Origin and seasonality of subfossil caprine dung from the discovery site of the Iceman (Eastern Alps)

The discovery of a Neolithic glacier mummy (dated to 3300–3100 cal b.c.) on a remote site of an Alpine pass at 3,200 m in the Ötztal Mountains is still puzzling. In the initial phase of the Iceman research, four hypotheses were suggested to explain the find in its entirety. The speculations vary from a hunter or warrior to a shaman, a miner or a shepherd. None of these proposals is accepted or corroborated by archaeological findings, but on the basis of palynological investigations conducted in the vicinity of the discovery site the assumption that the Iceman was involved in an early form of transhumance has now gained general acceptance. Concerning this assumption we present in this paper a recent study conducted on about a hundred caprine (sheep/goat or ibex/chamois) dung pellets recovered from the find spot of the Iceman and which were dated from 5400 to 2000 cal b.c. The approach was to determine through plant remains from these faeces whether they were droppings derived from animals grazing in anthropogenic habitats at low altitudes or in alpine grasslands. The former case would suggest they were livestock, the latter game. The results showed that all droppings derive from animals grazing at high altitudes.     

The genome and variation of Bacillus anthracis

The Bacillus anthracis genome reflects its close genetic ties to Bacillus cereus and Bacillus thuringiensis but has been shaped by its own unique biology and evolutionary forces. The genome is comprised of a chromosome and two large virulence plasmids, pXO1 and pXO2. The chromosome is mostly co-linear among B. anthracis strains and even with the closest near neighbor strains. An exception to this pattern has been observed in a large inversion in an attenuated strain suggesting that chromosome co-linearity is important to the natural biology of this pathogen. In general, there are few polymorphic nucleotides among B. anthracis strains reflecting the short evolutionary time since its derivation from a B. cereus-like ancestor. The exceptions to this lack of diversity are the variable number tandem repeat (VNTR) loci that exist in genic and non genic regions of the chromosome and both plasmids. Their variation is associated with high mutability that is driven by rapid insertion and deletion of the repeats within an array. A notable example is found in the vrrC locus which is homologous to known DNA translocase genes from other bacteria.     

Induction of Therapeutic Antibodies by Vaccination against External Loops of Tumor-Associated Viral Latent Membrane Protein

Some human herpesviruses (HHV) are etiological contributors to a wide range of malignant diseases. These HHV express latent membrane proteins (LMPs), which are type III membrane proteins consistently exposed at the cell surface in these malignancies. These LMPs have relatively large cytoplasmic domains but only short extracellular loops connecting transmembrane segments that are accessible at the surface of infected cells, but they do not elicit antibodies in the course of natural infection and tumorigenesis. We report here that conformational peptides mimicking two adjacent loops of the Epstein-Barr virus (EBV) LMP1 (2LS peptides) induce high-affinity antibodies with remarkable antitumor activities in mice. In active immunization experiments, LMP1-targeting 2LS vaccine conferred tumor protection in BALB/c mice. Moreover, this tumor protection is dependent upon a humoral anti-2LS immune response as demonstrated in DO11.10 (TCR-OVA) mice challenged with LMP1-expressing tumor and in SCID mice xenografted with human EBV-positive lymphoma cells. These data provide a proof of concept for 2LS immunization against short external loops of viral LMPs. This approach might possibly be extended to other infectious agents expressing type III membrane proteins.After the primary infection, some viruses, especially human herpesviruses (HHV) such as Epstein-Barr virus (EBV), cytomegalovirus, Kaposi''s sarcoma herpesvirus (HHV8), varicella-zoster virus, and herpes simplex virus, persist lifelong in all infected individuals, most often in an asymptomatic latent form. However, in the long term, some HHV can be involved in the emergence of malignant diseases in a small subset of infected individuals. EBV-associated lymphomas and carcinomas (22, 37), HHV8-associated Kaposi''s sarcomas (30), and human cytomegalovirus-associated glioblastomas (24) are examples of beta- and gammaherpesvirus-related human malignancies. All these malignancy-associated viruses encode type III membrane proteins which are expressed during the latent state of infection and thus can be called latent membrane proteins (LMPs). These viral LMPs (vLMPs), or “multipass” membrane proteins, appeared to be necessary for virus-driven host cell survival and/or transforming activity (1, 3, 28, 31). They are regarded by some authors as evolutionary mimics of cellular chemokine/cytokine receptors, and, like cellular receptors, they recruit numerous cytoplasmic adaptors. The several transmembrane domains of these vLMPs seem to mimic activated cellular chemokine/cytokine receptor structures and to function with versatile signaling devices, reprogramming cellular signaling networks to modulate cellular function after infection. They contribute prominently to virus survival in latently infected individuals and to virus-related human pathologies, including cancer (8, 14, 19, 34, 36). Despite expressing vLMP antigens at their membrane surface, these latently infected cells are very poor in initiating effective immune responses in infected individuals, thus facilitating viral persistence in humans (2, 17, 38). One reason for this poor immunogenicity may be the constitutive cell signaling property reported for these vLMPs in latently infected cells (3, 16, 35, 38). Consequently, unnecessary overexpression and large extracellular domains for ligand binding may facilitate vLMP immune escape (3, 35, 38). Thus, a major therapeutic approach involved the discovery of naturally active compounds or pharmacological agents that specifically block viral receptor functioning (12, 35). Compounds emerged from high-throughput screening of synthetic chemical libraries, but we still lack specific agents for vLMPs, as they cross-react with cellular chemokine/cytokine receptors and cellular signaling pathways (35). Functional antibodies (Abs) recognizing membrane proteins for anticancer therapies have recently emerged, but there are very few of these and they resulted mostly from serendipity rather than from a systematic design strategy (5). To date, LMPs as a target for a virus-specific immunotherapeutic Ab strategy have not been explored extensively. Some studies have been conducted with purified full-length LMPs from EBV, a gammaherpesvirus, but these studies failed to produce or detect Abs recognizing LMP extracellular domains (10, 20, 29). One reason for this poor immunogenicity could be the too-short extracellular structure of these LMPs, which could explain the failure of latently infected individuals to produce cytolytic Abs (21). To test this hypothesis, we used as an LMP model the EBV-encoded oncoprotein LMP1 which mimics a constitutively active tumor necrosis factor receptor-like molecule and is expressed during EBV latent infection (16). This LMP1 expression was observed in most EBV-carrying malignancies (16, 22, 37), therefore causing EBV to be classified as a class I human carcinogenic agent (11). Here, we report an original humoral approach, because Abs have unlimited diversity and are often exquisitely specific and readily produced. Indeed, to overcome the too-short extracellular size of LMP, we hypothesized that synthesis of a peptide mimicking several extracellular loops of LMP would be a successful general strategy for the development of Abs with the high-pressure liquid chromatography affinity necessary for neutralizing and cytolytic effectiveness, as described previously (4, 33a). We argue here that this new process (D. Tranchand Bunel, 28 January 2003, French patent application FR0300943; D. Tranchand Bunel, 28 July 2005, U.S. Patent Office, US069140) was rewarding, as by vaccinating mice with peptides that covered two adjacent extracellular loops of LMP1 (2LS peptides), we obtained the production of neutralizing and cytolytic high-affinity Abs. Moreover, these Abs induced by 2LS peptide vaccination appeared to confer protection of mice against the development of tumors expressing LMP1.     

A preliminary phylogeny of the 'didymocarpoid Gesneriaceae' based on three molecular data sets: Incongruence with available tribal classifications

The 'didymocarpoid Gesneriaceae' (traditional subfam. Cyrtandroideae excluding Epithemateae) are the largest group of Old World Gesneriaceae, comprising 85 genera and 1800 species. We attempt to resolve their hitherto poorly understood generic relationships using three molecular markers on 145 species, of which 128 belong to didymocarpoid Gesneriaceae. Our analyses demonstrate that consistent topological relationships can be retrieved from data sets with missing data using subsamples and different combinations of gene sequences. We show that all available classifications in Old World Gesneriaceae are artificial and do not reflect natural relationships. At the base of the didymocarpoids are grades of clades comprising isolated genera and small groups from Asia and Europe. These are followed by a clade comprising the African and Madagascan genera. The remaining clades represent the advanced Asiatic and Malesian genera. They include a major group with mostly twisted capsules. The much larger group of remaining genera comprises exclusively genera with straight capsules and the huge genus Cyrtandra with indehiscent fruits. Several genera such as Briggsia, Henckelia, and Chirita are not monophyletic; Chirita is even distributed throughout five clades. This degree of incongruence between molecular phylogenies, traditional classifications, and generic delimitations indicates the problems with classifications based on, sometimes a single, morphological characters.     

Think locally: control of ubiquitin‐dependent protein degradation in neurons

The nervous system coordinates many aspects of body function such as learning, memory, behaviour and locomotion. Therefore, it must develop and maintain an intricate network of differentiated neuronal cells, which communicate efficiently with each other and with non‐neuronal target cells. Unlike most somatic cells, differentiated neurons are post‐mitotic and characterized by a highly polarized morphology that determines the flow of information. Among other post‐translational modifications, the ubiquitination of specific protein substrates was recently shown to have a crucial role in the regulation of neuronal development and differentiation. Here, we review recent findings that illustrate the mechanisms that mediate the temporal and spatial control of neuronal protein turnover by the ubiquitin–proteasome system (UPS), which is crucial for the development and function of the nervous system.     

Recombinant protein expression by targeting pre-selected chromosomal loci

Background  

Recombinant protein expression in mammalian cells is mostly achieved by stable integration of transgenes into the chromosomal DNA of established cell lines. The chromosomal surroundings have strong influences on the expression of transgenes. The exploitation of defined loci by targeting expression constructs with different regulatory elements is an approach to design high level expression systems. Further, this allows to evaluate the impact of chromosomal surroundings on distinct vector constructs.     

Effector proteins of the bacterial pathogen Pseudomonas syringae alter the extracellular proteome of the host plant, Arabidopsis thaliana

In plants, potential pathogenic bacteria do not enter the host cell. Therefore, a large portion of the molecular interaction between microbial pathogen and host occurs in the extracellular space. To investigate potential mechanisms of disease resistance and susceptibility, we analyzed changes in the extracellular proteome, or secretome, using the Arabidopsis-Pseudomonas syringae pathosystem. This system provides the possibility to directly compare interactions resulting in basal resistance, susceptibility, and gene-specific resistance by using different genotypes of Pseudomonas on the same host. After infecting suspension-cultured cells of Arabidopsis with the Pseudomonas strain of interest, we isolated protein from the cell culture medium representing the secretome. After one-dimensional gel separation and in-gel digestion of proteins, we used iTRAQ (isobaric tags for relative and absolute quantitation) labeling in conjunction with LC-MS/MS to perform relative quantitative comparisons of the secretomes from each of these interactions. We obtained quantitative information from 45 Arabidopsis proteins that were present in all three biological experiments. We observed complex patterns of accumulation, ranging from proteins that decreased in abundance in the presence of all three bacterial strains to proteins that specifically increased or decreased during only one of the interactions. A particularly intriguing result was that the virulent bacteria (e.g. a susceptible interaction) caused the extracellular accumulation of a specific subset of host proteins lacking traditional signal peptides. These results indicate that the pathogen may manipulate host secretion to promote the successful invasion of plants.     

Ecological barcoding of corallivory by second internal transcribed spacer sequences: hosts of coralliophiline gastropods detected by the cnidarian DNA in their stomach

The second internal transcribed spacer (ITS2) of the nuclear ribosomal RNA cluster (rDNA) is significantly smaller in the Cnidaria (120–260 bp) than in the rest of the Metazoa. ITS2 is one of the fastest evolving DNA regions among those commonly used in molecular systematics and has been proposed as a possible barcoding gene for Cnidaria to replace the currently problematic mitochondrial sequences used. We have reviewed the intraspecific and interspecific variation of ITS2 rRNA sequences in the Anthozoa. We have observed that the lower limits of the interspecific DNA divergence ranges very often overlap with intraspecific ranges, and identical sequences from individuals of different species are not rare. This finding can result in problems similar to those encountered with the mitochondrial COI, and we conclude that ITS2 does not prove significantly better than COI for standard taxonomic DNA barcoding in Anthozoa. However, ITS2 appears to be a promising gene in the ecological DNA barcoding of corallivory, where taxonomic accuracy at genus or even family level may represent a significant improvement of current knowledge. We have successfully amplified and sequenced ITS2 from template DNA extracted from foot muscle and from stomach contents of corallivorous gastropods, and from their anthozoan hosts. The small size of cnidarian ITS2 makes it a very easy and efficient tool for ecological barcoding of associations. Ecological barcoding of corallivory is an indispensable approach to the study of the associations in deep water, where direct observation is severely limited by logistics and costs.