95 research outputs found
SIP1/ZEB2 induced epthelial to mesenchymal transition promotes metastasis and chemoresistance in colorectal cancer
No full textColorectal cancer (CRC) is the second commonest cause of cancer-associated mortality in Europe, and a key public health issue. Cancer metastasis is the principle cause of death and occurs in up to 30% at presentation, and subsequently develops in 50% after curative surgery. The majority of patients with metastases are incurable, and can expect a median survival of only up to 2 years, even with the latest chemotherapeutic and biological agents. Additionally, not all patients respond and side effects are frequent and at times life threatening. These findings highlight the pressing need for identification of new markers of metastatic capability and chemotherapy response, to improve precision with which therapy can be tailor to patients. Although development of primary CRC has served as a paradigm for understanding multistage carcinogenesis, the mechanisms influencing metastasis and chemoresistance are still poorly understood.Epithelial-Mesenchymal Transition (EMT) is an embryologically conserved genetic program by which cancer cells down regulate epithelial junctions, express mesenchymal markers, and manifest a migratory phenotype. While the significance of EMT during development and embryogenesis is well established, an emerging role is its involvement in metastasis and chemo/radio resistance in cancer. EMT is activated by TGFβ, FGF, EGF, WNT and Notch signalling pathways, which converge to activate transcription factors that subsequently repress the expression of critical epithelial genes. Key transcription factors in this process include members of the SNAIL, Twist, and ZEB families, which promote cellular phenotypic switch. In addition to enhanced migration, metastatic cells also acquire apoptosis resistance to chemo/radio therapy through currently poorly understood mechanism. Despite growing evidence that EMT promotes apoptosis resistance to DNA damaging agents, ZEB family of transcription factors have been sparsely studied in gastrointestinal malignancies and the molecular mechanism mediating apoptosis resistance poorly understood.Based on these observations the following hypothesis was formulated:• SMAD interacting protein (SIP1/ZEB2) induced EMT promotes metastasis and apoptosis resistance in colorectal cancer (CRC).The primary objectives of the study are: -1. Assess if SIP1/ZEB2 induces EMT in CRC.2. Investigate whether expression of SIP1/ZEB2 could serve as a biomarker to detect patients at high risk or recurrence after surgical resection in CRC.3. Study the molecular mechanisms that promote SIP1/ZEB2 induced apoptosis resistance to chemotherapeutic and radiotherapeutic treatment regimens.4. Validate in-vitro findings in a murine model SIP1/ZEB2 expression resulted in the acquisition of all the cardinal features of EMT, namely E-cadherin down regulation, increased metastatic capacity and apoptosis resistance to chemotherapeutic agents commonly using in clinical practice.SIP/ZEB2 expression in primary CRC, exhibited a statistically significant association with increased risk of distant recurrence in two independent patient cohorts. Addition of SIP1/ZEB2 expression status to the TNM staging system improved precision in the ability to identify patients at high risk of disease recurrence after curative surgery. Further studied also highlighted an important association between SIP1/ZEB2 expression and chemoresistance to cytotoxic drugs used to in the FOLFOX regimen. A qPCR array, with a focus on DNA damage response highlighted SIP1/ZEB2 induced EMT associated with increased expression of multiple components of the nucleotide excision repair (NER) pathway, in particular excision repair cross complementation group 1 (ERCC1).ERCC1 hetero-dimerises with excision repair cross complementation group 4, which functions as an exonuclease during repair of DNA crosslinks generated by platinum based chemotherapeutic agents such as oxaliplatin. Stable over expression of ERCC1; lead to attenuate DNA damage, apoptosis resistance and enhanced viability. Whilst siRNA mediated knockdown (KD) sensitise cells to oxaliplatin treatment. Assessment of DNA repair kinetics, as a mechanism of repair kinetics revealed higher expression levels of ERCC1 associated with faster kinetics of DNA cross-link clearance. The influence of ERCC1 over expression in vivo was demonstrated by impaired tumour regression in ERCC1 over-expressing cells in an orthotopic murine model of primary CRC.ZEB proteins have also been implicated with the enhanced ability to repair DNA DSB’s and consequently promote resistance to ionising radiation. For many decades, models of DNA DSB repair have highlighted the critical influence of the histone architecture in accessing damaged DNA and subsequently undertaking DNA repair. Heterochromatin rich DNA domains are known to be prone to accruing mutations, due to attenuated DNA repair. Recent studies have suggested EMT leads to epigenetic reprograming, which results in genome wide loss of heterochromatin rich domains. SIP1/ZEB2 expression in DLD-SIP1 cells enhanced apoptosis resistance secondary to faster repair of DNA DSB’s. ChIP-Seq analysis of SIP1/ZEB2 expressing mesenchymal cells highlighted genome wide loss of heterochromatin mark H3K27me3. The mechanism responsible for this epigenetic change was found to be direct transcriptional repression of the methyltransferase EZH2, by SIP1/ZEB2. Inhibition of EZH2 by small molecule inhibitor GSK126 in uninduced DLDSIP1 cells enhanced apoptosis resistance and viability in response to IR. The above results suggest the epigenetic architecture of mesenchymal cancer can influence DNA repair kinetics and consequently resistance to IR. The above body of work clearly demonstrates SIP1/ZEB2 plays a central role in promoting metastasis and treatment resistance in CRC. Further in vitro studies and clinical trials to dissect the impact of SIP1/ZEB2 expression in CRC will facilitate clinical translation in future years
ERCC1 abundance is an indicator of DNA repair-apoptosis decision upon DNA damage
No full textDNA repair is essential for successful propagation of genetic material and fidelity of transcription. Nucleotide excision repair (NER) is one of the earliest DNA repair mechanisms, functionally conserved from bacteria to human. The fact that number of NER genes vary significantly between prokaryotes and metazoans gives the insight that NER proteins have evolved to acquire additional functions to combat challenges associated with a diploid genome, including being involved in the decision between DNA repair and apoptosis. However, no direct association between apoptosis and NER proteins has been shown to date. In this study, we induced apoptosis with a variety of agents, including oxaliplatin, doxorubicin and TRAIL, and observed changes in the abundance and molecular weight of NER complex proteins. Our results showed that XPA, XPC and ERCC1 protein levels change during DNA damage-induced apoptosis. Among these, ERCC1 decrease was observed as a pre-mitochondria depolarisation event which marks the “point of no return” in apoptosis signalling. ERCC1 decrease was due to proteasomal degradation upon lethal doses of oxaliplatin exposure. When ERCC1 protein was stabilised using proteasome inhibitors, the pro-apoptotic activity of oxaliplatin was attenuated. These results explain why clinical trials using proteasome inhibitors and platinum derivatives showed limited efficacy in carcinoma treatment and also the importance of how deep understanding of DNA repair mechanisms can improve cancer therapy
Risk assessment using a novel scoring system (NUn score) to predict major complications after oesophageal resection
No full textBackground: the aim of this study was to establish a numerical scoring system that categorises a patients’ risk of developing major post-operative complications after oesophageal resection based on routine blood tests.Methods: a prospective database of all upperGI resectionswith an oesophageal anastomosis between 2005 and 2010 was reviewed. C-reactive protein (CRP), white cell count (WCC) and albumin were recorded once pre-operatively and post-operatively daily until discharge or day 14. All post-operative complications were recorded using the Clavien-Dindo (CD) classification. The diagnostic accuracy of CRP,WCCand albumin levels were analysed by receiver operating characteristic (ROC) curve analysis with anastomotic leak and major complication or death (CD 3–5) as outcome measures.Results: a total of 258 patients were identified (Median age 67 (37–85) years, Male 78%, Female 22%). A minimally invasive procedure was performed in 101 (40%) cases. A total of 63 (25%) patients developed a major complication and there were 7 (2•7%) deaths. 27 (10•5%) patients were diagnosed with an anastomotic leak at median post-operative day (POD) 7 (Range: 5–15). On univariable analysis there were no pre-operative patient or tumour characteristics that could predict post-operative complications. CRP (p=0•08), WCC (p=0•08) and albumin (p=0•003) were independent predictors of a major complication or death at POD 5. After multivariable analysis these factors were combined to create a novel scoring system (NUn score). On POD 4 the NUn score was highly predictive of an anastomotic leak (NUn score >0•97: sensitivity 100%, specificity 66%, diagnostic accuracy 0•78 (95%CI 0•655–0•905, p<0•0001)) and a major complication or death (NUn >0•9: sensitivity 73%, specificity 79%, diagnostic accuracy 0•71 (95%CI 0•609–0•81, p<0•0001)).Conclusion: we describe the development of a novel (NUn) scoring system that accurately categorises patients at risk of anastomotic leak and major complications following oesophageal resection. In this cohort the NUn score accurately identified patients at risk of anastomotic leak 3 days prior to diagnosis. The sensitivity of the POD4NUnscore for anastomotic leak is such that patients with a score <0•97 can be confidently fast-tracked to enteral feeding and early discharge<br/
Understanding the value-chain of counterfeit products: A multimethod investigation
Get PDFThe student, - Sreekumar Arun, accepted the attached license on 2021-04-13 at 23:09.The student, - Sreekumar Arun, submitted this Dissertation for approval on 2021-04-13 at 23:23.This Dissertation was approved for publication on 2021-04-15 at 11:53.DSpace SAF Submission Ingestion Package generated from Vireo submission #16317 on 2021-09-16 at 17:03:02Made available in DSpace on 2021-09-17T02:34:25Z (GMT). No. of bitstreams: 2
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Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemAuthor requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I OnlyThe context of this dissertation is the market for counterfeit products, which accounts for more than one trillion US dollars of trade globally every year. Entrepreneurs who manufacture and market these products are clandestine and operate in the black market. Drawing from this context, this dissertation seeks to advance knowledge on how entrepreneurs strategically use ambiguity in marketing communications, and in relationships with other firms. The first essay examines how and why equivocation is used as a persuasive strategy by sellers of counterfeit products. This essay develops a framework that can help qualitatively and quantitatively identify equivocation rhetoric in firm-generated text. The second essay examines how relationships between firms are managed when one of the firms employs ambiguity as a protection strategy. Specifically, the essay sheds light on how manufacturers and retailers of counterfeit products succeed in maintaining ambiguity, and in managing relationship tension arising from ambiguity. Put together, the essays present an investigation of how counterfeit manufacturers and retailers conduct their marketing functions despite being clandestine and illegal.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-05-0
Dataset for the study of various error measures steering adaptive model order reduction algorithms in vibroacoustic applications
No full textThe dataset is associated with the university dissertation titled "Surrogate modeling of high-dimensional vibroacoustic problems using parametric model order reduction" by Harikrishnan K. Sreekumar. To evaluate the accuracy of a reduced order model in the context of model order reduction in the frequency domain, a range of error measures are available. The error measures are extensively used in adaptive algorithms to build reduced order models of optimal dimensions with the least effort. The author performs a detailed study on some of the popular error measures using simple plate examples that are discussed in the thesis. This current dataset publication contains essential artifacts (computational notebook, model data and primary results) that enable reproducibility of the outcome presented in the dissertation
Facebook: Is it undermining Indian culture?
No full textIncreasing parental intervention in order to diminish the detrimental effects of social media sitesSpring 2012Accompanied by video fil
Beauty Leaf Tree (Calophyllum inophyllum L.) — its biogeographic variability for salinity tolerance and kernel oil content as determined by FTIR/FTNIR technologies
No full textOver-dependency on fossil fuel can result in depletion of natural resources and acceleration of global climate change. Thus, there is a need to find alternatives to fossil fuel to meet the growing energy demand. Establishment of biofuel crops on marginal lands could be a viable option. However, at present, little is known about such crops. There are many non-edible feedstocks that can grow well on marginal lands. Calophyllum inophyllum L. also known as beauty leaf tree (BLT) is one such tree crop that naturally occurs on marginal soils. Interestingly, its kernels contain up to 65% non-edible oil which can be converted into biofuel. At present, however, little information exists on its stress tolerance and high oil yielding genotypes.
The current study evaluated in pot trials, a wide range of BLT genotypes for seed germination, salinity tolerance and kernel oil content. The study also assessed the effectiveness of novel technologies such as fourier transform infrared (FTIR) and fourier transform near infrared (FTNIR) spectroscopy to predict kernel oil content and tissue chloride (Cl-) concentrations, respectively.
Seed germination studies showed significant variability between the three genotypes and the germination ranged from 82.8% to 98.6%. Based on the early seedling growth, superiority of three genotypes were ranked as RB2 (Rosslyn Bay)>Nash1 (Cairns)>CAS1 (Darwin). Screening of 12 genotypes in a glasshouse for salinity (75 mM NaCl) tolerance showed significant reduction in seedling height increment, leaf area, net CO2 assimilation rate (A), transpiration rate (E) and biomass, as compared to their controls. Principal component analysis of studied parameters ranked the genotypes BR35, 3A, BR23 and 29B as being the most tolerant and the genotypes 21A, 15A and 32A as the least salt tolerant.
Effects of NaCl concentrations (0, 50, 150, 300, 500 mM) on three genotypes (RB2, Nash1 and CAS1) showed little change in biomass accumulation at 50 mM, and up to 57% reduction at 500 mM. At 300 mM NaCl, Na concentration in the mature leaves was 6.5 times higher than that in the controls, whereas the Cl- concentration was higher by 28 times. In an outdoor experimental study, 3-year-old saplings of BLT were assessed for long term (16 months) responses to NaCl (75 mM). In this study no significant differences were observed between the control and NaCl-treated plants for growth, biomass, chlorophyll fluorescence and photosynthetic parameters. There was a significant difference between younger and older leaves in Cl- accumulation. While the leaves of control plants contained ~495 mg kg-1 Cl, those exposed to 75 mM NaCl accumulated ~1151 mg kg-1 of Cl. Results of this experiment helped confirm that the BLT is a moderately salt tolerant species.
FTIR-ATR spectroscopy was tested to predict leaf tissue Cl-. Clusters of wavenumbers were identified, with each wavelength displaying differing correlation with tissue Cl-. Application of exhaustive feature selection technique enabled selection of 806 spectra (out of 1746) that highly correlated (r=0.93) with the chemometrically determined Cl-. It was also found that a feature selection process can be a valuable exercise to predict tissue Cl- or to estimate the contribution of wave numbers to Cl-. Overall, this study demonstrated that the BLT tissue Cl- can be estimated using FTIR spectra.
Kernel oil, resin, press cake and residue content were determined using a screw press for 50 accessions of BLT that were collected from various parts of Australia. The same kernels were used to obtain FTNIR spectra. The resulting spectra were employed to develop calibration models using partial least squares regression. The model produced coefficient of determination in cross validation (R2) and standard error in cross validation (SECV) values of 0.60% and 4.15% for oil content, 0.78% and 2.6% for resin, 0.77% and 4.86% for cake and 0.76% and 2.8% for residue content, respectively. The results showed that the FTNIR technique could be successfully used as a faster and cheaper alternative technique to other laboratory methods to screen BLT genotypes for oil, resin and cake contents, as their residual predictive deviation (RPD) values ranged between 2 and 1.5.
In summary, this research has examined germination and salinity tolerance of various genotypes of BLT. Based on these results, the BLT has been declared as a moderately salt tolerant species as compared to other Australian tree species. The research has also demonstrated that the FTIR and FTNIR technologies can be employed to estimate leaf Cl- and kernel oil content non-destructively. These technologies will be invaluable in selecting salt tolerant genotypes that also contain high oil%, as the kernels having high oil% can be germinated and the resulting seedlings can be subsequently screened for salinity tolerance. The study helped identify superior genotypes and demonstrated that the infrared spectroscopy techniques could be used to rapidly screen BLT genotypes for low tissue Cl- (hence higher salt tolerance) and high kernel oil
Beauty Leaf Tree (Calophyllum inophyllum L.) — its biogeographic variability for salinity tolerance and kernel oil content as determined by FTIR/FTNIR technologies
No full textIn the present day, fossil fuels and petroleum are depleting at an alarming rate due to over-dependency on them for energy generation. Hence there is a great need for an alternate renewable source of energy, and biofuel can be a good alternative. Thus, looking into the huge global demand for biofuel, there is potential scope for the use of the seeds of Calophyllum inophyllum (Beauty Leaf Tree; BLT) for biofuel production. Since C. inophyllum thrives in coastal or saline condition and it is a high biodiesel yielding species, the proposed study has great significance. Since the production of biofuel from fertile land is not advisable due to food vs fuel competition, marginal soils are best suited for biofuel production. In this connection, BLT is considered a good candidate. However, its stress tolerance and physiological responses are not known at present. The proposed research will focus on elucidating the variability in morphology, growth rates, oil content and the mechanism of salt tolerance in C. inophyllum. It will also examine the suitability of modern novel technologies like Near Infrared (NIR) and Fourier transform infrared (FTIR) spectroscopy in assessing stress tolerance in plants, thereby allowing us to identify salt?tolerant genotypes in a very efficient, convenient and non-destructive way. The study will be adopting different experimental approaches, involving observations in the glasshouse, laboratory and field conditions to address the research questions and objectives.
The main dataset folder in the shared data storage named "beauty-leaf-tree" has three sub-folders: "COC", "Experiments" and "Thesis".
1. The folder "COC" contains important documents related to Confirmation of Candidature in word, pdf or xlsx format which includes clean and corrected version of section A, response to reviewers, COC budget and COC approval letter.
2. The folder "Experiments" contains all the data that have been collected and analysed in the research project. The folder is further divided experiment-wise/chapter-wise which contains all the data (raw data, analysed data, graphs, figures, photos) of the respective experiment. The data may be found stored in the following Microsoft Office formats: xlsx, unsb, CSV, RTF, TXT, JPG, PNG, pdf, docx and video recordings.
3. The folder "Thesis" contains all the versions of the thesis i.e., old versions, supervisor's reviewed versions, the proofread version and the final submitted version in word or pdf format. The sub-folder "THESIS SUBMISSION" contains the final version of the thesis- both before and after examiners' reviews in word and pdf formats.</p
Assessment of nuclear ZEB2 as a biomarker for colorectal cancer outcome and TNM risk stratification
No full textImportance: At present, patients with colorectal cancer (CRC) are risk stratified using TNM histologic features. More recently, an association between a mesenchymal phenotype and a high risk of disease recurrence and micrometastases has been recognized.Objective: To investigate the association of the epithelial to mesenchymal transition (EMT)-inducing transcription factor ZEB2 (zinc finger E box-binding homeobox 2), survival outcomes, and the efficacy of ZEB2 as a biomarker when added as refinement to TNM staging after curative intent surgery for CRC.Design, Setting, and Participants: ZEB2 expression was assessed using a previously validated scoring system as part of a prospective, observational, masked diagnostic study from January 1, 2008, to December 31, 2013. Data were prospectively collected and analyzed for association with oncologic outcomes from January 1, 2017, to December 31, 2018. An initial test cohort from an academic university medical center of 126 consecutive patients with CRC and, subsequently, an independent validation cohort of 210 patients were examined. ZEB2 positivity was scored by 2 independent, masked pathologists. External validity was tested using an open access gene expression portal. Nomograms were developed with or without ZEB2.Main Outcomes and Measures: Systemic and local recurrence of CRC.Results: The test cohort consisted of 126 consecutive patients (mean [SD] age, 72.7 [11.7] years; 61 [48.4%] male) and the validation cohort of 210 patients (mean [SD] age, 72.0 [10.6] years; 111 [52.9%] male). A total of 52 tumors (41.3%) in the test cohort and 104 (49.5%) in the validation cohort were scored nuclear ZEB2 positive. Survival analysis by the log-rank test found that ZEB2 expression was associated with a significant reduction in overall survival and disease-free survival in both cohorts. Cox proportional hazards regression analysis highlighted ZEB2 as an independent biomarker of shorter overall survival and disease-free survival. Analysis of node-negative disease (n = 222) identified ZEB2 as an independent biomarker of early recurrence and reduced survival. External validation confirmed these findings. Addition of ZEB2 expression to nomograms composed of conventional TNM risk factors improved the ability to identify patients at high risk of recurrence demonstrated by the improvement in concordance index in both test (0.73 to 0.77) and validation (0.82 to 0.87) cohorts.Conclusions and Relevance: The findings suggest that expression of ZEB2 is associated with poor oncologic outcome and distant recurrence. The study also found that the addition of ZEB2 to existing TNM classification improved the ability to stratify patients for risk of recurrence. The results of this study suggest that addition of ZEB2 expression status to the TNM staging system improves the ability to stratify patients at high risk of recurrence.</p
Strategies for Dendrite-free Lithium and Sodium Metal Anodes
No full textAs the public demand for electric vehicles and consumer electronics grows at an exponential rate, traditional energy storage systems like lithium-ion batteries are proving to be insufficient. A potential candidate to replace these conventional systems is the lithium metal battery. However, replacing the anode of lithium-ion batteries with lithium (Li) metal comes with its own challenges. Safety concerns and capacity loss during cycling (discharge-charge) are caused by internal dendrite formation and infinite volume change of the Li metal. In this work, two different strategies have been explored to counter these issues: 1. 3-dimensional metallic host for Li metal2. Surface layer deposition As the 3D metal host, a 3D porous nickel (3DPNi) substrate was used. It was fabricated in-house through a facile template-free electrodeposition process. Detailed electrochemical Li cycling tests were performed using a symmetric cell to investigate the performance of the substrate. Different aspects of the Li cycling like substrate structure and morphology, electrolyte modification (with LiNO3), kinetics of Li+ diffusion and the electrochemical impedance performance of the substrate were investigated. The 3DPNi substrate was also tested for its compatibility with sodium metal. To investigate the effect of surface layer deposits, atomic layer depositions (ALD) of Al2O3 and TiO2 were done on planar nickel substrates. Each of these were subjected to electrochemical Li cycling tests. Our results show that the 3DPNi substrate can be effectively cycled with Li for up to 300 cycles at a capacity of 0.5 mAh⋅cm-2 and a current rate of 1 mA⋅cm-2. Increasing the capacity to 3 mAh⋅cm-2 (6 times) at the same current rate resulted in up to 60 cycles. It was also found out that this substrate could be used for sodium metal cycling. ALD on planar substrates have enabled the Li metal to be cycled for more than 300 cycles without failure, albeit at a capacity of 0.25 mAh⋅cm-2 and a current rate of 0.125 mA⋅cm-2. Hence, our study confirms that both the methods significantly improve the performance of the lithium (and sodium) metal anodes
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