Contributions to the moss families Neckeraceae and Pterobryaceae of Bhutan

Three species previously thought to be Chinese endemics from the easternmost Himalayas are reported from Bhutan: Shevockia inunctocarpa Enroth & M.C. Ji and Taiwanobryum yunnanense (Enroth) Enroth comb. nov. of the Neckeraceae, and Calyptothecium acostatum J.X. Luo of the Pterobryaceae. The latter, originally described from Xizang, is also reported from Yunnan, China. Additionally, Noguchiodendron sphaerocarpum (Nog.) Ninh & Pócs is reported for the second time (since 1971) from Bhutan.Peer reviewe

Porotrichum saotomense sp. nov. (Neckeraceae) and other additions to the moss flora of São Tomé & Príncipe, Gulf of Guinea, West Africa

Peer reviewe

Rediscovery of the monospecific moss genus Cyptodontopsis (Cryphaeaceae) in China: a species restricted to flood plain habitats

Peer reviewe

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

Background: High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e. g. repetitive regions or non-specific antibody interactions. The noise will appear in the form of a background distribution of reads that must be taken into account in the downstream analysis, for example when detecting enriched regions (peak-calling). Several reported peak-callers can take experimental measurements of background tag distribution into account when analysing a data set. Unfortunately, the background is only used to adjust peak calling and not as a preprocessing step that aims at discerning the signal from the background noise. A normalization procedure that extracts the signal of interest would be of universal use when investigating genomic patterns. Results: We formulated such a normalization method based on linear regression and made a proof-of-concept implementation in R and C++. It was tested on simulated as well as on publicly available ChIP-seq data on binding sites for two transcription factors, MAX and FOXA1 and two control samples, Input and IgG. We applied three different peak-callers to (i) raw (un-normalized) data using statistical background models and (ii) raw data with control samples as background and (iii) normalized data without additional control samples as background. The fraction of called regions containing the expected transcription factor binding motif was largest for the normalized data and evaluation with qPCR data for FOXA1 suggested higher sensitivity and specificity using normalized data over raw data with experimental background. Conclusions: The proposed method can handle several control samples allowing for correction of multiple sources of bias simultaneously. Our evaluation on both synthetic and experimental data suggests that the method is successful in removing background noise

Notes on rediscovery of mosses Anomodon perlingulatus (Anomodontaceae) and Curvicladium kurzii (Neckeraceae) in Yunnan, China

Anomodon perlingulatus Broth. ex P.C. Wu & Y. Jia and Curvicladium kurzii (Kindberg) Enroth are reported as rheophytic mosses for the first time in China. They were so rarely collected that their habitat preferences remained unknown. The newly obtained specimens have expanded our understanding on their morphological variability and ecological preferences. After re-examining the type specimen held in H, the large size of median cells in A. perlingulatus is confirmed to be a measurement error made in the original description. An updated description is provided. Both A. perlingulatus and C. kurzii can be categorized as facultative rheophytes because of the limited number of specimens collected so far. We anticipate that with a better understanding of potential habitats of both species, that more occurrences in the neighboring provinces are likely to be discovered

Evolution of the Neckeraceae (Bryophyta): resolving the backbone phylogeny

Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.Earlier phylogenetic studies, including species belonging to the Neckeraceae, have indicated that this pleurocarpous moss family shares a strongly supported sister group relationship with the Lembophyllaceae, but the family delimitation of the former needs adjustment. To test the monophyly of the Neckeraceae, as well as to redefine the family circumscription and to pinpoint its phylogenetic position in a larger context, a phylogenetic study based on molecular data was carried out. Sequence data were compiled, combining data from all three genomes: nuclear ITS1 and 2, plastid trnS-rps4-trnT-trnL-trnF and rpl16, and mitochondrial nad5 intron. The Neckeraceae have sometimes been divided into the two families, Neckeraceae and Thamnobryaceae, a division rejected here. Both parsimony and Bayesian analyses of molecular data revealed that the family concept of the Neckeraceae needs several further adjustments, such as the exclusion of some individual species and smaller genera as well as the inclusion of the Leptodontaceae. Within the family three well-supported clades (A, B and C) can be distinguished. Members of clade A are mainly non-Asiatic and nontropical. Most species have a weak costa and immersed capsules with reduced peristomes (mainly Neckera spp.) and the teeth at the leaf margins are usually unicellular. Clade B members are also mainly non-Asiatic. They are typically fairly robust, distinctly stipilate, having a single, at least relatively strong costa, long setae (capsules exserted), and the peristomes are well developed or only somewhat reduced. Members of clade C are essentially Asiatic and tropical. The species of this clade usually have a strong costa and a long seta, the seta often being mammillose in its upper part. The peristome types in this clade are mixed, since both reduced and unreduced types are found. Several neckeraceous genera that were recognised on a morphological basis are polyphyletic (e.g. Neckera, Homalia, Thamnobryum, Porotrichum). Ancestral state reconstructions revealed that currently used diagnostic traits, such as the leaf asymmetry and costa strength are highly homoplastic. Similarly, the reconstructions revealed that the 'reduced' sporophyte features have evolved independently in each of the three clades.Peer reviewe

Laboratory verification of a new high flow differential mobility particle sizer, and field measurements in Hyytiälä

Measurement of atmospheric sub-10 nm nanoparticle number concentrations has been of substantial interest recently, which, however, is subject to considerable uncertainty. We report a laboratory characterization of a high flow differential mobility particle sizer (HFDMPS), which is based on the Half-mini type differential mobility analyzer (DMA) and nano condensation nuclei counter (A11), and show the first results from atmospheric observations. The HFDMPS utilizes the state-of-the-art aerosol technology, and is optimized for sub-10 nm particle size distribution measurements by a moderate resolution DMA, optimized and characterized low-loss particle sampling line and minimal dilution in the detector. We present an exhaustive laboratory calibration to the HFDMPS and compare the measured size data to the Hyytiala long-term DMPS and Neutral cluster and ion spectrometer. The HFDMPS detects about two times higher 3-10 nm particle concentrations than the long-term DMPS, and the counting uncertainties are halved as compared to the long-term DMPS. The HFDMPS did not observe any sub-2.5 nm particles in Hyytiala, and the reason for that was shown to be the inability of diethylene glycol to condense on such small biogenic particles. Last, we discuss the general implications of our results to the sub-10 nm DMPS based measurements.Peer reviewe

Ganglion Cell Adaptability: Does the Coupling of Horizontal Cells Play a Role?

Background: The visual system can adjust itself to different visual environments. One of the most well known examples of this is the shift in spatial tuning that occurs in retinal ganglion cells with the change from night to day vision. This shift is thought to be produced by a change in the ganglion cell receptive field surround, mediated by a decrease in the coupling of horizontal cells. Methodology/Principal Findings: To test this hypothesis, we used a transgenic mouse line, a connexin57-deficient line, in which horizontal cell coupling was abolished. Measurements, both at the ganglion cell level and the level of behavioral performance, showed no differences between wild-type retinas and retinas with decoupled horizontal cells from connexin57-deficient mice. Conclusion/Significance: This analysis showed that the coupling and uncoupling of horizontal cells does not play a dominant role in spatial tuning and its adjustability to night and day light conditions. Instead, our data suggest that anothe

Vertical profiles of sub-3nm particles over the boreal forest

This work presents airborne observations of sub-3 nm particles in the lower troposphere and investigates new particle formation (NPF) within an evolving boundary layer (BL). We studied particle concentrations together with supporting gas and meteorological data inside the planetary BL over a boreal forest site in Hyytiala, southern Finland. The analysed data were collected during three flight measurement campaigns: May-June 2015, August 2015 and April-May 2017, including 27 morning and 26 afternoon vertical profiles. As a platform for the instrumentation, we used a Cessna 172 aircraft. The analysed flight data were collected horizontally within a 30 km distance from SMEAR II in Hyytiala and vertically from 100 m above ground level up to 2700 m. The number concentration of 1.5-3 nm particles was observed to be, on average, the highest near the forest canopy top and to decrease with increasing altitude during the mornings of NPF event days. This indicates that the precursor vapours emitted by the forest play a key role in NPF in Hyytiala. During daytime, newly formed particles were observed to grow in size and the particle population became more homogenous within the well-mixed BL in the afternoon. During undefined days with respect to NPF, we also detected an increase in concentration of 1.5-3 nm particles in the morning but not their growth in size, which indicates an interrupted NPF process during these undefined days. Vertical mixing was typically stronger during the NPF event days than during the undefined or non-event days. The results shed light on the connection between boundary layer dynamics and NPF.Peer reviewe

An annotated checklist of bryophytes of Europe, Macaronesia and Cyprus

Introduction. Following on from work on the European bryophyte Red List, the taxonomically and nomenclaturally updated spreadsheets used for that project have been expanded into a new checklist for the bryophytes of Europe. Methods. A steering group of ten European bryologists was convened, and over the course of a year, the spreadsheets were compared with previous European checklists, and all changes noted. Recent literature was searched extensively. A taxonomic system was agreed, and the advice and expertise of many European bryologists sought. Key results. A new European checklist of bryophytes, comprising hornworts, liverworts and mosses, is presented. Fifteen new combinations are proposed. Conclusions. This checklist provides a snapshot of the current European bryophyte flora in 2019. It will already be out-of-date on publication, and further research, particularly molecular work, can be expected to result in many more changes over the next few years.Peer reviewe