• 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.
    • 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.
    • 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.
    • Spatial genetic and epigenetic structure of Thlaspi arvense (field pennycress) in China

      Guan, Yabin; Qu, Peng; Lu, Shugang; Crabbe, M. James C.; Zhang, Ti-Cao; Geng, Yu-peng; Yunnan University; Oxford University; Shanxi University; University of Bedfordshire; et al. (Genetics Society of Japan, 2020-11-11)
      (Received 13 May 2020, accepted 15 July 2020; J-STAGE Advance published date: 11 November 2020) Thlaspi arvense (field pennycress) is widespread in temperate regions of the northern hemisphere. We estimated the genetic and epigenetic structure of eight T. arvense populations (131 individuals) in China using amplified fragment length polymorphism and methylation-sensitive amplified polymorphism molecularmarker techniques. We detected low diversity at both genetic (mean = 0.03; total = 0.07) and epigenetic (mean = 0.04; total = 0.07) levels, while significant genetic (FST = 0.42, P < 0.001) and epigenetic (FST = 0.32, P < 0.001) divergence was found across the distribution range. Using Mantel testing, we found spatial genetic and epigenetic differentiation, consistent with isolation-by-distance models. We also identified a strong correlation between genetic and epigenetic differentiation (r = 0.7438, P < 0.001), suggesting genetic control of the epigenetic variation. Our results indicate that mating system, natural selection and gene flow events jointly structure spatial patterns of genetic and epigenetic variation. Moreover, epigenetic variation may serve as a basis of natural selection and ecological evolution to enable species to adapt to heterogeneous habitats. Our study provides novel clues for the adaptation of T. arvense.
    • COVID-19 and Parkinson’s disease: shared inflammatory pathways under oxidative stress

      Chaudhry, Zahara Latif; Klenja, Donika; Janjua, Najma; Cami-Kobeci, Gerta; Ahmed, Bushra Y.; University of Bedfordshire; University of Bristol; Kawasaki Medical School (MDPI, 2020-10-31)
      The current coronavirus pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in a serious global health crisis. It is a major concern for individuals living with chronic disorders such as Parkinson’s disease (PD). Increasing evidence suggests an involvement of oxidative stress and contribution of NFκB in the development of both COVID-19 and PD. Though, it is early to identify if SARS-CoV-2 led infection enhances PD complications, it is likely that oxidative stress may exacerbate PD progression in COVID-19 affected individuals and/or vice versa. In the current study, we sought to investigate whether NFκB-associated inflammatory pathways following oxidative stress in SARS-CoV-2 and PD patients are correlated. Toward this goal, we have integrated bioinformatics analysis obtained from BLASTP search for similarities between SARS-CoV-2 proteins and human proteome, literature review, and laboratory data obtained in a human cell model of PD. A Parkinson’s like state was created in 6OHDA-induced differentiated dopaminergic neurons (dDCNs) obtained from ReNVM cell line. The results indicated that SARS-CoV-2 infection and 6OHDA-induced toxicity triggered stimulation of caspases -2, -3 and -8 via the NFκB pathway resulting in death of dDCNs. Furthermore, specific inhibitors for NFκB and studied caspases reduced the death of stressed dDCNs. The findings suggest that knowledge of the selective inhibition of caspases and NFκB activation may contribute to development of potential therapeutic approaches for the treatment of COVID-19 and PD.
    • Establishment of a stable complex formed from whey protein isolate and chitosan and its stability under environmental stresses

      Xu, Weili; Tang, Yinzhao; Yang, Yang; Wang, Guijie; Zhou, Shaobo; Harbin Institute of Technology; University of Bedfordshire (Elsevier, 2020-10-22)
      This study aimed to investigate the stability of a complex formed with whey protein isolate (WPI) and chitosan under environmental stress. The optical density, particle size, zeta potential, chemical characteristics, electrostatic interactions, and surface morphology were evaluated for the stable complexes; the optimum conditions for the generation of the stable complex were 0.2% (wt/wt) whey protein with 0.05% (wt/wt) chitosan at pH 5.7. Under these conditions, the complex particle size was 217.8 ± 11.3 nm and the zeta potential was 16.7 ± 0.92 mV. The complex was formed through electrostatic interactions between the amine groups of chitosan (-NH3+) and carboxyl groups of whey protein (-COO−), and contained a porous network interspaced by heterogeneously sized vacuoles. The complex displayed stable physiochemical characteristics under environmental stresses including NaCl (0–75 mM) or sugar (0–5%) at ambient temperature and upon heating for 15 min at 25–65 °C, up to 65 °C for 30 min. Moreover, the complex could be stably stored for 30 d at 4 °C and for 20 d at 25 °C. The present results provide theoretical insights into the industrial production of chitosan-protein complexes and for microencapsulation of sensitive food or medicinal ingredients to increase their intestinal absorption.
    • Dissolved oxygen forecasting in aquaculture: a hybrid model approach

      Eze, Elias Chinedum; Ajmal, Tahmina; University of Bedfordshire (MDPI AG, 2020-10-12)
      Dissolved oxygen (DO) concentration is a vital parameter that indicates water quality. We present here DO short term forecasting using time series analysis on data collected from an aquaculture pond. This can provide the basis of data support for an early warning system, for an improved management of the aquaculture farm. The conventional forecasting approaches are commonly characterized by low accuracy and poor generalization problems. In this article, we present a novel hybrid DO concentration forecasting method with ensemble empirical mode decomposition (EEMD)-based LSTM (long short-term memory) neural network (NN). With this method, first, the sensor data integrity is improved through linear interpolation and moving average filtering methods of data preprocessing. Next, the EEMD algorithm is applied to decompose the original sensor data into multiple intrinsic mode functions (IMFs). Finally, the feature selection is used to carefully select IMFs that strongly correlate with the original sensor data, and integrate into both inputs for the NN. The hybrid EEMD-based LSTM forecasting model is then constructed. The performance of this proposed model in training and validation sets was compared with the observed real sensor data. To obtain the exact evaluation accuracy of the forecasted results of the hybrid EEMD-based LSTM forecasting model, four statistical performance indices were adopted: mean absolute error (MAE), mean square error (MSE), root mean square error (RMSE), and mean absolute percentage error (MAPE). Results are presented for the short term (12-h) and the long term (1-month) that are encouraging, indicating suitability of this technique for forecasting DO values.
    • 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.
    • 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.
    • 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.
    • Architecture and self-assembly of Clostridium sporogenes and Clostridium botulinum spore surfaces illustrate a general protective strategy across spore formers

      Janganan, Thamarai K.; Mullin, Nic; Dafis-Sagarmendi, Ainhoa; Brunt, Jason; Tzokov, Svetomir B.; Stringer, Sandra; Moir, Anne; Chaudhuri, Roy R.; Fagan, Robert P.; Hobbs, Jamie K.; et al. (American Society for Microbiology, 2020-07-01)
      Spores, the infectious agents of many Firmicutes, are remarkably resilient cell forms. Even distant relatives can have similar spore architectures although some display unique features; they all incorporate protective proteinaceous envelopes. We previously found that Bacillus spores can achieve these protective properties through extensive disulfide cross-linking of self-assembled arrays of cysteine-rich proteins. We predicted that this could be a mechanism employed by spore formers in general, even those from other genera. Here, we tested this by revealing in nanometer detail how the outer envelope (exosporium) in Clostridium sporogenes (surrogate for C. botulinum group I), and in other clostridial relatives, forms a hexagonally symmetric semipermeable array. A cysteine-rich protein, CsxA, when expressed in Escherichia coli, self-assembles into a highly thermally stable structure identical to that of the native exosporium. Like the exosporium, CsxA arrays require harsh “reducing” conditions for disassembly. We conclude that in vivo, CsxA self-organizes into a highly resilient, disulfide cross-linked array decorated with additional protein appendages enveloping the forespore. This pattern is remarkably similar to that in Bacillus spores, despite a lack of protein homology. In both cases, intracellular disulfide formation is favored by the high lattice symmetry. We have identified cysteine-rich proteins in many distantly related spore formers and propose that they may adopt a similar strategy for intracellular assembly of robust protective structures.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • 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.
    • Risk management analysis for novel Coronavirus in Wuhan, China

      Yue, Xiao-Guang; Shao, Xue-Feng; Li, Rita Yi Man; Crabbe, M. James C.; Mi, Lili; Hu, Siyan; Baker, Julien S.; Liang, Gang; European University Cyprus; Polytechnic Institute of Porto; et al. (MDPI, 2020-02-03)
      Recently, a novel coronavirus pneumonia (2019–nCoV) outbreak occurred in Wuhan, China, rapidly spreading first to the whole country, and then globally, causing widespread concern. From the perspectives of early warning and identification of risk, risk monitoring, and analysis, as well as risk management and handling, we propose corresponding solutions and recommendations, which include institutional cooperation, and to inform national and international policy-makers.