PathwayNexus: a tool for interactive metabolic data analysis.

MOTIVATION: High-throughput omics methods increasingly result in large datasets including metabolomics data, which are often difficult to analyse. RESULTS: To help researchers to handle and analyse those datasets by mapping and investigating metabolomics data of multiple sampling conditions (e.g. different time points or treatments) in the context of pathways, PathwayNexus has been developed, which presents the mapping results in a matrix format, allowing users to easily observe the relations between the compounds and the pathways. It also offers functionalities like ranking, sorting, clustering, pathway views, and further analytical tools. Its primary objective is to condense large sets of pathways into smaller, more relevant subsets that align with the specific interests of the user. AVAILABILITY AND IMPLEMENTATION: The methodology presented here is implemented in PathwayNexus, an open-source add-on for Vanted available at www.cls.uni-konstanz.de/software/pathway-nexus. CONTACT: falk.schreiber@unikonstanz.de. SUPPLEMENTARY INFORMATION: Website: www.cls.uni-konstanz.de/software/pathway-nexus.

Placental growth factor promotes neural invasion and predicts disease prognosis in resectable pancreatic cancer.

BACKGROUND: Surgery represents the only curative treatment option for pancreatic ductal adenocarcinoma (PDAC), but recurrence in more than 85% of patients limits the success of curative-intent tumor resection. Neural invasion (NI), particularly the spread of tumor cells along nerves into extratumoral regions of the pancreas, constitutes a well-recognized risk factor for recurrence. Hence, monitoring and therapeutic targeting of NI offer the potential to stratify recurrence risk and improve recurrence-free survival. Based on the evolutionary conserved dual function of axon and vessel guidance molecules, we hypothesize that the proangiogenic vessel guidance factor placental growth factor (PlGF) fosters NI. To test this hypothesis, we correlated PlGF with NI in PDAC patient samples and functionally assessed its role for the interaction of tumor cells with nerves. METHODS: Serum levels of PlGF and its soluble receptor sFlt1, and expression of PlGF mRNA transcripts in tumor tissues were determined by ELISA or qPCR in a retrospective discovery and a prospective validation cohort. Free circulating PlGF was calculated from the ratio PlGF/sFlt1. Incidence and extent of NI were quantified based on histomorphometric measurements and separately assessed for intratumoral and extratumoral nerves. PlGF function on reciprocal chemoattraction and directed neurite outgrowth was evaluated in co-cultures of PDAC cells with primary dorsal-root-ganglia neurons or Schwann cells using blocking anti-PlGF antibodies. RESULTS: Elevated circulating levels of free PlGF correlated with NI and shorter overall survival in patients with PDAC qualifying for curative-intent surgery. Furthermore, high tissue PlGF mRNA transcript levels in patients undergoing curative-intent surgery correlated with a higher incidence and greater extent of NI spreading to tumor-distant extratumoral nerves. In turn, more abundant extratumoral NI predicted shorter disease-free and overall survival. Experimentally, PlGF facilitated directional and dynamic changes in neurite outgrowth of primary dorsal-root-ganglia neurons upon exposure to PDAC derived guidance and growth factors and supported mutual chemoattraction of tumor cells with neurons and Schwann cells. CONCLUSION: Our translational results highlight PlGF as an axon guidance factor, which fosters neurite outgrowth and attracts tumor cells towards nerves. Hence, PlGF represents a promising circulating biomarker of NI and potential therapeutic target to improve the clinical outcome for patients with resectable PDAC.

Mycobacterium chelonae-abscessus complex associated with sinopulmonary disease, Northeastern USA.

Members of the Mycobacterium chelonae-abscessus complex represent Mycobacterium species that cause invasive infections in immunocompetent and immunocompromised hosts. We report the detection of a new pathogen that had been misidentified as M. chelonae with an atypical antimicrobial drug susceptibility profile. The discovery prompted a multicenter investigation of 26 patients. Almost all patients were from the northeastern United States, and most had underlying sinus or pulmonary disease. Infected patients had clinical features similar to those with M. abscessus infections. Taxonomically, the new pathogen shared molecular identity with members of the M. chelonae-abscessus complex. Multilocus DNA target sequencing, DNA-DNA hybridization, and deep multilocus sequencing (43 full-length genes) support a new taxon for these microorganisms. Because most isolates originated in Pennsylvania, we propose the name M. franklinii sp. nov. This investigation underscores the need for accurate identification of Mycobacterium spp. to detect new pathogens implicated in human disease.

Nocardia niwae sp. nov., isolated from human pulmonary sources.

Members of the genus Nocardia are responsible for cutaneous, pulmonary and disseminated human infections. From 2003 to 2008, four nocardioform strains (W8027, W8681, W9071 and W9241(T)) were isolated from patients in the state of Florida, USA. Ribosomal gene sequencing analysis suggested that a novel species of the genus Nocardia had been isolated. These strains were subjected to a taxonomic analysis using a polyphasic approach. Phenotypic analyses included morphological examination, biochemical profiling and antimicrobial susceptibility testing. Molecular studies included 16S rRNA and DNA gyrase B subunit (gyrB) gene sequence analyses and DNA-DNA hybridization. Phylogenetic neighbours were determined through 16S rRNA and gyrB gene sequence analyses. Phenotypic characteristics that differentiated the novel isolates from phylogenetically related species were growth at 45 °C, and three of the four novel strains utilized l-rhamnose. The antimicrobial profiles could not reliably distinguish the novel species from related nocardiae. Analysis showed that the 16S rRNA gene sequences of the four novel isolates were identical. The blast analysis of the near full-length 16S rRNA gene showed 99.2 % sequence similarity to Nocardia araoensis DSM 44729(T), Nocardia arthritidis DSM 44731(T) and Nocardia beijingensis JCM 10666(T), 98.7 % to Nocardia amamiensis DSM 45066(T), 98.2 % to Nocardia pneumoniae JCM 12119(T) and 97.8 % to Nocardia takedensis JCM 13313(T). Analysis of partial gyrB gene sequences showed that the novel isolates had 95.4 % similarity to N. arthritidis DSM 44731(T), 95.3 % to Nocardia gamkensis DSM 44956(T), 94.4 % to N. pneumoniae JCM 12119(T), 93.8 % to Nocardia asiatica DSM 44668(T), 93.5 % to N. amamiensis DSM 45066(T), 93.4 % to N. beijingensis JCM 10666(T) and 93.2 % to N. araoensis DSM 44729(T). The DNA-DNA relatedness values between the four novel strains were 86-89 %; the relatedness value for strain W9241(T) compared with N. beijingensis JCM 10666(T) was 47 % and 46 % with N. araoensis DSM 44729(T), 44 % with N. arthritidis DSM 44731(T), 32 % with N. amamiensis DSM 45066(T) and 20 % with N. asiatica DSM 44668(T). The results of the taxonomic analysis suggested that the new isolates represent a novel species of the genus Nocardia for which the name Nocardia niwae sp. nov. is proposed. The type strain is W9241(T) (=DSM 45340(T)=CCUG 57756(T)).

Visceral Varicella-Zoster Virus Infection in An Immunocompromised Patient: Uncommon Endoscopic Differential Diagnosis.

Varicella-Zoster virus (VZV) infection is well-known for its dermatological appearances, such as chickenpox and shingles. In addition to its dermal disease, we report a case of visceral dissemination of VZV in immunocompromised patients. A 38-year-old male Caucasian with a history of bone marrow transplantation due to diffuse large B-cell-lymphoma presented himself with severe abdominal pain. Immediate endoscopy revealed numerous gastric and duodenal ulcerations, while histological and molecular evaluation on tissue biopsies and blood samples confirmed VZV infection. Positive serological findings and history of chickenpox during childhood supported visceral VZV dissemination due to reactivation of VZV. The patient received Aciclovir treatment and fully recovered. This case illustrates that visceral dissemination of VZV may lead to acute abdominal pain due to severe mucosal ulcerations even in the absence of dermatological manifestations. Early endoscopic evaluation may therefore be crucial and the only means to immediately guide differential diagnosis, especially in immunocompromised patients. Characteristic histomorphological findings from mucosal ulcerations should lead to the immediate initiation of antiviral therapy and specific molecular evaluation in order to avoid detrimental spread of visceral VZV infection.

Evaluation of five commercial nucleic acid extraction kits for their ability to inactivate Bacillus anthracis spores and comparison of DNA yields from spores and spiked environmental samples.

This study evaluated five commercial extraction kits for their ability to recover DNA from Bacillus anthracis spores and spiked environmental samples. The kits evaluated represent the major types of methodologies which are commercially available for DNA or total nucleic acid extraction, and included the ChargeSwitch gDNA Mini Bacteria Kit, NucliSens Isolation Kit, Puregene Genomic DNA Purification Kit, QIAamp DNA Blood Mini Kit, and the UltraClean Microbial DNA Isolation Kit. Extraction methods were performed using the spores of eight virulent strains of B. anthracis. Viability testing of nucleic acid extracts showed that the UltraClean kit was the most efficient at depleting samples of live B. anthracis spores. TaqMan real-time PCR analysis revealed that the NucliSens, QIAamp and UltraClean kits yielded the best level of detection from spore suspensions. Comparisons of processed samples from spiked swabs and three powder types indicated that DNA extraction using the UltraClean kit resulted in the most consistently positive results and the lowest limit of detection. This study demonstrated that different nucleic extraction methodologies, represented here by various commercial extraction kits, differ in their ability to inactivate live B. anthracis spores as well as DNA yield and purity. In addition, the extraction method used can influence the sensitivity of real-time PCR assays for B. anthracis.

Deep Sequencing in Conjunction with Expression and Functional Analyses Reveals Activation of FGFR1 in Ewing Sarcoma.

PURPOSE: A low mutation rate seems to be a general feature of pediatric cancers, in particular in oncofusion gene-driven tumors. Genetically, Ewing sarcoma is defined by balanced chromosomal EWS/ETS translocations, which give rise to oncogenic chimeric proteins (EWS-ETS). Other contributing somatic mutations involved in disease development have only been observed at low frequency. EXPERIMENTAL DESIGN: Tumor samples of 116 Ewing sarcoma patients were analyzed here. Whole-genome sequencing was performed on two patients with normal, primary, and relapsed tissue. Whole-exome sequencing was performed on 50 Ewing sarcoma and 22 matched normal tissues. A discovery dataset of 14 of these tumor/normal pairs identified 232 somatic mutations. Recurrent nonsynonymous mutations were validated in the 36 remaining exomes. Transcriptome analysis was performed in a subset of 14 of 50 Ewing sarcomas and DNA copy number gain and expression of FGFR1 in 63 of 116 Ewing sarcomas. RESULTS: Relapsed tumors consistently showed a 2- to 3-fold increased number of mutations. We identified several recurrently mutated genes at low frequency (ANKRD30A, CCDC19, KIAA0319, KIAA1522, LAMB4, SLFN11, STAG2, TP53, UNC80, ZNF98). An oncogenic fibroblast growth factor receptor 1 (FGFR1) mutation (N546K) was detected, and the FGFR1 locus frequently showed copy number gain (31.7%) in primary tumors. Furthermore, high-level FGFR1 expression was noted as a characteristic feature of Ewing sarcoma. RNA interference of FGFR1 expression in Ewing sarcoma lines blocked proliferation and completely suppressed xenograft tumor growth. FGFR1 tyrosine kinase inhibitor (TKI) therapy in a patient with Ewing sarcoma relapse significantly reduced 18-FDG-PET activity. CONCLUSIONS: FGFR1 may constitute a promising target for novel therapeutic approaches in Ewing sarcoma.

Integrating optical fiber force sensors into microforceps for ORL microsurgery.

The delicate anatomy of the ear require surgeons to use great care when operating on its internal structures. One example for such an intervention is the stapedectomy, where a small crook shaped piston is placed in the oval window of the cochlea and connected to the incus through crimping thus bypassing the diseased stapes. Performing the crimp process with the correct force is necessary since loose crimps poorly transmit sound whereas tight crimps will eventually result in necrosis of the incus. Clinically, demand is high to reproducibly conduct the crimp process through a precise force measurement. For this reason, we have developed a fiber Bragg grating (FBG) integrated microforceps for use in such interventions. This device was calibrated, and tested in cadaver preparations. With this instrument we were able to measure for the first time forces involved in crimping a stapes prosthesis to the incus. We also discuss a method of attaching and actuating such forceps in conjunction with a robot currently under development in our group. Each component of this system can be used separately or combined to improve surgical accuracy, confidence and outcome.