Phylogenetic signal in growth and reproductive traits and in their plasticity: the D escurainia radiation in the C anary I slands

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106137/1/boj12139.pd

Genome size and phenotypic variation of Nymphaea (Nymphaeaceae) species from Eastern Europe and temperate Asia

Despite long-term research, the aquatic genus Nymphaea still possesses major taxonomic challenges. High phenotypic plasticity and possible interspecific hybridization often make it impossible to identify individual specimens. The main aim of this study was to assess phenotypic variation in Nymphaea taxa sampled over a wide area of Eastern Europe and temperate Asia. Samples were identified based on species-specific genome sizes and diagnostic morphological characters for each taxon were then selected. A total of 353 specimens from 32 populations in Poland, Russia and Ukraine were studied, with nine biometric traits being examined. Although some specimens morphologically matched N. ×borealis (a hybrid between N. alba and N. candida) according to published determination keys, only one hybrid individual was revealed based on genome size data. Other specimens with intermediate morphology possessed genome size corresponding to N. alba, N. candida or N. tetragona. This indicates that natural hybridization between N. alba and N. candida is not as frequent as previously suggested. Our results also revealed a considerably higher variation in the studied morphological traits (especially the quantitative ones) in N. alba and N. candida than reported in the literature. A determination key for the investigated Nymphaea species is provided, based on taxonomically-informative morphological characters identified in our study

MizAR 60 for Mizar 50

As a present to Mizar on its 50th anniversary, we develop an AI/TP system that automatically proves about 60% of the Mizar theorems in the hammer setting. We also automatically prove 75% of the Mizar theorems when the automated provers are helped by using only the premises used in the human-written Mizar proofs. We describe the methods and large-scale experiments leading to these results. This includes in particular the E and Vampire provers, their ENIGMA and Deepire learning modifications, a number of learning-based premise selection methods, and the incremental loop that interleaves growing a corpus of millions of ATP proofs with training increasingly strong AI/TP systems on them. We also present a selection of Mizar problems that were proved automatically

Identification of candidates for cyclotide biosynthesis and cyclisation by expressed sequence tag analysis of Oldenlandia affinis

<p>Abstract</p> <p>Background</p> <p>Cyclotides are a family of circular peptides that exhibit a range of biological activities, including anti-bacterial, cytotoxic, anti-HIV activities, and are proposed to function in plant defence. Their high stability has motivated their development as scaffolds for the stabilisation of peptide drugs. <it>Oldenlandia affinis</it> is a member of the Rubiaceae (coffee) family from which 18 cyclotides have been sequenced to date, but the details of their processing from precursor proteins have only begun to be elucidated. To increase the speed at which genes involved in cyclotide biosynthesis and processing are being discovered, an expressed sequence tag (EST) project was initiated to survey the transcript profile of <it>O. affinis</it> and to propose some future directions of research on in vivo protein cyclisation.</p> <p>Results</p> <p>Using flow cytometry the holoploid genome size (1C-value) of <it>O. affinis </it>was estimated to be 4,210 - 4,284 Mbp, one of the largest genomes of the Rubiaceae family. High-quality ESTs were identified, 1,117 in total, from leaf cDNAs and assembled into 502 contigs, comprising 202 consensus sequences and 300 singletons. ESTs encoding the cyclotide precursors for kalata B1 (<it>Oak1</it>) and kalata B2 (<it>Oak4</it>) were among the 20 most abundant ESTs. In total, 31 ESTs encoded cyclotide precursors, representing a distinct commitment of 2.8% of the <it>O. affinis </it>transcriptome to cyclotide biosynthesis. The high expression levels of cyclotide precursor transcripts are consistent with the abundance of mature cyclic peptides in <it>O. affinis</it>. A new cyclotide precursor named <it>Oak5 </it>was isolated and represents the first cDNA for the bracelet class of cyclotides in <it>O. affinis</it>. Clones encoding enzymes potentially involved in processing cyclotides were also identified and include enzymes involved in oxidative folding and proteolytic processing.</p> <p>Conclusion</p> <p>The EST library generated in this study provides a valuable resource for the study of the cyclisation of plant peptides. Further analysis of the candidates for cyclotide processing discovered in this work will increase our understanding and aid in reconstructing cyclotide production using transgenic systems and will benefit their development in pharmaceutical applications and insect-resistant crop plants.</p

Distribution and habitat segregation on different spatial scales among diploid, tetraploid and hexaploid cytotypes of Senecio carniolicus (Asteraceae) in the Eastern Alps

The spatial distribution of cytotypes can provide valuable insights into evolutionary patterns of polyploid complexes. In a previous study the macro-scale distribution of the three main cytotypes in Senecio carniolicus (Asteraceae) within the Eastern Alps was characterized. Employing a roughly 12-fold extended sampling, the present study focuses on unravelling patterns of cytotype distribution on the meso- and microscale and on correlating those with ecological properties of the growing sites. DAPI flow cytometry of dried samples was used to determine DNA ploidy level in 5033 individuals from 100 populations spread over the entire Eastern Alpine distribution area of S. carniolicus. Descriptors of microhabitats as well as spatial data were recorded in the field, and analysed with a mixed-effects ANOVA. Extensive variation in DNA ploidy levels (2x, 3x, 4x, 5x, 6x, 7x, 8x, 9x) was detected. Of the main cytotypes, diploids and hexaploids were widespread and had strongly overlapping distributions resulting in the frequent occurrence of cytotype mixtures (half of the investigated populations), whereas tetraploids were disjunctly distributed and occurred in the south-west and the east of the species' distribution area. In spite of the frequent co-occurrence of cytotypes, only 1 % of the samples belonged to secondary cytotypes (3x, 5x, 7x, 8x, 9x). Diploids, tetraploids and hexaploids were altitudinally segregated, but with broad overlap. Similarly, highly significant differences in vegetation and rock cover as well as microhabitat exposure were found between the main cytotypes. Senecio carniolicus shows a remarkable diversity of cytotypes. The distribution of the three main cytotypes (2x, 4x, 6x) has been shaped by Pleistocene glaciations to different extents. Whereas tetraploids are nearly entirely restricted to refugia, hexaploids colonized areas that were extensively glaciated. Diploid and hexaploid individuals often co-occur in mixed populations, where they are spatially and ecologically segregated at both the meso-scale (altitudinal differentiation, exposure of the growing site) and the micro-scale (cover of vegetation and bare rock). With regard to the ecological parameters investigated, the tetraploid cytotype occupies an intermediate position. The rareness of secondary cytotypes suggests the presence of strong pre- or post-zygotic mating barriers

Antibacterial Bioactive Glass, S53P4, for Chronic Bone Infections - A Multinational Study

Correction: Volume: 971 Pages: 115-116 DOI: 10.1007/5584_2017_13 Published: 2017 WOS:000446017300010Osteomyelitis is an infectious process in bone that occasionally leads to bone destruction. Traditionally, the surgical treatment procedure is performed in combination with systemic and local antibiotics as a two-stage procedure that uses autograft or allograft bone for filling of the cavitary defect. Bioactive glass (BAG-S53P4) is a bone substitute with proven antibacterial and bone bonding properties. One hundred and sixteen patients who had verified chronic osteomyelitis was treated using BAG-S53P4 as part of the treatment. Most of the patients had previously undergone numerous procedures, sometimes for decades. A register of patient data obtained from 11 centers from Finland, Italy, the Netherlands, Germany, Azerbaijan and Poland was set-up and continuously maintained at Helsinki University Central Hospital. The location of the osteomyelitis was mainly in the tibia followed by the femur and then the calcaneus. The median age of the patients was 48 years (15-87). The patients were either treated according to a one-stage procedure without local antibiotics (85 %) or by a two-stage procedure using antibiotic beads in the first procedure (15 %). The minimum follow-up was 1 year (12-95 months, median 31). The cure rate was 104/116, the total success rate 90 % and most of the patients showed a rapid recovery. The study shows that (BAG-S53P4) can be used in a one-stage procedure in treatment of osteomyelitis with excellent results.Peer reviewe

The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat "communities" are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat "community" composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat "communities".JP was supported by a Ramón y Cajal Fellowship (RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SB was funded by a Garfield Weston Foundation postdoctoral fellowship. PN and JM were supported by the ELIXIR CZ Research Infrastructure Project (Czech Ministry of Education, Youth and Sports; grant no. LM2018131).IntroductionMaterials and Methods Plant material collection and genome size measurement Phylogenetic, environmental and genomic data collection Modelling relationships between genome size and environmental variables DNA repeat profiling Assessing repeat dynamics in palm genomesResults Palm genome size variation Aridity preferences of palm species help explain genome size variation Ecological metrics of palm repeat ‘communities’ vary with genome size Repeat abundances correlate with genome size Aridity preferences of palm species explain abundances of certain repeat lineagesDiscussion Palm genome size variation Aridity thresholds best explain palm genome size diversity The ‘community ecology’ of repeats correlates with genome size Repeat dynamics may be modulated by aridityConclusionsAcknowledgementsAuthor contributionsPeer reviewe