Ancient DNA sequences reveal unsuspected phylogenetic relationships within New Zealand wrens (Acanthisittidae)

Ancient DNA sequences from preserved specimens are increasingly being used for the investigation of Pacific Island ecosystems prior to the large scale modification and extinction of endemic biota associated with human colonization. However, many difficulties are associated with the use of ancient DNA sequences in studies of genetically close taxa. In this paper, these difficulties are discussed as they relate to a study involving extinct and extant members of an ancient New Zealand avian family, the New Zealand wrens (Acanthisittidae).Sequences of the mitochondrial small ribosomal subunit RNA gene (12S) were obtained from museum specimens of several wren taxa in order to investigate their phylogenetic relationships and the taxonomic status of a rock wren (Xenicus gilviventris) subspecies. Limitations due to sample size and 12S sequence variability as well as the difficulties in authenticating ancient DNA sequences prevent firm conclusions but the data suggest unsuspected phylogenetic relationships exist and raise the possibility that conservation management of rock wren populations is required.     

The biochemistry of ancient DNA in bone

The amount of DNA in ancient bone was determined by ethidium bromide staining after the removal of the potent Taq inhibitor, fulvic acid. A complete decalcification and a perfusion protocol were used to recover DNA from bone. A variety of purification techniques including molecular sieve, hydroxyapatite binding and Magic preparations yielded DNA that spanned from 3.4g/g of bone to below detectable limits. Fulvic acid was shown to interfere with the quantification of DNA derived from ancient human skeletal material one hundred to over seven thousand years old. Scanning UV in the 300 to 230 nm range is a simple and sensitive technique for documenting fulvic acid contamination in ancient bone extracts.     

Mitochondrial DNA variation in geographic populations of Colorado potato beetle,Leptinotarsa decemlineata (Coleoptera; Chrysomelidae)

Summary This study demonstrates variability in restriction enzyme cleavage sites of mitochondrial DNA (mtDNA) among four popalations of Colorado potato beetle (CPB). A suite of three enzymes (EcoRI,HpaI,PstI) was sufficient to discriminate among the populations tested. Individuals heteroplasmic for restriction enzyme patterns were found in some populations. Variability in CPB mtDNA should prove useful in efforts to trace the origin and dispersal of the species in North America.     

Mitochondrial DNA variation in social wasps (Hymenoptera,Vespidae)

Summary Patterns of restriction fragment length polymorphisms (RFLP) of European Vespinae were more similar within genera than between them. Distance trees were constructed that support the hypothesis of monophyly of the generaVespula andDolichovespula. Within the genusVespula, V. germanica was more closely related toV. rufa than toV. vulgaris. The position of the genusVespa remained uncertain due to the precision limits of the RFLP technique.     

Infra-red study of the carbonate in bone,teeth and francolite

Résumé La diffraction des rayons X et la spectrographie infrarouge ont été employées pour rechercher la présence de calcite et de magnésite dans la fraction minérale de l'os et des dents ainsi que dans le minéral qui lui est le plus proche au point de vue chimique, la francolite. Le résultat positif obtenu dans l'infra-rouge indique la présence de liaisons CaCO₃ et MgCO₃ associées à la matrice fondamentale du type apatite de ces substances.

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This work was partially sponsored by theAir Research and Development Command, United States Air Force, through its European Office under contract n° AF 61 (514) 647 C.     

Sea urchin embryo as a model for analysis of the signaling pathways linking DNA damage checkpoint,DNA repair and apoptosis

DNA integrity checkpoint control was studied in the sea urchin early embryo. Treatment of the embryos with genotoxic agents such as methyl methanesulfonate (MMS) or bleomycin induced the activation of a cell cycle checkpoint as evidenced by the occurrence of a delay or an arrest in the division of the embryos and an inhibition of CDK1/cyclin B activating dephosphorylation. The genotoxic treatment was shown to induce DNA damage that depended on the genotoxic concentration and was correlated with the observed cell cycle delay. At low genotoxic concentrations, embryos were able to repair the DNA damage and recover from checkpoint arrest, whereas at high doses they underwent morphological and biochemical changes characteristic of apoptosis. Finally, extracts prepared from embryos were found to be capable of supporting DNA repair in vitro upon incubation with oligonucleotides mimicking damage. Taken together, our results demonstrate that sea urchin early embryos contain fully functional and activatable DNA damage checkpoints. Sea urchin embryos are discussed as a promising model to study the signaling pathways of cell cycle checkpoint, DNA repair and apoptosis, which upon deregulation play a significant role in the origin of cancer. Received 10 April 2007; accepted 23 April 2007     

Molecular ecology of a Neolithic meadow: The DNA of the grass remains from the archaeological site of the Tyrolean Iceman

The paper reports on the molecular analysis of samples of approximately 5,300-year-old grass found at the alpine archaeological site where the so-called Tyrolean Iceman was discovered. The grass comes from a cloak made of long grass blades and/or the stuffing of the snow footwear worn by the Iceman. The results show that while the largest fraction of the DNA extractable from the grass is of foreign origin, a much smaller part belongs to the original genetic material of the grass itself, and can be used as a valuable taxonomic clue to the plant species utilized by neolithic men to manufacture their equipment. On the other hand, the foreign DNA, or at least a portion of it, comes from microorganisms-mainly filamentous fungi and unicellular algae-which seem to have been associated with the grass since the time the grass was harvested.     

化学发光技术在蛋白质和DNA分析中的新进展

化学发光技术在生物技术、分子生物学、药学、临床和环境等许多领域都获得了广泛的应用，有关化学发光的评论文章近年来也有许多报道。本文就化学发光技术在蛋白质和DNA分析中的较有特色的新进展(2000年以来)进行了评述，引用文献30篇。     

Polymorphisms in mitochondrial DNA of european and Africanized honeybees (Apis mellifera)

Summary This study demonstrates polymorphisms in both the length and in the restriction enzyme cleavage sites of honeybee mitochondrial DNA (mtDNA). The levels of variation are typical of those found in other metazoan species. These polymorphisms are potentially useful for the identification of Africanized bees in the western hemisphere and for study of honeybee phylogenetics.     

An analysis of allozyme,mitochondrial DNA and morphological variation in mussel (Mytilus galloprovincialis) populations from Greece

Three populations ofM. galloprovincialis from northern Greece were investigated using isozyme analysis, discriminant analysis of morphological characteristics and analysis of restriction fragments of mtDNA. For all three types of analysis significant intra- and interpopulation differentiation was found. This differentiation is very noticeable at the mtDNA genotype frequencies. Furthermore, the restriction patterns of mtDNA were different from those reported for Atlantic populations of this species.     

Peptides as DNA mimics: cross-reactivity and mimicry in systemic autoimmune diseases

No Abstract. Received 21 February 2002; received after revision 16 May 2002; accepted 14 June 2002     

Geographic populations of the medfly may be differentiated by mitochondrial DNA variation

Restriction enzyme cleavage sites of mitochondrial DNA (mtDNA) from the Mediterranean fruit fly were found to vary among introduced populations in the Neotropics. The survey included samples from 15 established natural populations and 5 laboratory cultures from Hawaii, Central America, South America and West Africa and samples from recent California infestations (1989, 1991). Based on restriction fragment length polymorphisms from 2 enzymes, Hawaii is an unlikely source for the 1989 and 1991 California infestations. Interpopulational variation in mtDNA demonstrates the potential for the technique to trace the process of colonization (geographic spread) by this insect.     

Genomic sources of regulatory variation in cis and in trans

Regulatory variation results from genetic changes with both cis and trans acting effects on gene expression. Here I describe the types of genetic variants that alter cis and trans regulation and discuss differences in the potential for cis and trans changes among different classes of genes. I argue that the molecular function of the protein encoded by each gene and how the gene is wired into the genomic regulatory network may influence its propensity for cis and trans regulatory changes.Received 15 February 2005; received after revision 12 April 2005; accepted 26 April 2005     

PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus)

DNA from 30-million-year-old amber preserved termites (Mastotermes electrodominicus) was PCR amplified with nuclear ribosomal RNA small subunit primers and cloned into the TA vector (INVITROGEN). We obtained several classes of recombinant clones as a result. AuthenticMastotermes electrodominicus clones were identified. The source of other classes of clones was identified as contaminants of the ancient DNA template. Several of the clones appeared to be chimeric in structure with half of the clone identical to the termite sequence and the other half identical to contaminant sequences. The phenomenon of PCR jumping was identified as a possible source for the chimeric clones.     

Localization of integrated adenovirus DNA in the hamster genome

Adenovirus DNA integrated into the genomes of adenovirus-transformed hamster cells or of adenovirus type 12 (Ad12)-induced hamster tumor cells can be located at many different chromosomal sites. This raises the question as to whether distinct isochores of the hamster cell genome might be more accessible to recombination with adenovirus DNA. In Ad12- or Ad2-transformed hamster cell lines, and in Ad12 revertants, the investigated integrated viral DNA sequences were assigned to isochore families by analyzing DNA fractions from preparative CsCl density gradients for their buoyant densities (and, therefore, GC levels) and for the presence of viral DNA. Adenovirus DNA sequences were found in different isochores, which did not generally match the base composition of viral sequences. This is in apparent contrast to what was previously observed with retroviral integration. However, in cell lines carried in culture for many years, the viral DNA sequences might have been transposed to different isochore positions, since the host sequences flanking the viral DNA appear to have been conserved.Received 6 July 2004; received after revision 23 August 2004; accepted 6 October 2004     

Regulation of the cell cycle following DNA damage in normal and Ataxia telangiectasia cells

A proportion of the population is exposed to acute doses of ionizing radiation through medical treatment or occupational accidents, with little knowledge of the immedate effects. At the cellular level, ionizing radiation leads to the activation of a genetic program which enables the cell to increase its chances of survival and to minimize detrimental manifestations of radiation damage. Cytotoxic stress due to ionizing radiation causes genetic instability, alterations in the cell cycle, apoptosis, or necrosis. Alterations in the G1, S and G2 phases of the cell cycle coincide with improved survival and genome stability. The main cellular factors which are activated by DNA damage and interfere with the cell cycle controls are: p53, delaying the transition through the G1-S boundary; p21^WAF1/CIPI, preventing the entrance into S-phase; proliferating cell nuclear antigen (PCNA) and replication protein A (RPA), blocking DNA replication; and the p53 variant protein p53as together with the retinoblastoma protein (Rb), with less defined functions during the G2 phase of the cell cycle. By comparing a variety of radioresistant cell lines derived from radiosensitive ataxia talangiectasia cells with the parental cells, some essential mechanisms that allow cells to gain radioresistance have been identified. The results so far emphasise the importance of an adequate delay in the transition from G2 to M and the inhibition of DNA replication in the regulation of the cell cycle after exposure to ionizing radiation.     

Chromatin assembly during S phase: contributions from histone deposition, DNA replication and the cell division cycle

During S phase of the eukaryotic cell division cycle, newly replicated DNA is rapidly assembled into chromatin. Newly synthesised histones form complexes with chromatin assembly factors, mediating their deposition onto nascent DNA and their assembly into nucleosomes. Chromatin assembly factor 1, CAF-1, is a specialised assembly factor that targets these histones to replicating DNA by association with the replication fork associated protein, proliferating cell nuclear antigen, PCNA. Nucleosomes are further organised into ordered arrays along the DNA by the activity of ATP-dependent chromatin assembly and spacing factors such as ATP-utilising chromatin assembly and remodelling factor ACF. An additional level of controlling chromatin assembly pathways has become apparent by the observation of functional requirements for cyclin-dependent protein kinases, casein kinase II and protein phosphatases. In this review, we will discuss replication-associated histone deposition and nucleosome assembly pathways, and we will focus in particular on how nucleosome assembly is linked to DNA replication and how it may be regulated by the cell cycle control machinery.     

The range of life in amber: significance and implications in DNA studies

A survey of the major fossiliferous amber deposits is provided, including ages and various categories of life forms reported from each. The frequence of occurrence of the major groups of plants and animals in these amber deposits is also given. Thus far, DNA from four insect and one plant species has been extracted from amber fossils. In the case of the stingless bee in Dominican amber, evidence of reproducibility is provided, since two independent laboratories isolated DNA from six or more different specimens of the same insect.Amber sources for DNA studies are listed together with their advantages and disadvantages. The important points are the availability of desired pieces, the proper identification of the fossil, verification of the amber deposit, the cost involved, and the feasibility of causing damage to the specimen. The availability of several types of amber (Mexican, Dominican, Baltic, Chinese, Canadian, Siberian and Lebanese) at four major sources (academic collections, commercial dealers, private collections and amber mines) is discussed. The scientific implications of obtaining DNA from amber inclusions are presented.