Recent Submissions

  • Nance-Horan Syndrome-like 1 protein negatively regulates Scar/WAVE-Arp2/3 activity and inhibits lamellipodia stability and cell migration

    Law, Ah-Lai; Jalal, Shamsinar; Pallett, Tommy; Mosis, Fuad; Guni, Ahmad; Brayford, Simon; Yolland, Lawrence; Marcotti, Stefania; Levitt, James A.; Poland, Simon P.; et al. (Nature Research, 2021-09-28)
    Cell migration is important for development and its aberrant regulation contributes to many diseases. The Scar/WAVE complex is essential for Arp2/3 mediated lamellipodia formation during mesenchymal cell migration and several coinciding signals activate it. However, so far, no direct negative regulators are known. Here we identify Nance-Horan Syndrome-like 1 protein (NHSL1) as a direct binding partner of the Scar/WAVE complex, which co-localise at protruding lamellipodia. This interaction is mediated by the Abi SH3 domain and two binding sites in NHSL1. Furthermore, active Rac binds to NHSL1 at two regions that mediate leading edge targeting of NHSL1. Surprisingly, NHSL1 inhibits cell migration through its interaction with the Scar/WAVE complex. Mechanistically, NHSL1 may reduce cell migration efficiency by impeding Arp2/3 activity, as measured in cells using a Arp2/3 FRET-FLIM biosensor, resulting in reduced F-actin density of lamellipodia, and consequently impairing the stability of lamellipodia protrusions.
  • Purification and identification of novel xanthine oxidase inhibitory peptides derived from round scad (Decapterus maruadsi) protein hydrolysates

    Hu, Xiao; Zhou, Ya; Zhou, Shaobo; Chen, Shengjun; Wu, Yanyan; Li, Laihao; Yang, Xianqing; Chinese Academy of Fishery Sciences; Jiangsu Ocean University; Shanghai Ocean University; et al. (MDPI, 2021-09-24)
    The objective of the present study was to investigate the xanthine oxidase (XO) inhibitory effects of peptides purified and identified from round scad (Decapterus maruadsi) hydrolysates (RSHs). In this study, RSHs were obtained by using three proteases (neutrase, protamex and alcalase). Among them, the RSHs of 6-h hydrolysis by neutrase displayed the strongest XO inhibitory activity and had an abundance of small peptides (<500 Da). Four novel peptides were purified by immobilized metal affinity chromatography and identified by nano-high-performance liquid chromatography mass/mass spectrometry. Their amino acid sequences were KGFP (447.53 Da), FPSV (448.51 Da), FPFP (506.59 Da) and WPDGR (629.66 Da), respectively. Then the peptides were synthesized to evaluate their XO inhibitory activity. The results indicated that the peptides of both FPSV (5 mM) and FPFP (5 mM) exhibited higher XO inhibitory activity (22.61 +- 1.81% and 20.09 +- 2.41% respectively). Fluorescence spectra assay demonstrated that the fluorescence quenching mechanism of XO by these inhibitors (FPSV and FPFP) was a static quenching procedure. The study of inhibition kinetics suggested that the inhibition of both FPSV and FPFP was reversible, and the type of their inhibition was a mixed one. Molecular docking revealed the importance of π-π stacking between Phe residue (contained in peptides) and Phe914 (contained in the XO) in the XO inhibitory activity of the peptides.
  • ABL1 and Cofilin1 promote T-cell acute lymphoblastic leukemia cell migration

    Luo, Jixian; Zheng, Huiguang; Wang, Sen; Li, Dingyun; Ma, Wenli; Wang, Lan; Crabbe, M. James C. (Oxford University Press, 2021-09-11)
    The fusion gene of ABL1 is closely related to tumor proliferation, invasion, and migration. It has been reported recently that ABL1 itself is required for T-cell acute lymphoblastic leukemia (T-ALL) cell migration induced by CXCL12. Further experiments revealed that ABL1 inhibitor Nilotinib inhibited leukemia cell migration induced by CXCL12, indicating the possible application of Nilotinib in T-ALL leukemia treatment. However, the interacting proteins of ABL1 and the specific mechanisms of their involvement in this process need further investigation. In the present study, ABL1 interacting proteins were characterized and their roles in the process of leukemia cell migration induced by CXCL12 were investigated. Co-immunoprecipitation in combination with mass spectrometry analysis identified 333 proteins that interact with ABL1, including Cofilin1. Gene ontology analysis revealed that many of them were enriched in the intracellular organelle or cytoplasm, including nucleic acid binding components, transfectors, or co-transfectors. Kyoto Encyclopedia of Genes and Genomes analysis showed that the top three enriched pathways were translation, glycan biosynthesis, and metabolism, together with human diseases. ABL1 and Cofilin1 were in the same complex. Cofilin1 binds the SH3 domain of ABL1 directly; however, ABL1 is not required for the phosphorylation of Cofilin1. Molecular docking analysis shows that ABL1 interacts with Cofilin1 mainly through hydrogen bonds and ionic interaction between amino acid residues. The mobility of leukemic cells was significantly decreased by Cofilin1 siRNA. These results demonstrate that Cofilin1 is a novel ABL1 binding partner. Furthermore, Cofilin1 participates in the migration of leukemia cells induced by CXCL12. These data indicate that ABL1 and Cofilin1 are possible targets for T-ALL treatment.
  • Repeated parallel losses of inflexed stamens in Moraceae: phylogenomics and generic revision of the tribe Moreae and the reinstatement of the tribe Olmedieae (Moraceae)

    Gardner, Elliot M.; Garner, Mira; Cowan, Robyn S.; Dodsworth, Steven; Epitawalage, Niroshini; Arifiani, Deby; Baker, William J.; Forest, Felix; Maurin, Olivier; Zerega, Nyree JC; et al. (Wiley, 2021-07-06)
    We present a densely sampled phylogenomic study of the mulberry tribe (Moreae, Moraceae), an economically important clade with a global distribution, revealing multiple losses of inflexed stamens, a character traditionally used to circumscribe Moreae. Inflexed stamens facilitate ballistic pollen release and are associated with wind pollination, and the results presented here suggest that losses of this character state may have evolved repeatedly in Moraceae. Neither Moreae nor several of its major genera (Morus, Streblus, Trophis) were found to be monophyletic. A revised system for a monophyletic Moreae is presented, including the reinstatement of the genera Ampalis, Maillardia, Taxotrophis, and Paratrophis, and the recognition of the new genus Afromorus. Pseudostreblus is reinstated and transferred to the Parartocarpeae, and Sloetiopsis is reinstated and transferred to the Dorstenieae. The tribe Olmedieae is reinstated, replacing the Castilleae, owing to the reinstatement of the type Olmedia and its exclusion from Moreae. Streblus s.str. is excluded from Moreae and transferred to the Olmedieae, which is characterized primarily by involucrate inflorescences without regard to stamen position. Nine new combinations are made.
  • A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

    Maurin, Olivier; Anest, Artemis; Bellot, Sidonie; Biffin, Edward; Brewer, Grace E.; Charles-Dominique, Tristan; Cowan, Robyn S.; Dodsworth, Steven; Epitawalage, Niroshini; Gallego, Berta; et al. (Wiley, 2021-07-31)
    To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
  • Exploring Angiosperms353: an open, community toolkit for collaborative phylogenomic research on flowering plants

    Baker, William J.; Dodsworth, Steven; Forest, Felix; Graham, Sean W.; Johnson, Matthew G.; McDonnell, Angela J.; Pokorny, Lisa; Tate, Jennifer; Wicke, Susann; Wickett, Norman J.; et al. (Wiley, 2021-07-22)
    The unveiling of the angiosperm (flowering plant) tree of life over the past three decades has been one of the great success stories of modern plant biology. Flowering plants underpin most terrestrial biomes: they fix vast amounts of terrestrial carbon, in turn producing a substantial fraction of planetary oxygen, and drive major biogeochemical cycles. The bulk of human calories are derived either directly (crops) or indirectly (fodder) from angiosperms, as are many medicines, fuel, dyes, beverages, timber, fibers, and other materials. Countless indispensable and mundane items that impact human existence find their origins in flowering plants, and without them, life would be decidedly drearier—imagine a world without herbs, spices, or garden flowers, for example. In this context, the importance of a comprehensive understanding of the angiosperm tree of life cannot be overstated. The tree of life is the fundamental, biological roadmap to the evolution and properties of plants (e.g., Wong et al., 2020). For evolutionary biologists, phylogenies allow us to better understand the spectacular rise of the flowering plants to dominance over the past 140 million or so years (e.g., Lutzoni et al., 2018; Ramírez-Barahona et al., 2020). Information about angiosperm phylogenetic relationships also underpins modern angiosperm classification (e.g., APG IV, 2016), and helps us to better understand species origins and boundaries (e.g., Fazekas et al., 2009). Today, tree of life research is undergoing a renaissance due to the development of powerful, new phylogenomic methods (Dodsworth et al., 2019). In this special issue of the American Journal of Botany, together with a companion issue of Applications in Plant Sciences, we gather a set of papers that focus on a new, common phylogenomic toolkit, the Angiosperms353 probe set (Johnson et al., 2019), and illustrate its potential for evolutionary synthesis by promoting open collaboration across our community.
  • Exploring Angiosperms353: developing and applying a universal toolkit for flowering plant phylogenomics

    McDonnell, Angela J.; Baker, William J.; Dodsworth, Steven; Forest, Felix; Graham, Sean W.; Johnson, Matthew G.; Pokorny, Lisa; Tate, Jennifer; Wickett, Norman J.; Wicke, Susann; et al. (Wiley, 2021-07-26)
    Special Issue Introduction. Target enrichment represents a useful, cost-effective method for researchers working on the phylogenomics of non-model organisms (e.g., Cronn et al., 2012; Hale et al., 2020). The ability to sequence a customizable predefined genomic subset for several dozens or even hundreds of taxa allows in-depth analyses and the testing of phylogenetic hypotheses in ways that were not previously possible (reviewed in McKain et al., 2018). The most popular methods for targeted sequencing of genomic loci in phylogenomics include (long-)amplicon sequencing (Rothfels et al., 2017) and hybridization capture (Mandel et al., 2014; Weitemier et al., 2014). Targeted amplicon sequencing is based on single-fragment PCR amplification or by using multiplexing methods such as a microfluidic PCR-based amplification of multiple pre-selected genomic regions (e.g., Zhang and Ozdemir, 2009; Ho et al., 2014), which can then be pooled and sequenced. Massively parallel amplicon sequencing was first used in medical diagnostics (Turner et al., 2009) and was later applied to metazoan phylogenetics (Bybee et al., 2011; O’Neill et al., 2013). Microfluidic PCR and long-amplicon sequencing were subsequently applied in plant systematics (Uribe-Convers et al., 2014, 2016; Gostel et al., 2015). Amplicon-based methods can be time consuming as they require careful optimization and validation of primers. These methods are also susceptible to many of the common problems in PCR (such as nonspecific products, inability to amplify large loci in their entirety, or simply no products). Recently, amplicon approaches have been largely supplanted by hybridization-based targeted enrichment, which allows for relatively rapid probe design with reference to a few related transcriptomes or genomes, and allows simultaneous and efficient recovery of many hundreds of genes.
  • Management of environmental streaming data to optimize Arctic shipping routes.

    Zhang, Zhihua; Crabbe, M. James C.; University of Bedfordshire; Shandong University (Springer Nature, 2021-07-20)
    Dynamic accurate predictions of Arctic sea ice, ocean, atmosphere, and ecosystem are necessary for safe and efficient Arctic maritime transportation; however a related technical roadmap has not yet been established. In this paper, we propose a management system for trans-Arctic maritime transportation supported by near real-time streaming data from air-space-ground-sea integrated monitoring networks and high spatio-temporal sea ice modeling. As the core algorithm of integrated monitoring networks, a long short-term memory (LSTM) neural network is embedded to improve Arctic sea ice mapping algorithms.Since the LSTM is localized in time and space, it can make full use of streaming data characteristics. The sea ice–related parameters from satellite remote sensing raw data are used as the input of the LSTM, while streaming data from shipborne radar networks and/or buoy measurements are used as training datasets to enhance the accuracy and resolution of environmental streaming data from outputs of LSTM. Due to large size of streaming data, the proposed management system of trans-Arctic shipping should be built on a cloud distribution platform using existing wireless communications networks among vessels and ports. Our management system will be used by the ongoing European Commission Horizon 2020 Programme “ePIcenter.”
  • Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

    Geng, Yu-peng; Guan, Yabin; Qiong, La; Lu, Shugang; An, Miao; Crabbe, M. James C.; Qi, Ji.; Zhao, Fangqing; Qiao, Qin; Zhang, Ti-Cao; et al. (Springer Nature, 2021-07-22)
    Background: Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results: We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two highand two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions: Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.
  • Genetic modifications of metallothionein enhance the tolerance and bioaccumulation of heavy metals in Escherichia coli

    Li, Xuefen; Ren, Zhumei; Crabbe, M. James C.; Wang, Lan; Ma, Wenli; Shanxi University; University of Oxford; University of Bedfordshire (Elsevier, 2021-07-13)
    Metallothioneins (MTs) are low molecular weight cysteine-rich proteins that bind to metals. Owing to their high cysteine (Cys) content, MTs are effective mediators of heavy metal detoxification. To enhance the heavy metal binding ability of MT from the freshwater crab Sinopotamon henanense (ShMT), sequence-based multiple sequence alignment (MSA) and structure-based molecular docking simulation (MDS) were conducted in order to identify amino acid residues that could be mutated to bolster such metal-binding activity. Site-directed mutagenesis was then used to modify the primary structure of ShMT, and the recombinant proteins were further enhanced using the SUMO fusion expression system to yield SUMO-ShMT1, SUMO-ShMT2, and SUMO-ShMT3 harboring one-, two-, and three- point mutations, respectively. The resultant modified proteins were primarily expressed in a soluble form and exhibited the ability to readily bind to heavy metals. Importantly, these modified proteins exhibited significantly enhanced heavy metal binding capacities, and they improved Cd2+, Cu2+ and Zn2+ tolerance and bioaccumulation in Escherichia coli (E. coli) in a manner dependent upon the number of introduced point mutations (SUMO-ShMT3 > SUMO-ShMT2 > SUMO-ShMT1 > SUMO-ShMT > control). Indeed, E. coli cells harboring the pET28a-SUMO-ShMT3 expression vector exhibited maximal Cd2+, Cu2+, and Zn2+ bioaccumulation that was increased by 1.86 ± 0.02-, 1.71 ± 0.03-, and 2.13 ± 0.02-fold relative to that in E. coli harboring the pET28a-SUMO-ShMT vector. The present study offers a basis for the preparation of genetically engineered bacteria that are better able to bioaccumulate and tolerate heavy metals, thus providing a foundation for biological heavy metal water pollution treatment.
  • Evaluation of genetic diversity and population structure of Fragaria nilgerrensis using EST-SSR markers

    Liu, Jie; Zhang, Yichen; Diao, Xia; Yu, Kun; Dai, Xiongwei; Qu, Peng; Crabbe, M. James C.; Zhang, Ti-Cao; Qiao, Qin; Yunnan University; et al. (Elsevier, 2021-06-25)
    Fragaria nilgerrensis is a diploid wild strawberry widely distributed in Southwest China. Its white color and “peach-like” fragrance of fruits are valuable characters for the genetic improvement of cultivated strawberry plants. Its strong biotic and abiotic resistance and tolerance also enable it to survive in different habitats in the field. In this study, we evaluated the level of genetic variation within and between 16 populations with 169 individuals of F. nilgerrensis using 16 newly developed EST-SSR (expressed sequence tag-simple sequence repeats) markers. The results show that the genetic diversity of this species was high, based on Nei’s genetic diversity (0.26) and polymorphic loci (0.41), although it is self-compatible and has clonal propagation. Significant genetic differentiation among populations was also detected by AMOVA analysis (Fst = 0.34), which could be indicative of little gene flow (Nm = 0.43) in F. nilgerrensis. The phylogenetic tree indicates that most of individuals from the same population have clustered together. These populations were not grouped based on the geographical distance, consistent with the Mantel test result (R2 = 0.0063, P > 0.05). All the populations were assigned into two ancestral groups, with some individuals admixed, suggesting ancestral gene flow had occurred between these two groups. Our developed EST-SSR markers as well as the genetic diversity and population structure analysis of F. nilgerrensis are important for genetic improvement in the breeding process. Moreover, the populations that contain high genetic diversity would be a priority for collection and conservation.
  • Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA

    Costa, Lucas; Marques, André; Buddenhagen, Chris; Thomas, William Wayt; Huettel, Bruno; Schubert, Veit; Dodsworth, Steven; Houben, Andreas; Souza, Gustavo; Pedrosa-Harand, Andrea (Oxford University Press, 2021-05-29)
    With the advance of high-throughput sequencing (HTS), reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information, particularly from coding regions. As the off-target reads from such sequencing are expected to be similar to genome skimming (GS), we assessed the quality of repeat characterization in plant genomes using this data. Repeat composition obtained from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. In addition, a FISH probe was designed based on the most abundant satellite found in the TCS dataset of Rhynchospora cephalotes. Finally, repeat-based phylogenies of the five Rhynchospora species were constructed based on the GS and TCS dataset and the topologies were compared with a gene-alignment based phylogenetic tree. All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01% in the GS data. Rank correlation between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS was also reliable to develop a cytogenetic probe of a new variant of the holocentromeric satellite Tyba. Repeat-based phylogenies from TCS data were congruent with those obtained from GS data and the gene-alignment tree. Our results show that off-target TCS reads can be recycled to identify repeats for cyto- and phylogenomic investigations. Given the growing availability of TCS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.
  • Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

    Ottenlips, Michael V.; Mansfield, Donald H.; Buerki, Sven; Feist, Mary Ann E.; Downie, Stephen R.; Dodsworth, Steven; Forest, Felix; Plunkett, Gregory M.; Smith, James F.; Boise State University; et al. (Wiley, 2021-06-08)
    Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.
  • Encapsulation of α-tocopherol in whey protein isolate/chitosan particles using oil-in-water emulsion with optimal stability and bioaccessibility

    Xu, Weili; Lv, Kangxing; Mu, Wei; Zhou, Shaobo; Yang, Yang; University of Bedfordshire; Harbin Institute of Technology (Elsevier, 2021-05-23)
    The aim of this study was to develop an oil-in-water (O/W) emulsion using whey protein isolate (WPI)-chitosan (CN) complex to encapsulate α-tocopherol and to characterize their stability and bioaccessibility in vitro. The O/W emulsions prepared under the optimal conditions (mass ratio of WPI:CN = 1: 1, corn oil containing 5 g/100 g of α-tocopherol) exhibited a monomodal distribution (d = 803.3 ± 6.9 nm) with encapsulation rate of 86.3 ± 2.3%. The emulsions were stable under NaCl (0–150 mmol/L), sugar (0–5 g/100 g), 55 °C for 30 min, pH 5–6.5, even storage for 20 d at 4 °C and 25 °C. During gastric digestion, WPI situated at the surface of emulsion particles can be digested into small molecular peptides by pepsin, but the structure of the core-shell particles remained due to the cross-linking with CN. During intestinal digestion, the structure of the particles disintegrated over the digestion time, and the inner-oil phase was released. Release profiles of the α-tocopherol and free fatty acids showed a burst effect followed by slow release. These results suggest that the WPI-CN complex could be used to achieve a controlled and sustainable release of liposoluble bioactive compounds from O/W emulsions.
  • A comprehensive phylogenomic platform for exploring the angiosperm tree of life

    Baker, William J.; Bailey, Paul; Barber, Vanessa; Barker, Abigail; Bellot, Sidonie; Bishop, David; Botigué, Laura R.; Brewer, Grace E.; Carruthers, Tom; Clarkson, James J.; et al. (Oxford University Press, 2021-05-13)
    The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer ( ). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A "first pass" angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world's natural history collections.
  • Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

    Serna-Sánchez, Maria Alejandra; Pérez-Escobar, Oscar A.; Bogarín, Diego; Torres-Jimenez, María Fernanda; Alvarez-Yela, Astrid Catalina; Arcila-Galvis, Juliana E.; Hall, Climbie F.; de Barros, Fábio; Pinheiro, Fábio; Dodsworth, Steven; et al. (SpringerNature, 2021-03-25)
    Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
  • Extensive plastid-nuclear discordance in a recent radiation of Nicotiana section Suaveolentes (Solanaceae)

    Dodsworth, Steven; Christenhusz, Maarten J.M.; Conran, John G.; Guignard, Maite S.; Knapp, Sandra; Struebig, Monika; Leitch, Andrew R.; Chase, Mark W. (Oxford University Press, 2020-05-24)
    Nicotiana section Suaveolentes is the largest section of Nicotiana and is a monophyletic group of allotetraploid species. Most of the species are endemic to Australia, but three species occur on islands in the South Pacific as far east as French Polynesia and one species is native to Namibia. Here, we present phylogenetic results based on genome skimming, with near-complete taxon sampling and multiple accessions sampled for several species. These represent the first phylogenetic results for the section that include most recognized taxa, using wild-sourced material wherever possible. Despite known chromosome number and genome size changes in the section, there is little divergence in the ribosomal DNA operon (26S, 18.S and 5.8S plus associated spacers) and plastid genomes, with little to no taxonomic signal in plastome phylogenetic results and clear plastid-nuclear discordance. These results contrast with strong morphological differentiation (both floral and vegetative) between most of the core Australian taxa and obvious differences in ecological preferences. Together, these initial results portray Nicotiana section Suaveolentes as experiencing recent and ongoing radiation in the arid zone of Australia.
  • Liqui-pellet: the emerging next-generation oral dosage form which stems from liquisolid concept in combination with pelletization technology

    Lam, Matthew; Ghafourian, Taravat; Nokhodchi, Ali (Springer New York LLC, 2019-06-24)
    In spite of the major advantages that the liquisolid technology offers, particularly in tackling poor bioavailability of poorly water-soluble drugs (i.e., BCS Class II drugs), there are a few critical drawbacks. The inability of a high liquid load factor, poor flowability, poor compactibility, and an inability to produce a high dose dosage form of a reasonable size for swallowing are major hurdles, hampering this technology from being commercially feasible. An attempt was therefore made to overcome these drawbacks whilst maintaining the liquisolid inherent advantages. This resulted in the emerging next generation of oral dosage forms called the liqui-pellet. All formulations were incorporated into capsules as the final product. Solubility studies of naproxen were conducted in different liquid vehicles, namely polyethylene glycol 200, propylene glycol, Tween 80, Labrafil, Labrasol, and Kolliphor EL. The scanning electron microscopy studies indicated that the liquid vehicle tends to reduce the surface roughness of the pellet. X-ray powder diffraction (XRPD) indicated no significant differences in the crystalline structure or amorphous content between the physical mixture and the liqui-pellet formulation. This was due to the presence of a high concentration of amorphous Avicel in the formulation which overshadowed the crystalline structure of naproxen in the physical mixtures. Flowability and dissolution tests confirmed that this next-generation oral dosage form has excellent flowability, whilst maintaining the typical liquisolid enhanced drug release performance in comparison to its physical mixture counterpart. The liqui-pellet also had a high liquid load factor of 1, where ~ 29% of the total mass was the liquid vehicle. This shows that a high liquid load factor can be achieved in a liqui-pellet without compromising flowability. Overall, the results showed that the poor flowability of a liquisolid formulation could be overcomed with the liqui-pellet, which is believed to be a major advancement into the commercial feasibility of the liquisolid concept.
  • Optimising the release rate of naproxen liqui-pellet: a new technology for emerging novel oral dosage form

    Lam, Matthew; Ghafourian, Taravat; Nokhodchi, Ali; (Springer, 2019-07-08)
    Liqui-pellet is a new dosage form stemming from pelletisation technology and concept from liquisolid technology. In spite of liqui-pellet overcoming a major hurdle in liquisolid technology through achieving excellent flow property with high liquid load factor, the formulation requires to be optimised in order to improve drug release rate. Liqui-pellets of naproxen containing Tween 80, Primojel, Avicel and Aerosil were extruded and spheronised. Flowability test confirmed that all liqui-pellet formulations have excellent-good flow property (Carr’s index between 3.9–11.17%), including liqui-pellets with a high liquid load factor of 1.52, where 38% of the total mass is co-solvent. This shows a relatively high liquid load factor can be achieved in liqui-pellet without compromising the flowability, which is one of the key novelty of this work. It was found that the improved drug release rate was due to the remarkably improved disintegration of the supposedly non-disintegrating microcrystalline-based pellet; the optimised liqui-pellet seems to explode into fragments in the dissolution medium. At pH 1.2, the optimised formulation had ~ 10% more drug release than non-optimised formulation after 2 h, and at pH 7.4, the drug release of the optimised pellet was nearing 100% at ~ 15 min, whereas the none-optimised pellet only achieved ~ 79% drug release after 2 h. DSC and XRPD indicated an increase in the dissolution rate could be due to molecularly dispersion of naproxen in the pellets. Overall results showed that liqui-pellet exhibited an enhanced drug release and the capacity for high liquid load factor whilst maintaining excellent flowability, rendering it a potentially commercially feasible drug delivery system.
  • Critical role of the maternal immune system in the pathogenesis of autism spectrum disorder

    Ravaccia, Davide; Ghafourian, Taravat; University of Sussex (MDPI AG, 2020-12-01)
    Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders characterised by impairments in communication, social interaction, and the presence of restrictive and repetitive behaviours. Over the past decade, most of the research in ASD has focused on the contribution of genetics, with the identification of a variety of different genes and mutations. However, the vast heterogeneity in clinical presentations associated with this disorder suggests that environmental factors may be involved, acting as a “second hit” in already genetically susceptible individuals. To this regard, emerging evidence points towards a role for maternal immune system dysfunctions. This literature review considered evidence from epidemiological studies and aimed to discuss the pathological relevance of the maternal immune system in ASD by looking at the proposed mechanisms by which it alters the prenatal environment. In particular, this review focuses on the effects of maternal immune activation (MIA) by looking at foetal brain-reactive antibodies, cytokines and the microbiome. Despite the arguments presented here that strongly implicate MIA in the pathophysiology of ASD, further research is needed to fully understand the precise mechanisms by which they alter brain structure and behaviour. Overall, this review has not only shown the importance of the maternal immune system as a risk factor for ASD, but more importantly, has highlighted new promising pathways to target for the discovery of novel therapeutic interventions for the treatment of such a life-changing disorder.

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