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Background: Riccia fluitans, an amphibious liverwort, exhibits a fascinating adaptation mechanism to transition between terrestrial and aquatic environments. Utilizing nanopore direct RNA sequencing, we try to capture the complex epitranscriptomic changes undergone in response to land-water transition. Results: A significant finding is the identification of 45 differentially expressed genes (DEGs), with a split of 33 downregulated in terrestrial forms and 12 upregulated in aquatic forms, indicating a robust transcriptional response to environmental changes. Analysis of N6-methyladenosine (m6A) modifications revealed 173 m6A sites in aquatic and only 27 sites in the terrestrial forms, indicating a significant increase in methylation in the former, which could facilitate rapid adaptation to changing environments. The aquatic form showed a global elongation bias in poly(A) tails, which is associated with increased mRNA stability and efficient translation, enhancing the plant's resilience to water stress. Significant differences in polyadenylation signals were observed between the two forms, with nine transcripts showing notable changes in tail length, suggesting an adaptive mechanism to modulate mRNA stability and translational efficiency in response to environmental conditions. This differential methylation and polyadenylation underline a sophisticated layer of post-transcriptional regulation, enabling Riccia fluitans to fine-tune gene expression in response to its living conditions. Conclusions: These insights into transcriptome dynamics offer a deeper understanding of plant adaptation strategies at the molecular level, contributing to the broader knowledge of plant biology and evolution. These findings underscore the sophisticated post-transcriptional regulatory strategies Riccia fluitans employs to navigate the challenges of aquatic versus terrestrial living, highlighting the plant's dynamic adaptation to environmental stresses and its utility as a model for studying adaptation mechanisms in amphibious plants. [ABSTRACT FROM AUTHOR]

Orthotrichum camanchacanum is presented as a newly described species from Chile. The species is primarily distinguished by its emergent capsule with cryptoporous stomata, a double peristome, linear-lanceolate stem leaves with a long hyaline aristae in apex, conspicuously differentiated perichaetial leaves, and a densely hairy vaginula. The species was discovered in the mountain massif of the Andes in the Coquimbo region, notable for its unique climatic conditions. Molecular data and a brief discussion comparing the newly described species with the most closely related taxa are also provided. [ABSTRACT FROM AUTHOR]

In this comprehensive review, we explore the significant role that nanopore sequencing technology plays in the study of plant organellar genomes, particularly mitochondrial and chloroplast DNA. To date, the application of nanopore sequencing has led to the successful sequencing of over 100 plant mitochondrial genomes and around 80 chloroplast genomes. These figures not only demonstrate the technology's robustness but also mark a substantial advancement in the field, highlighting its efficacy in decoding the complex and dynamic nature of these genomes. Nanopore sequencing, known for its long-read capabilities, significantly surpasses traditional sequencing techniques, especially in addressing challenges like structural complexity and sequence repetitiveness in organellar DNA. This review delves into the nuances of nanopore sequencing, elaborating on its benefits compared to conventional methods and the groundbreaking applications it has fostered in plant organellar genomics. While its transformative impact is clear, the technology's limitations, including error rates and computational requirements, are discussed, alongside potential solutions and prospects for technological refinement. [ABSTRACT FROM AUTHOR]

The mitogenome of theOrthotrichum rogeri(GenBank accession number KM873610) has a total length of 106,634 bp and consist of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA. The gene order is identical to other known moss mitogenomes. A complete mitochondrial genome sequence ofO. rogeriwill help the development of primers for examining mitochondrial variation across bryophytes. [ABSTRACT FROM AUTHOR]

The mitogenome ofNiphotrichum ericoides(GenBank accession number KP 233863) has a total length of 106,727 bp and consists of 40 protein-coding genes, three ribosomal RNAs (rRNAs), and 24 transfer RNAs. The gene order is identical to that known in other moss mitogenomes. [ABSTRACT FROM AUTHOR]

The mitogenome of theCodriophorus laevigatus(GenBank accesion number KM506905) has a total length of 106,809 bp and consist of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA. The gene order is identical to other known moss mitogenomes. [ABSTRACT FROM PUBLISHER]

The mitogenome of theOrthotrichum speciousum(GenBank accession number KM288416) has a total length of 104,747 bp and consist of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA. The gene order is identical to other known moss mitogenomes. [ABSTRACT FROM PUBLISHER]

Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts—109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes. [ABSTRACT FROM AUTHOR]

Pulsatilla patens is a rare and endangered species in Europe and its population resources have significantly decreased over the past decades. Previous genetic studies of this species made it possible to estimate the genetic diversity of the European population and to describe the structure of chloroplast and mitochondrial genomes. The main aim of these studies was to characterize the variability of chloroplast and mitochondrial genomes in more detail at the intra-population and inter-population levels. Our study presents new organelle genome reference sequences that allow the design of novel markers that can be the starting point for testing hypotheses, past and modern biogeography of rare and endangered species P. patens, and adaptive responses of this species to changing environments. The study included sixteen individuals from five populations located in Northeastern Poland. Comparative analysis of 16 P. patens plastomes from 5 populations enabled us to identify 160 point mutations, including 64 substitutions and 96 InDels. The most numerous detected SNPs and Indels (75%) were accumulated in three intergenic spacers: ndhD—ccsA, rps4—rps16, and trnL(UAG)—ndhF. The mitogenome dataset, which was more than twice as large as the plastome (331 kbp vs. 151 kbp), revealed eight times fewer SNPs (8 vs. 64) and six times fewer InDels (16 vs. 96). Both chloroplast and mitochondrial genome identified the same number of haplotypes—11 out of 16 individuals, but both organellar genomes slightly differ in haplotype clustering. Despite the much lower variation, mitogenomic data provide additional resolution in the haplotype detection of P. patens, enabling molecular identification of individuals, which were unrecognizable based on the plastome dataset. [ABSTRACT FROM AUTHOR]

Background: The mitogenomes of vascular plants are one of the most structurally diverse molecules. In the present study we characterize mitogenomes of a rare and endangered species Pulsatilla patens. We investigated the gene content and its RNA editing potential, repeats distribution and plastid derived sequences. Results: The mitogenome structure of early divergent eudicot, endangered Pulsatilla patens does not support the master chromosome hypothesis, revealing the presence of three linear chromosomes of total length 986 613 bp. The molecules are shaped by the presence of extremely long, exceeding 87 kbp repeats and multiple chloroplast-derived regions including nearly complete inverted repeat. Since the plastid IR content of Ranunculales is very characteristic, the incorporation into mitogenome could be explained rather by intracellular transfer than mitochondrial HGT. The mitogenome contains almost a complete set of genes known from other vascular plants with exception of rps10 and sdh3, the latter being present but pseudogenized. Analysis of long ORFs enabled the identification of genes which are rarely present in plant mitogenomes, including RNA and DNA polymerases, albeit their presence even at species level is variable. Mitochondrial transcripts of P. patens were edited with a high frequency, which exceeded the level known in other analyzed angiosperms, despite the strict qualification criteria of counting the editing events and taking into analysis generally less frequently edited leaf transcriptome. The total number of edited sites was 902 and nad4 was identified as the most heavily edited gene with 65 C to U changes. Non-canonical, reverse U to C editing was not detected. Comparative analysis of mitochondrial genes of three Pulsatilla species revealed a level of variation comparable to chloroplast CDS dataset and much higher infrageneric differentiation than in other known angiosperm genera. The variation found in CDS of mitochondrial genes is comparable to values found among Pulsatilla plastomes. Despite the complicated mitogenome structure, 14 single copy regions of 329 kbp, not splitted by repeats or plastid-derived sequences (MTPT), revealed the potential for phylogenetic, phylogeographic and population genetics studies by revealing intra- and interspecific collinearity. Conclusions: This study provides valuable new information about mitochondrial genome of early divergent eudicots, Pulsatilla patens, revealed multi-chromosomal structure and shed new light on mitogenomics of early eudicots. [ABSTRACT FROM AUTHOR]

The study focused on the verification of the preferential site-specific concept hypothesizing, that mineral elements could be playing an initiating role in the biological speciation within Aneura pinguis cryptic species. A. pinguis species A and soil materials were collected from three ecological sites of Poland. They underwent genetic (Aneura pinguis) and chemical analyses (soil materials) for pH, total and water soluble (active) forms of Ca, Mg, K, Na fractions. Data revealed trends in the site preference of three genetic lineages (A1, A2 and A3) of A. pinguis cryptic species A. Lineage adaptability index Ca/(Mg + K + Na) reflecting the dynamic character of site pH implied, that lineages A1 and A2 were both calciphilous. The A3 lineages were intrinsically acidophilous and this characteristics was also observed at some A1 lineages. Site concentrations of Ca and in some cases Mg too were crucial in shaping pH, but this process could have been controlled by each mineral element, individually. Calciphilous or acidophilous A. pinguis species may be "remotely" attracted by high or low Ca (or Mg) concentrations, for alkalinity or acidity emergence, respectively. Mineral richness at investigated ecological sites has possibly initiated opportunistic and specific site colonisation by A. pinguis lineages. [ABSTRACT FROM AUTHOR]

Background: Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification. Results: On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%. Conclusions: This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data. [ABSTRACT FROM AUTHOR]

Plastomes serve as the main resources in the study of plant phylogeny, phylogeography, and barcode development. To date, only 5 complete plastomes of acrocarpous mosses are known. This study analyzes the complete plastome sequence of 5 mosses from Orthotrichaceae: Nyholmiella obtusifolia (Brid.) Holmen & E. Warncke; Orthotrichum rogeri Brid.; Stoneobryum bunyaense D.H. Norris & H. Rob.; Lewinskya incana F. Lara, Garilleti & Goffinet; and Ulota bruchii Hornsch. The plastomes of all studied species are similar in length (ca. 123 kbp) and have a quadripartite structure with 118 unique genes. A total of 278 simple sequence repeats were found, and the mononucleotide repeats were the most abundant. Dinucleotide, trinucleotide, and tetranucleotide repeats were also observed. Tandem repeats were observed in all studied genomes in similar amounts. A total of 6331 single nucleotide polymorphisms and 779 indels were found in the analyzed genomes. The most variable spacer was located between rpl14 and rps8 (π = 0.366), and matK (π = 0.046) was the most variable of the genes. Phylogenetic reconstruction based on protein coding sequences confirmed the recent division of the tribe. [ABSTRACT FROM AUTHOR]

Oil bodies are the unique feature of most liverworts. Their shape, color and distribution pattern in leaf and underleaf cells are important taxonomic features of the genus Calypogeia. Most species of the genus Calypogeia have pellucid and colorless oil bodies, whereas colored, including gray to pale brown, purple-brown or blue oil bodies, are rare. To date, C. azurea was the only species with blue oil bodies to have been considered as a species of the Holarctic range. This species has been noted in various parts of the northern hemisphere–from North America, through Europe to the Far East. The aim of this study was to determine the genetic diversity of C. azurea from different parts of its distribution range and to ascertain whether blue oil bodies appeared once or several times in the evolution of the genus Calypogeia. The phylogenetic analyses based on four plastid regions (rbcL, trnG, trnL, trnH-psbA) and one nuclear region (ITS2) revealed that C. azurea is presently a paraphyletic taxon, with other Calypogeia species nested among C. azurea accessions that were clustered into four different clades. Based on the level of genetic divergence (1.03–2.17%) and the observed morphological, ecological and geographical differences, the evaluated clades could be regarded as previously unrecognized species. Four species were identified: C. azurea Stotler & Crotz (a European species corresponding to the holotype), two new species from Pacific Asia—C. orientalis Buczkowska & Bakalin and C. sinensis Bakalin & Buczkowska, and a North American species which, due to the lack of identifiable morphological features, must be regarded as the cryptic species of C. azurea with a provisional name of C. azurea species NA. [ABSTRACT FROM AUTHOR]

Liverwort mitogenomes are considered to be evolutionarily stable. A comparative analysis of four Calypogeia species revealed differences compared to previously sequenced liverwort mitogenomes. Such differences involve unexpected structural changes in the two genes, cox1 and atp1, which have lost three and two introns, respectively. The group I introns in the cox1 gene are proposed to have been lost by two-step localized retroprocessing, whereas one-step retroprocessing could be responsible for the disappearance of the group II introns in the atp1 gene. These cases represent the first identified losses of introns in mitogenomes of leafy liverworts (Jungermanniopsida) contrasting the stability of mitochondrial gene order with certain changes in the gene content and intron set in liverworts. [ABSTRACT FROM AUTHOR]

A new species, Bucklandiella seppeltii Bednarek-Ochyra, Ochyra, Sawicki & Szczecińska, is delimited by its distinct morphology and biogeography. The geographical range of the new species is restricted to the southern-temperate and southern-cool-temperate zones of Tasmania and New Zealand, with maximum occurrence on the South Island of the latter insular country. he species is described and illustrated and its distribution is mapped. The systematic position of B. seppeltii is revealed to be a sister to New Zealand B. allanfifei Bednarek-Ochyra & Ochyra by molecular evidence based on parsimony analysis of nuclear sequences. In some morphological and anatomical traits, B. seppeltii is similar to southern South American cool-temperate B. heterostichoides (Cardot) Bednarek-Ochyra & Ochyra but is distinct by its smooth laminal cells, strict hyaline leaf hair points, erect growth form, and very broadly recurved leaf margin in the distal portion. [ABSTRACT FROM AUTHOR]

Background: Diabetes reduces the activity of CYP3A4 and may increase the exposure for the drugs metabolized by the isoenzyme. Sorafenib is a multi-targeted tyrosine kinase inhibitor (TKI), used for the treatment of advanced renal cell carcinoma, hepatocellular carcinoma and radioactive iodine resistant thyroid carcinoma. The TKI undergoes CYP3A4-dependent oxidative transformation, which may be influenced by hyperglycaemia. The aim of the study was to compare the oxidation for sorafenib between healthy and streptozotocin-induced diabetic rats. Additionally, the effect of sorafenib on glucose levels was investigated., Methods: The rats were assigned to the groups: streptozotocin-induced diabetic (DG, n = 8) or healthy (HG, n = 8). The rats received sorafenib orally as a single dose of 100 mg/kg. The plasma concentrations of sorafenib and its metabolite N-oxide were measured with the validated high-performance liquid chromatography with ultraviolet detection., Results: The difference between groups in C max and AUC 0-t values for sorafenib were significant (p = 0.0004, p = 0.0104), and similarly for the metabolite (p = 0.0008, p = 0.0011). Greater exposure for the parent drug and analysed metabolite was achieved in diabetic group. However, the C max , AUC 0-t , and AUC 0-∞ ratios between the metabolite and sorafenib were similar in both groups. The significant reduction of glycaemia was observed only in the diabetic animals., Conclusion: The findings of the study provide evidence that diabetes significantly influence on the exposition for sorafenib and its metabolite, but similar ratios N-oxide/sorafenib for AUC and C max in healthy and diabetic animals suggest that oxidation of the TKI is rather unchanged. Additionally, sorafenib-associated hypoglycaemia was confirmed in diabetic animals.

Elevated homocysteine levels and low vitamin B12 and folate levels have been associated with deteriorated bone health. This systematic literature review with dose-response meta-analyses summarizes the available scientific evidence on associations of vitamin B12, folate, and homocysteine status with fractures and bone mineral density (BMD). Twenty-seven eligible cross-sectional (n = 14) and prospective (n = 13) observational studies and one RCT were identified. Meta-analysis on four prospective studies including 7475 people showed a modest decrease in fracture risk of 4% per 50 pmol/L increase in vitamin B12 levels, which was borderline significant (RR = 0.96, 95% CI = 0.92 to 1.00). Meta-analysis of eight studies including 11511 people showed an increased fracture risk of 4% per μ mol/L increase in homocysteine concentration (RR = 1.04, 95% CI = 1.02 to 1.07). We could not draw a conclusion regarding folate levels and fracture risk, as too few studies investigated this association. Meta-analyses regarding vitamin B12, folate and homocysteine levels, and BMD were possible in female populations only and showed no associations. Results from studies regarding BMD that could not be included in the meta-analyses were not univocal.

Aims: To systematically review the literature on daily losses and bioavailability of vitamin B12. These estimates could be used for deriving recommendations on vitamin B12 intake for adults and elderly., Methods: We identified publications on daily vitamin B12 losses (July 2011) and publications on the bioavailability of vitamin B12 from foods or diets (June 2010) in MEDLINE, EMBASE and the Cochrane Library., Results: A pooled analysis of five studies (52 subjects) showed that 0.13 ± 0.03% of the total body store is lost per day. Absorption of vitamin B12 ranged from 4.5 (dose of 38 µg from consumption of liver) to 83% (dose of 3.0 µg from consumption of mutton meat). Data from eight studies including 83 subjects suggested that the amount of vitamin B12 absorbed from food (Ai) increased with increasing doses of vitamin B12 (Di) as described by the equation: ln(Ai) = 0.7694 * ln(Di) - 0.9614., Conclusion: Daily vitamin B12 losses in apparently healthy adults and elderly probably range from 1.4 to 5.1 µg. Vitamin B12 intakes needed to compensate for these losses seem to range from 3.8 to 20.7 µg. More evidence is needed on the relationships between biochemical markers of vitamin B12 status, vitamin B12 body store and long-term health outcomes to evaluate whether current recommendations on vitamin B12 intake (1.4-3 µg) need to be changed., (Copyright © 2013 S. Karger AG, Basel.)

The aim of the study was to meet the opinions of NHs' residents about the meals quality and nutrition system, with special consideration of meal ambience in canteens (appearance, atmosphere, etc.). Besides, other information about residents was collected: their self-perceived health status, psychical condition, physical activity, appetite and nutritional habits. Most of the subjects were single women, mainly with medium/technical education level, living in NHs over 3 years. Most of the NHs' residents evaluated their health status as average or bad, independently of the age or gender. Every second person indicated that health, loneliness and the feeling of isolation in their homes were the main reasons for coming to NH. Every third person still felt the loneliness or depression after staying in NH. The physical and intellectual activity of elderly depended on self-perceived health status. Over half of the subjects assessed their appetite as good, and said that their body mass was stable during staying in NH. The statistically significant relationship was found between the self-evaluated weight change and both age and gender. Additionally, the relationship was observed between psychical condition of residents and their appetite as also between the psychical condition and weight change during living in NH. The majority of the subjects (85%) said that they liked the canteen appearance, and they did not want to change anything in it. More women than men thought that canteens were spacious, clean and furnished with good taste, and those differences were significant. Part of studied population (25%) had some reservations about the atmosphere in canteen during the meals, mostly because of too much noise. In the opinions of most of the residents (over 80%) the nutrition organisation in NHs was good. Over half of the subjects assessed the meals quality in NHs also as good. Only some comments were about insufficient quantities of fruits and vegetables and meal monotony.