Convergent biochemical pathways for xanthine alkaloid production in plants evolved from ancestral enzymes with different catalytic properties

Convergent evolution is widespread but the extent to which common ancestral conditions are necessary to facilitate the independent acquisition of similar traits remains unclear. In order to better understand how ancestral biosynthetic catalytic capabilities might lead to convergent evolution of similar modern-day biochemical pathways, we resurrected ancient enzymes of the caffeine synthase (CS) methyltransferases that are responsible for theobromine and caffeine production in flowering plants. Ancestral CS enzymes of Theobroma, Paullinia, and Camellia exhibited similar substrate preferences but these resulted in the formation of different sets of products. From these ancestral enzymes, descendants with similar substrate preference and product formation independently evolved after gene duplication events in Theobroma and Paullinia. Thus, it appears that the convergent modern-day pathways likely originated from ancestral pathways with different inferred flux. Subsequently, the modern-day enzymes originated independently via gene duplication and their convergent catalytic characteristics evolved to partition the multiple ancestral activities by different mutations that occurred in homologous regions of the ancestral proteins. These results show that even when modern-day pathways and recruited genes are similar, the antecedent conditions may be distinctive such that different evolutionary steps are required to generate convergence

The whole and its parts : why and how to disentangle plant communities and synusiae in vegetation classification

Most plant communities consist of different structural and ecological subsets, ranging from cryptogams to different tree layers. The completeness and approach with which these subsets are sampled have implications for vegetation classification. Non‐vascular plants are often omitted or sometimes treated separately, referring to their assemblages as “synusiae” (e.g. epiphytes on bark, saxicolous species on rocks). The distinction of complete plant communities (phytocoenoses or holocoenoses) from their parts (synusiae or merocoenoses) is crucial to avoid logical problems and inconsistencies of the resulting classification systems. We here describe theoretical differences between the phytocoenosis as a whole and its parts, and outline consequences of this distinction for practise and terminology in vegetation classification. To implement a clearer separation, we call for modifications of the International Code of Phytosociological Nomenclature and the EuroVegChecklist. We believe that these steps will make vegetation classification systems better applicable and raise the recognition of the importance of non‐vascular plants in the vegetation as well as their interplay with vascular plants

Factors influencing epiphytic bryophyte and lichen species richness at different spatial scales in managed temperate forests

The effect of management related factors on species richness of epiphytic bryophytes and lichens was studied in managed deciduous-coniferous mixed forests in Western-Hungary. At the stand level, the potential explanatory variables were tree species composition, stand structure, microclimate and light conditions, landscape and historical variables; while at tree level host tree species, tree size and light were studied. Species richness of the two epiphyte groups was positively correlated. Both for lichen and bryophyte plot level richness, the composition and diversity of tree species and the abundance of shrub layer were the most influential positive factors. Besides, for bryophytes the presence of large trees, while for lichens amount and heterogeneity of light were important. Tree level richness was mainly determined by host tree species for both groups. For bryophytes oaks, while for lichens oaks and hornbeam turned out the most favourable hosts. Tree size generally increased tree level species richness, except on pine for bryophytes and on hornbeam for lichens. The key variables for epiphytic diversity of the region were directly influenced by recent forest management; historical and landscape variables were not influential. Forest management oriented to the conservation of epiphyte s should focus on: (i) the maintenance of tree species diversity in mixed stands; (ii) increment the proportion of deciduous trees (mainly oaks); (iii) conserving large trees within the stands; (iv) providing the presence of shrub and regeneration layer; (v) creating heterogeneous light conditions. For these purposes tree selection and selective cutting management seem more appropriate than shelterwood system

Validation, Deployment, and Real-World Implementation of a Modular Toolbox for Alzheimer’s Disease Detection and Dementia Risk Reduction: The AD-RIDDLE Project

The Real-World Implementation, Deployment, and Validation of Early Detection Tools and Lifestyle Enhancement (AD-RIDDLE) project, recently launched with the support of the EU Innovative Health Initiative (IHI) public-private partnership and UK Research and Innovation (UKRI), aims to develop, test, and deploy a modular toolbox platform that can reduce existing barriers to the timely detection, and therapeutic approaches in Alzheimer’s disease (AD), thus accelerating AD innovation. By focusing on health system and health worker practices, AD-RIDDLE seeks to improve and smooth AD management at and between each key step of the clinical pathway and across the disease continuum, from at-risk asymptomatic stages to early symptomatic ones. This includes innovation and improvement in AD awareness, risk reduction and prevention, detection, diagnosis, and intervention. The 24 partners in the AD-RIDDLE interdisciplinary consortium will develop and test the AD-RIDDLE toolbox platform and its components individually and in combination in six European countries. Expected results from this cross-sectoral research collaboration include tools for earlier detection and accurate diagnosis; validated, novel digital cognitive and blood-based biomarkers; and improved access to individualized preventative interventions (including multimodal interventions and symptomatic/disease-modifying therapies) across diverse populations, within the framework of precision medicine. Overall, AD-RIDDLE toolbox platform will advance management of AD, improving outcomes for patients and their families, and reducing costs

First Results from HERA Phase I: Upper Limits on the Epoch of Reionization 21 cm Power Spectrum

We report upper limits on the Epoch of Reionization 21 cm power spectrum at redshifts 7.9 and 10.4 with 18 nights of data (∼36 hr of integration) from Phase I of the Hydrogen Epoch of Reionization Array (HERA). The Phase I data show evidence for systematics that can be largely suppressed with systematic models down to a dynamic range of ∼109 with respect to the peak foreground power. This yields a 95% confidence upper limit on the 21 cm power spectrum of 212≤(30.76)2mK2 at k = 0.192 h Mpc-1 at z = 7.9, and also 212≤(95.74)2mK2 at k = 0.256 h Mpc-1 at z = 10.4. At z = 7.9, these limits are the most sensitive to date by over an order of magnitude. While we find evidence for residual systematics at low line-of-sight Fourier k π modes, at high k π modes we find our data to be largely consistent with thermal noise, an indicator that the system could benefit from deeper integrations. The observed systematics could be due to radio frequency interference, cable subreflections, or residual instrumental cross-coupling, and warrant further study. This analysis emphasizes algorithms that have minimal inherent signal loss, although we do perform a careful accounting in a companion paper of the small forms of loss or bias associated with the pipeline. Overall, these results are a promising first step in the development of a tuned, instrument-specific analysis pipeline for HERA, particularly as Phase II construction is completed en route to reaching the full sensitivity of the experiment

OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs

<p>Abstract</p> <p>Background</p> <p>The ancestry of mitochondria and chloroplasts traces back to separate endosymbioses of once free-living bacteria. The highly reduced genomes of these two organelles therefore contain very distant homologs that only recently have been shown to recombine inside the mitochondrial genome. Detection of gene conversion between mitochondrial and chloroplast homologs was previously impossible due to the lack of suitable computer programs. Recently, I developed a novel method and have, for the first time, discovered recurrent gene conversion between chloroplast mitochondrial genes. The method will further our understanding of plant organellar genome evolution and help identify and remove gene regions with incongruent phylogenetic signals for several genes widely used in plant systematics. Here, I implement such a method that is available in a user friendly web interface.</p> <p>Results</p> <p><monospace>OrgConv</monospace> (<b>Org</b>anellar <b>Conv</b>ersion) is a computer package developed for detection of gene conversion between mitochondrial and chloroplast homologous genes. <monospace>OrgConv</monospace> is available in two forms; source code can be installed and run on a Linux platform and a web interface is available on multiple operating systems. The input files of the feature program are two multiple sequence alignments from different organellar compartments in FASTA format. The program compares every examined sequence against the consensus sequence of each sequence alignment rather than exhaustively examining every possible combination. Making use of consensus sequences significantly reduces the number of comparisons and therefore reduces overall computational time, which allows for analysis of very large datasets. Most importantly, with the significantly reduced number of comparisons, the statistical power remains high in the face of correction for multiple tests.</p> <p>Conclusions</p> <p>Both the source code and the web interface of <monospace>OrgConv</monospace> are available for free from the <monospace>OrgConv</monospace> website <url>http://www.indiana.edu/~orgconv</url>. Although <monospace>OrgConv</monospace> has been developed with main focus on detection of gene conversion between mitochondrial and chloroplast genes, it may also be used for detection of gene conversion between any two distinct groups of homologous sequences.</p

Identification and Characterization of RcMADS1, an AGL24 Ortholog from the Holoparasitic Plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae)

10.1371/journal.pone.0067243PLoS ONE86-POLN

On plexus representation of dissimilarities

Correspondence analysis has found widespread application in analysing vegetation gradients. However, it is not clear how it is robust to situations where structures other than a simple gradient exist. The introduction of instrumental variables in canonical correspondence analysis does not avoid these difficulties. In this paper I propose to examine some simple methods based on the notion of the plexus (sensu McIntosh) where graphs or networks are used to display some of the structure of the data so that an informed choice of models is possible. I showthat two different classes of plexus model are available. These classes are distinguished by the use in one case of a global Euclidean model to obtain well-separated pair decomposition (WSPD) of a set of points which implicitly involves all dissimilarities, while in the other a Riemannian view is taken and emphasis is placed locally, i.e., on small dissimilarities. I showan example of each of these classes applied to vegetation data

Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147147/1/tax25065680.pd

Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets

<p>Abstract</p> <p>Background</p> <p>In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters.</p> <p>To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations.</p> <p>Results</p> <p>Based on our simulation study we suggest that the editing ‘noise’ in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (<it>rps3</it>, <it>matR</it> and <it>atp1</it>) no differences in the comparison between inferred genomic and cDNA topologies could be detected.</p> <p>Conclusions</p> <p>Our findings by the here reported <it>in silico</it> and <it>in vivo</it> computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0%) and reduced in length (shorter than 500 bp).</p> <p>In the current lack of direct experimental evidence the results presented here encourage, thus, the use of genomic mitochondrial rather than cDNA sequences for reconstructing phylogenetic events in land plants.</p