On the phylogenetic position of the genus Claopodium: a revival of a 19th century idea

Molecular phylogenetic analysis of nuclear ITS and plastid rps4–trnS found species of the genus Claopodium in the clade formed by species of Brachytheciaceae and Meteoriaceae, including Trachypodaceae. Claopodium is resolved as sister to Brachytheciaceae, thus we suggest its placement in this family, despite it will be the only taxon of the family with pluripapillose laminal cells. The taxonomic value of the papillose leaf cells in pleurocarpous mosses is discussed.</p

Alleniella aegaea Blockeel & Hugonnot (Neckeraceae), a new moss species from the Aegean islands of Greece

A new moss species, Alleniella aegaea (Neckeraceae) is described and illustrated from the Greek islands of Crete, Samos and Evvia based on morphological and molecular evidence. According to phylogenetic analysis of nuclear ITS and plastid trnS-F sequences it is sister to A. complanata, which it also morphologically resembles, but it differs from that species e.g. in its distinctly flattened habit, lack of caducous branchlets, more rounded leaf apices, and shorter median laminal cells. Alleniella aegaea is dioicous and the sporophytes remain unknow

What is Atraphaxis L. (Polygonaceae, Polygoneae): cryptic taxa and resolved taxonomic complexity instead of the formal lumping and the lack of morphological synapomorphies

Background: The recently proposed recircumscription of the genus Atraphaxis (incl. Atraphaxis section Ovczinnikovia O.V. Yurtseva ex. S. Tavakkoli and Polygonum sect. Spinescentia Boissier (=A. sect. Polygonoides S. Tavakkoli, Kaz. Osaloo & Mozaff.) makes this genus fairly heterogeneous and therefore almost undefinable based on morphology. A critical comprehensive reappraisal of the group is necessary. Methods: Using the DNA sequence data (ITS1&2 regions of nrDNA and combined trnL intron + trnL–F IGS and rpl32–trnL(UAG) IGS regions of plastid genome), Maximum Likelihood (ML) and Bayesian analyses (BI) were applied for phylogenetic reconstructions of the tribe Polygoneae with special attention to Atraphaxis, and related taxa. Maximum parsimony reconstructions of the evolution of perianth morphology and sporoderm ornamentation in the tribe Polygoneae were also performed. Life history, morphology of shoots, leaf blades, ocreas, perianth and achene morphology, ultrasculpture of achene surface, and pollen morphology were compared, and SEM and LM images were provided. Principal findings: The genera Atraphaxis and Polygonum were found to be widely polyphyletic. The rarest and morphologically remarkable endemic of Tian-Shan and Pamir Atraphaxis ovczinnikovii (Atraphaxis sect. Ovczinnikovia O.V. Yurtseva ex. S. Tavakkoli) was confirmed to be a sister of the clade (Atraphaxis + Polygonum sect. Spinescentia) in plastid topology. The genus Bactria (=Atraphaxis sect. Ovczinnikovia), which circumscribes two species, is newly established as a result of this analyses. Morphological data confirm the originality of the taxon. Discussion: We are arguing for a narrow delimitation of Atraphaxis with petalloid segments and striato-perforate sporoderm ornamentation as morphological synapomorphies. The recently proposed inclusion of Polygonum sect. Spinescentia in Atraphaxis is fairly questionable from a morphological standpoint. The rank of Polygonum sect. Spinescentia requires further clarification. The generic composition of the tribe Polygoneae also requires future reappraisals

On moss genera Hylocomiadelphus Ochyra & Stebel and Rhytidiadelphus (Limpr.) Warnst.

The moss family Hylocomiaceae is studied for the generic level taxonomy within a molecular phylogenetic approach. We confirm segregating of the species formerly known as Rhytidiadelphus triquetrus to Hylocomiadelphus Ochyra & Stebel from the genus Rhytidiadelphus. Hylocomiadelphus forms a clade with Loeskeobryum and Meteoriella, sharing with both genera cordate to auriculate leaf bases and non-squarrose leaves, and with the former undulate leaves and reticulate exostome teeth ornamentation. However, Loeskeobryum differs from Hylocomiadelphus in having paraphyllia, while Meteoriella has a straight capsule and reduced peristome, likely caused by its epiphytic ecology. In the group of species closely related to R. squarrosus, in addition to R. subpinnatus, the third species with North Pacific distribution is described as R. pacificum. Macrothamnium is found deeply nested in Rhytidiadelphus, although no nomenclatural implications are suggested at the moment due to insufficient sampling. Hylocomium splendens var. splendens and var. obtusifolium were found intermingled in the phylogenetic tree, indicating no correlation between morphology and variation in ITS region, thus supporting a view that these taxa are merely environmentally induced morphs

Alleniella aegaea Blockeel & Hugonnot (Neckeraceae), a New Moss Species from the Aegean Islands of Greece

A new moss species, Alleniella aegaea (Neckeraceae) is described and illustrated from the Greek islands of Crete, Samos and Evvia based on morphological and molecular evidence. According to phylogenetic analysis of nuclear ITS and plastid trnS-F sequences it is sister to A. complanata, which it also morphologically resembles, but it differs from that species e.g. in its distinctly flattened habit, lack of caducous branchlets, more rounded leaf apices, and shorter median laminal cells. Alleniella aegaea is dioicous and the sporophytes remain unknown

Complete mitochondrial genome sequence of the “copper moss” Mielichhoferia elongata reveals independent nad7 gene functionality loss

The mitochondrial genome of moss Mielichhoferia elongata has been sequenced and assembled with Spades genome assembler. It consists of 100,342 base pairs and has practically the same gene set and order as in other known bryophyte chondriomes. The genome contains 66 genes including three rRNAs, 24 tRNAs, and 40 conserved mitochondrial proteins genes. Unlike the majority of previously sequenced bryophyte mitogenomes, it lacks the functional nad7 gene. The phylogenetic reconstruction and scrutiny analysis of the primary structure of nad7 gene carried out in this study suggest its independent pseudogenization in different bryophyte lineages. Evaluation of the microsatellite (simple sequence repeat) content of the M. elongata mitochondrial genome indicates that it could be used as a tool in further studies as a phylogenetic marker. The strongly supported phylogenetic tree presented here, derived from 33 protein coding sequences of 40 bryophyte species, is consistent with other reconstructions based on a number of different data sets

The Mitochondrial Genome of Nematodontous Moss Polytrichum commune and Analysis of Intergenic Repeats Distribution Among Bryophyta

An early-branched moss Polytrichum commune is a widely accepted model object for ecological, environmental, physiological, and genetic studies. Its mitochondrial genome has been sequenced and annotated. The genome contains 67 genes in total and has a length equal to 114,831 bp, which exceeds the length of most known mitochondrial genomes for mosses. A phylogenetic tree based on 33 coding sequences of mitochondrial genome was constructed, and the pairwise identity of whole mitogenome sequences was estimated for 44 Bryophyta species. Based on the analysis of pairwise identity, it was shown that mitogenomes of Tetraphis pellucida and Buxbaumia aphylla sufficiently differ from those of other Bryophyta species. The first known Bryophyta mitogenome rearrangement was identified in Pogonatum inflexum within Polytrichopsida. Based on the intergenic repeats occurrence in 44 bryophyte mitochondrial genomes and available data on repetitive elements content in other Viridiplantae groups, it was noted for the first time that greater stability of the moss’s mitogenomes is probably associated mainly with the absence of long (&gt;1 kb) repeats. The phenomenon of absence of the intergenic repetitive elements in the terminal clades species was discovered

Applying of Hierarchical Clustering to Analysis of Protein Patterns in the Human Cancer-Associated Liver

<div><p>Background</p><p>There are two ways that statistical methods can learn from biomedical data. One way is to learn classifiers to identify diseases and to predict outcomes using the training dataset with established diagnosis for each sample. When the training dataset is not available the task can be to mine for presence of meaningful groups (clusters) of samples and to explore underlying data structure (unsupervised learning).</p><p>Results</p><p>We investigated the proteomic profiles of the cytosolic fraction of human liver samples using two-dimensional electrophoresis (2DE). Samples were resected upon surgical treatment of hepatic metastases in colorectal cancer. Unsupervised hierarchical clustering of 2DE gel images (n = 18) revealed a pair of clusters, containing 11 and 7 samples. Previously we used the same specimens to measure biochemical profiles based on cytochrome P450-dependent enzymatic activities and also found that samples were clearly divided into two well-separated groups by cluster analysis. It turned out that groups by enzyme activity almost perfectly match to the groups identified from proteomic data. Of the 271 reproducible spots on our 2DE gels, we selected 15 to distinguish the human liver cytosolic clusters. Using MALDI-TOF peptide mass fingerprinting, we identified 12 proteins for the selected spots, including known cancer-associated species.</p><p>Conclusions/Significance</p><p>Our results highlight the importance of hierarchical cluster analysis of proteomic data, and showed concordance between results of biochemical and proteomic approaches. Grouping of the human liver samples and/or patients into differing clusters may provide insights into possible molecular mechanism of drug metabolism and creates a rationale for personalized treatment.</p></div

The number of protein spots after manual processing of 19 2DE gel images for the human liver cytosol using the proprietary GelEditor software.

<p>Gels belonging to cluster 1 are shown in white columns. Gels belonging to cluster 2 are shown in gray columns. Gel which removed from all subsequent data processing is shown in the shaded column.</p

Hierarchical clustering applied to 2DE gel images of the human liver cytosol (a) and cytochrome P450 enzymes activities (mol/min/nmol P450) of the human liver microsomes (b).

<p>Two major clusters can be seen.</p