Recent Submissions

  • Deep sea mining for renewable technologies: a case study for using Big Data

    Crabbe, M. James C.; Oxford University; University of Bedfordshire; Shanxi University (World Scientific Publishing Company, 2022-10-18)
    Depleting terrestrial deposits and rising demand for metals in this time of climate change are stimulating interest in the deep sea — the area of the ocean below 200m — with commercial mining of mineral deposits imminent. Environmental impact assessments, effective regulation and mitigation strategies are needed to limit the impacts of deep-sea mining. This is a potential catastrophe for marine biodiversity, and use of Big Data will be needed to follow mining activities as well as chart impacts on known and unknown marine species and their habitats.
  • Cost–benefit analysis of synergistic CO2 and NOx energy-efficient technologies for the road transport sector in China

    Ping, Liying; Wang, Yuan; Lee, Lien-Chieh; Peng, Binbin; Ahmed, Bushra Y.; Zhang, Hongyu; Ma, Wenchao; Tianjin University; Hubei Polytechnic University; University of Bedfordshire; et al. (MDPI, 2022-09-20)
    The transportation sector is a major source of greenhouse gases and air pollutants, and it has a crucial effect on the synergistic reduction of NOx and carbon. In order to find the energy-efficient vehicle technologies with the highest net reduction potential and lowest net reduction cost over the life cycle, this study traced the CO2 and NOx emission streams of 33 energy-efficient technologies, hidden in the supply chain during the production phase, through structural path analysis, and measured the emission reductions during the use phase using the emission factor method. Moreover, we applied structural decomposition analysis to quantify the three main drivers, including emission intensity, industrial structure, and final demand, of changes in CO2 and NOx emissions from 11 transport subsectors during 2012–2018. Results indicate that CO2 emissions of the transport sector more than doubled from 2012 to 2018; however, the influence of NOx was less significant. The final demand of the road subsector was the most significant driver contributing to CO2 emission changes, with an increase of 109.27 Mt. The emission intensity of road transportation caused the greatest mitigation effect on NOx emission changes, with a decrease of 1902 Kt. The findings of the scenario analysis demonstrate that the most efficient action of the pure electric technology for passenger cars reduces 20.92 Mt NOx emissions, and the parallel hybrid technology for heavy trucks offers the greatest cost effectiveness with a net abatement of 2577 Mt CO2 over its life cycle. Consequently, the aggressive development of new energy technology has become a prerequisite strategy to synergistically reduce CO2 and NOx emissions.
  • microRNA 1307 is a potential target for SARS-CoV-2 infection: an in vitro model

    Arisan, Elif Damla; Dart, Alwyn; Grant, Guy H.; Dalby, Andrew; Kancagi, Derya Dilek; Turan, Raife Dilek; Yurtsever, Bulut; Karakus, Gozde Sir; Ovali, Ercument; Lange, Sigrun; et al. (American Chemical Society, 2022-10-25)
    microRNAs (miRs) are proposed as critical molecular targets in SARS-CoV-2 infection. Our recent in silico studies identified seven SARS-CoV-2 specific miR-like sequences, which are highly conserved with humans, including miR-1307-3p, with critical roles in COVID-19. In this current study, Vero cells were infected with SARS-CoV-2, and miR expression profiles were thereafter confirmed by qRT-PCR. miR-1307-3p was the most highly expressed miR in the infected cells; we, therefore, transiently inhibited its expression in both infected and uninfected cells. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) cell proliferation assay assessed cell viability following SARS-CoV-2 infection, identifying that miR-1307 expression is inversely correlated with cell viability. Lastly, changes in miR-1307-dependent pathways were analyzed through a detailed miRNOME and associated in silico analysis. In addition to our previously identified miRs, including miR-1307-3p, the upregulation of miR-193a-5p, miR-5100, and miR-23a-5p and downregulation of miR-130b-5p, miR34a-5p, miR-505-3p, miR181a-2-3p, miR-1271-5p, miR-598-3p, miR-34c-3p, and miR-129-5p were also established in Vero cells related to general lung disease-related genes following SARS-CoV-2 infection. Targeted anti-miR-1307-3p treatment rescued cell viability in infection when compared to SARS CoV-2 mediated cell cytotoxicity only. We furthermore identified by in silico analysis that miR-1307-3p is conserved in all SARS-CoV-2 sequences/strains, except in the BA.2 variant, possibly contributing to the lower disease severity of this variant, which warrants further investigation. Small RNA seq analysis was next used to evaluate alterations in the miRNOME, following miR-1307-3p manipulation, identifying critical pathobiological pathways linked to SARS-CoV-2 infection-mediated upregulation of this miR. On the basis of our findings, miRNAs like miR-1307-3p play a critical role in SARS-CoV-2 infection, including via effects on disease progression and severity.
  • Investigation into antiepileptic effect of ganoderic acid A and its mechanism in seizure rats induced by pentylenetetrazole

    Pang, Wei; Lu, Shuqing; Zheng, Rong; Li, Xin; Yang, Shunbo; Feng, Yuxia; Wang, Shuqiu; Guo, Jin; Zhou, Shaobo; ; et al. (Hindawi, 2022-09-01)
    Ganoderic acid A (GAA) exhibited neuron protection in in vitro epilepsy study, but no study has been done in vivo. Rats were administered (i.p.) pentylenetetrazole daily for 28 days to induce seizure. Rats with grade II or above of epileptic score were divided into three groups and given placebo, sodium valproate, or GAA treatment, respectively, for 7 days. The electrical signals of brain were monitored with electroencephalography (EGG); epileptic behavior was assessed using the Racine scale; morphological changes and apoptosis rate of cortical neurons were assessed with H&E staining and TUNEL staining, respectively. Protein expression of calcium-sensing receptor, p-ERK, p-JNK, and p-p38 in hippocampal tissue and Bcl-2, cleaved caspase-3, and Bax in cortical tissues was observed by Western blot and immunohistochemistry assay, respectively. After GAA treatment, apparent seizure-like EEG with significant arrhythmic disorder and spike waves was reduced or disappeared, and wave amplitude of EEG was reduced significantly. GAA showed similar effect with sodium valproate treatments on epilepsy. There were an apparent improvement of the epileptic behavior and a significant increase in the epileptic latency and shortening of the epileptic duration in the treatment group compared to control. GAA treatment ameliorated the nuclear pyknosis of neurons which appeared seriously in the epilepsy group. GAA treatment significantly reduced the cortical neuron apoptosis of epilepsy and the expression of calcium-sensing receptor, p-P38, p-JNK, cleaved caspase-3, and Bax but increased the expression of both p-ERK and Bcl-2. In conclusion, GAA treatment showed strong antiepileptic effect by decreasing apoptosis in cortical neuron and the expression of calcium-sensing receptor and stimulating the MAPK pathway.
  • Detoxification gene families at the genome-wide level of Rhus gall aphid Schlechtendalia chinensis

    He, Hongli; Crabbe, M. James C.; Ren, Zhumei; Shanxi University; Oxford University; University of Bedfordshire (MDPI, 2022-09-10)
    The Rhus gall aphid Schlechtendalia chinensis uses the species Rhus chinensis as its primary host plant, on which galls are produced. The galls have medicinal properties and can be used in various situations due to their high tannin content. Detoxification enzymes play significant roles in the insect lifecycle. In this study, we focused on five detoxification gene families, i.e., glutathione-Stransferase (GST), ABC transporter (ABC), Carboxylesterase (CCE), cyto-chrome P450 (CYP), and UDP-glycosyltransferase (UDP), and manually annotated 144 detoxification genes of S. chinensis using genome-wide techniques. The detoxification genes appeared mostly on chromosome 1, where a total of two pair genes were identified to show tandem duplications. There were 38 gene pairs between genomes of S. chinensis and Acyrthosiphon pisum in the detoxification gene families by collinear comparison. Ka/Ks ratios showed that detoxification genes of S. chinensis were mainly affected by purification selection during evolution. The gene expression numbers of P450s and ABCs by transcriptome sequencing data were greater, while gene expression of CCEs was the highest, suggesting they might be important in the detoxification process. Our study has firstly identified the genes of the different detoxification gene families in the S. chinensis genome, and then analyzed their general features and expression, demonstrating the importance of the detoxification genes in the aphid and providing new information for further research.
  • Identification of the antigens recognised by colorectal cancer patients using sera from patients who exhibit a Crohn's-like lymphoid reaction

    Boncheva, Viktoriya Bogdanova; Linnebacher, Michael; Kdimati, Said; Draper, Hannah; Orchard, Laurence; Mills, Ken I.; O'Sullivan, Gerald; Tangney, Mark; Guinn, Barbara-Ann; University of Bedfordshire; et al. (MDPI, 2022-07-29)
    A Crohn's-like lymphoid reaction (CLR) is observed in about 15% of colorectal cancer (CRC) patients and is associated with favourable outcomes. To identify the immune targets recognised by CRC CLR patient sera, we immunoscreened a testes cDNA library with sera from three patients. Immunoscreening of the 18 antigens identified by SEREX with sera from normal donors showed that only the heavy chain of IgG3 (IGHG3) and a novel antigen we named UOB-COL-7, were solely recognised by sera from CRC CLR patients. ELISA showed an elevation in IgG3 levels in patients with CRC (p = 0.01). To extend our studies we analysed the expression of our SEREX-identified antigens using the RNA-sequencing dataset (GSE5206). We found that the transcript levels of multiple IGHG probesets were highly significant (p < 0.001) in their association with clinical features of CRC while above median levels of DAPK1 (p = 0.005) and below median levels of GTF2H5 (p = 0.004) and SH3RF2 (p = 0.02) were associated with improved overall survival. Our findings demonstrate the potential of SEREX-identified CRC CLR antigens to act as biomarkers for CRC and provide a rationale for their further characterization and validation.
  • The pioneer transcription factor Foxa2 modulates T helper differentiation to reduce mouse allergic airway disease

    Yánez, Diana C.; Lau, Ching-In; Papaioannou, Eleftheria; Chawda, Mira Manilal; Rowell, Jasmine; Ross, Susan; Furmanski, Anna L.; Crompton, Tessa; ; UCL Great Ormond Street Institute of Child Health; et al. (Frontiers, 2022-08-08)
    Foxa2, a member of the Forkhead box (Fox) family of transcription factors, plays an important role in the regulation of lung function and lung tissue homeostasis. FOXA2 expression is reduced in the lung and airways epithelium of asthmatic patients and in mice absence of Foxa2 from the lung epithelium contributes to airway inflammation and goblet cell hyperplasia. Here we demonstrate a novel role for Foxa2 in the regulation of T helper differentiation and investigate its impact on lung inflammation. Conditional deletion of Foxa2 from T-cells led to increased Th2 cytokine secretion and differentiation, but decreased Th1 differentiation and IFN-γ expression in vitro. Induction of mouse allergic airway inflammation resulted in more severe disease in the conditional Foxa2 knockout than in control mice, with increased cellular infiltration to the lung, characterized by the recruitment of eosinophils and basophils, increased mucus production and increased production of Th2 cytokines and serum IgE. Thus, these experiments suggest that Foxa2 expression in T-cells is required to protect against the Th2 inflammatory response in allergic airway inflammation and that Foxa2 is important in T-cells to maintain the balance of effector cell differentiation and function in the lung.
  • Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)

    Zhang, Ti-Cao; Qiao, Qin; Du, Xiao; Zhang, Xiao; Hou, Yali; Wei, Xin; Sun, Chao; Zhang, Rengang; Yun, Quanzheng; Crabbe, M. James C.; et al. (Wiley, 2022-06-24)
    Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosome-level genome sequence of the hawthorn cultivar “Qiu Jinxing.” We assembled an 823.41 Mb genome encoding 40 571 genes and further anchored the 779.24 Mb sequence into 17 pseudo-chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole-genome duplication event was specifically detected in hawthorn. The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleo-polyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new high-quality reference genome provides a useful resource for the horticultural improvement of hawthorn.
  • Genetically modified metallothionein/cellulose composite material as an efficient and environmentally friendly biosorbent for Cd2+ removal

    Li, Xuefen; Wang, Yuxia; Crabbe, M. James C.; Wang, Lan; Ma, Wenli; Ren, Zhumei; Shanxi University; University of Oxford; University of Bedfordshire (Elsevier, 2022-07-25)
    Metallothioneins (MTs) are a class of cysteine-rich metal-binding proteins. Cadmium (Cd) is one of the toxic heavy metal pollutants. In our previous research, the full-length cDNA of MT (Cd specificity) from freshwater crab (Sinopotamon henanense) (ShMT) was cloned and genetically modified to ShMT3 by site-directed mutagenesis to enhance the tolerance for Cd2+, however, it was limited in actual Cd2+ adsorption due to instability. Here, ShMT3-CBM, a novel recombinant fusion protein, was prepared. CBM is a carbohydrate binding module that can specifically bind cellulose while ShMT3 can effectively chelate Cd2+. The biosorbent Cellulose1-ShMT3-CBM was obtained by screening suitable cellulose materials. The selective adsorption experiments showed that Cellulose1-ShMT3-CBM had a preference for Cd2+. In low-concentration Cd2+ solutions, the removal efficiency was >99 %, and the adsorption equilibrium was reached within 15 min. The saturated adsorption capacity of Cellulose1-ShMT3-CBM for Cd2+ is 180.35 ± 4.67 mg/g (Dry Weight). Regeneration experiments showed that adsorption efficiency was maintained after six cycles. The MTT experiment showed that Cellulose1-ShMT3-CBM had low cytotoxicity. Meanwhile, Cellulose1-ShMT3-CBM can preferentially remove Cd2+ in actual water samples and boiler sewage. In this study, an environmentally friendly biosorbent which can adsorb Cd2+ efficiently and quickly was prepared for actual water treatment.
  • Preparation, purification, and identification of novel antioxidant peptides derived from Gracilariopsis lemaneiformis protein hydrolysates

    Hu, Xiao; Liu, Jing; Li, Jun; Song, Yuqiong; Chen, Shengjun; Zhou, Shaobo; Yang, Xianqing; ; Chinese Academy of Fishery Sciences; Jiangsu Ocean University; et al. (Frontiers, 2022-07-22)
    Gracilariopsis lemaneiformis (G. lemaneiformis) protein was hydrolyzed with alkaline protease to obtain antioxidant peptides. The enzymatic hydrolysis conditions were optimized through single-factor and orthogonal experiments. The results showed that the optimal process parameters were using 2% of alkaline protease, and substrate concentration of 1 g/100 mL and hydrolyzed 2 h at pH 8.0. Gel filtration chromatography and RP-HPLC were adopted for isolating and purifying the antioxidant peptides from the G. lemaneiformis protein hydrolysate (GLPH). Three novel antioxidant peptides were identified as LSPGEL (614.68 Da), VYFDR (698.76 Da), and PGPTY (533.57 Da) by nano-HPLC-MS/MS. The results of ABTS free radical scavenging rate demonstrated PGPTY exhibited the best antioxidant activity (IC50 = 0.24 mg/mL). Moreover, LSPGEL, VYFDR, and PGPTY were docked with Keap1, respectively. The molecular docking results suggested PGPTY had smaller docking energy and inhibition constants than the other two peptides. Finally, the cell viability assay evidenced the protective effect exerted by the antioxidant peptide on H2O2-induced oxidative damage. Above findings showed the potential of using antioxidant peptides from GLPH as antioxidants.
  • NRF2-ARE signaling is responsive to haloacetonitrile-induced oxidative stress in human keratinocytes

    Xue, Peng; Wang, Huihui; Yang, Lili; Jiang, Zhiqiang; Li, Hongliang; Liu, Qinxin; Zhang, Qiang; Andersen, Melvin E.; Crabbe, M. James C.; Hao, Lipeng; et al. (Elsevier, 2022-07-14)
    Humans are exposed to disinfection by-products through oral, inhalation, and dermal routes, during bathing and swimming, potentially causing skin lesions, asthma, and bladder cancer. Nuclear factor E2-related factor 2 (NRF2) is a master regulator of the adaptive antioxidant response via the antioxidant reaction elements (ARE) orchestrating the transcription of a large group of antioxidant and detoxification genes. Here we used an immortalized human keratinocyte model HaCaT cells to investigate NRF2-ARE as a responder and protector in the acute cytotoxicity of seven haloacetonitriles (HANs), including chloroacetonitrile (CAN), bromoacetonitrile (BAN), iodoacetonitrile (IAN), bromochloroacetonitrile (BCAN), dichloroacetonitrile (DCAN), dibromoacetonitrile (DBAN), and trichloroacetonitrile (TCAN) found in drinking water and swimming pools. The rank order of cytotoxicity among the HANs tested was IAN ≈ BAN ˃ DBAN ˃ BCAN ˃ CAN ˃ TCAN ˃ DCAN based on their LC50. The HANs induced intracellular reactive oxygen species accumulation and activated cellular antioxidant responses in concentration- and time-dependent fashions, showing elevated NRF2 protein levels and ARE activity, induction of antioxidant genes, and increased glutathione levels. Additionally, knockdown of NRF2 by lentiviral shRNAs sensitized the HaCaT cells to HANs-induced cytotoxicity, emphasizing a protective role of NRF2 against the cytotoxicity of HANs. These results indicate that HANs cause oxidative stress and activate NRF2-ARE-mediated antioxidant response, which in turn protects the cells from HANs-induced cytotoxicity, highlighting that NRF2-ARE activity could be a sensitive indicator to identify and characterize the oxidative stress induced by HANs and other environmental pollutants.
  • Comparative genomic and phylogenetic analysis of chloroplast genomes of hawthorn (Crataegus spp.) in southwest China

    Wu, Xien; Luo, Dengli; Zhang, Yingmin; Yang, Congwei; Crabbe, M. James C.; Zhang, Ti-Cao; Li, Guodong; Yunnan University of Chinese Medicine; Oxford University; University of Bedfordshire; et al. (Frontiers, 2022-07-04)
    The hawthorns (Crataegus spp.) are widely distributed and famous for their edible and medicinal values. There are ~18 species and seven varieties of hawthorn in China distributed throughout the country. We now report the chloroplast genome sequences from C. scabrifolia, C. chungtienensis and C. oresbia, from the southwest of China and compare them with the previously released six species in Crataegus and four species in Rosaceae. The chloroplast genome structure of Crataegus is typical and can be divided into four parts. The genome sizes are between 159,654 and 159,898bp. The three newly sequenced chloroplast genomes encode 132 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis of the chloroplast genomes revealed six divergent hotspot regions, including ndhA, rps16-trnQ-UUG, ndhF-rpl32, rps16-psbK, trnR-UCU-atpA and rpl32-trnL-UAG. According to the correlation and cooccurrence analysis of repeats with indels and SNPs, the relationship between them cannot be ignored. The phylogenetic tree constructed based on the complete chloroplast genome and intergenic region sequences indicated that C. scabrifolia has a different origin from C. chungtienensis and C. oresbia. We support the placement of C. hupehensis, C. cuneata, C. scabrifolia in C. subg. Crataegus and C. kansuensis, C. oresbia, C. kansuensis in C. subg. Sanguineae. In addition, based on the morphology, geographic distribution and phylogenetic relationships of C. chungtienensis and C. oresbia, we speculate that these two species may be the same species. In conclusion, this study has enriched the chloroplast genome resources of Crataegus and provided valuable information for the phylogeny and species identification of this genus.
  • An insight into the impact of thermal process on dissolution profile and physical characteristics of theophylline tablets made through 3D printing compared to conventional methods

    Nashed, Nour; Lam, Matthew; Ghafourian, Taravat; Pausas, Lluis; Jiri, Memory; Majumder, Mridul; Nokhodchi, Ali; University of Sussex; University of Bedfordshire; M2M Pharmaceuticals Ltd (MDPI, 2022-06-06)
    The dissolution profile is of great importance in drug delivery and is affected by the manufacturing method. Thus, it is important to study the influence of the thermal process on drug release in emerging technologies such as 3D printing-fused deposition modeling (FDM). For this purpose, the characteristics of 3D printed tablets were compared to those of tablets prepared by other thermal methods such as hot-melt extrusion (HME) and non-thermal methods such as physical mixture (PM). Theophylline was used as a drug model and blends of ethyl cellulose (EC) and hydroxypropyl cellulose (HPC) were used as a matrix former. The solid state of the drug in all formulations was investigated by differential scanning calorimetry, X-ray powder diffraction, and Fourier-transformed infrared spectroscopy. All studied tablets had the same weight and surface area/volume (SA/V). Dissolution data showed that, for some formulations, printed tablets interestingly had a faster release profile despite having the highest hardness values (>550 N) compared to HME and PM tablets. Porosity investigations showed that 100% infill printed tablets had the highest porosity (~20%) compared to HME (<10%) and PM tablets (≤11%). True density records were the lowest in printed tablets (~1.22 g/m3) compared to tablets made from both HME and PM methods (~1.26 g/m3), reflecting the possible increase in polymer specific volume while printing. This increase in the volume of polymer network may accelerate water and drug diffusion from/within the matrix. Thus, it is a misconception that the 3D printing process will always retard drug release based on increased tablet hardness. Hardness, porosity, density, solid-state of the drug, SA/V, weight, and formulation components are all factors contributing to the release profile where the total balance can either slow down or accelerate the release profile.
  • Statistical learning-based spatial downscaling models for precipitation distribution

    Wu, Yichen; Zhang, Zhihua; Crabbe, M. James C.; Das, Lipon Chandra (Hindawi, 2022-06-07)
    The downscaling technique produces high spatial resolution precipitation distribution in order to analyze impacts of climate change in data-scarce regions or local scales. In this study, based on three statistical learning algorithms, such as support vector machine (SVM), random forest regression (RF), and gradient boosting regressor (GBR), we proposed an effcient downscaling approach to produce high spatial resolution precipitation. In order to demonstrate effciency and accuracy of our models over traditional multilinear regression (MLR) downscaling models, we did a downscaling analysis for daily observed precipitation data from 34 monitoring sites in Bangladesh. Validation revealed that R2 of GBR could reach 0.98, compared with RF (0.94), SVM (0.88), and multilinear regression (MLR) (0.69) models, so the GBR-based downscaling model had the best performance among all four downscaling models. We suggest that the GBR-based downscaling models should be used to replace traditional MLR downscaling models to produce a more accurate map of high-resolution precipitation for flood disaster management, drought forecasting, and long-term planning of land and water resources.
  • Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility.

    Cauz-Santos, Luiz A.; Dodsworth, Steven; Samuel, Rosabelle; Christenhusz, Maarten J.M.; Patel, Denise; Shittu, Taiwo Adewale; Jakob, Aljaž; Paun, Ovidiu; Chase, Mark W.; ; et al. (Wiley, 2022-05-10)
    One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and evolution of N. benthamiana across its wide distribution in Australia remains relatively underexplored. Here, we have used multispecies coalescent methods on genome-wide single nuclear polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.
  • ER stress in COVID-19 and Parkinson's Disease: in vitro and in silico evidences

    Chaudhry, Zahara Latif; Gamal, Mahmoud; Ferhati, Ingrid; Warda, Mohamad; Ahmed, Bushra Y.; ; University of Bedfordshire; Cairo University (MDPI, 2022-04-16)
    The outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) signifies a serious worldwide concern to public health. Both transcriptome and proteome of SARS-CoV-2-infected cells synergize the progression of infection in host, which may exacerbate symptoms and/or progression of other chronic diseases such as Parkinson's disease (PD). Oxidative stress is a well-known cause of endoplasmic reticulum (ER) stress observed in both SARS-CoV-2 and PD. In the current study, we aimed to explore the influence of PKR-like ER kinase (PERK) stress pathway under SARS-CoV-2-mediated infection and in human cell model of PD. Furthermore, we investigated whether they are interconnected and if the ER stress inhibitors could inhibit cell death and provide cellular protection. To achieve this aim, we have incorporated in silico analysis obtained from gene set enrichment analysis (GSEA), a literature review and laboratory data. The neurotoxin, 6-hydroxy dopamine (6OHDA), was used to mimic the biochemical and neuropathological characteristics of PD by inducing oxidative stress in dopamine-containing neurons differentiated from ReNVM cell line (dDCNs). Furthermore, we explored if ER stress influences activation of caspases-2, -4 and -8 in SARS-CoV-2 and in stressed dDCNs. Our laboratory data using Western blot, immunocytochemistry and 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) analyses indicated that 6OHDA-induced toxicity triggered activation of caspases-2, -4 and -8 in dDCNs. Under SARS-CoV-2 infection of different cell types, GSEA revealed cell-specific sensitivities to oxidative and ER stresses. Cardiomyocytes and type II alveolar epithelial-like cells were more vulnerable to oxidative stress than neural cells. On the other side, only cardiomyocytes activated the unfolded protein response, however, the PERK pathway was operative in both cardiomyocytes and neural cells. In addition, caspase-4 activation by a SARS-CoV-2 was observed via in silico analyses. These results demonstrate that the ER stress pathway under oxidative stress in SARS-CoV-2 and PD are interconnected using diverse pathways. Furthermore, our results using the ER stress inhibitor and caspase specific inhibitors provided cellular protection suggesting that the use of specific inhibitors can provide effective therapeutic approaches for the treatment of COVID-19 and PD.
  • Regulation of cell cycle and differentiation markers by pathogenic, non-pathogenic and opportunistic skin bacteria

    Younis, Sidra; Deeba, Farah; Fatima Saeed, Rida; Mothana, Ramzi A.; Ullah, Riaz; Faheem, Muhammad; Javed, Qamar; Blumenberg, Miroslav; National University of Medical Sciences, Pakistan; Quaid-e-Azam University; et al. (Elsevier B.V., 2021-11-02)
    Skin is the first line of defense against the physical, chemical and the biological environment. It is an ideal organ for studying molecular responses to biological infections through a variety of skin cells that specialize in immune responses. Comparative analysis of skin response to pathogenic, non-pathogenic, and commensal bacteria would help in the identification of disease specific pathways for drug targets. In this study, we investigated human breast reduction skin responses to Cutibacterium acnes (C. acnes), Staphylococcus aureus (S. aureus), Staphylococcus epidermidis (S. epidermidis), and TLR1/2 agonist using Affymetrix microarray chips. The Pam3CSK4 solution and bacterial cultures were prepared and inoculated in steel rings, that were placed on the acetone treated epidermis in a petri dish. After 24 h incubation, 8 mm punch biopsies were taken from the center of the ring, and RNA was extracted. The genome-wide expression was then analyzed using Affymetrix HG-133A gene chip microarray. We found that the C. acnes and S. aureus boosted the production of extracellular matrix components and attenuated the expression of differentiation markers. The above responses were mediated through the TLR2 pathway. Skin also responded to S. aureus and C. acnes by inducing the genes of the cell cycle machinery; this response was not TLR2-dependent. S. aureus induced, whereas C. acnes suppressed the genes associated with apoptosis; this was also not TLR2-dependent. Moreover, S. epidermis apparently did not lead to changes in gene expression. We conclude that the breast reduction skin is a very useful model to study the global gene expression in response to bacterial treatments.
  • Effects and mechanism of Ganoderma lucidum polysaccharides in the treatment of diabetic nephropathy in streptozotocin-induced diabetic rats

    Hu, Yu; Wang, Shu-Xiang; Wu, Fu-Yu; Wu, Ke-Jia; Shi, Rui-Ping; Qin, Li-Hong; Lu, Chun-Feng; Wang, Shu-Qiu; Wang, Fang-Fang; Zhou, Shaobo; et al. (Hindawi, 2022-03-08)
    Ganoderma lucidum polysaccharides (GLP) have renal protection effect but there was no study on the diabetic nephropathy. This study was designed to investigate its effect and mechanism using a diabetic rat model induced by streptozotocin (50 mg/kg, i.p.). The diabetic rats were treated with GLP (300 mg/kg/day) for 10 weeks. The blood glucose, glycated hemoglobin, body weight, and the levels of blood creatinine, urea nitrogen, and urine protein were assessed. And renal pathologies were assessed by the tissue sections stained with hematoxylin-eosin, Masson’s trichome, and periodic acid-Schiff. The expression of phosphorylated phosphoinositide 3 kinase (p-PI3K), phosphorylated protein kinase B (p-Akt), and phosphorylated mammalian target of rapamycin (p-mTOR), the autophagy proteins beclin-1, LC3-II, LC3-I, and P62; the apoptosis-related proteins caspase-3 and caspase-9; and the inflammation markers IL-6, IL-1β, and TNF-ɑ were assessed. Results showed that GLP alleviated the impairment of renal function by reducing urinary protein excretion and the blood creatinine level and ameliorated diabetic nephropathy. The expression of p-PI3K, p-Akt, and p-mTOR in the diabetic kidney were significantly reduced in the GLP treatment group compared to the without treatment group. GLP treatment activated the autophagy indicators of beclin-1 and the ratio of LC3-II/LC3-I but reduced p62 and also inhibited the expression of caspase-3, caspase-9 and IL-6, IL-1β, and TNF-ɑ. In conclusion, the effect of GLP amelioration diabetic nephropathy may be via the PI3k/Akt/mTOR signaling pathway by inhibition of the apoptosis and inflammation and activation of the autophagy process.
  • Study on the association of dietary fatty acids intake and serum lipid profiles with cognition in aging subjects with type 2 diabetes mellitus

    Li, Pengfei; Gao, Yanyan; Ma, Xiaojun; Zhou, Shaobo; Guo, Yujie; Xu, Jingjing; Wang, Xixiang; Van Halm-Lutterodt, Nicholas; Yuan, Linhong; Capital Medical University, Beijing; et al. (Frontiers, 2022-03-31)
    Background: The correlation between dietary fatty acid (FA) intake and serum lipid profile levels with cognition in the aged population has been reported by previous studies. However, the association of dietary FA intake and serum lipid profile levels with cognition in subjects with type 2 diabetes mellitus (T2DM) is seldom reported. Objective: A cross-sectional study was conducted to explore the correlation between dietary FA intake and serum lipid profiles with cognition in the aged Chinese population with T2DM. Methods: A total of 1,526 aged Chinese subjects were recruited from communities. Fasting blood samples were collected for parameter measurement. The food frequency questionnaire (FFQ) method was applied for a dietary survey. Cognition was assessed using the Montreal Cognitive Assessment (MoCA) test. Dietary FA intake and serum lipid levels were compared between subjects with T2DM and control subjects. A logistic regression analysis was carried out for analyzing the association of FA intake and serum lipid levels with the risk of mild cognitive impairment (MCI) in subjects with T2DM and control subjects. Results: There was a significant difference in the serum lipid level between the T2DM group and the control group. Results of the logistic regression analysis demonstrated the potential associations of serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c), and dietary n-3 polyunsaturated fatty acids (PUFAs) intake with the risk of MCI in subjects with T2DM, but the associations were not observed in control subjects. Conclusion: The T2DM phenotype might affect the relationship between dietary FA intake, circulating lipids, and cognitive performance. Large prospective cohort studies are needed to uncover the underlying mechanism of how dietary FA intake and serum lipid levels affect cognition in aged subjects with T2DM.
  • Prospective association of dietary soy and fibre intake with puberty timing: a cohort study among Chinese children

    Xiong, Jingyuan; Xu, Yujie; Liu, Xueting; Wang, Xiaoyu; Shan, Shufang; Crabbe, M. James C.; Zhao, Li; Fang, He; Cheng, Guo; ; et al. (BMC, 2022-04-04)
    Background: Dietary phytoestrogens have been suggested to influence puberty timing, a critical stage for wellbeing in adulthood. We hypothesized that childhood soy intake might prospectively influence puberty timing and that dietary fibre and the key isoflavone metabolite equol might play roles. Methods: Cox proportional hazard regression models were performed in 4781 children (2152 girls and 2629 boys) aged 6–8 years old from the Chinese Adolescent Cohort Study for whom a food frequency questionnaire at baseline and information about potential confounders were available. Anthropometry and pubertal status including age at Tanner stage 2 for breast development (B2) or age at the initiation of gonadal growth (G2), and age at menarche (M) or voice break (VB) were assessed annually. Equol excretion was determined by urine samples from 1311 participants. Results: Among girls and boys, higher soy intake was associated with later puberty timing (hazard ratio (HR)-B2: 0.88 (95% CI, 0.80–0.96), p=0.02; HR-M, 0.87 (0.77–0.94), p=0.01; HR-G2, 0.91 (0.82–0.98), p=0.013; HR-VB, 0.90 (0.82–0.9), p=0.02), independent of prepubertal body fatness and fibre intake. These associations were more pronounced among children with a high urinary equol level (pfor-interaction ≤ 0.04) or with a high cereal fibre intake (pfor-interaction ≤ 0.06). Intake of dietary fibre or its subtype was not prospectively associated with puberty onset after adjusting for dietary soy intake (p≥0.06). Conclusion: Higher childhood soy intake is prospectively associated with later puberty timing in both Chinese girls and boys, independent of prepubertal body fatness, and the association is particularly pronounced among individuals with a higher urinary equol level.

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