Open Source Technology : Design Principles, Methodology and Applications - A Literature Review

Closed source has a great significance in monopoly of software industries. Software users have been witnessing this monopoly of various software companies for the past many years. As an alternative to these closed sources, the concept of Open Source is originated. The term �Open Source�, literally means a consortium of like-minded individuals or corporations who try to come up with products/services that conforms to standards to one specific vertical sector of software industry. In this paper, the major focus is given on various open source technology concepts, development methodology and its significance along with various categories of open source applications

Engineered Bacteriophage Enabled Nanoprobes for SKBR-3 Cancer Cell Specific Imaging and Therapy

With the recent progress in nanoscience and great deal of understanding in molecular biology, it is now possible to combine genetic tools with synthetic nano- constructs for improved biotechnology applications. Viruses with its inherent nanosize architecture, genetic flexibility, stability to harsh conditions, circulatory behavior and targeting ability, in combination with nano science, are currently an excellent source for designing nano based therapeutics for cancer diagnosis and treatment.Here, we integrate phage display technology (PDT) with nanotechnology to synthesize novel nano-conjguates for potential biomedical applications.The first part of this dissertation is focused on the identification and characterization of novel SKBR-3 breast cancer cell targeting/internalizing ligands using landscape phage libraries. We used several computational methods and biochemical approaches to characterize the specificity, affinity and selectivity of the screened bacteriophage against target SKBR-3 breast cancer cells. In order to understand the mechanism of entry, we investigated the actin dynamics by using live cell and fluorescence imaging during selected phage internalization into target SKBR-3 cells. In conclusion, we demonstrate that phage harboring VSSTQDFP and DGSIPWST peptides could selectively internalize into SKBR-3 cells with high affinity and show rapid involvement of membrane ruffling and rearrangements of actin cytoskeleton during phage entry.The second part of this dissertation is focused on the isolation of major coat proteins, pVIII from screened bacteriophage, its conjugation on functionalized gold nanorod using appropriate chemistry and its multipurpose applications. The successful conjugation of coat proteins on functionalized gold nanorods was verified by using spectroscopic and microscopic techniques. In conclusion, we demonstrate that the resulting protein/peptide- nanoconjugates can be used for imaging and selective photo thermal destruction of SKBR-3 breast cancer cells upon exposure to near-infrared (NIR) light. In order, to gain insight into the mechanism and understand the key cellular processes involved following the treatment of these nanoconjugates, we used illumina microarray technique to explore the molecular interactions with in our model SKBR-3 breast cancer cells. We identified 76 genes to be up regulated and 26 genes are down regulated following the treatment of protein nanoconjugates. Our recent preliminary animal studies in SKBR-3 tumor model (nude mice) shows that these protein-nanoconjugates are feasible for in vivo applications. However, more in vivo experiments are under investigations before its clinical significance is realized.The third part of this dissertation is focused on the assembly of coat proteins on functionalized carbon nanotubes and other biomedical applications of engineered bacteriophage in nanoscience. Using various spectroscopic and microscopic studies, we demonstrate phage proteins assembled on carbon nanotubes can be used for imaging purpose, and SKBR-3 specific bacteriophage can be used as a template for conjugation of photosensitizer, pyropheophorbid-a for targeted photo dynamic therapy. We also demonstrate filamentous bacteriophage displayed with eight glutamic acid residues [E8] on the N-terminus of major coat protein using phage display can be used as a template to assemble liposomes and form phage-liposome complex for targeted drug delivery

Coomassie staining provides routine (sub)femtomole in‐gel detection of intact proteoforms: Expanding opportunities for genuine Top‐down Proteomics

Modified colloidal Coomassie Brilliant Blue (cCBB) staining utilising a novel destain protocol and near‐infrared fluorescence detection (nIRFD) rivals the in‐gel protein detection sensitivity (DS) of SYPRO Ruby. However, established DS estimates are likely inaccurate in terms of 2DE‐resolved proteoform ‘spots’ since DS is routinely measured from comparatively diffuse protein ‘bands’ following wide‐well 1DE. Here, cCBB DS for 2DE‐based proteomics was more accurately determined using narrow‐well 1DE. As precise estimates of protein standard monomer concentrations are essential for accurate quantitation, coupling UV absorbance with gel‐based purity assessments is described. Further, as cCBB is compatible with both nIRFD and densitometry, the impacts of imaging method (and image resolution) on DS were assessed. Narrow‐well 1DE enabled more accurate quantitation of cCBB DS for 2DE, achieving (sub)femtomole DS with either nIRFD or densitometry. While densitometry offers comparative simplicity and affordability, nIRFD has the unique potential for enhanced DS with Deep Imaging. Higher‐resolution nIRFD also improved analysis of a 2DE‐resolved proteome, surpassing the DS of standard nIRFD and densitometry, with nIRFD Deep Imaging further maximising proteome coverage. cCBB DS for intact proteins rivals that of mass spectrometry (MS) for peptides in complex mixtures, reaffirming that 2DE‐MS currently provides the most routine, broadly applicable, robust, and information‐rich Top‐down approach to Discovery Proteomics.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141479/1/elps6323.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141479/2/elps6323_am.pd

Examining phospho-modulation of regulated exocytosis and the release-ready state of native secretory vesicles

Regulated exocytosis enables numerous critical cellular functions such as wound healing, fertilisation, and neurotransmission. In most eukaryotic cells, proteins and other compounds that need to be secreted into the extracellular space are sorted into secretory vesicles, which then translocate to the plasma membrane where they dock and undergo priming reactions. Upon elevation of intracellular calcium levels (caused by a physiological stimulus), release-ready secretory vesicles fuse with the plasma membrane and release their contents. The late, calcium regulated steps of exocytosis (including docking, priming, and fusion) have been studied using a variety of model systems; in particular, studies utilising sea urchin eggs, cell surface complexes (large sheets of plasma membrane with endogenous, docked vesicles) and isolated cortical vesicles have provided numerous original insights into fundamental, conserved molecular mechanisms (Reviewed in Chapter One, and methods pertaining to the use of the model are detailed in Chapter Two). In Chapter Three, using intact eggs and cell surface complexes, I test the hypothesis that the fully primed, release-ready state is one of stable hemifusion (i.e. with the contacting monolayers of the vesicle and plasma membrane having already merged). Studies utilising fluorescent dyes with well-defined membrane properties and membrane permeable cationic amphiphiles capable of disrupting hemifusion intermediates indicate that, contrary to current opinion, the release-ready state is dynamic, and capable of transiently transitioning between hemifusion and close bilayer apposition. The phosphorylation of proteins and lipids has been implicated in modulating all stages of regulated exocytosis, and in Chapter Four I use cortical vesicles and minimised docking and membrane fusion assays to screen a range of well characterised small molecule modulators of phosphorylation. Data from the screen implicate phosphatases and casein kinase 2 in modulating the calcium sensitivity of fusion, and sphingosine kinase in modulating the ability to fuse. As detailed in Chapter Five, combined molecular and functional analysis of cell surface complexes and cortical vesicles with altered membrane sphingolipid levels confirmed that a critical balance of sphingolipids and sphingolipid metabolites is needed to maintain efficient docking, calcium sensitivity, and capacity to fuse

Enhancing Business Data Sharing in the Supply Chain Domain: A Framework of Infrastructural and Institutional Instruments

Effective data sharing plays a pivotal role in optimizing supply chain management and driving the operational excellence of businesses. However, certain barriers and challenges exist among the supply chain partners in communication and data exchange. This thesis investigates these barriers and proposes potential solutions, referred to as instruments, for data sharing in supply chains. The objective is to develop and validate a framework that addresses feasible barriers in high-tech supply chain organizations. Single case study interviews in a high-tech supply chain firm assess the framework's applicability, followed by a validation phase to test its generalizability. Infrastructural instruments include ICT, Blockchain, AI, ML, data standardization, and data security measures. Institutional instruments encompass cultural factors, trust-building techniques, contractual agreements, education and training programs, leadership practices, and ethical data sharing. The research contribution extends to a strategic deployment plan for these instruments, offering valuable insights to supply chain professionals. Additionally, the research emphasizes the significance of viewing risk as a comprehensive concept in relation to trust, technology, privacy, and governance-related barriers. Management of Technology (MoT

Application of High-Throughput Assays to Examine Phospho-Modulation of the Late Steps of Regulated Exocytosis

Abstract: Regulated exocytosis enables a range of physiological functions including neurotransmission, and the late steps (i.e., docking, priming and Ca2+-triggered membrane fusion) are modulated by a highly conserved set of proteins and lipids. Many of the molecular components and biochemical interactions required have been identified; the precise mechanistic steps they modulate and the biochemical interactions that need to occur across steps are still the subject of intense investigation. Particularly, although the involvement of phosphorylation in modulating exocytosis has been intensively investigated over the past three decades, it is unclear which phosphorylation events are a conserved part of the fundamental fusion mechanism and/or serve as part of the physiological fusion machine (e.g., to modulate Ca2+ sensitivity). Here, the homotypic fusion of cortical vesicles was monitored by utilizing new high-throughput, cost-effective assays to assess the influence of 17 small molecule phospho-modulators on docking/priming, Ca2+ sensitivity and membrane fusion. Specific phosphatases and casein kinase 2 are implicated in modulating the Ca2+ sensitivity of fusion, whereas sphingosine kinase is implicated in modulating the ability of vesicles to fuse. These results indicate the presence of multiple kinases and phosphatases on the vesicles and critical phosphorylation sites on vesicle membrane proteins and lipids that directly influence late steps of regulated exocytosis

Sphingolipids modulate docking, Ca2+ sensitivity and membrane fusion of native cortical vesicles

Docking, priming, and membrane fusion of secretory vesicles (i.e. regulated exocytosis) requires lipids and proteins. Sphingolipids, in particular, sphingosineand sphingosine-1-phosphate, have been implicated in the modulation of exocytosis. However, the specific exocytotic steps that sphingolipids modulate and the enzymes that regulate sphingolipid concentrations on native secretory vesicle membranes remain unknown. Here we use tightly coupled functional and molecular analyses of fusion-ready cell surface complexes and cortical vesicles isolated from oocytes to assess the role of sphingolipids in the late, Ca2+-triggered steps of exocytosis. The molecular changes resulting from treatments with sphingolipid modifying compounds coupled with immunoblotting analysis revealed the presence of sphingosine kinase on native vesicles; the presence of a sphingosine-1-phosphate phosphatase is also indicated. Changes in sphingolipid concentrations on vesicles altered their docking/priming, Ca2+-sensitivity, and ability to fuse, indicating that sphingolipid concentrations are tightly regulated and maintained at optimal levels and ratios to ensure efficient exocytosis

Design of Robust Hybrid Recommender System For Optimal Business Decision Model In E-Commerce Digital Systems

Now a day’s many e-commerce applications amount of data like products and its details, images, description, reviews etc. Recommender systems make life easier by making recommendations. In e-commerce, often some products doesn’t get sold or less profits are earned from the product. Identification of the reason behind the less profits from the product, was a difficult task. So we are proposing a hybrid recommender system that helps the item manufacturer to improve his product. We built a hybrid recommender system by combining various regression algorithms  along with backward elimination, CAR(Context-Aware Recommendation)model, user to user collaborative filtering. Finally the optimal business decision is taken by the manufacturer