Sex diagnosis of subadult specimens from Medieval Polish archaeological sites: metric analysis of deciduous dentition.

The subject of this work is the characterisation of the metric features of deciduous dentition in a Medieval population of central Poland with the use of the jackknife technique leave one out (LOO)-supporting multivariate methods, which are important for deriving discrimination equations that would result in sex determination of children's skeletal remains. The sex of the individuals was assessed through analysis of sex-specific DNA sequences (AMELY/AMELX, SRY and alpha satellite sequences). Discriminant analysis concerned only teeth of those individuals whose sex was confirmed by the primary structure of three DNA sequences. The deciduous tooth diameters of males were found to be significantly larger than those of females in four respects: MD diameter of the maxillary second molar, MD and BL diameters of the mandibular first molar and BL diameter of the mandibular second molar. A two-group discriminant analysis considered all those measurements as independent variables. A multiple regression procedure produced a linear equation predicting the sex of children's skeletons with a significant probability amounting to approximately 78%. The accuracy of the sex assessment of an individual, using dental measurements, was established at 69% in deciduous male and 88% in deciduous female teeth.     

Hominid carnivory and foraging strategies, and the socio-economic function of early archaeological sites.

New evidence for the tissue types exploited by early hominids from carcasses possibly acquired through scavenging is derived from the larger mammal bone assemblages from FLK I, level 22 (Zinjanthropus floor), and FLKN levels 1 and 2 from Bed I, Olduvai Gorge, Tanzania. Published skeletal part profiles from the two archaeological sites are evaluated using (i) modern observations on the sequence by which carnivores consume carcass parts in order to assess the timing of hominid access to carcasses, and (ii) measurements of flesh and marrow yields to assess the tissue types sought and acquired. These results suggest that the maximization of marrow (fat) yields, not flesh (protein) yields, was the criterion shaping decisions about carcass processing. Because of evidence for density-dependent destruction of some flesh-bearing parts by scavengers of the hominid-butchered assemblages, however, it is uncertain whether carcass parts were transported and acquired by hominids in a largely defleshed condition. The results on tissue types acquired are combined with a discussion of predation risk, feeding competition and the equipment needs of carcass processing in an attempt to identify archaeological test implications of competing hypotheses for the socio-economic function of the earliest archaeological sites.     

Depth of burial,an important factor in controlling bacterial decay of waterlogged archaeological poles

Wood discs from two waterlogged softwood poles were investigated for variations in bacterial decay. Exterior and interior degradation was observed using light, transmission and scanning electron microscopy. Maximum water content (U_max) was measured and extent of decay from the surface towards the wood interior was investigated. Despite a well preserved appearance, the majority of the tracheids were heavily degraded. Erosion bacteria were identified as the main degraders and a significant difference in degree of decay was found between the upper and lower parts of each pole. Small differences in oxygen concentration, derived from depth of burial, are suggested as the controlling factor. Active erosion bacterial decay was found in the inner parts of the 1200-year old wooden poles.     

Epigenetic markers in migrating population burial sites of the Mid-Elbe-Saale area

The distribution of 122 epigenetic traits of the cranium and the postcranial skeleton (180 skeletal individuals) of six sites of the period of the Middleelbe-Saale-Region was analyzed. Based on these frequencies and using the method of biodistance analysis (MMD after Sj?vold 1973) the relationships of these population groups were investigated which are different concerning their geographical origin. The results did not show distinct differences between these groups, but suggested a possible homogeneity of our populations.     

Biodeterioration of Mayan archaeological sites in the Yucatan Peninsula, Mexico

Many of the monuments of the Mayan civilization are suffering deterioration caused by environmental factors (high temperatures and relative humidities), increasing contamination from natural and anthropogenic sources, and by the action of micro- and macro-biological communities. Archaeological sites and historical monuments in the Mayan area were constructed with different limestones which offer different resistances to degradation by the various types of contamination. Two different sampling sites were chosen at the archaeological site of Uxmal in the Yucatan Peninsula, Mexico. Heterotrophic bacteria, cyanobacteria and different fungi were isolated and classified taxonomically. The other archaeological site chosen for this study was the fortress of Tulum, located at the side of the Caribbean Sea and exposed to chloride of marine spray and sand erosion. In this case, heterotrophic aerobic and anaerobic bacteria, cyanobacteria and fungi were isolated from the four sampling areas selected. In both archaeological sites crust deposits were observed by using light microscopy, SEM and ESEM. Surface analyses were made by means of EDAX and electron microprobe. Possible mechanisms of stone decay, based on the type of microorganisms isolated, the physico-chemical characteristics of the constructional materials and environmental factors are discussed.     

DNA decay rate in papyri and human remains from Egyptian archaeological sites

The writing sheets made with strips from the stem (caulis) of papyri (Cyperus papyrus) are one of the most ingenious products of ancient technology. We extracted DNA from samples of modern papyri varying in age from 0-100 years BP and from ancient specimens from Egypt, with an age-span from 1,300-3,200 years BP. The copy number of the plant chloroplast DNA in the sheets was determined using a competitive PCR system designed on the basis of a short (90 bp) tract of the chloroplast's ribulose bisphosphate carboxylase large subunit (rbcL) gene sequence. The results allowed us to establish that the DNA half-life in papyri is about 19-24 years. This means that the last DNA fragments will vanish within no more than 532-672 years from the sheets being manufactured. In a parallel investigation, we checked the archaeological specimens for the presence of residual DNA and determined the extent of racemization of aspartic (Asp) acid in both modern and ancient specimens, as a previous report (Poinar et al. [1996], Science 272:864-866) showed that racemization of aspartic acid and DNA decay are linked. The results confirmed the complete loss of authentic DNA, even in the less ancient (8th century AD) papyri. On the other hand, when the regression for Asp racemization rates in papyri was compared with that for human and animal remains from Egyptian archaeological sites, it proved, quite surprisingly, that the regressions are virtually identical. Our study provides an indirect argument against the reliability of claims about the recovery of authentic DNA from Egyptian mummies and bone remains.     

The effect of early social deprivation on rhesus monkeys: Social responsiveness

Twelve rhesus infants were subjected to early total social deprivation in a free-ranging environmental situation for the periods of 6, 12, and 18 months. After the termination of treatment at the end of each period, a group of four subjects was tested for social responsiveness with six stimulus animals belonging to both the sexes and three age groups. Responses of the subjects were compared with similarly tested, naturally reared controls. Purpose of the experiment was to separate the effect of social deprivation from that of physical restrictions which had confounded the results of earlier experiments. It is concluded that the deficit in social responsiveness indicated by quantitative measures should be interpreted in the light of qualitative observations. Subjects were found deficit in “social communication” and “social manners” that interfered with social interactions. It is suggested that appropriate social experience enabling the subjects to learn social communication should benefit them as they possess primary social response tendencies to an appreciable degree.     

Platelet-reactive sites in collagens type I and type III. Evidence for separate adhesion and aggregatory sites.

The adhesion of human and rabbit platelets to collagens and collagen-derived fragments immobilized on plastic was investigated. Adhesion appeared to be independent of collagen conformation, since similar attachment occurred to collagen (type I) in monomeric form, as fibres or in denatured state. The adhesion of human platelets was stimulated to a variable degree by Mg2+, but rabbit platelet adhesion showed little if any dependence on this cation. Collagens type I, III, V and VI were all able to support adhesion, although that to collagen type V (native) was lower than that to the other collagens. Adhesion to a series of peptides derived from collagens I and III was measured. Attachment did not require the presence of peptides in triple-helical configuration. The extent of adhesion ranged from relatively high, as good as to the intact parent collagen molecule, to little if any adhesive activity beyond the non-specific (background) level. The existence of very different degrees of activity suggests that platelet adhesion is associated with specific structural sites in the collagen molecule. Adhesion in many instances was essentially in accord with the known platelet-aggregatory activity of individual peptides. However, two peptides, alpha 1(I)CB3 and alpha 1(III)CB1,8,10,2, exhibited good adhesive activity although possessing little if any aggregatory activity. Of particular interest, despite its near-total lack of aggregatory activity, adhesion to peptide alpha 1(I)CB3 was as good as that to the structurally homologous peptide alpha 1(III)CB4, in which is located a highly reactive aggregatory site. This implies that platelet adhesion to collagen may involve sites in the collagen molecule distinct from those more directly associated with aggregation.     

Molecular genetic analysis of 400-year-old human remains found in two Yakut burial sites

The excavation of five frozen graves at the Sytygane Syhe and Istekh-Myrane burial sites (dated at 400 years old) in central Yakutia revealed five human skeletons belonging to the Yakut population. To investigate the origin and evolution of the Yakut population as well as the kinship system between individuals buried in these two sites, DNA was extracted from bone samples and analyzed by autosomal short tandem repeats (STRs) and by sequencing hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed a diversity of sepulchral organizations linked probably to the social or genetic background of the subjects. Comparison of STR profiles, mitochondrial haplotypes, and haplogroups with data from Eurasian populations indicated affinities with Asian populations and suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last five centuries. Moreover, our results did not support a Central Asian (with the exception of maternal lineage of West Eurasian origin) or Siberian origin of the maternal lineages of these ancient Yakut subjects, implying an ethnogenesis of the Yakut population probably more complex than previously proposed.     

Recognition of functional sites in protein structures

Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.     

Molecular characterization of mitochondrial Amerindian haplogroups and the amelogenin gene in human ancient DNA from three archaeological sites in Lambayeque - Peru

Important pre-Inca civilizations, known by their great political and religious structures, inhabited the northern coast of Peru. Archeological and anthropological studies have shown that people from these villages have hierarchical strata, but the genetic structure has been poorly studied. Here, we aimed to perform a molecular characterization of the Amerindian maternal lineages and the amelogenin gene in skeletons collected from three archeological sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial haplogroup B and the identification of haplogroups A, C, and D were obtained with PCR-RFLP experiments. The sex was characterized via amplification of the AMEL(X/Y) locus. Haplogroup frequencies were compared with available data from other ancient and modern civilizations from the Peruvian coast and highlands using statistical methods. Our results showed that haplogroup C had the highest frequency, while haplogroup B showed variable diversity in the analyzed populations. The meta-analysis revealed a positive correlation among some coastal villages. We concluded that ancient populations analyzed in our study showed the presence of four Amerindian mitochondrial haplogroups, which is consistent with previous studies.     

Capillaria spp. eggs in Patagonian archaeological sites: statistical analysis of morphometric data

Discriminant analysis was used to identify eggs of Capillaria spp. at specific level found in organic remains from an archaeological site in Patagonia, Argentina, dated of 6,540 +/- 110 years before present. In order to distinguish eggshell morphology 149 eggs were measured and grouped into four arbitrary subsets. The analysis used on egg width and length discriminated them into different morphotypes (Wilks' lambda = 0.381, p < 0.05). The correlation analysis suggests that width was the most important variable to discriminate among the Capillaria spp. egg morphotypes (Pearson coefficient = 0.950, p < 0.05). The study of eggshell patterns, the relative frequency in the sample, and the morphometric data allowed us to correlate the four morphotypes with Capillaria species.     

Lipid peroxidation in the synaptosomal and mitochondrial fractions of separate brain structures in hypoxia

The paper studies intensification of lipid peroxide oxidation in separate brain structures (the medulla oblongata, cerebellum, visual and sensomotor cortex), synaptosomal and mitochondrial fractions under hypoxia. It has been established that acute hypoxia increases accumulation of lipid peroxidation (LPO) products, hydroperoxide and malonyl dialdehyde. Intensification of LPO in synaptosomes and mitochondria is more pronounced as compared to the whole structures. Preliminary treatment with antioxidants (vitamin E and ionol) considerably suppressed LPO intensity under both hypoxia and hypoxia with reoxygenation. Intensification of LPO in synaptosomes and mitochondria is suggested to be the key point in structural-functional disturbances of the nervous system under hypoxia and ischemia.     

Urea-induced transformation of native estrogen receptor and evidence for separate DNA-and ATP-binding sites

We have investigated the involvement of hydrophobic receptor domains during transformation of the native estrogen receptor to a form(s) with high affinity for immobilized DNA and ATP. In the presence of 6 M urea the intact estrogen-receptor complex was completely (greater than 90%, n = 12) transformed into a DNA-binding configuration but only partially (35-45%, n = 8) transformed into an ATP-binding state. Similar experiments performed with unliganded receptor preparations further distinguished the receptor's DNA and ATP binding properties. While the urea-induced increase in receptor affinity for DNA-agarose was estrogen-dependent, the urea-induced increase in affinity for ATP-agarose was steroid-independent. This is the first direct evidence that hydrophobic receptor domains may be involved in the steroid-dependent exposure of the DNA binding site. This event is partially reversible and suggests that electrostatic interactions alone may not be sufficient to accurately describe receptor recognition of specific DNA acceptor sites.     

Evidence for separate binding sites for progesterone and RU486 in the chick oviduct

Binding characteristics of synthetic steroid, mifepristone (RU38486 - also referred to as RU486), were examined in cytosol prepared from the chick oviduct and the calf uterus, and were compared with those of progesterone and synthetic progestin R5020. Unlike [³H]progesterone binding, the [³H]RU486 binding in the oviduct cytosol did not saturate at 50 nM ligand concentration. The [³H]progesterone binding could not be eliminated in the presence of excess RU486, and [³H]RU486 binding was seen to be indisplaceable upon pretreatment of the chick oviduct cytosol with a 1000-fold excess progesterone. It is apparent that the chick oviduct cytosol is endowed with two separate sets of sites which interact with progesterone and RU486 independently. Furthermore, [³H]RU486 binding in the chick oviduct cytosol remained intact when incubated for 60 min at 37°C; it exhibited a single ionic form upon elution from DEAE-Sephacel and the [³H]RU486-associated radioactivity sedimented in the 4 S region both in salt-free and 0.3 M KCl-containing 5–20% sucrose gradients. In the calf uterus cytosol, both steroids exhibited comparable binding profiles. Our results provide evidence that chick oviduct possesses distinct binding sites that accept either progesterone or RU486, but not both, as is the case in the calf uterus.