The substantial increase in nuclear surface area resulting from these grooves and invaginations, their apparent preference for association with nucleoli, and the presence in them of actin bundles that support vesicle motility suggest that the structures might function both in mRNA export from the nucleus and in protein import from the cytoplasm to the nucleus.

Technical advance: stringent control of transgene expression in Arabidopsis thaliana using the Top10 promoter system

We show that the tightly regulated tetracycline-sensitive Top10 promoter system (Weinmann et al. Plant J. 1994, 5, 559-569) is functional in Arabidopsis thaliana. A pure breeding A. thaliana line (JL-tTA/8) was generated which expressed a chimeric fusion of the tetracycline repressor and the activation domain of Herpes simplex virus (tTA), from a single transgenic locus. Plants from this line were crossed with transgenics carrying the ER-targeted green fluorescent protein coding sequence (mGFP5) under control of the Top10 promoter sequence. Progeny from this cross displayed ER-targeted GFP fluorescence throughout the plant, indicating that the tTA-Top10 promoter interaction was functional in A. thaliana. GFP expression was repressed by 100 ng ml-1 tetracycline, an order of magnitude lower than the concentration used previously to repress expression in Nicotiana tabacum. Moreover, the level of GFP expression was controlled by varying the concentration of tetracycline in the medium, allowing a titred regulation of transgenic activity that was previously unavailable in A. thaliana. The kinetics of GFP activity were determined following de-repression of the Top10:mGFP5 transgene, with a visible ER-targeted GFP signal appearing from 24 to 48 h after de-repression.

Ultrastructure and affinity of Lower Carboniferous megaspores from the Moscow Basin, Russia

Ten megaspore species isolated from Moscow Basin lignites of Lower Carboniferous (Viséan) age have been studied by scanning and transmission electron microscopy (SEM and TEM). These species belong to seven megaspore genera: Lagenicula, Sublagenicula, Crassilagenicula, Setosisporites, Zonalesporites, Caudatosporites, and Cystosporites. Megaspores of the genus Caudatosporites have only been described previously from the Duckmantian (Westphalian B); a new species is duly erected. The ultrastructure of megaspore walls from the genera Crassilagenicula and Zonalesporites has not been previously described. This study also places them in context with other contemporaneous megaspores. The study shows that during the Viséan, in the Moscow Basin, megaspores expressed a similar wall ultrastructure despite large differences in external appearance. The genus Crassilagenicula may represent a group of megaspores from plants that had evolved from those bearing gulate megaspores here typified by Lagenicula acuminata, Setosisporites brevispinosus, and Sublagenicula hirsutoida. Zonalesporites brasserti also appears to show affinities to this group, and may be representative of a plant species in a transitional state between the Lagenicula bearing lycopsids and those more isoetalean in nature.

Chronic heart failure in the elderly: value of cardiopulmonary exercise testing in risk stratification

OBJECTIVE

To assess the value of cardiopulmonary exercise testing in predicting prognosis in a cohort of elderly patients with chronic heart failure (CHF).

DESIGN

A retrospective cohort study of all patients with CHF over the age of 70 years assessed between January 1992 and May 1997.

SETTING

Tertiary centre.

PATIENTS

50 patients (mean (SD) age 75.9 (4.5) years, 8 women) with CHF New York Heart Association (NYHA) class I (3 patients), II (25 patients), III (20 patients), and IV (2 patients). Follow up was complete for two years in all patients.

RESULTS

The patients underwent cardiopulmonary exercise testing (peak oxygen consumption 15.2 (4.5) ml/kg/min, minute ventilation/carbon dioxide production (VE/VCO(2)) slope 38.7 (11.8)); radionucleide ventriculography (left ventricular ejection fraction 32.8 (14.3)%); serum sodium measurement (139 (2.8) mmol/l); and echocardiography (left ventricular end diastolic dimension 6.1 (1.1) cm, left ventricular end systolic dimension 4.7 (1.5) cm). At the end of follow up in May 1999, 26 patients had died. The median follow up of the survivors was 47.7 months (interquartile range 31. 5-53.5 months). On univariate analysis VE/VCO(2) slope (p < 0.0001), NYHA class (p < 0.001), peak oxygen uptake (VO(2)) (p < 0.01), left ventricular end systolic dimension (p < 0.05), and serum sodium concentration (p < 0.05) had significant predictive power. Stepwise multivariate analysis identified only VE/VCO(2) slope (p < 0.01), NYHA class (p < 0.05), and peak VO(2) (p< 0.05) as conveying significant independent prognostic information.

CONCLUSION

Elderly patients with CHF have a high mortality, with the majority dead within two years. Cardiopulmonary exercise testing provides important information for risk stratification within this group and its use should not be neglected.

Changes in cytosolic pH within Arabidopsis root columella cells play a key role in the early signaling pathway for root gravitropism

Ratiometric wide-field fluorescence microscopy with 1',7'- bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein (BCECF)-dextran demonstrated that gravistimulation leads to rapid changes in cytoplasmic pH (pHc) in columella cells of Arabidopsis roots. The pHc of unstimulated columella cells in tiers 2 and 3, known sites of graviperception (E.B. Blancaflor, J.B. Fasano, S. Gilroy [1998] Plant Physiol 116: 213-222), was 7.22 +/- 0.02 pH units. Following gravistimulation, the magnitude and direction of pHc changes in these cells depended on their location in the columella. Cells in the lower side of tier 2 became more alkaline by 0.4 unit within 55 s of gravistimulation, whereas alkalinization of the cells on the upper side was slower (100 s). In contrast, all cells in tier 3 acidified by 0.4 pH unit within 480 s after gravistimulation. Disrupting these pHc changes in the columella cells using pHc modifiers at concentrations that do not affect root growth altered the gravitropic response. Acidifying agents, including bafilomycin A1, enhanced curvature, whereas alkalinizing agents disrupted gravitropic bending. These results imply that pHc changes in the gravisensing cells and the resultant pH gradients across the root cap are important at an early stage in the signal cascade leading to the gravitropic response.

Adductor transfers in cerebral palsy: long-term results studied by gait analysis

Thirty-three ambulatory patients with spastic cerebral palsy underwent evaluation and gait analysis an average of 9.6 years after bilateral posterior adductor transfers to the ischium. All patients showed functional improvement postoperatively, which was maintained at long-term follow-up in 94%. Gait analysis, however, documented pelvic obliquity in 85% of this group of patients. Associated with pelvic obliquity was a 36% incidence of unilateral hip subluxation. These complications of posterior adductor transfers have been difficult to treat and have resulted in the abandonment of this procedure at our institution.