A multidisciplinary study of archaeological grape seeds

We report here the first integrated investigation of both ancient DNA and proteins in archaeobotanical samples: medieval grape (Vitis vinifera L.) seeds, preserved by anoxic waterlogging, from an early medieval (seventh–eighth century A.D.) Byzantine rural settlement in the Salento area (Lecce, Italy) and a late (fourteenth–fifteenth century A.D.) medieval site in York (England). Pyrolysis gas chromatography mass spectrometry documented good carbohydrate preservation, whilst amino acid analysis revealed approximately 90% loss of the original protein content. In the York sample, mass spectrometry-based sequencing identified several degraded ancient peptides. Nuclear microsatellite locus (VVS2, VVMD5, VVMD7, ZAG62 and ZAG79) analysis permitted a tentative comparison of the genetic profiles of both the ancient samples with the modern varieties. The ability to recover microsatellite DNA has potential to improve biomolecular analysis on ancient grape seeds from archaeological contexts. Although the investigation of five microsatellite loci cannot assign the ancient samples to any geographic region or modern cultivar, the results allow speculation that the material from York was not grown locally, whilst the remains from Supersano could represent a trace of contacts with the eastern Mediterranean.     

Proving the Authenticity of Ancient DNA by Comparative Genomic Hybridization

 In PCR-supported amplification of ancient, degraded DNA, contamination with contemporary DNA can lead to false-positive results, which frequently give rise to discussions in which the mere existence of ancient DNA is doubted. Our confirmation of ancient DNA using comparative genome hybridization (CGH) eliminates these doubts. Unlike PCR methods, CGH requires no amplification of the DNA to be analyzed if adequate amounts of specimen DNA is used. Thus, false results traceable to contaminations are practically ruled out. The examples provided here prove the authenticity of ancient DNA for a 250-year-old and a 3000-year-old sample. At the same time, the CGH of ancient DNA offers the chance to gain insight into the pattern of DNA degradation and to monitor the preservation of certain chromosomal segments. Received: 10 May 1999 / Accepted in revised form: 29 July 1999     

Trace elements in buried human bones: intra-population variability of Sr/Ca and Ba/Ca ratios – diet or diagenesis?

A comparative analysis of trace element data of human skeletal material from four archaeological sites is presented. We show that the state of histomorphological preservation of bone, which is a measurement for the degree of its diagenetic alteration, closely corresponds to the Sr/Ca and Ba/Ca ratios at an intra-population level. This study challenges the validity of dietary studies that are based on the presently used procedures for sample preparation and subsequent evaluation of strontium and barium concentrations.     

Dodo remains from an in situ context from Mare aux Songes, Mauritius

Since 2005, excavations at Mare aux Songes, Mauritius, have revealed the presence of a very rich, ∼4,200-year-old fossil bone bed including dodo (Raphus cucullatus) bones and bone fragments. The recently excavated dodo assemblage comprises at least 17 individuals and is characterised by the presence of small and fragile skeletal elements, a dominance of leg elements and an absence of juveniles. The hydrology of the area suggests that dodos, like many other species, were probably lured to Mare aux Songes by the presence of freshwater during times of drought. The most likely scenario for the origin of the fossil deposit is that animals became trapped in the sediment in repeated miring events, which would favour the conservation of hindlimbs. Such a scenario is fully in accordance with the taphonomic characteristics of the bone assemblage.     

Carrier detection of duchenne muscular dystrophy through analysis of dna from deciduous teeth of a dead affected child

The sister of a child affected by Duchenne muscular dystrophy (DMD) was referred for genetic counselling to assess the risk of her being a carrier. Her brother had died 15 years previously at the age of 8. There were no other affected males in the family. There were no methods for DNA investigation at the time of the child's death and the family had never been studied for linkage with polymorphic probes on the chromosomal region Xp21. The only tissue from which an assessment of the risk could be made by DNA linkage analysis was two of the child's deciduous teeth that the parents had kept. DNA was extracted using a protocol described for the recovery of ancient DNA from museum specimens and archaeological finds. Multiplex amplification did not reveal deletions in 19 exons spanning the hot-spot regions for deletions within the dystrophin gene in Xp21. Linkage analysis using three highly polymorphic microsatellites demonstrated that the sister had not received the X chromosome borne by her brother. These results show that DNA extracted from teeth is a reliable source for molecular diagnosis.     

Metabolism and water loss are not related to environmental heterogeneity in two mygalomorph spiders

Laboratory water flumes are artificial troughs of moving water widely used in hydraulic studies of fluvial systems to investigate real-world problems at smaller, more manageable scales. Water flumes have also been used to understand bone transportation sorting and bone orientation found in the fossil record using actual bones. To date, these studies have not involved scaled bones. A 1/12 scale model of a 21.8-m long skeleton of Apatosaurus, a long-necked sauropod dinosaur from the Late Jurassic, was used to explore three problems at Dinosaur National Monument (USA) that cannot be explained by tradition bone flume studies: (1) why there is an abrupt bend in articulated vertebrae, (2) why articulated dorsals are inverted relative to the pelvis, and (3) how bone jams form. The flume experiments established that (1) bed friction with the wing-like transverse processes of vertebrae resists the force of the water flow, whereas those vertebrae lacking the processes are free to pivot in the flow; (2) elevation of the dorsal vertebrae by the transverse processes subjects the vertebrae to the energy of the flow stream, which causes the vertebrae to flip. Computation fluid dynamics (CFD) software shows this flip was due to differential pressure on the upstream and downstream sides. (3) The formation and growth of bone clusters or jams (analogous to log jams in rivers) occur as transported bones pile against an initial obstruction and jammed bones themselves become obstacles. These preliminary studies show that scale models can provide valuable insights into certain taphonomic problems that cannot be obtained by traditional bone flume studies.

     

Search for biochemical fossils on earth and non-biological organic molecules on Jupiter,Saturn and Titan

Recognizable remnants of ancient biochemicals may survive under mild/moderate geological environments. Acyclic isoprenoid hydrocarbons, cyclic hydrocarbons with terpenoid carbon skeletons (e.g. hopanes) and vanadyl and nickel porphyrins have been isolated from organic matter, including petroleum, in Phanerozoic sedimentary rocks. Remnants of lignin have also been found. Usually, carbohydrates do not survive long; they degrade and/or react with other organic substances to form macromolecular matter. Proteins, e.g. apparently those in dinosaur bone collagen, break down relatively rapidly. Life arose during the Precambrian and potential biochemical fossils, e.g. n-alkanes, 2,5-dimethylfuran have been isolated from Precambrian kerogens. Traces of hydrocarbons, NH₃, PH₃ occur on Jupiter and Saturn. Hydrocarbons, N₂ and HCN, the latter a key intermediary in the laboratory abiological syntheses of amino acids and nucleic acid bases, are present on Titan where life could not have evolved. Precursor abiological organic molecules of some complexity may have been synthesized on Titan and the Jovian planets.     

The integument of Psittacosaurus from Liaoning Province, China: taphonomy, epidermal patterns and color of a ceratopsian dinosaur

Preserved skin of small dinosaurs is rare. Here, a specimen of the ceratopsian dinosaur, Psittacosaurus, presents some of the best preserved epidermal scales observed to date in a relatively small dinosaur, over wide areas extending from the head to the tail. We study the preserved epidermis of SMF R 4970, the different types of scales, color, and patterns, and their respective locations in the body. We use modern application of high-power digital imaging for close-up analysis of the tubercles and fragments of preserved color. Three types of scales are preserved, large plate-like scales, smaller polygonal scales or tubercles, and round pebble-like scales. The sizes of the plate-like scales vary in different parts of the body and vanish altogether posteriorly. Light and dark cryptic patterns are created by the associations of the tubercle and plate-like scales, and there is also evidence of countershading in the proximal caudal region, the body darker dorsally and lighter ventrally. Perhaps most impressive are the distinctive pigmented impressions of scales over most of the skeletal elements. The pigmentation follows the curvature of the bones implying that when it was deposited, the skin was still pliable and able to wrap around the visible parts of the elements. The present record of color is the first in a non-theropod dinosaur and only the second record in a non-avian dinosaur. Because of its resistance to degradation and ability to produce various color tones from yellows to blacks, we suggest that melanin was the dominant chemical involved in the coloration of Psittacosaurus. The data here enable us to reconstruct the colors of Psittacosaurus as predominantly black and amber/brown, in cryptic patterns, somewhat dull, but useful to a prey animal. Indeed, skin pigment within a partially degraded bone indicates that Psittacosaurus was scavenged shortly after death. The theropod dinosaur Sinosauropteryx has recently been reported to have naturally pigmented integumental structures, which the authors interpret as proof that they are protofeathers and not support fibers of collagen. Our findings in Psittacosaurus, on the other hand, indicate a more parsimonious and less profound alternative explanation, i.e., decomposition of the skin releases pigments that readily permeate underlying structures.     

Stem cell transplantation before birth – a realistic option for treatment of osteogenesis imperfecta?

Osteogenesis imperfecta (OI) is characterized by severe bone deformities, growth retardation and bones that break easily, often from little or no apparent cause. OI is a genetic disorder primarily with defective type I collagen with a wide spectrum of clinical expression. In the more severe cases, it can be diagnosed before birth. Transplantation of mesenchymal stem cells (MSC) has the potential to improve the bone structure and stability, growth and fracture healing. Prenatal and postnatal cell transplantation has been investigated in preclinical and clinical studies of OI and suggests that this procedure is safe and has positive effects. Cell transplantation resulted in improved linear growth, mobility and reduced fracture incidence. However, the effect is transient and for this reason re-transplantation may be needed. So far there is limited experience in this area, and proper studies are required to accurately determine if MSC transplantation is of clinical benefit in the treatment of OI. In this review, we summarize what is currently known in this field. © 2015 John Wiley & Sons, Ltd.     

岩溶石漠化地区表土孢粉与植被关系的影响因素研究——以重庆南川区南平镇为例

根据表土孢粉分析和植被样方调查,重庆南平养兔场内外5个不同方位的表土孢粉组合较好地揭示了该区孢粉组合特点及其与植被的关系。通过对该区表土孢粉组合差异性的研究,探讨了影响表土孢粉与现代植被对应关系的主要因素,即外来孢粉、孢粉产量、孢粉保存和孢粉鉴定等。运用LuoPacias孢粉鉴定系统将孢粉鉴定到种,共132种,为在这一地区开展第四纪古植被、古气候和古环境等研究提供参考性依据。     

Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber

Microorganisms are the most ancient cells on this planet and they include key phyla for understanding cell evolution and Earth history, but, unfortunately, their microbial records are scarce. Here, we present a critical review of fossilized prokaryotic and eukaryotic microorganisms entrapped in Cretaceous ambers (but not exclusively from this geological period) obtained from deposits worldwide. Microbiota in ambers are rather diverse and include bacteria, fungi, and protists. We comment on the most important microbial records from the last 25 years, although it is not an exhaustive bibliographic compilation. The most frequently reported eukaryotic microfossils are shells of amoebae and protists with a cell wall or a complex cortex. Likewise, diverse dormant stages (palmeloid forms, resting cysts, spores, etc.) are abundant in ambers. Besides, viral and protist pathogens have been identified inside insects entrapped in amber. The situation regarding filamentous bacteria and fungi is quite confusing because in some cases, the same record was identified consecutively as a member of these phylogenetically distant groups. To avoid these identification errors in the future, we propose to apply a more resolute microscopic and analytical method in amber studies. Also, we discuss the most recent findings about ancient DNA repair and bacterial survival in remote substrates, which support the real possibility of ancient DNA amplification and bacterial resuscitation from Cretaceous resins.     

Middle-Eocene artiodactyls from Shanghuang (Jiangsu Province,Coastal China) and the diversity of basal dichobunoids in Asia

A new assemblage of basal dichobunoid artiodactyls from the middle-Eocene Shanghuang fissure fillings includes the diacodexeid Jiangsudon shanghuangensis gen. and sp. nov., a new species of the lantianine dichobunoid Elaschitotherium, Elaschitotherium crepaturus sp. nov., and an indeterminate suoid which is presently the earliest record of this clade. Diacodexeids are also represented by two forms provisionally referred to cf. Diacodexis sp. and to an indeterminate Diacodexeidae, respectively. The occurrence of diacodexeids in Shanghuang contrasts with the early and earliest middle-Eocene chronological range of the family in Europe and North America and suggests that the stratigraphic range of the family in Asia extends up to the middle Eocene. This may reflect particular habitats in coastal China that may have been relatively stable during the early and middle Eocene, thus preserving forest-dwelling artiodactyls that became extinct in the other Holarctic regions. Compared to other supposedly coeval North American, European, and Asian faunas, the Shanghuang mammalian assemblage is most similar to early Uintan faunas of North America but is also remarkable in recording forms close to taxa that are characteristic of the Wasatchian and Bridgerian North American Land Mammal Ages. The Irdinmanhan age of the Shanghuang fauna is supported by the mammalian assemblage recovered from the fissure D, but an Arshantan age cannot be completely ruled out at this point. Although the Shanghuang assemblage is biased towards preservation of small components of the mammalian fauna, the Shanghuang fauna provide an important and unique window into the Eocene diversity and early evolution of cetartiodactyls in eastern Asia.     

New insights on the systematics,palaeoecology and palaeobiology of a plesiosaurian with soft tissue preservation from the Toarcian of Holzmaden,Germany

The Posidonienschiefer Formation (Toarcian) of Holzmaden, Baden-Württemberg in southwestern Germany has yielded several excellently preserved plesiosaurian specimens and received considerable research attention. The plesiosaurians found within these deposits are always significantly outnumbered by ichthyosaurs, and close examination of these rare specimens is crucial to a better understanding of the diversity and palaeoecology of Plesiosauria in this very peculiar ecosystem. The plesiosaurian specimen SMNS 51945 found in this area is a juvenile individual consisting of a partial, crushed skull and an exquisitely preserved post-cranial skeleton. Its anatomical characters seem to differ from the long-necked plesiosauroids Microcleidus brachypterygius and Seeleyosaurus guilelmiimperatoris that are the most abundant taxa within the plesiosaurian assemblage. The post-cranial skeleton preserves very likely soft tissues composed of buff-coloured and dark-coloured structures around the vertebral column and hindlimb of the animal. A network of buff-coloured fibres located posterior to the hindlimb most likely represents phosphatised collagen fibres as already found in some ichthyosaur specimens, confirming that wing area in plesiosaurians was much larger than that suggested by skeletal remains alone. The specimen also contains gastroliths (sand-sized grains mainly composed of quartz) in the stomach cavity suggesting the animal spent at least some of its time in shallow coastal waters, tens or hundreds of kilometres from the final place of burial.     

湖泊沉积物古DNA揭示气候环境变化和生态演化

广泛分布的湖泊为连续沉积和保存历史时期多样化生物核酸分子提供了绝佳的自然档案。随着近年来古DNA提取和测序技术的进步以及组学技术的发展,利用湖泊沉积物古DNA重建古生态演化及其对气候变化和人类活动的差异性响应得到广泛而深入的研究。本文回顾了古DNA研究的历史背景、理论基础,以及湖泊沉积物古DNA保存的影响因素和生物信息学分析流程;重点评述了湖泊沉积物古DNA在揭示气候环境变化、生物多样性及流域生态系统演化、物种定殖与外来物种入侵、人类活动影响、环境生态功能基因演化及其在细胞器基因组和古生态时间序列分析研究中的诸多应用和进展。同时还介绍了当前研究面临的局限和挑战以及组学技术在古DNA研究中的发展概况,分析了当前研究尚存的不足,并展望了未来可能的努力方向。     

Did the Romans introduce the Egyptian mongoose (<Emphasis Type="Italic">Herpestes ichneumon</Emphasis>) into the Iberian Peninsula?

New finds of bones of the Egyptian Mongoose (Herpestes ichneumon), one from Portugal and one from Spain, were directly ¹⁴C dated to the first century AD. While the Portuguese specimen was found without connection to the Chalcolithic occupation of the Pedra Furada cave where it was recovered, the Spanish find, collected in the city of Mérida, comes from a ritual pit that also contained three human and 40 dog burials. The finds reported here show that the Egyptian mongoose, contrary to the traditional and predominant view, did not first arrive in the Iberian Peninsula during the Muslim occupation of Iberia. Instead, our findings are consistent with the hypothesis that the species was first introduced by the Romans, or at least sometime during the Roman occupation of Hispania. Therefore, radiocarbon dating of new archaeological finds of bones of the Egyptian Mongoose (Herpestes ichneumon) in the Iberian Peninsula push back the confirmed presence of the species in the region by approximately eight centuries, as the previously oldest dated record is from the ninth century. With these new dates, there are now a total of four ¹⁴C dated specimens of Egyptian mongooses from the Iberian Peninsula, and all of these dates fall within the last 2000 years. This offers support for the hypothesis that the presence of the species in Iberia is due to historical introductions and is at odds with a scenario of natural sweepstake dispersal across the Straits of Gibraltar in the Late Pleistocene (126,000–11,700 years ago), recently proposed based on genetic data.     

Reduced light avoidance in spiders from populations in light-polluted urban environments

New finds of bones of the Egyptian Mongoose (Herpestes ichneumon), one from Portugal and one from Spain, were directly ¹⁴C dated to the first century AD. While the Portuguese specimen was found without connection to the Chalcolithic occupation of the Pedra Furada cave where it was recovered, the Spanish find, collected in the city of Mérida, comes from a ritual pit that also contained three human and 40 dog burials. The finds reported here show that the Egyptian mongoose, contrary to the traditional and predominant view, did not first arrive in the Iberian Peninsula during the Muslim occupation of Iberia. Instead, our findings are consistent with the hypothesis that the species was first introduced by the Romans, or at least sometime during the Roman occupation of Hispania. Therefore, radiocarbon dating of new archaeological finds of bones of the Egyptian Mongoose (Herpestes ichneumon) in the Iberian Peninsula push back the confirmed presence of the species in the region by approximately eight centuries, as the previously oldest dated record is from the ninth century. With these new dates, there are now a total of four ¹⁴C dated specimens of Egyptian mongooses from the Iberian Peninsula, and all of these dates fall within the last 2000 years. This offers support for the hypothesis that the presence of the species in Iberia is due to historical introductions and is at odds with a scenario of natural sweepstake dispersal across the Straits of Gibraltar in the Late Pleistocene (126,000–11,700 years ago), recently proposed based on genetic data.

     

青海湖硅藻组合及其季节变化——来自沉积物捕获器的初步研究

通过对青海湖捕获器中2010年7月至2011年10月份沉积物样品与青海湖湖岸7个地点表层样品的分析,获得青海湖现代硅藻组合及季节变化特征。捕获器沉积物样品中共鉴定出硅藻2纲32属56种,主要为咸水种与微咸水种。其中,优势种为Berkeleya rutilans、Cocconeis placentula var. euglypta、Cyclotella choctawhatcheeana和Nitzschia inconspicua,此四种占总数的82%以上。硅藻组合变化具显著的季节性差异,冬季主要以浮游种Cyclotella choctawhatcheeana占优势;非冰封期则以附生种Berkeleya rutilans、Nitzschia inconspicua与Cocconeis placentula var. euglypta占优势。青海湖湖水具有高碱度,硅藻的保存率不高,其保存率具有夏季高、冬季低的季节性变化,但这不是造成硅藻组合显著季节性变化的主要原因,其季节性变化主要取决于水生植物的生长与湖区冰情。     

First-trimester screening for Down syndrome; the role of nasal bone assessment in the Korean population

Objectives The aim of this study was to evaluate the role of nasal bone assessment in first-trimester screening for Down syndrome (DS) in the Korean population. Methods From July 2004 to March 2006, we prospectively evaluated the fetal nasal bones at 11–14 weeks' gestation in the Korean population. Results A successful evaluation was possible in 6490 of 6787 fetuses (95.6%). Absent, hypoechoic, and short nasal bones were seen in 4 (26.7%), 4 (26.7%), and 1 (6.7%) of 15 fetuses with DS, respectively, whereas in 5 (0.1%), 11 (0.2%), and 246 (3.8%) of 6456 normal fetuses. The incidence of absent and hypoechoic nasal bone showed significant differences between normal fetuses and fetuses with DS (P < 0.0005, both). Screening for DS using an absent or hypoechoic nasal bone resulted in a sensitivity of 53.3%, a specificity of 99.8%, a positive likelihood ratio of 215.2, and a negative likelihood ratio of 0.5. Conclusion Our study showed that nasal bone abnormality at 11–14 weeks of gestation had a high association with DS in the Korean population. This suggests that nasal bone assessment can be used to supplement the current first-trimester screening for DS in the Korean population. Copyright © 2007 John Wiley & Sons, Ltd.     

Bone histology of the titanosaur <Emphasis Type="Italic">Lirainosaurus astibiae</Emphasis> (Dinosauria: Sauropoda) from the Latest Cretaceous of Spain

The titanosaur Lirainosaurus astibiae is the only sauropod species known from the Late Cretaceous of the Iberian Peninsula. Lirainosaurus did not reach a gigantic body size and is one of the smallest sauropods discovered to date. Histological analysis of Lirainosaurus bones, focused on diaphyseal transverse sections of appendicular elements, reveals that Lirainosaurus did not exhibit the osseous microstructure typical for large sauropods, but is comparable with that of the coeval titanosaurs Alamosaurus sanjuanensis, Ampelosaurus atacis, and Magyarosaurus dacus, and also shares histological traits with other small to medium-sized sauropodomorph dinosaurs. Lirainosaurus limb bones exhibit a laminar fibrolamellar bone microstructure interrupted by growth marks, fully obliterated in adulthood by intense secondary remodeling processes which tend to replace completely the primary cortex. Lirainosaurus attained smaller sizes than typical sauropods reducing the rate of primary periosteal osteogenesis and developing an extensive secondary remodeling well before the adult size was reached. Histological organization of Lirainosaurus long bones is more mature than observed in basal neosauropods at similar ontogenetic stage, documenting a case of peramorphosis by pre-displacement. This heterochronic growth would be a reversal of the accelerated pattern of bone deposition typical for the sauropod lineage.     

Web GIS信息系统对在南京考古遗址中的地理环境影响研究

考古文献是历史地理研究中一个重要的数据来源,在互联网时代对纸质文本进行数字化并根据考古遗址的时空特点建立信息系统,具有重要的意义.针对考古遗址的空间位置不明确,考古遗址信息系统注重空间特性但缺乏对原始文献的重视,基于WebGIS、关系型数据库技术以及MVC系统架构,设计并实现了南京考古遗址信息系统.从考古文献中提取考古遗址各种属性信息,构建考古遗址时空数据库,基于WebGIS信息系统发布南京考古遗址,实现考古遗址的时空可视化以及各个遗址点相关文献的原文阅读.提出了一种将考古遗址信息从单一的文本展示到融合时空信息的多维信息展示的技术流程,并为研究南京的历史地理学者提供了便捷的考古遗址资料共享平台.