New protein clustering of breast cancer tissue proteomics using actin content as a cellularity indicator

In the present study, we report the comparative proteome profiles of proteins solubilized from 37 breast cancer surgical tissues, normalized for the actin content. Blood-derived proteins were excluded from the analysis. Among the tumor-derived protein spots, a large proportion (39%) was found present in all patients. These included several glycolytic enzymes, detox and heat shock proteins, members of annexin and S100 protein families, cathepsin D, and two "rare" proteins, DDAH2 involved in the angiogenesis control, and the oncogene PARK7. Other proteins, such as psoriasin, galectin1, cofilin, peroredoxins, SH3L1, and others, showed sporadic presence and high expression level, which suggests their possible role for patient stratification.     

Complete mitochondrial genome sequence of the Tyrolean Iceman

The Tyrolean Iceman was a witness to the Neolithic-Copper Age transition in Central Europe 5350-5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations. This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.     

Optimization of human d-amino acid oxidase expression in Escherichia coli

Human d-amino acid oxidase (hDAAO) is a flavoprotein that plays a key role in the pathophysiology of schizophrenia. So far, the biochemical characterization of this enzyme has been hampered by the difficulty of expressing it in a common heterologous host such as Escherichia coli. Increasing amounts of recombinant hDAAO are indeed required for the investigation of its structure–function relationships and for the screening of new inhibitors to be used in the treatment of schizophrenia. A recombinant hDAAO has been over-expressed in BL21(DE3)Star E. coli cells. By alternating screenings of medium components at flask level and investigating physiological parameters in 2 L controlled batch fermentations, an improved, robust and scalable microbial process was set up giving almost a 40- and 4-fold improvement in volumetric productivity and specific activity, respectively. Under these conditions 770 U/L culture hDAAO with a specific activity of 0.4 U/mg protein and a specific productivity of 24.9 U/g biomass were produced. Optimization of medium ingredients, of the time and the amount of inducer’s addition, pH control at the moment of induction and harvest, low mechanical shear stress regime during recombinant protein production, represent the factors concurring to achieve the reported expression level. Notably, this expression level is higher than any previously described production of hDAAOs. A yield of 100 mg of pure hDAAO/L culture thus became available in comparison to the 1–10 mg/L previously reported.     

Population ecology of yew (<Emphasis Type="Italic">Taxus baccata</Emphasis> L.) in the Central Apennines: spatial patterns and their relevance for conservation strategies

Understanding the ecological mechanisms that allow a species to transition from an occasional understory component to the dominant type in the forest canopy is essential for predicting future shifts in the distribution of species. We investigated this issue with regard to yew, also because mature yew trees have been reported to inhibit self-regeneration and seedling survival, prompting concerns for the long-term preservation of the species. Our objectives were (a) to quantify spatial patterns of yew (Taxus baccata L.) populations near the southern limit of the species’ ecological distribution, (b) to determine the relationships between yew presence and topographic gradients, and (c) to answer the question of how yew regeneration is affected by such patterns and relationships. We analyzed three extensive yew populations (90–165 ha, including 3–12 thousand established individuals) that mostly occupy the understory of beech forests located in protected areas of the central Apennines (Italy). Overall, the realized niche of yew (either as established trees, saplings, or seedlings) followed the expected bell-shaped curve of a species response to an environmental gradient. Yew was mainly found at 1,000–1,600 m elevation on mesic exposures (north and west) and intermediate slopes (30–60%). Geostatistical analysis revealed that yew occurred in patches, as shown by variogram ranges of 40–110 m for yew tree basal area and regeneration abundance. Yew regeneration over the landscape was directly related to basal area of yew trees. At local scales (~10 m), presence of established trees favored regeneration in relatively less developed stands, whereas high density of mature yews suppressed regeneration. Healthy yew populations in beech forests had a minimum size of 0.5–3 ha. As yew density increased within these patches, regeneration dropped, so that yew conservation cannot be limited to presently occurring populations, despite the longevity and potential for vegetative reproduction of the species. Disturbance from grazing and wildfire was also found to impact yew survival. Long-term existence of yew in the Italian Apennines depends on maintaining and expanding old-growth beech forests that incorporate yew patches, and have a minimum continuous cover equivalent to a relatively undisturbed regime (10–50 ha).     

A retrospective study on IVF outcome in euthyroid patients with anti-thyroid antibodies: effects of levothyroxine, acetyl-salicylic acid and prednisolone adjuvant treatments

Background  

Anti-thyroid antibodies (ATA), even if not associated with thyroid dysfunction, are suspected to cause poorer outcome of in vitro fertilization (IVF).     

Comparison of the Immunomodulatory Properties of Three Probiotic Strains of Lactobacilli Using Complex Culture Systems: Prediction for In Vivo Efficacy

Background

While the use of probiotics to treat or prevent inflammatory bowel disease (IBD) has been proposed, to this point the clinical benefits have been limited. In this report we analyzed the immunological activity of three strains of Lactobacillus to predict their in vivo efficacy in protecting against experimental colitis.

Methodology/Principal Findings

We compared the immunological properties of Lactobacillus plantarum NCIMB8826, L. rhamnosus GG (LGG), L. paracasei {"type":"entrez-nucleotide","attrs":{"text":"B21060","term_id":"2396114","term_text":"B21060"}}B21060 and pathogenic Salmonella typhimurium (SL1344). We studied the stimulatory effects of these different strains upon dendritic cells (DCs) either directly by co-culture or indirectly via conditioning of an epithelial intermediary. Furthermore, we characterized the effects of these strains in vivo using a Dextran sulphate sodium (DSS) model of colitis.We found that the three strains exhibited different abilities to induce inflammatory cytokine production by DCs with L. plantarum being the most effective followed by LGG and L. paracasei. L. paracasei minimally induced the release of cytokines, while it also inhibited the potential of DCs to both produce inflammatory cytokines (IL-12 and TNF-α) and to drive Th1 T cells in response to Salmonella. This effect on DCs was found under both direct and indirect stimulatory conditions – i.e. mediated by epithelial cells - and was dependent upon an as yet unidentified soluble mediator. When tested in vivo, L. plantarum and LGG exacerbated the development of DSS-induced colitis and caused the death of treated mice, while, conversely L. paracasei was protective.

Conclusions

We describe a new property of probiotics to either directly or indirectly inhibit DC activation by inflammatory bacteria. Moreover, some immunostimulatory probiotics not only failed to protect against colitis, they actually amplified the disease progression. In conclusion, caution must be exercised when choosing a probiotic strain to treat IBD.     

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations

Trans/cis prolyl isomerisation is involved in several biological processes, including the development of numerous diseases. In the HIV-1 capsid protein (CA), such a process takes place in the uncoating and recruitment of the virion and is catalyzed by cyclophilin A (CypA). Here, we use metadynamics simulations to investigate the isomerization of CA's model substrate HAGPIA in water and in its target protein CypA. Our results allow us to propose a novel mechanistic hypothesis, which is finally consistent with all of the available molecular biology data.