Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi.

Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts

Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure

New antibacterial paper made of silver phosphate cellulose fibers: a preliminary study on the elimination of Staphylococcus aureus involved in diabetic foot ulceration

Aim. To evaluate in vitro the antibacterial effect of a paper made of silver phosphate cellulose fibers (SPCF) on Staphylococcus aureus, the most common diabetic foot ulceration (DFU) pathogen when compared with other common commercial products. Methods. The antibacterial activity of SPCF samples was evaluated through time with cell counting on agar plates. SPCF samples were then compared with commercial wound care products currently in use in DFU treatments (Silvercel™, Acticoat 7, and Aquacel Ag ExtraTM) through time on agar plates (growth inhibition zones). Results. After 6 hours, there was no viable bacterial cell detected on either plate (p < 0.05). There was a net growth inhibition zone for SPCF samples but no significant difference between the two silver concentrations. Compared with common commercial products, SPCF paper provides results equal to Acticoat 7 (p < 0.05) and superior to Aquacel AG ExtraTM and Silvercel™ at lower silver concentrations (p < 0.001). Conclusions. These results have shown the efficiency of SPCF paper to eliminate Staphylococcus aureus in these conditions. SPCF papers are effective when compared with other common commercial products and could have an industrial potential in wound care. Infected DFU could benefit from the antibacterial effectiveness of SPCF, but more relevant experimentations related to foot ulcers are needed

Mode identification from monochromatic amplitude and phase variations for the rapidly pulsating subdwarf B star EC 20338-1925

We obtain time-series spectrophotometry observations at the VLT with the aim of partially identifying the dominant oscillation modes in the rapidly pulsating subdwarf B star EC 20338-1925 on the basis of monochromatic amplitude and phase variations. From the data gathered, we detect four previously known pulsations with periods near 147, 168, 126 and 140 s and amplitudes between 0.2 and 2.3 % of the star's mean brightness. We also determine the atmospheric parameters of EC 20338-1925 by fitting our non-LTE model atmospheres to an averaged combined spectrum. The inferred parameters are Teff = 34,153+-94 K, log g =5.966+-0.017 and log[N(He)/N(H)] = - 1.642+-0.022, where the uncertainty estimates quoted refer to the formal fitting errors. Finally, we calculate the observed monochromatic amplitudes and phases for the periodicities extracted using least-squares fitting to the light curves obtained for each wavelength bin. These observed quantities are then compared to the corresponding theoretical values computed on the basis of dedicated model atmosphere codes and also taking into account non-adiabatic effects. We find that the quality of the data is sufficient to identify the dominant pulsation at 146.9 s as a radial mode, while two of the lower amplitude periodicities must be low-degree modes with l=0-2. This is the first time that monochromatic amplitudes and phases have been used for mode identification in a subdwarf B star, and the results are highly encouraging.Comment: 11 pages. Accepted for publication in Astronomy & Astrophysic

Proceedings of the International Haemophilia Prophylaxis Study Group Meeting, November 2003, Montreal, PQ, Canada

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72691/1/j.1365-2516.2005.01053.x.pd

A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions

<p>Abstract</p> <p>Background</p> <p>Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. However, this phylogenetic reconstruction is a very challenging task. For the most simple distance measures (the breakpoint distance and the reversal distance), the problem is NP-hard even if one considers only three genomes.</p> <p>Results</p> <p>In this paper, we present a new heuristic algorithm that directly constructs a phylogenetic tree w.r.t. the weighted reversal and transposition distance. Experimental results on previously published datasets show that constructing phylogenetic trees in this way results in better trees than constructing the trees w.r.t. the reversal distance, and recalculating the weight of the trees with the weighted reversal and transposition distance. An implementation of the algorithm can be obtained from the authors.</p> <p>Conclusion</p> <p>The possibility of creating phylogenetic trees directly w.r.t. the weighted reversal and transposition distance results in biologically more realistic scenarios. Our algorithm can solve today's most challenging biological datasets in a reasonable amount of time.</p

Combining Computational Prediction of Cis-Regulatory Elements with a New Enhancer Assay to Efficiently Label Neuronal Structures in the Medaka Fish

The developing vertebrate nervous system contains a remarkable array of neural cells organized into complex, evolutionarily conserved structures. The labeling of living cells in these structures is key for the understanding of brain development and function, yet the generation of stable lines expressing reporter genes in specific spatio-temporal patterns remains a limiting step. In this study we present a fast and reliable pipeline to efficiently generate a set of stable lines expressing a reporter gene in multiple neuronal structures in the developing nervous system in medaka. The pipeline combines both the accurate computational genome-wide prediction of neuronal specific cis-regulatory modules (CRMs) and a newly developed experimental setup to rapidly obtain transgenic lines in a cost-effective and highly reproducible manner. 95% of the CRMs tested in our experimental setup show enhancer activity in various and numerous neuronal structures belonging to all major brain subdivisions. This pipeline represents a significant step towards the dissection of embryonic neuronal development in vertebrates

Diabetic foot complications among Indigenous peoples in Canada: A scoping review through the PROGRESS-PLUS equity lens

Introduction Indigenous peoples in Canada face a disproportionate burden of diabetes-related foot complications (DRFC), such as foot ulcers, lower extremity amputations (LEA), and peripheral arterial disease. This scoping review aimed to provide a comprehensive understanding of DRFC among First Nations, Métis, and Inuit peoples in Canada, incorporating an equity lens Methods A scoping review was conducted based on Arksey and O’Malley refined by the Joanna Briggs Institute. The PROGRESS-Plus framework was utilized to extract data and incorporate an equity lens. A critical appraisal was performed, and Indigenous stakeholders were consulted for feedback. We identified the incorporation of patient-oriented/centered research (POR). Results Of 5,323 records identified, 40 studies were included in the review. The majority of studies focused on First Nations (92%), while representation of the Inuit population was very limited populations (< 3% of studies). LEA was the most studied outcome (76%). Age, gender, ethnicity, and place of residence were the most commonly included variables. Patient-oriented/centered research was mainly included in recent studies (16%). The overall quality of the studies was average. Data synthesis showed a high burden of DRFC among Indigenous populations compared to non-Indigenous populations. Indigenous identity and rural/remote communities were associated with the worse outcomes, particularly major LEA. Discussion This study provides a comprehensive understanding of DRFC in Indigenous peoples in Canada of published studies in database. It not only incorporates an equity lens and patient-oriented/centered research but also demonstrates that we need to change our approach. More data is needed to fully understand the burden of DRFC among Indigenous peoples, particularly in the Northern region in Canada where no data are previously available. Western research methods are insufficient to understand the unique situation of Indigenous peoples and it is essential to promote culturally safe and quality healthcare. Conclusion Efforts have been made to manage DRFC, but continued attention and support are necessary to address this population’s needs and ensure equitable prevention, access and care that embraces their ways of knowing, being and acting

Determining significance of pairwise co-occurrences of events in bursty sequences

<p>Abstract</p> <p>Background</p> <p>Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence. These events tend to occur in bursts: in some genomic regions there are more genes and therefore potentially more binding sites, while in some, possibly very long regions, hardly any events occur. Also some types of events may occur in the sequence more often than others.</p> <p>Tendencies of co-occurrence of binding sites of two or more TFs are interesting, as they may imply a co-operative role between the TFs in regulatory processes. Determining a numerical value to summarize the tendency for co-occurrence between two TFs can be done in a number of ways. However, testing for the significance of such values should be done with respect to a relevant null model that takes into account the global sequence structure.</p> <p>Results</p> <p>We extend the existing techniques that have been considered for determining the significance of co-occurrence patterns between a pair of event types under different null models. These models range from very simple ones to more complex models that take the burstiness of sequences into account. We evaluate the models and techniques on synthetic event sequences, and on real data consisting of potential transcription factor binding sites.</p> <p>Conclusion</p> <p>We show that simple null models are poorly suited for bursty data, and they yield many false positives. More sophisticated models give better results in our experiments. We also demonstrate the effect of the window size, i.e., maximum co-occurrence distance, on the significance results.</p

Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

<p>Abstract</p> <p>Background</p> <p>In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression.</p> <p>Results</p> <p>We develop a Bayesian network approach for identifying cis-regulatory modules likely to regulate tissue-specific expression. The network integrates predicted transcription factor binding site information, transcription factor expression data, and target gene expression data. At its core is a regression tree modeling the effect of combinations of transcription factors bound to a module. A new unsupervised EM-like algorithm is developed to learn the parameters of the network, including the regression tree structure.</p> <p>Conclusion</p> <p>Our approach is shown to accurately identify known human liver and erythroid-specific modules. When applied to the prediction of tissue-specific modules in 10 different tissues, the network predicts a number of important transcription factor combinations whose concerted binding is associated to specific expression.</p