• Identification of new antibacterial targets in RNA polymerase of Mycobacterium tuberculosis by detecting positive selection sites

      Wang, QingBiao; Xu, Yiqin; Gu, Zhuoya; Liu, Nian; Jin, Ke; Li, Yao; Crabbe, M. James C.; Zhong, Yang; Fudan University; Oxford University; et al. (Elsevier, 2017-11-21)
      Bacterial RNA polymerase (RNAP) is an effective target for antibacterial treatment. In order to search new potential targets in RNAP of Mycobacterium, we detected adaptive selections of RNAP related genes in 13 strains of Mycobacterium by phylogenetic analysis. We first collected sequences of 17 genes including rpoA, rpoB, rpoC, rpoZ, and sigma factor A-M. Then maximum likelihood trees were constructed, followed by positive selection detection. We found that sigG shows positive selection along the clade (M. tuberculosis, M. bovis), suggesting its important evolutionary role and its potential to be a new antibacterial target. Moreover, the regions near 933Cys and 935His on the rpoB subunit of M. tuberculosis showed significant positive selection, which could also be a new attractive target for anti-tuberculosis drugs.
    • Identification of survivin as a promising target for the immunotherapy of adult B-cell acute lymphoblastic leukemia

      Boullosa, Laura Freire; Savaliya, Payalben; Bonney, Stephanie A.; Orchard, Laurence; Wickenden, Hannah; Lee, Cindy; Smits, Evelien L.J.; Banham, Alison H.; Mills, Ken I.; Orchard, Kim H.; et al. (Impact Journals, 2017-12-17)
      B-cell acute lymphoblastic leukemia (B-ALL) is a rare heterogeneous disease characterized by a block in lymphoid differentiation and a rapid clonal expansion of immature, non-functioning B cells. Adult B-ALL patients have a poor prognosis with less than 50% chance of survival after five years and a high relapse rate after allogeneic haematopoietic stem cell transplantation. Novel treatment approaches are required to improve the outcome for patients and the identification of B-ALL specific antigens are essential for the development of targeted immunotherapeutic treatments. We examined twelve potential target antigens for the immunotherapy of adult B-ALL. RT-PCR indicated that only survivin and WT1 were expressed in B-ALL patient samples (7/11 and 6/11, respectively) but not normal donor control samples (0/8). Real-time quantitative (RQ)-PCR showed that survivin was the only antigen whose transcript exhibited significantly higher expression in the B-ALL samples (n = 10) compared with healthy controls (n = 4)(p = 0.015). Immunolabelling detected SSX2, SSX2IP, survivin and WT1 protein expression in all ten B-ALL samples examined, but survivin was not detectable in healthy volunteer samples. To determine whether these findings were supported by the analyses of a larger cohort of patient samples, we performed metadata analysis on an already published microarray dataset. We found that only survivin was significantly over-expressed in B-ALL patients (n = 215) compared to healthy B-cell controls (n = 12)(p = 0.013). We have shown that survivin is frequently transcribed and translated in adult B-ALL, but not healthy donor samples, suggesting this may be a promising target patient group for survivin-mediated immunotherapy.
    • The impact of climate change and the environment on coral growth.

      Crabbe, M. James C.; Goffredo, Stefano; Dubinsky, Zvy; University of Bologna; Bar-Ilan University; University of Bedfordshire (Springer Verlag, 2016-09-08)
      Knowledge of factors that are important in reef growth and resilience helps us understand how reefs react following major environmental disturbances including overfishing, destructive fishing practices, coral bleaching, ocean acidification, sea-level rise, algal blooms, agricultural run-off, coastal and resort development, marine pollution, increasing coral diseases, invasive species, hurricane/cyclone damage and bleaching. Research in both the Indo-Pacific and in the Caribbean show how temperature and environmental extremes have influenced coral growth, recruitment and mortality. Three dimensional topography and complexity is important for reef vitality and viability in the face of environmental stressors. Within the narrow temperature range for coral growth, corals can respond to rate of temperature change as well as to temperature per se. A rational polynomial function model for coral colony growth appears as the best-fitting model for coral growth, closely followed by exponential logistic, Gompertz, and von Bertalanffy models. Models have also been developed for many varieties of coral morphologies, as well as for polyp spacing in those morphologies. The chapter concludes with the suggestion that developing large Marine Protected Areas (MPAs) as part of an overall climate change policy for a country may be the best way of integrating climate change into MPA planning, management and evaluation.
    • In vitro bioaccessibility and physicochemical properties of phytosterol linoleic ester synthesized from soybean sterol and linoleic acid

      Yang, Fuming; Oyeyinka, Samson A.; Xu, Weili; Ma, Ying; Zhou, Shaobo; Harbin Institute of Technology; University of Ilorin; University of Bedfordshire (Elsevier, 2018-02-14)
      Phytosterols are bioactive components capable of reducing cholesterol level in serum and reducing risk of arteriosclerosis. In this study, conditions for the synthesis of maximum yield of phytosterol linoleic ester (PLE) was optimized and the physicochemical properties and in vitro bioaccessibility of the PLE were assessed. Under the optimized condition of 1:1.1 mol ratio of phytosterol and linoleoyl chloride at 80 °C for 1.5 h, the conversion rate of phytosterol reached 96.1%. Its solubility in oil increased 20 times, up to 33.8%. Also, peroxide value of PLE was much lower than linoleic acid (32.9 and 47.0 mmol/kg), which means better oxidative stability. Bioaccessibility of PLE was affected by time, concentration of bile extract, and dissolved medium. It was 4.93% alone, increased by 2.5 times compare to phytosterol; or 53.46% in oil, under the condition of 40 mg/mL bile extract for 120 min. In conclusion, under the tested condition, phytosterol conversion rate, its solubility in oil and bioaccessibility were improved significantly. The method showed great potential in manufacture high quality and quantity of PLE.
    • 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.
    • Inhibition effects of paeonol on mice bearing EMT6 breast cancer through inducing rumor cell apoptosis

      Song, Hanjun; Wang, Jianjie; Li, Lijiang; Wang, Molin; Dong, Hang; Luo, Wenzhe; Zhou, Shaobo; Jiamusi University; University of Bedfordshire (2014-11-11)
      Paeonol, a phenolic component from the root bark of Paeonia moutan, has been identified to possess antitumor effects on mice bearing EMT6 breast cancer in our previous studies. However, the underlying mechanisms remain unknown. In the present study the molecular mechanisms of paeonol were further investigated in EMT6 mice model. The results showed that treatment of mice with 175 and 350 mg/kg/day of paeonol significantly inhibited the growth of the EMT6 tumor in mice, and induced tumor cell apoptosis which were demonstrated by light microscopy after hematoxylin and eosin staining and apoptosis analysis by flow cytometry. In addition, compared with the control group, paeonol increased the number of tumor cells in G0/G1 phase but decreased the number of cells in S and G2/M phase. Paeonol treatment (350 mg/kg body weight) also resulted in a decrease of Bcl-2 and an increase in Bax and caspase-3 expressions, which were demonstrated by immunohistochemical and western blot analysis. These results indicate that the antitumor effects of paeonol might be associated with arresting tumor cells in the G0/G1 phase, inducing cell apoptosis and regulation of the expression of Bcl-2, Bax and activation of caspase-3.
    • Inhibition effects of paeonol on mice bearing EMT6 breast cancer through inducing tumor cell apoptosis

      Song, Hanjun; Wang, Jianjie; Li, Lijiang; Wang, Molin; Dong, Hang; Luo, Wenzhe; Zhou, Shaobo; ; Jiamusi University; University of Bedfordshire (2014-01-01)
      Paeonol, a phenolic component from the root bark of Paeonia moutan, has been identified to possess antitumor effects on mice bearing EMT6 breast cancer in our previous studies. However, the underlying mechanisms remain unknown. In the present study the molecular mechanisms of paeonol were further investigated in EMT6 mice model. The results showed that treatment of mice with 175 and 350 mg/kg/day of paeonol significantly inhibited the growth of the EMT6 tumor in mice, and induced tumor cell apoptosis which were demonstrated by light microscopy after hematoxylin and eosin staining and apoptosis analysis by flow cytometry. In addition, compared with the control group, paeonol increased the number of tumor cells in G0/G1 phase but decreased the number of cells in S and G2/M phase. Paeonol treatment (350 mg/kg body weight) also resulted in a decrease of Bcl-2 and an increase in Bax and caspase-3 expressions, which were demonstrated by immunohistochemical and western blot analysis. These results indicate that the antitumor effects of paeonol might be associated with arresting tumor cells in the G0/G1 phase, inducing cell apoptosis and regulation of the expression of Bcl-2, Bax and activation of caspase-3.
    • 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.
    • The interaction of Wnt-11 and signalling cascades in prostate cancer

      Koushyar, Sarah; Grant, Guy H.; Uysal-Onganer, Pinar (Springer Netherlands, 2016-08-11)
      Prostate cancer (PCa) is the second most common cancer among the male population. Conventional therapies target androgen signalling, which drives tumour growth; however, they provide limited survival benefits for patients. It is essential, therefore, to develop a more specific biomarker than the current gold standard, PSA testing. The Wnt signalling pathway induces expression of target genes through cell surface receptors. A non-canonical member of this family, Wnt-11, is evolutionarily highly conserved and is normally expressed by various cells in the developing embryo, as well as in the heart, liver and skeletal muscle of adult humans. We comprehensively review several cell signalling pathways to explain how they interact with Wnt-11, demonstrating its use as a potential biomarker for PCa. Several studies have shown that the expression of Wnt-11 is associated with gastric, renal and colorectal adenocarcinomas and PCa. Moreover, Wnt-11 affects extracellular matrix composition and cytoskeletal rearrangement, and it is required for proliferation and/or survival during cell differentiation. It was found that PCa cell lines express high levels of Wnt-11, which allows differentiation of the epithelial prostate tumour cells to neuron-like (NE) cells. The NE cells produce additional factors that can cause regression after treatment. Accumulating evidence shows that Wnt-11 could be a potential biomarker in diagnosing PCa. Many studies have shown both non-canonical and canonical Wnts interact with several signalling cascades such as PKC, JNK, NF-κB, Rho, PKA and PI3K. In particular, evidence demonstrates Wnt-11 is involved in the progression of PCa, thus it could have the potential to become both a specific disease marker and an important therapeutic target.
    • Intramolecular polyspecificity in CD4 T-cell recognition of Ad-restricted epitopes of proteoglycan aggrecan

      Falconer, Jane; Lowes, Katie; Furmanski, Anna L.; Dyson, Julian; Ng, Wan Fai; Robinson, John H. (Wiley, 2013-12-24)
      T-cell recognition of MHC–peptide complexes shows a high degree of polyspecificity extending to recognition of a large number of structurally unrelated peptides. Examples of polyspecificity reported to date are confined to recognition of epitopes from distinct proteins or synthetic peptide libraries. Here we describe intramolecular polyspecificity of CD4 T cells specific for several epitopes within proteoglycan aggrecan, a structural glycoprotein of cartilage and candidate autoantigen in rheumatoid arthritis. T-cell hybridomas from aggrecan-immunized mice recognized four structurally unrelated epitopes from the G1 domain of aggrecan, but not other aggrecan epitopes or a variety of other peptide epitopes restricted by the same MHC class II allele. We also showed that the hierarchy of cross-reactivity broadly correlated with the strength of peptide binding to MHC class II. Similar polyspecificity was observed in responses of lymph node cells from peptide-immunized mice, suggesting polyspecificity of a significant proportion of the in vivo aggrecan specific T-cell repertoire. Polyspecific recognition of several epitopes within the same autoantigen may provide a novel mechanism to reach the activation threshold of low-affinity autoreactive T cells in the initiation of autoimmune diseases.
    • The intrinsically disordered Tarp protein from chlamydia binds actin with a partially preformed helix

      Tolchard, James; Walpole, Samuel J.; Miles, Andrew J.; Maytum, Robin; Eaglen, Lawrence A.; Hackstadt, Ted; Wallace, B.A.; Blumenschein, Tharin M.A. (Nature, 2018-01-31)
      Tarp (translocated actin recruiting phosphoprotein) is an effector protein common to all chlamydial species that functions to remodel the host-actin cytoskeleton during the initial stage of infection. In C. trachomatis, direct binding to actin monomers has been broadly mapped to a 100-residue region (726-825) which is predicted to be predominantly disordered, with the exception of a ~10-residue α-helical patch homologous to other WH2 actin-binding motifs. Biophysical investigations demonstrate that a Tarp726-825 construct behaves as a typical intrinsically disordered protein; within it, NMR relaxation measurements and chemical shift analysis identify the ten residue WH2-homologous region to exhibit partial α-helix formation. Isothermal titration calorimetry experiments on the same construct in the presence of monomeric G-actin show a well defined binding event with a 1:1 stoichiometry and Kd of 102 nM, whilst synchrotron radiation circular dichroism spectroscopy suggests the binding is concomitant with an increase in helical secondary structure. Furthermore, NMR experiments in the presence of G-actin indicate this interaction affects the proposed WH2-like α-helical region, supporting results from in silico docking calculations which suggest that, when folded, this α-helix binds within the actin hydrophobic cleft as seen for other actin-associated proteins.
    • Is post-polyploidization diploidization the key to the evolutionary success of angiosperms?

      Dodsworth, Steven; Chase, Mark W.; Leitch, Andrew R. (Blackwell Publishing Ltd, 2015-12-24)
      Advances in recent years have revolutionized our understanding of both the context and occurrence of polyploidy in plants. Molecular phylogenetics has vastly improved our understanding of plant relationships, enabling us to better understand trait and character evolution, including chromosome number changes. This, in turn, has allowed us to appreciate better the frequent occurrence and extent of polyploidy throughout the history of angiosperms, despite the occurrence of low chromosome numbers in some groups, such as in Arabidopsis (A. thaliana was the first plant genome to be sequenced and assembled). In tandem with an enhanced appreciation of phylogenetic relationships, the accumulation of genomic data has led to the conclusion that all angiosperms are palaeopolyploids, together with better estimates of the frequency and type of polyploidy in different angiosperm lineages. The focus therefore becomes when a lineage last underwent polyploidization, rather than simply whether a plant is ‘diploid’ or ‘polyploid’. This legacy of past polyploidization in plants is masked by large-scale genome reorganization involving repetitive DNA loss, chromosome rearrangements (including fusions and fissions) and complex patterns of gene loss, a set of processes that are collectively termed ‘diploidization’. We argue here that it is the diploidization process that is responsible for the ‘lag phase’ between polyploidization events and lineage diversification. If so, diploidization is important in determining chromosome structure and gene content, and has therefore made a significant contribution to the evolutionary success of flowering plants.
    • Lamellipodin promotes invasive 3D cancer cell migration via regulated interactions with Ena/VASP and SCAR/WAVE

      Carmona, G.; Perera, U.; Gillett, C.; Naba, A.; Law, Ah-Lai; Sharma, V.P.; Wang, J.; Wyckoff, J.; Balsamo, M.; Mosis, F.; et al. (Nature Publishing Group, 2016-03-21)
      Cancer invasion is a hallmark of metastasis. The mesenchymal mode of cancer cell invasion is mediated by elongated membrane protrusions driven by the assembly of branched F-actin networks. How deregulation of actin regulators promotes cancer cell invasion is still enigmatic. We report that increased expression and membrane localization of the actin regulator Lamellipodin correlate with reduced metastasis-free survival and poor prognosis in breast cancer patients. In agreement, we find that Lamellipodin depletion reduced lung metastasis in an orthotopic mouse breast cancer model. Invasive 3D cancer cell migration as well as invadopodia formation and matrix degradation was impaired upon Lamellipodin depletion. Mechanistically, we show that Lamellipodin promotes invasive 3D cancer cell migration via both actin-elongating Ena/VASP proteins and the Scar/WAVE complex, which stimulates actin branching. In contrast, Lamellipodin interaction with Scar/WAVE but not with Ena/VASP is required for random 2D cell migration. We identified a phosphorylation-dependent mechanism that regulates selective recruitment of these effectors to Lamellipodin: Abl-mediated Lamellipodin phosphorylation promotes its association with both Scar/WAVE and Ena/VASP, whereas Src-dependent phosphorylation enhances binding to Scar/WAVE but not to Ena/VASP. Through these selective, regulated interactions Lamellipodin mediates directional sensing of epidermal growth factor (EGF) gradients and invasive 3D migration of breast cancer cells. Our findings imply that increased Lamellipodin levels enhance Ena/VASP and Scar/WAVE activities at the plasma membrane to promote 3D invasion and metastasis.
    • Lipid derivatives activate GPR119 and trigger GLP-1 secretion in primary murine L-cells

      Moss, Catherine E.; Glass, Leslie L.; Diakogiannaki, Eleftheria; Pais, Ramona; Lenaghan, Carol; Smith, David M.; Wedin, Marianne; Bohlooly-Y, Mohammad; Gribble, Fiona M.; Reimann, Frank; et al. (Elsevier Inc., 2015-07-02)
      Aims/hypothesis Glucagon-like peptide-1 (GLP-1) is an incretin hormone derived from proglucagon, which is released from intestinal L-cells and increases insulin secretion in a glucose dependent manner. GPR119 is a lipid derivative receptor present in L-cells, believed to play a role in the detection of dietary fat. This study aimed to characterize the responses of primary murine L-cells to GPR119 agonism and assess the importance of GPR119 for the detection of ingested lipid. Methods GLP-1 secretion was measured from murine primary cell cultures stimulated with a panel of GPR119 ligands. Plasma GLP-1 levels were measured in mice lacking GPR119 in proglucagon-expressing cells and controls after lipid gavage. Intracellular cAMP responses to GPR119 agonists were measured in single primary L-cells using transgenic mice expressing a cAMP FRET sensor driven by the proglucagon promoter. Results L-cell specific knockout of GPR119 dramatically decreased plasma GLP-1 levels after a lipid gavage. GPR119 ligands triggered GLP-1 secretion in a GPR119 dependent manner in primary epithelial cultures from the colon, but were less effective in the upper small intestine. GPR119 agonists elevated cAMP in ∼70% of colonic L-cells and 50% of small intestinal L-cells. Conclusions/interpretation GPR119 ligands strongly enhanced GLP-1 release from colonic cultures, reflecting the high proportion of colonic L-cells that exhibited cAMP responses to GPR119 agonists. Less GPR119-dependence could be demonstrated in the upper small intestine. In vivo, GPR119 in L-cells plays a key role in oral lipid-triggered GLP-1 secretion.
    • Liqui-pellet: the emerging next-generation oral dosage form which stems from liquisolid concept in combination with pelletization technology

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

      Cunningham, Phil; McDermott, Lindsay C. (Oxford University Press, 2009-04-30)
      Docosahexanoic (DHA)4 and arachidonic (ARA) acids are important for proper fetal development and accumulate in the fetus during gestation. They cannot be synthesized by the fetus and must be gained instead from the maternal blood supply via the syncytiotrophoblast, the transporting epithelium of the placenta. Cell biological experiments suggest that both membrane-associated placental plasma membrane fatty acid-binding protein (pFABPpm) and fatty acid transport protein (FATP) 4 are involved in DHA uptake while fatty acid-binding proteins (FABP) are thought to be involved in intracellular trafficking of long-chain fatty acids. FABP1, 3, and 4 have been detected in the syncytiotrophoblast and there is experimental and theoretical evidence to suggest that these three FABP are under the control of hypoxia inducible factor (HIF), perhaps playing a role in fetal protection from hypoxia. Biophysical measurements reveal these FABP have a higher affinity for DHA over ARA but that affinities for both are lower than those of nonessential fatty acids. Recent research is beginning to uncover the mechanisms of DHA and ARA transmembrane and intracellular transport in the placenta, and it is suggested that maternal health and nutrition during pregnancy could be important in determining fatty acid transport and binding protein expression and, thereby, essential fatty acid delivery to the fetus.
    • Management of environmental streaming data to optimize Arctic shipping routes.

      Zhang, Zhihua; Crabbe, M. James C.; University of Bedfordshire; Shandong University (Springer Nature, 2021-07-20)
      Dynamic accurate predictions of Arctic sea ice, ocean, atmosphere, and ecosystem are necessary for safe and efficient Arctic maritime transportation; however a related technical roadmap has not yet been established. In this paper, we propose a management system for trans-Arctic maritime transportation supported by near real-time streaming data from air-space-ground-sea integrated monitoring networks and high spatio-temporal sea ice modeling. As the core algorithm of integrated monitoring networks, a long short-term memory (LSTM) neural network is embedded to improve Arctic sea ice mapping algorithms.Since the LSTM is localized in time and space, it can make full use of streaming data characteristics. The sea ice–related parameters from satellite remote sensing raw data are used as the input of the LSTM, while streaming data from shipborne radar networks and/or buoy measurements are used as training datasets to enhance the accuracy and resolution of environmental streaming data from outputs of LSTM. Due to large size of streaming data, the proposed management system of trans-Arctic shipping should be built on a cloud distribution platform using existing wireless communications networks among vessels and ports. Our management system will be used by the ongoing European Commission Horizon 2020 Programme “ePIcenter.”
    • Mastermind-Like 3 controls proliferation and differentiation in neuroblastoma

      Heynen, Guus J.J.E.; Nevedomskaya, Ekaterina; Palit, Sander; Basheer, Noorjahan Jagalur; Lieftink, Cor; Schlicker, Andreas; Zwart, Wilbert; Bernards, René; Bajpe, Prashanth Kumar; ; et al. (American Association for Cancer Research Inc., 2016-01-19)
      Neuroblastoma cell lines can differentiate upon treatment with retinoic acid (RA), a finding that provided the basis for the clinical use of RA to treat neuroblastoma. However, resistance to RA is often observed, which limits its clinical utility. Using a gain-of-function genetic screen, we identified an unexpected link between RA signaling and mastermindlike 3 (MAML3), a known transcriptional coactivator for NOTCH. Our findings indicate that MAML3 expression leads to the loss of activation of a subset of RA target genes, which hampers RA-induced differentiation and promotes resistance to RA. The regulatory DNA elements of this subset of RA target genes show overlap in binding of MAML3 and the RA receptor, suggesting a direct role for MAML3 in the regulation of these genes. In addition, MAML3 has RA-independent functions, including the activation of IGF1R and downstream AKT signaling via upregulation of IGF2, resulting in increased proliferation. These results demonstrate an important mechanistic role for MAML3 in proliferation and RA-mediated differentiation.
    • Measurement of specific radioactivity in proteins separated by two-dimensional gel electrophoresis

      Zhou, Shaobo; Mann, Christopher J.; Dunn, Michael J.; Preedy, Victor R.; Emery, Peter W.; (Wiley, 2006-03-07)
      We report a method to quantify the specific radioactivity of proteins that have been separated by 2-DE. Gels are stained with SyproRuby, and protein spots are excised. The SyproRuby dye is extracted from each spot using DMSO, and the fluorescence is quantified automatically using a plate reader. The extracted gel piece is then dissolved in hydrogen peroxide and radioactivity is quantified by liquid scintillation counting. Gentle agitation with DMSO for 24 h was found to extract all the SyproRuby dye from gel fragments. The fluorescence of the extract was linearly related to the amount of BSA loaded onto a series of 1-D gels. When rat muscle samples were run on 2-DE gels, the fluorescence extracted from 54 protein spots showed a good correlation (r = 0.79, p < 0.001) with the corresponding spot intensity measured by conventional scanning and image analysis. DMSO extraction was found not to affect the amount of radioactive protein left in the gel. When a series of BSA solutions of known specific radioactivity were run on 2-DE gels, the specific radioactivity measured by the new method showed a good correlation (r = 0.98, p < 0.01, n = 5) with the specific radioactivity measured directly before loading. Reproducibility of the method was measured in a series of 2-DE gels containing proteins from the livers of rats and mice that had been injected with [35S]methionine. Variability tended to increase when the amount of radioactivity in the protein spot was low, but for samples containing at least 10 dpm above background the CV was around 30%, which is comparable to that obtained when measuring protein expression by conventional image analysis of SyproRuby-stained 2-DE gels. Similar results were obtained whether spots were excised manually or using a spot excision robot. This method offers a high-throughput, cost-effective and reliable method of quantifying the specific radioactivity of proteins from metabolic labelling experiments carried out in vivo, so long as sufficient quantities of radioactive tracer are used.
    • MFG-E8 induced differences in proteomic profiles in mouse C2C12 cells and its effect on PI3K/Akt and ERK signal pathways

      Li, He; Guan, Kaifang; Li, Xu; Ma, Ying; Zhou, Shaobo; Harbin Institute of Technology; Jilin University; University of Bedfordshire (Elsevier, 2018-11-28)
      Milk fat globule-EGF factor 8 (MFG-E8) is one of the major proteins in milk fat globule membrane. In this study, mouse-derived C2C12 myoblast cells were served as an experimentally tractable model system for investigating the molecular basis of skeletal muscle cell specification and development. To examine the biochemical adaptations associated with myocytes formation comprehensively, a liquid chromatography coupled with tandem mass spectrometry label-free semi-quantitative  approach was used to analyse the myogenic C2C12 proliferation program. Over 1987  proteins were identified in C2C12 cells. The MFG-E8 (200 mg/mL) and MFG-E8 (500 26 mg/mL) with significant differences were compared based on the relative abundance. The result profiles of regulation of MFG-E8 to the expression of proteins in C2C12 cells revealed that differential waves of expression of proteins linked to intracellular signaling, transcription, cytoarchitecture, adhesion, metabolism, and muscle contraction across during the C2C12 cell proliferation process. Based on the analysis of  KEGG and STRING database, further to verification the expression of PI3K and ERK phosphorylation levels by Western blot. This study found that the data of proteomic was complementary to recent MFG-E8 studies of protein expression patterns in developing myotubes and provided a holistic framework for understanding how diverse biochemical processes are coordinated at the cellular level during skeletal muscle development.