• 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.
    • 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.”
    • 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.
    • 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.
    • 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.
    • 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 (https://treeoflife.kew.org ). 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.
    • COVID-19 in Wuhan, China: pressing realities and city management

      Li, Rita Yi Man; Yue, Xiao-Guang; Crabbe, M. James C.; Hong Kong Shue Yan University; European University of Cyprus; Oxford University; University of Bedfordshire; Shanxi University (Frontiers, 2021-02-17)
      To most economists around the World, Covid-19 has provided an objective lesson in market failure. In the absence of complete information and sometimes even fake news, nobody knew what kind of pandemic it was at the beginning. Yet, there were 32,583 patients with laboratory-confirmed Covid-19 in Wuhan between December 8, 2019, and 8 March 8, 2020. The pandemic crippled and continues to cripple many health systems and has created unprecedented pressure on the psychological and physical aspects of millions of people's lives around the world. Over 200 countries and territories suffer from an acute shortage of medical personnel and medical equipment. The responses of different countries to Covid-19 has involved a range of measures that reflect national values, politics, and variations in scientific advice provided by local experts. Political considerations have often become more important than science. The Covid-19 outbreak in Wuhan was one of the most serious cases amongst all cities in the world, yet Wuhan managed and gain control of this pandemic. Health care systems and policies are important aspects that affect the control of infectious diseases like Covid-19. In China, 98% of primary health-care is complemented by traditional Chinese medicine (TCM) with allopathic approaches. Previous research has found that the cure rate increased by 33% among mild cases after adopting TCM with allopathic approaches. The hospital stay of severe patients with TCM's and nucleic acid turning negative was shortened by over 2 days. Prior to Covid-19, the government's Healthy China 2030 plan was already addressing chronic diseases in the aging population by raising healthcare expenditure. This is in sharp contrast to other countries with aging population problems such as Italy, where the government cut the healthcare budget substantially after the economic downturn. Hospital bed allocation went down from a maximum of four for every thousand inhabitants to a maximum of 3.7, despite the fact that 23.1% of the Italian population were aged 65 years and older in 2020. Likewise, the post-2008 financial crisis in Spain forced severe cuts to healthcare costs, which caused pressure on the system when there was an increase in demand for healthcare services. These measures particularly affected the elderly and disabled who are more vulnerable to Covid-19. Healthcare costs become underfunded at the level of 6.4% of GDP. Apart from scientific evidence on the effectiveness of TCM in curing covid, financial expenditures on health care is an important distal factor that helped Wuhan overcome Covid-19 quickly. In the following sections of this paper, we review the three city management stages adopted in Wuhan, to study proximal causes of success in combating the virus: (1) strong government intervention early in the outbreak; (2) the city lockdown; and, (3) the use of digital measures, such as a health code, when the city reopened.
    • Genome sequence of the biocontrol agent coniothyrium minitans conio (IMI 134523)

      Patel, Denise; Shittu, Taiwo Adewale; Baroncelli, Riccardo; Muthumeenakshi, Sreenivasaprasad; Osborne, Thomas H.; Janganan, Thamarai K.; Sreenivasaprasad, Surapareddy; University of Bedfordshire (American Phytopathological Society, 2021-02-16)
      Coniothyrium minitans (synonym, Paraphaeosphaeria minitans) is a highly specific mycoparasite of the wide host range crop pathogen Sclerotinia sclerotiorum. The capability of C. minitans to destroy the sclerotia of S. sclerotiorum has been well recognized and it is available as a widely used biocontrol product Contans WG. We present the draft genome sequence of C. minitans Conio (IMI 134523), which has previously been used in extensive studies that formed part of a registration package of the commercial product. This work provides a distinctive resource for further research into the molecular basis of mycoparasitism to harness the biocontrol potential of C. minitans.
    • Extreme climate response to marine cloud brightening in the arid Sahara-Sahel-Arabian Peninsula zone

      Zhu, Yuanzhuo; Zhang, Zhihua; Crabbe, M. James C.; Shandong University; Beijing Normal University; Oxford University; University of Bedfordshire; Shanxi University (Emerald, 2021-02-08)
      Purpose Climatic extreme events are predicted to occur more frequently and intensely and will significantly threat the living of residents in arid and semi-arid regions. Therefore, this study aims to assess climatic extremes’ response to the emerging climate change mitigation strategy using a marine cloud brightening (MCB) scheme. Design/methodology/approach Based on Hadley Centre Global Environmental Model version 2-Earth System model simulations of a MCB scheme, this study used six climatic extreme indices [i.e. the hottest days (TXx), the coolest nights (TNn), the warm spell duration (WSDI), the cold spell duration (CSDI), the consecutive dry days (CDD) and wettest consecutive five days (RX5day)] to analyze spatiotemporal evolution of climate extreme events in the arid Sahara-Sahel-Arabian Peninsula Zone with and without MCB implementation. Findings Compared with a Representative Concentration Pathways 4.5 scenario, from 2030 to 2059, implementation of MCB is predicted to decrease the mean annual TXx and TNn indices by 0.4–1.7 and 0.3–2.1°C, respectively, for most of the Sahara-Sahel-Arabian Peninsula zone. It would also shorten the mean annual WSDI index by 118–183 days and the mean annual CSDI index by only 1–3 days, especially in the southern Sahara-Sahel-Arabian Peninsula zone. In terms of extreme precipitation, MCB could also decrease the mean annual CDD index by 5–25 days in the whole Sahara and Sahel belt and increase the mean annual RX5day index by approximately 10 mm in the east part of the Sahel belt during 2030–2059. Originality/value The results provide the first insights into the impacts of MCB on extreme climate in the arid Sahara-Sahel-Arabian Peninsula zone.
    • MicroRNAs for virus pathogenicity and host responses, identified in SARS-CoV-2 genomes, may play roles in viral-host co-evolution in putative zoonotic host species

      Lange, Sigrun; Arisan, Elif Damla; Grant, Guy H.; Uysal-Onganer, Pinar; University of Westminster; Gebze Technical University; University of Bedfordshire (MDPI, 2021-01-16)
      Our recent study identified seven key microRNAs (miR-8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) similar between SARS-CoV-2 and the human genome, pointing at miR-related mechanisms in viral entry and the regulatory effects on host immunity. To identify the putative roles of these miRs in zoonosis, we assessed their conservation, compared with humans, in some key wild and domestic animal carriers of zoonotic viruses, including bat, pangolin, pig, cow, rat, and chicken. Out of the seven miRs under study, miR-3611 was the most strongly conserved across all species; miR-5197 was the most conserved in pangolin, pig, cow, bat, and rat; miR-1307 was most strongly conserved in pangolin, pig, cow, bat, and human; miR-3691-3p in pangolin, cow, and human; miR-3934-3p in pig and cow, followed by pangolin and bat; miR-1468 was most conserved in pangolin, pig, and bat; while miR-8066 was most conserved in pangolin and pig. In humans, miR-3611 and miR-1307 were most conserved, while miR-8066, miR-5197, miR-3334-3p and miR-1468 were least conserved, compared with pangolin, pig, cow, and bat. Furthermore, we identified that changes in the miR-5197 nucleotides between pangolin and human can generate three new miRs, with differing tissue distribution in the brain, lung, intestines, lymph nodes, and muscle, and with different downstream regulatory effects on KEGG pathways. This may be of considerable importance as miR-5197 is localized in the spike protein transcript area of the SARS-CoV-2 genome. Our findings may indicate roles for these miRs in viral-host co-evolution in zoonotic hosts, particularly highlighting pangolin, bat, cow, and pig as putative zoonotic carriers, while highlighting the miRs' roles in KEGG pathways linked to viral pathogenicity and host responses in humans. This in silico study paves the way for investigations into the roles of miRs in zoonotic disease.
    • Targeted editing of SlMAPK6 using CRISPR/Cas9 technology to promote the development of axillary buds in tomato plants

      Li, Yunzhou; Yue, Ningbo; Basit, Abdul; Li, Yulong; Zhang, Dalong; Qin, Lei; Crabbe, M. James C.; Xu, Wen; Wang, Yong; Yan, Jianmin; et al. (Canadian Center of Science and Education, 2021-01-15)
      The mitogen-activated protein kinase (MAPK) cascade signaling system has been relatively conserved throughout the evolution of eukaryotes and is involved in the regulation of growth and development and metabolism. In this study, dwarf tomato plants were used as the research material. First, the tissue-specific expression of SlMAPK6 was measured in wild-type plants by quantitative RT-PCR. The results showed that SlMAPK6 was highly expressed in the tissues of the stems, leaves and flowers but was expressed at low levels in the tissues of the roots, sepals and fruits. Second, SlMAPK6-knockout lines CRISPR-3 and CRISPR-7 were obtained by CRISPR-Cas9 technology and Agrobacterium-mediated transformation. Compared with wild-type, the mutant lines CRISPR-3 and CRISPR-7 showed significant phenotypic characteristics, such as increased numbers of axillary buds and true leaves, thickened stems, and longer leaflets. In addition, to explore the molecular mechanism by which MAPK regulates axillary bud growth, we also showed that SlMAPK6 positively regulates the strigolactone synthesis genes SlCCD7 and SlCCD8 and the gibberellin (GA) synthesis genes GA20ox3 and GA3ox1 and negatively regulates the axillary bud development-related genes Ls, BL and BRC1b/TCP8 and the GA synthesis inhibitory gene GAI. Therefore, SlMAPK6 appears to regulate the synthesis of strigolactone and GA to induce the growth and development of tomato axillary buds.
    • Migration of BEAS-2B cells enhanced by H1299 cell derived-exosomes

      Wang, Shuwei; Ju, Tuoyu; Wang, Jiajia; Yang, Fan; Qu, Kaige; Liu, Wei; Wang, Zuobin; Jilin University; Changchun University of Science and Technology; University of Bedfordshire (Elsevier Ltd, 2021-01-12)
      Previous studies reported that exosomes (Exos) secreted by tumor cells could affect the tumor cells themselves and normal cells. However, the effects of exosomes derived from tumor cells on normal cells’ migration and mechanical characteristics are rarely reported. This work explores the effects of H1299 cell-derived exosomes (H1299-Exos) on the migration of BEAS-2B cells, and analyzes possible mechanical mechanisms. In the experiments, exosomes were isolated from the culture supernatants of H1299 cells by ultracentrifugation. The H1299-Exos were confirmed by scanning electron microscope (SEM) and western blotting (WB). The BEAS-2B cell migration was assessed using scratch assays. Cytoskeletal structure changes were detected by immunofluorescence. Surface morphology and mechanical properties were measured by atomic force microscopy (AFM). After incubation with H1299-Exos for 48 h, BEAS-2B cells enhanced migration ability, with increased filopodia and cytoskeletal rearrangements. The changes in the morphology and mechanical properties of the cells caused by H1299-Exos were detected using AFM, including the increase in cell length and the decrease in cell height, Young's modulus and adhesion. In short, H1299-Exos promoted the BEAS-2B cell migrations. It indicates that the morphological and mechanical properties can be used as a means to assess normal cell alterations induced by tumor cell derived-exosomes. This provides a method for studying the effects of exosomes secreted by tumor cells on normal cells and the changes in their physical properties.
    • Bovine milk fat globule epidermal growth factor Ⅷ activates PI3K/Akt signaling pathway and attenuates sarcopenia in rat model induced by D-galactose

      Li, He; Wang, Rongchun; Wang, Lifeng; Li, Lin; Ma, Ying; Zhou, Shaobo; Jiangsu Normal University; Harbin Institute of Technology; Northeast Agriculture University; University of Bedfordshire (Elsevier, 2020-12-17)
      To develop a more effective and safer treatment for sarcopenia, this research investigated the anti-sarcopenia mechanism of Milk Fat Globule Epidermal Growth Factor Ⅷ (MFG-E8) from the liver function and metabolism in sarcopenic model rat. After 4 weeks nutritional intervention experiment, MFG-E8 can significantly increase the gastrocnemius mass in rat. The mechanism of MFG-E8 in improving sarcopenia was related to its promotional capacity to the activities of superoxide dismutase (SOD) activity in serum, Glutamic-oxaloacetic transaminase (GOT) and glutamic-pyruvic transaminase (GPT) in liver. Meanwhile, MFG-E8 could also down-regulate obesity-related indicators, such as triglyceride (TG) and Non-esterified fatty acid (NEFA). The analysis of liver and gastrocnemius histopathology found that MFG-E8 could reduce the accumulation of fatty vesicles, improve liver function, thereby alleviating gastrocnemius tissue inflammation. In vitro experiments, myoblasts obtained from gastrocnemius tissue showed that MFG-E8 could reduce mitochondrial autophagy and inhibit cell apoptosis. In addition, MFG-E8 could up-regulate the phosphorylation level of PI3K via activating PI3K/Akt signaling pathway in gastrocnemius tissue, and promote the formation of muscle fibers, thereby increasing muscle mass. Moreover, MFG-E8 could also promote the formation of neuromuscular junctions by up-regulating the mRNA and protein expression of MusK in gastrocnemius.
    • QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach

      Rosell-Hidalgo, Alicia; Young, Luke; Moore, Anthony L.; Ghafourian, Taravat; University of Sussex; University of Bedfordshire (Springer Science and Business Media Deutschland GmbH, 2020-12-08)
      The alternative oxidase (AOX) is a monotopic diiron carboxylate protein that catalyses the oxidation of ubiquinol and the reduction of oxygen to water. Although a number of AOX inhibitors have been discovered, little is still known about the ligand–protein interaction and essential chemical characteristics of compounds required for a potent inhibition. Furthermore, owing to the rapidly growing resistance to existing inhibitors, new compounds with improved potency and pharmacokinetic properties are urgently required. In this study we used two computational approaches, ligand–protein docking and Quantitative Structure–Activity Relationships (QSAR) to investigate binding of AOX inhibitors to the enzyme and the molecular characteristics required for inhibition. Docking studies followed by protein–ligand interaction fingerprint (PLIF) analysis using the AOX enzyme and the mutated analogues revealed the importance of the residues Leu 122, Arg 118 and Thr 219 within the hydrophobic cavity. QSAR analysis, using stepwise regression analysis with experimentally obtained IC50 values as the response variable, resulted in a multiple regression model with a good prediction accuracy. The model highlighted the importance of the presence of hydrogen bonding acceptor groups on specific positions of the aromatic ring of ascofuranone derivatives, acidity of the compounds, and a large linker group on the compounds on the inhibitory effect of AOX.
    • Effect and mechanism of Ganoderma lucidum spores on alleviation diabetic cardiomyopathy in a pilot in vivo study

      Shaher, Fahmi; Wang, Shuqiu; Qiu, Hong-Bin; Hu, Yu; Zhang, Yu; Wang, Weiqun; AL-ward, Hisham; Abdulghani, Mahfoudh A. M.; Baldi, Salem; Zhou, Shaobo; et al. (Dove Press, 2020-12-07)
      Background: Ganoderma lucidum spores (GLS) exhibit disease prevention properties, but no study has been carried out on the anti-diabetic cardiomyopathy property of GLS. The aim of this study is to evaluate the hyperglycemia-mediated cardiomyopathy protection and mechanisms of GLS in diabetic rats induced by streptozotocin (STZ). Methods: Male SD rats were randomly divided into three groups. Two groups were given STZ (50 mg/kg, i.p.) treatment and when their fasting plasma glucose was above 16.7 mmol/L, one group was given placebo, as diabetic group; and another group was given GLS (300 mg/kg) treatment. The group without STZ treatment was given placebo as a control group. The experiment lasted 70 days. The histology of myocardium and biomarkers of antioxidant, myocardial injury, pro-inflammatory cytokines, pro-apoptotic proteins and phosphorylation of key proteins in PI3K/AKT pathway were assessed. Results: Biochemical analysis showed that GLS treatment significantly reduced the blood glucose (-20.3%) and triglyceride (-20.4%) levels compared to diabetic group without treatment. GLS treatment decreased the content of MDA (-25.6%) and activity of lactate dehydrogenase (-18.9%) but increased the activity of GSH-Px (65.4%). Western blot analysis showed that GLS treatment reduced the expression of both alpha-smooth muscle actin and brain natriuretic peptide. Histological analysis on the cardiac tissue micrographs showed that GLS treatment reduced the collagen fibroses and glycogen reactivity in myocardium. Both western blot and immunohistochemistry analyses showed that GLS treatment decreased the expression levels of pro-inflammatory factors (cytokines IL-1β, and TNF-α) as well as apoptosis regulatory proteins (Bax, caspase-3 and -9), but increased the Bcl-2. Moreover, GLS treatment significantly increased the phosphorylation of key proteins involved in PI3K/AKT pathway, e.g. p-AKT p-PI3K and mTOR. Conclusion: The results indicated that GLS treatment alleviates diabetic cardiomyopathy by reducing hyperglycemia, oxidative stress, inflammation, apoptosis and further attenuating the fibrosis and myocardial dysfunction induced by STZ through the stimulation of the PI3K/Akt/mTOR signaling pathway.
    • 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.
    • Cellular mechanisms governing glucose-dependent insulinotropic polypeptide secretion.

      Reimann, Frank; Diakogiannaki, Eleftheria; Moss, Catherine E.; Gribble, Fiona M.; Wellcome Trust; University of Cambridge (Elsevier, 2020-11-19)
      Glucose-dependent insulinotropic polypeptide (GIP) is a gut hormone secreted from the upper small intestine, which plays an important physiological role in the control of glucose metabolism through its incretin action to enhance glucose-dependent insulin secretion. GIP has also been implicated in postprandial lipid homeostasis. GIP is secreted from enteroendocrine K-cells residing in the intestinal epithelium. K-cells sense a variety of components found in the gut lumen following food consumption, resulting in an increase in plasma GIP signal dependent on the nature and quantity of ingested nutrients. We review the evidence for an important role of sodium-coupled glucose uptake through SGLT1 for carbohydrate sensing, of free-fatty acid receptors FFAR1/FFAR4 and the monoacyl-glycerol sensing receptor GPR119 for lipid detection, of the calcium-sensing receptor CASR and GPR142 for protein sensing, and additional modulation by neurotransmitters such as somatostatin and galanin. These pathways have been identified through combinations of in vivo, in vitro and molecular approaches.