An alternative method to isoenzyme profile for cell line identification and interspecies cross-contaminations: cytochrome b PCR-RLFP analysis

One of the major risks in cell culture laboratories is the misidentification and cross-contamination of cell lines. Several methods have been used to authenticate cell lines, including isoenzyme profiling, the test suggested by European Farmacopeia, which is performed at the Tissue Culture Centre in Brescia. However, this method displays several disadvantages, such as high variability and low reproducibility, and it is time consuming and requires high cell concentrations to be performed. Therefore, an alternative method has been developed to confirm the specie of origin of 27 different animal cell cultures. A polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) assay was optimized, based on the use of a pair of primers that anneal to a portion of the cytochrome b gene in all the species. The amplification product was digested with a panel of six restriction enzymes, and the pattern derived was resolved on 3% high-resolution agarose gel. For 23 species, this protocol produced a unique restriction pattern, and the origin of these animal cells resulted to be confirmed by this analysis. Furthermore, results indicate that cytochrome b PCR-RFLP was able to amplify target sequences using very low amounts of deoxyribonucleic acid (DNA). Its sensitivity in detecting interspecies, cross-contamination was comparable to that of isoenzyme analysis (contaminating DNA should represent at least 10% of the total DNA). For 4 of the 27 species (sheep, dog, Guinea pig, and Rhesus monkey) the observed pattern, even if highly reproducible, showed additional bands; for these species, specific PCR was also performed.     

Animal xenodiversity in Italian inland waters: distribution, modes of arrival, and pathways

The paper provides a list of the non-indigenous animal species occurring today in Italian inland waters. Xenodiversity was found to amount to 112 species (64 invertebrates and 48 vertebrates), which contribute for about 2% to the inland-water fauna in Italy. Northern and central regions are most affected, and Asia, North America, and the rest of Europe are the main donor continents. The large majority of non-indigenous species entered Italy as a direct or indirect effect of human intervention. A difference between invertebrates and vertebrates was found for their mode of arrival (unintentional for invertebrates and intentional for vertebrates). Accidental transport, in association with both fish (for aquaculture or stock enhancement) and crops, has been the main vector of invertebrate introductions, whereas vertebrates were mostly released for stocking purposes. Overall stock enhancement (47.92%) and culture (37.5%) prevailed over the other pathways. Seventeen and 7 species of our list are included among the 100 worst invasive species of Europe (DAISIE) and of the world (IUCN), respectively. For some (but not all) non-indigenous species recorded in Italy the multilevel impact exerted on the recipient communities and ecosystems is known, even if rarely quantified, but knowledge on their chronic impact is still missing. Additional research is needed to provide criteria for prioritizing intervention against well established invaders and identify which new potential invader should be targeted as “unwanted”.     

An information theoretic exploratory method for learning patterns of conditional gene coexpression from microarray data

In this article, we introduce an exploratory framework for learning patterns of conditional co-expression in gene expression data. The main idea behind the proposed approach consists of estimating how the information content shared by a set of M nodes in a network (where each node is associated to an expression profile) varies upon conditioning on a set of L conditioning variables (in the simplest case represented by a separate set of expression profiles). The method is non-parametric and it is based on the concept of statistical co-information, which, unlike conventional correlation based techniques, is not restricted in scope to linear conditional dependency patterns. Moreover, such conditional co-expression relationships can potentially indicate regulatory interactions that do not manifest themselves when only pair-wise relationships are considered. A moment based approximation of the co-information measure is derived that efficiently gets around the problem of estimating high-dimensional multi-variate probability density functions from the data, a task usually not viable due to the intrinsic sample size limitations that characterize expression level measurements. By applying the proposed exploratory method, we analyzed a whole genome microarray assay of the eukaryote Saccharomices cerevisiae and were able to learn statistically significant patterns of conditional co-expression. A selection of such interactions that carry a meaningful biological interpretation are discussed.     

Treatment strategies for allergy and asthma

Allergic diseases have reached epidemic proportions worldwide. An understanding of the cellular and soluble mediators that are involved in allergic inflammatory responses not only helps in understanding the mechanisms of current treatments, but is also important for the identification of new targets that are amenable to both small-molecule and biological interventions. There is now considerable optimism with regards to tackling the allergy epidemic in light of improvements in systemic and mucosal allergen-specific immunotherapy, the identification of key cytokines and their receptors that drive T-helper-2-cell polarization, a clearer understanding of the pathways of leukocyte recruitment and the signalling pathways that are involved in cell activation and mediator secretion, and new approaches to vaccine development.     

Transketolase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase type I isoforms are specifically recognized by IgG autoantibodies in multiple sclerosis patients

The presence of autoantibodies in multiple sclerosis (MuS) is well known, but their target antigens have not been clearly identified. In the present study, IgG autoreactivity to neural antigens of normal human white matter separated by bidimensional electrophoresis was assessed in serum and cerebrospinal fluid of 18 MuS and 20 control patients. Broad IgG autoreactivity was detected by two-dimensional immunoblotting in all cases to neural antigens, most of which were identified by mass spectrometry. The comparative analysis of MuS and non-MuS reactive spots showed that a restricted number of neural protein isoforms were specifically recognized by MuS IgG. Almost all MuS patients had cerebrospinal fluid IgG directed to isoforms of one of the oligodendroglial molecules, transketolase, 2',3'-cyclic-nucleotide 3'-phosphodiesterase type I, collapsin response mediator protein 2, and tubulin beta 4. Interestingly 50% of MuS IgG recognized transketolase, which was mostly localized on oligodendrocytes in human white matter from normal and MuS samples. IgG autoreactivity to cytoskeletal proteins (radixin, sirtuin 2, and actin-interacting protein 1) was prevalent in secondary progressive MuS patients. Among the proteins recognized by serum IgG, almost all MuS patients specifically recognized a restricted number of neuronal/cytoskeletal proteins, whereas 2',3'-cyclic-nucleotide 3'-phosphodiesterase type I was the oligodendroglial antigen most frequently recognized (44%) by MuS seric IgG. Our immunomics approach shed new light on the autoimmune repertoire present in MuS patients revealing novel oligodendroglial and/or neuronal putative autoantigens with potential important pathogenic and diagnostic implications.     

Vinyl ester-based cyclic peptide proteasome inhibitors

The 20S proteasome is a multicatalytic protease complex responsible for the degradation of many proteins in mammalian cells. Specific inhibition of proteasome enzymatic subunits represents a topic of great interest for the development of new drug therapies. Following our previous development of a new class of peptide-based inhibitors bearing a C-terminal vinyl ester residue as a pharmacophoric unit that are able to interact with the catalytic threonine, we report here the synthesis and biological properties of a new series of vinyl ester cyclopeptide analogues. Some of these derivatives were shown to inhibit the chymotrypsin-like activity of the proteasome at nanomolar concentration and their potency was found to depend on the size of the tetrapeptidic cyclic portion.     

Design, synthesis, and biological evaluation of pirenzepine analogs bearing a 1,2-cyclohexanediamine and perhydroquinoxaline units in exchange for the piperazine ring as antimuscarinics

Pirenzepine (2) is one of the most selective muscarinic M(1) versus M(2) receptor antagonists known. A series of 2 analogs, in which the piperazyl moiety was replaced by a cis- and trans-cyclohexane-1,2-diamine (3-6) or a trans- and cis-perhydroquinoxaline rings (7 and 8) were prepared, with the aim to investigate the role of the piperazine ring of 2 in the interaction with the muscarinic receptors. The structural change leading to compounds 3-6 abolished in binding assays the muscarinic M(1)/M(2) selectivity of 2, due to an increased M(2) affinity. Rather, compounds 3-6 displayed a reversed selectivity showing more affinity at the muscarinic M(2) receptor than at all the other subtypes tested.     

Carbohydrate availability affects growth and metabolism in peach fruit

Along with sucrose, sorbitol represents the main photosynthetic product and form of translocated carbon in peach. This study aimed at determining whether peach fruit carbohydrate metabolism is affected by changes in source–sink balance , and specifically whether sorbitol or sucrose availability regulates fruit enzyme activities and growth. In various trials, different levels of assimilate availability to growing fruits were induced in vivo by varying crop load of entire trees, leaf : fruit ratio (L:F) of fruiting shoots, or by interrupting the phloem stream (girdling) to individual fruits. In vitro, fruit tissue was incubated in presence/absence of sorbitol and sucrose. Relative growth rate (RGR), enzyme activities and carbohydrates were measured at different fruit growth stages of various peach cultivars in different years. At stage III, high crop load induced higher acid invertase (AI, EC 3.2.1.26) activities and hexose : sucrose ratios. Both sorbitol and sucrose contents were proportional to L:F, while sorbitol dehydrogenase (SDH, EC 1.1.1.14) activity was the only enzyme activity directly related to L:F in both fruit growth stages. Girdling reduced fruit RGR and all major carbohydrates after 4 days and SDH activity already after 48 h, but it did not affect sucrose synthase (SS, EC 2.4.1.13), AI and neutral invertase (NI, EC 3.2.1.27). Fruit incubation in sorbitol for 24 h induced higher SDH activities than in buffer alone. In general, assimilate availability affected both sorbitol and sucrose metabolism in peach fruit, and sorbitol may function as a signal for modulating SDH activity. Under highly competitive conditions, AI activity may be enhanced by assimilate depletion, providing a mechanism to increase fruit sink strength by increasing hexose concentrations.     

Modified peptides in anti-cancer vaccines: are we eventually improving anti-tumour immunity?

The discovery of tumour antigens recognized by T cells and the features of immune responses directed against them has paved the way to a multitude of clinical studies aimed at boosting anti-tumour T cell immunity as a therapeutic tool for cancer patients. One of the different strategies explored to ameliorate the immunogenicity of tumour antigens in vaccine protocols is represented by the use of optimized peptides or altered peptide ligands, whose amino acid sequence has been modified for improving HLA binding or TCR interaction with respect to native epitopes. However, despite the promising results achieved with preclinical studies, the clinical efficacy of this approach has not yet met the expectations. Although multiple reasons could explain the relative failure of altered peptide ligands as more effective cancer vaccines, the possibility that T cells primed by modified tumour peptides might may be unable to effectively cross-recognize tumour cells has not been sufficiently addressed. Indeed, the introduction of conservative amino acid substitutions may still produce diverse and unpredictable changes in the HLA/peptide interface, with consequent modifications of the TCR repertoire that can interact with the complex. This could lead to the expansion of a broad array of T cells whose TCRs may not necessarily react with equivalent affinity with the original antigenic epitope. Considering the results presently achieved with this vaccine approach, and the emerging availability of alternative strategies for boosting anti-tumour immunity, the use of modified tumour peptides could be reconsidered. This article is a symposium paper from the conference “Immunotherapy—From Basic Research to Clinical Applications”, Symposium of the Collaborative Research Center (SFB) 685, held in Tübingen, Germany, 6–7 March 2008.