Comparison of rates and degrees of isoleucine epimerization in dipeptides and tripeptides

The degrees and rates of isoleucine epimerization in heating experiments with pure di- and tripeptides are dependent on: (1) the position of isoleucine in the peptide chain; (2) the formation from dipeptides of diketopiperazines, cyclic intermediates that are in equilbrium with, and hydrolyze to, both the parent and inverted dipeptides as follows: NH₂-terminal?diketopiperazine?COOH-terminal. The results of heating experiments show that isoleucine residues in diketopiperazine are the most highly epimerized form in both di- and tripeptide solutions. NH₂-terminal isoleucine also undergoes relatively rapid epimerization, while the rates of epimerization of COOH-terminal and free isoleucine are much slower. Through hydrolysis reactions, high degrees of isoleucine epimerization are transferred to slower epimerizing species. Consequently, the relative rate of isoleucine epimerization in the various positions differs from the relative degree of epimerization.The relative rates of isoleucine epimerization are: NH₂ ? diketopiperazine ? COOH ≈ interior ≈ free, while the relative degrees of isoleucine epimerization are: diketopiperazine > NH₂ > COOH ? interior. The high degree of epimerization exhibited by COOH-terminal isoleucine in fossil dipeptides is due to prior preferential epimerization in diketopiperazine. The high degree of epimerization of free isoleucine in carbonate fossils is due to the hydrolysis of highly epimerized terminal isoleucine. These results are applicable to peptides both in fossil shells and in aqueous solutions and form the basis for a revised model of isoleucine epimerization in fossil shells.     

Epimerization of COOH-terminal isoleucine in fossil dipeptides

Using procedures employed for protein sequencing to remove NH₂-terminal amino acids, the degree of epimerization of COOH-terminal isoleucine in dipeptides from fossil mollusc shells has been measured directly. The results show that isoleucine in this position is highly epimerized in fossil dipeptides and that the COOH-terminal isoleucine is more highly epimerized than the free amino acid. Hydrolysis of the highly epimerized terminal isoleucine leads to the high alloisoleucine/isoleucine values found in the free amino acid fraction. The results also provide evidence for the formation of diketopiperazines in fossils as a mechanism to account for the high degree of epimerization of COOH-terminal isoleucine.     

Kinetics and mechanism of the epimerization and decomposition of threonine in fossil foraminifera

Determination of alloThr/Thr ratios in foraminiferal tests ranging in age from Recent to ～ 700,000 yr B.P. has shown that threonine epimerization ratios approach a steady-state value of ～0.2. This is well below the equilibrium ratio of ～0.9 as measured in buffered aqueous solutions. It has also been found that the initial rate of decomposition of threonine in fossil foraminfera is about an order of magnitude faster than would be predicted on the basis of extrapolation from high temperature kinetic studies on free threonine in buffered aqueous solution. These results are apparently a consequence of metal cation catalysis of both the decomposition and the epimerization of free threonine, which is being continually released by the slow hydrolysis of peptide and proteinaceous material present in the fossil shells.     

Amino acids in fossil corals: racemization (epimerization) reactions and their implications for diagenetic models and geochronological studies

Thirty-eight fossil coral samples of known age from late Pleistocene uplifted reef terraces have been analyzed for amino acid composition and for the degree of racemization of selected amino acids. Particular attention has been given to the epimerization (racemization about the α-carbon) of isoleucine. The $\text{D}\text{L}$ ratios observed in many of these samples do not conform to the concept of increasing racemization being associated with increasing fossil age. It is shown that sixteen of the samples demonstrate concordance between their known age and the age estimated from racemization data. Racemization ages are based upon a kinetic model derived from the kinetics observed in foraminifera in marine sediments and published estimates of the temperature dependence of the isoleucine epimerization reaction. Lack of concordance for the remaining samples is explained by either of two separate diagenetic phenomena: extensive leaching of free amino acids from the fossil, or contamination by ‘young’ amino acids. Ambiguities observed in many of the results may be due to the fact that coralline organic matter can have a complex history because of variations in its source and in its relation to the mineral phase. Neither of these factors has been observed to exert such a significant effect on racemization kinetics observed in fossil foraminifera or molluscs. Fossil corals are of only modest value as specimens for amino acid geochronological studies.     

Unraveling the sequence and structure of the protein osteocalcin from a 42 ka fossil horse

We report the first complete amino acid sequence and evidence of secondary structure for osteocalcin from a temperate fossil. The osteocalcin derives from a 42 ka equid bone excavated from Juniper Cave, Wyoming. Results were determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-MS) and Edman sequencing with independent confirmation of the sequence in two laboratories. The ancient sequence was compared to that of three modern taxa: horse (Equus caballus), zebra (Equus grevyi), and donkey (Equus asinus). Although there was no difference in sequence among modern taxa, MALDI-MS and Edman sequencing show that residues 48 and 49 of our modern horse are Thr, Ala rather than Pro, Val as previously reported (Carstanjen B., Wattiez, R., Armory, H., Lepage, O.M., Remy, B., 2002. Isolation and characterization of equine osteocalcin. Ann. Med. Vet.146(1), 31-38). MALDI-MS and Edman sequencing data indicate that the osteocalcin sequence of the 42 ka fossil is similar to that of modern horse. Previously inaccessible structural attributes for ancient osteocalcin were observed. Glu₃₉ rather than Gln₃₉ is consistent with deamidation, a process known to occur during fossilization and aging. Two post-translational modifications were documented: Hyp₉ and a disulfide bridge. The latter suggests at least partial retention of secondary structure. As has been done for ancient DNA research, we recommend standards for preparation and criteria for authenticating results of ancient protein sequencing.     

Comparison of pedogenic CO2-containing carbonates in fossil soil and loess from the Antarctic ice core

Doklady Earth Sciences -     

Thermal structure of a fossil subduction wedge in the Western Alps

New peak metamorphic temperatures are obtained by Raman spectroscopy of Carbonaceous Material to document the thermal structure of the central Western Alps with high sampling resolution. We show that peak metamorphic T gradually increases eastward from <330 to 350 °C (ultra-Dauphinois to subbriançonnais units), ∼350 to more than 400 °C (Briançonnais domain including the Zone Houillère where metamorphic index minerals are rare) and from 350 to more than 500 °C (Liguro–Piemontese domain). Combined with other constraints on the metamorphic evolution, this dataset reveals a good preservation of the overall thermal structure of the fossil subduction wedge, with no particular thermal overprint during collision. However, local confrontation with P – T estimates and radiometric ages reveals more subtle variations within tectonic units and across the main contacts that are linked to the past activity of the major thrusts and extensional shear zones during subduction and exhumation.     

Comparison of a karst groundwater model with and without discrete conduit flow

Karst aquifers exhibit a dual flow system characterized by interacting conduit and matrix domains. This study evaluated the coupled continuum pipe-flow framework for modeling karst groundwater flow in the Madison aquifer of western South Dakota (USA). Coupled conduit and matrix flow was simulated within a regional finite-difference model over a 10-year transient period. An existing equivalent porous medium (EPM) model was modified to include major conduit networks whose locations were constrained by dye-tracing data and environmental tracer analysis. Model calibration data included measured hydraulic heads at observation wells and estimates of discharge at four karst springs. Relative to the EPM model, the match to observation well hydraulic heads was substantially improved with the addition of conduits. The inclusion of conduit flow allowed for a simpler hydraulic conductivity distribution in the matrix continuum. Two of the high-conductivity zones in the EPM model, which were required to indirectly simulate the effects of conduits, were eliminated from the new model. This work demonstrates the utility of the coupled continuum pipe-flow method and illustrates how karst aquifer model parameterization is dependent on the physical processes that are simulated.     

First report of a dipterocarpaceous fossil wood from Manipur

A fossil wood resembling Shorea and other allied genera of the Dipterocarpaceae is described from the Tipam Group of Manipur. This is for the first time any angiosperm wood is recorded from this state. The fossil collected from Jiribam district is considered as late Miocene in age. Its occurrence indicates warm and humid climate in the region during the deposition of the sediments.     

Flash floods and panic in the fossil record: a tale of 25 titanotheres

The Eocene rocks of southern Wyoming have provided a spectacular discovery of fossil bones and teeth. The remains of 25 titanotheres were found all together in one place less than 100 m square. Some of these horse-like mammals were young, some very old; and they were part of a herd. The geological and social evidence indicates that they perished together in a flash flood.     

Colloidal and polymeric nature of fossil amber

Fossilized ambers from several geographical origins, copal from the Kauri pine tree of New Zealand and modern white spruce tree resin have been analyzed by the following analytical techniques: dynamic light scattering, optical and scanning electron microscopy, gel permeation chromatography, IR spectroscopy, rheology and viscometry. The results dispute the prevailing view that amber is largely an insoluble, continuously crosslinked, integral polymer network. Rather, the data indicate that a large portion of amber consists of insoluble though solvent-swellable colloidal particles, ranging from submicron to multimicron in size, which can be dispersed in organic solvents such as N,N-dimethyl-formamide. The presence of colloidal particles in fossil amber, copal and even fresh resin suggests a mechanism for resin exudation involving the presence or formation of discrete ‘packets’ of resin, where the surface of each packet has been modified by the interaction with oxygen and water.     

Mineralogy of fossil resins in Northern Eurasia

The investigation is focused on identification and origin of fossil resins from the Cretaceous, Tertiary, and Quaternary sediments of Northern Eurasia on the basis of detailed study of their physical and chemical characteristics: morphology; size; mass; density; optical, mechanical, and thermal properties; chemical composition; etc. The composition of amorphous organic minerals with polymeric structure, fossil resins included, is studied with IR spectrometry, the EPR method, derivatography at low heating rates, XRD, chemical analysis, emission spectrometry, etc. The results of investigation summarized for the Baltic-Dnieper, North Siberian, and Far East amber-bearing provinces show some similarity of fossil resins in combination with specific features inherent to each province. Resins from the Baltic-Dnieper province should be termed as amber (succinite). Their variety is the most characteristic of Northern and Eastern Europe. Amber-like fossil resins from the North Siberian and Far East provinces are irrelevant to succinite. They usually occur as brittle resins, namely, retinite and gedanite, without jewelry value. Viscous fossil resin rumänite with an expected high economic value occurs in the Far East, on the shore of Sakhalin Island.     

Sphericity as a characteristic of solids from fossil fuel burning in a Lake Michigan sediment

The property of sphericity is used to identify some anthropogenic particles in a Lake Michigan sediment. Three classes of products from high temperature processes, primarily fossil fuel burning, have been isolated: charcoals, iron oxides and aluminosilicates. The morphologies, structures and surface characteristics are indicative of the combustion process.     

Ion subtraction — a computer-aided step in the geochemical analysis of fossil fuels

The subtraction of the signal intensities of the ion fragments m/e 149 and m/e 151 in the GLC-MS computer analysis of the saturated hydrocarbons of a fossil fuel, reveals the distribution of the 5α and 5β steranes. This technique is a convenient method of establishing the efficacity of the thiourea clathration step, and simplifies routine geochemical analysis. Subtraction of the signal intensities of the ion fragments m/e 218 and m/e 217 reveals the distribution of 14α and 14β sterane isomers, and is a further refinement in the study of geological steroids.     

Stegosauria: a historical review of the body fossil record and phylogenetic relationships

The first partial skeleton of a stegosaurian dinosaur was discovered in a brick pit in Swindon, UK in 1874. Since then, numerous stegosaurian remains have been discovered from Europe, North America, Africa and Asia, and continue to be discovered regularly. Stegosaurs are known from the Middle Jurassic to the Early Cretaceous; no definitive evidence of the clade is known from younger deposits. New discoveries are improving our understanding of stegosaur biology and showing that stegosaurs were more morphologically diverse than was previously realized. A new phylogeny, which includes all valid stegosaurian taxa, largely agrees with previous studies and shows the European Dacentrurinae was sister taxon to Stegosaurus. Poor resolution at the base of Stegosauria is probably due to the fragmentary nature of many of the Chinese taxa.     

The Soom Shale: a unique Ordovician fossil horizon in South Africa

The recent discovery of fossils with preserved soft tissues in the Cedarberg Mountains of the Cape Province has opened a new window on Ordovician life.     

New specimens of a fossil ostrich from the Miocene of Kenya

Fossilised hind limb bones from the late Middle Miocene (approximately 14 million-year-old [MYA]) Fort Ternan, Kadianga West and Ngorora localities in Western Kenya indicate the presence of a new representative of the ostrich genus Struthio. These new fossils represent some of the oldest known records for Struthio yet described, slightly younger than Struthio coppensi, from the Lower Miocene of Namibia. Because the four sub-species of the modern-day ostrich (Struthio camelus camelus, Struthio camelus australis, Struthio camelus massaicus, and Struthio camelus molybdophanes) inhabit the plains of Africa, and as recently as the 1940s, a fifth sub-species was also present in the Middle East and Saudi Arabia (Struthio camelus syriacus), records of Struthio from Kenya and Namibia testify to the much wider distribution of these cursorial birds in the relatively recent past. This is further supported by the very high frequency of ostrich eggshell fragments found across Africa and Eurasia, which vastly outweighs the amount of skeletal material uncovered over the last century.