Single-Institution Prospective Evaluation of Moderately Hypofractionated Whole-Breast Radiation Therapy With Simultaneous Integrated Boost With or Without Lymphatic Drainage Irradiation After Breast-Conserving Surgery.

Purpose: We report treatment outcomes for patients who received adjuvant moderate hypofractionated whole-breast radiation therapy with simultaneous integrated boost (SIB-mhWBRT) after breast-conserving surgery.

Methods And Materials: SIB-mhWBRT for patients with breast cancer was introduced in our department in July 2017. This prospective evaluation includes 424 consecutive patients treated with SIB-mhWBRT for stage I-III invasive breast cancer (n = 391) and/or ductal carcinoma in situ (n = 33) until December 2021.

Strains Induce Transcriptional and Morphological Changes and Reduce Root Colonization of spp.

Phytopathogenic Verticillia cause Verticillium wilt on numerous economically important crops. Plant infection begins at the roots, where the fungus is confronted with rhizosphere inhabiting bacteria. The effects of different fluorescent pseudomonads, including some known biocontrol agents of other plant pathogens, on fungal growth of the haploid and/or the amphidiploid were compared on pectin-rich medium, in microfluidic interaction channels, allowing visualization of single hyphae, or on roots.

Elicits Media-Dependent Secretome Responses With Capacity to Distinguish Between Plant-Related Environments.

Verticillia cause a vascular wilt disease affecting a broad range of economically valuable crops. The fungus enters its host plants through the roots and colonizes the vascular system. It requires extracellular proteins for a successful plant colonization.

Divergent co-transcriptomes of different host cells infected with Toxoplasma gondii reveal cell type-specific host-parasite interactions.

The apicomplexan parasite Toxoplasma gondii infects various cell types in avian and mammalian hosts including humans. Infection of immunocompetent hosts is mostly asymptomatic or benign, but leads to development of largely dormant bradyzoites that persist predominantly within neurons and muscle cells. Here we have analyzed the impact of the host cell type on the co-transcriptomes of host and parasite using high-throughput RNA sequencing.

Non-targeted metabolomics by high resolution mass spectrometry in HPRT knockout mice.

Aims: Lesch-Nyhan disease (LND) is characterized by hyperuricemia as well as neurological and neuropsychiatric symptoms including repetitive self-injurious behavior. Symptoms are caused by a deficiency of the enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT) as a result of a mutation on the X chromosome. To elucidate the pathophysiology of LND, we performed a metabolite screening for brain and serum extracts from HPRT knockout mice as an animal model for LND.

MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data.

A central aim in the evaluation of non-targeted metabolomics data is the detection of intensity patterns that differ between experimental conditions as well as the identification of the underlying metabolites and their association with metabolic pathways. In this context, the identification of metabolites based on non-targeted mass spectrometry data is a major bottleneck. In many applications, this identification needs to be guided by expert knowledge and interactive tools for exploratory data analysis can significantly support this process.

Membrane-bound methyltransferase complex VapA-VipC-VapB guides epigenetic control of fungal development.

Epigenetic and transcriptional control of gene expression must be coordinated in response to external signals to promote alternative multicellular developmental programs. The membrane-associated trimeric complex VapA-VipC-VapB controls a signal transduction pathway for fungal differentiation. The VipC-VapB methyltransferases are tethered to the membrane by the FYVE-like zinc finger protein VapA, allowing the nuclear VelB-VeA-LaeA complex to activate transcription for sexual development.

Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software.

State of the art high-throughput technologies allow comprehensive experimental studies of organism metabolism and induce the need for a convenient presentation of large heterogeneous datasets. Especially, the combined analysis and visualization of data from different high-throughput technologies remains a key challenge in bioinformatics. We present here the MarVis-Graph software for integrative analysis of metabolic and transcriptomic data.

Meta-analysis of pathway enrichment: combining independent and dependent omics data sets.

A major challenge in current systems biology is the combination and integrative analysis of large data sets obtained from different high-throughput omics platforms, such as mass spectrometry based Metabolomics and Proteomics or DNA microarray or RNA-seq-based Transcriptomics. Especially in the case of non-targeted Metabolomics experiments, where it is often impossible to unambiguously map ion features from mass spectrometry analysis to metabolites, the integration of more reliable omics technologies is highly desirable. A popular method for the knowledge-based interpretation of single data sets is the (Gene) Set Enrichment Analysis.

Targeting novel chemical and constitutive primed metabolites against Plectosphaerella cucumerina.

Priming is a physiological state for protection of plants against a broad range of pathogens, and is achieved through stimulation of the plant immune system. Various stimuli, such as beneficial microbes and chemical induction, activate defense priming. In the present study, we demonstrate that impairment of the high-affinity nitrate transporter 2.

Soluble phenylpropanoids are involved in the defense response of Arabidopsis against Verticillium longisporum.

Verticillium longisporum is a soil-borne vascular pathogen causing economic loss in rape. Using the model plant Arabidopsis this study analyzed metabolic changes upon fungal infection in order to identify possible defense strategies of Brassicaceae against this fungus. Metabolite fingerprinting identified infection-induced metabolites derived from the phenylpropanoid pathway.

Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots.

Six transcription regulatory genes of the Verticillium plant pathogen, which reprogrammed nonadherent budding yeasts for adhesion, were isolated by a genetic screen to identify control elements for early plant infection. Verticillium transcription activator of adhesion Vta2 is highly conserved in filamentous fungi but not present in yeasts. The Magnaporthe grisea ortholog conidiation regulator Con7 controls the formation of appressoria which are absent in Verticillium species.

Arabidopsis mutants of sphingolipid fatty acid α-hydroxylases accumulate ceramides and salicylates.

In Arabidopsis, the fatty acid moiety of sphingolipids is mainly α-hydroxylated. The consequences of a reduction in this modification were analysed. Mutants of both Fatty Acid Hydroxylase genes (AtFAH1 and AtFAH2) were analysed for sphingolipid profiles.

MarVis-Filter: ranking, filtering, adduct and isotope correction of mass spectrometry data.

Statistical ranking, filtering, adduct detection, isotope correction, and molecular formula calculation are essential tasks in processing mass spectrometry data in metabolomics studies. In order to obtain high-quality data sets, a framework which incorporates all these methods is required. We present the MarVis-Filter software, which provides well-established and specialized methods for processing mass spectrometry data.

The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development.

The COP9 signalosome complex (CSN) is a crucial regulator of ubiquitin ligases. Defects in CSN result in embryonic impairment and death in higher eukaryotes, whereas the filamentous fungus Aspergillus nidulans survives without CSN, but is unable to complete sexual development. We investigated overall impact of CSN activity on A.

MarVis: a tool for clustering and visualization of metabolic biomarkers.

Background: A central goal of experimental studies in systems biology is to identify meaningful markers that are hidden within a diffuse background of data originating from large-scale analytical intensity measurements as obtained from metabolomic experiments. Intensity-based clustering is an unsupervised approach to the identification of metabolic markers based on the grouping of similar intensity profiles. A major problem of this basic approach is that in general there is no prior information about an adequate number of biologically relevant clusters.

Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps.

Background: One of the goals of global metabolomic analysis is to identify metabolic markers that are hidden within a large background of data originating from high-throughput analytical measurements. Metabolite-based clustering is an unsupervised approach for marker identification based on grouping similar concentration profiles of putative metabolites. A major problem of this approach is that in general there is no prior information about an adequate number of clusters.