Transcriptome sequencing of Mycosphaerella fijiensis during association with Musa acuminata reveals candidate pathogenicity genes

Figure S4. Phylogenetic tree of fusicoccadiene synthase protein sequences. A maximum likelihood tree was created of the M. fijiensis fusicoccadiene synthase sequence and its top 50 hits using blastp with the non-redundant protein sequence database on NCBI. Bootstrap values are indicated on the tree, and the scale bar of branch lengths indicate substitutions per site. A description of each blast hit is shown, along with an abbreviation for species. Ab = Alternaria brassicicola; Ac = Acremonium chrysogenum; Af = Aspergillus flavus; Ak = Aspergillus kawachii; An = Aspergillus niger; Ao = Aspergillus oryzae; Ar = Aspergillus ruber; Bm = Bipolaris maydis; Bo = Bipolaris oryzae; Bp = Baudoinia panamericana; Bs = Bipolaris sorokiniana; Bv = Bipolaris victoriae; Bz = Bipolaris zeicola; Cg = Chaetomium globosum; Ci = Coccidioides immitis; Cp = Coccidioides posadasii; Da = Diaporthe amygdali; Fg = Fusarium graminearum; Fp = Fusarium pseudograminearum; Gl = Gymnopus luxurians; Mo = Magnaporthe oryzae; Mp = Macrophomina phaseolina; Nf = Neosartorya fischeri; Nu = Neosartorya udagawae; Om = Oidiodendron maius; Pp = Pseudogymnoascus pannorum; Ptt = Pyrenophora teres f. teres; Tc = Talaromyces cellulolyticus; Ti = Talaromyces islandicus; Tm = Talaromyces marneffei; To = Tolypocladium ophioglossoides; Ts = Talaromyces stipitatus; Tt = Thielavia terrestris. (TIF 303 kb

Rate dependent shear bands in a shear transformation zone model of amorphous solids

We use Shear Transformation Zone (STZ) theory to develop a deformation map for amorphous solids as a function of the imposed shear rate and initial material preparation. The STZ formulation incorporates recent simulation results [Haxton and Liu, PRL 99 195701 (2007)] showing that the steady state effective temperature is rate dependent. The resulting model predicts a wide range of deformation behavior as a function of the initial conditions, including homogeneous deformation, broad shear bands, extremely thin shear bands, and the onset of material failure. In particular, the STZ model predicts homogeneous deformation for shorter quench times and lower strain rates, and inhomogeneous deformation for longer quench times and higher strain rates. The location of the transition between homogeneous and inhomogeneous flow on the deformation map is determined in part by the steady state effective temperature, which is likely material dependent. This model also suggests that material failure occurs due to a runaway feedback between shear heating and the local disorder, and provides an explanation for the thickness of shear bands near the onset of material failure. We find that this model, which resolves dynamics within a sheared material interface, predicts that the stress weakens with strain much more rapidly than a similar model which uses a single state variable to specify internal dynamics on the interface.Comment: 10 pages, 13 figures, corrected typos, added section on rate strengthening vs. rate weakening material

Dynamite Voices: The Broadside Press of Detroit, 1985-1998

"Dynamite Vocies" celebrates the acquisition of the archive of the Broadside Press by the University of Michigan Special Collections Library. The archive was acquired from Hilda and Don Vest, owners of the Press from 1985 to 1998, and includes correspondence, business records, grant applications, audio and video recordings, photographs, posters, and publications of the Broadside Press from its beginnings in 1965 to the present.http://deepblue.lib.umich.edu/bitstream/2027.42/120247/1/dynamite_voices_01.pd

Portrait of a people: the Jewish Heritage Collection dedicated to Mark and Dave Harris

The Jewish Heritage Collection was a gift made jointly to the Frankel Center for Judaic Studies and the University Library, which aptly reflects the comprehensive and unique nature of this collection. This collection combines materials traditionally found in libraries (e.g., books, pamphlets, printed ephemera, and manuscripts) with objects of museum quality (artwork and historical artifacts) and an assortment of items of humbler nature used in everyday life. The curators have chosen several themes around which to organize the display, in order to demonstrate both interesting items from the collection and topics for study it can easily support. The full Portrait of a People Online Exhibit follows a brief biography of Constance Harris and an excerpt from her book, The Way Jews Lived. as well as essays on how the collection was assembled and how it will be used written by the Elliot Gertel and Erica Lehrer.Special Collections Libraryhttp://deepblue.lib.umich.edu/bitstream/2027.42/108167/1/Portrait-of-a-people.pd

"Makeup on Empty Space": a Celebration of Anne Waldman: An Exhibit

"Makeup on empty space" celebrates the opening of the Anne Waldman archive at the University of Michigan Library. This archive is as exciting and dynamic as the poet herself, showing many fascinating examples of how Anne Waldman works through her correspondence, working manuscripts, published books, audio and video tapes, and photographs covering her life and career.http://deepblue.lib.umich.edu/bitstream/2027.42/120261/1/makeup_on_empty_space_02.pd

Patterns of positive selection in seven ant genomes.

The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of positive selection on amino-acid changes in proteins. We identified 24 functional categories of genes which were enriched for positively selected genes in the ant lineage. We also reanalyzed genome-wide data sets in bees and flies with the same methodology to check whether positive selection was specific to ants or also present in other insects. Notably, genes implicated in immunity were enriched for positively selected genes in the three lineages, ruling out the hypothesis that the evolution of hygienic behaviors in social insects caused a major relaxation of selective pressure on immune genes. Our scan also indicated that genes implicated in neurogenesis and olfaction started to undergo increased positive selection before the evolution of sociality in Hymenoptera. Finally, the comparison between these three lineages allowed us to pinpoint molecular evolution patterns that were specific to the ant lineage. In particular, there was ant-specific recurrent positive selection on genes with mitochondrial functions, suggesting that mitochondrial activity was improved during the evolution of this lineage. This might have been an important step toward the evolution of extreme lifespan that is a hallmark of ants

Signal sequence analysis of expressed sequence tags from the nematode Nippostrongylus brasiliensis and the evolution of secreted proteins in parasites

BACKGROUND: Parasitism is a highly successful mode of life and one that requires suites of gene adaptations to permit survival within a potentially hostile host. Among such adaptations is the secretion of proteins capable of modifying or manipulating the host environment. Nippostrongylus brasiliensis is a well-studied model nematode parasite of rodents, which secretes products known to modulate host immunity. RESULTS: Taking a genomic approach to characterize potential secreted products, we analyzed expressed sequence tag (EST) sequences for putative amino-terminal secretory signals. We sequenced ESTs from a cDNA library constructed by oligo-capping to select full-length cDNAs, as well as from conventional cDNA libraries. SignalP analysis was applied to predicted open reading frames, to identify potential signal peptides and anchors. Among 1,234 ESTs, 197 (~16%) contain predicted 5' signal sequences, with 176 classified as conventional signal peptides and 21 as signal anchors. ESTs cluster into 742 distinct genes, of which 135 (18%) bear predicted signal-sequence coding regions. Comparisons of clusters with homologs from Caenorhabditis elegans and more distantly related organisms reveal that the majority (65% at P < e(-10)) of signal peptide-bearing sequences from N. brasiliensis show no similarity to previously reported genes, and less than 10% align to conserved genes recorded outside the phylum Nematoda. Of all novel sequences identified, 32% contained predicted signal peptides, whereas this was the case for only 3.4% of conserved genes with sequence homologies beyond the Nematoda. CONCLUSIONS: These results indicate that secreted proteins may be undergoing accelerated evolution, either because of relaxed functional constraints, or in response to stronger selective pressure from host immunity

Efficient Entropy Estimation for Mutual Information Analysis Using B-Splines

International audienceThe Correlation Power Analysis (CPA) is probably the most used side-channel attack because it seems to fit the power model of most standard CMOS devices and is very efficiently computed. However, the Pearson correlation coefficient used in the CPA measures only linear statistical dependences where the Mutual Information (MI) takes into account both linear and nonlinear dependences. Even if there can be simultaneously large correlation coefficients quantified by the correlation coefficient and weak dependences quantified by the MI, we can expect to get a more profound understanding about interactions from an MI Analysis (MIA). We study methods that improve the non-parametric Probability Density Functions (PDF) in the estimation of the entropies and, in particular, the use of B-spline basis functions as pdf estimators. Our results indicate an improvement of two fold in the number of required samples compared to a classic MI estimation. The B-spline smoothing technique can also be applied to the rencently introduced Cramér-von-Mises test