Still searching for graves: an analytical strategy for interpreting geophysical data used in the search for “unmarked” graves

Searching for and mapping the physical extent of unmarked graves using geophysical techniques has proven difficult in many cases. The success of individual geophysical techniques for detecting graves depends on a site-by-site basis. Significantly, detection of graves often results from measured contrasts that are linked to the background soils rather than the type of archaeological feature associated with the grave. It is evident that investigation of buried remains should be considered within a 3D space as the variation in burial environment can be extremely varied through the grave. Within this paper, we demonstrate the need for a multi-method survey strategy to investigate unmarked graves, as applied at a “planned” but unmarked pauper’s cemetery. The outcome from this case study provides new insights into the strategy that is required at such sites. Perhaps the most significant conclusion is that unmarked graves are best understood in terms of characterization rather than identification. In this paper, we argue for a methodological approach that, while following the current trends to use multiple techniques, is fundamentally dependent on a structured approach to the analysis of the data. The ramifications of this case study illustrate the necessity of an integrated strategy to provide a more holistic understanding of unmarked graves that may help aid in management of these unseen but important aspects of our heritage. It is concluded that the search for graves is still a current debate and one that will be solved by methodological rather than technique-based arguments.

Estrogen regulation of chicken riboflavin carrier protein gene is mediated by ERE half sites without direct binding of estrogen receptor

Estrogen is an important steroid hormone that mediates most of its effects on regulation of gene expression by binding to intracellular receptors. The consensus estrogen response element (ERE) is a 13 bp palindromic inverted repeat with a three nucleotide spacer. However, several reports suggest that many estrogen target genes are regulated by diverse elements, such as imperfect EREs and ERE half sites (ERE 1/2), which are either the proximal or the distal half of the palindrome. To gain more insight into ERE half site-mediated gene regulation, we used a region from the estrogen-regulated chicken riboflavin carrier protein (RCP) gene promoter that contains ERE half sites. Using moxestrol, an analogue of estrogen and transient transfection of deletion and mutation containing RCP promoter/reporter constructs in chicken hepatoma (LMH2A) cells, we identified an estrogen response unit (ERU) composed of two consensus ERE 1/2 sites and one non-consensus ERE 1/2 site. Mutation of any of these sites within this ERU abolishes moxestrol response. Further, the ERU is able to confer moxestrol responsiveness to a heterologous promoter. Interestingly, RCP promoter is regulated by moxestrol in estrogen responsive human MCF-7 cells, but not in other cell lines such as NIH3T3 and HepG2 despite estrogen receptor-alpha (ER-�) co transfection. Electrophoretic mobility shift assays (EMSAs) with promoter regions encompassing the half sites and nuclear extracts from LMH2A cells show the presence of a moxestrol-induced complex that is abolished by a polyclonal anti-ER� antibody. Surprisingly, estrogen receptor cannot bind to these promoter elements in isolation. Thus, there appears to be a definite requirement for some other factor(s) in addition to estrogen receptor, for the generation of a suitable response of this promoter to estrogen. Our studies therefore suggest a novel mechanism of gene regulation by estrogen, involving ERE half sites without direct binding of ER to the cognate elements.

In silico identification and characterization of protein-ligand binding sites

Protein–ligand binding site prediction methods aim to predict, from amino acid sequence, protein–ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein–ligand interactions has become extremely important to help determine a protein’s functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein–ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein–ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein–ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

Surface Urban Energy and Water Balance Scheme (SUEWS): development and evaluation at two UK sites

The Surface Urban Energy and Water Balance Scheme (SUEWS) is evaluated at two locations in the UK: a dense urban site in the centre of London and a residential suburban site in Swindon. Eddy covariance observations of the turbulent fluxes are used to assess model performance over a twoyear period (2011-2013). The distinct characteristics of the sites mean their surface energy exchanges differ considerably. The model suggests the largest differences can be attributed to surface cover (notably the proportion of vegetated versus impervious area) and the additional energy supplied by human activities. SUEWS performs better in summer than winter, and better at the suburban site than the dense urban site. One reason for this is the bias towards suburban summer field campaigns in observational data used to parameterise this (and other) model(s). The suitability of model parameters (such as albedo, energy use and water use) for the UK sites is considered and, where appropriate, alternative values are suggested. An alternative parameterisation for the surface conductance is implemented, which permits greater soil moisture deficits before evaporation is restricted at non-irrigated sites. Accounting for seasonal variation in the estimation of storage heat flux is necessary to obtain realistic wintertime fluxes.

Alternative body sites for heat stress measurement in milking cows under tropical conditions and their relationship to the thermal discomfort of the animals

This study was conducted to determine the relationship among temperatures measured at different anatomical sites of the animal body and their daily pattern as indicative of the thermal stress in lactating dairy cows under tropical conditions. Environmental dry bulb (DBT) and black globe (BGT) temperatures and relative humidity (RH) were recorded. Rectal temperature (RT), respiratory frequency (RF), body surface (BST), internal base of tail (TT), vulva (VT) and auricular temperatures (AT) were collected, from 37 Black and White Holstein cows at 0700, 1300 and 1800 hours. RT showed a moderately and positive correlations with all body temperatures, ranging from 0.59 with TT to 0.64 with BST. Correlations among AT, VT and TT with RF were very similar (from 0.63 to 0.64) and were greater than those observed for RF with RT (0.55) or with BST (0.54). RF and RT were positively correlated to TT (0.63 and 0.59, respectively), AT (r = 0.63 for both) and VT (r = 0.64 and 0.63, respectively). Positive and very high correlations were observed among AT, VT and TT (from 0.94 to 0.97) indicating good association of temperatures measured in these anatomical sites. Correlations of BST with AT and VT were positive and very similar (0.71 and 0.72, respectively) and lower with TT (0.66). The AT, TT, VT and BST presented similar patterns and follow the variations of DBT through the day. Temperatures measured at different anatomical sites of the animal body have the potential to be used as indicative of the thermal stress in lactating dairy cows.

Relationship Between Expression of Voltage-Dependent Anion Channel (VDAC) Isoforms and Type of Hexokinase Binding Sites on Brain Mitochondria

Voltage-dependent anion channels (VDAC) are pore-forming proteins found in the outer mitochondrial membrane of eukaryotes. VDACs are known to play an essential role in cellular metabolism and in early stages of apoptosis. In mammals, three VDAC isoforms have been identified. A proteomic approach was exploited to study the expression of VDAC isoforms in rat, bovine, and chicken brain mitochondria. Given the importance of mitochondrially bound hexokinase in regulation of aerobic glycolysis in brain, we studied the possibility that differences in the relative expression of VDAC isoforms may be a factor in determining the species-dependent ratio of type A/type B hexokinase binding sites on brain mitochondria. The spots were characterized, and the signal intensities among spots were compared. VDAC1 was the most abundantly expressed of the three isoforms. Moreover the expression of VDAC1 plus VDAC2 was significantly higher in bovine than in rat brain. Chicken brain mitochondria showed the highest VDAC1 expression and the lowest of VDAC2. Bovine brain mitochondria had the highest VDAC2 levels. We concluded that the nature of hexokinase binding site is not determined by the expression of a single VDAC isoform.

Light and scanning electron microscopy of Henneguya arapaima n. sp (Myxozoa: Myxobolidae) and histology of infected sites in pirarucu (Arapaima gigas: Pisces: Arapaimidae) from the Araguaia River, Brazil

In this report, we describe Henneguya arapaima n. sp., a parasite of the gill arch and gall bladder of Arapaima gigas (pirarucu) collected in the Araguaia River, in the municipality of Nova Crixas, Goias State, central Brazil. The plasmodia were white, round or ellipsoidal and measured 200-600 mu m. Parasite development was asynchronous and the mature spores were fusifonn and had smooth wall. The spores measurements were (range, with means +/- S.D. in parentheses): total length-48.4-53.1 mu m (51.6 +/- 3.4 mu m), body length-13.5-15.2 mu m (14.2 +/- 0.8 mu m), body width-5.1-6.1 mu m (5.7 +/- 0.5 mu m), body thickness-4.7-5.3 mu m (4.9 +/- 0.2 mu m) and caudal process length-38.0-41.2 mu m (38.3 +/- 2.9 mu m). The polar capsules were elongated and of unequal size, with lengths of 6.3-6.8 mu m (6.5 +/- 0.2) and 6.2-6.6 mu m (6.3 +/- 0.1) for the longest and shortest axes, respectively. Capsule width was 1.4-1.6 mu m (1.5 +/- 0.1). Histological analysis showed that the plasmodia occurred in the tunica adventitia of the gall bladder and were delimited by a thin capsule of connective tissue. In the gill arch, the plasmodia were also surrounded by connective tissue similar to the endomesium, of striated skeletal muscle cells. Sixty-five juvenile specimens of A. gigas weighing 1.0-25.0 kg were examined, 17 (26.1%) of which were infected. Of these, 14 (82.3%) had cysts in the gall bladder, two (11.7%) had cysts in the gill arch and only one (5.9%) had cysts in both organs. When the fish were grouped by weight, the prevalence of infection in fish weighing up to 10.0 kg (20.7%) was significantly lower than in fish weighing 10.1-25.0 kg (50%) (G = 3.93; d.f. = 1; p < 0.05). (C) 2008 Elsevier B.V. All rights reserved.

Regional representativity of AERONET observation sites during the biomass burning season in South America determined by correlation studies with MODIS Aerosol Optical Depth

This paper presents an analysis of ground-based Aerosol Optical Depth (AOD) observations by the Aerosol Robotic Network (AERONET) in South America from 2001 to 2007 in comparison with the satellite AOD product of Moderate Resolution Imaging Spectroradiometer (MODIS), aboard TERRA and AQUA satellites. Data of 12 observation sites were used with primary interest in AERONET sites located in or downwind of areas with high biomass burning activity and with measurements available for the full time range. Fires cause the predominant carbonaceous aerosol emission signal during the dry season in South America and are therefore a special focus of this study. Interannual and seasonal behavior of the observed AOD at different sites were investigated, showing clear differences between purely fire and urban influenced sites. An intercomparison of AERONET and MODIS AOD annual correlations revealed that neither an interannual long-term trend may be observed nor that correlations differ significantly owing to different overpass times of TERRA and AQUA. Individual anisotropic representativity areas for each AERONET site were derived by correlating daily AOD of each site for all years with available individual MODIS AOD pixels gridded to 1 degrees x 1 degrees. Results showed that for many sites a good AOD correlation (R(2) > 0.5) persists for large, often strongly anisotropic, areas. The climatological areas of common regional aerosol regimes often extend over several hundreds of kilometers, sometimes far across national boundaries. As a practical application, these strongly inhomogeneous and anisotropic areas of influence are being implemented in the tropospheric aerosol data assimilation system of the Coupled Chemistry-Aerosol-Tracer Transport Model coupled to the Brazilian Regional Atmospheric Modeling System (CCATT-BRAMS) at the Brazilian National Institute for Space Research (INPE). This new information promises an improved exploitation of local site sampling and, thus, chemical weather forecast.

Forest structure in a mosaic of rainforest sites: The effect of fragmentation and recovery after clear cut

A variety of human-induced disturbances such as forest fragmentation and recovery after deforestation for pasture or agricultural activities have resulted in a complex landscape mosaic in the Una region of northeastern Brazil. Using a set of vegetation descriptors, we investigated the main structural changes observed in forest categories that comprise the major components of the regional landscape and searched for potential key descriptors that could be used to discriminate among different forest categories. We assessed the forest structure of five habitat categories defined as (I) interiors and (2) edges of large fragments of old-growth forest (>1000 ha), (3) interiors and (4) edges of small forest fragments (<100 ha), and (5) early secondary forests. Forest descriptors used here were: frequency of herbaceous lianas and woody climbers, number of standing dead trees, number of fallen trunks, litter depth, number of pioneer plants (early secondary and shade-intolerant species), vertical foliage stratification profile and distribution Of trees in different diameter classes. Edges and interiors of forest fragments were significantly different only in the number of standing dead trees. Secondary forests and edges of fragments showed differences in litter depth, fallen trunks and number of pioneer trees, and secondary forests were significantly different from fragment interiors in the number of standing dead trees and the number of pioneer trees. Horizontal and vertical structure evaluated via ordination analysis showed that fragment interiors, compared to secondary forests, were characterized by a greater number of medium (25-35 cm) and large (35-50 cm) trees and smaller numbers of thin trees (5-10 cm). There was great heterogeneity at the edges of small and large fragments, as these sites were distributed along almost the entire gradient. Most interiors of large and small fragments presented higher values of foliage densities at higher strata ( 15-20 m and at 20-25 m height), and lower densities at 1-5 m. All secondary forests and some fragment edge sites showed an opposite tendency. A discriminant function highlighted differences among forest categories, with transects of large fragment interiors and secondary forests representing two extremes along a disturbance gradient determined by foliage structure (densities at 15-20 m and 20-25 m), with the edges of both large and small fragments and the interiors of small fragments scattered across the gradient. The major underlying processes determining patterns of forest disturbance in the study region are discussed, highlighting the importance of forest fragments, independently of its size, as forests recovery after clear cut show a greatly distinct structure, with profound implications on fauna movements. (C) 2009 Elsevier BY. All rights reserved.

Potential sites of triple-helical nucleic acid formation in chromosomes of Rhynchosciara (Diptera: Sciaridae) and Drosophila melanogaster

Antibodies to specific nucleic acid conformations are amongst the methods that have allowed the study of non-canonical (Watson-Crick) DNA structures in higher organisms. In this work, the structural limitations for the immunological detection of DNA.RNA hybrid duplexes were examined using specific RNA homopolymers as probes for homopolymer polydeoxyadenylic acid (poly(dA)).polydeoxythymidylic acid (poly(dT))-rich regions of Rhynchosciara americana (Diptera: Sciaridae) chromosomes. Anti-DNA.RNA duplexes did not react with the complex formed between chromosomal poly(dA) and exogenous polyuridylic acid (poly(rU)). Additionally, poly(rU) prevented the detection of polyadenylic acid.poly(dT) hybrid duplexes preformed in situ. These results raised the possibility that three-stranded structures rather than duplexes were formed in chromosomal sites. To test this hypothesis, the specificity of antibodies to triple-helical nucleic acids was reassessed employing distinct nucleic acid configurations. These antibodies were raised to the poly(dA).poly(rU).poly(rU) complex and have been used here for the first time in immunocytochemistry. Anti-triplex antibodies recognised the complex poly(dA).poly(rU).poly(rU) assembled with poly(rU) in poly(dA).poly(dT)-rich homopolymer regions of R. americana chromosomes. The antibodies could not detect short triplex stretches, suggesting the existence of constraints for triple-helix detection, probably related to triplex tract length. In addition, anti-poly(dA).poly(rU).poly(rU) antibodies reacted with the pericentric heterochromatin of RNase-treated polytene chromosomes of R. americana and Drosophila melanogaster. In apparent agreement with data obtained in cell types from other organisms, the results of this work suggest that significant triple-helix DNA extensions can be formed in pericentric regions of these species.