Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

BACKGROUND: During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed. RESULTS: A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service , users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available. DISCUSSION: The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases contain a thorough sampling of taxonomically well-annotated sequences. Taxonomy, held by some to be an old-fashioned trade, has accordingly never been more important. emerencia does not automate the taxonomic process, but it does allow researchers to focus their efforts elsewhere than countless manual BLAST runs and arduous sieving of BLAST hit lists. The emerencia system is available on an open source basis for local installation with any organism and gene group as targets

Follow-up study of the treatment outcomes at a psychiatric trauma clinic for refugees

Purpose: To describe change in mental health after treatment with antidepressants and trauma-focused cognitive behavioral therapy. Methods: Patients receiving treatment at the Psychiatric Trauma Clinic for Refugees in Copenhagen completed self-ratings of level of functioning, quality of life, and symptoms of PTSD, depression, and anxiety before and after treatment. Changes in mental state and predictors of change were evaluated in a sample that all received well-described and comparable treatment. Results: 85 patients with PTSD or depression were included in the analysis. Significant improvement and effect size were observed on all rating scales (p-value <0.01 and Cohen’s d 45-0.68). Correlation analysis showed no association between severity of symptoms at baseline and the observed change. Conclusion: Despite methodological limitations, the finding of a significant improvement on all rating scales is important considering that previous follow-up studies of comparable patient populations have not found significant change in the patients’ condition after treatment

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra- and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3% threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names

Patch Testing with a Textile Dye Mix in a Baseline Series in Two Countries

Disperse dyes are the most common contact sensitizers among textile dyes. The main aim of this study was to investigate the outcome of patch testing with a textile dye mix 6.6%. A total of 2,049 patients from Sweden and 497 from Belgium were tested with the mix, consisting of Disperse (D) Blue 35, D Yellow 3, D Orange 1 and 3, D Red 1 and 17, 1.0% each, and D Blue 106 and D Blue 124, 0.3% each. Of the total number, 65 patients, 2.6%, tested positively to the mix, 4.2% of the Belgian patients and 2.1% of the Swedish patients. Patch testing with the mix 6.6% revealed significantly more patients with contact allergy compared with testing with a previous mix 3.2% (p<0.01). Contact allergy to the mix was significantly more common in the Belgian than in the Swedish patients

Styrning av kunskapsarbetare- via normaitv styrning och direkt övervakning

Undersökningen visar på att styrning av kunskapsarbetare inte bara görs via normativ styrning, det förekommer också andra typer av styrning så som direkt övervakning/styrning. Studien visar på att kunskapsarbetares aversioner mot mer direkta former av styrning kan överkommas om denna legitimeras och paketeras på ett attraktivt sätt

Cognitive behavioral psychotherapeutic treatment at a psychiatric trauma clinic for refugees: description and evaluation

Introduction: Cognitive behavioural therapy (CBT) with trauma focus is the most evidence supported psychotherapeutic treatment of PTSD, but few CBT treatments for traumatized refugees have been described in detail. Purpose: To describe and evaluate a manualized cognitive behavioral therapy for traumatized refugees incorporating exposure therapy, mindfulness and acceptance, and commitment therapy. Material and methods: 85 patients received six months’ treatment at a Copenhagen Trauma Clinic for Refugees and completed self-ratings before and after treatment. The treatment administered to each patient was monitored in detail. The changes in mental state and the treatment components associated with change in state were analyzed statistically. Results: Despite the low level of functioning and high co-morbidity of patients, 42% received highly structured CBT, which was positively associated with all treatment outcomes. The more methods used and the more time each method was used, the better the outcome. The majority of patients were able to make homework assignments and this was associated with better treatment outcome. Correlation analysis showed no association between severity of symptoms at baseline and the observed change. Conclusion: The study suggests that CBT treatment incorporating mindfulness and acceptance and commitment therapy is promising for traumatized refugees and punctures the myth that this group of patients are unable to participate fully in structured CBT. However, treatment methods must be adapted to the special needs of refugees and trauma exposure should be further investigated.&nbsp

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

<p>Abstract</p> <p>Background</p> <p>The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus <it>Inocybe </it>(<it>Basidiomycota</it>) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified <it>Inocybe </it>sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of <it>Inocybe </it>was contrasted to that of other mycorrhizal genera.</p> <p>Results</p> <p>Most species of <it>Inocybe </it>were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified <it>Inocybe </it>sequences to species level. A total of 177 unidentified <it>Inocybe </it>ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight <it>Inocybe </it>species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, <it>Inocybe </it>sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution.</p> <p>Conclusion</p> <p>Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework.</p

Symptoms, Quality of Life and level of functioning of traumatized refugees at Psychiatric Trauma Clinic in Copenhagen

Objective: To characterize physical and mental health in trauma-exposed refugees by describing a population of patients with regard to background, mental health history, and current health problems; and to identify pre- and post-migratory predictors of mental health. Method: All patients receiving treatment at the Psychiatric Trauma Clinic for Refugees in Copenhagen from April 2008 to February 2010 completed self-rating inventories on symptoms of PTSD, depression, and anxiety as well as level of functioning and quality of life before treatment. Then, associations of pre and post-migratory factors with mental health were explored using linear and logistic regression and Pearson’s correlation coefficients. Results: Among the patients, the prevalence of depression, somatic disease, pain, psychotic symptoms co-existing with PTSD and very low level of functioning was high. Persecution, being an ex-combatant and living currently in social isolation were significantly associated with PTSD arousal symptoms and self-reported pain. Conclusions: New treatment modalities should seek to address all of the symptoms and challenges of the patients including psychotic and somatic symptoms and social isolation, and studies of treatment effect should clarify all co-morbidities so that comparable populations can be included in treatment evaluation studies

When mycologists describe new species, not all relevant information is provided (clearly enough)

Taxonomic mycology struggles with what seems to be a perpetual shortage of resources. Logically, fungal taxonomists should therefore leverage every opportunity to highlight and visualize the importance of taxonomic work, the usefulness of taxonomic data far beyond taxonomy, and the integrative and collaborative nature of modern taxonomy at large. Is mycology really doing that, though? In this study, we went through ten years' worth (2009-2018) of species descriptions of extant fungal taxa - 1,097 studies describing at most ten new species - in five major mycological journals plus one plant journal. We estimated the frequency at which a range of key words, illustrations, and concepts related to ecology, geography, taxonomy, molecular data, and data availability were provided with the descriptions. We also considered a range of science-demographical aspects such as gender bias and the rejuvenation of taxonomy and taxonomists as well as public availability of the results. Our results show that the target audience of fungal specks descriptions appears to be other fungal taxonomists, because many aspects of the new species were presented only implicitly, if at all. Although many of the parameters we estimated show a gradual, and in some cases marked, change for the better over time, they still paint a somewhat bleak picture of mycological taxonomy as a male-dominated field where the wants and needs of an extended target audience are often not understood or even considered. This study hopes to leave a mark on the way fungal species are described by putting the focus on ways in which fungal taxonomy can better anticipate the end users of species descriptions - be they mycologists, other researchers, the public at large, or even algorithms. In the end, fungal taxonomy, too, is likely to benefit from such measures

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