Metabolic pathways in immune senescence and inflammaging: Novel therapeutic strategy for chronic inflammatory lung diseases. An EAACI position paper from the Task Force for Immunopharmacology

The accumulation of senescent cells drives inflammaging and increases morbidity of chronic inflammatory lung diseases. Immune responses are built upon dynamic changes in cell metabolism that supply energy and substrates for cell proliferation, differentiation, and activation. Metabolic changes imposed by environmental stress and inflammation on immune cells and tissue microenvironment are thus chiefly involved in the pathophysiology of allergic and other immune-driven diseases. Altered cell metabolism is also a hallmark of cell senescence, a condition characterized by loss of proliferative activity in cells that remain metabolically active. Accelerated senescence can be triggered by acute or chronic stress and inflammatory responses. In contrast, replicative senescence occurs as part of the physiological aging process and has protective roles in cancer surveillance and wound healing. Importantly, cell senescence can also change or hamper response to diverse therapeutic treatments. Understanding the metabolic pathways of senescence in immune and structural cells is therefore critical to detect, prevent, or revert detrimental aspects of senescence-related immunopathology, by developing specific diagnostics and targeted therapies. In this paper, we review the main changes and metabolic alterations occurring in senescent immune cells (macrophages, B cells, T cells). Subsequently, we present the metabolic footprints described in translational studies in patients with chronic asthma and chronic obstructive pulmonary disease (COPD), and review the ongoing preclinical studies and clinical trials of therapeutic approaches aiming at targeting metabolic pathways to antagonize pathological senescence. Because this is a recently emerging field in allergy and clinical immunology, a better understanding of the metabolic profile of the complex landscape of cell senescence is needed. The progress achieved so far is already providing opportunities for new therapies, as well as for strategies aimed at disease prevention and supporting healthy aging.

Double migration of the endangered Tricyrtis formosana (Liliaceae) in Japan

The Ryukyu Islands of Japan are a biodiversity hotspot due to geographical and historical factors. Tricyrtis formosana is a perennial herbaceous plant that commonly found in Taiwan. But only a few populations have been identified in a limited habitat on Iriomote Island, while populations of unknown origin occur near human settlements in an area on the main island of Okinawa. To better understand these populations of the phylogenetic uniqueness and intrinsic vulnerability, we conducted comparative analyses including (1) phylogeny and population structure with MIG-seq data, (2) photosynthesis-related traits of plants grown under common conditions and (3) transcriptome analysis to detect deleterious variations. Results revealed that T. formosana was split into two clades by the congeners and that Iriomote and Okinawa populations independently derived from ancestral Taiwanese populations in each clade. Photosynthetic efficiency was lowest in the Iriomote population, followed by Okinawa and Taiwan. Transcriptome analysis showed that the Iriomote population accumulated more deleterious variations, suggesting intrinsic vulnerability. These results indicate that each T. formosana population in Japan is phylogenetically unique and has been independently dispersed from Taiwan, and that the Iriomote population presents a high conservation difficulty with a unique photosynthesis-related characteristic and a larger amount of deleterious variations.

Systematics and biogeography of the Old World fern genus Antrophyum

Antrophyum is one of the largest genera of vittarioid ferns (Pteridaceae) and is most diverse in tropical Asia and the Pacific Islands, but also occurs in temperate Asia, Australia, tropical Africa and the Malagasy region. The only monographic study of Antrophyum was published more than a century ago and a modern assessment of its diversity is lacking. Here, we reconstructed a comprehensively sampled and robustly supported phylogeny for the genus based on four chloroplast markers using Bayesian inference, maximum likelihood and maximum parsimony analyses. We then explored the evolution of the genus from the perspectives of morphology, systematics and historical biogeography. We investigated nine critical morphological characters using a morphometric approach and reconstructed their evolution on the phylogeny. We describe four new species and provide new insight into species delimitation. We currently recognize 34 species for the genus and provide a key to identify them. The results of biogeographical analysis suggest that the distribution of extant species is largely shaped by both ancient and recent dispersal events.

The contrary conservation situations of two local critically endangered species, Vaccinium emarginatum (Ericaceae) and Elatostema platyphyllum (Urticaceae), growing on the eastern edge of the distribution

As biodiversity loss continues, there is an urgent need to develop efficient conservation measures to protect diversity with limited conservation resources. Conservation targets have generally been selected based on their population size, but more detailed assessments clarifying the phylogenetic genetic status, history, and phylogenetic uniqueness of rare species is crucial to set more appropriate and effective conservation measures. In Japan, the Act on Conservation of Endangered Species of Wild Fauna and Flora designated endangered plants with high conservation priority, but >40% of these species also grow overseas. We conducted comparative analyses based on ddRADseq and MIG-seq to evaluate the population conservation status and value of Vaccinium emarginatum and Elatostema platyphyllum which are growing across national borders at the eastern edge of their species distribution range. The analyses revealed contrasting conservation status between the two species; the Japanese population of V. emarginatum had lower genetic diversity at the individual level and phylogenetically differentiated from Taiwanese populations, while that of E. platyphyllum had higher diversity at the individual level and is a relatively recent migrant with little phylogenetical differentiation from Taiwanese populations. The two species, which share the common feature of being critically rare in Japan, showed contrasting genetic/phylogenetic characteristics. This study provided useful information for appropriate conservation measures based on species’ phylogenetic traits and genetic diversity.

Langbiangia, a new genus of Gesneriaceae endemic to Langbiang Plateau, southern Vietnam and a taxonomic endeavor to achieve key targets of the post-2020 global biodiversity framework

Situated in the southern end of the Annamite Mountain Range, Langbiang Plateau is a major biodiversity hotspot of southern Vietnam known for high species diversity and endemicity. To achieve effective conservation, parts of the plateau were designated as the Langbiang Biosphere Reserve, an UNESCO World Network aiming to improve relationships between inhabitants and their environments. Amongst the rich endemic flora of the plateau are three gesneriads ascribed to Primulina, a calciphilous genus with high species diversity in the vast limestone karsts stretching from southern China to northern Vietnam. However, a recent phylogenetic study questioned the generic placement of the Langbiang Primulina, corroborating with observations on the geographical distribution, habitat preference, and phyllotaxy of the three species. Based on phylogenetic analyses of nuclear ITS and plastid trnL-F DNA sequences of a comprehensive sampling covering nearly all genera of the Old World Gesneriaceae, we demonstrate that the three Langbiang Primulina species form a fully supported clade distantly related to other Primulina. As this clade is biogeographically, ecologically, morphologically, and phylogenetically distinct worthy of generic recognition, we propose to name it Langbiangia gen. nov. to highlight the rich and unique biodiversity of the Langbiang Plateau. By means of this taxonomic endeavor, we are hoping to raise the conservation awareness of this biodiversity heritage of southern Vietnam and promote the importance of Langbiang Biosphere Reserve that is crucial for achieving action-oriented global targets of the post-2020 global biodiversity framework (GBF) of the UN Convention on Biological Diversity (CBD)-effective conservation and management of at least 30% of biodiverse terrestrial, inland water, and costal and marine areas by 2030-that has been agreed at the COP15 in Montréal in December 2022.

Broadband ultra-compact polarization splitter-rotator using diagonally overlapped bi-layer architecture

A broadband and ultra-compact polarization splitter-rotator based on diagonally overlapped bi-layer architecture and an asymmetrical directional coupler is proposed on a silicon-on-insulator platform. By leveraging the structure over supermode theory, a 1-dB bandwidth of 220 nm, extinction ratio (ER) of <19dB, and cross talk (XT) of <-15.85dB within the span of 1400-1700 nm and coupling length of 4.62 µm are achieved. In addition, TM₀-TE₀ conversion loss of ∼0.19dB, ER of 35.88 dB, and XT of -30.46dB can be obtained at 1550 nm. The fabrication tolerances are also analyzed, indicating that the insertion losses remain below 1 dB over 1460-1620 nm in terms of width errors and layer-to-layer misalignments within ±10nm. The results show that the proposed device is very suitable to utilize between fibers and for polarization diversity of on-chip systems for broadband operation as well as ultra-compact integration.

Demonstration of a bi-directionally tunable arrayed waveguide grating with ultra-low thermal power using S-shaped architecture and parallel-circuit configuration

A thermally bi-directionally tunable arrayed waveguide grating (TBDTAWG) is proposed and demonstrated on a silicon-on-insulator (SOI) platform. The device is composed of passive and active designs for realizations of an AWG and fine tuning of its filtering responses. Given that the required length difference between adjacent arrayed waveguides for the SOI platform is considerably short (∼3-5 µm) due to a high index contrast, an S-shaped architecture with a larger footprint instead of a rectangular one is employed in the AWG. Bi-directionally tunable functions, i.e., both red- and blue-shift tunable functions, can be achieved by using two triangular thermal-tuning regions with complementary phase distributions in the S-shaped architecture despite using only materials with positive thermo-optic coefficients, i.e., Si and SiO₂. Measurement results illustrate that both red- or blue-shifted spectra can be achieved and a linear bi-directional shift-to-power ratio of ±30.5 nm/W as well as a wide tuning range of 8 nm can be obtained under an electrical voltage range of 0-2.5 V, showing an agreement between the measurement results and two-dimensional simulation results. This also shows the potential of the proposed TBDTAWG for automatically stabilizing the spectral responses of AWG-based (de)multiplexers for coarse or dense wavelength division multiplexing communication systems by using a feedback control circuit.

Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages

The ecology and genetic diversity of the model yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe the ancestral species’ diversity. We found that S. cerevisiae is distributed ubiquitously at low abundance in the forests. Whole-genome sequencing of 121 isolates revealed nine distinct lineages that diverged from Asian lineages during the Pleistocene, when a transient continental shelf land bridge connected Taiwan to other major landmasses. Three lineages are endemic to Taiwan and six are widespread in Asia, making this region a focal biodiversity hotspot. Both ancient and recent admixture events were detected between the natural lineages, and a genetic ancestry component associated with isolates from fruits was detected in most admixed isolates. Collectively, Taiwanese isolates harbor genetic diversity comparable to that of the whole Asia continent, and different lineages have coexisted at a fine spatial scale even on the same tree. Patterns of variations within each lineage revealed that S. cerevisiae is highly clonal and predominantly reproduces asexually in nature. We identified different selection patterns shaping the coding sequences of natural lineages and found fewer gene family expansion and contractions that contrast with domesticated lineages. This study establishes that S. cerevisiae has rich natural diversity sheltered from human influences, making it a powerful model system in microbial ecology.

Plastome phylogenomics of Allaeanthus, Broussonetia and Malaisia (Dorstenieae, Moraceae) and the origin of B. × kazinoki

Species of Broussonetia have been essential in the development of papermaking technology. In Japan and Korea, a hybrid between B. monoica and B. papyrifera (= B. × kazinoki) known as kōzo and daknamu is still the major source of raw materials for making traditional paper washi and hanji, respectively. Despite their cultural and practical significance, however, the origin and taxonomy of kōzo and daknamu remain controversial. Additionally, the long-held generic concept of Broussonetia s.l., which included Sect. Allaeanthus and Sect. Broussonetia, was challenged as phylogenetic analyses showed Malaisia is sister to the latter section. To re-examine the taxonomic proposition that recognizes Allaeanthus, Broussonetia, and Malaisia (i.e., Broussonetia alliance), plastome and nuclear ribosomal DNA (nrDNA) sequences of six species of the alliance were assembled. Characterized by the canonical quadripartite structure, genome alignments and contents of the six plastomes (160,121-162,594 bp) are highly conserved, except for the pseudogenization and/or loss of the rpl22 gene. Relationships of the Broussonetia alliance are identical between plastome and nrDNA trees, supporting the maintenance of Malaisia and the resurrection of Allaeanthus. The phylogenomic relationships also indicate that the monoecy in B. monoica is a derived state, possibly resulting from hybridization between the dioecious B. kaempferi (♀) and B. papyrifera (♂). Based on the hypervariable ndhF-rpl32 intergenic spacer selected by sliding window analysis, phylogeographic analysis indicates that B. monoica is the sole maternal parent of B. × kazinoki and that daknamu carries multiple haplotypes, while only one haplotype was detected in kōzo. Because hybridizations between B. monoica and B. papyrifera are unidirectional and have occurred rarely in nature, our data suggest that daknamu might have originated via deliberate hybrid breeding selected for making hanji in Korea. On the contrary, kōzo appears to have a single origin and the possibility of a Korean origin cannot be ruled out.

Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae's taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

A dated molecular phylogeny and biogeographical analysis reveals the evolutionary history of the trans-pacifically disjunct tropical tree genus Ormosia (Fabaceae)

The papilionoid legume genus Ormosia (Fabaceae) comprises about 150 species of trees and exhibits a striking disjunct geographical distribution between the New World- and Asian and Australasian wet tropics and subtropics. Modern classifications of Ormosia are not grounded on a well-substantiated phylogenetic hypothesis and have been limited to just portions of the geographical range of the genus. The lack of an evolutionarily-based foundation for systematic studies has hindered taxonomic work on the genus and prevented the testing of biogeographical hypotheses related to the origin of the Old World/New World disjunction and the individual dispersal histories within both areas. Here, we present the most comprehensively sampled molecular phylogeny of Ormosia to date, based on analysis of both nuclear (ITS) and plastid (matK and trnL-F) DNA sequences from 82 species of the genus. Phylogenetically-based divergence times and ancestral range estimations are employed to test hypotheses related to the biogeographical history of the genus. We find strong support for the monophyly of Ormosia and the grouping of all sampled Asian species of the genus into two comparably sized clades, one of which is sister to another large clade containing all sampled New World species. Within the New World clade, additional resolution supports the grouping of most species into three mutually exclusive subordinate clades. The remaining New World species form a fourth well-supported clade in the analyses of plastid sequences, but that result is contradicted by the analysis of ITS. With few exceptions the supported clades have not been previously recognized as taxonomic groups. The biogeographical analysis suggests that Ormosia originated in continental Asia and dispersed to the New World in the Oligocene or early Miocene via long-distance trans-oceanic dispersal. We reject the hypothesis that the inter-hemispheric disjunction in Ormosia resulted from fragmentation of a more continuous "Boreotropical" distribution since the dispersal post-dates Eocene climatic maxima. Both of the Old World clades appear to have originated in mainland Asia and subsequently dispersed into the Malay Archipelago and beyond, at least two lineages dispersing across Wallace's Line as far as the Solomon Islands and northeastern Australia. In the New World, the major clades all originated in Amazonia. Dispersal from Amazonia into peripheral areas in Central America, the Caribbean, and Extra-Amazonian Brazil occurred multiple times over varying time scales, the earliest beginning in the late Miocene. In a few cases, these dispersals were followed by local diversification, but not by reverse migration back to Amazonia. Within each of the two main areas of distribution, multiple modest bouts of oceanic dispersal were required to achieve the modern distributions.

Extracellular matrix degradation pathways and fatty acid metabolism regulate distinct pulmonary vascular cell types in pulmonary arterial hypertension

Pulmonary arterial hypertension describes a group of diseases characterised by raised pulmonary vascular resistance, resulting from vascular remodelling in the pre-capillary resistance arterioles. Left untreated, patients die from right heart failure. Pulmonary vascular remodelling involves all cell types but to date the precise roles of the different cells is unknown. This study investigated differences in basal gene expression between pulmonary arterial hypertension and controls using both human pulmonary microvascular endothelial cells and human pulmonary artery smooth muscle cells. Human pulmonary microvascular endothelial cells and human pulmonary artery smooth muscle cells from pulmonary arterial hypertension patients and controls were cultured to confluence, harvested and RNA extracted. Whole genome sequencing was performed and after transcript quantification and normalisation, we examined differentially expressed genes and applied gene set enrichment analysis to the differentially expressed genes to identify putative activated pathways. Human pulmonary microvascular endothelial cells displayed 1008 significant (p ≤ 0.0001) differentially expressed genes in pulmonary arterial hypertension samples compared to controls. In human pulmonary artery smooth muscle cells, there were 229 significant (p ≤ 0.0001) differentially expressed genes between pulmonary arterial hypertension and controls. Pathway analysis revealed distinctive differences: human pulmonary microvascular endothelial cells display down-regulation of extracellular matrix organisation, collagen formation and biosynthesis, focal- and cell-adhesion molecules suggesting severe endothelial barrier dysfunction and vascular permeability in pulmonary arterial hypertension pathogenesis. In contrast, pathways in human pulmonary artery smooth muscle cells were mainly up-regulated, including those for fatty acid metabolism, biosynthesis of unsaturated fatty acids, cell–cell and adherens junction interactions suggesting a more energy-driven proliferative phenotype. This suggests that the two cell types play different mechanistic roles in pulmonary arterial hypertension pathogenesis and further studies are required to fully elucidate the role each plays and the interactions between these cell types in vascular remodelling in disease progression.

Six new species of Begonia from Guangxi, China

BACKGROUND

With currently 1980 described species, the mega-diverse Begonia is now perhaps the 5th largest flowering plant genus, expanding rapidly from ca. 900 species in 1997 to its current size in merely two decades. In continuation of our studies of Asian Begonia, we report six additional new species from Guangxi, the region/province harboring the second richest Begonia flora of China.

RESULTS

Based on morphological and molecular data, the new species B. aurora belongs to Begonia sect. Platycentrum, while the other five new species (viz. B. larvata, B. longiornithophylla, B. lui, B. scabrifolia, and B. zhuoyuniae) are members of Sect. Coelocentrum. Somatic chromosome numbers of B. longiornithophylla and B. zhuoyuniae at metaphase were counted as 2n = 30, consistent with previously reports for Sect. Coelocentrum.

CONCLUSIONS

With the addition of the six new species, the total number of Begonia species in Guangxi increases from 86 to 92. Detailed description, line drawings, and color plates are provided to aid in identification.

Correlation between work impairment, scores of rhinitis severity and asthma using the MASK-air® App

BACKGROUND

In allergic rhinitis, a relevant outcome providing information on the effectiveness of interventions is needed. In MASK-air (Mobile Airways Sentinel Network), a visual analogue scale (VAS) for work is used as a relevant outcome. This study aimed to assess the performance of the work VAS work by comparing VAS work with other VAS measurements and symptom-medication scores obtained concurrently.

METHODS

All consecutive MASK-air users in 23 countries from 1 June 2016 to 31 October 2018 were included (14 189 users; 205 904 days). Geolocalized users self-assessed daily symptom control using the touchscreen functionality on their smart phone to click on VAS scores (ranging from 0 to 100) for overall symptoms (global), nose, eyes, asthma and work. Two symptom-medication scores were used: the modified EAACI CSMS score and the MASK control score for rhinitis. To assess data quality, the intra-individual response variability (IRV) index was calculated.

RESULTS

A strong correlation was observed between VAS work and other VAS. The highest levels for correlation with VAS work and variance explained in VAS work were found with VAS global, followed by VAS nose, eye and asthma. In comparison with VAS global, the mCSMS and MASK control score showed a lower correlation with VAS work. Results are unlikely to be explained by a low quality of data arising from repeated VAS measures.

CONCLUSIONS

VAS work correlates with other outcomes (VAS global, nose, eye and asthma) but less well with a symptom-medication score. VAS work should be considered as a potentially useful AR outcome in intervention studies.

In memoriam Ching-I Peng (1950-2018)-an outstanding scientist and mentor with a remarkable legacy

Ching-I Peng, the most prolific and internationally recognized Taiwanese plant taxonomist of his generation, passed away on May 1, 2018. Dr. Peng was an eminent worker on the taxonomy of East Asian plants and the genus Ludwigia, and the foremost expert on Asian Begonia. He served as associate editor, co-editor in chief, and editor-in-chief of Botanical Studies and its predecessor Botanical Bulletin of Academia Sinica during the period 1992-2016. He gathered over 25,000 plant specimens, name 121 plant taxa, and has left a remarkable legacy of literature, collaborations and collections. This article summarizes Dr. Peng's academic career and commemorates his enduring contribution.

Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure

BACKGROUND

Sino-Vietnamese limestone karsts (SVLK) are a biodiversity hotspot rich in endemic plant species associated with caves and cave-like microhabitats. Based on phylogenetic studies of Begonia sect. Coelocentrum, a species-rich and characteristic SVLK clade, geographic isolation caused by extensive and continuous karstification was proposed as the major driving force triggering population diversification and geographic speciation. To test this proposition, population genetics and phylogeography of Begonia luzhaiensis were investigated using EST-SSR markers and the chloroplast trnC-ycf6 intergenic spacer.

RESULTS

F statistics, Bayesian clustering analysis, AMOVA, and PCoA of both data sets all indicated substantial population differentiation and significant isolation by distance. Nested clade phylogeographic analyses inferred that historical fragmentations have been prominent, congruent with Guangxi's geohistory of karstification as well as suggesting a mountain chain in northeastern Guangxi could have also acted as a major geographic barrier. A Bayesian skyline plot (BSP) indicated a slight decline in effective population size at 75,000 years ago (75 Kya), coinciding with the last glacial period during which the increased aridity in East Asia had retarded karstification, negatively affecting the populations of B. luzhaiensis. However, BSP detected a continuous and further population decline until the present time even though summer monsoons have resumed since the end of the last glacial maximum.

CONCLUSIONS

The microevolution patterns of B. luzhaiensis support that limited gene flow would have greatly enhanced the effects of random genetic drift and has been a major factor promoting diversification in Begonia, highly congruent with previous proposition. Based our study, we further propose that the arrival of Paleolithic Homo sapiens whose activities centered around limestone caves could have had further impacts on the populations of B. luzhaiensis, resulting in additional population decline. Further habitat destruction could have resulted from the transition from hunter gathering to food-producing societies ca. 20-10 Kya and the development of agriculture ca. 10 Kya in South China. Implications of the current study for SVLK plant conservation are also discussed.

Molecular systematics of Chiritopsis-like Primulina (Gesneriaceae): one new species, one new name, two new combinations, and new synonyms

BACKGROUND

The Gesneriaceae genus Chiritopsis, confined almost exclusively to cave or cave-like microhabitats of limestone karsts of southern China, was described to distinguish it from Chirita by much smaller flowers and generally miniature plant sizes in the former genus. However, molecular phylogenetic analyses showed that Chiritopsis is polyphyletic and its species delimitation has been problematic. To understand how many times Chiritopsis-like species have evolved from within the recircumscribed Primulina and to further clarify their species identification, we sampled all but two recently described species of Chiritopsis-like Primulina and reconstructed their phylogenetic relationship based on DNA sequences of nuclear ITS and chloroplast trnL-F and trnH-psbA.

RESULTS

With 182 accessions of 165 taxa of Primulina sampled, our analyses placed the 40 accessions of 25 taxa of Chiritopsis-like Primulina in 17 unrelated positions, indicating at least 17 independent origins of the traits associated with caves or cave-like microhabitats. Of the 17 clades containing Chiritopsis-like Primulina, Clade 1 is composed of P. bipinnatifida, P. cangwuensis, P. jianghuaensis, P. lingchuanensis, and P. zhoui, as well as additional samples that show variable and overlapping morphology in leaf shapes. Clade 10 includes P. cordifolia, P. huangii, and P. repanda, while Primulina repanda var. guilinensis is not placed within Clade 10. Primulina glandulosa var. yangshuoensis is not placed in the same clade of P. glandulosa.

CONCLUSIONS

Based on our data, P. cangwuensis, P. jianghuaensis, and P. lingchuanensis are proposed to synonymize under P. bipinnatifida, with P. zhoui treated as a variety of P. bipinnatifida. Primulina repanda var. guilinensis is transferred as P. subulata var. guilinensis comb. nov. and Primulina pseudoglandulosa nom. nov. is proposed for P. glandulosa var. yangshuoensis. One new species is named P. chingipengii to honor the late Dr. Ching-I Peng (1950-2018).

Human mediated translocation of Pacific paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)]: Genetic evidence of dispersal routes in Remote Oceania

Paper mulberry, Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae), a dioecious species, was transported by humans from Taiwan to the islands of Remote Oceania. Its introduction and cultivation in Remote Oceania was intentional due to its cultural importance as a fiber source for barkcloth textiles. The aim of this study was to explore the genetic diversity and structure of paper mulberry populations within Remote Oceania in order to infer dispersal patterns that may reflect past human interaction among island groups. We present the integrated analysis of 380 samples (313 contemporary and 67 herbarium specimens) collected in Near and Remote Oceania. Genetic characterization was based on a set of ten microsatellites developed for B. papyrifera and complemented with the analysis of the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker and the chloroplast ndhF–rpl32 intergenic spacer. Microsatellite data identify a total of 64 genotypes, despite this being a clonally propagated crop, and show three major dispersal hubs within Remote Oceania, centered on the islands of Fiji, Tonga, and Pitcairn. Of 64 genotypes identified, 55 correspond to genotypes associated to female-sexed plants that probably descend from plants introduced by the prehistoric Austronesian-speaking voyagers. The ratio of accessions to genotypes between herbarium and contemporary samples, suggests recent loss of genetic diversity. In addition to the chloroplast haplotypes described previously, we detected two new haplotypes within Remote Oceania both originating in Taiwan. This is the first study of a commensal species to show genetic structuring within Remote Oceania. In spite of the genetic bottleneck, the presence of only one sex, a timespan of less than 5000 years, and asexual propagation of this crop in Remote Oceania, we detect genetic diversity and regional structuring. These observations suggest specific migration routes between island groups within Remote Oceania.

Sputum proteomic signature of gastro-oesophageal reflux in patients with severe asthma

Gastro-oesophageal reflux disease (GORD) has long been associated with poor asthma control without an established cause-effect relationship. 610 asthmatics (421 severe/88 mild-moderate) and 101 healthy controls were assessed clinically and a subset of 154 severe asthmatics underwent proteomic analysis of induced sputum using untargeted mass spectrometry, LC-IMS-MS^E. Univariate and multiple logistic regression analyses (MLR) were conducted to identify proteins associated with GORD in this cohort. When compared to mild/moderate asthmatics and healthy individuals, respectively, GORD was three- and ten-fold more prevalent in severe asthmatics and was associated with increased asthma symptoms and oral corticosteroid use, poorer quality of life, depression/anxiety, obesity and symptoms of sino-nasal disease. Comparison of sputum proteomes in severe asthmatics with and without active GORD showed five differentially abundant proteins with described roles in anti-microbial defences, systemic inflammation and epithelial integrity. Three of these were associated with active GORD by multiple linear regression analysis: Ig lambda variable 1-47 (p = 0·017) and plasma protease C1 inhibitor (p = 0·043), both in lower concentrations, and lipocalin-1 (p = 0·034) in higher concentrations in active GORD. This study provides evidence which suggests that reflux can cause subtle perturbation of proteins detectable in the airways lining fluid and that severe asthmatics with GORD may represent a distinct phenotype of asthma.

PGAM5 expression and macrophage signatures in non-small cell lung cancer associated with chronic obstructive pulmonary disease (COPD)

Background

COPD patients are at increased risk of developing non-small cell lung carcinoma that has a worse prognosis. Oxidative stress contributes to carcinogenesis and is increased in COPD patients due to mitochondrial dysfunction. We determined whether mitochondrial dysfunction is a contributing factor to the reduced survival of COPD patients with non-small cell lung carcinoma (NSCLC).

Methods

Using a transcriptomic database and outcome data of 3553 NSCLC samples, we selected mitochondrial-related genes whose levels in the tumour correlated with patient mortality. We further selected those genes showing a ≥ 2 fold expression in cancer compared to normal tissue. Cell-type specific expression of these proteins in lung tissue from NSCLC patients who were non-smokers or smokers with or without COPD (healthy smokers) was determined by immunohistochemistry. Gene set variation analysis was used in additional NSCLC datasets to determine the relative expression of specific macrophage transcriptomic signatures within lung cancer tissue.

Results

The expression of 14 mitochondrial-related genes was correlated with patient mortality and these were differentially expressed between cancer and normal lung tissue. We studied further the expression of one of these genes, PGAM5 which is a regulator of mitochondrial degradation by mitophagy. In background lung tissue, PGAM5 was only expressed in alveolar macrophages, with the highest expression in smokers with COPD compared to healthy smokers and non-smokers. In cancerous tissue, only the malignant epithelial cells and associated macrophages at the periphery of the cancer expressed PGAM5. Pre-neoplastic epithelium also showed the expression of PGAM5. There was no difference in expression in cancer tissue between COPD, healthy smoker and non-smoker groups. Macrophages at the edge of the cancer from COPD patients showed a trend towards higher expression of PGAM5 compared to those from the other groups. There was a significant correlation between PGAM5 expression in cancer tissue and the level of expression of 9 out of 49 previously-defined macrophage transcriptomic signatures with a particular one associated with patient mortality (p < 0.05).

Conclusion

PGAM5 is expressed in pre-neoplastic tissue and NSCLC, but not in normal epithelium. The association between PGAM5 expression and patient mortality may be mediated through the induction of specific macrophage phenotypes.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-5140-9) contains supplementary material, which is available to authorized users.

Molecular recircumscription of Broussonetia (Moraceae) and the identity and taxonomic status of B. kaempferi var. australis

BACKGROUND

Despite being a relatively small genus, the taxonomy of the paper mulberry genus Broussonetia remains problematic. Much of the controversy is related to the identity and taxonomic status of Broussonetia kaempferi var. australis, a name treated as a synonym in the floras of Taiwan and yet accepted in the floras of China. At the generic level, the monophyly of Corner (Gard Bull Singap 19:187-252, 1962)'s concept of Broussonetia has not been tested. In recent studies of Broussonetia of Japan, lectotypes of the genus were designated and three species (B. kaempferi, Broussonetia monoica, and Broussonetia papyrifera) and a hybrid (B. ×kazinoki) were recognized. Based on the revision and molecular phylogenetic analyses, this article aims to clarify these issues.

RESULTS

Herbarium studies, field work, and molecular phylogenetic analyses indicate that all Taiwanese materials identifiable to B. kaempferi var. australis are conspecific with B. monoica of Japan and China. Molecular phylogenetic analyses showed that Broussonetia sensu Corner (Gard Bull Singap 19:187-252, 1962) contains two clades corresponding to sect. Broussonetia and sect. Allaeanthus, with Malaisia scandens sister to sect. Broussonetia.

CONCLUSIONS

Based on our analyses, B. kaempferi var. australis is treated as a synonym of B. monoica and that B. kaempferi is not distributed in Taiwan. To correct the non-monophyly of Broussonetia sensu Corner (Gard Bull Singap 19:187-252, 1962), Broussonetia is recircumscribed to contain only sect. Broussonetia and the generic status of Allaeanthus is reinstated.

Three new species of Paraboea (Gesneriaceae) from limestone karsts of China based on morphological and molecular evidence

BACKGROUND

The limestone karsts of Southeast Asia and South China are a major biodiversity hotspot of global terrestrial biomes. With more than 130 described species, Paraboea has become one of the most characteristic plant groups in the Southeast Asian limestone flora. During the course of extensive field work on the limestone formations of southern and southwestern China, three unknown species of Paraboea were collected.

RESULTS

Molecular phylogenetic analyses based on nuclear ITS and chloroplast trnL-F sequences strongly confirm the placements of the three new species in Paraboea sensu Puglisi et al. (Taxon 65:277-292. https://doi.org/10.12705/652.5 , 2016). Moreover, these three novelties can be distinguished from known Paraboea species with distinct morphological characters, further supporting their recognition as new species.

CONCLUSIONS

With the support of detailed morphological studies and molecular phylogenetic analyses, Paraboea dushanensis, P. sinovietnamica and P. xiangguiensis are recognized as three species new to science.

Three new species of Begonia sect. Baryandra from Panay Island, Philippines

BACKGROUND

The flora of Panay Island is under-collected compared with the other islands of the Philippines. In a joint expedition to the island, botanists from Taiwan and the Philippines found three unknown Begonia species and compared them with potentially allied species.

RESULTS

The three species are clearly assignable to Begonia sect. Baryandra which is largely endemic to the Philippines. Studies of literature, herbarium specimens, and living plants support the recognition of the three new species: Begonia culasiensis, B. merrilliana, and B. sykakiengii. Somatic chromosomes at metaphase were determined to be 2n = 30 for B. culasiensis and 2n = 28 for both B. merrilliana and B. sykakiengii, congruent with those of most species in sect. Baryandra. Molecular phylogenetic evidence is consistent with B. culasiensis being a relict from the late Miocene and B. merrilliana and B. sykakiengii being younger species of Pleistocene origin.

CONCLUSION

The continuing discovery of endemic Philippine species means the remaining fragments of both primary and secondary native vegetation in the archipelago are of increasing value in terms of natural capital. A secure future for the species could be realized through ex situ conservation collections and raising awareness with community groups.

Begonia myanmarica (Begoniaceae), a new species from Myanmar, and molecular phylogenetics of Begonia sect. Monopteron

BACKGROUND

A new species, Begonia myanmarica, was discovered from Myanmar and herein documented. Characterized by a single developed wing in the ovary/fruit, this species would be assigned to sect. Monopteron (sensu Doorenbos et al. in The sections of Begonia including descriptions, keys and species lists: studies in Begoniaceae VI. Wageningen Agricultural University, Wageningen, 1998) that is known by B. griffithiana and B. nepalensis from the Himalaya. To confirm its sectional assignment, we conducted morphological, phylogenetic and cytological studies.

RESULTS

Morphological observations indicated that B. myanmarica was distinguishable from the two known species of sect. Monopteron by the leaf shape and size, 1-locular ovary, parietal placentation and chromosome number. Molecular phylogenetic analysis using nrITS sequences showed that B. myanmarica was not allied with the clade of sect. Monopteron, though both were nested within sect. Platycentrum-sect. Sphenanthera clade.

CONCLUSIONS

Studies of morphology, molecular phylogenetics and cytology support the recognition of the new species, Begonia myanmarica, which is fully described and illustrated. Our results also indicate that B. myanmarica is not closely related to species previously assigned to sect. Monopteron, suggesting that the fruit morphology of a single developed wing in the ovary/fruit characterizing sect. Monopteron is homoplasious.

Phylogenetic Classification of Seed Plants of Taiwan

BACKGROUND

Biological classification, the hierarchical arrangement of scientific names of organisms, constitutes the core infrastructure of biological databases. For an efficient management of biological databases, adopting a stable and universal biological classification system is crucial. Currently in Taiwan Biodiversity Information Facility (TaiBIF; http://taibif.tw/ ), the national portal website that integrates Taiwan's biodiversity information databases, angiosperms are arranged according to Cronquist's System of Classification, which is not compatible with current trend of the Angiosperm Phylogeny Group (APG) classification. To consolidate the function and management of the database, TaiBIF is moving to adopt the APG IV classification and Christenhusz et al. (Phytotaxa 19:55-70, 2011)'s classification of gymnosperms, which we summarize as the Phylogenetic Classification of Seed Plants of Taiwan.

RESULTS

The Phylogenetic Classification of Seed Plants of Taiwan places gymnosperms in five families [vs. eight families in the Flora of Taiwan (FOT)] and angiosperms in 210 families (vs. 193 families in FOT). Three FOT gymnosperm families are synonymized in current treatment. Of the 210 APG IV families, familial circumscriptions of 114 families are identical with FOT and 50 families are recircumscription of FOT, with 46 families newly added. Of the 29 FOT families not included in current classification, two families are excluded and 27 families are synonymized.

CONCLUSIONS

The adoption of the Phylogenetic Classification of Seed Plants of Taiwan in TaiBIF will provide better service and efficient management of the nation's biodiversity information databases.

Phylogeography of herbarium specimens of asexually propagated paper mulberry [Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae)] reveals genetic diversity across the Pacific

BACKGROUND AND AIMS

Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred.

METHODS

DNA from 47 herbarium specimens of B. papyrifera collected from 1882 to 2006 from different islands of the Pacific was obtained under ancient DNA protocols. Genetic characterization was based on the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker, the chloroplast ndhF-rpl32 intergenic spacer and a set of ten microsatellites developed for B. papyrifera.

KEY RESULTS

Microsatellites allowed detection of 15 genotypes in Near and Remote Oceanian samples, in spite of the vegetative propagation of B. papyrifera in the Pacific. These genotypes are structured in two groups separating West and East Polynesia, and place Pitcairn in a pivotal position. We also detected the presence of male plants that carry the Polynesian chloroplast DNA (cpDNA) haplotype, in contrast to findings in contemporary B. papyrifera populations where only female plants bear the Polynesian cpDNA haplotype.

CONCLUSIONS

For the first time, genetic diversity was detected among paper mulberry accessions from Remote Oceania. A clear separation between West and East Polynesia was found that may be indicative of pulses during its dispersal history. The pattern linking the genotypes within Remote Oceania reflects the importance of central Polynesia as a dispersal hub, in agreement with archaeological evidence.

Characterization of microsatellite markers for Broussonetia papyrifera (Moraceae)

PREMISE OF THE STUDY

Broussonetia papyrifera (Moraceae) is native to Asia and is used as a medicinal plant and as a source of fiber for making paper. It was dispersed into the Pacific region as a fiber source for making nonwoven textiles (barkcloth). Microsatellites were developed to trace the human-mediated dispersal of this species into the Pacific region.

METHODS AND RESULTS

A set of 36 microsatellites was isolated and initially assayed on 10 accessions to assess polymorphism. We found that 20 markers were polymorphic, with the number of alleles per marker ranging from four to 35 in 70 accessions genotyped from three Asian populations. Observed and expected heterozygosities ranged from 0.04 to 0.85 and from 0.19 to 0.94, respectively. These markers were tested in four Moraceae species and one Rosaceae species.

CONCLUSIONS

These markers will be useful for the assessment of genetic diversity in B. papyrifera. They show low transferability to other species tested.

Convergence, Consilience, and the Evolution of Temperate Deciduous Forests

The deciduous habit of northern temperate trees and shrubs provides one of the most obvious examples of convergent evolution, but how did it evolve? Hypotheses based on the fossil record posit that deciduousness evolved first in response to drought or darkness and preadapted certain lineages as cold climates spread. An alternative is that evergreens first established in freezing environments and later evolved the deciduous habit. We monitored phenological patterns of 20 species of Viburnum spanning tropical, lucidophyllous (subtropical montane and warm temperate), and cool temperate Asian forests. In lucidophyllous forests, all viburnums were evergreen plants that exhibited coordinated leaf flushes with the onset of the rainy season but varied greatly in the timing of leaf senescence. In contrast, deciduous species exhibited tight coordination of both flushing and senescence, and we found a perfect correlation between the deciduous habit and prolonged annual freezing. In contrast to previous stepwise hypotheses, a consilience of independent lines of evidence supports a lockstep model in which deciduousness evolved in situ, in parallel, and concurrent with a gradual cooling climate. A pervasive selective force combined with the elevated evolutionary accessibility of a particular response may explain the massive convergence of adaptive strategies that characterizes the world's biomes.

Development and characterization of EST-SSR markers for Begonia luzhaiensis (Begoniaceae)

PREMISE OF THE STUDY

Microsatellite primers were developed for Begonia luzhaiensis (Begoniaceae) to assess genetic diversity and population genetic structure.

METHODS AND RESULTS

Based on the transcriptome data of B. luzhaiensis, 60 primer pairs were selected for initial validation, of which 16 yielded polymorphic microsatellite loci in 57 individuals. The number of alleles observed for these 16 loci ranged from one to nine. The observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.804 with averages of 0.370 and 0.404, respectively. Five loci could be successfully amplified in B. leprosa.

CONCLUSIONS

The expressed sequence tag-simple sequence repeat markers are the first specifically developed for B. luzhaiensis and the first developed in Begonia sect. Coelocentrum. These markers will be useful for future studies of the genetic structure and phylogeography of B. luzhaiensis.

Building Bridges for Innovation in Ageing: Synergies between Action Groups of the EIP on AHA

The Strategic Implementation Plan of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA) proposed six Action Groups. After almost three years of activity, many achievements have been obtained through commitments or collaborative work of the Action Groups. However, they have often worked in silos and, consequently, synergies between Action Groups have been proposed to strengthen the triple win of the EIP on AHA. The paper presents the methodology and current status of the Task Force on EIP on AHA synergies. Synergies are in line with the Action Groups' new Renovated Action Plan (2016-2018) to ensure that their future objectives are coherent and fully connected. The outcomes and impact of synergies are using the Monitoring and Assessment Framework for the EIP on AHA (MAFEIP). Eight proposals for synergies have been approved by the Task Force: Five cross-cutting synergies which can be used for all current and future synergies as they consider overarching domains (appropriate polypharmacy, citizen empowerment, teaching and coaching on AHA, deployment of synergies to EU regions, Responsible Research and Innovation), and three cross-cutting synergies focussing on current Action Group activities (falls, frailty, integrated care and chronic respiratory diseases).

ARIA 2016: Care pathways implementing emerging technologies for predictive medicine in rhinitis and asthma across the life cycle

The Allergic Rhinitis and its Impact on Asthma (ARIA) initiative commenced during a World Health Organization workshop in 1999. The initial goals were (1) to propose a new allergic rhinitis classification, (2) to promote the concept of multi-morbidity in asthma and rhinitis and (3) to develop guidelines with all stakeholders that could be used globally for all countries and populations. ARIA—disseminated and implemented in over 70 countries globally—is now focusing on the implementation of emerging technologies for individualized and predictive medicine. MASK [MACVIA (Contre les Maladies Chroniques pour un Vieillissement Actif)-ARIA Sentinel NetworK] uses mobile technology to develop care pathways for the management of rhinitis and asthma by a multi-disciplinary group and by patients themselves. An app (Android and iOS) is available in 20 countries and 15 languages. It uses a visual analogue scale to assess symptom control and work productivity as well as a clinical decision support system. It is associated with an inter-operable tablet for physicians and other health care professionals. The scaling up strategy uses the recommendations of the European Innovation Partnership on Active and Healthy Ageing. The aim of the novel ARIA approach is to provide an active and healthy life to rhinitis sufferers, whatever their age, sex or socio-economic status, in order to reduce health and social inequalities incurred by the disease.

Sex Distribution of Paper Mulberry (Broussonetia papyrifera) in the Pacific

Background

Paper mulberry (Broussonetia papyrifera (L.) L'Hér. ex Vent) is a dioecious tree native to East Asia and mainland Southeast-Asia, introduced prehistorically to Polynesia as a source of bark fiber by Austronesian-speaking voyagers. In Oceania, trees are coppiced and harvested for production of bark-cloth, so flowering is generally unknown. A survey of botanical records of paper mulberry revealed a distributional disjunction: the tree is apparently absent in Borneo and the Philippines. A subsequent study of chloroplast haplotypes linked paper mulberry of Remote Oceania directly to a population in southern Taiwan, distinct from known populations in mainland Southeast-Asia.

Methodology

We describe the optimization and use of a DNA marker designed to identify sex in paper mulberry. We used this marker to determine the sex distribution in selected localities across Asia, Near and Remote Oceania. We also characterized all samples using the ribosomal internal transcribed spacer sequence (ITS) in order to relate results to a previous survey of ITS diversity.

Results

In Near and Remote Oceania, contemporary paper mulberry plants are all female with the exception of Hawaii, where plants of both sexes are found. In its natural range in Asia, male and female plants are found, as expected. Male plants in Hawaii display an East Asian ITS genotype, consistent with modern introduction, while females in Remote Oceania share a distinctive variant.

Conclusions

Most paper mulberry plants now present in the Pacific appear to be descended from female clones introduced prehistorically. In Hawaii, the presence of male and female plants is thought to reflect a dual origin, one a prehistoric female introduction and the other a modern male introduction by Japanese/Chinese immigrants. If only female clones were dispersed from a source-region in Taiwan, this may explain the absence of botanical records and breeding populations in the Philippines and Borneo, and Remote Oceania.

Avoiding artefacts during electron microscopy of silver nanomaterials exposed to biological environments

Electron microscopy has been applied widely to study the interaction of nanomaterials with proteins, cells and tissues at nanometre scale. Biological material is most commonly embedded in thermoset resins to make it compatible with the high vacuum in the electron microscope. Room temperature sample preparation protocols developed over decades provide contrast by staining cell organelles, and aim to preserve the native cell structure. However, the effect of these complex protocols on the nanomaterials in the system is seldom considered. Any artefacts generated during sample preparation may ultimately interfere with the accurate prediction of the stability and reactivity of the nanomaterials. As a case study, we review steps in the room temperature preparation of cells exposed to silver nanomaterials (AgNMs) for transmission electron microscopy imaging and analysis. In particular, embedding and staining protocols, which can alter the physicochemical properties of AgNMs and introduce artefacts thereby leading to a misinterpretation of silver bioreactivity, are scrutinized. Recommendations are given for the application of cryogenic sample preparation protocols, which simultaneously fix both particles and diffusible ions. By being aware of the advantages and limitations of different sample preparation methods, compromises or selection of different correlative techniques can be made to draw more accurate conclusions about the data.