MicroRNA Control of Invasion and Metastasis Pathways

Despite recent advances, cancer remains a leading cause of death worldwide. In developed countries, the incidence of colorectal and breast cancer has been stable, but no improvement in prognosis has been observed if the patient presents with metastases at diagnosis. This fact highlights the importance of therapeutic approaches targeting cellular invasion and metastasis programs as the next step in cancer treatment. During carcinoma progression a process called epithelial–mesenchymal transition (EMT) results in enhanced invasion and motility which is directly linked with loss of epithelial polarity and epithelial junctions, migration permissive cytoskeleton alterations, and the acquisition of mesenchymal properties. The recent discovery of microRNAs (miRNAs) controlling key cellular pathways has opened a new era in understanding how EMT pathways are modulated. In this review, we classify EMT regulating proteins according to their cellular localization (membrane, cytoplasmic, and nuclear), and summarize the current knowledge on how they are controlled by miRNAs and propose potential miRNAs for the transcripts that may control their expression

Block Cave Mine Ventilation: Research Findings

The primary objective of this research is to provide practical mine ventilation engineering tools (i.e., cave resistances and pollutant emission rates) to model and predict adequate airflows and pressure drops across the cave with respect to cave propagation in underground block or panel cave mines. We used several research methods to investigate the phenomenon of cave ventilation and pollutant gas emissions in block or panel cave mines. The research methods include computational fluid dynamics (CFD)—continuum and discrete approaches in conjunction with advanced geo-mechanical analysis through numerical modeling, scale model studies, mathematical modeling, field observations, discrete fracture network (DFN), flow through porous media, particle flow code (PFC), Ventsim, MATLAB, and Python programming. The study investigated the several research questions related to block or panel cave mines: immature and mature cave properties, radon and airflow behavior, radon control measures, cave characteristics, ventilation on demand, blasting fumes, prediction of porosity, and permeability of different cave zones, the effect of undercut ventilation, forcing, exhaust and the push-pull system, the effect of airgap, and broken rock porosity and permeability on the cave ventilation system. The findings from this study provide useful information for optimizing the block or panel cave mine ventilation systems

Interpreting Metabolomic Profiles using Unbiased Pathway Models

Human disease is heterogeneous, with similar disease phenotypes resulting from distinct combinations of genetic and environmental factors. Small-molecule profiling can address disease heterogeneity by evaluating the underlying biologic state of individuals through non-invasive interrogation of plasma metabolite levels. We analyzed metabolite profiles from an oral glucose tolerance test (OGTT) in 50 individuals, 25 with normal (NGT) and 25 with impaired glucose tolerance (IGT). Our focus was to elucidate underlying biologic processes. Although we initially found little overlap between changed metabolites and preconceived definitions of metabolic pathways, the use of unbiased network approaches identified significant concerted changes. Specifically, we derived a metabolic network with edges drawn between reactant and product nodes in individual reactions and between all substrates of individual enzymes and transporters. We searched for “active modules”—regions of the metabolic network enriched for changes in metabolite levels. Active modules identified relationships among changed metabolites and highlighted the importance of specific solute carriers in metabolite profiles. Furthermore, hierarchical clustering and principal component analysis demonstrated that changed metabolites in OGTT naturally grouped according to the activities of the System A and L amino acid transporters, the osmolyte carrier SLC6A12, and the mitochondrial aspartate-glutamate transporter SLC25A13. Comparison between NGT and IGT groups supported blunted glucose- and/or insulin-stimulated activities in the IGT group. Using unbiased pathway models, we offer evidence supporting the important role of solute carriers in the physiologic response to glucose challenge and conclude that carrier activities are reflected in individual metabolite profiles of perturbation experiments. Given the involvement of transporters in human disease, metabolite profiling may contribute to improved disease classification via the interrogation of specific transporter activities

Daksha: On Alert for High Energy Transients

We present Daksha, a proposed high energy transients mission for the study of electromagnetic counterparts of gravitational wave sources, and gamma ray bursts. Daksha will comprise of two satellites in low earth equatorial orbits, on opposite sides of earth. Each satellite will carry three types of detectors to cover the entire sky in an energy range from 1 keV to >1 MeV. Any transients detected on-board will be announced publicly within minutes of discovery. All photon data will be downloaded in ground station passes to obtain source positions, spectra, and light curves. In addition, Daksha will address a wide range of science cases including monitoring X-ray pulsars, studies of magnetars, solar flares, searches for fast radio burst counterparts, routine monitoring of bright persistent high energy sources, terrestrial gamma-ray flashes, and probing primordial black hole abundances through lensing. In this paper, we discuss the technical capabilities of Daksha, while the detailed science case is discussed in a separate paper.Comment: 9 pages, 3 figures, 1 table. Additional information about the mission is available at https://www.dakshasat.in

Science with the Daksha High Energy Transients Mission

We present the science case for the proposed Daksha high energy transients mission. Daksha will comprise of two satellites covering the entire sky from 1~keV to $>1$~MeV. The primary objectives of the mission are to discover and characterize electromagnetic counterparts to gravitational wave source; and to study Gamma Ray Bursts (GRBs). Daksha is a versatile all-sky monitor that can address a wide variety of science cases. With its broadband spectral response, high sensitivity, and continuous all-sky coverage, it will discover fainter and rarer sources than any other existing or proposed mission. Daksha can make key strides in GRB research with polarization studies, prompt soft spectroscopy, and fine time-resolved spectral studies. Daksha will provide continuous monitoring of X-ray pulsars. It will detect magnetar outbursts and high energy counterparts to Fast Radio Bursts. Using Earth occultation to measure source fluxes, the two satellites together will obtain daily flux measurements of bright hard X-ray sources including active galactic nuclei, X-ray binaries, and slow transients like Novae. Correlation studies between the two satellites can be used to probe primordial black holes through lensing. Daksha will have a set of detectors continuously pointing towards the Sun, providing excellent hard X-ray monitoring data. Closer to home, the high sensitivity and time resolution of Daksha can be leveraged for the characterization of Terrestrial Gamma-ray Flashes.Comment: 19 pages, 7 figures. Submitted to ApJ. More details about the mission at https://www.dakshasat.in

SIP1/ZEB2 induced epthelial to mesenchymal transition promotes metastasis and chemoresistance in colorectal cancer

Colorectal 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

Beauty Leaf Tree (Calophyllum inophyllum L.) — its biogeographic variability for salinity tolerance and kernel oil content as determined by FTIR/FTNIR technologies

Over-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

In 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

Pattern of Seed Germination in Different Accessions of Calophyllum inophyllum L. in South Gujarat

The main objective of the present study is to assess seed germination performance of C. inophyllum in south Gujarat condition. Therefore, seeds were collected from different seed sources of Karnataka and Maharashtra and a preliminary study was carried out in the College of Forestry, ACHF, Navsari Agricultural University during 2015. Seeds were collected from 15 trees (good bearing) representing five populations of Maharashtra and Karnataka, and assessed for seed parameters and germination. Seed kernels were used for germination trials. Germination started from 10 to 20 days after sowing and completed maximum germination within 20-25 days after sowing. Seeds collected from CIMV1, CIMV2 and CIMN3 accessions resulted in early germination. The overall result showed that seed germination among 15 accessions ranged between 40% (CIMP4) to 100% (CIKK1; CIKK2). Considering each seed source, the seed germination was found to be highest in the seeds collected from Kumta, Karnataka. Tree to tree variation within a seed source for germination was also recorded and ranges of germination within each seed source are as follows: Dapoli (73.33-90%), Navare (60-93.33%), Purnagharh (40-93.33%), Vettye (93.33-96.67%) and Kumta (63.33-100%). In conclusion, the seed germination of C. inophyllum under south Gujarat condition showed a positive performance. This study may help for further assessment of seedlings at field condition of this region.The main objective of the present study is to assess seed germination performance of C. inophyllum in south Gujarat condition. Therefore, seeds were collected from different seed sources of Karnataka and Maharashtra and a preliminary study was carried out in the College of Forestry, ACHF, Navsari Agricultural University during 2015. Seeds were collected from 15 trees (good bearing) representing five populations of Maharashtra and Karnataka, and assessed for seed parameters and germination. Seed kernels were used for germination trials. Germination started from 10 to 20 days after sowing and completed maximum germination within 20-25 days after sowing. Seeds collected from CIMV1, CIMV2 and CIMN3 accessions resulted in early germination. The overall result showed that seed germination among 15 accessions ranged between 40% (CIMP4) to 100% (CIKK1; CIKK2). Considering each seed source, the seed germination was found to be highest in the seeds collected from Kumta, Karnataka. Tree to tree variation within a seed source for germination was also recorded and ranges of germination within each seed source are as follows: Dapoli (73.33-90%), Navare (60-93.33%), Purnagharh (40-93.33%), Vettye (93.33-96.67%) and Kumta (63.33-100%). In conclusion, the seed germination of C. inophyllum under south Gujarat condition showed a positive performance. This study may help for further assessment of seedlings at field condition of this region

Koch Curve Polar Coordinate Transform for UWB Antenna Applications

Fractal antennas allow for the design of Ultrawide-band (UWB) antennas with a reduced footprint; we present a novel technique for generating antenna geometries which extend the Koch snowflake to angles other than 60 degrees. This is achieved by generating a Koch curve of an arbitrary indentation angle and then circumscribing the curve about the origin. Using our method, we achieve a 36% footprint area reduction compared to a traditional Koch snowflake antenna with center frequency of 4.1GHz