Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress

The response to proteotoxic stresses such as heat shock allows organisms to maintain protein homeostasis under changing environmental conditions. We asked what happens if an organism can no longer react to cytosolic proteotoxic stress. To test this, we deleted or depleted, either individually or in combination, the stress-responsive transcription factors Msn2, Msn4, and Hsf1 in Saccharomyces cerevisiae. Our study reveals a combination of survival strategies, which together protect essential proteins. Msn2 and 4 broadly reprogram transcription, triggering the response to oxidative stress, as well as biosynthesis of the protective sugar trehalose and glycolytic enzymes, while Hsf1 mainly induces the synthesis of molecular chaperones and reverses the transcriptional response upon prolonged mild heat stress (adaptation).

Human genetic defects in SRP19 and SRPRA cause severe congenital neutropenia with distinctive proteome changes

The mechanisms of coordinated changes in proteome composition and their relevance for the differentiation of neutrophil granulocytes are not well studied. Here, we discover 2 novel human genetic defects in signal recognition particle receptor alpha (SRPRA) and SRP19, constituents of the mammalian cotranslational targeting machinery, and characterize their roles in neutrophil granulocyte differentiation. We systematically study the proteome of neutrophil granulocytes from patients with variants in the SRP genes, HAX1, and ELANE, and identify global as well as specific proteome aberrations. Using in vitro differentiation of human induced pluripotent stem cells and in vivo zebrafish models, we study the effects of SRP deficiency on neutrophil granulocyte development. In a heterologous cell-based inducible protein expression system, we validate the effects conferred by SRP dysfunction for selected proteins that we identified in our proteome screen. Thus, SRP-dependent protein processing, intracellular trafficking, and homeostasis are critically important for the differentiation of neutrophil granulocytes.

The 2021 Magnonics Roadmap

Magnonics is a budding research field in nanomagnetism and nanoscience that addresses the use of spin waves (magnons) to transmit, store, and process information. The rapid advancements of this field during last one decade in terms of upsurge in research papers, review articles, citations, proposals of devices as well as introduction of new sub-topics prompted us to present the first roadmap on magnonics. This is a collection of 22 sections written by leading experts in this field who review and discuss the current status besides presenting their vision of future perspectives. Today, the principal challenges in applied magnonics are the excitation of sub-100 nm wavelength magnons, their manipulation on the nanoscale and the creation of sub-micrometre devices using low-Gilbert damping magnetic materials and its interconnections to standard electronics. To this end, magnonics offers lower energy consumption, easier integrability and compatibility with CMOS structure, reprogrammability, shorter wavelength, smaller device features, anisotropic properties, negative group velocity, non-reciprocity and efficient tunability by various external stimuli to name a few. Hence, despite being a young research field, magnonics has come a long way since its early inception. This roadmap asserts a milestone for future emerging research directions in magnonics, and hopefully, it will inspire a series of exciting new articles on the same topic in the coming years.

The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins

Life is resilient because living systems are able to respond to elevated temperatures with an ancient gene expression program called the heat shock response (HSR). In yeast, the transcription of hundreds of genes is upregulated at stress temperatures. Besides stress protection conferred by chaperones, the function of the majority of the upregulated genes under stress has remained enigmatic. We show that those genes are required to directly counterbalance increased protein turnover at stress temperatures and to maintain the metabolism. This anaplerotic reaction together with molecular chaperones allows yeast to efficiently buffer proteotoxic stress. When the capacity of this system is exhausted at extreme temperatures, aggregation processes stop translation and growth pauses. The emerging concept is that the HSR is modular with distinct programs dependent on the severity of the stress.

Comparison of six breast cancer classifiers using qPCR

MOTIVATION

Several gene expression-based risk scores and subtype classifiers for breast cancer were developed to distinguish high- and low-risk patients. Evaluating the performance of these classifiers helps to decide which classifiers should be used in clinical practice for personal therapeutic recommendations. So far, studies that compared multiple classifiers in large independent patient cohorts mostly used microarray measurements. qPCR-based classifiers were not included in the comparison or had to be adapted to the different experimental platforms.

RESULTS

We used a prospective study of 726 early breast cancer patients from seven certified German breast cancer centers. Patients were treated according to national guidelines and the expressions of 94 selected genes were measured by the mid-throughput qPCR platform Fluidigm. Clinical and pathological data including outcome over five years is available. Using these data, we could compare the performance of six classifiers (scmgene and research versions of PAM50, ROR-S, recurrence score, EndoPredict and GGI). Similar to other studies, we found a similar or even higher concordance between most of the classifiers and most were also able to differentiate high- and low-risk patients. The classifiers that were originally developed for microarray data still performed similarly using the Fluidigm data. Therefore, Fluidigm can be used to measure the gene expressions needed by several classifiers for a large cohort with little effort. In addition, we provide an interactive report of the results, which enables a transparent, in-depth comparison of classifiers and their prediction of individual patients.

AVAILABILITY AND IMPLEMENTATION

https://services.bio.ifi.lmu.de/pia/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Toward a gold standard for benchmarking gene set enrichment analysis

MOTIVATION

Although gene set enrichment analysis has become an integral part of high-throughput gene expression data analysis, the assessment of enrichment methods remains rudimentary and ad hoc. In the absence of suitable gold standards, evaluations are commonly restricted to selected datasets and biological reasoning on the relevance of resulting enriched gene sets.

RESULTS

We develop an extensible framework for reproducible benchmarking of enrichment methods based on defined criteria for applicability, gene set prioritization and detection of relevant processes. This framework incorporates a curated compendium of 75 expression datasets investigating 42 human diseases. The compendium features microarray and RNA-seq measurements, and each dataset is associated with a precompiled GO/KEGG relevance ranking for the corresponding disease under investigation. We perform a comprehensive assessment of 10 major enrichment methods, identifying significant differences in runtime and applicability to RNA-seq data, fraction of enriched gene sets depending on the null hypothesis tested and recovery of the predefined relevance rankings. We make practical recommendations on how methods originally developed for microarray data can efficiently be applied to RNA-seq data, how to interpret results depending on the type of gene set test conducted and which methods are best suited to effectively prioritize gene sets with high phenotype relevance.

AVAILABILITY

http://bioconductor.org/packages/GSEABenchmarkeR.

CONTACT

ludwig.geistlinger@sph.cuny.edu.

A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock

BACKGROUND

One of the main obstacles preventing solventogenic clostridia from achieving higher yields in biofuel production is the toxicity of produced solvents. Unfortunately, regulatory mechanisms responsible for the shock response are poorly described on the transcriptomic level. Although the strain Clostridium beijerinckii NRRL B-598, a promising butanol producer, has been studied under different conditions in the past, its transcriptional response to a shock caused by butanol in the cultivation medium remains unknown.

RESULTS

In this paper, we present a transcriptional response of the strain during a butanol challenge, caused by the addition of butanol to the cultivation medium at the very end of the acidogenic phase, using RNA-Seq. We resequenced and reassembled the genome sequence of the strain and prepared novel genome and gene ontology annotation to provide the most accurate results. When compared to samples under standard cultivation conditions, samples gathered during butanol shock represented a well-distinguished group. Using reference samples gathered directly before the addition of butanol, we identified genes that were differentially expressed in butanol challenge samples. We determined clusters of 293 down-regulated and 301 up-regulated genes whose expression was affected by the cultivation conditions. Enriched term "RNA binding" among down-regulated genes corresponded to the downturn of translation and the cluster contained a group of small acid-soluble spore proteins. This explained phenotype of the culture that had not sporulated. On the other hand, up-regulated genes were characterized by the term "protein binding" which corresponded to activation of heat-shock proteins that were identified within this cluster.

CONCLUSIONS

We provided an overall transcriptional response of the strain C. beijerinckii NRRL B-598 to butanol shock, supplemented by auxiliary technologies, including high-pressure liquid chromatography and flow cytometry, to capture the corresponding phenotypic response. We identified genes whose regulation was affected by the addition of butanol to the cultivation medium and inferred related molecular functions that were significantly influenced. Additionally, using high-quality genome assembly and custom-made gene ontology annotation, we demonstrated that this settled terminology, widely used for the analysis of model organisms, could also be applied to non-model organisms and for research in the field of biofuels.

MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins

Mass spectrometry based proteomics is the method of choice for quantifying genome-wide differential changes of protein expression in a wide range of biological and biomedical applications. Protein expression changes need to be reliably derived from many measured peptide intensities and their corresponding peptide fold changes. These peptide fold changes vary considerably for a given protein. Numerous instrumental setups aim to reduce this variability, whereas current computational methods only implicitly account for this problem. We introduce a new method, MS-EmpiRe, which explicitly accounts for the noise underlying peptide fold changes. We derive data set-specific, intensity-dependent empirical error fold change distributions, which are used for individual weighing of peptide fold changes to detect differentially expressed proteins (DEPs).In a recently published proteome-wide benchmarking data set, MS-EmpiRe doubles the number of correctly identified DEPs at an estimated FDR cutoff compared with state-of-the-art tools. We additionally confirm the superior performance of MS-EmpiRe on simulated data. MS-EmpiRe requires only peptide intensities mapped to proteins and, thus, can be applied to any common quantitative proteomics setup. We apply our method to diverse MS data sets and observe consistent increases in sensitivity with more than 1000 additional significant proteins in deep data sets, including a clinical study over multiple patients. At the same time, we observe that even the proteins classified as most insignificant by other methods but significant by MS-EmpiRe show very clear regulation on the peptide intensity level. MS-EmpiRe provides rapid processing (< 2 min for 6 LC-MS/MS runs (3 h gradients)) and is publicly available under github.com/zimmerlab/MS-EmpiRe with a manual including examples.

Bone Manifestation of Faulty Perinatal Hormonal Imprinting: A Review

Hormonal imprinting takes place at the first encounter between the developing receptor and its target hormone and the encounter determines the receptor's binding capacity for life. In the critical period of development, when the window for imprinting is open, the receptor can be misdirected by related hormones, synthetic hormones, and industrial or communal endocrine disruptors which cause faulty hormonal imprinting with life-long consequences. Considering these facts, the hormonal imprinting is a functional teratogen provoking alterations in the perinatal (early postnatal) period. One single encounter with a low dose of the imprinter in the critical developmental period is enough for the formation of faulty imprinting, which is manifested later, in adult age. This has been justified in the immune system, in sexuality, in animal behavior and brain neurotransmitters etc. by animal experiments and human observations. This review points to the faulty hormonal imprinting in the case of bones (skeleton), by single or repeated treatments. The imprinting is an epigenetic alteration which is inherited to the progeny generations. From clinical aspect, the faulty imprinting can have a role in the pathological development of the bones as well, as in the risk of osteoporotic fractures, etc.

YESdb: integrative analysis of environmental stress in yeast

The stress response in the model organisms Saccharomyces cerevisiae is a well-studied system for which many data sets are available. Already in 2000, it was discovered that yeast cells trigger a similar transcriptional response when different types of stress are applied. However, the exact regulatory mechanisms and differences between the different types of stress are still not understood.

Here, we present the Yeast Environmental Stress database (YESdb), a database containing all high-throughput experiments measuring various kinds of stress in yeast. The goal of the database is to allow the user to execute complex, integrative analyses of selected data sets, e.g. the comparison of measurements of the same stress using different platforms or differences between strains, stress strengths or types of stress. The analyses can be visualized in various ways and can be compiled into interactive reports to summarize and communicate the results.

The data sets are available as differential conditions (typically stressed vs control), which are grouped to time or concentration series when multiple measurements over time or concentrations are done in one experiment. An annotation ontology has been constructed to annotate the data sets with the type, duration and strength of the applied stress, the used strain and experimental platform as well as the publication date. These annotations can easily be combined to select all relevant data sets for an analysis.

YESdb allows to construct and execute Petri net-based workflows to perform predefined and custom analyses. E.g. to compare two types of stress (e.g. salt vs oxidative stress), the corresponding data sets are selected from the database, the consistently changed genes are defined and combined and the shared genes are characterized by enrichment analysis.

A broad collection of visualizations is available most of which are also interactive. The results of all analyses can be summarized in an interactive report. Visualizations of individual steps (transitions) of YESdb workflows can be automatically added to this report or customized visualizations as well as interpretive text can manually be added to the report.

Overall, YESdb aims at making all published data sets on yeast stress immediately available and comparable for integrated analysis of data sets and sets of genes in order to identify and assess hypotheses and mechanisms.

RelExplain-integrating data and networks to explain biological processes

Motivation

The goal of many genome-wide experiments is to explain the changes between the analyzed conditions. Typically, the analysis is started with a set of differential genes DG and the first step is to identify the set of relevant biological processes BP . Current enrichment methods identify the involved biological process via statistically significant overrepresentation of differential genes in predefined sets, but do not further explain how the differential genes interact with each other or which other genes might be important for the enriched process. Other network-based methods determine subnetworks of interacting genes containing many differential genes, but do not employ process knowledge for a more focused analysis.

Results

RelExplain is a method to analyze a given biological process bp (e.g. identified by enrichment) in more detail by computing an explanation using the measured DG and a given network. An explanation is a subnetwork that contains the differential genes in the process bp and connects them in the best way given the experimental data using also genes that are not differential or not in bp . RelExplain takes into account the functional annotations of nodes and the edge consistency of the measurements. Explanations are compact networks of the relevant part of the bp and additional nodes that might be important for the bp . Our evaluation showed that RelExplain is better suited to retrieve manually curated subnetworks from unspecific networks than other algorithms. The interactive RelExplain tool allows to compute and inspect sub-optimal and alternative optimal explanations.

Availability and Implementation

A webserver is available at https://services.bio.ifi.lmu.de/relexplain .

Contact

berchtold@bio.ifi.lmu.de.

Supplementary information

Supplementary data are available at Bioinformatics online.

Vitamin-caused faulty perinatal hormonal imprinting and its consequences in adult age

Lipid-soluble vitamins (vitamins A, D, E, and K) are actually hormones (exohormones), as they can be directly bound by hormone receptors or are in connection with molecules, which influence hormone receptors. Vitamin D is a transition between endo- and exohormones and the possibility of similar situation in case of other lipid-soluble hormones is discussed. The perinatal exposition with these “vitamins” can cause faulty perinatal hormonal imprinting with similar consequences as the faulty imprinting by the synthetic endohormones, members of the same hormone family or industrial, communal, or medical endocrine disruptors. The faulty imprinting leads to late (lifelong) consequences with altered hormone binding by receptors, altered sexuality, brain function, immunity, bone development, and fractures, etc. In addition, as hormonal imprinting is an epigenetic process, the effect of a single exposure by fat-soluble vitamins is inherited to the progeny generations. As vitamins are handled differently from hormones; however, perinatal treatments take place frequently and sometimes it is forced, the negative late effect of faulty perinatal vitamin-caused hormonal imprinting must be considered.

Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data

Several methods predict activity changes of transcription factors (TFs) from a given regulatory network and measured expression data. But available gene regulatory networks are incomplete and contain many condition-dependent regulations that are not relevant for the specific expression measurement. It is not known which combination of active TFs is needed to cause a change in the expression of a target gene. A method to systematically evaluate the inferred activity changes is missing. We present such an evaluation strategy that indicates for how many target genes the observed expression changes can be explained by a given set of active TFs. To overcome the problem that the exact combination of active TFs needed to activate a gene is typically not known, we assume a gene to be explained if there exists any combination for which the predicted active TFs can possibly explain the observed change of the gene. We introduce the i-score (inconsistency score), which quantifies how many genes could not be explained by the set of activity changes of TFs. We observe that, even for these minimal requirements, published methods yield many unexplained target genes, i.e. large i-scores. This holds for all methods and all expression datasets we evaluated. We provide new optimization methods to calculate the best possible (minimal) i-score given the network and measured expression data. The evaluation of this optimized i-score on a large data compendium yields many unexplained target genes for almost every case. This indicates that currently available regulatory networks are still far from being complete. Both the presented Act-SAT and Act-A* methods produce optimal sets of TF activity changes, which can be used to investigate the difficult interplay of expression and network data. A web server and a command line tool to calculate our i-score and to find the active TFs associated with the minimal i-score is available from https://services.bio.ifi.lmu.de/i-score.

Exchange coupling between laterally adjacent nanomagnets

We experimentally demonstrate exchange-coupling between laterally adjacent nanomagnets. Our results show that two neighboring nanomagnets that are each antiferromagnetically exchange-coupled to a common ferromagnetic bottom layer can be brought into strong ferromagnetic interaction. Simulations show that interlayer exchange coupling effectively promotes ferromagnetic alignment between the two nanomagnets, as opposed to antiferromagnetic alignment due to dipole-coupling. In order to experimentally demonstrate the proposed scheme, we fabricated arrays of pairs of elongated, single-domain nanomagnets. Magnetic force microscopy measurements show that most of the pairs are ferromagnetically ordered. The results are in agreement with micromagnetic simulations. The presented scheme can achieve coupling strengths that are significantly stronger than dipole coupling, potentially enabling far-reaching applications in Nanomagnet Logic, spin-wave devices and three-dimensional storage and computing.

Resolving Lipid Mediators Maresin 1 and Resolvin D2 Prevent Atheroprogression in Mice

RATIONALE

Atheroprogression is a consequence of nonresolved inflammation, and currently a comprehensive overview of the mechanisms preventing resolution is missing. However, in acute inflammation, resolution is known to be orchestrated by a switch from inflammatory to resolving lipid mediators. Therefore, we hypothesized that lesional lipid mediator imbalance favors atheroprogression.

OBJECTIVE

To understand the lipid mediator balance during atheroprogression and to establish an interventional strategy based on the delivery of resolving lipid mediators.

METHODS AND RESULTS

Aortic lipid mediator profiling of aortas from Apoe^-/- mice fed a high-fat diet for 4 weeks, 8 weeks, or 4 months revealed an expansion of inflammatory lipid mediators, Leukotriene B4 and Prostaglandin E2, and a concomitant decrease of resolving lipid mediators, Resolvin D2 (RvD2) and Maresin 1 (MaR1), during advanced atherosclerosis. Functionally, aortic Leukotriene B4 and Prostaglandin E2 levels correlated with traits of plaque instability, whereas RvD2 and MaR1 levels correlated with the signs of plaque stability. In a therapeutic context, repetitive RvD2 and MaR1 delivery prevented atheroprogression as characterized by halted expansion of the necrotic core and accumulation of macrophages along with increased fibrous cap thickness and smooth muscle cell numbers. Mechanistically, RvD2 and MaR1 induced a shift in macrophage profile toward a reparative phenotype, which secondarily stimulated collagen synthesis in smooth muscle cells.

CONCLUSIONS

We present evidence for the imbalance between inflammatory and resolving lipid mediators during atheroprogression. Delivery of RvD2 and MaR1 successfully prevented atheroprogression, suggesting that resolving lipid mediators potentially represent an innovative strategy to resolve arterial inflammation.

Nanopatterning reconfigurable magnetic landscapes via thermally assisted scanning probe lithography

The search for novel tools to control magnetism at the nanoscale is crucial for the development of new paradigms in optics, electronics and spintronics. So far, the fabrication of magnetic nanostructures has been achieved mainly through irreversible structural or chemical modifications. Here, we propose a new concept for creating reconfigurable magnetic nanopatterns by crafting, at the nanoscale, the magnetic anisotropy landscape of a ferromagnetic layer exchange-coupled to an antiferromagnetic layer. By performing localized field cooling with the hot tip of a scanning probe microscope, magnetic structures, with arbitrarily oriented magnetization and tunable unidirectional anisotropy, are reversibly patterned without modifying the film chemistry and topography. This opens unforeseen possibilities for the development of novel metamaterials with finely tuned magnetic properties, such as reconfigurable magneto-plasmonic and magnonic crystals. In this context, we experimentally demonstrate spatially controlled spin wave excitation and propagation in magnetic structures patterned with the proposed method.

Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins

Alternative splicing often affects structured and highly conserved regions of proteins, generating so called non-trivial splicing variants of unknown structure and cellular function. The human small G-protein Rab1A is involved in the regulation of the vesicle transfer from the ER to Golgi. A conserved non-trivial splice variant lacks nearly 40% of the sequence of the native Rab1A, including most of the regulatory interaction sites. We show that this variant of Rab1A represents a stable and folded protein, which is still able to bind nucleotides and co-localizes with membranes. Nevertheless, it should be mentioned that compared to other wild-typeRabGTPases, the measured nucleotide binding affinities are dramatically reduced in the variant studied. Furthermore, the Rab1A variant forms hetero-dimers with wild-type Rab1A and its presence in the cell enhances the efficiency of alkaline phosphatase secretion. However, this variant shows no specificity for GXP nucleotides, a constantly enhanced GTP hydrolysis activity and is no longer controlled by GEF or GAP proteins, indicating a new regulatory mechanism for the Rab1A cycle via alternative non-trivial splicing.

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

BACKGROUND

Enrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-based) or incorporate (network-based) known interactions between genes. However, the often subtle benefits and disadvantages of the individual methods are confusing for most biological end users and there is currently no convenient way to combine methods for an enhanced result interpretation.

RESULTS

We present the EnrichmentBrowser package as an easily applicable software that enables (1) the application of the most frequently used set-based and network-based enrichment methods, (2) their straightforward combination, and (3) a detailed and interactive visualization and exploration of the results. The package is available from the Bioconductor repository and implements additional support for standardized expression data preprocessing, differential expression analysis, and definition of suitable input gene sets and networks.

CONCLUSION

The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. It combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.

The Faulty Perinatal Hormonal Imprinting as Functional Teratogen

Perinatally, the developmental window for the adjustment of hormone receptors to their target hormones is open. The hormonal imprinting which determines the relationship of hormones and receptors for life takes place in this period. The recognition ability of developing receptors is not yet entirely specific, so they could be 'cheated' by false imprinters such as related hormones, drugs, environmental pollutants or certain food components and faulty imprinting may result. This causes a functional developmental abnormality, which is then manifested, at any later time in life, as the alteration of the binding capacity of hormone receptors. With or without the presence of other factors this could cause problems in hormone regulated functions or may result in diseases. So it may be stated that faulty hormonal imprinting, caused by a broad spectrum of receptor level molecules, is acting as a functional teratogen. This means that functional maldevelopment is not restricted to intrauterine life, but can also occur after birth, in the perinatal period. The inclusion of faulty imprinting as maldevelopment widens both the list of functional teratogens and the period of teratogenicity. The importance and danger of faulty imprinting is high, especially considering its heritable (transgenerational) character. Considering the facts, the attitudes in the present-day perinatal treatments and medical training must be changed.

Alternative Splicing in Next Generation Sequencing Data of Saccharomyces cerevisiae

mRNA splicing is required in about 4% of protein coding genes in Saccharomyces cerevisiae. The gene structure of those genes is simple, generally comprising two exons and one intron. In order to characterize the impact of alternative splicing on the S. cerevisiae transcriptome, we perform a systematic analysis of mRNA sequencing data. We find evidence of a pervasive use of alternative splice sites and detect several novel introns both within and outside protein coding regions. We also find a predominance of alternative splicing on the 3’ side of introns, a finding which is consistent with existing knowledge on conservation of exon-intron boundaries in S. cerevisiae. Some of the alternatively spliced transcripts allow for a translation into different protein products.

ContextMap 2: fast and accurate context-based RNA-seq mapping

Background

Mapping of short sequencing reads is a crucial step in the analysis of RNA sequencing (RNA-seq) data. ContextMap is an RNA-seq mapping algorithm that uses a context-based approach to identify the best alignment for each read and allows parallel mapping against several reference genomes.

Results

In this article, we present ContextMap 2, a new and improved version of ContextMap. Its key novel features are: (i) a plug-in structure that allows easily integrating novel short read alignment programs with improved accuracy and runtime; (ii) context-based identification of insertions and deletions (indels); (iii) mapping of reads spanning an arbitrary number of exons and indels. ContextMap 2 using Bowtie, Bowtie 2 or BWA was evaluated on both simulated and real-life data from the recently published RGASP study.

Conclusions

We show that ContextMap 2 generally combines similar or higher recall compared to other state-of-the-art approaches with significantly higher precision in read placement and junction and indel prediction. Furthermore, runtime was significantly lower than for the best competing approaches. ContextMap 2 is freely available at http://www.bio.ifi.lmu.de/ContextMap.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0557-5) contains supplementary material, which is available to authorized users.

"Memory" of First Interaction with Physiological or Biologically Active Foreign Molecules (Benzpyrene, Gibberelline) in a Unicellular ( Tetrahymena) Model System

Gibberelline, prednisolon and benzpyrene stimulated the growth of Tetrahymena at the first interaction, while epinephrine did not. On a second exposure following upon the first 24 h treatment after a rest period of 6 h, epinephrine, too, developed a stimulatory action, and the other three molecules gave rise to a still greater increase in the growth rate. Obviously, imprinting effected by the first interaction accounts for a greater responsiveness to physio­ logical materials (hormones) also if these are indifferent in respect of the given function, and non-physiological, but biologically active materials can also give rise to imprinting in exposed target cells.

Mining RNA-seq data for infections and contaminations

RNA sequencing (RNA-seq) provides novel opportunities for transcriptomic studies at nucleotide resolution, including transcriptomics of viruses or microbes infecting a cell. However, standard approaches for mapping the resulting sequencing reads generally ignore alternative sources of expression other than the host cell and are little equipped to address the problems arising from redundancies and gaps among sequenced microbe and virus genomes. We show that screening of sequencing reads for contaminations and infections can be performed easily using ContextMap, our recently developed mapping software. Based on mapping-derived statistics, mapping confidence, similarities and misidentifications (e.g. due to missing genome sequences) of species/strains can be assessed. Performance of our approach is evaluated on three real-life sequencing data sets and compared to state-of-the-art metagenomics tools. In particular, ContextMap vastly outperformed GASiC and GRAMMy in terms of runtime. In contrast to MEGAN4, it was capable of providing individual read mappings to species and resolving non-unique mappings, thus allowing the identification of misalignments caused by sequence similarities between genomes and missing genome sequences. Our study illustrates the importance and potentials of routinely mining RNA-seq experiments for infections or contaminations by microbes and viruses. By using ContextMap, gene expression of infecting agents can be analyzed and novel insights in infection processes and tumorigenesis can be obtained.

A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae

Existing machine-readable resources for large-scale gene regulatory networks usually do not provide context information characterizing the activating conditions for a regulation and how targeted genes are affected. Although this information is essentially required for data interpretation, available networks are often restricted to not condition-dependent, non-quantitative, plain binary interactions as derived from high-throughput screens. In this article, we present a comprehensive Petri net based regulatory network that controls the diauxic shift in Saccharomyces cerevisiae. For 100 specific enzymatic genes, we collected regulations from public databases as well as identified and manually curated >400 relevant scientific articles. The resulting network consists of >300 multi-input regulatory interactions providing (i) activating conditions for the regulators; (ii) semi-quantitative effects on their targets; and (iii) classification of the experimental evidence. The diauxic shift network compiles widespread distributed regulatory information and is available in an easy-to-use machine-readable form. Additionally, we developed a browsable system organizing the network into pathway maps, which allows to inspect and trace the evidence for each annotated regulation in the model.

Effect of a single neonatal oxytocin treatment (hormonal imprinting) on the biogenic amine level of the adult rat brain: could oxytocin-induced labor cause pervasive developmental diseases?

Perinatal single-hormone treatment causes hormonal imprinting with lifelong consequences in receptor-binding capacity, hormone production as well as in social and sexual behavior. In the present experiments, newborn rats were treated with a single dose of oxytocin, and the levels of biogenic amines and their metabolites were studied in 8 different brain regions and in the sera when the male and female animals were 4 months old. Both dopaminergic and serotonergic neurotransmission was found to be significantly influenced. The levels of 3,4-dihydroxyphenylacetic acid, homovanillic acid, and 5-hydroxyindole acetic acid metabolites decreased in the hypothalamus and striatum. Dopamine, serotonin, norepinephrine, and 5-hydroxytryptophol levels were hardly altered, and there was no difference in the epinephrine levels. The results show that dopamine and serotonin metabolism of hypothalamus and striatum are deeply and lifelong influenced by a single neonatal oxytocin treatment Oxytocin imprinting resulted in decreased dopamine turnover in the hypothalamus and decreased serotonin turnover in the hypothalamus, medulla oblongata, and striatum of females. As the disturbance of brain dopamine and serotonin system has an important role in the development of pervasive developmental diseases (eg, autism) and neuropsychiatric disorders (eg, schizophrenia), the growing number of oxytocin-induced labor as a causal factor, cannot be omitted.

Effect of glucose on the insulin production and insulin binding of Tetrahymena

As the unicellular ciliate, Tetrahymena has insulin receptors and produces insulin itself, which can regulate its glucose metabolism and other cell functions, in the present experiments the feed-back, the effect of glucose on the insulin binding and insulin production was studied. The cells were kept partly in tryptone-yeast medium, partly in Losina salt solution. The duration of treatment (in 0.1, 1.0, 10.0 mg/ml glucose) in the binding study was 10 min, in the hormone production study 30 min. FITC-insulin binding was significantly decreased only by 0.1 mg/ml glucose treatment in medium and by 10 mg/ml glucose in salt. The insulin production was significantly lower only in cells treated with 10 mg/ml glucose in medium. The insulin binding in salt was always higher and the insulin production always lower, than in medium. Earlier results demonstrated that the hormonal system (presence of hormones, receptors and signal pathways) of higher ranked animals can be deduced to a unicellular level, however, the feed-back mechanism is not really present here, only the traces can be observed in these protozoa.

Some New Data concerning the Biology of Tumours: The Effects of Heparin Inhibitors on Tumour Growth

Images

A context-based approach to identify the most likely mapping for RNA-seq experiments

Background

Sequencing of mRNA (RNA-seq) by next generation sequencing technologies is widely used for analyzing the transcriptomic state of a cell. Here, one of the main challenges is the mapping of a sequenced read to its transcriptomic origin. As a simple alignment to the genome will fail to identify reads crossing splice junctions and a transcriptome alignment will miss novel splice sites, several approaches have been developed for this purpose. Most of these approaches have two drawbacks. First, each read is assigned to a location independent on whether the corresponding gene is expressed or not, i.e. information from other reads is not taken into account. Second, in case of multiple possible mappings, the mapping with the fewest mismatches is usually chosen which may lead to wrong assignments due to sequencing errors.

Results

To address these problems, we developed ContextMap which efficiently uses information on the context of a read, i.e. reads mapping to the same expressed region. The context information is used to resolve possible ambiguities and, thus, a much larger degree of ambiguities can be allowed in the initial stage in order to detect all possible candidate positions. Although ContextMap can be used as a stand-alone version using either a genome or transcriptome as input, the version presented in this article is focused on refining initial mappings provided by other mapping algorithms. Evaluation results on simulated sequencing reads showed that the application of ContextMap to either TopHat or MapSplice mappings improved the mapping accuracy of both initial mappings considerably.

Conclusions

In this article, we show that the context of reads mapping to nearby locations provides valuable information for identifying the best unique mapping for a read. Using our method, mappings provided by other state-of-the-art methods can be refined and alignment accuracy can be further improved.

Availability

http://www.bio.ifi.lmu.de/ContextMap.

Nanomagnet logic: progress toward system-level integration

Quoting the International Technology Roadmap for Semiconductors (ITRS) 2009 Emerging Research Devices section, 'Nanomagnetic logic (NML) has potential advantages relative to CMOS of being non-volatile, dense, low-power, and radiation-hard. Such magnetic elements are compatible with MRAM technology, which can provide input–output interfaces. Compatibility with MRAM also promises a natural integration of memory and logic. Nanomagnetic logic also appears to be scalable to the ultimate limit of using individual atomic spins.' This article reviews progress toward complete and reliable NML systems. More specifically, we (i) review experimental progress toward fundamental characteristics a device must possess if it is to be used in a digital system, (ii) consider how the NML design space may impact the system-level energy (especially when considering the clock needed to drive a computation), (iii) explain--using both the NML design space and a discussion of clocking as context—how reliable circuit operation may be achieved, (iv) highlight experimental efforts regarding CMOS friendly clock structures for NML systems, (v) explain how electrical I/O could be achieved, and (vi) conclude with a brief discussion of suitable architectures for this technology. Throughout the article, we attempt to identify important areas for future work.

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

MOTIVATION

Current gene set enrichment approaches do not take interactions and associations between set members into account. Mutual activation and inhibition causing positive and negative correlation among set members are thus neglected. As a consequence, inconsistent regulations and contextless expression changes are reported and, thus, the biological interpretation of the result is impeded.

RESULTS

We analyzed established gene set enrichment methods and their result sets in a large-scale investigation of 1000 expression datasets. The reported statistically significant gene sets exhibit only average consistency between the observed patterns of differential expression and known regulatory interactions. We present Gene Graph Enrichment Analysis (GGEA) to detect consistently and coherently enriched gene sets, based on prior knowledge derived from directed gene regulatory networks. Firstly, GGEA improves the concordance of pairwise regulation with individual expression changes in respective pairs of regulating and regulated genes, compared with set enrichment methods. Secondly, GGEA yields result sets where a large fraction of relevant expression changes can be explained by nearby regulators, such as transcription factors, again improving on set-based methods. Thirdly, we demonstrate in additional case studies that GGEA can be applied to human regulatory pathways, where it sensitively detects very specific regulation processes, which are altered in tumors of the central nervous system. GGEA significantly increases the detection of gene sets where measured positively or negatively correlated expression patterns coincide with directed inducing or repressing relationships, thus facilitating further interpretation of gene expression data.

AVAILABILITY

The method and accompanying visualization capabilities have been bundled into an R package and tied to a grahical user interface, the Galaxy workflow environment, that is running as a web server.

CONTACT

Ludwig.Geistlinger@bio.ifi.lmu.de; Ralf.Zimmer@bio.ifi.lmu.de.

Thyrotropin (TSH) regulates triiodothyronine (T3) production in the unicellular Tetrahymena

The aim of the experiments was to study the regulation of triiodothyronine (T3) production in the unicellular Tetrahymena. Untreated and troph-hormone treated specimen were prepared and in different timepoints T3 content was measured and compared by immunocytochemical flow cytometry. 0.1 or 0.001 IU TSH in tryptone-yeast medium stimulated T3 synthesis at 10, 20, 30 min, but does not stimulate after 1 h. The overlapping gonadotropic hormone (GTH) also did it, however only at 10 min. In Losina salt solution (physiological for Tetrahymena) the effect was weaker, however outer amino acid source was not absolutely needed for the production of the hormone. The results show that the TSH regulation of thyroid hormone synthesis (storage, secretion) and troph-hormone overlap can be deduced to a unicellular level. This may allow the hypothesis that the endocrine mechanisms proved at a low level of phylogeny are preserved for the higher ranked organisms.

Effect of different concentrations of serotonin, histamine and insulin on the hormone (serotonin and ACTH) production of Tetrahymena in nutrient-free physiological milieu

Cell populations of Tetrahymena pyriformisGL were kept in nutrient-free (Losina) milieu and treated with different (10(-6)-10(-21)M) concentrations of serotonin, histamine or insulin for 30 min. Following that the hormone (serotonin and adrenocorticotropin (ACTH) content of the cells were measured by immunocytochemical flow cytometric method. Serotonin reduced histamine when applied in 10(-12) and 10(-15)M concentrations, while elevated ACTH levels when applied in 10(-6), 10(-9) and 10(-21)M concentrations. Histamine reduced serotonin concentration at 10(-9)-10(-21)M concentrations and increased ACTH in 10(-6)M. Insulin elevated both hormones' content in each concentration except at 10(-12)M. The results demonstrate that (1) in nutrient-free conditions the hormonal effects differ from that of nutrient-rich (tryptone+yeast) condition; (2) there is an optimal hormone concentration, which causes the strongest effect and this is different for each hormones; (3) the hormone receptors of Tetrahymena are very sensitive; as they react to zeptomolar concentrations. Such small concentration is even more effective than higher ones. Since hormones must become highly diluted in the natural environment of Tetrahymena, it seems that such low concentrations are the actual physiological concentrations.

Investigations on the triiodothyronine (T3)-specificity of thyrotropic (TSH) and gonadotropic (HCG) hormone in the unicellular Tetrahymena

In a previous experiment thyrotropin (TSH) increased the triiodothyronine (T3) production of Tetrahymena and chorionic gonadotropin (HCG) moderately overlapped the effect. At present the production of three amino acid type (histamine, serotonin, epinephrine) and one peptide (endorphin) hormones were studied under the effect of TSH or HCG, in tryptone-yeast (TY) or salt (Losina-Losinsky) medium. The duration of the effect was 10 min. TSH significantly (with almost 20%) decreased epinephrine production in TY medium and HCG similarly decreased epinephrine and increased histamine level. In salt solution TSH as well as HCG decreased the level of serotonin. The results show that at this low level of phylogeny TSH effect is not completely thyroxine-specific, however it is not general. HCG overlaps TSH effect on epinephrine and serotonin production, however its effect is broader. The experiments also demonstrate that the effect of pituitary trop-hormones can be bidirectional in Tetrahymena, as histamine level was increased and epinephrine level was decreased by HCG, in the same cells.

Effect of perinatal stress on the biogenic amine neurotransmitter level of the adult rat's brain

The amount of biogenic amines (dopamine and serotonin) and their metabolites (DOPAC, HVA, 5-HIAA, and 5-HTOL) in five regions of the brain (frontal cortex, hypothalamus, hippocampus, striatum, and brainstem) was studied in the male and female offspring of control and perinatally (48 h before birth or 48 h after birth) food and water deprived dams, when they were three months old, by using HPLC-EC determination. The increase of amine or metabolite level was dominant (19 values increased and 10 decreased related to control). Before-birth stress caused increase in 9 case and only 2 decreased, while in the case of after-birth stress 10 increased and 8 decreased. However, though there is no possibility to decide an exact tendency of direction, the after-birth stress (transmitted by milk) has more expressed effect. Striatum and brainstem were the most touched regions. There was a gender dependence with the dominance of males, except striatum. Blood plasma nociceptin level was also studied and there was a significant elevation in males after pre- and postnatal deprivation, while in females only after postnatal deprivation. The importance of the results in correlation with other stress effects is discussed.

Decreased hormone content of immune cells in children during acute lymphocytic leukemia (ALL) - effect of treatment

Histamine, serotonin and triiodothyronine (T3) content of different circulating lymphocyte subsets of leukemic (acute lymphocytic leukemia, ALL) and non-leukemic (control) children were investigated by multicolor flow cytometry. The hormone contents of the cells were followed from the time of diagnosis till the end of treatment. Each hormone could be detected in every time in the investigated cell types, although the amounts of them changed during the treatment.T lymphocytes: Significantly lower amount of serotonin was found in each T cell subsets (Th, Tc and activated T lymphocytes) of leukemic children compared to the healthy control group at the time of diagnosis and it was permanently low during the maintenance therapy. The decreased amount of serotonin could be demonstrated in Tc and Th cells even at one year after the end of treatment. However, there was no alteration in the histamine and T3 content of T cell subsets in the time of diagnosis, but significant decrease was detected during the maintenance therapy and after treatment.NK cells: The serotonin and T3 contents of NK cells (both NK and NKT subsets) were significantly lower at the time of diagnosis and during the maintenance therapy. Similar decrease was detected in the case of serotonin in B cells. Although there was no difference in the T3 content of B cells at the time of diagnosis, significantly lower amounts could be detected during the therapy compared to the healthy control group. The serotonin concentration remained low for years after the end of treatment, both in B and NK cells. These observations might have diagnostic and prognostic importance.

Hormonal effects on Tetrahymena: change in case of combined treatment

In order to approach their natural conditions, populations of Tetrahymena were kept in Losina-Losinky's salt solution for 1 h, than in the tryptone+yeast medium. During this time they were treated with histamine, serotonin or insulin, or with the combinations of these hormones. Effect of the combined treatments on the production of serotonin (5HT), or adrenocorticotropic hormone (ACTH) or triiodothyronine (T₃) by the cells was compared to the effect of single-hormone treatments. Significant differences were seen between the results obtained following the single or combined treatments. There was no summation of the effects, however an elevation or diminution of the hormone production was observed after the combined treatment, as compared with the untreated controls or with the use of one of the hormones in the samples. The experiments demonstrate that there is a hormonal regulation between the Tetrahymena cells and the hormones influence each other's effect.

Vorescore--fold recognition improved by rescoring of protein structure models

Summary: The identification of good protein structure models and their appropriate ranking is a crucial problem in structure prediction and fold recognition. For many alignment methods, rescoring of alignment-induced models using structural information can improve the separation of useful and less useful models as compared with the alignment score. Vorescore, a template-based protein structure model rescoring system is introduced. The method scores the model structure against the template used for the modeling using Vorolign. The method works on models from different alignment methods and incorporates both knowledge from the prediction method and the rescoring.

Results: The performance of Vorescore is evaluated in a large-scale and difficult protein structure prediction context. We use different threading methods to create models for 410 targets, in three scenarios: (i) family members are contained in the template set; (ii) superfamily members (but no family members); and (iii) only fold members (but no family or superfamily members). In all cases Vorescore improves significantly (e.g. 40% on both Gotoh and HHalign at the fold level) on the model quality, and clearly outperforms the state-of-the-art physics-based model scoring system Rosetta. Moreover, Vorescore improves on other successful rescoring approaches such as Pcons and ProQ. In an additional experiment we add high-quality models based on structural alignments to the set, which allows Vorescore to improve the fold recognition rate by another 50%.

Availability: All models of the test set (about 2 million, 44 GB gzipped) are available upon request.

Contact:csaba@bio.ifi.lmu.de; ralf.zimmer@ifi.lmu.de

Effects of different fixatives on demonstrating epinephrine and ACTH hormones in Tetrahymena

The unicellular Tetrahymena produces, contains, and secretes many hormones characteristic of higher animals. We tested three fixatives, formaldehyde, N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDAC), and glutaraldehyde for suitability for immunocytochemical demonstration of epinephrine and adrenocorticotropic harmone (ACTH) in Tetrahymena. Using flow cytometric immunocytochemistry, staining of ACTH was highest after EDAC fixation and that of epinephrine after glutaraldehyde fixation. Using laser scanning confocal microscopy, formaldehyde fixation prevented staining. Glutaraldehyde fixation produced high autofluorescence, which obscured specific staining. After EDAC fixation, ACTH was localized in the ciliary row; however, demonstration of epinephrine was not improved. Our results show that there is no "fixative for any hormone." Different fixatives are needed to demonstrate different hormones in Tetrahymena.

miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature

Background

MicroRNAs have been discovered as important regulators of gene expression. To identify the target genes of microRNAs, several databases and prediction algorithms have been developed. Only few experimentally confirmed microRNA targets are available in databases. Many of the microRNA targets stored in databases were derived from large-scale experiments that are considered not very reliable. We propose to use text mining of publication abstracts for extracting microRNA-gene associations including microRNA-target relations to complement current repositories.

Results

The microRNA-gene association database miRSel combines text-mining results with existing databases and computational predictions. Text mining enables the reliable extraction of microRNA, gene and protein occurrences as well as their relationships from texts. Thereby, we increased the number of human, mouse and rat miRNA-gene associations by at least three-fold as compared to e.g. TarBase, a resource for miRNA-gene associations.

Conclusions

Our database miRSel offers the currently largest collection of literature derived miRNA-gene associations. Comprehensive collections of miRNA-gene associations are important for the development of miRNA target prediction tools and the analysis of regulatory networks. miRSel is updated daily and can be queried using a web-based interface via microRNA identifiers, gene and protein names, PubMed queries as well as gene ontology (GO) terms. miRSel is freely available online at http://services.bio.ifi.lmu.de/mirsel.

Influence of perinatal stress on the hormone content in immune cells of adult rats: dominance of ACTH

Rat dams were stressed by total deprivation of food and water for 48 h just before or directly after delivery and the offspring were studied when adult. The immune cells' hormone content (ACTH, histamine, serotonin, and T(3)) was measured by immunocytochemical flow cytometry. The elevation of ACTH content in males was convincing in each cell type (lymphocytes, monocytes and granulocytes, and mast cells). The change in histamine and T(3) content was inconsistent, while serotonin level did not change at all. As ACTH is the key hormone in the General Adaptation Syndrome, it seems likely that the perinatal stress primarily caused elevation in ACTH level and it was provoking the life-long hormonal imprinting. There was a difference between the reaction of males and females (with males' advance), which points to the gender dependence of the phenomenon. It is important that the effect of stress on the offspring was similar in case of direct (prenatal, in the mother) and indirect (postnatal, transmitted by milk) stress treatment, which calls attention to the danger of stress during this latter period.

Hormones in the nucleus of mast cells: confocal microscopic immunocytochemical observations

In earlier experiments, the presence of histamine and serotonin in the nucleus of mast cells was demonstrated. At present we studied the presence or absence of four hormones: adrenocorticotropine (ACTH), growth hormone (GH), triiodothyronine (T(3)), and progesterone. Cells of the (adult female) rat peritoneal fluid were fixed by EDAC and studied by laser-scanning confocal microscope, after treatment with primary antibodies and FITC-labeled secondary antibody. Strong ACTH and growth hormone fluorescence can be seen in the nucleus. ACTH fluorescence is present also in the granules. The cytoplasm of lymphocytes contains both ACTH and GH. T(3) shows very pale fluorescence, and progesterone is negative. The conclusion is that the nucleus of mast cells contains two polypeptide hormones studied. This was demonstrated by using EDAC fixation as this is a cross-linking agent and does not allow the escape of the minute amounts of hormones from the nucleus. Earlier observations on peptide hormones' nuclear presence and their importance are discussed.

Impact of Neonatal Catecholamine Treatment on Adult Response to Vasopressin and Norepinephrine

The present experiments have shown that neonatal imprinting with certain catecholamines had a significant impact on adult vascular adrenergic response, and on adult response to vasopressin as well. This finding not only substantiates the existence of a hormonal imprinting mechanism, but also suggests a certain (receptor-level) interaction between the vasopressin and catecholamine receptors involved in vascular contraction.

Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis

Background

SCOP and CATH are widely used as gold standards to benchmark novel protein structure comparison methods as well as to train machine learning approaches for protein structure classification and prediction. The two hierarchies result from different protocols which may result in differing classifications of the same protein. Ignoring such differences leads to problems when being used to train or benchmark automatic structure classification methods. Here, we propose a method to compare SCOP and CATH in detail and discuss possible applications of this analysis.

Results

We create a new mapping between SCOP and CATH and define a consistent benchmark set which is shown to largely reduce errors made by structure comparison methods such as TM-Align and has useful further applications, e.g. for machine learning methods being trained for protein structure classification. Additionally, we extract additional connections in the topology of the protein fold space from the orthogonal features contained in SCOP and CATH.

Conclusion

Via an all-to-all comparison, we find that there are large and unexpected differences between SCOP and CATH w.r.t. their domain definitions as well as their hierarchic partitioning of the fold space on every level of the two classifications. A consistent mapping of SCOP and CATH can be exploited for automated structure comparison and classification.

Availability

Benchmark sets and an interactive SCOP-CATH browser are available at .