Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.

Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.

A genomic Neolithic time transect of hunter-farmer admixture in central Poland.

Ancient DNA genome-wide analyses of Neolithic individuals from central and southern Europe indicate an overall population turnover pattern in which migrating farmers from Anatolia and the Near East largely replaced autochthonous Mesolithic hunter-gatherers. However, the genetic history of the Neolithic transition in areas lying north of the European Neolithic core region involved different levels of admixture with hunter-gatherers. Here we analyse genome-wide data of 17 individuals spanning from the Middle Neolithic to the Early Bronze Age (4300-1900 BCE) in order to assess the Neolithic transition in north-central Poland, and the local impacts of hunter-farmer contacts and Late Neolithic steppe migrations. We evaluate the influence of these on local populations and assess if and how they change through time, reporting evidence of recurrent hunter-farmer admixture over three millennia, and the co-existence of unadmixed hunter-gatherers as late as 4300 BCE. During the Late Neolithic we report the appearance of steppe ancestry, but on a lesser scale than previously described for other central European regions, with evidence of stronger affinities to hunter-gatherers than to steppe pastoralists. These results help understand the Neolithic palaeogenomics of another central European area, Kuyavia, and highlight the complexity of population interactions during those times.

Characterization of MHC class II-presented peptides generated from an antigen targeted to different endocytic compartments.

We evaluated the capacity of the secretory pathway or of different endocytic compartments in B cell lines to generate MHC class II-presented peptides from the antigen ovalbumin (OVA). Sorting signals from the transferrin receptor (TFR), targeted a chimeric OVA fusion protein to early endosomes and led to the generation of 8 of 12 presented peptides. Sorting signals from the lysosome-associated membrane protein 1 (LAMP-1), targeted an OVA fusion protein to lysosomes, and led to the generation of 9 of 12 peptides. In contrast, OVA with only a signal sequence led to the generation of only 2 presented peptides. There were both qualitative and quantitative differences in the generation of peptides from the different fusion proteins, suggesting that multiple distinct compartments are involved in generating different epitopes. One peptide was presented better from the TFR fusion protein, while all others were presented better from the LAMP-1 construct. Twelve peptides were generated from exogenously supplied OVA, including 3 peptides that were not generated from any of the fusion proteins. Since most endogenously synthesized foreign antigens are rarely presented on class II molecules, these studies further suggest a strategy whereby antigens in DNA-based vaccines could be targeted to endocytic compartments to enhance immunogenicity.

A monoclonal antibody reactive with a 40-kDa molecule on fetal thymocytes and tumor cells blocks proliferation and stimulates aggregation and apoptosis.

E710.2.3 is a murine thymic lymphoma cell line with an immature phenotype (CD4-CD8-) that proliferates in response to thymocytes or PMA when cultured at low density and proliferates spontaneously when grown at high density. To identify functional molecules on this cell line, we screened for mAbs that could block its proliferation. A hamster mAb, DMF10.62.3, inhibited the spontaneous, thymocyte-induced, and PMA-stimulated proliferation of E710.2.3 in vitro and induced these cells to undergo apoptosis. The mAb also caused homotypic aggregation of E710.2.3, which was inhibited by cytochalasin B, trifluoperazine, a combination of sodium azide and 2-deoxyglucose, EDTA, incubation at 4 degrees C, or treatment with paraformaldehyde. The DMF10 62.3 mAb stained a number of immortalized murine and human cell lines and, where tested, blocked their proliferation and caused death to varying extents by apoptosis. The molecule recognized by the mAb DMF10.62.3 was expressed on day 14 fetal thymus Thy1.2-positive cells. However, it was not detected on adult murine thymocytes, splenocytes, or bone marrow cells or on splenic LPS-activated B cells or Con A-activated T cells. The Ab immunoprecipitated a 40-kDa molecule from E710.2.3 that was not glycosylphosphatidylinositol linked. The data suggest that the molecule recognized by DMF62.3 is a novel cell surface molecule that may be involved in cell proliferation and/or cell death.

Comparison of T cell cytokines in resistant and susceptible mice infected with virulent Brucella abortus strain 2308.

C57BL/10 and BALB/c mice differ in their abilities to clear infections with the intracellular bacterium Brucella abortus strain 2308. We have previously reported that in vivo of IL-10 in the susceptible BALB/c mice results in significantly fewer bacteria in their spleens 1 week after infection with 5 x 10(3) colony forming units (CFU) of 2308. Here we extend those studies and report a similar effect when IL-4 is neutralized. In contrast, in the more resistant C57BL/10 mice infected with 5 x 10(3) CFU, neither neutralization of IL-4 significantly decreased the level of infection nor did it in either BALB/c or C57BL/10 mice infected with a 1000-fold higher dose of strain 2308. While splenocytes from the later mentioned groups of mice produced IL-10 in response to stimulation with brucella antigen, they also produced higher levels of interferon (IFN)-gamma than those from BALB/c mice with the low challenge dose of 5 x 10(3) CFU. Results of in vivo neutralization of IFN-gamma by monoclonal antibodies (MAb) reported here and elsewhere indicated that IFN-gamma is important for control; thus, we postulate that the higher levels of IFN-gamma override the detrimental effects of Th2 cytokines. In vitro studies also showed that macrophages from the more resistant C57BL/10 mice were less susceptible to the ability of IL-10 to decrease anti-brucella activities than were BALB/c macrophages. CD4+ T cells were principally responsible for the production of IL-10 in BALB/c but not C57BL/10 splenocyte populations. C57BL/10 splenocytes produced more IFN-gamma than those from BALB/c mice in response to stimulation with brucella antigens. These differences between BALB/c and C57BL/10 mice may contribute to the superior capacity of C57BL/10 mice to control infections with B. abortus strain 2308.

Lack of a role for natural killer cells in early control of Brucella abortus 2308 infections in mice.

Studies were conducted to determine if natural killer (NK) cells are important for early control of the virulent strain Brucella abortus 2308 following infection of mice with high or low challenge doses. Splenocytes from C57BL/10 and BALB/c mice that had been infected with the lower dose of B. abortus displayed increased cytotoxicity against YAC-1 cells during the first week after infection, while infection of C57BL/10 mice with the higher challenge dose either did not alter the level of NK cytotoxic activity or decreased it, depending upon the time postinfection. In vivo depletion of NK cells by monoclonal antibody anti-NK1.1 or polyclonal anti-asialoGM1 antiserum did not result in an increase in the number of brucellae recovered from the spleens or livers of the brucella-resistant C57BL/10 mice or from the spleens of the susceptible BALB/c mice during the first week after infection. Treatment of control mice with the NK-reactive antibodies, however, decreased killing of the NK-sensitive target YAC-1, indicating that the NK cell depletion regimes were effective. Our results suggest that NK cells are not crucial for early control of B. abortus 2308 even though they may be activated following infection. Further experiments indicated that treatment of C57BL/10 mice with poly(A:U) did not decrease the number of brucellae recovered from their spleens although it did decrease the CFU in livers of mice infected with the high challenge dose.

Interleukin-10 downregulates protective immunity to Brucella abortus.

In vivo neutralization of interleukin-10 (IL-10) with an anti-IL-10 monoclonal antibody resulted in up to 10-fold fewer bacteria in the spleens of BALB/c mice infected with the virulent Brucella abortus strain 2308. In vitro neutralization of endogenous IL-10 in brucella antigen-stimulated cultures of splenocytes from infected mice resulted in increased gamma interferon production in these cultures, whereas exogenous recombinant IL-10 inhibited the ability of peptone-elicited peritoneal macrophages to control intracellular brucellae. These data suggest that IL-10 may be downregulating the immune response to B. abortus by affecting both macrophage effector function and the production of the protective Th1 cytokine gamma interferon.

Macrophage control of Brucella abortus: influence of cytokines and iron.

Brucella abortus is a facultative intracellular bacterium that can infect and replicate in mononuclear phagocytes. Recent work has elucidated the role of cytokines in activating macrophages to inhibit the intracellular replication of brucellae, and in recruiting macrophages to the site of infection in vivo. There is also evidence that iron increases the ability of cytokine-activated macrophages to control intracellular brucellae by mechanisms involving reactive oxygen intermediates.