The gene family-free median of three

Background

The gene family-free framework for comparative genomics aims at providing methods for gene order analysis that do not require prior gene family assignment, but work directly on a sequence similarity graph. We study two problems related to the breakpoint median of three genomes, which asks for the construction of a fourth genome that minimizes the sum of breakpoint distances to the input genomes.

Methods

We present a model for constructing a median of three genomes in this family-free setting, based on maximizing an objective function that generalizes the classical breakpoint distance by integrating sequence similarity in the score of a gene adjacency. We study its computational complexity and we describe an integer linear program (ILP) for its exact solution. We further discuss a related problem called family-free adjacencies for k genomes for the special case of \(k \le 3\) and present an ILP for its solution. However, for this problem, the computation of exact solutions remains intractable for sufficiently large instances. We then proceed to describe a heuristic method, FFAdj-AM, which performs well in practice.

Results

The developed methods compute accurate positional orthologs for genomes comparable in size of bacterial genomes on simulated data and genomic data acquired from the OMA orthology database. In particular, FFAdj-AM performs equally or better when compared to the well-established gene family prediction tool MultiMSOAR.

Conclusions

We study the computational complexity of a new family-free model and present algorithms for its solution. With FFAdj-AM, we propose an appealing alternative to established tools for identifying higher confidence positional orthologs.

     

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics

Introduction

Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.

Objectives

The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.

Methods

NMRProcFlow was developed to be a graphical and interactive 1D NMR (¹H & ¹³C) spectra processing tool.

Results

NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.

Conclusion

Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.

     

Predicting ovarian cancer recurrence by plasma metabolic profiles before and after surgery

Background

Previous metabolomic studies have revealed that plasma metabolic signatures may predict epithelial ovarian cancer (EOC) recurrence. However, few studies have performed metabolic profiling of pre- and post-operative specimens to investigate EOC prognostic biomarkers.

Objective

The aims of our study were to compare the predictive performance of pre- and post-operative specimens and to create a better model for recurrence by combining biomarkers from both metabolic signatures.

Methods

Thirty-five paired plasma samples were collected from 35 EOC patients before and after surgery. The patients were followed-up until December, 2016 to obtain recurrence information. Metabolomics using rapid resolution liquid chromatography–mass spectrometry was performed to identify metabolic signatures related to EOC recurrence. The support vector machine model was employed to predict EOC recurrence using identified biomarkers.

Results

Global metabolomic profiles distinguished recurrent from non-recurrent EOC using both pre- and post-operative plasma. Ten common significant biomarkers, hydroxyphenyllactic acid, uric acid, creatinine, lysine, 3-(3,5-diiodo-4-hydroxyphenyl) lactate, phosphohydroxypyruvic acid, carnitine, coproporphyrinogen, l-beta-aspartyl-l-glutamic acid and 24,25-hydroxyvitamin D3, were identified as predictive biomarkers for EOC recurrence. The area under the receiver operating characteristic (AUC) values in pre- and post-operative plasma were 0.815 and 0.909, respectively; the AUC value after combining the two sets reached 0.964.

Conclusion

Plasma metabolomic analysis could be used to predict EOC recurrence. While post-operative biomarkers have a predictive advantage over pre-operative biomarkers, combining pre- and post-operative biomarkers showed the best predictive performance and has great potential for predicting recurrent EOC.

     

Metabolic response of porcine colon explants to in vitro infection by <Emphasis Type="Italic">Brachyspira hyodysenteriae</Emphasis>: a leap into disease pathophysiology

Introduction

Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.

Objective

The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.

Methods

Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.

Results

Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.

Conclusions

The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.

     

rDolphin: a GUI R package for proficient automatic profiling of 1D <Superscript>1</Superscript>H-NMR spectra of study datasets

Introduction

Adoption of automatic profiling tools for ¹H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices.

Objectives

To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process.

Methods

rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality.

Results

The information and quality achieved in two public datasets of complex matrices are maximized.

Conclusion

rDolphin is an open-source R package (http://github.com/danielcanueto/rDolphin) able to provide the best balance between accuracy, reproducibility and ease of use.

     

Accumulation of Fascin<Superscript>+</Superscript> cells during experimental autoimmune neuritis

Background

Experimental autoimmune neuritis (EAN) is a well-known animal model of human demyelinating polyneuropathies and is characterized by inflammation and demyelination in the peripheral nervous system. Fascin is an evolutionarily highly conserved cytoskeletal protein of 55 kDa containing two actin binding domains that cross-link filamentous actin to hexagonal bundles.

Methods

Here we have studied by immunohistochemistry the spatiotemporal accumulation of Fascin?+?cells in sciatic nerves of EAN rats.

Results

A robust accumulation of Fascin?+?cell was observed in the peripheral nervous system of EAN which was correlated with the severity of neurological signs in EAN.

Conclusion

Our results suggest a pathological role of Fascin in EAN.

Virtual slides

The virtual slides for this article can be found here: http://www.diagnosticphatology.diagnomx.eu/vs/6734593451114811

     

A metabolomics approach to uncover effects of different exercise modalities in type 1 diabetes

Introduction

Exercise-associated metabolism in type 1 diabetes (T1D) remains under-studied due to the complex interplay between exogenous insulin, counter-regulatory hormones and insulin-sensitivity.

Objective

To identify the metabolic differences induced by two exercise modalities in T1D using ultra high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC–HRMS) based metabolomics.

Methods

Twelve T1D adults performed intermittent high-intensity (IHE) and continuous-moderate-intensity (CONT) exercise. Serum samples were analysed by UHPLC–HRMS.

Results

Metabolic profiling of IHE and CONT highlighted exercise-induced changes in purine and acylcarnitine metabolism.

Conclusion

IHE may increase beta-oxidation through higher ATP-turnover. UHPLC–HRMS based metabolomics as a data-driven approach without an a priori hypothesis may help uncover distinctive metabolic effects during exercise in T1D.Clinical trial registration number is www.clinicaltrials.gov: NCT02068638.

     

Generation of Cas9 transgenic zebrafish and their application in establishing an ERV-deficient animal model

Objectives

To investigate the effect of endogenous Cas9 on genome editing efficiency in transgenic zebrafish.

Results

Here we have constructed a transgenic zebrafish strain that can be screened by pigment deficiency. Compared with the traditional CRISPR injection method, the transgenic zebrafish can improve the efficiency of genome editing significantly. At the same time, we first observed that the phenotype of vertebral malformation in early embryonic development of zebrafish after ZFERV knockout.

Conclusions

The transgenic zebrafish with expressed Cas9, is more efficient in genome editing. And the results of ZFERV knockout indicated that ERV may affect the vertebral development by Notch1/Delta D signal pathway.

     

Models and algorithms for genome rearrangement with positional constraints

Background

Traditionally, the merit of a rearrangement scenario between two gene orders has been measured based on a parsimony criteria alone; two scenarios with the same number of rearrangements are considered equally good. In this paper, we acknowledge that each rearrangement has a certain likelihood of occurring based on biological constraints, e.g. physical proximity of the DNA segments implicated or repetitive sequences.

Results

We propose optimization problems with the objective of maximizing overall likelihood, by weighting the rearrangements. We study a binary weight function suitable to the representation of sets of genome positions that are most likely to have swapped adjacencies. We give a polynomial-time algorithm for the problem of finding a minimum weight double cut and join scenario among all minimum length scenarios. In the process we solve an optimization problem on colored noncrossing partitions, which is a generalization of the Maximum Independent Set problem on circle graphs.

Conclusions

We introduce a model for weighting genome rearrangements and show that under simple yet reasonable conditions, a fundamental distance can be computed in polynomial time. This is achieved by solving a generalization of the Maximum Independent Set problem on circle graphs. Several variants of the problem are also mentioned.

     

The degradation of nucleotide triphosphates extracted under boiling ethanol conditions is prevented by the yeast cellular matrix

Introduction

Boiling ethanol extraction is a frequently used method for metabolomics studies of biological samples. However, the stability of several central carbon metabolites, including nucleotide triphosphates, and the influence of the cellular matrix on their degradation have not been addressed.

Objectives

To study how a complex cellular matrix extracted from yeast (Saccharomyces cerevisiae) may affect the degradation profiles of nucleotide triphosphates extracted under boiling ethanol conditions.

Methods

We present a double-labelling LC–MS approach with a ¹³C-labeled yeast cellular extract as complex surrogate matrix, and ¹³C¹⁵N-labeled nucleotides as internal standards, to study the effect of the yeast matrix on the degradation of nucleotide triphosphates.

Results

While nucleotide triphosphates were degraded to the corresponding diphosphates in pure solutions, degradation was prevented in the presence of the yeast matrix under typical boiling ethanol extraction conditions.

Conclusions

Extraction of biological samples under boiling ethanol extraction conditions that rapidly inactivate enzyme activity are suitable for labile central energy metabolites such as nucleotide triphosphates due to the stabilizing effect of the yeast matrix. The basis of this phenomenon requires further study.

Graphical abstract

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Estimating the subcritical transmissibility of the Zika outbreak in the State of Florida,USA, 2016

Background

Florida State has reported autochthonous transmission of Zika virus since late July 2016. Here we assessed the transmissibility associated with the outbreak and generated a short-term forecast.

Methods

Time-dependent dynamics of imported cases reported in the state of Florida was approximated by a logistic growth equation. We estimated the reproduction number using the renewal equation in order to predict the incidence of local cases arising from both local and imported primary cases. Using a bootstrap method together with the logistic and renewal equations, a short-term forecast of local and imported cases was carried out.

Results

The reproduction number was estimated at 0.16 (95 % Confidence Interval: 0.13, 0.19). Employing the logistic equation to capture a drastic decline in the number of imported cases expected through the course of 2016, together with the low estimate of the local reproduction number in Florida, the expected number of local reported cases was demonstrated to show an evident declining trend for the remainder of 2016.

Conclusions

The risk of local transmission in the state of Florida is predicted to dramatically decline by the end of 2016.

     

The Association Between Depression,Suicidal Ideation and Psychological Strains in College Students: A Cross-National Study

Objective

This study examined the differences of psychological strains between Chinese and American college students and discussed how strains may influence individuals’ suicidal ideation and depression.

Participants/methods

A total of 539 college students (298 from China and 241 from the U.S.) were recruited in March 2016 to complete the survey study. Multiple linear regressions were used in data analysis.

Results

Students in America had higher scores on depression and stress than students in China, while students in China rated higher on suicidal ideation than students in America. In contrast of students in America facing more coping strains, students in China were confronting more value strains in their life.

Conclusion

The cross-cultural variations in the effect of psychological strains have been substantiated in current study, indicating that understanding the psychological strains in different cultural contexts is necessary for the early intervention and prevention in college aged populations.

     

Resolution effects in reconstructing ancestral genomes

Background

The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions.

Results

We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses.

Conclusions

We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.

     

Pseudo current density maps of electrophysiological heart,nerve or brain function and their physical basis

Background

In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.

Methods

The physical basis of these intuitive maps is clarified by means of analytically solvable problems.

Results

Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.

Conclusion

Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

Structure elucidation of metabolite x17299 by interpretation of mass spectrometric data

Introduction

A major bottleneck in metabolomic studies is metabolite identification from accurate mass spectrometric data. Metabolite x17299 was identified in plasma as an unknown in a metabolomic study using a compound-centric approach where the associated ion features of the compound were used to determine the true molecular mass.

Objectives

The aim of this work is to elucidate the chemical structure of x17299, a new compound by de novo interpretation of mass spectrometric data.

Methods

An Orbitrap Elite mass spectrometer was used for acquisition of mass spectra up to MS⁴ at high resolution. Synthetic standards of N,N,N-trimethyl-l-alanyl-l-proline betaine (l,l-TMAP), a diastereomer, and an enantiomer were chemically prepared.

Results

The planar structure of x17299 was successfully proposed by de novo mechanistic interpretation of mass spectrometric data without any laborious purification and nuclear magnetic resonance spectroscopic analysis. The proposed structure was verified by deuterium exchanged mass spectrometric analysis and confirmed by comparison to a synthetic standard. Relative configuration of x17299 was determined by direct chromatographic comparison to a pair of synthetic diastereomers. Absolute configuration was assigned after derivatization of x17299 with a chiral auxiliary group followed by its chromatographic comparison to a pair of synthetic standards.

Conclusion

The chemical structure of metabolite x17299 was determined to be l,l-TMAP.

     

Towards pan-genome read alignment to improve variation calling

Background

Typical human genome differs from the reference genome at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences from different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single human reference genome. Identification and genotyping of genetic variants is typically carried out on short-read data aligned to a single reference, disregarding the underlying variation.

Results

We propose a new unified framework for variant calling with short-read data utilizing a representation of human genetic variation – a pan-genomic reference. We provide a modular pipeline that can be seamlessly incorporated into existing sequencing data analysis workflows. Our tool is open source and available online: https://gitlab.com/dvalenzu/PanVC.

Conclusions

Our experiments show that by replacing a standard human reference with a pan-genomic one we achieve an improvement in single-nucleotide variant calling accuracy and in short indel calling accuracy over the widely adopted Genome Analysis Toolkit (GATK) in difficult genomic regions.

     

Secure top most significant genome variants search: iDASH 2017 competition

Background

One of the 3 tracks of iDASH Privacy & Security Workshop 2017 competition was to execute a whole genome variants search on private genomic data. Particularly, the search application was to find the top most significant SNPs (Single-Nucleotide Polymorphisms) in a database of genome records labeled with control or case. In this paper we discuss the solution submitted by our team to this competition.

Methods

Privacy and confidentiality of genome data had to be ensured using Intel SGX enclaves. The typical use-case of this application is the multi-party computation (each party possessing one or several genome records) of the SNPs which statistically differentiate control and case genome datasets.

Results

Our solution consists of two applications: (i) compress and encrypt genome files and (ii) perform genome processing (top most important SNPs search). We have opted for a horizontal treatment of genome records and heavily used parallel processing. Rust programming language was employed to develop both applications.

Conclusions

Execution performance of the processing applications scales well and very good performance metrics are obtained. Contest organizers selected it as the best submission amongst other received competition entries and our team was awarded the first prize on this track.

     

The effect for Japanese workers of a self-help computerized cognitive behaviour therapy program with a supplement soft drink

Background

Computerized cognitive behaviour therapy (CCBT) programs can provide a useful self-help approach to the treatment of psychological problems. Previous studies have shown that CCBT has moderate effects on depression, insomnia, and anxiety. The present study investigated whether a supplement drink that includes L-carnosine enhances the effect of CCBT on psychological well-being.

Methods

Eighty-seven participants were randomly allocated to a control group, CCBT, or CCBT with supplement drink. The CCBT and CCBT with supplement drink groups received six weekly self-help CCBT program instalments, which consisted of psycho-education about stress management and coping, behaviour activation, and cognitive restructuring. The CCBT group consumed a bottle of the supplement soft drink every morning through the 6 weeks. This program was delivered by an e-learning system on demand and also included a self-help guidebook. Seventy-two participants completed the program or were assess at the end of the study.

Results

ANOVA revealed that there were significant interactions (times × groups) for POMS tension-anxiety and fatigue. The CCBT group showed significantly improved tension-anxiety scores, whereas the CCBT with drink group showed significant improvements on fatigue.

Conclusion

The self-help CCBT program reduced the subjective experience of tension-anxiety in this group of workers. The addition of a supplement drink enhanced the effect of CCBT on fatigue, providing one possible approach to enhancement of such programs.

Trial registration

This study was registered on September 2, 2016 at UMIN. The registration number is UMIN000023903.

     

An ILP solution for the gene duplication problem

Background

The gene duplication (GD) problem seeks a species tree that implies the fewest gene duplication events across a given collection of gene trees. Solving this problem makes it possible to use large gene families with complex histories of duplication and loss to infer phylogenetic trees. However, the GD problem is NP-hard, and therefore, most analyses use heuristics that lack any performance guarantee.

Results

We describe the first integer linear programming (ILP) formulation to solve instances of the gene duplication problem exactly. With simulations, we demonstrate that the ILP solution can solve problem instances with up to 14 taxa. Furthermore, we apply the new ILP solution to solve the gene duplication problem for the seed plant phylogeny using a 12-taxon, 6, 084-gene data set. The unique, optimal solution, which places Gnetales sister to the conifers, represents a new, large-scale genomic perspective on one of the most puzzling questions in plant systematics.

Conclusions

Although the GD problem is NP-hard, our novel ILP solution for it can solve instances with data sets consisting of as many as 14 taxa and 1, 000 genes in a few hours. These are the largest instances that have been solved to optimally to date. Thus, this work can provide large-scale genomic perspectives on phylogenetic questions that previously could only be addressed by heuristic estimates.