Incorporating molecular data in fungal systematics: a guide for aspiring researchers

The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching changes as disciplines in the wake of continual improvement in DNA sequencing technology. A taxonomic study that draws from molecular data involves a long series of steps, ranging from taxon sampling through the various laboratory procedures and data analysis to the publication process. All steps are important and influence the results and the way they are perceived by the scientific community. The present paper provides a reflective overview of all major steps in such a project with the purpose to assist research students about to begin their first study using DNA-based methods. We also take the opportunity to discuss the role of taxonomy in biology and the life sciences in general in the light of molecular data. While the best way to learn molecular methods is to work side by side with someone experienced, we hope that the present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology - comments most welcom

La Piezosurgery come metodica alternativa alla strumentazione rotante tradizionale nell'estrazione di ottavi inferiori inclusi. Revisione della letteratura

La presente dissertazione si occupa di esporre la validità della piezosurgery nell'estrazione di ottavi inclusi inferiori come alternativa alla strumentazione rotante tradizionale. Ne vengono illustrati vantaggi e svantaggi con particolare attenzione al tempo impiegato per l'intervento, alla riduzione delle complicanze e al miglioramento del decorso postoperatorio, il tutto sulla base di una revisione sistematica che la letteratura propone su questo argomento corredata dall' esposizione di una serie di casi clinici

Consistent melanophore spot patterns allow long-term individual recognition of Atlantic salmon Salmo salar

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Small molecule screening platform for assessment of cardiovascular toxicity on adult zebrafish heart

<p>Abstract</p> <p>Background</p> <p>Cardiovascular toxicity is a major limiting factor in drug development and requires multiple cost-effective models to perform toxicological evaluation. Zebrafish is an excellent model for many developmental, toxicological and regenerative studies. Using approaches like morpholino knockdown and electrocardiogram, researchers have demonstrated physiological and functional similarities between zebrafish heart and human heart. The close resemblance of the genetic cascade governing heart development in zebrafish to that of humans has propelled the zebrafish system as a cost-effective model to conduct various genetic and pharmacological screens on developing embryos and larvae. The current report describes a methodology for rapid isolation of adult zebrafish heart, maintenance <it>ex vivo</it>, and a setup to perform quick small molecule throughput screening, including an in-house implemented analysis script.</p> <p>Results</p> <p>Adult zebrafish were anesthetized and after rapid decapitation the hearts were isolated. The short time required for isolation of hearts allows dissection of multiple fishes, thereby obtaining a large sample size. The simple protocol for <it>ex vivo </it>culture allowed maintaining the beating heart for several days. The in-house developed script and spectral analyses allowed the readouts to be presented either in time domain or in frequency domain. Taken together, the current report offers an efficient platform for performing cardiac drug testing and pharmacological screens.</p> <p>Conclusion</p> <p>The new methodology presents a fast, cost-effective, sensitive and reliable method for performing small molecule screening. The variety of readouts that can be obtained along with the in-house developed analyses script offers a powerful setup for performing cardiac toxicity evaluation by researchers from both academics and industry.</p

The proteomic landscape of glioma stem-like cells

AbstractGlioma stem-like cells (GSCs) are hypothesized to provide a repository of cells in tumors that can self-replicate and are radio- and chemo-resistant. GSC lines, representing several glioma subtypes, have been isolated and characterized at the transcript level. We sought to characterize 35 GSC lines at the protein level using label-free quantitative proteomics. Resulting relative fold changes were used to drive unsupervised hierarchical clustering for the purpose of classifying the cell lines based on proteomic profiles. Bioinformatics analysis identified synoviolin, serine/arginine-rich splicing factor 2, symplekin, and IL-5 as molecules of interest in progression and/or treatment of glioma

Acute sleep deprivation increases portion size and affects food choice in young men

SummaryAcute sleep loss increases food intake in adults. However, little is known about the influence of acute sleep loss on portion size choice, and whether this depends on both hunger state and the type of food (snack or meal item) offered to an individual. The aim of the current study was to compare portion size choice after a night of sleep and a period of nocturnal wakefulness (a condition experienced by night-shift workers, e.g. physicians and nurses). Sixteen men (age: 23±0.9 years, BMI: 23.6±0.6kg/m2) participated in a randomized within-subject design with two conditions, 8-h of sleep and total sleep deprivation (TSD). In the morning following sleep interventions, portion size, comprising meal and snack items, was measured using a computer-based task, in both fasted and sated state. In addition, hunger as well as plasma levels of ghrelin were measured. In the morning after TSD, subjects had increased plasma ghrelin levels (13%, p=0.04), and chose larger portions (14%, p=0.02), irrespective of the type of food, as compared to the sleep condition. Self-reported hunger was also enhanced (p<0.01). Following breakfast, sleep-deprived subjects chose larger portions of snacks (16%, p=0.02), whereas the selection of meal items did not differ between the sleep interventions (6%, p=0.13). Our results suggest that overeating in the morning after sleep loss is driven by both homeostatic and hedonic factors. Further, they show that portion size choice after sleep loss depend on both an individual's hunger status, and the type of food offered

Introducing ribosomal tandem repeat barcoding for fungi

Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. The quality of the Nanopore generated sequences was 99.85%, which is comparable with the 99.78% accuracy described for Sanger sequencing. With this work, we hope to stimulate the generation of a new comprehensive standard of ribosomal reference data with the ultimate aim to close the huge gaps in our reference datasets

Clinical categories of patients and encounter rates in primary health care – a three-year study in defined populations

BACKGROUND: The objective was to estimate the proportion of inhabitants with a diagnosis-registered encounter with a general practitioner, and to elucidate annual variations of clinical categories of patients in terms of their individual comorbidity. METHODS: A three-year retrospective study of encounter data from electronic patient records, with an annual-based application of the Johns Hopkins Adjusted Clinical Groups (ACG) system. Data were retrieved from every patient with a diagnosis-registered encounter with a GP during the period 2001–2003 at 13 publicly managed primary health care centres in Blekinge county, southeastern Sweden, with about 150000 inhabitants. Main outcome measures: Proportions of inhabitants with a diagnosis-registered encounter, and ranges of the annual proportions of categories of patients according to ACGs. RESULTS: The proportion of inhabitants with a diagnosis-registered encounter ranged from about 64.0% to 90.6% for the primary health care centres, and averaged about 76.5% for all inhabitants. In a three-year perspective the average range of categories of patients was about 0.4% on the county level, and about 0.9% on the primary health care centre level. About one third of the patients each year had a constellation of two or more types of morbidity. CONCLUSION: About three fourths of all inhabitants had one or more diagnosis-registered encounters with a general practitioner during the three-year period. The annual variation of categories of patients according to ACGs was small on both the county and the primary health care centre level. The ACG system seems useful for demonstrating and predicting various aspects of clinical categories of patients in Swedish primary health care

Coding of procedures documented by general practitioners in Swedish primary care-an explorative study using two procedure coding systems

<p>Abstract</p> <p>Background</p> <p>Procedures documented by general practitioners in primary care have not been studied in relation to procedure coding systems. We aimed to describe procedures documented by Swedish general practitioners in electronic patient records and to compare them to the Swedish Classification of Health Interventions (KVÅ) and SNOMED CT.</p> <p>Methods</p> <p>Procedures in 200 record entries were identified, coded, assessed in relation to two procedure coding systems and analysed.</p> <p>Results</p> <p>417 procedures found in the 200 electronic patient record entries were coded with 36 different Classification of Health Interventions categories and 148 different SNOMED CT concepts. 22.8% of the procedures could not be coded with any Classification of Health Interventions category and 4.3% could not be coded with any SNOMED CT concept. 206 procedure-concept/category pairs were assessed as a complete match in SNOMED CT compared to 10 in the Classification of Health Interventions.</p> <p>Conclusions</p> <p>Procedures documented by general practitioners were present in nearly all electronic patient record entries. Almost all procedures could be coded using SNOMED CT.</p> <p>Classification of Health Interventions covered the procedures to a lesser extent and with a much lower degree of concordance. SNOMED CT is a more flexible terminology system that can be used for different purposes for procedure coding in primary care.</p