Testing the suitability of harpacticoid copepods as food for marine fish larvae

While capture fisheries have been stagnating since the 1990’s, aquaculture production has increased steadily from being negligible in the 1980’s to sharing now 40% of the world fish supply. This increase entails a growing demand of fingerlings which results in an intensification in rearing fish larvae. Intensive rearing systems imply exogenous feeding which in turn led to a research activity to find food for fish larvae which is nutritious and can be produced cost effectively, since food is the highest cost factor in aquaculture production. Brachionus and Artemia are nowadays the normally used prey items for fish larvae. They can be produced in high densities with relatively low labour costs. However, they have to be enriched, e.g. with certain fatty acids, to fulfil the nutritional requirements of fish larvae and are still outperformed by copepods which are the natural food of marine fish larvae. Fish larvae fed with copepods show higher survival and growth rates as well as fewer malpigmentation and malformations. For this reason, this study focused on the rearing of copepods, especially harpacticoids as food for marine fish larvae. Harpacticoids can be reared in higher densities than calanoids and are more robust to salinity and temperature changes, which promise an easier and a more cost effective production. A copepod screening revealed Tachidius discipes as a possible new species as food for marine fish larvae. In the first chapter the effect of algal species on the growth performance, reproduction and fatty acid composition of T. discipes was investigated and compared to Tisbe sp. Additionally, the food saturation density was determined to allow an economical feeding procedure of the copepods. The two algal species Rhodomonas sp. and Phaeodactylum tricornutum revealed the best performance of both copepod species meeting the recommended ratio of essential fatty acids. T. discipes can compete with Tisbe sp. in terms of development time and reproduction when feeding on a nutritious food source, but Tisbe sp. had a higher fatty acid desaturation capacity and/or is a more opportunistic species which can compensate an inadequate food source by switching to other sources such as bacteria compared to T. discipes. Nevertheless, T. discipes was evaluated as a new food source for Baltic herring larvae (Clupea harengus) and compared with Brachionus plicatilis (Chapter 2). A surprisingly low performance of the herring larvae fed with T. discipes led to an in-vitro trypsin digestibility test of several prey types used in aquaculture. This study revealed a lower digestibility of T. discipes than Tisbe sp. The most digestible prey item was Artemia sp. Subsequently, a 2D-video analysis was conducted to investigate if the benthic living mode of harpacticoid copepods is posing a problem for pelagic fish larvae in terms of feeding success and energy demand (Chapter 3). Benthic copepods are obviously detected by pelagic fish larvae, but the larvae had a lower feeding success when feeding on copepods compared to B. plicatilis, especially at first feeding. However, this improved with ontogeny. Providing harpacticoid copepods via a floating sieve improved the feeding success and lowered presumably the energetic expenditure of fish larvae. In conclusion, harpacticoid copepods can be a valuable food source for marine fish larvae, but their digestibility is a critical point, which should be considered when evaluating new species and conducting further feeding experiments. Furthermore, although harpacticoid copepods are cultured in relatively high densities, they do not reach the densities obtained with B. plicatilis. Consequently, copepods will be a food supplement rather than the sole food source.Während der Fischfang seit den 90er Jahren stagniert, steigt die Aquakulturproduktion stetig an. War die Fischzucht in den 80er Jahren nur in geringem Maße vorhanden, so nimmt sie jetzt 40% der weltweiten Fischversorgung ein. Diese Zunahme brachte auch einen steigenden Bedarf an Setzlingen mit sich, der eine Intensivierung der Fischlarvenzucht notwendig machte. Intensive Aquakultursysteme benötigen eine Fütterung von außen. Dadurch erhöht sich die Forschungsaktivität, Futter zu finden, welches nahrhaft ist, aber auch kosteneffizient produziert werden kann. Brachionus und Artemia sind momentan die zwei meist genutzten Futterarten für Fischlarven. Sie können zwar mit geringem Arbeitsaufwand kultiviert werden, aber sie müssen mit Nährstoffen - insbesondere Fettsäuren - angereichert werden, um die Fischlarven adäquat zu versorgen. Für marine Fischlarven sind Copepoden ein Hauptbestandteil der natürlichen Nahrungsquelle. Werden Fischlarven mit diesen gefüttert, zeigen sie oftmals eine höhere Überlebensrate, ein besseres Wachstum und weniger Fehlpigmentierungen und Missbildungen im Vergleich zur Ernährung mit angereicherten Brachionus und Artemia. Aus diesem Grund liegt der Fokus dieser Studie auf der Zucht von Copepoden, insbesondere harpacticiden Copepoden als Futter mariner Fischlarven. Harpacticide Copepoden können in höheren Dichten als calanide kultiviert werden und sind robuster gegenüber Temperatur- und Salinitätsschwankungen. Dies verspricht eine leichtere und kosteneffizientere Zucht im Vergleich zu calaniden Copepoden. In einem Copepoden-Screening erwies sich Tachidius discipes als ein möglicher neuer Kandidat zur Aufzucht von Fischlarven. Im ersten Kapitel wurde die Eignung der neuen Art im Hinblick auf Wachstum, Reproduktion und Fettsäurezusammensetzung untersucht und mit Tisbe sp. verglichen. Außerdem wurde die Futtersättigungskonzentration bestimmt, um eine ökonomische Fütterung der Copepoden zu ermöglichen. Mit den beiden Algenarten Rhodomonas sp. und Phaeodactylum tricornutum zeigten die Copepoden die beste Performance und das empfohlene Verhältnis der essentiellen Fettsäuren wurde erreicht. T. discipes und Tisbe sp. wiesen gleiche Wachstums- und Reproduktionsraten auf bei Fütterung mit optimalem Futter. Aber Tisbe sp. hatte anscheinend eine höhere Kapazität Fettsäuren zu desaturieren und/oder es ist eine opportunistischere Art, die inadäquates Futter kompensieren kann, indem sie zu anderen Futterarten wie z.B. Bakterien wechselt. Dennoch wurde T. discipes als eine neue Futterart für Heringslarven (Clupea harengus) evaluiert und mit Brachionus plicatilis verglichen (Kapitel 2). Eine überraschend schlechte Konstitution der Heringslarven bei Fütterung mit T. discipes führte zu einem anschließenden In-vitro-Verdauungstest mittels des Enzyms Trypsin. Diese Untersuchung zeigte, dass T. discipes schlechter verdaulich ist als Tisbe sp. Eine noch weitaus höhere Verdaubarkeit wies Artemia sp. auf. Anschließend wurde eine 2D-Videoanalyse durchgeführt um zu untersuchen, ob die benthische Lebensweise der harpacticiden Copepoden ein Problem für die pelagisch lebenden Fischlarven in Bezug auf Fangerfolg und Energieverbrauch darstellt (Kapitel 3). Benthische Copepoden wurden von den Fischlarven wahrgenommen. Aber die Fischlarven hatten seltener Futter im Darm, wenn sie mit Copepoden anstatt mit B. plicatilis gefüttert wurden. Dies verbesserte sich jedoch mit Entwicklung der Fischlarve. Die Verfütterung der Copepoden mittels eines schwimmenden Siebes verbesserte den Fangerfolg und verringerte wahrscheinlich den Energieverbrauch der Fischlarven. Abschließend lässt sich sagen, dass harpacticide Copepoden ein hochwertiges Futter für marine Fischlarven sind, aber ihre Verdaubarkeit ist ein kritischer Punkt, der bei künftigen Evaluierungen neuer Arten und bei Fütterungsversuchen berücksichtigt werden sollte. Obwohl harpacticide Copepoden in relativ hohen Dichten kultiviert werden können, werden nicht so hohe Dichten erzielt wie mit B. plicatilis. Somit werden Copepoden eher eine Nahrungsergänzung als das alleinige Futter für Fischlarven darstellen

Evaluation of Prognostic Parameters to Identify Aggressive Penile Carcinomas

Background: Advanced penile carcinoma is characterized by poor prognosis. Most data on prognostic factors are based on small study cohorts, and even meta-analyses are limited in patient numbers. Therefore, there is still a lack of evidence for clinical decisions. In addition, the most recent TNM classification is questionable; in line with previous studies, we found that it has not improved prognosis estimation. Methods: We evaluated 297 patients from Germany, Russia, and Portugal. Tissue samples from 233 patients were re-analyzed by two experienced pathologists. HPV status, p16, and histopathological parameters were evaluated for all patients. Results: Advanced lymph node metastases (N2, N3) were highly significantly associated with reductions in metastasis-free (MFS), cancer-specific (CS), and overall survival (OS) rates (p = <0.001), while lymphovascular invasion was a significant parameter for reduced CS and OS (p = 0.005; p = 0.007). Concerning the primary tumor stage, a significant difference in MFS was found only between pT1b and pT1a (p = 0.017), whereas CS and OS did not significantly differ between T categories. In patients without lymph node metastasis at the time of primary diagnosis, lymphovascular invasion was a significant prognostic parameter for lower MFS (p = 0.032). Histological subtypes differed in prognosis, with the worst outcome in basaloid carcinomas, but without statistical significance. HPV status was not associated with prognosis, either in the total cohort or in the usual type alone. Conclusion: Lymphatic involvement has the highest impact on prognosis in penile cancer, whereas HPV status alone is not suitable as a prognostic parameter. The pT1b stage, which includes grading, as well as lymphovascular and perineural invasion in the T stage, seems questionable; a revision of the TNM classification is therefore required

A model of implant-associated infection in the tibial metaphysis of rats

Objective. Implant-associated infections remain serious complications in orthopaedic and trauma surgery. A main scientific focus has thus been drawn to the development of anti-infective implant coatings. Animal models of implant-associated infections are considered helpful in the in vivo testing of new anti-infective implant coatings. The aim of the present study was to evaluate a novel animal model for generation of implant-associated infections in the tibial metaphysis of rats. Materials and Methods. A custom-made conical implant made of Ti6Al4V was inserted bilaterally at the medial proximal tibia of 26 female Sprague-Dawley rats. Staphylococcus aureus in amounts spanning four orders of magnitude and each suspended in 15 l phosphate buffered saline (PBS) was inoculated into the inner cavity of the implant after the implantation into the defined position. Controls were treated accordingly with PBS alone. Animals were then followed for six weeks until sacrifice. Implant-associated infection was evaluated by microbiological investigation using swabs and determination of viable bacteria in the bone around the implant and the biofilm on the implants after sonification. Results. Irrespective of the initial inoculum, all animals in the various groups harbored viable bacteria in the intraoperative swabs as well as the sonication fluid of the implant and the bone samples. No correlation could be established between initially inoculated CFU and population sizes on implant surfaces at sacrifice. However, a significantly higher viable count was observed from peri-implant bone samples for animals inoculated with 10 6 CFU. Macroscopic signs of animal infection (pus and abscess formation) were only observed for implants inoculated with at least 10 5 CFU S. aureus. Discussion/Conclusion. The results demonstrate the feasibility of this novel animal model to induce an implant-associated infection in the metaphysis of rats, even with comparatively low bacterial inocula. The specific design of the implant allows an application of bacteria in reproducible numbers at well-defined contact sites to the animal bone

Whole-exome sequencing reveals novel cancer genes and actionable targets in biliary tract cancers in primary sclerosing cholangitis.

BACKGROUND People with primary sclerosing cholangitis (PSC) have a 20% lifetime risk of biliary tract cancer (BTC). Using whole-exome sequencing, we characterized genomic alterations in tissue samples from BTC with underlying PSC. METHODS We extracted DNA from formalin-fixed, paraffin-embedded tumor and paired nontumor tissue from 52 resection or biopsy specimens from patients with PSC and BTC and performed whole-exome sequencing. Following copy number analysis, variant calling, and filtering, putative PSC-BTC-associated genes were assessed by pathway analyses and annotated to targeted cancer therapies. RESULTS We identified 53 candidate cancer genes with a total of 123 nonsynonymous alterations passing filtering thresholds in 2 or more samples. Of the identified genes, 19% had not previously been implicated in BTC, including CNGA3, KRT28, and EFCAB5. Another subset comprised genes previously implicated in hepato-pancreato-biliary cancer, such as ARID2, ELF3, and PTPRD. Finally, we identified a subset of genes implicated in a wide range of cancers such as the tumor suppressor genes TP53, CDKN2A, SMAD4, and RNF43 and the oncogenes KRAS, ERBB2, and BRAF. Focal copy number variations were found in 51.9% of the samples. Alterations in potential actionable genes, including ERBB2, MDM2, and FGFR3 were identified and alterations in the RTK/RAS (p = 0.036), TP53 (p = 0.04), and PI3K (p = 0.043) pathways were significantly associated with reduced overall survival. CONCLUSIONS In this exome-wide characterization of PSC-associated BTC, we delineated both PSC-specific and universal cancer genes. Our findings provide opportunities for a better understanding of the development of BTC in PSC and could be used as a platform to develop personalized treatment approaches

Responsiveness of the EQ-5D in breast cancer patients in their first year after treatment

<p>Abstract</p> <p>Background/aim</p> <p>The EQ-5D is a generic health-related quality of life (HRQoL) measure that is used for the purpose of economic evaluations of health interventions. Therefore, it has to be responsive to meaningful changes in health in the patient population under investigation. The aim of this study was to investigate the responsiveness of the EQ-5D in breast cancer patients in their first year after treatment.</p> <p>Methods</p> <p>The subscale global health of the disease-specific HRQoL measure EORTC QLQ-C30 was used as a reference instrument to determine meaningful changes in health and identify subgroups of patients: patients reporting a moderate-large deterioration, small deterioration, a small improvement, moderate-large improvement, or no change in health status. Responsiveness was evaluated by calculating standardized response means (SRMs) in the five subgroups of patients and performing analysis of variance procedures. The two HRQoL measures were filled out two weeks and one year after finalizing curative treatment for breast cancer (n = 192).</p> <p>Results</p> <p>The EQ-5D was able to capture both improvements and deteriorations in HRQoL. SRMs of the EQ VAS and EQ-5D Index were close to zero in the subgroup reporting no change and increased and decreased adequately in the subgroups reporting small and moderate changes. Additional analysis of variance procedures showed that the EQ-5D was able to differentiate between subgroups of patients with no change and moderate-large deterioration or improvement in health.</p> <p>Conclusion</p> <p>The EQ-5D seems an appropriate measure for the purpose of economic evaluations of health intervention in breast cancer patients after treatment.</p> <p>Trial registration</p> <p>Current Controlled Trials ISRCTN74071417.</p

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment