Ancient genomics

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field''s focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.     

The glycosylated IgII Extracellular domain of EMMPRIN is implicated in the induction of MMP-2

Insulin-like growth factor (IGF)-I and IGF-II play major roles in the regulation of skeletal muscle growth and differentiation, and both are locally expressed in muscle cells. Recent studies have demonstrated that IGF-II up-regulates its own gene expression during myogenesis and this auto-regulatory loop is critical for muscle differentiation. How local IGF-I is regulated in this process is unclear. Here, we report that while IGF-II up-regulated its own gene expression, it suppressed IGF-I gene expression during myogenesis. These opposite effects of IGF-II on IGF-I and IGF-II genes expression were time dependent and dose dependent. It has been shown that IGFs activate the PI3K-Akt-mTOR, p38 MAPK, and Erk1/2 MAPK pathways. In myoblasts, we examined their role(s) in mediating the opposite effects of IGF-II. Our results showed that both the PI3K-Akt-mTOR and p38 MAPK pathways played critical roles in increasing IGF-II mRNA expression. In contrast, mTOR was required for down-regulating the IGF-I gene expression by IGF-II. In addition, Akt, Erk1/2 MAPK, and p38 MAPK pathways were also involved in the regulation of basal levels of IGF-I and IGF-II genes during myogenesis. These findings reveal a previously unrecognized negative feedback mechanism and extend our knowledge of IGF-I and IGF-II gene expression and regulation during myogenesis.     

An essential role for TNF in modulating thresholds for survival, activation, and tolerance of CD8+ T cells

TNF and its receptors p55 and p75 are known to be important in the homeostasis of the peripheral immune system. Previous studies have presented apparently contradictory evidence for an in vivo role of TNF in T cells. In this study, we analyzed TNF-deficient mice crossed with the F5 TCR-transgenic animals. We show that endogenous TNF modulates several aspects of homeostasis of peripheral F5 CD8 T cells. We found that F5/TNF(-/-)mice had reduced numbers of peripheral F5 T cells, F5/TNF(-/-) CD8 T cells exhibited reduced survival potential, and furthermore that T cell-derived TNF is required for optimum recovery of naive CD8 T cells in lymphopenic hosts, suggesting its involvement in the survival of peripheral CD8 T cells. Both peptide activation and ensuing Ag-induced apoptosis are quantitatively reduced in TNF(-/-) CD8 T cells. The latter observations can be related to decreased binding activities of NF-kappaB and NF-ATp observed in Ag-stimulated F5/TNF(-/-) T cells. Finally, in a CD8 T cell tolerance model, endogenous TNF was necessary for several parameters of CD8 T cell tolerance induction. Collectively, our results provide evidence that endogenous TNF modulates thresholds in several ligand-driven T cell responses.     

Transposition of the Drosophila hydei Minos transposon in the mouse germ line

We tested the suitability of the fly transposon Minos, a member of the Tc1/mariner superfamily, for insertional mutagenesis in the mouse germ line. We generated a transgenic mouse line expressing Minos transposase in growing oocytes and another carrying a tandem array of nonautonomous transposons. The frequency of transposition in the progeny derived from oocytes carrying both transgenes is 8.2%. Analysis of the new integration sites shows a high frequency of transpositions to a different chromosome. Thus Minos transposition could be an effective system for insertional mutagenesis and functional genomic analysis in the mouse.     

Iron regulatory and bactericidal properties of human recombinant hepcidin expressed in Pichia pastoris

Hepcidin is a circulating cysteine-rich peptide with antimicrobial properties. It functions as a hormonal regulator of iron homeostasis by controlling iron efflux from target cells via ferroportin (FPN1), which is internalized and degraded upon hepcidin binding. Because of its profound biomedical significance, hepcidin has become the target of intense biochemical studies. The aim of this study was to produce functional recombinant hepcidin in sufficient quantities for advanced research or potential clinical use, as the native hepcidin can be isolated from urine in very low yield. We report the expression, purification and functional characterization of hepcidin variants in yeast P. pastoris. The yield of untagged hepcidin 20- and 25-mer peptides was too low for complete functional characterization. By contrast, Hep20 and Hep25 tagged with either single 6xHis or double Myc-6xHis epitopes were expressed at high quantities (5-7mg/l of culture), yet mostly in oligomeric forms. Purification of monomeric tagged hepcidins was achieved by size exclusion chromatography, with a yield of 0.5-1mg/l of culture. All recombinant hepcidins exhibited bacteriostatic activity and the ability to control cellular iron homeostasis, with Hep25-His being the most potent. Thus, Hep25-His promoted an increase in the levels of the labile iron pool (LIP) in macrophages and consistently bound to ferroportin (FPN1) causing its internalization and the subsequent downregulation of transferrin receptor 1 (TfR1) expression. Analysis by mass-spectrometry suggested that all eight cysteines participated in disulfide bond formation. Our results suggest that only the recombinant Hep25-His monomer was a fully active peptide. As Hep25-His faithfully recapitulates the functional properties of native Hep25, it represents a powerful tool for biochemical studies and potential diagnostic and therapeutic applications.     

Effect of food preservation on the grazing behavior and on the gut flora of the harpacticoid copepod Paramphiascella fulvofasciata

Harpacticoids owe their ‘reputation’ as primary consumers in aquatic food webs to their substantial grazing on diatoms, thus assuring an efficient energy flow to higher trophic levels. Due to the complex feeding behavior of harpacticoids, the nature and dynamics of diatom-harpacticoid trophic interactions remain poorly understood. In addition, there is a growing interest from aquaculture industry in mass-culturing harpacticoids with algal foods but the labor costs of maintaining algal stock cultures are high. This study focuses on the palatability of preserved diatoms for copepods and considers the possible role of bacterially mediated effects on diatom food uptake.The grazing of Paramphiascella fulvofasciata on a preserved freeze-dried diatom diet was tested and compared to the grazing on fresh cells. P. fulvofasciata assimilated the preserved diet, but assimilation of fresh cells was higher. When both cell types were mixed, no selective feeding was observed. Community fingerprinting of the bacteria associated with diatoms and fecal pellets suggests that the copepod gut flora was modified depending on the food source. Furthermore, the results suggest that the egestion of gut bacteria enriches the microenvironment and this can have an additional influence on the feeding behavior of the copepod.Experimental research using preserved foods must take into account that copepod grazing assimilations of fresh foods are likely to be significantly higher. Yet, the stated high assimilation of the mixed diet, encourages further exploration of the application of preserved ‘balanced’ foods for harpacticoid mass-culturing.     

Deletion analysis of the human CD2 gene locus control region in transgenic mice.

Genomic sequences located at the 3' flanking region of the human CD2 gene confer high level tissue-specific, position-independent expression of the gene when introduced in the germ line of mice. In order to further characterize these sequences a range of deletions, from the 3' end were produced and transgenic mice were generated with the human CD2 (hCD2) gene linked to these deleted fragments. This allowed us to establish the minimum sequences necessary for the copy-dependent transgene expression. 2.1 kb or 1.5 kb of 3' flanking sequences linked to a hCD2 mini-gene is sufficient to allow T-cell specific, copy-dependent, integration-independent expression in transgenic mice. 1.1 kb of 3' sequences results in the gene being expressed in a T-cell specific manner, but copy-dependent, integration-independent expression was not observed in a small number of transgenic animals. 0.2 or 0.5 kb of 3' flanking sequences were insufficient to allow expression above the level previously found with a human CD2 gene which lacked 3' flanking sequences. We conclude that the Locus Control Region (LCR) effect is caused by 1.5 kb of flanking sequences immediately 3' to the polyadenylation signal of the gene.     

Molecular Size of the γ-Aminobutyric AcidA Receptor Purified from Mammalian Cerebral Cortex

The hydrodynamic behaviour of both the soluble and purified gamma-aminobutyric acidA (GABAA) receptor of bovine or rat cerebral cortex has been investigated in solution in Triton X-100 or in 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulphonate (CHAPS). In all the hydrodynamic separations made, it was found that the binding activities for GABA, benzodiazepine, and (where detectable) t-butylbicyclophosphorothionate comigrated. Conditions were established for gel exclusion chromatography and for sucrose density gradient velocity sedimentation that maintain the GABAA receptor in a nonaggregated form. Using these conditions, the molecular weight of the bovine GABAA receptor in the above-mentioned detergents was calculated using the H2O/2H2O method. A value of Mr 230,000-240,000 was calculated for the bovine pure GABAA receptor purified in sodium deoxycholate/Triton X-100 media. A value of Mr 284,000-290,000 was calculated for the nonaggregated bovine or rat cortex receptor in CHAPS, but the Stokes radius is smaller in the latter than in the former medium and the detergent binding in CHAPS is underestimated. Thus the deduced Mr, 240,000, is the best estimate by this method.