Carbon storage and DNA absorption in allophanic soils and paleosols

Andisols and andic paleosols dominated by the nanocrystalline mineral allophane sequester large amounts of carbon (C), attributable mainly to its chemical bonding with charged hydroxyl groups on the surface of allophane together with its physical protection in nanopores within and between allophane nanoaggregates. C near-edge X-ray absorption fine structure (NEXAFS) spectra for a New Zealand Andisol (Tirau series) showed that the organic matter (OM) mainly comprises quinonic, aromatic, aliphatic, and carboxylic C. In different buried horizons from several other Andisols, C contents varied but the C species were similar, attributable to pedogenic processes operating during developmental upbuilding, downward leaching, or both. The presence of OM in natural allophanic soils weakened the adsorption of DNA on clay; an adsorption isotherm experiment involving humic acid (HA) showed that HA-free synthetic allophane adsorbed seven times more DNA than HA-rich synthetic allophane. Phosphorus X-ray absorption near-edge structure (XANES) spectra for salmonsperm DNA and DNA-clay complexes indicated that DNA was bound to the allophane clay through the phosphate group, but it is not clear if DNA was chemically bound to the surface of the allophane or to OM, or both. We plan more experiments to investigate interactions among DNA, allophane (natural and synthetic), and OM. Because DNA shows a high affinity to allophane, we are studying the potential to reconstruct late Quaternary palaeoenvironments by attempting to extract and characterise ancient DNA from allophanic paleosol

Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects

Palaeoenvironmental DNA (PalEnDNA) is defined as ancient DNA (aDNA) originating from disseminated genetic material within palaeoenvironmental samples. Sources of PalEnDNA include marine and lake sediments, peat, loess, till, ice, permafrost, palaeosols, coprolites, preserved gut contents, dental calculus, tephras, and soils as well as deposits in caves/rockshelters and at archaeological sites. PalEnDNA analysis provides a relatively new tool for Quaternary and archaeological sciences and its applications have included palaeoenvironmental and palaeodietary reconstructions, testing hypotheses regarding megafaunal extinctions, human–environment interactions, taxonomic studies and studies of DNA damage. Because PalEnDNA samples comprise markedly different materials, and represent wide-ranging depositional and taphonomic contexts, various issues must be addressed to achieve robust, reproducible findings. Such issues include climatic and temporal limitations, the biological origin and state (free versus bound) of PalEnDNA, stratigraphic reliability, sterile sampling, ability to distinguish modern from aDNA signals, DNA damage and PCR amplification, DNA extraction methods, and taxonomic resolution. In this review, we provide a non-specialist introduction to the use of PalEnDNA for Quaternary and archaeological researchers, assess attributes and limitations of this palaeoenvironmental tool, and discuss future prospects of using PalEnDNA to reconstruct past environments

Machine Learning Methods for Prediction of CDK-Inhibitors

Progression through the cell cycle involves the coordinated activities of a suite of cyclin/cyclin-dependent kinase (CDK) complexes. The activities of the complexes are regulated by CDK inhibitors (CDKIs). Apart from its role as cell cycle regulators, CDKIs are involved in apoptosis, transcriptional regulation, cell fate determination, cell migration and cytoskeletal dynamics. As the complexes perform crucial and diverse functions, these are important drug targets for tumour and stem cell therapeutic interventions. However, CDKIs are represented by proteins with considerable sequence heterogeneity and may fail to be identified by simple similarity search methods. In this work we have evaluated and developed machine learning methods for identification of CDKIs. We used different compositional features and evolutionary information in the form of PSSMs, from CDKIs and non-CDKIs for generating SVM and ANN classifiers. In the first stage, both the ANN and SVM models were evaluated using Leave-One-Out Cross-Validation and in the second stage these were tested on independent data sets. The PSSM-based SVM model emerged as the best classifier in both the stages and is publicly available through a user-friendly web interface at http://bioinfo.icgeb.res.in/cdkipred

Quantitative EEG findings in patients with acute, brief depression combined with other fluctuating psychiatric symptoms: a controlled study from an acute psychiatric department

<p>Abstract</p> <p>Background</p> <p>Patients with brief depressive episodes and concurrent rapidly fluctuating psychiatric symptoms do not fit current diagnostic criteria and they can be difficult to diagnose and treat in an acute psychiatric setting. We wanted to study whether these patients had signs of more epileptic or organic brain dysfunction than patients with depression without additional symptomatology.</p> <p>Methods</p> <p>Sixteen acutely admitted patients diagnosed with a brief depressive episode as well as another concurrent psychiatric diagnosis were included. Sixteen patients with major depression served as controls. Three electroencephalographic studies (EEG) were visually interpreted and the background activity was also analysed with quantitative electroencephalography (QEEG).</p> <p>Results</p> <p>The group with brief depression and concurrent symptoms had multiple abnormal features in their standard EEG compared to patients with major depression, but they did not show significantly more epileptiform activity. They also had significantly higher temporal QEEG delta amplitude and interhemispheric temporal delta asymmetry.</p> <p>Conclusion</p> <p>Organic brain dysfunction may be involved in the pathogenesis of patients with brief depressive episodes mixed with rapidly fluctuating psychiatric symptoms. This subgroup of depressed patients should be investigated further in order to clarify the pathophysiology and to establish the optimal evaluation scheme and treatment in an acute psychiatric setting.</p

Differences and Commonalities in Physical, Chemical and Mineralogical Properties of Zanzibari Geophagic Soils

The function of human geophagy has long been questioned. We sought to test hypotheses concerning its potential physiological effects through analysis of soils and patterns in geophagy behavior. Eleven samples of geophagic soils consumed by pregnant women on Pemba Island, Zanzibar, Tanzania, were characterized according to their color, texture, major element chemistry, trace element chemistry, bulk mineralogy, and clay mineralogy. An epidemiological study (N = 2367) and ethnographic interviews (N = 57) on Pemba yielded information about geophagic behaviors and socio-demographic and biological characteristics of those who consumed earth. The soils varied widely in color, ranging from light red to white through various shades of brown and yellow, and texture ranged from clay to sand. Major element chemistry of the soils also varied greatly; most were low in Fe and Ca. Trace elements, whether of biological or non-biological significance, were uniformly low when compared with normal ranges of mineral soils. The sole commonality among the samples is that all clay fractions were dominated by a kaolin mineral: kaolinite, halloysite, or a mixture of both. Geophagy behavior also varied greatly, with one major exception: a greater proportion of pregnant women (7.1%) and young children (4.5%) consumed earth than non-pregnant women (0.2%) or men (0%). The presence of kaolin mineral in all samples, its palliative and detoxifying properties, and the highest prevalence of geophagy among those most biologically vulnerable suggest that geophagy may be a protective behavior

Tephrochronology

Tephrochronology is the use of primary, characterized tephras or cryptotephras as chronostratigraphic marker beds to connect and synchronize geological, paleoenvironmental, or archaeological sequences or events, or soils/paleosols, and, uniquely, to transfer relative or numerical ages or dates to them using stratigraphic and age information together with mineralogical and geochemical compositional data, especially from individual glass-shard analyses, obtained for the tephra/cryptotephra deposits. To function as an age-equivalent correlation and chronostratigraphic dating tool, tephrochronology may be undertaken in three steps: (i) mapping and describing tephras and determining their stratigraphic relationships, (ii) characterizing tephras or cryptotephras in the laboratory, and (iii) dating them using a wide range of geochronological methods. Tephrochronology is also an important tool in volcanology, informing studies on volcanic petrology, volcano eruption histories and hazards, and volcano-climate forcing. Although limitations and challenges remain, multidisciplinary applications of tephrochronology continue to grow markedly

Toward a Comprehensive Approach to the Collection and Analysis of Pica Substances, with Emphasis on Geophagic Materials

Pica, the craving and subsequent consumption of non-food substances such as earth, charcoal, and raw starch, has been an enigma for more than 2000 years. Currently, there are little available data for testing major hypotheses about pica because of methodological limitations and lack of attention to the problem.In this paper we critically review procedures and guidelines for interviews and sample collection that are appropriate for a wide variety of pica substances. In addition, we outline methodologies for the physical, mineralogical, and chemical characterization of these substances, with particular focus on geophagic soils and clays. Many of these methods are standard procedures in anthropological, soil, or nutritional sciences, but have rarely or never been applied to the study of pica.Physical properties of geophagic materials including color, particle size distribution, consistency and dispersion/flocculation (coagulation) should be assessed by appropriate methods. Quantitative mineralogical analyses by X-ray diffraction should be made on bulk material as well as on separated clay fractions, and the various clay minerals should be characterized by a variety of supplementary tests. Concentrations of minerals should be determined using X-ray fluorescence for non-food substances and inductively coupled plasma-atomic emission spectroscopy for food-like substances. pH, salt content, cation exchange capacity, organic carbon content and labile forms of iron oxide should also be determined. Finally, analyses relating to biological interactions are recommended, including determination of the bioavailability of nutrients and other bioactive components from pica substances, as well as their detoxification capacities and parasitological profiles.This is the first review of appropriate methodologies for the study of human pica. The comprehensive and multi-disciplinary approach to the collection and analysis of pica substances detailed here is a necessary preliminary step to understanding the nutritional enigma of non-food consumption