Unexpected inhibition of peptidoglycan LD-transpeptidase from Enterococcus faecium by the beta-lactam imipenem

The beta-lactam antibiotics mimic the D-alanyl(4)-D-alanine(5) extremity of peptidoglycan precursors and act as "suicide" substrates of the DD-transpeptidases that catalyze the last cross-linking step of peptidoglycan synthesis. We have previously shown that bypass of the dd-transpeptidases by the LD-transpeptidase of Enterococcus faecium (Ldt(fm)) leads to high level resistance to ampicillin. Ldt(fm) is specific for the L-lysyl(3)-D-alanine(4) bond of peptidoglycan precursors containing a tetrapeptide stem lacking D-alanine(5). This specificity was proposed to account for resistance, because the substrate of Ldt(fm) does not mimic beta-lactams in contrast to the D-alanyl(4)-D-alanine(5) extremity of pentapeptide stems used by the DD-transpeptidases. Here, we unexpectedly show that imipenem, a beta-lactam of the carbapenem class, totally inhibited Ldt(fm) at a low drug concentration that was sufficient to inhibit growth of the bacteria. Peptidoglycan cross-linking was also inhibited, indicating that Ldt(fm) is the in vivo target of imipenem. Stoichiometric and covalent modification of Ldt(fm) by imipenem was detected by mass spectrometry. The modification was mapped into the trypsin fragment of Ldt(fm) containing the catalytic Cys residue, and the Cys to Ala substitution prevented imipenem binding. The mass increment matched the mass of imipenem, indicating that inactivation of Ldt(fm) is likely to involve rupture of the beta-lactam ring and acylation of the catalytic Cys residue. Thus, the spectrum of activity of beta-lactams is not restricted to transpeptidases of the DD-specificity, as previously thought. Combination therapy with imipenem and ampicillin could therefore be active against E. faecium strains having the dual capacity to manufacture peptidoglycan with transpeptidases of the LD- and DD-specificities.     

Long-term study on symptomless human metapneumovirus infection in hematopoietic stem cell transplant recipients

From October 2004 through October 2006 a study was performed to evaluate the prevalence of human Metapneumovirus (hMPV) infection in adult hematopoietic stem cell transplant (HSCT) recipients. Sequential nasopharyngeal aspirates (NPA) were collected independently from respiratory symptoms and evaluated for hMPV-RNA by polymerase chain reaction (PCR) and sequence analysis. Results indicate epidemiological and molecular differences between the 2004-2005 and 2005-2006 periods and that hMPV seems not to symptomatically affect HSCT patients or cause late respiratory sequelae. In addition, data collected suggest a hospital origin of hMPV infection in most HSCT patients during the 2004-2005 period.     

Selective observation of the disordered import signal of a globular protein by in-cell NMR: The example of frataxins

We have exploited the capability of in-cell NMR to selectively observe flexible regions within folded proteins to carry out a comparative study of two members of the highly conserved frataxin family which are found both in prokaryotes and in eukaryotes. They all contain a globular domain which shares more than 50% identity, which in eukaryotes is preceded by an N-terminal tail containing the mitochondrial import signal. We demonstrate that the NMR spectrum of the bacterial ortholog CyaY cannot be observed in the homologous E. coli system, although it becomes fully observable as soon as the cells are lysed. This behavior has been observed for several other compact globular proteins as seems to be the rule rather than the exception. The NMR spectrum of the yeast ortholog Yfh1 contains instead visible signals from the protein. We demonstrate that they correspond to the flexible N-terminal tail indicating that this is flexible and unfolded. This flexibility of the N-terminus agrees with previous studies of human frataxin, despite the extensive sequence diversity of this region in the two proteins. Interestingly, the residues that we observe in in-cell experiments are not visible in the crystal structure of a Yfh1 mutant designed to destabilize the first helix. More importantly, our results show that, in cell, the protein is predominantly present not as an aggregate but as a monomeric species.     

Antiproliferative activity and cell cycle analysis of 2-(3,5-dihydroxyphenyl)-6-hydroxybenzothiazole on MCF-7 breast and HCT-15 colon cancer cell lines

The antiproliferative activity of 2-(3,5-Dihydroxyphenyl)-6-hydroxybenzothiazole (DHB) is reported here. DHB inhibits the growth of human colon cancer HCT-15 with a 50% cell growth inhibition value of 23?μM and breast cancer MCF-7 with a 50% cell growth inhibition value of 41?μM in a dose/time dependent manner by using sulforhodamine B assay. Cell cycle analysis by flow cytometry showed that DHB-induced growth arrest could be associated with apoptosis in both cell lines. Moreover, suppression of clonogenic activity occurs after exposure to DHB at a concentration of 25?μM for HCT-15 and of 40?μM for MCF-7.     

Volatile components of whole and different plant parts of bastard balm (Melittis melissophyllum L., Lamiaceae) collected in Central Italy and Slovakia

The aim of this work was to trap the volatiles released from whole frozen and dry aerial parts, and, separately, from different organs (leaves, stems, corolla and calyx) of bastard balm (Melittis melissophyllum L., Lamiaceae) populations collected in Italy and Slovakia by HS-SPME, and to identify the headspace constituents responsible for the characteristic aroma impression by GC/FID and GC/MS techniques. Among more than 100 volatile components detected, the C(8) alcohol oct-1-en-3-ol, responsible for the typical mushroom-like odor, and the phenolic coumarin, with a characteristic sweet and creamy vanilla bean odor, played a major role in the aroma of whole aerial parts and different plant organ samples. In particular, dry calyx parts could be proposed as flavoring agent in food products as mushroom aroma enhancer. Multivariate chemometric techniques, such as cluster analysis and principal component analysis, were used to characterize the sample populations according to the geographical origin and processing of plant material.     

Who Is the Best Player Ever? A Complex Network Analysis of the History of Professional Tennis

We considered all matches played by professional tennis players between 1968 and 2010, and, on the basis of this data set, constructed a directed and weighted network of contacts. The resulting graph showed complex features, typical of many real networked systems studied in literature. We developed a diffusion algorithm and applied it to the tennis contact network in order to rank professional players. Jimmy Connors was identified as the best player in the history of tennis according to our ranking procedure. We performed a complete analysis by determining the best players on specific playing surfaces as well as the best ones in each of the years covered by the data set. The results of our technique were compared to those of two other well established methods. In general, we observed that our ranking method performed better: it had a higher predictive power and did not require the arbitrary introduction of external criteria for the correct assessment of the quality of players. The present work provides novel evidence of the utility of tools and methods of network theory in real applications.     

Traditions in spider monkeys are biased towards the social domain

Cross-site comparison studies of behavioral variation can provide evidence for traditions in wild species once ecological and genetic factors are excluded as causes for cross-site differences. These studies ensure behavior variants are considered within the context of a species' ecology and evolutionary adaptations. We examined wide-scale geographic variation in the behavior of spider monkeys (Ateles geoffroyi) across five long-term field sites in Central America using a well established ethnographic cross-site survey method. Spider monkeys possess a relatively rare social system with a high degree of fission-fusion dynamics, also typical of chimpanzees (Pan troglodytes) and humans (Homo sapiens). From the initial 62 behaviors surveyed 65% failed to meet the necessary criteria for traditions. The remaining 22 behaviors showed cross-site variation in occurrence ranging from absent through to customary, representing to our knowledge, the first documented cases of traditions in this taxon and only the second case of multiple traditions in a New World monkey species. Of the 22 behavioral variants recorded across all sites, on average 57% occurred in the social domain, 19% in food-related domains and 24% in other domains. This social bias contrasts with the food-related bias reported in great ape cross-site comparison studies and has implications for the evolution of human culture. No pattern of geographical radiation was found in relation to distance across sites. Our findings promote A. geoffroyi as a model species to investigate traditions with field and captive based experiments and emphasize the importance of the social domain for the study of animal traditions.     

Finding statistically significant communities in networks

Community structure is one of the main structural features of networks, revealing both their internal organization and the similarity of their elementary units. Despite the large variety of methods proposed to detect communities in graphs, there is a big need for multi-purpose techniques, able to handle different types of datasets and the subtleties of community structure. In this paper we present OSLOM (Order Statistics Local Optimization Method), the first method capable to detect clusters in networks accounting for edge directions, edge weights, overlapping communities, hierarchies and community dynamics. It is based on the local optimization of a fitness function expressing the statistical significance of clusters with respect to random fluctuations, which is estimated with tools of Extreme and Order Statistics. OSLOM can be used alone or as a refinement procedure of partitions/covers delivered by other techniques. We have also implemented sequential algorithms combining OSLOM with other fast techniques, so that the community structure of very large networks can be uncovered. Our method has a comparable performance as the best existing algorithms on artificial benchmark graphs. Several applications on real networks are shown as well. OSLOM is implemented in a freely available software (http://www.oslom.org), and we believe it will be a valuable tool in the analysis of networks.