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

Chloroplast magnesium transporters play essential but differential roles in maintaining magnesium homeostasis

Magnesium (Mg2+) is essential for photosynthesis in the chloroplasts of land plants and algae. Being the central ion of chlorophyll, cofactor and activator of many photosynthetic enzymes including RuBisCO, magnesium-deficient plants may suffer from leaf chlorosis symptoms and retarded growth. Therefore, the chloroplast Mg2+ concentration is tightly controlled by magnesium transport proteins. Recently, three different transporters from two distinct families have been identified in the chloroplast inner envelope of the model plant Arabidopsis thaliana: MGT10, MGR8, and MGR9. Here, we assess the individual roles of these three proteins in maintaining chloroplast Mg2+ homeostasis and regulating photosynthesis, and if their role is conserved in the model green alga Chlamydomonas reinhardtii. Phylogenetic analysis and heterologous expression revealed that the CorC-like MGR8 and MGR9 transport Mg2+ by a different mechanism than the CorA-like MGT10. MGR8 and MGT10 genes are highest expressed in leaves, indicating a function in chloroplast Mg2+ transport. MGR9 is important for chloroplast function and plant adaptation in conditions of deficiency or excess of Mg2+. Transmission electron microscopy indicated that MGT10 plays a differential role in thylakoid stacking than MGR8 and MGR9. Furthermore, we report that MGR8, MGR9, and MGT10 are involved in building up the pH gradient across the thylakoid membrane and activating photoprotection in conditions of excess light, however the mechanism has not been resolved yet. While there are no chloroplast MGR-like transporters in Chlamydomonas, we show that MRS4 is a homolog of MGT10, that is required for photosynthesis and cell growth. Taken together, our findings reveal that the studied Mg2+ transporters play essential but differential roles in maintaining chloroplast Mg2+ homeostasis

Chloroplast magnesium transporters play essential but differential roles in maintaining magnesium homeostasis

Magnesium (Mg2+) is essential for photosynthesis in the chloroplasts of land plants and algae. Being the central ion of chlorophyll, cofactor and activator of many photosynthetic enzymes including RuBisCO, magnesium-deficient plants may suffer from leaf chlorosis symptoms and retarded growth. Therefore, the chloroplast Mg2+ concentration is tightly controlled by magnesium transport proteins. Recently, three different transporters from two distinct families have been identified in the chloroplast inner envelope of the model plant Arabidopsis thaliana: MGT10, MGR8, and MGR9. Here, we assess the individual roles of these three proteins in maintaining chloroplast Mg2+ homeostasis and regulating photosynthesis, and if their role is conserved in the model green alga Chlamydomonas reinhardtii. Phylogenetic analysis and heterologous expression revealed that the CorC-like MGR8 and MGR9 transport Mg2+ by a different mechanism than the CorA-like MGT10. MGR8 and MGT10 genes are highest expressed in leaves, indicating a function in chloroplast Mg2+ transport. MGR9 is important for chloroplast function and plant adaptation in conditions of deficiency or excess of Mg2+. Transmission electron microscopy indicated that MGT10 plays a differential role in thylakoid stacking than MGR8 and MGR9. Furthermore, we report that MGR8, MGR9, and MGT10 are involved in building up the pH gradient across the thylakoid membrane and activating photoprotection in conditions of excess light, however the mechanism has not been resolved yet. While there are no chloroplast MGR-like transporters in Chlamydomonas, we show that MRS4 is a homolog of MGT10, that is required for photosynthesis and cell growth. Taken together, our findings reveal that the studied Mg2+ transporters play essential but differential roles in maintaining chloroplast Mg2+ homeostasis

The Elbow-EpiTrainer : A method of delivering graded resistance to the extensor carpi radialis brevis. Effectiveness of a prototype device in a healthy population

This document is the Accepted Manuscript version of the following article: Navsaria R, Ryder DM, Lewis JS, et al, 'The Elbow-EpiTrainer: a method of delivering graded resistance to the extensor carpi radialis brevi:. Effectiveness of a prototype device in a healthy population', British Journal of Sports Medicine, Vol. 49(5):318-322, March 2015, available online at: http://bjsm.bmj.com/content/49/5/318. Published by the BMJ Publishing Group Limited.Background: Tennis elbow or lateral epicondylopathy (LE) is experienced as the lateral elbow has a reported prevalence of 1.3%, with symptoms lasting up to 18 months. LE is most commonly attributed to tendinopathy involving the extensor carpi radialis brevis (ECRB) tendon. The aim of tendinopathy management is to alleviate symptoms and restore function that initially involves relative rest followed by progressive therapeutic exercise. Objective: To assess the effectiveness of two prototype exercises using commonly available clinical equipment to progressively increase resistance and activity of the ECRB. Method: Eighteen healthy participants undertook two exercise progressions. Surface electromyography was used to record ECRB activity during the two progressions, involving eccentric exercises of the wrist extensors and elbow pronation exercises using a prototype device. The two progressions were assessed for their linearity of progression using repeated ANOVA and linear regression analysis. Five participants repeated the study to assess reliability. Results: The exercise progressions led to an increase in ECRB electromyographic (EMG) activity (p0.7) between the first and second tests for five participants. Conclusions: Manipulation of resistance and leverage with the prototype exercises was effective in creating significant increases of ECRB normalised EMG activity in a linear manner that may, with future research, become useful to clinicians treating LE. In addition, between trial reliability for the device to generate a consistent load was acceptable.Peer reviewe

Coping strategies and health-related quality of life in children and adolescents with type 1 diabetes

The aim of this study was to identify relationships between coping strategies and different aspects of health-related quality of life in children with type 1 diabetes measured with the Croatian translation of the PedsQL 4.0 Generic Core Scales and PedsQL Diabetes Module. The sample consisted of 199 schoolchildren: 47 patients with type 1 diabetes and 152 healthy children. Children health problems were rated with PedsQL 4.0 Generic Core Scale and with PedsQL Diabetes Module. Coping strategies were measured with The Coping Strategies Inventory for Children and Adolescents. The results showed that all subscales of the PedsQL 4.0 Generic Core Scales and the PedsQL Diabetes Module have satisfactory reliability with the majority of scales exceeding a Cronbach α of 0,70. Significant correlations were found between coping strategies and different aspects of health-related quality of life and those correlations were higher in girls than in boys. The findings of the present study suggest that child psychologists and clinicians treating children and adolescents suffering diabetes should address coping strategies related to specific health-related problems and assist them in developing more effective ways of coping

First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses

The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus (TBEV). We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses about the ecological conditions that could account for the observed recombination

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Seagrasses colonized the sea(1) on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet(2). Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes(3), genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae(4) and that is important for ion homoeostasis, nutrient uptake and O-2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming(5,6), to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants(7)

Phylogenetic and phyloclimatic inference of the evolution of Potentilleae (Rosaseae)

Polyploidization has occurred many times during the evolution of angiosperms. Allopolyploidization is believed to be the process behind many of these genome duplications, and has resulted in a genetically diverse angiosperm flora. I have investigated the patterns of allopolyploidization in the tribe Potentilleae (Rosaceae), where many species have been proposed to have an allopolyploid origin. I have assessed the extent of allopolyploization in the group, with special emphasis on genus Potentilla, by comparing a topology based on nuclear data to one based on plastid data. This led to the identification of several incongruences that supports the notion of a reticulated evolution of the group. However, this has to be confirmed as not all incongruences identified with this method have to be the result of hybridization. Instead, further phylogenetic inference of relationships among the proposed allopolyploid species has to utilise low-copy nuclear genes. For future prospects, I have therefore evaluated Temperature Gradient Gel Electrophoresis (TGGE) for separating paralogues of low-copy nuclear genes. The method was found to require fewer PCR and sequencing reactions, compared to bacterial subcloning, a method routinely used to separate heterogeneous DNA samples. TGGE was therefore found it to be an efficient and applicable method for separating gene copies for phylogenetic investigations of allopolyploid species. The work presented in this thesis has also provided new insights into the evolution of Potentilleae. The phylogenetic analysis show that the ivesioid Potentilleae, a morphologically aberrant and diverse group comprising the three North American genera Ivesia, Horkelia and Horkeliella, form a well-supported clade nested within the Potentilla clade. Furthermore, a dated phylogeny of the family Rosaceae finds this clade to have originated approximately 25 Ma, a time when climate change is believed to have reshaped the flora of western North America. The analysis using phyloclimatic modeling of the evolution of the group reveals a close connection to climate change. The results indicate Great Basin as the area of origin and a westward range expansion to Sierra Nevada during Miocene. Several lineages were found to have crossed the mountain range after a Mediterranean type of climate had established in California. The analysis of microsatellite and AFLP data propose that climate change also have influenced the genetic diversity in Arctic populations. Geographical patterns of this diversity corroborate the hypothesis that Beringia served as a refugium for plants during the Wisconsinan glaciation. Evidence of additional refugia on Banks, Prince Patrick and Melville Islands was also found and further supported by geological data on ice expansion at the last glacial maximum. From the results of the investigations conducted during my thesis work I therefore conclude that allopolyploidization and climate change have had a great influence on the evolution of Potentilleae

Tic20 phylogenetic tree (pdf)

<p>Tic20 phylogeny.</p