text:
@article{zarnowski2018,
  title = {Candida Albicans Biofilm\textendash{}Induced Vesicles Confer Drug Resistance through Matrix Biogenesis},
  volume = {16},
  issn = {1545-7885},
  abstract = {Cells from all kingdoms of life produce extracellular vesicles (EVs). Their cargo is protected from the environment by the surrounding lipid bilayer. EVs from many organisms have been shown to function in cell\textendash{}cell communication, relaying signals that impact metazoan development, microbial quorum sensing, and pathogenic host\textendash{}microbe interactions. Here, we have investigated the production and functional activities of EVs in a surface-associated microbial community or biofilm of the fungal pathogen Candida albicans. Crowded communities like biofilms are a context in which EVs are likely to function. Biofilms are noteworthy because they are encased in an extracellular polymeric matrix and because biofilm cells exhibit extreme tolerance to antimicrobial compounds. We found that biofilm EVs are distinct from those produced by free-living planktonic cells and display strong parallels in composition to biofilm matrix material. The functions of biofilm EVs were delineated with a panel of mutants defective in orthologs of endosomal sorting complexes required for transport (ESCRT) subunits, which are required for normal EV production in diverse eukaryotes. Most ESCRT-defective mutations caused reduced biofilm EV production, reduced matrix polysaccharide levels, and greatly increased sensitivity to the antifungal drug fluconazole. Matrix accumulation and drug hypersensitivity of ESCRT mutants were reversed by addition of wild-type (WT) biofilm EVs. Vesicle complementation showed that biofilm EV function derives from specific cargo proteins. Our studies indicate that C. albicans biofilm EVs have a pivotal role in matrix production and biofilm drug resistance. Biofilm matrix synthesis is a community enterprise; prior studies of mixed cell biofilms have demonstrated extracellular complementation. Therefore, EVs function not only in cell\textendash{}cell communication but also in the sharing of microbial community resources.},
  language = {en},
  number = {10},
  journal = {PLOS Biology},
  doi = {10.1371/journal.pbio.2006872},
  author = {Zarnowski, Robert and Sanchez, Hiram and Covelli, Antonio S. and Dominguez, Eddie and Jaromin, Anna and Bernhardt, J{\"o}rg and Mitchell, Kaitlin F. and Heiss, Christian and Azadi, Parastoo and Mitchell, Aaron and Andes, David R.},
  month = oct,
  year = {2018},
  keywords = {Antimicrobial resistance,Biofilm culture,Biofilms,Candida albicans,Extracellular matrix,Extracellular matrix composition,Extracellular matrix proteins,Vesicles},
  pages = {e2006872},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Candida EVs\\Research\\Zarnowski et al_2018_Candida albicans biofilm–induced vesicles confer drug resistance through matrix.pdf;C:\\Users\\charl\\Zotero\\storage\\8IKV2F9B\\article.html}
}

@article{li2012,
  title = {{{RhoA}} Triggers a Specific Signaling Pathway That Generates Transforming Microvesicles in Cancer Cells},
  volume = {31},
  copyright = {2012 Nature Publishing Group},
  issn = {1476-5594},
  abstract = {Vesicular structures called microvesicles (MVs) that are shed from the surfaces of cancer cells are capable of transferring oncogenic cargo to recipient cancer cells, as well as to normal cells, sending mitogenic signals that greatly enhance tumor growth. Because MVs are stable in the circulation, they also may have a key role in secondary colonization and metastasis. Thus, understanding how MVs are generated could have important consequences for interfering with cancer progression. Here we report that the small GTPase RhoA triggers a specific signaling pathway essential for MV biogenesis in various human cancer cells. Inhibiting the activity of different proteins comprising this pathway blocks MV biogenesis in the donor cancer cells and prevents oncogenic transformation in cell culture as well as tumor growth in mice. Although RhoA has often been implicated in human cancer, these findings now highlight a previously unappreciated role for this GTPase in malignant transformation, and demonstrate that blocking MV biogenesis may offer novel approaches for interfering with malignant transformation.},
  language = {en},
  number = {45},
  journal = {Oncogene},
  doi = {10.1038/onc.2011.636},
  author = {Li, B. and Antonyak, M. A. and Zhang, J. and Cerione, R. A.},
  month = nov,
  year = {2012},
  pages = {4740-4749},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\EV biogenesis\\Research\\Li et al_2012_RhoA triggers a specific signaling pathway that generates transforming.pdf;C:\\Users\\charl\\Zotero\\storage\\X778YLK9\\onc2011636.html}
}

@article{skrzypek2017,
  title = {The {{Candida Genome Database}} ({{CGD}}): Incorporation of {{Assembly}} 22, Systematic Identifiers and Visualization of High Throughput Sequencing Data},
  volume = {45},
  issn = {0305-1048},
  shorttitle = {The {{Candida Genome Database}} ({{CGD}})},
  abstract = {Abstract.  The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence infor},
  language = {en},
  number = {D1},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gkw924},
  author = {Skrzypek, Marek S. and Binkley, Jonathan and Binkley, Gail and Miyasato, Stuart R. and Simison, Matt and Sherlock, Gavin},
  month = jan,
  year = {2017},
  pages = {D592-D596},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Online tools\\Skrzypek et al_2017_The Candida Genome Database (CGD).pdf;C:\\Users\\charl\\Zotero\\storage\\TLI75JAS\\2282824.html}
}

@article{ritchie2015,
  title = {Limma Powers Differential Expression Analyses for {{RNA}}-Sequencing and Microarray Studies},
  volume = {43},
  issn = {0305-1048},
  abstract = {Abstract.  limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains ric},
  language = {en},
  number = {7},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gkv007},
  author = {Ritchie, Matthew E. and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W. and Shi, Wei and Smyth, Gordon K.},
  month = apr,
  year = {2015},
  pages = {e47-e47},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\R packages\\Ritchie et al_2015_limma powers differential expression analyses for RNA-sequencing and microarray.pdf;C:\\Users\\charl\\Zotero\\storage\\NHHCD9TY\\2414268.html}
}

@article{arnaud2005,
  title = {The {{Candida Genome Database}} ({{CGD}}), a Community Resource for {{Candida}} Albicans Gene and Protein Information},
  volume = {33},
  issn = {0305-1048},
  abstract = {Abstract.   The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans . CGD},
  language = {en},
  number = {suppl\_1},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gki003},
  author = {Arnaud, Martha B. and Costanzo, Maria C. and Skrzypek, Marek S. and Binkley, Gail and Lane, Christopher and Miyasato, Stuart R. and Sherlock, Gavin},
  month = jan,
  year = {2005},
  pages = {D358-D363},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Online tools\\Arnaud et al_2005_The Candida Genome Database (CGD), a community resource for Candida albicans.pdf;C:\\Users\\charl\\Zotero\\storage\\PKVPJW86\\2505193.html}
}

@article{kullberg2015,
  title = {Invasive {{Candidiasis}}},
  volume = {373},
  issn = {0028-4793, 1533-4406},
  language = {en},
  number = {15},
  journal = {New England Journal of Medicine},
  doi = {10.1056/NEJMra1315399},
  author = {Kullberg, Bart Jan and Arendrup, Maiken C.},
  editor = {Campion, Edward W.},
  month = oct,
  year = {2015},
  pages = {1445-1456},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida pathogenesis\\Epidemiology\\Kullberg_Arendrup_2015_Invasive Candidiasis.pdf}
}

@article{tyanova2016,
  title = {The {{MaxQuant}} Computational Platform for Mass Spectrometry-Based Shotgun Proteomics},
  volume = {11},
  copyright = {2016 Nature Publishing Group},
  issn = {1750-2799},
  abstract = {MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C\# and is freely available at http://www.maxquant.org.},
  language = {en},
  number = {12},
  journal = {Nature Protocols},
  doi = {10.1038/nprot.2016.136},
  author = {Tyanova, Stefka and Temu, Tikira and Cox, Juergen},
  month = dec,
  year = {2016},
  pages = {2301-2319},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\MS search\\Tyanova et al_2016_The MaxQuant computational platform for mass spectrometry-based shotgun.pdf;C:\\Users\\charl\\Zotero\\storage\\ZWHVH48T\\nprot.2016.html}
}

@article{bielska2018,
  title = {Pathogen-Derived Extracellular Vesicles Mediate Virulence in the Fatal Human Pathogen {{Cryptococcus}} Gattii},
  volume = {9},
  copyright = {2018 The Author(s)},
  issn = {2041-1723},
  abstract = {Highly virulent cells of the fungal pathogen Cryptococcus gattiigrow rapidly within phagocytes by stimulating the growth of neighbouring fungal cells. Here, Bielska et al. show that this effect is mediated by the release of fungal extracellular vesicles that can be taken up by infected macrophages.},
  language = {En},
  number = {1},
  journal = {Nature Communications},
  doi = {10.1038/s41467-018-03991-6},
  author = {Bielska, Ewa and Sisquella, Marta Arch and Aldeieg, Maha and Birch, Charlotte and O'Donoghue, Eloise J. and May, Robin C.},
  month = apr,
  year = {2018},
  pages = {1556},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Gattii EVs\\Bielska et al_2018_Pathogen-derived extracellular vesicles mediate virulence in the fatal human.pdf;C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Gattii EVs\\Bielska et al_2018_Supplementary.pdf;C:\\Users\\charl\\Zotero\\storage\\RUYXQCIK\\s41467-018-03991-6.html}
}

@article{gross2012,
  title = {Active {{Wnt}} Proteins Are Secreted on Exosomes},
  volume = {14},
  copyright = {2012 Nature Publishing Group},
  issn = {1476-4679},
  abstract = {Wnt signalling has important roles during development and in many diseases. As morphogens, hydrophobic Wnt proteins exert their function over a distance to induce patterning and cell differentiation decisions. Recent studies have identified several factors that are required for the secretion of Wnt proteins; however, how Wnts travel in the extracellular space remains a largely unresolved question. Here we show that Wnts are secreted on exosomes both during Drosophila development and in human cells. We demonstrate that exosomes carry Wnts on their surface to induce Wnt signalling activity in target cells. Together with the cargo receptor Evi/WIs, Wnts are transported through endosomal compartments onto exosomes, a process that requires the R-SNARE Ykt6. Our study demonstrates an evolutionarily conserved functional role of extracellular vesicular transport of Wnt proteins.},
  language = {en},
  number = {10},
  journal = {Nature Cell Biology},
  doi = {10.1038/ncb2574},
  author = {Gross, Julia Christina and Chaudhary, Varun and Bartscherer, Kerstin and Boutros, Michael},
  month = oct,
  year = {2012},
  pages = {1036-1045},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Other organism EVs\\Drosophila\\Gross et al_2012_Active Wnt proteins are secreted on exosomes.pdf;C:\\Users\\charl\\Zotero\\storage\\83F4YK9C\\ncb2574.html}
}

@article{joffe2016,
  title = {Potential {{Roles}} of {{Fungal Extracellular Vesicles}} during {{Infection}}},
  volume = {1},
  copyright = {Copyright \textcopyright{} 2016 Joffe et al.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.},
  issn = {2379-5042},
  abstract = {Extracellular vesicles (EVs) are produced by virtually all cell types. Within the past few years, work in this field has revealed more information about fungal EVs. Fungal EVs have been shown to carry proteins, lipids, pigments, polysaccharides, and RNA; these components are known virulence factors, a fact which supports the hypothesis that fungal EVs concentrate pathogenic determinants. Additionally, recent studies have demonstrated that fungal EVs stimulate the host immune system. In this review, putative roles of fungal EVs are discussed, including their potential as vaccination tools and their possible contribution to pathogenesis in invasive fungal diseases.},
  language = {en},
  number = {4},
  journal = {mSphere},
  doi = {10.1128/mSphere.00099-16},
  author = {Joffe, Luna S. and Nimrichter, Leonardo and Rodrigues, Marcio L. and Poeta, Maurizio Del},
  month = aug,
  year = {2016},
  pages = {e00099-16},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review Fungal EV\\Joffe et al_2016_Potential Roles of Fungal Extracellular Vesicles during Infection.pdf;C:\\Users\\charl\\Zotero\\storage\\VDQV2FDG\\e00099-16.html},
  pmid = {27390779}
}

@article{corvest2013,
  title = {Spatiotemporal Regulation of {{Rho1}} and {{Cdc42}} Activity during {{Candida}} Albicans Filamentous Growth},
  volume = {89},
  issn = {0950-382X},
  abstract = {Summary Rho G-proteins are critical for polarized growth, yet little is known about the dynamics of their activation during fungal filamentous growth. We first investigated the roles of Rho1 and Rho2 during Candida albicans filamentous growth. Our results show that Rho1 is required for invasive filamentous growth and that Rho2 is not functionally redundant with Rho1. Using fluorescent reporters, we examined the dynamics of the active form of Rho1 and Cdc42 during initiation and maintenance of hyphal growth. Quantitative analyses indicated that the distribution, but not the level, of these active G-proteins is altered during initial polarization upon germ tube emergence. A comparison of the dynamics of these active G-proteins during budding and hyphal growth indicates that a higher concentration of active Cdc42 was recruited to the germ tube tip than to the bud tip. During hyphal elongation, active Cdc42 remained tightly restricted to the hyphal tip, whereas active Rho1 was broadly associated with the apex and subsequently recruited to the cell division site. Furthermore, our data suggest that phosphoinositide-bis-phosphates are critical to stabilize active Rho1 at the growth site. Together, our results point towards different regulation of Cdc42 and Rho1 activity during initiation and maintenance of filamentous growth.},
  number = {4},
  journal = {Molecular Microbiology},
  doi = {10.1111/mmi.12302},
  author = {Corvest, Vincent and Bogliolo, St{\'e}phanie and Follette, Peter and Arkowitz, Robert A. and Bassilana, Martine},
  month = jun,
  year = {2013},
  pages = {626-648},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\GFP fusions\\Corvest et al_2013_Spatiotemporal regulation of Rho1 and Cdc42 activity during Candida albicans.pdf;C:\\Users\\charl\\Zotero\\storage\\K99F4JIM\\mmi.html}
}

@article{cox2014,
  title = {Accurate {{Proteome}}-Wide {{Label}}-Free {{Quantification}} by {{Delayed Normalization}} and {{Maximal Peptide Ratio Extraction}}, {{Termed MaxLFQ}}},
  volume = {13},
  copyright = {\textcopyright{} 2014 by The American Society for Biochemistry and Molecular Biology, Inc.. Author's Choice\textemdash{}Final version full access.},
  issn = {1535-9476, 1535-9484},
  abstract = {Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide quantification with label-free approaches remains a challenge. We developed a new intensity determination and normalization procedure called MaxLFQ that is fully compatible with any peptide or protein separation prior to LC-MS analysis. Protein abundance profiles are assembled using the maximum possible information from MS signals, given that the presence of quantifiable peptides varies from sample to sample. For a benchmark dataset with two proteomes mixed at known ratios, we accurately detected the mixing ratio over the entire protein expression range, with greater precision for abundant proteins. The significance of individual label-free quantifications was obtained via a t test approach. For a second benchmark dataset, we accurately quantify fold changes over several orders of magnitude, a task that is challenging with label-based methods. MaxLFQ is a generic label-free quantification technology that is readily applicable to many biological questions; it is compatible with standard statistical analysis workflows, and it has been validated in many and diverse biological projects. Our algorithms can handle very large experiments of 500+ samples in a manageable computing time. It is implemented in the freely available MaxQuant computational proteomics platform and works completely seamlessly at the click of a button.},
  language = {en},
  number = {9},
  journal = {Molecular \& Cellular Proteomics},
  doi = {10.1074/mcp.M113.031591},
  author = {Cox, J{\"u}rgen and Hein, Marco Y. and Luber, Christian A. and Paron, Igor and Nagaraj, Nagarjuna and Mann, Matthias},
  month = sep,
  year = {2014},
  pages = {2513-2526},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\MS search\\Cox et al_2014_Accurate Proteome-wide Label-free Quantification by Delayed Normalization and.pdf;C:\\Users\\charl\\Zotero\\storage\\QNK7RBKY\\2513.html},
  pmid = {24942700}
}

@article{zamith-miranda2018,
  series = {20th {{Anniversary}} of {{Microbes}} \& {{Infection}}},
  title = {Fungal Extracellular Vesicles: Modulating Host\textendash{}Pathogen Interactions by Both the Fungus and the Host},
  volume = {20},
  issn = {1286-4579},
  shorttitle = {Fungal Extracellular Vesicles},
  abstract = {The secretion of biomolecules by fungal cells occurs via the conventional export of signal peptide-coupled soluble molecules, but it also results from transport within extracellular vesicles (EV). During the last ten years since the description of this non-conventional secretion pathway, varied, interesting biological roles have been associated with EV release by fungi. The various organic molecules carried by these structures are involved in pathogenesis and immune evasion, and may be associated with cell\textendash{}cell communication. In regards to host\textendash{}pathogen interactions, EV roles are diverse and organism-specific, although some features seem to be conserved among the pathogenic fungal organisms studied to date. This review aims to highlight our current understanding of the biologically relevant findings regarding EV released by the pathogenic fungal organisms and describes our knowledge of the roles of EV in host\textendash{}pathogen interactions.},
  number = {9},
  journal = {Microbes and Infection},
  doi = {10.1016/j.micinf.2018.01.011},
  author = {{Zamith-Miranda}, D. and Nimrichter, L. and Rodrigues, M. L. and Nosanchuk, J. D.},
  month = oct,
  year = {2018},
  keywords = {Candida,Cryptococcus,Extracellular vesicles,Fungus,Histoplasma,Paracoccidioides},
  pages = {501-504},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review Fungal EV\\Zamith-Miranda et al_2018_Fungal extracellular vesicles.pdf;C:\\Users\\charl\\Zotero\\storage\\BJ9VKAVS\\S1286457918300443.html}
}

@article{douglas2011,
  title = {Membrane {{Compartment Occupied}} by {{Can1}} ({{MCC}}) and {{Eisosome Subdomains}} of the {{Fungal Plasma Membrane}}},
  volume = {1},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  abstract = {Studies on the budding yeast Saccharomyces cerevisiae have revealed that fungal plasma membranes are organized into different subdomains. One new domain termed MCC/eisosomes consists of stable punctate patches that are distinct from lipid rafts. The MCC/eisosome domains correspond to furrows in the plasma membrane that are about 300 nm long and 50 nm deep. The MCC portion includes integral membrane proteins, such as the tetraspanners Sur7 and Nce102. The adjacent eisosome includes proteins that are peripherally associated with the membrane, including the BAR domains proteins Pil1 and Lsp1 that are thought to promote membrane curvature. Genetic analysis of the MCC/eisosome components indicates these domains broadly affect overall plasma membrane organization. The mechanisms regulating the formation of MCC/eisosomes in model organisms will be reviewed as well as the role of these plasma membrane domains in fungal pathogenesis and response to antifungal drugs.},
  language = {en},
  number = {4},
  journal = {Membranes},
  doi = {10.3390/membranes1040394},
  author = {Douglas, Lois M. and Wang, Hong X. and Li, Lifang and Konopka, James B.},
  month = dec,
  year = {2011},
  keywords = {cell wall,eisosome,hyphae,Lsp1,MCC,Nce102,Pil1,plasma membrane,Sur7,yeast},
  pages = {394-411},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\MCC eisosome\\Douglas et al_2011_Membrane Compartment Occupied by Can1 (MCC) and Eisosome Subdomains of the.pdf;C:\\Users\\charl\\Zotero\\storage\\HNKSH65P\\394.html}
}

@article{benjamini1995,
  title = {Controlling the {{False Discovery Rate}}: {{A Practical}} and {{Powerful Approach}} to {{Multiple Testing}}},
  volume = {57},
  issn = {0035-9246},
  shorttitle = {Controlling the {{False Discovery Rate}}},
  abstract = {The common approach to the multiplicity problem calls for controlling the familywise error rate (FWER). This approach, though, has faults, and we point out a few. A different approach to problems of multiple significance testing is presented. It calls for controlling the expected proportion of falsely rejected hypotheses-the false discovery rate. This error rate is equivalent to the FWER when all hypotheses are true but is smaller otherwise. Therefore, in problems where the control of the false discovery rate rather than that of the FWER is desired, there is potential for a gain in power. A simple sequential Bonferroni-type procedure is proved to control the false discovery rate for independent test statistics, and a simulation study shows that the gain in power is substantial. The use of the new procedure and the appropriateness of the criterion are illustrated with examples.},
  number = {1},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  author = {Benjamini, Yoav and Hochberg, Yosef},
  year = {1995},
  pages = {289-300},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\Bioinformatics\\Benjamini_Hochberg_1995_Controlling the False Discovery Rate.pdf}
}

@article{foderaro2017,
  title = {{{MCC}}/{{Eisosomes Regulate Cell Wall Synthesis}} and {{Stress Responses}} in {{Fungi}}},
  volume = {3},
  copyright = {http://creativecommons.org/licenses/by/3.0/},
  abstract = {The fungal plasma membrane is critical for cell wall synthesis and other important processes including nutrient uptake, secretion, endocytosis, morphogenesis, and response to stress. To coordinate these diverse functions, the plasma membrane is organized into specialized compartments that vary in size, stability, and composition. One recently identified domain known as the Membrane Compartment of Can1 (MCC)/eisosome is distinctive in that it corresponds to a furrow-like invagination in the plasma membrane. MCC/eisosomes have been shown to be formed by the Bin/Amphiphysin/Rvs (BAR) domain proteins Lsp1 and Pil1 in a range of fungi. MCC/eisosome domains influence multiple cellular functions; but a very pronounced defect in cell wall synthesis has been observed for mutants with defects in MCC/eisosomes in some yeast species. For example, Candida albicans MCC/eisosome mutants display abnormal spatial regulation of cell wall synthesis, including large invaginations and altered chemical composition of the walls. Recent studies indicate that MCC/eisosomes affect cell wall synthesis in part by regulating the levels of the key regulatory lipid phosphatidylinositol 4,5-bisphosphate (PI4,5P2) in the plasma membrane. One general way MCC/eisosomes function is by acting as protected islands in the plasma membrane, since these domains are very stable. They also act as scaffolds to recruit \>20 proteins. Genetic studies aimed at defining the function of the MCC/eisosome proteins have identified important roles in resistance to stress, such as resistance to oxidative stress mediated by the flavodoxin-like proteins Pst1, Pst2, Pst3 and Ycp4. Thus, MCC/eisosomes play multiple roles in plasma membrane organization that protect fungal cells from the environment.},
  language = {en},
  number = {4},
  journal = {Journal of Fungi},
  doi = {10.3390/jof3040061},
  author = {Foderaro, Jenna E. and Douglas, Lois M. and Konopka, James B.},
  month = nov,
  year = {2017},
  keywords = {cell wall,eisosome,morphogenesis,<i>Candida albicans</i>,chitin,fungal,Membrane Compartment of Can1 (MCC) domain,β-glucan},
  pages = {61},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\MCC eisosome\\Foderaro et al_2017_MCC-Eisosomes Regulate Cell Wall Synthesis and Stress Responses in Fungi.pdf;C:\\Users\\charl\\Zotero\\storage\\VC893ZR6\\61.html}
}

@article{thery2018,
  title = {Minimal Information for Studies of Extracellular Vesicles 2018 ({{MISEV2018}}): A Position Statement of the {{International Society}} for {{Extracellular Vesicles}} and Update of the {{MISEV2014}} Guidelines},
  volume = {7},
  issn = {null},
  shorttitle = {Minimal Information for Studies of Extracellular Vesicles 2018 ({{MISEV2018}})},
  abstract = {The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (``MISEV'') guidelines for the field in 2014. We now update these ``MISEV2014'' guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.},
  number = {1},
  journal = {Journal of Extracellular Vesicles},
  doi = {10.1080/20013078.2018.1535750},
  author = {Th{\'e}ry, Clotilde and Witwer, Kenneth W. and Aikawa, Elena and Alcaraz, Maria Jose and Anderson, Johnathon D. and Andriantsitohaina, Ramaroson and Antoniou, Anna and Arab, Tanina and Archer, Fabienne and {Atkin-Smith}, Georgia K. and Ayre, D. Craig and Bach, Jean-Marie and Bachurski, Daniel and Baharvand, Hossein and Balaj, Leonora and Baldacchino, Shawn and Bauer, Natalie N. and Baxter, Amy A. and Bebawy, Mary and Beckham, Carla and Zavec, Apolonija Bedina and Benmoussa, Abderrahim and Berardi, Anna C. and Bergese, Paolo and Bielska, Ewa and Blenkiron, Cherie and {Bobis-Wozowicz}, Sylwia and Boilard, Eric and Boireau, Wilfrid and Bongiovanni, Antonella and Borr{\`a}s, Francesc E. and Bosch, Steffi and Boulanger, Chantal M. and Breakefield, Xandra and Breglio, Andrew M. and Brennan, Meadhbh {\'A} and Brigstock, David R. and Brisson, Alain and Broekman, Marike LD and Bromberg, Jacqueline F. and {Bryl-G{\'o}recka}, Paulina and Buch, Shilpa and Buck, Amy H. and Burger, Dylan and Busatto, Sara and Buschmann, Dominik and Bussolati, Benedetta and Buz{\'a}s, Edit I. and Byrd, James Bryan and Camussi, Giovanni and Carter, David RF and Caruso, Sarah and Chamley, Lawrence W. and Chang, Yu-Ting and Chen, Chihchen and Chen, Shuai and Cheng, Lesley and Chin, Andrew R. and Clayton, Aled and Clerici, Stefano P. and Cocks, Alex and Cocucci, Emanuele and Coffey, Robert J. and {Cordeiro-da-Silva}, Anabela and Couch, Yvonne and Coumans, Frank AW and Coyle, Beth and Crescitelli, Rossella and Criado, Miria Ferreira and {D'Souza-Schorey}, Crislyn and Das, Saumya and Chaudhuri, Amrita Datta and de Candia, Paola and Junior, Eliezer F. De Santana and Wever, Olivier De and del Portillo, Hernando A. and Demaret, Tanguy and Deville, Sarah and Devitt, Andrew and Dhondt, Bert and Vizio, Dolores Di and Dieterich, Lothar C. and Dolo, Vincenza and Rubio, Ana Paula Dominguez and Dominici, Massimo and Dourado, Mauricio R. and Driedonks, Tom AP and Duarte, Filipe V. and Duncan, Heather M. and Eichenberger, Ramon M. and Ekstr{\"o}m, Karin and Andaloussi, Samir EL and {Elie-Caille}, Celine and Erdbr{\"u}gger, Uta and {Falc{\'o}n-P{\'e}rez}, Juan M. and Fatima, Farah and Fish, Jason E. and {Flores-Bellver}, Miguel and F{\"o}rs{\"o}nits, Andr{\'a}s and {Frelet-Barrand}, Annie and Fricke, Fabia and Fuhrmann, Gregor and Gabrielsson, Susanne and {G{\'a}mez-Valero}, Ana and Gardiner, Chris and G{\"a}rtner, Kathrin and Gaudin, Raphael and Gho, Yong Song and Giebel, Bernd and Gilbert, Caroline and Gimona, Mario and Giusti, Ilaria and Goberdhan, Deborah CI and G{\"o}rgens, Andr{\'e} and Gorski, Sharon M. and Greening, David W. and Gross, Julia Christina and Gualerzi, Alice and Gupta, Gopal N. and Gustafson, Dakota and Handberg, Aase and Haraszti, Reka A. and Harrison, Paul and Hegyesi, Hargita and Hendrix, An and Hill, Andrew F. and Hochberg, Fred H. and Hoffmann, Karl F. and Holder, Beth and Holthofer, Harry and Hosseinkhani, Baharak and Hu, Guoku and Huang, Yiyao and Huber, Veronica and Hunt, Stuart and Ibrahim, Ahmed Gamal-Eldin and Ikezu, Tsuneya and Inal, Jameel M. and Isin, Mustafa and Ivanova, Alena and Jackson, Hannah K. and Jacobsen, Soren and Jay, Steven M. and Jayachandran, Muthuvel and Jenster, Guido and Jiang, Lanzhou and Johnson, Suzanne M. and Jones, Jennifer C. and Jong, Ambrose and {Jovanovic-Talisman}, Tijana and Jung, Stephanie and Kalluri, Raghu and Kano, Shin-ichi and Kaur, Sukhbir and Kawamura, Yumi and Keller, Evan T. and Khamari, Delaram and Khomyakova, Elena and Khvorova, Anastasia and Kierulf, Peter and Kim, Kwang Pyo and Kislinger, Thomas and Klingeborn, Mikael and II, David J. Klinke and Kornek, Miroslaw and Kosanovi{\'c}, Maja M. and Kov{\'a}cs, {\'A}rp{\'a}d Ferenc and {Kr{\"a}mer-Albers}, Eva-Maria and Krasemann, Susanne and Krause, Mirja and Kurochkin, Igor V. and Kusuma, Gina D. and Kuypers, S{\"o}ren and Laitinen, Saara and Langevin, Scott M. and Languino, Lucia R. and Lannigan, Joanne and L{\"a}sser, Cecilia and Laurent, Louise C. and Lavieu, Gregory and {L{\'a}zaro-Ib{\'a}{\~n}ez}, Elisa and Lay, Soazig Le and Lee, Myung-Shin and Lee, Yi Xin Fiona and Lemos, Debora S. and Lenassi, Metka and Leszczynska, Aleksandra and Li, Isaac TS and Liao, Ke and Libregts, Sten F. and Ligeti, Erzsebet and Lim, Rebecca and Lim, Sai Kiang and Lin{\=e}, Aija and Linnemannst{\"o}ns, Karen and Llorente, Alicia and Lombard, Catherine A. and Lorenowicz, Magdalena J. and L{\"o}rincz, {\'A}kos M. and L{\"o}tvall, Jan and Lovett, Jason and Lowry, Michelle C. and Loyer, Xavier and Lu, Quan and Lukomska, Barbara and Lunavat, Taral R. and Maas, Sybren LN and Malhi, Harmeet and Marcilla, Antonio and Mariani, Jacopo and Mariscal, Javier and {Martens-Uzunova}, Elena S. and {Martin-Jaular}, Lorena and Martinez, M. Carmen and Martins, Vilma Regina and Mathieu, Mathilde and Mathivanan, Suresh and Maugeri, Marco and McGinnis, Lynda K. and McVey, Mark J. and Jr, David G. Meckes and Meehan, Katie L. and Mertens, Inge and Minciacchi, Valentina R. and M{\"o}ller, Andreas and J{\o}rgensen, Malene M{\o}ller and {Morales-Kastresana}, Aizea and Morhayim, Jess and Mullier, Fran{\c c}ois and Muraca, Maurizio and Musante, Luca and Mussack, Veronika and Muth, Dillon C. and Myburgh, Kathryn H. and Najrana, Tanbir and Nawaz, Muhammad and Nazarenko, Irina and Nejsum, Peter and Neri, Christian and Neri, Tommaso and Nieuwland, Rienk and Nimrichter, Leonardo and Nolan, John P. and Hoen, Esther NM Nolte-'t and Hooten, Nicole Noren and O'Driscoll, Lorraine and O'Grady, Tina and O'Loghlen, Ana and Ochiya, Takahiro and Olivier, Martin and Ortiz, Alberto and Ortiz, Luis A. and Osteikoetxea, Xabier and {\O}stergaard, Ole and Ostrowski, Matias and Park, Jaesung and Pegtel, D. Michiel and Peinado, Hector and Perut, Francesca and Pfaffl, Michael W. and Phinney, Donald G. and Pieters, Bartijn CH and Pink, Ryan C. and Pisetsky, David S. and von Strandmann, Elke Pogge and Polakovicova, Iva and Poon, Ivan KH and Powell, Bonita H. and Prada, Ilaria and Pulliam, Lynn and Quesenberry, Peter and Radeghieri, Annalisa and Raffai, Robert L. and Raimondo, Stefania and Rak, Janusz and Ramirez, Marcel I. and Raposo, Gra{\c c}a and Rayyan, Morsi S. and {Regev-Rudzki}, Neta and Ricklefs, Franz L. and Robbins, Paul D. and Roberts, David D. and Rodrigues, Silvia C. and Rohde, Eva and Rome, Sophie and Rouschop, Kasper MA and Rughetti, Aurelia and Russell, Ashley E. and Sa{\'a}, Paula and Sahoo, Susmita and {Salas-Huenuleo}, Edison and S{\'a}nchez, Catherine and Saugstad, Julie A. and Saul, Meike J. and Schiffelers, Raymond M. and Schneider, Raphael and Sch{\o}yen, Tine Hiorth and Scott, Aaron and Shahaj, Eriomina and Sharma, Shivani and Shatnyeva, Olga and Shekari, Faezeh and Shelke, Ganesh Vilas and Shetty, Ashok K. and Shiba, Kiyotaka and Siljander, Pia R.-M. and Silva, Andreia M. and Skowronek, Agata and II, Orman L. Snyder and Soares, Rodrigo Pedro and S{\'o}dar, Barbara W. and Soekmadji, Carolina and Sotillo, Javier and Stahl, Philip D. and Stoorvogel, Willem and Stott, Shannon L. and Strasser, Erwin F. and Swift, Simon and Tahara, Hidetoshi and Tewari, Muneesh and Timms, Kate and Tiwari, Swasti and Tixeira, Rochelle and Tkach, Mercedes and Toh, Wei Seong and Tomasini, Richard and Torrecilhas, Ana Claudia and Tosar, Juan Pablo and Toxavidis, Vasilis and Urbanelli, Lorena and Vader, Pieter and van Balkom, Bas WM and van der Grein, Susanne G. and Deun, Jan Van and van Herwijnen, Martijn JC and {Keuren-Jensen}, Kendall Van and van Niel, Guillaume and van Royen, Martin E. and van Wijnen, Andre J. and Vasconcelos, M. Helena and Jr, Ivan J. Vechetti and Veit, Tiago D. and Vella, Laura J. and Velot, {\'E}milie and Verweij, Frederik J. and Vestad, Beate and Vi{\~n}as, Jose L. and Visnovitz, Tam{\'a}s and Vukman, Krisztina V. and Wahlgren, Jessica and Watson, Dionysios C. and Wauben, Marca HM and Weaver, Alissa and Webber, Jason P. and Weber, Viktoria and Wehman, Ann M. and Weiss, Daniel J. and Welsh, Joshua A. and Wendt, Sebastian and Wheelock, Asa M. and Wiener, Zolt{\'a}n and Witte, Leonie and Wolfram, Joy and Xagorari, Angeliki and Xander, Patricia and Xu, Jing and Yan, Xiaomei and {Y{\'a}{\~n}ez-M{\'o}}, Mar{\'i}a and Yin, Hang and Yuana, Yuana and Zappulli, Valentina and Zarubova, Jana and {\v Z}{\.e}kas, Vytautas and Zhang, Jian-ye and Zhao, Zezhou and Zheng, Lei and Zheutlin, Alexander R. and Zickler, Antje M. and Zimmermann, Pascale and Zivkovic, Angela M. and Zocco, Davide and {Zuba-Surma}, Ewa K.},
  month = jan,
  year = {2018},
  keywords = {ectosomes,exosomes,extracellular vesicles,guidelines,microparticles,microvesicles,minimal information requirements,reproducibility,rigor,standardization},
  pages = {1535750},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\ISEV\\Théry et al_2018_Minimal information for studies of extracellular vesicles 2018 (MISEV2018).pdf;C:\\Users\\charl\\Zotero\\storage\\ZT3HPTNL\\20013078.2018.html}
}

@article{lotvall2014,
  title = {Minimal Experimental Requirements for Definition of Extracellular Vesicles and Their Functions: A Position Statement from the {{International Society}} for {{Extracellular Vesicles}}},
  volume = {3},
  issn = {null},
  shorttitle = {Minimal Experimental Requirements for Definition of Extracellular Vesicles and Their Functions},
  abstract = {Secreted membrane-enclosed vesicles, collectively called extracellular vesicles (EVs), which include exosomes, ectosomes, microvesicles, microparticles, apoptotic bodies and other EV subsets, encompass a very rapidly growing scientific field in biology and medicine. Importantly, it is currently technically challenging to obtain a totally pure EV fraction free from non-vesicular components for functional studies, and therefore there is a need to establish guidelines for analyses of these vesicles and reporting of scientific studies on EV biology. Here, the International Society for Extracellular Vesicles (ISEV) provides researchers with a minimal set of biochemical, biophysical and functional standards that should be used to attribute any specific biological cargo or functions to EVs.},
  number = {1},
  journal = {Journal of Extracellular Vesicles},
  doi = {10.3402/jev.v3.26913},
  author = {L{\"o}tvall, Jan and Hill, Andrew F. and Hochberg, Fred and Buz{\'a}s, Edit I. and Vizio, Dolores Di and Gardiner, Christopher and Gho, Yong Song and Kurochkin, Igor V. and Mathivanan, Suresh and Quesenberry, Peter and Sahoo, Susmita and Tahara, Hidetoshi and Wauben, Marca H. and Witwer, Kenneth W. and Th{\'e}ry, Clotilde},
  month = jan,
  year = {2014},
  keywords = {ectosomes,exosomes,extracellular RNA,extracellular vesicles,microparticles,microvesicles},
  pages = {26913},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\ISEV\\Lötvall et al_2014_Minimal experimental requirements for definition of extracellular vesicles and.pdf;C:\\Users\\charl\\Zotero\\storage\\6VSZVCGY\\jev.v3.html}
}

@article{nobile2015,
  title = {Candida Albicans {{Biofilms}} and {{Human Disease}}},
  volume = {69},
  issn = {0066-4227},
  abstract = {In humans, microbial cells (including bacteria, archaea, and fungi) greatly outnumber host cells. Candida albicans is the most prevalent fungal species of the human microbiota; this species asymptomatically colonizes many areas of the body, particularly the gastrointestinal and genitourinary tracts of healthy individuals. Alterations in host immunity, stress, resident microbiota, and other factors can lead to C. albicans overgrowth, causing a wide range of infections, from superficial mucosal to hematogenously disseminated candidiasis. To date, most studies of C. albicans have been carried out in suspension cultures; however, the medical impact of C. albicans (like that of many other microorganisms) depends on its ability to thrive as a biofilm, a closely packed community of cells. Biofilms are notorious for forming on implanted medical devices, including catheters, pacemakers, dentures, and prosthetic joints, which provide a surface and sanctuary for biofilm growth. C. albicans biofilms are intrinsically resistant to conventional antifungal therapeutics, the host immune system, and other environmental perturbations, making biofilm-based infections a significant clinical challenge. Here, we review our current knowledge of biofilms formed by C. albicans and closely related fungal species.},
  number = {1},
  journal = {Annual Review of Microbiology},
  doi = {10.1146/annurev-micro-091014-104330},
  author = {Nobile, Clarissa J. and Johnson, Alexander D.},
  month = oct,
  year = {2015},
  pages = {71-92},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida biofilm\\Review\\Nobile_Johnson_2015_Candida albicans Biofilms and Human Disease.pdf;C:\\Users\\charl\\Zotero\\storage\\LRM8P9NW\\annurev-micro-091014-104330.html}
}

@article{bobrie2011,
  title = {Exosome {{Secretion}}: {{Molecular Mechanisms}} and {{Roles}} in {{Immune Responses}}},
  volume = {12},
  issn = {1398-9219},
  shorttitle = {Exosome {{Secretion}}},
  abstract = {Exosomes are small membrane vesicles, secreted by most cell types from multivesicular endosomes, and thought to play important roles in intercellular communications. Initially described in 1983, as specifically secreted by reticulocytes, exosomes became of interest for immunologists in 1996, when they were proposed to play a role in antigen presentation. More recently, the finding that exosomes carry genetic materials, mRNA and miRNA, has been a major breakthrough in the field, unveiling their capacity to vehicle genetic messages. It is now clear that not only immune cells but probably all cell types are able to secrete exosomes: their range of possible functions expands well beyond immunology to neurobiology, stem cell and tumor biology, and their use in clinical applications as biomarkers or as therapeutic tools is an extensive area of research. Despite intensive efforts to understand their functions, two issues remain to be solved in the future: (i) what are the physiological function(s) of exosomes in vivo and (ii) what are the relative contributions of exosomes and of other secreted membrane vesicles in these proposed functions? Here, we will focus on the current ideas on exosomes and immune responses, but also on their mechanisms of secretion and the use of this knowledge to elucidate the latter issue.},
  number = {12},
  journal = {Traffic},
  doi = {10.1111/j.1600-0854.2011.01225.x},
  author = {Bobrie, Ang{\'e}lique and Colombo, Marina and Raposo, Gra{\c c}a and Th{\'e}ry, Clotilde},
  month = jun,
  year = {2011},
  keywords = {antigen presentation,immune responses,intracellular trafficking,RNA,secreted membrane vesicles},
  pages = {1659-1668},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review exosome\\Bobrie et al_2011_Exosome Secretion.pdf;C:\\Users\\charl\\Zotero\\storage\\MVKQY92L\\j.1600-0854.2011.01225.html}
}

@article{kowal2016,
  title = {Proteomic Comparison Defines Novel Markers to Characterize Heterogeneous Populations of Extracellular Vesicle Subtypes},
  volume = {113},
  copyright = {\textcopyright{}  . http://www.pnas.org/preview\_site/misc/userlicense.xhtml},
  issn = {0027-8424, 1091-6490},
  abstract = {Extracellular vesicles (EVs) have become the focus of rising interest because of their numerous functions in physiology and pathology. Cells release heterogeneous vesicles of different sizes and intracellular origins, including small EVs formed inside endosomal compartments (i.e., exosomes) and EVs of various sizes budding from the plasma membrane. Specific markers for the analysis and isolation of different EV populations are missing, imposing important limitations to understanding EV functions. Here, EVs from human dendritic cells were first separated by their sedimentation speed, and then either by their behavior upon upward floatation into iodixanol gradients or by immuno-isolation. Extensive quantitative proteomic analysis allowing comparison of the isolated populations showed that several classically used exosome markers, like major histocompatibility complex, flotillin, and heat-shock 70-kDa proteins, are similarly present in all EVs. We identified proteins specifically enriched in small EVs, and define a set of five protein categories displaying different relative abundance in distinct EV populations. We demonstrate the presence of exosomal and nonexosomal subpopulations within small EVs, and propose their differential separation by immuno-isolation using either CD63, CD81, or CD9. Our work thus provides guidelines to define subtypes of EVs for future functional studies.},
  language = {en},
  number = {8},
  journal = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1521230113},
  author = {Kowal, Joanna and Arras, Guillaume and Colombo, Marina and Jouve, Mabel and Morath, Jakob Paul and {Primdal-Bengtson}, Bjarke and Dingli, Florent and Loew, Damarys and Tkach, Mercedes and Th{\'e}ry, Clotilde},
  month = feb,
  year = {2016},
  keywords = {extracellular vesicles,microvesicles,ectosomes,exosomes,dendritic cells},
  pages = {E968-E977},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Proteomics\\Mammalian EV\\Kowal et al_2016_Proteomic comparison defines novel markers to characterize heterogeneous.pdf;C:\\Users\\charl\\Zotero\\storage\\MGCVJERM\\E968.html},
  pmid = {26858453}
}

@article{cox2011,
  title = {Andromeda: {{A Peptide Search Engine Integrated}} into the {{MaxQuant Environment}}},
  volume = {10},
  issn = {1535-3893},
  shorttitle = {Andromeda},
  abstract = {A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. Furthermore, it can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, such as highly phosphorylated peptides, and accommodates extremely large databases. The algorithms of Andromeda are provided. Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www.maxquant.org. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer. For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides.},
  number = {4},
  journal = {Journal of Proteome Research},
  doi = {10.1021/pr101065j},
  author = {Cox, J{\"u}rgen and Neuhauser, Nadin and Michalski, Annette and Scheltema, Richard A. and Olsen, Jesper V. and Mann, Matthias},
  month = apr,
  year = {2011},
  pages = {1794-1805},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\MS search\\Cox et al_2011_Andromeda.pdf;C:\\Users\\charl\\Zotero\\storage\\DFIPESA9\\pr101065j.html}
}

@article{fingerhut2018,
  title = {Shotgun {{Proteomics Analysis}} of {{Saliva}} and {{Salivary Gland Tissue}} from the {{Common Octopus Octopus}} Vulgaris},
  volume = {17},
  issn = {1535-3893},
  abstract = {The salivary apparatus of the common octopus (Octopus vulgaris) has been the subject of biochemical study for over a century. A combination of bioassays, behavioral studies and molecular analysis on O.~vulgaris and related species suggests that its proteome should contain a mixture of highly potent neurotoxins and degradative proteins. However, a lack of genomic and transcriptomic data has meant that the amino acid sequences of these proteins remain almost entirely unknown. To address this, we assembled the posterior salivary gland transcriptome of O.~vulgaris and combined it with high resolution mass spectrometry data from the posterior and anterior salivary glands of two adults, the posterior salivary glands of six paralarvae and the saliva from a single adult. We identified a total of 2810 protein groups from across this range of salivary tissues and age classes, including 84 with homology to known venom protein families. Additionally, we found 21 short secreted cysteine rich protein groups of which 12 were specific to cephalopods. By combining protein expression data with phylogenetic analysis we demonstrate that serine proteases expanded dramatically within the cephalopod lineage and that cephalopod specific proteins are strongly associated with the salivary apparatus.},
  number = {11},
  journal = {Journal of Proteome Research},
  doi = {10.1021/acs.jproteome.8b00525},
  author = {Fingerhut, Legana C. H. W. and Strugnell, Jan M. and Faou, Pierre and Labiaga, {\'A}lvaro Roura and Zhang, Jia and Cooke, Ira R.},
  month = nov,
  year = {2018},
  pages = {3866-3876},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\MS parameters\\Fingerhut et al_2018_Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common.pdf;C:\\Users\\charl\\Zotero\\storage\\AXEJNPWJ\\acs.jproteome.html}
}

@incollection{greening2015,
  address = {{New York, NY}},
  series = {Methods in {{Molecular Biology}}},
  title = {A {{Protocol}} for {{Exosome Isolation}} and {{Characterization}}: {{Evaluation}} of {{Ultracentrifugation}}, {{Density}}-{{Gradient Separation}}, and {{Immunoaffinity Capture Methods}}},
  isbn = {978-1-4939-2550-6},
  shorttitle = {A {{Protocol}} for {{Exosome Isolation}} and {{Characterization}}},
  abstract = {Exosomes are 40\textendash{}150 nm extracellular vesicles that are released from a multitude of cell types, and perform diverse cellular functions including intercellular communication, antigen presentation, and transfer of tumorigenic proteins, mRNA and miRNA. Exosomes are important regulators of the cellular niche, and their altered characteristics in many diseases, such as cancer, suggest their importance for diagnostic and therapeutic applications, and as drug delivery vehicles. Exosomes have been purified from biological fluids and in vitro cell cultures using a variety of strategies and techniques. In this chapter, we reveal the protocol and key insights into the isolation, purification and characterization of exosomes, distinct from shed microvesicles and apoptotic blebs. Using the colorectal cancer cell line LIM1863 as a cell model, a comprehensive evaluation of exosome isolation methods including ultracentrifugation (UC-Exos), OptiPrep\texttrademark{} density-based separation (DG-Exos), and immunoaffinity capture using anti-EpCAM-coated magnetic beads (IAC-Exos) were examined. All exosome isolation methodologies contained 40\textendash{}150 nm vesicles based on electron microscopy, and positive for exosome markers (Alix, TSG101, HSP70) based on immunoblotting. This protocol employed a proteomic profiling approach to characterize the protein composition of exosomes, and label-free spectral counting to evaluate the effectiveness of each method in exosome isolation. Based on the number of MS/MS spectra identified for exosome markers and proteins associated with their biogenesis, trafficking, and release, IAC-Exos was shown to be the most effective method to isolate exosomes. However, the use of density-based separation (DG-Exos) provides significant advantages for exosome isolation when the use of immunoaffinity capture is limited (due to antibody availability and suitability of exosome markers).},
  language = {en},
  booktitle = {Proteomic {{Profiling}}: {{Methods}} and {{Protocols}}},
  publisher = {{Springer New York}},
  author = {Greening, David W. and Xu, Rong and Ji, Hong and Tauro, Bow J. and Simpson, Richard J.},
  editor = {Posch, Anton},
  year = {2015},
  keywords = {Density,EpCAM,Exosome,Extracellular vesicle,Immunoaffinity capture,Isolation,Proteomics,Protocol,Purification,Shed microvesicles},
  pages = {179-209},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\MS sample prep\\Greening et al_2015_A Protocol for Exosome Isolation and Characterization.pdf},
  doi = {10.1007/978-1-4939-2550-6_15}
}

@article{stacklies2007,
  title = {{{pcaMethods}}\textemdash{}a Bioconductor Package Providing {{PCA}} Methods for Incomplete Data},
  volume = {23},
  issn = {1367-4803},
  abstract = {Abstract.  Summary:pcaMethods is a Bioconductor compliant library for computing principal component analysis (PCA) on incomplete data sets. The results can be a},
  language = {en},
  number = {9},
  journal = {Bioinformatics},
  doi = {10.1093/bioinformatics/btm069},
  author = {Stacklies, Wolfram and Redestig, Henning and Scholz, Matthias and Walther, Dirk and Selbig, Joachim},
  month = may,
  year = {2007},
  pages = {1164-1167},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\R packages\\Stacklies et al_2007_pcaMethods—a bioconductor package providing PCA methods for incomplete data.pdf;C:\\Users\\charl\\Zotero\\storage\\4HJ9YYC9\\272597.html}
}

@article{priebe2015,
  title = {{{FungiFun2}}: A Comprehensive Online Resource for Systematic Analysis of Gene Lists from Fungal Species},
  volume = {31},
  issn = {1367-4803},
  shorttitle = {{{FungiFun2}}},
  abstract = {Abstract.  Summary : Systematically extracting biological meaning from omics data is a major challenge in systems biology. Enrichment analysis is often used to},
  language = {en},
  number = {3},
  journal = {Bioinformatics},
  doi = {10.1093/bioinformatics/btu627},
  author = {Priebe, Steffen and Kreisel, Christian and Horn, Fabian and Guthke, Reinhard and Linde, J{\"o}rg},
  month = feb,
  year = {2015},
  pages = {445-446},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Online tools\\Priebe et al_2015_FungiFun2.pdf;C:\\Users\\charl\\Zotero\\storage\\6529E382\\2365387.html}
}

@article{gil-bona2015b,
  title = {Proteomics {{Unravels Extracellular Vesicles}} as {{Carriers}} of {{Classical Cytoplasmic Proteins}} in {{Candida}} Albicans},
  volume = {14},
  issn = {1535-3893},
  abstract = {The commensal fungus Candida albicans secretes a considerable number of proteins and, as in different fungal pathogens, extracellular vesicles (EVs) have also been observed. Our report contains the first proteomic analysis of EVs in C. albicans and a comparative proteomic study of the soluble secreted proteins. With this purpose, cell-free culture supernatants from C. albicans were separated into EVs and EV-free supernatant and analyzed by LC\textendash{}MS/MS. A total of 96 proteins were identified including 75 and 61 proteins in EVs and EV-free supernatant, respectively. Out of these, 40 proteins were found in secretome by proteomic analysis for the first time. The soluble proteins were enriched in cell wall and secreted pathogenesis related proteins. Interestingly, more than 90\% of these EV-free supernatant proteins were classical secretory proteins with predicted N-terminal signal peptide, whereas all the leaderless proteins involved in metabolism, including some moonlighting proteins, or in the exocytosis and endocytosis process were exclusively cargo of the EVs. We propose a model of the different mechanisms used by C. albicans secreted proteins to reach the extracellular medium. Furthermore, we tested the potential of the Bgl2 protein, identified in vesicles and EV-free supernatant, to protect against a systemic candidiasis in a murine model.},
  number = {1},
  journal = {Journal of Proteome Research},
  doi = {10.1021/pr5007944},
  author = {{Gil-Bona}, Ana and {Llama-Palacios}, Arancha and Parra, Claudia Marcela and Vivanco, Fernando and Nombela, C{\'e}sar and Monteoliva, Luc{\'i}a and Gil, Concha},
  month = jan,
  year = {2015},
  pages = {142-153},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Candida EVs\\Research\\Gil-Bona et al_2015_Proteomics Unravels Extracellular Vesicles as Carriers of Classical Cytoplasmic.pdf;C:\\Users\\charl\\Zotero\\storage\\PSR722QR\\pr5007944.html}
}

@article{kondoh1997,
  title = {Cloning of the {{RHO1}} Gene from {{Candida}} Albicans and Its Regulation of Beta-1,3-Glucan Synthesis.},
  volume = {179},
  issn = {0021-9193, 1098-5530},
  abstract = {The Saccharomyces cerevisiae RHO1 gene encodes a low-molecular-weight GTPase. One of its recently identified functions is the regulation of beta-1,3-glucan synthase, which synthesizes the main component of the fungal cell wall (J. Drgonova et al., Science 272:277-279, 1996; T. Mazur and W. Baginsky, J. Biol. Chem. 271:14604-14609, 1996; and H. Qadota et al., Science 272:279-281, 1996). From the opportunistic pathogenic fungus Candida albicans, we cloned the RHO1 gene by the PCR and cross-hybridization methods. Sequence analysis revealed that the Candida RHO1 gene has a 597-nucleotide region which encodes a putative 22.0-kDa peptide. The deduced amino acid sequence predicts that Candida albicans Rho1p is 82.9\% identical to Saccharomyces Rho1p and contains all the domains conserved among Rho-type GTPases from other organisms. The Candida albicans RHO1 gene could rescue a S. cerevisiae strain containing a rho1 deletion. Furthermore, recombinant Candida albicans Rho1p could reactivate the beta-1,3-glucan synthesis activities of both C. albicans and S. cerevisiae membranes in which endogenous Rho1p had been depleted by Tergitol NP-40-NaCl treatment. Candida albicans Rho1p was copurified with the beta-1,3-glucan synthase putative catalytic subunit, Candida albicans Gsc1p, by product entrapment. Candida albicans Rho1p was shown to interact directly with Candida albicans Gsc1p in a ligand overlay assay and a cross-linking study. These results indicate that Candida albicans Rho1p acts in the same manner as Saccharomyces cerevisiae Rho1p to regulate beta-1,3-glucan synthesis.},
  language = {en},
  number = {24},
  journal = {Journal of Bacteriology},
  doi = {10.1128/jb.179.24.7734-7741.1997},
  author = {Kondoh, O. and Tachibana, Y. and Ohya, Y. and Arisawa, M. and Watanabe, T.},
  month = dec,
  year = {1997},
  pages = {7734-7741},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Candida EVs\\Cargo\\M-R\\Kondoh et al_1997_Cloning of the RHO1 gene from Candida albicans and its regulation of.pdf;C:\\Users\\charl\\Zotero\\storage\\84LEYU2P\\7734.html},
  pmid = {9401032}
}

@article{hikita2018,
  title = {Sensitive and Rapid Quantification of Exosomes by Fusing Luciferase to Exosome Marker Proteins},
  volume = {8},
  copyright = {2018 The Author(s)},
  issn = {2045-2322},
  abstract = {Exosomes have emerged as important mediators of intercellular communication. Although their modes of action have been elucidated, the molecular mechanisms underlying their secretion, sorting of molecules, uptake into recipient cells, and biological distribution in vivo remain elusive. Here, we present a novel system for quantifying secreted exosomes by introducing ectopic or CRISPR/Cas9-mediated knock-in of luciferase-fusion exosome markers such as CD63. This luciferase-based method makes it possible to measure exosomes secreted into the culture medium with high linearity and wide dynamic range in a high-throughput manner. We demonstrate that data obtained by luminescent quantification are well correlated with data obtained by conventional nanoparticle tracking analysis under multiple conditions. In addition, our system is capable of evaluating the recipient cells or tissues that take up exosomes, as well as visualizing exosomes in vivo. The proposed system represents a powerful tool for understanding the molecular mechanisms underlying exosome production, uptake, and long-term distribution.},
  language = {En},
  number = {1},
  journal = {Scientific Reports},
  doi = {10.1038/s41598-018-32535-7},
  author = {Hikita, Tomoya and Miyata, Mamiko and Watanabe, Risayo and Oneyama, Chitose},
  month = sep,
  year = {2018},
  pages = {14035},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\EV marker usage\\Hikita et al_2018_Sensitive and rapid quantification of exosomes by fusing luciferase to exosome.pdf;C:\\Users\\charl\\Zotero\\storage\\BE4AUCDM\\s41598-018-32535-7.html}
}

@article{noble2010,
  title = {Systematic Screens of a {{Candida}} Albicans Homozygous Deletion Library Decouple Morphogenetic Switching and Pathogenicity},
  volume = {42},
  copyright = {2010 Nature Publishing Group},
  issn = {1546-1718},
  abstract = {Candida albicans is the most common cause of serious fungal disease in humans. Creation of isogenic null mutants of this diploid organism, which requires sequential gene targeting, allows dissection of virulence mechanisms. Published analyses of such mutants show a near-perfect correlation between C. albicans pathogenicity and the ability to undergo a yeast-to-hypha morphological switch in vitro. However, most studies have used mutants constructed with a marker that is itself a virulence determinant and therefore complicates their interpretation. Using alternative markers, we created {$\sim$}3,000 homozygous deletion strains affecting 674 genes, or roughly 11\% of the C. albicans genome. Screening for infectivity in a mouse model and for morphological switching and cell proliferation in vitro, we identified 115 infectivity-attenuated mutants, of which nearly half demonstrated normal morphological switching and proliferation. Analysis of such mutants revealed that virulence requires the glycolipid glucosylceramide. To our knowledge, this is the first C. albicans small molecule that has been found to be required specifically for virulence.},
  language = {en},
  number = {7},
  journal = {Nature Genetics},
  doi = {10.1038/ng.605},
  author = {Noble, Suzanne M. and French, Sarah and Kohn, Lisa A. and Chen, Victoria and Johnson, Alexander D.},
  month = jul,
  year = {2010},
  pages = {590-598},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Tetraspanins\\EVP1\\Noble et al_2010_Systematic screens of a iCandida albicans-i homozygous deletion library.pdf;C:\\Users\\charl\\Zotero\\storage\\V48ZQJV6\\ng.html}
}

@article{garcia-sanchez2005,
  title = {Global {{Roles}} of {{Ssn6}} in {{Tup1}}- and {{Nrg1}}-Dependent {{Gene Regulation}} in the {{Fungal Pathogen}}, {{Candida}} Albicans},
  volume = {16},
  issn = {1059-1524},
  abstract = {In budding yeast, Tup1 and Ssn6/Cyc8 form a corepressor that regulates a large number of genes. This Tup1-Ssn6 corepressor appears to be conserved from yeast to man. In the pathogenic fungus Candida albicans, Tup1 regulates cellular morphogenesis, phenotypic switching, and metabolism, but the role of Ssn6 remains unclear. We show that there are clear differences in the morphological and invasive phenotypes of C. albicans ssn6 and tup1 mutants. Unlike Tup1, Ssn6 depletion promoted morphological events reminiscent of phenotypic switching rather than filamentous growth. Transcript profiling revealed minimal overlap between the Ssn6 and Tup1 regulons. Hypha-specific genes, which are repressed by Tup1 and Nrg1, were not derepressed in ssn6 cells under the conditions studied. In contrast, the phase specific gene WH11 was derepressed in ssn6 cells, but not in tup1 or nrg1 cells. Hence Ssn6 and Tup1 play distinct roles in C. albicans. Nevertheless, both Ssn6 and Tup1 were required for the Nrg1-mediated repression of an artificial NRE promoter, and lexA-Nrg1 mediated repression in the C. albicans one-hybrid system. These observations are explained in models that are generally consistent with the Tup1-Ssn6 paradigm in budding yeast.},
  number = {6},
  journal = {Molecular Biology of the Cell},
  doi = {10.1091/mbc.e05-01-0071},
  author = {{Garc{\'i}a-S{\'a}nchez}, Susana and Mavor, Abigail L. and Russell, Claire L. and Argimon, Silvia and Dennison, Paul and Enjalbert, Brice and Brown, Alistair J.P.},
  month = apr,
  year = {2005},
  pages = {2913-2925},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Tetraspanins\\EVP1\\García-Sánchez et al_2005_Global Roles of Ssn6 in Tup1- and Nrg1-dependent Gene Regulation in the Fungal.pdf;C:\\Users\\charl\\Zotero\\storage\\I7UB7S5X\\mbc.html}
}

@article{pitarch2006,
  title = {Decoding {{Serological Response}} to {{Candida Cell Wall Immunome}} into {{Novel Diagnostic}}, {{Prognostic}}, and {{Therapeutic Candidates}} for {{Systemic Candidiasis}} by {{Proteomic}} and {{Bioinformatic Analyses}}},
  volume = {5},
  copyright = {\textcopyright{} 2006 The American Society for Biochemistry and Molecular Biology},
  issn = {1535-9476, 1535-9484},
  abstract = {In an effort to bring novel diagnostic and prognostic biomarkers or even potential targets for vaccine design for systemic candidiasis (SC) into the open, a systematic proteomic approach coupled with bioinformatic analysis was used to decode the serological response to Candida wall immunome in SC patients. Serum levels of IgG antibodies against Candida wall-associated proteins (proteins secreted from protoplasts in active wall regeneration, separated by two-dimensional gel electrophoresis, and identified by mass spectrometry) were measured in 45 SC patients, 57 non-SC patients, and 61 healthy subjects by Western blotting. Two-way hierarchical clustering and principal component analysis of their serum anti-Candida wall antibody expression patterns discriminated SC patients from controls and highlighted the heterogeneity of their expression profiles. Multivariate logistic regression models demonstrated that high levels of antibodies against glucan 1,3-{$\beta$}-glucosidase (Bgl2p) and the anti-wall phosphoglycerate kinase antibody seropositivity were the only independent predictors of SC. Receiver operating characteristic curve analysis revealed no difference between their combined evaluation and measurement of anti-Bgl2p antibodies alone. In a logistic regression model adjusted for known prognostic factors for mortality, SC patients with high anti-Bgl2p antibody levels or a positive anti-wall enolase antibody status, which correlated with each other, had a reduced 2-month risk of death. After controlling for each other, only the seropositivity for anti-wall enolase antibodies was an independent predictor of a lower risk of fatality, supporting that these mediated the protective effect. No association between serum anti-cytoplasmic enolase antibody levels and outcomes was established, suggesting a specific mechanism of enolase processing during wall biogenesis. We conclude that serum anti-Bgl2p antibodies are a novel accurate diagnostic biomarker for SC and that, at high levels, they may provide protection by modulating the anti-wall enolase antibody response. Furthermore serum anti-wall enolase antibodies are a new prognostic indicator for SC and confer protection against it. Bgl2p and wall-associated enolase could be valuable candidates for future vaccine development.},
  language = {en},
  number = {1},
  journal = {Molecular \& Cellular Proteomics},
  doi = {10.1074/mcp.M500243-MCP200},
  author = {Pitarch, Aida and Jim{\'e}nez, Antonio and Nombela, C{\'e}sar and Gil, Concha},
  month = jan,
  year = {2006},
  keywords = {BGL2},
  pages = {79-96},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Candida EVs\\Cargo\\A-F\\Pitarch et al_2006_Decoding Serological Response to Candida Cell Wall Immunome into Novel.pdf;C:\\Users\\charl\\Zotero\\storage\\WYK5JKL6\\79.html},
  pmid = {16195222}
}

@article{hessvik2018,
  title = {Current Knowledge on Exosome Biogenesis and Release},
  volume = {75},
  issn = {1420-9071},
  abstract = {Exosomes are nanosized membrane vesicles released by fusion of an organelle of the endocytic pathway, the multivesicular body, with the plasma membrane. This process was discovered more than 30 years ago, and during these years, exosomes have gone from being considered as cellular waste disposal to mediate a novel mechanism of cell-to-cell communication. The exponential interest in exosomes experienced during recent years is due to their important roles in health and disease and to their potential clinical application in therapy and diagnosis. However, important aspects of the biology of exosomes remain unknown. To explore the use of exosomes in the clinic, it is essential that the basic molecular mechanisms behind the transport and function of these vesicles are better understood. We have here summarized what is presently known about how exosomes are formed and released by cells. Moreover, other cellular processes related to exosome biogenesis and release, such as autophagy and lysosomal exocytosis are presented. Finally, methodological aspects related to exosome release studies are discussed.},
  language = {en},
  number = {2},
  journal = {Cellular and Molecular Life Sciences},
  doi = {10.1007/s00018-017-2595-9},
  author = {Hessvik, Nina Pettersen and Llorente, Alicia},
  month = jan,
  year = {2018},
  keywords = {Autophagy,Endosomes,Exosomes,Extracellular vesicles,Lysosomes,Microvesicles,MVB biogenesis,MVBs,Release,Secretion},
  pages = {193-208},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review exosome\\Hessvik_Llorente_2018_Current knowledge on exosome biogenesis and release2.pdf;C:\\Users\\charl\\Zotero\\storage\\4UIHI5CC\\Hessvik and Llorente - 2018 - Current knowledge on exosome biogenesis and releas.pdf}
}

@article{marwick2018,
  title = {Packaging {{Data Analytical Work Reproducibly Using R}} (and {{Friends}})},
  volume = {72},
  issn = {0003-1305},
  abstract = {Computers are a central tool in the research process, enabling complex and large-scale data analysis. As computer-based research has increased in complexity, so have the challenges of ensuring that this research is reproducible. To address this challenge, we review the concept of the research compendium as a solution for providing a standard and easily recognizable way for organizing the digital materials of a research project to enable other researchers to inspect, reproduce, and extend the research. We investigate how the structure and tooling of software packages of the R programming language are being used to produce research compendia in a variety of disciplines. We also describe how software engineering tools and services are being used by researchers to streamline working with research compendia. Using real-world examples, we show how researchers can improve the reproducibility of their work using research compendia based on R packages and related tools.},
  number = {1},
  journal = {The American Statistician},
  doi = {10.1080/00031305.2017.1375986},
  author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
  month = jan,
  year = {2018},
  pages = {80-88},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Model papers\\Research compendium\\Boettiger_Mullen_2018_Packaging Data Analytical Work Reproducibly Using R (and Friends) AU -.pdf;C:\\Users\\charl\\Zotero\\storage\\Q4TJL5UK\\00031305.2017.html}
}

@article{chen2011,
  title = {{{VennDiagram}}: A Package for the Generation of Highly-Customizable {{Venn}} and {{Euler}} Diagrams in {{R}}},
  volume = {12},
  issn = {1471-2105},
  shorttitle = {{{VennDiagram}}},
  abstract = {Visualization of orthogonal (disjoint) or overlapping datasets is a common task in bioinformatics. Few tools exist to automate the generation of extensively-customizable, high-resolution Venn and Euler diagrams in the R statistical environment. To fill this gap we introduce VennDiagram, an R package that enables the automated generation of highly-customizable, high-resolution Venn diagrams with up to four sets and Euler diagrams with up to three sets.},
  number = {1},
  journal = {BMC Bioinformatics},
  doi = {10.1186/1471-2105-12-35},
  author = {Chen, Hanbo and Boutros, Paul C.},
  month = jan,
  year = {2011},
  pages = {35},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\R packages\\Chen_Boutros_2011_VennDiagram.pdf;C:\\Users\\charl\\Zotero\\storage\\A2PLVRJ8\\1471-2105-12-35.html}
}

@article{theuniprotconsortium2019,
  title = {{{UniProt}}: A Worldwide Hub of Protein Knowledge},
  volume = {47},
  issn = {0305-1048},
  shorttitle = {{{UniProt}}},
  abstract = {The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotation},
  language = {en},
  number = {D1},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gky1049},
  author = {{The UniProt Consortium}},
  month = jan,
  year = {2019},
  pages = {D506-D515},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Online tools\\2019_UniProt.pdf;C:\\Users\\charl\\Zotero\\storage\\N3RJFW46\\5160987.html}
}

@article{phipson2016,
  title = {Robust Hyperparameter Estimation Protects against Hypervariable Genes and Improves Power to Detect Differential Expression},
  volume = {10},
  issn = {1932-6157, 1941-7330},
  abstract = {One of the most common analysis tasks in genomic research is to identify genes that are differentially expressed (DE) between experimental conditions. Empirical Bayes (EB) statistical tests using moderated genewise variances have been very effective for this purpose, especially when the number of biological replicate samples is small. The EB procedures can, however, be heavily influenced by a small number of genes with very large or very small variances. This article improves the differential expression tests by robustifying the hyperparameter estimation procedure. The robust procedure has the effect of decreasing the informativeness of the prior distribution for outlier genes while increasing its informativeness for other genes. This effect has the double benefit of reducing the chance that hypervariable genes will be spuriously identified as DE while increasing statistical power for the main body of genes. The robust EB algorithm is fast and numerically stable. The procedure allows exact small-sample null distributions for the test statistics and reduces exactly to the original EB procedure when no outlier genes are present. Simulations show that the robustified tests have similar performance to the original tests in the absence of outlier genes but have greater power and robustness when outliers are present. The article includes case studies for which the robust method correctly identifies and downweights genes associated with hidden covariates and detects more genes likely to be scientifically relevant to the experimental conditions. The new procedure is implemented in the limma software package freely available from the Bioconductor repository.},
  language = {EN},
  number = {2},
  journal = {The Annals of Applied Statistics},
  doi = {10.1214/16-AOAS920},
  author = {Phipson, Belinda and Lee, Stanley and Majewski, Ian J. and Alexander, Warren S. and Smyth, Gordon K.},
  month = jun,
  year = {2016},
  keywords = {Empirical Bayes,gene expression,microarrays,outliers,robustness},
  pages = {946-963},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\R packages\\Phipson et al_2016_Robust hyperparameter estimation protects against hypervariable genes and.pdf;C:\\Users\\charl\\Zotero\\storage\\U663GDJ8\\1469199900.html}
}

@article{suetsugu2013,
  series = {Exosomes; a Key to Delivering Genetic Materials},
  title = {Imaging Exosome Transfer from Breast Cancer Cells to Stroma at Metastatic Sites in Orthotopic Nude-Mouse Models},
  volume = {65},
  issn = {0169-409X},
  abstract = {Exosomes play an important role in cell-to-cell communication to promote tumor metastasis. In order to image the fate of cancer-cell-derived exosomes in orthotopic nude mouse models of breast cancer, we used green fluorescent protein (GFP)-tagged CD63, which is a general marker of exosomes. Breast cancer cells transferred their own exosomes to other cancer cells and normal lung tissue cells in culture. In orthotopic nude-mouse models, breast cancer cells secreted exosomes into the tumor microenvironment. Tumor-derived exosomes were incorporated into tumor-associated cells as well as circulating in the blood of mice with breast cancer metastases. These results suggest that tumor-derived exosomes may contribute to forming a niche to promote tumor growth and metastasis. Our results demonstrate the usefulness of GFP imaging to investigate the role of exosomes in cancer metastasis.},
  number = {3},
  journal = {Advanced Drug Delivery Reviews},
  doi = {10.1016/j.addr.2012.08.007},
  author = {Suetsugu, Atsushi and Honma, Kimi and Saji, Shigetoyo and Moriwaki, Hisataka and Ochiya, Takahiro and Hoffman, Robert M.},
  month = mar,
  year = {2013},
  keywords = {Breast cancer,CD63,Exosome,GFP,Imaging,Metastasis,RFP},
  pages = {383-390},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\EV isolation\\Suetsugu et al_2013_Imaging exosome transfer from breast cancer cells to stroma at metastatic sites.pdf;C:\\Users\\charl\\Zotero\\storage\\5QTARZ24\\S0169409X12002426.html}
}

@incollection{oksvold2015,
  address = {{New York, NY}},
  series = {Methods in {{Molecular Biology}}},
  title = {Magnetic {{Bead}}-{{Based Isolation}} of {{Exosomes}}},
  isbn = {978-1-4939-1538-5},
  abstract = {Exosomes are here defined as extracellular vesicles (EVs) in the approximate size range of 30\textendash{}100 nm in diameter, and are observed in most body fluids containing typical exosomal markers such as CD9, CD63, and CD81. Potential subpopulations of exosomes can be captured by targeting these markers using magnetic beads. Magnetic beads are versatile tools for exosome isolation and downstream analysis. Here, we describe the workflow of immuno magnetic isolation and analysis of exosomes by flow cytometry, Western immunoblotting, and electron microscopy.},
  language = {en},
  booktitle = {{{RNA Interference}}: {{Challenges}} and {{Therapeutic Opportunities}}},
  publisher = {{Springer New York}},
  author = {Oksvold, Morten P. and Neurauter, Axl and Pedersen, Ketil W.},
  editor = {Sioud, Mouldy},
  year = {2015},
  keywords = {Dynabeads,Electron microscopy,Exosomes,Extracellular vesicles,Magnetic bead isolation},
  pages = {465-481},
  doi = {10.1007/978-1-4939-1538-5_27}
}

@article{gamez-valero2016,
  title = {Size-{{Exclusion Chromatography}}-Based Isolation Minimally Alters {{Extracellular Vesicles}}' Characteristics Compared to Precipitating Agents},
  volume = {6},
  issn = {2045-2322},
  abstract = {Extracellular vesicles (EVs) have become an attractive field among the scientific community. Yet, a major challenge is to define a consensus method for EVs isolation. Ultracentrifugation has been the most widely used methodology but rapid methods, including Size Exclusion Chromatography (SEC) and/or precipitating agents such as Polyethylene glycol (PEG) or PRotein Organic Solvent PRecipitation (PROSPR) have emerged. To evaluate the impact of these different methods on the resulting EV preparations, plasma EVs were isolated using SEC, PEG and PROSPR, and their total protein content, NTA and Cryo-electron microscopy profiles, and EV-markers were compared. Also, their effect on recipient cells was tested. Low protein content and Cryo-EM analysis showed that SEC removed most of the overabundant soluble plasma proteins, which were not removed using PEG and partially by PROSPR. Moreover, only SEC allowed the detection of the EV-markers CD9, CD63 and CD81, LGALS3BP and CD5L, suggesting a putative interference of the precipitating agents in the structure/composition of the EVs. Furthermore, PEG and PROSPR-based EV isolation resulted in reduced cell viability in vitro. These results stress that appropriate EV-isolation method should be considered depending on the forthcoming application of the purified EVs.},
  language = {en},
  journal = {Scientific Reports},
  doi = {10.1038/srep33641},
  author = {{G{\'a}mez-Valero}, Ana and {Mongui{\'o}-Tortajada}, Marta and {Carreras-Planella}, Laura and Franquesa, Marcel{$\cdot$}la and Beyer, Katrin and Borr{\`a}s, Francesc E.},
  month = sep,
  year = {2016},
  pages = {33641},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\EV isolation\\Gámez-Valero et al_2016_Size-Exclusion Chromatography-based isolation minimally alters Extracellular.pdf;C:\\Users\\charl\\Zotero\\storage\\9ZFJYLJA\\srep33641.html}
}

@article{taff2012,
  title = {A {{Candida Biofilm}}-{{Induced Pathway}} for {{Matrix Glucan Delivery}}: {{Implications}} for {{Drug Resistance}}},
  volume = {8},
  issn = {1553-7374},
  shorttitle = {A {{Candida Biofilm}}-{{Induced Pathway}} for {{Matrix Glucan Delivery}}},
  abstract = {Extracellular polysaccharides are key constituents of the biofilm matrix of many microorganisms. One critical carbohydrate component of Candida albicans biofilms, {$\beta$}-1,3 glucan, has been linked to biofilm protection from antifungal agents. In this study, we identify three glucan modification enzymes that function to deliver glucan from the cell to the extracellular matrix. These enzymes include two predicted glucan transferases and an exo-glucanase, encoded by BGL2, PHR1, and XOG1, respectively. We show that the enzymes are crucial for both delivery of {$\beta$}-1,3 glucan to the biofilm matrix and for accumulation of mature matrix biomass. The enzymes do not appear to impact cell wall glucan content of biofilm cells, nor are they necessary for filamentation or biofilm formation. We demonstrate that mutants lacking these genes exhibit enhanced susceptibility to the commonly used antifungal, fluconazole, during biofilm growth only. Transcriptional analysis and biofilm phenotypes of strains with multiple mutations suggest that these enzymes act in a complementary fashion to distribute matrix downstream of the primary {$\beta$}-1,3 glucan synthase encoded by FKS1. Furthermore, our observations suggest that this matrix delivery pathway works independently from the C. albicans ZAP1 matrix formation regulatory pathway. These glucan modification enzymes appear to play a biofilm-specific role in mediating the delivery and organization of mature biofilm matrix. We propose that the discovery of inhibitors for these enzymes would provide promising anti-biofilm therapeutics.},
  language = {en},
  number = {8},
  journal = {PLOS Pathogens},
  doi = {10.1371/journal.ppat.1002848},
  author = {Taff, Heather T. and Nett, Jeniel E. and Zarnowski, Robert and Ross, Kelly M. and Sanchez, Hiram and Cain, Mike T. and Hamaker, Jessica and Mitchell, Aaron P. and Andes, David R.},
  month = aug,
  year = {2012},
  keywords = {Antifungals,Antimicrobial resistance,Biofilms,Candida albicans,Cell walls,Extracellular matrix,Glucans,Mutant strains},
  pages = {e1002848},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida biofilm\\Research\\Taff et al_2012_A Candida Biofilm-Induced Pathway for Matrix Glucan Delivery.pdf;C:\\Users\\charl\\Zotero\\storage\\64F35DQH\\article.html}
}

@article{dasilva2015a,
  title = {Extracellular Vesicles from {{Paracoccidioides}} Pathogenic Species Transport Polysaccharide and Expose Ligands for {{DC}}-{{SIGN}} Receptors},
  volume = {5},
  copyright = {2015 Nature Publishing Group},
  issn = {2045-2322},
  abstract = {Extracellular vesicles (EVs) mediate non-conventional transport of molecules across the fungal cell wall. We aimed at describing the carbohydrate composition and surface carbohydrate epitopes of EVs isolated from the pathogenic fungi Paracoccidioides brasiliensis and P. lutzii using standard procedures. Total EV carbohydrates were ethanol-precipitated from preparations depleted of lipids and proteins, then analyzed by chemical degradation, gas chromatography-mass spectrometry, nuclear magnetic resonance and size-exclusion chromatography. EV glycosyl residues of Glc, Man, and Gal comprised most probably two major components: a high molecular mass 4,6-{$\alpha$}-glucan and a galactofuranosylmannan, possibly an oligomer, bearing a 2-{$\alpha$}-Manp main chain linked to {$\beta$}-Galf (1,3) and {$\alpha$}-Manp (1,6) end units. The results also suggested the presence of small amounts of a (1\textrightarrow6)-Manp polymer, (1\textrightarrow3)-glucan and (1\textrightarrow6)-glucan. Glycan microarrays allowed identification of EV surface lectin(s), while plant lectin microarray profiling revealed terminal Man and GlcNAc residues exposed at the EVs surface. Mammalian lectin microarray profiling showed that DC-SIGN receptors recognized surface carbohydrate in Paracoccidioides EVs. Our results suggest that oligosaccharides, cytoplasmic storage, and cell wall polysaccharides can be exported in fungal EVs, which also expose surface PAMPs and lectins. The role of these newly identified components in the interaction with the host remains to be unraveled.},
  language = {en},
  journal = {Scientific Reports},
  doi = {10.1038/srep14213},
  author = {{da Silva}, Roberta Peres and Heiss, Christian and Black, Ian and Azadi, Parastoo and Gerlach, Jared Q. and Travassos, Luiz R. and Joshi, Lokesh and Kilcoyne, Michelle and Puccia, Rosana},
  month = sep,
  year = {2015},
  pages = {14213},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Para EVs\\Peres da Silva et al_2015_Extracellular vesicles from Paracoccidioides pathogenic species transport.pdf;C:\\Users\\charl\\Zotero\\storage\\NDZUG5Z8\\srep14213.html}
}

@article{dasilva2015,
  title = {Extracellular Vesicle-Mediated Export of Fungal {{RNA}}},
  volume = {5},
  copyright = {2015 Nature Publishing Group},
  issn = {2045-2322},
  abstract = {Extracellular vesicles (EVs) play an important role in the biology of various organisms, including fungi, in which they are required for the trafficking of molecules across the cell wall. Fungal EVs contain a complex combination of macromolecules, including proteins, lipids and glycans. In this work, we aimed to describe and characterize RNA in EV preparations from the human pathogens Cryptococcus neoformans, Paracoccidiodes brasiliensis and Candida albicans, and from the model yeast Saccharomyces cerevisiae. The EV RNA content consisted mostly of molecules less than 250 nt long and the reads obtained aligned with intergenic and intronic regions or specific positions within the mRNA. We identified 114 ncRNAs, among them, six small nucleolar (snoRNA), two small nuclear (snRNA), two ribosomal (rRNA) and one transfer (tRNA) common to all the species considered, together with 20 sequences with features consistent with miRNAs. We also observed some copurified mRNAs, as suggested by reads covering entire transcripts, including those involved in vesicle-mediated transport and metabolic pathways. We characterized for the first time RNA molecules present in EVs produced by fungi. Our results suggest that RNA-containing vesicles may be determinant for various biological processes, including cell communication and pathogenesis.},
  language = {en},
  journal = {Scientific Reports},
  doi = {10.1038/srep07763},
  author = {{da Silva}, Roberta Peres and Puccia, Rosana and Rodrigues, Marcio L. and Oliveira, D{\'e}bora L. and Joffe, Luna S. and C{\'e}sar, Gabriele V. and Nimrichter, Leonardo and Goldenberg, Samuel and Alves, Lysangela R.},
  month = jan,
  year = {2015},
  pages = {7763},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Candida EVs\\Research\\Peres da Silva et al_2015_Extracellular vesicle-mediated export of fungal RNA.pdf;C:\\Users\\charl\\Zotero\\storage\\J5B4KYI8\\srep07763.html}
}

@article{dasilva2016,
  title = {Extracellular Vesicles from {{Paracoccidioides}} Brasiliensis Induced {{M1}} Polarization in Vitro},
  volume = {6},
  copyright = {2016 Nature Publishing Group},
  issn = {2045-2322},
  abstract = {Extracellular vesicles (EVs) released by eukaryotes, archaea, and bacteria contain proteins, lipids, polysaccharides, and other molecules. The cargo analysis of EVs shows that they contain virulence factors suggesting a role in the pathogenesis of infection. The proteome, lipidome, RNA content, and carbohydrate composition of EVs from Paracoccidioides brasiliensis and Paracoccidioides lutzii were characterized. However, the effects of P. brasiliensis EVs on the host immune system have not yet been investigated. Herein, we verified that EVs from P. brasiliensis induce the production of proinflammatory mediators by murine macrophages in a dose-dependent manner. Addition of EV to macrophages also promoted transcription of the M1-polarization marker iNOs and diminish that of the M2 markers Arginase-1, Ym-1, and FIZZ-1. Furthermore, the augmented expression of M2-polarization markers, stimulated by IL-4 plus IL-10, was reverted toward an M1 phenotype in response to secondary stimulation with EVs from P. brasiliensis. The ability of EVs from P. brasiliensis to promote M1 polarization macrophages favoring an enhanced fungicidal activity, demonstrated by the decreased CFU recovery of internalized yeasts, with comparable phagocytic efficacy. Our results suggest that EVs from P. brasiliensis can modulate the innate immune response and affect the relationship between P. brasiliensis and host immune cells.},
  language = {en},
  journal = {Scientific Reports},
  doi = {10.1038/srep35867},
  author = {{da Silva}, Thiago Aparecido and {Roque-Barreira}, Maria Cristina and Casadevall, Arturo and Almeida, Fausto},
  month = oct,
  year = {2016},
  pages = {35867},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Fungal EVs\\Para EVs\\da Silva et al_2016_Extracellular vesicles from Paracoccidioides brasiliensis induced M1.pdf;C:\\Users\\charl\\Zotero\\storage\\IPXMLWKK\\srep35867.html}
}

@article{maas2017,
  title = {Extracellular {{Vesicles}}: {{Unique Intercellular Delivery Vehicles}}},
  volume = {27},
  issn = {0962-8924, 1879-3088},
  shorttitle = {Extracellular {{Vesicles}}},
  abstract = {{$<$}p{$>$}Extracellular vesicles (EVs) are a heterogeneous collection of membrane-bound carriers with complex cargoes including proteins, lipids, and nucleic acids. While the release of EVs was previously thought to be only a mechanism to discard nonfunctional cellular components, increasing evidence implicates EVs as key players in intercellular and even interorganismal communication. EVs confer stability and can direct their cargoes to specific cell types. EV cargoes also appear to act in a combinatorial manner to communicate directives to other cells. This review focuses on recent findings and knowledge gaps in the area of EV biogenesis, release, and uptake. In addition, we highlight examples whereby EV cargoes control basic cellular functions, including motility and polarization, immune responses, and development, and contribute to diseases such as cancer and neurodegeneration.{$<$}/p{$>$}},
  language = {English},
  number = {3},
  journal = {Trends in Cell Biology},
  doi = {10.1016/j.tcb.2016.11.003},
  author = {Maas, Sybren L. N. and Breakefield, Xandra O. and Weaver, Alissa M.},
  month = mar,
  year = {2017},
  pages = {172-188},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review EV\\Maas et al_2017_Extracellular Vesicles.pdf;C:\\Users\\charl\\Zotero\\storage\\MJCND75T\\S0962-8924(16)30179-9.html},
  pmid = {27979573}
}

@article{pathirana2016,
  title = {Bacterial Membrane Vesicles: {{Biogenesis}}, Immune Regulation and Pathogenesis},
  volume = {18},
  copyright = {\textcopyright{} 2016 John Wiley \& Sons Ltd},
  issn = {1462-5822},
  shorttitle = {Bacterial Membrane Vesicles},
  abstract = {Outer membrane vesicles were first described approximately 50 years ago and for many years were considered to be an artifact of bacterial growth. Since that initial discovery, it has become evident that outer membrane vesicles are produced by almost all Gram-negative bacteria as part of their normal growth in addition to driving pathogenesis within the host. More recently, the identification of membrane vesicle (MV) production by some Gram-positive bacteria, parasites, fungi, mycobacteria and infected host cells has significantly broadened the field of MV research and emphasized their importance to pathogenesis. In this review, we will focus on discussing recent advances in the field of bacterial MV biogenesis and the mechanisms whereby they modulate immunity and contribute to pathogenesis. We will highlight findings identifying the contribution of extracellular vesicles produced by Gram-positive bacteria, fungi, parasites, and infected host cells in mediating pathogenesis in addition to the functions of MVs produced by commensal bacteria. Finally, we will discuss recent progress in the development of bacterial MVs as novel vaccines capable of mediating cellular and humoral immune responses.},
  language = {en},
  number = {11},
  journal = {Cellular Microbiology},
  doi = {10.1111/cmi.12658},
  author = {Pathirana, Rishi D. and Kaparakis-Liaskos, Maria},
  year = {2016},
  pages = {1518-1524},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review EV\\Pathirana_Kaparakis‐Liaskos_2016_Bacterial membrane vesicles.pdf;C:\\Users\\charl\\Zotero\\storage\\CXEFKX3P\\cmi.html}
}

@article{quek2017,
  series = {{{SI}}: {{Neurodegeneration}}},
  title = {The Role of Extracellular Vesicles in Neurodegenerative Diseases},
  volume = {483},
  issn = {0006-291X},
  abstract = {Extracellular vesicles, including exosomes, are small membranous vesicles released from many biotypes, contributing to the disease progression and spreading. These extracellular vesicles provide an important mode of cell-to-cell communication by delivering proteins, lipids and RNA to target cells. Exosomes are found associated with neurodegenerative diseases, which are characterised by progressive degeneration of neurons and often associated with misfolded protein. The common diseases include Parkinson's disease (PD), Alzheimer's diseases (AD), amyotrophic lateral sclerosis (ALS), and the prion diseases. Of all neurodegenerative diseases, prion diseases are classified as the distinctive group owing to its transmissible and infectious nature of misfolded prion protein. The infectious prion particles have been demonstrated to be present in exosomes to spread prion infectivity within cells. Similarly, misfolded proteins involved in other neurodegenerative diseases such as Amyloid-{$\beta$} and tau in AD, {$\alpha$}-synuclein in PD, and superoxide dismutase 1 in ALS have been demonstrated to exploit exosomes for induced spreading of misfolded proteins in a prion-like mechanism. Furthermore, RNA molecules can be taken up by the recipient cells as cargo in exosomes. These RNAs can module the expression of the target genes by repressing or inhibiting protein translation. Here we review the role of exosomes in prion diseases and other common neurodegenerative diseases, and discuss the potential of these vesicles for disease pathogenesis.},
  number = {4},
  journal = {Biochemical and Biophysical Research Communications},
  doi = {10.1016/j.bbrc.2016.09.090},
  author = {Quek, Camelia and Hill, Andrew F.},
  month = feb,
  year = {2017},
  keywords = {Alzheimer's disease,Exosomes,Extracellular vesicles,Parkinson's disease,Prions},
  pages = {1178-1186},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review EV\\Quek_Hill_2017_The role of extracellular vesicles in neurodegenerative diseases.pdf;C:\\Users\\charl\\Zotero\\storage\\Y7429AWP\\S0006291X16315571.html}
}

@article{xu2018,
  title = {Extracellular Vesicles in Cancer - Implications for Future Improvements in Cancer Care},
  volume = {15},
  copyright = {2018 Macmillan Publishers Ltd., part of Springer Nature},
  issn = {1759-4782},
  abstract = {Emerging evidence indicates that tumour-derived extracellular vesicles (EVs), notably exosomes, mediate intercellular communication to promote cancer development and progression. Herein, the authors discuss EV properties and physiological functions, particularly their pro-metastatic effects, and highlight the diagnostic and therapeutic potential of EVs in cancer.},
  language = {En},
  number = {10},
  journal = {Nature Reviews Clinical Oncology},
  doi = {10.1038/s41571-018-0036-9},
  author = {Xu, Rong and Rai, Alin and Chen, Maoshan and Suwakulsiri, Wittaya and Greening, David W. and Simpson, Richard J.},
  month = oct,
  year = {2018},
  pages = {617-638},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Review EV\\Xu et al_2018_Extracellular vesicles in cancer — implications for future improvements in.pdf;C:\\Users\\charl\\Zotero\\storage\\9E4YFGUS\\s41571-018-0036-9.html}
}

@article{pappas2016,
  title = {Clinical {{Practice Guideline}} for the {{Management}} of {{Candidiasis}}: 2016 {{Update}} by the {{Infectious Diseases Society}} of {{America}}},
  volume = {62},
  issn = {1058-4838},
  shorttitle = {Clinical {{Practice Guideline}} for the {{Management}} of {{Candidiasis}}},
  abstract = {Abstract.  It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician},
  language = {en},
  number = {4},
  journal = {Clinical Infectious Diseases},
  doi = {10.1093/cid/civ933},
  author = {Pappas, Peter G. and Kauffman, Carol A. and Andes, David R. and Clancy, Cornelius J. and Marr, Kieren A. and {Ostrosky-Zeichner}, Luis and Reboli, Annette C. and Schuster, Mindy G. and Vazquez, Jose A. and Walsh, Thomas J. and Zaoutis, Theoklis E. and Sobel, Jack D.},
  month = feb,
  year = {2016},
  pages = {e1-e50},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida antifungals\\Resistance\\Pappas et al_2016_Clinical Practice Guideline for the Management of Candidiasis.pdf;C:\\Users\\charl\\Zotero\\storage\\APIVMTDI\\2462830.html}
}

@article{fisher2018,
  title = {Worldwide Emergence of Resistance to Antifungal Drugs Challenges Human Health and Food Security},
  volume = {360},
  copyright = {Copyright \textcopyright{} 2018, American Association for the Advancement of Science. http://www.sciencemag.org.ez.library.latrobe.edu.au/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.},
  issn = {0036-8075, 1095-9203},
  abstract = {The recent rate of emergence of pathogenic fungi that are resistant to the limited number of commonly used antifungal agents is unprecedented. The azoles, for example, are used not only for human and animal health care and crop protection but also in antifouling coatings and timber preservation. The ubiquity and multiple uses of azoles have hastened the independent evolution of resistance in many environments. One consequence is an increasing risk in human health care from naturally occurring opportunistic fungal pathogens that have acquired resistance to this broad class of chemicals. To avoid a global collapse in our ability to control fungal infections and to avoid critical failures in medicine and food security, we must improve our stewardship of extant chemicals, promote new antifungal discovery, and leverage emerging technologies for alternative solutions.},
  language = {en},
  number = {6390},
  journal = {Science},
  doi = {10.1126/science.aap7999},
  author = {Fisher, Matthew C. and Hawkins, Nichola J. and Sanglard, Dominique and Gurr, Sarah J.},
  month = may,
  year = {2018},
  pages = {739-742},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida antifungals\\Resistance\\Fisher et al_2018_Worldwide emergence of resistance to antifungal drugs challenges human health.pdf;C:\\Users\\charl\\Zotero\\storage\\3GT5CFD3\\739.html},
  pmid = {29773744}
}

@article{perlin2017,
  title = {The Global Problem of Antifungal Resistance: Prevalence, Mechanisms, and Management},
  volume = {17},
  issn = {1473-3099},
  shorttitle = {The Global Problem of Antifungal Resistance},
  abstract = {Summary
All serious fungal infections need appropriate antifungal therapy for successful patient outcome. Only a few classes of antifungal drugs are available, so the emergence of resistance to single drug classes and now multidrug resistance greatly hampers patient management. Azole resistance among Candida and Aspergillus species is one of the greatest challenges to clinical success, followed by echinocandin and multidrug resistance among some Candida species, especially Candida glabrata. The spread of agriculturally derived azole-resistant Aspergillus fumigatus and emerging threats such as multidrug resistant Candida auris are also alarming. The molecular mechanisms that cause drug resistance are naturally occurring in less susceptible species and are acquired in strains of susceptible organisms. Drug resistance mechanisms include altered drug-target interactions, reduced cellular drug concentrations mediated by drug efflux transporters, and permeability barriers associated with biofilms. Although C auris is inherently multidrug resistant, other strains typically develop resistance through stepwise selection of multiple drug-resistance mechanisms. Cellular stress induced by drug treatment promotes adaptation, which contributes to breakthrough resistance. Drug exposure also drives the emergence of resistance. An effective antifungal stewardship programme is essential to control drug resistance, and should incorporate rapid fungal diagnostics, therapeutic drug monitoring, and clinical intervention teams. The development of better diagnostic tools and strategies that allow targeted use of antifungals is essential to preserve drug effectiveness.},
  number = {12},
  journal = {The Lancet Infectious Diseases},
  doi = {10.1016/S1473-3099(17)30316-X},
  author = {Perlin, David S and {Rautemaa-Richardson}, Riina and {Alastruey-Izquierdo}, Ana},
  month = dec,
  year = {2017},
  pages = {e383-e392},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida antifungals\\Resistance\\Perlin et al_2017_The global problem of antifungal resistance.pdf;C:\\Users\\charl\\Zotero\\storage\\HH95LGQD\\S147330991730316X.html}
}

@article{perlin2015,
  title = {Mechanisms of Echinocandin Antifungal Drug Resistance},
  volume = {1354},
  copyright = {\textcopyright{} 2015 New York Academy of Sciences.},
  issn = {1749-6632},
  abstract = {Fungal infections due to Candida and Aspergillus species cause extensive morbidity and mortality, especially among immunosuppressed patients, and antifungal therapy is critical to patient management. Yet only a few drug classes are available to treat invasive fungal diseases, and this problem is compounded by the emergence of antifungal resistance. Echinocandin drugs are the preferred choice to treat candidiasis. They are the first cell wall\textendash{}active agents and target the fungal-specific enzyme glucan synthase, which catalyzes the biosynthesis of {$\beta$}-1,3-glucan, a key cell wall polymer. Therapeutic failures occur rarely among common Candida species, with the exception of Candida glabrata, which is frequently multidrug resistant. Echinocandin resistance in susceptible species is always acquired during therapy. The mechanism of resistance involves amino acid changes in hot-spot regions of Fks subunits of glucan synthase, which decrease the sensitivity of the enzyme to drug. Cellular stress response pathways lead to drug adaptation, which promotes the formation of resistant fks strains. Clinical factors promoting echinocandin resistance include empiric therapy, prophylaxis, gastrointestinal reservoirs, and intra-abdominal infections. A better understanding of the echinocandin-resistance mechanism, along with cellular and clinical factors promoting resistance, will facilitate more effective strategies to overcome and prevent echinocandin resistance.},
  language = {en},
  number = {1},
  journal = {Annals of the New York Academy of Sciences},
  doi = {10.1111/nyas.12831},
  author = {Perlin, David S.},
  year = {2015},
  keywords = {caspofungin,chitin synthase,echinocandin,FKS,glucan synthase,micafungin},
  pages = {1-11},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida antifungals\\Echinocandins\\Perlin_2015_Mechanisms of echinocandin antifungal drug resistance.pdf;C:\\Users\\charl\\Zotero\\storage\\H7I43AVX\\nyas.html}
}

@article{whaley2017,
  title = {Azole {{Antifungal Resistance}} in {{Candida}} Albicans and {{Emerging Non}}-Albicans {{Candida Species}}},
  volume = {7},
  issn = {1664-302X},
  abstract = {Within the limited antifungal armamentarium, the azole antifungals are the most frequent class used to treat Candida infections. Azole antifungals such as fluconazole are often preferred treatment for many Candida infections as they are inexpensive, exhibit limited toxicity, and are available for oral administration. There is, however, extensive documentation of intrinsic and developed resistance to azole antifungals among several Candida species. As the frequency of azole resistant Candida isolates in the clinical setting increases, it is essential to elucidate the mechanisms of such resistance in order to both preserve and improve upon the azole class of antifungals for the treatment of Candida infections. This review examines azole resistance in infections caused by C. albicans as well as the emerging non-albicans Candida species C. parapsilosis, C. tropicalis, C. krusei, and C. glabrata and, in particular, describes the current understanding of molecular basis of azole resistance in these fungal species.},
  language = {English},
  journal = {Frontiers in Microbiology},
  doi = {10.3389/fmicb.2016.02173},
  author = {Whaley, Sarah G. and Berkow, Elizabeth L. and Rybak, Jeffrey M. and Nishimoto, Andrew T. and Barker, Katherine S. and Rogers, P. David},
  year = {2017},
  keywords = {Antifungal,azole,Candida albicans,Candida glabrata,Candida krusei,Candida parapsilosis,Candida tropicalis,Resistance},
  pages = {2173},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida antifungals\\Azoles\\Whaley et al_2017_Azole Antifungal Resistance in Candida albicans and Emerging Non-albicans.pdf}
}

@article{havlickova2008,
  title = {Epidemiological Trends in Skin Mycoses Worldwide},
  volume = {51},
  copyright = {\textcopyright{} 2008 The Authors. Journal compilation \textcopyright{} 2008 Blackwell Publishing Ltd},
  issn = {1439-0507},
  abstract = {Fungal infections of the skin and nails are a common global problem. The high prevalence of superficial mycotic infections shows that 20\textendash{}25\% of the world's population has skin mycoses, making these one of the most frequent forms of infection. Pathogens responsible for skin mycoses are primarily anthropophilic and zoophilic dermatophytes from the genera Trichophyton (T.), Microsporum (M.) and Epidermophyton (E.). There appears to be considerable inter- and intra-continental variability in the global incidence of these fungal infections. Trichophyton rubrum, T. interdigitale (mentagrophytes var. interdigitale), M. canis, M. audouinii, T. tonsurans and T. verrucosum are the most common, but the attack rates and incidence of specific mycoses can vary widely. Local socio-economic conditions and cultural practices can also influence the prevalence of a particular infection in a given area. For example, tinea pedis (athlete's foot) is more prevalent in developed countries than in emerging economies and is likely to be caused by the anthropophilic germ T. rubrum. In poorer countries, scalp infections (tinea capitis) caused by T. soudanense or M. audouinii are more prevalent. This review summarises current epidemiological trends for fungal infections and focuses on dermatomycosis of glabrous skin on different continents.},
  language = {en},
  number = {s4},
  journal = {Mycoses},
  doi = {10.1111/j.1439-0507.2008.01606.x},
  author = {Havlickova, Blanka and Czaika, Viktor A. and Friedrich, Markus},
  year = {2008},
  keywords = {Candida,epidemiology,Skin mycoses,tinea,Trichophyton},
  pages = {2-15},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida pathogenesis\\Epidemiology\\Havlickova et al_2008_Epidemiological trends in skin mycoses worldwide.pdf;C:\\Users\\charl\\Zotero\\storage\\4GXLFZR6\\j.1439-0507.2008.01606.html}
}

@article{davis2002,
  title = {Candida Albicans {{Mds3p}}, a {{Conserved Regulator}} of {{pH Responses}} and {{Virulence Identified Through Insertional Mutagenesis}}},
  volume = {162},
  copyright = {Copyright \textcopyright{} 2002 by the Genetics Society of America},
  issn = {0016-6731, 1943-2631},
  abstract = {Candida albicans is a commensal fungus that causes diverse infections after antibiotic use or immune debilitation. Gene discovery has been limited because the organism is an asexual diploid. We have developed a strategy that yields random homozygous insertion mutants. The strategy has permitted identification of several prospective essential genes. Many of these genes are homologous to nonessential Saccharomyces cerevisiae genes, and some have no S. cerevisiae homolog. These findings may expand the range of antifungal drug targets. We have also identified new genes required for pH-dependent filamentation, a trait previously associated with virulence. One newly identified gene, MDS3, is required for expression in alkaline media of two filamentation-associated genes, HWP1 and ECE1, but is not required for expression of other pH-response genes. In S. cerevisiae, the two MDS3 homologs are required for growth in alkaline media, thus arguing that Mds3p function in adaptation to external pH changes is conserved. Epistasis tests show that Mds3p contributes to virulence and alkaline pH responses independently of the well-characterized Rim101p pH-response pathway.},
  language = {en},
  number = {4},
  journal = {Genetics},
  author = {Davis, Dana A. and Bruno, Vincent M. and Loza, Lucio and Filler, Scott G. and Mitchell, Aaron P.},
  month = dec,
  year = {2002},
  pages = {1573-1581},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida strains\\Davis et al_2002_Candida albicans Mds3p, a Conserved Regulator of pH Responses and Virulence.pdf;C:\\Users\\charl\\Zotero\\storage\\U7VS657C\\1573.html},
  pmid = {12524333}
}

@article{rcoreteam2018,
  title = {R: {{A Language}} and {{Environmental}} for {{Statistical Computing}}},
  volume = {R Foundation for Statistical Computing.},
  doi = {https://www.R-project.org},
  author = {R Core Team},
  month = dec,
  year = {2018}
}

@article{greening2016,
  title = {Human {{Endometrial Exosomes Contain Hormone}}-{{Specific Cargo Modulating Trophoblast Adhesive Capacity}}: {{Insights}} into {{Endometrial}}-{{Embryo Interactions}}},
  volume = {94},
  issn = {0006-3363},
  shorttitle = {Human {{Endometrial Exosomes Contain Hormone}}-{{Specific Cargo Modulating Trophoblast Adhesive Capacity}}},
  abstract = {Abstract.  Embryo implantation into receptive endometrium requires synergistic endometrial-blastocyst interactions within the uterine cavity and is essential fo},
  language = {en},
  number = {2},
  journal = {Biology of Reproduction},
  doi = {10.1095/biolreprod.115.134890},
  author = {Greening, David W. and Nguyen, Hong P. T. and Elgass, Kirstin and Simpson, Richard J. and Salamonsen, Lois A.},
  month = feb,
  year = {2016},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Methods\\MS sample prep\\Greening et al_2016_Human Endometrial Exosomes Contain Hormone-Specific Cargo Modulating.pdf;C:\\Users\\charl\\Zotero\\storage\\X9GSL5XU\\2434419.html}
}

@article{bleackley2019,
  title = {Fungal {{Extracellular Vesicles}} with a {{Focus}} on {{Proteomic Analysis}}},
  volume = {19},
  copyright = {\textcopyright{} 2019 WILEY-VCH Verlag GmbH \& Co. KGaA, Weinheim},
  issn = {1615-9861},
  abstract = {Extracellular vesicles (EVs) perform crucial functions in cell\textendash{}cell communication. The packaging of biomolecules into membrane-enveloped vesicles prior to release into the extracellular environment provides a mechanism for coordinated delivery of multiple signals at high concentrations that is not achievable by classical secretion alone. Most of the understanding of the biosynthesis, composition, and function of EVs comes from mammalian systems. Investigation of fungal EVs, particularly those released by pathogenic yeast species, has revealed diverse cargo including proteins, lipids, nucleic acids, carbohydrates, and small molecules. Fungal EVs are proposed to function in a variety of biological processes including virulence and cell wall homeostasis with a focus on host\textendash{}pathogen interactions. EVs also carry signals between fungal cells allowing for a coordinated attack on a host during infection. Research on fungal EVs in still in its infancy. Here a review of the literature thus far with a focus on proteomic analysis is provided with respect to techniques, results, and prospects.},
  language = {en},
  number = {8},
  journal = {PROTEOMICS},
  doi = {10.1002/pmic.201800232},
  author = {Bleackley, Mark R. and Dawson, Charlotte S. and Anderson, Marilyn A.},
  year = {2019},
  keywords = {extracellular vesicles,fungi,yeast},
  pages = {1800232},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\My papers\\Bleackley et al_2019_Fungal Extracellular Vesicles with a Focus on Proteomic Analysis.pdf;C:\\Users\\charl\\Zotero\\storage\\K67VILED\\pmic.html}
}

@article{benedict2018,
  title = {Estimation of {{Direct Healthcare Costs}} of {{Fungal Diseases}} in the {{United States}}},
  volume = {68},
  abstract = {To provide insight into the burden of fungal diseases in the United States, we used several administrative data sources to estimate their total direct healthcar},
  language = {en},
  number = {11},
  journal = {Clinical Infectious Diseases},
  doi = {10.1093/cid/ciy776},
  author = {Benedict, Kaitlin and Jackson, Brendan R. and Chiller, Tom and Beer, Karlyn D.},
  year = {2018},
  pages = {1791--1797},
  file = {C:\\Users\\charl\\OneDrive\\zotero\\Honours\\Candida pathogenesis\\Epidemiology\\Benedict et al_Estimation of Direct Healthcare Costs of Fungal Diseases in the United States.pdf;C:\\Users\\charl\\Zotero\\storage\\NCRGPZV6\\5094714.html}
}

@article{ren2008,
  title = {{{CSS}}-{{Palm}} 2.0: An Updated Software for Palmitoylation Sites Prediction},
  volume = {21},
  issn = {1741-0126},
  shorttitle = {{{CSS}}-{{Palm}} 2.0},
  abstract = {Abstract.  Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes},
  language = {en},
  number = {11},
  journal = {Protein Engineering, Design and Selection},
  doi = {10.1093/protein/gzn039},
  author = {Ren, Jian and Wen, Longping and Gao, Xinjiao and Jin, Changjiang and Xue,

repository: csdaw/candidaev

repo_name: csdaw/candidaev