Identification of conserved gene clusters in multiple genomes based on synteny and homology

<p>Abstract</p> <p>Background</p> <p>Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on <it>gene teams</it> and <it>homology teams.</it></p> <p>Results</p> <p>Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.</p> <p>Conclusions</p> <p>The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.</p

MammaPrint Molecular Diagnostics on Formalin-Fixed, Paraffin-Embedded Tissue

MammaPrint, a prognostic 70-gene profile for early-stage breast cancer, has been available for fresh tissue. Improvements in RNA processing have enabled microarray diagnostics for formalin-fixed, paraffin-embedded (FFPE) tissue. Here, we describe method optimization, validation, and performance of MammaPrint using analyte from FFPE tissue. Laboratory procedures for enabling the assay to be run on FFPE tissue were determined using 157 samples, and the assay was established using 125 matched FFPE and fresh tissues. Validation of MammaPrint-FFPE, compared with MammaPrint-fresh, was performed on an independent series of matched tissue from five hospitals (n = 211). Reproducibility, repeatability, and precision of the FFPE assay (n = 87) was established for duplicate analysis of the same tumor, inter-laboratory performance, 20-day repeat experiments, and repeated analyses over 12 months. FFPE sample processing had a success rate of 97%. The MammaPrint assay using FFPE analyte demonstrated an overall equivalence of 91.5% (95% confidence interval, 86.9% to 94.5%) between the 211 independent matched FFPE and fresh tumor samples. Precision was 97.3%, and repeatability was 97.8%, with highly reproducible results between replicate samples of the same tumor and between two laboratories (concordance, 96%). Thus, with 580 tumor samples, MammaPrint was successfully translated to FFPE tissue. The assay has high precision and reproducibility, and FFPE results are substantially equivalent to results derived from fresh tissue

Hygromechanical properties of grenadilla wood (Dalbergia melanoxylon)

International audienceGrenadilla wood (Dalbergia melanoxylon Guill. & Perr.) is a hardwood species found in Tanzania, Mozambique, and other countries in the tropical part of Africa, especially in the Eastern-Central region. Thanks to its high density and good hygro-scopic stability, it is used in the making of various musical instruments and fine furniture. Due to the scarcity of published data on this wood species, more studies on its properties are needed to improve its processing and use, and even to search for sustainable alternative materials as its trade is increasingly limited by new regulations. This work is focused on the hygromechanical properties, which hold an important role in the applications of this wood: diffusion coefficients and adsorption-desorp-tion curve (both measured at T = 20 • C), swelling-shrinkage coefficients and full orthotropic elastic constants using an ultrasonic method. Results show that grenadilla wood possesses small water diffusion coefficients (from 1.54 ± 0.49 × 10 −7 cm 2 ∕s in T direction to 4.58 ± 0.84 × 10 −7 cm 2 ∕s in L direction), which is probably related to its high density (1250.0 ± 26.2 kg∕m 2); unique equilibrium moisture content (sorp-tion) curve with a lower fiber saturation point (0.173 ± 0.003); smaller swelling-shrinkage coefficients (0.20 ± 0.03 and 0.32 ± 0.05 in T and R directions, respectively); and elastic constants lower in the longitudinal direction (15.56 ± 1.79 GPa) and higher in the transverse ones (5.10 ± 0.46 GPa and 4.05 ± 0.35 GPa in R and T directions, respectively) than what could be expected with a standard model based on the density only. Several explanations were described here, from the effects of a high extractive content to the possibility of a high microfibril and/or fiber angle