Geologically ancient DNA: fact or artefact?

Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.

Evidence of ancient papillomavirus recombination

An open question amongst papillomavirus taxonomists is whether recombination has featured in the evolutionary history of these viruses. Since the onset of the global AIDS epidemic, the question is somewhat less academic, because immune-compromised human immunodeficiency virus patients are often co-infected with extraordinarily diverse mixtures of human papillomavirus (HPV) types. It is expected that these conditions may facilitate the emergence of HPV recombinants, some of which might have novel pathogenic properties. Here, a range of rigorous analyses is applied to full-genome sequences of papillomaviruses to provide convincing statistical and phylogenetic evidence that evolutionarily relevant papillomavirus recombination can occur. © 2006 SGM.

A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family

Background. We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera. Results. Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses. Similarly, while ECSV has the same unusual TAAGATTCC virion strand replication origin nonanucleotide found in another recently described divergent geminivirus, Beet curly top Iran virus (BCTIV), the rest of the transcription and replication origin is structurally more similar to those found in begomoviruses and curtoviruses than it is to those found in BCTIV and mastreviruses. ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions. Conclusion. Although it superficially resembles a chimaera of geminiviruses from different genera, the ECSV genome is not obviously recombinant, implying that the features it shares with other geminiviruses are those that were probably present within the last common ancestor of these viruses. In addition to inferring how the ancestral geminivirus genome may have looked, we use the discovery of ECSV to refine various hypotheses regarding the recombinant origins of the major geminivirus lineages. © 2009 Varsani et al; licensee BioMed Central Ltd.

Chlamydia pneumoniae : modern insights into an ancient pathogen

Chlamydia pneumoniae is an enigmatic human and animal pathogen. Originally discovered in association with acute human respiratory disease, it is now associated with a remarkably wide range of chronic diseases as well as having a cosmopolitan distribution within the animal kingdom. Molecular typing studies suggest that animal strains are ancestral to human strains and that C. pneumoniae crossed from animals to humans as the result of at least one relatively recent zoonotic event. Whole genome analyses appear to support this concept – the human strains are highly conserved whereas the single animal strain that has been fully sequenced has a larger genome with several notable differences. When compared to the other, better known chlamydial species that is implicated in human infection, Chlamydia trachomatis, C. pneumoniae demonstrates pertinent differences in its cell biology, development, and genome structure. Here, we examine the characteristic facets of C. pneumoniae biology, offering insights into the diversity and evolution of this silent and ancient pathogen.

The ancient gene C12orf29 : an exploration of its role in the chordate body plan

The sheep (Ovis aries) is commonly used as a large animal model in skeletal research. Although the sheep genome has been sequenced there are still only a limited number of annotated mRNA sequences in public databases. A complementary DNA (cDNA) library was constructed to provide a generic resource for further exploration of genes that are actively expressed in bone cells in sheep. It was anticipated that the cDNA library would provide molecular tools for further research into the process of fracture repair and bone homeostasis, and add to the existing body of knowledge. One of the hallmarks of cDNA libraries has been the identification of novel genes and in this library the full open reading frame of the gene C12orf29 was cloned and characterised. This gene codes for a protein of unknown function with a molecular weight of 37 kDa. A literature search showed that no previous studies had been conducted into the biological role of C12orf29, except for some bioinformatics studies that suggested a possible link with cancer. Phylogenetic analyses revealed that C12orf29 had an ancient pedigree with a homologous gene found in some bacterial taxa. This implied that the gene was present in the last common eukaryotic ancestor, thought to have existed more than 2 billion years ago. This notion was further supported by the fact that the gene is found in taxa belonging to the two major eukaryotic branches, bikonts and unikonts. In the bikont supergroup a C12orf29-like gene was found in the single celled protist Naegleria gruberi, whereas in the unikont supergroup, encompassing the metazoa, the gene is universal to all chordate and, therefore, vertebrate species. It appears to have been lost to the majority of cnidaria and protostomes taxa; however, C12orf29-like genes have been found in the cnidarian freshwater hydra and the protostome Pacific oyster. The experimental data indicate that C12orf29 has a structural role in skeletal development and tissue homeostasis, whereas in silico analysis of the human C12orf29 promoter region suggests that its expression is potentially under the control of the NOTCH, WNT and TGF- developmental pathways, as well SOX9 and BAPX1; pathways that are all heavily involved in skeletogenesis. Taken together, this investigation provides strong evidence that C12orf29 has a very important role in the chordate body plan, in early skeletal development, cartilage homeostasis, and also a possible link with spina bifida in humans.

An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotyp

Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.

Analysis of ancient pottery and ceramic objects using X-ray fluorescence spectrometry

Archaeology has been called 'the science of the artefact' and nothing demonstrates this point better than the current interest displayed in provenance studies of archaeological objects. In theory, every vessel carries a chemical compositional pattern or 'fingerprint' identical with the clay from which it was made and this relationship is basic to provenance studies. The reasoning behind provenance or sourcing studies is to probe into this past and attempt to re-create prehistory by obtaining information on exchange and social interaction. This paper discusses the use of XRF spectrometry for the analysis of ancient pottery and ceramics to examine whether it is possible to predict prehictoric cultural exchanges.

The function of the RNA-binding protein TEL1 in moss reveals ancient regulatory mechanisms of shoot development

The shoot represents the basic body plan in land plants. It consists of a repeated structure composed of stems and leaves. Whereas vascular plants generate a shoot in their diploid phase, non-vascular plants such as mosses form a shoot (called the gametophore) in their haploid generation. The evolution of regulatory mechanisms or genetic networks used in the development of these two kinds of shoots is unclear. TERMINAL EAR1-like genes have been involved in diploid shoot development in vascular plants. Here, we show that disruption of PpTEL1 from the moss Physcomitrella patens, causes reduced protonema growth and gametophore initiation, as well as defects in gametophore development. Leafy shoots formed on ΔTEL1 mutants exhibit shorter stems with more leaves per shoot, suggesting an accelerated leaf initiation (shortened plastochron), a phenotype shared with the Poaceae vascular plants TE1 and PLA2/LHD2 mutants. Moreover, the positive correlation between plastochron length and leaf size observed in ΔTEL1 mutants suggests a conserved compensatory mechanism correlating leaf growth and leaf initiation rate that would minimize overall changes in plant biomass. The RNA-binding protein encoded by PpTEL1 contains two N-terminus RNA-recognition motifs, and a third C-terminus non-canonical RRM, specific to TEL proteins. Removal of the PpTEL1 C-terminus (including this third RRM) or only 16–18 amino acids within it seriously impairs PpTEL1 function, suggesting a critical role for this third RRM. These results show a conserved function of the RNA-binding PpTEL1 protein in the regulation of shoot development, from early ancestors to vascular plants, that depends on the third TEL-specific RRM.

The Phraseology and Structure of Latin Building Inscriptions in Roman North Africa

This study analyses the diction of Latin building inscriptions. Despite its importance, this topic has rarely been discussed before: the most substantial contribution on the subject is a short dissertation by Klaus Gast (1965) that focuses on 100 inscriptions dating mostly from the Republican period. Marietta Horster (2001) also touched upon this theme in her thesis on imperial building inscriptions. I have collected my source material in North Africa because more Latin building inscriptions dating from the Imperial period have survived there than in any other area of the Roman Empire. By means of a thorough and independent survey, I have assembled all relevant African Latin building inscriptions datable to the Roman period (between 146 BC and AD 425), 1002 texts, into a corpus. These inscriptions are all fully edited in Appendix 1; Appendix 2 contains references to earlier editions. To facilitate search operations, both are also available in electronic form. They are downloadable from the address http://www.helsinki.fi/hum/kla/htm/jatkoopinnot.htm. Chapter one is an introduction dealing with the nature of building inscriptions as source material. Chapter two offers a statistical overview of the material. The following main section of the work falls into five chapters, each of which analyses one main part of a building inscription. An average building inscription can be divided into five parts: the starting phrase opens the inscription (a dedication to gods, for example), the subject part identifies the builder, the object part describes the constructed or repaired building, the predicate part records the building activity and the supplement part offers additional information on the project (it can specify the funding, for instance). These chapters are systematic and chronological and their purpose is to register and interpret the phrases used, to analyse reasons for their use and for their popularity among the different groups of builders. Chapter eight, which follows the main section of the work, creates a typology of building inscriptions based on their structure. It also presents the most frequently attested types of building inscriptions. The conclusion describes, on a general level, how the diction of building inscriptions developed during the period of study and how this striking development resulted from socio-economic changes that took place in Romano-African society during Antiquity. This study shows that the phraseology of building inscriptions had a clear correlation both with the type of builder and with the date of carving. Private builders tended to accentuate their participation (especially its financial side) in the project; honouring the emperor received more emphasis in the building inscriptions set up by communities; the texts produced by the army were concise. The chronological development is so clear that it enables stylistic dating. At the beginning of the imperial period the phrases were clear, concrete, formal and stereotyped but by Late Antiquity they have become vague, subjective, flexible, varied and even rhetorically or poetically coloured.

Ancient Philosophers on Mental Illness

This dissertation is about ancient philosophers notions of mental illness, from Plato onwards. Mental illness here means disorders that, in ancient medical thought, were believed to originate in the body but to manifest themselves predominantly through mental symptoms. These illnesses were treated by physical means, which were believed to address the bodily cause of the illness, conceived of as an elemental imbalance or a state of cephalic stricture , for example. Sometimes the mental symptoms were addressed directly by psychotherapeutic means. The first and most important question explored concerns how the ancient philosophers responded to the medical notion of mental illness, and how they explained such illnesses in their theories of physiology and psychology. Although the illnesses are seldom discussed extensively, the philosophers were well aware of their existence and regarded their occurrence an indication of the soul s close dependence on the body. This called for a philosophical account. The second question addressed has to do with the ancient philosophers role as experts in mental problems of a non-medical kind, such as unwanted emotions. These problems were dubbed diseases of the soul , and the philosophers thus claimed to be doctors of the soul. Although the distinction between mental illnesses and diseases of the soul was often presented as rather obvious, there was some vagueness and overlap. There is still a third question that is explored, concerning the status of both mental illnesses and diseases of the soul as unnatural conditions, the role of the human body in the philosophical aetiologies of evil, and the medico-philosophical theories of psycho-physiological temperaments. This work consists of an introduction and five main chapters, focusing on Plato, Aristotle, the Stoics and Galen, and the Sceptics, the Epicureans and later Platonists. The sources drawn on are the original Greek and Latin philosophical and medical texts. It appears that the philosophers accepted the medical notion of mental illness, but interpreted it in various ways. The differences in interpretation were mostly attributable to differences in their theories of the soul. Although the distinction between mental illness and diseases of the soul was important, marking the boundary between the fields of expertise of medicine and philosophy, and of the individual s moral responsibilities, the problematic aspects of establishing it are discussed rather little in ancient philosophy. There may have been various reasons for this. The medical descriptions of mental illness are often extreme, symptoms of the psychotic type excluding the possibility of the condition being of the non-medical kind. In addition, the rigid normativeness of ancient philosophical anthropologies and their rigorous notion of human happiness decreased the need to assess the acceptability of individual variation in their emotional and intellectual lives and external behaviour.