How Many Loci Does it Take to DNA Barcode a Crocus?

BACKGROUND: DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species. METHODOLOGY AND PRINCIPAL FINDINGS: Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will--as is the case in crocus--undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached--even in a taxonomic context. CONCLUSIONS/SIGNIFICANCE: The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting

Phylogeny of Triticeae (Poaceae) Based on Three Organelle Genes, Two Single-Copy Nuclear Genes, and Morphology

Triticeae are renowned for their complicated taxonomy, but their phylogeny is equally intricate and perplexing, and remains largely unresolved. Based on morphology and nucleotide sequences from two plastid genes (rbcL, rpoA), one mitochondrial gene (coxII), and two single-copy nuclear genes (DMC1, EF-G), the most comprehensive hypothesis (both with respect to taxa and data points) of the phylogeny of diploid Triticeae to date is presented. The incongruence length difference tests clearly indicate that the four logical data partitions (morphology and the three genome compartments) are mutually incongruent, except the mitochondrial and nuclear sequences. Nonetheless, a total evidence approach results in a highly resolved, strongly supported consensus tree, though partitioned Bremer support points to a high level of conflict among the individual data sets

Genomes, Chromosomes, and Genes and the Concept of Homology

The traditional application of genome analysis in phylogenetic inference is questionable. Hypotheses about phylogeny are based upon the analysis of homologous characters, existing as a consequence of common descent. The concept of homology in morphology and molecular biology is well-defined: To count as an homology any character must pass the similarity, congruence, and conjunction tests. In genome analysis homology is related to the behaviour of chromosomes during meiosis: homologous chromosomes pair, nonhomologous chromosomes do not. Thus, in genome analysis homology becomes a purely operational concept. How well does this operational concept work? And what are the relationships, if any, between this operational concept of homology and the homology concept of morphology and molecular biology

Occupational Therapist contributions within everyday rehabilitation in community mental health services

Masteroppgave, psykisk helsearbeid, 2013Norsk sammendrag; Hensikten med denne studien er å bidra til å utvikle kunnskap om hverdagsrehabilitering innen psykisk helsearbeid, samt kunnskap om ergoterapeutens faktiske og potensielle rolle og bidrag innenfor hverdagsrehabilitering for mennesker med psykiske lidelser. Det er benyttet kvalitativ metode i studien, og en eksplorativ og deskriptiv tilnærming. Eksplorativ fordi det finnes lite litteratur om hverdagsrehabilitering knyttet til psykisk helsearbeid, og deskriptiv fordi det gir mulighet for åpne og nyanserte beskrivelser fra informantene. Videre er det benyttet en fenomenologisk-hermeneutisk forståelse. Det fenomenologiske perspektivet brukes for å kunne gi presise beskrivelser av informantenes opplevelser og erfaringer knyttet til hverdagsrehabilitering, psykisk helsearbeid og ergoterapeutens bidrag. Mens hermeneutikken har gitt mulighet for en dypere forståelse for informantenes bidrag gjennom fortolkning av datamaterialet. Det er foretatt et strategisk utvalg av ti informanter hvor alle er ergoterapeuter. De arbeider eller har erfaring fra arbeid innen psykisk helsearbeid og/eller har kunnskap om hverdagsrehabilitering. Datainnsamlingen ble gjennomført ved hjelp av semistrukturerte kvalitative intervju. Studiens data er empiriske og Malteruds modell for kvalitativ innholdsanalyse er benyttet. Funnene i studien er samlet i fire hovedkategorier; hverdagsrehabilitering, sentrale momenter ved hverdagsrehabilitering, aktivitet versus passivitet og ergoterapeuter ser vitenskapelig på hverdagsaktiviteter. Det beskrives at det allerede finnes et rehabiliteringsfokus innen psykisk helsearbeid i kommunene, men at det har kommet i skyggen av et stort fokus på pleie og omsorg. Derfor ønskes en større tyngde på hverdagsrehabilitering med fokus på forebyggende og helsefremmende arbeid i fremtiden. Målgruppen anses å være alle med psykiske lidelser, men i denne studien henviser informantene hovedsakelig til mennesker med alvorlige psykiske lidelser. Hovedmålet for hverdagsrehabilitering for mennesker med psykiske lidelser vil være å forebygge psykoser og innleggelser. Det legges stor vekt på at alt arbeidet skal gjøres i samarbeid med bruker, og med respekt for den enkelte og menneskeverdet. Noe av det mest betydningsfulle helsepersonell kan bidra med i denne sammenheng er å formidle et håp om at forandring er mulig. Hjelp til selvhjelp i form av empowerment anses som viktig for å kunne hjelpe mennesker til å mestre hverdagen og oppleve kontroll over eget liv. Videre er fokus på at betydningen av det selvfølgelige hverdagslivet og de ordinære hverdagsaktivitetene må ha et sentralt aspekt i dette arbeidet. Mange med psykiske lidelser er ensomme og isolerer seg, så det å ha et sosialt nettverk og forsøke å finne sosiale arenaer er noe av det mest elementære. Her kan pårørende i mange tilfeller være en viktig og ubenyttet ressurs. Mange av momentene som knyttes til hverdagsrehabilitering i studien, kan relateres til recovery/bedringsprosesser. Ergoterapeuter anses å ha en helt sentral rolle i arbeidet med hverdagsrehabilitering og hverdagsmestring. Deres kunnskap om, forståelse for og bruk av aktivitet viser seg å være en god tilnærming til mennesker med psykiske lidelser. I denne sammenheng vises det til betydningen av aktivitetsanalyser for å kunne oppnå denne kunnskapen. Videre trekkes spesielt ergoterapeuters helhetlige tankegang med samspillet mellom person, aktivitet og omgivelser frem, samt deres systematiske kartlegging, vurderinger og intervensjoner.English abstract: The purpose of this study is to contribute to developement of knowledge about everyday rehabilitation in mental health, as well as knowledge about occupational therapist actual and potential role and contribution within everyday rehabilitation for people with mental illness. The method of the study is qualitative and the approach is exploratory and descriptive. Exploratory because there is little literature on everyday rehabilitation related to mental health, and descriptive because it allows open and nuanced descriptions from the informants. Further on it uses a phenomenological-hermeneutic understanding. The phenomenological perspective is used to provide precise descriptions of the informants' experiences related to daily rehabilitation, mental health and occupational therapists contributions. While hermeneutics has provided the opportunity for a deeper understanding of the informants' contributions through the interpretation of the data. A strategic sample of ten informants have been made, all of which are occupational therapists. They work or have experience of working in mental health and/or have knowledge of everyday rehabilitation. The data collection was conducted using semi-structured qualitative interviews. The study data are empirical and Malteruds model for qualitative content analysis was used. The findings of the study are contained in four main categories: everyday rehabilitation, significant aspects of daily rehabilitation, activity versus passivity and occupational therapists scientific look at everyday activities. It is described that there is already a rehabilitation focus in community mental health services, but it has been overshadowed by a major focus of care. Therefore a greater emphasis on everyday rehabilitation, with a focus on prevention and health promotion in the future, is desired. The target group is considered to be all mental disorders, but in this study informants refer mainly to people with severe psychiatric disability. The main objective of everyday rehabilitation for people with mental illness will be to prevent psychosis and hospitalizations. It is emphasized that all the work will be done in cooperation with the user and with respect for the individual and human dignity. One of the most significant things health care professionals can contribute is to convey a hope that change is possible. Self-help in the form of empowerment is considered important to help people cope with everyday life and experience control over their own lives. Furthermore, focusing on the importance of the obvious everyday life and the ordinary everyday activities must be a central aspect of this work. Many people with mental illness are lonely and isolated, so having a social network and attempting to find social venues are some of the most elementary. Next of kins can in many cases be an important and untapped resource. Many of the factors associated with daily rehabilitation in the study, may be related to recovery. Occupational therapists are considered to have a central role in everyday rehabilitation and everyday coping. Their knowledge, understanding and use of activity turns out to be a good approach to people with mental disorders. In this context, reference is made to the importance of activity analysis in order to obtain this knowledge. Furthermore are particularly occupational therapists holistic thinking with the interaction between person, task and environment highlighted, as well as their systematic mapping, assessments and interventions

Plastome evolution in hemiparasitic mistletoes

Santalales is an order of plants consisting almost entirely of parasites. Some, such as Osyris, are facultative root parasites whereas others, such as Viscum, are obligate stem parasitic mistletoes. Here, we report the complete plastome sequences of one species of Osyris and three species of Viscum, and we investigate the evolutionary aspects of structural changes and changes in gene content in relation to parasitism. Compared with typical angiosperms plastomes, the four Santalales plastomes are all reduced in size (10–22% compared with Vitis), and they have experienced rearrangements, mostly but not exclusively in the border areas of the inverted repeats. Additionally, a number of protein-coding genes (matK, infA, ccsA, rpl33, and all 11 ndh genes) as well as two transfer RNA genes (trnG-UCC and trnV-UAC) have been pseudogenized or completely lost. Most of the remaining plastid genes have a significantly changed selection pattern compared with other dicots, and the relaxed selection of photosynthesis genes is noteworthy. Although gene loss obviously reduces plastome size, intergenic regions were also shortened. As plastome modifications are generally most prominent in Viscum, they are most likely correlated with the increased nutritional dependence on the host compared with Osyris

Differentiating instruction using authentic, performance assessments and technology integration

A major challenge in education today is to be able to reach and teach all learners. Methodologies and strategies come and go. The philosophy of differentiated instruction, while not new, is being bandied about as the answer to working with all students of all abilities. The beliefs associated with differentiated instruction envelope methodologies and strategies associated with authentic assessment, performance-based assessment, and technology integration. A common bond inherent within these philosophies is the growing emphasis on assessing students based on their ability to perform real-life tasks, and technology integration is the connecting link. Educators must become facilitators of meaningful learning experiences for all students. Differentiating instruction through authentic, performance-based tasks that integrate technology provides students the skills necessary for the world awaiting them

Massive gene loss in mistletoe (<em>Viscum</em>, Viscaceae) mitochondria

Parasitism is a successful survival strategy across all kingdoms and has evolved repeatedly in angiosperms. Parasitic plants obtain nutrients from other plants and some are agricultural pests. Obligate parasites, which cannot complete their lifecycle without a host, may lack functional photosystems (holoparasites), or have retained photosynthesis (hemiparasites). Plastid genomes are often reduced in parasites, but complete mitochondrial genomes have not been sequenced and their mitochondrial respiratory capacities are largely unknown. The hemiparasitic European mistletoe (Viscum album), known from folklore and postulated therapeutic properties, is a pest in plantations and forestry. We compare the mitochondrial genomes of three Viscum species based on the complete mitochondrial genome of V. album, the first from a parasitic plant. We show that mitochondrial genes encoding proteins of all respiratory complexes are lacking or pseudogenized raising several questions relevant to all parasitic plants: Are any mitochondrial gene functions essential? Do any genes need to be located in the mitochondrial genome or can they all be transferred to the nucleus? Can parasitic plants survive without oxidative phosphorylation by using alternative respiratory pathways? More generally, our study is a step towards understanding how host- and self-perception, host integration and nucleic acid transfer has modified ancestral mitochondrial genomes