Recent Submissions

  • Increased epigenetic diversity and transient epigenetic memory in response to salinity stress in Thlaspi arvense.

    Geng, Yu-peng; Chang, Na; Zhao, Yuewan; Qin, Xiaoying; Lu, Shugang; Crabbe, M. James C.; Guan, Yabin; Zhang, Ti-Cao (Wiley, 2020-09-20)
    Epigenetic diversity could play an important role in adaptive evolution of organisms, especially for plant species occurring in new and stressful environments. Thlaspi arvense (field pennycress), a valuable oilseed crop, is widespread in temperate regions of the northern hemisphere. In this study, we investigated the effect of salinity stress on the epigenetic variation of DNA methylation and epigenetic stress memory in pennycress using methylation-sensitive amplification polymorphism (MSAP) markers. We examined how the status of DNA methylation changes across individuals in response to salinity stress and whether such an effect of maternal stress could be transferred to offspring for one or two generations in nonstressed environments. Our results based on 306 epiloci indicated no consistent change of DNA methylation status in specific epiloci across individuals within the same conditions. In contrast, we found that the epigenetic diversity at population level increased significantly in response to the stimulation of salinity stress; and this “stimulation effect” could be transferred partially in the form of stress memory to at least two generations of offspring in nonstressed environments. In addition, we observed a parallel change in functionally important traits, that is, phenotypic variation was significantly higher in plants grown under salinity stress compared with those of control groups. Taken together, our results provide novel clues for the increased spontaneous epimutation rate in response to stress in plants, of potential adaptive significance.
  • The solution structure of the complement deregulator FHR5 reveals a compact dimer and provides new insights into CFHR5 nephropathy

    Kadkhodayi-Kholghi, Nilufar; Gor, Jayesh; McDermott, Lindsay C.; Gale, Daniel P.; Perkins, Stephen J.; Bhatt, Jayesh S. (American Society for Biochemistry and Molecular Biology (United States), 2020-09-14)
    The human complement Factor H-related 5 protein (FHR5) antagonizes the main circulating complement regulator Factor H, resulting in the deregulation of complement activation. FHR5 normally contains nine short complement regulator (SCR) domains, but a FHR5 mutant has been identified with a duplicated N-terminal SCR-1/2 domain pair that causes CFHR5 nephropathy. To understand how this duplication causes disease, we characterized the solution structure of native FHR5 by analytical ultracentrifugation and small-angle X-ray scattering. Sedimentation velocity and Xray scattering indicated that FHR5 was dimeric, with a radius of gyration RG of 5.5 ± 0.2 nm and a maximum protein length of 20 nm for its 18 domains. This result indicated that FHR5 was even more compact than the main regulator Factor H which showed an overall length of 26-29 nm for its 20 SCR domains. Atomistic modelling for FHR5 generated a library of 250,000 physically-realistic trial arrangements of SCR domains for scattering curve fits. Only compact domain structures in this library fit well to the scattering data, and these structures readily accommodated the extra SCR-1/2 domain pair present in CFHR5 nephropathy. This model indicated that mutant FHR5 can form oligomers that possess additional binding sites for C3b in FHR5. We conclude that the deregulation of complement regulation by the FHR5 mutant can be rationalized by the enhanced binding of FHR5 oligomers to C3b deposited on host cell surfaces. Our FHR5 structures thus explained key features of the mechanism and pathology of CFHR5 nephropathy.
  • The prediction of miRNAs in SARS-CoV-2 genomes: hsa-miR databases identify 7 key miRs linked to host responses and virus pathogenicity-related KEGG pathways significant for comorbidities

    Arisan, Elif Damla; Dart, Alwyn; Grant, Guy H.; Arisan, Serdar; Cuhadaroglu, Songul; Lange, Sigrun; Uysal-Onganer, Pinar; ; Gebze Technical University; St George’s University of London; et al. (MDPI, 2020-06-04)
    Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the betacoronavirus family, which causes COVID-19 disease. SARS-CoV-2 pathogenicity in humans leads to increased mortality rates due to alterations of significant pathways, including some resulting in exacerbated inflammatory responses linked to the "cytokine storm" and extensive lung pathology, as well as being linked to a number of comorbidities. Our current study compared five SARS-CoV-2 sequences from different geographical regions to those from SARS, MERS and two cold viruses, OC43 and 229E, to identify the presence of miR-like sequences. We identified seven key miRs, which highlight considerable differences between the SARS-CoV-2 sequences, compared with the other viruses. The level of conservation between the five SARS-CoV-2 sequences was identical but poor compared with the other sequences, with SARS showing the highest degree of conservation. This decrease in similarity could result in reduced levels of transcriptional control, as well as a change in the physiological effect of the virus and associated host-pathogen responses. MERS and the milder symptom viruses showed greater differences and even significant sequence gaps. This divergence away from the SARS-CoV-2 sequences broadly mirrors the phylogenetic relationships obtained from the whole-genome alignments. Therefore, patterns of mutation, occurring during sequence divergence from the longer established human viruses to the more recent ones, may have led to the emergence of sequence motifs that can be related directly to the pathogenicity of SARS-CoV-2. Importantly, we identified 7 key-microRNAs (miRs 8066, 5197, 3611, 3934-3p, 1307-3p, 3691-3p, 1468-5p) with significant links to KEGG pathways linked to viral pathogenicity and host responses. According to Bioproject data (PRJNA615032), SARS-CoV-2 mediated transcriptomic alterations were similar to the target pathways of the selected 7 miRs identified in our study. This mechanism could have considerable significance in determining the symptom spectrum of future potential pandemics. KEGG pathway analysis revealed a number of critical pathways linked to the seven identified miRs that may provide insight into the interplay between the virus and comorbidities. Based on our reported findings, miRNAs may constitute potential and effective therapeutic approaches in COVID-19 and its pathological consequences.
  • Inhibition on JNK mimics silencing of Wnt-11 mediated cellular response in androgen-independent prostate cancer cells

    Arisan, Elif Damla; Rencuzogullari, Ozge; Keskin, Buse; Grant, Guy H.; Uysal-Onganer, Pinar; Gebze Technical University; Istanbul Kultur University; University of Bedfordshire; University of Westminster (MDPI, 2020-06-27)
    Prostate cancer (PCa) is one of the most common cancers among men, and one of the leading causes of cancer death for men. The c-Jun N-terminal kinase (JNK) pathway is required for several cellular functions, such as survival, proliferation, differentiation, and migration. Wnt-11, a member of the Wnt family, has been identified for its upregulation in PCa; however, downstream signalling of Wnt-11 remains to be fully characterized. In this study, we investigated the role of the JNK pathway as a potential downstream factor for Wnt-11 signalling. For this purpose, LNCaP, DU145, and PC-3 PCa cells and normal epithelial PNT1A cells were treated with a specific JNK kinase inhibitor: JNKVIII. Our results showed that JNK inhibition decreased mitochondrial membrane potential and promoted cell death in a cell type-dependent manner. We found that JNK inhibition led to an increase in autophagy and prevented epithelial-mesenchymal transition (EMT) in independently growing androgen cells. JNK inhibition and the silencing of Wnt-11 showed similar responses in DU145 and PC-3 cells and decreased metastasis-related biomarkers, cell migration, and invasion. Overall, our results suggest that JNK signalling plays a significant role in the pathophysiology of PCa by mediating Wnt-11 induced signals. Our data highlights that both the JNK pathway and Wnt-11 could be a useful therapeutic target for the combinatory application of current PCa.
  • Oral ingestion of bacterially expressed dsrna can silence genes and cause mortality in a highly invasive, tree-killing pest, the emerald ash borer

    Leelesh, Ramya Shanivarsanthe; Rieske, Lynne K.; University of Kentucky; University of Bedfordshire (MDPI, 2020-07-14)
    RNA interference (RNAi) is a naturally occurring process inhibiting gene expression, and recent advances in our understanding of the mechanism have allowed its development as a tool against insect pests. A major challenge for deployment in the field is the development of convenient and efficient methods for production of double stranded RNA (dsRNA). We assessed the potential for deploying bacterially produced dsRNA as a bio-pesticide against an invasive forest pest, the emerald ash borer (EAB). EAB feeds on the cambial tissue of ash trees (Fraxinus spp.), causing rapid death. EAB has killed millions of trees in North America since its discovery in 2002, prompting the need for innovative management strategies. In our study, bacterial expression and synthesis of dsRNA were performed with E. coli strain HT115 using the L4440 expression vector. EAB-specific dsRNAs (shi and hsp) over-expressed in E. coli were toxic to neonate EAB after oral administration, successfully triggering gene silencing and subsequent mortality; however, a non-specific dsRNA control was not included. Our results suggest that ingestion of transformed E. coli expressing dsRNAs can induce an RNAi response in EAB. To our knowledge, this is the first example of an effective RNAi response induced by feeding dsRNA-expressing bacteria in a forest pest.
  • On the origin of giant seeds: the macroevolution of the double coconut (Lodoicea maldivica) and its relatives (Borasseae, Arecaceae)

    Bellot, Sidonie; Bayton, Ross P.; Couvreur, Thomas L.P.; Dodsworth, Steven; Eiserhardt, Wolf L.; Guignard, Maite S.; Pritchard, Hugh W.; Roberts, Lucy; Toorop, Peter E.; Baker, William J. (Wiley, 2020-06-16)
    Seed size shapes plant evolution and ecosystems, and may be driven by plant size and architecture, dispersers, habitat and insularity. How these factors influence the evolution of giant seeds is unclear, as are the rate of evolution and the biogeographical consequences of giant seeds. We generated DNA and seed size data for the palm tribe Borasseae (Arecaceae) and its relatives, which show a wide diversity in seed size and include the double coconut (Lodoicea maldivica), the largest seed in the world. We inferred their phylogeny, dispersal history and rates of change in seed size, and evaluated the possible influence of plant size, inflorescence branching, habitat and insularity on these changes. Large seeds were involved in 10 oceanic dispersals. Following theoretical predictions, we found that: taller plants with fewer-branched inflorescences produced larger seeds; seed size tended to evolve faster on islands (except Madagascar); and seeds of shade-loving Borasseae tended to be larger. Plant size and inflorescence branching may constrain seed size in Borasseae and their relatives. The possible roles of insularity, habitat and dispersers are difficult to disentangle. Evolutionary contingencies better explain the gigantism of the double coconut than unusually high rates of seed size increase.
  • Changes of synovial fluid protein concentrations in supra-patellar bursitis patients after the injection of different molecular weights of hyaluronic acid

    Chen, Carl P.C.; Hsu, Chin Chin; Pei, Yu-Cheng; Chen, Ruoli; Zhou, Shaobo; Shen, Hsuan-Chen; Lin, Shih-Cherng; Tsai, Wen-Chung; ; Chang Gung University; et al. (Elsevier, 2014-01-30)
    Knee pain is commonly seen in orthopedic and rehabilitation outpatient clinical settings, and in the aging population. Bursitis of the knee joint, especially when the volume of the synovial fluid is large enough, can compress and distend the nearby soft tissues, causing pain in the knee joint. Out of all the bursae surrounding the knee joint, supra-patellar bursitis is most often associated with knee pain. Treatment strategies in managing supra-patellar bursitis include the aspiration of joint synovial fluid and then followed by steroid injection into the bursa. When supra-patellar bursitis is caused by degenerative disorders, the concept of viscosupplementation treatment may be effective by injecting hyaluronic acid into the bursa. However, the rheology or the changes in the concentrations of proteins (biomarkers) that are related to the development of bursitis in the synovial fluid is virtually unexplored. Therefore, this study aimed to identify the concentration changes in the synovial fluid total protein amount and individual proteins associated with supra-patellar bursitis using the Bradford protein assay and western immunoglobulin methods. A total of 20 patients were divided into two groups with 10 patients in each group. One group received the high molecular weight hyaluronic acid product of Synvisc Hylan G-F 20 and the other group received the low molecular weight hyaluronic acid product of Hya-Joint Synovial Fluid Supplement once per week injection into the bursa for a total of 3. weeks. Significant decreases in the synovial fluid total protein concentrations were observed after the second dosage of high molecular weight hyaluronic acid injections. Apolipoprotein A-I, interleukin 1 beta, alpha 1 antitrypsin, and matrix metalloproteinase 1 proteins revealed a trend of decreasing western immunoblotting band densities after hyaluronic acid injections. The decreases in apolipoprotein A-I and interleukin 1 beta protein band densities were significant in the high molecular weight hyaluronic acid injection group. Transthyretin, complement 5, and matrilin 3 proteins revealed a trend of increasing western immunoblotting band densities after hyaluronic acid injections. Transthyretin revealed significant increases in protein band densities in both the high and low molecular weight hyaluronic acid injection groups. This study may provide the rationale for targeting several biomarkers associated with lipid transport, inflammation, and anti-aging as possible disease modifying therapies for the treatment of supra-patellar bursitis and even degenerative joint disorders. © 2014 Elsevier B.V.
  • Characterization of Colletotrichum gloeosporioides, as the main causal agent of citrus anthracnose, and C. karstii as species preferentially associated with lemon twig dieback in Portugal

    Ramos, Ana Paula; Talhinhas, Pedro; Sreenivasaprasad, Surapareddy; Oliveira, Helena (Springer Netherlands, 2016-09-13)
    In the last two decades significant losses in citrus production in Portugal related to anthracnose symptoms have been recorded. These symptoms were attributed to Colletotrichum gloeosporioides, but preliminary population diversity evidence suggested that other Colletotrichum species could be involved in the disease. In this work, a field survey of the main citrus growing areas in Portugal was conducted and the pathogenicity of a group of Colletotrichum spp. isolates was studied along with morphological and genetic variability characterization [including Inter-Simple Sequence Repeats (ISSR) profiles and DNA sequence data of rDNA-ITS and β-tubulin 2 gene regions]. Colletotrichum karstii (from the C. boninense species complex) and C. gloeosporioides were identified from symptoms on leaves, branches, flowers and fruits of several citrus cultivars. However, C. acutatum, the species most commonly associated with citrus anthracnose in the Americas, was never detected. While C. gloeosporioides was isolated at higher frequency overall (87 %), C. karstii was more frequent in branches and leaves of lemon in specific geographic locations. Only C. gloeosporioides was detected in flowers. Colletotrichum karstii and C. gloeosporioides were pathogenic to sweet orange flowers and fruits and to leaves of sweet orange, mandarin and lemon, while reference C. acutatum citrus isolates were pathogenic to Key lime flowers and leaves.
  • Fungal biomolecules: sources, applications and recent developments

    Gupta, V.J.; Mach, R.L.; Sreenivasaprasad, Surapareddy (Wiley, 2015-04-30)
    Fungi have an integral role to play in the development of the biotechnology and biomedical sectors. The fields of chemical engineering, Agri-food,Biochemical, pharmaceuticals, diagnostics and medical device development all employ fungal products, with fungal biomolecules currently used in a wide range of applications, ranging from drug development to food technology and agricultural biotechnology. Understanding the biology of different fungi in diverse ecosystems, as well as their biotropic interactions with other microorganisms, animals and plants, is essential to underpin effective and innovative technological developments. Fungal Biomolecules is a keystone reference, integrating branches of fungal product research into a comprehensive volume of interdisciplinary research. As such, it: reflects state-of-the-art research and current emerging issues in fungal biology and biotechnology reviews the methods and experimental work used to investigate different aspects of fungal biomolecules provides examples of the diverse applications of fungal biomolecules in the areas of food, health and the environment is edited by an experienced team, with contributions from international specialists This book is an invaluable resource for industry-based researchers, academic institutions and professionals working in the area of fungal biology and associated biomolecules for their applications in food technology, microbial and biochemical process, biotechnology, natural products, drug development and agriculture.
  • Electrochemical detection of non-esterified fatty acid by layer-by-layer assembled enzyme electrodes

    Kang, Jing; Hussain, Anisah T.; Catt, Michael; Trenell, Michael I.; Haggett, Barry G.D.; Yu, Eileen Hao; Newcastle University; University of Bedfordshire (Elsevier, 2013-09-12)
    In this study, detection and measurement of non-esterified fatty acids (NEFA) concentration has been achieved by electrochemical method in one operation step. Multilayer films of poly(dimethyldiallyammonium chloride) (PDA) wrapped multi-wall carbon nanotubes (MWCNTs) and two enzymes acyl-CoA synthetase (ACS) and acyl-CoA oxidase (ACOD) were assembled on a carbon screen printed electrode by the layer-by-layer (LbL) immobilization. The fine polymer-enzyme layers produced by the LbL method, allowed mass transport from the reactant cascading down the layers to accomplish the two-step enzyme reactions. The polymer-CNTs and enzyme modified electrode exhibited good electrocatalytical property retaining enzyme activity. Linear increase of anodic current from H2O2 produced from NEFA oxidation was observed with the increasing concentrations of oleic acid. These results indicate a promising technique for a simple, rapid one-step determination of NEFA for diabetes management.
  • Associated targets of the antioxidant cardioprotection of Ganoderma lucidum in diabetic cardiomyopathy by using open targets platform: a systematic review

    Shaher, Fahmi; Qiu, Hong-Bin; Wang, Shuqiu; Hu, Yu; Wang, Weiqun; Zhang, Yu; Wei, Yao; AL-ward, Hisham; Abdulghani, Mahfoudh A. M.; Alenezi, Sattam Khulaif; et al. (Hindawi, 2020-07-25)
    Even with substantial advances in cardiovascular therapy, the morbidity and mortality rates of diabetic cardiomyopathy (DCM) continually increase. Hence, a feasible therapeutic approach is urgently needed. Objectives. This work is aimed at systemically reviewing literature and addressing cell targets in DCM through the possible cardioprotection of G. lucidum through its antioxidant effects by using the Open Targets Platform (OTP) website. Methods. The OTP website version of 19.11 was accessed in December 2019 to identify the studies in DCM involving G. lucidum. Results. Among the 157 cell targets associated with DCM, the mammalian target of rapamycin (mTOR) was shared by all evidence, drug, and text mining data with 0.08 score association. mTOR also had the highest score association 0.1 with autophagy in DCM. Among the 1731 studies of indexed PubMed articles on G. lucidum published between 1985 and 2019, 33 addressed the antioxidant effects of G. lucidum and its molecular signal pathways involving oxidative stress and therefore were included in the current work. Conclusion. mTOR is one of the targets by DCM and can be inhibited by the antioxidative properties of G. lucidum directly via scavenging radicals and indirectly via modulating mTOR signal pathways such as Wnt signaling pathway, Erk1/2 signaling, and NF-κB pathways.
  • DNA methylation and body-mass index: a genome-wide analysis

    Dick, Katherine J.; Nelson, Christopher P.; Tsaprouni, Loukia G.; Sandling, Johanna K.; Aïssi, Dylan; Wahl, Simone; Meduri, Eshwar; Morange, Pierre-Emmanuel; Gagnon, France; Grallert, Harald; et al. (Lancet Publishing Group, 2014-06-09)
    Background Obesity is a major health problem that is determined by interactions between lifestyle and environmental and genetic factors. Although associations between several genetic variants and body-mass index (BMI) have been identified, little is known about epigenetic changes related to BMI. We undertook a genome-wide analysis of methylation at CpG sites in relation to BMI. Methods 479 individuals of European origin recruited by the Cardiogenics Consortium formed our discovery cohort. We typed their whole-blood DNA with the Infinium HumanMethylation450 array. After quality control, methylation levels were tested for association with BMI. Methylation sites showing an association with BMI at a false discovery rate q value of 0·05 or less were taken forward for replication in a cohort of 339 unrelated white patients of northern European origin from the MARTHA cohort. Sites that remained significant in this primary replication cohort were tested in a second replication cohort of 1789 white patients of European origin from the KORA cohort. We examined whether methylation levels at identified sites also showed an association with BMI in DNA from adipose tissue (n=635) and skin (n=395) obtained from white female individuals participating in the MuTHER study. Finally, we examined the association of methylation at BMI-Associated sites with genetic variants and with gene expression. Findings 20 individuals from the discovery cohort were excluded from analyses after quality-control checks, leaving 459 participants. After adjustment for covariates, we identified an association (q value ≤middot&05) between methylation at five probes across three different genes and BMI. The associations with three of these probes - cg22891070, cg27146050, and cg16672562, all of which are in intron 1 of HIF3A - were confirmed in both the primary and second replication cohorts. For every 0·1 increase in methylation β value at cg22891070, BMI was 3·6% (95% CI 2·9) higher in the discovery cohort, 2·7% (1·2) higher in the primary replication cohort, and 0·8% (0·4) higher in the second replication cohort. For the MuTHER cohort, methylation at cg22891070 was associated with BMI in adipose tissue (p=1·72×10) but not in skin (p=0·882). We observed a significant inverse correlation (p=0·005) between methylation at cg22891070 and expression of one HIF3A gene-expression probe in adipose tissue. Two single nucleotide polymorphisms - rs8102595 and rs3826795 - had independent associations with methylation at cg22891070 in all cohorts. However, these single nucleotide polymorphisms were not significantly associated with BMI. Interpretation Increased BMI in adults of European origin is associated with increased methylation at the HIF3A locus in blood cells and in adipose tissue. Our findings suggest that perturbation of hypoxia inducible transcription factor pathways could have an important role in the response to increased weight in people. Funding The European Commission, National Institute for Health Research, British Heart Foundation, and Wellcome Trust.
  • Effect of culture medium on morphogenic processes in vitro in Cinchona officinalis L.

    Moreno Serrano, José Antonio; Pérez Ruíz, César; Moreno Fierro, Ivonne; Moreno Fierro, Jorge (Facultad de Ciencias Agrarias. Universidad Nacional de Cuyo, 2019-06-30)
    This paper describes the effect of the various plant growth regulators of the culture medium on morphogenic processes in vitro in Cinchona officinalis L, a highly vulnerable species from southern Ecuador. To do this, different concentrations of NaOCl were used in combination with different immersion times for seed disinfection; for seed germination in vitro GA3 was added to the MS basal culture medium in different concentrations, and for morphogenic processes in vitro, different concentrations of auxins and cytokinins were combined. The decrease in the contamination rate was with high concentrations of NaOCl and an increase in the germination rate in 45 days with the addition of 1.0 mg L-1 GA3 to the culture medium the hormonal combination of 0.5 mg L-1 NAA + 2.5 mg L-1 BAP showed a high rate of shoot proliferation and with 1.0 mg L-1 NAA a high number of roots was obtained. In the callogenesis phase, the best results were obtained with 1.0 mg L-1 2,4-D + 0.5 mg L-1 BAP for callus proliferation. In vitro propagation protocols were generated in Cinchona officinalis L, for the preservation and conservation of the species.
  • ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis

    Huang, Ji; Nguyen, Vinh H.; Hamblin, Karleigh; Maytum, Robin; van der Giezen, Mark; Fraser, Marie E.; (International Union of Crystallography, 2019-07-08)
    Succinyl‐CoA synthetase (SCS) catalyzes the only step of the tricarboxylic acid cycle that leads to substrate‐level phosphorylation. Some forms of SCS are specific for ADP/ATP or for GDP/GTP, while others can bind all of these nucleotides, generally with different affinities. The theory of `gatekeeper' residues has been proposed to explain the nucleotide‐specificity. Gatekeeper residues lie outside the binding site and create specific electrostatic interactions with incoming nucleotides to determine whether the nucleotides can enter the binding site. To test this theory, the crystal structure of the nucleotide‐binding domain in complex with Mg2+‐ADP was determined, as well as the structures of four proteins with single mutations, K46βE, K114βD, V113βL and L227βF, and one with two mutations, K46βE/K114βD. The crystal structures show that the enzyme is specific for ADP/ATP because of interactions between the nucleotide and the binding site. Nucleotide‐specificity is provided by hydrogen‐bonding interactions between the adenine base and Gln20β, Gly111β and Val113β. The O atom of the side chain of Gln20β interacts with N6 of ADP, while the side‐chain N atom interacts with the carbonyl O atom of Gly111β. It is the different conformations of the backbone at Gln20β, of the side chain of Gln20β and of the linker that make the enzyme ATP‐specific. This linker connects the two subdomains of the ATP‐grasp fold and interacts differently with adenine and guanine bases. The mutant proteins have similar conformations, although the L227βF mutant shows structural changes that disrupt the binding site for the magnesium ion. Although the K46βE/K114βD double mutant of Blastocystis hominis SCS binds GTP better than ATP according to kinetic assays, only the complex with Mg2+‐ADP was obtained.
  • Genomics evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes

    Armitage, Andrew D.; Cockerton, Helen M.; Sreenivasaprasad, Surapareddy; Woodhall, James; Lane, Charles R.; Harrison, Richard; Clarkson, John P. (Frontiers, 2020-01-23)
    The Alternaria section alternaria (Alternaria alternata species group) represents a diverse group of saprotroph, human allergens, and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear, and strawberry pathotypes, providing new tools for pathogen diagnostics.
  • Confocal microscopy provides visual evidence and confirms the feasibility of dsRNA delivery to emerald ash borer through plant tissues

    Pampolini, Flavia; Rodrigues, Thais B.; Leelesh, Ramya Shanivarsanthe; Kawashima, Tomokazu; Rieske, Lynne K. (Springer, 2020-05-15)
    Double-stranded RNA (dsRNA)-mediated gene silencing, or RNA interference (RNAi), is an emerging biotechnology that has been a breakthrough tool for crop protection. Exogenous dsRNA triggers the RNAi pathway, silences genes, disrupts protein function, and can cause insect mortality. However, effective delivery of the dsRNA is problematic, particularly in systems with long-lived, endophagous insects such as the emerald ash borer (EAB), Agrilus planipennis, a tree-killing nonnative invader that attacks ash, Fraxinus spp. Larvae feed on cambial tissue causing rapid tree death. EAB is susceptible to RNAi, but we lack a practical means of delivery. Here we evaluated delivery of dsRNA to green, F. pennsylvanica, and tropical ash, F. uhdei, through root and/or petiole absorption, and also demonstrated dsRNA absorption through the EAB egg chorion. We labeled exogenous dsRNA using a fluorescing label and then used confocal microscopy and RT-qPCR to evaluate its distribution in plant and insect tissues. Labeled dsRNAs are detectable in root, stem, and leaf tissues 48-h postapplication. In excised ash branches, labeled dsRNA is detectable in the inner bark and in recovered EAB neonates 8-day postapplication. Eggs and larvae emerging from treated eggs also presented fluorescing dsRNA under confocal imaging. Adult EAB-fed tropical ash leaves treated with in vitro synthesized EAB-specific dsSHI through petiole absorption experience a significant knockdown of the shi gene and a significant mortality. Our findings provide a proof of concept that delivery of dsRNAs through topical or systemic application methods is a feasible means of suppressing EAB, providing hope for future tree protection.
  • Reconstructing phylogenetic relationships based on repeat sequence similarities

    Vitales, Daniel; Garcia, Sonia; Dodsworth, Steven; Institut Botànic de Barcelona; Universitat de Barcelona; University of Bedfordshire (Elsevier, 2020-02-28)
    A recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.
  • Repetitive DNA restructuring across multiple Nicotiana allopolyploidisation events shows a lack of strong cytoplasmic bias in influencing repeat turnover

    Dodsworth, Steven; Guignard, Maite S.; Pérez-Escobar, Oscar A.; Struebig, Monika; Chase, Mark W.; Leitch, Andrew R.; ; University of Bedfordshire; Queen Mary University of London; Royal Botanic Gardens, Kew; et al. (MDPI, 2020-02-19)
    Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following three allotetraploid events, and how these are inherited from the closest extant relatives of the maternal and paternal subgenome donors. In all three cases, there was a lack of clear maternal, cytoplasmic bias in repeat evolution, i.e., lack of a predicted bias towards maternal subgenome-derived repeats, with roughly equal contributions from both parental subgenomes. Different overall repeat dynamics were found across timescales of <0.5 (N. rustica L.), 4 (N. repanda Willd.) and 6 (N. benthamiana Domin) Ma, with nearly additive, genome upsizing, and genome downsizing, respectively. Lower copy repeats were inherited in similar abundance to the parental subgenomes, whereas higher copy repeats contributed the most to genome size change in N. repanda and N. benthamiana. Genome downsizing post-polyploidisation may be a general long-term trend across angiosperms, but at more recent timescales there is species-specific variance as found in Nicotiana.
  • Non-destructive genome skimming for aquatic copepods

    Vakati, Vinod; Dodsworth, Steven; Neijiang Normal University; Hanyang University; University of Bedfordshire (Springer, 2020-01-21)
    Copepods are important ecologically and represent a large amount of aquatic biomass in both freshwater and marine systems. Despite this, the taxonomy of copepods and other meiofauna is not well understood, hampered by tiny sizes, cryptic taxa, intraspecific polymorphisms and total specimen destruction where DNA methods are employed. In this article we highlight these issues and propose a more up-to-date approach for dealing with them. Namely, we recommend non-destructive DNA extraction methods, coupled with high-throughput sequencing (HTS). Whilst DNA yields may be low, they should still be sufficient for HTS library preparation and DNA sequencing. At the same time morphological specimens can be preserved and the crucial link between morphology and DNA sequence is maintained. This is critical for an integrative taxonomy and a fuller understanding of biodiversity patterns as well as evolutionary processes in meiofauna.
  • Risk prediction and assessment: duration, infections, and death toll of the COVID-19 and its impact on China’s economy

    Yue, Xiao-Guang; Shao, Xue-Feng; Li, Rita Yi Man; Crabbe, M. James C.; Mi, Lili; Hu, Siyan; Baker, Julien S.; Liu, Liting; Dong, Kechen; University of Bedfordshire; et al. (MDPI, 2020-04-03)
    This study first analyzes the national and global infection status of the Coronavirus Disease that emerged in 2019 (COVID-19). It then uses the trend comparison method to predict the inflection point and Key Point of the COVID-19 virus by comparison with the severe acute respiratory syndrome (SARS) graphs, followed by using the Autoregressive Integrated Moving Average model, Autoregressive Moving Average model, Seasonal Autoregressive Integrated Moving-Average with Exogenous Regressors, and Holt Winter’s Exponential Smoothing to predict infections, deaths, and GDP in China. Finally, it discusses and assesses the impact of these results. This study argues that even if the risks and impacts of the epidemic are significant, China’s economy will continue to maintain steady development.

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