The synthesis and study of novel fluorescence probes for Nitroreductase

This Thesis entitled ‘The synthesis and study of novel fluorescence probes for NTR’ is divided in 7 chapters. Chapter 1, provides an introduction to cancer, reductive stress and some techniques to detect the tumour cells. A range of relevant examples of fluorescence sensors for NTR are also given. This Chapter also includes the objectives for the research conducted in Chapters 2, 3 and 4. Chapter 2 describes the synthesis of a set of novel fluorescence sensors where variation of naphthalimide substituents is described. The synthesis of each compound is discussed, followed by an evaluation of their photophysical characteristics and response to nitroreductase (NTR) in a biological setting. Chapter 3 explores synthetic modifications to the compounds described in Chapter 2 in order to increase NTR sensitivity. A set of novel fluorescence sensors are described where the sensitivity is modulated using a range of reducible nitroaromatic moieties. The synthesis of each compound is also discussed, in addition to the preliminary test for NTR. Chapter 4 discusses a novel family of NTR sensors amenable to bioconjugation through various biocompatible linkages. Structural modification of compounds described in Chapter 2 provides access for conjugation to peptides, sugars, oligonucleotides and various other important biomolecules. The synthesis of each compound is discussed. Chapter 5 outlines the overall conclusion of the work carried out during this research. Chapter 6 describes general experimental procedures and the characterisation of each compound discussed throughout the thesis. Finally, in Chapter 7, the Appendix shows all supporting information

A multi-protein receptor-ligand complex underlies combinatorial dendrite guidance choices in C. elegans.

Ligand receptor interactions instruct axon guidance during development. How dendrites are guided to specific targets is less understood. The C. elegans PVD sensory neuron innervates muscle-skin interface with its elaborate dendritic branches. Here, we found that LECT-2, the ortholog of leukocyte cell-derived chemotaxin-2 (LECT2), is secreted from the muscles and required for muscle innervation by PVD. Mosaic analyses showed that LECT-2 acted locally to guide the growth of terminal branches. Ectopic expression of LECT-2 from seam cells is sufficient to redirect the PVD dendrites onto seam cells. LECT-2 functions in a multi-protein receptor-ligand complex that also contains two transmembrane ligands on the skin, SAX-7/L1CAM and MNR-1, and the neuronal transmembrane receptor DMA-1. LECT-2 greatly enhances the binding between SAX-7, MNR-1 and DMA-1. The activation of DMA-1 strictly requires all three ligands, which establishes a combinatorial code to precisely target and pattern dendritic arbors

Long non-coding RNA DLGAP1 antisense RNA 1 accelerates glioma progression via the microRNA-628-5p/DEAD-box helicase 59 pathway

Objectives: Abnormal expression of long non-coding RNAs (lncRNAs) plays a prominent role in glioma progression. However, the biological function and mechanism of lncRNA DLGAP1 antisense RNA 1 (DLGAP1-AS1) in gliomas are still unknown. Methods: The authors assessed DLGAP1-AS1 and miR-628-5p expression in glioma tissues and cell lines using quantitative real-time polymerase chain reaction (qRT-PCR) and evaluated their effects on glioma cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) using the cell counting kit-8 (CCK-8) assay, 5-Ethynyl-2′-deoxyuridine (EdU) assay, Transwell assay, and western blot, respectively. The expression of DEAD-box helicase 59 (DDX59) was quantified using western blotting, and a dual-luciferase reporter gene assay was performed to detect the interaction between DLGAP1-AS1 and miR-628-5p. Results: The authors observed increased DLGAP1-AS1 expression in glioma tissues and cell lines with higher WHO grades and shorter survival time. DLGAP1-AS1 promoted the proliferation, migration, invasion, and EMT of glioma cells, while miR-628-5p counteracted these effects. The authors identified DLGAP1-AS1 as a molecular sponge of miR-628-5p in glioma cells as the biological functions of DLGAP1-AS1 are partially mediated via miR-628-5p. In addition, DLGAP1-AS1 upregulated DDX59 expression by inhibiting miR-628-5p expression. Conclusion: The DLGAP1-AS1/miR-628-5p/DDX59 axis regulates glioma progression

Field-aware Calibration: A Simple and Empirically Strong Method for Reliable Probabilistic Predictions

It is often observed that the probabilistic predictions given by a machine learning model can disagree with averaged actual outcomes on specific subsets of data, which is also known as the issue of miscalibration. It is responsible for the unreliability of practical machine learning systems. For example, in online advertising, an ad can receive a click-through rate prediction of 0.1 over some population of users where its actual click rate is 0.15. In such cases, the probabilistic predictions have to be fixed before the system can be deployed. In this paper, we first introduce a new evaluation metric named field-level calibration error that measures the bias in predictions over the sensitive input field that the decision-maker concerns. We show that existing post-hoc calibration methods have limited improvements in the new field-level metric and other non-calibration metrics such as the AUC score. To this end, we propose Neural Calibration, a simple yet powerful post-hoc calibration method that learns to calibrate by making full use of the field-aware information over the validation set. We present extensive experiments on five large-scale datasets. The results showed that Neural Calibration significantly improves against uncalibrated predictions in common metrics such as the negative log-likelihood, Brier score and AUC, as well as the proposed field-level calibration error.Comment: WWW 202