Methodological strategies to assess the degree of bone preservation for ancient DNA studies.

BACKGROUND: Archaeological bones contain only small amounts of DNA due to post-mortem DNA degradation and the changes endogenous DNA is subjected to during diagenesis. An important step before undertaking such time-consuming and costly analyses as ancient DNA investigation is to predict the presence of DNA in ancient samples. To date, the leading screening method has been amino acid racemization; however, other analytical techniques can also be used to assess the degree of bone preservation. AIM: The aim of the present study was to relate the presence of DNA with bone preservation in order to select samples potentially suitable for ancient DNA analysis. SUBJECTS AND METHODS: Bones collected from several archaeological sites, different locations (cave, rockshelter or sub divo) and diachronic periods were selected for analytical and spectroscopic analysis in order to correlate bone tissue preservation with the presence of DNA. Different techniques were combined to assess the degree of preservation of organic and inorganic components. RESULTS: As determined by different analytical methods, preservation of the inorganic component was best associated with the presence of DNA. CONCLUSION: Evaluation of the bone preservation state may be an efficient step to predict the presence of DNA in ancient samples prior to aDNA analysis.

Effects of merohedric twinning on the diffraction pattern.

In merohedric twinning, the lattices of the individuals are perfectly overlapped and the presence of twinning is not easily detected from the diffraction pattern, especially in the case of inversion twinning (class I). In general, the investigator has to consider three possible structural models: a crystal with space-group type H and point group P, either untwinned (H model) or twinned through an operation t in vector space (t-H model), and an untwinned crystal with space group G whose point group P' is obtained as an extension of P through the twin operation t (G model). In 71 cases, consideration of the reflection conditions may directly rule out the G model; in seven other cases the reflection conditions suggest a space group which does not correspond to the extension of H by the twin operation and the structure solution or at least the refinement will fail. When the twin operation belongs to a different crystal family (class IIB twinning: the crystal has a specialized metric), the presence of twinning can often be recognized by the peculiar effect it has on the reflection conditions.

Two new silicate structures based on a rhodesite-type heteropolyhedral microporous framework.

Two new members of the mero-plesiotype rhodesite series [Sr(2)Na(2)(Si(8)O(19)).4H(2)O, abbreviated as TR09; SrNa(4)(Si(8)O(19)).4H(2)O, TR10] have been hydrothermally synthesized in Teflon-lined autoclaves at 503 K and structurally characterized using X-ray diffraction single-crystal data. The crystal structures were solved by direct methods and refined to R = 0.021 [TR09; 3317 reflections with I(o) > 2sigma(I(o))] and R = 0.033 [TR10; 5007 reflections with I(o) > 2sigma(I(o))]. Both structures are based on a rhodesite-type microporous heteropolyhedral framework, where two types of channels are within the double silicate layer that alternates with an ;octahedral' O sheet. The large Sr(2+) cation constrains to the roughly ellipsoidal shape of the channels. The H(2)O molecules are located both in the O sheets and in the channels, where they are loosely hydrogen bonded. The crystal-chemical features that allow flexibility to the rhodesite-type microporous heteropolyhedral framework and make it interesting for possible technological applications are discussed.

New RE microporous heteropolyhedral silicates containing 4(1)5(1)6(1)8(2) tetrahedral sheets.

Four heteropolyhedral microporous silicates, A(3)RESi(6)O(15).2.25H(2)O, crystallizing in the Cmm2 space group and based on 4(1)5(1)6(1)8(2) tetrahedral sheets [A(3) = Na(2.74)K(0.26), RE = Ce, abbreviated as TR05; TR06: A(3) = Na(2.72)K(0.28), RE = La; TR07: A(3) = Na(3), RE = La; TR08: A(3) = Na(2.74)(H(3)O)(0.26), RE = La(0.68)Eu(0.32)] have been hydrothermally synthesized in Teflon-lined autoclaves at 503 K and structurally characterized using X-ray diffraction single-crystal data. Except for TR05, diffraction data have been collected on {001} twins by merohedry. The four structures are isotypic and based on strongly corrugated 4(1)5(1)6(1)8(2) silicate sheets interconnected along [010] by seven-coordinated RE polyhedra to form a microporous heteropolyhedral framework. The framework is crossed by three systems of ellipsoidal channels that host H(2)O molecules and alkaline ions. The channels run either parallel or perpendicular to the silicate sheets; the largest effective channel width is 4.7 x 2 A. In TR08 some (H(3)O)(+) replaces alkalis. Although the H atoms have not been localized, the configuration of the hydrogen bonding has been deduced from bond lengths and angles.

Penkvilksite-2O: Na2TiSi4O11.2H2O.

The crystal structure of synthetic penkvilksite-2O, disodium titanium tetrasilicate dihydrate, Na(2)TiSi(4)O(11).2H(2)O, a microporous titanosilicate, confirms the major features of a previous model that had been obtained by order-disorder (OD) theory from the known structure of penkvilksite-1M. An important difference from the previous model involves the hydrogen bonding of the water molecule which, on the basis of a Raman spectrum and the finding of only one of the two H atoms, is proposed to be disordered about a fixed O-H direction. The structure of penkvilksite-2O is based on (100) silicate layers linked by isolated TiO(6) octahedra to form a heteropolyhedral framework. The layer is strongly corrugated, based on interlaced spiral chains, and is crossed by two different channels that have an effective channel width of about 3 A.

Order-disorder character and twinning in the structure of a new synthetic titanosilicate: (Ba,Sr)4Ti6Si4O24 x H2O.

Prismatic crystals of the title compound, up to 100 microm long and {001} twinned by metric merohedry, were obtained as a side-product of a hydrothermal run devoted to synthesizing the heterophyllosilicate lamprophyllite. Single-crystal X-ray diffraction data were collected on a Bruker-AXS Smart Apex diffractometer from a crystal with approximate composition (Ba(0.80)Sr(0.20))(4)Ti6Si4O24 x H2O. The structure was solved and refined as a disordered structure in the space group Cmmm [a(o) = 5.906 (2), b(o) = 20.618 (8), c(o) = 16.719 (6) A, R = 0.089 for 682 reflections with I(o) > 2sigma(I(o))], and then deciphered by the order-disorder (OD) theory as an ordered structure and refined in the space group P2/c [a = 5.906, b = 16.719, c = 10.724 A, beta = 105.99 degrees , R = 0.083 for 1090 reflections with I(o) > 2sigma(I(o))]. The discussion based on the OD theory shows that the refined ordered structure corresponds to one (2M) of two maximum degree of order (MDO) polytypes. The structure of the second MDO polytype (4O) was modelled but not refined because it does not substantially occur in our sample. In the structure, infinite (001) ribbons of Ti octahedra elongated along the [100] direction are connected by (SiO3)4 four-membered rings, thus realising a new type of heteropolyhedral framework. The ribbons are three-octahedra wide and one-octahedron thick; they are formed by linking, via edge-sharing, rutile-type edge-sharing rows of octahedra. This ribbon represents a slice of the octahedral sheet that occurs in perrierite-(Ce), Ce4MgFe2Ti2O8(Si2O7)2. The (Ba,Sr) ions are hosted within two independent [100] narrow channels both delimited by four Ti octahedra and four Si tetrahedra. The disorder of H2O is discussed on the basis of a Raman spectrum.

Overlooked problems in manifold twins: twin misfit in zero-obliquity TLQS twinning and twin index calculation.

It is shown that the twin index n calculated, according to Friedel, as a function of the indices (hkl) and [uvw] of the lattice plane and lattice direction defining the cell of the twin lattice applies only to twofold twins, i.e. twins where the twin element is of order 2. For manifold twins, where the twin operation is a three-, four- or sixfold (direct or inverse) rotation, it is shown that the generalized formula becomes n=NXi/xi, where N is the number of lattice planes of the (hkl) family passing within the cell of the twin lattice, Xi the two-dimensional coincidence index for a plane of the (hkl) family and xi the number of planes out of N of that family that are partially restored by the twin operation. The existence of twin lattice quasi-symmetry (TLQS) twins with zero-obliquity in manifold twins leads to the introduction of a new parameter as a general measure of the pseudo-symmetry of TLQS rotation twins: the twin misfit delta, defined as the distance between the first nodes along the two shortest directions in the plane of LT (quasi-)perpendicular to the twin axes that are quasi-restored by the twin operation. Taking the example of staurolite twins, several inconsistencies in the treatment of manifold twins are pointed out.

The derivation of twin laws in non-merohedric twins. Application to the analysis of hybrid twins.

An algorithm is presented to derive the twin laws in non-merohedric twins through the systematic search for quasi-perpendicular lattice planes/directions. The twin lattice, i.e. the sublattice common to the whole crystalline edifice built by the twinned individuals, is based on a supercell of the individual defined by a pair of quasi-perpendicular lattice elements (hkl)/[uvw]. Starting from a (real or supposed) twin element, (hkl) or [uvw], the set of quasi-perpendicular lattice elements with user-defined limits on the twin index and obliquity is explored. The degree of lattice quasi-restoration is commonly measured by the classical twin index but in some cases, especially for large supercells, this index represents only a first approximation of the degree of lattice quasi-restoration, because more than one pair (hkl)/[uvw] may exist, and more than one concurrent sublattices of nodes, based on the same twin element, may be quasi-restored, although within different obliquities. These twins, whose existence has been recently recognized, are termed hybrid twins. In hybrid twins, the degree of lattice quasi-restoration is measured by the effective twin index n(E), a generalization of the classical twin index: in the limiting case of only one (quasi-)restored sublattice, the effective twin index and the classical twin index coincide. A number of examples previously reported simply as 'non-Friedelian' twins (with a twin index higher than the empirical limit of 6 established by Friedel) are analysed and reinterpreted as hybrid twins. A Fortran program is made available, which derives the possible twin laws according to this algorithm and analyses the pseudosymmetry of the concurrent sublattices defined by each pair (hkl)/[uvw]. The occurrence of hybrid concurrent components in twinning does not affect the normal procedures of dealing with diffraction patterns of twinned crystals.

Applied geminography--symmetry analysis of twinned crystals and definition of twinning by reticular polyholohedry.

The common classification of twinning into the four categories of twinning by merohedry (complete and exact overlap of the lattices of the twinned crystals), pseudomerohedry (complete but approximate overlap), reticular merohedry (partial but exact overlap) and reticular pseudomerohedry (partial and approximate overlap) is revised in terms of the complete (translational and point) lattice symmetry of the twin and of the individual. The new category of reticular polyholohedry is introduced for twins where the twin lattice has the same point symmetry but a different orientation of the individual lattice. It is shown that the degeneration to twin index 1 relates, in a parallel way, reticular merohedry to metric merohedry and reticular polyholohedry to syngonic merohedry. Some examples from the recent literature are analysed in terms of this revised classification.