Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Outcomes and complications of fibular head resection

The fibular head is often used as donor graft material for reconstruction of defects of the distal radius. However little is known on the safety of such a procedure. This report describes the long-term donor-site morbidity following the procedure. Fourteen patients who underwent simple or marginal resections of the proximal fibula between 1990 and 2007 were reviewed. Subjective donor-site morbidity, knee and ankle range of motion and instability, presence of sensory or motor function loss, gait and fibular regeneration were assessed. The mean age at surgery was 25 years; six were male, eight were female and the mean follow-up was 11 years. Abnormal clinical findings were present in 10 patients (71.4 %): nine patients (64.3 %) had Grade 2 varus laxity at the knee confirmed by stress radiographs; one had sensory loss in the distribution of the superficial peroneal nerve. Patients with varus laxity had significantly higher mean age at surgery than those without varus laxity (p = 0.001). None had deformity at the knee or ankle. The range of joint movements was normal. All had a normal tibiotalar angle and none had proximal migration of the fibula. One patient demonstrated near-complete regeneration of the fibula. Donor-site morbidity following simple and marginal resection of the proximal fibula is acceptable. Older patients had a higher risk of demonstrable varus laxity at the knee but proximal fibula resection in children appears to be safe

Relative Abundance of Transcripts (RATs):Identifying differential isoform abundance from RNA-seq [version 1; referees: 1 approved, 2 approved with reservations]

The biological importance of changes in RNA expression is reflected by the wide variety of tools available to characterise these changes from RNA-seq data. Several tools exist for detecting differential transcript isoform usage (DTU) from aligned or assembled RNA-seq data, but few exist for DTU detection from alignment-free RNA-seq quantifications. We present the RATs, an R package that identifies DTU transcriptome-wide directly from transcript abundance estimates. RATs is unique in applying bootstrapping to estimate the reliability of detected DTU events and shows good performance at all replication levels (median false positive fraction < 0.05). We compare RATs to two existing DTU tools, DRIM-Seq & SUPPA2, using two publicly available simulated RNA-seq datasets and a published human RNA-seq dataset, in which 248 genes have been previously identified as displaying significant DTU. RATs with default threshold values on the simulated Human data has a sensitivity of 0.55, a Matthews correlation coefficient of 0.71 and a false discovery rate (FDR) of 0.04, outperforming both other tools. Applying the same thresholds for SUPPA2 results in a higher sensitivity (0.61) but poorer FDR performance (0.33). RATs and DRIM-seq use different methods for measuring DTU effect-sizes complicating the comparison of results between these tools, however, for a likelihood-ratio threshold of 30, DRIM-Seq has similar FDR performance to RATs (0.06), but worse sensitivity (0.47). These differences persist for the simulated drosophila dataset. On the published human RNA-seq dataset the greatest agreement between the tools tested is 53%, observed between RATs and SUPPA2. The bootstrapping quality filter in RATs is responsible for removing the majority of DTU events called by SUPPA2 that are not reported by RATs. All methods, including the previously published qRT-PCR of three of the 248 detected DTU events, were found to be sensitive to annotation differences between Ensembl v60 and v87

A Grid Computing Based Power System Monitoring Tool Using Gridgain

With the advancement of civilization, Power Sector is undergoing drastic upheavals. With the ever increasing demand and dependence on electric power, protection of power system against failures remains a major challenge, particularly against cascading failures that lead to blackouts. There is a great demand for power systems protection that is scattered all around the globe. Effective monitoring of the power system parameters is a prerequisite in providing effective control and protection schemas. This paper advocates the use of grid computing in power system monitoring which discusses the suitability of grid computing to address the requirements of distinguished power system protection. Albeit, the Supervisory Control And Data Acquisition (SCADA) system is presently implied for monitoring power systems; yet it has its limitations. This paper proposes to use Grid Computing as an aid to the existing SCADA based power system monitoring & control framework and demonstrates is applicability by means of a grid based real-time power system monitoring system. The afore mentioned system has been deployed in desktop computers with GridGain 2.0 as middleware has been employed to set up the grid environment, all relevant details of the design framework has been shown

Regional conductivity structure of Cascadia : preliminary results form 3D inversion of USArray transportable array magnetotelluric data

In conjunction with the USArray component of EarthScope, long period magnetotelluric (MT) data are being acquired in a series of arrays across the continental US. Initial deployments in 2006 and 2007 acquired data (10– 10,000 s) at 110 sites covering the US Pacific Northwest, distributed with the same nominal spacing as the USArray seismic transportable array (~75 km). The most striking and robust features revealed by initial three-dimensional inversion of this dataset are extensive areas of high conductivity in the lower crust beneath all of southeastern Oregon, and beneath the Cascade Mountains, contrasting with very resistive crust in Siletzia and the Columbia Embayment. Significant variations in upper mantle conductivity are also revealed by the inversions, with the most conductive mantle beneath the Washington backarc, and the most resistive corresponding to subducting oceanic mantle

BaRTv1.0:an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

Background: The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.Results: A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427-433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20-28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5' and 3' UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage.Conclusion: A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.</p

HSRA: Hadoop-based spliced read aligner for RNA sequencing data

[Abstract] Nowadays, the analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference genome or transcriptome is considered a crucial step that remains as one of the most time-consuming. With the steady development of Next Generation Sequencing (NGS) technologies, unprecedented amounts of genomic data introduce significant challenges in terms of storage, processing and downstream analysis. As cost and throughput continue to improve, there is a growing need for new software solutions that minimize the impact of increasing data volume on RNA read alignment. In this work we introduce HSRA, a Big Data tool that takes advantage of the MapReduce programming model to extend the multithreading capabilities of a state-of-the-art spliced read aligner for RNA-seq data (HISAT2) to distributed memory systems such as multi-core clusters or cloud platforms. HSRA has been built upon the Hadoop MapReduce framework and supports both single- and paired-end reads from FASTQ/FASTA datasets, providing output alignments in SAM format. The design of HSRA has been carefully optimized to avoid the main limitations and major causes of inefficiency found in previous Big Data mapping tools, which cannot fully exploit the raw performance of the underlying aligner. On a 16-node multi-core cluster, HSRA is on average 2.3 times faster than previous Hadoop-based tools. Source code in Java as well as a user’s guide are publicly available for download at http://hsra.dec.udc.es.Ministerio de Economía, Industria y Competitividad; TIN2016-75845-PXunta de Galicia; ED431G/0

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline

Diminishing potential to replace damaged tissues is a hallmark for ageing of somatic stem cells, but the mechanisms remain elusive. Here, we present proteome-wide atlases of age-associated alterations in human haematopoietic stem and progenitor cells (HPCs) and five other cell populations that constitute the bone marrow niche. For each, the abundance of a large fraction of the ~12,000 proteins identified is assessed in 59 human subjects from different ages. As the HPCs become older, pathways in central carbon metabolism exhibit features reminiscent of the Warburg effect, where glycolytic intermediates are rerouted towards anabolism. Simultaneously, altered abundance of early regulators of HPC differentiation reveals a reduced functionality and a bias towards myeloid differentiation. Ageing causes alterations in the bone marrow niche too, and diminishes the functionality of the pathways involved in HPC homing. The data represent a valuable resource for further analyses, and for validation of knowledge gained from animal models

Unraveling the pathogenomics of Rhizoctonia solani infecting proso millet (Panicum miliaceum L.): genomic perspective on ruthless virulence and adaptive evolution

IntroductionBanded sheath blight (Bsb), caused by Rhizoctonia solani, is an emerging threat to proso millet cultivation, significantly impacting yield and grain quality. This study on the pathogenomics of R. solani seeks to unravel its genetic mechanisms, identify key virulence factors, decode host-pathogen interactions, and pinpoint molecular targets for effective control strategies.MethodsR. solani isolates were collected from various regions across India, resulting in six distinct isolates. These isolates were comprehensively characterized through morphological observations, molecular analyses, and virulence assessments to gain comprehensive insights into their diversity and pathogenic potential. The most virulent strain, designated VAP-1, infecting proso millet, was sequenced using the Illumina platform and de novo assembled using the SPAdes assembler, resulting in a highly complete genome. Functional regions of the genome were predicted and annotated using Funannotate. A subsequent comparative genomics study and secretome analysis were conducted to support functional genomic investigations.ResultsThe VAP-1 genome assembly resulted in a total size of 47.12 Mb, with approximately 17.62% of the genome consisting of repetitive sequences, predominantly dominated by interspersed elements (around 97.8%). These interspersed elements were primarily classified as retrotransposons (72%), with DNA transposons comprising a smaller proportion (5%), while the remaining interspersed sequences were not fully annotated. Functional analysis of the genome revealed significant enrichment in KEGG pathways, including “Carbohydrate metabolism,” “Translation,” “Signal transduction,” and “Transport and catabolism.” In addition, Gene Ontology (GO) terms such as “Proteolysis,” “Membrane,” and “ATP binding” were notably enriched. The secretory protein profile of the VAP-1 genome from R. solani features key proteins from the major facilitator superfamily (MFS) transporters, (Trans) glycosidases, P-loop containing nucleoside triphosphate hydrolases, and galactose oxidase, all within the central domain superfamily. Glycoside hydrolases represent the largest class of CAZymes in the VAP-1 genome. Comparative genomic analysis of VAP-1 with other R. solani strains infecting Poaceae (e.g., rice) and non-Poaceae (e.g., sugar beet and tobacco) hosts showed that VAP-1 clusters closely with rice-infecting strains at the species level, yet exhibits a greater divergence in genomic similarity from strains infecting sugar beet and tobacco. Notably, variations were observed in important secretory proteins, such as multiple base deletions in MFS proteins across strains infecting proso millet, rice, and sugar beet.DiscussionFunctional analysis of the VAP-1 genome has unveiled a wealth of insights, though we have only begun to scratch the surface. KEGG and GO annotations point to critical proteins that are essential for host infection, providing the pathogen with a potent arsenal for successful penetration, survival, and dissemination within the host. The secretory proteins encoded in the VAP-1 genome play a pivotal role in equipping the pathogen with the necessary tools to degrade plant cell wall polymers, release cell wall-bound saccharides, and break down polysaccharides for energy utilization and host colonization. Notable variations were observed in several secretome superfamily proteins within the VAP-1 strain. These findings underscore the genomic diversity present within R. solani strains and suggest possible adaptations that may contribute to host specificity