Pseudocercospora species on Piperaceae from Viçosa, Minas Gerais, Brazil

Three Pseudocercospora species were found associated with leaf spots on five different members of the family Piperaceae in a stretch of Atlantic rain forest in the municipality of Viçosa, Minas Gerais, Brazil. Pseudocercospora piperis is newly recorded on Piper crassinervium and Piper mollicomum. It was also found in association with Pothomorphe umbellata, which is already known to be a host. Pseudocercospora piperis-arborei sp. nov. and Pseudocercospora piperis-gigantifolii sp. nov. were recorded on Piper arboreum and Piper gigantifolium, respectively. These three species are fully described and illustrated in the present work.     

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.     

Functional representation of enzymes by specific peptides

Predicting the function of a protein from its sequence is a long-standing goal of bioinformatic research. While sequence similarity is the most popular tool used for this purpose, sequence motifs may also subserve this goal. Here we develop a motif-based method consisting of applying an unsupervised motif extraction algorithm (MEX) to all enzyme sequences, and filtering the results by the four-level classification hierarchy of the Enzyme Commission (EC). The resulting motifs serve as specific peptides (SPs), appearing on single branches of the EC. In contrast to previous motif-based methods, the new method does not require any preprocessing by multiple sequence alignment, nor does it rely on over-representation of motifs within EC branches. The SPs obtained comprise on average 8.4 +/- 4.5 amino acids, and specify the functions of 93% of all enzymes, which is much higher than the coverage of 63% provided by ProSite motifs. The SP classification thus compares favorably with previous function annotation methods and successfully demonstrates an added value in extreme cases where sequence similarity fails. Interestingly, SPs cover most of the annotated active and binding site amino acids, and occur in active-site neighboring 3-D pockets in a highly statistically significant manner. The latter are assumed to have strong biological relevance to the activity of the enzyme. Further filtering of SPs by biological functional annotations results in reduced small subsets of SPs that possess very large enzyme coverage. Overall, SPs both form a very useful tool for enzyme functional classification and bear responsibility for the catalytic biological function carried out by enzymes.     

No evidence of inhibition of horizontal gene transfer by CRISPR–Cas on evolutionary timescales

The CRISPR (clustered, regularly, interspaced, short, palindromic repeats)–Cas (CRISPR-associated genes) systems of archaea and bacteria provide adaptive immunity against viruses and other selfish elements and are believed to curtail horizontal gene transfer (HGT). Limiting acquisition of new genetic material could be one of the sources of the fitness cost of CRISPR–Cas maintenance and one of the causes of the patchy distribution of CRISPR–Cas among bacteria, and across environments. We sought to test the hypothesis that the activity of CRISPR–Cas in microbes is negatively correlated with the extent of recent HGT. Using three independent measures of HGT, we found no significant dependence between the length of CRISPR arrays, which reflects the activity of the immune system, and the estimated number of recent HGT events. In contrast, we observed a significant negative dependence between the estimated extent of HGT and growth temperature of microbes, which could be explained by the lower genetic diversity in hotter environments. We hypothesize that the relevant events in the evolution of resistance to mobile elements and proclivity for HGT, to which CRISPR–Cas systems seem to substantially contribute, occur on the population scale rather than on the timescale of species evolution.     

Radial compression of microtubules and the mechanism of action of taxol and associated proteins

Microtubules (MTs) are hollow cylindrical polymers composed of alphabeta-tubulin heterodimers that align head-to-tail in the MT wall, forming linear protofilaments that interact laterally. We introduce a probe of the interprotofilament interactions within MTs and show that this technique gives insight into the mechanisms by which MT-associated proteins (MAPs) and taxol stabilize MTs. In addition, we present further measurements of the mechanical properties of MT walls, MT-MT interactions, and the entry of polymers into the MT lumen. These results are obtained from a synchrotron small angle x-ray diffraction (SAXRD) study of MTs under osmotic stress. Above a critical osmotic pressure, P(cr), we observe rectangular bundles of MTs whose cross sections have buckled to a noncircular shape; further increases in pressure continue to distort MTs elastically. The P(cr) of approximately 600 Pa provides, for the first time, a measure of the bending modulus of the interprotofilament bond within an MT. The presence of neuronal MAPs greatly increases P(cr), whereas surprisingly, the cancer chemotherapeutic drug taxol, which suppresses MT dynamics and inhibits MT depolymerization, does not affect the interprotofilament interactions. This SAXRD-osmotic stress technique, which has enabled measurements of the mechanical properties of MTs, should find broad application for studying interactions between MTs and of MTs with MAPs and MT-associated drugs.     

Multicultural society and everyday cultural racism: second generation of Ethiopian Jews in Israel's ‘crisis of modernization’

Abstract

The core of this article sets out to examine the extent to which a multicultural society can prevent cultural racism, which, like multiculturalism, is by definition based on a culture of diversity and separation. The ‘first modernity’ was organized along national lines, with a centralist state that opted to create an essentialist and uncontested national identity. Immigrants, especially those who came from ‘third world’ countries, were expected to undergo a process of assimilation, and to integrate into the dominant culture by relinquishing their particular past and tradition. Multiculturalism, which emerged historically as a criticism of that perspective, aims at creating a kaleidoscope of associations and cultural communities, which inevitably presents a challenge to the one ‘truth’ of the nation-state with the argument that this ‘truth’ favours some groups over others. Within the multicultural model, identity politics of various groups is perceived as a means to achieve recognition, acceptance, respect and even public affirmation of differences. However, do multicultural society and identity-related differences provide a solution to cultural racism as well?

Investigating the second generation of the Ethiopian Jews, who migrated to Israel during its transformation from ethno-national republicanism to a neo-liberal, multicultural society, can help answer this question. By presenting their patterns of association, character of protest activities and the newly formed hybrid identity that Ethiopian youth have developed as a means to liberate themselves from a discriminating reality, and by examining the Others’ reaction to that challenge, this article uncovers certain mechanisms and methods of action through which a multicultural society, having a thin and mild version of multiculturalism, does not diminish cultural racism, particularly its everyday non-institutional version, but in fact augments it.