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PubMed2002

Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior.

Effects of amino acid substitutions at four fully buried sites of the ubiquitin molecule on the thermodynamic parameters (enthalpy, Gibbs energy) of unfolding were evaluated experimentally using differential scanning calorimetry. The same set of substitutions has been incorporated at each of four sites. These substitutions have been designed to perturb packing (van der Waals) interactions, hydration, and/or hydrogen bonding. From the analysis of the thermodynamic parameters for these ubiquitin variants we conclude that: (i) packing of non-polar groups in the protein interior is favorable and is largely defined by a favorable enthalpy of van der Waals interactions. The removal of one methylene group from the protein interior will destabilize a protein by approximately 5 kJ/mol, and will decrease the enthalpy of a protein by 12 kJ/mol. (ii) Burial of polar groups in the non-polar interior of a protein is highly destabilizing, and the degree of destabilization depends on the relative polarity of this group. For example, burial of Thr side-chain in the non-polar interior will be less destabilizing than burial of Asn side-chain. This decrease in stability is defined by a large enthalpy of dehydration of polar groups upon burial. (iii) The destabilizing effect of dehydration of polar groups upon burial can be compensated if these buried polar groups form hydrogen bonding. The enthalpy of this hydrogen bonding will compensate for the unfavorable dehydration energy and as a result the effect will be energetically neutral or even slightly stabilizing.

Amino Acids↗
PubMedDate not supplied

Holocene age of the Yuha burial: direct radiocarbon determinations by accelerator mass spectrometry.

The view that human populations may not have arrived in the Western Hemisphere before about 12,000 radiocarbon yr BP has been challenged by claims of much greater antiquity for a small number of archaeological sites and human skeleton samples. One such site is the Homo sapiens sapiens cairn burial excavated in 1971 from the Yuha desert, Imperial County, California. Radiocarbon analysis of caliche coating one of the bones of the skeleton yielded a radiocarbon age of 21,500 +/- 1,000 yr BP, while radiocarbon and uranium series analyses of caliche coating a cairn boulder yielded ages of 22,125 +/- 400 and 19,000 +/- 3,000 yr BP, respectively. The late Pleistocene age assignment to the Yuha burial has been challenged by comparing the cultural context of the burial with other cairn burials in the same region, on the basis of the site's geomorphological context and from radiocarbon analyses of soil caliches. In rebuttal, arguments in defence of the original age assignment have been presented as well as an amino acid recemization analysis on the Yuha skeleton indicating an age of 23,600 +/- 2,600 yr BP. The tandem accelerator mass spectrometer at the University of Arizona has now been used to measure the ratio of 14C/13C in several organic and inorganic fractions of post-cranial bone from the Yuha H. sapiens sapiens skeleton. Isotope ratios from six chemical fractions all yielded radiocarbon ages for the skeleton of less than 4,000 yr BP. These results indicate that the Yuha skeleton is of Holocene age, in agreement with the cultural context of the burial, and in disagreement with the previously assigned Pleistocene age of 19,000-23,000 yr.

Animals↗
PubMed2001

Heat capacity analysis of oxidized Escherichia coli thioredoxin fragments (1--73, 74--108) and their noncovalent complex. Evidence for the burial of apolar surface in protein unfolded states.

We have calculated the absolute heat capacities of fragments 1--73 (N fragment) and 74--108 (C fragment) from thioredoxin, their complex and the uncleaved protein, from the concentration dependence of the apparent heat capacities of the solutions determined by differential scanning calorimetry. We find that, while the absolute heat capacities of uncleaved, unfolded thioredoxin and the C fragment are in good agreement with the theoretical values expected for fully solvated chains (calculated as the sum of the contributions of the constituent amino acids), the absolute heat capacities of the N fragment and the unfolded complex are about 2 kJ x K(-1) x mol(-1) lower than the fully solvated-chain values. We attribute this discrepancy to burial of the apolar surface in the N fragment (as burial of the polar area is expected to lead to an increase in heat capacity). Illustrative calculations suggest that burial of about 1000--1600 A(2) of apolar surface takes place in the N fragment (probably accompanied by the burial of a smaller amount of polar surface). In general, this work is supportive of heat capacity measurements on protein fragments being useful as probes of surface burial in studies to characterize protein unfolded states and the high regions of protein folding landscapes.

Buffers↗
PubMed2004

The effect of the method of burial on adipocere formation.

A controlled laboratory experiment was conducted in order to investigate the effect of the method of burial (i.e. the presence of coffin and clothing) on the formation of adipocere. This study follows previous studies by the authors who have investigated the effect of physical conditions on the formation of adipocere present in a controlled burial environment. The study utilises infrared spectroscopy to provide a preliminary lipid profile of the remains following a 12 month decomposition period. Inductively coupled plasma-mass spectrometry was employed as a technique for determining the salts of fatty acids present in adipocere. Gas chromatography-mass spectrometry (GC-MS) was used as the confirmatory test for the identification and determination of the chemical composition of adipocere which formed in the controlled burial environments. The results suggest that coffins will retard the rate at which adipocere forms but that clothing enhances its formation. The results concur with previous observations on adipocere formation in burial environments.

Adipose Tissue↗
PubMed2005

U-series and ESR analyses of bones and teeth relating to the human burials from Skhul.

In order to resolve long-standing issues surrounding the age of the Skhul early modern humans, new analyses have been conducted, including the dating of four well-provenanced fossils by ESR and U-series. If the Skhul burials took place within a relatively short time span, then the best age estimate lies between 100 and 135 ka. This result agrees very well with TL ages obtained from burnt flint of 119+/-18 ka (Mercier et al., 1993). However, we cannot exclude the possibility that the material associated with the Skhul IX burial is older than those of Skhul II and Skhul V. These and other recent age estimates suggest that the three burial sites, Skhul, Qafzeh and Tabun are broadly contemporaneous, falling within the time range of 100 to 130 ka. The presence of early representatives of both early modern humans and Neanderthals in the Levant during Marine Isotope Stage 5 inevitably complicates attempts at segregating these populations by date or archaeological association. Nevertheless, it does appear that the oldest known symbolic burials are those of early modern humans at Skhul and Qafzeh. This supports the view that, despite the associated Middle Palaeolithic technology, elements of modern human behaviour were represented at Skhul and Qafzeh prior to 100 ka.

Animals↗
PubMed1989

Ethical and legal aspects to death: the burial.

As a form of ritualized behaviour, the burial promotes and maintains the emotional well-being of the individual and the social cohesion of the group. Sources of burial law in Southern Africa are summarized and the present legal situation with regard to burial is given in some detail. Fulton sums up the essence of our subject historically and comparatively as follows: 'Burial of the dead is an ancient practice among men. From paleolithic times to the present, man has responded to the death of his fellow man with solemnity and ceremony. The event of death has evoked not only a religious awe in men, but its threat to the survival of communal life has also engendered fear, just as its disruption of family life has aroused sorrow.'

Attitude to Death↗
PubMed2005

Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts.

Electrostatics calculations with proteins that are uniformly charged over volume can aid enzyme/non-enzyme discrimination. For known enzymes, such methods locate active sites to within 5% on the enzyme surface, in 77% of a test set. We now report that removing the dielectric boundary improves active site location to 80%, with optimal discrimination between enzymes and non-enzymes of around 80% specificity and 80% sensitivity. This calculation quantifies burial of solvent-accessible regions. Many of the true enzymes incorrectly assigned as non-enzymes have active sites at subunit boundaries. These are missed in monomer-based calculations. Catalytic and non-catalytic antibodies are studied in this context of active/binding site burial. Whilst catalytic antibodies, on average, have marginally higher active site burial than non-catalytic antibodies, these values are generally smaller than for non-antibody enzymes, possibly contributing to their relatively low turnover. Prediction of active site location improves further when sequence profile-based weights replace the uniform charge distribution, so that a combination of burial and amino acid conservation is assessed. Accuracy rises to 93% of active sites to within 5%, in the test set, for the optimal profile weights scheme. The equivalent value in a separate validation set is 89% to within 5%. Enzyme/non-enzyme and enzyme functional site predictions are made for structural genomics proteins, suggesting that a substantial majority of these are non-enzymes.

Antibodies↗
PubMed2002

Influence of nematophagous fungi, earthworms and dung burial on development of the free-living stages of Ostertagia (Teladorsagia) circumcincta in New Zealand.

Biological options for nematode parasite control are being sought, as the long-term efficacy of conventional anthelmintics comes increasingly under threat from drug-resistant parasites. Three biological methods with the potential to reduce pasture contamination by parasitic nematode larvae were examined: (a) killing of larvae developing in dung by nematophagous fungi; (b) removal of dung through earthworm ingestion; (c) burial of dung in soil as might occur through the action of dung beetles. Field trials with the test bio-control agents were carried out in autumn and spring by adding dung from sheep infected with Ostertagia (Teladorsagia) circumcincta to pots of ryegrass/white clover. The factorial treatment structure included five fungal treatments (individual applications of Duddingtonia flagrans, Monacrosporium gephyropagum and Harposporium helicoides, a combination of all the three fungi together and an untreated control), two dung burial treatments (dung buried or deposited on the soil surface) and two earthworm treatments (earthworms present or absent). D. flagrans and H. helicoides, individually or in combination, reduced recovery of infective stage larvae in experiment 1, while only H. helicoides reduced recovery in experiment 2. In both the experiments, dung burial increased the total number of larvae recovered, while the number of infective larvae were reduced by the action of earthworms. Increased recovery following burial, along with the fact that larvae moved rapidly from soil onto herbage, suggests that soil may provide a protective reservoir for infective larvae infesting herbage.

Animals↗
PubMed2001

Normal oxygenation and ventilation during snow burial by the exclusion of exhaled carbon dioxide.

OBJECTIVE: To confirm that the accumulation of exhaled carbon dioxide (CO2) is the principal cause of nonmechanical asphyxiation during avalanche burial by demonstrating that complete exclusion of exhaled CO2 during experimental snow burial results in normal oxygenation and ventilation utilizing the air within the snowpack. METHODS: In the experimental group, 8 healthy volunteers (mean age 32 years, range 19-44 years) were fully buried up to 90 minutes in compacted snow with a density ranging from 300 to 680 kg/ m3 at an elevation of 2385 m. The 6 men and 2 women breathed directly from the snow utilizing a device containing no air pocket around the inhalation intake, in addition to an extended exhalation tube running completely out of the snowpack to remove all exhaled CO2. Continuous physiologic monitoring included oxygen saturation, end-tidal CO2, inspired CO2, electrocardiogram, rectal core temperature, and respiratory rate. As controls, 5 of the 8 subjects repeated the study protocol breathing directly into a small, fist-sized air pocket with no CO2 removal device. RESULTS: In the experimental group, the mean burial time was 88 minutes, despite the absence of an air pocket. No significant changes occurred in any physiologic parameters in this group compared to baseline values. In contrast, the controls remained buried for a mean of 10 minutes (P = .003) and became significantly hypercapnic (P < .01) and hypoxic (P < .02). CONCLUSIONS: There is sufficient oxygen contained within a densified snowpack comparable to avalanche debris to sustain normal oxygenation and ventilation for at least 90 minutes during snow burial if exhaled CO2 is removed. The prolonged oxygenation observed during CO2 exclusion is irrespective of the presence of an air pocket.

Adult↗
PubMed2000

Tomicus piniperda (Coleoptera: Scolytidae) emergence in relation to burial depth of brood logs.

The pine shoot beetle, Tomicus piniperda (L.), is an exotic pest of pines, Pinus spp., that was first found in the United States in 1992. A federal quarantine currently regulates movement of pine Christmas trees and pine nursery stock from infested to uninfested counties. The current national Pine Shoot Beetle Compliance Management Program requires T. piniperda-infested brood material to be disposed of by burning, chipping, or burial. The burial option requires that the infested pine material be buried at a depth of at least 30 cm. We tested this requirement by burying logs with similar levels of infestation at 0, 15, 30, 45, 61 and 76 cm and then monitoring for T. piniperda emergence. Logs were buried at two times during larval development (early and late) and in two soil types (sandy loam and loam). Emergence patterns from the two soil types were similar. Overall, 1,747 T. piniperda adults were collected from the 24 exposed control logs, but only 34 adults from the 120 buried logs, including 24 adults from logs buried at 15 cm, eight adults from 30 cm, one adult from 45 cm, and one adult from 61 cm. In comparing mean emergence density from buried logs with that of exposed logs, 98.6% mortality occurred at 15 cm, 99.5% at 30 cm, and > 99.9% at > or = 45 cm. Mean date of T. piniperda emergence to the soil surface was affected by burial depth and burial date, but not soil type.

Animals↗
PubMed2004

Accidental burials in sand: a potentially fatal summertime hazard.

Accidental burial in sand is a tragically unrecognized risk associated with a popular childhood recreational activity. We describe 4 boys, aged 10 to 13 years, who were accidentally buried by sand. One boy died after his self-made tunnel in a sandbox collapsed. In a separate incident at a construction site, 1 boy died, and 2 were injured after a 30-foot sandpile collapsed as they ran down the embankment; all 3 were buried by the sand. In both incidents, play was unsupervised, and burial was sudden and complete. The calculated weight of the sand exceeded the expected maximal muscle effort of the chest, leading to traumatic asphyxiation secondary to restrictive compression of the chest. Only 15 accidental burials have been reported in the literature. To our knowledge, this is the first report describing children who died of respiratory asphyxia due to overwhelming thoracic compression after sand burial. Greater awareness by public health and safety officials at beaches, sandboxes, sandpiles, and natural play areas may prevent potentially lethal accidents.

Accidents↗
PubMed1997

Different element ratios of red cosmetics excavated from ancient burials of Japan.

Marker elements of red cosmetics, collected from ancient burials of Matsuyama, Tokushima and Nara Japan, were determined by emission spectrometry (ICP/AES). The mass ratios of Hg, Fe, Cu, and Zn were different between samples. Element levels were compared with reference to relative amounts of sulfur. Of the possible contaminants from the bone and sand of burials, the relative amounts of Hg and Fe to S were most commonly available to evaluate the difference between the cosmetics. The cosmetics were divided into four groups; type I (high Hg with less Fe), type II (both moderate Hg and Fe), type III (moderate Hg with high Fe) and type IV (less Hg with high Fe). The main constituents of cosmetics are mercury sulfide (cinnabar) or ferric oxide mixed with trace metals. Zinc contents differ between the Fe and Hg amounts for the three areas. Cosmetic compositions varied with each burial site, suggesting that they were derived from different mines of ancient Japan.

Anthropology↗
PubMedDate not supplied

Intentions of burial: mourning, politics, and memorials following the massacre at Srebrenica.

In the aftermath of tragedy, memorials and grave sites are frequently constructed. Research needs to pay attention to the goals of mourners for such places. The 1995 massacre at Srebrenica in Bosnia-Herzegovina left over 7,000 Muslim men missing and presumed dead. Five years later, families fought to bury the remains that had been collected. Qualitative interviews with 67 people, including survivors and key informants were completed over the summer of 2000. This article examines the intentions of the burial from the perspective of two groups of family members who lost loved ones: survivors who remain politically isolated and those involved in advocacy or political organizations. For the politically isolated, burial was important in reshaping individual mourning after mass death and in the face of unidentified remains. For those involved in advocacy groups, burial was a means of recognizing the past massacre, understanding the massacre's impact on current political divisions, and shaping future directions. Both mourning and political functions are elaborated on in the setting of Bosnian culture and society.

Bosnia and Herzegovina↗
PubMed2006

Sequential monitoring of burials containing large pig cadavers using ground-penetrating radar.

Ground-penetrating radar (GPR) was used to monitor 12 pig burials in Florida, each of which contained a large pig cadaver. Six of the cadavers were buried in sand at a depth of 0.50-0.60 m, and the other six were buried at a depth of 1.00-1.10 m and were in contact with the upper surface of a clay horizon. Control excavations with no pig internment were also constructed as blank graves and monitored with GPR. The burials were monitored with GPR for durations of either 12-13 or 21-21.5 months when they were then excavated to correlate the decomposition state of the cadaver with the GPR imagery. Overall, cadavers in sand were easily detected for the duration of this study at 21.5 months, even when completely skeletonized. Conversely, in clay it became increasingly difficult to image the pig cadavers over the first year of burial, even when they still retained extensive soft tissue structures.

Animals↗
PubMed2004

Double child burial from Sunghir (Russia): pathology and inferences for upper paleolithic funerary practices.

The double child burial from Sunghir (Russia) is a spectacular Mid Upper Palaeolithic funerary example dated to about 24,000 BP. A boy (Sunghir 2) and a girl (Sunghir 3), about 12-13 and 9-10 years old, respectively, were buried at the same time, head to head, covered by red ocher and ornamented with extraordinarily rich grave goods. Examination of the two skeletons reveals that the Sunghir 3 femora are short and exhibit marked antero-posterior bowing. The two femora do not show any asymmetry in the degree of shortening and bowing. Bowing affects the whole diaphysis and shows a regularly incurved profile, with the highest point at midshaft. Pathology is confined to the femora, and no other part of this well-preserved specimen shows abnormality. The isolated nature of the Sunghir 3 anomalies points to cases reported in the medical literature under the label of "congenital bowing of long bones" (CBLB). These are a group of rare conditions exhibiting localized, sometimes bilateral, bowing and shortening which are nonspecific and may result from different causes, including abnormalities of the primary cartilaginous anlage (i.e., the aggregation of cells representing the first trace of an organ). Localized ossification disturbances, possibly linked to a diabetic maternal condition, might explain the shortening and the coincidence of maximum midshaft curvature with the position of the primary ossification center, as well as the lack of involvement of other skeletal parts. This scenario, rather than other possibilities (early bilateral midshaft fracture, acute plastic bowing deformities, or faulty fetal posture), provides the most likely explanation for the Sunghir 3 femoral deformities. The intriguing combination of a pathological condition apparent since birth with a spectacular burial of unusually positioned young individuals of different sexes recalls significant aspects of the triple burial from the contemporary site of Dolní Vestonice (Moravia), evoking a patterned relationship between physical abnormality and extraordinary Upper Paleolithic funerary behavior.

Adolescent↗
PubMed2001

The Upper Paleolithic triple burial of Dolní Vestonice: pathology and funerary behavior.

This work focuses on paleopathological analysis of one of the skeletons from the Gravettian triple burial of Dolní Vestonice (Moravia) and addresses issues of Upper Paleolithic funerary behavior. The burial includes the well-preserved skeletons of three young individuals. The skeleton in the middle (DV 15) is pathological and very problematic to sex; the other two (DV 13 and DV 14) are males and lie in an unusual position. The young age, the possibility of a simultaneous interment, and the position of the three specimens have given rise to speculations about the symbolic significance of this spectacular and intriguing funerary pattern. The pathological condition of the skeleton in the middle further emphasizes its peculiarity. Main pathological changes of the DV 15 skeleton include: asymmetric shortening of the right femur and of left forearm bones, bowing of the right femur, right humerus, and left radius, elongation of fibulae, dysplasias of the vertebral column, and very marked enamel hypoplasias. Scrutiny of the medical literature suggests that the most likely etiology is chondrodysplasia calcificans punctata (CCP) complicated by trauma and early fractures of the upper limbs. CCP is a rare inherited disorder characterized by stippled ossification of the epiphyses. The cartilaginous stippling is a transient phenomenon that disappears during infancy, leaving permanent deformities on affected bones. Among the different forms of CCP, the X-linked dominant form is that resulting in asymmetric shortening and is lethal during early infancy in males. Thus, survival of DV 15 until young adult age would require the specimen to be a female. Clinical findings often associated with the disease (erythemas, ichthyosis, alopecia, cataracts, and joint contractures, among others) would emphasize the singular aspect of this individual, pointing to a condition that should be carefully taken into account when speculating on the significance of that peculiar burial.

Adult↗
PubMed2004

Quantifying the effect of burial of amino acid residues on protein stability.

The average contribution of individual residue to folding stability and its dependence on buried accessible surface area (ASA) are obtained by two different approaches. One is based on experimental mutation data, and the other uses a new knowledge-based atom-atom potential of mean force. We show that the contribution of a residue has a significant correlation with buried ASA and the regression slopes of 20 amino acid residues (called the buriability) are all positive (pro-burial). The buriability parameter provides a quantitative measure of the driving force for the burial of a residue. The large buriability gap observed between hydrophobic and hydrophilic residues is responsible for the burial of hydrophobic residues in soluble proteins. Possible factors that contribute to the buriability gap are discussed.

Amino Acids↗
PubMed2001

Litter burial and exhumation: spatial and temporal distribution on a cobble pocket beach.

A cobble beach (-6 diameter to -8 diameter) located on the South Wales coastline, UK, was studied over a three-month winter period to assess litter input levels. After total beach litter clearance, six surveys were conducted at consecutive spring tides which involved marking of previously unrecorded litter. The beach was soon inundated with debris, predominantly plastic beverage containers. Some marked litter was found to disappear from the beach surface, re-emerging weeks later which suggests that the potential for litter burial has been underestimated in litter research. Higher wave energies between surveys coincided with higher levels of previously unseen litter. These new inputs consisted of sea borne and exhumed litter. Items larger than the surrounding cobbles were found to work their way back to the surface of the beach after burial, smaller items remained buried. Pits dug into the cobble ridge confirmed the burial of mainly small items.

Environmental Monitoring↗